title: Muscle biopsies from trained COPD patient #30 with normal Body Mass Index

description: Gene expression data from muscle biopsies of a trained COPD individual with normal BMI.

source_name: Trained COPD with normal BMI

value: normal


title: N3D cell line Biological replicate in antisense orientation replicate 3

status: Public on Nov 16 2013

type: RNA

city: Baltimore

first: Kathleen

middle: Helen

last: Burns

state: MD

address: 720 Rutland Ave Ross 524

department: Pathology

country: USA

institute: Johns Hopkins University School of Medicine

description: Control experiment showing the specificity of the transposable element array.

hyb_protocol: Arrays were hybridized following the manufacturer’s protocol for 17h. Longer hybridization times up to 65 h were attempted in order to verify saturation at the recommended 17h.

scan_protocol: Arrays were washed and scanned on an Agilent 2mm scanner at 70% PMT (photomultiplier tubes) for both green and red channels. Agilent's Feature Extractor was used for generating data files.

data_processing: Probe intensities from the two-channel arrays were log2 transformed and LOESS normalized.

molecule: total RNA

organism: Mus musculus

source_name: Control Mouse cell line N3D biological replicate 3

label_protocol: Poly-A RNA was reverse transcribed to double stranded cDNA using MMLV RT. T7 promoter was ligated to the 3’ end corresponding to poly-A. T7 was used to generate single stranded, labeled cRNA. RNA was labeled using Quick amp kit (Agilent) with Cy-dye labeled Cytosine.

extract_protocol: N1G and N3D were derived from primary breast cancer overexpressing Rat Her2/Neu in Balbc mice. Cell lines were maintained in D-MEM with 10% FBS and 100 units/ml penicillin/streptomycin. After reaching 75% confluence, Trizol was added directly onto the plates and total RNA was extracted following the standard Trizol prescribed protocol.

tag: age

tag: strain

value: Balbc

source_name: Control Mouse cell line N3D Total RNA extracted from different culture plates of same cell line replicate 3


title: 24c

type: genomic

city: Beijing

first: Yunfeng

last: Yang

state: Beijing

address: Qinghuayuan Street

department: School of Environment

country: China

institute: Tsinghua University

description: GeoChip data for soil sample collected at the 3400 m elevation sourced from 3200m after 3 years transplant, from gassland without grazing, replicate 3

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

molecule: genomic DNA

organism: uncultured bacterium

source_name: Soil microbes in Tibetan grasslands

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

treatment_protocol: In August 2009, soil samples were collected from all of the plots. Five soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

tag: sourced elevations

tag: transplanted elevations

tag: grazing condition

value: Ungrazing

tag: vegetation landsape

value: Grassland


title: Muscle biopsies from sedentary COPD patient #41 with low Body Mass Index

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

description: Gene expression data from muscle biopsies of a sedentary COPD individual with low BMI.

hyb_protocol: Affymetrix GeneChip technology was performed using Human U133 Plus2 GeneChips according to the manufacturer's suggested protocols.

scan_protocol: Affymetrix Scanner 3000 7G.

data_processing: The data were quantile normalized using the R package RMA.

label: biotin

organism: Homo sapiens

source_name: Sedentary COPD with low BMI

label_protocol: Amplification and labeling of cRNA was performed with the Affymetrix IVT labeling  kit.

extract_protocol: RNA was isolated using the RNeasy extraction kit (QIAGEN, USA) according to the manufacturer's instructions.

treatment_protocol: 8 weeks of exercise training.

tag: tissue

value: musculus vastus lateralis

tag: disease state

value: chronic obstructive pulmonary disease (COPD)

tag: exercise state

value: sedentary

tag: bmi

value: low

tag: individual


title: Muscle biopsies from sedentary COPD patient #37 with low Body Mass Index


title: Muscle biopsies from sedentary COPD patient #36 with low Body Mass Index


title: Muscle biopsies from sedentary COPD patient #38 with low Body Mass Index


title: 3200a

description: GeoChip data for soil sample collected at the 3200 m elevation grassland without grazing, replicate 1


title: Muscle biopsies from trained COPD patient #34 with normal Body Mass Index

value: trained


title: N1G cell line Biological replicate in antisense orientation replicate 6

source_name: Control Mouse cell line N1G biological replicate 6

source_name: Control Mouse cell line N1G Total RNA extracted from different culture plates of same cell line replicate 6


title: Muscle biopsies from trained COPD patient #25 with normal Body Mass Index


title: N1G cell line Biological replicate in antisense orientation replicate 5

source_name: Control Mouse cell line N1G biological replicate 5

source_name: Control Mouse cell line N1G Total RNA extracted from different culture plates of same cell line replicate 5


title: Muscle biopsies from trained COPD patient #27 with normal Body Mass Index


title: Muscle biopsies from trained COPD patient #22 with normal Body Mass Index


title: N3D cell line Technical replicate in antisense orientation replicate 4

source_name: Control Mouse cell line N3D technical replicate 4

source_name: Control Mouse cell line N3D Total RNA extracted from same culture plate replicate 4


title: Muscle biopsies from trained COPD patient #20 with normal Body Mass Index


title: N1G cell line Biological replicate in antisense orientation replicate 3

source_name: Control Mouse cell line N1G biological replicate 3

source_name: Control Mouse cell line N1G Total RNA extracted from different culture plates of same cell line replicate 3


title: N1G cell line Biological replicate in antisense orientation replicate 1

source_name: Control Mouse cell line N1G biological replicate 1

source_name: Control Mouse cell line N1G Total RNA extracted from different culture plates of same cell line replicate 1


title: N1G cell line Biological replicate in antisense orientation replicate 4

source_name: Control Mouse cell line N1G biological replicate 4

source_name: Control Mouse cell line N1G Total RNA extracted from different culture plates of same cell line replicate 4


title: Muscle biopsies from trained COPD patient #24 with normal Body Mass Index

source_name: Trained COPD with normal BMI


title: N3D cell line Technical replicate in antisense orientation replicate 1

source_name: Control Mouse cell line N3D technical replicate 1

source_name: Control Mouse cell line N3D Total RNA extracted from same culture plate replicate 1


title: Muscle biopsies from trained COPD patient #17 with normal Body Mass Index


title: N3D cell line Technical replicate in antisense orientation replicate 3

source_name: Control Mouse cell line N3D technical replicate 3

source_name: Control Mouse cell line N3D Total RNA extracted from same culture plate replicate 3


title: N3D cell line Technical replicate in antisense orientation replicate 2

source_name: Control Mouse cell line N3D technical replicate 2

source_name: Control Mouse cell line N3D Total RNA extracted from same culture plate replicate 2


title: Muscle biopsies from sedentary COPD patient #27 with normal Body Mass Index

description: Gene expression data from muscle biopsies of a sedentary COPD individual with normal BMI.

source_name: Sedentary COPD with normal BMI


title: Muscle biopsies from trained COPD patient #18 with normal Body Mass Index


title: N1G cell line Technical replicate in antisense orientation replicate 3

source_name: Control Mouse cell line N1G technical replicate 3

source_name: Control Mouse cell line N1G Total RNA extracted from same culture plate replicate 3


title: Muscle biopsies from sedentary COPD patient #24 with normal Body Mass Index


title: N1G cell line Technical replicate in antisense orientation replicate 2

source_name: Control Mouse cell line N1G technical replicate 2

source_name: Control Mouse cell line N1G Total RNA extracted from same culture plate replicate 2


title: Muscle biopsies from sedentary COPD patient #30 with normal Body Mass Index


title: N1G cell line Biological replicate in antisense orientation replicate 2

source_name: Control Mouse cell line N1G biological replicate 2

source_name: Control Mouse cell line N1G Total RNA extracted from different culture plates of same cell line replicate 2


title: Testis compared to pooled tissue reference on sense oriented array replicate 1

description: Comparison of normal tissue RNA against reference pooled tissue RNA in sense orientation arrays to identify transposable element transcripts present in the sense orientation.

source_name: Normal tissue harvested from 12 week old C57BL/6 mouse

extract_protocol: Normal tissue experiments used 12 week old C57BL/6 mice. Animals were sacrificed. The tissues were dissected and flash frozen on dry ice. Tissue subsections were homogenized in Trizol (Invitrogen, Carlsbad, CA) and total RNA was extracted and ethanol precipitated (Ambion, Carlsbad, CA). RNA was quantified using Nanodrop (Thermo Fisher Scientific, Wilmington, DE) and its integrity measured using Bioanalyzer 2100 (Agilent, Santa Clara, CA) according to the manufacturer’s directions. Normal somatic tissue RNA pools of 6 mg were made by combining 600ng of RNA from each of the following tissues: lung (2 male animals, 300ng each and 1 female animal, 600ng), brain (3 males, 200ng each and 3 females 200ng each), liver (1 male, 600ng and 1 female, 600ng), kidney (1 male, 600ng and 1 female, 600ng) and heart (1 male, 600ng and 1 female, 600ng).

value: 12 weeks

source_name: Pooled tissue reference


title: Testis compared to pooled tissue reference on sense oriented array replicate 2


title: Muscle biopsies from sedentary COPD patient #18 with normal Body Mass Index


title: N1G cell line Technical replicate in antisense orientation replicate 1

source_name: Control Mouse cell line N1G technical replicate 1

source_name: Control Mouse cell line N1G Total RNA extracted from same culture plate replicate 1


title: Male lung compared to pooled tissue reference on sense oriented array replicate 2


title: Male lung compared to pooled tissue reference on sense oriented array replicate 3


title: Muscle biopsies from sedentary COPD patient #34 with normal Body Mass Index


title: Muscle biopsies from sedentary COPD patient #17 with normal Body Mass Index


title: Testis compared to pooled tissue reference on sense oriented array replicate 3


title: Female lung compared to pooled tissue reference on sense oriented array


title: Muscle biopsies from sedentary COPD patient #20 with normal Body Mass Index


title: Muscle biopsies from healthy individual #8 after 8w training

description: Gene expression data from muscle biopsies of a trained healthy individual.

source_name: Trained healthy

value: healthy


title: Male lung compared to pooled tissue reference on sense oriented array replicate 1


title: Male liver compared to pooled tissue reference on sense oriented array replicate 3


title: Muscle biopsies from healthy individual #9 after 8w training


title: Muscle biopsies from healthy individual #7 after 8w training


title: Muscle biopsies from sedentary COPD patient #22 with normal Body Mass Index


title: Muscle biopsies from healthy individual #5 after 8w training


title: Male liver compared to pooled tissue reference on sense oriented array replicate 2


title: Muscle biopsies from sedentary COPD patient #25 with normal Body Mass Index


title: Male kidney compared to pooled tissue reference on sense oriented array replicate 3


title: Muscle biopsies from healthy individual #4 after 8w training


title: Male liver compared to pooled tissue reference on sense oriented array replicate 1


title: Muscle biopsies from healthy individual #2 after 8w training


title: Male kidney compared to pooled tissue reference on sense oriented array replicate 2


title: Muscle biopsies from healthy individual #15 after 8w training


title: Male heart compared to pooled tissue reference on sense oriented array replicate 3


title: Muscle biopsies from healthy sedentary individuals #9

description: Gene expression data from muscle biopsies of a sedentary healthy individual.

source_name: Sedentary healthy


title: Male heart compared to pooled tissue reference on sense oriented array replicate 1


title: Muscle biopsies from healthy individual #10 after 8w training


title: Male heart compared to pooled tissue reference on sense oriented array replicate 2


title: Muscle biopsies from healthy individual #13 after 8w training


title: Muscle biopsies from healthy individual #12 after 8w training


title: Male kidney compared to pooled tissue reference on sense oriented array replicate 1


title: Muscle biopsies from healthy individual #1 after 8w training


title: Muscle biopsies from healthy sedentary individuals #7


title: Breast compared to pooled tissue reference on sense oriented array replicate 1


title: Breast compared to pooled tissue reference on sense oriented array replicate 2


title: Male brain compared to pooled tissue reference on sense oriented array replicate3


title: Muscle biopsies from healthy sedentary individuals #8


title: Muscle biopsies from healthy sedentary individuals #5


title: Muscle biopsies from healthy sedentary individual #4


title: Male brain compared to pooled tissue reference on antisense oriented array

description: Comparison of normal tissue RNA against reference pooled tissue RNA in antisense orientation arrays to identify transposable element transcripts present in the antisense orientation.


title: Muscle biopsies from healthy individual #11 after 8w training


title: Female brain compared to pooled tissue reference on antisense oriented array


title: Muscle biopsies from healthy sedentary individuals #13


title: Muscle biopsies from healthy sedentary individuals #15


title: Breast compared to pooled tissue reference on antisense oriented array


title: Female lung compared to pooled tissue reference on antisense oriented array


title: Male brain compared to pooled tissue reference on sense oriented array replicate 1


title: Male brain compared to pooled tissue reference on sense oriented array replicate 2


title: Female brain compared to pooled tissue reference on sense oriented array


title: Muscle biopsies from healthy sedentary individual #2


title: Muscle biopsies from healthy sedentary individuals #12


title: Muscle biopsies from healthy sedentary individuals #11


title: Male lung compared to pooled tissue reference on antisense oriented array


title: Muscle biopsies from healthy sedentary individual #10


title: Muscle biopsies from healthy sedentary individual #1


title: SK_A2_2C

status: Public on Nov 15 2013

city: Boston

first: Susan

last: Kandarian

state: MA

address: 635commonwealth ave, Rm444

department: Health Sciences

institute: Boston University

description: Whole transcript expression profiling

hyb_protocol: Fragmented, biotinylated DNA samples were hybridized on a mouse Gene 1.0 ST array acorrding to manufacture's recommendation.

