title: control HUVEC (4)

city: Toronto

first: Philip

middle: A

last: Marsden

address: 209 Victoria Street, Room 522

department: Medicine

country: Canada

institute: University of Toronto

description: Gene expression after 48hr of transfection

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505C)

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 8 out of 8 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 8/8 samples prior to any data processing (e.g. prior to fold-change filtering). There was a considerable number of probes not detected in this experiment.
Gene and lncRNA expression

source_name: HUVEC (prep ID 4) treated with universal negative control 48hr

growth_protocol: HUVECs were isolated from umbilical cords from male and female live births and cultured in supplemented M199 medium for at least 2 passages before use. All biological samples were used at passage 3 and 4.

extract_protocol: RNA was recovered from samples using RNeasy mini plus kit (Qiagen). Exogenous luciferase RNA was introduced in a known amount during to extraction to assess RNA recovery

treatment_protocol: Dicer substrate siRNAs designed against LIVE1 and Dicer substrate universal negative control (scrambled) was used at 40uM per 6cm plate. RNA was then collected at 48 hour post-transfection

tag: cell type

value: human umbilical vein endothelial cells

tag: culture

value: 6cm plate monolayer

value: control


title: actinomycin D treatment_0h_rep1

status: Public on Jun 30 2015

type: RNA

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

description: replicate 1 of 4. actinomycin D treated cells - 0h vs. untreated control cells.

hyb_protocol: Agilent Gene Expression Hybridization Kit were used and samples were applied to microarrays enclosed in Agilent  Microarray Hybridization Chamber. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent High-Resolution Microarray scanner . Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing:
Filtering was performed prior to normalization and statistical analysis.
Agilent Feature Extraction Software (version 9.5) was used for background subtraction (BGSubSignal was used). 5,874 probes with significant expression in the reference sample as determined by a 2-sided t-test (IsPosAndSignif flag in Feature Extraction output) and signal at least two-fold greater than the background measurement in at least three of the four replicates of each time-point treatment were further analyzed. The time-course expression data set was normalized by the expression level that was measured prior to treatment (0h), which was set to 1 (log2 = 0).

molecule: total RNA

organism: Homo sapiens

source_name: actinomycin D treated cells - 0h

label_protocol: 200 ng of total RNA were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit following manufacturer's instructions

growth_protocol: HeLa cells were grown in culture medium according to ATCC recomendations

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

tag: cell line

value: HeLa (ATCC CCL-2)

tag: agent

value: actinomycin D

tag: time

source_name: pooled samples treated with DMSO vehicle (control)

tag: control composition

value: pooled samples, untreated


title: 2004-T54-rec-RMS_N

type: genomic

city: Tokyo

first: Masafumi

last: Seki

state: Tokyo

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Pediatrics

country: Japan

institute: The University of Tokyo

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing:
CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR 3.0
primary_data_description = Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

source_name: RMS tumor tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from fresh frozen tumor of rhabdomyosarcoma. DNA quality and quantity was assessed using a Nanodrop Spectrophotometers and agarose gel electrophoresis.

tag: tumor

value: Rhabdomyosarcoma


title: mouse spleen at 6 dpi, biological rep1

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

country: USA

institute: University of Rochester

description: Gene expression data from mouse spleen 6 days post-infection with A/HK-x31 influenza virus.

hyb_protocol: cDNA was hybridized with Affymetrix Mouse Gene ST 1.0 arrays overnight using conditions specified in the NuGEN kit. Arrays were washed and stained with phycoerythrin-streptavidin in an Affymetrix hybridization station as recommended by Affyemtrix.

scan_protocol: Stained arrays were scanned with an Affymetrix scanner controlled by Expression Console software, which converted the raw data files to cel files.

data_processing: Cel file data were normalized with the Affymetrix PLIER algorithm using Affymetrix Expresiion Console software. Transcript-level PLIER signals were then quantile-normalized.

organism: Mus musculus

source_name: mouse spleen 6 days post-infection with influenza A

label_protocol: Biotinylated cDNA was prepared from RNA using Ovation kits purchased from NuGEN according to instructions provided by NuGEN.

growth_protocol: Mice were housed in microisolator cages with same-sex siblings. They were allowed free access to water and rodent chow.

extract_protocol: Spleens were disrupted by pressing through a strainer with a syringe piston. Cells were were filtered through Nitex mesh (Thermo-Fisher, Waltham, MA) and layered on Lympholyte (Cedarlane, Burlington, NC). TER-119 immunomagnetic beads (BD Bioscience, San Diego, CA) were used to remove red blood cells. RNA was extracted with Qiagen Rneasy kits. RNA integrity was confirmed with an Agilent Bioanalyzer.

treatment_protocol: Mice were anesthetized with Avertin, then inoculated intranasally with 0.03 ml H3N2/Hong Kong/X31 influenza A virus ( 10^5 EID50).

tag: tissue

value: spleen

tag: subject

tag: timepoint

tag: Sex

value: Female

tag: mousestrain

tag: weightbaseline

tag: weightunits

value: g

tag: ageatinfection

tag: ageunits

value: weeks

tag: treatment

value: infected

tag: virussubtype

tag: virusstrain

tag: infectionroute

tag: infectionvolume

tag: infectionvolumeunits

value: ug

tag: infectiondose

tag: weightatsacrifice


title: mouse spleen at 7 dpi, biological rep1

description: Gene expression data from mouse spleen 7 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 7 days post-infection with influenza A

tag: tissue


title: mouse spleen at 4 dpi, biological rep3

description: Gene expression data from mouse spleen 4 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 4 days post-infection with influenza A

tag: subject


title: Knockdown of LIVE1 HUVEC (2)

source_name: HUVEC (prep ID 2) treated with dsiRNA(I) against LIVE1 48hr

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

tag: cell type

tag: culture

value: LIVE1 knockdown


title: 2000-T60-rec-RMS_N

description: Hybridized to 250K_Nsp

tag: tumor


title: Knockdown of LIVE1 HUVEC (4)

source_name: HUVEC (prep ID 4) treated with dsiRNA(II) against LIVE1 48hr


title: mouse spleen at 5 dpi, biological rep3

description: Gene expression data from mouse spleen 5 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 5 days post-infection with influenza A

tag: timepoint

tag: Sex

tag: mousestrain

tag: weightbaseline


title: mouse spleen at 5 dpi, biological rep1

tag: weightunits

tag: ageatinfection

tag: ageunits

tag: treatment


title: Mia PaCa 2_5-Aza treatment_replicate 4

description: Replicate 4 of 4. 5-Aza treated cells  vs. untreated control cells.

scan_protocol: Scanned on a GenePix 4000B (Molecular Devices Corporation) scanner . Images were quantified using Agilent Feature Extraction Software (version 11).

data_processing:
Filtering was performed prior to normalization and statistical analysis.
Agilent Feature Extraction Software (version 9.5) was used for background subtraction and LOWESS normalization. 10,658 probes with expression significantly greater than the corresponding background (2-sided t-test, flag ‘IsPosAndSignif’) in at least  three of the four replicates were defined as expressed and further analyzed.

source_name: Untreated Mia PaCa 2 cells

label_protocol: 500 ng of total RNA were DNAse-treated, amplified and labeled using Agilent Low RNA Input Fluorescent Linear Amplification Kit following manufacturer's instructions.

growth_protocol: Mia PaCa 2 cells were grown in culture medium according to ATCC recomendations.

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

tag: cell line

value: Mia PaCa 2 (ATCC CRL-1420)

tag: agent

value: Untreated

source_name: 5-Aza treated Mia PaCa 2 cells


title: mouse spleen at 3 dpi, biological rep3

description: Gene expression data from mouse spleen 3 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 3 days post-infection with influenza A

tag: virussubtype

tag: virusstrain

tag: infectionroute

tag: infectionvolume

tag: infectionvolumeunits

tag: infectiondose


title: mouse spleen at 4 dpi, biological rep1

tag: tissue

tag: subject

tag: weightatsacrifice


title: Mia PaCa 2_5-Aza treatment_replicate 3

description: Replicate 3 of 4. 5-Aza treated cells  vs. untreated control cells.


title: Knockdown of LIVE1 HUVEC (1)

source_name: HUVEC (prep ID 1) treated with dsiRNA(I) against LIVE1 48hr

tag: cell type

tag: culture


title: mouse spleen at 4 dpi, biological rep2

tag: timepoint

tag: Sex

tag: mousestrain

tag: weightbaseline

tag: weightunits


title: mouse spleen at 3 dpi, biological rep2

tag: ageatinfection

tag: ageunits

tag: treatment


title: Knockdown of LIVE1 HUVEC (3)

source_name: HUVEC (prep ID 3) treated with dsiRNA(II) against LIVE1 48hr


title: control HUVEC (3)

source_name: HUVEC (prep ID 3) treated with universal negative control 48hr


title: 2002-T67-rec-RMS_N

description: Hybridized to 250K_Nsp

tag: tumor


title: mouse spleen at 3 dpi, biological rep1

tag: virussubtype

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: control HUVEC (2)

source_name: HUVEC (prep ID 2) treated with universal negative control 48hr


title: mouse spleen at 2 dpi, biological rep4

description: Gene expression data from mouse spleen 2 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 2 days post-infection with influenza A

tag: tissue

tag: subject

tag: infectionvolumeunits

tag: infectiondose


title: control HUVEC (1)

source_name: HUVEC (prep ID 1) treated with universal negative control 48hr

tag: cell type

tag: culture


title: mouse spleen at 2 dpi, biological rep3

tag: timepoint

tag: Sex

tag: mousestrain

tag: weightatsacrifice


title: Mia PaCa 2_5-Aza treatment_replicate 2

description: Replicate 2 of 4. 5-Aza treated cells  vs. untreated control cells.

tag: cell line

tag: agent


title: HUVEC (prep ID 8) 3D Matrigel mock treatment

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.  Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).  After quantile normalization of the raw data, lncRNAs and mRNAs that at least 6 out of 16 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering.  Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 6/16 samples prior to any  data processing (e.g. prior to fold-change filtering).  There was a considerable number of probes not detected in this experiment.
Gene and lncRNA expression

source_name: HUVEC (prep ID 8) cultured in Matrigel treated with mock treatment

extract_protocol: RNA was extracted from HUVEC isolated from female and male births cultured in 2D conventional culture and 3D Matrigel (BD). Cells were recovered from 3D Matrigel using a 3D cell collection kit (Trevigen). RNA was then recovered from samples using RNeasy mini plus kit (Qiagen). Exogenous luciferase RNA was introduced in a known amount during to extraction to assess RNA recovery and first strand efficiency.

treatment_protocol: Each biological sample were subject to four treatment conditions, mock treatment or 100 ng/ml of VEGF-A165 every 12 hours in 2 dimensional monolayer gelatin culture as well as 3 dimensional Matrigel culture (tumor-derived extracellular matrix that induces vascular network formation) and supplemented 30 minutes pre-collection

tag: treatment

value: mock

value: matrigel


title: HUVEC (prep ID 4) 3D Matrigel mock treatment

source_name: HUVEC (prep ID 4) cultured in Matrigel treated with mock treatment

value: human umbilical vein endothelial cells


title: Mia PaCa 2_5-Aza treatment_replicate 1

description: Replicate 1 of 4. 5-Aza treated cells  vs. untreated control cells.


