title: Fish sample 9 slide 2

status: Public on Aug 31 2014

type: RNA

city: Laval

first: Jennifer

last: Arstikaitis

state: Quebec

address: 531, boulevard des Prairies

department: Toxicology/Cellular and Molecular Biology

country: Canada

institute: INRS-Institut Armand Frappier Universite du Quebec

hyb_protocol: A 40ul aliquot of labeled cRNA was hybridized to each microarray using the In Situ Hybridization Kit Plus (Agilent, Santa Clara, USA) according to the manufacturer's protocol.

scan_protocol: The microarray slides were scanned immediately after washing (see hybridization protocol) using a ScanArray Express laser scanner (Perkin Elmer).

data_processing: The fluorescent images were processed using Gene Pix Pro 7 software (Molecular Devices Inc).  Data was imported into GeneSpring GX11 software (Agilent Technologies) for further analysis.  The intensity of each spot was characterized by the median pixel intensity and between-array scale normalization on median intensities.

molecule: total RNA

organism: Pimephales promelas

source_name: liver, control

label_protocol: An aliquot of 500 ng of total RNA was prepared for amplification and labeling with Cy3 using the Low RNA Input Linear Amplification kit and Quick Amp Labeling Kit (Agilent, Santa Clara, USA) according to the maufacturer's instructions.  The cRNA concentration was determined using the Nanodrop (TheramoScientific, Waltham, USA).

extract_protocol: Frozen liver samples were ground under liquid nitrogen using a mortar and pestle and total RNA was extracted using the Illustra RNAspin Mini Kit (GE Healthcare) according to the maufacturer's protocol.  The quality and quantity of the RNA was determined using the2100 BioAnalyzer (Agilent, Santa Clara, USA) and the Nanodrop (TheramoScientific, Waltham, USA).

treatment_protocol: Immature Pimephales promelas were raised at the Quebec Aquarium (Quebec, QC) and transferred to the Montreal wastewater treatmen tplant (Montreal, QC).  Fish were mainted in 15 L glass aquariums with flowing water at a constant temperature (25˚C ± 2˚C) under 16 hrs of light and 8 hrs of dark.  Fish were exposed to either 0 (control) or 20% v/v Montreal wastewater effluent in a flow-through system.  Fish were fed 4 mL of bring shrimp (Ocean Nutrition, Dartmouth, NS) twice per day.  After 21 days, fish were anesthetized in 3-aminobenzoic-ethyl-ester-acid (MS222; 0.05g/L) and euthanized.  Fish were euthanized and liver tissue was removed, frozen and stored at -80˚C.

tag: developmental stage

value: juvenile

tag: treatment

value: 0% municipal effluent


title: Fish sample 10 slide 2


title: Fish sample 2 slide 1


title: Fish sample 16 slide 2

source_name: liver, exposed

value: 20% municipal effluent


title: Fish sample 11 slide 2


title: Fish sample 8 slide 1


title: Fish sample 13 slide 2


title: Fish sample 12 slide 2


title: Fish sample 7 slide 1


title: Fish sample 15 slide 2


title: Fish sample 4 slide 1


title: Fish sample 3 slide 1


title: Fish sample 5 slide 1


title: Fish sample 14 slide 2


title: Fish sample 1 slide 1


title: Fish sample 6 slide 1


title: Tiso Juvenile Replicate 2

city: Rimouski

first: Sleiman

last: Bassim

address: 310, Allée des Ursulines

department: Oceanography

institute: UQAR

description: custom build de novo assembly transcriptome

hyb_protocol: The whole design resulted in a custom gene expression glass slide, custom designed probes spotted on eight high-definition 60K arrays (Agilent SurePrint G3 format). High-quality oligonucletides were in situ synthesized and printed using Agilent's 60-mer SurePrint inkjet technology. Complimentary RNA was synthesized with the Illustra CyScribe GFX purification kit (GE Healthcare) according to the manufacturers instructions.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Limma R package was used for preprocessing of probe signals. Background correction (60 offset; method normexp). Normalize within arrays (method loess). Normalize between arrays (method quantile).

organism: Mytilus edulis

source_name: blue mussel spats (42 DPF) – Tiso diet

label_protocol: Probes were labeled with Agilent's Low Input Quick Amp labeling kit (Agilent) for two-channel microarray-based gene expression analysis, following manufacturers instructions. The common reference design was dye-labeled with cyanine 3 and experimental samples were dye-labeled with cyanine 5. Isolated RNAs from all developmental stages were pooled to prepare the reference sample.

growth_protocol: Gametes from different individual parents were used in a pool-cross designed to produce one random larval family carried out at the Aquacole Station in Rimouski, Quebec. Adult blue mussels were obtained from the Havres-aux-Maisons lagoon (Magdalen Islands) in Quebec. Mussel larvae and postlarvae were collected from cultures at each development interval. Morphological criteria enabled the level of competence to be determined for metamorphosis of larvae dependent on eyespot and foot formation.

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

treatment_protocol: Three independent cultures constituting biological replicates were each stocked with fertilized eggs. All larvae were fed continuously at 30,000 cells/ml either with a cocktail (COC) of three different algae species (Isochrysis galbana, Pavlova lutherii, Nannochloropsis oculata) or with a Tiso diet (Nannochloropsis oculata).

value: Juvenile

value: Tiso

source_name: pooled all stages

value: pooled all stages


title: Tiso Pediveliger Replicate 2

source_name: blue mussel pediveligers (22 DPF) – Tiso diet

value: Pediveliger


title: Tiso Juvenile Replicate 1


title: COC Juvenile Replicate 2

source_name: blue mussel spats (42 DPF) – COC diet

value: Cocktail (COC)


title: MINO  Untreated

city: Hong Kong

first: Chor Sang

last: Chim

address: Queen Mary Hospital

department: Medicine

country: Hong Kong

institute: The University of Hong Kong

description: Control

data_processing: For the normalization it uses the average of three housekeeping microRNAs (U6snRNA, RNU44 and RNU48) on corresponding LDA card. Relative microRNA levels were determined by ΔΔCt using endogenous controls and untreated controls using SDS 2.4 and RQ manager 1.2..

label: FAM

organism: Homo sapiens

source_name: MCL Cell line

label_protocol: RNA were converted into cDNA by MegaplexTM RT Primers and TaqMan® MicroRNA Reverse Transcription Kit following the Manufacturer’s instructions. cDNA was pre-amplified using MegaplexTM PreAmp Primer following the Manufacturer’s instructions. Taqman based quantitative real-time PCR were performed (7900HT Real-Time PCR system , ABI) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

growth_protocol: Cell lines were maintained in RPMI-1640 supplemented with 15% fetal bovine serum, 50U/mL of penicillin and 50ug/mL streptomycin in a humidified atmosphere of 5% CO2 at 37oC

extract_protocol: total RNA including microRNA were extracted from mirVana™ miRNA Isolation Kit (Ambion) following manufacturer’s instruction.

treatment_protocol: Cells were seeded at a density of 1x106 cells/ml and cultured with 1.5uM of 5-aza-2’-deoxycytidine (5-azadC) (Sigma–Aldrich) for 5 days

tag: cell line

value: MINO

tag: cell type

value: naïve neoplastic B-cell


title: Tiso Pediveliger Replicate 3


title: MINO 5-azadC

description: Test


title: Tiso Veliger Replicate 2

source_name: blue mussel veligers (15 DPF) – Tiso diet

value: Veliger


title: JEKO-1  5-azadC

description: Test


title: COC Pediveliger Replicate 2

source_name: blue mussel pediveligers (22 DPF) – COC diet


title: Tiso Pediveliger Replicate 1


title: Tiso Veliger Replicate 1


title: JEKO-1  Untreated

description: Control


title: COC Veliger Replicate 2

source_name: blue mussel veligers (15 DPF) – COC diet


title: Control Trocophore Replicate 2

source_name: blue mussel trocophores (1 DPF) – no diet

value: Trocophore


title: COC Pediveliger Replicate 1


title: COC Juvenile Replicate 3


title: Control Eggs Replicate 2

source_name: blue mussel eggs (0 DPF) – no diet

value: EGG


title: COC Veliger Replicate 1


title: COC Juvenile Replicate 1


title: Tiso Veliger Replicate 3


title: Control Trocophore Replicate 1


title: COC Pediveliger Replicate 3


title: Control Eggs Replicate 1


title: ECL003_mock_0h_2

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

country: USA

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. 250ng of each RNA sample was hybridized to one Agilent 8X60K human HG array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Calu-3 2B4 cells, a clonal population of Calu-3 cells sorted for ACE2 expression, were grown in MEM (Gibco) supplemented with 20% fetal bovine serum (Hyclone) and 1% antibiotic antimycotic (Gibco).  Viral titrations and propagation HCoV-EMC were performed in VeroE6 cells using standard methods.  Human Coronavirus EMC 2012 (HCoV-EMC) was received from Bart L. Haagmans, Erasmus Medical Center, Rotterdam, Netherlands via MTA.

extract_protocol: At 0, 3, 7, 12, 18 and 24 hours post-infection (hpi), triplicate wells of virus and mock-infected Calu-3 2B-4 monolayers were washed with 5 ml cold phosphate buffered saline (PBS) and lysed directly with 1 ml of Trizol (Invitrogen), according to the manufacturer’s recommendation, and resulting lysates were stored at -80°C until further processing.  All Trizol lysates were processed simultaneously:  they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative real-time PCR (qPCR) and microarray analyses.

treatment_protocol: Cells were washed with phosphate-buffered saline (PBS) and inoculated with virus at a multiplicity of infection (MOI) of 5 plaque-forming unit (PFU) per cell or mock diluted in PBS for 40 min at 37°C, as previously described (Josset et al., mBio 2012).  Following inoculation, cells were washed 3 times, and fresh medium was added.  Triplicate infected Calu-3 2B4 cultures and triplicate time-matched mock-infected controls were harvested at 0, 3, 7, 12, 18 and 24 hours post-infection (hpi).

tag: timepoint

tag: infection

value: Mock  Infected

value: Calu-3 2B4


title: ECL003_mock_0h_3


title: Control Trocophore Replicate 3


title: ECL003_LoCov_7h_3

value: LoCoV


title: ECL003_LoCov_24h_1


title: Control Eggs Replicate 3


title: ECL003_mock_18h_1


title: ECL003_mock_12h_1


title: ECL003_mock_3h_3


title: ECL003_mock_12h_3


title: ECL003_LoCov_12h_3


title: ECL003_LoCov_24h_2


title: ECL003_mock_18h_3


title: ECL003_LoCov_3h_1


title: ECL003_LoCov_24h_3


title: ECL003_mock_7h_1


title: ECL003_mock_18h_2


title: ECL003_mock_12h_2


title: ECL003_LoCov_0h_3


title: ECL003_LoCov_18h_2


title: ECL003_LoCov_7h_2


title: ECL003_LoCov_12h_2


title: ECL003_mock_7h_3


title: ECL003_LoCov_0h_1


title: ECL003_LoCov_3h_2


title: ECL003_mock_3h_2


title: ECL003_LoCov_3h_3


title: ECL003_mock_0h_1


title: ECL003_LoCov_7h_1


title: ECL003_LoCov_12h_1


title: ECL003_LoCov_18h_3


title: ECL003_LoCov_0h_2


title: ECL003_mock_3h_1


title: ECL003_mock_7h_2


title: Col WT, rep1

city: Singapore

first: Toshiro

last: Ito

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

description: Total RNA from wild-type plants were used in this experiment. This is the first sample of the two biological replicates.

hyb_protocol: Hybridization was performed  following NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed  following NimbleGen standard operating protocol. See www.nimblegen.com.

