title: E18.5 KO_1


title: P. syringae pv tomato DC3000 wildtype 11 hours biorep B

status: Public on Jun 02 2015

type: RNA

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

description: Randomised loop design providing dye-swaps between treatments, time points and bioreps

hyb_protocol: The order in which the 288 slides were hybridized and scanned was randomised to minimise the impact on differences between samples of any potential variation in the processing conditions. According to this randomised experimental design combinations of labelled samples were hybridized to slides overnight at 42oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5). Scanned data were quantified using Imagene 7.5.0 software (BioDiscovery, Inc.).

data_processing: Quantified microarray data were Lowess normalized within pintip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003). Oligo sequences of CATMA array probes were mapped to individual mRNA sequences of transcripts from the TAIR9 genome assembly using BLASTn with e-value cutoff of 0.01.  Additionally, alignments were filtered to exclude alignments shorter than 30bp or with less than 80% sequence identity.

label: Cy3 or Cy5

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis plants Col-0 were grown under a 16:8 hr light:dark cycle (lights on 04:00 to 20:00) at 20°C, 60% humidity and light intensity of 100 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1).

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

tag: strain

tag: treatment

value: Infected P. syringae pv tomato DC3000 wildtype

tag: tissue

value: leaf


title: P. syringae pv tomato DC3000 wildtype 12 hours biorep B


title: P. syringae pv tomato DC3000 wildtype 10 hours biorep B


title: P. syringae pv tomato DC3000 wildtype 5 hours biorep C


title: P. syringae pv tomato DC3000 wildtype 8 hours biorep C


title: P. syringae pv tomato DC3000 wildtype 13 hours biorep B


title: P. syringae pv tomato DC3000 wildtype 2 hours biorep C


title: P. syringae pv tomato DC3000 wildtype 1 hours biorep C


title: E18.5 KO_3

city: South San Francisco

first: Matthew

last: Brauer

state: California

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 11.

data_processing: Agilent Feature Extraction Software version 11 was used for background subtraction and LOWESS normalization.

organism: Mus musculus

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene).

extract_protocol: Total RNA was prepared by Qiagen RNeasy kit with on column DNase digestion.

value: Liver

tag: genotype

value: GCGR knockout

tag: age

source_name: Universal mouse reference (UMR) from Stratagene

tag: sample type

value: pooled mouse reference RNA


title: P. syringae pv tomato DC3000 wildtype 9 hours biorep C


title: P. syringae pv tomato DC3000 wildtype 4 hours biorep C


title: P. syringae pv tomato DC3000 wildtype 7 hours biorep C


title: E18.5 KO_2


title: P7.5 wt_3

source_name: P7.5 wt

value: wildtype


title: P2.5 KO_2

source_name: P2.5 KO


title: P. syringae pv tomato DC3000 wildtype 6 hours biorep C


title: P. syringae pv tomato DC3000 wildtype 9 hours biorep B


title: P. syringae pv tomato DC3000 wildtype 8 hours biorep B


title: P7.5 wt_1


title: P. syringae pv tomato DC3000 wildtype 7 hours biorep B


title: P. syringae pv tomato DC3000 wildtype 4 hours biorep B


title: P2.5 wt_2

source_name: P2.5 wt


title: P. syringae pv tomato DC3000 wildtype 5 hours biorep B


title: P. syringae pv tomato DC3000 wildtype 1 hours biorep B


title: P. syringae pv tomato DC3000 wildtype 9 hours biorep A


title: P. syringae pv tomato DC3000 wildtype 3 hours biorep B


title: P. syringae pv tomato DC3000 wildtype 10 hours biorep A


title: P7.5 wt_2


title: E18.5 wt_3


title: P. syringae pv tomato DC3000 wildtype 12 hours biorep A


title: P. syringae pv tomato DC3000 wildtype 2 hours biorep B


title: P. syringae pv tomato DC3000 wildtype 11 hours biorep A


title: PA001

city: Taipei

first: Ming Che

last: Shih

address: No.128, Sec. 2, Academia Rd., Nangang Dist

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica, Taiwan

description: gene expression profile of mature flower petal

hyb_protocol: All microarray hybridizations were followed Agilent Hybridization procedure at 65℃ for 17 hours.

scan_protocol: All chips were scanned by Agilent Microarray Scanner and scan settings were followed the manufacture suggestion.

data_processing: All Microarray data were processed using 75% percentile normalization in GeneSpring GX 11 (Agilent, CA, USA)

organism: Phalaenopsis aphrodite

source_name: Petal

label_protocol: RNA amplification was performed with MessageAmp™ II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) starting with 1 µg total RNA and following the manufacture procedures including first strand cDNA synthesis, second strand cDNA synthesis and in vitro transcription for cRNA synthesis. Finally, 1.65 µg of amplified aminallyl labeled cRNA was coupled with Alex Fluor 555 dye (Cy 3) and then the dye-coupled aRNA was fragmented before hybridization.

extract_protocol: Orchid total RNA was isolated as described previously with minor modification (Yu and Goh 2000). Plant tissues were frozen and ground in liquid nitrogen. RNA was extracted by vortexing with 5 to10 volumes (w/v) of extraction buffer (2% hexadecyltrimethylammonium bromide, 1% polyvinylpyrrolidone 40, 100 mM Tris-HCl pH 7.5, 20 mM EDTA, 2 M NaCl, 2% 2-mercaptoethanol) pre-warmed at 65°C. The homogenate was incubated at 65°C for 15 minutes with frequent mixing. The homogenate was centrifuged at 3,000xg for 10 minutes at room temperature. The supernatant was extracted twice with an equal volume of chloroform:isoamyl alcohol (24:1, v/v) and centrifuged at 8,000xg for 15 minutes. One-third volume of 8M lithium chloride was added to the aqueous phase to precipitate total RNA at -20°C overnight. The RNA pellet was harvested by centrifugation at 12,000xg for 30 minutes at 4°C, washed with ice-cold 75% ethanol, and resuspended in RNase-free water. RNA purity and concentration were determined by Nanodrop 2000 (Thermo Scientific, MA, USA) or Qubit (Invitrogen, CA, USA) measurement. The quality of RNA was evaluated on an Agilent 2100 Bioanalyzer (Agilent, CA, USA).

value: Phalaenopsis V3 hybrid, tetraploid

value: Petal


title: P. syringae pv tomato DC3000 wildtype 4 hours biorep A


title: PA003

description: gene expression profile of mature flower sepal

source_name: Sepal

value: Sepal


title: P. syringae pv tomato DC3000 wildtype 7 hours biorep A


title: P. syringae pv tomato DC3000 wildtype 8 hours biorep A


title: E18.5 wt_4


title: P. syringae pv tomato DC3000 wildtype 3 hours biorep A


title: E18.5 wt_2


title: P2.5 wt_3


title: E18.5 wt-1


title: P2.5 wt_1


title: P. syringae pv tomato DC3000 hrpA- mutant 13 hours biorep D

value: Infected P. syringae pv tomato DC3000 hrpA- mutant


title: aFGFR1/KLB 43

description: Brown Adipose Tissue gene expression from mice treated with aFGFR1/KLB

hyb_protocol: Hyb and wash by Affymetrix commercial methods

scan_protocol: Affymetrix commercial

data_processing: RMA normalization

label: biotin

source_name: BAT aFGFR1/KLB

label_protocol: Labeling by Affy Express

growth_protocol: Mice fed high-fat diet

extract_protocol: Five days post-treatment brown adipose tissue isolated and extracted for RNA

treatment_protocol: single intraperitoneal injection of 10 mg/kg anti-FGFR1/KLB agonistic antibody (bFKB1) or human FGF21 at 1 mg/kg b.i.d. (2 mg/kg/day)

value: Interscapular Brown Adipose Tissue

value: wt

value: adult


title: P. syringae pv tomato DC3000 hrpA- mutant 8 hours biorep D


title: P. syringae pv tomato DC3000 hrpA- mutant 10 hours biorep D


title: P. syringae pv tomato DC3000 hrpA- mutant 6 hours biorep D


title: P. syringae pv tomato DC3000 hrpA- mutant 5 hours biorep D


title: FGF21 40

description: Brown Adipose Tissue gene expression from mice treated with FGF21

source_name: BAT FGF21


title: P. syringae pv tomato DC3000 hrpA- mutant 11 hours biorep D


title: P. syringae pv tomato DC3000 hrpA- mutant 12 hours biorep D


title: P. syringae pv tomato DC3000 hrpA- mutant 9 hours biorep D


title: aFGFR1/KLB 44


title: P. syringae pv tomato DC3000 wildtype 2 hours biorep A


title: P. syringae pv tomato DC3000 hrpA- mutant 7 hours biorep D


title: P. syringae pv tomato DC3000 hrpA- mutant 3 hours biorep D


title: P. syringae pv tomato DC3000 hrpA- mutant 4 hours biorep D


title: P. syringae pv tomato DC3000 wildtype 1 hours biorep D


title: P. syringae pv tomato DC3000 wildtype 1 hours biorep A


title: aFGFR1/KLB 41


title: aFGFR1/KLB 45


title: aFGFR1/KLB 42


title: P. syringae pv tomato DC3000 hrpA- mutant 1 hours biorep D


title: P. syringae pv tomato DC3000 hrpA- mutant 13 hours biorep C


title: P7.5 KO_1

source_name: P7.5 KO


title: P. syringae pv tomato DC3000 wildtype 13 hours biorep A


title: FGF21 39


title: P2.5 wt_4


title: P. syringae pv tomato DC3000 hrpA- mutant 2 hours biorep D


title: FGF21 38


title: P. syringae pv tomato DC3000 hrpA- mutant 12 hours biorep C


title: P. syringae pv tomato DC3000 hrpA- mutant 11 hours biorep C


title: P. syringae pv tomato DC3000 hrpA- mutant 10 hours biorep C


title: P. syringae pv tomato DC3000 hrpA- mutant 4 hours biorep C


title: P. syringae pv tomato DC3000 hrpA- mutant 13 hours biorep B


title: FGF21 36


title: control 32

description: Brown Adipose Tissue gene expression from mice treated with control

source_name: BAT control


title: P. syringae pv tomato DC3000 hrpA- mutant 11 hours biorep B


title: control 35


title: control 31


title: P. syringae pv tomato DC3000 hrpA- mutant 5 hours biorep C


title: P. syringae pv tomato DC3000 wildtype 6 hours biorep A


title: P. syringae pv tomato DC3000 hrpA- mutant 9 hours biorep B


title: P. syringae pv tomato DC3000 hrpA- mutant 6 hours biorep C


title: P. syringae pv tomato DC3000 hrpA- mutant 9 hours biorep C


title: control 33


title: P. syringae pv tomato DC3000 hrpA- mutant 8 hours biorep C


title: P. syringae pv tomato DC3000 hrpA- mutant 10 hours biorep B


title: control 34


title: P. syringae pv tomato DC3000 hrpA- mutant 2 hours biorep C


title: P. syringae pv tomato DC3000 hrpA- mutant 3 hours biorep C


title: P. syringae pv tomato DC3000 hrpA- mutant 7 hours biorep C


title: P. syringae pv tomato DC3000 hrpA- mutant 8 hours biorep B


title: Roblin,spikelet F2, 48 hrs after noxABΔ inoculation in F0, rep 3

city: Ottawa

first: Thérèse

last: Ouellet

state: ON

address: 960 Carling Ave, room 2091

department: Eastern Cereal and Oilseed Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

description:
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of Fg noxABΔ in F0, biol. replicate 3
NoxAB_48_R3_F2

hyb_protocol: According to Affymetrix instructions for the GeneChip® 3' IVT Express Kit. All samples were processed in one experimental batch.

