title: Lung fibroblasts treated with miR-NC

city: chuo-ku

first: Yu

last: Fujita

state: Tokyo

address: 5-1-1 Tsukiji

department: Research of Molecular Functions and Targets

institute: National Cancer Center Research Institute

description: Sample name: lung fibroblast_miR-NC

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Lung fibroblasts treated with miR-NC

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

extract_protocol: Total RNA was extracted from cultured cells using QIAzol and the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: The miRNA transfection at 25 nM was conducted with DharmaFECT 1 reagent (Thermo Scientific, San Jose, CA) according to the manufacturer’s protocol.

value: primary lung fibroblasts

tag: transfection

value: miR-NC


title: MRC5 cells treated with miR-NC

status: Public on Feb 19 2018

type: RNA

country: Japan

description: Sample name: MRC5_miR-NC

molecule: total RNA

organism: Homo sapiens

source_name: MRC5 cells treated with miR-NC

tag: cell line


title: 1_L28_C39

type: SRA

city: Stanford

first: Mark

last: Krasnow

state: Ca

address: Beckman Center, B400 279 W. Campus Dr.

country: USA

institute: Stanford University

description: Adult distal lung mesenchymal cell 24

library_source: transcriptomic

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Column headers include: tracking_id, class_code,  nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, q0_FPKM, q0_FPKM_lo, q0_FPKM_hi, q0_status.

organism: Mus musculus

source_name: adult mouse lung_single cell

extract_protocol:
To obtain mesenchymal cells from the adult lung, the pulmonary vasculature was cleared and lungs were gently inflated with digestion buffer prior to isolation and mincing of the lung. All tissue was digested at 37C for 45 min using Elastase and DNase I, triturated and subsequently filtered using 100µm and 40µm strainers to obtain a single cell suspension. Mesenchymal cells were enriched by magnetic-assisted cell sorting using CD45, Pecam, and EpCAM depletion. Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions. As a bulk control, cDNA was prepared from approximately 200 cells in a PCR tube using the same protocol and reagents as used for the single cells.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

tag: tissue

value: lung

tag: developmental stage

value: adult

tag: cell type

value: mesenchymal cells

tag: strain


title: 1D_L28_C33

description: Adult distal lung mesenchymal cell 22


title: 1_L28_C26

description: Adult distal lung mesenchymal cell 23


title: 1_L28_C08

description: Adult distal lung mesenchymal cell 26


title: MRC5 cells treated with miR-210

description: Sample name: MRC5_miR-210

source_name: MRC5 cells treated with miR-210


title: 1_L28_C66

description: Adult distal lung mesenchymal cell 25


title: smoking-induced primary HBEC-derived EVs

description:
Sample name: CSE (+)
Human bronchial epithelial cell

hyb_protocol: Labeled RNA was hybridized to the Human miRNA Microarray version 2 8x15K (G4470B Agilent Technologies) with the miRNA Complete Labeling Reagent and Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: Images were quantified using Agilent Feature Extraction software version 10.7.3.1 (Agilent) using default parameters (Grid: 046064_D_F_20121223) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Exosome

label_protocol: RNA sample was labeled with the miRNA Complete Labeling Reagent and Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from EVs using QIAzol and the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Cigarette smoke extract (CSE) was prepared for smoking exposure model in vitro. Forty milliliters of cigarette smoke was drawn into the syringe and slowly bubbled into sterile serum-free cell culture media in a 15-ml BD falcon tube. One cigarette was used for the preparation of 10 mL of solution. CSE solution was filtered (0.22 μm) to remove insoluble particles and was designated as a 100% CSE solution. We analyzed the role of CSE induced HBEC-derived EVs in the airway microenvironment. After HBECs were incubated in the non-FBS containing medium with or without a low-concentration CSE (1.0%) for 2 days, we collected conditioned medium (on day 4, 6) and isolated EVs by ultracentrifugation.

