title: ET 4_D12

description: Gene expression array


title: ET 4_A03

status: Public on Mar 31 2015

type: RNA

city: New York

first: Mike

last: Harr

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial Sloan-Ketering Cancer Center

description: Gene expression array

hyb_protocol: Please see Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (http://www.affymetrix.com/support/technical/byproduct.affx?product=amplification)

data_processing: RMA : log2 transromation : quantile normalization : median polish using Partek GS version 6.5

label: Biotin

molecule: total RNA

organism: Homo sapiens

extract_protocol: Extracted using Trizol according to manufacturure's recommendations

treatment_protocol: de novo MPN patients

tag: disease status

value: ET


title: ET 4_E11

description: Gene expression array

scan_protocol: Please see Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (http://www.affymetrix.com/support/technical/byproduct.affx?product=amplification)


title: AMM 4_C05

description: Gene expression array

label_protocol: Please see Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (http://www.affymetrix.com/support/technical/byproduct.affx?product=amplification)

value: AMM


title: ET 4_G03

description: Gene expression array


title: AMM H05

description: Gene expression array


title: ET 4_A08

description: Gene expression array


title: ET A01

description: Gene expression array


title: AMM G08

description: Gene expression array


title: ET 4_E08

description: Gene expression array


title: ET 4_G06

description: Gene expression array


title: ET 4_G05

description: Gene expression array


title: ET 4_B07

description: Gene expression array


title: ET 4_B06

description: Gene expression array


title: PV G06

description: Gene expression array

value: PV


title: PV G03

description: Gene expression array


title: PV G05

description: Gene expression array


title: ET 4_C09

description: Gene expression array


title: AMM H04

description: Gene expression array


title: AMM G11

description: Gene expression array


title: ET 4_E06

description: Gene expression array


title: Normal F08

description: Gene expression array

value: Normal


title: AMM F11

description: Gene expression array


title: PV E05

description: Gene expression array


title: AMM E02

description: Gene expression array


title: Normal F04

description: Gene expression array


title: PV E11

description: Gene expression array


title: ET D09

description: Gene expression array


title: Root_4hrs

city: Dallas

first: Roel

last: Rabara

state: Texas

address: 17360 Coit Road

institute: Texas A&M AgriLife Research

description:
Root_4hrs_rep1
Root_4hrs_rep2
Root_4hrs_rep3

hyb_protocol: NimbleGen expression array hybridization using NimbleGen Hybridization Kit.

scan_protocol: NimbleGen MS-200 scanner with auto-gain - 2um scan

data_processing: NimbleScan v. 2.6

organism: Nicotiana tabacum

source_name: Root, Dehydrated for 4 hrs

label_protocol: total RNA was amplified using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Ref. 11917-020).  Amplified product was labeled using NimbleGen DNA Labeling Kit.

growth_protocol: Tobacco cv Burley 21 were germinated in half-strength MS agar medium and transferred to container with half-strength MS liquid medium in a growth chamber with constant light and 25oC temperature.

extract_protocol: Total RNA was isloated for both tissues using Qiagen RNAeasy Mini Kit.

treatment_protocol: After two weeks, seedlings were subjected to dehydration by removing them from their container without touching the plants and air dry  the plants at different time points. Leaves and Roots were harvested and flash freezing in liquid nitrogen. Twenty plants were utilized for each replicate to ensure enough materials were harvested for the roots. Three biological replicates were made for each dehydration time point.

tag: cultivar

value: Burley 21

tag: tissue

value: Root

tag: stress

value: dehydrated

tag: time

value: 4 hrs


title: Normal F05

description: Gene expression array


title: Normal G02

description: Gene expression array


title: Leaf_2hrs

description:
Leaf_2hrs_rep1
Leaf_2hrs_rep2
Leaf_2hrs_rep3

source_name: Leaf, Dehydrated for 2 hrs

value: Leaf

value: 2 hrs


title: Root_0min

description:
Root_0min_rep1
Root_0min_rep2
Root_0min_rep3

source_name: Root, unstressed

value: unstressed

value: control


title: Normal F01

description: Gene expression array


title: PV F06

description: Gene expression array


title: AMM D10

description: Gene expression array


title: AMM E03

description: Gene expression array


title: Root_1hr

description:
Root_1hr_rep1
Root_1hr_rep2
Root_1hr_rep3

source_name: Root, Dehydrated for 1 hr

value: 1 hr


title: Root_20min

description:
Root_20min_rep1
Root_20min_rep2
Root_20min_rep3

source_name: Root, Dehydrated for 20 min

value: 20 min


title: AMM F02

description: Gene expression array


title: Leaf_0min

description:
Leaf_0min_rep1
Leaf_0min_rep2
Leaf_0min_rep3

source_name: Leaf, unstressed


title: Leaf_1hr

description:
Leaf_1hr_rep1
Leaf_1hr_rep2
Leaf_1hr_rep3

source_name: Leaf, Dehydrated for 1 hr


title: PV E04

description: Gene expression array


title: AMM D07

description: Gene expression array


title: AMM E01

description: Gene expression array


title: PV D05

description: Gene expression array


title: Leaf_40min

description:
Leaf_40min_rep1
Leaf_40min_rep2
Leaf_40min_rep3

source_name: Leaf, Dehydrated for 40 min

value: 40 min


title: Root_2hrs

description:
Root_2hrs_rep1
Root_2hrs_rep2
Root_2hrs_rep3

source_name: Root, Dehydrated for 2 hrs


title: Leaf_4hrs

description:
Leaf_4hrs_rep1
Leaf_4hrs_rep2
Leaf_4hrs_rep3

source_name: Leaf, Dehydrated for 4 hrs


title: Root_40min

description:
Root_40min_rep1
Root_40min_rep2
Root_40min_rep3

source_name: Root, Dehydrated for 40 min


title: AMM C03

description: Gene expression array


title: ET D08

description: Gene expression array


title: PV D04

description: Gene expression array


title: AMM A08

description: Gene expression array


title: AMM C06

description: Gene expression array


title: Leaf_20min

description:
Leaf_20min_rep1
Leaf_20min_rep2
Leaf_20min_rep3

source_name: Leaf, Dehydrated for 20 min


title: PV C10

description: Gene expression array


title: Normal A06

description: Gene expression array


title: Normal D02

description: Gene expression array


title: Normal A12

description: Gene expression array


title: PV C12

description: Gene expression array


title: PV A11

description: Gene expression array


title: Normal B04

description: Gene expression array


title: PV A04

description: Gene expression array


title: p_F1_d7_96

city: Bogota

first: Carolina

last: Pardo-Diaz

address: Carrera 24 # 63C-69

department: Programa de Biología

country: Colombia

institute: Universidad del Rosario

description:
MA_96
The sample comes from pupal wings.

hyb_protocol: Hybridization was performed in the FlyChip Genomics Facility (Cambridge, United Kingdom) following NimbleGen standard operating protocol.

scan_protocol: Scanning was performed in the FlyChip Genomics Facility (Cambridge, United Kingdom) following their standard operating protocol.

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: Heliconius melpomene plesseni

source_name: Proximal forewing, day 7, plesseni

label_protocol: Labeling was performed in the FlyChip Genomics Facility (Cambridge, United Kingdom) following NimbleGen standard operating protocol.

extract_protocol: Total RNA was isolated with hybrid TRIzol (Invitrogen)/RNeasy (Qiagen) protocol where wings were homogenized in TRIzol and then RNA was extracted by adding 0.2 volumes of chloroform and one volume of 70% ethanol to the aqueous layer. The RNA was subsequently purified using the RNeasy purification column (Qiagen) and DNase treated with the DNA-free kit (Ambion).

treatment_protocol: The wing tissue was stored in RNAlater at -80°C until RNA extractions were performed.

tag: race

value: plesseni

value: proximal forewing

tag: developmental stage

value: day 7


title: AMM A03

description: Gene expression array

value: AMM


title: m_F1_d7_91

description:
MA_91
The sample comes from pupal wings.

organism: Heliconius melpomene malleti

source_name: Proximal forewing, day 7, malleti

value: malleti


title: p_F2_d7_94

description:
MA_94
The sample comes from pupal wings.

source_name: Distal forewing, day 7, plesseni

value: distal forewing


title: p_F1_d7_92

description:
MA_92
The sample comes from pupal wings.


title: AMM C11

description: Gene expression array


title: Normal A07

description: Gene expression array

value: Normal


title: Normal A09

description: Gene expression array


title: p_Eye_d5_90

description:
MA_90
The sample comes from pupal eyes.

source_name: Eye, day 5, plesseni

value: eye

value: day 5


title: p_F2_d5_88

description:
MA_88
The sample comes from pupal wings.

source_name: Distal forewing, day 5, plesseni


title: m_F2_d7_93

description:
MA_93
The sample comes from pupal wings.

source_name: Distal forewing, day 7, malleti


title: m_F1_d5_85

description:
MA_85
The sample comes from pupal wings.

source_name: Proximal forewing, day 5, malleti


title: m_F2_d5_87

description:
MA_87
The sample comes from pupal wings.

source_name: Distal forewing, day 5, malleti


title: p_F1_d3_84

description:
MA_84
The sample comes from pupal wings.

source_name: Proximal forewing, day 3, plesseni

value: day 3


title: p_F2_d5_86

description:
MA_86
The sample comes from pupal wings.


title: D9

type: genomic

city: Miami

first: John

last: Gilbert

state: FL

address: 1535 NW 10th Ave

department: John P. Hussman Institute for Human Genomics

institute: University of Miami

description: post-mortem brain tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing: Sample analysis was done according to the Illumina protocol; The unmethylated and methylated signal intensities are located on the series level and in the .idat files.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: temporal pole_dementia_with_lewy_bodies

label_protocol: Sample preparation were done according to the Illumina protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: disease

value: Dementia with Lewy Bodies

value: brain

tag: brain region

value: temporal pole

tag: gender

value: Male


title: p_Eye_d3_82

description:
MA_82
The sample comes from pupal eyes.

source_name: Eye, day 3, plesseni


title: m_Eye_d5_89

description:
MA_89
The sample comes from pupal eyes.

source_name: Eye, day 5, malleti


title: m_Eye_d3_81

description:
MA_81
The sample comes from pupal eyes.

source_name: Eye, day 3, malleti


title: p_F1_d3_80

description:
MA_80
The sample comes from pupal wings.


title: D7

description: post-mortem brain tissue


title: D3

description: post-mortem brain tissue


title: D5

description: post-mortem brain tissue


title: m_F1_d3_83

description:
MA_83
The sample comes from pupal wings.

source_name: Proximal forewing, day 3, malleti


title: m_F1_d3_79

description:
MA_79
The sample comes from pupal wings.


title: p_F1_d1_78

description:
MA_78
The sample comes from pupal wings.

source_name: Proximal forewing, day 1, plesseni

value: day 1


title: D8

description: post-mortem brain tissue


title: m_F1_d1_77

description:
MA_77
The sample comes from pupal wings.

source_name: Proximal forewing, day 1, malleti


title: p_F1_d1_76

description:
MA_76
The sample comes from pupal wings.


title: m_F1_d1_75

description:
MA_75
The sample comes from pupal wings.


title: D4

description: post-mortem brain tissue


title: D1

description: post-mortem brain tissue


title: p_Eye_d1_74

description:
MA_74
The sample comes from pupal eyes.

source_name: Eye, day 1, plesseni


title: m_Eye_d1_73

description:
MA_73
The sample comes from pupal eyes.

