title: B. subtilis_CHG medium_rep2

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

description: growth rate: μ=1.7 h-1

hyb_protocol: 600 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2505C (Agilent Technologies).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).

organism: Bacillus subtilis

source_name: B. subtilis wild type_exponential growth in CHG medium

label_protocol:
For cDNA synthesis, 10 µg of total RNA were mixed with random primers (Promega) and spike-ins (One-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added:
10 µl of 5x First Strand Buffer, 5 µl of 0.1 M DTT, 0.5 µl of dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP (GE Healthcare) and 2 µl of SuperScript II reverse transcriptase (Invitrogen). The reaction was incubated at 42°C for 60 min
and then heated to 70 °C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare).

growth_protocol: B. subtilis BSB1 was grown aerobically at 37 °C in S medium, CH medium, CHG medium (Sharpe et al., 1998; PMID 9457856) or M9SE medium (M9 succinate/glutamate) (PMID 22383849).

extract_protocol: Cells were harvested and total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002; PMID 11948165).

value: Bacillus subtilis BSB1 (Trp+ derivative of strain 168)


title: B. subtilis_CHG medium_rep1

status: Public on Apr 18 2016

type: RNA

country: Germany

description: growth rate: μ=1.7 h-1

molecule: total RNA

tag: strain


title: Survivor2_Day0

city: Stanford

first: David

middle: S

last: Schneider

state: CALIFORNIA

address: 299 Campus Drive

department: Microbiology and Immunology

country: USA

institute: Stanford University

hyb_protocol: Standard Illumina hybridization protocol using streptavidin-Cy3 for detection.

scan_protocol: Standard Illumina scanning protocol. Slides were scanned on an Illumina Beadstation.

data_processing: Data was normalized using percentile normalization with GeneSpring 12.1-GX and a baseline transformation (median of all samples) was applied.

organism: Mus musculus

source_name: Whole blood

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

extract_protocol: RNA was extracted from 10 ul of whole blood using the Mouse RiboPure Blood RNA isolation kit (Ambion-Life Technologies). Quality control was performed using the Agilent 2100 BioAnalyzer. RNA was amplified using Ambion Illumina RNA amplificicatin kit with biotin UTP labeling.

treatment_protocol: Whole blood was stored in 500 ul of RNA later in -80 C until further processed.

tag: mouse

tag: red blood cells

tag: parasite density

tag: temperature

tag: weight

tag: days post infection

tag: outcome

value: Survivor


title: B. subtilis_CH medium_rep4

description: growth rate: μ=1.2 h-1

source_name: B. subtilis wild type_exponential growth in CH medium


title: control non-infected plant ecotype Wt-1_plant 2

city: Valencia

first: Julia

last: Hillung

state: Valencia

address: Ingeniero Fausto Elio s/n

department: IBMCP

country: Spain

institute: CSIC-UPV

description: negative control

scan_protocol: GenePix

data_processing: Agilent ProcessedSignal (Agilent Feature Extraction Software) was standardized using quantile normalization.

organism: Arabidopsis thaliana

source_name: whole plant, non-infected

label_protocol: See Agilent Technologies's web site at http://www.agilent.com/ Quick Amp Labeling Kit One Color labeled with Cy3

growth_protocol: plants were mantained in a BSL-2 greenhouse at 16:8h light:dark and 24:20 day:night temperature until sample collection on 21 days post infection.

extract_protocol: Invitek, InviTrap® Spin Plant RNA Mini Kit, following manual

treatment_protocol: Plants infected with tobacco etch potyvirus isolate At17b (TEV-At17b), with in each host ecotype evolved isolates derived from TEV-At17b and control non-infected plants.