title: HUVEC (prep ID 1) 3D Matrigel mock treatment

source_name: HUVEC (prep ID 1) cultured in Matrigel treated with mock treatment


title: MCF-7_5-Aza treatment_replicate 4

data_processing:
Filtering was performed prior to normalization and statistical analysis.
Agilent Feature Extraction Software (version 9.5) was used for background subtraction and LOWESS normalization. 12,328 probes with expression significantly greater than the corresponding background (2-sided t-test, flag ‘IsPosAndSignif’) in at least  three of the four replicates were defined as expressed and further analyzed.

source_name: Untreated MCF-7 cells

growth_protocol: MCF-7 cells were grown in culture medium according to ATCC recomendations.

value: MCF7 (ATCC HTB-22)

source_name: 5-Aza treated MCF-7 cells


title: mouse spleen at 2 dpi, biological rep2

tag: weightbaseline

tag: weightunits

tag: ageatinfection

tag: ageunits

tag: virussubtype


title: mouse spleen at 2 dpi, biological rep1

tag: tissue

tag: subject

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: mouse spleen at 1 dpi, biological rep1

description: Gene expression data from mouse spleen 1 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 1 days post-infection with influenza A

tag: timepoint

tag: infectionvolumeunits

tag: infectiondose


title: MCF-7_5-Aza treatment_replicate 2


title: MCF-7_5-Aza treatment_replicate 1


title: mouse spleen at 1 dpi, biological rep2

tag: Sex

tag: mousestrain

tag: weightatsacrifice


title: HUVEC (prep ID 2)3D Matrigel mock treatment

source_name: HUVEC (prep ID 2) cultured in Matrigel treated with mock treatment

tag: cell type

tag: treatment

tag: culture


title: DU-145_5-Aza treatment_replicate 4

data_processing:
Filtering was performed prior to normalization and statistical analysis.
Agilent Feature Extraction Software (version 9.5) was used for background subtraction and LOWESS normalization. 13,111 probes with expression significantly greater than the corresponding background (2-sided t-test, flag ‘IsPosAndSignif’) in at least  three of the four replicates were defined as expressed and further analyzed.

source_name: Untreated DU-145 cells

label_protocol: 500 ng of total RNA were DNAse-treated and amplified and labeled using Agilent Low RNA Input Fluorescent Linear Amplification Kit following manufacturer's instructions.

growth_protocol: DU-145 cells were grown in culture medium according to ATCC recomendations.

tag: cell line

value: DU 145 (ATCC HTB-81)

tag: agent

source_name: 5-Aza treated DU-145 cells


title: mouse spleen non-infected, biological rep2

description: Gene expression data from mouse spleen non-infected.

source_name: mouse spleen non-infected

tag: weightbaseline

tag: weightunits

tag: ageatinfection

tag: ageunits

value: non-infected

tag: virussubtype


title: MCF-7_5-Aza treatment_replicate 3


title: mouse lymph node at 10 dpi, biological rep3

description: Gene expression data from mouse lymph node 10 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 10 days post-infection with influenza A

extract_protocol: Lymph nodes were disrupted by pressing through a strainer with a syringe piston. Cells were were filtered through Nitex mesh (Thermo-Fisher, Waltham, MA) and layered on Lympholyte (Cedarlane, Burlington, NC). TER-119 immunomagnetic beads (BD Bioscience, San Diego, CA) were used to remove red blood cells. RNA was extracted with Qiagen Rneasy kits. RNA integrity was confirmed with an Agilent Bioanalyzer.

tag: tissue

value: lymph node

tag: subject

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: mouse lymph node at 10 dpi, biological rep2

tag: timepoint

tag: Sex

tag: mousestrain

tag: infectionvolumeunits

tag: infectiondose


title: mouse spleen non-infected, biological rep3

tag: treatment

tag: weightatsacrifice


title: mouse spleen at 1 dpi, biological rep3

tag: weightbaseline


title: mouse spleen at 0 dpi, biological rep3

description: Gene expression data from mouse spleen 0 days post-infection with A/HK-x31 influenza virus.

source_name: mouse spleen 0 days post-infection with influenza A

tag: weightunits


title: HUVEC (Prep ID 8)3D Matrigel VEGF-A165

source_name: HUVEC (Prep ID 8) cultured in Matrigel treated with 100ng/ml of VEGF-A165

tag: cell type

tag: culture


title: HUVEC (Prep ID 4)3D Matrigel VEGF-A165

source_name: HUVEC (Prep ID 4) cultured in Matrigel treated with 100ng/ml of VEGF-A165


title: mouse spleen at 0 dpi, biological rep2

tag: ageatinfection

tag: ageunits

tag: virussubtype


title: mouse spleen non-infected, biological rep1

tag: tissue

tag: subject

tag: virusstrain


title: mouse spleen at 0 dpi, biological rep1

tag: timepoint

tag: infectionroute

tag: infectionvolume


title: HUVEC (Prep ID 2) 3D Matrigel VEGF-A165

source_name: HUVEC (Prep ID 2) cultured in Matrigel treated with 100ng/ml of VEGF-A165


title: DU-145_5-Aza treatment_replicate 3

tag: cell line

tag: agent


title: mouse lymph node at 10 dpi, biological rep1

tag: Sex

tag: mousestrain

tag: treatment

tag: infectionvolumeunits

tag: infectiondose


title: mouse lymph node at 9 dpi, biological rep3

description: Gene expression data from mouse lymph node 9 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 9 days post-infection with influenza A

tag: weightbaseline

tag: weightunits

tag: weightatsacrifice


title: HUVEC (Prep ID 1) 3D Matrigel VEGF-A165

source_name: HUVEC (Prep ID 1) cultured in Matrigel treated with 100ng/ml of VEGF-A165

tag: cell type

tag: culture


title: mouse lymph node at 9 dpi, biological rep1

tag: tissue

tag: subject

tag: ageatinfection

tag: ageunits

tag: virussubtype


title: mouse lymph node at 8 dpi, biological rep3

description: Gene expression data from mouse lymph node 8 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 8 days post-infection with influenza A

tag: timepoint

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: mouse lymph node at 6 dpi, biological rep2

description: Gene expression data from mouse lymph node 6 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 6 days post-infection with influenza A

tag: Sex

tag: mousestrain

tag: treatment


title: mouse lymph node at 7 dpi, biological rep3

description: Gene expression data from mouse lymph node 7 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 7 days post-infection with influenza A

tag: weightbaseline

tag: infectionvolumeunits

tag: infectiondose


title: mouse lymph node at 8 dpi, biological rep2

tag: weightunits

tag: weightatsacrifice


title: mouse lymph node at 7 dpi, biological rep2

tag: tissue


title: DU-145_5-Aza treatment_replicate 1

tag: cell line

tag: agent


title: HUVEC (prep ID 8) 2D monolayer mock treatment

source_name: HUVEC (prep ID 8) cultured in monolayer treated with mock treatment

tag: cell type

tag: culture

value: monolayer


title: mouse lymph node at 6 dpi, biological rep1

tag: subject

tag: timepoint

tag: ageatinfection

tag: ageunits

tag: virussubtype


title: HUVEC (prep ID 2)  2D monolayer mock treatment

source_name: HUVEC (prep ID 2) cultured in monolayer treated with mock treatment


title: HUVEC (prep ID 0) 2D monolayer mock treatment

source_name: HUVEC (prep ID 0) cultured in monolayer treated with mock treatment


title: mouse lymph node at 7 dpi, biological rep1

tag: Sex

tag: mousestrain

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: HUVEC (Prep ID 2) 2D monolayer VEGF-A165

source_name: HUVEC (Prep ID 2) cultured in monolayer treated with 100ng/ml of VEGF-A165

tag: treatment


title: DU-145_5-Aza treatment_replicate 2

source_name: Untreated DU-145 cells


title: HUVEC (prep ID 1)  2D monolayer mock treatment

source_name: HUVEC (prep ID 1) cultured in monolayer treated with mock treatment


title: HUVEC (Prep ID 8) 2D monolayer VEGF-A165

source_name: HUVEC (Prep ID8) cultured in monolayer treated with 100ng/ml of VEGF-A165


title: mouse lymph node at 4 dpi, biological rep1

description: Gene expression data from mouse lymph node 4 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 4 days post-infection with influenza A

tag: weightbaseline

tag: weightunits

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: mouse lymph node at 9 dpi, biological rep2

tag: tissue


title: mouse lymph node at 4 dpi, biological rep2

tag: subject


title: mouse lymph node at 6 dpi, biological rep3

tag: timepoint


title: mouse lymph node at 8 dpi, biological rep1

tag: ageatinfection


title: mouse lymph node at 5 dpi, biological rep2

description: Gene expression data from mouse lymph node 5 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 5 days post-infection with influenza A

tag: ageunits


title: mouse lymph node at 4 dpi, biological rep3

tag: virussubtype


title: HUVEC (Prep ID 1) 2D monolayer VEGF-A165

source_name: HUVEC (Prep ID 1) cultured in monolayer treated with 100ng/ml of VEGF-A165

tag: cell type

tag: culture


title: mouse lymph node at 5 dpi, biological rep3

tag: Sex

tag: mousestrain

tag: virusstrain


title: mouse lymph node at 5 dpi, biological rep1

tag: treatment

tag: infectionroute

tag: infectionvolume


title: HUVEC (prep ID 0) 2D monolayer VEGF-A165

source_name: HUVEC (prep ID 0) cultured in monolayer treated with 100ng/ml of VEGF-A165


title: Nasopharyngeal Carcinoma tissue 20

city: Guangzhou

first: Xin

last: Li

state: Province

address: Southern medical university

department: Cancer research institute

country: China

institute: Southern medical university

description:
Biological replicate 20 of 20. Nasopharyngeal Carcinoma tissue 20
NPC20

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in LF-I molecular hybridization chambers(Scientz, China). After hybridization, slides were washed sequential

scan_protocol: Scanned on an CapitalBio LuxScan 10K scanner. Images were quantified using Genepix pro Software (version 6.0).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Madb and  BRB ArrayTools were used.