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

organism: Arabidopsis thaliana

source_name: Col WT, 13 DAG, 29°C LD

label_protocol: Labeling was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: The seeds of the indicated genotype were planted on soil, and grown at 22°C under long day (LD, 16 hour light, 8 hour dark) conditions until treatment.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNaseI digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: Plants were shift to elevated temperature conditions (29°C, LD) at 3 DAG. Samples were harvested at 13 DAG.

tag: genetic background

tag: tissue

value: seedling

tag: genotype

value: wild-type

tag: phenotype


title: Col WT, rep2

description: Total RNA from wild-type plants were used in this experiment. This is the second sample of the two biological replicates.


title: jmj30 jmj32, rep1

description: Total RNA from jmj30 jmj32 plants were used in this experiment. This is the first sample of the two biological replicates.

source_name: jmj30 jmj32, 13 DAG, 29°C LD

value: Flowered earlier than WT grown at similar condition


title: LF8 -F pump

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

description: unfertilized eggs from female equipped with cortisol pump

hyb_protocol: Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Scanning was performed with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 4x44K oligoarray (channels: Green, resolution: 5µm, TIFF: 20 bit)

data_processing: Data were then obtained with the Agilent Feature Extraction software (v10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Before analysis, saturated spot, non-uniform spots and spots not significantly different from background (k=5) were flagged using the Agilent GeneSpring GX software (v.10.0.2). Probes were considered valid when corresponding spots remained present in at least 80% of the replicates of each experimental condition after the flagging procedure. Data were subsequently scale-normalized using the median value of each array.

organism: Salmo salar

label_protocol: 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop. 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array.

extract_protocol: Total RNA was obtained using a Trizol® Reagent kit (Applied Biosystem, Foster city, CA, USA) following the manufacturer´s instructions and further purified using a Nucleospin RNA II kit. RNA integrity was checked with the Agilent Bioanalyzer (Agilent Technologies, Massy, France) and yield was estimated using a Nanodrop ND-1000 spectrophotometer (Labtech, Palaiseau, France).

value: unfertilized eggs


title: jmj30 jmj32, rep2

description: Total RNA from jmj30 jmj32 plants were used in this experiment. This is the second sample of the two biological replicates.


title: LF12 -Ctr pump

description: unfertilized eggs from female equipped with control pump


title: LF13 -F pump

source_name: unfertilized eggs from female equipped with control pump


title: LF15 -Ctr pump


title: LF17 -F pump

source_name: unfertilized eggs from female equipped with cortisol pump


title: LF9 -F pump


title: LF11 -Ctr pump


title: LF7 -F+Oinj

description: unfertilized eggs from cortisol injected female


title: LF10 -F pump


title: LF16 -F pump


title: LF5 - F+Oinj

source_name: unfertilized eggs from cortisol injected female


title: LF4 -Ctr

description: unfertilized eggs from control female

source_name: unfertilized eggs from control female


title: LF2 -F+Oinj


title: LF6 - Ctr

description: unfertilized eggs from control female


title: LF3 -Ctr

description: unfertilized eggs from control female


title: LF1 -Ctr

description: unfertilized eggs from control female


title: Fyn-null mice, PFC, saline-treated, biological replicate 2, experimental group 14

city: Richmond

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

description: Medial PFC brain dissection, saline IP injected Fyn-null genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 14)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr to murine 430 2.0 microarrays with hybridization and washing procedures per the manufacturer's protocols.

scan_protocol: Arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR) and scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: Microarray data analysis was conducted using the Bioconductor affy package for R. Array quality was assessed by inspecting the distributions of log-transformed probe intensity values, as well as scanning for outlier chips using a standard battery of quality measurements, including: average background, scaling factor, percentage of probe-sets called present and 3'-5' actin ratios. Expression data from the saline and ethanol treatment groups were background corrected, quantile normalized and summarized using the robust multi-array average (RMA) expression measure. Outlier arrays were identified by principal component analysis and groups trimmed to 3 arrays per treatment/genotype group for detailed analysis. S-score analysis was performed as detailed in manuscript.

label: biotin

organism: Mus musculus

source_name: Fyn-null mice, PFC, saline-treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA.

extract_protocol: Tissue pooled from three mice of the same genotype/treatment group was homogenized in PureZol Reagent (Bio-Rad Laboratories, Hercules, CA) using a Tekmar homogenizer, and total RNA was isolated with the Aurum Total RNA fatty and Fibrous Tissue Kit according to the manufacturer's instructions.

treatment_protocol: Control and Fyn-null mice (n=24 of each genotype) were administered intraperitoneal injections of saline for 3 days to habituate them to the injection process; on day 4 mice received either an injection of saline (n=12 of each genotype) or 3 g/kg (20% v/v) of ethanol (n=12 of each genotype). Animals were sacrificed by cervical dislocation and decapitation at a 4-hour time-point.

value: brain, medial prefrontal cortex

tag: gender

value: male

value: adult

tag: age

value: 12 weeks

value: saline


title: Fyn-null mice, PFC, saline-treated, biological replicate 3, experimental group 15

description: Medial PFC brain dissection, saline IP injected Fyn-null genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 15)


title: Control mice, PFC, saline-treated, biological replicate 3, experimental group 7

description: Medial PFC brain dissection, saline IP injected control genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 7)

source_name: Control mice, PFC, saline-treated


title: Fyn-null mice, PFC, ethanol-treated, biological replicate 2, experimental group 11

description: Medial PFC brain dissection, ethanol (3.0 g/kg) IP injected Fyn-null genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 11)

source_name: Fyn-null mice, PFC, ethanol-treated

value: ethanol


title: st.35 XY somatic cells_rep3

city: Okazaki

first: Toshiya

last: Nishimura

address: 5-1 Higashiyama Myodaiji-cho

country: Japan

institute: National Institute for Basic Biology

description: Gene expression of XY gonadal somatic cells at st.35

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 125 µl containing 1x Agilent fragmentation buffer and 2x GE blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 125 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Custom Oligo Microarrays (design ID: 027381) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 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-v5_95 and Grid: 027381_D_AA_20100222) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Raw signal intensity processed by Subio (Import Signals for Same IDs: Median).

organism: Oryzias latipes

source_name: sox9b-DsRed positive XY somatic cells at st.35_rep3

label_protocol: In each sample, the whole amount of total RNA (>25ng) was used for cRNA labeling using the One-Color Low Input Quick Amp Labeling  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Germ cells (olvas-EGFP positive cells ) and gonadal somatic cells (sox9b-DsRed positive cells) were isolated by flow FACS (Beckman Coulter, COULTER EPICS ALTRA) according to fluorescence intensity and size. Total RNA was extracted from 8000–10000 cells using an RNaqueous-Micro Kit (Ambion).

value: gonadal somatic cells

tag: Sex

value: XY


title: Fyn-null mice, PFC, saline-treated, biological replicate 4, experimental group 16

description: Medial PFC brain dissection, saline IP injected Fyn-null genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 16)


title: Control mice, PFC, saline-treated, biological replicate 2, experimental group 6

description: Medial PFC brain dissection, saline IP injected control genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 6)


title: Control mice, PFC, saline-treated, biological replicate 1, experimental group 5

description: Medial PFC brain dissection, saline IP injected control genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 5)


title: ECL003_LoCov_18h_1


title: st.35 XY somatic cells_rep2

source_name: sox9b-DsRed positive XY somatic cells at st.35_rep2


title: st.35 XY somatic cells_rep1

source_name: sox9b-DsRed positive XY somatic cells at st.35_rep1


title: st.35 XX somatic cells_rep3

description: Gene expression of XX gonadal somatic cells at st.35

source_name: sox9b-DsRed positive XX somatic cells at st.35_rep3

value: XX


title: Control mice, PFC, ethanol-treated, biological replicate 4, experimental group 4

description: Medial PFC brain dissection, ethanol (3.0 g/kg) IP injected control genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 4)

source_name: Control mice, PFC, ethanol-treated


title: st.35 XX somatic cells_rep1

source_name: sox9b-DsRed positive XX somatic cells at st.35_rep1


title: Aorta-PPE_4

city: Stanford

first: Joshua

middle: M.

last: Spin

state: CA

address: 300 Pasteur Drive

institute: Stanford University

hyb_protocol: GE Blocking agent and Hi-RPM hybridization buffer were added to the samples, which were incubated at 100° C for 5 min, and transferred to an ice-water bath. Samples and arrays were then loaded using Agilent SureHyb chambers and gaskets, hybridized at 55° C for 20 hours, and washed (Gene Expression wash buffers 1 and 2).

