title: T B6 476 X LOW male

description:
476Xlow-m
Independent sample 3 of 3


title: Fg_Wheat_4d_BR3_cy3 vs mock

status: Public on Sep 30 2015

type: RNA

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

description: Wheat infected with Fusarium graminearum for 96hrs vs mock infected wheat

hyb_protocol: Hybridizations were incubated overnight at 65ºC in a Robbins 400 oven outfitted with a Hybridization Oven Rotator (Agilent G2530-60029). Slides were washed as recommended by Agilent: Wash with Stabilization and Drying Solution.

scan_protocol: Slides were scanned on the Genepix 4200a (Molecular Devices) at 5µ resolution. Images were quantified using Genepix Pro 6.0 (Molecular Devices)

data_processing: Array results files (.gpr) were imported in Acuity 4.0 and normalized by ratio-based method using spike-in control (+)E1A_r60_1, which has a cy5:cy3 ratio of 1:1. There are 20 copies of (+)E1A_r60_1 on each array. Two datasets were formed with all arrays and the datatypes were changed to F532-B532 and F635-B635 respectively to remove false signals from dust or other contaminants. After the removal of false signals, for each dataset, features that did not have intensities higher than 250 in at least 1 of 8 replicates were removed. A new dataset was formed with the remaining features from each , and the datatype was changed to Ratio of Medians. Spike-in controls were removed. Cy3 test array data were swapped to cy5. Technical replicates were combined.

molecule: total RNA

organism: Triticum aestivum

label_protocol: 500ng of total RNA was labelled using reagents and procedure described in the Two-color Quick Amp Labeling protocol version 5.7 (Agilent Technologies) except only half the amounts of reagents were used in Step 2 of the labelling reaction.

growth_protocol: Maize inbred B73 was grown in the field on the Central Experimental Farm, Ottawa, ON in 2004 and 2006. Wheat cultivar Roblin and barley cultivar Encore were grown in the greenhouse under conditons of 16 h light (20oC) and 8h dark (16oC).

extract_protocol: Total RNA was extracted using a guanidine isothiocyanate-cesium chloride method (Ohan and Heikkila 1995).

treatment_protocol: All three plant species were inoculated with F. graminearum strain DAOM180378 (15ADON-producer). Field-grown maize (Zea mays) inbred B73 ears were sib-crossed and developing kernels (eleven days post-fertilization) were inoculated through the husks with 0.1 ml of macroconidia suspension (5 x 105  spores/ml) (between 8 am and 10 am) and fields were irrigated for 15 min every afternoon during the inoculation period. The spring wheat (Triticum aestivum) cultivar Roblin and barley (Hordeum vulgare) cultivar Encore were grown in a controlled-environment cabinet with 16h light (20°C) and 8h dark (16°C).  At mid-anthesis, each biological replicate of six wheat heads were point inoculated by pipetting 10 µl of a 10,000 spores/mL F. graminearum macroconidia suspension between lemma and plea of two primary florets in each spikelet. All fully developed spikelets on each head were inoculated.  In the case of barley, at mid-anthesis, each fully developed floret of only two central rows was inoculated and florets from laterals rows were stripped from the rachis. In each inoculated barley floret, the tip of the lemma that includes the awn was excised and 1000 F. graminearum macroconidia were pipetted inside the lemma.  A mock inoculation using water was carried out in parallel. Inoculated wheat and barley plants were misted overhead for 20 sec every 30 min for 2 days to maintain high humidity during the initial infection period and then moved to a non-misted bench in the same cabinet. Infected ears or spikelets were harvested 1, 2 and 4 days post inoculation, flash-frozen in liquid nitrogen, and stored at -80oC.

tag: time

value: 2 days

tag: biorep

tag: growth condition

value: Greenhouse

tag: cultivar

value: Roblin

organism: Triticum

value: 4 days


title: Myocardium_MI_4w_rep5

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

description:
8324341115_A
remote non-infarcted LV posterior and inferior wall

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol for iSCAN.

data_processing: Data variance stabilizing transformation (VST) and robust spline normalization (RSN) were conducted with the lumi R package implemented in BRB-ArrayTools 4.3.2, Bioconductor v. 2.12, and R v. 3.0.1.

label: biotin

organism: Mus musculus

source_name: Left ventricle, untreated myocardial infarction, 4 weeks

label_protocol: RNA was used to generate biotinylated, linearly amplified RNA (cRNA) by Total Prep RNA Amplification Kit (Life Technologies), according to manufacturer’s manual.

growth_protocol: Animals were fed ad libitum with standard chow and water.

extract_protocol: Total RNA was extracted using silica-membrane RNeasy spin columns (Qiagen) following recommended manufacturer's instructions. RNA was treated with Turbo RNase-free DNase (Life Technologies) as described by the manufacturer's protocol. RNA quantity and purity were assessed by micro-volume spectrophotometry using an Infinite 200 PRO plate reader (Tecan). The quality and integrity of the total RNA were checked by the RNA 6000 Nano Assay kit in a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Infarcted mice with an ejection fraction (EF), obtained by CMR at 24 h, within the range 35-45% were randomized to 1:1 to Valsartan 1 mg/Kg/die in drinking water or water only for 4 weeks.

tag: gender

value: female

tag: strain

tag: age

value: 8-10 weeks

tag: stress

value: myocardial infarction

tag: agent

value: control

tag: tissue

value: cardiac muscle (non-infarcted left ventricle)


title: T B6 462 X+G male

city: Madrid

first: Javier

last: Santos

address: Nicolás Cabrera, 1,

country: Spain

institute: Department of Cellular Biology and Immunology. Severo Ochoa Molecular Biology Center. Autonomous University (CBMSO-UAM)

description:
462X+G-m
Independent sample 1 of 3

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

data_processing:
Data from hybridized microarray images were quantitated, backgound subtracted, corrected by additive detrending and submitted to intra-array Lowess global normalization with Agilent FeatureExtraction (FE) Software.
Lowess normalization reduces spurious bias by merging two-color data, and applying a smoothing adjustment that corrects non-linear dye-specific variation.
Raw data signals are thresholded to 1, and replicated probe signals for the individual channels (Cy5 and Cy3) are summarized by computing their geometric mean. Normalized signal values are obtained by Cy5/Cy3 ratio computing and Log base2 transformation. These manipulations are done with GeneSpring GX12 software.
Thresholding is a simple substitution step that removes very small expression values or negative values, so that there would not be large negative values or missing values in the log transformed data.
Normalization involves Log2 data transformation, which generates a roughly normal distribution and allows to use statistical parametric tests (student’s t-test, etc).

source_name: thymocyte sample

label_protocol:
Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases.
Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores.
Labeled samples are purified with silica-based spin columns.
Microarray: Mouse Gene Expression G3 60K (Agilent microarray design ID 028005, P/N G4852A). Microarray sequences and annotations are listed in sheet '028005_mm9_20121126'.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Thymocytes were irradiated under three different radiation conditions: (1) priming low dose radiation (0.075 Gy of X-rays) 6 hour before high dose radiation (1.75 Gy of gamma rays); (2) low dose radiation (0.075 Gy of X-rays); (3) high dose radiation (1.75 Gy of gamma rays).

tag: cell type

value: primary thymocytes

value: male

tag: group

value: radio-adapted

source_name: Universal Mouse RNA (Stratagene)

tag: reference

value: Pool of amplified RNAs


title: Fg_Wheat_2d_BR3_cy3 vs mock

description: Wheat infected with Fusarium graminearum for 48hrs vs mock infected wheat


title: Myocardium_MI_4w_rep3

description:
8324341055_E
remote non-infarcted LV posterior and inferior wall


title: Fg_Wheat_4d_BR3_cy5 vs mock


title: T B6 463 X+G male

description:
463X+G-m
Independent sample 2 of 3


title: T B6 467 G male

description:
467G-m
Independent sample 3 of 3

value: treated with high dose irradiation


title: Myocardium_MI_4w_rep2

description:
8324341055_C
remote non-infarcted LV posterior and inferior wall


title: Sirolimus Monotherapy, ITN013ST_307165_062

city: Bethesda

first: Adam

last: Asare

state: MD

address: 7500 Old Georgetown Road, Suite 800

department: Bioinformatics Group

country: USA

institute: Immune Tolerance Network

description:
ITN013ST_307165 Visit 62
cDNA

scan_protocol: Products were resolved on a linear MALDI-TOF mass spectrometer (MassARRAY Compact, Sequenom, San Diego, CA.). Signal acquisition, allele assignment and peak area integration per spectrum were conducted with the MassARRAY RT Workstation v3.4 (Sequenom, San Diego, CA).

data_processing:
Data was analyzed using MassARRAY QGE Analyzer v3.4 (Sequenom, San Diego, CA.) with copy numbers for each transcript per sample determined based on the EC50 of standard curve titrations of known competitor amounts per assay vs. a fixed amount of cDNA template.
Normalization of copy numbers between samples for the different assays was conducted using a multiplexed set of ten well-characterized human housekeeping (normalization) transcripts plus an 18s RNA assay and geNorm software. Normalization factors per sample were calculated using the geometric mean of the most stable combination of these normalization assays, determined by the measure of their pairwise variation as calculated by geNorm.

organism: Homo sapiens

source_name: Sirolimus Monotherapy, cohort ITN013

label_protocol: Multiplexed primer and competitive template designs were created using the MassARRAY quantitative gene expression (MassARRAY QGE) Assay Design software for random hexamer priming, such that at least 1 PCR primer spanned an exonic boundary per transcript assayed.

extract_protocol: RNA was extracted from whole blood collected in ABI Tempus tubes. Extraction was performed using the ABI6100 instrument.

treatment_protocol: Participants in this study received no protocol related treatment.

value: peripheral whole blood

tag: disease state

value: renal transplant

value: Sirolimus monotherapy

tag: patient id

tag: visit

tag: cohort


title: Sirolimus Monotherapy, ITN013ST_187319_062

description:
ITN013ST_187319 Visit 62
cDNA


title: Sirolimus Monotherapy, ITN013ST_371019_062

description:
ITN013ST_371019 Visit 62
cDNA


title: T B6 466 G male

description:
466G-m
Independent sample 2 of 3


title: SI Multiagent, ITN013ST_145787_062

description:
ITN013ST_145787 Visit 62
cDNA

source_name: SI Multiagent, cohort ITN013

value: standard immunosuppression multiagent


title: TOL, FACTOR_987079_004

description:
FACTOR_987079 Visit 4
cDNA

source_name: TOL, cohort ITN507

value: tolerant


title: Fg_Wheat_2d_BR3_cy5 vs mock

tag: time

value: 2 days

value: Greenhouse

value: Roblin


title: TOL, FACTOR_987079_000

description:
FACTOR_987079 Visit 0
cDNA


title: Fg_Wheat_1d_BR3_cy5 vs mock

description: Wheat infected with Fusarium graminearum for 24hrs vs mock infected wheat

value: 1 day

tag: biorep


title: T B6 465 G male

description:
465G-m
Independent sample 1 of 3


title: T B6 477 Control male

description:
477C-m
Independent sample 1 of 3


title: Myocardium_MI_4w_rep1

description:
8324341055_B
remote non-infarcted LV posterior and inferior wall

value: female

value: 8-10 weeks

value: myocardial infarction


title: Fg_Wheat_1d_BR3_cy3 vs mock

tag: growth condition


title: HMRN_75_v3_rep

city: Leeds

first: Chulin

last: Sha

address: Woodhouse Lane

department: School of Mole&Cell Biology

country: United Kingdom

institute: University of Leeds

description: replicate sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: The data were normalised using lumi package in R

label: Biotin

source_name: Biopsy

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was extracted from 5mm paraffin sections using the Ambion RecoverAll kit standard protocol, with the exception of a 16-hour protease digestion. These were routinely collected tissue samples and no attempt was made to standardise fixation or processing protocols