source_name: Eye, day 1, malleti


title: m_F2_d7_71

description:
MA_71
The sample comes from pupal wings.


title: D10

description: post-mortem brain tissue


title: P5 EM 2

city: Paterna

first: Estéfani

last: García-Ríos

state: Valencia

address: Avenue Agustín Escardino, 7

department: Biotechnology

country: Spain

institute: Institute of Agrochemistry and Food Technology (IATA-CSIC)

hyb_protocol: The hybridization mixture was prepared according to the Affymetrix protocol. Each sample was hybridized to a GeneChip Yeast Genome 2.0 Array (Affymetrix).

scan_protocol: Arrays were washed and stained in a Fluidics Station 450 and scanned in a GeneChip Scanner 3000 (both Affymetrix) according to the manufacturer’s recommendations.

data_processing:
CEL files were generated from DAT files using the GCOS software (Affymetrix). To generate the log2 expression estimates, overall array intensity was normalized between arrays and the probe intensity of all probes in a probe set was summarized to a single value with the RMA (Robust Multichip Average) algorithm (Irizarry et al, 2003) in Genomics Suite 6.6 (Partek).
Log2 ratios were used to calculate the differential expression between strains. The genes with at least 2-fold differences in the transcript levels (log2ratio was <-1 or >1) between strains were tested. Genes were considered to have a significant differential expression if the p-values of the Student’s t-test were <0.05 after applying the Benjamini and Hochberg (BH) method to adjust for the false discovery rate (FDR) (Benjamini and Hochberg, 1995). To group genes into functional categories, the GO term Finder in the MIPS Functional Catalog was used (http://mips.helmholtz-muenchen.de/funcatDB/).

organism: Saccharomyces cerevisiae

source_name: P5 evolved strain growing at 12ºC

label_protocol: RNA expression profiling was performed following the Pico Profiling method (Gonzalez-Roca et al, 2010). Briefly, cDNA library preparation and amplification were carried out from 25 ng total RNA using WTA2 (Sigma-Aldrich) with 17 amplification cycles. Eight µg of cDNA were subsequently fragmented by DNaseI and biotinylated by terminal transferase obtained from the GeneChip Mapping 250K Nsp Assay Kit (Affymetrix).

growth_protocol: Yeast cells (108 cells/mL) were collected in the exponential growth phase during fermentation at 12 ºC from three independently cultured replicates

extract_protocol: RNA was isolated as described by Sierkstra et al. (1992) and was re-suspended in 50 µL of DEPC-treated water. Total RNA suspensions were purified by the High Pure Isolation kit (Roche Applied Science, Germany) according to the manufacturer’s instructions. Solutions and equipment were treated so that they were RNase-free, as outlined in Sambrook et al. (1989).

tag: growth temperature

tag: sample group

value: evolved strain

tag: growth phase


title: P5 EM 3

value: exponential growth phase during fermentation at 12 ºC


title: p_F2_d7_72

description:
MA_72
The sample comes from pupal wings.

source_name: Distal forewing, day 7, plesseni

value: plesseni


title: p_Eye_d7_68

description:
MA_68
The sample comes from pupal eyes.

source_name: Eye, day 7, plesseni


title: P5 EM 1


title: p_F1_d7_70

description:
MA_70
The sample comes from pupal wings.

source_name: Proximal forewing, day 7, plesseni

value: proximal forewing


title: AD7

description: post-mortem brain tissue

source_name: temporal pole_Alzheimer's

value: Alzheimer's Disease


title: AD8

description: post-mortem brain tissue


title: m_Eye_d7_67

description:
MA_67
The sample comes from pupal eyes.

source_name: Eye, day 7, malleti

value: day 7


title: m_F1_d7_95

description:
MA_95
The sample comes from pupal wings.

source_name: Proximal forewing, day 7, malleti

value: malleti


title: P5 3

source_name: P5 strain growing at 12ºC


title: m_F1_d7_69

description:
MA_69
The sample comes from pupal wings.


title: P5 1


title: AD4

description: post-mortem brain tissue


title: m_Hw_d5_65

description:
MA_65
The sample comes from pupal wings.

source_name: Hindwing, day 5, malleti

value: hindwing


title: p_Hw_d5_66

description:
MA_66
The sample comes from pupal wings.

source_name: Hindwing, day 5, plesseni


title: AD5

description: post-mortem brain tissue


title: Mouse 6h Penumbra 4

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

organism: Mus musculus

source_name: 6h Saline Ischemia Penumbra Cy3

label_protocol: Manual:  Low Input Quick Amp Labeling Kit, Two-Color  (Agilent)

growth_protocol: Animal care and experimental procedures were used as approved by the Institutional Animal Care and Use Committee of Showa University (School of Medicine), Tokyo, Japan. Thirty male mice (C57BL/6J) of 9-weeks-old (25 ~ 35 g body weight) were purchased from Charles River (Kanagawa, Japan). Mice were housed at the Animal Institution in Showa University in acrylic cages (8 mice/cage) maintained at 23 ºC with a standard 12 h light/dark cycle, optimum humidity, and temperature control. Animals were given access to tap water and laboratory chow ad libitum

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Mice were first anesthetized with 4% sevoflurane (induction) and 2 % sevoflurane (maintenance) in a 30% O2 and 70% N2O gas mixture via a face mask, followed by an incision in the cervical skin, opening of salivary gland, resulting in visualization of the right common carotid artery. A midline cervical incision was made to expose the external carotid artery, and using intraluminal filament technique the PMCAO model was generated. PACAP38 (1 l containing 1 pmol) or 1 µl of saline (0.9% NaCl, as control) was injected intracerebroventrically, immediately after PMCAO. PACAP38 (Peptide Institute Inc., Osaka, Japan; supplier temperature was -20 ºC) was dissolved at 10-5M concentration by saline, and stored at -80 ºC. PACAP test solution (for injection) was diluted ×10 times with 0.9% NaCl just before use. After injections, the animals were returned to their cages. A total of four groups were prepared

tag: strain

value: ischemia penumbra

source_name: 6h Saline Healthy Penumbra Cy5

value: healthy penumbra


title: AD3

description: post-mortem brain tissue


title: Mouse 6h Penumbra 3

source_name: 6h Saline Healthy Penumbra Cy3

source_name: 6h Saline Ischemia Penumbra Cy5


title: p_F1_d5_64

description:
MA_64
The sample comes from pupal wings.

source_name: Proximal forewing, day 5, plesseni

value: day 5


title: Mouse 6h Ischemia Core 2

source_name: 6h Saline Ischemia Core Cy3

value: ischemia core

source_name: 6h Saline Healthy Core Cy5

value: healthy core


title: m_F1_d5_63

description:
MA_63
The sample comes from pupal wings.

source_name: Proximal forewing, day 5, malleti


title: P5 2


title: AD10

description: post-mortem brain tissue

value: brain


title: Mouse 6h Ischemia Core 1

source_name: 6h Saline Healthy Core Cy3

source_name: 6h Saline Ischemia Core Cy5


title: AD1

description: post-mortem brain tissue

value: temporal pole


title: AD2

description: post-mortem brain tissue

value: Male


title: p_Eye_d3_60

description:
MA_60
The sample comes from pupal eyes.

source_name: Eye, day 3, plesseni

value: eye

value: day 3


title: recA730_vs_recA730,dcd

city: Warszawa

first: Iwona

last: Fijalkowska

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics

hyb_protocol: Labeled probes were hybridized to E. coli Gene Expression Microarray, 8x15K (catalog no. G4813A-020097) using Gene Expression Hybridization Kit, Hybridization Chamber and Hybridization oven (all from Agilent) for 17 hours at 65°C.

scan_protocol: After washing using Gene Expression Wash Buffer Set (Agilent) the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5μm and 100% laser power. PMT gain was set to around 600 and 750 for 532 nm and 635 nm excitation respectively with minor adjustments to normalize images. Feature extraction was done using GenePix Pro 6.1 (Molecular Devices, USA).

data_processing: GPR files were analyzed further with Acuity 4.0 software (Molecular Devices, USA) starting with lowess normalization. Normalized log2 ratio data from biological replicates and technical replicates (dye swap) were averaged and the statistical significance (p-value) was calculated.

organism: Escherichia coli

source_name: bacterial cells grown to OD600=0.5

label_protocol: cRNA labeling was performed with the use of FairPlay III Microarray Labeling Kit (Agilent Technologies) and CyDye Cy5 and Cy3 mono-reactive dyes (GE Healthcare), according to the manufacturer’s protocol.

growth_protocol: Bacterial strains were grown in LB. Overnight cultures were diluted 1:100 in fresh LB and grown at 37°C with shaking to an OD600 = 0.5.

extract_protocol: RNA was isolated using the RNeasy Protect Bacteria Mini Kit (Qiagen), following manufacturer's instructions.

value: MC4100 derivative, recA730

value: MC4100 derivative, recA730, dcd::kan


title: m_Eye_d3_59

description:
MA_59
The sample comes from pupal eyes.

source_name: Eye, day 3, malleti


title: hMSC cells expressing EWS-FLI1 (+EF), biological rep #2

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

description: Exogenous expression of EWS-FLI1.

hyb_protocol: Approximately 5.5ug of labeled DNA target was hybridized to the Affymetrix GeneChip Human Exon 1.0 ST Array at 45C for 16 hours, per manufacturer's recommendation. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) on an Affymetrix GeneChip Scanner 7G Plus.

data_processing:
All data processing was done in the R programming environment using Bioconductor packages. Intensity values stored in CEL format files were normalized and background-corrected using RMA, followed by batch correction using ComBat.
Probe group file: HuEx-1_0-st-v2.r2.pgf

label: biotin

source_name: Human mesenchymal stem cells (hMSC) cells, +EF

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

growth_protocol: Ewing's sarcoma cell lines TC32 and A673i were grown in 10% fetal bovine serum in RPMI at 37°C in 5% CO2 and passaged every 3 to 4 days. Human mesenchymal stem cells (hMSC) were obtained from Lonza (Walkersville, MD, USA) and maintained according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein kit from each of the derived cell lines (with/without EWS-FLI1), according to the manufacturer’s instructions. The RNA quality was measured using Agilent 2100 Bioanalyzer, and RNA Integrity number (RIN) above 9.60 were used for Exon array experiments.

treatment_protocol: TC32 and A673i RNA were collected from wild-type cells, as well as from cells with reduced EWS-FLI1 expression. TC32 EWS-FLI1 expression was reduced using lentiviral transient shFli1, and A673i EWS-FLI1 expression was reduced using an inducible construct. Expression of EWS-FLI1 was induced in hMSC cells using a retroviral vector.

tag: cell type

value: mesenchymal stem cells

tag: ews-fli1 expression

value: +EF


title: hMSC cells expressing EWS-FLI1 (+EF), biological rep #3

description: Exogenous expression of EWS-FLI1.


title: WT_vs_dcd

value: MC4100 derivative

value: MC4100 derivative, dcd::kan


title: p_F1_d5_62

description:
MA_62
The sample comes from pupal wings.

value: plesseni

value: proximal forewing


title: hMSC wild-type cells not expressing EWS-FLI1 (-EF), biological rep #2

description: Wild-type

source_name: Human mesenchymal stem cells (hMSC) cells, WT

value: -EF


title: m_F2_d5_61

description:
MA_61
The sample comes from pupal wings.

source_name: Distal forewing, day 5, malleti

value: malleti

value: distal forewing

value: day 5


title: hMSC cells expressing EWS-FLI1 (+EF), biological rep #1

description: Exogenous expression of EWS-FLI1.