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner and Feature Extractor (software version A.10.7.3.1).

data_processing:
QC reports were generated by the Feature Extraction software, and the array data were analyzed with Genespring GX 12.5 (Agilent). Arrays were examined with Quality Control metrics, principal components analysis (PCA), and hierachical agglomerative clustering (HAC). All chips clustered properly and were included in further analysis. The 10 arrays were subjected to one-way ANOVA at a cutoff of p < 0.05, with Benjamini-Hochberg correction for multiple testing. Significant miRNAs were required to show > 1.5-fold expression change from sham-operated Control.
The sample data table includes normalized, background subtracted and processed data using the Feature Extractor. However, replicates of the same miRNA have not been averaged, a process that occurs when the data is uploaded to Genespring. Also all Control Flagged spots have been removed.

source_name: Infrarenal Aorta-PPE-Infused_D7

label_protocol: Per manufacturer’s protocol, 100 ng of total RNA per sample was dephosphorylated using calf intestine alkaline phosphatase at 37° C for 30 min, then denatured in DMSO at 100° C for 5 min and placed in an ice-water bath. Ligation to Cyanine 3-pCp was performed using T4 Ligase at 16° C for 2 hours, and labeled miRNA samples were purified using Micro Bio-spin 6 columns.

growth_protocol: Male 10-week-old C57/Bl6 mice (Jackson Labs)  fed a normal diet were treated as described below.

extract_protocol: Total RNA was isolated using a TRIzol-based (Invitrogen) RNA isolation protocol. RNA was quantified by Nanodrop (Agilent Technologies), and RNA and miRNA quality were verified using an Agilent 2100 Bioanalyzer (Agilent Technologies). Samples required 260/280 ratios >1.8, and sample RNA integrity numbers >9 for inclusion.

treatment_protocol: The PPE infusion model to induce mouse AAA was performed as follows. Temporary ligatures were placed around the proximal and distal infrarenal abdominal aorta. An aortotomy was created at the bifurcation and an insertion catheter was used to infuse the aorta for 5 minutes at 100  mmHg with saline, or saline containing type I porcine pancreatic elastase (1.5 U/mL).  After removing the infusion catheter, the aortotomy was repaired without constriction of the lumen. Aortic segments were harvested at 7 post-surgery at the induced AAA (area between the left renal artery and the bifurcation). Samples were snap-frozen in liquid nitrogen, and then stored at -80°C pending further processing.

tag: strain

tag: treatment group

value: AAA-induction with PPE

tag: harvest time point

value: 7d post-surgery

value: infrarenal aorta


title: Aorta-PPE_5


title: Aorta-PPE_2


title: st.33 XY somatic cells_rep3

description: Gene expression of XY gonadal somatic cells at st.33

source_name: sox9b-DsRed positive XY somatic cells at st.33_rep3


title: Control mice, PFC, ethanol-treated, biological replicate 2, experimental group 2

description: Medial PFC brain dissection, ethanol (3.0 g/kg) IP injected control genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 2)


title: Aorta-PPE_3


title: st.33 XY somatic cells_rep1

source_name: sox9b-DsRed positive XY somatic cells at st.33_rep1


title: Fyn-null mice, PFC, ethanol-treated, biological replicate 1, experimental group 10

description: Medial PFC brain dissection, ethanol (3.0 g/kg) IP injected Fyn-null genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 10)


title: Control mice, PFC, ethanol-treated, biological replicate 1, experimental group 1

description: Medial PFC brain dissection, ethanol (3.0 g/kg) IP injected control genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 1)


title: st.33 XX somatic cells_rep2

description: Gene expression of XX gonadal somatic cells at st.33

source_name: sox9b-DsRed positive XX somatic cells at st.33_rep2


title: st.35 XX somatic cells_rep2

source_name: sox9b-DsRed positive XX somatic cells at st.35_rep2


title: Aorta-PPE_1


title: st.33 XY somatic cells_rep2

source_name: sox9b-DsRed positive XY somatic cells at st.33_rep2


title: st.33 XX somatic cells_rep3

source_name: sox9b-DsRed positive XX somatic cells at st.33_rep3


title: 20% Op5

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

source_name: human umbilical cord fibroblast

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

growth_protocol: Human umbilical cord (UC) tissues were washed at least twice with phosphate buffered saline (PBS) to remove blood cells and cut into two pieces. One was placed in high glucose (HG, 25 mM), the other in  low glucose (LG, 5.6 mM) DMEM medium, respectively. Tissues were minced into 1–2 mm3 fragments with scissors and placed into a 48-well plate (one small piece per well, 12 wells for HG and 12 wells LG medium, respectively) that had been coated with 0.1% gelatin in HG/LG medium containing 10% FBS, 1% NEAA, 2mM glutamine, 0.1mM 2-mercaptoethanol and 4ng/ml FGF2, and cultured at 37C in an atmosphere of either 4 % O2/5 % CO2/91 % N2 or 5 % CO2/air (20 % O2) respectively to generate outgrowths of adherent cells.

extract_protocol: RNA was isolated from early passages (< p5) of UC fibroblast lines (15 PE and 9 CTL lines, grown in T25 flasks) when they reached ~90% confluency in 4 % O2 conditions. In order to collect RNA from cells under 20 % O2, cell lines at either p 4, 5, or 6 were switched from 4 % O2 conditions to 20 % O2 conditions when they were approximately 20 % confluent. When they reached ~90% confluency (generally 2 days in 4 % O2 and 3-4 days in 20 % O2 conditions), medium was removed and RNA STAT60 (I ml; Tel-Test, Friendswood, TX) was immediately added to each T25 flask and RNA extracted by following the manufacturer?s instructions. The samples of RNA were submitted to University Texas Southwestern Medical Center Microarray Core Facility (https://microarray.swmed.edu/) and microarray analysis performed with Illumina HumanHT-12 v4 expression BeadChips. Raw intensity data were background subtracted by using BeadStudio software and analyzed further by GeneSpring 12.6 software (Agilent Technologies Inc., Santa Clara CA), according to the advanced workflow protocol: percentile shift and filter by flags (detected).

treatment_protocol: All cells for RNA collection were cultured in low glucose (5.6 mM)-DMEM medium containing 10% FBS, 1% NEAA, 2mM glutamine, 0.1mM beta-mercaptoethanol and 4ng/ml FGF2 under 4% or 20 O2 in 37 ℃ incubator. The human umbilical cord fibroblast cultures were maintained and expanded by media in every two days. When the culture reached 80-90% confluency, cells were detached dissociated with TrypLE and split at ratio of 1:4 into new T-25 flasks coated with 0.1% gelatin.

tag: cell id

value: PE O

tag: passage #

value: umbilical cord fibroblast


title: Fyn-null mice, PFC, ethanol-treated, biological replicate 3, experimental group 12

description: Medial PFC brain dissection, ethanol (3.0 g/kg) IP injected Fyn-null genotype, tissue harvested 4 hours after injection, RNA isolated from pooled tissue of 3 animals of same genotype/treatment group (group 12)

tag: developmental stage

tag: treatment


title: Liver H3K9me2 Rep1

type: genomic

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

description:
ChIP-chip: Liver, H3K9me2, rep1
L2_K9_new

hyb_protocol: Samples were hybridized onto a NimbleGen 2.1M Deluxe Human Promoter Array following NimbleGen’s protocol.

scan_protocol: The microarray slides were scanned using the Agilent G2565BA DNA Microarray Scanner.  Images were processed using the NimbleScan software.

data_processing:
The log2(Cy5) values were normalized using loess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173. The normalized values presented here are the residuals obtained from loess regression (log2(cy5) was treated as dependent and log2(cy3) as explanatory variables) for CG count bin. These approach is similar to localized MA loess normalization the difference being that instead of predicting M (log2(Cy5/cy3)) using A (log2(cy5*cy3)) locally (using subset of probes) we attempt to predict log2(cy5) using log2(cy3) using probes that are similar in terms of their CG count.
The multple signal values from same probe within array were averaged. Furthermore, the resulting signal values for MIRA and ChIP-antibody samples were quantile normalized independently to adjust for between sample variations.

molecule: genomic DNA

source_name: H3K9me2 ChIP DNA from Liver

label_protocol: Input and ChIP DNA were amplified (WGA2; Sigma-Aldrich), labeled with Cy3 and Cy5 (TriLink Biotechnologies), respectively, according to NimbleGen’s protocol.

extract_protocol:
For MIRA (methylated-CpG island recovery assay), Genomic DNA purified from B cells and liver were sonicated using a Bioruptor (Diagenode) to generate 200–500-bp fragments. Methylated DNA fragments were enriched from 500 ng of sonicated DNA using the MethylCollector Ultra kit (Active Motif) according to the manufacturer’s protocol.
For ChIP, about 10 million B cells were treated with 1% formaldehyde in PBS and incubated 10 min at room temperature and 30 mg of liver tissue was pulverized then incubated in 1% formaldehyde in PBS for 15 min at room temperature. Cross-linking was terminated by addition of glycine. The cells were spun down and rinsed in ice-cold PBS two times. The cell lysates were sonicated using a Bioruptor (Diagenode) to generate 150–350 bp fragments for immunoprecipitation. The following antibodies were used for ChIP: H3K4me3 (Active Motif), H3K27me3 (Active Motif), H3K9me2 (Abcam).

treatment_protocol: Liver was dissected and washed in PBS then was snap frozen on dry ice.

tag: strain background

value: Liver

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: replicate

source_name: Liver_input DNA


title: st.35 XY germ cells_rep2

description: Gene expression of XY germ cells at st.35

source_name: olvas-EGFP positive XY germ cells at st.35_rep2

tag: cell type

value: germ cells


title: COC Veliger Replicate 3

description: custom build de novo assembly transcriptome

source_name: blue mussel veligers (15 DPF) – COC diet

value: Veliger

value: Cocktail (COC)

source_name: pooled all stages

value: pooled all stages


title: st.33 XX somatic cells_rep1

source_name: sox9b-DsRed positive XX somatic cells at st.33_rep1


title: 20% Pp4

description: replicate 1

value: PE P

tag: diagnosis

value: preeclampsia


title: B-cells H3K9me2 Rep2

description:
ChIP-chip: B-cells, H3K9me2, rep2
B4_h3k9me2

source_name: H3K9me2 ChIP DNA from B-cells

treatment_protocol: B cells were purified from spleen using CD19-microbeads (MB) (Miltenyi Biotec).