data_processing: The probe-level data for the whole profiling experiment were assembled into one dataset using the Robust Multichip Analysis (Irizarry et al, 2002) implemented in the software Acuity 4.0 (Molecular Devices, CA, USA), with quantile normalization and summarization by median polish.

organism: Triticum aestivum

source_name: Roblin, F2, noxABΔ

growth_protocol: Plants were grown in growth cabinets at 20 C/16 hrs daylight; 16 C/8 hrs night until heads reached mid anthesis; then they were moved to the misting room.

extract_protocol: Total RNA from each sample was isolated using a modified version of the Trizol method (Invitrogen Life Technologh, ON, Canada).  The RNA samples were treated with an RNase-free DNase (Qiagen, Mississauga, Canada) and cleaned up using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Wheat heads at mid-anthesis were inoculated as follow: 10 µl of either water (mock inoculation) or a 100,000 spores/ml suspension of the Fusarium graminearum mutant strain  noxABΔ (DAOM 239571) was point-inoculated into each of two basal florets of one developed spikelet (F0) of 30 wheat heads (grouped into biological replicates of 5 heads each).  The inoculated plants were mist-irrigated for 10 second intervals every 15 minutes for 24 hours to maintain high humidity, at a temperature of 25 oC.  Spikelets F0and F2 of each inoculated head were sampled at 48 hours after inoculation.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

tag: cultivar

value: spring wheat cv Roblin

value: spikelet F2

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment on f0

value: Fg noxABΔ

tag: hours after inoculation

tag: biological replicate


title: P. syringae pv tomato DC3000 hrpA- mutant 1 hours biorep C


title: Roblin,spikelet F2, 48 hrs after noxABΔ inoculation in F0, rep 2

description:
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of Fg noxABΔ in F0, biol. replicate 2
NoxAB_48_R2_F2

scan_protocol: According to Affymetrix instructions for the GeneChip® 3' IVT Express Kit. All samples were processed in one experimental batch.


title: P. syringae pv tomato DC3000 hrpA- mutant 12 hours biorep B


title: FGF21 37


title: P. syringae pv tomato DC3000 hrpA- mutant 7 hours biorep B


title: Roblin,spikelet F2, 48 hrs after noxABΔ inoculation in F0, rep 1

description:
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of Fg noxABΔ in F0, biol. replicate 1
NoxAB_48_R1_F2

label_protocol: According to Affymetrix instructions for the GeneChip® 3' IVT Express Kit. All samples were processed in one experimental batch.


title: P. syringae pv tomato DC3000 hrpA- mutant 5 hours biorep B


title: Roblin,spikelet F0, 48 hrs after noxABΔ inoculation in F0, rep 3

description:
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of Fg noxABΔ in F0, biol. replicate 3
NoxAB_48_R3_F0

source_name: Roblin, F0, noxABΔ

value: spikelet F0


title: control 6h [EV110113-6]

city: Pittsburgh

first: Luai

last: Huleihel

state: PA

address: 450 technology drive

department: Regenerative medicine

institute: University of Pittsburgh

description: ex-vivo at time point 6

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55C on Agilent 8X60K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters.

organism: Homo sapiens

source_name: control 6h

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The EVLP consist in the perfusion of the lungs out of the body during 6 hours. It is a well established protocol in where basically lungs are on a table connected to a close circuit containing a special perfusion solution that is circulated through the pulmonary vein and artery using a pump. The circuit contains also a deoxygenator. The perfusion temperature and flow are adjusted gradually and after 20 mins of perfusion the ventilation is initiated. Every hour lungs are recruited in order to assess pulmonary function and collect perfusate samples. In addition to perfusate, tissue samples from the lower lobe of the left lung and bronchial alveolar lavage (BAL) are collected at times T0, 3 and 6 hr.

value: lung

tag: gender

value: female

tag: age (yr)


title: P. syringae pv tomato DC3000 wildtype 6 hours biorep B

value: Infected P. syringae pv tomato DC3000 wildtype

value: leaf


title: Roblin,spikelet F0, 48 hrs after noxABΔ inoculation in F0, rep 2

description:
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of Fg noxABΔ in F0, biol. replicate 2
NoxAB_48_R2_F0


title: P. syringae pv tomato DC3000 hrpA- mutant 3 hours biorep B


title: control 3h [EV110113-3]

description: ex-vivo at time point 3

source_name: control 3h


title: Roblin,spikelet F2, 48 hrs after water inoculation in F0, rep 2

description:
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of water in F0, biol. replicate 2
dH2O_48_R2_F2

source_name: Roblin, F2, water

value: water


title: P. syringae pv tomato DC3000 hrpA- mutant 6 hours biorep B


title: control 6h [EV100713-6]

description: ex-vivo at time point 6


title: Roblin,spikelet F2, 48 hrs after water inoculation in F0, rep 3

description:
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of water in F0, biol. replicate 3
dH2O_48_R3_F2


title: Roblin,spikelet F2, 48 hrs after water inoculation in F0, rep 1

description:
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of water in F0, biol. replicate 1
dH2O_48_R1_F2


title: Roblin,spikelet F0, 48 hrs after noxABΔ inoculation in F0, rep 1

description:
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of Fg noxABΔ in F0, biol. replicate 1
NoxAB_48_R1_F0


title: P. syringae pv tomato DC3000 hrpA- mutant 4 hours biorep B


title: P. syringae pv tomato DC3000 hrpA- mutant 1 hours biorep B


title: P. syringae pv tomato DC3000 hrpA- mutant 12 hours biorep A


title: P. syringae pv tomato DC3000 hrpA- mutant 2 hours biorep B


title: control 0h [EV100713-0]

description: ex-vivo at time point 0

source_name: control 0h


title: control 3h [EV100713-3]

description: ex-vivo at time point 3


title: Roblin,spikelet F0, 48 hrs after water inoculation in F0, rep 3

description:
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of water in F0, biol. replicate 3
dH2O_48_R3_F0

source_name: Roblin, F0, water


title: PAH 6h [EV091113-6]

description: ex-vivo at time point 6

source_name: PAH 6h


title: control 0h [EV110113-0]

description: ex-vivo at time point 0


title: PAH 3h [EV091113-3]

description: ex-vivo at time point 3

source_name: PAH 3h


title: Roblin,spikelet F0, 48 hrs after water inoculation in F0, rep 1

description:
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of water in F0, biol. replicate 1
dH2O_48_R1_F0


title: P. syringae pv tomato DC3000 wildtype 5 hours biorep A

description: Randomised loop design providing dye-swaps between treatments, time points and bioreps


title: Roblin,spikelet F0, 48 hrs after water inoculation in F0, rep 2

description:
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of water in F0, biol. replicate 2
dH2O_48_R2_F0


title: P. syringae pv tomato DC3000 hrpA- mutant 11 hours biorep A


title: PAH 6h [EV090413-6]

description: ex-vivo at time point 6


title: Roblin,spikeled F4, 48 hrs after water inoculation in F0, rep 3

description:
W-48-R3-F4
Gene expression data from Roblin spikelet F4, 48 hr after inoculation of water in F0, biol. replicate 3

hyb_protocol: According to Affymetrix instructions for the GeneChip® HT One-Cycle Target Labeling and Controls Kit. All samples were processed in one experimental batch.

scan_protocol: According to Affymetrix instructions for the GeneChip® HT One-Cycle Target Labeling and Controls Kit, using the Affymetrix GeneChip® 3000 Scanner.

data_processing:
The probe-level data for the whole profiling experiment were assembled into one dataset using the Robust Multichip Analysis (Irizarry et al, 2002) implemented in the software Acuity 4.0 (Molecular Devices, CA, USA), with quantile normalization and summarization by median polish.
Signal from Acuity 4.0 RMA (using quantile normalization and summarization by median polish)

source_name: spikeled F4_48 hrs after water inoculation in F0

treatment_protocol: Wheat heads at mid-anthesis were inoculated as follow: 10 µl of either water (mock inoculation) or a 100,000 spores/ml suspension of the Fusarium graminearum mutant strain  tri6Δ (DAOM 237993) was point-inoculated into each of two basal florets of one developed spikelet (F0) of 4 or 5 wheat heads for each biological replicate, and 3 biological replicates were done for each condition.  The inoculated plants were mist-irrigated for 10 second intervals every 15 minutes for 24 hours to maintain high humidity, at a temperature of 25 oC.  Spikelets F0, F2 and F4 of each inoculated head were sampled at 0, 24 and 48 hours after inoculation.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

tag: cultivar/genotype

tag: inoculated with

value: water  (control)

value: spikelet F4


title: P. syringae pv tomato DC3000 hrpA- mutant 9 hours biorep A


title: Roblin,spikeled F2, 48 hrs after water inoculation in F0, rep 3

description:
W-48-R3-F2
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of water in F0, biol. replicate 3

source_name: spikeled F2_48 hrs after water inoculation in F0

label_protocol: According to Affymetrix instructions for the GeneChip® HT One-Cycle Target Labeling and Controls Kit. All samples were processed in one experimental batch.


title: PAH 0h [EV091113-0]

description: ex-vivo at time point 0

source_name: PAH 0h


title: P. syringae pv tomato DC3000 hrpA- mutant 8 hours biorep A


title: P. syringae pv tomato DC3000 hrpA- mutant 10 hours biorep A


title: Roblin,spikeled F0, 48 hrs after water inoculation in F0, rep 3

description:
W-48-R3-F0
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of water in F0, biol. replicate 3

source_name: spikeled F0_48 hrs after water inoculation in F0


title: P. syringae pv tomato DC3000 hrpA- mutant 7 hours biorep A


title: P. syringae pv tomato DC3000 hrpA- mutant 6 hours biorep A


title: P. syringae pv tomato DC3000 hrpA- mutant 13 hours biorep A


title: PAH 3h [EV090413-3]

description: ex-vivo at time point 3


title: P. syringae pv tomato DC3000 hrpA- mutant 3 hours biorep A


title: P. syringae pv tomato DC3000 hrpA- mutant 4 hours biorep A


title: Roblin,spikeled F0, 48 hrs after water inoculation in F0, rep 2

description:
W-48-R2-F0
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of water in F0, biol. replicate 2


title: PAH 0h [EV090413-0]

description: ex-vivo at time point 0


title: Roblin,spikeled F2, 48 hrs after water inoculation in F0, rep 2

description:
W-48-R2-F2
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of water in F0, biol. replicate 2


title: Roblin,spikeled F2, 48 hrs after water inoculation in F0, rep 1

description:
W-48-R1-F2
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of water in F0, biol. replicate 1


title: Roblin,spikeled F4, 24 hrs after water inoculation in F0, rep 3

description:
W-24-R3-F4
Gene expression data from Roblin spikelet F4, 24 hr after inoculation of water in F0, biol. replicate 3

source_name: spikeled F4_24 hrs after water inoculation in F0


title: P. syringae pv tomato DC3000 hrpA- mutant 2 hours biorep A


title: Roblin,spikeled F4, 48 hrs after water inoculation in F0, rep 1

description:
W-48-R1-F4
Gene expression data from Roblin spikelet F4, 48 hr after inoculation of water in F0, biol. replicate 1


title: Mock 12 hours biorep D

source_name: Mock 12 hours biorep D

value: Mock


title: Mock 13 hours biorep D

source_name: Mock 13 hours biorep D


title: P. syringae pv tomato DC3000 hrpA- mutant 5 hours biorep A

value: Infected P. syringae pv tomato DC3000 hrpA- mutant


title: Mock 11 hours biorep D

source_name: Mock 11 hours biorep D


title: Roblin,spikeled F0, 48 hrs after water inoculation in F0, rep 1

description:
W-48-R1-F0
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of water in F0, biol. replicate 1


title: HC_DZY

city: Beijing

first: Nannan

last: Wang

address: Fuxing Road NO.28

department: Department of Nephrology

country: China

institute: Chinese PLA General Hospital, Chinese PLA Institute of Nephrology,National Clinical Research Center for Kidney Diseases

description: MicroRNA expression data from unrine sediments

hyb_protocol: The labled RNA were hybridized for 16 hr at 48C on Affymetrix miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with miRNA QCTool using Affymetrix default analysis settings and quantile as normalization method.

source_name: human urine sediments

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit. This kit can be used to label any RNA sample, including total RNA, severely degraded RNA, plant RNA, and low molecular weight RNA.