value: HBEC

tag: treatment

value: CSE (+)

tag: isolated by ultracentrifugation

value: extracellular vesicles (EVs)


title: Lung fibroblasts treated with miR-210

description: Sample name: lung fibroblast_miR-210

source_name: Lung fibroblasts treated with miR-210


title: 1p_L28_C13

description: Adult distal lung mesenchymal cell 21


title: 1_L28_C61

description: Adult distal lung mesenchymal cell 20


title: 1_L28_C31

description: Adult distal lung mesenchymal cell 28


title: 1_L28_C54

description: Adult distal lung mesenchymal cell 12


title: 1_L28_C36

description: Adult distal lung mesenchymal cell 17


title: 1_L28_C18

description: Adult distal lung mesenchymal cell 15


title: 1_L28_C15

description: Adult distal lung mesenchymal cell 9


title: 1_L28_C63

description: Adult distal lung mesenchymal cell 16


title: 1p_L28_C51

description: Adult distal lung mesenchymal cell 19


title: 1_L28_C81

description: Adult distal lung mesenchymal cell 10


title: 1_L28_C72

description: Adult distal lung mesenchymal cell 11


title: non-treated primary HBEC-derived EVs

description:
Sample name: CSE (-)
Human bronchial epithelial cell

value: CSE (-)


title: 1_L28_C58

description: Adult distal lung mesenchymal cell 8


title: 1_L28_C10

description: Adult distal lung mesenchymal cell 14


title: 1_L28_C01

description: Adult distal lung mesenchymal cell 6


title: 1_L28_C68

description: Adult distal lung mesenchymal cell 18


title: 1_L28_C55

description: Adult distal lung mesenchymal cell 7


title: 1_L28_C40

description: Adult distal lung mesenchymal cell 5


title: 1_L28_C83

description: Adult distal lung mesenchymal cell 1


title: 1_L28_C87

description: Adult distal lung mesenchymal cell 13


title: 1_L28_C19

description: Adult distal lung mesenchymal cell 3


title: 1_L28_C73

description: Adult distal lung mesenchymal cell 4


title: 1_L28_C60

description: Adult distal lung mesenchymal cell 2


title: S27_paxgene_d28_100

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: paxgene 9224523003_F d28

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the quantified output data was conducted using the limma version 3.4.3 from the R statistical language and other software packages from Bioconductor version 3.6.  Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: biotin

organism: Macaca mulatta

source_name: paxgene

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: Total RNA extraction was performed using the Paxgene Blood RNA kit (QIAGEN, Hilden, Germany)

tag: donor id

tag: samplegroup

tag: time point

tag: acutetg

tag: sampleID


title: S30_paxgene_d28_0

description: paxgene 9224523003_D d28


title: S13_paxgene_d7_100

description: paxgene 9224523003_G d7


title: S07_paxgene_d0_100

description: paxgene 9224523003_A d0


title: Control leaf in light - Rep3

status: Public on Feb 20 2018

city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

description: Gene expression data for control leaves grown in light

hyb_protocol: Hybridization was carried out at 45 °C for 16 h, and the arrays were washed and stained according to the protocol described in the Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays (P/N 703174 Rev.2, Affymetrix)

scan_protocol: The arrays were scanned using GeneAtlas Imaging Station (Affymetrix)

data_processing: Array data was read into R using the oligo package that retrieved the pd.aragene.1.1.st array information, which features (probeset) were annotated using Affymetrix online resources through the getNetAffx function. The technical quality of the arrays was assessed using the arrayQualityMetrics (Kauffmann et al., 2009) R package (data not shown). Next, the resulting microarray data was subjected to a variance stabilizing transformation (within-array normalization) and to cyclic-loess between-array normalization.