title: A673i wild-type cells expressing EWS-FLI1 (+EF), biological rep #1

description: Wild-type

source_name: Ewing's sarcoma A673i, WT

tag: cell line

value: Ewing's sarcoma cell line


title: hMSC wild-type cells not expressing EWS-FLI1 (-EF), biological rep #3

description: Wild-type


title: recA730_vs_recA730,ndk

value: MC4100 derivative, recA730, ndk::cam


title: WT_vs_ndk

value: MC4100 derivative, ndk::cam


title: m_Hw_d3_57

description:
MA_57
The sample comes from pupal wings.

source_name: Hindwing, day 3, malleti

value: hindwing


title: A673i wild-type cells expressing EWS-FLI1 (+EF), biological rep #3

description: Wild-type


title: p_Hw_d3_58

description:
MA_58
The sample comes from pupal wings.

source_name: Hindwing, day 3, plesseni

value: day 3


title: A673i doxycycline-inducible shRNA reduction of EWS-FLI1 (-EF), biological rep #2

description: sh EWS-FLI1

source_name: Ewing's sarcoma A673i, shEF


title: TC32 cells with shRNA reduction of EWS-FLI1 (-EF), biological rep #2

description: sh EWS-FLI1

source_name: Ewing's sarcoma TC32, shEF


title: WT_vs_recA730

value: MC4100 derivative, recA730


title: A673i doxycycline-inducible shRNA reduction of EWS-FLI1 (-EF), biological rep #3

description: sh EWS-FLI1


title: A673i wild-type cells expressing EWS-FLI1 (+EF), biological rep #2

description: Wild-type


title: A673i doxycycline-inducible shRNA reduction of EWS-FLI1 (-EF), biological rep #1

description: sh EWS-FLI1


title: Technical replicate to sample 7668610068_R02C01 (SAMPLE 29)

city: Vejle

first: Anders

last: Bojesen

address: Kabbeltoft 25

department: Department of Clinical Genetics

country: Denmark

institute: Vejle Hospital

description:
SAMPLE 59
Sample name: 9297962144_R05C02

hyb_protocol: Illumina Infinium HumanMethylation450 Beadchip Kit standard protocol (Illumina Inc., San Diego, CA, USA)

scan_protocol: Beadchips were scanned with an Illumina HiScanSQ scanner using standard settings

data_processing: Initial quality control, background subtraction and raw data normalization were done using the standard algorithms provided in Illumina Genome studio Methylation module v1.0.

source_name: chorionic villus

extract_protocol: QIAamp DNA Mini kit (QIAGEN Inc., Valencia, CA, USA)

tag: individual

value: male fetus

value: chorionic villus

tag: pregnancy

value: trisomy 21


title: m_F2_d1_53

description:
MA_53
The sample comes from pupal wings.

source_name: Distal forewing, day 1, malleti

tag: tissue

value: day 1


title: TC32 cells with shRNA reduction of EWS-FLI1 (-EF), biological rep #3

description: sh EWS-FLI1


title: TC32 cells with shRNA reduction of EWS-FLI1 (-EF), biological rep #1

description: sh EWS-FLI1


title: p_F2_d1_54

description:
MA_54
The sample comes from pupal wings.

source_name: Distal forewing, day 1, plesseni


title: p_F2_d3_56

description:
MA_56
The sample comes from pupal wings.

source_name: Distal forewing, day 3, plesseni


title: hMSC wild-type cells not expressing EWS-FLI1 (-EF), biological rep #1

description: Wild-type

value: mesenchymal stem cells


title: Technical replicate to sample 8795207029_R02C02 (SAMPLE 15)

description:
SAMPLE 58
Sample name: 9297962144_R04C02

label_protocol: Illumina Infinium HumanMethylation450 Beadchip Kit standard protocol (Illumina Inc., San Diego, CA, USA)

value: normal pregnancy


title: m_Eye_d1_51

description:
MA_51
The sample comes from pupal eyes.

source_name: Eye, day 1, malleti

value: eye


title: Technical replicate to sample 8795207029_R03C02 (SAMPLE 27)

description:
SAMPLE 60
Sample name: 9297962144_R06C02


title: Technical replicate to sample 7668610068_R01C01 (SAMPLE 17)

description:
SAMPLE 57
Sample name: 9297962144_R03C02


title: p_Eye_d1_52

description:
MA_52
The sample comes from pupal eyes.

source_name: Eye, day 1, plesseni

value: plesseni


title: TC32 wild-type cells expressing EWS-FLI1 (+EF), biological rep #2

description: Wild-type

source_name: Ewing's sarcoma TC32, WT

value: +EF


title: m_Hw_d1_49

description:
MA_49
The sample comes from pupal wings.

source_name: Hindwing, day 1, malleti

value: malleti


title: p_Hw_d7_48

description:
MA_48
The sample comes from pupal wings.

source_name: Hindwing, day 7, plesseni

value: day 7


title: m_Eye_d7_45

description:
MA_45
The sample comes from pupal eyes.

source_name: Eye, day 7, malleti


title: p_Hw_d7_44

description:
MA_44
The sample comes from pupal wings.


title: m_Hw_d7_47

description:
MA_47
The sample comes from pupal wings.

source_name: Hindwing, day 7, malleti


title: m_Hw_d7_43

description:
MA_43
The sample comes from pupal wings.


title: TC32 wild-type cells expressing EWS-FLI1 (+EF), biological rep #1

description: Wild-type

value: Ewing's sarcoma cell line


title: m_F2_d3_55

description:
MA_55
The sample comes from pupal wings.

source_name: Distal forewing, day 3, malleti

value: distal forewing


title: p_Eye_d7_46

description:
MA_46
The sample comes from pupal eyes.

source_name: Eye, day 7, plesseni


title: p_F2_d5_42

description:
MA_42
The sample comes from pupal wings.

source_name: Distal forewing, day 5, plesseni

value: day 5


title: p_Hw_d5_40

description:
MA_40
The sample comes from pupal wings.

source_name: Hindwing, day 5, plesseni

value: hindwing


title: m_Hw_d5_39

description:
MA_39
The sample comes from pupal wings.

source_name: Hindwing, day 5, malleti


title: Technical replicate to sample 7668610068_R04C02 (SAMPLE 6)

description:
SAMPLE 55
Sample name: 9297962144_R01C02

source_name: maternal whole blood

extract_protocol: Standard salt extraction method.

value: Female

value: maternal whole blood


title: p_Hw_d1_50

description:
MA_50
The sample comes from pupal wings.

source_name: Hindwing, day 1, plesseni


title: chorionic_villus_trisomy13_rep5

description:
SAMPLE 53
Sample name: 9297962141_R05C02

source_name: chorionic villus

value: male fetus

value: trisomy 13


title: p_Eye_d5_38

description:
MA_38
The sample comes from pupal eyes.

source_name: Eye, day 5, plesseni


title: p_Hw_d3_36

description:
MA_36
The sample comes from pupal wings.

source_name: Hindwing, day 3, plesseni

value: day 3


title: Technical replicate to sample 8795207029_R01C02 (SAMPLE 3)

description:
SAMPLE 56
Sample name: 9297962144_R02C02


title: chorionic_villus_trisomy13_rep6

description:
SAMPLE 54
Sample name: 9297962141_R06C02

value: chorionic villus


title: TC32 wild-type cells expressing EWS-FLI1 (+EF), biological rep #3

description: Wild-type


title: m_F2_d5_41

description:
MA_41
The sample comes from pupal wings.

source_name: Distal forewing, day 5, malleti


title: chorionic_villus_trisomy18_rep12

description:
SAMPLE 48
Sample name: 9297962144_R06C01

value: female fetus

value: trisomy 18


title: chorionic_villus_trisomy18_rep10

description:
SAMPLE 46
Sample name: 9297962144_R04C01


title: chorionic_villus_trisomy13_rep1

description:
SAMPLE 49
Sample name: 9297962141_R01C02


title: chorionic_villus_trisomy13_rep2

description:
SAMPLE 50
Sample name: 9297962141_R02C02


title: chorionic_villus_trisomy13_rep4

description:
SAMPLE 52
Sample name: 9297962141_R04C02


title: m_Hw_d3_35

description:
MA_35
The sample comes from pupal wings.

source_name: Hindwing, day 3, malleti


title: chorionic_villus_trisomy18_rep11

description:
SAMPLE 47
Sample name: 9297962144_R05C01


title: m_Eye_d5_37

description:
MA_37
The sample comes from pupal eyes.

source_name: Eye, day 5, malleti

value: eye


title: chorionic_villus_trisomy18_rep8

description:
SAMPLE 44
Sample name: 9297962144_R02C01


title: m_Hw_d3_31

description:
MA_31
The sample comes from pupal wings.


title: m_Eye_d1_29

description:
MA_29
The sample comes from pupal eyes.

source_name: Eye, day 1, malleti

value: day 1


title: chorionic_villus_trisomy13_rep3

description:
SAMPLE 51
Sample name: 9297962141_R03C02


title: p_Eye_d1_30

description:
MA_30
The sample comes from pupal eyes.

source_name: Eye, day 1, plesseni

value: plesseni


title: chorionic_villus_trisomy18_rep7

description:
SAMPLE 43
Sample name: 9297962144_R01C01


title: p_Hw_d1_28

description:
MA_28
The sample comes from pupal wings.


title: p_Hw_d3_32

description:
MA_32
The sample comes from pupal wings.


title: chorionic_villus_trisomy18_rep1

description:
SAMPLE 37
Sample name: 9297962141_R01C01


title: p_F2_d3_34

description:
MA_34
The sample comes from pupal wings.

source_name: Distal forewing, day 3, plesseni


title: chorionic_villus_trisomy18_rep5

description:
SAMPLE 41
Sample name: 9297962141_R05C01


title: m_F2_d3_33

description:
MA_33
The sample comes from pupal wings.

value: malleti


title: chorionic_villus_trisomy21_rep12

description:
SAMPLE 36
Sample name: 8795194156_R06C02

value: trisomy 21


title: chorionic_villus_trisomy18_rep3

description:
SAMPLE 39
Sample name: 9297962141_R03C01


title: m_Hw_d1_27

description:
MA_27
The sample comes from pupal wings.

source_name: Hindwing, day 1, malleti


title: m_F2_d1_25

description:
MA_25
The sample comes from pupal wings.

source_name: Distal forewing, day 1, malleti


title: chorionic_villus_trisomy18_rep2

description:
SAMPLE 38
Sample name: 9297962141_R02C01


title: chorionic_villus_trisomy18_rep6

description:
SAMPLE 42
Sample name: 9297962141_R06C01


title: chorionic_villus_trisomy18_rep4

description:
SAMPLE 40
Sample name: 9297962141_R04C01


title: p_F2_d1_26

description:
MA_26
The sample comes from pupal wings.

source_name: Distal forewing, day 1, plesseni


title: m_Eye_d7_23

description:
MA_23
The sample comes from pupal eyes.

source_name: Eye, day 7, malleti

value: day 7


title: chorionic_villus_trisomy18_rep9

description:
SAMPLE 45
Sample name: 9297962144_R03C01


title: p_Eye_d7_24

description:
MA_24
The sample comes from pupal eyes.

source_name: Eye, day 7, plesseni


title: chorionic_villus_trisomy21_rep11

description:
SAMPLE 35
Sample name: 8795194156_R06C01


title: p_F2_d7_20

description:
MA_20
The sample comes from pupal wings.