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

treatment_protocol:
[collection protocol] A whole-stream early-morning urine specimen was collected into sterile tubes before renal biopsy and processed within 3 hours.
Urine sample was centrifuged at 3,000 g for 30 min and at 13,000 g for 5 min at 4 °C. Urinary cell pellet was lysed by TRIzol® Reagent (Invitrogen™). Specimens were then stored at –80 °C until use.

value: urine sediments

tag: ethnicity

value: Han

tag: disease state

value: HC


title: Roblin,spikeled F2, 24 hrs after water inoculation in F0, rep 3

description:
W-24-R3-F2
Gene expression data from Roblin spikelet F2, 24 hr after inoculation of water in F0, biol. replicate 3

source_name: spikeled F2_24 hrs after water inoculation in F0

value: spring wheat cv Roblin


title: HC_LD


title: Roblin,spikeled F0, 24 hrs after water inoculation in F0, rep 3

description:
W-24-R3-F0
Gene expression data from Roblin spikelet F0, 24 hr after inoculation of water in F0, biol. replicate 3

source_name: spikeled F0_24 hrs after water inoculation in F0


title: P. syringae pv tomato DC3000 hrpA- mutant 1 hours biorep A

tag: strain


title: HC_ZDL

value: male


title: Mock 10 hours biorep D

source_name: Mock 10 hours biorep D

tag: treatment


title: Roblin,spikeled F4, 24 hrs after water inoculation in F0, rep 2

description:
W-24-R2-F4
Gene expression data from Roblin spikelet F4, 24 hr after inoculation of water in F0, biol. replicate 2

tag: tissue

value: heads after mid-anthesis


title: Mock 9 hours biorep D

source_name: Mock 9 hours biorep D


title: HC_MJ


title: Roblin,spikeled F2, 24 hrs after water inoculation in F0, rep 2

description:
W-24-R2-F2
Gene expression data from Roblin spikelet F2, 24 hr after inoculation of water in F0, biol. replicate 2

value: spikelet F2


title: HC_QK


title: Roblin,spikeled F4, 24 hrs after water inoculation in F0, rep 1

description:
W-24-R1-F4
Gene expression data from Roblin spikelet F4, 24 hr after inoculation of water in F0, biol. replicate 1


title: Roblin,spikeled F0, 24 hrs after water inoculation in F0, rep 2

description:
W-24-R2-F0
Gene expression data from Roblin spikelet F0, 24 hr after inoculation of water in F0, biol. replicate 2

value: spikelet F0


title: Mock 7 hours biorep D

description: Randomised loop design providing dye-swaps between treatments, time points and bioreps

source_name: Mock 7 hours biorep D


title: HC_WSY


title: Mock 5 hours biorep D

source_name: Mock 5 hours biorep D


title: Mock 8 hours biorep D

source_name: Mock 8 hours biorep D


title: MCD_MY

value: MCD


title: Mock 6 hours biorep D

source_name: Mock 6 hours biorep D


title: Roblin,spikeled F0, 24 hrs after water inoculation in F0, rep 1

description:
W-24-R1-F0
Gene expression data from Roblin spikelet F0, 24 hr after inoculation of water in F0, biol. replicate 1


title: Roblin,spikeled F2, 24 hrs after water inoculation in F0, rep 1

description:
W-24-R1-F2
Gene expression data from Roblin spikelet F2, 24 hr after inoculation of water in F0, biol. replicate 1


title: MCD_YHY


title: MCD_WYG

value: female


title: Mock 3 hours biorep D

source_name: Mock 3 hours biorep D


title: Mock 4 hours biorep D

source_name: Mock 4 hours biorep D


title: Roblin,spikeled F2, 0 hrs after water inoculation in F0, rep 3

description:
W-0-R3-F2
Gene expression data from Roblin spikelet F2, 0 hr after inoculation of water in F0, biol. replicate 3

source_name: spikeled F2_0 hrs after water inoculation in F0


title: MCD_LY


title: Roblin,spikeled F4, 0 hrs after water inoculation in F0, rep 3

description:
W-0-R3-F4
Gene expression data from Roblin spikelet F4, 0 hr after inoculation of water in F0, biol. replicate 3

source_name: spikeled F4_0 hrs after water inoculation in F0


title: Mock 1 hours biorep D

source_name: Mock 1 hours biorep D


title: Roblin,spikeled F0, 0 hrs after water inoculation in F0, rep 3

description:
W-0-R3-F0
Gene expression data from Roblin spikelet F0, 0 hr after inoculation of water in F0, biol. replicate 3

source_name: spikeled F0_0 hrs after water inoculation in F0


title: Mock 2 hours biorep D

source_name: Mock 2 hours biorep D


title: MN_AJY

value: MN


title: Mock 13 hours biorep C

source_name: Mock 13 hours biorep C

value: leaf


title: MN_HXD

source_name: human urine sediments


title: Roblin,spikeled F2, 0 hrs after water inoculation in F0, rep 2

description:
W-0-R2-F2
Gene expression data from Roblin spikelet F2, 0 hr after inoculation of water in F0, biol. replicate 2


title: Mock 12 hours biorep C

source_name: Mock 12 hours biorep C


title: MN_YST


title: Roblin,spikeled F0, 0 hrs after water inoculation in F0, rep 2

description:
W-0-R2-F0
Gene expression data from Roblin spikelet F0, 0 hr after inoculation of water in F0, biol. replicate 2


title: Roblin,spikeled F4, 48 hrs after water inoculation in F0, rep 2

description:
W-48-R2-F4
Gene expression data from Roblin spikelet F4, 48 hr after inoculation of water in F0, biol. replicate 2

source_name: spikeled F4_48 hrs after water inoculation in F0


title: MN_DLT


title: IgAN IV-V Grade_CCY

value: IgAN

tag: disease grade

value: IV-V


title: Roblin,spikeled F4, 0 hrs after water inoculation in F0, rep 1

description:
W-0-R1-F4
Gene expression data from Roblin spikelet F4, 0 hr after inoculation of water in F0, biol. replicate 1

value: water  (control)

value: spikelet F4


title: IgAN IV-V Grade_YJ

description: MicroRNA expression data from unrine sediments

tag: age


title: Roblin,spikeled F2, 0 hrs after water inoculation in F0, rep 1

description:
W-0-R1-F2
Gene expression data from Roblin spikelet F2, 0 hr after inoculation of water in F0, biol. replicate 1


title: Mock 10 hours biorep C

source_name: Mock 10 hours biorep C

value: Mock


title: IgAN IV-V Grade_ZAS

tag: sample type

value: urine sediments


title: Roblin,spikeled F0, 0 hrs after water inoculation in F0, rep 1

description:
W-0-R1-F0
Gene expression data from Roblin spikelet F0, 0 hr after inoculation of water in F0, biol. replicate 1


title: case-37

type: genomic

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

description: Hybridized to Affymetrix Cytogenetics Array

hyb_protocol: DNA was whole-genome amplified, purified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files generated by Affymetrix Command Console and CYCHP files generated byAffymetrix Chromosome Analysis Suite software (ChAS).  DNA copy number  analysis were performed using Affymetrix ChAS, which compares all hybridization intensities against a built-in reference data set.

molecule: genomic DNA

source_name: Diffuse Large B-cell Lymphoma

label_protocol: Biotin, affymetrix protocol for the  Cytogenetics array 2.7M

growth_protocol: No culture-just DNA from frozen tissue

extract_protocol: Qiagen kit for DNA extraction

value: M

tag: ebv

value: negative

tag: immune status

value: Immunocompetent

tag: survival [months]

tag: cytogenetics

value: Not Done


title: Mock 9 hours biorep C

source_name: Mock 9 hours biorep C


title: Roblin,spikeled F4, 0 hrs after water inoculation in F0, rep 2

description:
W-0-R2-F4
Gene expression data from Roblin spikelet F4, 0 hr after inoculation of water in F0, biol. replicate 2

value: spring wheat cv Roblin

tag: tissue age

value: heads after mid-anthesis

tag: hours after inoculation


title: IgAN IV-V Grade_XBY

tag: gender

value: male

value: Han


title: case-32


title: case-35

value: F


title: Mock 11 hours biorep C

source_name: Mock 11 hours biorep C


title: IgAN IV-V Grade_DJG


title: IgAN IV-V Grade_WJ


title: Mock 7 hours biorep C

source_name: Mock 7 hours biorep C


title: case-36


title: case-34


title: Roblin,spikeled F0, 48 hrs after tri6Δ inoculation in F0, rep 3

description:
T6-48-R3-F0
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of Fg tri6Δ in F0, biol. replicate 3

source_name: spikeled F0_48 hrs after tri6Δ inoculation in F0

tag: cultivar/genotype

value: F. graminearum  tri6Δ mutant

value: spikelet F0


title: Roblin,spikeled F2, 48 hrs after tri6Δ inoculation in F0, rep 3

description:
T6-48-R3-F2
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of Fg tri6Δ in F0, biol. replicate 3

source_name: spikeled F2_48 hrs after tri6Δ inoculation in F0

tag: inoculated with

value: spikelet F2


title: case-38


title: case-31


title: Mock 6 hours biorep C

description: Randomised loop design providing dye-swaps between treatments, time points and bioreps

source_name: Mock 6 hours biorep C

value: leaf


title: Mock 5 hours biorep C

source_name: Mock 5 hours biorep C


title: Roblin,spikeled F4, 48 hrs after tri6Δ inoculation in F0, rep 2

description:
T6-48-R2-F4
Gene expression data from Roblin spikelet F4, 48 hr after inoculation of Fg tri6Δ in F0, biol. replicate 2

source_name: spikeled F4_48 hrs after tri6Δ inoculation in F0


title: IgAN III Grade_HYZ

value: female

tag: ethnicity

value: IgAN

value: III


title: IgAN III Grade_DSL

value: urine sediments

tag: disease state


title: Mock 4 hours biorep C

source_name: Mock 4 hours biorep C

tag: strain

value: Mock


title: case-33

value: M

value: negative


title: IgAN III Grade_WZY


title: Roblin,spikeled F0, 48 hrs after tri6Δ inoculation in F0, rep 2

description:
T6-48-R2-F0
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of Fg tri6Δ in F0, biol. replicate 2