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf, in light (short day conditions)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana ecotype Col-0 was grown at 22 0C under short day conditions (8 h light and 16 h dark) with 180 µmol m2 s-1 white light

extract_protocol: About 40 mg frozen material was used for RNA isolation using a RNAeasy kit from QIAGEN and followed by a DNase treatment.

treatment_protocol: For the whole darkened plant (DP), plants were isolated from light by dark boxes and were placed back in the same chamber to conserve the same temperature shift. For the individually darkened leaves (IDL), one fully expanded leaf was covered on each side of the plant (total of 2 covered leaves/plant) with plastic mittens coated with aluminum foil while the rest of the rosette remained under normal light/dark cycle (Keech et al., 2007)

tag: days in darkness

value: leaf

tag: ecotype


title: S21_paxgene_d21_100

description: paxgene 9224522085_K d21


title: S01_paxgene_d-35_100

description: paxgene 9224522085_G d-35


title: S10_paxgene_d0_0

description: paxgene 9224522085_H d0


title: S28_paxgene_d28_100

description: paxgene 9224522045_J d28


title: S25_paxgene_d21_0

description: paxgene 9224523003_K d21


title: S11_paxgene_d7_100

description: paxgene 9224522085_I d7


title: S04_paxgene_d-35_10

description: paxgene 9224522085_A d-35


title: S15_paxgene_d7_0

description: paxgene 9224522085_E d7


title: S16_paxgene_d14_100

description: paxgene 9224522045_F d14


title: S12_paxgene_d7_100

description: paxgene 9224522085_F d7


title: S14_paxgene_d7_10

description: paxgene 9224522045_C d7


title: S18_paxgene_d14_100

description: paxgene 9224522085_B d14


title: S26_paxgene_d28_100

description: paxgene 9224522045_B d28


title: S06_paxgene_d0_100

description: paxgene 9224522085_C d0


title: S24_paxgene_d21_10

description: paxgene 9224523003_E d21


title: S19_paxgene_d14_10

description: paxgene 9224523003_I d14


title: S09_paxgene_d0_10

description: paxgene 9224522045_H d0


title: S05_paxgene_d-35_0

description: paxgene 9224523003_B d-35


title: S08_paxgene_d0_100

description: paxgene 9224522085_D d0


title: S23_paxgene_d21_100

description: paxgene 9224522085_J d21


title: S29_paxgene_d28_10

description: paxgene 9224522045_D d28


title: S03_paxgene_d-35_100

description: paxgene 9224522045_L d-35


title: S17_paxgene_d14_100

description: paxgene 9224522045_E d14


title: S22_paxgene_d21_100

description: paxgene 9224522045_K d21


title: S019_paxgene_d7_100

description: paxgene 8659387134_F d7


title: S036_paxgene_d7_0

description: paxgene 8659387134_G d7


title: S064_paxgene_d21_100

description: paxgene 8659387122_G d21


title: S050_paxgene_d14_100

description: paxgene 8659387112_H d14


title: S029_paxgene_d7_10

description: paxgene 8659387111_L d7


title: S066_paxgene_d21_0

description: paxgene 8659387122_B d21


title: S035_paxgene_d7_0

description: paxgene 8659387134_B d7


title: S052_paxgene_d14_10

description: paxgene 8659387122_A d14


title: S086_paxgene_d28_100

description: paxgene 8659387111_J d28


title: S069_paxgene_d21_10

description: paxgene 8659387111_B d21


title: S058_paxgene_d21_0

description: paxgene 8659387134_C d21


title: S055_paxgene_d21_100

description: paxgene 8659387111_A d21


title: S093_paxgene_d-35_10

description: paxgene 8659387134_K d-35


title: S022_paxgene_d7_0

description: paxgene 8659387112_B d7


title: S088_paxgene_d28_10

description: paxgene 8659387111_K d28


title: S010_paxgene_d0_100

description: paxgene 8659387134_A d0


title: S101_paxgene_d-35_10

description: paxgene 8659387112_F d-35


title: S089_paxgene_d28_0

description: paxgene 8659387134_H d28


title: S072_paxgene_d21_0