source_name: Distal forewing, day 7, plesseni

value: distal forewing


title: m_Hw_d7_21

description:
MA_21
The sample comes from pupal wings.

source_name: Hindwing, day 7, malleti


title: p_Hw_d7_22

description:
MA_22
The sample comes from pupal wings.

source_name: Hindwing, day 7, plesseni


title: m_F2_d7_19

description:
MA_19
The sample comes from pupal wings.

source_name: Distal forewing, day 7, malleti


title: chorionic_villus_trisomy21_rep5

description:
SAMPLE 29
Sample name: 7668610068_R02C01

source_name: chorionic villus


title: p_F1_d5_18

description:
MA_18
The sample comes from pupal wings.

source_name: Proximal forewing, day 5, plesseni

value: proximal forewing

value: day 5


title: m_F1_d5_17

description:
MA_17
The sample comes from pupal wings.

source_name: Proximal forewing, day 5, malleti


title: chorionic_villus_trisomy21_rep7

description:
SAMPLE 31
Sample name: 7668610068_R06C01


title: p_Eye_d5_16

description:
MA_16
The sample comes from pupal eyes.

source_name: Eye, day 5, plesseni


title: chorionic_villus_trisomy21_rep9

description:
SAMPLE 33
Sample name: 8795194156_R03C01


title: chorionic_villus_trisomy21_rep10

description:
SAMPLE 34
Sample name: 8795194156_R03C02


title: m_Eye_d5_15

description:
MA_15
The sample comes from pupal eyes.

source_name: Eye, day 5, malleti


title: chorionic_villus_trisomy21_rep2

description:
SAMPLE 26
Sample name: 8795207029_R03C01


title: chorionic_villus_trisomy21_rep6

description:
SAMPLE 30
Sample name: 7668610068_R04C01


title: p_F2_d3_12

description:
MA_12
The sample comes from pupal wings.


title: p_Hw_d5_14

description:
MA_14
The sample comes from pupal wings.

source_name: Hindwing, day 5, plesseni

value: hindwing


title: m_Hw_d5_13

description:
MA_13
The sample comes from pupal wings.

source_name: Hindwing, day 5, malleti


title: chorionic_villus_normal_rep12

description:
SAMPLE 24
Sample name: 8795194156_R05C02

value: normal pregnancy


title: chorionic_villus_trisomy21_rep4

description:
SAMPLE 28
Sample name: 8795207029_R06C02

value: male fetus


title: chorionic_villus_trisomy21_rep3

description:
SAMPLE 27
Sample name: 8795207029_R03C02


title: p_F1_d3_10

description:
MA_10
The sample comes from pupal wings.

source_name: Proximal forewing, day 3, plesseni


title: chorionic_villus_trisomy21_rep8

description:
SAMPLE 32
Sample name: 7668610068_R02C02


title: chorionic_villus_trisomy21_rep1

description:
SAMPLE 25
Sample name: 8795207029_R01C01


title: chorionic_villus_normal_rep11

description:
SAMPLE 23
Sample name: 8795194156_R05C01


title: m_F1_d3_9

description:
MA_9
The sample comes from pupal wings.

source_name: Proximal forewing, day 3, malleti


title: chorionic_villus_normal_rep10

description:
SAMPLE 22
Sample name: 8795194156_R02C02


title: m_F2_d3_11

description:
MA_11
The sample comes from pupal wings.

source_name: Distal forewing, day 3, malleti


title: chorionic_villus_normal_rep9

description:
SAMPLE 21
Sample name: 8795194156_R02C01


title: chorionic_villus_normal_rep7

description:
SAMPLE 19
Sample name: 7668610068_R05C01


title: chorionic_villus_normal_rep5

description:
SAMPLE 17
Sample name: 7668610068_R01C01


title: m_Eye_d3_7

description:
MA_7
The sample comes from pupal eyes.

source_name: Eye, day 3, malleti


title: p_Eye_d3_8

description:
MA_8
The sample comes from pupal eyes.

source_name: Eye, day 3, plesseni


title: chorionic_villus_normal_rep6

description:
SAMPLE 18
Sample name: 7668610068_R03C01


title: chorionic_villus_normal_rep8

description:
SAMPLE 20
Sample name: 7668610068_R01C02


title: p_F1_d1_2

description:
MA_2
The sample comes from pupal wings.

source_name: Proximal forewing, day 1, plesseni


title: m_F1_d1_1

description:
MA_1
The sample comes from pupal wings.

source_name: Proximal forewing, day 1, malleti


title: chorionic_villus_normal_rep3

description:
SAMPLE 15
Sample name: 8795207029_R02C02


title: chorionic_villus_normal_rep4

description:
SAMPLE 16
Sample name: 8795207029_R05C02


title: p_F2_d1_4

description:
MA_4
The sample comes from pupal wings.

source_name: Distal forewing, day 1, plesseni


title: p_Hw_d1_6

description:
MA_6
The sample comes from pupal wings.

source_name: Hindwing, day 1, plesseni


title: m_F2_d1_3

description:
MA_3
The sample comes from pupal wings.

source_name: Distal forewing, day 1, malleti


title: maternal_whole_blood_rep12

description:
SAMPLE 12
Sample name: 8795194156_R04C02

source_name: maternal whole blood

value: Female

value: maternal whole blood


title: chorionic_villus_normal_rep1

description:
SAMPLE 13
Sample name: 8795207029_R02C01

source_name: chorionic villus

value: chorionic villus


title: m_Hw_d1_5

description:
MA_5
The sample comes from pupal wings.

source_name: Hindwing, day 1, malleti


title: chorionic_villus_normal_rep2

description:
SAMPLE 14
Sample name: 8795207029_R05C01


title: WTD0_a

city: Montpellier

first: Pierre

last: BERTHOMIEU

address: Place Viala

department: UMR BPMP

country: France

institute: Montpellier SupAgro

description: Yeast expressing the plant defensin and grown in control condition (WTD0) repetition 1

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 016322 completed with the 39 genes from the new region of EC1118 (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7

data_processing: Data normalization and statistical analysis were performed using R 2.14.2 software and the limma package. Normalization was done by the quantile method considering all arrays

source_name: WTD_control medium (WTD0)

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)

growth_protocol: WT yeast cells (BY4741; Mat a, his3∆1, leu2∆0, met15∆0, ura3∆0) expressing the empty pFL38H vector harboring a HIS3 marker gene and expressing or not the AhPDF1.1b plant defensin (accession number AY961376) under the yeast Triose Phosphate Isomerase promoter in plasmid pYX212 were plated at the 50 UFC/cm2 density on solid YNB-derived medium (1.43 g/l Yeast Nitrogen Base w/o amino acids w/o ammonium sulfate (Ref. 233520, Difco), 20 g/l glucose, 6.4 g/l NH4NO3, 50 mM succinic acid-KOH pH 4.5, 20 mg/l methionine, 60 mg/l leucine, 20 g/l agarose (Réf. D5, Euromedex)) and grown at 30°C until the colony diameters were 0.48 ± 0.02 mm

extract_protocol: Total RNA extraction were perform with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then with RNeasy kit (Qiagen).

treatment_protocol: Plates were supplemented or not with ZnSO4 at the final concentration of 20 mM.

tag: strain background

tag: genotype/variation

value: WTD; expressing the AhPDF1.1b defensin

tag: growth medium

value: control medium

tag: array id

tag: array block id


title: WT20_b

description: WT yeast grown in the presence of 20 mM ZnSO4 (WT20) repetition 2

source_name: WT_20 mM ZnSO4 (WT20)

value: WT; wild type

value: supplemented with 20 mM ZnSO4


title: WT0_b

description: WT yeast grown in control condition (WT0) repetition 2

source_name: WT_control condition (WT0)


title: maternal_whole_blood_rep9

description:
SAMPLE 9
Sample name: 8795194156_R01C01


title: maternal_whole_blood_rep8

description:
SAMPLE 8
Sample name: 7668610068_R06C02


title: Sca6-StageE-SA-3

city: University Park

first: Mark

last: Guiltinan

state: Pennsylvania

address: 422 Life Sciences Bldg.

department: Plant Molecular Biology

institute: Penn State University

hyb_protocol: Hybridizations were performed by the Genomics Core Facility at PSU according to published facility protocols for NimbleGen microarrays, as described in Mejía LC, Herre EA, Sparks JP, Winter K, García MN, Van Bael SA, Stitt J, Shi Z, Zhang Y, Guiltinan MJ, Maximova SN. 2014. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree. Frontiers in Microbiology 5.

scan_protocol: Scannings were performed by the Genomics Core Facility at PSU according to published facility protocols for NimbleGen microarrays, as described in Mejía LC, Herre EA, Sparks JP, Winter K, García MN, Van Bael SA, Stitt J, Shi Z, Zhang Y, Guiltinan MJ, Maximova SN. 2014. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree. Frontiers in Microbiology 5.

data_processing: After log2 adjustment of expression data, only those probe sets with mean log2 expression over all samples greater than 8.0 were kept for statistical test based on overall expression histograms. Differential expression between genotypes on per-treatment and per-treatment+per-leaf-stage bases were assessed by generalized linear hypothesis (GLH) tests via the R multcomp package version 1.3(Bretz et al., 2010). Differential expression between treatments was assessed on a per-genotype+per-leaf-stage basis with two-sided student’s t-tests on expression differences (testing whether mean differential expression equaled 0) between replicates paired by sampling day per group. Differential expression between treatments overall and on per-genotype bases were assessed with GLH tests. On the microarrays, a number of genes were represented by additional probe sets generated from 3’ UTR regions. For those genes with multiple probe sets that passed expression cutoffs, a mixed linear model treating probe set as a random factor was used for the GLH tests rather than a simple linear model. All p-values were corrected with Benjamini-Hochberg correction on a per-test basis (Benjamini and Hochberg, 1995).

organism: Theobroma cacao

source_name: Scavina 6 cacao

label_protocol: Labelings were performed by the Genomics Core Facility at PSU according to published facility protocols for NimbleGen microarrays, as described in Mejía LC, Herre EA, Sparks JP, Winter K, García MN, Van Bael SA, Stitt J, Shi Z, Zhang Y, Guiltinan MJ, Maximova SN. 2014. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree. Frontiers in Microbiology 5.

growth_protocol: Three to four month old Scavina 6 and Imperial College Selection 1 rooted cuttings were used for the experiment and were grown under greenhouse conditions as described in Swanson et al., 2008.

extract_protocol: Plants treated with only water served as negative controls. Twenty-four hours after treatment, leaf samples from different developmental stages A, C and E (Mejia et al., 2012) were collected, three biological replicates for each genotype, each treatment and each developmental stage, except for Stage A Sca6 and Stage E ICS1, both of which had only two replicates per treatment. Thus, 32 samples were collected in total. RNA from each sample were isolated as previously described in Verica et a., 2006.

treatment_protocol: Sca6 and ICS1 were treated with 2mM SA dissolved in water or with only water served as negative controls. Twenty-four hours after treatment, leaf samples from different developmental stages A, C and E (Mejia et al., 2012) were collected, three biological replicates for each genotype, each treatment and each developmental stage, except for Stage A Sca6 and Stage E ICS1, both of which had only two replicates per treatment. Thus, 32 samples were collected in total.