title: Mock 3 hours biorep C

source_name: Mock 3 hours biorep C

tag: treatment


title: case-29

value: Immunocompetent

value: no mitosis


title: Roblin,spikeled F2, 48 hrs after tri6Δ inoculation in F0, rep 2

description:
T6-48-R2-F2
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of Fg tri6Δ in F0, biol. replicate 2

value: spring wheat cv Roblin

tag: tissue

value: heads after mid-anthesis


title: Roblin,spikeled F4, 48 hrs after tri6Δ inoculation in F0, rep 3

description:
T6-48-R3-F4
Gene expression data from Roblin spikelet F4, 48 hr after inoculation of Fg tri6Δ in F0, biol. replicate 3

value: spikelet F4


title: Mock 2 hours biorep C

source_name: Mock 2 hours biorep C


title: case-28

value: Not Done


title: IgAN III Grade_XB

value: male

value: Han

tag: disease grade


title: Roblin,spikeled F4, 48 hrs after tri6Δ inoculation in F0, rep 1

description:
T6-48-R1-F4
Gene expression data from Roblin spikelet F4, 48 hr after inoculation of Fg tri6Δ in F0, biol. replicate 1

value: F. graminearum  tri6Δ mutant


title: case-30

tag: age


title: IgAN III Grade_ZC

tag: sample type


title: Roblin,spikeled F2, 48 hrs after tri6Δ inoculation in F0, rep 1

description:
T6-48-R1-F2
Gene expression data from Roblin spikelet F2, 48 hr after inoculation of Fg tri6Δ in F0, biol. replicate 1

value: spikelet F2


title: Mock 1 hours biorep C

source_name: Mock 1 hours biorep C

value: leaf


title: Mock 13 hours biorep B

source_name: Mock 13 hours biorep B


title: Roblin,spikeled F4, 24 hrs after tri6Δ inoculation in F0, rep 3

description:
T6-24-R3-F4
Gene expression data from Roblin spikelet F4, 24 hr after inoculation of Fg tri6Δ in F0, biol. replicate 3

source_name: spikeled F4_24 hrs after tri6Δ inoculation in F0


title: IgAN III Grade_YNN

source_name: human urine sediments

value: IgAN


title: Roblin,spikeled F0, 48 hrs after tri6Δ inoculation in F0, rep 1

description:
T6-48-R1-F0
Gene expression data from Roblin spikelet F0, 48 hr after inoculation of Fg tri6Δ in F0, biol. replicate 1

value: spikelet F0


title: IgAN I-II Grade_LCX

value: urine sediments

value: female

value: I-II


title: case-25

value: M

tag: ebv

value: negative

value: Immunodeficient

tag: graft

value: liver

tag: tx-ptld interval (months)


title: Mock 8 hours biorep C

source_name: Mock 8 hours biorep C

value: Mock


title: Mock 12 hours biorep B

source_name: Mock 12 hours biorep B


title: case-23

source_name: Diffuse Large B-cell Lymphoma

tag: immune status

tag: survival [months]

tag: cytogenetics


title: IgAN I-II Grade_ZY

tag: gender


title: Roblin,spikeled F2, 24 hrs after tri6Δ inoculation in F0, rep 3

description:
T6-24-R3-F2
Gene expression data from Roblin spikelet F2, 24 hr after inoculation of Fg tri6Δ in F0, biol. replicate 3

source_name: spikeled F2_24 hrs after tri6Δ inoculation in F0

tag: cultivar/genotype

value: spring wheat cv Roblin

tag: tissue age

value: heads after mid-anthesis

tag: hours after inoculation


title: Mock 10 hours biorep B

source_name: Mock 10 hours biorep B


title: IgAN I-II Grade_LX

description: MicroRNA expression data from unrine sediments

tag: ethnicity

tag: disease state


title: case-21

value: positive

value: Heart

value: Not Done


title: case-19

value: Kidney


title: case-20

value: F

value: no mitosis


title: Roblin,spikeled F4, 24 hrs after tri6Δ inoculation in F0, rep 2

description:
T6-24-R2-F4
Gene expression data from Roblin spikelet F4, 24 hr after inoculation of Fg tri6Δ in F0, biol. replicate 2

tag: inoculated with

value: F. graminearum  tri6Δ mutant

value: spikelet F4


title: case-24


title: IgAN I-II Grade_ZW

value: urine sediments

value: male

value: Han

value: IgAN


title: Roblin,spikeled F2, 24 hrs after tri6Δ inoculation in F0, rep 2

description:
T6-24-R2-F2
Gene expression data from Roblin spikelet F2, 24 hr after inoculation of Fg tri6Δ in F0, biol. replicate 2

tag: tissue

value: spikelet F2


title: Mock 11 hours biorep B

source_name: Mock 11 hours biorep B

tag: strain

tag: treatment

value: leaf


title: IgAN I-II Grade_LMY

tag: sample type

tag: age

tag: disease grade

value: I-II


title: Roblin,spikeled F0, 24 hrs after tri6Δ inoculation in F0, rep 3

description:
T6-24-R3-F0
Gene expression data from Roblin spikelet F0, 24 hr after inoculation of Fg tri6Δ in F0, biol. replicate 3

source_name: spikeled F0_24 hrs after tri6Δ inoculation in F0

value: spring wheat cv Roblin

value: spikelet F0


title: Roblin,spikeled F4, 24 hrs after tri6Δ inoculation in F0, rep 1

description:
T6-24-R1-F4
Gene expression data from Roblin spikelet F4, 24 hr after inoculation of Fg tri6Δ in F0, biol. replicate 1

value: heads after mid-anthesis


title: Mock 8 hours biorep B

source_name: Mock 8 hours biorep B

value: Mock


title: case-26

description: Hybridized to Affymetrix Cytogenetics Array

tag: ebv

value: negative

value: Immunodeficient

tag: graft

tag: tx-ptld interval (months)

value: Not Done


title: S aureus ATCC29213_Celecoxib & Ampicillin treated cells_dup

city: HYDERABAD

first: Arunasree

middle: M.

last: Kalle

state: -- Please Select --

address: GACHIBOWLI

department: Department of Animal Sciences

country: India

institute: UNIVERSITY OF HYDERABAD

description: Gene expression after 40 min of celecoxib & ampicillin treated cells

hyb_protocol: Samples that pass the QC for specific activity were taken for hybridization. 2000ng of Cy3 labeled cRNA samples were fragmented and hybridized on Agilent Custom Staphylococcus aureus 8x15k designed by Genotypic Technology Private Limited (AMADID: 27491)using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.7)

data_processing: Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Staphylococcus aureus

source_name: S aureus, celecoxib & ampicillin treated, 40 min

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using Random hexamer primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized cRNA strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop

growth_protocol: S aureus ATCC 29213 was grown overnight in LB medium at 37 °C, 180 rpm from glycerol stock.

extract_protocol: Total RNA isolation was performed using Trizol method as per the manufacturer’s instructions.

treatment_protocol: For treatments, 50ml of LB broth was inoculated with 1% overnight culture and grown till the log phase (OD 600 = 0.4). The cells were treated with celecoxib (25μM) or ampicillin (3μg/ml) and incubated for 40 min. For treatment of cells with both celecoxib and ampicillin, celecoxib was added after 20 min of incubation of cells with ampicillin. The untreated cells served as control.  The cells were harvested by centrifugation at 5000 rpm, 4 oC for 5 min, washed with 25 mM Tris pH 7.5, snap freezed in liquid nitrogen and stored at – 80 oC for RNA isolation.


title: Roblin,spikeled F0, 24 hrs after tri6Δ inoculation in F0, rep 2

description:
T6-24-R2-F0
Gene expression data from Roblin spikelet F0, 24 hr after inoculation of Fg tri6Δ in F0, biol. replicate 2


title: Mock 6 hours biorep B

description: Randomised loop design providing dye-swaps between treatments, time points and bioreps

source_name: Mock 6 hours biorep B


title: case-18

value: M

value: positive

tag: immune status

value: hematopoietic stem cell

tag: survival [months]

tag: cytogenetics


title: S aureus ATCC29213_Celecoxib & Ampicillin treated cells


title: case-22

tag: gender

value: liver

value: no mitosis


title: case-27

value: Kidney


title: Mock 7 hours biorep B

source_name: Mock 7 hours biorep B


title: IgAN I-II Grade_LDH

value: urine sediments

value: male

value: Han

value: IgAN


title: Mock 5 hours biorep B

source_name: Mock 5 hours biorep B

value: leaf


title: S aureus ATCC29213_Ampicillin treated cells_dup

description: Gene expression after 40 min of ampicillin treated cells

source_name: S aureus, ampicillin treated, 40 min


title: Mock 9 hours biorep B

source_name: Mock 9 hours biorep B


title: case-17


title: Roblin,spikeled F2, 24 hrs after tri6Δ inoculation in F0, rep 1

description:
T6-24-R1-F2
Gene expression data from Roblin spikelet F2, 24 hr after inoculation of Fg tri6Δ in F0, biol. replicate 1

tag: cultivar/genotype

value: spring wheat cv Roblin

value: F. graminearum  tri6Δ mutant

value: spikelet F2

tag: tissue age

tag: hours after inoculation


title: Mock 4 hours biorep B

source_name: Mock 4 hours biorep B

value: Mock


title: S aureus ATCC29213_Celecoxib treated cells_dup

description: Gene expression after 40 min of celecoxib treated cells

source_name: S aureus, celecoxib treated, 40 min


title: Roblin,spikeled F0, 24 hrs after tri6Δ inoculation in F0, rep 1

description:
T6-24-R1-F0
Gene expression data from Roblin spikelet F0, 24 hr after inoculation of Fg tri6Δ in F0, biol. replicate 1

tag: inoculated with

value: spikelet F0

value: heads after mid-anthesis


title: Frontal cortex pyramidal neurons, low DNA damage response 4

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description: Gene expression data from human astrocytes

hyb_protocol: 12.5µg of cRNA molecules were heat fragmented and applied to the Human Genome HGU133 Plus 2.0 GeneChip in a hybridization solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridization platform at 45°C for 16 hours. Post hybridization stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: The data were prepared using Expression Console software