source_name: human biopsy of nasopharyngeal carcinoma

label_protocol: 6 µg of  total RNA were labeled with labeling protocal of miRCURY LNA microRNA Array, Power labeling Kit

tag: biopsy

tag: diagnosis

source_name: Total RNA from Human lung fibroblasts cells

growth_protocol: HLF cells were cultured in RPMI-1640 with 10% Fetal Cow Serum

tag: cell line

value: HLF

tag: passage

value: HLF drived from Human lung fibroblasts


title: Nasopharyngeal Carcinoma tissue 19

description:
Biological replicate 19 of 20. Nasopharyngeal Carcinoma tissue 19
NPC19

value: human biopsy of nasopharyngeal carcinoma


title: Nasopharyngeal Carcinoma tissue 17

description:
Biological replicate 17 of 20. Nasopharyngeal Carcinoma tissue 17
NPC17


title: Nasopharyngeal Carcinoma tissue 18

description:
Biological replicate 18 of 20. Nasopharyngeal Carcinoma tissue 18
NPC18


title: Nasopharyngeal Carcinoma tissue 16

description:
Biological replicate 16 of 20. Nasopharyngeal Carcinoma tissue 16
NPC16


title: Nasopharyngeal Carcinoma tissue 14

description:
Biological replicate 14 of 20. Nasopharyngeal Carcinoma tissue 14
NPC14


title: Nasopharyngeal Carcinoma tissue 15

description:
Biological replicate 15 of 20. Nasopharyngeal Carcinoma tissue 15
NPC15


title: mouse lymph node at 3 dpi, biological rep1

description: Gene expression data from mouse lymph node 3 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 3 days post-infection with influenza A

tag: tissue

tag: subject

value: Female

tag: weightbaseline

tag: weightunits

value: g

value: weeks

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: Nasopharyngeal Carcinoma tissue 13

description:
Biological replicate 13 of 20. Nasopharyngeal Carcinoma tissue 13
NPC13

tag: cell type


title: mouse lymph node at 2 dpi, biological rep3

description: Gene expression data from mouse lymph node 2 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 2 days post-infection with influenza A

tag: timepoint

tag: Sex

tag: mousestrain

tag: ageatinfection

tag: ageunits

value: infected

tag: virussubtype

value: ug


title: Nasopharyngeal Carcinoma tissue 12

description:
Biological replicate 12 of 20. Nasopharyngeal Carcinoma tissue 12
NPC12

tag: biopsy

tag: diagnosis


title: mouse lymph node at 1 dpi, biological rep3

description: Gene expression data from mouse lymph node 1 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 1 days post-infection with influenza A

tag: treatment

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: mouse lymph node at 1 dpi, biological rep2

tag: tissue

tag: subject

tag: weightbaseline

tag: weightunits


title: Nasopharyngeal Carcinoma tissue 10

description:
Biological replicate 10 of 20. Nasopharyngeal Carcinoma tissue 10
NPC10

tag: cell line

tag: passage

tag: cell type


title: Nasopharyngeal Carcinoma tissue 11

description:
Biological replicate 11 of 20. Nasopharyngeal Carcinoma tissue 11
NPC11


title: mouse lymph node at 0 dpi, biological rep2

description: Gene expression data from mouse lymph node 0 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lymph node 0 days post-infection with influenza A

tag: timepoint

tag: Sex

tag: mousestrain

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: mouse lymph node non-infected, biological rep1

description: Gene expression data from mouse lymph node non-infected.

source_name: mouse lymph node non-infected

tag: ageatinfection

tag: ageunits

tag: treatment

tag: virussubtype


title: mouse lung at 9 dpi, biological rep2

description: Gene expression data from mouse lung 9 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 9 days post-infection with influenza A

extract_protocol: Lung tissue was disrupted by pressing through a strainer with a syringe piston. Cells were were filtered through Nitex mesh (Thermo-Fisher, Waltham, MA) and layered on Lympholyte (Cedarlane, Burlington, NC). TER-119 immunomagnetic beads (BD Bioscience, San Diego, CA) were used to remove red blood cells. RNA was extracted with Qiagen Rneasy kits. RNA integrity was confirmed with an Agilent Bioanalyzer.

tag: tissue

value: lung

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: mouse lymph node at 0 dpi, biological rep1

tag: subject

tag: weightbaseline

tag: weightunits


title: mouse lymph node at 2 dpi, biological rep2

tag: timepoint


title: mouse lymph node at 0 dpi, biological rep3

tag: Sex


title: Nasopharyngeal Carcinoma tissue 8

description:
Biological replicate 8 of 20. Nasopharyngeal Carcinoma tissue 8
NPC8

tag: biopsy

tag: diagnosis

tag: cell line

tag: passage

tag: cell type


title: Nasopharyngeal Carcinoma tissue 9

description:
Biological replicate 9 of 20. Nasopharyngeal Carcinoma tissue 9
NPC9


title: mouse lymph node non-infected, biological rep2

tag: mousestrain

tag: ageatinfection

tag: ageunits

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: mouse lung at 10 dpi, biological rep2

description: Gene expression data from mouse lung 10 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 10 days post-infection with influenza A

tag: tissue

tag: treatment

tag: virussubtype

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: mouse lung at 7 dpi, biological rep2

description: Gene expression data from mouse lung 7 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 7 days post-infection with influenza A

tag: subject

tag: timepoint

tag: Sex

tag: weightbaseline

tag: weightunits


title: mouse lymph node at 1 dpi, biological rep1

tag: mousestrain


title: mouse lymph node at 3 dpi, biological rep3

tag: ageatinfection


title: mouse lymph node at 2 dpi, biological rep1

tag: ageunits


title: mouse lymph node non-infected, biological rep3

tag: infectionvolumeunits


title: mouse lymph node at 3 dpi, biological rep2

tag: infectiondose


title: mouse lung at 8 dpi, biological rep2

description: Gene expression data from mouse lung 8 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 8 days post-infection with influenza A

tag: weightatsacrifice


title: mouse lung at 10 dpi, biological rep3

tag: tissue


title: mouse lung at 9 dpi, biological rep1

tag: treatment


title: mouse lung at 7 dpi, biological rep1

tag: virussubtype


title: mouse lung at 10 dpi, biological rep1

tag: virusstrain


title: mouse lung at 8 dpi, biological rep1

tag: infectionroute


title: mouse lung at 5 dpi, biological rep3

description: Gene expression data from mouse lung 5 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 5 days post-infection with influenza A

tag: infectionvolume


title: Nasopharyngeal Carcinoma tissue 7

description:
Biological replicate 7 of 20. Nasopharyngeal Carcinoma tissue 7
NPC7

tag: biopsy

tag: diagnosis

tag: cell line

tag: passage

tag: cell type


title: mouse lung at 6 dpi, biological rep1

description: Gene expression data from mouse lung 6 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 6 days post-infection with influenza A

tag: subject

tag: timepoint

tag: Sex

tag: mousestrain

tag: weightbaseline

tag: weightunits


title: Nasopharyngeal Carcinoma tissue 5

description:
Biological replicate 5 of 20. Nasopharyngeal Carcinoma tissue 5
NPC5


title: mouse lung at 5 dpi, biological rep1

tag: tissue

tag: ageatinfection

tag: ageunits

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: mouse lung at 4 dpi, biological rep2

description: Gene expression data from mouse lung 4 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 4 days post-infection with influenza A

tag: treatment

tag: virussubtype

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: Nasopharyngeal Carcinoma tissue 4

description:
Biological replicate 4 of 20. Nasopharyngeal Carcinoma tissue 4
NPC4

tag: biopsy

tag: diagnosis

tag: cell line

tag: passage

tag: cell type


title: Nasopharyngeal Carcinoma tissue 1

description:
Biological replicate 1 of 20. Nasopharyngeal Carcinoma tissue 1
NPC1


title: Chronic Nasopharyngitis tissue 20

description:
Biological replicate 20 of 20. Chronic Nasopharyngitis tissue 20
CNP20

source_name: human biopsy of chronic nasopharyngitis

value: human biopsy of chronic nasopharyngitis

value: chronic nasopharyngitis


title: Nasopharyngeal Carcinoma tissue 3

description:
Biological replicate 3 of 20. Nasopharyngeal Carcinoma tissue 3
NPC3


title: Nasopharyngeal Carcinoma tissue 6

description:
Biological replicate 6 of 20. Nasopharyngeal Carcinoma tissue 6
NPC6


title: Nasopharyngeal Carcinoma tissue 2

description:
Biological replicate 2 of 20. Nasopharyngeal Carcinoma tissue 2
NPC2


title: Chronic Nasopharyngitis tissue 18

description:
Biological replicate 18 of 20. Chronic Nasopharyngitis tissue 18
CNP18


title: Chronic Nasopharyngitis tissue 17

description:
Biological replicate 17 of 20. Chronic Nasopharyngitis tissue 17
CNP17


title: mouse lung at 0 dpi, biological rep1

description: Gene expression data from mouse lung 0 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 0 days post-infection with influenza A

tag: subject

tag: timepoint

tag: Sex

tag: mousestrain

tag: weightbaseline

tag: weightunits


title: mouse lung at 4 dpi, biological rep1

tag: tissue

tag: ageatinfection

tag: ageunits

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: mouse blood at 8 dpi, biological rep3

description:
Gene expression data from mouse blood 8 days post-infection with A/HK-x31 influenza virus.
blood_T8_rep3

source_name: mouse blood 8 days post-infection with influenza A

extract_protocol: Blood monocytes were separated from erythrocytes by density gradient centrifugation. RNA was extracted from monocytes with Qiagen Rneasy kits. RNA integrity was confirmed with an Agilent Bioanalyzer.

value: blood

value: peripheral blood monocyte

tag: gender

tag: treatment

tag: virussubtype

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: mouse blood at 10 dpi, biological rep2

description:
Gene expression data from mouse blood 10 days post-infection with A/HK-x31 influenza virus.
blood_T10_rep2

source_name: mouse blood 10 days post-infection with influenza A

tag: cell type

tag: subject

tag: timepoint


title: mouse lung at 3 dpi, biological rep1

description: Gene expression data from mouse lung 3 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 3 days post-infection with influenza A

tag: Sex

tag: mousestrain

tag: weightbaseline


title: Chronic Nasopharyngitis tissue 19

description:
Biological replicate 19 of 20. Chronic Nasopharyngitis tissue 19
CNP19

tag: biopsy

tag: diagnosis

source_name: Total RNA from Human lung fibroblasts cells

tag: cell line

tag: passage


title: Chronic Nasopharyngitis tissue 16

description:
Biological replicate 16 of 20. Chronic Nasopharyngitis tissue 16
CNP16


title: mouse lung non-infected, biological rep3

description: Gene expression data from mouse lung non-infected.

source_name: mouse lung non-infected

tag: tissue

tag: weightunits

tag: ageatinfection

tag: ageunits

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: mouse lung at 1 dpi, biological rep1

description: Gene expression data from mouse lung 1 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 1 days post-infection with influenza A

tag: treatment

tag: virussubtype

tag: virusstrain

tag: infectionroute

tag: infectionvolume


title: mouse lung non-infected, biological rep1

tag: subject

tag: timepoint

tag: Sex

tag: mousestrain

tag: weightbaseline


title: mouse lung at 5 dpi, biological rep2

description: Gene expression data from mouse lung 5 days post-infection with A/HK-x31 influenza virus.

tag: tissue


title: mouse lung non-infected, biological rep2

tag: weightunits


title: mouse lung at 3 dpi, biological rep2

tag: ageatinfection


title: mouse blood at 9 dpi, biological rep3

description:
Gene expression data from mouse blood 9 days post-infection with A/HK-x31 influenza virus.
blood_T9_rep3

source_name: mouse blood 9 days post-infection with influenza A

tag: cell type

tag: gender

tag: ageunits


title: mouse lung at 2 dpi, biological rep1

description: Gene expression data from mouse lung 2 days post-infection with A/HK-x31 influenza virus.

