title: Blood_H56+Alum_24hr_animal5

description:
Gene expression after 24hr in H56+Alum-treated mouse whole blood
C14_WB


title: Blood_H56+Alum_24hr_animal6

status: Public on Jan 09 2017

type: RNA

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

country: Germany

institute: MPIIB

description:
Gene expression after 24hr in H56+Alum-treated mouse whole blood
C12_WB

hyb_protocol: Quantity and labelling efficiency were verified before hybridization to human whole genome microarrays (Agilent Technologies)

scan_protocol: Scanned on an Agilent Scanner G2505B. Image analysis was performed with Feature Extraction software (version 6.1.1, Agilent Technologies).

data_processing: Data were processed, quantile normalized and analyzed using the R package Lima (Ritchie et al (2015). Nucleic Acids Research, 43(7), pp. e47)

molecule: total RNA

organism: Mus musculus

source_name: Whole blood

label_protocol: RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

extract_protocol: RNA was extracted from lymph nodes and whole blood using the RNeasy Mini QIAcube kit (Qiagen) and PAXgene kit (Qiagen), respectively.

treatment_protocol: Anesthesized mice were injected sub cuntaneous with 100 microliter vaccine/adjuvants combination

tag: group

tag: tissue

value: whole blood

tag: treatment

tag: timepoint


title: Blood_H56+Alum_24hr_animal4

description:
Gene expression after 24hr in H56+Alum-treated mouse whole blood
C8_WB


title: Blood_H56+Alum_24hr_animal3

description:
Gene expression after 24hr in H56+Alum-treated mouse whole blood
C11_WB


title: Blood_H56+Alum_6hr_animal6

description:
Gene expression after 6hr in H56+Alum-treated mouse whole blood
C5_WB


title: Blood_H56+Alum_6hr_animal5

description:
Gene expression after 6hr in H56+Alum-treated mouse whole blood
C7_WB


title: Blood_H56+Alum_24hr_animal1

description:
Gene expression after 24hr in H56+Alum-treated mouse whole blood
C10_WB


title: Blood_H56+Alum_6hr_animal7

description:
Gene expression after 6hr in H56+Alum-treated mouse whole blood
C6_WB


title: Blood_H56+Alum_24hr_animal2

description:
Gene expression after 24hr in H56+Alum-treated mouse whole blood
C9_WB


title: Blood_H56+Alum_6hr_animal3

description:
Gene expression after 6hr in H56+Alum-treated mouse whole blood
C1_WB


title: Blood_H56+Alum_6hr_animal4

description:
Gene expression after 6hr in H56+Alum-treated mouse whole blood
C2_WB


title: Blood_H56+Alum_6hr_animal1

description:
Gene expression after 6hr in H56+Alum-treated mouse whole blood
C3_WB


title: Blood_H56_168hr_animal7

description:
Gene expression after 168hr in H56-treated mouse whole blood
B25_WB


title: Blood_H56_168hr_animal6

description:
Gene expression after 168hr in H56-treated mouse whole blood
B26_WB


title: Blood_H56_168hr_animal5

description:
Gene expression after 168hr in H56-treated mouse whole blood
B27_WB


title: Blood_H56_168hr_animal4

description:
Gene expression after 168hr in H56-treated mouse whole blood
B22_WB


title: Blood_H56_168hr_animal3

description:
Gene expression after 168hr in H56-treated mouse whole blood
B24_WB


title: Blood_H56_168hr_animal2

description:
Gene expression after 168hr in H56-treated mouse whole blood
B23_WB


title: Blood_H56_168hr_animal1

description:
Gene expression after 168hr in H56-treated mouse whole blood
B28_WB


title: Non-Cachectic controls [7254]

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Ave

department: Laboratory medicine and pathology

country: Canada

institute: University of Alberta

description: Total RNA was used for labeling and hybridisation. .CEL files were generated for downstream analysis

hyb_protocol: Hybridization was performed for 16 hours in Genechip hybridization oven 645 using the standard procedures (http://www.affymetrix.com)

scan_protocol: The HTA 2.0 arrays were scanned using Affymetrix GCS 3000 7G scanner to generate the raw intensity CEL files for downstream analyses.

data_processing:
Exon level intensity estimates were generated using RMA method which includes background correction, quantile normalization and log 2 transformation. Exons that were not expressed in all of the samples were excluded from further analysis. In the AS analysis, PGS generates two results – at the transcript (isoform) level and at the exon level. Initially, at a transcript level, DE between cases and controls at a p-value of < 0.05 were identified as ASGs (Partek defines this as “alt-splice p-value”). At the exon level, the expression between cases and controls with p < 0.05 and FC > 1.4 were identified using one-way ANOVA and these exons were mapped to their corresponding transcripts (isoforms). Final representation of data would therefore reflect a composite signature of the alternatively spliced gene transcripts overlapped with exon level results (p < 0.05, FC > 1.4). These overlapped transcripts were called differentially expressed alternatively spliced genes (DASGs).
Human Transcriptome 2.0

label: Biotin

organism: Homo sapiens

source_name: Rectus abdominis

label_protocol: 100 ng of total RNA was used as a starting material for labeling and hybridization.

growth_protocol: Muscle biposies were preserved as Fresh frozen tissues

extract_protocol: Total RNA was isolated using TRIzol and Qiagen Rneasy kit according to manufacturer's instructions

value: Muscle biopsy


title: Non-Cachectic controls [7409]


title: Non-Cachectic controls [7257]


title: Blood_H56+Alum_6hr_animal2

description:
Gene expression after 6hr in H56+Alum-treated mouse whole blood
C4_WB


title: Non-Cachectic controls [7347]


title: Blood_H56_72hr_animal7

description:
Gene expression after 72hr in H56-treated mouse whole blood
B20_WB


title: Non-Cachectic controls [7245]


title: Non-Cachectic controls [7353]


title: Non-Cachectic controls [7227]


title: Blood_H56_72hr_animal5

description:
Gene expression after 72hr in H56-treated mouse whole blood
B18_WB


title: Non-Cachectic controls [7212]


title: Non-Cachectic controls [7359]


title: Blood_H56_72hr_animal4

description:
Gene expression after 72hr in H56-treated mouse whole blood
B15_WB


title: Cachectic cases [7308]


title: Non-Cachectic controls [7050]


title: Blood_H56_72hr_animal1

description:
Gene expression after 72hr in H56-treated mouse whole blood
B17_WB


title: Blood_H56_72hr_animal3

description:
Gene expression after 72hr in H56-treated mouse whole blood
B16_WB


title: Cachectic cases [7156]


title: Blood_H56_72hr_animal6

description:
Gene expression after 72hr in H56-treated mouse whole blood
B19_WB


title: Non-Cachectic controls [7192]


title: Non-Cachectic controls [6144]


title: Non-Cachectic controls [7135]


title: Non-Cachectic controls [7139]


title: Cachectic cases [7100]


title: Cachectic cases [7455]


title: Blood_H56_24hr_animal6

description:
Gene expression after 24hr in H56-treated mouse whole blood
B12_WB


title: Blood_H56_24hr_animal7

description:
Gene expression after 24hr in H56-treated mouse whole blood
B13_WB


title: Non-Cachectic controls [6142]


title: Cachectic cases [5159]


title: Non-Cachectic controls [6147]


title: Non-Cachectic controls [2066]


title: Non-Cachectic controls [3016]


title: Non-Cachectic controls [3027]


title: Blood_H56_6hr_animal6

description:
Gene expression after 6hr in H56-treated mouse whole blood
B5_WB


title: Cachectic cases [7180]


title: Blood_H56_72hr_animal2

description:
Gene expression after 72hr in H56-treated mouse whole blood
B21_WB


title: Blood_H56_6hr_animal4

description:
Gene expression after 6hr in H56-treated mouse whole blood
B2_WB


title: Cachectic cases [7056]


title: Blood_H56_24hr_animal2

description:
Gene expression after 24hr in H56-treated mouse whole blood
B9_WB


title: Cachectic cases [6181]


title: Cachectic cases [6189]


title: Blood_H56_6hr_animal3

description:
Gene expression after 6hr in H56-treated mouse whole blood
B1_WB


title: Blood_H56_6hr_animal7

description:
Gene expression after 6hr in H56-treated mouse whole blood
B6_WB


title: Blood_H56_6hr_animal2

description:
Gene expression after 6hr in H56-treated mouse whole blood
B4_WB


title: Blood_H56_24hr_animal3

description:
Gene expression after 24hr in H56-treated mouse whole blood
B11_WB


title: met1-3_rep3

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: met1-3 Arabidopsis RNA chip 3

hyb_protocol: Approximately 7.5 μg of fragmented cDNA was hybridized for 16 hours at 60 rpm.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
Data was processed in R as described in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94. Briefly, RMA was used for normalization, and the 'limma' and 'QValue' packages from Bioconductor were used for statistical analysis.
met1-1_processed.csv; met1-3_processed.csv
The resulting csv files were generated in Bioconductor (R software environment) and report normalized log2 genes expression differences for met1-1 and met1-3 compared to wild type, with p-values and corrections for multiple comparison (FDR).