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol:
[staining_protocol] 7um frozen frontal cortex sections were fixed in acetone and stained using Toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 95%, 100%) and cleared in xylene.
[isolation_protocol] From each individual case, approximately 1000 pyramidal neurones were isolated using a PixCell II laser-capture microdissection system (Applied Biosystems)
PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

tag: tissue

value: frontal cortex

tag: cell type

value: pyramidal neuron

tag: neuronal ddr

value: Low DNA damage


title: Roblin,spikeled F0, 0 hrs after tri6Δ inoculation in F0, rep 3

description:
T6-0-R3-F0
Gene expression data from Roblin spikelet F0, 0 hr after inoculation of Fg tri6Δ in F0, biol. replicate 3

source_name: spikeled F0_0 hrs after tri6Δ inoculation in F0


title: Mock 3 hours biorep B

source_name: Mock 3 hours biorep B

tag: strain

tag: treatment


title: case-14

value: M

tag: age

value: positive

value: Immunodeficient

value: hematopoietic stem cell


title: Frontal cortex pyramidal neurons, low DNA damage response 3


title: Mock 2 hours biorep B

source_name: Mock 2 hours biorep B


title: case-16

source_name: Diffuse Large B-cell Lymphoma

tag: ebv

value: Not Done


title: Mock 1 hours biorep B

source_name: Mock 1 hours biorep B


title: S aureus ATCC29213_Ampicillin treated cells


title: S aureus ATCC29213_Control cells_dup

description: Gene expression after 40 min untreated cells

source_name: S aureus, untreated, 40 min


title: case-13

tag: graft

value: Kidney


title: S aureus ATCC29213_Celecoxib treated cells


title: Roblin,spikeled F0, 0 hrs after tri6Δ inoculation in F0, rep 2

description:
T6-0-R2-F0
Gene expression data from Roblin spikelet F0, 0 hr after inoculation of Fg tri6Δ in F0, biol. replicate 2


title: S aureus ATCC29213_Control cells


title: Frontal cortex pyramidal neurons, low DNA damage response 2


title: Mock 12 hours biorep A

source_name: Mock 12 hours biorep A


title: Mock 13 hours biorep A

source_name: Mock 13 hours biorep A


title: dasR_vs_wt_48h_rep2

city: Shanghai

first: Chengheng

last: Liao

address: 130 Meilong Road

department: State Key Laboratory of Bioreactor Engineering

institute: East China University of Science and Technology

description: Biological replicate 2 of 2. Control wild-type train NRRL23338, harvested at 48 h.

hyb_protocol: Each Slide was hybridized with 300ng Cy3-labeled cRNA and 300ng Cy-5 labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Red&Green, Scan resolution=5μm, PMT 100%, 10% , 16bit. and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

data_processing: Raw data were normalized by Lowess(locally weighted scatter plot smoothing) algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Saccharopolyspora erythraea

source_name: dasR null mutant

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, Two-Color (Cat#5190-2306, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Each strain was grown in liquid TSB medium, and total RNA were extracted from the mycelia sample harvested at 24 h and 48 h, respectively.

extract_protocol: RNA was extracted from samples derived from two independent culture samples collected at two time points (24 h and 48 h) using the RNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer's instructions.

value: dasR null mutant

tag: time

source_name: wild-type strain NRRL23338

value: wild-type strain NRRL23338


title: Frontal cortex pyramidal neurons, high DNA damage response 4

value: High DNA damage


title: case-9

value: F

tag: immune status

tag: tx-ptld interval (months)


title: dasR_vs_wt_48h_rep1

description: Biological replicate 1 of 2. Control wild-type train NRRL23338, harvested at 48 h.


title: case-10

value: Heart-Lung

tag: survival [months]

tag: cytogenetics


title: case-11

tag: gender


title: Mock 10 hours biorep A

source_name: Mock 10 hours biorep A

value: Mock

value: leaf


title: case-12

value: no mitosis


title: Frontal cortex pyramidal neurons, high DNA damage response 3

value: frontal cortex


title: Frontal cortex pyramidal neurons, high DNA damage response 2

value: pyramidal neuron


title: Dog-HNSCC-938

city: New York

first: Deli

last: Liu

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

hyb_protocol: Using NimbleGen Hybridization System (following the NimbleGen official Manual)

scan_protocol: Scanning two-color NimbleGen arrays with GenePix 4000B Scanner and associated software(following the NimbleGen official Manual)

data_processing: Analyzing the data with the segMNT algorithm (following the NimbleGen official Manual), and background correction as implemented in the NimbleScan software package, version 2.6.0.0 (Roche NimbleGen, Inc.).

organism: Canis lupus familiaris

source_name: DNA from HNSCC tumor tissue of dog 938

label_protocol: Labeling test samples with Cy3 following the NimbleGen official Manual, see more at NimbleGen website, and labeling reference samples with Cy5 following the NimbleGen official Manual, see more at NimbleGen website.

extract_protocol: Genomic DNA was extracted from the dissected tissues using a Qiagen Tissue DNeasy purification kit (exactly following the kit manual)

tag: genotype

value: Head and neck squamous cell carcinoma

value: HNSCC

value: Unknown

source_name: DNA from head and neck normal tissue of dog 938

value: Normal

value: Normal cell


title: Frontal cortex pyramidal neurons, low DNA damage response 1

value: Low DNA damage


title: Mock 11 hours biorep A

source_name: Mock 11 hours biorep A


title: dasR_vs_wt_24h_rep2

description: Biological replicate 2 of 2. Control wild-type train NRRL23338, harvested at 24 h.


title: case-8

value: M

value: positive

value: Immunodeficient

value: Kidney

value: Not Done


title: case-7

value: hematopoietic stem cell


title: Dog-HNSCC-840

source_name: DNA from HNSCC tumor tissue of dog 840

source_name: DNA from head and neck normal tissue of dog 840


title: Mock 9 hours biorep A

source_name: Mock 9 hours biorep A

value: Mock


title: Frontal cortex pyramidal neurons, high DNA damage response 1

value: High DNA damage


title: dasR_vs_wt_24h_rep1

description: Biological replicate 1 of 2. Control wild-type train NRRL23338, harvested at 24 h.

value: dasR null mutant

value: wild-type strain NRRL23338


title: case-4

value: Heart


title: Mock 7 hours biorep A

source_name: Mock 7 hours biorep A

value: leaf


title: BARX1 overexpressed intestine at E13.5, Biological replicate 1

first: Chenura

last: Jayewickreme

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medical College

description: Gene expression data from 3 day cultured E13.5 intestine overexpressing BARX1

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Resources at GenePattern.org were used to normalize files using RMA and to identify differentially expressed genes

source_name: Mouse intestines overexpressing BARX1 at E13.5, cultured for 3 days

label_protocol: Affymetrix protocol

growth_protocol: Embryos were harvested from pregnant dams at E13.5

extract_protocol: Tissues were excised, washed in cold Hank's Balanced Salt Solution (HBSS), and digested sequentially in 0.1% Collagenase-Dispase in HBSS at 37 degrees Celsius for 30 min and 0.25% Trypsin-EDTA in HBSS for 10 min. After a short centrifugation to collect cells, the pellet was washed in Dulbecco's Modified Eager Medium (DMEM) and cultured for 3 days in DMEM supplemented with 20% fetal bovine serum and 1% Penicillin-Streptomycin.

value: Embryonic Intestine

value: Rosa26+/Barx1;Bapx1+/Cre (OE)

tag: development stage


title: Mock 5 hours biorep A

source_name: Mock 5 hours biorep A


title: BARX1 overexpressed intestine at E13.5, Biological replicate 2


title: iHCs_Dox+RA Day 8, biological rep3

city: Edinburgh

first: Aida

last: Santos da Costa

state: Edinburgh

address: Old College, South Bridge

institute: University of Edinburgh

description: Gene expression data from purified iHCs (iMyo7a+ cells) obtained from floating embryoid bodies treated with Dox + RA at day 4 and harvested day 8

hyb_protocol: 3.5 µg of end-labeled, fragmented cDNA was used in a 150-µl hybridization cocktail containing added hybridization controls (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix), of which 120 ul were hybridized on array strips for 20 h at 48°C. Standard post hybridization wash and double-stain protocols (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix) were used on an Affymetrix GeneAtlas system.

scan_protocol: Array strips were scanned on an Affymetrix GeneAtlas scanner

data_processing: The 16 scanned arrays were analyzed first with Affymetrix Expression Console software using RMA to obtain expression values and for quality control. Control probe sets were removed and log2 expression values of the remaining  33708 transcripts were imported into Chipster 2.4. Differential expression was determined by empirical Bayes two-group test with Benjamini-Hochberg multiple testing correction and a p-value cut-off of 0.01.

source_name: iMyo7a+ cells, FACS-sorted from day 8 embryoid bodies, treated with Dox + RA for 4 days

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) Mouse Genome 2.1 ST Arrays Strip by using the Ambion WT Expression Kit (Life Technologies, CA, USA) and Affymetrix GeneChip WT Terminal Labeling Kit, according to the manufacturer’s protocols. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (Ambion WT Expression Kit) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (Ambion WT Expression Kit). 15 ug of this cRNA was used for a second cycle of first-strand cDNA synthesis (Ambion WT Expression Kit). 5.5 ug of single stranded cDNA was fragmented and end-labeled (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: EBs were grown in at 370C in a 5% CO2 incubator in Dulbecco's Modified Eagle’s Medium (DMEM, Invitrogen), supplemented with 10% fetal bovine serum (FBS) (ES-qualified, Invitrogen), on 60-mm bacterial-grade Petri dishes.

extract_protocol: Total RNA was extracted from 10e6 cells using High Pure RNA Isolation kit (Roche Diagnostics) according to manufacturer's instructions.

treatment_protocol: EBs were dissociated using 0.25% trypsin-EDTA (Invitrogen) in PBS and resuspended in 4% FBS in PBS. Cell sorting of iMyo7a:venus+ populations were done on a FACS Aria cell sorter (Becton Dickinson).

value: Embryonic Stem Cell

tag: cell line

value: Culture day 8


title: Wildtype intestine at E13.5, Biological replicate 2

description: Gene expression data from 3 day cultured E13.5 intestine

source_name: Mouse intestine at E13.5, cultured for 3 days

tag: tissue

value: Rosa26+/Barx1 or Bapx1+/Cre (WT)


title: Mock 6 hours biorep A

source_name: Mock 6 hours biorep A


title: Mock 8 hours biorep A

source_name: Mock 8 hours biorep A


title: iHCs_Dox+RA Day 12, biological rep3

description: Gene expression data from purified iHCs (iMyo7a+ cells) obtained from floating embryoid bodies treated with Dox + RA at day 4 and harvested day 12

source_name: iMyo7a+ cells, FACS-sorted from day 12 embryoid bodies, treated with Dox + RA for 8 days

tag: cell type

value: Culture day 12


title: Dog-HNSCC-573

source_name: DNA from HNSCC tumor tissue of dog 573

value: Head and neck squamous cell carcinoma

value: HNSCC

value: Unknown

source_name: DNA from head and neck normal tissue of dog 573

value: Normal

value: Normal cell


title: Roblin,spikeled F0, 0 hrs after tri6Δ inoculation in F0, rep 1

description:
T6-0-R1-F0
Gene expression data from Roblin spikelet F0, 0 hr after inoculation of Fg tri6Δ in F0, biol. replicate 1

source_name: spikeled F0_0 hrs after tri6Δ inoculation in F0

tag: cultivar/genotype

value: spring wheat cv Roblin

tag: inoculated with

value: F. graminearum  tri6Δ mutant

value: spikelet F0

tag: tissue age

value: heads after mid-anthesis

tag: hours after inoculation


title: iHCs_Dox Day 8, biological rep3

description: Gene expression data from purified iHCs (iMyo7a+ cells) obtained from floating embryoid bodies treated with Dox at day 4 and harvested day 8

source_name: iMyo7a+ cells, FACS-sorted from day 8 embryoid bodies, treated with Dox for 4 days

tag: age


title: Wildtype intestine at E13.5, Biological replicate 1

tag: strain


title: case-6

description: Hybridized to Affymetrix Cytogenetics Array

source_name: Diffuse Large B-cell Lymphoma

value: F

tag: ebv

value: positive

value: Immunodeficient

tag: graft

value: Lung

value: Not Done


title: Mock 4 hours biorep A

description: Randomised loop design providing dye-swaps between treatments, time points and bioreps