tag: tissue

value: B-cells

source_name: B-cells_input DNA


title: st.35 XY germ cells_rep3

source_name: olvas-EGFP positive XY germ cells at st.35_rep3


title: 20% Mp5

description: replicate 1

value: PE M


title: Liver H3K27me3 Rep1

description:
ChIP-chip: Liver, H3K27me3, rep1
L4_h3k27me3

source_name: H3K27me3 ChIP DNA from Liver

value: Active Motif


title: Aorta-Sham_5

source_name: Infrarenal Aorta-Sham Operated_D7

tag: age

tag: gender

value: male

value: sham operated


title: B-cells H3K9me2 Rep1

description:
ChIP-chip: B-cells, H3K9me2, rep1
B3_h3k9me2


title: st.35 XX germ cells_rep2

description: Gene expression of XX germ cells at st.35

source_name: olvas-EGFP positive XX germ cells at st.35_rep2

tag: Sex

value: XX


title: st.35 XX germ cells_rep3

source_name: olvas-EGFP positive XX germ cells at st.35_rep3


title: Aorta-Sham_2

tag: strain

tag: treatment group

value: 7d post-surgery

value: infrarenal aorta


title: 20% Lp5

description: replicate 1

tag: cell id

value: PE L

value: umbilical cord fibroblast


title: Liver H3K9me2 Rep2

description:
ChIP-chip: Liver, H3K9me2, rep2
L4_K9_new

value: Liver

value: Abcam


title: st.35 XY germ cells_rep1

source_name: olvas-EGFP positive XY germ cells at st.35_rep1

value: germ cells

value: XY


title: 20% Np4

description: replicate 1

value: PE N

tag: passage #


title: Liver H3K4me3 Rep1

description:
ChIP-chip: Liver, H3K4me3, rep1
L2_h3k4me3

source_name: H3K4me3 ChIP DNA from Liver


title: Aorta-Sham_1

tag: harvest time point


title: Aorta-Sham_4


title: B-cells H3K27me3 Rep1

description:
ChIP-chip: B-cells, H3K27me3, rep1
B1_h3k27me3

source_name: H3K27me3 ChIP DNA from B-cells


title: B-cells H3K27me3 Rep2

description:
ChIP-chip: B-cells, H3K27me3, rep2
B2_h3k27me3


title: B-cells H3K4me3 Rep2

description:
ChIP-chip: B-cells, H3K4me3, rep2
B2_h3k4me3

source_name: H3K4me3 ChIP DNA from B-cells


title: 20% Jp5

description: replicate 1

source_name: human umbilical cord fibroblast

value: PE J


title: Aorta-Sham_3


title: st.35 XX germ cells_rep1

source_name: olvas-EGFP positive XX germ cells at st.35_rep1


title: st.33 XY germ cells_rep3

description: Gene expression of XY germ cells at st.33

source_name: olvas-EGFP positive XY germ cells at st.33_rep3


title: B-cells H3K4me3 Rep1

description:
ChIP-chip: B-cells, H3K4me3, rep1
B1_h3k4me3


title: 20% Ip5

description: replicate 1

value: PE I

value: preeclampsia


title: 20% Fp5

description: replicate 1

value: PE F


title: st.33 XY germ cells_rep1

source_name: olvas-EGFP positive XY germ cells at st.33_rep1


title: 20% Gp5

description: replicate 1

value: PE G


title: 20% Hp5

description: replicate 1

value: PE H


title: st.33 XY germ cells_rep2

source_name: olvas-EGFP positive XY germ cells at st.33_rep2


title: 20% Dp5

description: replicate 1

value: PE D


title: 20% Cp3

description: replicate 1

value: PE C


title: 20% Bp6

description: replicate 1

value: PE B


title: st.33 XX germ cells_rep1

description: Gene expression of XX germ cells at st.33

source_name: olvas-EGFP positive XX germ cells at st.33_rep1

value: XX


title: st.33 XX germ cells_rep3

source_name: olvas-EGFP positive XX germ cells at st.33_rep3


title: 20% Ap5

description: replicate 1

value: PE A


title: 20% 10p5

description: replicate 1

value: CTL #10

value: umbilical cord fibroblast


title: 20% 8p5

description: replicate 1

value: CTL #8


title: ovary from old, biological rep3

city: guangzhou

first: hengxi

last: wei

address: No. 483, wushan

country: China

institute: scau

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0 Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with  R bioconductor software (v. 1.28.0) using RMA algorithm [PMID 14960456].

organism: Macaca mulatta

source_name: ovary_18-19 years old monkey

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Different aged monkeys were deeply anaesthetized and transcardially perfused with 4 L of Krebs-Heinseleit buffer at 4°C. The ovaries were collected and immediately frozen in liquid nitrogen.

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: The tissue of ovary was crashed in liquid nitrogen with mortar, and placed on ice in the Trizol solution (GibcoBRL).

tag: sample age group

value: old; 18-19 years

value: ovary


title: 20% 6p5

description: replicate 1

value: CTL #6


title: st.33 XX germ cells_rep2

source_name: olvas-EGFP positive XX germ cells at st.33_rep2

value: germ cells


title: 20% 9p5

description: replicate 1

value: CTL #9


title: ovary from old, biological rep2


title: ovary from old, biological rep1


title: ovary from middle-age, biological rep1

source_name: ovary_7-8 years old monkey

value: middle-age; 7-8 years


title: ovary from middle-age, biological rep3


title: ovary from Young, biological rep2

source_name: ovary_3-4 years old monkey

value: young; 3-4 years


title: 20% 4p4

description: replicate 1

value: CTL #4

value: preeclampsia


title: 20% 3p5

description: replicate 1

value: CTL #3


title: 20% 5p4

description: replicate 1

value: CTL #5


title: 20% 7p5

description: replicate 1

value: CTL #7


title: Malignant Pleural Mesothelioma 41

city: Houston

first: Milind

middle: Bhalchandra

last: Suraokar

address: 1515 Holcombe Blvd.

institute: Univ. of Texas M. D Anderson Cancer Center

description: Gene expression data from frozen resected tissues

hyb_protocol: Labeled cRNA hybridizing to Affymetrix U133 plus 2.0 chips according to manufacturer's protocol (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: Chips scanned using the Affymetrix GeneChip Scanner 3000 with 7G upgrade

data_processing: Affymetrix U133 Plus 2.0 gene expression arrays were processed and analyzed using R packages in Bioconductor to obtain GC-RMA probe set summary data. Bioinformatic analysis of the RNA microarray data involved using a linear regression model, which accounted for the branch effect seen in samples, to discover differentially expressed genes between normal and tumor pairs.

source_name: Malignant Pleural Mesothelioma

label_protocol: Two hundred and fifty nanograms of total RNA was labeled via the double in-vitro transcription (IVT) protocol, using oligo (dT) and random hexamer primers, to obtain cRNA according to manufacturer's protocol (Affymetrix, Inc., Santa Clara, CA).

growth_protocol: Resected tissue specimens

extract_protocol: The tumor and non-malignant frozen tissues were processed on the Leica CM1850 cryostat (Leica Microsystems, Inc., 1700 Leider Lane, IL, USA) to generate multiple 5-micron thick shaved sections for subsequent homogenization by Omni TH electric homogenizer using disposable Omni-tips (Omni International, Marietta, GA, USA). Total RNA, from homogenized sections, was extracted using TRIREAGENT (Applied Biosystems/Ambion, Austin, TX) according to manufacturer’s protocol. The nanodrop spectrophotometer (Thermo Fisher, Nanodrop products, Wilmington, DE) was used to estimate the concentration of RNA and the quality of the RNA was assessed on Nano Series II RNA LAB-chips using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA).

treatment_protocol: Flash-Frozen and stored at -80 C

tag: sample type

value: Malignant Pleural Mesothelioma

value: Frozen Resected Tissue


title: ovary from middle-age, biological rep2


title: ovary from Young, biological rep3


title: ovary from Young, biological rep1


title: 4% Op3

description: replicate 1

value: PE O


title: 4% Pp2

description: replicate 1

value: PE P

value: umbilical cord fibroblast


title: Malignant Pleural Mesothelioma 40


title: Normal Paired Lung Parenchyma Tissue 40

source_name: Normal Paired lung Parenchyma tissue

value: Normal Paired lung Parenchyma tissue


title: 4% Mp4

description: replicate 1

value: PE M


title: 4% Np2

description: replicate 1

value: PE N


title: 4% Jp4

description: replicate 1

value: PE J


title: Malignant Pleural Mesothelioma 39


title: Normal Paired Lung Parenchyma Tissue 38


title: 20% Kp4

description: replicate 1

value: PE K


title: Normal Paired Lung Parenchyma Tissue 41


title: Malignant Pleural Mesothelioma 37


title: 20% 2p4

description: replicate 1

value: CTL #2


title: 4% Kp2

description: replicate 1


title: Malignant Pleural Mesothelioma 36


title: 4% Dp2

description: replicate 1

value: PE D


title: 4% Fp4

description: replicate 1

value: PE F


title: Normal Paired Lung Parenchyma Tissue 37


title: 4% Ip4

description: replicate 1

value: PE I

value: preeclampsia


title: Normal Paired Lung Parenchyma Tissue 39


title: 4% Gp4

description: replicate 1

value: PE G


title: Malignant Pleural Mesothelioma 38


title: 4% Cp1

description: replicate 1

value: PE C


title: 4% Hp2

description: replicate 1

value: PE H


title: 4% Bp4

description: replicate 1

value: PE B


title: 4% Ap3

description: replicate 1

value: PE A


title: Malignant Pleural Mesothelioma 50

value: Malignant Pleural Mesothelioma

value: Frozen Resected Tissue


title: 4% 9p4

description: replicate 1

value: CTL #9

value: umbilical cord fibroblast

value: healthy


title: 4% 10p5

description: replicate 1

value: CTL #10


title: 4% 8p4

description: replicate 1

value: CTL #8


title: Malignant Pleural Mesothelioma 47


title: Malignant Pleural Mesothelioma 45


title: Malignant Pleural Mesothelioma 35


title: Malignant Pleural Mesothelioma 48


title: 4% 6p3

description: replicate 1

value: CTL #6


title: Malignant Pleural Mesothelioma 46


title: Malignant Pleural Mesothelioma 51


title: Normal Paired Lung Parenchyma Tissue 33

value: Normal Paired lung Parenchyma tissue


title: Normal Paired Lung Parenchyma Tissue 36


title: 4% 7p4

description: replicate 1

value: CTL #7


title: Malignant Pleural Mesothelioma 44


title: 4% 2p2

description: replicate 1

value: CTL #2


title: Malignant Pleural Mesothelioma 42


title: Malignant Pleural Mesothelioma 33


title: 4% 3p2

description: replicate 1

value: CTL #3


title: Normal Paired Lung Parenchyma Tissue 34


title: Malignant Pleural Mesothelioma 43


title: 4% 4p2

description: replicate 1

value: CTL #4


title: 4% 5p2

description: replicate 1

value: CTL #5


title: Malignant Pleural Mesothelioma 34


title: Malignant Pleural Mesothelioma 49


title: Malignant Pleural Mesothelioma 32


title: Normal Paired Lung Parenchyma Tissue 32


title: Malignant Pleural Mesothelioma 30


title: Normal Paired Lung Parenchyma Tissue 31


title: TCL007_TNFa_6h_2

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. 250ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

growth_protocol: Calu-3 2B4 cells, a clonal population of Calu-3 cells sorted for ACE2 expression, were grown in MEM (Gibco) supplemented with 20% fetal bovine serum (Hyclone) and 1% antibiotic antimycotic (Gibco).

extract_protocol: At 3, 6 and 24h for IL-1a and 6 and 24h for TNF post-exposure, triplicate wells of virus and mock-infected Calu-3 2B-4 monolayers were washed with 5 ml cold phosphate buffered saline (PBS) and lysed directly with 1 ml of Trizol (Invitrogen), according to the manufacturer’s recommendation, and resulting lysates were stored at -80°C until further processing.  All Trizol lysates were processed simultaneously:  they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative real-time PCR (qPCR) and microarray analyses.

treatment_protocol: Cells were washed with phosphate-buffered saline (PBS) and treated with either IL-1a (0.001ng/ml) or TNFa (0.05ng/ml) or mock diluted in PBS for 40 min at 37°C.  Following treatment, cells were washed 3 times, and fresh medium was added.  Triplicate Calu-3 2B4 cultures and triplicate time-matched mock-infected controls were harvested at 3, 6 and 24h for IL-1a and 6 and 24h for TNF post-exposure.