label: biotin

organism: Arabidopsis thaliana

label_protocol: Libraries were prepared with the GeneChip Whole Transcript Amplified Double-Stranded Target Assay (Affymetrix), according to the manufacturer’s protocol.

growth_protocol: Plants were grown in plates under long-day conditions (21°C, 16 h light, 8 h dark)

extract_protocol: Total RNA was extracted using the Trizol (Invitrogen) method according to the manufacturer’s instructions.

tag: genotype/variation

tag: ecotype

value: seedling

tag: age

value: 2 weeks


title: met1-3_rep2

description: met1-3 Arabidopsis RNA chip 2


title: met1-3_rep1

description: met1-3 Arabidopsis RNA chip 1


title: Blood_H56_6hr_animal5

description:
Gene expression after 6hr in H56-treated mouse whole blood
B7_WB


title: Blood_H56_24hr_animal4

description:
Gene expression after 24hr in H56-treated mouse whole blood
B8_WB


title: WT_for_met1-3_rep3

description: wt Arabidopsis RNA chip 6

source_name: wild type

value: WT


title: Cachectic cases [3053]

description: Total RNA was used for labeling and hybridisation. .CEL files were generated for downstream analysis


title: Blood_H56_6hr_animal1

description:
Gene expression after 6hr in H56-treated mouse whole blood
B3_WB


title: Blood_H56_24hr_animal5

description:
Gene expression after 24hr in H56-treated mouse whole blood
B14_WB


title: Blood_H56_24hr_animal1

description:
Gene expression after 24hr in H56-treated mouse whole blood
B10_WB


title: Blood_untreated_0hr_animal6

description:
Gene expression in untreated mouse whole blood
A5_WB

value: untreated


title: WT_for_met1-3_rep1

description: wt Arabidopsis RNA chip 4


title: Blood_untreated_0hr_animal7

description:
Gene expression in untreated mouse whole blood
A6_WB


title: WT_for_met1-3_rep2

description: wt Arabidopsis RNA chip 5


title: Blood_untreated_0hr_animal5

description:
Gene expression in untreated mouse whole blood
A7_WB


title: Blood_untreated_0hr_animal1

description:
Gene expression in untreated mouse whole blood
A3_WB


title: met1-1_rep2

description: met1-1 Arabidopsis RNA chip 2


title: LymphNode_H56+GLA-SE_168hr_animal3

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse lymph node
F24_LN

source_name: Lymph node

value: lymph node


title: LymphNode_H56+GLA-SE_168hr_animal5

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse lymph node
F26_LN


title: LymphNode_H56+GLA-SE_168hr_animal7

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse lymph node
F28_LN


title: Blood_untreated_0hr_animal2

description:
Gene expression in untreated mouse whole blood
A4_WB


title: met1-1_rep1

description: met1-1 Arabidopsis RNA chip 1


title: LymphNode_H56+GLA-SE_168hr_animal4

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse lymph node
F25_LN


title: Cachectic cases [5134]


title: WT_for_met1-1_rep3

description: wt Arabidopsis RNA chip 3


title: Cachectic cases [5211]


title: Cachectic cases [6170]


title: Blood_untreated_0hr_animal3

description:
Gene expression in untreated mouse whole blood
A1_WB


title: WT_for_met1-1_rep2

description: wt Arabidopsis RNA chip 2


title: LymphNode_H56+GLA-SE_72hr_animal7

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse lymph node
F21_LN


title: LymphNode_H56+GLA-SE_168hr_animal1

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse lymph node
F22_LN


title: LymphNode_H56+GLA-SE_168hr_animal2

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse lymph node
F23_LN


title: LymphNode_H56+GLA-SE_72hr_animal6

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse lymph node
F20_LN


title: met1-1_rep3

description: met1-1 Arabidopsis RNA chip 3


title: LymphNode_H56+GLA-SE_168hr_animal6

description:
Gene expression after 168hr in H56+GLA-SE-treated mouse lymph node
F27_LN


title: WT_for_met1-1_rep1

description: wt Arabidopsis RNA chip 1


title: LymphNode_H56+GLA-SE_72hr_animal5

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse lymph node
F19_LN


title: LymphNode_H56+GLA-SE_72hr_animal4

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse lymph node
F18_LN


title: LymphNode_H56+GLA-SE_72hr_animal2

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse lymph node
F16_LN


title: LymphNode_H56+GLA-SE_72hr_animal3

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse lymph node
F17_LN


title: LymphNode_H56+GLA-SE_24hr_animal7

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse lymph node
F14_LN


title: LymphNode_H56+GLA-SE_72hr_animal1

description:
Gene expression after 72hr in H56+GLA-SE-treated mouse lymph node
F15_LN


title: LymphNode_H56+GLA-SE_24hr_animal6

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse lymph node
F13_LN


title: VPM_16_week0

description: Gene expression in whole blood before vaccination

extract_protocol: RNA was extracted from whole blood stored in RNAlater solution (Sigma) using the RiboPure -Blood kit (Ambion)

treatment_protocol: Infants were vaccinated with standard dose of BCG or VPM1002

tag: timepoint (weeks post vaccination)


title: LymphNode_H56+GLA-SE_24hr_animal5

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse lymph node
F12_LN


title: LymphNode_H56+GLA-SE_24hr_animal2

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse lymph node
F9_LN


title: VPM_15_week26

description: Gene expression in whole blood 26 weeks after vaccination


title: VPM_15_week18

description: Gene expression in whole blood 18 weeks after vaccination


title: LymphNode_H56+GLA-SE_24hr_animal1

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse lymph node
F8_LN


title: Cachectic cases [3005]

description: Total RNA was used for labeling and hybridisation. .CEL files were generated for downstream analysis


title: LymphNode_H56+GLA-SE_6hr_animal7

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse lymph node
F7_LN


title: Cachectic cases [5186]


title: Cachectic cases [4093]


title: Cachectic cases [7147]


title: LymphNode_H56+GLA-SE_6hr_animal2

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse lymph node
F2_LN


title: VPM_15_week12

description: Gene expression in whole blood 12 weeks after vaccination


title: Cachectic cases [4219]


title: LymphNode_H56+GLA-SE_6hr_animal6

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse lymph node
F6_LN


title: LymphNode_H56+GLA-SE_24hr_animal3

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse lymph node
F10_LN


title: LymphNode_H56+GLA-SE_6hr_animal5

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse lymph node
F5_LN


title: VPM_15_week2

description: Gene expression in whole blood 2 weeks after vaccination


title: VPM_15_week6

description: Gene expression in whole blood 6 weeks after vaccination


title: LymphNode_H56+GLA-SE_6hr_animal4

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse lymph node
F4_LN


title: VPM_14_week26


title: LymphNode_H56+GLA-SE_6hr_animal1

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse lymph node
F1_LN


title: Cachectic cases [3003]


title: LymphNode_H56+GLA-SE_6hr_animal3

description:
Gene expression after 6hr in H56+GLA-SE-treated mouse lymph node
F3_LN


title: Blood_untreated_0hr_animal4

description:
Gene expression in untreated mouse whole blood
A2_WB


title: VPM_15_week0

description: Gene expression in whole blood before vaccination


title: VPM_21_week6


title: LymphNode_H56+IC31_168hr_animal1

description:
Gene expression after 168hr in H56+IC31-treated mouse lymph node
E22_LN


title: Cachectic cases [5128]


title: LymphNode_H56+IC31_72hr_animal7

description:
Gene expression after 72hr in H56+IC31-treated mouse lymph node
E21_LN


title: VPM_21_week2


title: LymphNode_H56+IC31_168hr_animal3

description:
Gene expression after 168hr in H56+IC31-treated mouse lymph node
E24_LN


title: LymphNode_H56+IC31_72hr_animal3

description:
Gene expression after 72hr in H56+IC31-treated mouse lymph node
E17_LN


title: LymphNode_H56+IC31_72hr_animal6

description:
Gene expression after 72hr in H56+IC31-treated mouse lymph node
E20_LN


title: LymphNode_H56+IC31_168hr_animal5

description:
Gene expression after 168hr in H56+IC31-treated mouse lymph node
E26_LN


title: VPM_21_week0


title: LymphNode_H56+IC31_72hr_animal5

description:
Gene expression after 72hr in H56+IC31-treated mouse lymph node
E19_LN


title: VPM_16_week18

description: Gene expression in whole blood 18 weeks after vaccination


title: LymphNode_H56+IC31_168hr_animal2

description:
Gene expression after 168hr in H56+IC31-treated mouse lymph node
E23_LN