source_name: Mock 4 hours biorep A

tag: treatment

value: Mock

value: leaf


title: iHCs_Dox+RA Day 12, biological rep2

value: Embryonic Stem Cell

value: Culture day 12


title: Dog-HNSCC-571

source_name: DNA from HNSCC tumor tissue of dog 571

value: Head and neck squamous cell carcinoma

value: HNSCC

source_name: DNA from head and neck normal tissue of dog 571


title: Wildtype stomach at E13.5, Biological replicate 2

description: Gene expression data from 3 day cultured E13.5 stomach

source_name: Mouse stomach at E13.5, cultured for 3 days

value: Embryonic Stomach

value: Rosa26+/Barx1 or Bapx1+/Cre (WT)


title: Dog-HNSCC-465

source_name: DNA from HNSCC tumor tissue of dog 465

value: Unknown

source_name: DNA from head and neck normal tissue of dog 465

value: Normal

value: Normal cell


title: case-1

value: M

tag: immune status

value: Heart

tag: tx-ptld interval (months)

tag: survival [months]


title: iHCs_Dox Day 12, biological rep3

description: Gene expression data from purified iHCs (iMyo7a+ cells) obtained from floating embryoid bodies treated with Dox at day 4 and harvested day 12

source_name: iMyo7a+ cells, FACS-sorted from day 12 embryoid bodies, treated with Dox for 8 days


title: Mock 3 hours biorep A

source_name: Mock 3 hours biorep A


title: Dog-HNSCC-419

source_name: DNA from HNSCC tumor tissue of dog 419

tag: genotype

source_name: DNA from head and neck normal tissue of dog 419


title: Dog-HNSCC-419_2

source_name: DNA from HNSCC tumor tissue of dog 419_2

source_name: DNA from head and neck normal tissue of dog 419_2


title: Wildtype stomach at E13.5, Biological replicate 1

tag: development stage


title: case-3

tag: gender

value: F

value: positive

value: Kidney

tag: cytogenetics


title: Dog-HNSCC-404

source_name: DNA from HNSCC tumor tissue of dog 404

tag: cell type

source_name: DNA from head and neck normal tissue of dog 404


title: 14A overexpression_H1299_rep2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: miRNAs expression

hyb_protocol: The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labeled miRNA sample was incubated for 5 min at 100 °C and immediately kept on ice. Each 45 ul sample was hybridized onto a microarray at 55 °C for 20 h. Slides were washed for 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes.

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: The normalization was done using GeneSpring GX 12 Software. 90th Percentile Shift Normalization

source_name: H1299 cell line

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit(Agilent Technologies, Part Number: 5190-0456). 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 7 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 hrs. The labeled samples were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: Trizol-RNA extraction

tag: cell line

value: 14A overexpression

tag: tissue

value: lung


title: Mock 2 hours biorep A

source_name: Mock 2 hours biorep A

value: Mock

value: leaf


title: EBs_Control Day 12, biological rep2

description: Gene expression data from floating embryoid bodies at day 12

source_name: Embryoid bodies harvested at day 12, untreated

value: Embryonic Stem Cell

value: Culture day 12


title: Mock 1 hours biorep A

source_name: Mock 1 hours biorep A


title: iHCs_Dox+RA Day 8, biological rep2

source_name: iMyo7a+ cells, FACS-sorted from day 8 embryoid bodies, treated with Dox + RA for 4 days

value: Culture day 8


title: EGFP overexpression_H1299_rep2

description: miRNAs expression

value: EGFP overexpression


title: 14A overexpression_H1299_rep1

description: miRNAs expression


title: Liver_ko_5

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software version 10.7.

data_processing: Agilent Feature Extraction Software version 10.7 was used for background subtraction and LOWESS normalization.

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference.

extract_protocol: Total RNA was extracted from mouse livers using Qiagen RNAeasy Lipid Tissue Kit with in-column DNase I treatment.

value: GCGR ko/ko

tag: Sex

value: Male

value: liver

source_name: Universal mouse reference (UMR) from Stratagene

tag: sample type

value: pooled mouse reference RNA


title: case-2

source_name: Diffuse Large B-cell Lymphoma

value: M

tag: age

value: Immunodeficient


title: EGFP overexpression_H1299_rep1

description: miRNAs expression


title: Liver_wt_4

value: wt/wt

value: Female


title: Dog-HNSCC-1172

source_name: DNA from HNSCC tumor tissue of dog 1172

value: Head and neck squamous cell carcinoma

value: HNSCC

tag: strain

value: Unknown

source_name: DNA from head and neck normal tissue of dog 1172

value: Normal

value: Normal cell


title: Liver_wt_5


title: ∆N-p53 overexpression_H1299_rep2

description: miRNAs expression

value: ∆N-p53 overexpression

value: lung


title: Liver_ko_4


title: Liver_wt_3


title: iHCs_Dox Day 12, biological rep1

source_name: iMyo7a+ cells, FACS-sorted from day 12 embryoid bodies, treated with Dox for 8 days

value: Embryonic Stem Cell

value: Culture day 12


title: EBs_Control Day 12, biological rep1


title: Dog-HNSCC-240

source_name: DNA from HNSCC tumor tissue of dog 240

source_name: DNA from head and neck normal tissue of dog 240


title: Liver_ko_3

value: GCGR ko/ko


title: ∆N-p53 overexpression_H1299_rep1

description: miRNAs expression


title: iHCs_Dox+RA Day 12, biological rep1

source_name: iMyo7a+ cells, FACS-sorted from day 12 embryoid bodies, treated with Dox + RA for 8 days


title: Dog-HNSCC-734

source_name: DNA from HNSCC tumor tissue of dog 734

source_name: DNA from head and neck normal tissue of dog 734


title: EBs_Control Day 8, biological rep2

description: Gene expression data from floating embryoid bodies at day 8

source_name: Embryoid bodies harvested at day 8, untreated

value: Culture day 8


title: case-5

value: F

tag: ebv

value: positive

value: hematopoietic stem cell

value: no mitosis


title: Liver_ko_2

value: liver

value: pooled mouse reference RNA


title: iHCs_Dox Day 8, biological rep1

source_name: iMyo7a+ cells, FACS-sorted from day 8 embryoid bodies, treated with Dox for 4 days


title: iHCs_Dox+RA Day 8, biological rep1


title: Liver_wt_2

value: wt/wt

value: Male


title: Liver_wt_1


title: Dog-HNSCC-1152

source_name: DNA from HNSCC tumor tissue of dog 1152

value: Head and neck squamous cell carcinoma

value: HNSCC

value: Unknown

source_name: DNA from head and neck normal tissue of dog 1152


title: ARO80 GEV Overexpression Strain T=180 minutes

status: Public on Jun 01 2015

city: Princeton

first: Megan

middle: Nicole

last: McClean

state: New Jersey

address: 120 Carl Ican

department: Lewis-Sigler Institute

institute: Princeton University

description: ARO80 GEV overexpression strain 180 minutes after addition of 1 micromolar beta-estradiol

hyb_protocol: Hybridization buffer, blocking agent, and fragmentation buffer (Agilent) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were washed sequentially in Gene Expression Buffers 1 and 2 (Agilent)

scan_protocol: Agilent Technologies Scanner G2505B US22502626 Aglient Feature Extraction Software version 9.5.3.1

data_processing: Princeton PUMAdb to retrieve unflagged spots with red and green intensities well above background.  Matlab to perform zero timepoint substraction and normalization.

organism: Saccharomyces cerevisiae

source_name: Yeast strain S288C HAP1+ background

label_protocol: 415ng of total RNA was labeled using the Agilent QuickAmp labeling kit following manufacturer's protocols.  Labelled RNA was again purified using an RNeasy kit.

growth_protocol: Yeast cells were grown to mid-log phase in low fluorescence media with 1g/L urea as the nitrogen source.  Cells were grown at 30C.

extract_protocol: Total RNA was extracted using an acid phenol protocol followed by ethanol precipitation and Qiagen RNeasy cleanup.

treatment_protocol: Cells were treated with 1uM beta-estradiol at T=0 minutes.  Timepoints were taken at 30, 90, and 180 minutes after this treatment.

tag: strain number

source_name: DBY12021 from phosphate-limited chemostat


title: Control Strain T=90 minutes

description: Control strain 90 minutes after addition of 1 micromolar beta-estradiol


title: Control Strain T=180 minutes

description: Control strain 180 minutes after addition of 1 micromolar beta-estradiol


title: ARO80 GEV Overexpression Strain T=30 minutes

description: ARO80 GEV overexpression strain 30 minutes after addition of 1 micromolar beta-estradiol


title: ARO80 GEV Overexpression Strain T=0 minutes

description: ARO80 GEV overexpression strain before addition of 1 micromolar beta-estradiol


title: case-15

value: M

value: Immunodeficient

tag: graft


title: ARO80 GEV Overexpression Strain T=90 minutes

description: ARO80 GEV overexpression strain 90 minutes after addition of 1 micromolar beta-estradiol


title: Control Strain T=30 minutes

description: Control strain 30 minutes after addition of 1 micromolar beta-estradiol


title: iHCs_Dox Day 12, biological rep2

value: Embryonic Stem Cell


title: EBs_Control Day 8, biological rep1


title: citrate nanoparticles treatment, replicate 32

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

hyb_protocol: 500 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed withFeature extraction (Agilent) using default parameters and Agilient-provided GEML grid file 036574_D_F_20110917.xml to obtain signal intensities. GeneSpring GX (Agilent Technologies) was used to normalize data by quantile normalizaton and baseline transformation to the median of all samples. Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA to test for significant differential expression of microarray targets.

organism: Pimephales promelas

source_name: gill

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Fathead minnow gills were dissected to perform microarray analysis.

extract_protocol: Qiagen Rneasy

treatment_protocol: Fathead minnows were exposed to 20 nm PVP- or citrate-coated silver nanoparticles (PVP-AgNP; citrate-AgNP) at the nominal concentration of 200 μg/L or AgNO3 at nominal 6 μg/L for 96 hr.

value: gill

tag: treatment

value: 20 nm citrate-AgNP for 96 hr


title: p53 overexpression_H1299_rep2

description: miRNAs expression

source_name: H1299 cell line

value: p53 overexpression

value: lung


title: PVP nanoparticles treatment, replicate 24

value: 20 nm PVP-AgNP for 96 hr


title: p53 overexpression_H1299_rep1

description: miRNAs expression


title: AgNO3 treatment, replicate 19

value: AgNO3 at 6 ug/L for 96 hr


title: PVP nanoparticles treatment, replicate 26


title: PVP nanoparticles treatment, replicate 22


title: PVP nanoparticles treatment, replicate 25


title: PVP nanoparticles treatment, replicate 21


title: citrate nanoparticles treatment, replicate 36


title: citrate nanoparticles treatment, replicate 32-2


title: Dog-HNSCC-251

source_name: DNA from HNSCC tumor tissue of dog 251

source_name: DNA from head and neck normal tissue of dog 251

value: Normal

value: Normal cell


title: Control Strain T=0 minutes

description: Control strain before addition of 1micromolar beta-estradiol


title: AgNO3 treatment, replicate 11


title: AgNO3 treatment, replicate 17


title: Liver_ko_1

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

value: GCGR ko/ko

value: liver

source_name: Universal mouse reference (UMR) from Stratagene

value: pooled mouse reference RNA


title: control, replicate 6


title: control, replicate 3


title: control, replicate 5


title: AgNO3 treatment, replicate 13


title: Piri_Athal_14dpi R3

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

country: Germany

institute: Fraunhofer ITEM

description: A. thaliana plants were pre-grown for 14 days prior to inoculation

hyb_protocol: Hybridization and washing was performed according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (gProcessedSignal).
For the current manuscript, we analyzed (a) S. vermifera probes/genes responsive to A. thaliana colonization (using fungal probes from samples 4-15) and (b) A. thaliana probes/genes responsive to either S. vermifera or P. indics colonization (using plant probes from all samples except 13-15).
For the analysis of fungal genes, the plant probes in the dataset were set to null and vice versa as they would bias the normalization.
Furthermore all control probes (e.g. dark corner, spike ins, etc) were set to null as they are unimportant for the analysis.