scan_protocol: A total of 6 array images were acquired by GeneChip Scanner 3000 TG and quality assessed by Affymetrix Expression Console (Santa Clara, CA).

data_processing:
Gene expression signal values were generated by the Expression File Creator module of the GenePattern platform (Broad Institute, Cambridge, MA) and robust multi-array analysis algorithm (RMA) and quantile normalization was used for data preprocessing {Bolstad, 2003 #4365}.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: Brainarray MoGene 1.0 ST custom CDF file v.13 was used for probe annotation {Allan, 2005 #4379}.

label: Btiotin

source_name: gastrocnemius/plantaris muscles

label_protocol: Whole-transcript expression profiling experiments were carried out by the Boston University Microarray Core Facility.  The Affy standard WT Sense Target Labeling assay protocol was followed to synthesize biotinylated DNA.

growth_protocol: Eight-week-old, male CDF1 mice purchased from Charles River Laboratories (Wilmington, MA, USA) were used for all experiments. The use of animals was approved by the Boston University Institutional Animal Care and Use Committee. Animals were maintained on a 12:12 L/D cycle, were housed individually, and were given access to food and water ad libitum.  After three days of acclimation, animals were randomly assigned to a non-tumor control group or a C26 tumor-bearing group.  Control animals received an inoculum of 150 μL 1 x PBS/matrigel (1:1) subcutaneously into the right and left flanks.  Tumor-bearing animals received an inoculum of 5.0 x 105 C26 cells suspended in 150 μL PBS/matrigel (1:1) injected subcutaneously into the right and left flanks.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.  The extracted total RNA was further purified using an RNase-Free DNase I kit (Qiagen, Valencia, CA, USA) and an RNeasy Mini kit (Qiagen, Valencia, CA, USA) as previously described {Wu, 2011 #4036}.  Extracted RNA was quantitated by UV spectrophotometry and quality checked by a 1% denaturing agarose gel.  Samples were also verified by Bioanalyzer 2100 analysis and had a minimal RIN number of 8.0 (Agilent, Palo Alto, CA, USA).

treatment_protocol: The gastrocnemius/plantaris muscles from a total of 7 mice were used, including 4 C26 tumor-bearing mice, and 3 control non tumor-bearing mice. Gastrocnemius and plantaris muscles were harvested from anesthetized non-tumor and tumor-bearing mice, snap-frozen in liquid nitrogen, and stored at -80°C until further processing.

tag: sample type

value: healthy, non-tumor bearing mice

tag: gender

value: male


title: SK_A5_3E

description: Whole transcript expression profiling

value: atrophied C26-tumor bearing mice


title: Testis compared to pooled tissue reference on antisense oriented array


title: HeLa cells transfected with L1 transposon containing plasmid

description: Positive control experiment to study the upregulation of L1 transposon when HeLa cells are transfected with an L1 containing plasmid as compared to a GFP containing plasmid.

source_name: LINE1 (L1) transposon construct containing plasmid versus GFP plasmid transfected HeLa comparison on sense oriented human array

extract_protocol: HeLa-HA cells were maintained in Dulbecco’s Modified Eagle Medium (D-MEM) supplemented with 10% fetal bovine serum and 100units/ml penicillin/streptomycin. HeLa were seeded in 6-well plates (2x105 cells/well) the day before transfection. pLD107 (pCEP puro -eGFP) was made by cloning eGFP gene into pCEP puro plasmid after the CMV promoter (between NheI and BamHI sites). pLD190 (pCEP puro L1.3-GFPAI) was made by replacing L1RP sequence (NotI/BstZ17I fragment) within pLD223 [45] with L1.3 fragment from JM101 (Not I/BstZ17I) [46]. The next day each well was transfected with 1 mg of either pLD107 or pLD190 plasmid using Fugene 6 (Roche Applied Science, Indianapolis, IN) according to the manufacturer’s protocol. The day after transfection, cells were trypsinized and transferred to a 6 cm plate with 4 mL DMEM medium containing puromycin (2.5mg/ml). After 3 days of puromycin selection, total RNA was extracted using RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

source_name: HeLa cells transfected with GFP construct containing plasmid.


title: SK_A6_4E

description: Whole transcript expression profiling


title: SK_A1_1C

description: Whole transcript expression profiling


title: SK_A4_1E

description: Whole transcript expression profiling


title: 0cGy-NOTRT6hr-m3 (2666_7848_33941)

city: durham

first: lingling

last: zheng

address: research dr

institute: duke university

hyb_protocol: Hybridization protocol was that of the manufacturer protocol by Affymertrix.

scan_protocol: Scanning protocol was that of the manufacturer protocol by Affymetrix.

data_processing: The data was analyzed using RMA from the affy package to pre-process Affymetrix arrays.

label: Biotin

source_name: 0cGy,no treatment,6hr

label_protocol: 500ngs of total RNA was amplified according to the MessageAmp Premier protocol (Ambion).  Affymetrix GeneChip analysis was prepared according to the manufacturer’s instructions, and targets were hybridized to the Mouse 430A 2.0 GeneChip (Affymetrix, Santa Clara, CA).

extract_protocol: Blood was collected in PAXgene fluid and total RNA was extracted using the RNeasy Protect Animal Blood Kit.  RNA was beta globin reduced using Ambion Mouse/Rat GLOBINclear kit for the mouse studies.  RNA was purified using the Qiagen RNEasy Mini Kit.  All total RNA samples were assessed for quality using a NanoDrop ND8000 Spectrophotometer for absorbance ratios, and the Agilent Bioanalyzer 2100 for RIN scores.

treatment_protocol: Ten to 12 week old female and male C57Bl6 mice (Jackson Laboratory, Bar Harbor, ME) were housed in the Duke Cancer Center Isolation Facility and all protocols were approved by the Duke University Animal Care and Use Committee (Protocol Number A037-10-02).  Mice were exposed to 0, 100, 150, 200, 300, 450, 600, 800 or 1050 cGy total body irradiation (TBI) via a Cs137 irradiator at a dose rate of 480 cGy/min.  Peripheral blood samples were collected via terminal cardiac puncture at 6, 24, 48 and 72 hrs, as well as day +5 and +7 following TBI.

tag: stress

value: control (no ionizing radiation)

tag: dose

tag: treatment

value: no treatment

tag: time

value: peripheral blood


title: 600cGy-LPS24hr-m3 (2666_7848_33937)

value: female

value: ionizing radiation

value: LPS


title: SK_A3_3C

description: Whole transcript expression profiling


title: 600cGy-GCSF24hr-m3 (2666_7848_33936)

value: GCSF


title: 0cGy-GCSF6hr-m3 (2666_7848_33939)


title: 200cGy-GCSF6hr-m3 (2666_7848_33942)


title: 300cGy-LPS24hr-m3 (2666_7848_33934)


title: 600cGy-NOTRT6hr-m3 (2666_7848_33927)

source_name: 600cGy,no treatment,6hr


title: 200cGy-LPS24hr-m3 (2666_7848_33932)


title: 300cGy-NOTRT24hr-m3 (2666_7848_33935)

source_name: 300cGy,no treatment,24hr


title: 600cGy-LPS6hr-m3 (2666_7848_33926)


title: 600cGy-NOTRT24hr-m3 (2666_7848_33938)

source_name: 600cGy,no treatment,24hr


title: 200cGy-NOTRT24hr-m3 (2666_7848_33933)

source_name: 200cGy,no treatment,24hr


title: 0cGy-LPS6hr-m3 (2666_7848_33940)


title: 0cGy-LPS24hr-m3 (2666_7848_33929)


title: 0cGy-GCSF24hr-m3 (2666_7848_33928)


title: 300cGy-LPS6hr-m3 (2666_7848_33923)


title: 300cGy-GCSF6hr-m3 (2666_7848_33922)


title: 0cGy-NOTRT24hr-m3 (2666_7848_33930)

source_name: 0cGy,no treatment,24hr


title: 200cGy-NOTRT6hr-m3 (2666_7848_33921)

source_name: 200cGy,no treatment,6hr


title: 300cGy-NOTRT6hr-m3 (2666_7848_33924)

source_name: 300cGy,no treatment,6hr


title: 0cGy-NOTRT6hr-m3 (2666_7848_33918)


title: 200cGy-GCSF6hr-m3 (2666_7848_33919)


title: 600cGy-GCSF6hr-m3 (2666_7848_33925)


title: 200cGy-GCSF24hr-m3 (2666_7848_33931)


title: 600cGy-LPS24hr-m2 (2666_7848_33914)


title: 0cGy-NOTRT24hr-m2 (2666_7848_33909)


title: 300cGy-GCSF24hr-m2 (2666_7848_33912)


title: 600cGy-GCSF24hr-m2 (2666_7848_33913)


title: 600cGy-NOTRT24hr-m9 (2666_7848_33915)


title: 0cGy-GCSF6hr-m3 (2666_7848_33916)


title: 200cGy-LPS6hr-m3 (2666_7848_33920)


title: 200cGy-LPS24hr-m2 (2666_7848_33910)


title: 200cGy-NOTRT6hr-m2 (2666_7848_33900)


title: 0cGy-LPS24hr-m2 (2666_7848_33908)


title: 600cGy-NOTRT6hr-m2 (2666_7848_33906)


title: 600cGy-LPS6hr-m2 (2666_7848_33905)


title: 300cGy-LPS6hr-m2 (2666_7848_33902)


title: 300cGy-GCSF6hr-m2 (2666_7848_33901)


title: 600cGy-GCSF6hr-m2 (2666_7848_33904)


title: 300cGy-NOTRT6hr-m2 (2666_7848_33903)


title: 0cGy-GCSF24hr-m2 (2666_7848_33907)


title: 600cGy-NOTRT24hr-m2 (2666_7848_33894)


title: 0cGy-LPS6hr-m2 (2666_7848_33896)


title: 200cGy-GCSF6hr-m2 (2666_7848_33898)


title: 0cGy-GCSF6hr-m2 (2666_7848_33895)


title: 200cGy-LPS6hr-m2 (2666_7848_33899)


title: 300cGy-GCSF24hr-m2 (2666_7848_33890)


title: 300cGy-LPS24hr-m2 (2666_7848_33891)


title: 200cGy-LPS24hr-m2 (2666_7848_33888)


title: 600cGy-GCSF6hr-m2 (2666_7848_33881)


title: 200cGy-GCSF24hr-m2 (2666_7848_33887)


title: 0cGy-GCSF24hr-m2 (2666_7848_33884)


title: 600cGy-LPS6hr-m2 (2666_7848_33882)


title: 0cGy-NOTRT6hr-m2 (2666_7848_33897)


title: 0cGy-NOTRT24hr-m2 (2666_7848_33886)


title: 0cGy-LPS24hr-m2 (2666_7848_33885)


title: 600cGy-LPS24hr-m2 (2666_7848_33893)


title: 600cGy-NOTRT6hr-m2 (2666_7848_33883)


title: 600cGy-GCSF24hr-m2 (2666_7848_33892)


title: ChIP sample 3 (Hypothyroid)

city: Ottawa

first: Martin

last: Paquette

address: 50 Colombine

country: Canada

institute: Health Canada

hyb_protocol: TI and IP samples (5 μg each) were hybridized to Agilent SurePrint G3 Mouse Promoter Microarray, 1x1M (G4875A) at 65 ºC, 20 RPM for 40 hours.

scan_protocol: Slides were scanned on an Agilent Microarray Scanner (G2565CA).

data_processing: The log2 ratio(IP/TI) median probe intensity for each array was subtracted from its median and then divided by the standard deviation. Data for each array were then submitted to Splitter (Shulha et al., 2007) for peak discovery. Splitter uses the extreme right section of the log2 ratio intensity distribution to find binding events. A cut-off median +2.35 standard deviations (98th percentile assuming normal distribution) was selected. From this high log2 ratio distribution section, a peak would be identified if a minimum of two consecutive probes were present at a genomic distance of less than 420 bp.

source_name: Hypothyroid Liver - total input

label_protocol: The Agilent Mammalian ChIP-on-chip protocol (version 10.2, Agilent Technologies, Mississauga, ON, Canada) was used for sample labelling, hybridization, washes and scanning. Briefly, amplified TI and IP DNA samples (2 μg) were labelled with cyanine 3-dUTP and cyanine 5-dUTP respectively, using the Genomic DNA Enzymatic Labelling Kit (Agilent Technologies) as per the manufacturer’s instructions.

growth_protocol: C57BL/6 mice were purchased from Charles River (St. Constant, QC, Canada) and were housed in hanging polycarbonate cages under a 12:12 hr light-dark cycle at 23°C. Animals were provided with shelters, nesting material, food ad libitum (Purina rodent chow 5010; Ralston-Purina, St. Louis, MO, USA) and drinking water containing 1% (wt/vol) sucrose (ad libitum). Mice were acclimated for 10 days.

extract_protocol: Pup livers were rapidly dissected and flash frozen in liquid nitrogen. Total RNA was extracted from liver samples with TRIzol reagent (Invitrogen, Burlington, ON, Canada) followed by RNeasy Mini Kit (Qiagen, Missisauga, ON, Canada) clean-up according to the manufacturer’s instructions. RNA quality assessment was determined by Nanodrop (Thermo Scientific, Billerica, MA, USA) and Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies, Mississauga, ON, Canada). All samples had 260/280 ratios over 2.1, and RNA integrity numbers over 9.0.