title: LymphNode_H56+IC31_168hr_animal4

description:
Gene expression after 168hr in H56+IC31-treated mouse lymph node
E25_LN


title: LymphNode_H56+IC31_24hr_animal7

description:
Gene expression after 24hr in H56+IC31-treated mouse lymph node
E14_LN


title: LymphNode_H56+IC31_72hr_animal1

description:
Gene expression after 72hr in H56+IC31-treated mouse lymph node
E15_LN


title: VPM_16_week6

description: Gene expression in whole blood 6 weeks after vaccination


title: VPM_16_week12

description: Gene expression in whole blood 12 weeks after vaccination


title: LymphNode_H56+IC31_72hr_animal4

description:
Gene expression after 72hr in H56+IC31-treated mouse lymph node
E18_LN


title: VPM_16_week26

description: Gene expression in whole blood 26 weeks after vaccination


title: LymphNode_H56+IC31_24hr_animal5

description:
Gene expression after 24hr in H56+IC31-treated mouse lymph node
E12_LN


title: LymphNode_H56+IC31_72hr_animal2

description:
Gene expression after 72hr in H56+IC31-treated mouse lymph node
E16_LN


title: LymphNode_H56+IC31_24hr_animal4

description:
Gene expression after 24hr in H56+IC31-treated mouse lymph node
E11_LN


title: LymphNode_H56+IC31_168hr_animal7

description:
Gene expression after 168hr in H56+IC31-treated mouse lymph node
E28_LN


title: VPM_16_week2

description: Gene expression in whole blood 2 weeks after vaccination


title: Cachectic cases [5100]

description: Total RNA was used for labeling and hybridisation. .CEL files were generated for downstream analysis


title: LymphNode_H56+IC31_24hr_animal3

description:
Gene expression after 24hr in H56+IC31-treated mouse lymph node
E10_LN


title: LymphNode_H56+IC31_24hr_animal2

description:
Gene expression after 24hr in H56+IC31-treated mouse lymph node
E9_LN


title: VPM_14_week12


title: LymphNode_H56+IC31_24hr_animal6

description:
Gene expression after 24hr in H56+IC31-treated mouse lymph node
E13_LN


title: LymphNode_H56+IC31_6hr_animal7

description:
Gene expression after 6hr in H56+IC31-treated mouse lymph node
E7_LN


title: LymphNode_H56+IC31_6hr_animal6

description:
Gene expression after 6hr in H56+IC31-treated mouse lymph node
E6_LN


title: VPM_13_week18

description: Gene expression in whole blood 18 weeks after vaccination


title: LymphNode_H56+IC31_6hr_animal1

description:
Gene expression after 6hr in H56+IC31-treated mouse lymph node
E1_LN


title: LymphNode_H56+IC31_6hr_animal5

description:
Gene expression after 6hr in H56+IC31-treated mouse lymph node
E5_LN


title: VPM_13_week26


title: LymphNode_H56+IC31_6hr_animal2

description:
Gene expression after 6hr in H56+IC31-treated mouse lymph node
E2_LN


title: LymphNode_H56+CAF01_168hr_animal7

description:
Gene expression after 168hr in H56+CAF01-treated mouse lymph node
D28_LN


title: VPM_14_week0

description: Gene expression in whole blood before vaccination


title: VPM_13_week12

description: Gene expression in whole blood 12 weeks after vaccination


title: LymphNode_H56+CAF01_168hr_animal4

description:
Gene expression after 168hr in H56+CAF01-treated mouse lymph node
D25_LN


title: LymphNode_H56+IC31_6hr_animal3

description:
Gene expression after 6hr in H56+IC31-treated mouse lymph node
E3_LN


title: LymphNode_H56+CAF01_168hr_animal5

description:
Gene expression after 168hr in H56+CAF01-treated mouse lymph node
D26_LN


title: VPM_13_week0


title: LymphNode_H56+CAF01_168hr_animal3

description:
Gene expression after 168hr in H56+CAF01-treated mouse lymph node
D24_LN


title: LymphNode_H56+CAF01_168hr_animal6

description:
Gene expression after 168hr in H56+CAF01-treated mouse lymph node
D27_LN


title: VPM_12_week6

description: Gene expression in whole blood 6 weeks after vaccination


title: LymphNode_H56+CAF01_72hr_animal6

description:
Gene expression after 72hr in H56+CAF01-treated mouse lymph node
D21_LN


title: LymphNode_H56+GLA-SE_24hr_animal4

description:
Gene expression after 24hr in H56+GLA-SE-treated mouse lymph node
F11_LN


title: LymphNode_H56+CAF01_168hr_animal1

description:
Gene expression after 168hr in H56+CAF01-treated mouse lymph node
D22_LN


title: VPM_12_week0


title: LymphNode_H56+CAF01_168hr_animal2

description:
Gene expression after 168hr in H56+CAF01-treated mouse lymph node
D23_LN


title: VPM_12_week12


title: LymphNode_H56+CAF01_72hr_animal2

description:
Gene expression after 72hr in H56+CAF01-treated mouse lymph node
D17_LN


title: VPM_10_week12


title: VPM_10_week6


title: VPM_10_week0


title: LymphNode_H56+CAF01_72hr_animal1

description:
Gene expression after 72hr in H56+CAF01-treated mouse lymph node
D16_LN


title: LymphNode_H56+CAF01_24hr_animal7

description:
Gene expression after 24hr in H56+CAF01-treated mouse lymph node
D13_LN


title: LymphNode_H56+CAF01_24hr_animal6

description:
Gene expression after 24hr in H56+CAF01-treated mouse lymph node
D12_LN


title: LymphNode_H56+CAF01_24hr_animal5

description:
Gene expression after 24hr in H56+CAF01-treated mouse lymph node
D11_LN


title: LymphNode_H56+CAF01_6hr_animal7

description:
Gene expression after 6hr in H56+CAF01-treated mouse lymph node
D7_LN


title: LymphNode_H56+CAF01_24hr_animal4

description:
Gene expression after 24hr in H56+CAF01-treated mouse lymph node
D10_LN


title: LymphNode_H56+CAF01_24hr_animal1

description:
Gene expression after 24hr in H56+CAF01-treated mouse lymph node
D8_LN


title: VPM_08_week6


title: LymphNode_H56+IC31_6hr_animal4

description:
Gene expression after 6hr in H56+IC31-treated mouse lymph node
E4_LN


title: LymphNode_H56+CAF01_6hr_animal6

description:
Gene expression after 6hr in H56+CAF01-treated mouse lymph node
D6_LN


title: VPM_08_week18

description: Gene expression in whole blood 18 weeks after vaccination


title: LymphNode_H56+CAF01_24hr_animal2

description:
Gene expression after 24hr in H56+CAF01-treated mouse lymph node
D15_LN


title: LymphNode_H56+CAF01_6hr_animal3

description:
Gene expression after 6hr in H56+CAF01-treated mouse lymph node
D3_LN


title: VPM_08_week0

description: Gene expression in whole blood before vaccination


title: LymphNode_H56+CAF01_6hr_animal4

description:
Gene expression after 6hr in H56+CAF01-treated mouse lymph node
D4_LN


title: LymphNode_H56+CAF01_24hr_animal3

description:
Gene expression after 24hr in H56+CAF01-treated mouse lymph node
D9_LN


title: LymphNode_H56+IC31_168hr_animal6

description:
Gene expression after 168hr in H56+IC31-treated mouse lymph node
E27_LN


title: VPM_08_week12

description: Gene expression in whole blood 12 weeks after vaccination


title: VPM_07_week26

description: Gene expression in whole blood 26 weeks after vaccination


title: LymphNode_H56+CAF01_6hr_animal5

description:
Gene expression after 6hr in H56+CAF01-treated mouse lymph node
D5_LN


title: patient # 027 pre placebo treatment

city: Baltimore

first: Seakwoo

last: Lee

state: Maryland

address: 600 N. Wolfe Street

country: USA

institute: Johns Hopkins University, School of Medicine

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Affiymetrix GeneChip scanner 3000 with G7 upgrade (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA).

data_processing:
Raw gene expression data, Affymetrix exon CEL files, were extracted and RMA (Robust Multi-array Average) (Bolstad BM et al 2003, Irizarry RA et al. 2003) normalized using Partek Genomics Suite v6.6 analytic platform (Partek Inc. St. Louis, MO)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.na32.hg19.probeset_extended.mps

label_protocol: cDNA (5 µg) was fragmented and labeled using Encore® Biotin Module (Nugen Encore® Biotin Mocule user guide, Nugen Technologies Inc., San Carlos, CA).