tag: host ecotype

tag: viral lineage

value: mock

tag: block


title: Survivor2_Day6


title: control non-infected plant ecotype Wt-1_plant 5

description: negative control

hyb_protocol: See Agilent Technologies's web site at http://www.agilent.com/


title: Survivor2_Day1


title: B. subtilis_CH medium_rep1

description: growth rate: μ=1.2 h-1


title: B. subtilis_CH medium_rep3

description: growth rate: μ=1.2 h-1


title: Survivor1_Day24


title: B. subtilis_S medium_rep4

description: growth rate: μ=0.6 h-1

source_name: B. subtilis wild type_exponential growth in S medium


title: B. subtilis_CH medium_rep2

description: growth rate: μ=1.2 h-1


title: B. subtilis_CHG medium_rep3

description: growth rate: μ=1.7 h-1


title: B. subtilis_CHG medium_rep4

description: growth rate: μ=1.7 h-1


title: Survivor1_Day25


title: control non-infected plant ecotype St-0_plant 5

description: negative control


title: B. subtilis_S medium_rep2

description: growth rate: μ=0.6 h-1


title: B. subtilis_S medium_rep3

description: growth rate: μ=0.6 h-1


title: Di-2 infected replicate 3

description: non-evolved

source_name: whole plant, infected

value: ancestral, TEV-At17b


title: control non-infected plant ecotype St-0_plant 4

description: negative control


title: Survivor1_Day23


title: control non-infected plant ecotype St-0_plant 2

description: negative control


title: B. subtilis_M9SE medium_rep4

description: growth rate: μ=0.4 h-1

source_name: B. subtilis wild type_exponential growth in M9SE medium


title: B. subtilis_S medium_rep1

description: growth rate: μ=0.6 h-1


title: B. subtilis_M9SE medium_rep3

description: growth rate: μ=0.4 h-1


title: control non-infected plant ecotype Ei-2_plant 5

description: negative control


title: B. subtilis_M9SE medium_rep1

description: growth rate: μ=0.4 h-1


title: control non-infected plant ecotype Ei-2_plant 4

description: negative control


title: Survivor1_Day21


title: B. subtilis_M9SE medium_rep2

description: growth rate: μ=0.4 h-1


title: control non-infected plant ecotype Di-2_plant 3

description: negative control


title: Survivor1_Day19


title: Survivor1_Day16


title: Survivor1_Day17


title: Survivor1_Day14


title: Survivor1_Day20


title: Survivor1_Day22


title: control non-infected plant ecotype Ler-0_plant 3

description: negative control


title: Survivor1_Day13


title: control non-infected plant ecotype Ler-0_plant 2

description: negative control


title: Survivor1_Day18


title: control non-infected plant ecotype Di-2_plant 2

description: negative control


title: Survivor1_Day15


title: control non-infected plant ecotype Ei-2_plant 2

description: negative control


title: control non-infected plant ecotype Di-2_plant 5

description: negative control


title: ecotype Ei-2_infected with lineage 3 of virus evolved in Ei-2_plant 4

description: local host


title: ecotype Ei-2_infected with lineage 2 of virus evolved in Ei-2_plant 5

description: local host


title: control non-infected plant ecotype Ler-0_plant 1

description: negative control


title: ecotype Ei-2_infected with lineage 3 of virus evolved in Ei-2_plant 1

description: local host


title: Survivor1_Day11


title: Survivor1_Day10


title: ecotype Ei-2_infected with lineage 2 of virus evolved in Ei-2_plant 3

description: local host


title: Survivor1_Day9


title: ecotype Ei-2_infected with lineage 2 of virus evolved in Ei-2_plant 2

description: local host


title: Survivor1_Day8


title: Survivor1_Day6


title: Survivor1_Day12


title: ecotype Ei-2_infected with lineage 1 of virus evolved in Ei-2_plant 5

description: local host


title: Survivor1_Day2


title: ecotype Ei-2_infected with lineage 1 of virus evolved in Ei-2_plant 4

description: local host


title: Survivor1_Day3


title: Survivor1_Day5


title: Survivor1_Day1


title: Survivor1_Day7


title: ecotype Ei-2_infected with lineage 3 of virus evolved in St-0_plant 3

description: most specialist viral strain


title: ecotype Wt-1_infected with lineage 3 of virus evolved in Wt-1_plant 4

description: local host


title: ecotype Wt-1_infected with lineage 2 of virus evolved in Wt-1_plant 6

description: local host


title: ecotype Ei-2_infected with lineage 3 of virus evolved in St-0_plant 4

description: most specialist viral strain


title: ecotype Wt-1_infected with lineage 3 of virus evolved in Wt-1_plant 2

description: local host


title: ecotype Ei-2_infected with lineage 3 of virus evolved in St-0_plant 1

description: most specialist viral strain


title: ecotype Ei-2_infected with lineage 1 of virus evolved in Ei-2_plant 1

description: local host


title: Survivor1_Day0


title: ecotype Wt-1_infected with lineage 1 of virus evolved in Wt-1_plant 6

description: local host


title: Survivor1_Day4


title: ecotype Wt-1_infected with lineage 3 of virus evolved in St-0_plant 3

description: most specialist viral strain


title: ecotype Wt-1_infected with lineage 3 of virus evolved in St-0_plant 2

description: most specialist viral strain


title: ecotype Wt-1_infected with lineage 3 of virus evolved in Wt-1_plant 5

description: local host


title: ecotype Wt-1_infected with lineage 1 of virus evolved in Wt-1_plant 5

description: local host


title: ecotype Wt-1_infected with lineage 1 of virus evolved in Wt-1_plant 3

description: local host


title: ecotype Wt-1_infected with lineage 2 of virus evolved in Wt-1_plant 1

description: local host


title: ecotype Di-2_infected with lineage 3 of virus evolved in Di-2_plant 5

description: local host


title: ecotype Di-2_infected with lineage 3 of virus evolved in Di-2_plant 3

description: local host


title: ecotype Wt-1_infected with lineage 3 of virus evolved in St-0_plant 1

description: most specialist viral strain


title: ecotype St-0_infected with lineage 3 of virus evolved in St-0_plant 6

description: local host


title: ecotype Di-2_infected with lineage 3 of virus evolved in St-0_plant 3

description: most specialist viral strain


title: ecotype St-0_infected with lineage 3 of virus evolved in St-0_plant 7

description: local host


title: ecotype Di-2_infected with lineage 2 of virus evolved in Di-2_plant 2

description: local host


title: ecotype Wt-1_infected with lineage 2 of virus evolved in Wt-1_plant 2

description: local host


title: ecotype Di-2_infected with lineage 1 of virus evolved in Di-2_plant 3

description: local host


title: ecotype St-0_infected with lineage 2 of virus evolved in St-0_plant 5

description: local host


title: ecotype Di-2_infected with lineage 2 of virus evolved in Di-2_plant 3

description: local host


title: ecotype St-0_infected with lineage 3 of virus evolved in St-0_plant 8

description: local host


title: ecotype Di-2_infected with lineage 3 of virus evolved in Di-2_plant 2

description: local host


title: ecotype Di-2_infected with lineage 3 of virus evolved in St-0_plant 1

description: most specialist viral strain


title: ecotype Wt-1_infected with lineage 1 of virus evolved in Ler-0_plant 3

description: most generalist viral strain


title: ecotype St-0_infected with lineage 1 of virus evolved in St-0_plant 7

description: local host


title: ecotype Di-2_infected with lineage 3 of virus evolved in St-0_plant 2

description: most specialist viral strain


title: ecotype St-0_infected with lineage 1 of virus evolved in St-0_plant 1

description: local host


title: ecotype Di-2_infected with lineage 1 of virus evolved in Di-2_plant 4

description: local host


title: ecotype Wt-1_infected with lineage 1 of virus evolved in Ler-0_plant 1

description: most generalist viral strain


title: ecotype Ei-2_infected with lineage 1 of virus evolved in Ler-0_plant 2

description: most generalist viral strain


title: ecotype Ei-2_infected with lineage 1 of virus evolved in Ler-0_plant 1

description: most generalist viral strain


title: ecotype Di-2_infected with lineage 1 of virus evolved in Ler-0_plant 3

description: most generalist viral strain


title: ecotype Di-2_infected with lineage 1 of virus evolved in Ler-0_plant 1

description: most generalist viral strain


title: ecotype St-0_infected with lineage 1 of virus evolved in Ler-0_plant 5

description: most generalist viral strain


title: ecotype St-0_infected with lineage 1 of virus evolved in Ler-0_plant 4

description: most generalist viral strain


title: ecotype St-0_infected with lineage 2 of virus evolved in St-0_plant 4

description: local host


title: ecotype Di-2_infected with lineage 1 of virus evolved in Ler-0_plant 5

description: most generalist viral strain


title: ecotype St-0_infected with lineage 1 of virus evolved in St-0_plant 6

description: local host


title: ecotype St-0_infected with lineage 2 of virus evolved in St-0_plant 3

description: local host


title: ecotype Di-2_infected with lineage 2 of virus evolved in Di-2_plant 1

description: local host


title: ecotype Wt-1_infected with lineage 1 of virus evolved in Ler-0_plant 2

description: most generalist viral strain


title: ecotype Ei-2_infected with lineage 1 of virus evolved in Ler-0_plant 5

description: most generalist viral strain


title: miR-33* mimic 2

city: New York

first: Kathryn

last: Moore

state: New York

address: 522 First Ave, Smilow 707

department: Medicine

institute: NYU Medical Center

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes (per each sample group); 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]. Therefore, sample data table contains non_normalized data for each sample.
the fold_change.txt reports test/control (representative)

label: SYBR

source_name: peritoneal macrophage_miR-33* mimic

label_protocol: Mouse Autophagy RT2 Profiler PCR Arrays (PAMM-084Z, SABiosciences) as per the manufacturer’s protocol.

growth_protocol: Peritoneal macrophages from adult mice were harvested by peritoneal lavage four days after intraperitoneal injection of thioglycollate.  The cells were maintained in culture as adherent monolayer in medium containing DMEM, 10% FBS, and 20% L929-conditioned medium.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo Research)

treatment_protocol: cells were transfected with  miRNA mimics (miR-mimic-33/miR-mimic-33*) or  miRNA inhibitors (anti-miR-33 ASO/anti-miR-33* ASO) Lipofectamine RNAiMax Transfection Reagent

tag: strain background

tag: cell type

value: peritoneal macrophage

tag: transfected with

value: 80-120 nM miRIDIAN miRNA mimics (miR-mimic-33*)

tag: time

value: 48h post txf


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Ei-2_plant 3

description: alternative host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Ei-2_plant 2

description: alternative host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Ei-2_plant 1

description: alternative host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Ei-2_plant 2

description: alternative host


title: ecotype St-0_infected with lineage 1 of virus evolved in Ler-0_plant 3

description: most generalist viral strain


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Ei-2_plant 1

description: alternative host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Ei-2_plant 4

description: alternative host


title: control ASO -4

description: control aso4

source_name: peritoneal macrophage_control ASO

value: inhibitor negative control sequence


title: anti-mir-33 ASO -3

description: anti-miR-33 ASO 3

source_name: peritoneal macrophage_anti-mir-33 ASO

value: 80-120 nM miRIDIAN miRNA inhibitors (anti-miR-33 ASO)


title: anti-mir-33* ASO -3

description: anti-miR-33* ASO 3

source_name: peritoneal macrophage_anti-mir-33* ASO

value: 80-120 nM miRIDIAN miRNA inhibitors (anti-miR-33* ASO)


title: control mimic -3

description: control mim3

source_name: peritoneal macrophage_control mimic

value: non-targeting control mimics sequence


title: anti-mir-33* ASO -2

description: anti-miR-33* ASO 2


title: anti-mir-33* ASO -4

description: anti-miR-33* ASO 4


title: control ASO -6

description: control aso6


title: control ASO -7

description: control aso7


title: control ASO -5

description: control aso5


title: anti-mir-33* ASO -1

description: anti-miR-33* ASO  1


title: control mimic -4

description: control mim4


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Ei-2_plant 1

description: alternative host


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Ei-2_plant 4

description: alternative host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Wt-1_plant 2

description: alternative host


title: miR-33* mimic 1


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Ei-2_plant 3

description: alternative host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Wt-1_plant 5

description: alternative host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Wt-1_plant 5

description: alternative host


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Wt-1_plant 4

description: alternative host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Wt-1_plant 4

description: alternative host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Wt-1_plant 1

description: alternative host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Wt-1_plant 1

description: alternative host


title: anti-mir-33 ASO -2

description: anti-miR-33 ASO 2


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Wt-1_plant 3

description: alternative host


title: control ASO -2

description: control aso2


title: mimic-33 -1

source_name: peritoneal macrophage_mimic-33

value: 80-120 nM miRIDIAN miRNA mimics (miR-mimic-33)


title: mimic-33 -3


title: mimic-33 -2


title: mimic-33 -4


title: control mimic -2

description: control mim2


title: control mimic -1

description: control mim1


title: control ASO -3

description: control aso3


title: anti-mir-33 ASO -1

description: anti-miR-33 ASO  1


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Di-2_plant 2

description: alternative host


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Di-2_plant 3

description: alternative host


title: control ASO -1

description: control aso1


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Di-2_plant 4

description: alternative host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in St-0_plant 4

description: most specialist viral strain


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Di-2_plant 3

description: alternative host


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Di-2_plant 2

description: alternative host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in St-0_plant 1

description: most specialist viral strain


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Di-2_plant 3

description: alternative host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Di-2_plant 4

description: alternative host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in St-0_plant 4

description: alternative host


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Di-2_plant 4

description: alternative host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Di-2_plant 1

description: alternative host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in St-0_plant 3

description: alternative host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Ler-0_plant 2

description: local host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in St-0_plant 5

description: alternative host


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Ler-0_plant 3

description: local host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Ler-0_plant 4

description: local host


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Ler-0_plant 3

description: local host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Ler-0_plant 1

description: local host


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Ler-0_plant 2

description: local host


title: ecotype Ler-0_infected with lineage 1 of virus evolved in Ler-0_plant 4

description: local host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in Ler-0_plant 3

description: local host


title: ecotype Ler-0_infected with lineage 3 of virus evolved in St-0_plant 3

description: most specialist viral strain


title: Aspergillus nidulans grown in 0.7M of cholinium chloride media for fifteen days, biological rep. 3

city: Lisboa

first: Cristina

middle: Silva

last: Pereira

address: Rua da Quinta Grande nº6

country: Portugal

institute: Instituto de Tecnologia Química e Biológica (ITQB)

description: Gene expression data A. nidulans grown in 0.7M of cholinium chloride media for fifteen days

hyb_protocol: A total of 200µl of the hybridisation mixture containing 10µg of fragmented cRNA was hybridised on arrays for 16 hours at 45 °C.  Standard post hybridisation washes and double-stain protocols (FS450_0001) were used on an Affymetrix GeneChip Fluidics Station 450, in conjunction with the GeneChip Hybridisation Wash and Stain Kit (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Subsequent analysis was carried out with DNA-Chip Analyzer (dChip) 2010 (http://www.dchip.org) applying a probeset mask file considering only the A. nidulans probes on the array representing 9674 transcripts. The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the 9 arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model.

label: biotin

organism: Aspergillus nidulans

source_name: Aspergillus nidulans mycelia after growth in 0.7M of cholinium chloride media for fifteen days

label_protocol: RNA was processed for use on Affymetrix custom dual species FungiANC arrays,  according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Fungal cultures with a density of Aspergillus nidulans (FGSC A4) conidia of 1.00E+5 per mL (50 mL, minimal media containing 0.1% w/v glucose) were incubated in the dark, at 27 °C and with 70% humidity, under orbital agitation (90 rpm).

extract_protocol: Total RNA was isolated from fungal mycelia (grounded to powder using mortar and pestle in liquid nitrogen) using the RNeasy Plant Mini Kit (QIAGEN) and further purified following a standard ethanol precipitation.

treatment_protocol: Aspergillus nidulans (FGSC A4) cultures were incubated with 1.00E+5 conidia per mL (50 mL), in the dark, at 27 °C and with 70% humidity and under orbital agitation (90 rpm), for fifteen days. The media used was  minimal media containing 0.1% w/v glucose (control), minimal media with 0.1% w/v glucose supplemented with cholinium chloride (0.7M) and  minimal media with 0.1% w/v glucose supplemented with 1-ethyl-3-methylimidazolium chloride (0.7M). After fifteen days the mycelia and the culture media were recovered and preserved at -80 °C.

tag: culture conditions

value: Fifteen days in 0.7M of cholinium chloride media


title: Aspergillus nidulans grown in 0.7M of 1-ethyl-3-methylimidazolium chloride media for fifteen days, biological rep. 1

description: Gene expression data A. nidulans grown in 0.7M of 1-ethyl-3-methylimidazolium chloride media for fifteen days

source_name: Aspergillus nidulans mycelia after growth in 0.7M of 1-ethyl-3-methylimidazolium chloride media for fifteen days

value: Fifteen days in 0.7M of 1-ethyl-3-methylimidazolium chloride media


title: Aspergillus nidulans grown in 0.7M of cholinium chloride media for fifteen days, biological rep. 2


title: Aspergillus nidulans grown in 0.7M of 1-ethyl-3-methylimidazolium chloride media for fifteen days, biological rep. 3


title: Aspergillus nidulans grown in 0.7M of 1-ethyl-3-methylimidazolium chloride media for fifteen days, biological rep. 2


title: Aspergillus nidulans grown in glucose media for fifteen days, biological rep. 3

description: Gene expression data A. nidulans grown in glucose media for fifteen days

source_name: Aspergillus nidulans mycelia after growth in glucose media for fifteen days

value: Fifteen days in glucose media


title: Aspergillus nidulans grown in glucose media for fifteen days, biological rep. 2


title: Aspergillus nidulans grown in 0.7M of cholinium chloride media for fifteen days, biological rep. 1


title: Aspergillus nidulans grown in glucose media for fifteen days, biological rep. 1


title: ecotype Ler-0_infected with lineage 2 of virus evolved in Ler-0_plant 4

description: local host


title: 15h Pneumococcus-infected, non-epithelial cells, biological rep2

city: Boston

first: Hirofumi

last: Kamata

state: Massachusetts

address: 72 East Concord Street

department: The Pulmonary Center

institute: Boston University, School of Medicine

description: Gene expression data from adult mouse lungs

hyb_protocol: The labeled, fragmented DNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7GPlus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene10stv1mmentrezg R package (version 14.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.download/MoGene10stv1_Mm_ENTREZG_14.0.0.zip).