tag: leaf stage

value: Stage E Leaf

tag: genotype

value: Scavina 6

tag: treatment

value: 2mM SA

tag: age

value: 3-4 Months

tag: propagation

value: Rooted Cutting


title: maternal_whole_blood_rep11

description:
SAMPLE 11
Sample name: 8795194156_R04C01


title: WTD20_b

description: Yeast expressing the plant defensin and grown in the presence of 20 mM ZnSO4 (WTD20) repetition 2

source_name: WTD_20 mM ZnSO4 (WTD20)


title: Sca6-StageE-SA-2


title: Sca6-StageC-SA-1

value: Stage C Leaf


title: WT20_a

description: WT yeast grown in the presence of 20 mM ZnSO4 (WT20) repetition 1


title: WTD0_b

description: Yeast expressing the plant defensin and grown in control condition (WTD0) repetition 2


title: Sca6-StageE-Water-3

value: Water


title: Sca6-StageE-Water-2


title: Sca6-StageC-SA-3


title: maternal_whole_blood_rep2

description:
SAMPLE 2
Sample name: 8795207029_R06C01


title: Sca6-StageE-SA-1


title: maternal_whole_blood_rep7

description:
SAMPLE 7
Sample name: 7668610068_R05C02


title: Sca6-StageE-Water-1


title: maternal_whole_blood_rep6

description:
SAMPLE 6
Sample name: 7668610068_R04C02


title: maternal_whole_blood_rep5

description:
SAMPLE 5
Sample name: 7668610068_R03C02


title: maternal_whole_blood_rep10

description:
SAMPLE 10
Sample name: 8795194156_R01C02


title: genomic DNA from cold plasma effected MDA-MB-231

city: Seoul

first: Sung-bin

last: Park

address: Dongguk university, Pil-dong, Joong-gu

department: Life Science

country: South Korea

institute: Dongguk Univ.

description: SAMPLE 2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing:
Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Methylatioin Module v1.9.0) and R 3.0.2
The non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy3, Cy5

source_name: MDA-MB-231_cold plasma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from MDA-MB-231 using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to standard instructions

value: estrogene receptor negative breast cancer cell line

tag: tissue source

value: breast, mammary gland

tag: treated with

value: atmospheric cold plasma


title: maternal_whole_blood_rep4

description:
SAMPLE 4
Sample name: 8795207029_R04C02

value: Female

value: normal pregnancy


title: WT0_a

description: WT yeast grown in control condition (WT0) repetition 1


title: Sca6-StageC-SA-2


title: Sca6-StageA-SA-2

value: Stage A Leaf


title: maternal_whole_blood_rep3

description:
SAMPLE 3
Sample name: 8795207029_R01C02

value: maternal whole blood


title: genomic DNA from MDA-MB-231

description: SAMPLE 1

tag: cell type

value: none (control)


title: ICS1-StageE-SA-2

source_name: Imperial College Selection 1 cacao

value: Imperial College Selection 1


title: WTD20_a

description: Yeast expressing the plant defensin and grown in the presence of 20 mM ZnSO4 (WTD20) repetition 1

value: WTD; expressing the AhPDF1.1b defensin

value: supplemented with 20 mM ZnSO4


title: genomic DNA from MCF-7

description: SAMPLE 1

data_processing:
GenomeStudio 2011, R 3.0.2
The non_normalized.txt contains unmethylated and methylated signal intensities.

extract_protocol: genomic DNA was extracted and purified from MCF-7 using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to standard instructions

tag: cell line

value: estrogene receptor postive breast cancer cell line


title: Sca6-StageA-SA-1

value: Scavina 6

value: 2mM SA


title: Sca6-StageC-Water-1

value: 3-4 Months

value: Rooted Cutting


title: Differentiated NS sample #3

city: Seville

first: Ricardo

last: Pardal

address: Avda. Manuel Siurot, s/n.

department: Medical Physiology and Biophysics

institute: University of Seville

description: Gene expression data from CB differentiated NS.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Rat Gene ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip® Command Console Software (AGCC) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Rattus norvegicus

source_name: Adult rat carotid body

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: Dispersed rat carotid body cells were cultured for 10 days in neural crest medium at 37ºC in ultra-low 6-well plates for the formation of neurospheres.

extract_protocol: Total RNA was extracted using a commercial kit (RNeasy MICRO kit; QIAGEN), according to manufacturer's instruction guidelines.

treatment_protocol: Undifferentiated sample was cultured in complete neural crest medium plus mitogens (FGF, IGF-1, EGF, and ET-1) and normoxic conditions; Differentiated sample was cultured in neural crest medium without mitogens and in hypoxic conditions (3%O2).

value: cultured CB cells

value: differentiated NS


title: ICS1-StageE-SA-1

value: Stage E Leaf


title: Sca6-StageC-Water-2

value: Stage C Leaf

value: Water


title: Differentiated NS sample #2


title: Differentiated NS sample #1


title: Undifferentiated NS sample #3

description: Gene expression data from CB undifferentiated NS.

value: undifferentiated NS


title: Undifferentiated NS sample #1


title: Undifferentiated NS sample #2


title: ICS1-StageC-Water-2


title: ICS1-StageE-Water-2


title: Sca6-StageC-Water-3


title: Sca6-StageA-Water-2

value: Stage A Leaf


title: ICS1-StageC-SA-1


title: ICS1-StageC-SA-3


title: GFP_A2

city: London

first: Lucie

last: Abeler-Dörner

address: Great Maze Pond

department: Immunobiology

country: United Kingdom

institute: King's College London

description:
replicate 1
5511176056_D

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization with no Background subtraction using Genome Studio.

source_name: MODE-K cells, transduced with empty vector (GFP), medium, 18h

label_protocol: Standard Illumina biotin labelling protocol

growth_protocol: MODE-K cells stably transfected with Btnl1 or vector alone  were seeded in 6-well plates the day before the experiment.

extract_protocol: Total RNA was extracted using a Qiagen RNEasy extraction kit.

treatment_protocol: MODE-K cells were stimulated with unstimulated or stimulated (on anti-CD3) cultured IEL supernatant or a combination of TNF (1 µg/ml) and IL-1_ (100 pg/ml) for 18 hours.

tag: strain

value: female

value: SV40 T transformed intestinal epithelial cell line

tag: retroviral vector

value: pMX-IRES-GFP


title: maternal_whole_blood_rep1

description:
SAMPLE 1
Sample name: 8795207029_R04C01

tag: individual

value: Female

tag: tissue

value: maternal whole blood

tag: pregnancy

value: normal pregnancy


title: BTN_C2

description:
replicate 2
5511176056_H

source_name: MODE-K cells, transduced with Btnl1, SN unstimulated IEL, 18h


title: genomic DNA from cold plasma effected MCF-7

description: SAMPLE 2

source_name: MCF-7_cold plasma

value: estrogene receptor postive breast cancer cell line

value: breast, mammary gland

value: atmospheric cold plasma


title: ICS1-StageA-SA-2

value: Imperial College Selection 1

value: 2mM SA

value: 3-4 Months

value: Rooted Cutting


title: BTN_C3

description:
replicate 3
5511176052_H


title: Sca6-StageA-Water-1

value: Scavina 6


title: ICS1-StageC-Water-3

value: Stage C Leaf

value: Water


title: GFP_D2

description:
replicate 2
5511176056_F

source_name: MODE-K cells, transduced with empty vector (GFP), SN stimulated IEL, 18h


title: ICS1-StageC-SA-2


title: ICS1-StageE-Water-1

value: Stage E Leaf


title: GFP_D3

description:
replicate 3
5511176056_C

value: female


title: GFP_B2

description:
replicate 2
5511176052_G

source_name: MODE-K cells, transduced with empty vector (GFP), TNF+IL-1_, 18h

value: SV40 T transformed intestinal epithelial cell line


title: ICS1-StageA-SA-1

value: Stage A Leaf


title: BTN_D2

description:
replicate 2
5511176056_G

source_name: MODE-K cells, transduced with Btnl1, SN stimulated IEL, 18h


title: ICS1-StageA-Water-2


title: ICS1-StageA-SA-3


title: BTN_D1

description:
replicate 1
5511176056_B


title: ICS1-StageC-Water-1


title: GFP_C2

description:
replicate 1
5511176052_D

source_name: MODE-K cells, transduced with empty vector (GFP), SN unstimulated IEL, 18h

value: pMX-IRES-GFP


title: BTN_B2

description:
replicate 2
5511176052_A

source_name: MODE-K cells, transduced with Btnl1, TNF+IL-1_, 18h


title: ICS1-StageA-Water-3


title: ICS1-StageA-Water-1


title: BTN_B1

description:
replicate 1
5511176031_E


title: GFP_C3

description:
replicate 2
5511176031_G


title: BTN_C1

description:
replicate 1
5511176052_E


title: BTN_A1

description:
replicate 1
5511176031_H

source_name: MODE-K cells, transduced with Btnl1, medium, 18h


title: BTN_A2

description:
replicate 2
5511176052_C


title: GFP_A3

description:
replicate 2
5511176052_B


title: GFP_D1

description:
replicate 1
5511176031_C


title: GFP_B3

description:
replicate 3
5511176052_F


title: BTN_D3

description:
replicate 3
5511176031_D


title: GFP_B1

description:
replicate 1
5511176031_B


title: BTN_A3

description:
replicate 3
5511176031_F


title: LNCaP cells Treated with MK591 for 8 hours_2

city: Detroit

first: Jagadananda

last: Ghosh

state: MI

address: 1 Ford Place

department: Urology

institute: Henry Ford Health System

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

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

growth_protocol: LNCaP human prostate cancer cells were cultured in RPMI medium 1640 supplemented with 10% FBS and antibiotics.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Exponentially growing cells were treated with 30 micromolar MK591 for 8 or 16 hours at 37oC in the CO2 incubator.

value: LNCaP

value: prostate adenocarcinoma


title: UES patient 3

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

description:
UES3
Gene expression in primary tumor sample.

hyb_protocol: Gene expression analysis was performed using SurePrint G3 Human GE 8x60K microarrays (G4851A) according to the one-color microarray-based expression analysis protocol (Agilent Technologies, SantaClara, CA, USA).

scan_protocol: The microarray slides were scanned using the Agilent G2565A DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Image analysis was done using the Feature Extraction V10.10.1.1 software (Agilent Technologies, SantaClara, CA, USA). Microarray data were analyzed using GeneSpring GX default workflow parameters for Agilent one-color expression experiments (Agilent Technologies, SantaClara, CA, USA).

source_name: tumor sample, UES

label_protocol: Total RNA (25ng) was reverse transcribed into cDNA by incorporating a T7 oligo-dT promoter primer prior to the generation of fluorescent cRNA using an Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

extract_protocol: Total RNA were extracted from 11 frozen EST specimens using the miRNeasy Mini Kit (Qiagen) with optional DNase treatment using RNase-free DNase Set (Qiagen). RNA quality was checked using the Bio-Rad Experion system (Bio-Rad Laboratories).

value: primary undifferentiated endometrial sarcoma

tag: histosubtype

value: undifferentiated stromal tumor


title: LNCaP cells Treated with MK591 for 8 hours_1


title: LNCaP cells Treated with MK591 for 16 hours_1


title: LNCaP cells Treated with MK591 for 16 hours_2


title: UES patient 5

description:
UES5
Gene expression in primary tumor sample.


title: Low-grade ESS patient 8

description:
ESSlow8
Gene expression in primary tumor sample.

source_name: tumor sample, low-grade ESS

value: primary endometrial stromal sarcoma

value: low-grade endometrial stromal tumor


title: triple mutant of myb3r1 myb3r3 myb3r5, first leaf pairs, 15d-old, rep1

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

institute: NAIST

hyb_protocol: Following fragmentation, 15 micro g of cRNA were hybridized for 16 hrs at 45 Celsius degree on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 micro g of total RNA.