value: BL

value: Burkitt lymphoma

value: yes


title: T B6 479 Control male

description:
479C-m
Independent sample 3 of 3

value: primary thymocytes

value: male

value: control

value: Pool of amplified RNAs


title: TOL, FACTOR_974351_006

description:
FACTOR_974351 Visit 6
cDNA

value: peripheral whole blood

value: renal transplant


title: Fg_Wheat_4d_BR2_cy3 vs mock

tag: cultivar

value: 4 days


title: T B6 482 X LOW female

description:
482Xlow-f
Independent sample 3 of 3

tag: gender

value: treated with low dose irradiation


title: Myocardium_sham_4w_rep1

description:
8324341055_D
remote non-infarcted LV posterior and inferior wall

source_name: Left ventricle, sham operated control, 4 weeks

tag: strain

value: sham operation

value: cardiac muscle (non-infarcted left ventricle)


title: Myocardium_MI+Val_4w_rep1

description:
8324341055_A
remote non-infarcted LV posterior and inferior wall

source_name: Left ventricle, Valsartan-treated myocardial infarction, 4 weeks

tag: age

value: Valsartan


title: HMRN_76_v3

value: DLBCL

value: Diffuse Large B-cell Lymphoma

value: unknown


title: Fg_Wheat_2d_BR2_cy5 vs mock

value: 2 days

value: Greenhouse

value: Roblin


title: Fg_Wheat_4d_BR2_cy5 vs mock


title: HMRN_73_v3


title: T B6 478 Control male

description:
478C-m
Independent sample 2 of 3

value: primary thymocytes


title: HMRN_74_v3

value: BL

value: Burkitt lymphoma

value: yes


title: TOL, FACTOR_974351_004

description:
FACTOR_974351 Visit 4
cDNA

value: peripheral whole blood

value: tolerant


title: T B6 480 X LOW female

description:
480Xlow-f
Independent sample 1 of 3

value: female

value: Pool of amplified RNAs


title: HMRN_75_v3


title: HMRN_72_v3

value: no


title: Fg_Wheat_2d_BR2_cy3 vs mock


title: T B6 474 X LOW male

description:
474Xlow-m
Independent sample 1 of 3

value: male

value: treated with low dose irradiation


title: TOL, FACTOR_974351_000

description:
FACTOR_974351 Visit 0
cDNA

value: renal transplant


title: TOL, FACTOR_948987_006

description:
FACTOR_948987 Visit 6
cDNA


title: TOL, FACTOR_948987_004

description:
FACTOR_948987 Visit 4
cDNA


title: TOL, FACTOR_944735_006

description:
FACTOR_944735 Visit 6
cDNA


title: TOL, FACTOR_948987_000

description:
FACTOR_948987 Visit 0
cDNA


title: Fg_Wheat_1d_BR2_cy5 vs mock

value: 1 day


title: T B6 468 X+G female

description:
468X+G-f
Independent sample 1 of 3

value: radio-adapted


title: Fg_Wheat_1d_BR2_cy3 vs mock

value: 2 days


title: T B6 470 X+G female

description:
470X+G-f
Independent sample 3 of 3


title: HMRN_69_v3


title: HMRN_71_v3


title: Fg_Wheat_2d_BR1_cy3 vs mock

value: Greenhouse


title: Fg_Wheat_4d_BR1_cy5 vs mock

value: 4 days

value: Roblin


title: T B6 469 X+G female

description:
469X+G-f
Independent sample 2 of 3

value: primary thymocytes


title: Fg_Wheat_4d_BR1_cy3 vs mock


title: Fg_Wheat_1d_BR1_cy3 vs mock


title: TOL, FACTOR_948987_002

description:
FACTOR_948987 Visit 2
cDNA


title: HMRN_68_v3_rep

description: replicate sample

value: BL

value: Burkitt lymphoma

tag: treatment

value: COP/COPAD/COPADM


title: T B6 473 G female

description:
473G-f
Independent sample 3 of 3

value: treated with high dose irradiation


title: HMRN_69_v3_rep

description: replicate sample

value: yes


title: T B6 471 G female

description:
471G-f
Independent sample 1 of 3

value: female

value: Pool of amplified RNAs


title: Fg_Wheat_1d_BR1_cy5 vs mock


title: HMRN_70_v3

value: DLBCL

value: Diffuse Large B-cell Lymphoma MYC rearranged

value: R-CHOP


title: HMRN_67_v3

value: CODOX-M/IVAC


title: T B6 472 G female

description:
472G-f
Independent sample 2 of 3


title: T B6 485 Control female

description:
485C-f
Independent sample 3 of 3

value: control


title: HMRN_68_v3


title: Fg_Maize_4d_BR2_cy3 field vs mock

description: Field grown maize infected with Fusarium graminearum for 96hrs vs mock infected maize

organism: Zea mays

value: 2 days

value: Field

value: Field grown


title: Fg_Wheat_2d_BR1_cy5 vs mock

value: Greenhouse

value: Roblin


title: TOL, FACTOR_944735_004

description:
FACTOR_944735 Visit 4
cDNA

value: peripheral whole blood

value: renal transplant

value: tolerant


title: SI, FACTOR_936912_006

description:
FACTOR_936912 Visit 6
cDNA

source_name: SI, cohort ITN507

value: standard immunosuppression


title: Fg_Maize_4d_BR2_cy5 field vs mock

value: 4 days


title: HMRN_66_v3

value: Burkitt lymphoma

value: yes


title: SI, FACTOR_930968_006

description:
FACTOR_930968 Visit 6
cDNA


title: T B6 483 Control female

description:
483C-f
Independent sample 1 of 3

value: primary thymocytes

value: female

value: Pool of amplified RNAs


title: T B6 484 Control female

description:
484C-f
Independent sample 2 of 3


title: HMRN_65_v3_rep

description: replicate sample

value: BL

value: CODOX-M/IVAC


title: SI, FACTOR_930960_006

description:
FACTOR_930960 Visit 6
cDNA


title: TOL, FACTOR_911411_006

description:
FACTOR_911411 Visit 6
cDNA


title: TOL, FACTOR_919105_000

description:
FACTOR_919105 Visit 0
cDNA


title: SI, FACTOR_930968_000

description:
FACTOR_930968 Visit 0
cDNA


title: TOL, FACTOR_911411_002

description:
FACTOR_911411 Visit 2
cDNA


title: TOL, FACTOR_911411_004

description:
FACTOR_911411 Visit 4
cDNA


title: Fg_Maize_1d_BR2_cy5 field vs mock

description: Field grown maize infected with Fusarium graminearum for 24hrs vs mock infected maize

value: 1 day

value: 2 days


title: poolC/poolM -DyeSwap- (II)

city: Boston

first: Sebastian

middle: Christoph

last: Hasenfuss

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

hyb_protocol: Microarray: Mouse Gene Expression G3 8x60K (Agilent microarray design ID 028005, P/N G4852A). Microarray sequences and annotations are listed in sheet. Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours. '028005_AllAnnotations_20120201'.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 10.7), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

data_processing: Images were analyzed using the Feature Extraction Software Version 10.7 (Agilent)

source_name: C57BL/6J wt pool

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit.Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).Amplification: by RNA polymerases.

growth_protocol: Mice were housed under standard conditions

extract_protocol: RNA was isolated using the RNEasy Midi kit (Qiagen) and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. Samples of RNA integrity score above 7.8 were used for microarray analysis.

treatment_protocol: no treatment

value: liver

value: 26-28 weeks

value: C57BL/6J wt

source_name: Fra-1 hep mice (C57BL/6J) pool

value: Fra-1 hep mice (C57BL/6J)


title: Fg_Maize_4d_BR1_cy3 field vs mock

value: Field

value: Field grown


title: Fg_Maize_2d_BR2_cy3 field vs mock

description: Field grown maize infected with Fusarium graminearum for 48hrs vs mock infected maize


title: Fg_Maize_1d_BR2_cy3 field vs mock


title: mutant 3/pool (II)

source_name: Fra-1 hep mice (C57BL/6J)


title: Fg_Maize_4d_BR1_cy5 field vs mock


title: HMRN_63_v3

value: COP/COPAD/COPADM


title: mutant 5/pool (II)


title: HMRN_63_v3_rep

description: replicate sample


title: TOL, FACTOR_911411_000

description:
FACTOR_911411 Visit 0
cDNA

value: peripheral whole blood

value: renal transplant

value: tolerant


title: Fg_Maize_2d_BR2_cy5 field vs mock


title: HMRN_65_v3

value: DLBCL

value: Burkitt lymphoma

value: yes


title: mutant 4/pool (II)


title: Fg_Maize_2d_BR1_cy3 field vs mock

source_name: Fg_Maize_2d_BR1 field


title: mutant 1/pool (II)


title: HMRN_64_v3

value: Diffuse Large B-cell Lymphoma

value: no


title: HMRN_62_v3_rep

description: replicate sample

value: BL

value: CODOX-M/IVAC


title: mutant 2/pool (II)

value: liver


title: Fg_Maize_2d_BR1_cy5 field vs mock

value: 2 days


title: HMRN_62_v3


title: TOL, FACTOR_909034_006

description:
FACTOR_909034 Visit 6
cDNA


title: HMRN_61_v3


title: poolC/poolM -DyeSwap-

treatment_protocol: Mice received HFD (45 % kcal fat) starting at 4 weeks of age.

value: 26-28 weeks

value: C57BL/6J wt


title: HMRN_60_v3


title: mutant 4/pool

value: Fra-1 hep mice (C57BL/6J)


title: TOL, FACTOR_909034_004

description:
FACTOR_909034 Visit 4
cDNA


title: Fg_Maize_1d_BR1_cy3 field vs mock

value: Field

source_name: Fg_Maize_1d_BR1 field

value: 1 day

value: Field grown


title: TOL, FACTOR_909034_000

description:
FACTOR_909034 Visit 0
cDNA

value: peripheral whole blood

value: renal transplant


title: mutant 3/pool


title: Fg_Maize_1d_BR1_cy5 field vs mock


title: SI, FACTOR_908887_000

description:
FACTOR_908887 Visit 0
cDNA

value: standard immunosuppression


title: SI, FACTOR_908887_004

description:
FACTOR_908887 Visit 4
cDNA


title: SI, FACTOR_884046_006

description:
FACTOR_884046 Visit 6
cDNA


title: TOL, FACTOR_987079_002

description:
FACTOR_987079 Visit 2
cDNA

value: tolerant


title: Fg_Maize_4d_BR3_cy3 field vs mock

source_name: Fg_Maize_4d_BR3 field

value: 4 days


title: SI, FACTOR_884046_000

description:
FACTOR_884046 Visit 0
cDNA


title: Fg_Maize_4d_BR3_cy5 field vs mock


title: mutant 2/pool


title: Fg_Maize_2d_BR3_cy5 field vs mock

source_name: Fg_Maize_2d_BR3 field


title: HMRN_59_v3_rep

description: replicate sample

value: Burkitt lymphoma

value: yes


title: mutant 1/pool


title: New TOL, FACTOR_882447_004

description:
FACTOR_882447 Visit 4
cDNA

source_name: New TOL, cohort ITN507

value: new tolerant


title: Fg_Maize_1d_BR3_cy3 field vs mock

source_name: Fg_Maize_1d_BR3 field


title: HMRN_59_v3

value: BL


title: HMRN_57_v3

value: DLBCL

value: CODOX-M/IVAC


title: New TOL, FACTOR_882447_002

description:
FACTOR_882447 Visit 2
cDNA


title: HMRN_58_v3_rep

description: replicate sample


title: T B6 481 X LOW female

description:
481Xlow-f
Independent sample 2 of 3

source_name: thymocyte sample

value: primary thymocytes

value: female

value: treated with low dose irradiation

source_name: Universal Mouse RNA (Stratagene)