label: Biotin

source_name: Lung non-epithelial cells from infected mouse

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was purified from sorted cells using the Qiagen RNeasy Micro Kit accordint to manufacturer's instructions.

tag: tissue

value: Lung

tag: infection

value: 15h intratracheal Pneumococcus


title: 15h Pneumococcus-infected, non-epithelial cells, biological rep1

tag: strain


title: 15h Pneumococcus-infected, non-epithelial cells, biological rep3


title: Uninfected, epithelial cells, biological rep2

source_name: Lung epithelial cells from uninfected mouse

value: No treatment


title: Control 6-28-10

status: Public on Apr 16 2016

city: Palo Altp

first: Mollie

middle: Elizabeth

last: Jacobs

state: CA

address: 3801 Miranda AVE

description: treated with ethanol

hyb_protocol: standard Affymetrix protocol; conducted by Stanford University Protein and Nucleic Acid Facility

data_processing:
Affymetric Expression Console RMA normalization using miRNA-1_0_2Xgain
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

growth_protocol: mpkCCD c14 cells were seeded onto 24-mm permeable supports (0.4 μm pore size, Costar, Corning, NY) and grown in defined medium until transepithelial resistance (Rte) reached values between 800 and 1200 Ω·cm2

extract_protocol: RNA was isolated using the miRNeasy Mini Kit

treatment_protocol: Cells were then switched to supplement and serum-free media for 48 hours before treatment with aldosterone (10-6 M) or 100% ethanol vehicle.

tag: cell line

tag: tissus source

value: mouse cortical collecting duct,

tag: treated with

value: ethanol (vehicle)


title: Uninfected, epithelial cells, biological rep1


title: P14 24h

status: Public on Apr 17 2016

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004)

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour and 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 10.10 to produce spatially detrended and background subtracted gProcessedSignal intensities. Genespring was used for quantile normalizaton.

organism: Homo sapiens

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

growth_protocol: Human tendon fibroblasts were cultured in high glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 2 mm L-glutamine, 100 units/ml penicillin, 100 mg/ml streptomycin and 50 µg/ml ascorbic acid in a humidified incubator containing 5% CO2 at 37ºC

extract_protocol: not provided

treatment_protocol: Human tendon fibroblasts isolated from 3 individuals were treated with recombinant human Angiopoietin-like 4 at a concentration of 5 µg/ml for 4 or 24 hours. Control cells were left untreated for the same time periods

value: tendon fibroblasts

tag: time point

tag: patient id


title: 15h Pneumococcus-infected, epithelial cells, biological rep1

source_name: Lung epithelial cells from infected mouse


title: P16 24h


title: P13 24h


title: Control 7-13-10

description: treated with ethanol

scan_protocol: standard Affymetrix protocol; conducted by Stanford University Protein and Nucleic Acid Facility


title: P13 ctrl

source_name: tendon fibroblasts_untreated

value: 0h (untreated)


title: Uninfected, epithelial cells, biological rep3


title: P13 4h


title: P16 4h


title: P14 ctrl


title: 15h Pneumococcus-infected, epithelial cells, biological rep3


title: Aldo 7-13-10

description: treated with 1uM aldosterone

label_protocol: standard Affymetrix protocol; conducted by Stanford University Protein and Nucleic Acid Facility

value: 1uM aldosterone


title: P14 4h


title: P16 ctrl


title: YF454A-2

city: Shanghai

first: Xiufeng

last: Pang

address: 500 Dongchuan Road

department: School of Life Sciences

country: China

institute: East China Normal University

description: Gene expression data from erlotinib resistance PC9 NSCLC cells treat with 0.2μM YF454A

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using Affymetrix GeneChip® Human Transcriptome Array 2.0

data_processing: The data were analyzed with R 3.2.2 using Bioconductor's oligo package and Robust Multichip Analysis (RMA) algorithm was used as normalization method

source_name: erlotinib resistance PC9 NSCLC cells,0.2μM YF454A

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

growth_protocol: Erlotinib resistance PC9 cells were grown at 37°C under a humidified 95:5 (%; v/v) mixture of air and CO2

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

treatment_protocol: A549 cells were treated with Erlotinib (5 nM), YF454A (0.2 µM), or the combination of erlotinib and YF454A for 12 h as indicated.

value: epithelial cell

tag: genotype

value: EGFR exon 19 deletion, activating mutation

tag: disease

value: Carcinoma

tag: treatment


title: Aldo 6-28-10

description: treated with 1uM aldosterone


title: 15h Pneumococcus-infected, epithelial cells, biological rep2


title: YF454A-3


title: YF454A-1


title: Erlotinib-3

description: Gene expression data from erlotinib resistance PC9 NSCLC cells treat with 5μM erlotinib

source_name: erlotinib resistance PC9 NSCLC cells,5μM erlotinib

value: 5μM erlotinib


title: Combination-3

description: Gene expression data from erlotinib resistance PC9 NSCLC cells treat with 5μM erlotinib and 0.2μM YF454A

source_name: erlotinib resistance PC9 NSCLC cells,5μM erlotinib+0.2μM YF454A

value: 5μM erlotinib and 0.2μM YF454A


title: Erlotinib-2


title: Erlotinib-1


title: Normal_3

status: Public on Apr 15 2016

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: 2555 miRNAs were spotted on each array.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: Castleman normal tissues

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

value: Liver

tag: disease status

value: normal


title: Tumor_3

description: 2555 miRNAs were spotted on each array.

source_name: Castleman tumor tissues

value: Castleman tumor


title: Tumor_1

description: 2555 miRNAs were spotted on each array.


title: Tumor_2

description: 2555 miRNAs were spotted on each array.


title: Normal_2

description: 2555 miRNAs were spotted on each array.


title: Combination-2


title: Normal_1

description: 2555 miRNAs were spotted on each array.


title: Activated 2

city: Lyon

first: Fabien

last: Le Grand

address: 8 avenue Rockefeller

department: Melis

country: France

institute: Institut Neuromyogene

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

source_name: Primary myoblasts

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: Cells were grown in Ham F10 media with 20%FBS and 2ng/ml bFGF for 5 passage. Differentiation was induced by serum removal and 24hours of culture in DMEM with 2% HS.

treatment_protocol: Differentiating myocytes were either treated with 4-OH tamoxifen (diluted in ethanol) to induce recombination of beta-catenin gene or with ethanol alone for control cells.

tag: expression

value: active form of beta-catenin


title: Control 3

value: control


title: Activated 1


title: Activated 3


title: Control-3

description: Gene expression data from A549 cells with no treatment.

source_name: erlotinib resistance PC9 NSCLC cells, no treatment (control)

value: Lung

tag: cell type


title: Control-2


title: Aldo 6-18-10

description: treated with 1uM aldosterone


title: Control 2


title: Control 1


title: Control 6-18-10

description: treated with ethanol


title: CD14 monocyte_75

city: Gaithersburg

first: Mustimbo

last: Roberts

state: MD

address: One MedImmune Way

institute: MedImmune

description:
HGU133 Plus array data
PBMCs from whole blood

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed ArrayAssist Lite

source_name: CD14 monocyte

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

extract_protocol: Qiagen RNeasy Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: CD14, CD8 and CD4 T cells isolated by magnetic bead positive selection from PBMCs from whole blood

