title: Mtb H37Rv versus 98_1663, TPC-4

city: Montreal

first: Pilar

last: Domenech

state: Quebec

address: 1001 Décarie Boulevard

department: IDIGH Program

country: Canada

institute: Research Institute of McGill University Health Centre

description: Transcriptional profile comparison_4

hyb_protocol: Microarray hybridization was carried out in GE Healthcare hybridization buffer in the presence of yeast tRNA (0.2µg ml-1) at 42°C for 16 hours. Following hybridization, microarray slides were washed three times (15 mins/wash) with 0.5X SSC + 0.01% SDS, 0.06X SSC + 0.01% SDS and 0.06X SSC.

scan_protocol: Scanned on ScanArray Lite (Packard). Images were quantified using ScanArray Express software (Packard).

data_processing: Mean fluorescence values for each spot, minus the surrounding background, were used in the analysis. Spots flagged as misrepresentative or those with a negative value following background correction were subsequently excluded from further analysis. The fluorescence intensity ratios (Cy3/Cy5 or Cy5/Cy3, representing test/reference) were calculated for each spot, log10 transformed and then normalized with respect to the mean value of all fluorescence ratios. A Z- score [Z = (log10 fluorescence ratio - mean)/standard deviation] was calculated for each spot.

organism: Mycobacterium tuberculosis

source_name: Mtb H37Rv

label_protocol: 4µg samples of RNA were used in the preparation of cDNA labeled with either Cy3- or Cy5-NHS esters (GE Healthcare) via the aminoallyl indirect labeling method (Yu et al., 2002) in the presence of RevertAid M-MuLV Reverse Transcriptase (Fermentas). Labeled cDNA was subsequently purified using the QIAquick PCR Purification Kit (Qiagen) and samples to be co-hybridized on the same array were mixed and concentrated to 6µl in a Savant SpeedVac Concentrator.

extract_protocol: Bacterial pellets were flash frozen on dry ice, resuspended in Trizol, and bead-beaten 3 x 40 seconds. Resulting cell lysates were added to chloroform, centrifuged and nucleic acids were then precipitated from the aqueous phase with isopropanol. RNA was washed in 75% ethanol, then DNase treated. For further purification, the Qiagen RNeasy kit was used according to the manufacturer's instructions.

tag: strain/background

value: H37Rv ATCC27294

tag: properties

value: Laboratory strain, Euro-American or lineage 4

value: Clinical isolate, East-Asian or lineage 2, group 1 (pre-Beijing)


title: Doxorubicin3 vs Control3, 1 week post treatment, reverse labelling

status: Public on Jun 24 2016

type: RNA

city: Didcot

first: Emma

middle: Louise

last: Marczylo

state: Oxfordshire

address: Harwell Campus, Chilton

department: Toxicology

country: United Kingdom

institute: Public Health England

description: Biological replicate 3 of 6, reverse labelling, 1 week

hyb_protocol: Control and doxorubicin samples were randomly paired and pooled and treated according to the labelling kit's manufacturer's instructions. Samples were denatured for 3-10 min at 65oC and incubated for 30 min at 37oC prior to hybridisation overnight at 37oC using a Genetix hybridisation chamber. Arrays were washed on a rocking platform set at 50 oscillations per min for 5 min each at RT, firstly in 2X SSC containing 0.05% (w/v) SDS, secondly in 1X SSC and finally in 0.5X SSC, and dried by centrifugation.

scan_protocol: Slides scanned on a 4200 Axon scanner and data acquired using GenePix Pro v.6.0.

data_processing: Result files were normalised using the LOESS within array followed by the quantile between array commands in the Bioconductor limma library package of R version 2.15.2. Normalised log2[Cy5/Cy3] for forward labelling arrays and log2[Cy3/Cy5] for reverse labelling arrays were compiled into a single matrix file. All array control and empty values were removed and excluded from normalisation in R.

molecule: total RNA

organism: Mus musculus

source_name: Testis RNA, Doxorubicin3, 1 week post treatment

label_protocol: 500 ng of total RNA was labelled with either Flashtag RNA labelling kit (Genisphere) or Label IT miRNA labelling kit (Mirus) according to the manufacturer's instructions.

growth_protocol: Male C57BL/6J mice, 8-10 weeks old. 12 hour light/dark cycle. Food and water provided ad libitum, 24 hours a day.

extract_protocol: 1 whole testis was lysed in 1ml of Tri reagent (Sigma). RNA was extracted according to the manufacturer's instructions.

treatment_protocol: Mice were randomly assigned to groups. Dosing was performed via intraperitoneal injection. Treated mice received 3 x 3mg/kg of doxorubicin (in 0.85% (v/v) saline) per week (9mg/kg in total), controls received vehicle only; in a dose volume of 10ml/kg. 1, 4 or 7 wk after the final administration mice were sacrificed under isoflurane anaesthesia and exsanguinated. Testes were taken for analysis.

tag: gender

value: Male

tag: strain

tag: tissue

value: Testis

source_name: Testis RNA, Vehicle only3, 1 week post treatment


title: Doxorubicin6 vs Control6, 1 week post treatment, reverse labelling

description: Biological replicate 6 of 6, reverse labelling, 1 week

source_name: Testis RNA, Doxorubicin6, 1 week post treatment

source_name: Testis RNA, Vehicle only6, 1 week post treatment


title: Control3 vs Doxorubicin3, 1 week post treatment, forward labelling

description: Biological replicate 3 of 6, forward labelling, 1 week


title: Mtb H37Rv versus 98_1663, TPC-5

description: Transcriptional profile comparison_5


title: Mtb 98_1663 versus H37Rv, TPC-6

description: Transcriptional profile comparison_6


title: Mtb HN878 versus H37Rv, TPC-2

description: Transcriptional profile comparison_2

source_name: Mtb HN878

value: Clinical isolate, East-Asian or lineage 2, group 5 (Beijing)


title: Mtb H37Rv versus HN878, TPC-1

description: Transcriptional profile comparison_1


title: Mtb H37Rv versus HN878, TPC-3

description: Transcriptional profile comparison_3


title: HCC827-Del+Decitabine+Vorinostat replicate 1

status: Public on Jun 23 2016

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: University of Alabama at Birmingham

description: SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensities of probes were log2-transformed and Quantile normalized (ArrayStudio from Omicsoft)

label: biotin

organism: Homo sapiens

source_name: HCC827-Del cell line

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

growth_protocol: HCC827-Del and HCC827-Del-TM cells were grown in RPMI-1640 media with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instruction

treatment_protocol: Cells were treated with DMSO or with the combination of Decitabine and Vorinostat

tag: cell line

tag: genotype/variation

tag: agent

value: Decitabine+Vorinostat


title: Biofilm versus planktonic cells replicate 1

city: Torrejón de Ardoz

first: Mercedes

last: Moreno

state: Madrid

address: Crta. de Ajalvir, km 4

country: Spain

institute: Centro de Astrobiología

description:
Samples were collected from a permanent spring coming out under a pile of pyrite-containing rocks accumulated by mining activities.
collection: Environmental samples were collected from a permanent spring coming out under a pile of pyrite-containing rocks accumulated by mining activity.

hyb_protocol: Microarrays were blocked by incubation in prehybridization buffer: 5XSSC (3 M sodium chloride and 300 mM trisodium citrate (adjusted to pH 7.0 with HCl)), 0.1% SDS, 0.1ug/ul of shared denatured salmon sperm DNA and 1% BSA) at 42ºC for 45min. Hybridizations were performed overnight, at 55ºC, with 1X HybIt® Hybridization Solution (Arrayit corporation) in a volume of 50ul. 22 X 60mm coverslips (Sigma) and an ArrayIt® Hybridization Cassette (AHC, Arrayit corporation) were used.  Three washing steps were carried out for 5 min in the following buffers: 1) 2xSSC + SDS 0.1%; 2)  0.2x SSC + SDS 0.1%; 3) 0.2x SSC.

scan_protocol: Images were quantified using Genepix pro 6.0 Software in a  Genepix personal 4100A scanner

data_processing: The local background was subtracted and the Log2 of processed Red signal/processed Green signal was calculated with Genepix  pro 6.0 software (Molecular Devices). LOWESS normalization and statistical student's t-test analyses were carried out using AlmaZen software (BioAlma).

organism: Leptospirillum ferrooxidans

source_name: Biofilm cells

label_protocol: Labeled cDNA synthesis was achieved from 2.5ug of amplified RNA with the CyScribe first-strand cDNA labeling kit. (Amersham) and purified with GFX columns (Amersham).

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions. RNA samples were amplified as described in Moreno-Paz, M and Parro V.(Environ. Microbiol 2006, 8:1064-1073).

treatment_protocol: Cells from water samples were collected by filtration and maintained in RNAlater. Filament samples growing in the same site were collected in RNA later. All samples were frozen on dry ice and kept at -20ºC until use.

tag: sample

value: Environmental sample

source_name: Planktonic cells


title: HCC827-Del replicate 3

description: SAMPLE 3

value: control


title: HCC827-Del+Decitabine+Vorinostat replicate 2

description: SAMPLE 5


title: HCC827-Del-TM+Decitabine+Vorinostat replicate 2

description: SAMPLE 11

source_name: HCC827-Del-TM cell line


title: HCC827-Del-TM replicate 2

description: SAMPLE 8


title: HCC827-Del-TM+Decitabine+Vorinostat replicate 3

description: SAMPLE 12


title: HCC827-Del-TM+Decitabine+Vorinostat replicate 1

description: SAMPLE 10


title: HCC827-Del replicate 1

description: SAMPLE 1


title: HCC827-Del-TM replicate 1

description: SAMPLE 7


title: HCC827-Del replicate 2

description: SAMPLE 2


title: Biofilm versus planktonic cells replicate 2


title: HCC827-Del+Decitabine+Vorinostat replicate 3

description: SAMPLE 6


title: HCC827-Del-TM replicate 3

description: SAMPLE 9


title: HCT116-10uM-GSK343-4hr

city: Taipei

first: Pei-Ming

last: Yang

address: 250 Wu-Hsing St

department: Graduate Institute of Cancer Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

extract_protocol: RNA was prepared using the GENEzo TriRNA Pure Kit (Geneaid Biotech; New Taipei City, Taiwan) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HCT116 cells were treated with drug in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 4 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cel line


title: Conjunctiva 1

city: Singapore

first: Wanwen

last: Lan

address: 9 Hospital Drive SON Blk C #02-03

country: Singapore

institute: Singapore Eye Research Institute

description: Gene expression after treatment with non-specific oligos for 48 h

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 human GE 8x60K microarray  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High Resolution Microarray scanner using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Conjunctiva tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 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: Pterygium and conjunctiva tissues were transported from the operating theatre in DMEM/F12 with 10% FBS

extract_protocol: Tissues were homogenized using pestle and mortar in liquid nitrogen. RNA was extracted using trizol and the RNAeasy mini kit (Qiagen) according to manufacturer's protocol

treatment_protocol: No treatment performed

value: Conjunctiva


title: Pterygium 1

source_name: Pterygium tissue

value: Pterygium


title: HCT116-control

source_name: HCT116, control


title: Conjunctiva 4

description: Gene expression after treatment with  siRNA targeting linc-9432 for 48 h


title: Conjunctiva 3


title: HCT116-5uM-UNC1999-4hr


title: Pterygium 3


title: Pterygium 4


title: Conjunctiva 2


title: Pterygium 2


title: Liver_Marine_rep4

city: St Pee sur nivelle

first: Inge

last: Geurden

address: Quartier Ibarron

department: PHASE

country: France

institute: INRA

description: Gene expression after 25 day challenge with plant-based diet in liver of juvenile rainbow trout with history of early exposure to marine diet