description: paxgene 8659387111_F d21


title: S028_paxgene_d7_100

description: paxgene 8659387111_H d7


title: S070_paxgene_d21_10

description: paxgene 8659387112_C d21


title: S038_paxgene_d14_10

description: paxgene 8659387122_F d14


title: S065_paxgene_d21_10

description: paxgene 8659387100_H d21


title: S075_paxgene_d28_10

description: paxgene 8659387111_I d28


title: S003_paxgene_d0_10

description: paxgene 8659387100_I d0


title: S053_paxgene_d14_0

description: paxgene 8659387122_D d14


title: S046_paxgene_d14_100

description: paxgene 8659387111_E d14


title: S030_paxgene_d7_0

description: paxgene 8659387100_J d7


title: S02_paxgene_d-35_100

description: paxgene 9224522045_A d-35


title: S071_paxgene_d21_0

description: paxgene 8659387100_G d21


title: S001_paxgene_d0_100

description: paxgene 8659387100_E d0


title: S002_paxgene_d0_10

description: paxgene 8659387099_B d0


title: S094_paxgene_d-35_0

description: paxgene 8659387100_C d-35


title: S015_paxgene_d0_10

description: paxgene 8659387099_C d0


title: S034_paxgene_d7_10

description: paxgene 8659387099_J d7


title: S049_paxgene_d14_0

description: paxgene 8659387099_F d14


title: S056_paxgene_d21_10

description: paxgene 8659387011_K d21


title: S085_paxgene_d28_0

description: paxgene 8659387099_G d28


title: S083_paxgene_d28_10

description: paxgene 8659387093_J d28


title: S102_paxgene_d-35_0

description: paxgene 8659387099_K d-35


title: S103_paxgene_d-35_0

description: paxgene 8659387093_L d-35


title: S012_paxgene_d0_0

description: paxgene 8659387093_G d0


title: S105_paxgene_d-35_10

description: paxgene 8659387093_B d-35


title: S051_paxgene_d14_10

description: paxgene 8659387093_H d14


title: S013_paxgene_d0_0

description: paxgene 8659387011_G d0


title: S082_paxgene_d28_100

description: paxgene 8659387011_H d28


title: S018_paxgene_d0_0

description: paxgene 8659387093_F d0


title: S048_paxgene_d14_0

description: paxgene 8659387100_F d14


title: S106_paxgene_d-35_10

description: paxgene 8659387099_I d-35


title: S039_paxgene_d14_10

description: paxgene 8659387011_I d14


title: S004_paxgene_d0_0

description: paxgene 8659387093_D d0


title: S090_paxgene_d28_0

description: paxgene 8659387093_E d28


title: S031_paxgene_d7_0

description: paxgene 8659387093_I d7


title: S032_paxgene_d7_100

description: paxgene 8659387099_E d7


title: S040_paxgene_d14_0

description: paxgene 8659387011_J d14


title: S107_paxgene_d-35_0

description: paxgene 8659387011_F d-35


title: S108_paxgene_d-35_0

description: paxgene 8659387011_B d-35


title: S057_paxgene_d21_10

description: paxgene 8659387011_E d21


title: S074_paxgene_d28_10

description: paxgene 8556388001_E d28


title: S054_paxgene_d14_0

description: paxgene 8556388001_L d14


title: S033_paxgene_d7_10

description: paxgene 8659387011_A d7


title: S020_paxgene_d7_10

description: paxgene 8556388001_K d7


title: S021_paxgene_d7_10

description: paxgene 8556388001_C d7


title: S017_paxgene_d0_0

description: paxgene 8546278060_K d0


title: S073_paxgene_d28_100

description: paxgene 8556388025_A d28


title: S014_paxgene_d0_100

description: paxgene 8556388025_C d0


title: S068_paxgene_d21_100

description: paxgene 8546278060_J d21


title: S067_paxgene_d21_0

description: paxgene 8546278060_I d21


title: S104_paxgene_d-35_100

description: paxgene 8556388001_J d-35


title: S092_paxgene_d-35_10

description: paxgene 8546278060_L d-35


title: MFE 296 PD res 4

city: London

first: Jun

last: Wang

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

description:
Resistant to PD173074 small molecule FGFR inhibitor.
Replicate 4

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with GenomeStudio.