value: blood

value: monocyte

tag: cell marker

tag: diagnosis

value: COPD


title: CD14 monocyte_74

value: Smoker


title: CD14 monocyte_71


title: CD14 monocyte_68


title: Control-1


title: Combination-1


title: CD14 monocyte_66


title: CD14 monocyte_67


title: CD14 monocyte_64


title: CD14 monocyte_73


title: CD14 monocyte_72


title: CD14 monocyte_63


title: CD14 monocyte_70


title: CD14 monocyte_57


title: CD14 monocyte_56


title: CD14 monocyte_58


title: CD14 monocyte_54


title: CD14 monocyte_65


title: CD14 monocyte_51


title: CD14 monocyte_60


title: CD14 monocyte_69


title: CD14 monocyte_59


title: CD14 monocyte_49


title: CD14 monocyte_50


title: CD14 monocyte_61


title: CD14 monocyte_62


title: CD14 monocyte_52


title: CD14 monocyte_48


title: CD14 monocyte_55


title: CD14 monocyte_47


title: CD14 monocyte_53


title: CD14 monocyte_44


title: CD14 monocyte_45


title: CD14 monocyte_38


title: CD14 monocyte_41


title: CD14 monocyte_39


title: CD14 monocyte_42


title: CD14 monocyte_43


title: CD14 monocyte_40


title: CD14 monocyte_46


title: CD14 monocyte_33


title: CD14 monocyte_35


title: CD14 monocyte_32


title: CD14 monocyte_37


title: CD14 monocyte_29


title: CD14 monocyte_36


title: CD14 monocyte_34


title: CD14 monocyte_30


title: CD14 monocyte_27


title: CD14 monocyte_26


title: CD14 monocyte_24


title: CD14 monocyte_31


title: CD14 monocyte_21


title: CD14 monocyte_22


title: CD14 monocyte_23


title: CD14 monocyte_14


title: CD14 monocyte_19


title: CD14 monocyte_28


title: CD14 monocyte_16


title: CD14 monocyte_17


title: CD14 monocyte_12


title: CD14 monocyte_13


title: CD14 monocyte_18


title: CD14 monocyte_11


title: CD14 monocyte_15


title: CD14 monocyte_25


title: CD14 monocyte_8


title: CD14 monocyte_10


title: CD14 monocyte_20


title: CD14 monocyte_5


title: CD14 monocyte_4


title: CD14 monocyte_2


title: CD14 monocyte_6


title: CD14 monocyte_9


title: CD14 monocyte_3


title: CD14 monocyte_7


title: CD14 monocyte_1


title: Blood T Cell_CD8_75

source_name: Blood T Cell_CD8

value: T cell


title: Blood T Cell_CD8_74


title: Blood T Cell_CD4_76

source_name: Blood T Cell_CD4


title: Blood T Cell_CD4_77


title: Blood T Cell_CD8_73


title: Blood T Cell_CD4_79


title: Blood T Cell_CD4_78


title: Blood T Cell_CD4_68


title: Blood T Cell_CD4_73


title: Blood T Cell_CD8_72


title: Blood T Cell_CD4_69


title: Blood T Cell_CD4_75


title: Blood T Cell_CD4_72


title: Blood T Cell_CD8_67


title: Blood T Cell_CD8_64


title: Blood T Cell_CD4_71


title: Blood T Cell_CD8_71


title: Blood T Cell_CD8_68


title: Blood T Cell_CD4_74


title: Blood T Cell_CD4_65


title: Blood T Cell_CD4_64


title: Blood T Cell_CD4_66


title: Blood T Cell_CD8_69


title: Blood T Cell_CD8_61


title: Blood T Cell_CD8_70


title: Blood T Cell_CD4_67


title: Blood T Cell_CD8_63


title: Blood T Cell_CD4_70


title: Blood T Cell_CD8_66


title: Blood T Cell_CD8_65


title: Blood T Cell_CD8_60


title: Blood T Cell_CD4_63


title: Blood T Cell_CD8_62


title: Blood T Cell_CD8_59


title: Blood T Cell_CD8_58


title: Blood T Cell_CD4_62


title: Blood T Cell_CD8_57


title: Blood T Cell_CD4_60


title: Blood T Cell_CD4_59


title: Blood T Cell_CD4_61


title: Blood T Cell_CD4_57


title: Blood T Cell_CD4_58


title: Blood T Cell_CD8_52


title: Blood T Cell_CD8_50


title: Blood T Cell_CD8_54


title: Blood T Cell_CD8_56


title: Blood T Cell_CD4_53


title: Blood T Cell_CD8_55


title: Blood T Cell_CD8_53


title: Blood T Cell_CD4_56


title: Blood T Cell_CD8_49


title: Blood T Cell_CD4_49


title: Blood T Cell_CD8_51


title: Blood T Cell_CD4_50


title: Blood T Cell_CD4_52


title: Blood T Cell_CD4_51


title: Blood T Cell_CD4_47


title: Blood T Cell_CD8_47


title: Blood T Cell_CD8_48


title: Blood T Cell_CD4_46

value: Never Smoker


title: Blood T Cell_CD4_45


title: Blood T Cell_CD4_48


title: Blood T Cell_CD4_55


title: Blood T Cell_CD8_46


title: Blood T Cell_CD4_54


title: Blood T Cell_CD8_44


title: Blood T Cell_CD8_41


title: Blood T Cell_CD8_45


title: Blood T Cell_CD8_42


title: Blood T Cell_CD4_44


title: Blood T Cell_CD4_41


title: Blood T Cell_CD8_40


title: Blood T Cell_CD4_43


title: Blood T Cell_CD4_39


title: Blood T Cell_CD4_40


title: Blood T Cell_CD4_42


title: Blood T Cell_CD8_37


title: Blood T Cell_CD4_38


title: Blood T Cell_CD8_38


title: Blood T Cell_CD8_35

value: Screen-fail


title: Blood T Cell_CD8_34


title: Blood T Cell_CD8_36


title: Blood T Cell_CD4_33


title: Blood T Cell_CD8_33


title: Blood T Cell_CD4_37


title: NCAIM789

type: genomic

first: Clara

last: Ibáñez

address: Avenue Agustín Escardino, 7

institute: Institute of Agrochemistry and Food Technology

description: Duplicate arrays and Cy5-dCTP and Cy3-dCTP dye-swap assays

hyb_protocol: The mixture of the required Cy3 and Cy5 labelled samples was adjusted to 60 μl with hybridization solution (50% formamide, 5X SSC, 0,1% SDS, 100 μg/ml salmon sperm DNA and water) incubated for 1 minute at 95 ºC and centrifuged at 13000 X g for 1 min. The supernatants were applied to microarrays and the hybridizations were allowed to proceed overnight at 65°C.

scan_protocol: Arrays scanned using an Axon GenePix 4100A scanner and GenePix Pro 6.0 software

data_processing: Using Acuity 4.0 software (Molecular Devices Corp., Union City, CA, USA), manually flagged bad spots were eliminated and the local background was subtracted before averaging the replicate features on the array. Log2 intensity ratios (M values) were then Median normalized to correct for differences in genomic DNA labelling efficiency between samples. The relative hybridization signal of each ORF was derived from the average of the two dye-swap hybridizations performed for each strain. The normalized log2 ratio (M value) was considered as a measure of the relative abundance of each ORF relatively to that of the reference strain S288C. Deviations from the 1:1 hybridization ratio were taken as indicative of changes in DNA copy number. Given that the variability usually observed between S. cerevisiae genomes, (either within laboratory strains or natural isolates), is much lower than this estimate (Adams et al. 1992, Carreto et al. 2008), we interpreted statistically significant variations in hybridization signal as ORF deletions or duplications. Data imported from Acuity was manipulated and clustered, using established algorithms implemented in the software program Genesis. Average linkage clustering with centered correlation was used to generate visual representations of clusters.

molecule: genomic DNA

organism: Saccharomyces uvarum

source_name: NCAIM789, YPD, 24h

label_protocol: Approximately 2 μg of these DNAs were labelled with fluorescently-tagged nucleotides (Amersham, Piscataway, NJ, USA), either Cy3-dCTP or Cy-5 dCTP for the reference and the studied strains, using Exo-Klenow Fragment and random primer Mix (Bioprime Array CGH Kit, Invitrogen). Dye-swap hybridizations were performed for each strain. After labeling, the reactions were heatinactivated, the experimental (Cy5 or Cy3-labeled) and reference (Cy3 or Cy5-labeled) DNAs were mixed and purified away from unincorporated label using the MinElute PCR Purification Kit (QUIAGEN). The degree of labeling was determined by measuring the absorbance at 260 nm and at 550 nm for Cy3- labelled DNA or at 260 nm and 650 nm for Cy5-labeled DNA. Samples with a base/dye ratio between 40 and 80 for both Cy3 and Cy5, were routinely obtained.

growth_protocol: Yeast strains were cultivated in 5ml YPD (1% yeast extract, 2% peptone, 2% glucose), at 28 ºC for 24 hours

extract_protocol: DNA was isolated according to standard procedures (Querol et al., 1992). After isolation the DNAs were digested with HinfI (Takara Bio Inc., Japan) and purified with High Pure PCR Product Purification Kit (Roche Molecular Biochemicals, Mannheim, Germany).

tag: isolation source

value: Oak, Hungary

organism: Saccharomyces cerevisiae S288C

tag: sample type

value: Reference strain


title: Blood T Cell_CD4_35

tag: tissue


title: Blood T Cell_CD8_31


title: Blood T Cell_CD8_32


title: Blood T Cell_CD8_39


title: Blood T Cell_CD4_32


title: Blood T Cell_CD4_31


title: Blood T Cell_CD8_30


title: BMV58

source_name: BMV58, YPD, 24h

tag: strain

value: Wine, Murviedro wineries, Valencia (Spain)


title: Blood T Cell_CD4_34


title: CECT 1969

value: CECT 1969

value: Currant juice


title: Blood T Cell_CD8_29


title: Blood T Cell_CD8_43


title: Blood T Cell_CD8_25


title: Blood T Cell_CD4_30


title: Blood T Cell_CD8_26


title: Blood T Cell_CD8_27


title: Blood T Cell_CD4_27


title: Blood T Cell_CD4_24


title: Blood T Cell_CD4_28


title: Blood T Cell_CD4_29


title: Blood T Cell_CD8_20


title: CECT 12600

value: Mistela, Alicante (Spain)


title: Blood T Cell_CD4_36


title: Blood T Cell_CD8_28


title: Blood T Cell_CD8_22


title: Blood T Cell_CD8_23


title: Blood T Cell_CD8_21


title: Blood T Cell_CD4_20


title: Blood T Cell_CD4_23


title: Blood T Cell_CD4_19


title: Blood T Cell_CD8_18


title: Blood T Cell_CD4_26


title: Blood T Cell_CD4_25


title: Blood T Cell_CD8_24


title: Blood T Cell_CD8_17


title: Blood T Cell_CD4_21


title: Blood T Cell_CD4_18


title: Blood T Cell_CD4_17


title: Blood T Cell_CD8_16


title: Blood T Cell_CD8_19


title: Blood T Cell_CD8_12


title: Blood T Cell_CD4_16


title: Blood T Cell_CD4_15


title: Blood T Cell_CD4_13


title: Blood T Cell_CD8_10


title: CIE mouse, BNST, sacrificed at 72 hours, biological replicate 63

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

hyb_protocol: Following fragmentation, cRNA samples were hybridized for 16 hr to GeneChip Mouse Genome 430 2.0 arrays by procedures outlined by Affymetrix.

scan_protocol: Arrays were washed, stained with streptavidin-phycoerythrin and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarrays were separated by RNA hybridization batch for initial normalization. Each batch was background corrected with the Robust Multi-array Average (RMA) technique and normalized by quantile normalization. The second step involved subjecting all microarrays together to another round of quantile normalization. Finally, ComBat with hybridization group as the batch effect was used to remove any remaining batch effects reflected in the data. Network analysis with WGCNA and bioinformatics analysis were used to identify modules of co-expressed genes representing specific biological pathways. Modules were overlapped with genes differentially expressed between CIE and Ctrl mice at each time-point to identify modules regulated at specific times after CIE.

source_name: BNST brain dissection, ethanol inhalation chamber, tissue harvested 72 hours after final inhalation chamber session

label_protocol: Botinylated cRNA samples were prepared according to Affymetrix protocols.

extract_protocol: Tissue from individual mice was homogenized using a Tekmar homogenizer, and total RNA was isolated with reagents and procedures provided by the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Adult male C57BL/6J mice were divided into two groups of 24. One group (CIE) received ethanol vapor exposure for 16 hours/day for 4 days while the other group was similarly handled but received only air exposure. For CIE mice, ethanol was volatized by passing air through an air stone submerged in 95% ethanol. Chamber ethanol concentrations were monitored daily and air flow was adjusted to maintain ethanol concentrations within a range (10-13 mg/l air). Before each chronic ethanol exposure cycle, intoxication was initiated in the CIE group by administration of ethanol (1.6 g/kg), and blood ethanol concentration was stabilized by injection of the alcohol dehydrogenase inhibitor pyrazole (1 mmol/kg).  Both ethanol and pyrazole were administered intraperitoneally (i.p.) in a volume of 0.02 ml/g body weight.  Ctrl mice were handled similarly, but administered saline and pyrazole (i.p.) prior to being placed in control chambers that delivered only air. Following 4 days in the inhalation chamber, mice underwent 7 days of complete abstinence from ethanol. At the end of the abstinence period, mice were returned to the inhalation chamber to begin the next cycle of CIE. This pattern of 4 days CIE (or control air) exposure followed by 7 days abstinence was repeated for four complete cycles.