tag: treatment

value: TNFa

tag: timepoint

tag: cell line

value: Calu-3 2B4 cells


title: Normal Paired Lung Parenchyma Tissue 29


title: Malignant Pleural Mesothelioma 31


title: TCL007_TNFa_6h_1


title: Malignant Pleural Mesothelioma 55


title: TCL007_TNFa_24h_3


title: Normal Paired Lung Parenchyma Tissue 30


title: TCL007_TNFa_24h_2


title: TCL007_TNFa_24h_1


title: Malignant Pleural Mesothelioma 29


title: TCL007_Mock_6h_3

value: Mock


title: TCL007_Mock_6h_2


title: Malignant Pleural Mesothelioma 28

value: Malignant Pleural Mesothelioma


title: Malignant Pleural Mesothelioma 54

value: Frozen Resected Tissue


title: Aorta-anti-miR-24-PPE_Day7_6

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

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing:
Arrays were Agilent Feature Extracted (software version A.10.7.3.1) with background subtraction and LOWESS normalization.  All data included, no missing values imputation performed. Controls spots removed.
Please note that values in the sample data table are Logbase2(rprocessedsignal/gprocessedsignal), while LogRatios in the raw data files are Logbase10.

label_protocol: Un-pooled total aortic RNA (500 ng) isolated as described was labeled using Cyanine-5-CTP, and labeled cRNAs were hybridized to the SurePrint G3 Mouse Whole Genome GE 8x60K Microarray G4852A platform with an equimolar concentration of Cyanine-3-CTP–labeled universal mouse reference (Stratagene, La Jolla, CA, USA).

treatment_protocol:
Male 10-week-old C57BL/6J mice (Jackson Labs) fed a normal diet were treated as described below:
The PPE infusion model to induce mouse AAA was performed as previously described. Briefly, temporary ligatures were placed around the proximal and distal infrarenal abdominal aorta. An aortotomy was created at the bifurcation and an insertion catheter was used to infuse the aorta for 5 minutes at 100  mmHg with saline (sham), or saline containing type I porcine pancreatic elastase (1.5 U/mL).  After removing the infusion catheter, the aortotomy was repaired without constriction of the lumen. The miR-24 pre-miR, scrambled miR (scr-miR) and miR-ZIP-anti-24 (System Biosciences, Mountain View, USA), were cloned into a human immunodeficiency virus lentiviral vector, containing a copGFP reporter with the miR precursor under constitutive CMV promoter control. The packaged lentiviral constructs were provided as frozen VSV-G pseudotyped particles, with their titer (IFU/ml) being defined with the UltraRapid Lentiviral Titer Kit (System Biosciences, Mountain View, USA). The precursor miR-24 sequence was: UUCACAGUGGCUAAGUUCUGC. Anti- and pre-miRs were injected intraperitoneally in 500 ml PBS with 7.6 x 107 IFU/mouse of loaded lentivirus. Modulators were injected one day after AAA induction.The entire involved aortic segment was harvested at 7 days post-surgery (area between the left renal artery and the bifurcation). Samples were snap-frozen in liquid nitrogen, and then stored at -80°C pending further processing.

value: male

value: AAA-induction with PPE

tag: injected with

value: miR-24 antagomir (anti-miR-24)

value: 7d post-surgery

value: infrarenal aorta

source_name: Stratagene Universal Mouse Reference

value: Reference


title: Aorta-anti-miR-24-PPE_Day7_5


title: Aorta-anti-miR-24-PPE_Day7_4


title: Normal Paired Lung Parenchyma Tissue 28

value: Normal Paired lung Parenchyma tissue


title: Malignant Pleural Mesothelioma 27


title: Normal Paired Lung Parenchyma Tissue 27


title: Aorta-anti-miR-24-PPE_Day7_3


title: TCL007_Mock_6h_1


title: TCL007_TNFa_6h_3


title: Aorta-pre-miR-24-PPE_Day7_3

value: miR-24 mimic (pre-miR-24)


title: TCL007_Mock_3h_2


title: TCL007_Mock_3h_1


title: Malignant Pleural Mesothelioma 26


title: Normal Paired Lung Parenchyma Tissue 26


title: TCL007_Mock_24h_3


title: Aorta-anti-miR-24-PPE_Day7_2


title: Malignant Pleural Mesothelioma 25


title: Aorta-anti-miR-24-PPE_Day7_1


title: TCL007_Mock_24h_2


title: TCL007_Mock_24h_1


title: Aorta-pre-miR-24-PPE_Day7_2


title: Aorta-Scr-miR-PPE_Day7_5

value: scrambled microRNA control (scr-miR)


title: TCL007_IL-1a_6h_2


title: Malignant Pleural Mesothelioma 53


title: Normal Paired Lung Parenchyma Tissue 25


title: TCL007_IL-1a_6h_3


title: Aorta-pre-miR-24-PPE_Day7_1


title: Malignant Pleural Mesothelioma 24


title: Normal Paired Lung Parenchyma Tissue 24


title: TCL007_Mock_3h_3


title: Normal Paired Lung Parenchyma Tissue 35


title: TCL007_IL-1a_6h_1


title: Aorta-ShamSaline_Day7_4

source_name: Infrarenal Aorta-ShamSaline Operated_D7

value: sham operated

value: saline


title: TCL007_IL-1a_3h_2


title: Aorta-Scr-miR-PPE_Day7_4


title: Malignant Pleural Mesothelioma 22


title: Aorta-Scr-miR-PPE_Day7_2


title: Aorta-Scr-miR-PPE_Day7_3


title: TCL007_IL-1a_24h_2


title: Aorta-ShamSaline_Day7_2


title: TCL007_IL-1a_24h_1


title: Malignant Pleural Mesothelioma 23


title: Normal Paired Lung Parenchyma Tissue 22


title: Normal Paired Lung Parenchyma Tissue 21


title: Aorta-ShamSaline_Day7_1


title: Normal Paired Lung Parenchyma Tissue 23


title: Malignant Pleural Mesothelioma 21


title: Aorta-ShamSaline_Day7_3


title: Aorta-Scr-miR-PPE_Day7_1


title: TCL007_IL-1a_3h_1


title: Malignant Pleural Mesothelioma 20


title: TCL007_IL-1a_24h_3


title: TCL007_IL-1a_3h_3


title: Normal Paired Lung Parenchyma Tissue 20


title: Normal Paired Lung Parenchyma Tissue 19


title: Aorta-PPE vs Ref_5

source_name: Infrarenal Aorta-PPE-Infused_D7_5

treatment_protocol:
Male 10-week-old C57BL/6J mice (Jackson Labs) fed a normal diet were treated as described below:
The PPE infusion model to induce mouse AAA was performed as previously described. Briefly, temporary ligatures were placed around the proximal and distal infrarenal abdominal aorta. An aortotomy was created at the bifurcation and an insertion catheter was used to infuse the aorta for 5 minutes at 100  mmHg with saline (sham), or saline containing type I porcine pancreatic elastase (1.5 U/mL).  After removing the infusion catheter, the aortotomy was repaired without constriction of the lumen. The entire involved aortic segment was harvested at 7 days post-surgery (area between the left renal artery and the bifurcation). Samples were snap-frozen in liquid nitrogen, and then stored at -80°C pending further processing.


title: Aorta-PPE vs Ref_4

source_name: Infrarenal Aorta-PPE-Infused_D7_4


title: Aorta-PPE vs Ref_1

source_name: Infrarenal Aorta-PPE-Infused_D7_1


title: 34_20_miN-20

city: tokushima city

first: Shinji

last: Kitamura

address: kuramotocho 3-18-15

institute: tokushima university

hyb_protocol: Labeled cRNA was hybridized to human whole genome microarray (4 X 44 K; Agilent) in accordance with the manufacturer’s procedure.

scan_protocol: The array was scanned with a laser scanner (G2565BA; Agilent).

data_processing: Feature Extraction 9.5 software (Agilent) was used to obtain the microarray raw data.

source_name: Gastric cancer

label_protocol: cRNA was amplified with a WT-Ovation FFPE RNA Amplification System V2 (NuGEN, Cincinnati, Ohio). The amplified cRNA was labeled with Cy3 using a FL-Ovation cDNA Fluorescent Module (NuGEN).

extract_protocol: Extraction protocol The miRNeasy mini kit (Qiagen, Valencia, CA) was used to extract total RNA.