growth_protocol: Human nasal epithelial cells were collected from various ages of cystic fibrosis patients

extract_protocol: Total RNA extracted by using QIAzol® lysis reagent was purified using RNeasy micro kit (Qiagen Inc., Valencia, CA) with on column DNase treatment.

treatment_protocol: All samples were placed in Trizol and snap frozen in liquid N2

tag: disease state

value: CF

tag: individual

value: patient # 027

value: placebo

tag: dosage

value: 100 micro gram/daily

tag: time

value: pre treatment

tag: cell type

value: nasal epithelial cells


title: VPM_07_week12


title: patient # 027 post placebo treatment

value: post treatment


title: LymphNode_H56+CAF01_72hr_animal4

description:
Gene expression after 72hr in H56+CAF01-treated mouse lymph node
D19_LN


title: LymphNode_H56+CAF01_6hr_animal2

description:
Gene expression after 6hr in H56+CAF01-treated mouse lymph node
D2_LN


title: VPM_08_week2

description: Gene expression in whole blood 2 weeks after vaccination


title: LymphNode_H56+CAF01_6hr_animal1

description:
Gene expression after 6hr in H56+CAF01-treated mouse lymph node
D1_LN


title: patient # 022 pre placebo treatment

value: patient # 022


title: patient # 022 post placebo treatment


title: LymphNode_H56+Alum_168hr_animal4

description:
Gene expression after 168hr in H56+Alum-treated mouse lymph node
C25_LN


title: LymphNode_H56+CAF01_72hr_animal3

description:
Gene expression after 72hr in H56+CAF01-treated mouse lymph node
D18_LN


title: LymphNode_H56+Alum_168hr_animal6

description:
Gene expression after 168hr in H56+Alum-treated mouse lymph node
C27_LN


title: LymphNode_H56+Alum_168hr_animal5

description:
Gene expression after 168hr in H56+Alum-treated mouse lymph node
C26_LN


title: VPM_01_week18

description: Gene expression in whole blood 18 weeks after vaccination


title: VPM_07_week6

description: Gene expression in whole blood 6 weeks after vaccination


title: VPM_07_week0

description: Gene expression in whole blood before vaccination


title: VPM_01_week26


title: LymphNode_H56+Alum_168hr_animal7

description:
Gene expression after 168hr in H56+Alum-treated mouse lymph node
C28_LN


title: patient # 018 post placebo treatment

value: patient # 018


title: patient # 018 pre placebo treatment


title: LymphNode_H56+CAF01_72hr_animal5

description:
Gene expression after 72hr in H56+CAF01-treated mouse lymph node
D20_LN


title: VPM_01_week12


title: LymphNode_H56+Alum_168hr_animal1

description:
Gene expression after 168hr in H56+Alum-treated mouse lymph node
C22_LN


title: VPM_14_week18


title: LymphNode_H56+Alum_168hr_animal3

description:
Gene expression after 168hr in H56+Alum-treated mouse lymph node
C24_LN


title: patient # 014 pre placebo treatment

value: patient # 014


title: LymphNode_H56+Alum_168hr_animal2

description:
Gene expression after 168hr in H56+Alum-treated mouse lymph node
C23_LN


title: patient # 014 post placebo treatment


title: patient # 010 pre placebo treatment

value: patient # 010


title: VPM_08_week26

description: Gene expression in whole blood 26 weeks after vaccination


title: LymphNode_H56+Alum_72hr_animal6

description:
Gene expression after 72hr in H56+Alum-treated mouse lymph node
C20_LN


title: patient # 010 post placebo treatment


title: VPM_14_week6


title: LymphNode_H56+IC31_24hr_animal1

description:
Gene expression after 24hr in H56+IC31-treated mouse lymph node
E8_LN


title: patient # 005 pre placebo treatment

value: patient # 005


title: VPM_12_week26


title: LymphNode_H56+Alum_72hr_animal4

description:
Gene expression after 72hr in H56+Alum-treated mouse lymph node
C18_LN


title: patient # 003 pre placebo treatment

value: patient # 003


title: VPM_12_week18


title: VPM_10_week2

description: Gene expression in whole blood 2 weeks after vaccination


title: BCG_09_week12

description: Gene expression in whole blood 12 weeks after vaccination

value: BCG


title: LymphNode_H56+Alum_72hr_animal3

description:
Gene expression after 72hr in H56+Alum-treated mouse lymph node
C17_LN


title: patient # 005 post placebo treatment


title: patient # 003 post placebo treatment


title: LymphNode_H56+Alum_24hr_animal6

description:
Gene expression after 24hr in H56+Alum-treated mouse lymph node
C13_LN


title: patient # 030 pre digitoxin treatment

value: patient # 030

value: digitoxin

value: 50 micro gram/daily


title: BCG_11_week26


title: patient # 031 pre digitoxin treatment

value: CF

value: patient # 031


title: VPM_22_week26


title: LymphNode_H56+Alum_72hr_animal2

description:
Gene expression after 72hr in H56+Alum-treated mouse lymph node
C16_LN

value: lymph node


title: LymphNode_H56+Alum_72hr_animal1

description:
Gene expression after 72hr in H56+Alum-treated mouse lymph node
C15_LN


title: patient # 030 post digitoxin treatment


title: LymphNode_H56+Alum_24hr_animal7

description:
Gene expression after 24hr in H56+Alum-treated mouse lymph node
C14_LN


title: LymphNode_H56+Alum_72hr_animal5

description:
Gene expression after 72hr in H56+Alum-treated mouse lymph node
C19_LN


title: VPM_22_week18

description: Gene expression in whole blood 18 weeks after vaccination


title: patient # 031 post digitoxin treatment


title: VPM_22_week12


title: LymphNode_H56+Alum_24hr_animal4

description:
Gene expression after 24hr in H56+Alum-treated mouse lymph node
C11_LN


title: VPM_22_week2


title: patient # 025 pre digitoxin treatment

value: patient # 025

value: 100 micro gram/daily


title: patient # 028 pre digitoxin treatment

value: patient # 028

value: pre treatment

value: nasal epithelial cells


title: VPM_22_week6

description: Gene expression in whole blood 6 weeks after vaccination


title: VPM_21_week18


title: VPM_01_week2


title: VPM_21_week12


title: VPM_22_week0

description: Gene expression in whole blood before vaccination


title: LymphNode_H56+Alum_6hr_animal7

description:
Gene expression after 6hr in H56+Alum-treated mouse lymph node
C7_LN


title: LymphNode_H56+Alum_24hr_animal1

description:
Gene expression after 24hr in H56+Alum-treated mouse lymph node
C8_LN


title: patient # 025 post digitoxin treatment

value: post treatment


title: VPM_01_week6


title: VPM_01_week0


title: LymphNode_H56+Alum_6hr_animal6

description:
Gene expression after 6hr in H56+Alum-treated mouse lymph node
C6_LN


title: patient # 024 pre digitoxin treatment

value: patient # 024


title: LymphNode_H56+Alum_24hr_animal5

description:
Gene expression after 24hr in H56+Alum-treated mouse lymph node
C12_LN


title: LymphNode_H56+Alum_6hr_animal5

description:
Gene expression after 6hr in H56+Alum-treated mouse lymph node
C5_LN


title: BCG_45_week26

description: Gene expression in whole blood 26 weeks after vaccination


title: LymphNode_H56+Alum_24hr_animal2

description:
Gene expression after 24hr in H56+Alum-treated mouse lymph node
C9_LN


title: LymphNode_H56+Alum_6hr_animal3

description:
Gene expression after 6hr in H56+Alum-treated mouse lymph node
C3_LN


title: LymphNode_H56+Alum_6hr_animal4

description:
Gene expression after 6hr in H56+Alum-treated mouse lymph node
C4_LN


title: patient # 020 post digitoxin treatment

value: patient # 020


title: patient # 020 pre digitoxin treatment


title: patient # 021 post digitoxin treatment

value: patient # 021


title: patient # 021 pre digitoxin treatment


title: BCG_45_week6


title: LymphNode_H56_168hr_animal6

description:
Gene expression after 168hr in H56-treated mouse lymph node
B27_LN


title: BCG_42_week26


title: LymphNode_H56_168hr_animal3

description:
Gene expression after 168hr in H56-treated mouse lymph node
B24_LN


title: BCG_45_week0


title: LymphNode_H56+Alum_6hr_animal2

description:
Gene expression after 6hr in H56+Alum-treated mouse lymph node
C2_LN


title: patient # 017 pre digitoxin treatment

value: patient # 017


title: BCG_45_week2

description: Gene expression in whole blood 2 weeks after vaccination

value: BCG


title: LymphNode_H56+Alum_6hr_animal1

description:
Gene expression after 6hr in H56+Alum-treated mouse lymph node
C1_LN