value: brain, bed nucleus of the stria terminalis

tag: sacrifice time

value: 72 hours post final vapor chamber session

tag: Sex

value: male


title: CIE mouse, BNST, sacrificed at 72 hours, biological replicate 3


title: CIE mouse, BNST, sacrificed at 7 days, biological replicate 65

source_name: BNST brain dissection, ethanol inhalation chamber, tissue harvested 7 days after final inhalation chamber session

value: 7 days post final vapor chamber session


title: CIE mouse, BNST, sacrificed at 72 hours, biological replicate 61


title: CIE mouse, BNST, sacrificed at 72 hours, biological replicate 35


title: CIE mouse, BNST, sacrificed at 7 days, biological replicate 59


title: Blood T Cell_CD8_14

value: blood


title: Blood T Cell_CD4_22


title: Blood T Cell_CD4_14


title: CIE mouse, BNST, sacrificed at 8 hours, biological replicate 41

source_name: BNST brain dissection, ethanol inhalation chamber, tissue harvested 8 hours after final inhalation chamber session

value: 8 hours post final vapor chamber session


title: Blood T Cell_CD8_15

value: COPD


title: CIE mouse, BNST, sacrificed at 72 hours, biological replicate 71


title: CIE mouse, BNST, sacrificed at 7 days, biological replicate 45


title: CIE mouse, BNST, sacrificed at 7 days, biological replicate 27


title: CIE mouse, BNST, sacrificed at 72 hours, biological replicate 29


title: Blood T Cell_CD8_13


title: Blood T Cell_CD4_12

value: Smoker


title: Blood T Cell_CD4_10

value: T cell


title: Blood T Cell_CD8_11


title: Blood T Cell_CD4_11


title: Blood T Cell_CD8_9


title: Blood T Cell_CD4_9


title: CIE mouse, BNST, sacrificed at 8 hours, biological replicate 23


title: CIE mouse, BNST, sacrificed at 8 hours, biological replicate 69


title: Blood T Cell_CD8_7


title: control mouse, BNST, sacrificed at 7 days, biological replicate 80

source_name: BNST brain dissection, air inhalation chamber, tissue harvested 7 days after final inhalation chamber session


title: CIE mouse, BNST, sacrificed at 0 hours, biological replicate 26

source_name: BNST brain dissection, ethanol inhalation chamber, tissue harvested 0 hours after final inhalation chamber session

value: 0 hour post final vapor chamber session


title: CIE mouse, BNST, sacrificed at 8 hours, biological replicate 15


title: Blood T Cell_CD4_8


title: Blood T Cell_CD4_7


title: Blood T Cell_CD8_8


title: Blood T Cell_CD8_6


title: CIE mouse, BNST, sacrificed at 0 hours, biological replicate 19


title: Blood T Cell_CD4_6


title: CIE mouse, BNST, sacrificed at 8 hours, biological replicate 21


title: CIE mouse, BNST, sacrificed at 0 hours, biological replicate 67


title: CIE mouse, BNST, sacrificed at 0 hours, biological replicate 43


title: Blood T Cell_CD8_5


title: CIE mouse, BNST, sacrificed at 0 hours, biological replicate 17


title: CIE mouse, BNST, sacrificed at 0 hours, biological replicate 57


title: Blood T Cell_CD4_5


title: Blood T Cell_CD4_4


title: control mouse, BNST, sacrificed at 7 days, biological replicate 70


title: control mouse, BNST, sacrificed at 7 days, biological replicate 62


title: Blood T Cell_CD4_3


title: Blood T Cell_CD8_4


title: Blood T Cell_CD8_2


title: Blood T Cell_CD8_3


title: control mouse, BNST, sacrificed at 7 days, biological replicate 28


title: control mouse, BNST, sacrificed at 7 days, biological replicate 36


title: Blood T Cell_CD8_1


title: Blood T Cell_CD4_2


title: control mouse, BNST, sacrificed at 7 days, biological replicate 46


title: control mouse, BNST, sacrificed at 72 hours, biological replicate 34

source_name: BNST brain dissection, air inhalation chamber, tissue harvested 72 hours after final inhalation chamber session


title: control mouse, BNST, sacrificed at 72 hours, biological replicate 68


title: control mouse, BNST, sacrificed at 72 hours, biological replicate 44


title: control mouse, BNST, sacrificed at 72 hours, biological replicate 52


title: CIE mouse, BNST, sacrificed at 8 hours, biological replicate 40


title: control mouse, BNST, sacrificed at 72 hours, biological replicate 24


title: Blood T Cell_CD4_1


title: stimulated whole blood_126

description: HGU133 Plus array data

source_name: whole blood

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

treatment_protocol: unstimulated whole blood and whole blood stimulated with anti-CD3 and anti-CD28 using the TruCulture ex-vivo method

value: whole blood

tag: stimulus

value: Unstimulated


title: stimulated whole blood_122

description: HGU133 Plus array data


title: control mouse, BNST, sacrificed at 72 hours, biological replicate 16


title: control mouse, BNST, sacrificed at 8 hours, biological replicate 58

source_name: BNST brain dissection, air inhalation chamber, tissue harvested 8 hours after final inhalation chamber session


title: stimulated whole blood_123

description: HGU133 Plus array data


title: stimulated whole blood_124

description: HGU133 Plus array data


title: control mouse, BNST, sacrificed at 8 hours, biological replicate 75


title: control mouse, BNST, sacrificed at 8 hours, biological replicate 66


title: stimulated whole blood_121

description: HGU133 Plus array data


title: stimulated whole blood_125

description: HGU133 Plus array data


title: control mouse, BNST, sacrificed at 0 hours, biological replicate 64

source_name: BNST brain dissection, air inhalation chamber, tissue harvested 0 hours after final inhalation chamber session


title: stimulated whole blood_120

description: HGU133 Plus array data


title: control mouse, BNST, sacrificed at 8 hours, biological replicate 50


title: control mouse, BNST, sacrificed at 8 hours, biological replicate 8


title: stimulated whole blood_118

description: HGU133 Plus array data


title: stimulated whole blood_119

description: HGU133 Plus array data


title: stimulated whole blood_117

description: HGU133 Plus array data


title: stimulated whole blood_110

description: HGU133 Plus array data


title: control mouse, BNST, sacrificed at 0 hours, biological replicate 56


title: stimulated whole blood_111

description: HGU133 Plus array data


title: stimulated whole blood_108

description: HGU133 Plus array data


title: stimulated whole blood_113

description: HGU133 Plus array data


title: stimulated whole blood_116

description: HGU133 Plus array data


title: stimulated whole blood_115

description: HGU133 Plus array data


title: control mouse, BNST, sacrificed at 8 hours, biological replicate 42


title: CIE mouse, CEA, sacrificed at 7 days, biological replicate 27

source_name: CEA brain dissection, ethanol inhalation chamber, tissue harvested 7 days after final inhalation chamber session

value: brain, central nucleus of the amygdala


title: control mouse, BNST, sacrificed at 0 hours, biological replicate 48


title: stimulated whole blood_109

description: HGU133 Plus array data


title: stimulated whole blood_114

description: HGU133 Plus array data


title: stimulated whole blood_106

description: HGU133 Plus array data


title: control mouse, BNST, sacrificed at 0 hours, biological replicate 38


title: CIE mouse, CEA, sacrificed at 7 days, biological replicate 65


title: stimulated whole blood_112

description: HGU133 Plus array data


title: CIE mouse, CEA, sacrificed at 7 days, biological replicate 9


title: CIE mouse, CEA, sacrificed at 7 days, biological replicate 13


title: control mouse, BNST, sacrificed at 0 hours, biological replicate 12


title: CIE mouse, CEA, sacrificed at 72 hours, biological replicate 35

source_name: CEA brain dissection, ethanol inhalation chamber, tissue harvested 72 hours after final inhalation chamber session


title: control mouse, BNST, sacrificed at 0 hours, biological replicate 30


title: stimulated whole blood_105

description: HGU133 Plus array data


title: CIE mouse, CEA, sacrificed at 7 days, biological replicate 45


title: CIE mouse, CEA, sacrificed at 72 hours, biological replicate 3


title: CIE mouse, CEA, sacrificed at 72 hours, biological replicate 71


title: CIE mouse, CEA, sacrificed at 72 hours, biological replicate 33


title: CIE mouse, CEA, sacrificed at 7 days, biological replicate 7


title: stimulated whole blood_102

description: HGU133 Plus array data


title: stimulated whole blood_103

description: HGU133 Plus array data


title: stimulated whole blood_104

description: HGU133 Plus array data


title: stimulated whole blood_107

description: HGU133 Plus array data


title: stimulated whole blood_98

description: HGU133 Plus array data


title: CIE mouse, CEA, sacrificed at 8 hours, biological replicate 23

source_name: CEA brain dissection, ethanol inhalation chamber, tissue harvested 8 hours after final inhalation chamber session


title: CIE mouse, CEA, sacrificed at 72 hours, biological replicate 29


title: CIE mouse, CEA, sacrificed at 8 hours, biological replicate 21


title: stimulated whole blood_101

description: HGU133 Plus array data


title: stimulated whole blood_100

description: HGU133 Plus array data


title: CIE mouse, CEA, sacrificed at 72 hours, biological replicate 10


title: CIE mouse, CEA, sacrificed at 8 hours, biological replicate 41


title: CIE mouse, CEA, sacrificed at 8 hours, biological replicate 51


title: stimulated whole blood_99

description: HGU133 Plus array data


title: stimulated whole blood_96

description: HGU133 Plus array data


title: stimulated whole blood_97

description: HGU133 Plus array data


title: stimulated whole blood_94

description: HGU133 Plus array data


title: stimulated whole blood_92

description: HGU133 Plus array data


title: stimulated whole blood_91

description: HGU133 Plus array data


title: stimulated whole blood_90

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 7 days, biological replicate 77

source_name: CEA brain dissection, air inhalation chamber, tissue harvested 7 days after final inhalation chamber session


title: stimulated whole blood_95

description: HGU133 Plus array data


title: CIE mouse, CEA, sacrificed at 8 hours, biological replicate 1


title: CIE mouse, CEA, sacrificed at 0 hours, biological replicate 19

source_name: CEA brain dissection, ethanol inhalation chamber, tissue harvested 0 hours after final inhalation chamber session