treatment_protocol: Females were cohoused for 4 days with sexually mature males and singly housed post-mating. Dams were allowed to litter naturally (day of birth = PND 0) and pup numbers were not adjusted. To produce hypothyroid (hypo) pups, dams were provided with drinking water containing methimizole (MMI, 0.05 % wt/vol) and perchlorate (1 % wt/vol) for three days (PND 12 to 15). Both control and hypo groups received a saline i.p. four hours before decapitation and tissue collection.

tag: background strain

value: liver

tag: antibody

value: none (input)

source_name: Hypothyroid Liver - Immunoprecipitated

value: Anti-TR polyclonal antibody (PA1-213, clone TR -62, Affinity BioReagents, Golden, CO, USA)


title: 300cGy-GCSF6hr-m2 (2666_7848_33878)

tag: strain


title: ChIP sample 1 (Euthyroid)

source_name: Euthyroid Liver - total input

source_name: Euthyroid Liver - Immunoprecipitated


title: 300cGy-LPS6hr-m2 (2666_7848_33879)


title: 0cGy-NOTRT6hr-m2 (2666_7848_33874)


title: 200cGy-GCSF6hr-m2 (2666_7848_33875)


title: 600cGy-LPS24hr-m1 (2666_7848_33870)


title: 300cGy-NOTRT6hr-m2 (2666_7848_33880)


title: 600cGy-NOTRT24hr-m8 (2666_7848_33871)


title: 200cGy-NOTRT6hr-m2 (2666_7848_33877)


title: 0cGy-GCSF6hr-m2 (2666_7848_33872)


title: 300cGy-NOTRT24hr-m1 (2666_7848_33868)


title: ChIP sample 2 (Hypothyroid)


title: 300cGy-GCSF24hr-m1 (2666_7848_33866)


title: 200cGy-LPS6hr-m2 (2666_7848_33876)


title: 0cGy-LPS6hr-m2 (2666_7848_33873)


title: 200cGy-NOTRT24hr-m1 (2666_7848_33865)


title: 200cGy-LPS24hr-m1 (2666_7848_33864)


title: 0cGy-GCSF24hr-m1 (2666_7848_33860)


title: 0cGy-NOTRT24hr-m1 (2666_7848_33862)


title: 200cGy-NOTRT6hr-m1 (2666_7848_33853)


title: 300cGy-GCSF6hr-m1 (2666_7848_33854)


title: 300cGy-LPS24hr-m1 (2666_7848_33867)


title: 200cGy-GCSF24hr-m1 (2666_7848_33863)


title: 600cGy-NOTRT6hr-m1 (2666_7848_33859)


title: 0cGy-LPS24hr-m1 (2666_7848_33861)


title: 600cGy-LPS6hr-m1 (2666_7848_33858)


title: 600cGy-GCSF24hr-m1 (2666_7848_33869)


title: 600cGy-GCSF6hr-m1 (2666_7848_33857)


title: 300cGy-LPS6hr-m1 (2666_7848_33855)


title: 300cGy-NOTRT6hr-m1 (2666_7848_33856)


title: 0cGy-LPS6hr-m1 (2666_7848_33849)


title: 0cGy-GCSF6hr-m1 (2666_7848_33848)


title: 0cGy-NOTRT6hr-m1 (2666_7848_33850)


title: 200cGy-GCSF6hr-m1 (2666_7848_33851)


title: 200cGy-LPS6hr-m1 (2666_7848_33852)


title: 600cGy-NOTRT24hr-m1 (2666_7848_33847)


title: 300cGy-NOTRT24hr-m1 (2666_7848_33844)


title: 600cGy-GCSF24hr-m1 (2666_7848_33845)


title: 300cGy-GCSF24hr-m1 (2666_7848_33842)


title: 600cGy-LPS24hr-m1 (2666_7848_33846)


title: 300cGy-LPS24hr-m1 (2666_7848_33843)


title: 200cGy-NOTRT24hr-m1 (2666_7848_33841)


title: 200cGy-LPS24hr-m1 (2666_7848_33840)


title: 200cGy-GCSF24hr-m1 (2666_7848_33839)


title: 0cGy-LPS24hr-m1 (2666_7848_33837)


title: 0cGy-GCSF24hr-m1 (2666_7848_33836)


title: 300cGy-NOTRT6hr-m1 (2666_7848_33832)


title: 0cGy-NOTRT24hr-m1 (2666_7848_33838)


title: 0cGy-NOTRT6hr-m1 (2666_7848_33826)


title: 200cGy-GCSF6hr-m1 (2666_7848_33827)


title: 1050cGy-168hr-m19 (2665_8455_34988)

source_name: 1050cGy,168hr,no treatment

value: unknown


title: 200cGy-LPS6hr-m1 (2666_7848_33828)


title: 600cGy-LPS6hr-m1 (2666_7848_33834)


title: 300cGy-LPS6hr-m1 (2666_7848_33831)


title: 300cGy-GCSF6hr-m1 (2666_7848_33830)


title: 0cGy-GCSF6hr-m1 (2666_7848_33825)


title: 600cGy-GCSF6hr-m1 (2666_7848_33833)


title: 600cGy-NOTRT6hr-m1 (2666_7848_33835)


title: 200cGy-NOTRT6hr-m1 (2666_7848_33829)


title: 200cGy-NOTRT24hr-m2 (2666_7848_33889)


title: 800cGy-168hr-m19 (2665_8455_34987)

source_name: 800cGy,168hr,no treatment


title: 100cGy-168hr-m5 (2665_8455_34982)

source_name: 100cGy,168hr,no treatment


title: 100cGy-120hr-m6 (2665_8455_34974)

source_name: 100cGy,120hr,no treatment


title: 300cGy-168hr-m5 (2665_8455_34984)

source_name: 300cGy,168hr,no treatment


title: 0cGy-168hr-m5 (2665_8455_34981)

source_name: 0cGy,168hr,no treatment


title: 1050cGy-72hr-m7 (2665_8455_34972)

source_name: 1050cGy,72hr,no treatment


title: 0cGy-120hr-m5 (2665_8455_34973)

source_name: 0cGy,120hr,no treatment


title: 450cGy-168hr-m5 (2665_8455_34985)

source_name: 450cGy,168hr,no treatment


title: 200cGy-168hr-m5 (2665_8455_34983)

source_name: 200cGy,168hr,no treatment


title: 1050cGy-120hr-m15 (2665_8455_34980)

source_name: 1050cGy,120hr,no treatment


title: 600cGy-168hr-m14 (2665_8455_34986)

source_name: 600cGy,168hr,no treatment


title: 450cGy-120hr-m6 (2665_8455_34977)

source_name: 450cGy,120hr,no treatment


title: 300cGy-120hr-m5 (2665_8455_34976)

source_name: 300cGy,120hr,no treatment


title: 800cGy-72hr-m12 (2665_8455_34971)

source_name: 800cGy,72hr,no treatment


title: 600cGy-120hr-m11 (2665_8455_34978)

source_name: 600cGy,120hr,no treatment


title: 200cGy-120hr-m5 (2665_8455_34975)

source_name: 200cGy,120hr,no treatment


title: 600cGy-72hr-m12 (2665_8455_34970)

source_name: 600cGy,72hr,no treatment


title: 0cGy-72hr-m5 (2665_8455_34965)

source_name: 0cGy,72hr,no treatment


title: 300cGy-72hr-m13 (2665_8455_34968)

source_name: 300cGy,72hr,no treatment


title: 800cGy-48hr-m13 (2665_8455_34963)

source_name: 800cGy,48hr,no treatment


title: 450cGy-48hr-m7 (2665_8455_34961)

source_name: 450cGy,48hr,no treatment


title: 450cGy-72hr-m11 (2665_8455_34969)

source_name: 450cGy,72hr,no treatment


title: 100cGy-72hr-m5 (2665_8455_34966)

source_name: 100cGy,72hr,no treatment


title: 200cGy-72hr-m13 (2665_8455_34967)

source_name: 200cGy,72hr,no treatment


title: 600cGy-48hr-m2 (2665_8455_34962)

source_name: 600cGy,48hr,no treatment


title: 100cGy-48hr-m9 (2665_8455_34958)

source_name: 100cGy,48hr,no treatment


title: 300cGy-48hr-m14 (2665_8455_34960)

source_name: 300cGy,48hr,no treatment


title: 200cGy-48hr-m14 (2665_8455_34959)

source_name: 200cGy,48hr,no treatment


title: 1050cGy-48hr-m13 (2665_8455_34964)

source_name: 1050cGy,48hr,no treatment


title: 0cGy-48hr-m6 (2665_8455_34957)

source_name: 0cGy,48hr,no treatment


title: 1050cGy-24hr-m7 (2665_8455_34956)

source_name: 1050cGy,24hr,no treatment


title: WT 140 mM NaCl Rep 4

city: Berkeley, CA

first: Stavroula

last: Hatzios

address: B84 Hildebrand Hall #1460

institute: UC Berkeley

description: Biological replicate 4 of 4.

hyb_protocol: Slides were prehybridized for at least 1 hour in pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA), washed with water (2 x 1 min washes) and isopropanol (5-10 seconds), and dried with filtered air.  Probe pairs were hybridized to slides in sealed incubation chambers in a 42 °C water bath overnight.  Post-hybridization washes: 2X SSC, 0.1% SDS for 5 min at 42 °C; 0.1X SSC, 0.1% SDS for 10 min at rt; 0.1X SSC for 1 min at rt (4 times); 0.01X SSC for 10 sec at rt.  Slides dried with filtered air.

scan_protocol: Arrays scanned using GenePix 4000B scanner and GenePix 6.0 software.  Channels roughly normalized by adjusting gain during preview scan.

data_processing: Data analyzed with Acuity 4.1 software.  Spots flagged as not found were discarded from the dataset and remaining features were Lowess-normalized.

organism: Mycobacterium tuberculosis

source_name: Wild-type Mtb, 0 mM NaCl for 0 h

label_protocol: Followed standard amino-allyl labeling protocol (TIGR).  Total RNA (5 ug per sample) was reverse-transcribed with Superscript III in the presence of aminoallyl dUTP, purified using a Qiaquick column (Qiagen), and covalently labeled with either Cy5 or Cy3 in sodium carbonate.  Excess dye was removed using a Qiaquick column.  Cy3- and Cy5-labeled cDNA samples were resuspended in hybridization buffer (50% formamide, 5X SSC, and 0.1% SDS).

growth_protocol: Bacteria were grown in 1-L roller bottles in a rolling-bottle incubator at 37 °C.  Cultures were prepared from frozen glycerol stocks and grown to mid-log phase in 7H9 medium.  Bacteria were washed and passaged once in Sauton’s medium, then grown for 2 days to early log phase in 60-mL Sauton's medium.

extract_protocol: Cell pellets were thawed on ice and resuspended in Trizol, disrupted by bead beating, and centrifuged to clarify cell lysates.  Following chloroform extraction with Heavy Phase Lock Gel, the aqueous layer was precipitated using a 50% isopropanol 50% high salt solution (0.8 M sodium citrate, 1.2 M NaCl).  RNA purification and DNAse treatment were performed with the RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Each 60-mL culture was divided into two 30-mL cultures.  One culture (t=0 sample) was centrifuged (10 min, 3500 rpm, rt), and the cell pellet was immediately frozen on dry ice and stored at -80 °C.  The second culture (t=1 h sample) was treated with 140 mM NaCl (~1.5 mL of Sauton’s medium containing 3 M NaCl) to increase the culture osmolarity by  ~280 mOsm/L and incubated for 1 h at 37 °C prior to harvesting and freezing the cells as before.

value: 0 mM NaCl for 0 h

source_name: Wild-type Mtb, 140 mM NaCl for 1 h

value: 140 mM NaCl for 1 h


title: WT 140 mM NaCl Rep 3

description: Biological replicate 3 of 4.


title: WT 140 mM NaCl Rep 2

description: Biological replicate 2 of 4.


title: 800cGy-24hr-m10 (2665_8455_34955)

source_name: 800cGy,24hr,no treatment


title: WT 140 mM NaCl Rep 1

description: Biological replicate 1 of 4.


title: 200cGy-24hr-m5 (2665_8455_34951)

source_name: 200cGy,24hr,no treatment


title: 300cGy-24hr-m5 (2665_8455_34952)

source_name: 300cGy,24hr,no treatment


title: 100cGy-24hr-m5 (2665_8455_34950)

source_name: 100cGy,24hr,no treatment


title: 450cGy-24hr-m5 (2665_8455_34953)

source_name: 450cGy,24hr,no treatment


title: 600cGy-6hr-m5 (2665_8455_34946)

source_name: 600cGy,6hr,no treatment


title: 0cGy-24hr-m5 (2665_8455_34949)

source_name: 0cGy,24hr,no treatment


title: 1050cGy-6hr-m5 (2665_8455_34948)

source_name: 1050cGy,6hr,no treatment


title: 450cGy-6hr-m5 (2665_8455_34945)

source_name: 450cGy,6hr,no treatment


title: 100cGy-6hr-m5 (2665_8455_34942)

source_name: 100cGy,6hr,no treatment


title: 300cGy-6hr-m5 (2665_8455_34944)

source_name: 300cGy,6hr,no treatment


title: 600cGy-24hr-m5 (2665_8455_34954)

source_name: 600cGy,24hr,no treatment


title: 1050cGy-168hr-m2 (2665_8454_34940)

source_name: 1050cGy,168hr,no treatment


title: 800cGy-6hr-m5 (2665_8455_34947)

source_name: 800cGy,6hr,no treatment


title: 200cGy-6hr-m5 (2665_8455_34943)

source_name: 200cGy,6hr,no treatment


title: WNV10-01

type: other

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

description:
Japanese encephalitis virus; Dengue virus types 1; 2; 4
Data used in Table 1

hyb_protocol: Hybridization was performed in-house at SSI, Denmark, according to manufacturer’s protocol (Gene expression analysis, Roche NimbleGen). Briefly, 8 µg of labelled DNA was used for hybridization. Hybridization was performed in a NimbleGen Hybridization system using the NimbleGen Hybridization kit (Roche NimbleGen).