title: BCG_42_week12

description: Gene expression in whole blood 12 weeks after vaccination


title: LymphNode_H56+Alum_72hr_animal7

description:
Gene expression after 72hr in H56+Alum-treated mouse lymph node
C21_LN


title: LymphNode_H56_168hr_animal5

description:
Gene expression after 168hr in H56-treated mouse lymph node
B26_LN


title: BCG_45_week12


title: BCG_42_week18

description: Gene expression in whole blood 18 weeks after vaccination


title: BCG_45_week18


title: LymphNode_H56_168hr_animal7

description:
Gene expression after 168hr in H56-treated mouse lymph node
B28_LN


title: LymphNode_H56_168hr_animal4

description:
Gene expression after 168hr in H56-treated mouse lymph node
B25_LN


title: LymphNode_H56_168hr_animal2

description:
Gene expression after 168hr in H56-treated mouse lymph node
B23_LN


title: patient # 015 pre digitoxin treatment

value: patient # 015


title: patient # 017 post digitoxin treatment

value: digitoxin


title: patient # 015 post digitoxin treatment


title: patient # 013 pre digitoxin treatment

value: patient # 013

value: 50 micro gram/daily


title: BCG_42_week6

description: Gene expression in whole blood 6 weeks after vaccination


title: patient # 019 post digitoxin treatment

value: CF

value: patient # 019


title: patient # 019 pre digitoxin treatment


title: patient # 013 post digitoxin treatment


title: patient # 009 pre digitoxin treatment

value: patient # 009


title: LymphNode_H56+Alum_24hr_animal3

description:
Gene expression after 24hr in H56+Alum-treated mouse lymph node
C10_LN

value: lymph node


title: LymphNode_H56_72hr_animal7

description:
Gene expression after 72hr in H56-treated mouse lymph node
B21_LN


title: BCG_42_week0

description: Gene expression in whole blood before vaccination


title: LymphNode_H56_168hr_animal1

description:
Gene expression after 168hr in H56-treated mouse lymph node
B22_LN


title: BCG_40_week2


title: LymphNode_H56_72hr_animal6

description:
Gene expression after 72hr in H56-treated mouse lymph node
B20_LN


title: LymphNode_H56_72hr_animal4

description:
Gene expression after 72hr in H56-treated mouse lymph node
B18_LN


title: patient # 006 post digitoxin treatment

value: patient # 006


title: BCG_40_week12


title: LymphNode_H56_72hr_animal2

description:
Gene expression after 72hr in H56-treated mouse lymph node
B16_LN


title: patient # 006 pre digitoxin treatment

value: pre treatment


title: BCG_33_week6


title: unstimulated rep3

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite

source_name: primary neonatal micoglia_unstimulated

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

tag: strain

value: 1-5 days old pups

value: primary microglia isolated from cortial tissue

tag: treated with

value: none (unstimulated control)


title: LymphNode_H56_72hr_animal5

description:
Gene expression after 72hr in H56-treated mouse lymph node
B19_LN


title: unstimulated rep2


title: BCG_42_week2

description: Gene expression in whole blood 2 weeks after vaccination


title: BCG_40_week0


title: BCG_33_week12

description: Gene expression in whole blood 12 weeks after vaccination


title: BCG_40_week6


title: LymphNode_H56_72hr_animal3

description:
Gene expression after 72hr in H56-treated mouse lymph node
B17_LN


title: patient # 004 post digitoxin treatment

value: patient # 004

value: post treatment

value: nasal epithelial cells


title: patient # 002 pre digitoxin treatment

value: patient # 002


title: patient # 002 post digitoxin treatment


title: patient # 004 pre digitoxin treatment


title: patient # 009 post digitoxin treatment


title: patient # 028 post digitoxin treatment

value: patient # 028

value: 100 micro gram/daily


title: LPS/IFNg rep3

source_name: primary neonatal micoglia_LPS/IFNg

value: LPS (100n/ml) and IFNγ (20 ng/ml) for 16hrs


title: unstimulated rep1


title: BCG_33_week2

value: BCG


title: LymphNode_H56_24hr_animal7

description:
Gene expression after 24hr in H56-treated mouse lymph node
B14_LN


title: patient # 001 pre digitoxin treatment

value: CF

value: patient # 001

value: digitoxin

value: 50 micro gram/daily


title: patient # 001 post digitoxin treatment


title: LymphNode_H56_24hr_animal5

description:
Gene expression after 24hr in H56-treated mouse lymph node
B12_LN

value: lymph node


title: LymphNode_H56_24hr_animal4

description:
Gene expression after 24hr in H56-treated mouse lymph node
B11_LN


title: OGA-3

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA

scan_protocol: Drosorphila whole genome expression array chips were washed and stained in the Affymetrix Fluidics Station 400s

data_processing:
Chips were scanned with an Affymetrix Scanner with standard settings
Data was analyzed by Micrarray Suite 5.0 (MAS5) and by RMA using the program Partek

organism: Drosophila melanogaster

source_name: OGA mutant

label_protocol: Trizol extraction of total RNA was performed according to standard affymetrix labeling protocols

growth_protocol: We used the standard growth protocol for Drosorphila as in our manuscript.

extract_protocol: Drosorphila were isolated for wild type and two mutant strains: OGA and SXC by Trizol protocol.

treatment_protocol: RNA were isolated from wild type and mutants.

tag: genotype

value: OGA mutant


title: BCG_30_week26

description: Gene expression in whole blood 26 weeks after vaccination


title: SXC-3

source_name: SXC mutant

value: SXC mutant


title: BCG_30_week6


title: LPS/IFNg rep2

value: 1-5 days old pups

value: primary microglia isolated from cortial tissue


title: BCG_33_week0


title: LymphNode_H56_24hr_animal6

description:
Gene expression after 24hr in H56-treated mouse lymph node
B13_LN


title: Control-3

source_name: WildType

value: WildType


title: LPS/IFNg rep1


title: LymphNode_H56_24hr_animal3

description:
Gene expression after 24hr in H56-treated mouse lymph node
B10_LN


title: SXC-2


title: OGA-2


title: LymphNode_H56_72hr_animal1

description:
Gene expression after 72hr in H56-treated mouse lymph node
B15_LN


title: IL-4 rep1

source_name: primary neonatal micoglia_IL-4

value: Interleukin-4 (IL-4) (100 U/ml) for 48hrs


title: IL-4 rep3


title: Control-2


title: patient # 024 post digitoxin treatment

value: patient # 024

value: post treatment

value: nasal epithelial cells


title: LymphNode_H56_24hr_animal2

description:
Gene expression after 24hr in H56-treated mouse lymph node
B9_LN


title: IL-4 rep2


title: BCG_30_week0

description: Gene expression in whole blood before vaccination


title: BCG_30_week12


title: cecum_control_replicate6

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations  (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.2)

source_name: cecum isolated from a mouse carrying only the ASF4 background microbiota since birth (control treatment)

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Germ-free C57Bl/6 mice were obtained from the Clean Mouse Facility (CMF) of the University of Bern, Switzerland and directly inoculated with a mixture of Altered Schaedler flora (ASF4) strains (ASF356, ASF361, SB2 (=reisolate of ASF502), ASF519). Mice were bred under germ-free conditions in an isolator with Hepa-filtered air and supplied with sterile chow and water. Animal experiments were approved by the regional ethics committee and performed according to authorities.

extract_protocol: RNA was purified from cecum samples using TRIzol (Life Technologies, Calsbad, CA, USA) followed by an additional round of purification with RNeasy Microkit columns (Qiagen, Venlo, the Netherlands). RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: C57BL/6 mice harboring a reduced Altered Schaedler flora (ASF4; n=6) or ASF4 mice colonized with M. schaedleri MCS for 10 days (n=6) were sacrificed. The cecum was washed in PBS and snap-frozen in liquid N2.