growth_protocol: Seedlings were grown in half strength of MS agar medium with 2% sucrose in continuous light at 22 Celcius degree.

extract_protocol: Total RNA was extracted using Plant RNeasy kit (QIAGEN) following instruction.

value: leaf

tag: genotype/variation

value: myb3r1 myb3r3 myb3r5


title: triple mutant of myb3r1 myb3r3 myb3r5, first leaf pairs, 15d-old, rep3


title: UES patient 4

description:
UES4
Gene expression in primary tumor sample.


title: Low-grade ESS patient 2

description:
ESSlow9
Patient 2 described in this study.
Gene expression in primary tumor sample.


title: LNCaP cells Control_1

source_name: LNCaP cells Control


title: wild-type, first leaf pairs, 15d-old, rep3

source_name: wild-type (Columbia), first leaf pairs, 15d-old

value: wild-type


title: triple mutant of myb3r1 myb3r3 myb3r5, first leaf pairs, 5d-old, rep2


title: triple mutant of myb3r1 myb3r3 myb3r5, first leaf pairs, 15d-old, rep2


title: BTN_B3

description:
replicate 3
5511176031_A


title: quaradple mutant of myb3r1 myb3r3 myb3r4 myb3r5, seedling, 9d-old

value: whole seedling

value: myb3r1 myb3r3 myb3r4 myb3r5


title: wild-type, first leaf pairs, 5d-old, rep1

source_name: wild-type (Columbia), first leaf pairs, 5d-old


title: triple mutant of myb3r1 myb3r3 myb3r5, first leaf pairs, 5d-old, rep1


title: wild-type, first leaf pairs, 15d-old, rep2


title: H37Rv in A549 #1 vs 7H9 replicate 3

city: New York

first: Suman

last: Laal

address: 423 Esat 23rd Street, 18N

department: Pathology

institute: VA/NYU

hyb_protocol: For hybridization, labeled cDNA probes generated from aRNA obtained from M. tb grown in A549 cells was mixed with the labeled reference cDNA probe prior to purification with Microcon YM10 filter (Millipore). For each A549 grown M. tb sample (two biological replicates), the M. tb arrays were hybridized overnight with the mixed labeled cDNA probes in duplicate including a Cy3/Cy5 dye swap (Fontan et al, 2008). For biological replicate 1, 4 technical replicated including two dye flip were used.

scan_protocol: The microarrays were scanned and processed with an Axon 4000B scanner and GenePix Pro 6.1 software, respectively.

data_processing: Normalized by the WinPrint-Tip Lowess method; intensity ratio data obtained used to perform Significance Analysis of Microarrays (SAM) with Multiarray Viewer Software on the TMEV website for determination of differentially expressed genes; ≥ 2 fold change at a false discovery rate of ≤2% were considered significantly differentially expressed.

source_name: Mycobacterium tuberculosis H37Rv 72 hr in A549 Expt #1

label_protocol: The synthesis and fluorescent labeling of cDNA with Cy3 or Cy5 from amplified RNA (aRNA) was accomplished by first performing reverse transcriptase (RT) reaction with Superscript II RT followed by labeling with Klenow fragment using Bioprime Kit (Invitrogen) following a published method (Schlingemann 2005).

growth_protocol: Monolayers of A549 cells in 4-5 T225 flasks were infected with M. tb H37Rv at an MOI of 5:1 bacteria to cell.  Extracellular bacteria were removed by washing at 1 hr post-infection. Infected cells were maintained in 37C 5% CO2 for 72 hr pi then lysed and intracellular bacteria isolated. For reference, M. tb H37Rv was grown in Middlebrook 7H9 broth to log phase.

extract_protocol: M. tb H37Rv infected cells monolayer lysed with GTC solution and bacteria pelleted. Pellets were washed in GTC, resuspended in TRI reagent containing polyacryl carrier and disrupted in bead beater using sterile 0.1 mm zirconia. Total RNA was extracted according to published protocol (Dubnau E. et al. 2002). RNA from log phase culture of M. tb H37Rv grown in 7H9 broth was also extracted. An RNA amplification strategy was used (MessageAmp II-bacteria RNA amplification kit- Ambion) (Schlingemann et al., 2005; Garton et al., 2008).

source_name: 7H9 broth grown M. tb


title: Low-grade ESS patient 1

description:
ESSlow7
Patient 1 described in this study.
Gene expression in primary tumor sample.


title: UES patient 1

description:
UES1
Gene expression in primary tumor sample.


title: H37Rv in A549 #1 vs 7H9 replicate 1


title: High-grade ESS patient 4

description:
ESShigh4
Gene expression in primary tumor sample.

source_name: tumor sample, high-grade ESS

value: high-grade endometrial stromal tumor


title: wild-type, first leaf pairs, 15d-old, rep1


title: Low-grade ESS patient 11

description:
ESSlow11
Gene expression in primary tumor sample.


title: H37Rv in A549 #1 vs 7H9 replicate 4 (dye flip)


title: single mutant of myb3r1, seedling, 9d-old


title: ExVivo-normal-PM-3N

city: Beijing

first: Yanshuang

last: Li

address: 5 Dong Dan San Tiao

department: National Laboratory of Medical Molecular Biology

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

description:
Sample name: fuM_NS
expression of microRNA

hyb_protocol: Each  slide  was  hybridized  with  100ng  Cy3-labeled  RNA  using  miRNA  Complete Labeling  and  Hyb  Kit(Agilent  technologies,  Santa  Clara,  CA, US) in hybridization Oven(Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization ection. After hybridization, slides were washed in staining dishes (Thermo handon, altham,  MA,  US)  with  Gene  Expression  Wash  Buffer  Kit（Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned immediately after washing on Agilent  Microarray  Scanner(G2565BA, Agilent technologies,  Santa  Clara,  CA,  US）  Feature  Extraction  software  10.7  (Agilent technologies, Santa Clara,CA, US)with default settings.

data_processing:
The scanned images were analyzed with  Feature  Extraction  software  10.7  (Agilent technologies, Santa Clara, CA, US)with default settings.
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: normal peritoneal macrophage

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Agilent technologies,Santa Clara,CA,US)followed the manufacturer’s instructions, labeling section.

extract_protocol: TAMs were isolated from tumor tissue and total RNA was extracted from cells using Trizol (Invitrogen, CA, USA) reagent.Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: BALB/c

tag: gender

value: PEC


title: ExVivo-late tumor-TAM-3L

description:
Sample name: TAM_417_M_NS
expression of microRNA

source_name: 4T1 transplanted late tumor

value: female

value: TAM (isolated from late tumor, 21 days after 4T1 cell injection)


title: ExVivo-normal-PM-2N

description:
Sample name: fu2M_NS
expression of microRNA


title: triple mutant of myb3r3 myb3r4 myb3r5, seedling, 9d-old

value: myb3r3 myb3r4 myb3r5


title: ExVivo-early tumor-TAM-2E

description:
Sample name: TAM33_330_CD_TAM_NS
expression of microRNA

source_name: 4T1 transplanted early tumor

value: TAM (isolated from early tumor, 12 days after 4T1 cell injection)


title: ExVivo-early tumor-TAM-3E

description:
Sample name: TAM612_NS
expression of microRNA


title: ExVivo-early tumor-TAM-1E

description:
Sample name: TAM32_NS
expression of microRNA


title: High-grade ESS patient 1

description:
ESShigh1
Gene expression in primary tumor sample.


title: ExVivo-late tumor-TAM-2L

description:
Sample name: TAM_417_L_NS
expression of microRNA


title: double mutant of myb3r1 myb3r4, seedling, 9d-old

value: myb3r1 myb3r4


title: ExVivo-late tumor-TAM-1L

description:
Sample name: TAM_417_H_NS
expression of microRNA


title: High-grade ESS patient 2

description:
ESShigh2
Gene expression in primary tumor sample.


title: wild-type, first leaf pairs, 5d-old, rep2


title: H37Rv in A549 #2 vs 7H9 replicate 2 (dye flip)

source_name: Mycobacterium tuberculosis H37Rv 72 hr in A549 Expt #2


title: single mutant of myb3r5, seedling, 9d-old


title: H37Rv in A549 #1 vs 7H9 replicate 2 (dye flip)


title: ExVivo-normal-PM-1N

description:
Sample name: PEC_37_Ia_NS
expression of microRNA


title: double mutant of myb3r3 myb3r5, seedling, 9d-old

value: myb3r3 myb3r5


title: LNCaP cells Control_2

value: LNCaP

value: prostate adenocarcinoma


title: wild-type, seedling, 9d-old

source_name: wild-type (Columbia), seedling, 9d-old


title: Sinorhizobium meliloti A2102 pS73, biological rep1

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G

data_processing: The data were analyzed using Affymetrix software GCOS v1.4 with Affymetrix default analysis setting and global scaling as the normalization method. The mean target intensity of each array was arbitrarily set to 500. Affymetrix Data Mining Tool v3.1 was used for data mining as previously described by Barnett et al. 2004.

organism: Sinorhizobium meliloti

source_name: nodD1D2D3 mutant with plasmid overexpressing syrM from the trp promoter

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol: Bacteria were cultured in TY medium supplemented with 10 ug/ml tetracycline and 500 ug/ml streptomycin. Cells were harvested at OD-600 = 0.59 - 0.67

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.

value: nodD1D2D3 mutant overexpressing syrM


title: single mutant of myb3r3, seedling, 9d-old


title: H37Rv in A549 #2 vs 7H9 replicate 1


title: Sinorhizobium meliloti A2102 pS73, biological rep2


title: DRG_Expt (VZV infected MEWO) 2

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

state: PA

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C to an Affymetrix Rat Genome 230 2.0 Array. Microarrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip 3000 Array scanner.

data_processing:
The data were analyzed with Affymetrix GCOS v1.4, which uses Microarray Suite version 5.0 (MAS 5.0) algorithms. Global scaling as normalization method, with the 2% trimmed mean target intensity of each array  arbitrarily set to 500.
*****The fold changes examined were smaller (1.3-fold) than the 2-fold threshold often used. Therefore, non-default analysis  values were used for the perturbation parameter (1.05 instead of 1.1),  and critical p value (gamma1: 0.005 instead of 0.002)********

source_name: Dorsal root ganglion, L4,5

label_protocol: Biotinylated cRNA was prepared from approx 160 ng total RNA using Affymetrix 3' IVT Express kit (#901228)

growth_protocol: Not applicable

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Samples subsequently were cleaned up using a QIAGEN RNeasy kit

treatment_protocol: Dorsal root ganglia corresponding to L4-5 were surgically removed from euthanized rats, snap frozen in liquid nitrogen and placed at -80oC until processed

value: Male

value: Sprague-Dawley


title: DRG_Expt (VZV infected MEWO) 1


title: DRG_Control (MEWO only) 3


title: whole embryo, actD treat, 3 hour chase

city: Merced

first: Michael

last: Cleary

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

description: TU-RNA present after 3 hour chase

hyb_protocol: 1.65 micrograms of Cy3 labeled cRNA was combined with the recommended dilution of spike-in control and hybridized following manufacturer's instructions

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000B scanner, with pixel size 10, scan power 100%, and 532nm PMTGain set between 500 and 700.

data_processing:
Spot alignments and data measurements were made using GenePix Pro 5.1 software. Post-processing of GenePix Pro data was performed in R.
Signal intensities within a pulse-chase series were normalized using the spike-in control.  Threshold F532 intensity (mean - background) for a spot to be considered present (signal above background) was determined for each pulse-chase series by averaging the signals for maternal mRNAs that should not be present in the TU-RNA samples at any timepoint.  Spots with signals below this average value were removed from analysis.