value: Pool of amplified RNAs


title: HMRN_56_v3

value: Diffuse Large B-cell Lymphoma MYC rearranged


title: Fg_Barley_4d_BR3_cy3 vs mock

description: Barley infected with Fusarium graminearum for 96hrs vs mock infected barley

organism: Hordeum vulgare

value: 2 days

value: Greenhouse

value: Encore


title: HMRN_58_v3


title: New TOL, FACTOR_882447_000

description:
FACTOR_882447 Visit 0
cDNA

value: peripheral whole blood

value: renal transplant


title: HMRN_55_v3

description: relapse sample


title: HMRN_54_v3_rep

description: replicate sample


title: Fg_Barley_4d_BR3_cy5 vs mock

value: 4 days


title: SI, FACTOR_853380_004

description:
FACTOR_853380 Visit 4
cDNA

value: standard immunosuppression


title: HMRN_54_v3

value: yes


title: Fg_Maize_1d_BR3_cy5 field vs mock

value: 1 day

value: Field

value: Field grown


title: Fg_Barley_1d_BR2_cy5 vs mock

description: Barley infected with Fusarium graminearum for 24hrs vs mock infected barley


title: Fg_Barley_1d_BR2_cy3 vs mock


title: SI, FACTOR_853380_006

description:
FACTOR_853380 Visit 6
cDNA


title: HMRN_52_v3

value: BL

value: Burkitt lymphoma

value: CODOX-M/IVAC


title: Fg_Barley_4d_BR1_cy3 vs mock


title: SI, FACTOR_853380_000

description:
FACTOR_853380 Visit 0
cDNA


title: SI, FACTOR_850120_005

description:
FACTOR_850120 Visit 5
cDNA


title: HMRN_53_v3

value: Burkitt lymphoma - HIV associated


title: TOL, FACTOR_841311_000

description:
FACTOR_841311 Visit 0
cDNA

value: tolerant


title: SI, FACTOR_850120_000

description:
FACTOR_850120 Visit 0
cDNA


title: HMRN_51_v3


title: New TOL, FACTOR_833683_004

description:
FACTOR_833683 Visit 4
cDNA

value: new tolerant


title: Fg_Barley_2d_BR1_cy3 vs mock

description: Barley infected with Fusarium graminearum for 48hrs vs mock infected barley

value: 2 days


title: HMRN_51_v3_rep

description: replicate sample

value: DLBCL


title: New TOL, FACTOR_833683_002

description:
FACTOR_833683 Visit 2
cDNA


title: Fg_Barley_4d_BR1_cy5 vs mock

value: Greenhouse

value: Encore


title: New TOL, FACTOR_833683_000

description:
FACTOR_833683 Visit 0
cDNA

value: peripheral whole blood

value: renal transplant


title: Fg_Barley_1d_BR1_cy3 vs mock


title: TOL, FACTOR_808379_006

description:
FACTOR_808379 Visit 6
cDNA


title: Fg_Barley_2d_BR1_cy5 vs mock


title: TOL, FACTOR_808379_004

description:
FACTOR_808379 Visit 4
cDNA


title: TOL, FACTOR_808379_002

description:
FACTOR_808379 Visit 2
cDNA


title: TOL, FACTOR_808379_000

description:
FACTOR_808379 Visit 0
cDNA


title: HMRN_48_v3

value: Diffuse Large B-cell Lymphoma MYC rearranged


title: SI, FACTOR_762897_006

description:
FACTOR_762897 Visit 6
cDNA

value: standard immunosuppression


title: HMRN_50_v3

value: yes


title: HMRN_49_v3

value: COP/COPAD/COPADM


title: SI, FACTOR_762897_000

description:
FACTOR_762897 Visit 0
cDNA


title: PDGFRa-GFP bright SHAM biological rep1

city: Palleja

first: Herbert

last: Auer

address: Calle Bellavista 53

institute: Functional GenOmics Consulting

description:
Sample name: AKP897
Gene expression data from PDGFRa-GFP bright cells

hyb_protocol: Affymetrix MG-430 PM array strips were hybridized with 8 mg of labeled cDNA, washed, stained and scanned according to the protocol described in GeneAtlas 3’IVT express kit User Manual

scan_protocol: Arrays were scanned with GeneAtlasImaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)

source_name: PDGFRa-GFP bright 5days post SHAM

label_protocol: cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Lungs were harvested 5 days post partial pneumonectomy or Sham surgery

extract_protocol: RNA isolation and cDNA amplification was performed as described by Gonzalez-Roca et al. (2010). In brief, cells were sorted into lysis buffer and RNA was purified using magnetic beads (RNAClean XP beads, Agencourt).RNA was reverse transcribed and cDNA was amplified using Whole Transcriptome Amplification chemistry (WTA2, Sigma Aldrich). For monitoring amplification, SYBR Green was added to the reaction; it was stopped after 25 cycles when SYBR Green signal reached a plateau. cDNA was purified using Genelute PCR Clean-Up kit (Sigma Aldrich).

treatment_protocol: Lungs were digested into single cell suspension using dispase. PDGFRa-GFP positive cells were isolated using FACS.

tag: protocol

value: sham surgery

value: lung

value: interstitial lung fibroblast

tag: cell subset

value: PDGFRa-GFP bright


title: SI, FACTOR_743013_006

description:
FACTOR_743013 Visit 6
cDNA

tag: tissue


title: PDGFRa-GFP dim  SHAM biological rep1

description:
Sample name: AKP898
Gene expression data from PDGFRa-GFP dim cells

source_name: PDGFRa-GFP dim 5days post SHAM

tag: cell type

value: PDGFRa-GFP dim


title: HMRN_43_v3

source_name: Biopsy

value: BL

value: R-CHOP


title: HMRN_47_v3

value: Burkitt lymphoma


title: HMRN_46_v3

value: DLBCL


title: PDGFRa-GFP dim PNX dnFGFR biological rep1

description:
Sample name: AKP894
Gene expression data from PDGFRa-GFP dim cells 5 days after pneumonectomy with dnFGFR

source_name: PDGFRa-GFP dim 5days post pneumonectomy dnFGFR

value: pneumonectomy with dnFGFR


title: SI, FACTOR_743013_000

description:
FACTOR_743013 Visit 0
cDNA

tag: group


title: PDGFRa-GFP bright SHAM biological rep2

description:
Sample name: AKP899
Gene expression data from PDGFRa-GFP bright cells


title: PDGFRa-GFP dim  SHAM biological rep2

description:
Sample name: AKP900
Gene expression data from PDGFRa-GFP dim cells


title: PDGFRa-GFP bright PNX dnFGFR biological rep2

description:
Sample name: AKP895
Gene expression data from PDGFRa-GFP bright cells 5 days after pneumonectomy with dnFGFR

source_name: PDGFRa-GFP bright 5days post pneumonectomy dnFGFR


title: HMRN_44_v3


title: HMRN_45_v3


title: LY_40_v3


title: PDGFRa-GFP dim PNX dnFGFR biological rep2

description:
Sample name: AKP896
Gene expression data from PDGFRa-GFP dim cells 5 days after pneumonectomy with dnFGFR


title: PDGFRa-GFP bright PNX dnFGFR biological rep1

description:
Sample name: AKP893
Gene expression data from PDGFRa-GFP bright cells 5 days after pneumonectomy with dnFGFR


title: LY_42_v3

value: Diffuse Large B-cell Lymphoma

value: CODOX-M/IVAC

value: no


title: PDGFRa-GFP bright PNX biological rep2

description:
Sample name: AKP891
Gene expression data from PDGFRa-GFP bright cells 5 days after pneumonectomy

source_name: PDGFRa-GFP bright 5days post pneumonectomy

value: pneumonectomy


title: LY_41_v3

value: Burkitt Lymphoma


title: PDGFRa-GFP dim PNX biological rep2

description:
Sample name: AKP892
Gene expression data from PDGFRa-GFP dim cells 5 days after pneumonectomy

source_name: PDGFRa-GFP dim 5days post pneumonectomy


title: TOL, FACTOR_712246_002

description:
FACTOR_712246 Visit 2
cDNA

source_name: TOL, cohort ITN507

value: peripheral whole blood

tag: disease state

value: renal transplant

value: tolerant


title: PDGFRa-GFP dim PNX biological rep1

description:
Sample name: AKP890
Gene expression data from PDGFRa-GFP dim cells 5 days after pneumonectomy

value: lung


title: LY_38_v3

value: yes


title: TOL, FACTOR_712246_000

description:
FACTOR_712246 Visit 0
cDNA

tag: patient id


title: LY_37_v3

value: Diffuse Large B-cell Lymphoma MYC rearranged


title: LY_39_v3


title: LY_36_v3


title: LY_35_v3


title: TOL, FACTOR_701789_006

description:
FACTOR_701789 Visit 6
cDNA

tag: visit


title: TOL, FACTOR_701789_004

description:
FACTOR_701789 Visit 4
cDNA

tag: cohort


title: TOL, FACTOR_701789_000

description:
FACTOR_701789 Visit 0
cDNA


title: SI, FACTOR_700990_000

description:
FACTOR_700990 Visit 0
cDNA

source_name: SI, cohort ITN507

value: standard immunosuppression


title: SI, FACTOR_700990_004

description:
FACTOR_700990 Visit 4
cDNA


title: High calcium shift 60 min time point

city: Manchester

first: Margherita

last: Bertuzzi

address: Core Technology Facility, 46 Grafton Street

department: Institute for Inflammation and Repair

institute: University of Manchester

description:
For CaCl2_60 min, ch1 = Cy5 and ch2 = Cy3
For CaCl2_60 min  flip dye, ch1 = Cy3 and ch2 = Cy5

hyb_protocol: The A. fumigatus oligonucleotide slides version 3 were used for microarray hybridization (http://pfgrc.tigr.org/slide_html/microarray_descriptions.shtml). Briefly, hybridizations were incubated for 18 h at 42°C. Post hybridization washes included (twice each) 55°C in 2X SSC, 0.1% SDS, RT in 0.1X SSC, 0.1% SDS and RT 0.1X SSC.

scan_protocol: After washing, slides were scanned with a GenePix 4000b scanner using GenePix Pro 3.0 software. PMT gains were changed in order to generate images with red:green ratios of as close to 1:1 as possible. Images were saved as .TIF files and TIGR Spotfinder (Saeed et al, 2003) was used to quantitate fluorescent intensities. Poor quality spots were identified manually and flagged. After Spotfinder analysis, results were exported as TIGR software compatible MEV files following local background subtraction.

data_processing: The phase- or strain-specific comparative analysis of gene expression datasets was conducted in Genespring GX 11.02 (Agilent). Normalised log2 expression ratios were filtered on expression level and differentially regulated transcripts were defined as having log2 (Cy5/Cy3) greater than the arbitrary thresholds of ± 1.5.

label: Cy5, Cy3

organism: Aspergillus fumigatus

source_name: high calcium shift, after 14 hours of growth at pH 5.0, 60 minutes shift to 200 mM CaCl2 pH 5.0

label_protocol: cDNA synthesis and labeling were performed as per JCVI PFGRC SOP m007 as described previously (McDonagh et al., 2008)(http://pfgrc.jcvi.org/index.php/microarray/protocols.html) Briefly, cDNA were generated using Invitrogen Superscript II, incorporating aminoallyl-dUTP. cDNA Samples were labeled with Cy3 or Cy5 during a 2 hour room temperature incubation followed by purification with a Qiagen PCR purification column to remove unbound dye.