tag: mouse id

tag: Sex

value: Male

tag: age (weeks)

value: 6 weeks

value: Control, i.e. only background microbiota comprised of a mixture of ASF4 strains (ASF356, ASF361, SB2 (=reisolate of ASF502), ASF519) that was present since birth

value: cecum


title: SXC-1


title: cecum_control_replicate5

value: 7 weeks

tag: treatment

tag: tissue


title: BCG_23_week18

description: Gene expression in whole blood 18 weeks after vaccination

tag: group

value: BCG


title: BCG_23_week26


title: LymphNode_H56_24hr_animal1

description:
Gene expression after 24hr in H56-treated mouse lymph node
B8_LN

tag: timepoint


title: OGA-1


title: BCG_23_week6

description: Gene expression in whole blood 6 weeks after vaccination


title: LymphNode_H56_6hr_animal4

description:
Gene expression after 6hr in H56-treated mouse lymph node
B4_LN


title: LymphNode_H56_6hr_animal6

description:
Gene expression after 6hr in H56-treated mouse lymph node
B6_LN


title: cecum_ASF457_replicate6

source_name: cecum isolated 10 days after inoculation with M. schaedleri ASF 457 MCS on top of the ASF4 background microbiota that was present since birth (ASF457 treatment)

value: ASF457, i.e. 10 days after inoculation with M. schaedleri ASF 457 MCS in a mouse that harbored the ASF4 background microbiota since birth


title: cecum_ASF457_replicate4


title: Control-1


title: BCG_23_week0


title: cecum_ASF457_replicate5


title: cecum_control_replicate4


title: BCG_23_week12


title: LymphNode_H56_6hr_animal5

description:
Gene expression after 6hr in H56-treated mouse lymph node
B5_LN

value: lymph node


title: BCG_20_week26


title: LymphNode_H56_6hr_animal2

description:
Gene expression after 6hr in H56-treated mouse lymph node
B2_LN


title: cecum_ASF457_replicate3

value: Female


title: BCG_20_week6


title: cecum_ASF457_replicate1


title: BCG_20_week12

description: Gene expression in whole blood 12 weeks after vaccination


title: cecum_control_replicate3


title: LymphNode_H56_6hr_animal1

description:
Gene expression after 6hr in H56-treated mouse lymph node
B1_LN


title: cecum_ASF457_replicate2


title: LymphNode_untreated_0hr_animal7

description:
Gene expression in untreated mouse lymph node
A7_LN

value: untreated


title: LymphNode_H56_6hr_animal3

description:
Gene expression after 6hr in H56-treated mouse lymph node
B3_LN


title: LymphNode_untreated_0hr_animal6

description:
Gene expression in untreated mouse lymph node
A6_LN


title: cecum_control_replicate2


title: LymphNode_untreated_0hr_animal3

description:
Gene expression in untreated mouse lymph node
A3_LN


title: LymphNode_untreated_0hr_animal4

description:
Gene expression in untreated mouse lymph node
A4_LN


title: BCG_20_week2

description: Gene expression in whole blood 2 weeks after vaccination


title: TT/CC_3

city: Granada

first: Jose

middle: Antonio

last: Lopez-Escamez

state: Granada

address: Av. Ilustracion 114

department: Genomics of vestibular disorders

country: Spain

institute: Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research (GENYO)

description:
Replicate 2
SAMPLE 6

data_processing: The data were normalised using quantile normalisation from IlluminaGUI interface in R

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

extract_protocol: RNA was extracted using the RNA isolatin Kit from Roche in accordance to the manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

tag: subject status

value: TT/CC haplotype-conditioned

tag: gender

value: male

value: peripheral blood mononuclear cells (PBMCs)


title: cecum_control_replicate1


title: LymphNode_untreated_0hr_animal5

description:
Gene expression in untreated mouse lymph node
A5_LN


title: BCG_11_week12

tag: timepoint (weeks post vaccination)


title: BCG_11_week18


title: BCG_11_week0

description: Gene expression in whole blood before vaccination


title: TT/CC_1

description:
Replicate 2
SAMPLE 4

value: female


title: BCG_09_week26

description: Gene expression in whole blood 26 weeks after vaccination


title: LymphNode_untreated_0hr_animal1

description:
Gene expression in untreated mouse lymph node
A1_LN


title: CC/TT_3

description:
Replicate 1
SAMPLE 3

value: CC/TT haplotype-conditioned


title: LymphNode_untreated_0hr_animal2

description:
Gene expression in untreated mouse lymph node
A2_LN


title: BCG_09_week18

description: Gene expression in whole blood 18 weeks after vaccination


title: BCG_09_week2


title: BCG_11_week2


title: BCG_09_week6

description: Gene expression in whole blood 6 weeks after vaccination


title: TT/CC_2

description:
Replicate 2
SAMPLE 5


title: BCG_09_week0


title: BCG_20_week0


title: BCG_03_week26


title: BCG_03_week12


title: BCG_03_week18


title: CC/TT_2

description:
Replicate 1
SAMPLE 2


title: CC/TT_1

description:
Replicate 1
SAMPLE 1


title: BCG_03_week6


title: BCG_03_week0


title: BCG_02_week18


title: BCG_03_week2


title: BCG_02_week0


title: BCG_40_week26


title: BCG_02_week6


title: BCG_30_week2


title: BCG_30_week18


title: BCG_02_week26


title: VPM_07_week18


title: Terbufos_57.5ugL_MaleBrain_72h_251959710321_1_2_X.txt

status: Public on Jan 08 2017

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

institute: US EPA

description: chemical abbreviations: EE2, 17a-ethynyl estradiol;  DMSO, Dimethyl sulfoxide

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: Agilent Technologies Scanner G2505B was used to scan microarray images at 3 or 5 µm resolution

data_processing:
Microarray image processing was performed using the latest Agilent's Feature Extraction software available at the time following the manufacturer’s protocol and recommendations.  Data pre-processing and analysis related to the identification of differentially expressed genes (DEGs) were based on individual chemical conditions and their conrresponding controls using the R package Limma, in the order of backgroundCorrect("normexp"), normalizeBetweenArrays("quantile"), and modified t-test. A subset of DEGs from each chemical treatment condition was then selected as a gene signature.  Individual chemical-treated microarray samples were also processed into rank-ordered gene lists (ROGLs) relative to their approriate controls.  This collection of ROGLs was subsequently interrogated by gene signatures computationally so their underlying chemical conditions could be connected.
supplementary files: log2 intensity after backgroundCorrect("normexp") and normalizeBetweenArrays("quantile") in Limma; various types of control probes were filtered

organism: Pimephales promelas

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling Kit; Agilent, Palo Alto, CA)

growth_protocol: Fry and sexually mature adult fathead minnows (5-7 month old) were obtained from an on-site aquatic culture facility at the US EPA Ecological Exposure Research Division, Cincinnati, Ohio, USA. Fish were held under a 16:8 light:dark photoperiod fed frozen adult brine shrimp (San Francisco Bay Brand, Newark, CA, USA). Fish survival, water temperature (mean ± SD; 25.0±0.3), and dissolved oxygen (mean ± SD; 7.0±0.2) were monitored daily over the duration of the exposure and did not vary significantly between treatment groups.

extract_protocol: Total RNA was isolated from ovary tissue of both fathead minnow using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and RNA was quantified spectrophotometrically (Nanodrop). Total RNA samples were stored at -80oC until used for microarray analyses.

treatment_protocol: Exposures were conducted in an either static or flow-through system.  To initiate a typical experiment, four males and four females were placed together in a glass test tank holding 10 L of water (4 µM filtered, UV sterilized) or test chemical dissolved in water and/or DMSO carrier. There were multiple tanks for each treatment condition. The animals were held at 25 +/- 0.5 °C under a 16:8 L:D photoperiod, and were fed brine shrimp to satiation twice per day.

tag: chemical

value: Terbufos

tag: dose

value: MaleBrain

tag: exposure duration

tag: age

value: 5-7 month

tag: arrayname

tag: featureextractiontime

tag: featureextractionsoftwareversion

tag: experimentid

value: Mixtures


title: VPM_13_week6


title: Terbufos_57.5ugL_MaleBrain_72h_251959710319_1_4_X.txt


title: BCG_11_week6


title: Terbufos_57.5ugL_MaleBrain_72h_251959710320_1_4_X.txt


title: Terbufos_57.5ugL_MaleBrain_72h_251959710319_2_3_X.txt


title: Terbufos_57.5ugL_MaleBrain_72h_251959710321_1_1_X.txt


title: VPM_10_week18


title: Terbufos_57.5ugL_MaleBrain_72h_251959710320_2_2_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710322_2_2_X.txt

value: Permethrin


title: Terbufos_57.5ugL_MaleBrain_72h_251959710318_1_2_X.txt


title: Terbufos_57.5ugL_MaleBrain_72h_251959710317_2_2_X.txt


title: Terbufos_57.5ugL_MaleBrain_72h_251959710319_2_1_X.txt


title: Terbufos_57.5ugL_MaleBrain_72h_251959710318_1_3_X.txt


title: Terbufos_57.5ugL_MaleBrain_72h_251959710321_2_4_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710321_2_2_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710322_1_4_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710318_2_1_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710320_1_3_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710319_1_2_X.txt


title: Terbufos_57.5ugL_MaleBrain_72h_251959710319_1_1_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710317_2_4_X.txt


title: Terbufos_57.5ugL_MaleBrain_72h_251959710318_2_2_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710317_1_2_X.txt


title: LymphNode_H56_6hr_animal7

description:
Gene expression after 6hr in H56-treated mouse lymph node
B7_LN


title: Permethrin_7.5ugL_MaleBrain_72h_251959710317_1_1_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710319_2_2_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710317_1_3_X.txt