organism: Drosophila melanogaster

source_name: whole embryo, actD treat, 3 hour chase RNA

label_protocol: Purified TU-RNA plus a spike-in control (One-Color RNA Spike-In Kit, Agilent) was used to generate Cy3 labeled cRNA (Low Input Quick Amp Labeling Kit, Agilent) and hybridized to Agilent 4x44K Drosophila gene expression microarrays.

growth_protocol: embryos were collected on standard apple juice, agar plates and reared at 18C or 25C to reach stage 12 - 15

extract_protocol: Total RNA was extracted using trizol purification protocols.  TU-RNA was purified as previously described.

treatment_protocol: Embryos were permeabilized and pulse-labeled in tagging media [D22 insect media, 5% FBS, and either 1mM 4-thiouridine (whole embryo tagging) or 1mM 4-thiouracil (neural-specific tagging)] for 1 hour at 30°C. Pulse-labeled embryos were then transferred for 1 or 3 hours to chase media containing uridine [D22 insect media, 5% FBS, 10mM uridine] at 30°C. Embryos were homogenized for 30 seconds and frozen in Trizol (Invitrogen) at -80°C.  Multiple samples for each time-point were pooled for RNA extraction and TU-RNA purification, as previously described

value: whole embryo

value: wildtype

tag: developmental stage

value: embryo

tag: embryonic stage

value: stage 12 - 15

value: UAS-T.g.UPRT (no GAL4)


title: whole embryo, uridine only chase, 1 hour pulse

description: TU-RNA present after 1 hour pulse

source_name: whole embryo, 1 hour pulse

tag: genotype


title: Sinorhizobium meliloti A2102 pTE3, biological rep3

source_name: nodD1D2D3 mutant with empty vector control plasmid

value: nodD1D2D3 mutant


title: whole embryo, uridine only chase, 3 hour chase

description: TU-RNA present after 3 hour chase

source_name: whole embryo, 3 hour chase


title: Sinorhizobium meliloti A2102 pS73, biological rep3


title: Sinorhizobium meliloti Rm1021 pMB89, biological rep1

source_name: wild type overexpressing syrA from trp promoter

growth_protocol: Bacteria were cultured in TY medium supplemented with 10 ug/ml tetracycline and 500 ug/ml streptomycin. Cells were harvested at OD-600 = 0.57 - 0.64

value: wild type overexpressing syrA


title: Sinorhizobium meliloti Rm1021 pMB89, biological rep2


title: Sinorhizobium meliloti A2102 pTE3, biological rep2


title: DRG_Expt (VZV infected MEWO) 3


title: single mutant of myb3r4, seedling, 9d-old

value: whole seedling

tag: age


title: Sinorhizobium meliloti A2102 pTE3, biological rep1


title: Sinorhizobium meliloti Rm1021 pMB89, biological rep3


title: whole embryo, uridine only chase, 1 hour chase

description: TU-RNA present after 1 hour chase

source_name: whole embryo, 1 hour chase


title: DRG_Control (MEWO only) 1


title: whole embryo, actD treat, 1 hour pulse

description: TU-RNA present after 1 hour pulse

source_name: whole embryo, actD treat, 1 hour pulse RNA


title: whole embryo, actD treat, 1 hour chase

description: TU-RNA present after 1 hour chase

source_name: whole embryo, actD treat, 1 hour chase RNA


title: Sinorhizobium meliloti Rm1021 pMB90, biological rep1

source_name: wild type with insert in the opposite orientation with respect to the trp promoter (control plasmid)

value: wild type


title: Sinorhizobium meliloti EC176 pMB90, biological rep2

data_processing: The data were analyzed using Affymetrix software GCOS v1.4 with Affymetrix default analysis setting and global scaling as the normalization method. The mean target intensity of each array was arbitrarily set to 500.

source_name: wild type with insert in the opposite orientation with respect to the trp promoter (control plasmid) (integrated pDW181)

growth_protocol: Bacteria were cultured in LB medium supplemented with 10 ug/ml tetracycline, 50 ug/ml hygromycin, and 500 ug/ml streptomycin. Cells were harvested at OD-600 = 0.63 - 0.74.

value: EC176 pMB90


title: Sinorhizobium meliloti EC176 pMB90, biological rep3


title: Sinorhizobium meliloti Rm1021 pMB90, biological rep3


title: Sinorhizobium meliloti Rm1021 pMB90, biological rep2


title: DRG_Control (MEWO only) 2


title: MB231  CEBPB

city: Shanghai

first: Pei Yi

last: Xia

address: 320 Yue Yang Road

institute: Shanghai Institute of biochemistry and cell biology, Chinese Academy of Sciences

description: CEBPB overexpressing MDA-MB231 cell

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: CEBPB overexpressing MDA-MB231 cell

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Cells were cultured in DMEM, supplemented with 10% FBS and 1% antibiotics in 5% CO2 at 37 °C

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

value: CEBPB overexpress


title: triple mutant of myb3r1 myb3r3 myb3r5, seedling, 9d-old

value: myb3r1 myb3r3 myb3r5


title: MB231  PCOH

description: MDA-MB231 control cell

source_name: MDA-MB231 control cell

value: control


title: Sinorhizobium meliloti EC176 pMB89, biological rep3

source_name: wild type overexpressing syrA from trp promoter (integrated pDW181)

value: EC176 pMB89


title: Sinorhizobium meliloti EC69 pMB89, biological rep1

source_name: chvI K214T overexpressing syrA from trp promoter (integrated pDW181)

value: EC69 pMB89

value: chvI K214T mutant overexpressing syrA


title: mESC-IVFWM 1

city: San Francisco

first: Rhodel

last: Simbulan

address: 513 Parnassus Ave

department: Obstetrics, Gynecology & Reproductive Sciences

institute: University of California San Francisco

hyb_protocol: Samples were hybridized onto Affymetrix MoGene 1.0 ST Arrays was performed by the UCSF Genomics Core.

scan_protocol: Array scans were performed by the UCSF Genomics Core.

data_processing:
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187
The microarray data were further analyzed using R software version 3.1.0 along with the appropriate Bioconductor (http://www.bioconductor.org/) packages. We conducted a non-parametrical test which applies a P-value correction (here named pfp correction) akin to false-positive discovery rate (FDR) using the RankProd package to narrow down the list of significant genes.

source_name: mESC-IVFWM

label_protocol: Biotin labeling was performed by the UCSF Genomics Core.

growth_protocol: Blastocysts were derived from their respective experimental group and derived into embryonic stem cells and treated equally to study the impact of culture on the derivation process.

extract_protocol: Total RNA was isolated from three female lines per experimental condition using RNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.

tag: strain background

tag: Sex

value: female

tag: cell line source

value: blastocysts conceived after IVF

value: mouse embryonic stem cell

tag: ivf condition

value: suboptimal (Whitten's Medium+20% O2, mESCWM)


title: Sinorhizobium meliloti EC69 pMB90, biological rep3

source_name: chvI K214T with insert in the opposite orientation with respect to the trp promoter (control plasmid) (integrated pDW181)

value: EC69 pMB90

value: chvI K214T mutant


title: Sinorhizobium meliloti EC69 pMB90, biological rep2


title: mESC-IVFWM 3

tag: cell type


title: Sinorhizobium meliloti EC176 pMB89, biological rep2

tag: strain


title: Sinorhizobium meliloti EC69 pMB89, biological rep3


title: mESC-IVFKAA 3

source_name: mESC-IVFKAA

value: optimal (KSOM+5% O2; mESCKAA)


title: Sinorhizobium meliloti EC176 pMB89, biological rep1

value: wild type overexpressing syrA


title: mESC-control 1

source_name: mESC-control

value: blastocysts conceived after natural mating (mESCFB)


title: mESC-IVFKAA 1


title: Sinorhizobium meliloti EC69 pMB89, biological rep2


title: Sinorhizobium meliloti EC69 pMB90, biological rep1


title: mESC-IVFKAA 2


title: Sinorhizobium meliloti EC176 pMB90, biological rep1

value: wild type


title: SXR_VK2

city: Tokyo

first: Kotaro

last: Azuma

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

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

data_processing: The data were analyzed with Robust Multi-array Average (RMA) procedure using Affymetrix default analysis settings and global scaling as normalization method.

source_name: ATDC5 cells infected with adeno-SXR and treated with vitamin K2

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

growth_protocol: ATDC5 cells were maintained in in the medium consisting of a 1:1 mixture of Dulbecco's modified Eagle medium (DMEM) and Ham's F-12 (Invitrogen) supplemented with 10% fetal calf serum (FCS), at 37°C under 5% CO2.

extract_protocol: Total RNA was extracted from the cells using the ToTALLY RNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.

treatment_protocol: ATDC5 cells were cultured in phenol red-free DMEM with 5% charcoal/dextran-treated FCS from 24 h prior to rifampicin (Nacalai Tesque, Kyoto, Japan), MK-4 (gifted by Eisai Co., Ltd., Tokyo, Japan), or vehicle (0.1% ethanol) treatment. Recombinant adenoviruses were generated using the Adenovirus Expression Vector Kit (Takara Bio, Otsu, Japan) and used at a multiplicity of infection (MOI) of 40–100 according to the manufacturer's protocol.

tag: cell line

value: Chondrogenic cell line ATDC5

tag: infection

value: adeno-SXR

tag: agent

value: vitamin K2


title: mESC-IVFWM 2


title: mESC-control 3


title: High Day 28 Sample liver 161

city: Ottawa

first: Mainul

last: Husain

address: 50 Colombine Driveway

country: Canada

institute: Health Canada

description: Biological replicate Day 28, Treated

hyb_protocol: Each experimental cRNA sample was mixed with an equimolar amount of reference cRNA and was hybridized to Agilent mouse 4×44 oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada) for 17 h in a hybridization chamber at 60C with a rotation speed of 10 rpm.

scan_protocol: Arrays were washed according to manufacturer’s protocols (Agilent Technologies Inc., Mississauga, ON, Canada) and scanned on an Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1.). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Liver

label_protocol: Total RNA (250 ng) samples from individual mice (n = 5-6 per experimental and control group) and from universal reference total RNA (Agilent Technologies, Inc., Mississauga, ON, Canada) were used to synthesize double-stranded cDNA and cyanine labelled cRNA using Quick Amp Labeling Kit (Agilent Technologies Inc., Mississauga, ON, Canada) according to the manufacturer’s instruction. Control and nano-TiO2 treated cRNAs were labelled with Cyanine 5-CTP, and reference RNAs were labelled with Cyanine 3-CTP using a T7 RNA polymerase in vitro transcription kit (Agilent Technologies Inc., Mississauga, ON, Canada) and purified using RNeasy Mini kits (Qiagen, Mississauga, ON, Canada).

growth_protocol: Five-to-seven week old female C57BL/6 mice were purchased from Taconic (Ry, Denmark) and were acclimatized for 1-3 weeks prior to the commencement of the experiment. Mice were maintained in groups in polypropylene cages with sawdust bedding and enrichment, at 20-22°C room temperature and relative humidity of 40-60% with a 12 h light-to-dark cycle. All mice received food and water ad libitum throughout the experiment. All animal experiments were approved by the Danish “Animal Experiments Inspectorate” and performed according to their guidelines for ethical conduct and care of animals in research.