growth_protocol: A. fumigatus spores were harvested into sterile water from cultures grown on solid Aspergillus Complete Media (ACM) for 5 days and spore suspensions were filtered using Miracloth. Conidial suspensions were spun for 10 min at 4000 rpm, washed twice with sterile water. Following enumeration, spores were resuspended in Aspergillus Minimal Media (AMM) plus vitamin solution (10 ml/l vitamin solution [400 mg/l 4-aminobenzoic acid, 50 mg/l aneurin, 1 mg/l biotin, 24 g/l mesoinositol, 100 mg/l nicotinic acid, 200 mg/l DL-pantothenic acid (hemicalcium salt), 250 mg/l pyridoxine monohydrochloride, 100 mg/l riboflavin, 1.4 mg/l choline chloride]). Mycelia were cultured for 14 hours and then transferred to fresh AMM plus vitamin solution in the respective conditions for the shift.

extract_protocol: Total RNA was extracted with RNA-Bee (Amsbio, UK) following the manufacturer instruction. About 1ug of total RNA was treated with RNase-free DNaseI (Invitrogen, UK) in order to eliminate eventual genomic DNA contaminations. Quality of RNA used for microarray analysis was checked by Nanodrop ND-1000 Spectrophotometer. Only RNA with an A260/280 and an A260/230 ratio > 1.9 was used for the experiments.

treatment_protocol: Treated mycelia were washed thoroughly with sterile water, quickly frozen in liquid nitrogen, and disrupted by grinding.

tag: time point

value: 60 minutes time point

value: mycelia

label: Cy3, Cy5

source_name: time zero reference

value: 0 minutes time point


title: TOL, FACTOR_679149_006

description:
FACTOR_679149 Visit 6
cDNA


title: TOL, FACTOR_681387_000

description:
FACTOR_681387 Visit 0
cDNA


title: PDGFRa-GFP bright PNX biological rep1

description:
Sample name: AKP889
Gene expression data from PDGFRa-GFP bright cells 5 days after pneumonectomy

value: interstitial lung fibroblast

value: PDGFRa-GFP bright


title: High calcium shift 45 min time point

description:
For CaCl2_45 min, ch1 = Cy5 and ch2 = Cy3
For CaCl2_45 min  flip dye, ch1 = Cy3 and ch2 = Cy5

source_name: high calcium shift, after 14 hours of growth at pH 5.0, 45 minutes shift to 200 mM CaCl2 pH 5.0

value: 45 minutes time point


title: LY_34_v3

value: BL

value: Diffuse Large B-cell Lymphoma

value: CODOX-M/IVAC


title: LY_33_v3

value: DLBCL

value: Burkitt Lymphoma


title: TOL, FACTOR_679149_004

description:
FACTOR_679149 Visit 4
cDNA

value: peripheral whole blood

value: renal transplant


title: TOL, FACTOR_679149_000

description:
FACTOR_679149 Visit 0
cDNA

value: tolerant


title: High calcium shift 15 min time point

description:
For CaCl2_15 min, ch1 = Cy5 and ch2 = Cy3
For CaCl2_15 min  flip dye, ch1 = Cy3 and ch2 = Cy5

source_name: high calcium shift, after 14 hours of growth at pH 5.0, 15 minutes shift to 200 mM CaCl2 pH 5.0

value: 15 minutes time point


title: High calcium shift 30 min time point

description:
For CaCl2_30 min, ch1 = Cy5 and ch2 = Cy3
For CaCl2_30 min  flip dye, ch1 = Cy3 and ch2 = Cy5

source_name: high calcium shift, after 14 hours of growth at pH 5.0, 30 minutes shift to 200 mM CaCl2 pH 5.0

value: 30 minutes time point


title: Alkaline shift 45 min time point

description:
For ALK_45 min, ch1 = Cy5 and ch2 = Cy3
For  ALK_45 min flip dye, ch1 = Cy3 and ch2 = Cy5

source_name: alkaline shift, after 14 hours of growth at pH 5.0, 45 minutes shift to pH 8.0


title: High calcium shift 5 min time point

description:
For CaCl2_5 min, ch1 = Cy5 and ch2 = Cy3
For CaCl2_5 min  flip dye, ch1 = Cy3 and ch2 = Cy5

source_name: high calcium shift, after 14 hours of growth at pH 5.0, 5 minutes shift to 200 mM CaCl2 pH 5.0

value: 5 minutes time point


title: SI, FACTOR_671619_006

description:
FACTOR_671619 Visit 6
cDNA

value: standard immunosuppression


title: LY_32_v3

value: no


title: LY_30_v3

value: EPOCH

value: yes


title: Alkaline shift 30 min time point

description:
For ALK_30 min, ch1 = Cy5 and ch2 = Cy3
For  ALK_30 min flip dye, ch1 = Cy3 and ch2 = Cy5

source_name: alkaline shift, after 14 hours of growth at pH 5.0, 30 minutes shift to pH 8.0

value: mycelia

value: 0 minutes time point


title: LY_31_v3

value: BL


title: SI, FACTOR_671619_000

description:
FACTOR_671619 Visit 0
cDNA


title: Alkaline shift 60 min time point

description:
For ALK_60 min, ch1 = Cy5 and ch2 = Cy3
For  ALK_60 min flip dye, ch1 = Cy3 and ch2 = Cy5

source_name: alkaline shift, after 14 hours of growth at pH 5.0, 60 minutes shift to pH 8.0

value: 60 minutes time point


title: LY_28_v3

value: CODOX-M/IVAC


title: LY_29_v3

value: DLBCL

value: Diffuse Large B-cell Lymphoma


title: Alkaline shift 15 min time point

description:
For ALK_15 min, ch1 = Cy5 and ch2 = Cy3
For  ALK_15 min flip dye, ch1 = Cy3 and ch2 = Cy5

source_name: alkaline shift, after 14 hours of growth at pH 5.0, 15 minutes shift to pH 8.0


title: Alkaline shift 5 min time point

description:
For ALK_5 min, ch1 = Cy5 and ch2 = Cy3
For  ALK_5 min flip dye, ch1 = Cy3 and ch2 = Cy5

source_name: alkaline shift, after 14 hours of growth at pH 5.0, 5 minutes shift to pH 8.0


title: LY_27_v3_rep

description: replicate sample

source_name: Biopsy


title: SI, FACTOR_662711_006

description:
FACTOR_662711 Visit 6
cDNA

value: peripheral whole blood


title: SI, FACTOR_662711_004

description:
FACTOR_662711 Visit 4
cDNA

value: renal transplant


title: LY_27_v3


title: SI, FACTOR_662711_000

description:
FACTOR_662711 Visit 0
cDNA


title: LY_26_v3_rep

description: replicate sample

value: Burkitt Lymphoma


title: New TOL, FACTOR_645626_000

description:
FACTOR_645626 Visit 0
cDNA

source_name: New TOL, cohort ITN507

value: new tolerant


title: LY_25_v3_rep

description: replicate sample


title: LY_25_v3_rep_2

description: replicate sample


title: s24h_RAW_IN3_1A_NS

city: Hangzhou

first: Qian

last: Zhou

address: Yuhang Road 866

country: China

institute: College of Pharmaceutical Sciences, Zhejiang University

description: Gene expression after ATRA and IL13 treatment for 24hrs in RAW264.7 cells

hyb_protocol: each slide was hybridized with 1.65ug Cy3-labeled cRNA using Gene Expression Hybridization Kit(Cat#5188-5242,Agilent technologies,santa clara,CA,US)in hybridization Oven(Cat#G2545A,Agilent technologies,santa clara,CA,US),according to the manufacturer's instructions. After 17 hours hybridization,slides were washed in staining dishes(Cat#121,Thermo shandon,Waltham,MA,US)with gene expression wash buffer kit(Cat#5188-5327,Agilent technologies,santa clara,CA,US),followed the manufacturer's instructions.

scan_protocol: slides were scanned by agilent  microarray scanner(cat#G2565CA,agilent technologies,santa,CA,US)with default setting,Dye channel:green,scan resolution=3um,20bit.Data were extracted with feature extraction software 10.7(Agilent technologies,santa clara,CA,US).

source_name: raw264.7 cells

label_protocol: total RNA was amplified and labeled by low input quick amp labeling kit,one-color(cat#5190-2305,agilent technologies,santa clara,CA,US),following the manufacturer's instructions.Labeled cRNA were purified by Rneasy mini lit(Cat#74106,QIAGEN,GmBH,Germany).

growth_protocol: RAW264.7 cells were cultured in DMEM medium supplemented with 15% heat-inactivated fetal bovine serum.   The cultures were incubated for 12 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent(Cat#15596-018,Life technologies,Carlsbad,CA,US)following the manufacture's instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies,Santa clara,CA,US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106,QIAGEN,GmBH,Germany)and RNase-free DNase Set(Cat#79254,QIAGEN,GmBH,Germany)

treatment_protocol: The cultures were incubated for 12 or 24 hours with ATRA or IL13 at 37 ºC in a humidified incubator with 5% CO2.

tag: cells

value: mouse macrophages 24h

tag: polarization type

value: M2 polarization suppressed


title: SI, FACTOR_583976_006

description:
FACTOR_583976 Visit 6
cDNA

value: standard immunosuppression


title: SI, FACTOR_583976_004

description:
FACTOR_583976 Visit 4
cDNA


title: TOL, FACTOR_579210_004

description:
FACTOR_579210 Visit 4
cDNA

value: tolerant


title: LY_26_v3


title: SI, FACTOR_573541_006

description:
FACTOR_573541 Visit 6
cDNA


title: LY_24_v3


title: LY_24_v3_rep

description: replicate sample


title: s24h_RAW_1A_NS

description: Gene expression after ATRA treatment for 24hrs in RAW264.7 cells

data_processing: Data were extracted with feature extraction software 10.7(Agilent technologies,santa clara,CA,US).

value: unpolarized


title: LY_25_v3

value: yes


title: s24h_RAW_con_NS

description: Gene expression after 24hrs in RAW264.7 cells


title: SI, FACTOR_573541_004

description:
FACTOR_573541 Visit 4
cDNA


title: LY_23_v3_rep

description: replicate sample

value: no


title: s12h_RAW_IN3_1A_NS

description: Gene expression after ATRA and IL13 treatment for 12hrs in RAW264.7 cells

value: mouse macrophages 12h


title: LY_23_v3


title: LY_22_v3


title: SI, FACTOR_583976_000

description:
FACTOR_583976 Visit 0
cDNA


title: lung_PBS-rep6

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profiling after 20hrs PBS

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: Mock

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from harvested lungs using Trizol/phenol chloroform extraction followed by precipitation.  RNA quality assessed using Agilent Bioanalyzer.

treatment_protocol: , mice were first exposed to either aerosolized PBS, Francisella tularensis subsp tularensis (FT SchuS4), the live vaccine strain of Francisella tularensis subsp. holarctica (FT LVS), or Francisella novicida (FN). Approximately 18hrs post-exposure, infected and control animals were exposed to aerosolized E. coli LPS, a potent TLR4 agonist. [25].  Lung samples were harvested 2.5 hrs later to measure changes in host transcriptome using microarray technology.

value: Lung

tag: agent

value: PBS

tag: time p.i.