title: Mixture_7.5P57.5TugL_MaleBrain_72h_251959710322_1_3_X.txt

value: Mixture


title: Permethrin_7.5ugL_MaleBrain_72h_251959710322_1_2_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710319_2_4_X.txt


title: Mixture_7.5P57.5TugL_MaleBrain_72h_251959710320_2_3_X.txt


title: Mixture_7.5P57.5TugL_MaleBrain_72h_251959710320_1_2_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710322_1_1_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710317_2_3_X.txt


title: Mixture_7.5P57.5TugL_MaleBrain_72h_251959710317_2_1_X.txt


title: Mixture_7.5P57.5TugL_MaleBrain_72h_251959710318_1_4_X.txt


title: Permethrin_7.5ugL_MaleBrain_72h_251959710320_2_1_X.txt


title: Control_0_MaleBrain_72h_251959710322_2_4_X.txt

value: Control


title: Control_0_MaleBrain_72h_251959710321_2_3_X.txt


title: Mixture_7.5P57.5TugL_MaleBrain_72h_251959710320_1_1_X.txt


title: Control_0_MaleBrain_72h_251959710322_2_3_X.txt


title: Control_0_MaleBrain_72h_251959710322_2_1_X.txt


title: Control_0_MaleBrain_72h_251959710321_2_1_X.txt


title: Control_0_MaleBrain_72h_251959710321_1_4_X.txt


title: Control_0_MaleBrain_72h_251959710321_1_3_X.txt


title: Control_0_MaleBrain_72h_251959710318_2_3_X.txt


title: cypermethrin_Control_larva_48hr_251959710455_1_2_X.txt

value: cypermethrin

value: larva

value: 48h post hatch


title: Control_0_MaleBrain_72h_251959710319_1_3_X.txt


title: cypermethrin_Control_larva_48hr_251959710453_2_1_X.txt


title: permethrin_3.13ugL_larvae_48hr_253657410233_2_4_17.txt

value: permethrin

value: larvae


title: Control_0_MaleBrain_72h_251959710317_1_4_X.txt


title: permethrin_3.13ugL_larvae_48hr_253657410234_1_3_17.txt


title: cypermethrin_Control_larva_48hr_251959710462_1_3_X.txt


title: Control_0_MaleBrain_72h_251959710320_2_4_X.txt


title: Control_0_MaleBrain_72h_251959710318_2_4_X.txt


title: permethrin_3.13ugL_larvae_48hr_253657410232_1_1_17.txt


title: cypermethrin_Control_larva_48hr_251959710451_1_3_X.txt


title: permethrin_1.56ugL_larvae_48hr_253657410233_1_4_17.txt


title: permethrin_3.13ugL_larvae_48hr_253657410231_2_4_17.txt


title: cypermethrin_Control_larva_48hr_251959710452_2_4_X.txt


title: permethrin_3.13ugL_larvae_48hr_253657410225_1_4_17.txt


title: permethrin_3.13ugL_larvae_48hr_253657410229_2_2_17.txt


title: cypermethrin_Control_larva_48hr_251959710450_2_2_X.txt


title: permethrin_3.13ugL_larvae_48hr_253657410230_1_3_17.txt


title: permethrin_3.13ugL_larvae_48hr_253657410222_2_4_17.txt


title: Control_0_MaleBrain_72h_251959710318_1_1_X.txt


title: permethrin_1.56ugL_larvae_48hr_253657410232_2_1_17.txt


title: cypermethrin_Control_larva_48hr_251959710454_1_4_X.txt


title: permethrin_1.56ugL_larvae_48hr_253657410231_1_4_17.txt


title: permethrin_3.13ugL_larvae_48hr_253657410224_2_3_17.txt


title: permethrin_3.13ugL_larvae_48hr_253657410223_1_4_17.txt


title: permethrin_1.56ugL_larvae_48hr_253657410230_2_4_17.txt


title: cypermethrin_Control_larva_48hr_251959710324_2_3_X.txt


title: cypermethrin_Control_larva_48hr_251959710449_1_3_X.txt


title: cypermethrin_Control_larva_48hr_251959710448_1_1_X.txt


title: permethrin_1.56ugL_larvae_48hr_253657410234_2_2_17.txt


title: cypermethrin_Control_brain_72hr_251959710456_2_3_X.txt

value: brain


title: permethrin_1.56ugL_larvae_48hr_253657410229_1_4_17.txt


title: permethrin_1.56ugL_larvae_48hr_253657410230_1_1_17.txt


title: cypermethrin_Control_brain_72hr_251959710452_1_3_X.txt


title: permethrin_1.56ugL_larvae_48hr_253657410226_2_4_17.txt


title: permethrin_3.13ugL_larvae_48hr_253657410227_1_3_17.txt


title: cypermethrin_Control_brain_72hr_251959710461_2_2_X.txt


title: cypermethrin_Control_brain_72hr_251959710458_1_2_X.txt


title: cypermethrin_Control_brain_72hr_251959710450_2_4_X.txt


title: esfenvalerate_1ugL_larvae_48hr_253657410232_1_3_16.txt

value: esfenvalerate


title: cypermethrin_Control_brain_72hr_251959710449_2_1_X.txt


title: permethrin_1.56ugL_larvae_48hr_253657410220_2_1_17.txt


title: esfenvalerate_1ugL_larvae_48hr_253657410230_1_4_16.txt


title: permethrin_1.56ugL_larvae_48hr_253657410221_1_4_17.txt


title: esfenvalerate_0.5ugL_larvae_48hr_253657410233_2_3_16.txt


title: permethrin_1.56ugL_larvae_48hr_253657410227_2_4_17.txt


title: cypermethrin_Control_brain_72hr_251959710325_1_1_X.txt


title: cypermethrin_Control_brain_72hr_251959710455_2_2_X.txt


title: cypermethrin_Control_brain_72hr_251959710451_2_1_X.txt


title: cypermethrin_1ugL_larva_48hr_251959710456_2_1_X.txt


title: cypermethrin_1ugL_larva_48hr_251959710458_2_3_X.txt


title: esfenvalerate_1ugL_larvae_48hr_253657410231_2_2_16.txt


title: cypermethrin_1ugL_larva_48hr_251959710454_2_4_X.txt


title: esfenvalerate_0.5ugL_larvae_48hr_253657410227_1_2_16.txt


title: esfenvalerate_0.5ugL_larvae_48hr_253657410234_1_4_16.txt


title: cypermethrin_1ugL_larva_48hr_251959710452_1_1_X.txt


title: cypermethrin_1ugL_larva_48hr_251959710459_2_2_X.txt


title: cypermethrin_1ugL_larva_48hr_251959710327_1_4_X.txt


title: cypermethrin_1ugL_larva_48hr_251959710448_1_3_X.txt


title: esfenvalerate_0.5ugL_larvae_48hr_253657410223_1_2_16.txt


title: esfenvalerate_0.5ugL_larvae_48hr_253657410226_2_3_16.txt


title: esfenvalerate_0.5ugL_larvae_48hr_253657410224_2_2_16.txt


title: cypermethrin_1ugL_larva_48hr_251959710325_2_2_X.txt


title: cypermethrin_1ugL_larva_48hr_251959710449_1_1_X.txt


title: esfenvalerate_0.5ugL_larvae_48hr_253657410225_1_3_16.txt


title: esfenvalerate_0.5ugL_larvae_48hr_253657410221_1_3_16.txt


title: dmso_ControlugL_larvae_48hr_253657410234_2_4_17.txt

value: dmso

value: ControlugL


title: dmso_ControlugL_larvae_48hr_253657410232_2_4_16.txt


title: esfenvalerate_0.5ugL_larvae_48hr_253657410220_2_3_16.txt


title: dmso_ControlugL_larvae_48hr_253657410233_1_2_17.txt


title: cypermethrin_1ugL_larva_48hr_251959710324_1_2_X.txt


title: cypermethrin_1ugL_brain_72hr_251959710462_2_2_X.txt


title: cypermethrin_1ugL_brain_72hr_251959710461_1_3_X.txt


title: dmso_ControlugL_larvae_48hr_253657410231_1_3_16.txt


title: cypermethrin_1ugL_brain_72hr_251959710456_2_4_X.txt


title: cypermethrin_1ugL_brain_72hr_251959710455_2_1_X.txt


title: dmso_ControlugL_larvae_48hr_253657410230_2_1_14.txt


title: cypermethrin_1ugL_brain_72hr_251959710454_1_1_X.txt


title: cypermethrin_1ugL_brain_72hr_251959710326_1_2_X.txt


title: dmso_ControlugL_larvae_48hr_253657410231_1_2_15.txt