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

scan_protocol: Scanning was performed with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (channels: Green, resolution: 3µm, TIFF: 20 bit)

data_processing: Data were then obtained with the Agilent Feature Extraction software (v10.7) according to the appropriate GE protocol (GE1_107_Sep09). Before analysis, saturated spot, non-uniform spots and spots not significantly different from background (k=5) were flagged using the Agilent GeneSpring GX software (v.12.6.1). Probes were considered valid when corresponding spots remained present in at least 80% of the replicates of each experimental condition after the flagging procedure. Data were subsequently scale-normalized using the median value of each array.

organism: Oncorhynchus mykiss

source_name: Liver 91M

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

growth_protocol: Hatching and first-feeding (23 days following hatching) of rainbow trout (Oncorhynchus mykiss) took place at the INRA Lees-Athas fish farm, France (flow-through spring water, 7 ºC). For the first 21 days of exogenous feeding, the rainbow trout swim-up fry received either a plant-based diet (diet V, containing a blend of protein-rich plant ingredients (wheat gluten, extruded peas, corn gluten meal, soybean meal and white lupin) and plant oils (palmseed, rapeseed and linseed oil) as lipid source)) or marine-based diet (diet M, containing fishmeal and fish oil as protein and lipid source, respectively;), which was carefully distributed by hand on an hourly basis (8 to 10 meals per day) to duplicate groups (60 fry per tank). Each group was fed (7 min/ meal) in slight excess. This early feeding period is referred to as ‘nutritional history V or M’ and fish from the respective nutritional histories are termed ‘V- or M-fish’. At the end of this 3-week early exposure, a subset of swim-up fry fed diet V or diet M were flash frozen in liquid nitrogen and stored at -80 ºC until further analyses. Following this early exposure, the M- and V-fish were maintained on diet M (hand feeding, 2 meals per day until visual satiation) for an intermediary period of seven months. Intermediate growth and feed intake was followed by weighing the fish groups and amount of feed distributed on a three-week basis. Survival was monitored daily. For accelerating the juvenile growth phase, fish were reared from 2 g body weight at higher water temperature, 16.5 ºC (INRA Donzacq farm, flow-through spring water).

extract_protocol: Whole trout swim-up fry sampled at the end of 3 weeks of early nutrition exposure, or brain and liver from juvenile trout sampled at the end of the V-challenge were snap frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from the trout swim-up fry, brain or liver by homogenization in 1-2 ml TRIzol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. Total RNA was quantified using spectrophotometry based on absorbance at 260 nm (Nanodrop ND1000, LabTech) and the integrity of the RNA was determined by electrophoresis (Agilent Bioanalyser 2100) and samples with RNA integrity number above 8 were used for microarray analysis.

treatment_protocol: Three weeks prior to the V-challenge, fish were transferred for acclimating to the INRA facilities of St. Pee-sur-Nivelle, consisting of a recirculating water unit of 24 tanks (70 L volume, 7 L/min water exchange rate, 16.5 ± 1 ºC water temperature and artificial photoperiod set at 13 h light). The V-challenge was carried out with 4 replicate tanks (18 fish/tank) per treatment group and 3 replicate tanks (17 fish/tank). Feed intake (FI) was recorded during the last 7 days of acclimation (diet M), once stabilized in all groups. The challenge test with diet V (V-challenge) took place 7 months after the early nutritional history period. Here, the M-fish and V-fish groups received diet V for 25 days. Following V-challenge, the liver and brain of M- and V-fish were harvested and flash frozen in liquid nitrogen and stored at -80 ºC until further analyses.

tag: developmental stage

value: juvenile

value: Liver

tag: diet (history)

value: Marine

tag: treatment

value: 25 day challenge with plant-based diet


title: Liver_Marine_rep2

source_name: Liver 88M


title: Liver_Marine_rep3

source_name: Liver 89M


title: Twinpair43_twin1_time1

type: genomic

city: Odense C

first: Lene

last: Christiansen

address: J.B. Winsloews Vej 9B

department: Epidemiology, Biostatistics and Biodemography

country: Denmark

institute: University of Southern Denmark

hyb_protocol: Standard Illumina procedures

scan_protocol: Standard Illumina procedures using the iScan System

data_processing:
The genotype data was processed using the GenomeStudio Software (Illumina) with clustering on the project samples themselves. Samples genotyped on GPL20641 were loaded into GenomeStudio using the manifest humanomni25m-8v1-1_b (with 2,391,739 SNPs), samples genotyped on GPL13135 (except for 2_1_T1, 3_1_T1, 4_1_T1, 8_1_T1, 10_1_T1, and 12_1_T1) were loaded into GenomeStudio using the manifest HumanOmniExpress-12v1_J (with 730,526 SNPs), and 2_1_T1, 3_1_T1, 4_1_T1, 8_1_T1, 10_1_T1, and 12_1_T1 were loaded into GenomeStudio using the manifest HumanOmniExpress-12v1_A. In total, 172 samples were genotyped, but 3 (3_2_T1, 9_2_T2, and 36_1_T1) were excluded during quality control.
Processed data file contents: ID_REF - Illumina SNP name; Log R Ratio - Log R Ratio; B Allele Freq -  B Allele Frequency

label: Biotin

molecule: genomic DNA

source_name: Blood

label_protocol: Standard Illumina procedures

extract_protocol: Genomic DNA was extracted from whole blood using a standard salting out method

value: blood

value: Female


title: Twinpair43_twin2_time2


title: Twinpair43_twin2_time1


title: Twinpair43_twin1_time2


title: Twinpair42_twin2_time1


title: Twinpair42_twin2_time2


title: Twinpair42_twin1_time1


title: Twinpair42_twin1_time2


title: Twinpair41_twin2_time2


title: Liver_Plant-Based_rep2

description: Gene expression after 25 day challenge with plant-based diet in liver of juvenile rainbow trout with history of early exposure to plant-based diet

source_name: Liver 51V

value: Plant-based


title: Brain_Marine_rep4

description: Gene expression after 25 day challenge with plant-based diet in brain of juvenile rainbow trout with history of early exposure to marine diet

source_name: Brain 89M

value: Brain


title: Liver_Plant-Based_rep4

source_name: Liver 74V


title: Liver_Marine_rep1

source_name: Liver 67M


title: Brain_Plant-Based_rep4

description: Gene expression after 25 day challenge with plant-based diet in brain of juvenile rainbow trout with history of early exposure to plant-based diet

source_name: Brain 74V


title: Twinpair41_twin1_time2


title: Twinpair41_twin2_time1


title: Liver_Plant-Based_rep1

source_name: Liver 50V


title: Twinpair40_twin2_time2


title: Liver_Plant-Based_rep3

source_name: Liver 73V


title: Twinpair41_twin1_time1


title: Brain_Marine_rep3

source_name: Brain 88M


title: Twinpair40_twin1_time2


title: Brain_Plant-Based_rep2

source_name: Brain 51V


title: Twinpair40_twin2_time1


title: Twinpair39_twin1_time1


title: Brain_Plant-Based_rep3

source_name: Brain 73V


title: Twinpair39_twin2_time1


title: Brain_Marine_rep1

source_name: Brain 64M


title: 3-week_Plant-Based_rep2

description: Gene expression after 3 week early exposure to plant-based diet in rainbow trout swim-up fry

value: Swim-up fry


title: 3-week_Marine_rep4

description: Gene expression after 3 week early exposure to marine diet in rainbow trout swim-up fry


title: 3-week_Plant-Based_rep3


title: Twinpair38_twin2_time2

value: Male


title: Twinpair38_twin2_time1


title: Twinpair38_twin1_time1


title: Twinpair37_twin2_time2


title: Brain_Plant-Based_rep1

source_name: Brain 50V


title: Twinpair38_twin1_time2


title: Twinpair37_twin2_time1


title: Twinpair36_twin2_time1


title: 3-week_Marine_rep1


title: 3-week_Marine_rep2


title: 3-week_Marine_rep3


title: Brain_Marine_rep2

source_name: Brain 65M


title: 3-week_Plant-Based_rep1


title: Twinpair37_twin1_time2


title: Twinpair37_twin1_time1


title: Twinpair35_twin1_time2


title: Twinpair36_twin2_time2


title: Twinpair34_twin1_time1


title: Twinpair34_twin1_time2


title: Twinpair33_twin2_time1


title: Twinpair40_twin1_time1


title: Twinpair33_twin1_time2


title: Twinpair32_twin2_time2


title: Twinpair32_twin2_time1


title: Twinpair32_twin1_time1


title: Twinpair35_twin2_time1


title: Twinpair35_twin2_time2


title: Twinpair31_twin2_time1


title: Twinpair31_twin1_time1


title: Twinpair35_twin1_time1


title: Twinpair34_twin2_time2


title: Twinpair30_twin2_time2


title: Twinpair33_twin2_time2


title: Twinpair30_twin1_time2


title: Twinpair34_twin2_time1


title: Twinpair32_twin1_time2


title: Cold+1d+T-2.txt

city: Berlin

first: Reinhard

last: Kunze

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Institute of Biology

country: Germany

institute: Freie Universität Berlin

description: Gene expression in leaves after 'treatment'

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. Hybridization was performed in a Agilent hybridization oven at standard conditions as recommended by the manufacturer. Subsequently, microarrays were washed 1 minute with GE Wash Buffer 1 (Agilent) at 23°C and 1 minute with GE Wash buffer 2 (Agilent) at 37°C.

scan_protocol: Microarrays were scanned immediately after washing with an Agilent High-Resolution Scanner (G2600D) using default settings.

data_processing: The images were processed with the Agilent Feature Extraction software 10.1 using default settings  (protocol GE1_1105_Oct12 (Read Only) and Grid_Name 049286_D_F_20130524). The resulting processed signals of all individual hybridizations were normalized and log2-converted as described in Firtzlaff V, Oberländer J, Geiselhardt S, Hilker M and Kunze R, 2015, .

organism: Arabidopsis thaliana

label_protocol: Cy3-labeled cRNA was synthesized with the Agilent Quick Amp Labeling Kit one-cCy3-labeled cRNA was synthesized with the Quick Amp Labeling Kit, one-color (Agilent Technologies catalog number 5190-0442) according to the manufacturer's instructions.