title: SI, FACTOR_573541_000

description:
FACTOR_573541 Visit 0
cDNA


title: s24h_RAW_IN3_NS

description: Gene expression after IL13 treatment for 24hrs in RAW264.7 cells

value: M2 macrophages


title: s12h_RAW_1A_NS

description: Gene expression after ATRA treatment for 12hrs in RAW264.7 cells


title: SI, FACTOR_553535_000

description:
FACTOR_553535 Visit 0
cDNA


title: LY_20_v3

value: BL

value: CODOX-M/IVAC


title: SI, FACTOR_553478_004

description:
FACTOR_553478 Visit 4
cDNA

value: peripheral whole blood


title: SI, FACTOR_553478_000

description:
FACTOR_553478 Visit 0
cDNA

value: renal transplant


title: TOL, FACTOR_551339_006

description:
FACTOR_551339 Visit 6
cDNA

source_name: TOL, cohort ITN507


title: lung_PBS-rep3


title: LY_19_v3

value: DLBCL

value: Diffuse Large B-cell Lymphoma


title: lung_PBS-rep5


title: LY_18_v3


title: lung_PBS-rep4


title: lung_LPS-rep3 (LVS exposure group)

description: Gene expression profiling after 2.5hrs LPS

source_name: LPS (LVS exposure group)

value: LPS


title: LY_15_v3_rep

description: replicate sample


title: lung_PBS-rep1


title: lung_PBS-rep2


title: LY_17_v3

value: Diffuse Large B-cell Lymphoma MYC rearranged

value: R-CHOP


title: LY_16_v3

value: Burkitt Lymphoma


title: TOL, FACTOR_551339_004

description:
FACTOR_551339 Visit 4
cDNA

value: tolerant


title: TOL, FACTOR_551339_000

description:
FACTOR_551339 Visit 0
cDNA


title: SI, FACTOR_553478_006

description:
FACTOR_553478 Visit 6
cDNA

source_name: SI, cohort ITN507

value: standard immunosuppression


title: LY_13_v3

value: yes


title: TOL, FACTOR_541582_002

description:
FACTOR_541582 Visit 2
cDNA


title: lung_LPS-rep1 (LVS exposure group)


title: TOL, FACTOR_541582_000

description:
FACTOR_541582 Visit 0
cDNA


title: lung_LPS-rep2 (LVS exposure group)


title: TOL, FACTOR_541582_004

description:
FACTOR_541582 Visit 4
cDNA


title: SI, FACTOR_532410_006

description:
FACTOR_532410 Visit 6
cDNA


title: LY_15_v3

value: no


title: SI, FACTOR_505880_000

description:
FACTOR_505880 Visit 0
cDNA


title: SI, FACTOR_505880_004

description:
FACTOR_505880 Visit 4
cDNA


title: LY_21_v3


title: lung_LVS_rep3

description: Gene expression profiling after 20hrs LVS

source_name: FT LVS

value: Lung

value: FT LVS


title: SI, FACTOR_486391_006

description:
FACTOR_486391 Visit 6
cDNA


title: LY_14_v3


title: lung_FT LVS_LPS_rep2

description: Gene expression profiling after 20hrs LVS LPS

source_name: FT LVS LPS

value: FT LVS LPS


title: lung_FT LVS_LPS_rep3


title: s12h_RAW_IN3_NS

description: Gene expression after IL13 treatment for 12hrs in RAW264.7 cells

value: mouse macrophages 12h

value: M2 macrophages


title: LY_12_v3

value: BL

value: CODOX-M/IVAC


title: LY_10_v3

value: DLBCL


title: lung_LPS-rep1 (FN exposure group)

source_name: LPS (FN exposure group)


title: lung_LVS_rep1


title: LY_8_v3


title: SI, FACTOR_486391_000

description:
FACTOR_486391 Visit 0
cDNA

value: peripheral whole blood

value: renal transplant


title: LY_9_v3

value: Diffuse Large B-cell Lymphoma


title: New TOL, FACTOR_465810_000

description:
FACTOR_465810 Visit 0
cDNA

value: new tolerant


title: SI, FACTOR_445323_002

description:
FACTOR_445323 Visit 2
cDNA


title: lung_LVS_rep2


title: lung_FN_rep3

description: Gene expression profiling after 20hrs FN

source_name: FN

value: FN


title: SI, FACTOR_486391_004

description:
FACTOR_486391 Visit 4
cDNA


title: SI, FACTOR_445323_000

description:
FACTOR_445323 Visit 0
cDNA


title: lung_LPS-rep3 (FN exposure group)

value: LPS


title: s12h_RAW_con_NS

description: Gene expression after 12hrs in RAW264.7 cells

value: unpolarized


title: lung_FT LVS_LPS_rep1


title: lung_FN_rep2


title: LY_7_v3

value: Burkitt Lymphoma

value: yes


title: lung_FN_LPS_rep2

description: Gene expression profiling after 20hrs FN LPS

source_name: FN LPS

value: Lung

value: LPS FN


title: LY_4_v3

value: no


title: SI, FACTOR_439639_005

description:
FACTOR_439639 Visit 5
cDNA

value: standard immunosuppression


title: lung_FN_LPS_rep1


title: lung_FN_rep1


title: LY_6_v3


title: LY_1_v3


title: LY_2_v3


title: LY_3_v3


title: lung_LPS_rep3 (FT SchuS4 exposure group)

description: Gene expression profiling after 2.5hrs  LPS

source_name: LPS (FT SchuS4 exposure group)


title: lung_LPS-rep2 (FN exposure group)


title: lung_FN_LPS_rep3


title: Post-transplant_Muscle_30 minutes after exercise, 011

city: Tucson

first: Dawn

middle: K

last: Coletta

state: AZ

address: 1501 N. Campbell Ave

department: Medicine

institute: UNIVERSITY OF ARIZONA

description:
011 post exercise
Gene expression after exercise post-transplant.

hyb_protocol: Cy3-labeled aRNA was fragmented using Agilent Gene Expression Hybridization kit and hybridized to Agilent-014850 4x44K Whole Human Genome Microarray at 65C for 17 hours.

scan_protocol: After washing, slides were scanned with an Agilent DNA microarray scanner.

data_processing:
Feature Extraction software version 10.5.1.1 (Agilent) was used for analysis.
Quantile-normalized log2 signal intensities generated in GeneSpring V12. Log2 signal values for the unique genes (41K) generated.

source_name: Vastus lateralis muscle, 30 minutes post-exercise, post-transplant

label_protocol: Total RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA amplification kit and quantified for Cy3 dye labeled aRNA concentration, RNA absorbance ratio, A260, Adye, and dye/probe values.

extract_protocol: Muscle biopsy specimens were homogenized in RNAStat solution using a Polytron homogenizer, and the total RNA was purified with RNeasy and DNase I treatment.

treatment_protocol: Volunteers before and after kidney transplant (n=5, age 52±2) had glucose clamps (Rd) and an exercise bout with muscle biopsies (Bx) pre and 30 minutes after an exercise bout, and muscle biopsies were frozen in liquid nitrogen.

tag: gender

value: male

value: 40 yrs

tag: kidney transplant status

value: post-transplant

value: vastus lateralis muscle

tag: timepoint

value: after exercise


title: SI, FACTOR_439639_006

description:
FACTOR_439639 Visit 6
cDNA

value: peripheral whole blood

value: renal transplant


title: SI, FACTOR_432603_000

description:
FACTOR_432603 Visit 0
cDNA


title: SI, FACTOR_418828_004

description:
FACTOR_418828 Visit 4
cDNA


title: SI, FACTOR_418828_002

description:
FACTOR_418828 Visit 2
cDNA


title: lung_LPS_rep1 (FT SchuS4 exposure group)


title: SI, FACTOR_439639_000

description:
FACTOR_439639 Visit 0
cDNA


title: SI, FACTOR_405881_006

description:
FACTOR_405881 Visit 6
cDNA


title: SI, FACTOR_405881_000

description:
FACTOR_405881 Visit 0
cDNA


title: TOL, FACTOR_402941_012

description:
FACTOR_402941 Visit 12
cDNA

value: tolerant


title: Post-transplant_Muscle_Basal before exercise, 011

description:
011 post basal
Gene expression before exercise post-transplant.

source_name: Vastus lateralis muscle, basal pre-exercise, post-transplant

tag: age

value: before exercise


title: TOL, FACTOR_402941_000

description:
FACTOR_402941 Visit 0
cDNA


title: lung_FT SchuS4_rep2

description: Gene expression profiling after 20hrs FT Schu4

source_name: FT Schu4

value: FT Schu4


title: lung_FT SchuS4_LPS_rep2

description: Gene expression profiling after 20hrs FT SchuS4 LPS

source_name: FT Schu4 LPS

value: FT Schu4 LPS


title: lung_LPS_rep2 (FT SchuS4 exposure group)

value: LPS


title: Post-transplant_Muscle_Basal before exercise, 009

description:
009 post basal 2
Gene expression before exercise post-transplant.

value: 62 yrs


title: Pre-transplant_Muscle_Basal before exercise, 011

description:
011 pre basal
Gene expression before exercise pre-transplant.

source_name: Vastus lateralis muscle, basal pre-exercise, pre-transplant

value: pre-transplant


title: Post-transplant_Muscle_30 minutes after exercise, 009

description:
009 post exercise 2
Gene expression after exercise post-transplant.


title: lung_FT SchuS4_rep1

value: Lung


title: TOL, FACTOR_402941_006

description:
FACTOR_402941 Visit 6
cDNA


title: Pre-transplant_Muscle_30 minutes after exercise, 009

description:
009 pre exercise 2
Gene expression after exercise pre-transplant.

source_name: Vastus lateralis muscle, 30 minutes post-exercise, pre-transplant


title: lung_FT SchuS4_LPS_rep1


title: TOL, FACTOR_402941_004

description:
FACTOR_402941 Visit 4
cDNA


title: lung_TRIF KO_rep2

description: Gene expression profiling after 2.5hrs TRIF KO PBS

source_name: TRIF KO

value: PBS


title: LY_5_v3

source_name: Biopsy

value: DLBCL

value: Diffuse Large B-cell Lymphoma

tag: treatment

value: CODOX-M/IVAC

value: no


title: Pre-transplant_Muscle_Basal before exercise, 009

description:
009 pre basal 2
Gene expression before exercise pre-transplant.

value: male

tag: tissue

value: vastus lateralis muscle


title: Post-transplant_Muscle_Basal before exercise, 007

description:
007 post basal 2
Gene expression before exercise post-transplant.

value: 66 yrs

value: post-transplant


title: lung_TRIF KO_rep4


title: lung_TRIF KO_rep3


title: SI, FACTOR_278451_006

description:
FACTOR_278451 Visit 6
cDNA

value: peripheral whole blood

value: renal transplant

value: standard immunosuppression


title: Post-transplant_Muscle_30 minutes after exercise, 007

description:
007 post exercise 2
Gene expression after exercise post-transplant.

value: after exercise


title: lung_TRIF KO_rep1


title: SI, FACTOR_278451_002

description:
FACTOR_278451 Visit 2
cDNA


title: Pre-transplant_Muscle_30 minutes after exercise, 007

description:
007 pre exercise 2
Gene expression after exercise pre-transplant.


title: Post-transplant_Muscle_30 minutes after exercise, 005

description:
005 post exercise
Gene expression after exercise post-transplant.

value: female

value: 45 yrs


title: TOL, FACTOR_274363_006

description:
FACTOR_274363 Visit 6
cDNA

source_name: TOL, cohort ITN507

value: tolerant


title: SI, FACTOR_278451_000

description:
FACTOR_278451 Visit 0
cDNA


title: TOL, FACTOR_274363_002

description:
FACTOR_274363 Visit 2
cDNA


title: SI, FACTOR_249795_000

description:
FACTOR_249795 Visit 0
cDNA


title: SI, FACTOR_245217_006

description:
FACTOR_245217 Visit 6
cDNA


title: SI, FACTOR_245217_000

description:
FACTOR_245217 Visit 0
cDNA


title: Post-transplant_Muscle_Basal before exercise, 005

description:
005 post basal
Gene expression before exercise post-transplant.

value: before exercise


title: Post-transplant_Muscle_30 minutes after exercise, 003

description:
003 post exercise
Gene expression after exercise post-transplant.