scan_protocol: Microarrays were scanned in-house at SSI, Denmark using a MS 200 Scanner (Roche, Nimblegen)

data_processing: Data was analyzed using NimbleScan software and custom software developed at Lawrence Livermore National Laboratory, CA, USA and described in 'Gardner et al. A Micobial Detection Array (MDA) for Viral and Bacterial Detection. BMC Genomics 2010 Nov 25;11:668'. Additional stringency criteria were applied to exclude bacterial sequences and viruses having fewer than 20% of probes detected out of those expected. Probes were classified as detected if the intensity exceeded a threshold equal to the 99th percentile of intensities for negative control probes, except for the ORF+ skin lesion sample that was analyzed using the 95th percentile.

molecule: other

organism: Dengue virus

label_protocol: Labelling was performed in-house at SSI, Denmark, according to manufacturer’s protocol (Gene expression analysis, Roche NimbleGen). Briefly, 1 µg of heat-denatured WTA-amplified sample was labelled using nick translation with Cy3- or Cy5-labeled random nonamer primers and Klenow fragment (exo-) (NEB) at 37 ºC for 2 hours. Labelled DNA was iso-propanol precipitated and the pellet washed, dried, reconstituted and quantitated.

extract_protocol: Two-hundred and thirty microliters of sample was centrifuged at 17,000 g for 10 minutes. The supernatant was filtered through a 0.22 µm Ultrafree MC spin filter (Costar) at 2000 g for 2 minutes and DNase treated (5 U DNaseI (Invitrogen or New England Biolabs) for 30-1½ hours at room temperature (urine and CSF samples were considered free of genomic DNA and hence not DNAse treated). The viral nucleic acid (NA) was extracted using the PureLink Viral RNA/DNA kit (Invitrogen), without the addition of carrier RNA. The extracted viral NA was eluted with 30 µl DNase/RNase-free sterile water, and stored at -20 ºC or immediately used. Virus-positive supernatants suspended in RNA-extraction reagent were purified according to manufacturer (TRIzol, Life Technologies; TriFast, Peqlab; AVL buffer, Qiagen). The resulting RNA was further purified using QIAamp RNA viral Mini kit (Qiagen). The Extracted viral NA was eluted with 30µl DNase/RNase-free sterile water, and stored at -20 ºC or immediately used. To be able to amplify both DNA virus and RNA virus samples with the same protocol, we used the described Whole Transcriptome Amplification (WTA) method (Berthet et al. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Molecular Biology 2008, 9:77) by using the QuantiTect WTA kit (Qiagen) according to manufacturer’s protocol, except for the reverse transcription step that was replaced by the Superscript III Reverse Transcription kit (Invitrogen) combined with 5´-phosphorylated random hexamers (P-N6)(Eurofines MWG Operon). The WTA protocol includes 3 sequential reactions: firstly a reverse transcription reaction to generate cDNA, secondly a ligation of generated cDNA into larger transcriptomes and thirdly a Repli-g amplification of the generated transcriptomes. Neither of the two first reactions (cDNA synthesis and ligation) had any adverse effects when performed on a DNA-virus. Briefly, 11 µl of extracted viral NA was put into a 20 µl RT reaction and incubated at 42 ºC for 1 hour. The Superscript enzyme was inactivated at 95 ºC for 5 minutes, 10 µl of the cDNA reaction was added to 10 µl of ligation mix and incubated at 22 ºC for 2 hours. Thirty microliters of amplification mix containing Phi29 polymerase and random primers was then added and amplification performed at 30 ºC for 2-8 hours. The reaction was terminated by incubation at 95 ºC for 5 minutes. Amplified material was purified using QIAamp DNA mini kit (Qiagen) using a modified protocol (www.qiagen.com), and checked for purity and concentration using a NanoDrop spectrophotometer (Thermo Scientific) and agarose gel electrophoresis. The DNA was then stored at -80 ºC or immediately used for microarray analysis.

tag: isolation source

value: sample WNV10-01 from QCMD EQA panel


title: 800cGy-168hr-m13 (2665_8454_34939)

source_name: 800cGy,168hr,no treatment


title: WNV-4-clinical

description: Data used in Table 2

organism: West Nile virus

value: urine


title: WNV-3-clinical

description: Data used in Table 2


title: WNV10-07

description:
Tick-borne encephalitis virus; Dengue virus type 3; Yellow fever virus
Data used in Table 1

organism: Yellow fever virus

value: sample WNV10-07 from QCMD EQA panel


title: 600cGy-168hr-m22 (2665_8454_34938)

source_name: 600cGy,168hr,no treatment


title: WNV-6-clinical

description: Data used in Table 1


title: 450cGy-168hr-m4 (2665_8454_34937)

source_name: 450cGy,168hr,no treatment


title: 0cGy-6hr-m5 (2665_8455_34941)

source_name: 0cGy,6hr,no treatment


title: 300cGy-168hr-m4 (2665_8454_34936)

source_name: 300cGy,168hr,no treatment


title: 200cGy-168hr-m4 (2665_8454_34935)

source_name: 200cGy,168hr,no treatment


title: WNV-5-clinical

description: Data used in Table 2


title: WNV-1-clinical

description: Data used in Table 2


title: WNV-2-clinical

description: Data used in Table 2


title: SinNombre

description: Data used in Table 1

organism: Orthohantavirus sinnombreense

source_name: SinNombre

value: cell culture supernatant


title: 100cGy-168hr-m4 (2665_8454_34934)

source_name: 100cGy,168hr,no treatment


title: WNV

description: Data used in Table 2

source_name: WNV

value: purified RNA


title: Toscana-clinical

description: Data used in Table 1

organism: Toscana virus

source_name: Toscana-clinical

value: cerebrospinal fluid


title: Toscana

description: Data used in Table 2

source_name: Toscana


title: Usutu

description: Data used in Table 1

organism: Usutu virus

source_name: Usutu


title: 800cGy-120hr-m15 (2665_8454_34931)

source_name: 800cGy,120hr,no treatment

value: no treatment

value: peripheral blood


title: 1050cGy-120hr-m16 (2665_8454_34932)

source_name: 1050cGy,120hr,no treatment

value: ionizing radiation


title: 0cGy-168hr-m4 (2665_8454_34933)

source_name: 0cGy,168hr,no treatment

value: control (no ionizing radiation)


title: 600cGy-120hr-m16 (2665_8454_34930)

source_name: 600cGy,120hr,no treatment


title: hog1∆ contrl replicate2

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

hyb_protocol: 325ng of Cy3 labeled cRNA were hybridized to the custom C. glabrata GE 8x15K arrays (Agilent eArray Design 017617; GPL10713). Samples were hybridized for 17 hours at 65°C, 10rpm.

scan_protocol: Agilent G2505C Microarray Scanner System was used to scan the arrays.

data_processing: The Agilent Feature Extraction program (Version FE 10.5.1.1) was used to analyze the array images. Quantile Normalization according to Bioconductor

organism: Nakaseomyces glabratus

source_name: hog1∆ contrl

label_protocol: 1 µg of total RNA was used for labeling reaction (Agilent Quick Amp Labeling Kit, two-color, Cat.Nr. 5190-0444). The standard Agilent Protocol for one-color labeling was used (G4140-90041).

growth_protocol: BG14 and BG14hog1∆ cells were grown in rich medium in batch culture at 30°C for 4 generations to OD600nm of about 1.

extract_protocol: Frozen cells were broken using glassbeads. The total RNA was isolated via phenol-chloroform extraction and Ethanol precipitation.

treatment_protocol: The culture was split. For weak acid stress, potassium sorbate was added to a final concetration of 20mM. After 20 minutes incubation cells were harvested and frozen. Untreated references were harvested  and frozen.

tag: genotype

value: control


title: 800cGy-120hr-m17 (2665_8455_34979)


title: 300cGy-120hr-m4 (2665_8454_34928)

source_name: 300cGy,120hr,no treatment


title: hog1∆ 20'stress replicate2

source_name: hog1∆ 20'stress

value: sorbic acid


title: WT cntrl replicate2

source_name: WT cntrl


title: WT cntrl replicate3


title: WT 20'stress replicate2

source_name: WT 20'stress


title: Sicilian

description: Data used in Table 1

organism: sandfly fever Sicilian virus

source_name: Sicilian


title: WT 20'stress replicate3


title: 1050cGy-72hr-m4 (2665_8454_34924)

source_name: 1050cGy,72hr,no treatment


title: 0cGy-120hr-m4 (2665_8454_34925)

source_name: 0cGy,120hr,no treatment


title: hog1∆ 20'stress replicate3


title: 200cGy-120hr-m4 (2665_8454_34927)

source_name: 200cGy,120hr,no treatment


title: RVF-3

description: Data used in Table 3

organism: Rift Valley fever virus


title: RVF-4

description: Data used in Table 1


title: hog1∆ contrl replicate1


title: 450cGy-120hr-m4 (2665_8454_34929)

source_name: 450cGy,120hr,no treatment


title: 800cGy-72hr-m14 (2665_8454_34923)

source_name: 800cGy,72hr,no treatment


title: RVF-2

description: Data used in Table 3


title: Seoul

description: Data used in Table 1

organism: Orthohantavirus seoulense

source_name: Seoul


title: 600cGy-72hr-m3 (2665_8454_34922)

source_name: 600cGy,72hr,no treatment


title: 100cGy-120hr-m4 (2665_8454_34926)

source_name: 100cGy,120hr,no treatment


title: hog1∆ 20'stress replicate1


title: WT 20'stress replicate1


title: WT cntrl replicate1


title: 450cGy-72hr-m13 (2665_8454_34921)

source_name: 450cGy,72hr,no treatment


title: 300cGy-72hr-m12 (2665_8454_34920)

source_name: 300cGy,72hr,no treatment


title: 1050cGy-48hr-m12 (2665_8454_34916)

source_name: 1050cGy,48hr,no treatment


title: 300cGy-48hr-m13 (2665_8454_34912)

source_name: 300cGy,48hr,no treatment


title: 200cGy-72hr-m12 (2665_8454_34919)

source_name: 200cGy,72hr,no treatment


title: Orf-clinical

description: Data used in Table 2

organism: Orf virus

source_name: Orf-clinical

value: skin lesion


title: 100cGy-48hr-m7 (2665_8454_34910)

source_name: 100cGy,48hr,no treatment


title: 450cGy-48hr-m5 (2665_8454_34913)

source_name: 450cGy,48hr,no treatment


title: 0cGy-72hr-m4 (2665_8454_34917)

source_name: 0cGy,72hr,no treatment


title: 800cGy-48hr-m12 (2665_8454_34915)

source_name: 800cGy,48hr,no treatment


title: 200cGy-48hr-m13 (2665_8454_34911)

source_name: 200cGy,48hr,no treatment


title: 600cGy-48hr-m5 (2665_8454_34914)

source_name: 600cGy,48hr,no treatment


title: 100cGy-72hr-m4 (2665_8454_34918)

source_name: 100cGy,72hr,no treatment


title: RVF

description: Data used in Table 3

source_name: RVF


title: 1050cGy-24hr-m6 (2665_8454_34908)

source_name: 1050cGy,24hr,no treatment


title: Naples

description: Data used in Table 1

organism: Sandfly fever Naples virus

source_name: Naples


title: NegControlCSF

description: Data used in Table 2

organism: synthetic construct

source_name: NegControlCSF


title: 600cGy-24hr-m4 (2665_8454_34906)

organism: Mus musculus

source_name: 600cGy,24hr,no treatment


title: 0cGy-48hr-m5 (2665_8454_34909)

source_name: 0cGy,48hr,no treatment


title: NegControlUrine

description: Data used in Table 2

source_name: NegControlUrine


title: 450cGy-24hr-m4 (2665_8454_34905)

source_name: 450cGy,24hr,no treatment


title: Monkeypox

description: Data used in Table 1

organism: Monkeypox virus

source_name: Monkeypox

value: purified DNA


title: 300cGy-24hr-m4 (2665_8454_34904)

source_name: 300cGy,24hr,no treatment

value: unknown


title: 800cGy-24hr-m4 (2665_8454_34907)

source_name: 800cGy,24hr,no treatment


title: NegControlSerum

description: Data used in Table 2

source_name: NegControlSerum

value: serum


title: Puumala

description: Data used in Table 1

organism: Orthohantavirus puumalaense

source_name: Puumala


title: Marburg

description: Data used in Table 1

organism: Marburgvirus

source_name: Marburg


title: Polio

description: Data used in Table 1

organism: Human poliovirus sp.