growth_protocol: For cold treatment, Arabidopsis thaliana Col-0 plants were grown for 7 weeks on soil under short day conditions (10-h/14-h light/dark cycle, 120 μmol m−2 sec−1 light intensity, 50% relative humidity) and then transferred for five days to 4°C under short day conditions (8-h/16-h light/dark cycle, 120 μmol m−2 sec−1 light intensity, 50% relative humidity). Subsequently plants were retransferred to 20°C. Control plants were kept constantly at 20°C.  For egg deposition, a mated female P. brassicae butterfly was placed on the apex of leaf 17 of seven weeks old A. thaliana Col-0 plants grown under short day conditions (10 h/14 h light/dark). The female deposited one egg cluster with 40 eggs each on the lower surface of each leaf. The plants with the egg clusters grew for five days under short day conditions (8-h/16-h light/dark cycle, 120 μmol m−2 sec−1 light intensity, 20°C, 50% relative humidity). Afterwards the egg clusters were gently removed.  For larval feeding, P. brassicae larvae were transferred to leaves of untreated, chilling-treated and oviposition-treated plants and allowed to gregariously feed for two days.

extract_protocol: Total RNA was extracted from frozen and ground tissue according to Verwoerd et al. (1989. Nucleic Acids Res. 17, 2362) and purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA was photometrically quantified with a NanoPhotometer (Implen, München, Germany) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: 5d 4°C + 1d 20°C + 2d larval feeding

tag: cultivar

value: rosette leaf 17


title: Cold+1d+T-1.txt


title: Eggs+1d+T-2.txt

value: 5d Eggs + 3d Egg-free + 2d larval feeding


title: Cold+1d+T-3.txt


title: Eggs+1d+T-1.txt


title: T-1.txt

value: 6d 20°C + 2d larval feeding


title: Twinpair30_twin1_time1


title: T-3.txt


title: Twinpair29_twin2_time2


title: Eggs+3d-3.txt

value: 5d Eggs + 3d Egg-free


title: Twinpair33_twin1_time1


title: Twinpair29_twin1_time2


title: Twinpair29_twin1_time1


title: Twinpair29_twin2_time1


title: Eggs+1d+T-3.txt


title: Eggs+3d-1.txt


title: Cold+3d-2.txt

value: 5d 4°C + 3d 20°C


title: Eggs+3d-2.txt


title: Twinpair30_twin2_time1


title: Cold+3d-1.txt


title: Control 3-3.txt

source_name: Control 3-3

value: 8d 20°C


title: Control 3-2.txt

source_name: Control 3-2


title: Twinpair39_twin2_time2


title: Twinpair28_twin1_time1


title: Twinpair27_twin2_time1


title: T-2.txt


title: Twinpair27_twin2_time2


title: Twinpair28_twin1_time2


title: Twinpair39_twin1_time2


title: Twinpair31_twin2_time2


title: Control 3-4.txt

source_name: Control 3-4


title: Twinpair31_twin1_time2

source_name: Blood


title: Eggs+1d-2.txt

value: 5d Eggs + 1d Egg-free


title: Twinpair28_twin2_time1


title: Eggs+1d-1.txt


title: Cold+1d-3.txt

value: 5d 4°C + 1d 20°C


title: Cold+1d-2.txt


title: Twinpair27_twin1_time2


title: Lck-akt2 72/3237 +

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

description: 15; Gene expression data from lymphoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mogene Array.

scan_protocol: GeneChips were scanned using the Affemetrix scanner 7G.

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.0.187

source_name: Thymic tumor from Lck-MyrAkt2 Transgenic mouse founder line72 cell3237

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

growth_protocol: Mice were husbandried under normal condition

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

tag: age (months)

value: thymic T cell lymphoma


title: Twinpair27_twin1_time1


title: Twinpair26_twin2_time2


title: Twinpair21_twin2_time2


title: Eggs+1d-3.txt


title: Cold+1d-1.txt


title: Cold+3d-3.txt


title: Twinpair26_twin2_time1


title: Control 2-2.txt

source_name: Control 2-2

value: 6d 20°C


title: Twinpair21_twin1_time2

value: blood


title: Twinpair20_twin2_time2

value: Female


title: Control 2-3.txt

source_name: Control 2-3


title: Twinpair26_twin1_time2


title: Control 3-1.txt

source_name: Control 3-1


title: Eggs-3.txt

value: 5d Eggs


title: Twinpair20_twin1_time2


title: Twinpair26_twin1_time1


title: Eggs-2.txt


title: Twinpair25_twin2_time2


title: Twinpair19_twin2_time2


title: Cold-3.txt

value: 5d 4°C


title: Cold-2.txt


title: Twinpair25_twin2_time1


title: Twinpair19_twin1_time2


title: Control 2-1.txt

source_name: Control 2-1


title: Twinpair25_twin1_time2


title: Twinpair18_twin2_time2


title: Twinpair18_twin1_time2


title: Cold-1.txt


title: Twinpair17_twin2_time2


title: Control 1-3.txt

source_name: Control 1-3

value: 5d 20°C


title: Twinpair17_twin1_time2


title: Twinpair12_twin1_time2


title: Twinpair24_twin2_time1


title: Eggs-1.txt


title: Twinpair24_twin2_time2


title: Twinpair25_twin1_time1


title: Control 1-1.txt

source_name: Control 1-1


title: Twinpair24_twin1_time2


title: Twinpair12_twin1_time1

description: Raw data not available due to server breakdown and no back-up


title: Control 1-2.txt

source_name: Control 1-2


title: Twinpair10_twin2_time2

value: Male


title: Twinpair24_twin1_time1


title: Twinpair10_twin1_time1


title: Twinpair23_twin2_time1


title: Twinpair8_twin2_time2


title: Twinpair23_twin1_time2


title: Twinpair22_twin2_time2


title: Twinpair8_twin1_time2


title: Twinpair8_twin1_time1


title: Twinpair23_twin1_time1


title: Twinpair4_twin1_time2


title: Twinpair4_twin1_time1


title: Twinpair22_twin2_time1


title: Twinpair22_twin1_time2


title: Twinpair3_twin2_time2


title: Twinpair22_twin1_time1


title: Twinpair3_twin1_time1


title: Twinpair21_twin2_time1


title: Twinpair2_twin2_time2


title: Twinpair21_twin1_time1


title: Twinpair2_twin1_time2


title: Twinpair20_twin2_time1


title: Twinpair2_twin1_time1


title: Twinpair23_twin2_time2


title: Twinpair20_twin1_time1


title: Twinpair19_twin2_time1


title: Twinpair19_twin1_time1


title: Twinpair18_twin2_time1


title: E14 rep C

city: Cardiff

first: Anne

last: Rosser

state: SOUTH GLAMORGAN

address: Museum Ave

institute: Cardiff University

description: E14 WGE rep C

hyb_protocol: 10 μg fragmented cDNA was then hybridised overnight to the Affymetrix Mouse 430A GeneChip

scan_protocol: GeneChips were scanned using the Agilent Gene Array Scanner controlled by GCOS 1.2

data_processing: MAS5 signal intensity processed in the R statistical programming environment

source_name: E14 Whole gangionic emeince

label_protocol: 10 μg RNA was used to generate double-stranded cDNA by using a T7-linked oligo(dT) primer. Biotinylated cRNA was synthesised using the T7 RNA transcript labelling kit (Enzo Diagnostics, Farmingdale NY, USA)

extract_protocol: RNA was extracted using TriZol reagent performed according to the manufacturer's instructions.


title: E16 rep B

description: E16 WGE rep B

source_name: E16 Whole gangionic emeince


title: E16 rep A

description: E16 WGE rep A


title: E12 rep A

description: E12 WGE rep A

source_name: E12 Whole gangionic emeince


title: E14 rep B

description: E14 WGE rep B


title: E12 rep C

description: E12 WGE rep C


title: E16 rep C

description: E16 WGE rep C


title: NUP98-JARID1A LSC, line 3

first: Rui

last: Lu

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

description: gene expression data from NUP98-JARID1A LSCs

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Hybridization signals were retrieved and normalized by RMA

source_name: transformed leukemia stem cells

label_protocol: Standard Affymetrix protocol

growth_protocol: RH-RAS and other Leukemia stem cell (LSC) lines were cultured in Opti-MEM base medium supplemented with 10% FBS, 1% antibiotics, 50 _M mercaptoethanol and stem cell factor

extract_protocol: Trizol extraction of total RNA and further RNeasy Kit purification was performed according to the manufacturer's instructions.

treatment_protocol: Total RNA was isolated with the Rneasy Plus Miniprep Kit (Qiagen).

value: NUP98-JARID1A LSC


title: Twinpair18_twin1_time1


title: E14 rep A

description: E14 WGE rep A


title: E12 rep B

description: E12 WGE rep B


title: RH-RAS LSC, line 3

description: gene expression data from RH-RAS LSCs

value: RH-RAS LSC


title: RH-RAS LSC, line 4

description: gene expression data from RH-RAS LSCs


title: RH-RAS LSC, line 3, treated with Dot1l inhibitor

description: gene expression data from Dot1l inhibitor treated RH-RAS LSCs

value: Dot1l inhibitor


title: treatment 2 #6

city: Linköping

first: Mohammad

last: Atikuzzaman

address: Linköping

department: Clinical and Experimental Medicine

country: Sweden

institute: Linköping University

description: gene expression data by Affymetrix microarray

hyb_protocol: 3.5 μg of labeled cDNA was hybridized following GeneChip WT PLUS reagent kit's instructions

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner GCS3000

data_processing: The data were analyzed using Bioconductor R packages oligo and limma  with RMA normalization

organism: Sus scrofa

source_name: Sus scrofa oviductal sperm reservoir

label_protocol: standard Affymetrix protocol

growth_protocol: The utero-tubal junction tissues were collected within 24 h by surgery after insemination of BTS, or mating or sperm-free seminal plasma infusion.