tag: status

value: tumor

tag: response

value: effective


title: Malignant Pleural Mesothelioma 19

tag: tissue


title: 38_22_miN-22

value: normal

value: non-effective


title: Malignant Pleural Mesothelioma 17

value: Malignant Pleural Mesothelioma


title: 37_22_miL-22


title: Aorta-PPE vs Ref_3

source_name: Infrarenal Aorta-PPE-Infused_D7_3


title: Aorta-PPE vs Ref_2

source_name: Infrarenal Aorta-PPE-Infused_D7_2


title: Aorta-Sham vs Ref_5

source_name: Infrarenal Aorta-Sham Operated_D7_5


title: Aorta-Sham vs Ref_4

source_name: Infrarenal Aorta-Sham Operated_D7_4


title: Liver H3K4me3 Rep2

description:
ChIP-chip: Liver, H3K4me3, rep2
L4_h3k4me3

source_name: H3K4me3 ChIP DNA from Liver

tag: strain background

value: Liver

tag: chip antibody

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #

tag: replicate

source_name: Liver_input DNA


title: Normal Paired Lung Parenchyma Tissue 17

value: Frozen Resected Tissue


title: Malignant Pleural Mesothelioma 16


title: 35_21_miL-21


title: Normal Paired Lung Parenchyma Tissue 18


title: 31_19_miL-19


title: 33_20_miL-20


title: 32_19_miN-19


title: Liver DNAme Rep2

description:
DNAme: Liver, rep2
L3

source_name: Methylated DNA from Liver


title: B-cells DNAme Rep1

description:
DNAme: B-cells, rep1
B2

source_name: Methylated DNA from B-cells

value: B-cells

source_name: B-cells_input DNA


title: Aorta-Sham vs Ref_3

source_name: Infrarenal Aorta-Sham Operated_D7_3

tag: strain

tag: gender

value: male

tag: treatment group

value: 7d post-surgery


title: Liver H3K27me3 Rep2

description:
ChIP-chip: Liver, H3K27me3, rep2
L2_h3k27me3

source_name: H3K27me3 ChIP DNA from Liver


title: Aorta-Sham vs Ref_2

source_name: Infrarenal Aorta-Sham Operated_D7_2

tag: harvest time point

value: infrarenal aorta

source_name: Stratagene Universal Mouse Reference

value: Reference


title: B-cells DNAme Rep2

description:
DNAme: B-cells, rep2
B3


title: Liver DNAme Rep1

description:
DNAme: Liver, rep1
L2


title: 30_18_miN-18


title: Normal Paired Lung Parenchyma Tissue 15

source_name: Normal Paired lung Parenchyma tissue

tag: sample type

value: Normal Paired lung Parenchyma tissue


title: 29_18_miL-18


title: 27_17_miL-17


title: Malignant Pleural Mesothelioma 15

source_name: Malignant Pleural Mesothelioma


title: Malignant Pleural Mesothelioma 13


title: Aorta-Sham vs Ref_1

source_name: Infrarenal Aorta-Sham Operated_D7_1


title: Normal Paired Lung Parenchyma Tissue 13


title: 26_16_miN-16

source_name: Gastric cancer


title: Normal Paired Lung Parenchyma Tissue 16


title: 20_13_miN-13


title: Malignant Pleural Mesothelioma 12


title: Normal Paired Lung Parenchyma Tissue 14


title: 25_16_miL-16


title: 24_15_miN-15


title: 23_15_miL-15


title: 36_21_miN-21


title: 19_13_miL-13


title: 22_14_miN-14


title: 21_14_miL-14


title: Malignant Pleural Mesothelioma 11


title: 28_17_miN-17


title: Malignant Pleural Mesothelioma 10


title: Normal Paired Lung Parenchyma Tissue 11


title: Normal Paired Lung Parenchyma Tissue 10


title: Malignant Pleural Mesothelioma 14


title: Normal Paired Lung Parenchyma Tissue 12


title: Malignant Pleural Mesothelioma 18


title: Malignant Pleural Mesothelioma 9


title: 17_11_miL-11


title: 16_10_maN-10


title: Malignant Pleural Mesothelioma 52


title: 13_09_miL-9


title: 14_09_miN-9


title: Normal Paired Lung Parenchyma Tissue 8


title: Normal Paired Lung Parenchyma Tissue 9


title: Normal Paired Lung Parenchyma Tissue 7


title: Malignant Pleural Mesothelioma 8


title: Panc02_Standard Environment_Pooled RNA

city: Shanghai

first: Yu

last: Gan

address: 25/Ln. 2200 Xietu Road

institute: Shanghai Cancer Institute

description:
Gene expression in Panc02 pancreatic tumor of mice housed in standard environment
SE

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014868 Whole Mouse Genome 4x44K array 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 (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0 (Agilent). The probes that were flagged as Detected or Compromised in either sample were maintained.

source_name: Panc02 tumor, Standard Environment housing, 5weeks, Pooled RNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from homogenized tumors was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The RNA samples pooled from 6 mice for each group were subjected to microarray analysis.

treatment_protocol: Three-week-old C57BL/6 mice were randomized to live in either enriched environment or standard environment conditions. Mice from both groups were given subcutaneous injection of Panc02 murine pancreatic cancer cells (6 × 105 cells per mouse) and lived in their respective homes for 5 additional weeks. At the end of the experiment, the Panc02 tumors were harvested and processed for following analysis.

tag: environment

value: Standard

tag: treatment

tag: tissue (rna source)

value: Pancreatic cancer xenograft


title: Malignant Pleural Mesothelioma 7


title: Malignant Pleural Mesothelioma 5


title: Liver, rep2

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Liver

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to Agilent’s protocol.

extract_protocol: Total RNA was prepared using the Rneasy kit (Qiagen).

treatment_protocol: B cells were purified from spleen using CD19-microbeads (MB) (Miltenyi Biotec). Liver was dissected and washed in PBS then was snap frozen on dry ice.


title: Liver, rep3


title: 15_10_maL-10


title: Normal Paired Lung Parenchyma Tissue 6


title: 10_07_miN-7re


title: Malignant Pleural Mesothelioma 6


title: 91R replicate 1

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah

description:
Replicate 1 of 4.91R
91R1

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm.  Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each.  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.  The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  Data captured from the scanned microarray image is saved as a TIF file.

data_processing: TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 9.5.1.1. The software automatically positions a grid and finds the centroid positions of each feature on the microarray. This information is used to perform calculations that include feature intensities, background measurements and statistical analyses. Data generated by the software is recorded as a tab-delimited text file. The data were Lowess-normalized using R and are presented in log base 2

organism: Drosophila melanogaster

label_protocol: The Agilent Twoe-Color Quick Amp Labeling Kit is used to generate fluorescently labeled cRNA for one-color microarray hybridizations.  Agilent RNA spike-in controls are combined with input total RNA samples (50 to 1000 ng).  The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT.   Following cDNA synthesis, T7 RNA polymerase and dye-labeled nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate either cyanine 3-CTP or cyanine 5-CTP.  Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit.  The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

growth_protocol: Flies were raised on standard cornmeal/molasses/agar food at 20-25°C.

extract_protocol: Total RNA was extracted with Tripure (Roche) following manufacturer's instructions and purified RNAeasy columns (Qiagen)

treatment_protocol: RNA was extracted from mature adult 91R or 91C males  and subjected to micraoarray analysis.

tag: genotype/variation

value: CONTROL

value: MUTANT


title: Panc02_Enriched Environment_Pooled RNA

description:
Gene expression in Panc02 pancreatic tumor of mice housed in enriched environment
EE

source_name: Panc02 tumor, Enriched Environment housing, 5weeks, Pooled RNA

value: Enriched

value: subcutaneous injection of Panc02 murine pancreatic cancer cells


title: 11_08_miL-8

tag: status

value: tumor

value: non-effective


title: Liver, rep1

value: Liver


title: 12_08_miN-8

source_name: Gastyric cancer

value: normal

tag: response


title: 91R replicate 4

description:
Replicate 4 of 4.91R
91R4


title: Normal Paired Lung Parenchyma Tissue 5

tag: tissue

value: Frozen Resected Tissue


title: 91R replicate 3

description:
Replicate 3 of 4.91R
91R3


title: 18_11_miN-11

value: effective


title: 09_07_miL-7re


title: B-cells, rep1

source_name: B-cells

tag: strain background

value: B-cells


title: B-cells, rep2


title: Malignant Pleural Mesothelioma 4

value: Malignant Pleural Mesothelioma


title: Normal Paired Lung Parenchyma Tissue 4


title: Normal Paired Lung Parenchyma Tissue 3


title: Uninfected_0week_rep1

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

description:
Gene expression in the uninfected liver of C57BL/6 mice at 0 week
9254035024_H_0 week, Control (1)

hyb_protocol: Synthesized cRNA was hybridised to Illumina mouse Ref-8 v2 expression beadchips according to manufacturer instructions.

scan_protocol: Images on the arrays were scanned using Beadstation 500 at green factor level 2.

data_processing:
Feature extraction of the data was generated using GenomeStudio version 1.1.1 and analysed further using GeneSpring GX 11.
Non-normalised (Raw data) represent relative signal intensity; normalised data were normalised to the median of all samples and are presented in log2 scale.

source_name: Uninfected liver

label_protocol: cRNA was synthesised from total RNA using Illumina Total Prep RNA Amplication kit (Ambion).

growth_protocol: The complete life cycle of schistosoma japonicum was maintained in our laboratory. The cercarial of S. japonicum were shed from Oncomelania hupensis snail to infect the experimental mice.

extract_protocol: Total RNA of liver tissues were extracted by a combination use of Trizol (Invitrogen) and RNeasy Mini kit (Qiagen) method.

treatment_protocol: Mice were euthanised and whole liver from each experimental grouping were stored in Trizol reagent at -80C for RNA extraction.

value: Female

tag: age

value: 0 week

tag: infection

value: Non PZQ


title: 06_04_miN-4


title: 05_04_miL-4


title: Uninfected_0week_rep2

description:
Gene expression in the uninfected liver of C57BL/6 mice at 0 week
9257636048_H_0 week, Control (2)


title: 07_05_miL-5


title: 08_05_miN-5


title: 03_03_miL-3


title: Uninfected_PZQ_14weeks_rep1

description:
Gene expression in the PZQ-treated, uninfected liver of C57BL/6 mice at 14 weeks
9257636048_C_14 weeks, Control (1)

source_name: Uninfected liver, PZQ

value: 14 weeks

value: PZQ


title: Malignant Pleural Mesothelioma 2


title: Uninfected_PZQ_14weeks_rep3

description:
Gene expression in the PZQ-treated, uninfected liver of C57BL/6 mice at 14 weeks
9254035017_H_14 weeks, Control (3)


title: Adult CPC clones

city: Loma Linda

first: Mary

last: Kearns-Jonker

address: 25094 Daisy Ave

department: Anatomy

institute: Loma Linda University

description: Test

data_processing:
Data normalization and analysis was performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For normalization the average of 4 housekeeping genes (SNORD48, SNORD47, SNORD44, RNUG-2) was used.
The sabiosciences web-based software performs all statistical analysis and deltadeltaCt based fold-change calculations.
Fold change worksheet reports test/control  (i.e. Cardiovascular progenitor cells/human embryonic stem cell) and test/test  (i.e. adult cardiovascular progenitor cell clones/neonatal cardiovascular progenitor cell clones) ratios.

label: SYBER Green

source_name: Atrial Tissue, collagenase digested

label_protocol: PCR arrays were performed using the cell development & differentiation miRNA PCR array (SA Biosciences, Frederick, MD) following the Manufacturer's instructions.  Reverse transcription was performed using 200ng of total RNA with the RT2 miRNA First Strand Kit (SA Biosciences).  Quantitative real-time PCR were performed (IQ5, Bio-rad) with 40 cycles at 94oC for 15 seconds, 60oC for 60 seconds.

growth_protocol: Cells were grown in M199 media (Invitrogen, Grand Island, NY) supplemented with EGM-2 media (Invitrogen) at 5% CO2.

extract_protocol: Total RNA was extracted using Trizol Reagent Protocol.

value: Adult cardiovascular progenitor cell clones


title: hES-3 cells

description: Control

source_name: WiCell

value: Human Embryonic Stem Cell line


title: Malignant Pleural Mesothelioma 1


title: Normal Paired Lung Parenchyma Tissue 2

value: Normal Paired lung Parenchyma tissue


title: Uninfected_PZQ_13weeks_rep3

description:
Gene expression in the PZQ-treated, uninfected liver of C57BL/6 mice at 13 weeks
9254035017_E_13 weeks, Control (3)

value: 13 weeks


title: Infected_Non PZQ_14weeks_rep3

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 14 weeks post infection
9254035017_F_14 weeks, non PZQ (3)

source_name: Infected liver, non PZQ

value: S. japonicum


title: Uninfected_PZQ_14weeks_rep2

description:
Gene expression in the PZQ-treated, uninfected liver of C57BL/6 mice at 14 weeks
9254035003_F_14 weeks, Control (2)


title: 04_03_miN-3


title: 01_02_miL-2-2

value: tumor


title: 02_02_miN-2-2


title: Neonatal CPC clones

description: Test

value: Neonatal cardiovascular progenitor cell clones


title: Uninfected_PZQ_13weeks_rep1

description:
Gene expression in the PZQ-treated, uninfected liver of C57BL/6 mice at 13 weeks
9254035024_G_13 weeks, Control (1)

value: Liver


title: MC38 tumor cells isolated from tumor bearing livers of DT-treated CD11b DTR mice 2

city: Oxford

first: Su Yin

last: Lim

address: Old Road Campus Research Building

department: Oncology

country: United Kingdom

institute: University of Oxford

description:
DT2
Replicate 2

data_processing: The data was normalized and filtered to remove low and unexpressed probes using VSN (variance-stabilization and normalization) algorithm.