value: 48 yrs


title: New TOL, FACTOR_243751_000

description:
FACTOR_243751 Visit 0
cDNA

source_name: New TOL, cohort ITN507

value: new tolerant


title: lung_Myd88 KO_rep3

description: Gene expression profiling after 2.5hrs Myd88 KO PBS

source_name: Myd88 KO

value: Lung

value: PBS


title: Pre-transplant_Muscle_Basal before exercise, 005

description:
005 pre basal
Gene expression before exercise pre-transplant.

value: pre-transplant


title: Pre-transplant_Muscle_Basal before exercise, 007

description:
007 pre basal 2
Gene expression before exercise pre-transplant.

value: male


title: lung_C57BL6wt_rep4

description: Gene expression profiling after 2.5hrs C57BL6wt PBS


title: TOL, FACTOR_274363_004

description:
FACTOR_274363 Visit 4
cDNA


title: lung_C57BL6wt_rep2


title: Pre-transplant_Muscle_30 minutes after exercise, 005

description:
005 pre exercise
Gene expression after exercise pre-transplant.

value: vastus lateralis muscle


title: Post-transplant_Muscle_Basal before exercise, 003

description:
003 post basal
Gene expression before exercise post-transplant.


title: TOL, FACTOR_231375_004

description:
FACTOR_231375 Visit 4
cDNA


title: lung_C57BL6wt_rep3


title: wt at T4h

city: Turku

first: Heli

last: Elovaara

address: Tykistokatu 6A

department: Medicity research laboratory

country: Finland

institute: University of Turku

description: Gene expression data from wt E. Coli K-12 4h after the induction of tynA gene.

hyb_protocol: Samples were hybridized to GeneChip® E. coli Genome 2.0 Array at +45°C  for 16 h according to GeneChip® Expression Analysis Technical Manual (With Specific Protocols for Using the GeneChip® Hybridization, Wash and Stain Kit).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 with Autoloader.

data_processing: Data analysis was done using R language and environment for a statistical computing and Bioconductor.  Array data were normalized with gcRMA method.

organism: Escherichia coli

source_name: Escherichia coli K-12 wt 4h after the induction of tynA expression

label_protocol: Affymetrix based end-terminus labeling with biotin.

growth_protocol: Bacteria were cultured in an M9 minimal medium supplemented with 2 g/L lactose and 5 mM phenylethylamine (PEA, M9+L+PEA). To induce ECAO expression from tynA gene, o/n culture of wt E. coli in M9-lactose medium was diluted 1:20 in M9+L+PEA with 5 μM CuSO4. The bacteria were grown aerobically at +30°C with 250 rpm shaking.

extract_protocol: Total RNA was isolated using the RNeasy Mini-Kit (Qiagen) according to the manufacturer`s instruction and DNA was removed by using RNAse-Free DNAse Set (Qiagen).

treatment_protocol: Samples were treated with Prokaryotic Target Preparation protocol (GeneChip Expression Analysis Technical Manual).

tag: genotype

value: wild type

tag: strain


title: lung_C57BL6wt_rep1


title: lung_TRIF KO_LPS_rep4

description: Gene expression profiling after 2.5hrs TRIF KO LPS

source_name: TRIF KO LPS

value: LPS


title: lung_Myd88 KO_rep1


title: LY_11_v3

value: BL

value: Diffuse Large B-cell Lymphoma

value: CODOX-M/IVAC

value: no


title: lung_TRIF KO_LPS_rep3


title: lung_Myd88 KO_rep2


title: Pre-transplant_Muscle_30 minutes after exercise, 003

description:
003 pre exercise
Gene expression after exercise pre-transplant.

value: after exercise


title: lung_TRIF KO_LPS_rep2


title: Pre-transplant_Muscle_Basal before exercise, 003

description:
003 pre basal
Gene expression before exercise pre-transplant.


title: TOL, FACTOR_231375_000

description:
FACTOR_231375 Visit 0
cDNA

value: peripheral whole blood

tag: disease state

value: renal transplant

tag: group


title: lung_TRIF KO_LPS_rep1


title: lung_Myd88 KO_rep4


title: wt at T1h

description: Gene expression data from wt E. Coli K-12 1h after the induction of tynA gene.

source_name: Escherichia coli K-12 tynA- 4h after the induction of tynA expression


title: lung_Myd88 KO_LPS_rep4

description: Gene expression profiling after 2.5hrs Myd88 KO LPS

source_name: Myd88 KO LPS


title: SI, FACTOR_213935_004

description:
FACTOR_213935 Visit 4
cDNA

source_name: SI, cohort ITN507

value: standard immunosuppression

tag: patient id

tag: visit


title: TOL, FACTOR_208304_006

description:
FACTOR_208304 Visit 6
cDNA

value: tolerant

tag: cohort


title: SI, FACTOR_213935_002

description:
FACTOR_213935 Visit 2
cDNA


title: SI, FACTOR_213935_006

description:
FACTOR_213935 Visit 6
cDNA


title: tynA- at T4h

description: Gene expression data from E. Coli K-12 tynA- 4h after the induction of tynA gene.

source_name: Escherichia coli K-12 tynA- 1h after induction of tynA expression

value: tynA-


title: tynA- at T1h

description: Gene expression data from E. Coli K-12 tynA- 1h after the induction of tynA gene.

source_name: Escherichia coli K-12 wt at time of induction of tynA expression


title: TOL, FACTOR_208304_002

description:
FACTOR_208304 Visit 2
cDNA


title: tynA- at T0

description: Gene expression data from E. Coli K-12 tynA- at the time of induction of tynA gene.

source_name: Escherichia coli K-12 tynA- at time of induction of tynA expression


title: SI, FACTOR_193782_006

description:
FACTOR_193782 Visit 6
cDNA


title: TOL, FACTOR_208304_000

description:
FACTOR_208304 Visit 0
cDNA


title: wt at T0

description: Gene expression data from wt E. Coli K-12 at the time of induction of tynA gene.

source_name: Escherichia coli K-12 wt 1h after the induction of tynA expression


title: SI, FACTOR_193782_004

description:
FACTOR_193782 Visit 4
cDNA


title: lung_Myd88 KO_LPS_rep3

value: Lung


title: lung_Myd88 KO_LPS_rep2


title: SI, FACTOR_193782_002

description:
FACTOR_193782 Visit 2
cDNA


title: lung_Myd88 KO_LPS_rep1


title: UMR_control_1

city: Livermore

first: Aimy

last: Sebastian

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

description: gene expression data from UMR-106 cells cultured alone

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array or Rat 230.2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Microarray data analysis was conducted using Bioconductor. Data preprocessing and normalization were performed using Robust Multi-chip Average (RMA) protocol. Genes differentially expressed between different conditions were identified using the empirical Bayes method implemented in Linear Models for MicroArray package.

organism: Rattus norvegicus

source_name: UMR-106 cells cultured alone

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PC3 cells, UMR-106 cells and primary osteoblasts were cultured in either a 12 well plate or a 3.0 µm pore transwell insert until cells reached 50% confluency in DMEM/F-12 media supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin.Then the media was changed to serum-free DMEM/F-12 media and the cells were cultured for 48 hours prior to RNA isolation.

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini columns performed according to the manufacturer's instructions.

tag: cell line

value: UMR-106 osteoblast-like cells


title: UMR_control_2

growth_protocol: PC3 cells, UMR-106 cells and primary osteoblasts were cultured in either a 12 well plate or a 3.0 µm pore transwell insert until cells reached 50% confluency in DMEM/F-12 media supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin. Then the media was changed to serum-free DMEM/F-12 media and the cells were cultured for 48 hours prior to RNA isolation.


title: lung_C57BL6wt_LPS_rep3

description: Gene expression profiling after 2.5hrs C57BL6wt LPS

source_name: C57BL6wt  LPS


title: lung_C57BL6wt_LPS_rep1


title: UMR+PC3_2

description: gene expression data from UMR-106 cells co-cultured with PC3 cells


title: lung_C57BL6wt_LPS_rep4


title: ok778-PA14-prep15

city: Gettysburg

first: Jennifer

middle: R

last: Powell

state: PA

address: 300 N. Washington Street

department: Biology

institute: Gettysburg College

description: fshr-1 mutant worms, PA14 infection

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: GenePattern (Broad Institute)

organism: Caenorhabditis elegans

source_name: fshr-1(ok778) exposed to PA14 for 4 hours

label_protocol: Affymetrix

growth_protocol: Embryos were collected by bleaching and allowed to hatch and then arrest in the absence of food.  Arrested L1 larvae were placed onto NGM plates seeded with OP50 and grown at 20oC to the young adult stage.  Worms were washed from these plates and transferred to SK plates seeded with OP50 or PA14.  After 4 hours, animals were harvested for analysis.

extract_protocol: TRI reagent (Molecular Research Center)

treatment_protocol: Animals were transferred to SK plates seeded with OP50 or PA14 4 hours prior to harvesting.

tag: bacteria


title: UMR+PC3_1

source_name: UMR-106 cells co-cultured with PC3 cells

growth_protocol: PC3 cells, UMR-106 cells and primary osteoblasts were cultured in either a 12 well plate or a 3.0 µm pore transwell insert until cells reached 50% confluency in DMEM/F-12 media supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin.Then the media was changed to serum-free DMEM/F-12 media and the cells were cultured for 48 hours prior to RNA isolation


title: SI, FACTOR_193782_000

description:
FACTOR_193782 Visit 0
cDNA


title: TOL, FACTOR_191757_006

description:
FACTOR_191757 Visit 6
cDNA


title: TOL, FACTOR_191757_004

description:
FACTOR_191757 Visit 4
cDNA


title: HepG2_VECELL_3-1

city: Setagaya

first: Seiichi

last: Ishida

state: Tokyo

address: 1-18-1, Kamiyoga

department: Pharmacology

country: Japan

institute: National Institute of Health Sciences

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on HG U133A chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: HepG2 on VECELL

label_protocol: Biotinylated aRNA were prepared by 3'-IVT Express Kit according to the manufactuer's instruction from 100 ng of total RNA.

growth_protocol: HepG2 cells were cultured either on normal cell culture plate or on VECELL for three days at 37°C in humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA were prepared by RNeasy Mini Total RNA Extraction Kit (Qiagen, Hileden, Germany) according to the manufacturer’s instruction.

tag: culture vessel

value: VECELL 3

tag: hybridization replicate

value: hybridization 1


title: HepG2_VECELL_3-2

value: hybridization 2


title: ok778-PA14-prep30

description: fshr-1 mutant worms, PA14 infection


title: TOL, FACTOR_191757_002

description:
FACTOR_191757 Visit 2
cDNA

source_name: TOL, cohort ITN507


title: TOL, FACTOR_157168_006

description:
FACTOR_157168 Visit 6
cDNA


title: TOL, FACTOR_150776_010

description:
FACTOR_150776 Visit 10
cDNA


title: TOL, FACTOR_208304_004

description:
FACTOR_208304 Visit 4
cDNA


title: ok778-PA14-prep9

description: fshr-1 mutant worms, PA14 infection


title: TOL, FACTOR_150776_006

description:
FACTOR_150776 Visit 6
cDNA


title: TOL, FACTOR_150776_000

description:
FACTOR_150776 Visit 0
cDNA


title: HepG2_plate_3-2

source_name: HepG2 on plate

value: normal culture plate 3


title: HepG2_VECELL_2-1

value: VECELL 2


title: HepG2_VECELL_1-1

value: VECELL 1


title: SI, FACTOR_143335_000

description:
FACTOR_143335 Visit 0
cDNA


title: HepG2_VECELL_1-2


title: lung_C57BL6wt_LPS_rep2

tag: agent

value: LPS

tag: time p.i.