source_name: MFE-296 resistant to PD173074

label_protocol: 100 ng of total RNA was reverse transcribed and biotin labeled.

extract_protocol: Qiagen RNeasy Micro kit.

tag: parental cell line

tag: parental cell type

value: endometrial cancer cell line

tag: resistance


title: MFE 296 PD res 2

description:
Resistant to PD173074 small molecule FGFR inhibitor.
Replicate 2


title: S047_paxgene_d14_10

description: paxgene 8546278060_E d14


title: MFE 296 AZ res 4

description:
Resistant to AZD4547 small molecule FGFR inhibitor.
Replicate 4

source_name: MFE-296 resistant to AZD4547


title: S016_paxgene_d0_10

description: paxgene 8546278060_F d0


title: S084_paxgene_d28_0

description: paxgene 8546278060_A d28


title: MFE 296 parental 3

description:
Parental cell line.
Replicate 3

source_name: MFE-296 parental cell line

tag: cell line


title: S100_paxgene_d-35_100

description: paxgene 8546278060_H d-35


title: S091_paxgene_d-35_100

description: paxgene 8546278060_B d-35


title: MFE 296 PD res 3

description:
Resistant to PD173074 small molecule FGFR inhibitor.
Replicate 3


title: S037_paxgene_d14_100

description: paxgene 8546278060_G d14


title: MFE 296 parental 2

description:
Parental cell line.
Replicate 2


title: MFE 296 PD res 1

description:
Resistant to PD173074 small molecule FGFR inhibitor.
Replicate 1


title: S011_paxgene_d0_10

description: paxgene 8546278060_D d0


title: MFE 296 parental 1

description:
Parental cell line.
Replicate 1


title: MFE 296 AZ res 3

description:
Resistant to AZD4547 small molecule FGFR inhibitor.
Replicate 3


title: MFE 296 AZ res 2

description:
Resistant to AZD4547 small molecule FGFR inhibitor.
Replicate 2


title: MFE 296 AZ res 1

description:
Resistant to AZD4547 small molecule FGFR inhibitor.
Replicate 1


title: BloodGT3110

type: genomic

city: Wageningen

first: Veronika

last: Laine

address: Droevendaalsesteeg 10

department: Animal Ecology

country: Netherlands

institute: NIOO-KNAW

description: DishQualityControl 0.982

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
A total of 3.116 great tits were genotyped using a custom made Affymetrix® great tit 650K SNP chip at Edinburgh Genomics (Edinburgh, United Kingdom). SNP calling was done following the Affymetrix® best practices workflow by using the Axiom® Analysis Suite 1.1.
The processed data file "SamValuesAll.txt" includes the Genotype Call (SNP call): AA (0), AB (1), BB (2), and NoCall (3); Columns with header 'A' or 'B' represent the raw signal intensity from the probes targeting each allele (i.e. A and B).

label: Biotin

molecule: genomic DNA

organism: Parus major

source_name: wild

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Whole blood samples were stored in either 1 ml Cell Lysis Solution (Gentra Puregene Kit, Qiagen, USA) or Queens buffer. DNA was extracted by using the FavorPrep 96-Well Genomic DNA Extraction Kit (Favorgen Biotech corp.). DNA quality and DNA concentration were measured on a Nanodrop 2000 (Thermo Scientific).