source_name: Polio


title: Lassa

description: Data used in Table 1

organism: Mammarenavirus lassaense

source_name: Lassa


title: HCV-4

description: Data used in Table 3

organism: Hepacivirus hominis


title: HCV-3

description: Data used in Table 3


title: HCV-2

description: Data used in Table 3


title: Dobrava

description: Data used in Table 1

organism: Orthohantavirus dobravaense

source_name: Dobrava


title: Hantaan

description: Data used in Table 1

organism: Orthohantavirus hantanense

source_name: Hantaan


title: 0cGy-24hr-m4 (2665_8454_34901)

source_name: 0cGy,24hr,no treatment


title: 1050cGy-6hr-m4 (2665_8454_34900)

source_name: 1050cGy,6hr,no treatment


title: 600cGy-6hr-m4 (2665_8454_34898)

source_name: 600cGy,6hr,no treatment


title: 300cGy-6hr-m4 (2665_8454_34896)

source_name: 300cGy,6hr,no treatment


title: EEE

description: Data used in Table 1

organism: Eastern equine encephalitis virus

source_name: EEE


title: 800cGy-6hr-m4 (2665_8454_34899)

source_name: 800cGy,6hr,no treatment


title: 100cGy-6hr-m4 (2665_8454_34894)

source_name: 100cGy,6hr,no treatment


title: Dengue2-clinical2

description: Data used in Table 2

organism: dengue virus type 2


title: 200cGy-24hr-m4 (2665_8454_34903)

source_name: 200cGy,24hr,no treatment


title: Ebola

description: Data used in Table 1

organism: Zaire ebolavirus

source_name: Ebola


title: 100cGy-24hr-m4 (2665_8454_34902)

source_name: 100cGy,24hr,no treatment


title: CCHF

description: Data used in Table 1

organism: Orthonairovirus haemorrhagiae

source_name: CCHF


title: Chikungunya-clinical

description: Data used in Table 2

organism: Chikungunya virus

source_name: Chikungunya-clinical


title: 450cGy-6hr-m4 (2665_8454_34897)

source_name: 450cGy,6hr,no treatment


title: Cowpox

description: Data used in Table 1

organism: Cowpox virus

source_name: Cowpox


title: Dengue2-clinical1

description: Data used in Table 2


title: 200cGy-6hr-m4 (2665_8454_34895)

source_name: 200cGy,6hr,no treatment


title: 0cGy-6hr-m4 (2665_8454_34893)

source_name: 0cGy,6hr,no treatment


title: CCHF-Sam3-clinical

description: Data used in Table 2


title: spinal cord, injured, 3 days, rep3

city: Toronto

first: Mahmood

last: Chamankhah

state: Ontario

address: 399 Bathurst Street

institute: University Health Network

description: Gene expression data from injured spinal cord, epicenter

hyb_protocol: 2 ug of the fragmented and labeled cDNA was used for hybridization onto the Rat 230 2.0 GeneChip array according to Affymetrix GeneChip WT Terminal Labeling and Hybridization Kit.

scan_protocol: GeneChips were scanned using the GeneArray Scanner

data_processing: Data analysis was performed in R with the Affy package (v1.12.2) in BioConductor. Data were investigated for spatial and distributional homogeneity. Normalization was performed with the sequence-specific GCRMA algorithm (package v2.6.0) in BioConductor. Significance testing of this dataset was performed using linear models and pair-wise comparisons. Annotations derived from Affymetrix annotion build na32.

label: Biotin-11-dXTP Analog (DLR)

organism: Rattus norvegicus

source_name: T7 spinal cord epicenter, 3 days post-injury

label_protocol: 2nd cycle cDNAs were prepared according to the standard Ambion WT Expression Kit protocol from 0.5 ug total RNA. Fragmentation and DLR labeling of the cDNA was performed using Affymetrix GeneChip WT Terminal Labeling and Hybridization Kit.

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

treatment_protocol: Female Wistar rats underwent a T6-T8 laminectomy and then received a 35 g clip (Walsh) moderate to severe aneurysm clip impact-compression injury at T7 for 1 min.

value: Wistar

value: spinal cord


title: spinal cord, injured, 3 days, rep4


title: 1050cGy-168hr-m13 (2665_8453_34892)

source_name: 1050cGy,168hr,no treatment


title: 600cGy-168hr-m20 (2665_8453_34890)

source_name: 600cGy,168hr,no treatment


title: spinal cord, injured, 3 days, rep1


title: 800cGy-168hr-m14 (2665_8453_34891)

source_name: 800cGy,168hr,no treatment


title: spinal cord, injured, 3 days, rep2


title: spinal cord, injured, 1 day, rep4

source_name: T7 spinal cord epicenter, 1 day post-injury


title: spinal cord, injured, 1 day, rep3


title: 800cGy-120hr-m9 (2665_8453_34883)

source_name: 800cGy,120hr,no treatment


title: spinal cord, injured, 1 day, rep1


title: 1050cGy-120hr-m2 (2665_8453_34884)

source_name: 1050cGy,120hr,no treatment


title: spinal cord, injured, 1 week, rep1

source_name: T7 spinal cord epicenter, 1 week post-injury


title: 450cGy-168hr-m3 (2665_8453_34889)

source_name: 450cGy,168hr,no treatment


title: 300cGy-168hr-m3 (2665_8453_34888)

source_name: 300cGy,168hr,no treatment


title: 100cGy-168hr-m3 (2665_8453_34886)

source_name: 100cGy,168hr,no treatment


title: spinal cord, injured, 1 day, rep2


title: 200cGy-168hr-m3 (2665_8453_34887)

source_name: 200cGy,168hr,no treatment


title: spinal cord, injured, 1 week, rep2


title: 0cGy-168hr-m3 (2665_8453_34885)

source_name: 0cGy,168hr,no treatment


title: 200cGy-120hr-m3 (2665_8453_34879)

source_name: 200cGy,120hr,no treatment


title: spinal cord, injured, 2 weeks, rep2

source_name: T7 spinal cord epicenter, 2 weeks post-injury


title: spinal cord, injured, 2 weeks, rep1


title: 300cGy-120hr-m3 (2665_8453_34880)

source_name: 300cGy,120hr,no treatment


title: spinal cord, sham, rep4

source_name: T7 spinal cord epicenter, sham


title: 450cGy-120hr-m3 (2665_8453_34881)

source_name: 450cGy,120hr,no treatment


title: 100cGy-120hr-m3 (2665_8453_34878)

source_name: 100cGy,120hr,no treatment


title: 600cGy-120hr-m14 (2665_8453_34882)

source_name: 600cGy,120hr,no treatment


title: spinal cord, sham, rep2


title: spinal cord, injured, 2 weeks, rep3


title: spinal cord, injured, 1 week, rep3


title: 0cGy-120hr-m3 (2665_8453_34877)

source_name: 0cGy,120hr,no treatment


title: spinal cord, injured, 1 week, rep4


title: spinal cord, injured, 2 weeks, rep4


title: spinal cord, sham, rep1


title: 300cGy-72hr-m11 (2665_8453_34872)

source_name: 300cGy,72hr,no treatment


title: spinal cord, injured, 8 weeks, rep4

source_name: T7 spinal cord epicenter, 8 weeks post-injury


title: spinal cord, sham, rep3


title: 1050cGy-168hr-m13 (2665_8453_34892r)

source_name: 1050cGy,168hr,no treatment


title: 1050cGy-48hr-m11 (2665_8453_34868)

source_name: 1050cGy,48hr,no treatment


title: spinal cord, injured, 8 weeks, rep1


title: spinal cord, injured, 8 weeks, rep3


title: 450cGy-72hr-m6 (2665_8453_34873)

source_name: 450cGy,72hr,no treatment


title: 800cGy-48hr-m11 (2665_8453_34867)

source_name: 800cGy,48hr,no treatment


title: 100cGy-72hr-m3 (2665_8453_34870)

source_name: 100cGy,72hr,no treatment


title: 0cGy-72hr-m3 (2665_8453_34869)

source_name: 0cGy,72hr,no treatment


title: AA female RBP - Case 08

city: Rochester

first: Timothy

middle: B.

last: Niewold

state: MN

address: 200 1st St. SW

department: Division of Rheumatology and Department of Immunology

institute: Mayo Clinic

description: AA RBP - Cases

hyb_protocol: 2.5 ug of the fragmented and labeled cDNA was hybridized to Human Gene 1.0 ST array for 16 h at 45°C and 60 rpm in Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin, in Affymetrix Fluidics Station 450 using GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual V.4 (Affymetrix, Inc).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by Gene Chip Operating Software v. 1.4 (MicroArray Suite 5.0).

data_processing: The data (CEL files) were analyzed with Affymetrix Expression Console and normalized using RMA Sketch Quantile normalization

organism: Homo sapiens

source_name: subject blood

label_protocol: 250 ng of total RNA was used to generate sense strand cDNA with Ambion WT Expression Kit (Life Technology, Inc).  The cDNA was fragmented and biotin labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix, Inc).

extract_protocol: Whole blood from the subjects was collected in PAX gene tubes (Qiagen), and RNA was purified in spin columns per manufacture recommendations.

value: whole blood

value: female

tag: ancestry

value: African

tag: subject type

value: Subject RBP -

tag: age


title: 600cGy-48hr-m4 (2665_8453_34866)

organism: Mus musculus

source_name: 600cGy,48hr,no treatment

tag: tissue


title: AA female RBP - Case 07

description: AA RBP - Cases


title: 800cGy-72hr-m5 (2665_8453_34875)

source_name: 800cGy,72hr,no treatment


title: 300cGy-48hr-m12 (2665_8453_34864r)

source_name: 300cGy,48hr,no treatment


title: AA female RBP - Case 04

description: AA RBP - Cases


title: 300cGy-48hr-m12 (2665_8453_34864)


title: AA female RBP - Case 06

description: AA RBP - Cases


title: spinal cord, injured, 8 weeks, rep2


title: 450cGy-48hr-m4 (2665_8453_34865)

source_name: 450cGy,48hr,no treatment


title: AA female RBP - Case 05

description: AA RBP - Cases


title: 200cGy-48hr-m12 (2665_8453_34863)

source_name: 200cGy,48hr,no treatment


title: AA female RBP - Case 02

description: AA RBP - Cases


title: 200cGy-72hr-m11 (2665_8453_34871)

source_name: 200cGy,72hr,no treatment


title: AA female RBP - Case 03

description: AA RBP - Cases


title: 800cGy-24hr-m3 (2665_8453_34859)

source_name: 800cGy,24hr,no treatment


title: AA female RBP + Case 08

description: AA RBP + Cases

value: Subject RBP +


title: AA female RBP + Case 09

description: AA RBP + Cases


title: 0cGy-48hr-m3 (2665_8453_34861)

source_name: 0cGy,48hr,no treatment

value: no treatment


title: AA female RBP - Case 01

description: AA RBP - Cases


title: 100cGy-48hr-m6 (2665_8453_34862)

source_name: 100cGy,48hr,no treatment

value: peripheral blood


title: 200cGy-24hr-m3 (2665_8453_34855)

source_name: 200cGy,24hr,no treatment

value: ionizing radiation


title: 100cGy-24hr-m3 (2665_8453_34854)

source_name: 100cGy,24hr,no treatment


title: 450cGy-24hr-m3 (2665_8453_34857)

source_name: 450cGy,24hr,no treatment


title: AA female RBP + Case 05

description: AA RBP + Cases


title: 1050cGy-24hr-m5 (2665_8453_34860)

source_name: 1050cGy,24hr,no treatment


title: 300cGy-24hr-m3 (2665_8453_34856)

source_name: 300cGy,24hr,no treatment


title: AA female RBP + Case 06

description: AA RBP + Cases


title: AA female RBP + Case 07

description: AA RBP + Cases


title: AA female RBP + Case 03

description: AA RBP + Cases


title: AA female RBP + Case 04

description: AA RBP + Cases


title: 600cGy-24hr-m3 (2665_8453_34858)

source_name: 600cGy,24hr,no treatment


title: AA female RBP + Case 02

description: AA RBP + Cases


title: 0cGy-24hr-m3 (2665_8453_34853)

source_name: 0cGy,24hr,no treatment

value: control (no ionizing radiation)


title: 800cGy-6hr-m3 (2665_8453_34851)

source_name: 800cGy,6hr,no treatment


title: 1050cGy-6hr-m3 (2665_8453_34852)

source_name: 1050cGy,6hr,no treatment


title: AA female RBP + Case 01

description: AA RBP + Cases

source_name: subject blood


title: 200cGy-6hr-m3 (2665_8453_34847)

source_name: 200cGy,6hr,no treatment


title: EA female RBP - Case 06

description: EA RBP - Cases

value: European


title: EA female RBP - Case 04

description: EA RBP - Cases


title: 1050cGy-72hr-m2 (2665_8453_34876)

source_name: 1050cGy,72hr,no treatment


title: EA female RBP - Case 07

description: EA RBP - Cases


title: 600cGy-6hr-m3 (2665_8453_34850)

source_name: 600cGy,6hr,no treatment


title: 300cGy-6hr-m3 (2665_8453_34848)

source_name: 300cGy,6hr,no treatment


title: EA female RBP - Case 05

description: EA RBP - Cases


title: EA female RBP - Case 08

description: EA RBP - Cases


title: 0cGy-6hr-m3 (2665_8453_34845)

source_name: 0cGy,6hr,no treatment


title: EA female RBP - Case 03

description: EA RBP - Cases


title: EA female RBP - Case 01

description: EA RBP - Cases


title: EA female RBP + Case 07

description: EA RBP + Cases


title: 300cGy-168hr-m2 (2665_8452_34840)