title: ok778-OP50-prep30

description: fshr-1 mutant worms, no infection

source_name: fshr-1(ok778) exposed to OP50 for 4 hours


title: TOL, FACTOR_118518_000

description:
FACTOR_118518 Visit 0
cDNA


title: HepG2_plate_2-2

value: normal culture plate 2


title: HepG2_plate_2-1


title: HepG2_plate_3-1


title: ok778-OP50-prep15

description: fshr-1 mutant worms, no infection


title: SI, FACTOR_109622_006

description:
FACTOR_109622 Visit 6
cDNA


title: ok778-OP50-prep9

description: fshr-1 mutant worms, no infection


title: HepG2_plate_1-2

value: normal culture plate 1


title: N2-PA14-prep15

description: wild-type worms, PA14 infection

source_name: N2 exposed to PA14 for 4 hours


title: N2-PA14-prep9

description: wild-type worms, PA14 infection


title: N2-OP50-prep30

description: wild-type worms, no infection

source_name: N2 exposed to OP50 for 4 hours


title: Ag-B7+IL21 @72hr, biological rep1

city: Minneapolis

first: Lynn

last: Heltemes Harris

state: MN

address: 2101 6th St. SE

institute: University of Minnesota

description: OT-I CD8 T cells stimulated with Ag-B7+IL21 @72hr, biological rep1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45oC on Murine GeneChip U74Av2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 according to Affymetrix protocol at the University of Minnesota Microarray facility.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings as the normalization method with scaling target signal set to 1000.

source_name: In vitro stimulated OT-I TCR transgenic CD8 T lymphocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10ug total RNA (Expression Analysis Technical Manual, Affymetrix) using Enzo Bioarray HighYield RNA transcript labeling kit.

growth_protocol: CD44lo CD8+ T cells were negatively enriched from lymph nodes of OT-1 TCR transgenic mice and stimulated in vitro with H-2Kb:SINNFEKL peptide complex and B7-1 proteins coated on 5uM latex microspheres in presence or absence of murine IL-21. All cultures were supplemented with human rIL-2.  At 48h, and 72h the cells from cultures were harvested for analysis.

extract_protocol: Total RNA was extracted using Rneasy Mini Kit, Qiagen and performed according to the manufacturer's instructions.

treatment_protocol: At indicated times after stimulation, the cells were harvested, washed with PBS and subjected to RNA isolation procedure.

value: CD8 T lymphocyte

tag: genotype/variation

value: OT-1 TCR transgenic

value: 6 to 8 weeks

value: stimulated with Ag-B7+IL21

tag: time


title: N2-OP50-prep9

description: wild-type worms, no infection


title: HepG2_plate_1-1


title: Ag-B7+IL21 @48hr, biological rep2

description: OT-I CD8 T cells stimulated with Ag-B7+IL21 @48hr, biological rep2

tag: age

tag: treatment


title: HepG2_VECELL_2-2


title: Ag-B7@ 48hr, biological rep2

description: OT-I CD8 T cells stimulated with Ag-B7@ 48hr, biological rep2

tag: tissue

value: stimulated with Ag-B7


title: Ag-B7+IL21 @48hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7+IL21 @48hr, biological rep1

tag: strain


title: N2-OP50-prep15

description: wild-type worms, no infection

tag: genotype


title: Ag-B7@ 48hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7@ 48hr, biological rep1


title: SI, FACTOR_109622_002

description:
FACTOR_109622 Visit 2
cDNA

value: peripheral whole blood

tag: disease state

value: renal transplant

tag: group

value: standard immunosuppression


title: Rh4-PAX3-FOXO1 siRNA transfected for 72h-2

status: Public on Sep 29 2015

city: Zurich

first: Beat

last: Schäfer

state: ZH

address: Balgrist Campus Lengghalde 5

department: Oncology

country: Switzerland

institute: University Childrens Hospital

description: Gene expression data from Rh4 cells treated for 72h with siRNA directed against PAX3-FOXO1

hyb_protocol: Fifteen microg of labeled cRNA was fragmented at 94°C for 35 min in a buffer  containing 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, and 30 mM  magnesium acetate. Fragmented cRNA was mixed with a mixture containing  0.1 M 4-morpholinepropanesulfonic acid (pH 6.5–6.7), 1 M NaCl, 20 mM  EDTA, 0.01% Tween-20, 0.5 mg/ml acetylated bovine serum albumin, 0.1  mg/ml herring sperm DNA, 1x eukaryotic hybridization control mix, and 50  pM B2 control oligo (Affymetrix). This mixture was heated to 95°C for 5 min,  followed by incubation at 45°C for 5 min and centrifugation for 5 min at  maximum speed. The probe array was incubated at 45°C for 16 h at constant  rotation (60 rpm).

scan_protocol: Stained arrays were scanned in a Gene Array Scanner (Agilent)

data_processing: Data was imported in dCHIP and normalized

source_name: Rh4 cells treated with siRNA directed against PAX3-FOXO1 for 72h, sample 2

label_protocol: RNA amplification and labeling were done according to the GeneChip  eukaryotic small sample target labeling technical note (Affymetrix, Santa  Clara, CA).

growth_protocol: Rh4 cells were grown in DMEM/10% FBS

extract_protocol: Total RNA was extracted using the RNAeasy kit including the DNAse digestion step

treatment_protocol: Transfection was carried using 7 microl of GeneEraser (Stratagene, La Jolla, CA, USA) and 20 nm siRNA (final concentration) per 6-well

value: alveolar rhadomyosarcoma


title: Rh4-PAX3-FOXO1 siRNA transfected for 48h-1

description: Gene expression data from Rh4 cells treated for 48h with siRNA directed against PAX3-FOXO1

source_name: Rh4 cells treated with siRNA directed against PAX3-FOXO1 for 48h, sample 1


title: Rh4-sc siRNA transfected for 72h-1

description: Gene expression data from Rh4 cells treated for 72h with scrambled siRNA

source_name: Rh4 cells treated with sc siRNA for 72h, sample 1


title: Rh4-PAX3-FOXO1 siRNA transfected for 24h-1

description: Gene expression data from Rh4 cells treated for 24h with siRNA directed against PAX3-FOXO1

source_name: Rh4 cells treated with siRNA directed against PAX3-FOXO1 for 24h, sample 1


title: Rh4-PAX3-FOXO1 siRNA transfected for 72h-1

source_name: Rh4 cells treated with siRNA directed against PAX3-FOXO1 for 72h, sample 1


title: Rh4-sc siRNA transfected for 72h-2

source_name: Rh4 cells treated with sc siRNA for 72h, sample 2


title: Rh4-sc siRNA transfected for 48h-2

description: Gene expression data from Rh4 cells treated for 48h with scrambled siRNA

source_name: Rh4 cells treated with sc siRNA for 48h, sample 2


title: Rh4-untreated-1

description: Gene expression data from untreated Rh4 cells

source_name: Untreated Rh4 cells, sample 1


title: Rh4-sc siRNA transfected for 48h-1

source_name: Rh4 cells treated with sc siRNA for 48h, sample 1


title: Rh4-PAX3-FOXO1 siRNA transfected for 24h-2

source_name: Rh4 cells treated with siRNA directed against PAX3-FOXO1 for 24h, sample 2


title: Rh4-sc siRNA transfected for 24h-1

description: Gene expression data from Rh4 cells treated for 24h with scrambled siRNA

source_name: Rh4 cells treated with sc siRNA for 24h, sample 1


title: Rh4-untreated-2

source_name: Untreated Rh4 cells, sample 2


title: Rh4-PAX3-FOXO1 siRNA transfected for 48h-2

source_name: Rh4 cells treated with siRNA directed against PAX3-FOXO1 for 48h, sample 2


title: N2-PA14-prep30

description: wild-type worms, PA14 infection


title: Rh4-sc siRNA transfected for 24h-2

source_name: Rh4 cells treated with sc siRNA for 24h, sample 2


title: NAFLD Rat 6w-2

city: Xinxiang

first: Cunshuan

last: Xu

address: No. 46, Construction East Road

institute: Henan Normal University

description: Liver tissues from rats after high-fat emulsion feeding for 6w,technical rep2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Rat Genome 230 2.0 array. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).

data_processing:
The data were analyzed with Affymetrix GCOS 2.0 software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
When P value is < 0.05, it means that the gene is present (P), when < 0.065, means marginal (M), and when > 0.065, means marked absent (A). On the other hand, the normalized signal values in PH to that in control were used to calculate the relative value, that is, ratio value of gene expression abundance. When ratio value is ≥ 2, it means that gene expression change was significantly up-regulated, when ≤ 0.5, means significantly down-regulated, and when 0.5-2, means biologically insignificant. To minimize the technical errors from microarray analysis, each sample was tested at least three times using Rat Genome 230 2.0 microarray, and the average value was considered as a reliable value.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip In Vitro Transcript Labeling Kit, ENZO Biochemical, New York, USA).

extract_protocol: Total RNA was extracted according to the manual of Trizol reagent (Invitrogen Corporation, Carlsbad, California, USA) and purified following the RNeasy mini protocol (Qiagen, Inc, Valencia, CA, USA).

treatment_protocol: After the model of NAFLD  was established, the rats at corresponding time points were anaesthetized, and then the liver tissues from the middle part of the right lobe of the liver were collected in RNase-free tubes for use.

value: Sprague-Dawley

value: Liver


title: NAFLD Rat 0h-3

description: Normal liver tissues at 0h, technical rep3

source_name: Normal liver tissues


title: NAFLD Rat 4w-1

description: Liver tissues from rats after high-fat emulsion feeding for 4w,technical rep1


title: NAFLD Rat 6w-3

description: Liver tissues from rats after high-fat emulsion feeding for 6w,technical rep3


title: NAFLD Rat 2w-1

description: Liver tissues from rats after high-fat emulsion feeding for 2w,technical rep1


title: LC Rat 9w-3

description: Liver tissues from rats after carbon tetrachloride administration for 9w,technical rep3

treatment_protocol: After the model of LC  was established, the rats at corresponding time points were anaesthetized, and then the liver tissues from the middle part of the right lobe of the liver were collected in RNase-free tubes for use.


title: NAFLD Rat 4w-2

description: Liver tissues from rats after high-fat emulsion feeding for 4w,technical rep2


title: LC Rat 6w-1

description: Liver tissues from rats after carbon tetrachloride administration for 6w,technical rep1


title: LC Rat 9w-1

description: Liver tissues from rats after carbon tetrachloride administration for 9w,technical rep1


title: NAFLD Rat 4w-3

description: Liver tissues from rats after high-fat emulsion feeding for 4w,technical rep3


title: NAFLD Rat 2w-2

description: Liver tissues from rats after high-fat emulsion feeding for 2w,technical rep2


title: LC Rat 0h-1

description: Normal liver tissues at 0h, technical rep1


title: NAFLD Rat 0h-1


title: HC 18w-3

description: Liver tissues from HCs after diethylnitrosamine treatment for 18w,technical rep3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on HC Genome 230 2.0 array. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

data_processing:
The data were analyzed with Affymetrix GCOS 2.0 software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
When P value is < 0.05, it means that the gene is present (P), when < 0.065, means marginal (M), and when > 0.065, means marked absent (A). On the other hand, the normalized signal values in PH to that in control were used to calculate the relative value, that is, HCio value of gene expression abundance. When HCio value is ≥ 2, it means that gene expression change was significantly up-regulated, when ≤ 0.5, means significantly down-regulated, and when 0.5-2, means biologically insignificant. To minimize the technical errors from microarray analysis, each sample was tested at least three times using HC Genome 230 2.0 microarray, and the average value was considered as a reliable value.

extract_protocol: Total RNA was extracted according to the manual of Trizol reagent (Invitrogen CorpoHCion, Carlsbad, California, USA) and purified following the RNeasy mini protocol (Qiagen, Inc, Valencia, CA, USA).