extract_protocol: Trizol was used to extract RNA following manufacturer's instructions. The synthesis of cDNA was done using GeneChip WT PLUS Reagent kit

treatment_protocol: The tissues were immediately plunged into liquid nitrogen and then frozen until processs for RNA extraction

value: Oviductal tissues after 50 ml sperm-free seminal fluid infusion


title: treatment 2 #5


title: Twinpair17_twin1_time1


title: Twinpair17_twin2_time1


title: RH-RAS LSC, line 1, treated with Dot1l inhibitor


title: NUP98-JARID1A LSC, line 1


title: MLL-AF9 LSC

description: gene expression data from MLL-AF9 LSCs

value: MLL-AF9 LSC


title: NUP98-JARID1A LSC, line 2


title: treatment 2 #7


title: Twinpair16_twin2_time2


title: treatment 2 #8


title: treatment 2 #4


title: RH-RAS LSC, line 1

description: gene expression data from RH-RAS LSCs


title: RH-RAS LSC, line 2

description: gene expression data from RH-RAS LSCs


title: treatment 2 #3


title: Twinpair16_twin2_time1


title: Twinpair16_twin1_time2


title: Twinpair15_twin2_time2


title: Twinpair16_twin1_time1


title: treatment 2 #1


title: Twinpair15_twin1_time2


title: Twinpair15_twin2_time1


title: treatment 1 #8

value: Oviductal tissues after mating with a boar


title: Twinpair15_twin1_time1


title: Twinpair14_twin1_time2


title: Twinpair28_twin2_time2


title: Twinpair14_twin2_time1


title: Twinpair14_twin2_time2


title: Twinpair14_twin1_time1


title: Twinpair13_twin2_time1


title: treatment 1 #2


title: treatment 1 #1


title: treatment 1 #5


title: treatment 1 #6


title: treatment 1 #3


title: treatment 1 #4


title: Twinpair12_twin2_time2


title: control #8

value: oviductal tissues after infusion of 50 ml BTS


title: treatment 1 #7


title: control #7


title: Twinpair13_twin1_time1


title: control #6


title: treatment 2 #2


title: Twinpair12_twin2_time1


title: Twinpair13_twin2_time2


title: control #5


title: Twinpair11_twin2_time2


title: Twinpair11_twin2_time1


title: control #4


title: control #2


title: Twinpair11_twin1_time2


title: control #3


title: Twinpair13_twin1_time2


title: control #1


title: U87CR exposure to Carmustine and DMSO, rep3

city: Silver Spring

first: Salaheldin

middle: Sobhi

last: Hamed

state: Maryland

address: 10903 New Hampshire Ave

department: CDER/OTR

institute: U.S. FDA

description: Analysis of RNA from cells treated with DMSO as control vs. cells treated with carmustine.

hyb_protocol: Labelled microarray slides were placed in shaking water bath for 16 h at 42 °C. Arrays were then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.

scan_protocol: Microarrays were scanned on a GenePix 4000B scanner (Axon Instruments, Union City, CA).

data_processing: GPR files containing raw data were loaded into MATLAB (Mathworks, Natick, MA). Features were removed from each of the 4 replicates if one array had a negative flag or negative value after background subtraction (median spot intensity minus background). Data were normalized using LOWESS algorithm.

source_name: U87CR 1hr exposure to Carmustine

label_protocol: RNA from control (DMSO) or carmustine-treated cells was labeled indirectly using a dendrimer-based Genisphere 3DNA Array 350 labeling kit (Genisphere, Hatfield, PA). Remaining washing steps were performed according to manufacturer's protocols.

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS, 4 mM L-glutamine, and 100 U/mL Penicillin/Streptomycin. Cells were kept in 5% CO2 incubator at 37oC.

extract_protocol: Total RNA was isolated from exponentially growing cells using RNeasy mini kit (Qiagen, Valencia, CA) according to manufacturer's protocol. The quality of RNA was assessed via Agilent Bioanalyzer 2100 using the RNA nano kit (Agilent Technologies, Palo Alto, CA). cDNA synthesized from 5 mg of RNA using SuperScript® VILO cDNA synthesis kit.

treatment_protocol: Cells in treatment group were treated with 70 mg/mL carmustine for 1 hour and cells in control group were treated with DMSO (vehicle control) for 1 hour.

tag: cell type

value: glioma cell line

tag: carmustine sensitivity

value: resistant

value: Carmustine

tag: treatment duration

value: 1 hr

source_name: U87CR 1hr exposure to DMSO

value: DMSO


title: U87CR exposure to Carmustine and DMSO, rep2


title: U87CR exposure to Carmustine and DMSO, rep4


title: Twinpair10_twin2_time1

value: blood


title: Twinpair9_twin2_time1


title: U87CR exposure to Carmustine and DMSO, rep1


title: Twinpair8_twin2_time1

value: Female


title: Twinpair9_twin1_time2


title: Twinpair10_twin1_time2


title: Twinpair36_twin1_time2


title: Twinpair7_twin2_time2


title: Twinpair7_twin1_time2


title: Twinpair7_twin1_time1


title: Twinpair6_twin2_time2


title: U87 exposure to Carmustine and DMSO, rep1

source_name: U87 1hr exposure to Carmustine

value: sensitive

source_name: U87 1hr exposure to DMSO


title: Twinpair11_twin1_time1

source_name: Blood


title: U87 exposure to Carmustine and DMSO, rep3


title: U87 exposure to Carmustine and DMSO, rep4


title: U87 exposure to Carmustine and DMSO, rep2


title: Twinpair7_twin2_time1


title: SW1088CR exposure to Carmustine and DMSO, rep3

source_name: SW1088CR 1hr exposure to Carmustine

source_name: SW1088CR 1hr exposure to DMSO


title: SW1088CR exposure to Carmustine and DMSO, rep4


title: Twinpair6_twin2_time1


title: Twinpair9_twin1_time1


title: SW1088CR exposure to Carmustine and DMSO, rep1


title: SW1088 exposure to Carmustine and DMSO, rep4

source_name: SW1088 1hr exposure to Carmustine

source_name: SW1088 1hr exposure to DMSO


title: Twinpair6_twin1_time2


title: SW1088 exposure to Carmustine and DMSO, rep3


title: Twinpair5_twin2_time2


title: Twinpair6_twin1_time1


title: SW1088 exposure to Carmustine and DMSO, rep1


title: Twinpair5_twin1_time2


title: A172CR exposure to Carmustine and DMSO, rep3

source_name: A172CR 1hr exposure to Carmustine

source_name: A172CR 1hr exposure to DMSO


title: SW1088CR exposure to Carmustine and DMSO, rep2


title: Twinpair5_twin1_time1


title: A172CR exposure to Carmustine and DMSO, rep2


title: A172CR exposure to Carmustine and DMSO, rep4


title: SW1088 exposure to Carmustine and DMSO, rep2


title: WT_RAS_day16_2

hyb_protocol: Samples were hybridized with Affymetrix Mouse Gene 2.1 ST Array Strip (Affymetrix) according to the manifacture's instruction.

data_processing:
Hybridization signals were retrieved and normalized, followed by differential expression analysis and statistical analysis using GeneSpring Analysis Platform GX 12.6 (Agilent Technologies).
MoGene-2_1-st.pgf
MoGene-2_1-st.mps

source_name: HSPCs in vitro, WT;RAS transduced, day 16

label_protocol: The cDNA was fragmented and terminally labeled with biotin, using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA)

growth_protocol: Lin- enriched murine hematopoietic stem/progenitor cells leukemia progenitor cell lines were cultured in Opti-MEM base medium supplemented with 10% FBS, 1% antibiotics, 50 μM mercaptoethanol and stem cell factor

extract_protocol: Total RNA was isolated with the Rneasy Plus Miniprep Kit (Qiagen).

treatment_protocol: Primary HSPC Cells were retrovirally infected with NRAS G12D alone (EV-RAS), DNMT3A R882H with NRAS G12D (RH-RAS) or DNMT3A WT with NRAS G12D (WT-RAS)

tag: genotype

tag: time point

value: day 16 post-transduction

value: Lin- enriched hematopoietic stem/progenitor cells


title: A172CR exposure to Carmustine and DMSO, rep1


title: Twinpair4_twin2_time2

tag: gender

value: Male


title: WT_RAS_day16_1


title: Twinpair4_twin2_time1

tag: tissue


title: RH_RAS_day16_1

source_name: HSPCs in vitro, RH;RAS transduced, day 16


title: Twinpair3_twin1_time2


title: A172 exposure to Carmustine and DMSO, rep4

source_name: A172 1hr exposure to Carmustine

tag: cell line

source_name: A172 1hr exposure to DMSO


title: A172 exposure to Carmustine and DMSO, rep3


title: A172 exposure to Carmustine and DMSO, rep2


title: Twinpair5_twin2_time1


title: Twinpair1_twin2_time2


title: Twinpair1_twin2_time1


title: A172 exposure to Carmustine and DMSO, rep1


title: Twinpair1_twin1_time2


title: EV_RAS_day16_1

source_name: HSPCs in vitro, EV;RAS transduced, day 16


title: Twinpair1_twin1_time1


title: RH_RAS_day12_2

source_name: HSPCs in vitro, RH;RAS transduced, day 12

value: day 12 post-transduction


title: EV_RAS_day16_2


title: WT_RAS_day12_1

source_name: HSPCs in vitro, WT;RAS transduced, day 12


title: RH_RAS_day12_1


title: RH_RAS_day16_2


title: WT_RAS_day12_2


title: treatment 2 rep4

description: gene expression data from NimbleGen

hyb_protocol: The 4 µg of labeled cDNA was hybridized using NimbleGen hybridizer for 16 hours.

scan_protocol: The chip was scanne dusing NimbleGen scanner MS200

data_processing: The data was analyzed using Bioconductor R packages oligo and limma with RMA normalization

organism: Gallus gallus

source_name: Gallus gallus utero-vaginal junction

label_protocol: standard NimbleGen protocol

growth_protocol: The utero-vaginal junction was retrieved 24 h after treatment along with controls.

extract_protocol: Trizol was used to extract RNA following manufacturer's instructions. The cDNA was synthesized using RevertAid Premium First-Strand cDNA syntheis kit following manufacturer's instructions.

treatment_protocol: The utero-vaginal junction tissues was plunged into the liquid nitrogen and frozen thereafter until used for total RNA extraction.

value: utero-vaginal junction was retrieved from hen 24 h after insemination with sperm-free seminal fluid


title: Twinpair2_twin2_time1


title: treatment 2 rep3

description: gene expression data from NimbleGen


title: EV_RAS_day12_2

source_name: HSPCs in vitro, EV;RAS transduced, day 12


title: EV_RAS_day12_1


title: PFC 2014-04_linc-9432 knockdown

source_name: Pterygium fibroblast cell, knocked down, 48 h

growth_protocol: Cultured primary pterygium fibroblast cells are cultured in DMEM/F-12 with 10% FBS

extract_protocol: RNA was extracted using the RNAeasy mini kit (Qiagen) according to manufacturer's protocol

treatment_protocol: 21 nM pooled siRNA (Ambion, Life Technologies) or non-specific control oligonucleotides are added to cultured fibroblast cells for 48 hours

value: Linc-9432 knockdown


title: treatment 2 rep1

description: gene expression data from NimbleGen


title: treatment 2 rep2

description: gene expression data from NimbleGen


title: treatment 1 rep2

description: gene expression data from NimbleGen

value: utero-vaginal junction was retrieved from hen 24 h after mating with a male chicken


title: treatment 1 rep4

description: gene expression data from NimbleGen


title: PFC 2014-04_control

source_name: Pterygium fibroblast cell, control, 48 h

value: Random oligonucleotide


title: PFC No. 3_linc-9432 knockdown


title: U87_negative_control

city: Fukuoka

first: Ryota

last: Kurogi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Neurosurgery

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with the Bioconductor.

source_name: U87 transfected with miR negative control

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: U87 cells were maintained in α-MEM (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS; Invitrogen, Carlsbad, CA, USA) and 1% penicillin-streptomycin mixture (WAKO, Osaka, Japan). Cells were incubated at 37°C in a humidified atmosphere containing 5% CO2/95% air.