extract_protocol: Total RNA was isolated from random sections of the left lungs (n = 5-6 per group) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy Plus Mini kits (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instruction. Total RNA concentration was measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and RNA quality and integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Mississauga, ON, Canada) according to the manufacturer’s instruction. Samples with RNA integrity numbers of 7 and above were used to conduct microarray and qPCR experiments.

treatment_protocol: Naïve C57BL/6 mice were flushed twice with 0.6 ml of 0.9% NaCl to obtain approximately 1 ml of bronchoalveolar lavage fluid (BAL). BAL was centrifuged at 400 g for 10 min at 4°C to remove cells. The supernatant was used in the dispersant liquid. A total of 4.05 mg of nano-TiO2 was suspended in 1 ml of MilliQ water containing 0.9% NaCl and 10% v/v acellular BAL. Particle suspensions were prepared by sonicating the samples using a S-450D sonifier (Branson Ultrasonics Corp., Danbury, CT, USA) at 10% amplitude for a total of 16 minutes on ice with alternating 10 s pulses and pauses. One dilution of nano-TiO2 were prepared and used in this experiment: 162 µg. Control vehicle solutions were prepared without the nano-TiO2 (MilliQ water containing 90% of 0.9% NaCl and 10% acellular BAL fluid). The dose162 μg/mouse equals 15 working days at the Danish occupational exposure level for TiO2 (6.0 mg Ti/m3 ~ 9.75 mg TiO2/m3), respectively. Each treatment group consisted of a minimum of 5 animals. Mice in the experimental groups received a single intratracheal instillation of 162 µg of nano-TiO2 in a 40 µl suspension, followed by 150 μl air with a 250 µl SGE glass syringe (250F-LT-GT, MicroLab, Aarhus, Denmark). Intratracheal instillation was performed at 37 ºC on heating plates, under anesthesia using Hypnorm® (fentanyl citrate 0.315 mg/ml and fluanisone 10 mg/ml from Janssen Pharma) and Dormicum® (Midazolam 5 mg/mL from Roche). Control mice received 40 µl of dispersant vehicle only. Following instillation, mice were under observation until they recovered from anaesthesia. Mice were allowed to recover for 24 hours and 28 days following instillation before sacrificing under anaesthesia (Hypnorm/Dormicum). Blood, BAL fluid and tissues were collected. Liver tissues from each experimental and control mice were cut into small pieces, and stored in cryogenic vials and snap frozen immediately in liquid nitrogen. All tissues were stored at -80°C until analysis.

tag: tissue

value: liver

tag: treatment

tag: treatment type

value: High

tag: time point (day)

tag: dose

source_name: Agilent Universal Mouse Reference RNA (UMRR)

tag: sample type

value: Reference 11 mouse cell lines


title: SXR_Et

source_name: ATDC5 cells infected with adeno-SXR and treated with ethanol

value: ethanol


title: DsRed_Et

source_name: ATDC5 cells infected with adeno-DsRed and treated with ethanol

value: adeno-DsRed


title: SXR_RIF

source_name: ATDC5 cells infected with adeno-SXR and treated with rifampicine

value: rifampicine


title: DsRed_VK2

source_name: ATDC5 cells infected with adeno-DsRed and treated with vitamin K2


title: High Day 28 Sample liver 160

description: Biological replicate Day 28, Treated


title: mESC-control 2

value: female

value: mouse embryonic stem cell


title: High Day 28 Sample liver 162

description: Biological replicate Day 28, Treated


title: male islet graft, non-pregnant, biological rep 3

city: Leuven

first: Leentje

last: Van Lommel

address: Herestraat 49 bus 901

department: Molecular cell biology

country: Belgium

institute: KULeuven

description: Gene expression data from a male islet graft in non-pregnant condition

hyb_protocol: Labeled DNA was hybridized to the array during 16h at 45°C

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: All image files were generated using the Affymetrix GeneChip command console (AGCC). The raw data (.CEL files) were preprocessed with robust multichip analysis using the implementation in the aroma.affymetrix R package.

source_name: mouse islet graft, male, C57bl6/J, NP

label_protocol: according to manufacturer’s manual 701880Rev4 (Affymetrix, Santa Clara, CA). Briefly, in the first cycle, double stranded cDNA was prepared with random hexamers tagged with a T7 promoter sequence followed by the generation of cRNA using the GeneChip WT Synthesis and Amplification kit (Affymetrix). cRNA concentration after cleanup was measured with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW). In the second cycle, sense oriented single-stranded DNA containing dUTP is generated and the concentration is, after cleanup, measured using the nanodrop. The cRNA is hydrolysed and the single stranded DNA is fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) (GeneChip WT terminal Labeling kit, Affymetrix). The quality of fragmentation (fragments should be between 40 and 70 nucleotides) is checked on the bioanalyzer (Agilent, Waldbronn, Germany). The fragmented DNA is labeled by terminal deoxynucleotidyl transferase (TDT) with the Affymetrix DNA Labeling reagent that is covalently linked to biotin (GeneChip WT terminal Labeling kit, Affymetrix).

extract_protocol: The absolute RNA microprep kit of Strategene was used to extract total RNA according to the manufacturer's instructions. The total RNA quantity and quality was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW) and the 2100 Bioanalyzer (Agilent, Waldbronn, Germany), respectively. Total RNA profiles of all tested samples were similar with sharp 18S and 28S rRNA peaks on a flat baseline.

tag: genetic background

tag: gender

value: M

tag: pregnancy day

value: NP

value: pancreatic islets

tag: transplanted

value: yes


title: High Day 28 Sample liver 157

description: Biological replicate Day 28, Treated


title: High Day 28 Sample liver 158

description: Biological replicate Day 28, Treated


title: female islet graft, non-pregnant, biological rep 2

description: Gene expression data from a female islet graft in non-pregnant condition

source_name: mouse islet graft, female, C57bl6/J, NP

value: F


title: High Day 28 Sample liver 159

description: Biological replicate Day 28, Treated


title: female islet graft, non-pregnant, biological rep 3


title: High Day 1 Sample liver 125

description: Biological replicate Day 1, Treated


title: male islet graft, non-pregnant, biological rep 2


title: Control Day 28 Sample liver 587

description: Biological replicate Day 28, Control

value: Control


title: male islet graft, non-pregnant, biological rep 1


title: High Day 1 Sample liver 122

description: Biological replicate Day 1, Treated


title: male islet graft, pregnancy day 12.5, biological rep 2

description: Gene expression data from a male islet graft at pregnancy day 12.5

source_name: mouse islet graft, male, C57bl6/J, P12.5


title: High Day 1 Sample liver 123

description: Biological replicate Day 1, Treated


title: female islet graft, non-pregnant, biological rep 1


title: male islet graft, pregnancy day 12.5, biological rep 3


title: Control Day 28 Sample liver 586

description: Biological replicate Day 28, Control


title: High Day 1 Sample liver 121

description: Biological replicate Day 1, Treated


title: High Day 1 Sample liver 124

description: Biological replicate Day 1, Treated


title: Control Day 28 Sample liver 592

description: Biological replicate Day 28, Control


title: Control Day 28 Sample liver 585

description: Biological replicate Day 28, Control


title: islets of non-pregnant female mouse, biological rep 4 (reanalysis)

description: Gene expression data from islets of non-pregnant female mice

source_name: mouse islets, C57bl6/J, NP

value: no


title: Control Day 1 Sample liver 549

description: Biological replicate Day 1, Control


title: female islet graft, pregnancy day 12.5, biological rep 3

description: Gene expression data from a female islet graft at pregnancy day 12.5

source_name: mouse islet graft, female, C57bl6/J, P12.5


title: Control Day 1 Sample liver 548

description: Biological replicate Day 1, Control


title: High Day 1 Sample liver 126

description: Biological replicate Day 1, Treated


title: Control Day 1 Sample liver 552

description: Biological replicate Day 1, Control


title: islets of non-pregnant female mouse, biological rep 2 (reanalysis)


title: female islet graft, pregnancy day 12.5, biological rep 1


title: islets of non-pregnant female mouse, biological rep 1 (reanalysis)


title: islets of non-pregnant female mouse, biological rep 3 (reanalysis)


title: islets of pregnancy day 12.5, biological rep 3 (reanalysis)

description: Gene expression data from islets of mice that were 12.5 day pregnant

source_name: mouse islets, C57bl6/J, P12.5


title: male islet graft, pregnancy day 12.5, biological rep 1


title: islets of pregnancy day 12.5, biological rep 1 (reanalysis)


title: High (162 ug) Day 28 Sample 162

description: Biological replicate Day 28, Treated

source_name: Heart

treatment_protocol: Naïve C57BL/6 mice were flushed twice with 0.6 ml of 0.9% NaCl to obtain approximately 1 ml of bronchoalveolar lavage fluid (BAL). BAL was centrifuged at 400 g for 10 min at 4°C to remove cells. The supernatant was used in the dispersant liquid. A total of 4.05 mg of nano-TiO2 was suspended in 1 ml of MilliQ water containing 0.9% NaCl and 10% v/v acellular BAL. Particle suspensions were prepared by sonicating the samples using a S-450D sonifier (Branson Ultrasonics Corp., Danbury, CT, USA) at 10% amplitude for a total of 16 minutes on ice with alternating 10 s pulses and pauses. One dilution of nano-TiO2 were prepared and used in this experiment: 162 µg. Control vehicle solutions were prepared without the nano-TiO2 (MilliQ water containing 90% of 0.9% NaCl and 10% acellular BAL fluid). The dose162 μg/mouse equals 15 working days at the Danish occupational exposure level for TiO2 (6.0 mg Ti/m3 ~ 9.75 mg TiO2/m3), respectively. Each treatment group consisted of a minimum of 5 animals. Mice in the experimental groups received a single intratracheal instillation of 162 µg of nano-TiO2 in a 40 µl suspension, followed by 150 μl air with a 250 µl SGE glass syringe (250F-LT-GT, MicroLab, Aarhus, Denmark). Intratracheal instillation was performed at 37 ºC on heating plates, under anesthesia using Hypnorm® (fentanyl citrate 0.315 mg/ml and fluanisone 10 mg/ml from Janssen Pharma) and Dormicum® (Midazolam 5 mg/mL from Roche). Control mice received 40 µl of dispersant vehicle only. Following instillation, mice were under observation until they recovered from anaesthesia. Mice were allowed to recover for 24 hours and 28 days following instillation before sacrificing under anaesthesia (Hypnorm/Dormicum). Blood, BAL fluid and tissues were collected. Heart tissues from each experimental and control mice were cut into small pieces, and stored in cryogenic vials and snap frozen immediately in liquid nitrogen. All tissues were stored at -80°C until analysis.

value: heart

tag: sampleID


title: female islet graft, pregnancy day 12.5, biological rep 2


title: Control Day 1 Sample liver 547

description: Biological replicate Day 1, Control


title: islets of  PRLR+/+ mice day 9.5 of pregnancy, biological rep 1

description: Gene expression data from islets of PRLR+/+ mice that were pregnant (day 9.5)

source_name: mouse islets, PRLR+/+, 129Sv, P9.5

tag: genotype

value: PRLR WT


title: islets of pregnancy day 12.5, biological rep 4 (reanalysis)


title: islets of pregnancy day 12.5, biological rep 2 (reanalysis)


title: islets of  PRLR+/+ mice day 9.5 of pregnancye, biological rep 3


title: High (162 ug) Day 28 Sample 161

description: Biological replicate Day 28, Treated


title: Control Day 1 Sample liver 550

description: Biological replicate Day 1, Control

value: liver