source_name: mouse lung 2 days post-infection with influenza A

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: mouse blood at 8 dpi, biological rep1

description:
Gene expression data from mouse blood 8 days post-infection with A/HK-x31 influenza virus.
blood_T8_rep1

tag: treatment

tag: virussubtype

tag: virusstrain


title: mouse blood at 9 dpi, biological rep2

description:
Gene expression data from mouse blood 9 days post-infection with A/HK-x31 influenza virus.
blood_T9_rep2

tag: subject

tag: infectionroute

tag: infectionvolume


title: mouse blood at 10 dpi, biological rep1

description:
Gene expression data from mouse blood 10 days post-infection with A/HK-x31 influenza virus.
blood_T10_rep1

tag: timepoint

tag: mousestrain


title: mouse blood at 7 dpi, biological rep3

description:
Gene expression data from mouse blood 7 days post-infection with A/HK-x31 influenza virus.
blood_T7_rep3

source_name: mouse blood 7 days post-infection with influenza A

tag: tissue

tag: weightbaseline


title: mouse blood at 9 dpi, biological rep1

description:
Gene expression data from mouse blood 9 days post-infection with A/HK-x31 influenza virus.
blood_T9_rep1

tag: weightunits

tag: ageatinfection


title: mouse blood at 10 dpi, biological rep3

description:
Gene expression data from mouse blood 10 days post-infection with A/HK-x31 influenza virus.
blood_T10_rep3

tag: cell type

tag: gender


title: mouse blood at 7 dpi, biological rep2

description:
Gene expression data from mouse blood 7 days post-infection with A/HK-x31 influenza virus.
blood_T7_rep2

tag: ageunits

tag: infectionvolumeunits


title: Chronic Nasopharyngitis tissue 15

description:
Biological replicate 15 of 20. Chronic Nasopharyngitis tissue 15
CNP15

tag: biopsy

tag: diagnosis

tag: cell line

tag: passage


title: mouse blood at 7 dpi, biological rep1

description:
Gene expression data from mouse blood 7 days post-infection with A/HK-x31 influenza virus.
blood_T7_rep1

tag: subject

tag: treatment

tag: virussubtype

tag: virusstrain

tag: infectiondose

tag: weightatsacrifice


title: Chronic Nasopharyngitis tissue 14

description:
Biological replicate 14 of 20. Chronic Nasopharyngitis tissue 14
CNP14


title: Chronic Nasopharyngitis tissue 13

description:
Biological replicate 13 of 20. Chronic Nasopharyngitis tissue 13
CNP13


title: Chronic Nasopharyngitis tissue 12

description:
Biological replicate 12 of 20. Chronic Nasopharyngitis tissue 12
CNP12


title: Chronic Nasopharyngitis tissue 8

description:
Biological replicate 8 of 20. Chronic Nasopharyngitis tissue 8
CNP8


title: Chronic Nasopharyngitis tissue 7

description:
Biological replicate 7 of 20. Chronic Nasopharyngitis tissue 7
CNP7


title: Chronic Nasopharyngitis tissue 9

description:
Biological replicate 9 of 20. Chronic Nasopharyngitis tissue 9
CNP9


title: Chronic Nasopharyngitis tissue 11

description:
Biological replicate 11 of 20. Chronic Nasopharyngitis tissue 11
CNP11


title: Chronic Nasopharyngitis tissue 10

description:
Biological replicate 10 of 20. Chronic Nasopharyngitis tissue 10
CNP10


title: mouse blood at 6 dpi, biological rep3

description:
Gene expression data from mouse blood 6 days post-infection with A/HK-x31 influenza virus.
blood_T6_rep3

source_name: mouse blood 6 days post-infection with influenza A

tag: tissue

tag: timepoint

tag: mousestrain

tag: weightbaseline

tag: infectionroute

tag: infectionvolume


title: mouse blood at 4 dpi, biological rep2

description:
Gene expression data from mouse blood 4 days post-infection with A/HK-x31 influenza virus.
blood_T4_rep2

source_name: mouse blood 4 days post-infection with influenza A

tag: cell type

tag: gender

tag: weightunits

tag: ageatinfection

tag: ageunits

tag: infectionvolumeunits


title: mouse blood at 1 dpi, biological rep3

description:
Gene expression data from mouse blood 1 days post-infection with A/HK-x31 influenza virus.
blood_T1_rep3

source_name: mouse blood 1 days post-infection with influenza A

tag: subject

tag: treatment


title: mouse blood at 8 dpi, biological rep2

description:
Gene expression data from mouse blood 8 days post-infection with A/HK-x31 influenza virus.
blood_T8_rep2

tag: virussubtype

tag: virusstrain


title: mouse blood at 3 dpi, biological rep3

description:
Gene expression data from mouse blood 3 days post-infection with A/HK-x31 influenza virus.
blood_T3_rep3

source_name: mouse blood 3 days post-infection with influenza A

tag: infectiondose

tag: weightatsacrifice


title: mouse blood at 2 dpi, biological rep1

description:
Gene expression data from mouse blood 2 days post-infection with A/HK-x31 influenza virus.
blood_T2_rep1

source_name: mouse blood 2 days post-infection with influenza A

tag: tissue

tag: timepoint


title: mouse blood at 3 dpi, biological rep2

description:
Gene expression data from mouse blood 3 days post-infection with A/HK-x31 influenza virus.
blood_T3_rep2

tag: mousestrain

tag: weightbaseline


title: mouse blood at 4 dpi, biological rep1

description:
Gene expression data from mouse blood 4 days post-infection with A/HK-x31 influenza virus.
blood_T4_rep1

tag: infectionroute

tag: infectionvolume


title: mouse blood at 6 dpi, biological rep1

description:
Gene expression data from mouse blood 6 days post-infection with A/HK-x31 influenza virus.
blood_T6_rep1

tag: cell type

tag: gender


title: Chronic Nasopharyngitis tissue 6

description:
Biological replicate 6 of 20. Chronic Nasopharyngitis tissue 6
CNP6

tag: biopsy

tag: diagnosis

tag: cell line

tag: passage


title: mouse blood at 5 dpi, biological rep2

description:
Gene expression data from mouse blood 5 days post-infection with A/HK-x31 influenza virus.
blood_T5_rep2

source_name: mouse blood 5 days post-infection with influenza A

tag: subject

tag: weightunits

tag: ageatinfection

tag: ageunits

tag: treatment

tag: infectionvolumeunits


title: mouse blood at 1 dpi, biological rep1

description:
Gene expression data from mouse blood 1 days post-infection with A/HK-x31 influenza virus.
blood_T1_rep1

tag: tissue

tag: timepoint

tag: virussubtype

tag: virusstrain

tag: infectiondose

tag: weightatsacrifice


title: mouse blood at 2 dpi, biological rep3

description:
Gene expression data from mouse blood 2 days post-infection with A/HK-x31 influenza virus.
blood_T2_rep3

tag: cell type

tag: gender

tag: mousestrain

tag: weightbaseline

tag: infectionroute

tag: infectionvolume


title: mouse blood at 5 dpi, biological rep3

description:
Gene expression data from mouse blood 5 days post-infection with A/HK-x31 influenza virus.
blood_T5_rep3

tag: subject

tag: weightunits


title: mouse blood at 3 dpi, biological rep1

description:
Gene expression data from mouse blood 3 days post-infection with A/HK-x31 influenza virus.
blood_T3_rep1

tag: ageatinfection

tag: ageunits


title: mouse blood at 4 dpi, biological rep3

description:
Gene expression data from mouse blood 4 days post-infection with A/HK-x31 influenza virus.
blood_T4_rep3

tag: treatment

tag: infectionvolumeunits


title: mouse blood at 6 dpi, biological rep2

description:
Gene expression data from mouse blood 6 days post-infection with A/HK-x31 influenza virus.
blood_T6_rep2

tag: tissue

tag: timepoint


title: mouse blood at 5 dpi, biological rep1

description:
Gene expression data from mouse blood 5 days post-infection with A/HK-x31 influenza virus.
blood_T5_rep1

tag: virussubtype

tag: virusstrain


title: mouse blood at 1 dpi, biological rep2

description:
Gene expression data from mouse blood 1 days post-infection with A/HK-x31 influenza virus.
blood_T1_rep2

tag: infectiondose

tag: weightatsacrifice


title: mouse blood at 0 dpi, biological rep3

description:
Gene expression data from mouse blood 0 days post-infection with A/HK-x31 influenza virus.
blood_T0_rep3

source_name: mouse blood 0 days post-infection with influenza A

tag: cell type

tag: gender


title: Chronic Nasopharyngitis tissue 3

description:
Biological replicate 3 of 20. Chronic Nasopharyngitis tissue 3
CNP3

source_name: human biopsy of chronic nasopharyngitis

tag: biopsy

tag: diagnosis

tag: cell line

tag: passage


title: Chronic Nasopharyngitis tissue 4

description:
Biological replicate 4 of 20. Chronic Nasopharyngitis tissue 4
CNP4


title: Chronic Nasopharyngitis tissue 5

description:
Biological replicate 5 of 20. Chronic Nasopharyngitis tissue 5
CNP5


title: mouse blood at 0 dpi, biological rep2

description:
Gene expression data from mouse blood 0 days post-infection with A/HK-x31 influenza virus.
blood_T0_rep2

tag: subject

tag: mousestrain

tag: weightbaseline

tag: weightunits

tag: infectionroute

tag: infectionvolume


title: mouse blood at 2 dpi, biological rep2

description:
Gene expression data from mouse blood 2 days post-infection with A/HK-x31 influenza virus.
blood_T2_rep2

tag: tissue

tag: timepoint

tag: ageatinfection

tag: ageunits

tag: treatment

tag: infectionvolumeunits


title: Chronic Nasopharyngitis tissue 2

description:
Biological replicate 2 of 20. Chronic Nasopharyngitis tissue 2
CNP2

tag: cell type


title: Chronic Nasopharyngitis tissue 1

description:
Biological replicate 1 of 20. Chronic Nasopharyngitis tissue 1
CNP1

tag: biopsy


title: mouse blood at 0 dpi, biological rep1

description:
Gene expression data from mouse blood 0 days post-infection with A/HK-x31 influenza virus.
blood_T0_rep1

tag: gender

tag: virussubtype

tag: virusstrain

tag: infectiondose

tag: weightatsacrifice


city: Paris

first: Franck

last: Tirode

address: 26 Rue d'Ulm

department: Inserm U830

country: France

institute: Institut Curie

description: Gene expression data of IB120 cell line expressing CIC-DUX4 shRNA_2 (replicate1)

hyb_protocol: As according to the manufacturer's instructions.

scan_protocol: GCOS 1.4

data_processing: All data were normalized using the gcrma package version 2.34.0 in the R 3.0.2 environment (R Development Core Team, 2005) with Brainarray Entrez gene CDF v17 and with quantile normalisation

label: biotin

molecule: polyA RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using 2µg total RNA