extract_protocol: Cellular miRs were extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA) according to the manufacturer’s protocols. Purified total RNA was eluted in 100 µl of elution buffer.

treatment_protocol: After incubation overnight at 37°C, U87 cells were transfected with human mirVana miR Mimics or the mirVana miR mimic negative control #1 (Ambion, Carlsbad, CA, USA) using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s protocols.

tag: protocol

value: control


title: SG200_4dpi_2

city: Vienna

first: Armin

last: Djamei

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute of Molecular Plant Biology GmbH

hyb_protocol: Hybridization was performed according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies).

scan_protocol: Scanning was performed according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies).

data_processing: background correction by normexp; intra-array normalization by loess, data filtered to retain only probes targeting  U.maydis sense transcripts; in-between-array normalisation by quantile method

molecule: polyA RNA

organism:
Zea mays
Mycosarcoma maydis

source_name: leaf, 4 days after U.maydis infection

label_protocol: Labelling was performed according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis protocol using the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Infection of Z. mays cv. Early Golden Bantam by U. maydis strains indicated above was performed according to Doehlemann et al., 2008. Samples were collected in 3 independently conducted experiments by sampling 12 plants per experiment (2 cm of the third leaf were harvested 2 cm below the injection point).

extract_protocol: Infected plant material was ground in liquid nitrogen and RNA was extracted using TRIzol (Thermo Fisher Scientific) according to the manufacturer's protocol. RNA was additionally purified with the RNeasy Kit (Qiagen). 200 ng purified RNA was subjected to microarray analysis.

tag: u. maydis strain used for infection

tag: zea mays cultivar

value: Early Golden Bantam

value: common reference pool of all Ch1 samples


title: SG200_4dpi_3


title: treatment 1 rep3

description: gene expression data from NimbleGen


title: PFC No.  3_control


title: 233A-FABP4

city: Sapporo

first: Masato

last: Furuhashi

institute: Sapporo Medical University School of Medicine

description: Gene expression after 24 hr incubation in 233A cells with FABP4 (+) and FABP5 (-)

hyb_protocol: For each sample, the Cy3-labeled cRNA was fragmented and hybridized at 65 °C for 17 h in a rotating hybridization oven.

scan_protocol: After washing, microarrays were scanned using an Agilent microarray scanner (Agilent Technologies).

data_processing: Intensity values of each scanned feature were quantified using Agilent Feature Extraction Software, which performs background subtractions, such as error modeling, adjusting for additive and multiplicative noise. Normalization was performed using Agilent GeneSpring GX (per chip normalization: 75 percentile shift; per gene normalization: none).

label_protocol: Starting with 50 ng of total RNA, Cy3-labeled cRNA was produced according to the manufacturer’s protocol.

growth_protocol: ADSC and 233A cells were grown in MesenPRO-RS (Invitrogen, Carlsbad, CA) and Dulbecco's Modified Eagle's Medium (DMEM)/Ham’s F-12 (Invitrogen) supplemented with ITS (insulin, transferrin and selenite) mix and nicotinamide, respectively.

extract_protocol: Total RNA was extracted using an RNeasy Mini kit (Qiagen, Hilden, Germany), and RNA quality was assessed by using an Agilent 2100 Bioanalyzer.

treatment_protocol: The cells were stimulated with 1 µM recombinant FABP4 or recombinant FABP5 for 24 h.

value: 233A renal tubular stem/progenitor cells

value: 1uM recombinant FABP4


title: control rep4

description: gene expression data from NimbleGen

value: utero-vaginal junction tissue was retrieved from control hen


title: 233A-FABP5

description: Gene expression after 24 hr incubation in 233A cells with FABP4 (-) and FABP5 (+)

value: 1uM recombinant FABP5


title: SG200∆rss1_4dpi_2

value: SG200 delta rss1


title: SG200∆rss1_4dpi_3


title: PFC No. 2_control


title: treatment 1 rep1

description: gene expression data from NimbleGen


title: U87_overexpression (miR_145_and_31)

source_name: U87 co-overexpressing miR-145 and 31 mimics

value: transfected with miR-145 and 31 mimics


title: PFC  No. 2_linc-9432 knockdown


title: 233A-Control

description: Gene expression after 24 hr incubation in 233A cells with FABP4 (-) and FABP5 (-)

value: without FABP4 or FABP5


title: SG200_4dpi_1


title: SG200∆rss1_4dpi_1


title: ADSC-FABP5

description: Gene expression after 24 hr incubation in ADSC with FABP4 (-) and FABP5 (+)

source_name: ADSC, FABP4 (-), FABP5 (+)

value: Adipocyte-derived stem cells


title: control rep1

description: gene expression data from NimbleGen


title: PFC No. 1_linc-9432 knockdown

description: Gene expression after treatment with  siRNA targeting linc-9432 for 48 h


title: control rep3

description: gene expression data from NimbleGen


title: control rep2

description: gene expression data from NimbleGen


title: ADSC-Control

description: Gene expression after 24 hr incubation in ADSC with FABP4 (-) and FABP5 (-)

source_name: ADSC, FABP4 (-), FABP5 (-)


title: ADSC-FABP4

description: Gene expression after 24 hr incubation in ADSC with FABP4 (+) and FABP5 (-)

source_name: ADSC, FABP4 (+), FABP5 (-)


title: RSV DEE1 Subject 20, Hour 142

status: Public on Jun 22 2016

city: Ann Arbor

first: Alfred

last: Hero

state: MI

address: 1301 Beal Avenue

institute: University of Michigan

description:
RSV_DEE1_SAMPLE_419
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 142.

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Human Genome U133A 2.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing:
The data were analyzed with robust multi-array average (RMA) normalization using default background adjustment and quantile normalization settings. Then possible batch effect was removed by the parametric and nonparametric empirical Bayes frameworks.
Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: Brainarray Version 10, Hs133Av2_Hs_ENTREZG].

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

extract_protocol: RNA was extracted at Expression Analysis (Durham, NC) from whole blood using the PAXgene™ 96 Blood RNA Kit (PreAnalytiX, Valencia, CA) employing the manufacturer's recommended protocol. While whole blood RNA is initially extracted, a secondary procedure (B-globin reduction) was then employed to remove the contribution of red blood cell (RBC) RNA to the total RNA. A set of four peptide nucleic acid (PNA) oligomers whose sequences are complementary to the 3' portions of the alpha and beta hemoglobin RNA transcripts were added to reduce globin RNA transcription due to RBC. The inhibition of globin cDNA synthesis dramatically reduces the relative amount of anti-sense, biotin-labeled cRNA corresponding to the hemoglobin transcripts.

treatment_protocol: 148 human volunteer subjects under 4 different inoculation regimes (HRV, RSV, H1N1, H3N2). During each challenge study, subjects had peripheral blood taken prior to inoculation with virus (baseline), immediately prior to inoculation (pre-challenge) and at set intervals following challenge.

value: peripheral blood

tag: virus

value: RSV

value: hour 142

tag: subject

value: RSV DEE1 subject 20


title: RSV DEE1 Subject 20, Hour 132

description:
RSV_DEE1_SAMPLE_418
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 132.

value: hour 132


title: RSV DEE1 Subject 20, Hour 101

description:
RSV_DEE1_SAMPLE_414
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 101.

value: hour 101


title: RSV DEE1 Subject 20, Hour 125

description:
RSV_DEE1_SAMPLE_417
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 125.

value: hour 125


title: RSV DEE1 Subject 20, Hour 108

description:
RSV_DEE1_SAMPLE_415
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 108.

value: hour 108


title: RSV DEE1 Subject 20, Hour 118

description:
RSV_DEE1_SAMPLE_416
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 118.

value: hour 118


title: RSV DEE1 Subject 20, Hour 94

description:
RSV_DEE1_SAMPLE_413
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 94.

value: hour 94


title: RSV DEE1 Subject 20, Hour 166

description:
RSV_DEE1_SAMPLE_420
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 166.

value: hour 166


title: RSV DEE1 Subject 20, Hour 70

description:
RSV_DEE1_SAMPLE_410
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 70.

value: hour 70


title: RSV DEE1 Subject 20, Hour 77

description:
RSV_DEE1_SAMPLE_411
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 77.

value: hour 77


title: RSV DEE1 Subject 20, Hour 53

description:
RSV_DEE1_SAMPLE_408
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 53.

value: hour 53


title: RSV DEE1 Subject 20, Hour 36

description:
RSV_DEE1_SAMPLE_406
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 36.

value: hour 36


title: RSV DEE1 Subject 20, Hour 84

description:
RSV_DEE1_SAMPLE_412
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 84.

value: hour 84


title: RSV DEE1 Subject 20, Hour -38

description:
RSV_DEE1_SAMPLE_400
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour -38.

value: hour -38


title: RSV DEE1 Subject 20, Hour 5

description:
RSV_DEE1_SAMPLE_402
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 5.

value: peripheral blood

value: hour 5


title: RSV DEE1 Subject 20, Hour 60

description:
RSV_DEE1_SAMPLE_409
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 60.

value: RSV

value: hour 60


title: RSV DEE1 Subject 20, Hour 22

description:
RSV_DEE1_SAMPLE_404
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 22.

value: hour 22

value: RSV DEE1 subject 20


title: RSV DEE1 Subject 20, Hour 0

description:
RSV_DEE1_SAMPLE_401
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 0.

value: hour 0


title: PFC No. 1_control

description: Gene expression after treatment with non-specific oligos for 48 h

value: Random oligonucleotide


title: RSV DEE1 Subject 19, Hour 125

description:
RSV_DEE1_SAMPLE_396
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 125.

value: hour 125

value: RSV DEE1 subject 19


title: RSV DEE1 Subject 20, Hour 29

description:
RSV_DEE1_SAMPLE_405
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 29.

value: hour 29


title: RSV DEE1 Subject 19, Hour 94

description:
RSV_DEE1_SAMPLE_392
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 94.

value: hour 94


title: RSV DEE1 Subject 19, Hour 166

description:
RSV_DEE1_SAMPLE_399
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 166.

value: hour 166


title: RSV DEE1 Subject 19, Hour 101

description:
RSV_DEE1_SAMPLE_393
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 101.

value: hour 101


title: RSV DEE1 Subject 19, Hour 118

description:
RSV_DEE1_SAMPLE_395
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 118.

value: hour 118


title: RSV DEE1 Subject 19, Hour 84

description:
RSV_DEE1_SAMPLE_391
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 84.

value: hour 84


title: RSV DEE1 Subject 20, Hour 46

description:
RSV_DEE1_SAMPLE_407
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 46.

value: hour 46


title: RSV DEE1 Subject 19, Hour 77

description:
RSV_DEE1_SAMPLE_390
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 77.

value: peripheral blood

value: hour 77


title: RSV DEE1 Subject 20, Hour 12

description:
RSV_DEE1_SAMPLE_403
Gene expression profile from peripheral blood of RSV DEE1 subject 20, hour 12.