title: stimulated whole blood_93

description: HGU133 Plus array data


title: CIE mouse, CEA, sacrificed at 0 hours, biological replicate 72


title: control mouse, CEA, sacrificed at 7 days, biological replicate 70


title: CIE mouse, CEA, sacrificed at 0 hours, biological replicate 67


title: CIE mouse, CEA, sacrificed at 0 hours, biological replicate 11


title: CIE mouse, CEA, sacrificed at 8 hours, biological replicate 15


title: stimulated whole blood_89

description: HGU133 Plus array data


title: CIE mouse, CEA, sacrificed at 0 hours, biological replicate 5


title: stimulated whole blood_88

description: HGU133 Plus array data


title: stimulated whole blood_87

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 7 days, biological replicate 46


title: stimulated whole blood_84

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 7 days, biological replicate 36


title: stimulated whole blood_82

description: HGU133 Plus array data


title: stimulated whole blood_80

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 7 days, biological replicate 28


title: control mouse, CEA, sacrificed at 7 days, biological replicate 22


title: control mouse, CEA, sacrificed at 72 hours, biological replicate 44

source_name: CEA brain dissection, air inhalation chamber, tissue harvested 72 hours after final inhalation chamber session


title: stimulated whole blood_78

description: HGU133 Plus array data


title: CIE mouse, CEA, sacrificed at 0 hours, biological replicate 26


title: stimulated whole blood_85

description: HGU133 Plus array data


title: stimulated whole blood_86

description: HGU133 Plus array data


title: stimulated whole blood_81

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 72 hours, biological replicate 34


title: stimulated whole blood_76

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 72 hours, biological replicate 52


title: control mouse, CEA, sacrificed at 72 hours, biological replicate 76


title: stimulated whole blood_74

description: HGU133 Plus array data


title: stimulated whole blood_83

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 8 hours, biological replicate 75

source_name: CEA brain dissection, air inhalation chamber, tissue harvested 8 hours after final inhalation chamber session


title: control mouse, CEA, sacrificed at 8 hours, biological replicate 14


title: stimulated whole blood_71

description: HGU133 Plus array data


title: stimulated whole blood_79

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 8 hours, biological replicate 32


title: stimulated whole blood_77

description: HGU133 Plus array data


title: stimulated whole blood_69

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 8 hours, biological replicate 4


title: stimulated whole blood_70

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 0 hours, biological replicate 38

source_name: CEA brain dissection, air inhalation chamber, tissue harvested 0 hours after final inhalation chamber session


title: stimulated whole blood_65

description: HGU133 Plus array data


title: stimulated whole blood_75

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 72 hours, biological replicate 6


title: control mouse, CEA, sacrificed at 8 hours, biological replicate 50


title: control mouse, CEA, sacrificed at 72 hours, biological replicate 24


title: stimulated whole blood_73

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 0 hours, biological replicate 2


title: control mouse, CEA, sacrificed at 0 hours, biological replicate 30


title: control mouse, CEA, sacrificed at 8 hours, biological replicate 8


title: CIE mouse, HPC, sacrificed at 7 days, biological replicate 59

source_name: HPC brain dissection, ethanol inhalation chamber, tissue harvested 7 days after final inhalation chamber session

value: brain, hippocampus


title: stimulated whole blood_68

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 7 days, biological replicate 37


title: control mouse, CEA, sacrificed at 0 hours, biological replicate 78


title: control mouse, CEA, sacrificed at 0 hours, biological replicate 74


title: stimulated whole blood_62

description: HGU133 Plus array data


title: stimulated whole blood_61

description: HGU133 Plus array data


title: stimulated whole blood_60

description: HGU133 Plus array data


title: stimulated whole blood_72

description: HGU133 Plus array data


title: stimulated whole blood_66

description: HGU133 Plus array data


title: control mouse, CEA, sacrificed at 0 hours, biological replicate 48


title: stimulated whole blood_57

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 7 days, biological replicate 7


title: CIE mouse, HPC, sacrificed at 72 hours, biological replicate 33

source_name: HPC brain dissection, ethanol inhalation chamber, tissue harvested 72 hours after final inhalation chamber session


title: stimulated whole blood_63

description: HGU133 Plus array data


title: stimulated whole blood_53

description: HGU133 Plus array data


title: stimulated whole blood_51

description: HGU133 Plus array data


title: stimulated whole blood_67

description: HGU133 Plus array data


title: stimulated whole blood_59

description: HGU133 Plus array data


title: stimulated whole blood_50

description: HGU133 Plus array data


title: stimulated whole blood_55

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 7 days, biological replicate 9


title: CIE mouse, HPC, sacrificed at 7 days, biological replicate 45


title: stimulated whole blood_48

description: HGU133 Plus array data


title: stimulated whole blood_64

description: HGU133 Plus array data


title: stimulated whole blood_46

description: HGU133 Plus array data


title: stimulated whole blood_47

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 7 days, biological replicate 27


title: stimulated whole blood_58

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 8 hours, biological replicate 41

source_name: HPC brain dissection, ethanol inhalation chamber, tissue harvested 8 hours after final inhalation chamber session


title: CIE mouse, HPC, sacrificed at 72 hours, biological replicate 35


title: stimulated whole blood_56

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 72 hours, biological replicate 61


title: CIE mouse, HPC, sacrificed at 72 hours, biological replicate 71


title: CIE mouse, HPC, sacrificed at 72 hours, biological replicate 3


title: stimulated whole blood_52

description: HGU133 Plus array data


title: stimulated whole blood_54

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 8 hours, biological replicate 25


title: CIE mouse, HPC, sacrificed at 8 hours, biological replicate 21


title: CIE mouse, HPC, sacrificed at 0 hours, biological replicate 72

source_name: HPC brain dissection, ethanol inhalation chamber, tissue harvested 0 hours after final inhalation chamber session


title: CIE mouse, HPC, sacrificed at 8 hours, biological replicate 23


title: CIE mouse, HPC, sacrificed at 0 hours, biological replicate 19


title: CIE mouse, HPC, sacrificed at 72 hours, biological replicate 29


title: stimulated whole blood_45

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 0 hours, biological replicate 67


title: CIE mouse, HPC, sacrificed at 0 hours, biological replicate 11


title: stimulated whole blood_40

description: HGU133 Plus array data


title: stimulated whole blood_42

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 0 hours, biological replicate 57


title: stimulated whole blood_43

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 8 hours, biological replicate 15


title: control mouse, HPC, sacrificed at 7 days, biological replicate 80

source_name: HPC brain dissection, air inhalation chamber, tissue harvested 7 days after final inhalation chamber session


title: stimulated whole blood_39

description: HGU133 Plus array data


title: stimulated whole blood_44

description: HGU133 Plus array data


title: stimulated whole blood_38

description: HGU133 Plus array data


title: CIE mouse, HPC, sacrificed at 0 hours, biological replicate 43


title: stimulated whole blood_41

description: HGU133 Plus array data


title: stimulated whole blood_37

description: HGU133 Plus array data


title: stimulated whole blood_36

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 7 days, biological replicate 70


title: control mouse, HPC, sacrificed at 7 days, biological replicate 54


title: control mouse, HPC, sacrificed at 7 days, biological replicate 46


title: stimulated whole blood_34

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 7 days, biological replicate 18


title: stimulated whole blood_32

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 7 days, biological replicate 22


title: CIE mouse, HPC, sacrificed at 8 hours, biological replicate 69


title: stimulated whole blood_35

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 72 hours, biological replicate 68

source_name: HPC brain dissection, air inhalation chamber, tissue harvested 72 hours after final inhalation chamber session


title: stimulated whole blood_30

description: HGU133 Plus array data

source_name: whole blood


title: control mouse, HPC, sacrificed at 72 hours, biological replicate 44


title: control mouse, HPC, sacrificed at 72 hours, biological replicate 52


title: control mouse, HPC, sacrificed at 72 hours, biological replicate 24


title: stimulated whole blood_29

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 72 hours, biological replicate 6


title: stimulated whole blood_28

description: HGU133 Plus array data


title: stimulated whole blood_31

description: HGU133 Plus array data


title: stimulated whole blood_25

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 8 hours, biological replicate 42

source_name: HPC brain dissection, air inhalation chamber, tissue harvested 8 hours after final inhalation chamber session


title: stimulated whole blood_26

description: HGU133 Plus array data


title: stimulated whole blood_27

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 8 hours, biological replicate 66


title: stimulated whole blood_23

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 8 hours, biological replicate 79


title: control mouse, HPC, sacrificed at 8 hours, biological replicate 32


title: control mouse, HPC, sacrificed at 72 hours, biological replicate 16


title: stimulated whole blood_22

description: HGU133 Plus array data


title: stimulated whole blood_24

description: HGU133 Plus array data


title: stimulated whole blood_21

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 0 hours, biological replicate 56

source_name: HPC brain dissection, air inhalation chamber, tissue harvested 0 hours after final inhalation chamber session


title: stimulated whole blood_20

description: HGU133 Plus array data


title: stimulated whole blood_19

description: HGU133 Plus array data


title: stimulated whole blood_16

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 8 hours, biological replicate 4


title: control mouse, HPC, sacrificed at 8 hours, biological replicate 8


title: stimulated whole blood_15

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 0 hours, biological replicate 64


title: stimulated whole blood_14

description: HGU133 Plus array data


title: stimulated whole blood_18

description: HGU133 Plus array data


title: control mouse, HPC, sacrificed at 0 hours, biological replicate 38


title: control mouse, HPC, sacrificed at 0 hours, biological replicate 12


title: control mouse, HPC, sacrificed at 0 hours, biological replicate 2


title: CIE mouse, NAC, sacrificed at 7 days, biological replicate 45

source_name: NAC brain dissection, ethanol inhalation chamber, tissue harvested 7 days after final inhalation chamber session

value: brain, nucleus accumbens


title: stimulated whole blood_17

description: HGU133 Plus array data


title: stimulated whole blood_13

description: HGU133 Plus array data


title: stimulated whole blood_12

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 7 days, biological replicate 37


title: stimulated whole blood_11

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 7 days, biological replicate 27


title: CIE mouse, NAC, sacrificed at 7 days, biological replicate 65


title: CIE mouse, NAC, sacrificed at 7 days, biological replicate 13


title: stimulated whole blood_10

description: HGU133 Plus array data


title: stimulated whole blood_9

description: HGU133 Plus array data


title: stimulated whole blood_8

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 72 hours, biological replicate 63

source_name: NAC brain dissection, ethanol inhalation chamber, tissue harvested 72 hours after final inhalation chamber session