treatment_protocol: After the model of HC was established, the HCs at corresponding time points were anaesthetized, and then the liver tissues from the middle part of the right lobe of the liver were collected in RNase-free tubes for use.


title: NAFLD Rat 2w-3

description: Liver tissues from rats after high-fat emulsion feeding for 2w,technical rep3


title: NAFLD Rat 0h-2

description: Normal liver tissues at 0h, technical rep2


title: LC Rat 6w-3

description: Liver tissues from rats after carbon tetrachloride administration for 6w,technical rep3


title: LC Rat 6w-2

description: Liver tissues from rats after carbon tetrachloride administration for 6w,technical rep2


title: LC Rat 0h-2


title: LC Rat 3w-3

description: Liver tissues from rats after carbon tetrachloride administration for 3w,technical rep3


title: LC Rat 3w-2

description: Liver tissues from rats after carbon tetrachloride administration for 3w,technical rep2


title: LC Rat 0h-3

description: Normal liver tissues at 0h, technical rep3


title: Pre-transplant_Muscle_30 minutes after exercise, 011

description:
011 pre exercise
Gene expression after exercise pre-transplant.

source_name: Vastus lateralis muscle, 30 minutes post-exercise, pre-transplant

tag: gender

value: male

value: 40 yrs

tag: kidney transplant status

value: pre-transplant

value: vastus lateralis muscle

tag: timepoint

value: after exercise

tag: patient id


title: HC 18w-2

description: Liver tissues from HCs after diethylnitrosamine treatment for 18w,technical rep2


title: HC 16w-2

description: Liver tissues from HCs after diethylnitrosamine treatment for 16w,technical rep2


title: HC 18w-1

description: Liver tissues from HCs after diethylnitrosamine treatment for 18w,technical rep1


title: NAFLD Rat 6w-1

description: Liver tissues from rats after high-fat emulsion feeding for 6w,technical rep1


title: HC 8w-3

description: Liver tissues from HCs after diethylnitrosamine treatment for 8w,technical rep3


title: HC 8w-2

description: Liver tissues from HCs after diethylnitrosamine treatment for 8w,technical rep2


title: HC 5w-3

description: Liver tissues from HCs after diethylnitrosamine treatment for 5w,technical rep3


title: HC 0h-1

description: Normal liver tissues at 0h, technical rep1


title: HC 12w-1

description: Liver tissues from HCs after diethylnitrosamine treatment for 12w,technical rep1


title: HC 0h-2


title: HC 5w-2

description: Liver tissues from HCs after diethylnitrosamine treatment for 5w,technical rep2


title: HC 16w-1

description: Liver tissues from HCs after diethylnitrosamine treatment for 16w,technical rep1


title: HC 5w-1

description: Liver tissues from HCs after diethylnitrosamine treatment for 5w,technical rep1


title: HC 12w-2

description: Liver tissues from HCs after diethylnitrosamine treatment for 12w,technical rep2


title: LC Rat 3w-1

description: Liver tissues from rats after carbon tetrachloride administration for 3w,technical rep1


title: HC 12w-3

description: Liver tissues from HCs after diethylnitrosamine treatment for 12w,technical rep3


title: HC 16w-3

description: Liver tissues from HCs after diethylnitrosamine treatment for 16w,technical rep3


title: HC 8w-1

description: Liver tissues from HCs after diethylnitrosamine treatment for 8w,technical rep1


title: HC 0h-3

description: Normal liver tissues at 0h, technical rep3


title: AHF Rat 24h-3

description: Liver tissues from rats after carbon tetrachloride treatment for 24h,technical rep3

treatment_protocol: After the model of AHF was established, the rats at corresponding time points were anaesthetized, and then the liver tissues from the middle part of the right lobe of the liver were collected in RNase-free tubes for use.


title: AHF Rat 24h-2

description: Liver tissues from rats after carbon tetrachloride treatment for 24h,technical rep2


title: AHF Rat 12h-3

description: Liver tissues from rats after carbon tetrachloride treatment for 12h,technical rep3


title: AHF Rat 72h-2

description: Liver tissues from rats after carbon tetrachloride treatment for 72h,technical rep2


title: AHF Rat 72h-3

description: Liver tissues from rats after carbon tetrachloride treatment for 72h,technical rep3


title: AHF Rat 72h-1

description: Liver tissues from rats after carbon tetrachloride treatment for 72h,technical rep1


title: AHF Rat 24h-1

description: Liver tissues from rats after carbon tetrachloride treatment for 24h,technical rep1


title: AHF Rat 48h-3

description: Liver tissues from rats after carbon tetrachloride treatment for 48h,technical rep3


title: AHF Rat 48h-2

description: Liver tissues from rats after carbon tetrachloride treatment for 48h,technical rep2


title: AHF Rat 6h-2

description: Liver tissues from rats after carbon tetrachloride treatment for 6h,technical rep2


title: AHF Rat 6h-1

description: Liver tissues from rats after carbon tetrachloride treatment for 6h,technical rep1


title: AHF Rat 0h-1

description: Normal liver tissues at 0h, technical rep1


title: AHF Rat 3h-3

description: Liver tissues from rats after carbon tetrachloride treatment for 3h,technical rep3


title: AHF Rat 3h-2

description: Liver tissues from rats after carbon tetrachloride treatment for 3h,technical rep2


title: Colon, tubular adenoma, replicate 22

city: Portland

first: Amiee

middle: Bell

last: Potter

state: OR

address: 3181 SW Sam Jackson Park Rd, Mail Code #L581

department: Integrated Genomics Laboratory

institute: OHSU

description: miRNA expression in colonic adenoma

hyb_protocol: Labeled RNA was added to the hybridization cocktail following the Genisphere FlashTag technical manual specifically for Affymetrix miRNA microarray. Hyb cocktail was added to the miRNA microarray and hybridized for 16 hrs at 48 degrees C in the Affymetrix GeneChip hybridization Oven 640 with rotation at 60 RPM

scan_protocol: Arrays were washed and stained on the GeneChip Fluidics Station 450 with manufacturer recommended fluidics script. Arrays were scanned using the Affymetrix autoloader carousel and GeneChip Scanner 3000

data_processing: All .cel files as a single set were uploaded to Partek Genomics Suite 6.6 using the default RMA subroutine.  Default RMA includes RMA background correction followed by quantile normalization and median polish summarization. Data QC and array performance assessment was performed in Statistica using the RMA normalized log2 transformed signal data exported from Partek. Differential gene expression was statistically tested using ANOVA in Partek Genomics Suite 6.6 on the RMA normalized log2 transformed signal data.  More advanced statistical testing was conducted on the exported Partek file of RMA normalized log2 transformed signal data using SAS

source_name: colonic adenoma

label_protocol: Manufacturer's protocol: Genisphere FlashTag Biotin labelin. In sum - RNA was polyadenylated using poly(A) polymerase and ATP in stock reaction buffer. Polyadenylated miRNAs were labeled using the biotin ligation mix and T4 DNA ligase.

extract_protocol: Total RNA, including miRNA, was isolated from the region using the miRNeasy FFPE kit (Catalog #217504; Qiagen, Valencia, CA), per manufacturer’s recommended protocol.

treatment_protocol: Normal colonic mucosa was obtained as part of routine clinical pathology and distant to the adenoma at the time of biopsy. Polyp biopsies were also taken. Polyps were evaluated by two pathologists and classified as normal mucosa, tubular adenoma, sessile serrated adenoma, traditional serrated adenoma, and tubular villous/villous or adenoma with high grade dysplasia. A demarcated hematoxylin and eosin-stained slide was used to guide macrodissection of regions of interest containing the defined predominant histologic feature(s) on which the tissue was classified.

value: colon

tag: category

value: tubular adenoma


title: Colon, tubular adenoma, replicate 23

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 21

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 25

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 24

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 20

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 26

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 19

description: miRNA expression in colonic adenoma


title: AHF Rat 12h-2

description: Liver tissues from rats after carbon tetrachloride treatment for 12h,technical rep2


title: AHF Rat 6h-3

description: Liver tissues from rats after carbon tetrachloride treatment for 6h,technical rep3


title: AHF Rat 0h-3

description: Normal liver tissues at 0h, technical rep3


title: AHF Rat 3h-1

description: Liver tissues from rats after carbon tetrachloride treatment for 3h,technical rep1


title: AHF Rat 12h-1

description: Liver tissues from rats after carbon tetrachloride treatment for 12h,technical rep1


title: AHF Rat 0h-2

description: Normal liver tissues at 0h, technical rep2


title: AHF Rat 48h-1

description: Liver tissues from rats after carbon tetrachloride treatment for 48h,technical rep1


title: Colon, tubular adenoma, replicate 18

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 16

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 15

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 14

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 13

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 11

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 10

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 12

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 9

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 8

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 7

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 4

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 2

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 17

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 6

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 3

description: miRNA expression in colonic adenoma


title: Colon, tubular adenoma, replicate 5

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 10

description: miRNA expression in colonic adenoma

value: traditional serrate


title: Colon, tubular adenoma, replicate 1

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 9

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 3

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 8

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 6

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 7

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 5

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 4

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 2

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 1

description: miRNA expression in colonic adenoma


title: Colon, traditional serrate, replicate 11

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate8

description: miRNA expression in colonic adenoma

value: sessile serrate


title: Colon, sessile serrate, replicate9

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate12

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate10

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate11

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate13

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate5

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate3

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate4

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate6

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate2

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate1

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate37

description: miRNA expression in colonic adenoma

value: high grade, tubulovillous adenoma with highgrade dysplasia


title: Colon, high grade, replicate40

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate38

description: miRNA expression in colonic adenoma

value: high grade, tubulovillous adenoma without highgrade dysplasia


title: Colon, high grade, replicate35

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate39

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate34

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate28

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate33

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate29

description: miRNA expression in colonic adenoma

value: high grade, high grade dysplasia


title: Colon, high grade, replicate30

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate31

description: miRNA expression in colonic adenoma


title: Colon, sessile serrate, replicate7

description: miRNA expression in colonic adenoma


title: LC Rat 9w-2

description: Liver tissues from rats after carbon tetrachloride administration for 9w,technical rep2


title: Colon, high grade, replicate27

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate32

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate26

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate36

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate19

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate25

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate23

description: miRNA expression in colonic adenoma

value: high grade, sessile serrated adenoma with highgrade dysplasia


title: Colon, high grade, replicate20

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate22

description: miRNA expression in colonic adenoma

value: high grade, traditional serrated adenoma with highgrade dysplasia


title: Colon, high grade, replicate21

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate16

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate15

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate13

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate14

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate12

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate11

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate7

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate10

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate4

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate2

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate5

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate8

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate3

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate6

description: miRNA expression in colonic adenoma


title: Colon, hyperplastic polyp or normal mucosa, replicate 23

description: miRNA expression in colonic normal mucosa and hyperplastic polyp

source_name: colonic polyp or normal mucosa

value: hyperplastic polyp or normal mucosa


title: Colon, high grade, replicate1

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate24

description: miRNA expression in colonic adenoma

value: high grade, tubulovillous sessile serrated adenoma


title: Colon, high grade, replicate18

description: miRNA expression in colonic adenoma


title: Colon, high grade, replicate17

description: miRNA expression in colonic adenoma


title: Colon, hyperplastic polyp or normal mucosa, replicate 22


title: Colon, hyperplastic polyp or normal mucosa, replicate 19


title: Colon, hyperplastic polyp or normal mucosa, replicate 18


title: Colon, hyperplastic polyp or normal mucosa, replicate 15


title: Colon, hyperplastic polyp or normal mucosa, replicate 17


title: Colon, hyperplastic polyp or normal mucosa, replicate 14


title: Colon, high grade, replicate9

description: miRNA expression in colonic adenoma