source_name: 300cGy,168hr,no treatment


title: 100cGy-6hr-m3 (2665_8453_34846)

source_name: 100cGy,6hr,no treatment


title: 600cGy-168hr-m15 (2665_8452_34842)

source_name: 600cGy,168hr,no treatment


title: EA female RBP + Case 06

description: EA RBP + Cases


title: EA female RBP + Case 08

description: EA RBP + Cases


title: 1050cGy-168hr-m14 (2665_8452_34844)

source_name: 1050cGy,168hr,no treatment


title: 450cGy-6hr-m3 (2665_8453_34849)

source_name: 450cGy,6hr,no treatment


title: 800cGy-168hr-m17 (2665_8452_34843)

source_name: 800cGy,168hr,no treatment


title: EA female RBP - Case 02

description: EA RBP - Cases


title: 200cGy-168hr-m2 (2665_8452_34839)

source_name: 200cGy,168hr,no treatment


title: EA female RBP + Case 03

description: EA RBP + Cases


title: 450cGy-168hr-m2 (2665_8452_34841)

source_name: 450cGy,168hr,no treatment


title: 0cGy-168hr-m2 (2665_8452_34837)

source_name: 0cGy,168hr,no treatment


title: 100cGy-168hr-m2 (2665_8452_34838)

source_name: 100cGy,168hr,no treatment


title: EA female RBP + Case 01

description: EA RBP + Cases


title: EA female RBP + Case 02

description: EA RBP + Cases


title: EA female RBP + Case 04

description: EA RBP + Cases


title: 600cGy-120hr-m13 (2665_8452_34834)

source_name: 600cGy,120hr,no treatment


title: EA female RBP + Case 05

description: EA RBP + Cases

source_name: subject blood


title: 800cGy-120hr-m6 (2665_8452_34835)

source_name: 800cGy,120hr,no treatment


title: 1050cGy-120hr-m10 (2665_8452_34836)

source_name: 1050cGy,120hr,no treatment


title: AA female Control 8

description: AA Controls

value: Control


title: 450cGy-120hr-m2 (2665_8452_34833)

source_name: 450cGy,120hr,no treatment


title: AA female Control 7

description: AA Controls


title: 600cGy-72hr-m14 (2665_8453_34874)

source_name: 600cGy,72hr,no treatment


title: AA female Control 4

description: AA Controls


title: AA female Control 3

description: AA Controls


title: AA female Control 6

description: AA Controls


title: 100cGy-120hr-m2 (2665_8452_34830)

source_name: 100cGy,120hr,no treatment


title: AA female Control 2

description: AA Controls


title: 1050cGy-72hr-m8 (2665_8452_34828)

source_name: 1050cGy,72hr,no treatment


title: 800cGy-72hr-m13 (2665_8452_34827)

source_name: 800cGy,72hr,no treatment


title: AA female Control 1

description: AA Controls


title: 300cGy-120hr-m2 (2665_8452_34832)

source_name: 300cGy,120hr,no treatment


title: 200cGy-120hr-m2 (2665_8452_34831)

source_name: 200cGy,120hr,no treatment


title: 600cGy-72hr-m13 (2665_8452_34826)


title: EA female Control 8

description: EA Controls


title: AA female Control 5

description: AA Controls


title: 450cGy-72hr-m1 (2665_8452_34825)

source_name: 450cGy,72hr,no treatment


title: 200cGy-72hr-m10 (2665_8452_34823)

source_name: 200cGy,72hr,no treatment


title: EA female Control 4

description: EA Controls


title: EA female Control 3

description: EA Controls


title: 0cGy-72hr-m2 (2665_8452_34821)

source_name: 0cGy,72hr,no treatment


title: EA female Control 6

description: EA Controls


title: 100cGy-72hr-m2 (2665_8452_34822)

source_name: 100cGy,72hr,no treatment


title: 0cGy-120hr-m2 (2665_8452_34829)

source_name: 0cGy,120hr,no treatment


title: 1050cGy-48hr-m5 (2665_8452_34820)

source_name: 1050cGy,48hr,no treatment


title: 300cGy-72hr-m6 (2665_8452_34824)

source_name: 300cGy,72hr,no treatment


title: EA female Control 5

description: EA Controls

source_name: subject blood


title: EA female Control 1

description: EA Controls


title: 600cGy-48hr-m6 (2665_8452_34818)

source_name: 600cGy,48hr,no treatment


title: EA female Control 7

description: EA Controls


title: 800cGy-48hr-m1 (2665_8452_34819)

source_name: 800cGy,48hr,no treatment


title: EA female Control 2

description: EA Controls


title: PRAX study [gene-level] 160 186

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

description: Healthy Human platelets

hyb_protocol: Hybridization was performed at 45℃ for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were analyzed using Affymetrix Powertools (APT) using rma method (the command line option was -a rma-sketch) .

source_name: leukocyte-depleted platelets

label_protocol: Three hundred ng of total RNA was processed for cRNA synthesis, fragmentation, and terminal labeling with the GeneChip Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix).

extract_protocol: Total RNA was extracted with TRIzol® (Life Technologies, Carlsbad, CA)

treatment_protocol: Leukocyte depleted platelets (LDP) RNA were prepared by density centrifugation and immune-depletion of CD45+ cells as previously described, yielding less than 1 leukocyte per 5 million platelets.

tag: ethnicity

value: african american

tag: par4 agonist response score

tag: cell type

value: leukocyte-depleted platelets


title: PRAX study [gene-level] 163 189

description: Healthy Human platelets


title: PRAX study [gene-level] 159 185

description: Healthy Human platelets


title: PRAX study [gene-level] 161 187

description: Healthy Human platelets


title: 450cGy-48hr-m3 (2665_8452_34817)

source_name: 450cGy,48hr,no treatment

tag: gender

value: unknown


title: 100cGy-48hr-m2 (2665_8452_34814)

source_name: 100cGy,48hr,no treatment

tag: stress


title: PRAX study [gene-level] 158 184

description: Healthy Human platelets

value: caucasian


title: 0cGy-48hr-m2 (2665_8452_34813)

source_name: 0cGy,48hr,no treatment

tag: dose


title: PRAX study [gene-level] 154 180

description: Healthy Human platelets


title: PRAX study [gene-level] 157 183

description: Healthy Human platelets


title: 300cGy-48hr-m11 (2665_8452_34816)

source_name: 300cGy,48hr,no treatment

tag: treatment


title: PRAX study [gene-level] 162 188

description: Healthy Human platelets


title: PRAX study [gene-level] 156 182

description: Healthy Human platelets


title: 450cGy-24hr-m2 (2665_8452_34809)

source_name: 450cGy,24hr,no treatment

tag: time


title: 800cGy-24hr-m2 (2665_8452_34811)

source_name: 800cGy,24hr,no treatment


title: 1050cGy-24hr-m4 (2665_8452_34812)

source_name: 1050cGy,24hr,no treatment


title: 300cGy-24hr-m2 (2665_8452_34808)

source_name: 300cGy,24hr,no treatment


title: 100cGy-24hr-m2 (2665_8452_34806)

source_name: 100cGy,24hr,no treatment


title: PRAX study [gene-level] 153 179

description: Healthy Human platelets


title: PRAX study [gene-level] 152 178

description: Healthy Human platelets


title: 200cGy-24hr-m2 (2665_8452_34807)

source_name: 200cGy,24hr,no treatment


title: PRAX study [gene-level] 155 181

description: Healthy Human platelets


title: PRAX study [gene-level] 151 177

description: Healthy Human platelets


title: PRAX study [gene-level] 149 175

description: Healthy Human platelets


title: PRAX study [gene-level] 150 176

description: Healthy Human platelets


title: 1050cGy-6hr-m2 (2665_8452_34804)

source_name: 1050cGy,6hr,no treatment


title: 800cGy-6hr-m2 (2665_8452_34803)

source_name: 800cGy,6hr,no treatment


title: PRAX study [gene-level] 147 173

description: Healthy Human platelets


title: 600cGy-24hr-m2 (2665_8452_34810)

source_name: 600cGy,24hr,no treatment


title: PRAX study [gene-level] 146 172

description: Healthy Human platelets


title: 0cGy-24hr-m2 (2665_8452_34805)

source_name: 0cGy,24hr,no treatment


title: PRAX study [gene-level] 148 174

description: Healthy Human platelets


title: 600cGy-6hr-m2 (2665_8452_34802)

source_name: 600cGy,6hr,no treatment


title: 450cGy-6hr-m2 (2665_8452_34801)

source_name: 450cGy,6hr,no treatment


title: PRAX study [gene-level] 145 171

description: Healthy Human platelets

source_name: leukocyte-depleted platelets


title: 300cGy-6hr-m2 (2665_8452_34800)

source_name: 300cGy,6hr,no treatment


title: PRAX study [gene-level] 144 170

description: Healthy Human platelets


title: 0cGy-6hr-m2 (2665_8452_34797)

source_name: 0cGy,6hr,no treatment


title: 200cGy-6hr-m2 (2665_8452_34799)

source_name: 200cGy,6hr,no treatment


title: PRAX study [gene-level] 142 168

description: Healthy Human platelets


title: PRAX study [gene-level] 143 169

description: Healthy Human platelets


title: 800cGy-168hr-m1 (2665_8291_34588)

source_name: 800cGy,168hr,no treatment


title: 1050cGy-168hr-m1 (2665_8291_34589)

source_name: 1050cGy,168hr,no treatment


title: PRAX study [gene-level] 139 165

description: Healthy Human platelets


title: PRAX study [gene-level] 140 166

description: Healthy Human platelets


title: 100cGy-6hr-m2 (2665_8452_34798)

source_name: 100cGy,6hr,no treatment


title: 200cGy-48hr-m11 (2665_8452_34815)

source_name: 200cGy,48hr,no treatment


title: PRAX study [gene-level] 138 164

description: Healthy Human platelets


title: 600cGy-168hr-m2 (2665_8291_34587)

source_name: 600cGy,168hr,no treatment


title: PRAX study [gene-level] 137 163

description: Healthy Human platelets


title: 450cGy-168hr-m1 (2665_8291_34586)

source_name: 450cGy,168hr,no treatment


title: PRAX study [gene-level] 135 161

description: Healthy Human platelets


title: PRAX study [gene-level] 136 162

description: Healthy Human platelets


title: 1050cGy-120hr-m6 (2665_8291_34581)

source_name: 1050cGy,120hr,no treatment


title: 300cGy-168hr-m1 (2665_8291_34585)

source_name: 300cGy,168hr,no treatment


title: 200cGy-168hr-m1 (2665_8291_34584)

source_name: 200cGy,168hr,no treatment


title: PRAX study [gene-level] 133 159

description: Healthy Human platelets


title: 0cGy-168hr-m1 (2665_8291_34582)

source_name: 0cGy,168hr,no treatment


title: PRAX study [gene-level] 134 160

description: Healthy Human platelets


title: PRAX study [gene-level] 128 154

description: Healthy Human platelets


title: PRAX study [gene-level] 130 156

description: Healthy Human platelets


title: PRAX study [gene-level] 129 155

description: Healthy Human platelets


title: 100cGy-168hr-m1 (2665_8291_34583)

source_name: 100cGy,168hr,no treatment


title: 600cGy-120hr-m7 (2665_8291_34579)

source_name: 600cGy,120hr,no treatment


title: 300cGy-120hr-m1 (2665_8291_34577)

source_name: 300cGy,120hr,no treatment


title: PRAX study [gene-level] 132 158

description: Healthy Human platelets

source_name: leukocyte-depleted platelets


title: 800cGy-120hr-m7 (2665_8291_34580)

source_name: 800cGy,120hr,no treatment


title: 450cGy-120hr-m1 (2665_8291_34578)

source_name: 450cGy,120hr,no treatment


title: PRAX study [gene-level] 120 153

description: Healthy Human platelets


title: PRAX study [gene-level] 131 157

description: Healthy Human platelets


title: PRAX study [gene-level] 127 152

description: Healthy Human platelets


title: PRAX study [gene-level] 125 150

description: Healthy Human platelets


title: 0cGy-120hr-m1 (2665_8291_34574)

source_name: 0cGy,120hr,no treatment


title: 1050cGy-72hr-m1 (2665_8291_34573)

source_name: 1050cGy,72hr,no treatment


title: PRAX study [gene-level] 123 148

description: Healthy Human platelets


title: 200cGy-120hr-m1 (2665_8291_34576)

source_name: 200cGy,120hr,no treatment


title: 100cGy-120hr-m1 (2665_8291_34575)

source_name: 100cGy,120hr,no treatment


title: PRAX study [gene-level] 122 147

description: Healthy Human platelets


title: 800cGy-72hr-m1 (2665_8291_34572)

source_name: 800cGy,72hr,no treatment


title: 600cGy-72hr-m1 (2665_8291_34571)

source_name: 600cGy,72hr,no treatment


title: PRAX study [gene-level] 124 149

description: Healthy Human platelets


title: 450cGy-72hr-m2 (2665_8291_34570)

source_name: 450cGy,72hr,no treatment


title: PRAX study [gene-level] 121 146

description: Healthy Human platelets


title: PRAX study [gene-level] 118 143

description: Healthy Human platelets


title: PRAX study [gene-level] 119 144

description: Healthy Human platelets


title: 300cGy-72hr-m2 (2665_8291_34569)

source_name: 300cGy,72hr,no treatment


title: 200cGy-72hr-m7 (2665_8291_34568)

source_name: 200cGy,72hr,no treatment


title: 100cGy-72hr-m1 (2665_8291_34567)