value: RSV

value: hour 12


title: RSV DEE1 Subject 19, Hour 70

description:
RSV_DEE1_SAMPLE_389
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 70.

value: hour 70


title: RSV DEE1 Subject 19, Hour 53

description:
RSV_DEE1_SAMPLE_387
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 53.

value: hour 53


title: RSV DEE1 Subject 19, Hour 132

description:
RSV_DEE1_SAMPLE_397
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 132.

value: hour 132


title: RSV DEE1 Subject 19, Hour 142

description:
RSV_DEE1_SAMPLE_398
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 142.

value: hour 142


title: RSV DEE1 Subject 19, Hour 46

description:
RSV_DEE1_SAMPLE_386
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 46.


title: RSV DEE1 Subject 19, Hour 29

description:
RSV_DEE1_SAMPLE_384
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 29.


title: RSV DEE1 Subject 19, Hour 0

description:
RSV_DEE1_SAMPLE_380
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 0.

value: hour 0


title: RSV DEE1 Subject 19, Hour 12

description:
RSV_DEE1_SAMPLE_382
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 12.

value: RSV DEE1 subject 19


title: RSV DEE1 Subject 19, Hour 108

description:
RSV_DEE1_SAMPLE_394
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 108.

value: hour 108


title: RSV DEE1 Subject 19, Hour -38

description:
RSV_DEE1_SAMPLE_379
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour -38.

value: hour -38


title: RSV DEE1 Subject 18, Hour 166

description:
RSV_DEE1_SAMPLE_378
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 166.

value: hour 166

value: RSV DEE1 subject 18


title: RSV DEE1 Subject 19, Hour 60

description:
RSV_DEE1_SAMPLE_388
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 60.

value: hour 60


title: RSV DEE1 Subject 19, Hour 36

description:
RSV_DEE1_SAMPLE_385
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 36.

value: hour 36


title: RSV DEE1 Subject 18, Hour 125

description:
RSV_DEE1_SAMPLE_375
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 125.

value: hour 125


title: RSV DEE1 Subject 18, Hour 142

description:
RSV_DEE1_SAMPLE_377
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 142.

value: peripheral blood


title: RSV DEE1 Subject 18, Hour 132

description:
RSV_DEE1_SAMPLE_376
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 132.


title: RSV DEE1 Subject 18, Hour 118

description:
RSV_DEE1_SAMPLE_374
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 118.

value: hour 118


title: RSV DEE1 Subject 18, Hour 108

description:
RSV_DEE1_SAMPLE_373
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 108.

value: RSV


title: RSV DEE1 Subject 18, Hour 101

description:
RSV_DEE1_SAMPLE_372
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 101.

value: hour 101


title: RSV DEE1 Subject 18, Hour 84

description:
RSV_DEE1_SAMPLE_370
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 84.

value: hour 84


title: RSV DEE1 Subject 18, Hour 94

description:
RSV_DEE1_SAMPLE_371
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 94.

value: hour 94


title: RSV DEE1 Subject 18, Hour 36

description:
RSV_DEE1_SAMPLE_364
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 36.


title: RSV DEE1 Subject 18, Hour 46

description:
RSV_DEE1_SAMPLE_365
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 46.

value: hour 46


title: RSV DEE1 Subject 19, Hour 5

description:
RSV_DEE1_SAMPLE_381
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 5.

value: hour 5


title: RSV DEE1 Subject 19, Hour 22

description:
RSV_DEE1_SAMPLE_383
Gene expression profile from peripheral blood of RSV DEE1 subject 19, hour 22.

value: hour 22


title: RSV DEE1 Subject 18, Hour 22

description:
RSV_DEE1_SAMPLE_362
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 22.


title: RSV DEE1 Subject 18, Hour 29

description:
RSV_DEE1_SAMPLE_363
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 29.

value: hour 29


title: RSV DEE1 Subject 18, Hour 60

description:
RSV_DEE1_SAMPLE_367
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 60.


title: RSV DEE1 Subject 18, Hour 70

description:
RSV_DEE1_SAMPLE_368
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 70.

value: hour 70


title: RSV DEE1 Subject 18, Hour 0

description:
RSV_DEE1_SAMPLE_359
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 0.

value: hour 0


title: RSV DEE1 Subject 18, Hour 77

description:
RSV_DEE1_SAMPLE_369
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 77.

value: hour 77


title: RSV DEE1 Subject 18, Hour 53

description:
RSV_DEE1_SAMPLE_366
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 53.

value: hour 53

value: RSV DEE1 subject 18


title: RSV DEE1 Subject 18, Hour 5

description:
RSV_DEE1_SAMPLE_360
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 5.


title: RSV DEE1 Subject 18, Hour 12

description:
RSV_DEE1_SAMPLE_361
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour 12.

value: hour 12


title: RSV DEE1 Subject 17, Hour 125

description:
RSV_DEE1_SAMPLE_354
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 125.

value: hour 125

value: RSV DEE1 subject 17


title: RSV DEE1 Subject 17, Hour 132

description:
RSV_DEE1_SAMPLE_355
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 132.

value: peripheral blood

value: hour 132


title: RSV DEE1 Subject 17, Hour 142

description:
RSV_DEE1_SAMPLE_356
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 142.

value: RSV

value: hour 142


title: RSV DEE1 Subject 17, Hour 118

description:
RSV_DEE1_SAMPLE_353
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 118.

value: hour 118


title: RSV DEE1 Subject 17, Hour 108

description:
RSV_DEE1_SAMPLE_352
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 108.

value: hour 108


title: RSV DEE1 Subject 17, Hour 84

description:
RSV_DEE1_SAMPLE_349
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 84.

value: hour 84


title: RSV DEE1 Subject 17, Hour 70

description:
RSV_DEE1_SAMPLE_347
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 70.


title: RSV DEE1 Subject 17, Hour 77

description:
RSV_DEE1_SAMPLE_348
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 77.


title: RSV DEE1 Subject 17, Hour 36

description:
RSV_DEE1_SAMPLE_343
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 36.

value: hour 36


title: RSV DEE1 Subject 17, Hour 46

description:
RSV_DEE1_SAMPLE_344
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 46.

value: hour 46


title: RSV DEE1 Subject 17, Hour 101

description:
RSV_DEE1_SAMPLE_351
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 101.

value: hour 101


title: RSV DEE1 Subject 17, Hour 166

description:
RSV_DEE1_SAMPLE_357
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 166.

value: hour 166


title: RSV DEE1 Subject 18, Hour -38

description:
RSV_DEE1_SAMPLE_358
Gene expression profile from peripheral blood of RSV DEE1 subject 18, hour -38.

value: hour -38


title: RSV DEE1 Subject 17, Hour 94

description:
RSV_DEE1_SAMPLE_350
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 94.

value: hour 94


title: RSV DEE1 Subject 17, Hour 60

description:
RSV_DEE1_SAMPLE_346
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 60.

value: hour 60


title: RSV DEE1 Subject 17, Hour 22

description:
RSV_DEE1_SAMPLE_341
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 22.

value: hour 22


title: RSV DEE1 Subject 17, Hour 0

description:
RSV_DEE1_SAMPLE_338
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 0.

value: hour 0


title: RSV DEE1 Subject 17, Hour 5

description:
RSV_DEE1_SAMPLE_339
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 5.

value: hour 5

value: RSV DEE1 subject 17


title: RSV DEE1 Subject 17, Hour 12

description:
RSV_DEE1_SAMPLE_340
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 12.

value: peripheral blood

value: hour 12


title: RSV DEE1 Subject 16, Hour 101

description:
RSV_DEE1_SAMPLE_330
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 101.

value: RSV

value: RSV DEE1 subject 16


title: RSV DEE1 Subject 17, Hour -38

description:
RSV_DEE1_SAMPLE_337
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour -38.


title: RSV DEE1 Subject 16, Hour 125

description:
RSV_DEE1_SAMPLE_333
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 125.

value: hour 125


title: RSV DEE1 Subject 16, Hour 142

description:
RSV_DEE1_SAMPLE_335
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 142.

value: hour 142


title: RSV DEE1 Subject 16, Hour 166

description:
RSV_DEE1_SAMPLE_336
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 166.


title: RSV DEE1 Subject 16, Hour 108

description:
RSV_DEE1_SAMPLE_331
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 108.

value: hour 108


title: RSV DEE1 Subject 16, Hour 77

description:
RSV_DEE1_SAMPLE_327
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 77.

value: hour 77


title: RSV DEE1 Subject 16, Hour 118

description:
RSV_DEE1_SAMPLE_332
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 118.

value: hour 118


title: RSV DEE1 Subject 16, Hour 94

description:
RSV_DEE1_SAMPLE_329
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 94.


title: RSV DEE1 Subject 16, Hour 84

description:
RSV_DEE1_SAMPLE_328
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 84.

value: hour 84


title: RSV DEE1 Subject 16, Hour 70

description:
RSV_DEE1_SAMPLE_326
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 70.

value: hour 70


title: RSV DEE1 Subject 16, Hour 46

description:
RSV_DEE1_SAMPLE_323
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 46.

value: hour 46


title: RSV DEE1 Subject 17, Hour 29

description:
RSV_DEE1_SAMPLE_342
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 29.

value: hour 29


title: RSV DEE1 Subject 16, Hour 53

description:
RSV_DEE1_SAMPLE_324
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 53.

value: hour 53


title: RSV DEE1 Subject 15, Hour 142

description:
RSV_DEE1_SAMPLE_314
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 142.

value: RSV DEE1 subject 15


title: RSV DEE1 Subject 16, Hour 60

description:
RSV_DEE1_SAMPLE_325
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 60.

value: hour 60


title: RSV DEE1 Subject 16, Hour 36

description:
RSV_DEE1_SAMPLE_322
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 36.

value: hour 36


title: RSV DEE1 Subject 16, Hour 0

description:
RSV_DEE1_SAMPLE_317
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 0.

value: peripheral blood

value: hour 0


title: RSV DEE1 Subject 16, Hour 5

description:
RSV_DEE1_SAMPLE_318
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 5.

value: RSV

value: hour 5


title: RSV DEE1 Subject 15, Hour 108

description:
RSV_DEE1_SAMPLE_310
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 108.


title: RSV DEE1 Subject 16, Hour 22

description:
RSV_DEE1_SAMPLE_320
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 22.

value: hour 22

value: RSV DEE1 subject 16


title: RSV DEE1 Subject 16, Hour 12

description:
RSV_DEE1_SAMPLE_319
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 12.

value: hour 12


title: RSV DEE1 Subject 16, Hour 132

description:
RSV_DEE1_SAMPLE_334
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 132.

value: hour 132


title: RSV DEE1 Subject 15, Hour 166

description:
RSV_DEE1_SAMPLE_315
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 166.

value: hour 166


title: RSV DEE1 Subject 16, Hour -38

description:
RSV_DEE1_SAMPLE_316
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour -38.

value: hour -38


title: RSV DEE1 Subject 15, Hour 132

description:
RSV_DEE1_SAMPLE_313
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 132.