tag: tissue

value: blood

tag: Sex

value: female


title: BloodGT3111

description: DishQualityControl 0.987

source_name: captive


title: BloodGT3113

description: DishQualityControl 0.983


title: BloodGT3112

description: DishQualityControl 0.993

value: male


title: BloodGT3114

description: DishQualityControl 0.986


title: BloodGT3115

description: DishQualityControl 0.99


title: BloodGT3109

description: DishQualityControl 0.987


title: wild-type mock_1dpi_rep1

city: Madrid

first: Sara

last: Sopeña Torres

address: Campus Montegancedo - Autovia M40 km.38

country: Spain

institute: Centro de Biotecnologia y Genomica de Plantas (UPM-INIA)

description: Gene expression at 1 day post-inoculation in mock-treated wild-type plants, replicate 1

hyb_protocol: 1650 ng of Cy3 probes were mixed and hybridized to an Arabidopsis 4 Oligo Microarray 4x44K (G2519F_021169, Agilent Technologies) for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in an hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation.

scan_protocol: Arrays were scanned at 3mm resolution on Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent Technologies). Local background correction and normalization of expression data were performed using normexp and loess methods, respectively. To have similar distribution across arrays and to achieve consistency among arrays, log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate p-values were corrected by using the method of Benjamani and Hochberg . The expected false discovery rate was controlled to be less than 5%.

source_name: wild-type, mock treatment, 1dpi, replicate 1

label_protocol: 200 ng of total RNA was reverse transcribed using T7 promoter primer and the cDNA was converted to aRNA using T7 RNA polimerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP.

growth_protocol: Arabidopsis thaliana plants were grown in phytochambers on a sterilized mixture of soil and vermiculite (3:1) with a 10 h day/14 h night photoperiod, a temperature of 22ºC day/20ºC night and 50% relative humidity. Light intensity was fixed to 120–150 umol m-2 s-1 (Hernández-Blanco et al., 2007)

extract_protocol: Frozen samples were ground using mortar and pestle and total RNA was extracted with a phenol/chloroform method, as described in Berrocal-Lobo et al., 2002. Total RNA was further purified using the RNeasy Kit (Qiagen) and quantified with a NanoDrop ND-100 spectrophotometer (Thermo Scientific). RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies.

treatment_protocol: 18-day-old Arabidopsis plants were spray-inoculated with a spore suspension (4 x 10^6 spores/ml) of PcBMM (0.6 ml per pot containing 5 plants) or with water (mock treatment). After inoculation, plants were transferred to a growth chamber with a 10 h day/14 h night photoperiod, a temperature of 24ºC day/22ºC night, and light intensity was maintained at 120–150 umol m-2 s-1. Inoculated plants were kept under high humidity in covered trays. Samples were collected 1 day after inoculation and frozen in liquid nitrogen.

tag: background

tag: genotype

value: wild-type

value: water (mock)

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description: Gene expression at 1 day post-inoculation in PcBMM-infected wild-type plants, replicate 3

source_name: wild-type, PcBMM infection, 1 dpi, replicate 3

tag: treatment

value: PcBMM


title: CA-YDA PcBMM_1dpi_rep1

description: Gene expression at 1 day post-inoculation in PcBMM-infected CA-YDA plants, replicate 1

source_name: CA-YDA, PcBMM infection, 1dpi, replicate 1

value: CA-YDA


title: CA-YDA mock_1dpi_rep1

description: Gene expression at 1 day post-inoculation in mock-treated CA-YDA plants, replicate 1

source_name: CA-YDA, mock treatment, 1dpi, replicate 1


title: CA-YDA mock_1dpi_rep2

description: Gene expression at 1 day post-inoculation in mock-treated CA-YDA plants, replicate 2

source_name: CA-YDA, mock treatment, 1dpi, replicate 2


title: wild-type PcBMM_1dpi_rep1

description: Gene expression at 1 day post-inoculation in PcBMM-infected wild-type plants, replicate 1

source_name: wild-type, PcBMM infection, 1 dpi, replicate 1


title: MFE 296 parental 4

description:
Parental cell line.
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description: Gene expression at 1 day post-inoculation in PcBMM-infected CA-YDA plants, replicate 2

source_name: CA-YDA, PcBMM infection, 1dpi, replicate 2


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source_name: wild-type, PcBMM infection, 1 dpi, replicate 2


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