source_name: 100cGy,72hr,no treatment


title: 1050cGy-48hr-m7 (2665_8291_34565)

source_name: 1050cGy,48hr,no treatment


title: PRAX study [gene-level] 115 140

description: Healthy Human platelets


title: 600cGy-48hr-m3 (2665_8291_34563)

source_name: 600cGy,48hr,no treatment


title: PRAX study [gene-level] 117 142

description: Healthy Human platelets


title: 0cGy-72hr-m1 (2665_8291_34566)

source_name: 0cGy,72hr,no treatment


title: PRAX study [gene-level] 113 138

description: Healthy Human platelets


title: PRAX study [gene-level] 112 137

description: Healthy Human platelets


title: PRAX study [gene-level] 116 141

description: Healthy Human platelets


title: PRAX study [gene-level] 110 135

description: Healthy Human platelets


title: 200cGy-48hr-m5 (2665_8291_34560)

source_name: 200cGy,48hr,no treatment


title: 450cGy-48hr-m2 (2665_8291_34562)

source_name: 450cGy,48hr,no treatment


title: PRAX study [gene-level] 111 136

description: Healthy Human platelets

source_name: leukocyte-depleted platelets


title: PRAX study [gene-level] 109 134

description: Healthy Human platelets


title: 100cGy-48hr-m1 (2665_8291_34559)

source_name: 100cGy,48hr,no treatment


title: PRAX study [gene-level] 107 132

description: Healthy Human platelets


title: 300cGy-48hr-m4 (2665_8291_34561)

source_name: 300cGy,48hr,no treatment


title: 1050cGy-24hr-m2 (2665_8291_34557)

source_name: 1050cGy,24hr,no treatment


title: 800cGy-48hr-m4 (2665_8291_34564)

source_name: 800cGy,48hr,no treatment


title: PRAX study [gene-level] 106 131

description: Healthy Human platelets


title: 800cGy-24hr-m1 (2665_8291_34556)

source_name: 800cGy,24hr,no treatment


title: PRAX study [gene-level] 104 129

description: Healthy Human platelets


title: PRAX study [gene-level] 108 133

description: Healthy Human platelets


title: 0cGy-48hr-m1 (2665_8291_34558)

source_name: 0cGy,48hr,no treatment


title: PRAX study [gene-level] 103 128

description: Healthy Human platelets


title: 600cGy-24hr-m1 (2665_8291_34555)

source_name: 600cGy,24hr,no treatment


title: 450cGy-24hr-m1 (2665_8291_34554)

source_name: 450cGy,24hr,no treatment


title: PRAX study [gene-level] 105 130

description: Healthy Human platelets


title: 200cGy-24hr-m1 (2665_8291_34552)

source_name: 200cGy,24hr,no treatment


title: 300cGy-24hr-m1 (2665_8291_34553)

source_name: 300cGy,24hr,no treatment


title: 0cGy-24hr-m1 (2665_8291_34550)

source_name: 0cGy,24hr,no treatment


title: PRAX study [gene-level] 126 151

description: Healthy Human platelets


title: PRAX study [gene-level] 98 123

description: Healthy Human platelets


title: PRAX study [gene-level] 101 126

description: Healthy Human platelets


title: 800cGy-6hr-m1 (2665_8291_34548)

source_name: 800cGy,6hr,no treatment


title: PRAX study [gene-level] 97 122

description: Healthy Human platelets


title: 1050cGy-6hr-m1 (2665_8291_34549)

source_name: 1050cGy,6hr,no treatment


title: 100cGy-24hr-m1 (2665_8291_34551)

source_name: 100cGy,24hr,no treatment


title: PRAX study [gene-level] 99 124

description: Healthy Human platelets


title: 600cGy-6hr-m1 (2665_8291_34547)

source_name: 600cGy,6hr,no treatment


title: PRAX study [gene-level] 95 120

description: Healthy Human platelets


title: PRAX study [gene-level] 102 127

description: Healthy Human platelets


title: PRAX study [gene-level] 94 119

description: Healthy Human platelets


title: 100cGy-6hr-m1 (2665_8291_34543)

source_name: 100cGy,6hr,no treatment


title: 450cGy-6hr-m1 (2665_8291_34546)

source_name: 450cGy,6hr,no treatment


title: 200cGy-6hr-m1 (2665_8291_34544)

source_name: 200cGy,6hr,no treatment


title: PRAX study [gene-level] 91 116

description: Healthy Human platelets

source_name: leukocyte-depleted platelets


title: PRAX study [gene-level] 92 117

description: Healthy Human platelets


title: PRAX study [gene-level] 96 121

description: Healthy Human platelets


title: 300cGy-6hr-m1 (2665_8291_34545)

source_name: 300cGy,6hr,no treatment


title: PRAX study [gene-level] 93 118

description: Healthy Human platelets


title: PRAX study [gene-level] 90 115

description: Healthy Human platelets


title: 0cGy-6hr-m1 (2665_8291_34542)

source_name: 0cGy,6hr,no treatment


title: PRAX study [gene-level] 87 112

description: Healthy Human platelets


title: PRAX study [gene-level] 88 113

description: Healthy Human platelets


title: 150cGy-7d-m7 (2202_6087_30066)

source_name: 150cGy,7d,no treatment


title: PRAX study [gene-level] 85 110

description: Healthy Human platelets


title: PRAX study [gene-level] 86 111

description: Healthy Human platelets


title: 150cGy-7d-m10 (2202_6087_30069)


title: PRAX study [gene-level] 89 114

description: Healthy Human platelets


title: PRAX study [gene-level] 80 105

description: Healthy Human platelets


title: 0cGy-7d-m2 (2202_6087_30058)

source_name: 0cGy,7d,no treatment


title: 150cGy-7d-m8 (2202_6087_30067)


title: PRAX study [gene-level] 84 109

description: Healthy Human platelets


title: 150cGy-7d-m5 (2202_6087_30064)


title: 150cGy-7d-m1 (2202_6087_30060)


title: 150cGy-7d-m9 (2202_6087_30068)


title: PRAX study [gene-level] 81 106

description: Healthy Human platelets


title: 150cGy-7d-m6 (2202_6087_30065)


title: 150cGy-7d-m4 (2202_6087_30063)


title: 150cGy-7d-m2 (2202_6087_30061)


title: PRAX study [gene-level] 82 107

description: Healthy Human platelets


title: PRAX study [gene-level] 78 103

description: Healthy Human platelets


title: 150cGy-7d-m3 (2202_6087_30062)


title: 0cGy-7d-m3 (2202_6087_30059)


title: 0cGy-7d-m1 (2202_6087_30057)


title: PRAX study [gene-level] 76 101

description: Healthy Human platelets


title: PRAX study [gene-level] 75 100

description: Healthy Human platelets


title: PRAX study [gene-level] 83 108

description: Healthy Human platelets


title: PRAX study [gene-level] 77 102

description: Healthy Human platelets


title: 0cGy-24h-m2 (2202_6087_30055)


title: 0cGy-6h-m2 (2202_6087_30053)


title: PRAX study [gene-level] 74 99

description: Healthy Human platelets


title: 0cGy-24h-m3 (2202_6087_30056)


title: 0cGy-6h-m3 (2202_6087_30054)


title: PRAX study [gene-level] 69 94

description: Healthy Human platelets


title: PRAX study [gene-level] 73 98

description: Healthy Human platelets


title: PRAX study [gene-level] 72 97

description: Healthy Human platelets


title: 0cGy-noTRT6-m2 (2202_4866_28414)

source_name: 0cGy,no treatment,6hr


title: 0cGy-noTRT6-m8 (2202_4866_28416)


title: 0cGy-noTRT6-m3 (2202_4866_28415)


title: 0cGy-noTRT6-m9 (2202_4866_28417)


title: PRAX study [gene-level] 71 96

description: Healthy Human platelets


title: PRAX study [gene-level] 68 93

description: Healthy Human platelets


title: 0cGy-LPS6-m9 (2202_4866_28411)

value: LPS


title: PRAX study [gene-level] 70 95

description: Healthy Human platelets


title: PRAX study [gene-level] 67 92

description: Healthy Human platelets


title: PRAX study [gene-level] 63 88

description: Healthy Human platelets


title: PRAX study [gene-level] 66 91

description: Healthy Human platelets


title: 0cGy-noTRT6-m10 (2202_4866_28413)


title: 0cGy-noTRT6-m1 (2202_4866_28412)


title: 0cGy-6h-m1 (2202_6087_30052)


title: PRAX study [gene-level] 62 87

description: Healthy Human platelets


title: 0cGy-LPS6-m6 (2202_4866_28408)


title: 0cGy-LPS6-m7 (2202_4866_28409)


title: 0cGy-LPS6-m8 (2202_4866_28410)


title: PRAX study [gene-level] 61 86

description: Healthy Human platelets


title: PRAX study [gene-level] 64 89

description: Healthy Human platelets


title: PRAX study [gene-level] 60 85

description: Healthy Human platelets


title: 0cGy-LPS6-m3 (2202_4866_28407)


title: PRAX study [gene-level] 59 84

description: Healthy Human platelets


title: 0cGy-GCSF6-m8 (2202_4866_28405)

value: GCSF


title: 0cGy-LPS6-m1 (2202_4866_28406)


title: 600cGy-noTRT6-m7 (2202_4866_28399)

source_name: 600cGy,no treatment,6hr


title: PRAX study [gene-level] 56 80

description: Healthy Human platelets


title: 0cGy-GCSF6-m6 (2202_4866_28404)


title: PRAX study [gene-level] 54 78

description: Healthy Human platelets


title: PRAX study [gene-level] 52 76

description: Healthy Human platelets


title: 0cGy-GCSF6-m1 (2202_4866_28400)


title: PRAX study [gene-level] 53 77

description: Healthy Human platelets


title: 0cGy-GCSF6-m3 (2202_4866_28401)


title: PRAX study [gene-level] 55 79

description: Healthy Human platelets


title: PRAX study [gene-level] 50 74

description: Healthy Human platelets


title: 0cGy-GCSF6-m4 (2202_4866_28402)


title: 600cGy-noTRT6-m3 (2202_4866_28396)


title: 600cGy-noTRT6-m1 (2202_4866_28395)


title: 0cGy-GCSF6-m5 (2202_4866_28403)


title: PRAX study [gene-level] 57 81

description: Healthy Human platelets


title: PRAX study [gene-level] 45 82

description: Healthy Human platelets


title: PRAX study [gene-level] 51 75

description: Healthy Human platelets


title: PRAX study [gene-level] 58 83

description: Healthy Human platelets


title: 600cGy-noTRT6-m5 (2202_4866_28398)


title: 600cGy-noTRT6-m4 (2202_4866_28397)


title: PRAX study [gene-level] 49 73

description: Healthy Human platelets


title: 600cGy-LPS6-m5 (2202_4866_28393)


title: 600cGy-LPS6-m6 (2202_4866_28394)


title: PRAX study [gene-level] 46 70

description: Healthy Human platelets


title: PRAX study [gene-level] 48 72

description: Healthy Human platelets


title: PRAX study [gene-level] 44 68

description: Healthy Human platelets


title: 600cGy-LPS6-m2 (2202_4866_28390)


title: 600cGy-GCSF6-m4 (2202_4866_28386)


title: PRAX study [gene-level] 38 62

description: Healthy Human platelets


title: 600cGy-LPS6-m1 (2202_4866_28389)


title: 600cGy-GCSF6-m6 (2202_4866_28388)


title: 600cGy-LPS6-m4 (2202_4866_28392)


title: 600cGy-GCSF6-m3 (2202_4866_28385)


title: PRAX study [gene-level] 42 66

description: Healthy Human platelets


title: PRAX study [gene-level] 40 64

description: Healthy Human platelets


title: PRAX study [gene-level] 36 60

description: Healthy Human platelets


title: PRAX study [gene-level] 37 61

description: Healthy Human platelets


title: PRAX study [gene-level] 39 63

description: Healthy Human platelets


title: 600cGy-GCSF6-m1 (2202_4866_28384)


title: 150cGy-noTRT6-m8 (2202_4866_28383)

source_name: 150cGy,no treatment,6hr


title: PRAX study [gene-level] 43 67

description: Healthy Human platelets


title: PRAX study [gene-level] 34 58

description: Healthy Human platelets


title: 150cGy-noTRT6-m6 (2202_4866_28381)


title: PRAX study [gene-level] 32 56

description: Healthy Human platelets


title: PRAX study [gene-level] 31 55

description: Healthy Human platelets


title: 150cGy-noTRT6-m5 (2202_4866_28380)


title: PRAX study [gene-level] 30 54

description: Healthy Human platelets


title: 150cGy-noTRT6-m7 (2202_4866_28382)


title: 150cGy-noTRT6-m1 (2202_4866_28378)


title: PRAX study [gene-level] 26 50

description: Healthy Human platelets


title: PRAX study [gene-level] 28 52

description: Healthy Human platelets


title: PRAX study [gene-level] 27 51

description: Healthy Human platelets


title: 150cGy-LPS6-m8 (2202_4866_28376)


title: PRAX study [gene-level] 19 43

description: Healthy Human platelets


title: PRAX study [gene-level] 25 49

description: Healthy Human platelets


title: PRAX study [gene-level] 21 45

description: Healthy Human platelets


title: 150cGy-LPS6-m3 (2202_4866_28373)


title: PRAX study [gene-level] 33 57

description: Healthy Human platelets


title: 150cGy-GCSF6-m9 (2202_4866_28372)