label: Biotin

source_name: MC38 tumor cell line

label_protocol: Standard Illumina labeling protocol

growth_protocol: Mice were injected with MC38 tumor cells into spleen to develop liver metastasis. Tumor bearing livers were collected 10 days after injection.

extract_protocol: MC38 tumor cells were isolated from tumor bearing livers by FACS sorting. RNA was extracted from the MC38 cells with Trizol reagent. Quality control was performed with Agilent Bioanalyser. cDNA was synthesized using the OligoDT based Illumina TotalPrep-96 Amplification Kit from Ambion according to manufacturer's protocol.

treatment_protocol: Mice were given PBS or DT via intraperitoneal injections on Day 7 and Day 9 after intrasplenic injection.

value: CD11bDTR transgenic

value: DT

tag: source tissue

value: liver

tag: tumor cell line


title: Malignant Pleural Mesothelioma 3

value: Malignant Pleural Mesothelioma

value: Frozen Resected Tissue


title: 91R replicate 2

description:
Replicate 2 of 4.91R
91R2

tag: strain

value: male

value: CONTROL

value: MUTANT


title: Infected_PZQ_14weeks_rep3

description:
Gene expression in the PZQ-treated liver of infected C57BL/6 mice at 14 weeks post infection
9254035017_G_14 weeks, PZQ (3)

source_name: Infected liver, PZQ

tag: gender

value: Female

value: 14 weeks

value: PZQ


title: Peyer's Patch high endothelial cells 1

city: Palo Alto

first: Eugene

middle: C.

last: Butcher

address: 3801 Miranda Avenue

department: Pathology

institute: Stanford School of Medicine

description: Transcriptional profiling of sorted mouse vascular endothelial cells from lymphoid tissue

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Mouse Exon 1.0 ST Arrays and scanned by Expression Analysis, Inc.

scan_protocol: Array scanning was performed by Expression Analysis, Inc. according to the manufacturer's instruction

data_processing: GeneSpring GX 12.6 and Partek Genomic Suite (6.6) were used for processing and analyzing the data. Genespring preprocessing and default normalization (RMA-16) was applied to each dataset.

source_name: equal male/female mix of adult (6-8 weeks old) Balb/c

label_protocol: Single-stranded cDNA was generated from amplified cRNA (using Ambion WT Expression Kit) and then fragmented/labeled with the Affymetrix GeneChip WT Terminal Labeling and Controls Kit, performed by Expression Analysis, Inc.

extract_protocol: Total RNA was isolated from sorted mouse lymphoid endothelial cells using Qiagen RNeasy Plus Micro kit following manufacturer’s protocol

value: Balb/c

value: 6-8 weeks

value: Peyer's Patch


title: Infected_PZQ_14weeks_rep2

description:
Gene expression in the PZQ-treated liver of infected C57BL/6 mice at 14 weeks post infection
9254035003_E_14 weeks, PZQ (2)

value: S. japonicum


title: MC38 tumor cells isolated from tumor bearing livers of DT-treated CD11b DTR mice 3

description:
DT3
Replicate 3


title: Normal Paired Lung Parenchyma Tissue 1

source_name: Normal Paired lung Parenchyma tissue

value: Normal Paired lung Parenchyma tissue


title: Infected_PZQ_14weeks_rep1

description:
Gene expression in the PZQ-treated liver of infected C57BL/6 mice at 14 weeks post infection
9257636048_B_14 weeks, PZQ (1)

value: Liver


title: Infected_Non PZQ_14weeks_rep1

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 14 weeks post infection
9257636048_A_14 weeks, non PZQ (1)

value: Non PZQ


title: MC38 tumor cells isolated from tumor bearing livers of DT-treated CD11b DTR mice 1

description:
DT1
Replicate 1

value: CD11bDTR transgenic

value: DT


title: Infected_Non PZQ_13weeks_rep3

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 13 weeks post infection
9254035017_C_13 weeks, non PZQ (3)

value: 13 weeks


title: Infected_Non PZQ_14weeks_rep2

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 14 weeks post infection
9254035003_D_14 weeks, non PZQ (2)


title: Uninfected_PZQ_13weeks_rep2

description:
Gene expression in the PZQ-treated, uninfected liver of C57BL/6 mice at 13 weeks
9254035003_C_13 weeks, Control (2)


title: MC38 tumor cells isolated from tumor bearing livers of PBS-treated CD11b DTR mice 3

description:
PBS3
Replicate 3

value: PBS

value: liver


title: MC38 tumor cells isolated from tumor bearing livers of PBS-treated CD11b DTR mice 1

description:
PBS1
Replicate 1


title: Uninfected_PZQ_10weeks_rep2

description:
Gene expression in the PZQ-treated, uninfected liver of C57BL/6 mice at 10 weeks
9257636048_G_10 weeks, Control (2)

value: 10 weeks


title: Infected_PZQ_13weeks_rep3

description:
Gene expression in the PZQ-treated liver of infected C57BL/6 mice at 13 weeks post infection
9254035017_D_13 weeks, PZQ (3)


title: Diet study with EE2 in liver of female largemouth bass, 0.2mg/kg EE2, replicate 4

city: Gainesville

first: Reyna

middle: Cristina

last: Colli-Dula

state: Florida

address: Mowry Drive 471

department: CEHT

institute: University of Florida

description:
0.2mg/kgEE2_04
Gene expression in liver of female LMB after 60 days of 0.2 mg/kg EE2 exposure.

hyb_protocol: Agilent protocol titled One-color microarrays-based  gene expression analysis (document no. G4140-90040 v6.5) was used.

scan_protocol: Scanned on an Agilent G2505B microarray scanner. Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range. Data extraction was performed using Agilent Feature Extraction software.

data_processing: Background-subtracted raw expression data (gProcessedSignal) were imported into JMP Genomics v5 (SAS, Cary, NC). During import, data were log2-transformed and all control and non-uniform spots were removed prior to the final analysis. Raw intensity data for each microarray were normalized by median centering before performing ANOVA. Differentially regulated transcripts were identified using a one-way analysis of variance (false discovery rate [FDR] = 5%).

organism: Micropterus salmoides

source_name: Liver, 60 d, 0.2mg/kg EE2

growth_protocol: Adult female largemouth bass (LMB) were purchased from American Sport Fish Hatchery (Montgomery, AL). Fish were acclimated in aerated 104–250 gallon fiberglass tanks under constant conditions in accordance with the NIH Guide for the Care and Use of Laboratory Animals for at least 1 week prior to the experiment within the Aquatic Toxicology Laboratory at the University of Florida Center for Environmental and Human Toxicology (CEHT).

extract_protocol: Total RNA was extracted from LMB samples using RNA STAT-60 (Tel-test, Friendswood, TX) according to the manufacturer's protocol.  RNA was reconstituted in RNAsecure (Ambion) and Dnase-1 treated with DNA-free Turbo (Ambion).

treatment_protocol: LMB were fed chemically treated floating pellets, in which 17alpha-ethinylestradiol (EE2) from Sigma Chemical Company (St. Louis, MO) was incorporated, 5 days per week for 60 days. Feed concentration was 0.2 mg/kg of EE2. Samples were randomly collected (n=5-10) from each EE2 treatment after 60 days of dietary exposure. Fish were euthanized by submersion in a water bath containing 50-110 ppm tricaine methanesulfonate (MS-222) and sacrificed by a sharp blow to the head, followed by cervical transection in accordance with the University of Florida's Institutional Animal Care and Use Committee (IACUC) guidelines. Fish were immediately flash frozen in liquid nitrogen, and stored at -80C until RNA was isolated. The above-mentioned dose of EE2 was selected based on the results of preliminary experiments performed in our lab and based on previous studies of physiological responses found in fish (Denslow et al., 2001; Schultz et al., 2001; Parrot and Blunt, 2005; Skillman et al., 2006; Martyniuk et al., 2007; Garcia-Reyero et al., 2009; Martyniuk et al., 2010).

value: female

tag: developmental stage

value: adult

tag: treatment duration

value: 60 days


title: Peyer's Patch high endothelial cells 2


title: Uninfected_PZQ_10weeks_rep1

description:
Gene expression in the PZQ-treated, uninfected liver of C57BL/6 mice at 10 weeks
9254035024_D_10 weeks, Control (1)

value: Female

value: PZQ


title: Peyer's Patch high endothelial cells 3

value: Balb/c

value: 6-8 weeks


title: MC38 tumor cells isolated from tumor bearing livers of PBS-treated CD11b DTR mice 2

description:
PBS2
Replicate 2


title: Infected_PZQ_13weeks_rep1

description:
Gene expression in the PZQ-treated liver of infected C57BL/6 mice at 13 weeks post infection
9254035024_F_13 weeks, PZQ (1)

value: S. japonicum


title: Infected_PZQ_13weeks_rep2

description:
Gene expression in the PZQ-treated liver of infected C57BL/6 mice at 13 weeks post infection
9254035003_B_13 weeks, PZQ (2)


title: Peyer's Patch capillary 1

value: Peyer's Patch


title: Infected_PZQ_10weeks_rep3

description:
Gene expression in the PZQ-treated liver of infected C57BL/6 mice at 10 weeks post infection
9254035017_A_10 weeks, PZQ (3)

value: Liver


title: peripheral lymph nodes capillary 2

value: peripheral lymph nodes


title: Diet study with EE2 in liver of female largemouth bass, 0.2mg/kg EE2, replicate 2

description:
0.2mg/kgEE2_02
Gene expression in liver of female LMB after 60 days of 0.2 mg/kg EE2 exposure.

label_protocol: Agilent protocol titled One-color microarrays-based  gene expression analysis (document no. G4140-90040 v6.5) was used.


title: Peyer's Patch capillary 3


title: peripheral lymph nodes high endothelial cells 1


title: Peyer's Patch capillary 2


title: peripheral lymph nodes high endothelial cells 4


title: Diet study with EE2 in liver of female largemouth bass, 0.2mg/kg EE2, replicate 3

description:
0.2mg/kgEE2_03
Gene expression in liver of female LMB after 60 days of 0.2 mg/kg EE2 exposure.