organism: Serendipita indica

source_name: A. thaliana root, P. indica inoculated, 14 days post inoculation, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5) followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-1000 Spectrophotometer (Agilent)

growth_protocol: Piriformospora indica Sav. Verma, Aj. Varma, Rexer, G. Kost & P. Franken (DSM11827, Deutsche Sammlung von Mikroorganismen und Zellkulturen, DSMZ, Braunschweig, Germany) cultures were propagated at 28°C in liquid complete medium (CM) (Pham et al., 2004) supplemented with 2% glucose and 130 rpm shaking or on solid medium supplemented with 1.5% agar. For microarray experiments P. indica was cultivated on 1/10 PNM-agar plates (Basiewicz et al., 2011) for 3 days. Barley seeds (Hordeum vulgare cv. Golden Promise) were surface sterilized with 70% ethanol for 1 minute, 12% sodium hypochlorite for 1.5 hours and sterile distilled water for 3 hours. Sterilized seeds were kept in the dark for 3 days on sterile wet filter paper at room temperature. Incubation was performed in a Conviron phytochamber with a day/night cycle of 16/8 hours (light intensity: 110 µmol m-2 s-1) and temperature 22/18°C. Arabidopsis thaliana seeds (Ecotype Columbia-0) were incubated for 5 min in 70 % ethanol, surface sterilized for 5 min with 6 % sodium hypochlorite and washed 6 times for 5 min in sterile water. After stratification for 3 days at 4‹C in the dark on 1/10 PNM medium, Arabidopsis seedlings were grown for 14 days under sterile conditions in a phytochamber (Vötsch, Balingen-Frommern, Germany) at long day conditions (day: 16 h, 23‹C (350 µmol/m-2s-1); night: 8 h, 18‹C; 60% humidity).

extract_protocol: Barley root samples from four to five plants per jar were collected 14 dpi and carefully washed in distilled water. The differentiation zone (four cm below the seed) of the roots was excised and immediately frozen in liquid nitrogen. Arabidopsis root material was harvested in liquid nitrogen 3 and 14 dpi. For each time point roots from 80 to 100 plants were pooled. P. indica hyphae grown on plate were thoroughly scratched from the agar surface with a sterile scalpel 3 dpi and immediately frozen in liquid nitrogen. All experiments were performed in 3 independent biological replications. Total RNA from 200 mg grounded material was extracted with TRIzol (Invitrogen, Karlsruhe, Germany) following the manufacturerfs instructions. Amount and quality of the extracted RNA was estimated by NanoDrop-1000 Spectrophotometer (Agilent) and by a 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: For barley studies, three-day-old barley germlings were transferred into sterile jars containing 1/10 PNM medium and inoculated with 3 ml chlamydospore suspension (5×105 ml-1 in 0.002% TWEEN20). For inoculation of Arabidopsis roots with P. indica chlamydospores, plants of roughly the same size were first transferred to square petri dishes containing 1/10 PNM. Arabidopsis roots were inoculated directly with either 500.000 P. indica spores per 20 seedlings or mock treated.

tag: host

value: A. thaliana

tag: host tissue

value: root

tag: time (dpi)

tag: symbiont

value: P. indica


title: Piri_Athal_14dpi R2

source_name: A. thaliana root, P. indica inoculated, 14 days post inoculation, replicate 2


title: Piri_Athal_14dpi R1

source_name: A. thaliana root, P. indica inoculated, 14 days post inoculation, replicate 1


title: control, replicate 1


title: Piri_Athal_3dpi R2

source_name: A. thaliana root, P. indica inoculated, 3 days post inoculation, replicate 2


title: Piri_Athal_3dpi R3

source_name: A. thaliana root, P. indica inoculated, 3 days post inoculation, replicate 3


title: control, replicate 2


title: KitW/Wv LFD, 2

city: Heidelberg

first: Dario

middle: Alejandro

last: Gutierrez

state: BW

address: Im Neuenheimer Feld 280

department: Cellular Immunology

institute: German Cancer Research center

description:
Group 6
SAMPLE 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was normalized using the Chipster 3.1.1 software (Genome studio) by the quatile method

label: Biotin

source_name: Mouse epididymal AT

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was isolated using Quiagen RNA minikit

treatment_protocol:
Mice were fed a HFD (60% kcal from fat) or chow diet (6% fat) for 12 weeks
eAT was isolated after a 5h morning fast

tag: diet

value: LFD

tag: background

value: WBB6F1 (WB X C57Bl/6)

tag: genotype/variation

value: KitW/Wv


title: citrate nanoparticles treatment, replicate 31

value: gill


title: iHCs_Dox Day 8, biological rep2

tag: cell type

value: Embryonic Stem Cell

tag: cell line

value: Culture day 8


title: Cpa3Cre/+ HFD, 3

description:
Group 1
SAMPLE 13

value: HFD


title: KitW/Wv LFD, 3

description:
Group 6
SAMPLE 17


title: Piri_Athal_7dpi_R1

description:
SAMPLE 1
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, P. indica inoculated, 7 days post inoculation, replicate 1

growth_protocol: Piriformospora indica Sav. Verma, Aj. Varma, Rexer, G. Kost & P. Franken (DSM11827, Deutsche Sammlung von Mikroorganismen und Zellkulturen, DSMZ, Braunschweig, Germany) cultures were propagated at 28°C in liquid complete medium (CM) (Pham et al., 2004) supplemented with 2% glucose and 130 rpm shaking or on solid medium supplemented with 1.5% agar. S. vermifera cultures were propagated at 25°C in liquid MYP medium (0.7% w/v malt extract; 0.1% w/v peptone; 0.05% w/v yeast extract) and 120 rpm shaling or on solid medium supplemented with 1.5% agar. For microarray experiments P. indica and S. vermifera were cultivated on 1/10 PNM-agar plates (Basiewicz et al., 2011) for 3 days. Arabidopsis thaliana seeds (Ecotype Columbia-0) were incubated for 5 min in 70 % ethanol, surface sterilized for 5 min with 6 % sodium hypochlorite and washed 6 times for 5 min in sterile water. After stratification for 3 days at 4°C in the dark on 1/10 PNM medium, Arabidopsis seedlings were grown for 14 days under sterile conditions in a phytochamber (Vötsch, Balingen-Frommern, Germany) at long day conditions (day: 16 h, 23°C (350 µmol/m-2s-1); night: 8 h, 18°C; 60% humidity).

extract_protocol: Arabidopsis root material was harvested in liquid nitrogen 3, 7 and 14 dpi. For each time point roots from 45 to 60 plants were pooled. S. vermifera hyphae grown on plate were thoroughly scratched from the agar surface with a sterile scalpel 3 dpi and immediately frozen in liquid nitrogen. All experiments were performed in 3 independent biological replications. Total RNA from 200 mg grounded material was extracted with TRIzol (Invitrogen, Karlsruhe, Germany) following the manufacturer's instructions. Amount and quality of the extracted RNA was estimated by NanoDrop-1000 Spectrophotometer (Agilent) and by a 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: For inoculation of Arabidopsis roots with P. indica or S. vermifera, plants of roughly the same size were first transferred to square petri dishes containing 1/10 PNM. Arabidopsis roots were inoculated directly with either 500.000 P. indica spores per 20 seedlings or 2 plugs S. vermifera mycellium per plant root or mock treated with tween water (0.002% TWEEN20).

tag: inoculant

value: 7 days

value: 21  days


title: KitW/Wv HFD, 3

description:
Group 3
SAMPLE 14


title: Piri_Athal_3dpi R1

source_name: A. thaliana root, P. indica inoculated, 3 days post inoculation, replicate 1


title: Cpa3+/+ LFD, 3

description:
Group 5
SAMPLE 16


title: KitW/Wv LFD, 1

description:
Group 6
SAMPLE 11


title: Piri_Athal_7dpi_R2

description:
SAMPLE 2
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, P. indica inoculated, 7 days post inoculation, replicate 2

value: 21 days


title: Cpa3+/+ LFD, 1

description:
Group 5
SAMPLE 9


title: Piri_Athal_7dpi_R3

description:
SAMPLE 3
A. thaliana plants were pre-grown for 14 days prior to inoculation

source_name: A. thaliana root, P. indica inoculated, 7 days post inoculation, replicate 3


title: Cpa3+/+ LFD, 2

description:
Group 5
SAMPLE 10


title: 56251002_532

city: Madison

first: Gregory

middle: M

last: Gauthier

state: WI

address: 1550 Linden Drive

department: Medicine

institute: University of Wisconsin - Madison

description: B. dermatitidis SREBΔ incubated for 48-hrs at 22oC. It is the 3rd biological replicate for this time point, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.

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

organism: Blastomyces dermatitidis

source_name: Blastomyces dermatitidis SREBΔ

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.

growth_protocol: 3 biological replicates of SREBΔ and the isogenic wild-type control (ATCC 26199) were grown 37oC and for 6, 24, and 48-hrs at 22oC. All cultures were grown in liquid HMM (Histoplasma macrophage media) containing 10 uM FeSO4.  All glassware was pre-treated with 2N HCl and extensively washed with ddH2O.

extract_protocol: For all samples, total RNA was extracted using the phenol-guanidinium thiocyanate-1-bromo-3-chloropropane method [Sambrook J and Russell DW. Molecular cloning: a laboratory manual, 3rd Ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2001. pp. 7.4 – 7.8.].  B. dermatitidis cells were washed with PBS (pre-warmed to 37oC or 22oC), frozen in liquid nitrogen, lysed by grinding in a mortar and pestle, and treated with TRI Reagent followed by 1-bromo-3-chloropropane (Molecular Research Center Inc., Cincinnati, OH).  Total RNA was precipitated using a 1:1 concentration of isopropanol and high salt solution (Molecular Research Center, Inc., Cincinnati, OH), and washed with 75% ethanol.  Following resuspension in water pre-treated with diethyl pyrocarbonate (DEPC; Calbiochem, San Diego, CA), total RNA was treated with turboDNAase (Applied Biosystems/Ambion, Austin Texas), and purified using an RNeasy kit (Qiagen, Valencia, CA).  To optimally remove guanidine salts, an extra wash of RPE buffer was performed during RNAeasy purification.  RNA quality was assessed using an Agilent bioanalyzer (Agilent Technoligies, Santa Clara, CA).  Double-stranded cDNA was synthesized and purified at the Gene Expression Center at the University of Wisconsin – Madison.  Roche NimbleGen performed Cy3 labeling, hybridization, scanning, and RMA (Robust Multi-Array analysis) normalization for all 24 microarrays at their facility in Reykjavík, Iceland.