title: CIE mouse, NAC, sacrificed at 7 days, biological replicate 7


title: stimulated whole blood_49

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 72 hours, biological replicate 33


title: CIE mouse, NAC, sacrificed at 72 hours, biological replicate 61


title: CIE mouse, NAC, sacrificed at 8 hours, biological replicate 51

source_name: NAC brain dissection, ethanol inhalation chamber, tissue harvested 8 hours after final inhalation chamber session


title: CIE mouse, NAC, sacrificed at 72 hours, biological replicate 29


title: stimulated whole blood_5

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 8 hours, biological replicate 23


title: stimulated whole blood_3

description: HGU133 Plus array data


title: stimulated whole blood_1

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 8 hours, biological replicate 25


title: CIE mouse, NAC, sacrificed at 8 hours, biological replicate 1


title: stimulated whole blood_7

description: HGU133 Plus array data


title: whole blood_79

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 8 hours, biological replicate 15


title: CIE mouse, NAC, sacrificed at 0 hours, biological replicate 72

source_name: NAC brain dissection, ethanol inhalation chamber, tissue harvested 0 hours after final inhalation chamber session


title: whole blood_78

description: HGU133 Plus array data


title: stimulated whole blood_6

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 0 hours, biological replicate 43


title: whole blood_77

description: HGU133 Plus array data


title: stimulated whole blood_2

description: HGU133 Plus array data


title: stimulated whole blood_33

description: HGU133 Plus array data


title: stimulated whole blood_4

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 72 hours, biological replicate 3


title: CIE mouse, NAC, sacrificed at 0 hours, biological replicate 17


title: whole blood_80

description: HGU133 Plus array data


title: whole blood_75

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 0 hours, biological replicate 26


title: whole blood_76

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 0 hours, biological replicate 67


title: control mouse, HPC, sacrificed at 0 hours, biological replicate 20


title: whole blood_68

description: HGU133 Plus array data


title: whole blood_73

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 7 days, biological replicate 77

source_name: NAC brain dissection, air inhalation chamber, tissue harvested 7 days after final inhalation chamber session


title: control mouse, NAC, sacrificed at 7 days, biological replicate 80


title: control mouse, NAC, sacrificed at 7 days, biological replicate 36


title: control mouse, NAC, sacrificed at 7 days, biological replicate 54


title: control mouse, NAC, sacrificed at 7 days, biological replicate 62


title: whole blood_72

description: HGU133 Plus array data


title: CIE mouse, NAC, sacrificed at 0 hours, biological replicate 5


title: whole blood_67

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 72 hours, biological replicate 34

source_name: NAC brain dissection, air inhalation chamber, tissue harvested 72 hours after final inhalation chamber session


title: whole blood_69

description: HGU133 Plus array data


title: whole blood_64

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 72 hours, biological replicate 68


title: control mouse, NAC, sacrificed at 7 days, biological replicate 28


title: whole blood_70

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 8 hours, biological replicate 50

source_name: NAC brain dissection, air inhalation chamber, tissue harvested 8 hours after final inhalation chamber session


title: whole blood_63

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 72 hours, biological replicate 24


title: whole blood_61

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 72 hours, biological replicate 6


title: control mouse, NAC, sacrificed at 72 hours, biological replicate 52


title: whole blood_66

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 72 hours, biological replicate 44


title: control mouse, NAC, sacrificed at 8 hours, biological replicate 79


title: whole blood_71

description: HGU133 Plus array data


title: whole blood_65

description: HGU133 Plus array data


title: whole blood_62

description: HGU133 Plus array data


title: whole blood_60

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 0 hours, biological replicate 78

source_name: NAC brain dissection, air inhalation chamber, tissue harvested 0 hours after final inhalation chamber session


title: whole blood_57

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 8 hours, biological replicate 8


title: whole blood_58

description: HGU133 Plus array data


title: whole blood_56

description: HGU133 Plus array data


title: whole blood_53

description: HGU133 Plus array data


title: whole blood_52

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 8 hours, biological replicate 4


title: whole blood_59

description: HGU133 Plus array data


title: whole blood_55

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 0 hours, biological replicate 38


title: control mouse, NAC, sacrificed at 0 hours, biological replicate 30


title: control mouse, NAC, sacrificed at 8 hours, biological replicate 42


title: whole blood_50

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 0 hours, biological replicate 48


title: whole blood_54

description: HGU133 Plus array data


title: control mouse, NAC, sacrificed at 0 hours, biological replicate 74


title: Akita1

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

description: Replication 1 out of 4, Akita vs Reference

hyb_protocol: Cy3- and Cy5-labeled cRNA were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65 °C; Slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies)

scan_protocol: Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 10.5 with default parameter settings for GE two-color microarrays (GE2_107_Sep09). The data was transferred to limma (Smyth, 2005) for further statistical analysis. After background corrections, within- and between-array normalizations, differential expression was identified by a cut off of Fold Change and corrected p-value (Benjamini-Hochberg correction) at 2 and 0.05, respectively.

organism: Tetranychus urticae

source_name: Akita

label_protocol: Using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies), Cy3- or Cy5-labeled cRNA was generated using 100 ng of total RNA (excluding RNA-spike in controls).

growth_protocol: Both the susceptible and resistant mite strain were maintained in climatically controlled rooms at 26 °C, 60% RH and 16:8 h light:dark photoperiod

extract_protocol: Total RNA samples were isolated using the RNeasy minikit (Qiagen) and were subsequently treated with DNase (Turbo DNA-free kit, Ambion). RNA was extracted from 100-120 young adult female mites in four replicates from each strain.

tag: life stage

value: adult

tag: gender

value: female

source_name: Reference


title: whole blood_51

description: HGU133 Plus array data


title: Akita2

description: Replication 2 out of 4, Akita vs Reference


title: Akita3

description: Replication 3 out of 4, Akita vs Reference


title: CIE mouse, PFC, sacrificed at 7 days, biological replicate 45, repeat group 1

data_processing: Microarrays were separated by RNA hybridization batch for initial normalization. Each batch was background corrected with the Robust Multi-array Average (RMA) technique and normalized by quantile normalization. The second step involved subjecting all microarrays together to another round of quantile normalization. Finally, ComBat with hybridization group as the batch effect was used to remove any remaining batch effects reflected in the data. The only exception to this procedure was the prefrontal cortex where repeat group was used as only the batch effect correction factor. Network analysis with WGCNA and bioinformatics analysis were used to identify modules of co-expressed genes representing specific biological pathways. Modules were overlapped with genes differentially expressed between CIE and Ctrl mice at each time-point to identify modules regulated at specific times after CIE.

source_name: medial PFC brain dissection, ethanol inhalation chamber, tissue harvested 7 days after final inhalation chamber session

value: brain, medial prefrontal cortex


title: Akita4

description: Replication 4 out of 4, Akita vs Reference


title: control mouse, NAC, sacrificed at 0 hours, biological replicate 20


title: whole blood_49

description: HGU133 Plus array data


title: CIE mouse, PFC, sacrificed at 7 days, biological replicate 65, repeat group 1


title: cyenoR4

description: Replication 4 out of 4, JP-R vs JP-S

source_name: JP-R-whole organism

tag: developmental stage

source_name: JP-S-whole organism


title: whole blood_48

description: HGU133 Plus array data


title: CIE mouse, PFC, sacrificed at 7 days, biological replicate 37, repeat group 1


title: whole blood_46

description: HGU133 Plus array data


title: whole blood_47

description: HGU133 Plus array data


title: CIE mouse, PFC, sacrificed at 7 days, biological replicate 7, repeat group 1


title: cyenoR2

description: Replication 2 out of 4, JP-R vs JP-S


title: cyenoR1

description: Replication 1 out of 4, JP-R vs JP-S


title: CIE mouse, PFC, sacrificed at 7 days, biological replicate 13, repeat group 1


title: cyenoR3

description: Replication 3 out of 4, JP-R vs JP-S


title: CIE mouse, PFC, sacrificed at 72 hours, biological replicate 71, repeat group 1

source_name: medial PFC brain dissection, ethanol inhalation chamber, tissue harvested 72 hours after final inhalation chamber session

value: 72 hours post final vapor chamber session


title: whole blood_44

description: HGU133 Plus array data

source_name: whole blood


title: whole blood_41

description: HGU133 Plus array data

value: Never Smoker


title: Dark exposed, female WT mouse, biological replicate 3

city: Basel

first: Christoph

last: Handschin

address: Spitalstrasse 41

country: Switzerland

institute: Biozentrum, University of Basel

hyb_protocol: Following fragmentation, 4.25 ug of DNA were hybridized for 17 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed at the Functional Genomics Center Zurich (FGCZ), using the PARTEK Software Suite and Bioconductor.

source_name: retina, dark exposed, WT mouse

label_protocol: Sense target biotin labeling according to the  Mouse 1.0 ST Whole Gene Array from Affymetrix

value: Retina

tag: genotype

value: wild type


title: light exposed, male PGC-1alpha KO mouse, biological replicate 2

source_name: retina, light exposed, KO mouse

value: PGC-1 alpha knockout

value: male


title: light exposed, male WT mouse, biological replicate 1

source_name: retina, light exposed, WT mouse


title: light exposed, male WT mouse, biological replicate 2


title: CIE mouse, PFC, sacrificed at 7 days, biological replicate 27, repeat group 1

value: 7 days post final vapor chamber session


title: light exposed, male PGC-1alpha KO mouse, biological replicate 1


title: Dark exposed, female WT mouse, biological replicate 2


title: whole blood_45

description: HGU133 Plus array data


title: CIE mouse, PFC, sacrificed at 72 hours, biological replicate 63, repeat group 1


title: CIE mouse, PFC, sacrificed at 72 hours, biological replicate 35, repeat group 1


title: Dark exposed, female PGC-1alpha KO mouse, biological replicate 2

source_name: retina, dark exposed, KO mouse


title: Dark exposed, female PGC-1alpha KO mouse, biological replicate 3


title: light exposed, male WT mouse, biological replicate 3


title: Dark exposed, male WT mouse, biological replicate 4


title: light exposed, male PGC-1alpha KO mouse, biological replicate 3


title: CIE mouse, PFC, sacrificed at 72 hours, biological replicate 33, repeat group 1


title: Dark exposed, female WT mouse, biological replicate 1


title: whole blood_42

description: HGU133 Plus array data


title: whole blood_43

description: HGU133 Plus array data


title: whole blood_74

description: HGU133 Plus array data

value: COPD


title: T72_rep3_ses

city: CUERNAVACA

first: AGUSTIN

middle: REYES

last: PEREZ

state: MORELOS

address: UNIVERSITY AV.