title: RSV DEE1 Subject 16, Hour 29

description:
RSV_DEE1_SAMPLE_321
Gene expression profile from peripheral blood of RSV DEE1 subject 16, hour 29.


title: RSV DEE1 Subject 15, Hour 118

description:
RSV_DEE1_SAMPLE_311
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 118.

value: hour 118


title: RSV DEE1 Subject 15, Hour 125

description:
RSV_DEE1_SAMPLE_312
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 125.

value: hour 125


title: RSV DEE1 Subject 15, Hour 46

description:
RSV_DEE1_SAMPLE_302
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 46.

value: hour 46


title: RSV DEE1 Subject 15, Hour 60

description:
RSV_DEE1_SAMPLE_304
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 60.


title: RSV DEE1 Subject 15, Hour 53

description:
RSV_DEE1_SAMPLE_303
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 53.

value: hour 53


title: RSV DEE1 Subject 15, Hour 84

description:
RSV_DEE1_SAMPLE_307
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 84.

value: hour 84

value: RSV DEE1 subject 15


title: RSV DEE1 Subject 15, Hour 77

description:
RSV_DEE1_SAMPLE_306
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 77.

value: hour 77


title: RSV DEE1 Subject 15, Hour 101

description:
RSV_DEE1_SAMPLE_309
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 101.

value: peripheral blood

value: hour 101


title: RSV DEE1 Subject 15, Hour 94

description:
RSV_DEE1_SAMPLE_308
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 94.

value: RSV

value: hour 94


title: RSV DEE1 Subject 15, Hour 36

description:
RSV_DEE1_SAMPLE_301
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 36.

value: hour 36


title: RSV DEE1 Subject 15, Hour 70

description:
RSV_DEE1_SAMPLE_305
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 70.

value: hour 70


title: RSV DEE1 Subject 17, Hour 53

description:
RSV_DEE1_SAMPLE_345
Gene expression profile from peripheral blood of RSV DEE1 subject 17, hour 53.

value: RSV DEE1 subject 17


title: RSV DEE1 Subject 15, Hour 22

description:
RSV_DEE1_SAMPLE_299
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 22.

value: hour 22


title: RSV DEE1 Subject 15, Hour 29

description:
RSV_DEE1_SAMPLE_300
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 29.

value: hour 29


title: RSV DEE1 Subject 15, Hour 12

description:
RSV_DEE1_SAMPLE_298
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 12.

value: hour 12


title: RSV DEE1 Subject 15, Hour -38

description:
RSV_DEE1_SAMPLE_295
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour -38.

value: hour -38


title: RSV DEE1 Subject 14, Hour 46

description:
RSV_DEE1_SAMPLE_281
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 46.

value: RSV DEE1 subject 14


title: RSV DEE1 Subject 14, Hour 166

description:
RSV_DEE1_SAMPLE_294
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 166.

value: hour 166


title: RSV DEE1 Subject 14, Hour 84

description:
RSV_DEE1_SAMPLE_286
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 84.


title: RSV DEE1 Subject 15, Hour 0

description:
RSV_DEE1_SAMPLE_296
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 0.

value: hour 0


title: RSV DEE1 Subject 15, Hour 5

description:
RSV_DEE1_SAMPLE_297
Gene expression profile from peripheral blood of RSV DEE1 subject 15, hour 5.

value: hour 5


title: RSV DEE1 Subject 14, Hour 94

description:
RSV_DEE1_SAMPLE_287
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 94.


title: RSV DEE1 Subject 14, Hour 53

description:
RSV_DEE1_SAMPLE_282
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 53.

value: hour 53


title: RSV DEE1 Subject 14, Hour 101

description:
RSV_DEE1_SAMPLE_288
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 101.


title: RSV DEE1 Subject 14, Hour 60

description:
RSV_DEE1_SAMPLE_283
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 60.

value: hour 60


title: RSV DEE1 Subject 14, Hour 77

description:
RSV_DEE1_SAMPLE_285
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 77.

value: peripheral blood

value: hour 77


title: RSV DEE1 Subject 14, Hour 70

description:
RSV_DEE1_SAMPLE_284
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 70.

value: RSV


title: RSV DEE1 Subject 14, Hour 118

description:
RSV_DEE1_SAMPLE_290
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 118.

value: hour 118


title: RSV DEE1 Subject 14, Hour 125

description:
RSV_DEE1_SAMPLE_291
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 125.

value: hour 125


title: RSV DEE1 Subject 14, Hour 108

description:
RSV_DEE1_SAMPLE_289
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 108.

value: hour 108


title: RSV DEE1 Subject 14, Hour 142

description:
RSV_DEE1_SAMPLE_293
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 142.

value: hour 142


title: RSV DEE1 Subject 14, Hour 132

description:
RSV_DEE1_SAMPLE_292
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 132.

value: hour 132


title: RSV DEE1 Subject 14, Hour 22

description:
RSV_DEE1_SAMPLE_278
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 22.

value: hour 22


title: RSV DEE1 Subject 14, Hour 29

description:
RSV_DEE1_SAMPLE_279
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 29.

value: hour 29


title: RSV DEE1 Subject 14, Hour 5

description:
RSV_DEE1_SAMPLE_276
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 5.


title: RSV DEE1 Subject 14, Hour 36

description:
RSV_DEE1_SAMPLE_280
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 36.

value: hour 36


title: RSV DEE1 Subject 14, Hour 0

description:
RSV_DEE1_SAMPLE_275
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 0.

value: RSV DEE1 subject 14


title: RSV DEE1 Subject 13, Hour 166

description:
RSV_DEE1_SAMPLE_273
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 166.

value: hour 166

value: RSV DEE1 subject 13


title: RSV DEE1 Subject 14, Hour -38

description:
RSV_DEE1_SAMPLE_274
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour -38.

value: hour -38


title: RSV DEE1 Subject 13, Hour 142

description:
RSV_DEE1_SAMPLE_272
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 142.


title: RSV DEE1 Subject 13, Hour 132

description:
RSV_DEE1_SAMPLE_271
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 132.


title: RSV DEE1 Subject 14, Hour 12

description:
RSV_DEE1_SAMPLE_277
Gene expression profile from peripheral blood of RSV DEE1 subject 14, hour 12.

value: hour 12


title: RSV DEE1 Subject 13, Hour 84

description:
RSV_DEE1_SAMPLE_265
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 84.

value: hour 84


title: RSV DEE1 Subject 13, Hour 108

description:
RSV_DEE1_SAMPLE_268
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 108.

value: peripheral blood


title: RSV DEE1 Subject 13, Hour 70

description:
RSV_DEE1_SAMPLE_263
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 70.

value: hour 70


title: RSV DEE1 Subject 13, Hour 101

description:
RSV_DEE1_SAMPLE_267
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 101.

value: RSV

value: hour 101


title: RSV DEE1 Subject 13, Hour 77

description:
RSV_DEE1_SAMPLE_264
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 77.

value: hour 77


title: RSV DEE1 Subject 13, Hour 22

description:
RSV_DEE1_SAMPLE_257
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 22.


title: RSV DEE1 Subject 13, Hour 46

description:
RSV_DEE1_SAMPLE_260
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 46.

value: hour 46


title: RSV DEE1 Subject 13, Hour 94

description:
RSV_DEE1_SAMPLE_266
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 94.

value: hour 94


title: RSV DEE1 Subject 13, Hour 118

description:
RSV_DEE1_SAMPLE_269
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 118.

value: hour 118


title: RSV DEE1 Subject 13, Hour 12

description:
RSV_DEE1_SAMPLE_256
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 12.


title: RSV DEE1 Subject 13, Hour 60

description:
RSV_DEE1_SAMPLE_262
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 60.

value: hour 60


title: RSV DEE1 Subject 13, Hour 53

description:
RSV_DEE1_SAMPLE_261
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 53.

value: hour 53


title: RSV DEE1 Subject 12, Hour 142

description:
RSV_DEE1_SAMPLE_251
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 142.

value: hour 142

value: RSV DEE1 subject 12


title: RSV DEE1 Subject 13, Hour -38

description:
RSV_DEE1_SAMPLE_253
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour -38.


title: RSV DEE1 Subject 13, Hour 0

description:
RSV_DEE1_SAMPLE_254
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 0.

value: hour 0


title: RSV DEE1 Subject 13, Hour 5

description:
RSV_DEE1_SAMPLE_255
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 5.

value: hour 5

value: RSV DEE1 subject 13


title: RSV DEE1 Subject 13, Hour 125

description:
RSV_DEE1_SAMPLE_270
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 125.

value: hour 125


title: RSV DEE1 Subject 12, Hour 101

description:
RSV_DEE1_SAMPLE_246
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 101.


title: RSV DEE1 Subject 12, Hour 94

description:
RSV_DEE1_SAMPLE_245
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 94.


title: RSV DEE1 Subject 12, Hour 108

description:
RSV_DEE1_SAMPLE_247
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 108.

value: hour 108


title: RSV DEE1 Subject 12, Hour 125

description:
RSV_DEE1_SAMPLE_249
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 125.

value: peripheral blood


title: RSV DEE1 Subject 12, Hour 132

description:
RSV_DEE1_SAMPLE_250
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 132.

value: hour 132


title: RSV DEE1 Subject 12, Hour 84

description:
RSV_DEE1_SAMPLE_244
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 84.

value: RSV

value: hour 84


title: RSV DEE1 Subject 12, Hour 118

description:
RSV_DEE1_SAMPLE_248
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 118.


title: RSV DEE1 Subject 12, Hour 60

description:
RSV_DEE1_SAMPLE_241
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 60.


title: RSV DEE1 Subject 13, Hour 36

description:
RSV_DEE1_SAMPLE_259
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 36.

value: hour 36


title: RSV DEE1 Subject 13, Hour 29

description:
RSV_DEE1_SAMPLE_258
Gene expression profile from peripheral blood of RSV DEE1 subject 13, hour 29.

value: hour 29


title: RSV DEE1 Subject 12, Hour 70

description:
RSV_DEE1_SAMPLE_242
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 70.

value: hour 70


title: RSV DEE1 Subject 12, Hour 166

description:
RSV_DEE1_SAMPLE_252
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 166.

value: hour 166


title: RSV DEE1 Subject 12, Hour 77

description:
RSV_DEE1_SAMPLE_243
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 77.

value: hour 77


title: RSV DEE1 Subject 12, Hour 46

description:
RSV_DEE1_SAMPLE_239
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 46.

value: hour 46


title: RSV DEE1 Subject 12, Hour 53

description:
RSV_DEE1_SAMPLE_240
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 53.

value: hour 53


title: RSV DEE1 Subject 12, Hour 5

description:
RSV_DEE1_SAMPLE_234
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 5.

value: RSV DEE1 subject 12


title: RSV DEE1 Subject 12, Hour 22

description:
RSV_DEE1_SAMPLE_236
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 22.

value: hour 22


title: RSV DEE1 Subject 12, Hour 12

description:
RSV_DEE1_SAMPLE_235
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 12.