value: SREBΔ

tag: time point

value: 48-hrs 22oC

tag: replicate

value: C


title: 53895902_532

description: B. dermatitidis ATCC 26199 wild-type incubated for 48-hrs at 22oC. It is the 3rd biological replicate for this time point, each from separate cultures.

source_name: Blastomyces dermatitidis ATCC 26199 wild-type

tag: strain

value: wild-type


title: 56254402_532

description: B. dermatitidis ATCC 26199 wild-type incubated for 24-hrs at 22oC. It is the 2nd biological replicate for this time point, each from separate cultures.

value: 24-hrs 22oC

value: B


title: 56250802_532

description: B. dermatitidis SREBΔ incubated for 48-hrs at 22oC. It is the 1st biological replicate for this time point, each from separate cultures.

value: A


title: Cpa3Cre/+ LFD, 3

description:
Group 4
SAMPLE 15

value: LFD


title: Cpa3+/+ HFD, 1

description:
Group 2
SAMPLE 3

value: WBB6F1 (WB X C57Bl/6)


title: Cpa3Cre/+ LFD, 1

description:
Group 4
SAMPLE 7


title: KitW/Wv HFD, 1

description:
Group 3
SAMPLE 5

value: KitW/Wv


title: 56246702_532

description: B. dermatitidis SREBΔ incubated for 24-hrs at 22oC. It is the 3rdt biological replicate for this time point, each from separate cultures.


title: Cpa3+/+ HFD, 2

description:
Group 2
SAMPLE 4


title: 56250702_532

description: B. dermatitidis ATCC 26199 wild-type incubated for 48-hrs at 22oC. It is the 1st biological replicate for this time point, each from separate cultures.


title: KitW/Wv HFD, 2

description:
Group 3
SAMPLE 6


title: 56238602_532

description: B. dermatitidis ATCC 26199 wild-type incubated for 24-hrs at 22oC. It is the 3rd biological replicate for this time point, each from separate cultures.


title: Cpa3Cre/+ HFD, 1

description:
Group 1
SAMPLE 1


title: 56251102_532

description: B. dermatitidis SREBΔ incubated for 24-hrs at 22oC. It is the 1st biological replicate for this time point, each from separate cultures.


title: citrate nanoparticles treatment, replicate 34

source_name: gill

tag: tissue

value: gill

value: 20 nm citrate-AgNP for 96 hr


title: Cpa3Cre/+ HFD, 2

description:
Group 1
SAMPLE 2


title: 56249002_532

description: B. dermatitidis SREBΔ incubated for 48-hrs at 22oC. It is the 2nd biological replicate for this time point, each from separate cultures.


title: 56237602_532

description: B. dermatitidis SREBΔ incubated for 6-hrs at 22oC. It is the 2nd biological replicate for this time point, each from separate cultures.

value: 6-hrs 22oC


title: 56246202_532

description: B. dermatitidis SREBΔ incubated for 24-hrs at 22oC. It is the 2nd biological replicate for this time point, each from separate cultures.


title: 56248802_532

description: B. dermatitidis SREBΔ incubated for 6-hrs at 22oC. It is the 1st biological replicate for this time point, each from separate cultures.


title: 56246302_532

description: B. dermatitidis ATCC 26199 wild-type incubated for 6-hrs at 22oC. It is the 3rd biological replicate for this time point, each from separate cultures.


title: 56250602_532

description: B. dermatitidis ATCC 26199 wild-type incubated for 6-hrs at 22oC. It is the 2nd biological replicate for this time point, each from separate cultures.


title: 56245902_532

description: B. dermatitidis ATCC 26199 wild-type incubated for 6-hrs at 22oC. It is the 1st biological replicate for this time point, each from separate cultures.


title: 56246102_532

description: B. dermatitidis SREBΔ incubated at 37oC. It is the 3rd biological replicate for this time point, each from separate cultures.


title: 56240502_532

description: B. dermatitidis ATCC 26199 wild-type incubated at 37oC. It is the 1st biological replicate for this time point, each from separate cultures.


title: 56250902_532

description: B. dermatitidis SREBΔ incubated at 37oC. It is the 1st biological replicate for this time point, each from separate cultures.


title: 56251302_532

description: B. dermatitidis ATCC 26199 wild-type incubated at 37oC. It is the 3rd biological replicate for this time point, each from separate cultures.


title: 56246002_532

description: B. dermatitidis ATCC 26199 wild-type incubated at 37oC. It is the 2nd biological replicate for this time point, each from separate cultures.


title: 6p_1

city: Philadelphia

first: Nigel

last: Fraser

address: 3101 Walnut St

department: Dept. of Microbiology

institute: Upenn

description: cellular gDNA infected with viral DNA and PAA and harvested at 6hpi

hyb_protocol: CGH protocols were used for hybridization and washing (Oligo aCGH/CHiP Hybridization Kit and Wash Buffer Kit, Agilent #5188-5220 and #5188-5226, no Cot-1 DNA).  The following protocol modifications were used for hybridization: hybridization buffer contained 30% de-ionized formamide, hybridization was carried out at 60oC, and the final wash solution was heated to 60oC.  All other steps were carried out according to the manufacturer’s instructions.

scan_protocol: Microarray images were acquired using an Agilent Technologies High Resolution-C Scanner.  Data extraction was carried out using Agilent Feature Extraction software, version 9.5.3.  Scanning and data extraction were conducted according to the manufacturer’s instructions to produce a raw signal for each probe that incorporates background pixel correction and averaging of duplicate features.

data_processing: The raw signal was first processed by “backgroundCorrect” and “normalizeBetweenArrays” functions in the limma package in R/Biocoductor.  The normalized signal was then log2 transformed.

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: 6hpi infected DNA 1 with PAA treatment

label_protocol: 500ng of 150bp DNA were labeled with Cy3 dye (SureTag Complete DNA Labeling Kit, direct labeling option, Agilent #5190-4240)

growth_protocol: Two 175 cm2 flasks of SY5Y cells (human neuroblastoma cell line) at 100% confluence in RPMI 1640 medium supplemented with 10% fetal calf serum and penicillin (150u/ml) and streptomycin antibiotics (150u/ml)  were infected with HSV-1 F strain at a moi of 5 PFU per cell.

extract_protocol: For Mnase digestion, peleted nuclei were digested with Nuclease S7 Micrococcal nuclease (MNase) at 5U/ul of sample for complete digestion, added 12mM EDTA to stop reaction on ice, and treated with 100ug/ml of proteinase K for overnight at 37’C. DNA was purified by a Wizard DNA clean-up kit (Promega) according to the manufacturer’s instructions.  MNase digested DNA were checked by running on 1.5% low melting point (LMP) agarose gel and 150bp bands were extracted by a QIAEX II gel extraction kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Cells were harvested by scraping, re-suspended in 10ml RSB (10mM Tris, pH 7.5, 10mM 5M NaCl, and 3mM MgCl2), and incubated for 5min on ice. Following addition of 10ml 1%NP40 (in RSB), the cells were mixed, incubated for 2 min on ice, overlaid with 10ml of 0.33M sucrose (in RSB), and centrifuged at 1700rpm for 10min at 4’C.  The pelleted nuclei were re-suspended in 1ml of MNase buffer (20mM 1M Pipes, pH7, 1mM MgCl2, 10mM NaCl, 1mM CaCl2, 5mM 2-mercaptoethanol, 0.25M sucrose, and 0.1mM PMSF).

value: human neuroblastoma cell line and Herpes Simplex Virus 1

value: cellular and viral DNA 500ng

tag: virus strain

value: F strain


title: 6p_3

source_name: 6hpi infected DNA 3 with PAA treatment


title: 6no2

description:
human neuroblastoma cell line and Herpes Simplex Virus 1
cellular gDNA infected with viral DNA and harvested at 6hpi

source_name: 6hpi infected DNA 2


title: 6no1

source_name: 6hpi infected DNA 1


title: 56236902_532

description: B. dermatitidis ATCC 26199 wild-type incubated for 24-hrs at 22oC. It is the 1st biological replicate for this time point, each from separate cultures.


title: 6no3

source_name: 6hpi infected DNA 3


title: Vir2_10

description:
human neuroblastoma cell line and Herpes Simplex Virus 1
cellular gDNA mixed with 10ng purified virion DNA

source_name: Virion 2- 10ng

value: mixed with cellular gDNA 500ng


title: Vir2_5.0

description:
human neuroblastoma cell line and Herpes Simplex Virus 1
cellular gDNA mixed with 5ng purified virion DNA

source_name: Virion 2- 5ng


title: Vir1_10

source_name: Virion 1- 10ng


title: 56248602_532

description: B. dermatitidis SREBΔ incubated at 37oC. It is the 2nd biological replicate for this time point, each from separate cultures.

value: SREBΔ


title: Vir2_0.5

description:
human neuroblastoma cell line and Herpes Simplex Virus 1
cellular gDNA mixed with 0.5ng purified virion DNA

source_name: Virion 2- 0.5ng


title: Vir1_5.0

source_name: Virion 1- 5ng


title: Vir1_1.0

description:
human neuroblastoma cell line and Herpes Simplex Virus 1
cellular gDNA mixed with 1ng purified virion DNA

source_name: Virion 1- 1ng


title: Vir2_1.0

source_name: Virion 2- 1ng


title: 6p_2

source_name: 6hpi infected DNA 2 with PAA treatment


title: Vir3

description:
human neuroblastoma cell line and Herpes Simplex Virus 1
cellular gDNA mixed with 0.1ng purified virion DNA

source_name: Virion 3- 0.1ng


title: Vir1

source_name: Virion 1- 0.1ng


title: AgNO3 treatment, replicate 15

value: AgNO3 at 6 ug/L for 96 hr


title: 56251202_532

description: B. dermatitidis ATCC 26199 wild-type incubated for 48-hrs at 22oC. It is the 2nd biological replicate for this time point, each from separate cultures.

source_name: Blastomyces dermatitidis ATCC 26199 wild-type

value: 48-hrs 22oC


title: Vir2

source_name: Virion 2- 0.1ng


title: CP-23

first: Svetlana

middle: A

last: Yatsenko

address: 300 Halket St

description: copy number and homozygosity mapping

hyb_protocol: According to Agilent protocol

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Cytogenomics Software (2.5.8.1).

data_processing: Copy number variants (CNVs), including gains and losses, were identified using the Aberration Detection Method 2 (ADM-2) algorithm, with modifications that support the determination of the clonal fraction of genomic imbalances in cancer cells. A minimum of five consecutive probes per region, with absolute average log2 ratio of 0.3 for any given region or a minimum region of 1 Mb in size, with a minimum absolute average log2 ratio of 0.08 (Agilent mosaic protocol).  Loss of homozygosity (LOH) regions were detected according to the Agilent protocol.

source_name: Bone marrow

label_protocol: According to Agilent protocol

growth_protocol: uncultured

extract_protocol: DNA extracted using Puregene Kit following manufacturer's instructions

value: Bone marrow

tag: gender

value: Male

tag: disease

value: CLL

source_name: commercially-available DNA used as reference

tag: reference dna gender

tag: reference dna cell line