title: peripheral lymph nodes high endothelial cells 2


title: peripheral lymph nodes high endothelial cells 3


title: mesenteric lymph nodes high endothelial cells (MAdCAM1+) 4

value: mesenteric lymph nodes


title: Infected_Non PZQ_13weeks_rep1

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 13 weeks post infection
9254035024_E_13 weeks, non PZQ (1)

value: Non PZQ


title: Uninfected_PZQ_10weeks_rep3

description:
Gene expression in the PZQ-treated, uninfected liver of C57BL/6 mice at 10 weeks
9254035017_B_10 weeks, Control (3)


title: Infected_Non PZQ_13weeks_rep2

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 13 weeks post infection
9254035003_A_13 weeks, non PZQ (2)

value: 13 weeks


title: Stable

city: Nagoya

first: Kenta

last: IWASAKI

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Transplant Immunology

institute: Nagoya University School of Medicine

description: Each miRNA probe spottd in 4 well, and caluculate Median value.

hyb_protocol: The samples were incubated at 95 degree for 2 min and left the samples at room temperature.

scan_protocol: Apply the samples to plate chanber, wash several times, and scan the plate by GenePix4000B

data_processing:
The strength of fluorescence in each spot was measured by Array-Pro Analyzer Ver.4.5
Caluculate Net intensity by subtraction ((Raw intencity from each spots)-(Background))

source_name: PBMC

label_protocol: 1 ug total RNA were labeled with Hi-power labeling kit according manufactures protocol and dissolved into 350 ul Hybridization buffer.

extract_protocol: PBMCs were obtained from 5 ml whole blood by density gradient centrifugation using Ficoll-Paque (sigma). Combined same number of PBMCs in each group and Total RNA was isolated using miRNeasy Mini kit.

value: DSA (-), no rejection


title: Infected_Non PZQ_10weeks_rep3

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 10 weeks post infection
9254035003_H_10 weeks, non PZQ (3)


title: peripheral lymph nodes capillary 3

description: Transcriptional profiling of sorted mouse vascular endothelial cells from lymphoid tissue


title: Infected_PZQ_10weeks_rep2

description:
Gene expression in the PZQ-treated liver of infected C57BL/6 mice at 10 weeks post infection
9257636048_F_10 weeks, PZQ (2)


title: Potetial Risk

value: DSA (+), no rejection


title: mesenteric lymph nodes capillary 1


title: peripheral lymph nodes capillary 1


title: Infected_Non PZQ_6weeks_rep2

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 6 weeks post infection
9257636048_D_6 weeks p.i. (2)

value: 6 weeks


title: Diet study with EE2 in liver of female largemouth bass, 0.2mg/kg EE2, replicate 1

description:
0.2mg/kgEE2_01
Gene expression in liver of female LMB after 60 days of 0.2 mg/kg EE2 exposure.

value: liver

value: female


title: Infected_PZQ_10weeks_rep1

description:
Gene expression in the PZQ-treated liver of infected C57BL/6 mice at 10 weeks post infection
9254035024_C_10 weeks, PZQ (1)

value: 10 weeks


title: Infected_Non PZQ_10weeks_rep1

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 10 weeks post infection
9254035024_B_10 weeks, non PZQ (1)

value: Female


title: Infected_Non PZQ_6weeks_rep3

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 6 weeks post infection
9254035003_G_6 weeks p.i. (3)


title: CAMR

value: CAMR


title: mesenteric lymph nodes capillary 2

value: Balb/c


title: mesenteric lymph nodes high endothelial cells (MAdCAM1+) 3

value: 6-8 weeks


title: mesenteric lymph nodes high endothelial cells (MAdCAM1+/PNAd+) 1


title: Infected_Non PZQ_10weeks_rep2

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 10 weeks post infection
9257636048_E_10 weeks, non PZQ (2)

value: S. japonicum


title: mesenteric lymph nodes high endothelial cells (MAdCAM1+/PNAd+) 2


title: Infected_Non PZQ_6weeks_rep1

description:
Gene expression in the non PZQ-treated liver of infected C57BL/6 mice at 6 weeks post infection
9254035024_A_6 weeks p.i. (1)


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep4

status: Public on Aug 30 2014

city: Irvine

first: Arthur

middle: D

last: Lander

address: 2638 Biosciences 3

department: Developmental and Cell Biology

institute: University of California Irvine

description: Mutant

hyb_protocol: Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45C with rotation for 17 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array.  The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).  Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files

data_processing: These probe cell intensity files (.CEL) were analyzed  using Expression File Creator by GenePattern (Broad Insitute) using the RMA algorithm, quantile normalization and background correction.

source_name: Nipbl heterozygous E10.5 hindlimb buds

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip® WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence.  The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit.  10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.    The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual).  The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Embryos were dissected at day E10.5.

extract_protocol: Total RNA was extracted from hindlimbs of E10.5 mice using Qiagen's RNeasy mini kit with on-column DNA digestion.

treatment_protocol: Hindlimb limb buds (both right and left) were dissected from E10.5 wildtype and Nipbl+/- embryos

tag: genotype

value: Nipbl heterozygous

value: hindlimb buds


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep9

description: Mutant

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep10

description: Mutant


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep8

description: Mutant


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep12

description: Mutant


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep11

description: Mutant


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep3

description: Mutant


title: wildtype E10.5 hindlimb  buds, biological rep9

description: Control

source_name: wildtype E10.5 hindlimb buds

value: wildtype


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep5

description: Mutant


title: wildtype E10.5 hindlimb  buds, biological rep10

description: Control


title: wildtype E10.5 hindlimb  buds, biological rep7

description: Control


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep6

description: Mutant


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep1

description: Mutant


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep7

description: Mutant


title: wildtype E10.5 hindlimb  buds, biological rep12

description: Control


title: fr-1

city: Heidelberg

first: Manuel

last: Roehrich

state: Baden-Württemberg

address: INF 280

department: Molecular Radiation Oncology

country: Germany

institute: DKFZ Heidelberg

description: mRNA expression human glioblastoma stem cell like cells 6 h after treatment (treated with FG-3019 and irradiation)

hyb_protocol: 500 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (GPL 10332) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 014850_D_20060807).

data_processing: Data was quantile normalized with ChipSkipper Table Butler and SUMO software (http://angiogenesis.dkfz.de/oncoexpress/software/index.htm).

source_name: NMA 23_treated with FG-3019 + irradiation_6 hrs

label_protocol: 500 ng of total RNA were labeled with Cyanin-3 using the Agilent Low RNA Input Linear Amplification Kit following the detailed protocol described in the user´s manual.

growth_protocol: NMA-23 cells were maintained in their undifferentiated state using Neurobasal Media supplemented with epidermal growth factor and basic fibroblast growth factor (each at 10 μg/500 mL media), sodium pyruvate, glutamine, B27 supplement, non-essential amino acids and penicillin/ streptomycin (Gibco, Grand Island, NY). NMA 23 cells were maintained at 37C in a humidified incubator with 5% CO2

extract_protocol: 6 h after treatment exposures, CSLCs cells were solubilized and homogenized in TRIzol (Invitrogen, Carlsbad, CA). Total RNA was isolated according to the manufacturer´s instruction and purity and integrity of the RNA was assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: NMA-23 were treated with FG-3019 (30 μg/ml)  and/or irradiated with 4 Gy with 6 MV X-rays (Mevatron, Siemens, Erlangen, Germany) at a dose rate of 2,5 Gy/min. Then, the cultures were incubated for 6 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

tag: cell type

value: glioblastoma stem cell like cells

tag: treated with

value: FG-3019 + irradiation for 6hrs


title: Nipbl heterozygous E10.5 hindlimb buds, biological rep2

description: Mutant


title: wildtype E10.5 hindlimb  buds, biological rep8

description: Control


title: wildtype E10.5 hindlimb  buds, biological rep11

description: Control


title: wildtype E10.5 hindlimb  buds, biological rep5

description: Control


title: wildtype E10.5 hindlimb  buds, biological rep6

description: Control


title: fr-3


title: rt-1

description: mRNA expression human glioblastoma stem cell like cells 6 h after treatment (treated with irradiation)

source_name: NMA 23_treated with irradiation_6 hrs

value: irradiation for 6hrs


title: 8-3 (Parg C-3)

city: Logan

first: Ralph

middle: G

last: Meyer

address: 4700 Old Main Hill

department: School of Veterinary Medicine

institute: Utah State University

hyb_protocol: standard Affymetrix methods

scan_protocol: standard Affymetrix methods

data_processing: Gene expression profiles of individual embryos were generated by hybridization of the amplified cDNA to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix).  Gene expression data, as well as tiling microarray data (see below), were analyzed using Partek® Genomics SuiteTM software. Copyright, Partek Inc., St. Louis, MO.  Raw intensities were subjected to background correction, quantile normalization, log2 transformation and probe set summarization with the RMA (Robust Multichip Average) method.

source_name: 2-cell embryo

label_protocol: standard Affymetrix methods

growth_protocol: Natural mating

extract_protocol: RNA from individual embryos was isolated and amplified using the WT-Ovation One-Direct RNA Amplification kit (NuGen Technologies)

treatment_protocol: Genetic disruption of the Parg gene (Parg(110)-/-) in sires, wt mothers, embryos are heterozygous for deletion of exons 2 and 3 (Parg(110)-/+)

tag: father

value: 2-cell embryo

tag: background strain

value: 129SVE (=129S6/SvEvTac, Taconic)


title: fg-2

description: mRNA expression human glioblastoma stem cell like cells 6 h after treatment (treated with FG-3019)

source_name: NMA 23_treated with FG-3019_6 hrs

value: FG-3019 for 6hrs


title: fr-2


title: wildtype E10.5 hindlimb  buds, biological rep3

description: Control


title: 7-2 (Parg B-2)


title: ctrl-3

description: mRNA expression human glioblastoma stem cell like cells 6 h after treatment (untreated)

source_name: NMA 23_untreated_6 hrs

value: none for 6h (untreated control)


title: fg-1


title: rt3


title: wildtype E10.5 hindlimb  buds, biological rep4

description: Control


title: 7-1 (Parg B-1)


title: ctrl-2


title: rt2


title: wildtype E10.5 hindlimb  buds, biological rep2

description: Control


title: wildtype E10.5 hindlimb  buds, biological rep1

description: Control


title: WT_3-2

value: Wild-type


title: fg-3


title: 8-2 (Parg C-2)


title: 7-3 (Parg B-3)


title: WT_2-2


title: WT_2-1


title: WT_2-3


title: 8-1 (Parg C-1)