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

value: IB120 cell line

tag: growth medium

value: RPMI-1640 medium supplemented with 10% foetal calf serum


title: mouse blood non-infected, biological rep3

description:
Gene expression data from mouse blood non-infected.
blood_T-9_rep3

source_name: mouse blood non-infected

tag: subject

tag: mousestrain

tag: weightbaseline

tag: weightunits

value: non-infected


title: Arabidopsis-GK543B11-rep3

city: Aberdeen

first: David

middle: E

last: Salt

address: St Machar Drive

department: Institute of Biological and Environmental Sciences

country: United Kingdom

institute: University of Aberdeen

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA algorithm in R package 'oligo'

organism: Arabidopsis thaliana

source_name: myb36-2, root, 2-weeks-old

label_protocol: Standard Affymetrix protocol

growth_protocol: Plants were grown on MGRL medium solidified with 1.2% agar supplemented with 1% sucrose. After incubation for 2 days at 4˚C, the plates were placed vertically and the plants were grown at 22˚C under a 16-h light/8-h dark photoperiod. After two-weeks, RNA was prepared from roots and applied for the microarray analysis.

extract_protocol: Total RNA was prepared from plants with a PureLink RNA Mini Kit (lifetechnologies).

tag: line

tag: tissue

value: root

tag: age


title: mouse blood non-infected, biological rep1

description:
Gene expression data from mouse blood non-infected.
blood_T-9_rep1

tag: timepoint

tag: ageatinfection

tag: ageunits

tag: treatment

tag: infectionroute

tag: infectionvolume


description: Gene expression data of IB120 cell line transfected with empty vector (replicate1)


title: 231_CXCR6_sample

city: Shanghai

first: Gang

last: Xiao

address: 227 South Chongqing Road

institute: Shanghai Jiao-Tong University School of Medicine

description:
XG_002
Gene expression of cultured cells.

hyb_protocol: Each Slide was hybridized with 1.65μg 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) following the manufacturer’s instructions.

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

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 12.0 (Agilent Technologies, Santa Clara, CA, US).

source_name: MDA-MB-231, CXCR6 overexpression

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 Kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Human breast cancer cell lines MDA-MB-231 and MCF-7 were maintained in DMEM (Hyclone), supplemented with 10% FBS (GIBCO) and 1% penicillin/streptomycin. Cells were cultured at 37C water-saturated 5% CO2 atmosphere.

extract_protocol: Total RNA was 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: For restoring expression of CXCR6 in MDA-MB-231 and MCF-7 cells, human full-length CXCR6 cDNA was inserted into lentivirus vector pLenti-easy-HA. For the production of lentivirus, lenti-x cells were transfected with the PMD2.G, PSPAX2 and CXCR6 expression vector using the lipofectamine 2000 (Invitrogen). After 48 hours, culture supernatants were collected and passed through 0.45µm filters, mixed with fresh media (1:1) and polybrene (8μg/ml) to infect target cells. Infected cells were selected by G418 treatment at 100ng/ml.

tag: cell line

tag: cell type

value: breast cancer cell line

tag: overexpression


title: Arabidopsis-GK543B11-rep1


title: MCF-7_CXCR6_sample

description:
XG_004
Gene expression of cultured cells.

source_name: MCF-7, CXCR6 overexpression


description: Gene expression data of IB120 cell line expressing CIC-DUX4 shRNA_1 (replicate2)

tag: growth medium


title: Arabidopsis-11250-rep3

source_name: myb36-1, root, 2-weeks-old


description: Gene expression data of IB120 cell line transfected with empty vector (replicate2)


title: Arabidopsis-Col-rep2

source_name: Col-0, root, 2-weeks-old


description: Gene expression data of IB120 cell line expressing CIC-DUX4 shRNA_2 (replicate2)


title: Arabidopsis-Col-rep3


title: MCF-7_GFP_sample

description:
XG_003
Control of cultured cells.

source_name: MCF-7, control

value: control


title: 231_GFP_sample

description:
XG_001
Control of cultured cells.

source_name: MDA-MB-231, control


title: mouse blood non-infected, biological rep2

description:
Gene expression data from mouse blood non-infected.
blood_T-9_rep2

tag: subject

tag: gender

tag: virussubtype

tag: virusstrain

tag: infectionvolumeunits

tag: infectiondose

tag: weightatsacrifice


title: Arabidopsis-Col-rep1

tag: line

tag: tissue

tag: age


title: Arabidopsis-GK543B11-rep2


title: Arabidopsis-11250-rep2


title: Arabidopsis-11250-rep1


description: Gene expression data of IB120 cell line expressing CIC-DUX4 shRNA_1 (replicate1)


description: Gene expression data of hMSC cell line expressing EWSR1-NFATc2 (replicate2)

value: hMSC cell line


description: Gene expression data of hMSC cell line transfected with empty vector (replicate1)


title: EWSR1-NFATc2 tumor, sample RUS2

description: Gene expression data of EWSR1-NFATc2 tumor

source_name: EWSR1-NFATc2 tumor

value: EWSR1-NFATc2 tumor

value: Male


title: EWSR1-NFATc2 tumor biopsy, sample L1857

source_name: EWSR1-NFATc2 tumor biopsy

value: EWSR1-NFATc2 tumor biopsy


description: Gene expression data of hMSC cell line transfected with empty vector (replicate2)


title: EWSR1-NFATc2 tumor biopsy, sample L1231


title: EWSR1-NFATc2 tumor biopsy, sample EW697T


title: Calbicans_Nocodazole_3h_Biolrep3_Techrep2

city: Stuttgart

first: Steffen

last: Rupp

address: Nobelstr. 12

department: MBT

country: Germany

institute: Fraunhofer IGB

description: Dye Swap to Sample 17

hyb_protocol: 30 µL cDNA eluate, 6.5 µL SDS solution (1 %), 13 µL 20 x SSC and 15.5 µL RNase-free ddH2O were mixed and denatured at 100°C for 3 min. Hybridization was done over night (16 – 20 h) at 65 °C using LifterSlips (25 x 44 mm, VWR, Darmstadt, Germany). After hybridization, the LifterSlips were removed while rinsing for 1 min using 2 x SSC, 0.2 % SDS. Subsequently, DNA microarrays were washed for 10 min 2 x SSC, 0.2 % SDS, for 10 min in 2 x SSC and for 10 min in 0.2 x SSC. Afterwards, DNA microarrays were dried with compressed N2 gas, and stored protected from light in the dark until scanned.

scan_protocol: The completely dried DNA microarrays were scanned using the Genepix microarray scanner 4300A (Molecular Devices, Sunnyvale, CA) (resolution,  10 µm; PMT setting: auto-PMT). Pictures of both channels were saved as 16-bit TIFF files.

data_processing:
Raw data were created using Molecular Devices imaging software GenePix Pro 7.0 (Molecular Devices, Sunnyvale, CA).
The data were statistically analyzed using the software R (V. 2.10.1), the limma package (V. 3.2.1) and the statmod package (V. 1.4.2) (1, 2). An empirical Bayes method was chosen to take into account that in the classical t test, small variance values of the gene of interest tend to lead to high t-test statistics and therefore, erroneously, to a higher probability of significant differential expression (3). Background correction was performed using “normexp” with an offset of 50 (4). The data was normalized “print-tip-loess” (5). Spots which were classified as not found by the image analysis software were ignored for fitting of the linear model.
As thousands of hypotheses can be tested with DNA microarrays, the chance to make an α error increases with the number of hypotheses. Therefore, multiple-hypothesis testing was performed (6). Multiple-hypothesis testing correction was performed by the method of Benjamini and Hochberg, which controls the false discovery rate (FDR) (7). The quotient between expected false-positive genes and all differentially expressed genes allows an adjusted P value to be calculated, which can be used to make predictions about differential gene expression. Genes were regarded as differentially expressed and followed up, when the adjusted P values were 0.001, therefore nominally controlling the expected FDR to less than 0.001.
[1. R. (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing., RDevelopment Core Team.] [2. Smyth, G. K. (2005) Limma: Linear models for microarray data., In Bioinformatics and Computational Biology Solutions using R and Bioconductor (Gentleman, R., Carrey, V., Dudoit, S., Irizzary, I., Huber, W., Ed.), pp 397-420, Springer, New York.] [3. Lönnstedt, I., and Speed, T. P. (2002) Replicated microarray data., Stat.Sin. 12, 31-46.] [4. Ritchie, M. E., Silver, J., Oshlack, A., Holmes, M., Diyagama, D., Holloway, A., and Smyth, G. K. (2007) A comparison of background correction methods for two-colour microarrays, Bioinformatics 23, 2700-2707.] [5. Smyth, G. K., and Speed, T. (2003) Normalization of cDNA microarray data, Methods 31, 265-273.] [6. Dudoit, S., Popper Schaffer, J., and Boldrick, J. C. (2003) Multiple hypothesis testing in microarray experiments, Stat. Sci. 28, 71-103.] [7. Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing., J. R. Stat. Soc. B 57, 289-300.]

organism: Candida albicans

source_name: cultured cells, Nocodazole treated, 3h

label_protocol: Identical amounts of concentrated total RNA were reverse transcribed using LabelStar-Kit (Qiagen, Hilden, Germany) and labeled with Cy3-dCTPs or Cy5-dCTPs. All reactions were performed on ice according to manufacturers’ protocol. After reverse transcription, reference (Cy3 or Cy5 labeled, respectively) and sample (Cy5 or Cy3 labeled, respectively) were combined, purified and eluted using 30 µL buffer EB.

growth_protocol: 100 mL RPMI 1640 Medium (Invitrogen, Karlsruhe, Germany) + 10 % Fetal Calf Serum (FCS, Gibco Life Technologies GmbH, Karlsruhe, Germany) were inoculated with C. albicans SC5314 to an OD of 0.4 from an ON culture (10 mL YPD medium (1 % yeast extract, 2 %bacto peptone, 2 % glucose), 30°C) and grown for 3 h at 37 °C with or without treatment: ECM120B12 (0.125 µg/ml) or Fluconazole (1.0 µg/ml) or Nocodazole (7.5 µg/ml).

extract_protocol: Cell beads were destroyed using mortar and pestle. Grounded cell powder was transferred to a 15 mL falcon tube filled with 4 mL RLT-buffer (RNeasy Midi Kit, Qiagen, Hilden, Germany) and 40 µL ß-mercaptoethanol (Merck, Darmstadt, Germany) using an applicator. Prior to use, mortar, pestle, and applicator were cooled with liquid nitrogen. Liquid nitrogen was added during the cell destruction process whenever needed to avoid thawing.   RNA was isolated using RNeasy-Midi-Kit (Qiagen, Hilden, Germany) according to manufacturers protocol (Yeast II). On column DNAse digestion was performed (RNase-free DNase set; Qiagen, Hilden, Germany). RNA concentration and quality were assessed photometrically (Spectra-Photometer V630, Jasco, Gross-Umstadt, Germany) and by bioanalyzer analysis (RNA 6000 Nano LabChip kit, Agilent Bioanalyzer 2100; Agilent Technologies, CA). The RNA was precipitated using lithium chloride: 500 µL 4 M LiCl-solution was added to 500 µL RNA-solution and incubated at -20°C over night. RNA was centrifuged at 4°C and 13,000 g for 30 min, washed three times with 70 % ethanol and the precipitate dried for 5 min at 37 °C. RNA was redissolved in 50 µL RNase free ddH2O. Only RNA with a 260 nm/280 nm ratio of 1.8 to 2 as well as a 260 nm/230 nm ratio of 1.8 was used for DNA microarrays.   25 μg of total-RNA in a volume of maximal 19 μL was used for reverse transcription and labeling.