title: 150cGy-LPS6-m6 (2202_4866_28375)


title: 150cGy-GCSF6-m7 (2202_4866_28371)


title: PRAX study [gene-level] 65 90

description: Healthy Human platelets


title: 150cGy-GCSF6-m5 (2202_4866_28370)


title: 150cGy-LPS6-m4 (2202_4866_28374)


title: 150cGy-noTRT6-m4 (2202_4866_28379)


title: PRAX study [gene-level] 22 46

description: Healthy Human platelets


title: 150cGy-GCSF6-m3 (2202_4866_28368)


title: PRAX study [gene-level] 14 34

description: Healthy Human platelets


title: PRAX study [gene-level] 15 36

description: Healthy Human platelets


title: PRAX study [gene-level] 17 41

description: Healthy Human platelets


title: PRAX study [gene-level] 13 32

description: Healthy Human platelets


title: 300cGy-LPS24hr-m2 (2666_7960_34173)

value: male


title: 150cGy-GCSF6-m4 (2202_4866_28369)


title: 300cGy-NOTRT24hr-m2 (2666_7960_34174)

source_name: 300cGy,no treatment,24hr

value: female


title: PRAX study [gene-level] 11 25

description: Healthy Human platelets


title: 300cGy-NOTRT24hr-m3 (2666_7960_34176)


title: PRAX study [gene-level] 12 30

description: Healthy Human platelets


title: 300cGy-NOTRT24hr-m2 (2666_7960_34175)


title: PRAX study [gene-level] 29 53

description: Healthy Human platelets


title: 300cGy-GCSF24hr-m3 (2666_7960_34170)


title: 300cGy-LPS24hr-m5 (2666_7960_34172)


title: PRAX study [gene-level] 10 24

description: Healthy Human platelets


title: 200cGy-LPS24hr-m3 (2666_7960_34169)


title: 300cGy-GCSF24hr-m5 (2666_7960_34171)


title: PRAX study [gene-level] 6 11

description: Healthy Human platelets


title: PRAX study [gene-level] 9 20

description: Healthy Human platelets


title: PRAX study [gene-level] 8 15

description: Healthy Human platelets


title: PRAX study [gene-level] 5 8

description: Healthy Human platelets


title: PRAX study [gene-level] 7 12

description: Healthy Human platelets


title: 600cGy-GCSF24hr-m5 (2666_7848_34046)


title: PRAX study [gene-level] 4 6

description: Healthy Human platelets


title: PRAX study [gene-level] 3 4

description: Healthy Human platelets


title: 200cGy-NOTRT24hr-m5 (2666_7848_34043)

source_name: 200cGy,no treatment,24hr


title: 600cGy-LPS24hr-m5 (2666_7848_34047)


title: 150cGy-LPS6-m9 (2202_4866_28377)


title: PRAX study [gene-level] 2 2

description: Healthy Human platelets


title: 600cGy-NOTRT24hr-m10 (2666_7848_34048)

source_name: 600cGy,no treatment,24hr


title: PRAX study [gene-level] 1 1

description: Healthy Human platelets


title: 200cGy-GCSF24hr-m5 (2666_7848_34041)


title: 4CT

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description: RNA from Homo Sapiens Vastus Lateralis muscle biopsy after 27 hours of fasting

hyb_protocol: Samples were hybridized with GeneChip Human Gene 1.0 ST Arrays (Affymetrix) and scanned at the Genomics Corelab at the Cambridge Biomedical Research Centre.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were normalized using core gene-level RMA, data analysis and statistical evaluations were performed with Genespring GX12.5

label_protocol: cDNA was generated using Ambion WT Expression Kit (Life Technologies) in accordance with the manufacturerís protocol, and was then fragmented and labelled with Affymetrix GeneChipWT Terminal Labeling and Hybridization kit (Affymetrix)

growth_protocol: The skeletal muscle  biopsies are obtained after 27 hour fasting and was preceeded by a frequently sampled intravenous glucose tolerance test

extract_protocol: Total RNA was extracted using miRNeasy mini kit (Qiagen), and the miRNA was removed using RNeasy MinElute Cleanup Kit (Qiagen) according to manufacturer´s instructions

treatment_protocol: The biopsies were snapfrozen in liquid nitrogen and stored at -80

value: vastus lateralis muscle

tag: sample type

value: subjects with High IGF-I


title: 0cGy-NOTRT24hr-m5 (2666_7848_34040)

source_name: 0cGy,no treatment,24hr


title: 200cGy-LPS24hr-m5 (2666_7848_34042)


title: 2RL

source_name: Vastus Lateralis muscle biopsy after 27 hours of fasting


title: 200cGy-GCSF24hr-m2 (2666_7960_34168)


title: PRAX study [gene-level] 24 48

description: Healthy Human platelets


title: 0cGy-GCSF24hr-m5 (2666_7848_34038)


title: 600cGy-LPS6-m3 (2202_4866_28391)


title: 0cGy-LPS24hr-m5 (2666_7848_34039)


title: 600cGy-NOTRT6hr-m5 (2666_7848_34037)


title: 27DM


title: 21JH


title: 300cGy-NOTRT6hr-m5 (2666_7848_34034)

source_name: 300cGy,no treatment,6hr


title: 17AG


title: 15FM


title: 11NB


title: 600cGy-GCSF6hr-m5 (2666_7848_34035)


title: 18CM


title: 600cGy-LPS6hr-m5 (2666_7848_34036)


title: 1NS


title: 200cGy-LPS6hr-m5 (2666_7848_34030)


title: 3HL

value: subjects with Low IGF-I


title: 8LV


title: 200cGy-GCSF6hr-m5 (2666_7848_34029)


title: 200cGy-NOTRT6hr-m5 (2666_7848_34031)

source_name: 200cGy,no treatment,6hr

value: no treatment


title: 20SF


title: 600cGy-GCSF6-m5 (2202_4866_28387)

value: peripheral blood


title: 0cGy-NOTRT6hr-m5 (2666_7848_34028)


title: 0cGy-LPS6hr-m5 (2666_7848_34027)


title: 300cGy-GCSF6hr-m5 (2666_7848_34032)

value: ionizing radiation


title: 23PT


title: 0cGy-GCSF6hr-m5 (2666_7848_34026)

value: control (no ionizing radiation)


title: 19CA


title: 16PT


title: 14WT


title: 600cGy-NOTRT24hr-m5 (2666_7848_34025)


title: PRAX study [gene-level] 35 59

description: Healthy Human platelets


title: 13DR


title: 12BP


title: 200cGy-NOTRT24hr-m5 (2666_7848_34021)


title: 300cGy-NOTRT24hr-m5 (2666_7848_34022)


title: 200cGy-LPS24hr-m5 (2666_7848_34020)


title: 600cGy-GCSF24hr-m5 (2666_7848_34023)


title: 0cGy-GCSF24hr-m5 (2666_7848_34016)


title: preCC mouse OR4559m154

city: Chapel Hill

first: Samir

last: Kelada

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina

description: preCC mouse OR4559m154

hyb_protocol: 2 micrograms of labeled cRNAs were hybridized overnight to the Illumina MouseRef-8 plex using Illumina hybridization mixture and temperature.  The slides were washed and stained using standard Illumina's reagents and procedure.

scan_protocol: The Illumina BeadChips were scanned on the Illumina BeadArray scanner.

data_processing: The resulting data were initially processed using Illumina Genome Studio software and then imported into R (v2.9.2) for post-processing. Normalization was conducted using RMA with quantile normalization and log2 transformation.

source_name: mouse lung

label_protocol: 500 nanogram of total RNA was subjeceted to amplification and biotin labeling with the  Ambion Illumina® TotalPrep RNA Amplification Kit (Ambion kit cat# AMIL1791)

growth_protocol: The right lower lobe was inflated with OCT and then flash frozen in liquid nitrogen.

extract_protocol: Lung lobes were homogenized and then RNA was isolated using RNeasy Mini Kits (Qiagen), according to the manufacturer’s instructions. RNAs were DNAseI treated.

treatment_protocol: mice were  i.p. sensitized with 10 ug Der p 1 and then challenged with 50 ug Der p 1 on day 15.  All mice were harvested on day 18 (72 hours after challenge).

value: preCC  OR4559

value: lung


title: 600cGy-NOTRT6hr-m5 (2666_7848_34015)


title: preCC mouse OR167m167

description: preCC mouse OR167m167

value: preCC  OR167


title: preCC mouse OR3489m49

description: preCC mouse OR3489m49

value: preCC  OR3489


title: preCC mouse OR5091m144

description: preCC mouse OR5091m144

value: preCC  OR5091


title: 0cGy-NOTRT24hr-m5 (2666_7848_34018)


title: preCC mouse OR2291m70

description: preCC mouse OR2291m70

value: preCC  OR2291


title: preCC mouse OR4390m150

description: preCC mouse OR4390m150

value: preCC  OR4390


title: preCC mouse OR3289m52

description: preCC mouse OR3289m52

value: preCC  OR3289


title: 600cGy-LPS6hr-m5 (2666_7848_34014)

value: LPS


title: 600cGy-GCSF6hr-m5 (2666_7848_34013)

value: female

value: GCSF


title: preCC mouse OR5515m126

description: preCC mouse OR5515m126

value: preCC  OR5515


title: 0cGy-LPS24hr-m5 (2666_7848_34017)


title: 300cGy-NOTRT6hr-m5 (2666_7848_34012)


title: preCC mouse OR773m68

description: preCC mouse OR773m68

value: preCC  OR773


title: PRAX study [gene-level] 20 44

description: Healthy Human platelets

value: caucasian

value: leukocyte-depleted platelets


title: 300cGy-LPS6hr-m5 (2666_7848_34011)

value: ionizing radiation

value: peripheral blood


title: preCC mouse OR166m65

description: preCC mouse OR166m65

value: preCC  OR166


title: preCC mouse OR5389m137

description: preCC mouse OR5389m137

value: preCC  OR5389

value: lung


title: 300cGy-GCSF6hr-m5 (2666_7848_34010)


title: 200cGy-NOTRT6hr-m5 (2666_7848_34009)

value: no treatment


title: 200cGy-GCSF6hr-m5 (2666_7848_34008)


title: 0cGy-LPS6hr-m5 (2666_7848_34006)

value: control (no ionizing radiation)


title: 600cGy-NOTRT24hr-m4 (2666_7848_34004)

value: male


title: 600cGy-LPS24hr-m4 (2666_7848_34003)


title: 0cGy-NOTRT6hr-m5 (2666_7848_34007)


title: preCC mouse OR3046m53

description: preCC mouse OR3046m53

value: preCC  OR3046


title: preCC mouse OR3584m51

description: preCC mouse OR3584m51

value: preCC  OR3584


title: 0cGy-GCSF6hr-m5 (2666_7848_34005)


title: preCC mouse OR3091m49

description: preCC mouse OR3091m49

value: preCC  OR3091


title: 600cGy-GCSF24hr-m8 (2666_7848_34002)


title: preCC mouse OR1519m154

description: preCC mouse OR1519m154

value: preCC  OR1519


title: preCC mouse OR4650m146

description: preCC mouse OR4650m146

value: preCC  OR4650


title: preCC mouse OR5370m142

description: preCC mouse OR5370m142

value: preCC  OR5370


title: preCC mouse OR1112m142

description: preCC mouse OR1112m142

value: preCC  OR1112


title: preCC mouse OR3076m40

description: preCC mouse OR3076m40

value: preCC  OR3076


title: preCC mouse OR489m79

description: preCC mouse OR489m79

value: preCC  OR489


title: 200cGy-NOTRT24hr-m4 (2666_7848_33999)

value: ionizing radiation


title: 200cGy-GCSF24hr-m4 (2666_7848_33997)

value: GCSF

value: peripheral blood


title: 300cGy-NOTRT24hr-m4 (2666_7848_34001)


title: 200cGy-LPS24hr-m4 (2666_7848_33998)

value: LPS


title: 0cGy-NOTRT24hr-m4 (2666_7848_33996)


title: 0cGy-LPS24hr-m4 (2666_7848_33995)


title: 600cGy-LPS24hr-m5 (2666_7848_34024)

value: female


title: preCC mouse OR4010m155

description: preCC mouse OR4010m155

value: preCC  OR4010

value: lung


title: preCC mouse OR205m51

description: preCC mouse OR205m51

value: preCC  OR205


title: preCC mouse OR555m52

description: preCC mouse OR555m52

value: preCC  OR555


title: preCC mouse OR829m74

description: preCC mouse OR829m74

value: preCC  OR829


title: preCC mouse OR5232m137

description: preCC mouse OR5232m137

value: preCC  OR5232


title: preCC mouse OR2041m60

description: preCC mouse OR2041m60

value: preCC  OR2041


title: 300cGy-NOTRT6hr-m4 (2666_7848_33990)

value: male

value: no treatment


title: 600cGy-GCSF6hr-m4 (2666_7848_33991)


title: 600cGy-LPS6hr-m4 (2666_7848_33992)


title: 300cGy-LPS6hr-m4 (2666_7848_33989)


title: 600cGy-NOTRT6hr-m4 (2666_7848_33993)


title: preCC mouse OR305m87

description: preCC mouse OR305m87

value: preCC  OR305


title: 0cGy-GCSF24hr-m4 (2666_7848_33994)

value: control (no ionizing radiation)


title: preCC mouse OR3018m50

description: preCC mouse OR3018m50

value: preCC  OR3018