value: hour 12


title: RSV DEE1 Subject 12, Hour 0

description:
RSV_DEE1_SAMPLE_233
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 0.

value: hour 0


title: RSV DEE1 Subject 11, Hour 118

description:
RSV_DEE1_SAMPLE_227
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 118.

value: hour 118

value: RSV DEE1 subject 11


title: RSV DEE1 Subject 11, Hour 108

description:
RSV_DEE1_SAMPLE_226
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 108.

value: peripheral blood

value: hour 108


title: RSV DEE1 Subject 11, Hour 94

description:
RSV_DEE1_SAMPLE_224
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 94.

value: RSV

value: hour 94


title: RSV DEE1 Subject 12, Hour 36

description:
RSV_DEE1_SAMPLE_238
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 36.

value: hour 36


title: RSV DEE1 Subject 12, Hour -38

description:
RSV_DEE1_SAMPLE_232
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour -38.

value: hour -38


title: RSV DEE1 Subject 11, Hour 166

description:
RSV_DEE1_SAMPLE_231
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 166.


title: RSV DEE1 Subject 11, Hour 132

description:
RSV_DEE1_SAMPLE_229
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 132.

value: hour 132


title: RSV DEE1 Subject 11, Hour 125

description:
RSV_DEE1_SAMPLE_228
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 125.

value: hour 125


title: RSV DEE1 Subject 11, Hour 101

description:
RSV_DEE1_SAMPLE_225
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 101.

value: hour 101


title: RSV DEE1 Subject 11, Hour 142

description:
RSV_DEE1_SAMPLE_230
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 142.

value: hour 142


title: RSV DEE1 Subject 11, Hour 84

description:
RSV_DEE1_SAMPLE_223
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 84.

value: hour 84


title: RSV DEE1 Subject 11, Hour 70

description:
RSV_DEE1_SAMPLE_221
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 70.

value: hour 70


title: RSV DEE1 Subject 11, Hour 46

description:
RSV_DEE1_SAMPLE_218
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 46.

value: hour 46


title: RSV DEE1 Subject 11, Hour 36

description:
RSV_DEE1_SAMPLE_217
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 36.


title: RSV DEE1 Subject 12, Hour 29

description:
RSV_DEE1_SAMPLE_237
Gene expression profile from peripheral blood of RSV DEE1 subject 12, hour 29.

value: hour 29

value: RSV DEE1 subject 12


title: RSV DEE1 Subject 11, Hour 22

description:
RSV_DEE1_SAMPLE_215
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 22.

value: hour 22


title: RSV DEE1 Subject 11, Hour 77

description:
RSV_DEE1_SAMPLE_222
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 77.

value: hour 77

value: RSV DEE1 subject 11


title: RSV DEE1 Subject 11, Hour 12

description:
RSV_DEE1_SAMPLE_214
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 12.

value: peripheral blood

value: hour 12


title: RSV DEE1 Subject 11, Hour 29

description:
RSV_DEE1_SAMPLE_216
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 29.

value: RSV


title: RSV DEE1 Subject 11, Hour 53

description:
RSV_DEE1_SAMPLE_219
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 53.

value: hour 53


title: RSV DEE1 Subject 10, Hour 166

description:
RSV_DEE1_SAMPLE_210
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 166.

value: hour 166

value: RSV DEE1 subject 10


title: RSV DEE1 Subject 11, Hour 60

description:
RSV_DEE1_SAMPLE_220
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 60.

value: hour 60


title: RSV DEE1 Subject 10, Hour 132

description:
RSV_DEE1_SAMPLE_208
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 132.

value: hour 132


title: RSV DEE1 Subject 10, Hour 125

description:
RSV_DEE1_SAMPLE_207
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 125.

value: hour 125


title: RSV DEE1 Subject 11, Hour 0

description:
RSV_DEE1_SAMPLE_212
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 0.

value: hour 0


title: RSV DEE1 Subject 10, Hour 142

description:
RSV_DEE1_SAMPLE_209
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 142.

value: hour 142


title: RSV DEE1 Subject 11, Hour -38

description:
RSV_DEE1_SAMPLE_211
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour -38.

value: hour -38


title: RSV DEE1 Subject 11, Hour 5

description:
RSV_DEE1_SAMPLE_213
Gene expression profile from peripheral blood of RSV DEE1 subject 11, hour 5.

value: hour 5


title: RSV DEE1 Subject 10, Hour 108

description:
RSV_DEE1_SAMPLE_205
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 108.

value: hour 108


title: RSV DEE1 Subject 10, Hour 84

description:
RSV_DEE1_SAMPLE_202
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 84.

value: hour 84


title: RSV DEE1 Subject 10, Hour 118

description:
RSV_DEE1_SAMPLE_206
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 118.

value: hour 118


title: RSV DEE1 Subject 10, Hour 94

description:
RSV_DEE1_SAMPLE_203
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 94.

value: hour 94


title: RSV DEE1 Subject 10, Hour 77

description:
RSV_DEE1_SAMPLE_201
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 77.

value: peripheral blood

value: hour 77


title: RSV DEE1 Subject 10, Hour 46

description:
RSV_DEE1_SAMPLE_197
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 46.

value: RSV

value: hour 46


title: RSV DEE1 Subject 10, Hour 53

description:
RSV_DEE1_SAMPLE_198
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 53.

value: hour 53


title: RSV DEE1 Subject 10, Hour 70

description:
RSV_DEE1_SAMPLE_200
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 70.

value: hour 70

value: RSV DEE1 subject 10


title: RSV DEE1 Subject 10, Hour 12

description:
RSV_DEE1_SAMPLE_193
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 12.

value: hour 12


title: RSV DEE1 Subject 10, Hour 22

description:
RSV_DEE1_SAMPLE_194
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 22.

value: hour 22


title: RSV DEE1 Subject 10, Hour 0

description:
RSV_DEE1_SAMPLE_191
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 0.

value: hour 0


title: RSV DEE1 Subject 9, Hour 142

description:
RSV_DEE1_SAMPLE_188
Gene expression profile from peripheral blood of RSV DEE1 subject 9, hour 142.

value: hour 142

value: RSV DEE1 subject 9


title: RSV DEE1 Subject 10, Hour -38

description:
RSV_DEE1_SAMPLE_190
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour -38.

value: hour -38


title: RSV DEE1 Subject 9, Hour 166

description:
RSV_DEE1_SAMPLE_189
Gene expression profile from peripheral blood of RSV DEE1 subject 9, hour 166.

value: hour 166


title: RSV DEE1 Subject 9, Hour 132

description:
RSV_DEE1_SAMPLE_187
Gene expression profile from peripheral blood of RSV DEE1 subject 9, hour 132.

value: hour 132


title: RSV DEE1 Subject 10, Hour 101

description:
RSV_DEE1_SAMPLE_204
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 101.

value: hour 101


title: RSV DEE1 Subject 10, Hour 60

description:
RSV_DEE1_SAMPLE_199
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 60.

value: hour 60


title: RSV DEE1 Subject 10, Hour 29

description:
RSV_DEE1_SAMPLE_195
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 29.

value: peripheral blood

value: hour 29


title: RSV DEE1 Subject 10, Hour 36

description:
RSV_DEE1_SAMPLE_196
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 36.

value: RSV

value: hour 36


title: RSV DEE1 Subject 10, Hour 5

description:
RSV_DEE1_SAMPLE_192
Gene expression profile from peripheral blood of RSV DEE1 subject 10, hour 5.

value: hour 5


title: sample.361

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U219 Gene Chip Arrays.

scan_protocol: Washing and staining was performed in Affymetrix fluidics station 450 with the recommended programm. Arrays were scanned on a GCS 3000.

data_processing: The data were analysed using Bioconductor package 'oligo' 1.18.0 under R-2.14.0. Background correction, normalization and probe summarization was performed with RMA.

source_name: peripheral blood of donor.13 at timepoint 3, control treated

label_protocol: Biotinylated cRNA were prepared using the 3'IVT Express Kit (Ambion) from 100ng total RNA according to the manufacturer.

growth_protocol: not applicable

extract_protocol: LPS-stimulated and un-stimulated blood samples from both genders were transferred into PaxGene Blood RNA Tubes (PreAnalytiX/QIAGEN, Switzerland) and total RNA was isolated using the PaxGene Blood RNA kit (PreAnalytix/Switzerland) following the manufacturer’s protocol.

treatment_protocol: Whole blood (K3-EDTA) was cultured with vehicle or lipopolysaccharide (LPS)(10 ng/ml) for 1h.

tag: donor

tag: time (pre-exercise and post-exercise 30 min, 3h, 24h)

value: control

value: f


title: sample.323

source_name: peripheral blood of donor.6 at timepoint 3, LPS treated

tag: treatment

value: LPS

value: m


title: sample.317

source_name: peripheral blood of donor.5 at timepoint 3, LPS treated


title: sample.368

source_name: peripheral blood of donor.14 at timepoint 3, control treated


title: sample.329

source_name: peripheral blood of donor.7 at timepoint 3, LPS treated


title: sample.370

source_name: peripheral blood of donor.14 at timepoint 3, LPS treated


title: sample.305

source_name: peripheral blood of donor.3 at timepoint 3, LPS treated


title: sample.353

source_name: peripheral blood of donor.11 at timepoint 3, LPS treated


title: sample.355

source_name: peripheral blood of donor.12 at timepoint 3, control treated


title: sample.327

source_name: peripheral blood of donor.7 at timepoint 3, control treated


title: sample.269

source_name: peripheral blood of donor.13 at timepoint 2, LPS treated


title: sample.315

source_name: peripheral blood of donor.5 at timepoint 3, control treated


title: sample.274

source_name: peripheral blood of donor.14 at timepoint 2, LPS treated


title: sample.366

source_name: peripheral blood of donor.13 at timepoint 3, LPS treated


title: sample.351

source_name: peripheral blood of donor.11 at timepoint 3, control treated


title: sample.303

source_name: peripheral blood of donor.3 at timepoint 3, control treated


title: sample.321

source_name: peripheral blood of donor.6 at timepoint 3, control treated


title: sample.262

source_name: peripheral blood of donor.12 at timepoint 2, LPS treated


title: sample.258

source_name: peripheral blood of donor.11 at timepoint 2, LPS treated


title: sample.220

source_name: peripheral blood of donor.5 at timepoint 2, LPS treated


title: sample.205

source_name: peripheral blood of donor.3 at timepoint 2, control treated


title: sample.254

source_name: peripheral blood of donor.11 at timepoint 2, control treated


title: sample.265

source_name: peripheral blood of donor.13 at timepoint 2, control treated


title: sample.173

source_name: peripheral blood of donor.13 at timepoint 1, LPS treated


title: sample.165

source_name: peripheral blood of donor.12 at timepoint 1, control treated


title: sample.176

source_name: peripheral blood of donor.14 at timepoint 1, control treated


title: sample.230

source_name: peripheral blood of donor.7 at timepoint 2, control treated


title: sample.219

source_name: peripheral blood of donor.5 at timepoint 2, control treated