treatment_protocol: Cells were centrifuged (1200 g, 3 min) and the supernatant discarded. Subsequently, cells were resuspended in the remaining medium and dropped into liquid N2 to generate cell beads for RNA isolation. The experiment was performed three times.

tag: strain

source_name: cultured cells, untreated, 3h


title: Calbicans_Fluconazole_3h_Biolrep3_Techrep1

description: Dye Swap to Sample 12

source_name: cultured cells, Fluconazole treated, 3h


title: Calbicans_Nocodazole_3h_Biolrep2_Techrep1

description: Dye Swap to Sample 16


title: Calbicans_Fluconazole_3h_Biolrep3_Techrep2

description: Dye Swap to Sample 11


title: EWSR1-NFATc2 tumor biopsy, sample EW335T


title: Calbicans_Nocodazole_3h_Biolrep1_Techrep2

description: Dye Swap to Sample 13


title: EWSR1-NFATc2 tumor biopsy, sample EW331T


description: Gene expression data of hMSC cell line expressing EWSR1-NFATc2 (replicate1)


title: Calbicans_Nocodazole_3h_Biolrep1_Techrep1

description: Dye Swap to Sample 14


title: Calbicans_Nocodazole_3h_Biolrep2_Techrep2

description: Dye Swap to Sample 15


title: Calbicans_Nocodazole_3h_Biolrep3_Techrep1

description: Dye Swap to Sample 18


title: CIC-DUX4 tumor biopsy, sample EWN989T

description: Gene expression data of CIC-DUX4 tumor

source_name: CIC-DUX4 tumor biopsy

value: CIC-DUX4 tumor biopsy


title: Calbicans_Fluconazole_3h_Biolrep1_Techrep2

description: Dye Swap to Sample 7


title: Calbicans_Fluconazole_3h_Biolrep1_Techrep1

description: Dye Swap to Sample 8


title: Calbicans_Fluconazole_3h_Biolrep2_Techrep2

description: Dye Swap to Sample 9


title: EWSR1-NFATc2 tumor biopsy, sample EW327T

value: Female


title: CIC-DUX4 tumor biopsy, sample EWN1082T

description: Gene expression data of CIC-DUX4 tumor


title: CIC-DUX4 tumor biopsy, sample EWN1084T

description: Gene expression data of CIC-DUX4 tumor


title: Calbicans_Fluconazole_3h_Biolrep2_Techrep1

description: Dye Swap to Sample 10


title: St Col-0 con, replicate 2

city: Erlangen

first: Christian

last: Prasch

address: Staudtstrasse 5

department: Biochemistry division

institute: FAU Universität Erlangen-Nürnberg

description: Gene expression of WT- Col-0 under control conditions

hyb_protocol: 17 h at 65°C following Agilent One-Color_GE_5.7 protocol

scan_protocol: Agilent  G2565BA Microarray Scanner and Feature ExtractionVersion: 11.0, http://www.chem.agilent.com/Library/usermanuals/Public/G2566-90017.pdf, Scanner manual for software release 7.0. Data extraction using protocol GE1_1105_Oct12

data_processing: After importing text files via feature extraction software (Version 11.0; Agilent Technologies) into GeneSpring GX 11.0 (Silicon Genetics) microarray data were log2-transformed followed by normalization by Quantil and corrected to the median of all samples.  A one-way Anova (p ≤0.05, variance assumed as equal) enabled us to select genes which show differential behavior.

source_name: Arabidopsis Col-0, guard cell, control, replicate 2

label_protocol: 200ng RNA was used for labelling as described in the Agilent low input one color microarray-based gene expression analysis protocol

growth_protocol: After two days overnight 4°C treatment for stratification plants were grown on soil under short-day conditions (8 h light, 16 h dark), 60% humidity and 22°C (day) or 18/19°C (night). 14 days later young seedlings were further cultivated in single plant pots containing 160g soil and plants were watered with defined volumes of water as described by Prasch and Sonnewald, 2013. Controlled plant cultivation was achieved by a temperature regime followed the light/dark cycle with 22°C/18°C and a diurnal rhythm of 12h of light at approximately 80 µmol m-2 s-2 and exactly 60% humidity at day and night provided by a plant climate chamber (Plant-Master PGR 3045, CLF Plant Climatics GmbH, Germany).

extract_protocol: After plants have been treated with heat stress (3 days) 5-8 plants were grouped for one biological replicate. The stomata extraction procedure was performed as described by Bauer et al., 2013. After sampling, material was immediately frozen in liquid nitrogen. Stomatal RNA was isolated using the RNeasy Plant Mini Kit (www.quiagen.com) according to the manufacturer’s protocol. Two biological replicates were used for microarray hybridization.

treatment_protocol: Mild heat stress was given by 32°C at days and 28°C nights for three days according to Prasch and Sonnewald, 2013. Harvest of plant material was realized at the end of the light period. After determine the fresh weight of each plant, stomata-specific RNA of leaves was prepared.

tag: genotype/variation

value: WT

value: Stomata of leaves

value: guard cell

value: 5-week old plants

tag: stress


title: St Col-0 heat, replicate 2

description: Gene expression of WT- Col-0 after heat stress

source_name: Arabidopsis Col-0, guard cell, heat, replicate 2

value: heat


title: St bam1 heat, replicate 2

description: Gene expression of bam1 mutants after heat stress

source_name: Arabidopsis bam1, guard cell, heat, replicate 2

value: bam1 mutant


title: St bam1 con, replicate 2

description: Gene expression of bam1 mutants under control conditions

source_name: Arabidopsis bam1, guard cell, control, replicate 2


title: St Col-0 con, replicate 1

source_name: Arabidopsis Col-0, guard cell, control, replicate 1


title: CIC-DUX4 tumor biopsy, sample EWN1079T

description: Gene expression data of CIC-DUX4 tumor


title: CIC-DUX4 tumor biopsy, sample EWN1081T

description: Gene expression data of CIC-DUX4 tumor


title: CIC-DUX4 tumor biopsy, sample EWN1078T

description: Gene expression data of CIC-DUX4 tumor


title: St bam1 heat, replicate 1

source_name: Arabidopsis bam1, guard cell, heat, replicate 1


title: St bam1 con, replicate 1

source_name: Arabidopsis bam1, guard cell, control, replicate 1


title: CIC-DUX4 tumor biopsy, sample EWN1077T

description: Gene expression data of CIC-DUX4 tumor


title: CIC-DUX4 tumor biopsy, sample EWN1074T

description: Gene expression data of CIC-DUX4 tumor


title: leaf bam1 drought replicate 3

description: Experiment3: Gene expression in leaves of bam1 plants after 5 days of drought stress

hyb_protocol: following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent Arabidopsis_v4 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent G2565B Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.7.1 (Agilent Technologies Germany). Data extraction using protocol GE1_v5_95_Feb07

data_processing: After importing text files via feature extraction software (Version 11.7.1; Agilent Technologies) into GeneSpring GX 12.6 (Silicon Genetics) microarray data were log2-transformed followed by normalization to Quantile and corrected to the median of all samples.  After applying an one-way ANOVA (p ≤0.05, variance assumed as equal), Volcano plot analysis identified statistically significant (p ≤0.05; equal variances assumed), more than 2-fold differentially expressed genes between two conditions. For each experiment replicates of stressed plants were compared to their respective controls. Under drought stress conditions two to three replicates have been analyzed for each treatment and each genotype.

source_name: leaf bam1 drought replicate 3

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 80mg  total RNA after the method published by Logemann et al. (1987) (One-Color Microarray-based gene expression analysis v.5.5)

extract_protocol: After plants have been treated with drought stress (5 days) 5-8 plants were grouped for one biological replicate. The stomata extraction procedure was performed as described by Bauer et al., 2013. After sampling, material was immediately frozen in liquid nitrogen. Stomatal RNA was isolated using the RNeasy Plant Mini Kit (www.quiagen.com) according to the manufacturer’s protocol. Two to three biological replicates were used for microarray hybridization.

treatment_protocol: Six week old plants were exposed to mild drought stress (5 days). Mild drought stress was applied according to Prasch and Sonnewald, 2013. Harvest of plant material was realized at the end of the light period. After determine the fresh weight of each plant, stomata-specific and total RNA of leaves has been prepared.

tag: ecotype

value: leaf

tag: treatment

value: 5 days of drought stress


title: St Col-0 control replicate 3

description: Experiment3: Stomata-specific gene expression of Col-0 plants after 5 weeks under control conditions

source_name: St Col-0 control replicate 3

value: 5 weeks under control conditions


title: St Col-0 heat, replicate 1

source_name: Arabidopsis Col-0, guard cell, heat, replicate 1

tag: cell type


title: CIC-DUX4 tumor biopsy, sample EWN1072T

description: Gene expression data of CIC-DUX4 tumor


title: CIC-DUX4 tumor biopsy, sample EWN1069T

description: Gene expression data of CIC-DUX4 tumor


title: CIC-DUX4 tumor biopsy, sample EWN1076T

description: Gene expression data of CIC-DUX4 tumor


title: CIC-DUX4 tumor biopsy, sample EWN1075T

description: Gene expression data of CIC-DUX4 tumor


title: St bam1 control replicate 1

description: Experiment3: Stomata-specific gene expression in bam1 plants after 5 weeks under control conditions

source_name: St bam1 control replicate 1


title: CIC-DUX4 tumor biopsy, sample OD_089

description: Gene expression data of CIC-DUX4 tumor


title: St Col-0 drought replicate2

description: Experiment3: Stomata-specific gene expression of Col-0 plants after 5 days of drought stress

source_name: St Col-0 drought replicate2


title: leaf bam1 control replicate 1

description: Experiment3: Gene expression in leaves of bam1 plants after 5 weeks under control conditions

source_name: leaf bam1 control replicate 1


title: leaf Col-0 drought replicate 2

description: Experiment3: Gene expression in leaves of Col-0 plants after 5 days of drought stress

source_name: leaf Col-0 drought replicate 2


title: leaf bam1 control replicate 2

source_name: leaf bam1 control replicate 2


title: St bam1 control replicate 2

source_name: St bam1 control replicate 2


title: CIC-DUX4 tumor biopsy, sample EWN1073T

description: Gene expression data of CIC-DUX4 tumor

source_name: CIC-DUX4 tumor biopsy


title: St Col-0 drought replicate1


title: St Col-0 control replicate 2

source_name: St Col-0 control replicate 2


title: leaf Col-0 drought replicate 1

description: Experiment3: Gene expression in leaves of Col-0 after 5 days of drought stress

source_name: leaf Col-0 drought replicate 1


title: leaf bam1 control replicate 3

source_name: leaf bam1 control replicate 3


title: St bam1 drought replicate 1

description: Experiment3: Stomata-specific gene expression in bam1 plants after 5 days of drought stress

source_name: St bam1 drought replicate 1


title: leaf Col-0 control replicate 1

description: Experiment3: Gene expression in leaves of Col-0 after 5 weeks under control conditions

source_name: leaf Col-0 control replicate 1


title: leaf bam1 drought replicate 1

source_name: leaf bam1 drought replicate 1


title: leaf Col-0 control replicate 2

description: Experiment3: Gene expression in leaves of Col-0 plants after 5 weeks under control conditions

source_name: leaf Col-0 control replicate 2


title: leaf bam1 drought replicate 2

source_name: leaf bam1 drought replicate 2


title: St Col-0 control replicate 1

source_name: St Col-0 control replicate 1


title: St bam1 drought replicate 2

source_name: St bam1 drought replicate 2


title: leaf Col-0 control replicate 3

source_name: leaf Col-0 control replicate 3


title: PBMC stimulated with Borrelia rep7

city: Boston

first: Aylwin

last: Ng

state: MA

address: 185 Cambridge Street

institute: CCIB, MGH

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.wt.TT); PBMC stimulated with Borrelia rep7