department: FUNCTIONAL GENOMICS

country: Mexico

institute: UNAM

hyb_protocol: Pairs of Cy3- and Cy5-labeled cDNA samples were mixed and hybridized with the array as described by Hedge et al. (2000).

scan_protocol: After the arrays were washed, they were scanned using a pixel size of 10 mm with a Scan Array Lite microarray scanner (Perkin-Elmer, Boston, MA).

data_processing:
Spot detection, determination of mean signals and mean local background intensities, image segmentation, and signal quantification were performed for the microarray images using the Array-Pro Analyzer 4.0 software (Media Cybernetics, L.P.).
The analysis consisted of three steps: background subtraction and data normalization, analysis of variance, and controlling for the expected number of false positives (Quackenbush 2002). The raw data microarray data were normalized to have comparable signal values between the different microarray slides. After background subtraction, data were quantile-normalized using the q-spline method (Workman et al. 2002), attaining signal intensities with the same distributions between all microarray slides in the red and green channels. The signals were transformed to logarithmic scale (log2), and the resulting signals were examined using M-A plots
To determine the significance of the expression differences from planktonic and sessile samples, data were subjected to ANOVA analysis, and a p-value <0.01 was considered as significant. Thus an expected 10% of false positives were accepted. Microarray data were analyzed to assess the statistical significance of expression differences between planktonic and sessile organisms after 24 and 72 hours biofilm maturation stages. The analysis consisted of three steps: background subtraction and data normalization, analysis of variance, and controlling for the expected number of false positives (Quackenbush, 2002).

organism: Rhizobium etli CFN 42

source_name: Biofilm formation 72 hours

label_protocol: The RNA was differentially labeled with Cy3-dCTP and Cy5-dCTP using a CyScribe first-strand cDNA labeling Kitt (Amersham Biosciences).

growth_protocol: The bacteria cultures were incubated at 29ºC 60% of relative humidity and sessile and planktonic cells were cultured both in the same bootle and separed after 24 and 72 hours by centrifugation.

extract_protocol: We used 100 ml cultures samples (planktonic and sessile). Total RNA was isolated by acid hot phenol extraction as described previously by De Vries et al., (1993).

treatment_protocol: Separated after 24 hours and 72 hours by centrifugation (13,000g 10 min) using 150 mL culture and mixed with RNA later AMBION (RNA stabilization solution).

value: Sessile cells


title: T72_rep2_planck

source_name: Planktonic cell 72 hours

value: Planktonic cells


title: T72_rep3_planck


title: T72_rep2_ses


title: T24_rep2_ses

source_name: Biofilm formation 24 hours


title: T24_rep3_planc

source_name: Planktonic cell 24 hours


title: whole blood_38

description: HGU133 Plus array data

value: whole blood


title: whole blood_40

description: HGU133 Plus array data


title: CIE mouse, PFC, sacrificed at 8 hours, biological replicate 15, repeat group 2

source_name: medial PFC brain dissection, ethanol inhalation chamber, tissue harvested 8 hours after final inhalation chamber session

value: 8 hours post final vapor chamber session


title: T24_rep3_ses


title: T72_rep1_planck


title: Dark exposed, female PGC-1alpha KO mouse, biological replicate 1


title: T24_rep1_planck


title: T72_rep1_ses


title: T24_rep2_planc


title: CIE mouse, PFC, sacrificed at 72 hours, biological replicate 3, repeat group 1


title: whole blood_35

description: HGU133 Plus array data


title: whole blood_36

description: HGU133 Plus array data


title: CIE mouse, PFC, sacrificed at 72 hours, biological replicate 29, repeat group 1


title: CIE mouse, PFC, sacrificed at 8 hours, biological replicate 40, repeat group 1


title: whole blood_39

description: HGU133 Plus array data


title: T24_rep1_ses


title: whole blood_37

description: HGU133 Plus array data


title: CIE mouse, PFC, sacrificed at 8 hours, biological replicate 23, repeat group 2


title: whole blood_34

description: HGU133 Plus array data

value: Screen-fail


title: CIE mouse, PFC, sacrificed at 8 hours, biological replicate 51, repeat group 1


title: MLM#10 replicate B

city: Sioux Falls

first: Paola

middle: Drapkin

last: Vermeer

state: SD

address: 2301 East 60th street north

department: Cancer Biology and Immunotherapies Group

institute: Sanford Research

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanninig protocol

data_processing: Data were normalized using cubic spline normalization (GSGX Version 1.8.0)

source_name: mEERL Lung Metastasis lines (MLM)

growth_protocol: Standard cell culture in Emedia

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment  on Rneasy mini kits in accordance with the manufactures instructions for the kit. Quality control was performed with nano drop full spectrum scan.

treatment_protocol: no treatment

tag: isolation from metastatic site

value: lung

value: mEERL Lung Metastasis lines (MLM)


title: CIE mouse, PFC, sacrificed at 8 hours, biological replicate 69, repeat group 1


title: MLM#10 replicate C

description: replicate 3


title: whole blood_33

description: HGU133 Plus array data


title: CIE mouse, PFC, sacrificed at 0 hours, biological replicate 72, repeat group 1

source_name: medial PFC brain dissection, ethanol inhalation chamber, tissue harvested 0 hours after final inhalation chamber session

value: 0 hour post final vapor chamber session


title: MLM#10 replicate A

description: replicate 1


title: whole blood_32

description: HGU133 Plus array data

value: Smoker


title: whole blood_29

description: HGU133 Plus array data


title: whole blood_28

description: HGU133 Plus array data


title: whole blood_30

description: HGU133 Plus array data


title: MLM#3 replicate B

description: replicate 2


title: whole blood_27

description: HGU133 Plus array data


title: whole blood_31

description: HGU133 Plus array data


title: control mouse, PFC, sacrificed at 7 days, biological replicate 80, repeat group 1

source_name: medial PFC brain dissection, air inhalation chamber, tissue harvested 7 days after final inhalation chamber session

value: brain, medial prefrontal cortex


title: control mouse, PFC, sacrificed at 7 days, biological replicate 70, repeat group 1


title: MLM#3 replicate C

description: replicate 3


title: MLM#5 replicate D

description: replicate 4


title: CIE mouse, PFC, sacrificed at 0 hours, biological replicate 11, repeat group 1


title: CIE mouse, PFC, sacrificed at 0 hours, biological replicate 17, repeat group 1


title: CIE mouse, PFC, sacrificed at 0 hours, biological replicate 5, repeat group 1


title: MLM#5 replicate A

description: replicate 1


title: MLM#3 replicate A

description: replicate 1


title: whole blood_24

description: HGU133 Plus array data


title: CIE mouse, PFC, sacrificed at 0 hours, biological replicate 43, repeat group 1


title: control mouse, PFC, sacrificed at 7 days, biological replicate 28, repeat group 1


title: MLM#5 replicate C

description: replicate 3


title: MLM#5 replicate B

description: replicate 2


title: whole blood_26

description: HGU133 Plus array data


title: control mouse, PFC, sacrificed at 7 days, biological replicate 46, repeat group 1


title: whole blood_23

description: HGU133 Plus array data


title: whole blood_25

description: HGU133 Plus array data


title: MLM#1 replicate C

description: replicate 3


title: CIE mouse, PFC, sacrificed at 0 hours, biological replicate 67, repeat group 1


title: control mouse, PFC, sacrificed at 7 days, biological replicate 22, repeat group 1


title: MLM#1 replicate B

description: replicate 2


title: mEERL replicate B

description: replicate 2

source_name: mouse oropharyngeal cells expressing HPV16 E6/E7, hRas and luciferase (mEERL)

value: oropharyngeal cells expressing HPV16 E6/E7, hRas, and luciferase (mEERL)


title: control mouse, PFC, sacrificed at 72 hours, biological replicate 68, repeat group 1

source_name: medial PFC brain dissection, air inhalation chamber, tissue harvested 72 hours after final inhalation chamber session

value: 72 hours post final vapor chamber session


title: whole blood_19

description: HGU133 Plus array data


title: MLM#1 replicate A

description: replicate 1


title: whole blood_22

description: HGU133 Plus array data


title: control mouse, PFC, sacrificed at 7 days, biological replicate 18, repeat group 1


title: mEERL replicate A

description: replicate 1


title: mEERL replicate C

description: replicate 3


title: CL-Serum-Exo#1

city: Bonn

first: Yong

last: Chen

address: Sigmund-Freud-Strasse 25

institute: University of Bonn

description: exosomes in serum from CL-treated mice

data_processing: Data was processed by using DataAssist Software v3.01. Processed data was normalized by Global Normalization

label: FAM

source_name: serum exosome (Serum-Exo)

label_protocol: PCR assays were performed usingTaqMan® Low Density Array Rodent MicroRNA panel kit ( Thermo Fisher Scientific) according to manufacturer's instruction. Reverse transcription was performed from 100ng total RNA using TaqMan® MicroRNA Reverse Transcription Kit ( Thermo Fisher Scientific). Quantitative real-time PCR were performed with 40 cycles at 95˚C for 15 seconds and 60˚C for 60 seconds.

growth_protocol: BA-exosomes were from mature brown adipocytes in vitro. BAT-SVF cells were dissected from newborn C57BL/6 mice, then differentiated to mature brown adipocytes in proadipogenic medium

extract_protocol: exosome isolation from medium in vitro and serum in vivo by using Total Exosome Isolation Kits from life technologies. Total RNA was extracted from the exosomes by using Total Exosome RNA and Protein Isolation Kit from life technologies. All kits were used according to the User Guide supported by the manufacturer

treatment_protocol: mature brown adipocytes were treated with cAMP for 48 hours in vitro; C57BL/6 mice were either injected (I.P.) daily with CL316.243, or exposed to cold (4˚C) for 7 days

value: serum


title: whole blood_20

description: HGU133 Plus array data


title: whole blood_13

description: HGU133 Plus array data


title: whole blood_12

description: HGU133 Plus array data


title: whole blood_16

description: HGU133 Plus array data


title: control mouse, PFC, sacrificed at 8 hours, biological replicate 79, repeat group 1

source_name: medial PFC brain dissection, air inhalation chamber, tissue harvested 8 hours after final inhalation chamber session


title: control mouse, PFC, sacrificed at 8 hours, biological replicate 75, repeat group 1


title: CL-Serum-Exo#2

description: exosomes in serum from CL-treated mice


title: control mouse, PFC, sacrificed at 8 hours, biological replicate 32, repeat group 2


title: whole blood_17

description: HGU133 Plus array data

source_name: whole blood


title: control mouse, PFC, sacrificed at 8 hours, biological replicate 50, repeat group 2


title: control mouse, PFC, sacrificed at 8 hours, biological replicate 42, repeat group 2