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Gene expression data was exported using the Illumina BeadStudio software.

source_name: Blood

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

growth_protocol: PBMCs were washed twice in saline and suspended in RPMI.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: PBMCs were stimulated for 24h with RPMI alone, or RPMI containing heat-killed Borrelia burgdorferi (10 million microorganisms/ml), muramyl dipeptide, MDP (10μg/ml), or Pam3Cys (10μg/ml).

value: Peripheral blood mononuclear cells

value: stimulated with Borrelia


title: PBMC stimulated with Borrelia rep4

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with Borrelia rep4


title: PBMC stimulated with Borrelia rep6

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.wt.TT); PBMC stimulated with Borrelia rep6


title: PBMC stimulated with Borrelia rep2

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with Borrelia rep2


title: PBMC stimulated with Borrelia rep1

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.wt.TT); PBMC stimulated with Borrelia rep1


title: PBMC stimulated with Pam3 rep6

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.wt.TT); PBMC stimulated with Pam3 rep6

value: stimulated with Pam3


title: PBMC stimulated with Borrelia rep5

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with Borrelia rep5


title: PBMC stimulated with Pam3 rep2

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with Pam3 rep2


title: PBMC stimulated with Pam3 rep1

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with Pam3 rep1


title: PBMC stimulated with Pam3 rep5

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.wt.TT); PBMC stimulated with Pam3 rep5


title: PBMC stimulated with MDP rep3

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with MDP rep3

value: stimulated with MDP


title: PBMC stimulated with Pam3 rep4

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with Pam3 rep4


title: PBMC unstimulated (in RPMI) rep6

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.wt.TT); PBMC unstimulated (in RPMI) rep6

value: unstimulated (in RPMI)


title: PBMC stimulated with MDP rep2

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with MDP rep2


title: PBMC unstimulated (in RPMI) rep2

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC unstimulated (in RPMI) rep2


title: PBMC unstimulated (in RPMI) rep3

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC unstimulated (in RPMI) rep3


title: PBMC stimulated with Pam3 rep3

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with Pam3 rep3


title: PBMC stimulated with MDP rep4

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.wt.TT); PBMC stimulated with MDP rep4


title: PBMC unstimulated (in RPMI) rep5

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.wt.TT); PBMC unstimulated (in RPMI) rep5


title: PBMC stimulated with Borrelia rep3

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with Borrelia rep3


title: PBMC stimulated with MDP rep1

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC stimulated with MDP rep1


title: PBMC stimulated with MDP rep5

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.wt.TT); PBMC stimulated with MDP rep5


title: Cell_08_PAC_rep2

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

description:
Technical replicate 2
7980291034_H

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.

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: PBMNCs were seeded at a density of 5×10^5/cm2 on fibronectin-coated dishes with EGM2 complete medium for 7 days to obatin PACs.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen) following recommended manufacturer's instructions. RNA was treated with DNase Turbo (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: PACs where pretreated for 2 days with GM-CSF and IL-4 and then exposed to IL-1β and TNFα or ox-LDL for 3 days to obtain APCcy and APCox

value: Healthy volunteer

tag: cell type origin

value: Peripheral Blood Mononuclear Cells (PBMC)

value: pro-angiogenic cells (PACs)


title: Cell_07_APCcy_rep1

description:
Technical replicate 1
7980291034_I

tag: subject

value: cytokine-induced antigen presenting cells (APCcy)


title: PBMC unstimulated (in RPMI) rep4

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.300.AA); PBMC unstimulated (in RPMI) rep4


title: Cell_08_APCox_rep1

description:
Technical replicate 1
7980291034_F

value: ox-LDL-induced antigen presenting cells (APCox)


title: Cell_07_APCox_rep1

description:
Technical replicate 1
7980291034_B


title: Cell_09_PAC_rep2

description:
Technical replicate 2
7980291034_A


title: Cell_07_PAC_rep1

description:
Technical replicate 1
7980291034_G


title: Cell_08_APCcy_rep1

description:
Technical replicate 1
7980291034_E


title: Cell_09_PAC_rep1

description:
Technical replicate 1
7976997035_C


title: Cell_08_PAC_rep1

description:
Technical replicate 1
7976997035_L


title: Cell_10_APCcy_rep1

description:
Technical replicate 1
7976997035_H


title: Cell_09_APCox_rep1

description:
Technical replicate 1
7976997035_B


title: Cell_10_APCox_rep1

description:
Technical replicate 1
7976997035_I


title: Cell_11_PAC_rep2

description:
Technical replicate 2
6071811137_H


title: Cell_12_APCcy_rep1

description:
Technical replicate 1
6071811137_I


title: Cell_09_APCcy_rep1

description:
Technical replicate 1
7976997035_D


title: Cell_11_APCox_rep2

description:
Technical replicate 2
6071811137_G


title: Donor_Sample 65

city: Townsville

first: Erik

last: Biros

address: James Cook Drive

country: Australia

institute: James Cook University

description: normal aortic tissue

data_processing:
The data were normalized using standard normalization procedures recommended for the GeneSpring GX version 11.5.1 software for Illumina single-color array.
Percentile Shift Normalization with default settings to 75th percentile.
Filtering method: Probes were filtered based on their flag values using P (present) and M (marginal) flags using standard GeneSpring GX software settings for  Illumina single-color arrays.

source_name: Human abdominal aorta

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep RNA amplification kit (Cat. No. IL1791) for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: disease state

value: control

tag: subjects

value: heart-beating, brain-dead donors

value: full thickness aortic wall biopsies


title: Donor_Sample 62

description: normal aortic tissue


title: PBMC unstimulated (in RPMI) rep1

description:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers
Genotyped: (ATG16L1.wt.TT); PBMC unstimulated (in RPMI) rep1


title: Donor_Sample 61

description: normal aortic tissue


title: Donor_Sample 63

description: normal aortic tissue


title: Cell_10_PAC_rep1

description:
Technical replicate 1
7976997035_E


title: Donor_Sample 60

description: normal aortic tissue


title: Donor_Sample 59

description: normal aortic tissue


title: Cell_12_APCox_rep2

description:
Technical replicate 2
6071811137_L


title: Cell_11_APCcy_rep1

description:
Technical replicate 1
6071811137_E


title: Donor_Sample 66

description: normal aortic tissue


title: Cell_12_PAC_rep1

description:
Technical replicate 1
6071811137_F


title: Cell_12_APCox_rep1

description:
Technical replicate 1
6071811137_C


title: Donor_Sample 68

description: normal aortic tissue


title: Donor_Sample 67

description: normal aortic tissue


title: Cell_11_PAC_rep1

description:
Technical replicate 1
6071811137_A


title: AOD_Sample 56

description: aortic atheroma tissue

value: AOD

value: patients with AOD undergoing open surgery to treat chronic lower limb ischemia


title: AOD_Sample 57

description: aortic atheroma tissue


title: AOD_Sample 53

description: aortic atheroma tissue


title: large AAA_Sample 49

description: AAA tissue

value: large AAA

value: patients with AAA undergoing open surgery to treat AAA


title: AOD_Sample 54

description: aortic atheroma tissue


title: AOD_Sample 50

description: aortic atheroma tissue


title: hepatocytes_senkirkine_rep2

city: Berlin

first: Stefanie

last: Hessel

address: Max-Dohrn-Straße 8-10

institute: Federal Institute for Risk Assessment

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133 Plus 2.0 (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

source_name: primary hepatocytes

label_protocol: Biotinylated cRNA was prepared from 250 ng total RNA according to the 3`IVT express kit Affymetrix protocol.

growth_protocol: Clonetics® Normal Human Hepatocytes were received from Lonza (Walkersville, MD, USA) on collagen-coated 6-well plates. After shipment, medium was replaced with pre-warmed HCM™ (HCM™ BulletKit®, Lonza, Walkersville, MD, USA) and cells were cultured for 24 h at 37 °C and 5 % CO2.

extract_protocol: Prior to RNA isolation, cells were washed three times with pre-warmed PBS. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.

treatment_protocol: Cells were treated for 24 h with 100 µM echimidine, heliotrine, senecionine, senkirkine or solvent control (1 % acetonitrile) in triplicate.

tag: agent

value: senkirkine


title: large AAA_Sample 48

description: AAA tissue


title: AOD_Sample 51

description: aortic atheroma tissue


title: hepatocytes_senkirkine_rep1


title: large AAA_Sample 40

description: AAA tissue


title: large AAA_Sample 41

description: AAA tissue


title: hepatocytes_senkirkine_rep3


title: large AAA_Sample 45

description: AAA tissue


title: large AAA_Sample 42

description: AAA tissue


title: large AAA_Sample 38

description: AAA tissue


title: hepatocytes_senecionine_rep2

value: senecionine


title: AOD_Sample 52

description: aortic atheroma tissue


title: large AAA_Sample 43

description: AAA tissue


title: hepatocytes_control_rep3

value: vehicle ( 50:50 (v/v) acetonitrile :H2O)


title: hepatocytes_senecionine_rep3


title: large AAA_Sample 46

description: AAA tissue


title: large AAA_Sample 44

description: AAA tissue


title: large AAA_Sample 47

description: AAA tissue


title: hepatocytes_senecionine_rep1


title: hepatocytes_control_rep2


title: large AAA_Sample 39

description: AAA tissue


title: large AAA_Sample 37

description: AAA tissue


title: large AAA_Sample 32

description: AAA tissue


title: hepatocytes_heliotrine_rep3

value: heliotrine


title: hepatocytes_heliotrine_rep2


title: large AAA_Sample 35

description: AAA tissue


title: large AAA_Sample 36

description: AAA tissue


title: hepatocytes_heliotrine_rep1


title: hepatocytes_echimdine_rep2

value: echimidine


title: large AAA_Sample 30

description: AAA tissue


title: hepatocytes_control_rep1


title: large AAA_Sample 31

description: AAA tissue


title: large AAA_Sample 34

description: AAA tissue


title: large AAA_Sample 26

description: AAA tissue


title: large AAA_Sample 23

description: AAA tissue


title: large AAA_Sample 25

description: AAA tissue


title: large AAA_Sample 33

description: AAA tissue


title: large AAA_Sample 28

description: AAA tissue


title: large AAA_Sample 27

description: AAA tissue


title: large AAA_Sample 29

description: AAA tissue


title: large AAA_Sample 22

description: AAA tissue


title: Donor_Sample 64

description: normal aortic tissue


title: hepatocytes_echimdine_rep3


title: large AAA_Sample 21

description: AAA tissue


title: small AAA_Sample 19

description: AAA tissue

value: small AAA


title: large AAA_Sample 24

description: AAA tissue


title: hepatocytes_echimdine_rep1


title: small AAA_Sample 20

description: AAA tissue


title: small AAA_Sample 17

description: AAA tissue


title: small AAA_Sample 9

description: AAA tissue


title: small AAA_Sample 14

description: AAA tissue


title: small AAA_Sample 15

description: AAA tissue


title: small AAA_Sample 12

description: AAA tissue


title: pDC_Adult_3M003_6h_subj6

city: Vancouver

first: Kathleen

last: Wee

state: BC

address: 938 W 28th Ave.

institute: University of British Columbia

description: Sample name: 1848089057_C

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with no background subtraction using Illumina's BeadStudio software version 3.1.3.0

source_name: Peripheral blood

label_protocol: Biotinylated cRNA were prepared with the Ambion's Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with in-column DNAseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: gender

value: Female

tag: age group

value: Adult

tag: individual

value: pDC

tag: time


title: small AAA_Sample 18

description: AAA tissue

tag: tissue


title: small AAA_Sample 4

description: AAA tissue


title: small AAA_Sample 10

description: AAA tissue


title: pDC_Neonate_3M003_6h_subj6

description: Sample name: 1723260056_C

source_name: Cord blood

value: Male

value: Neonate


title: pDC_Adult_3M003_1h_subj6

description: Sample name: 1848089057_B


title: small AAA_Sample 7

description: AAA tissue


title: small AAA_Sample 16

description: AAA tissue


title: small AAA_Sample 5

description: AAA tissue


title: small AAA_Sample 2

description: AAA tissue


title: small AAA_Sample 6

description: AAA tissue


title: small AAA_Sample 13

description: AAA tissue


title: small AAA_Sample 8

description: AAA tissue


title: pDC_Neonate_3M003_6h_subj5

description: Sample name: 1723260009_F


title: pDC_Neonate_3M003_1h_subj5

description: Sample name: 1723260009_E


title: pDC_Neonate_Unstim_0h_subj6

description: Sample name: 1723260056_A

value: control


title: small AAA_Sample 1

description: AAA tissue

value: full thickness aortic wall biopsies


title: small AAA_Sample 3

description: AAA tissue


title: small AAA_Sample 11

description: AAA tissue


title: pDC_Neonate_3M003_1h_subj6

description: Sample name: 1723260056_B


title: pDC_Neonate_Unstim_0h_subj5

description: Sample name: 1723260009_D


title: Chn25_logarithmic phase_0 min_1

first: Lanming

last: Chen

address: 999 Hu Cheng Huan Road

department: College of Food Science and Technology

institute: Shanghai Ocean University

description:
Gene expression after 0 min in artificial gastric fluid at logarithmic phase
GE1_107_Sep09_1_1.txt

hyb_protocol: Each Slide was hybridized with 600ng 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 Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, photoelectric multiplication tube (PMT) 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Vibrio parahaemolyticus

source_name: Chn25_logarithmic phase_0 min

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), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Vibrio parahaemolyticus CHN25 was streaked from frozen stocks (stored at -80°C) onto LB (pH 8.5) agar and stored at 4°C for working stocks. For acid survival and microarray studies, one colony from the working stock was inoculated into 5 ml Tryptic Soy Broth (TSB, pH 8.5) supplemented with 3% NaCl (TSB-3% NaCl) and grown at 37°C overnight (12 to 18 h). The overnight culture was diluted 1:100 in 5 ml fresh TSB-3% NaCl shaking at 175 rpm at 37°C to an optical density at 600 nm (OD 600nm) of 0.7 and 1.3

extract_protocol: Total RNA was extracted using RNeasy Protect bacterial mini kit 74524(Qiagen, Hilden, Germany) following the manufacturer’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: Briefly, a 1 ml aliquot of culture was centrifuged with 3500 rpm for 2 min, then it was resuspended using 1 ml artificial gastric fluid, and added to 4 ml artificial gastric fluid (8.3 g/liter Proteose peptone, 3.5 g D-glucose, 2.05 g NaCl, 0.6 g KH2PO4, 0.147 g CaCl2•2H2O, 0.37 g KCl, adjusted to pH 4.9 with HCl). Acid-exposed cultures at log phase or stationary phase were subsequently incubated at 37°C for 30 min time.

tag: growth phase

value: logarithmic phase

tag: exposed to

value: none (0min control)


title: pDC_Neonate_3M003_6h_subj4

description: Sample name: 1723260009_C


title: AOD_Sample 55

description: aortic atheroma tissue

value: AOD

value: patients with AOD undergoing open surgery to treat chronic lower limb ischemia


title: AOD_Sample 58

description: aortic atheroma tissue


title: pDC_Adult_Unstim_0h_subj6

description: Sample name: 1848089057_A


title: Chn25_logarithmic phase_30 min_1

description:
Gene expression after 30 min in artificial gastric fluid at logarithmic phase
GE1_107_Sep09_1_3.txt

source_name: Chn25_logarithmic phase_30 min

tag: strain

value: artificial gastric fluid at 37°C for 30 min


title: Chn25_logarithmic phase_0 min_2

description:
Gene expression after 1 min in artificial gastric fluid at logarithmic phase
GE1_107_Sep09_1_2.txt


title: Chn25_logarithmic phase_30 min_2

description:
Gene expression after 31 min in artificial gastric fluid at logarithmic phase
GE1_107_Sep09_1_4.txt


title: Chn25_stationary phase_30 min_2

description:
Gene expression after 30 min in artificial gastric fluid at stationary phase
GE1_107_Sep09_2_4.txt

source_name: Chn25_stationary phase_30 min

value: stationary phase


title: Chn25_stationary phase_0 min_2

description:
Gene expression after 0 min in artificial gastric fluid at stationary phase
GE1_107_Sep09_2_2.txt

source_name: Chn25_stationary phase_0 min


title: Chn25_stationary phase_30 min_1

description:
Gene expression after 30 min in artificial gastric fluid at stationary phase
GE1_107_Sep09_2_3.txt


title: Chn25_stationary phase_0 min_1

description:
Gene expression after 0 min in artificial gastric fluid at stationary phase
GE1_107_Sep09_2_1.txt


title: pDC_Neonate_3M003_1h_subj4

description: Sample name: 1723260009_B


title: pDC_Neonate_Unstim_0h_subj4

description: Sample name: 1723260009_A


title: pDC_Adult_3M003_6h_subj4

description: Sample name: 1723260021_C


title: pDC_Adult_Unstim_0h_subj4

description: Sample name: 1723260021_A


title: ZT0, control pool 4

city: Nashville

first: Xiaofei

last: Wang

state: TN

address: 3500 John A Merritt blvd

department: Biological Sciences

institute: Tennessee State University

hyb_protocol: Each target cDNA was desiccated and resuspended in 25 µl of DIG Hyb solution (Roche) and mixed with a reference cDNA sample that was also resuspended in 25 µl,  and together with 2  µg of yeast tRNA (Sigma), 2 µg of salmon testes DNA (Sigma). The target mixture was heated at 70°C and applied to 13K chicken microarray, covered with Lifterslip cover slip, sealed in hybridization chamber, and hybridized at 42°C over night. Slides were washed once with 1× SSC/0.2% SDS in 50°C for 5 min, and 0.1× SSC/0.2% SDS for 5 min at room temperature with shaking.

scan_protocol: Slides were spun dried in a centrifuge at 1000 × g for 5 minutes and scanned immediately using an Axon 4100A Microarray Scanner (Axon Instruments) with GenePix 6.0 software. Each slide was then checked for background and morphological inconsistencies.  Data were converted to Excel spreadsheet containing clone identification numbers and gene names.

data_processing: Analyzed with Webarray, print tip loess normalization

organism: Gallus gallus

source_name: ZT0, dark

label_protocol: Total RNA (2 µg) was amplified using Message Amp II aRNA amplification kit (Ambion, Austin, TX, USA) following the protocol recommended by the manufacturer.  Amplified RNA (aRNA, 5 µg) was labeled with Alexa 555 using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen) following the recommendation of the manufacturer.  Reference RNA was prepared by pooling equal amount of total RNA from each of the test samples, and was amplified the same way as the test sample, and then labeled with Alexa 647. Quality of the labeled target cDNA was monitored with a NanoDrop spectrophotometer.

growth_protocol: Newly hatched birds were housed in brooder units setting air condintioned rooms. Starter feed and water were supplied ad libitum.

extract_protocol: Total RNA was extracted with Qiagen RNeasy mini kit, following the manufacturer's recommendation.

treatment_protocol: See overall design

value: male

tag: breed

value: rhode island red

tag: age

value: 1 week old

value: pineal gland

tag: sacrificed at

tag: light treatment

value: dark (control)

tag: paradigm

source_name: Reference pool

tag: reference pool

value: made by pooling equal amoung from each of the 16 primary pools (male rhode island red, 1 week old, pineal)


title: pDC_Adult_3M003_1h_subj5

description: Sample name: 1723260021_E

value: Adult

tag: cell type

value: pDC


title: pDC_Adult_3M003_1h_subj4

description: Sample name: 1723260021_B

value: Male


title: pDC_Adult_Unstim_0h_subj5

description: Sample name: 1723260021_D

value: control


title: pDC_Neonate_3M003_6h_subj3

description: Sample name: 1714460247_F

value: Female

value: Neonate


title: pDC_Neonate_3M003_1h_subj3

description: Sample name: 1714460247_E


title: pDC_Adult_3M003_6h_subj5

description: Sample name: 1723260021_F


title: ZT0, control pool 3


title: pDC_Neonate_3M003_6h_subj2

description: Sample name: 1714460247_C


title: pDC_Neonate_Unstim_0h_subj3

description: Sample name: 1714460247_D


title: ZT0, control pool 2


title: pDC_Neonate_3M003_1h_subj2

description: Sample name: 1714460247_B


title: pDC_Neonate_Unstim_0h_subj2

description: Sample name: 1714460247_A


title: ZT0, late night 2 h  light exposure, pool 3

source_name: ZT0, light

value: light


title: pDC_Adult_3M003_6h_subj3

description: Sample name: 1723260020_F


title: ZT0, control pool 1


title: ZT0, late night 2 h  light exposure, pool 2


title: ZT0, late night 2 h  light exposure, pool 4


title: pDC_Adult_Unstim_0h_subj3

description: Sample name: 1723260020_D


title: pDC_Adult_3M003_1h_subj3

description: Sample name: 1723260020_E


title: ZT14, 2 h extended light period, pool 2

source_name: ZT14, light


title: ZT0, late night 2 h  light exposure, pool 1