title: cypermethrin_1ugL_brain_72hr_251959710453_2_3_X.txt


title: cypermethrin_0.25ugL_larva_48hr_251959710456_1_3_X.txt


title: cypermethrin_1ugL_brain_72hr_251959710327_2_2_X.txt


title: cypermethrin_1ugL_brain_72hr_251959710451_2_3_X.txt


title: cypermethrin_1ugL_brain_72hr_251959710324_1_4_X.txt


title: dmso_ControlugL_larvae_48hr_253657410230_2_3_15.txt


title: cypermethrin_0.25ugL_larva_48hr_251959710459_2_1_X.txt


title: cypermethrin_0.25ugL_larva_48hr_251959710454_1_2_X.txt


title: dmso_ControlugL_larvae_48hr_253657410232_2_3_15.txt


title: dmso_ControlugL_larvae_48hr_253657410229_2_4_16.txt


title: dmso_ControlugL_larvae_48hr_253657410229_1_1_14.txt


title: dmso_ControlugL_larvae_48hr_253657410227_2_2_14.txt


title: dmso_ControlugL_larvae_48hr_253657410230_1_2_16.txt


title: dmso_ControlugL_larvae_48hr_253657410229_1_2_15.txt


title: dmso_ControlugL_larvae_48hr_253657410226_2_2_17.txt


title: dmso_ControlugL_larvae_48hr_253657410226_1_4_15.txt


title: dmso_ControlugL_larvae_48hr_253657410229_2_1_16.txt


title: dmso_ControlugL_larvae_48hr_253657410227_2_1_15.txt


title: dmso_ControlugL_larvae_48hr_253657410226_1_2_14.txt


title: cypermethrin_0.25ugL_larva_48hr_251959710448_1_4_X.txt


title: cypermethrin_0.25ugL_brain_72hr_251959710452_2_2_X.txt


title: cypermethrin_0.25ugL_brain_72hr_251959710455_1_3_X.txt


title: cypermethrin_0.25ugL_larva_48hr_251959710453_2_2_X.txt


title: cypermethrin_0.25ugL_brain_72hr_251959710456_1_2_X.txt


title: cypermethrin_0.25ugL_larva_48hr_251959710451_1_1_X.txt


title: cypermethrin_0.25ugL_brain_72hr_251959710459_1_1_X.txt


title: cypermethrin_0.25ugL_brain_72hr_251959710451_2_4_X.txt


title: cypermethrin_0.25ugL_larva_48hr_251959710449_2_3_X.txt


title: cypermethrin_0.25ugL_brain_72hr_251959710448_2_4_X.txt


title: cypermethrin_0.25ugL_brain_72hr_251959710326_1_4_X.txt


title: dmso_ControlugL_larvae_48hr_253657410224_1_1_14.txt


title: dmso_ControlugL_larvae_48hr_253657410222_2_2_17.txt


title: cypermethrin_0.25ugL_larva_48hr_251959710327_1_1_X.txt


title: dmso_ControlugL_larvae_48hr_253657410225_2_1_14.txt


title: dmso_ControlugL_larvae_48hr_253657410223_2_4_17.txt


title: dmso_ControlugL_larvae_48hr_253657410224_1_3_16.txt


title: cypermethrin_0.25ugL_brain_72hr_251959710450_2_3_X.txt


title: dmso_ControlugL_larvae_48hr_253657410223_2_1_15.txt


title: dmso_ControlugL_larvae_48hr_253657410226_1_1_16.txt


title: cypermethrin_0.25ugL_brain_72hr_251959710325_1_4_X.txt


title: dmso_ControlugL_larvae_48hr_253657410223_1_3_17.txt


title: dmso_ControlugL_larvae_48hr_253657410223_2_2_16.txt


title: cypermethrin_0.25ugL_brain_72hr_251959710324_2_1_X.txt


title: dmso_ControlugL_larvae_48hr_253657410224_2_4_17.txt


title: dmso_ControlugL_larvae_48hr_253657410225_1_1_17.txt


title: dmso_ControlugL_larvae_48hr_253657410222_1_3_16.txt


title: dmso_ControlugL_larvae_48hr_253657410221_1_1_17.txt


title: bifenthrin_Control_larva_48hr_251959710452_2_1_X.txt

value: bifenthrin


title: bifenthrin_Control_larva_48hr_251959710454_1_3_X.txt


title: bifenthrin_Control_larva_48hr_251959710448_2_2_X.txt


title: bifenthrin_Control_larva_48hr_251959710327_1_3_X.txt


title: bifenthrin_Control_larva_48hr_251959710451_1_4_X.txt


title: bifenthrin_Control_larva_48hr_251959710450_1_1_X.txt


title: dmso_ControlugL_larvae_48hr_253657410220_1_1_14.txt


title: dmso_ControlugL_larvae_48hr_253657410220_2_4_17.txt


title: dmso_ControlugL_larvae_48hr_253657410221_2_2_14.txt


title: cypermethrin_1ugL_larvae_48hr_253657410231_2_1_15.txt


title: cypermethrin_1ugL_larvae_48hr_253657410234_1_1_15.txt


title: cypermethrin_1ugL_larvae_48hr_253657410233_2_2_15.txt


title: bifenthrin_Control_brain_72hr_251959710461_1_4_X.txt


title: cypermethrin_1ugL_larvae_48hr_253657410232_1_2_15.txt


title: bifenthrin_Control_larva_48hr_251959710326_2_3_X.txt


title: bifenthrin_Control_brain_72hr_251959710456_1_4_X.txt


title: bifenthrin_Control_brain_72hr_251959710451_2_2_X.txt


title: bifenthrin_Control_brain_72hr_251959710462_1_4_X.txt


title: bifenthrin_Control_brain_72hr_251959710450_1_3_X.txt


title: bifenthrin_Control_larva_48hr_251959710324_2_2_X.txt


title: cypermethrin_1ugL_larvae_48hr_253657410221_1_2_15.txt


title: bifenthrin_Control_brain_72hr_251959710448_2_3_X.txt


title: cypermethrin_1ugL_larvae_48hr_253657410220_2_2_15.txt


title: cypermethrin_0.5ugL_larvae_48hr_253657410234_2_1_15.txt


title: cypermethrin_1ugL_larvae_48hr_253657410222_1_4_15.txt


title: cypermethrin_0.5ugL_larvae_48hr_253657410233_1_3_15.txt


title: cypermethrin_1ugL_larvae_48hr_253657410222_2_3_15.txt


title: bifenthrin_Control_larva_48hr_251959710455_2_4_X.txt


title: bifenthrin_0.593ugL_larva_48hr_251959710458_1_1_X.txt


title: bifenthrin_0.593ugL_larva_48hr_251959710459_1_4_X.txt


title: bifenthrin_0.593ugL_larva_48hr_251959710455_2_3_X.txt


title: bifenthrin_Control_brain_72hr_251959710326_2_4_X.txt


title: cypermethrin_0.5ugL_larvae_48hr_253657410225_1_2_15.txt


title: bifenthrin_0.593ugL_larva_48hr_251959710452_1_2_X.txt


title: bifenthrin_0.593ugL_larva_48hr_251959710454_2_3_X.txt


title: bifenthrin_Control_brain_72hr_251959710324_1_1_X.txt


title: bifenthrin_Control_brain_72hr_251959710325_2_1_X.txt


title: cypermethrin_0.5ugL_larvae_48hr_253657410226_2_1_15.txt


title: cypermethrin_0.5ugL_larvae_48hr_253657410223_1_1_15.txt


title: cypermethrin_0.5ugL_larvae_48hr_253657410220_1_4_15.txt


title: bifenthrin_0.3ugL_larvae_48hr_253657410231_1_1_14.txt


title: bifenthrin_0.593ugL_larva_48hr_251959710448_2_1_X.txt


title: bifenthrin_0.593ugL_larva_48hr_251959710449_2_2_X.txt


title: bifenthrin_0.593ugL_larva_48hr_251959710326_1_3_X.txt


title: cypermethrin_0.5ugL_larvae_48hr_253657410222_2_1_15.txt


title: bifenthrin_0.3ugL_larvae_48hr_253657410234_2_3_14.txt


title: cypermethrin_0.5ugL_larvae_48hr_253657410224_2_1_15.txt


title: bifenthrin_0.3ugL_larvae_48hr_253657410230_2_2_14.txt


title: bifenthrin_0.593ugL_larva_48hr_251959710324_2_4_X.txt


title: bifenthrin_0.3ugL_larvae_48hr_253657410227_2_3_14.txt


title: bifenthrin_0.3ugL_larvae_48hr_253657410229_1_3_14.txt


title: cypermethrin_0.5ugL_larvae_48hr_253657410221_2_3_15.txt


title: bifenthrin_0.3ugL_larvae_48hr_253657410225_2_2_14.txt


title: bifenthrin_0.593ugL_brain_72hr_251959710459_2_4_X.txt


title: bifenthrin_0.593ugL_brain_72hr_251959710456_1_1_X.txt


title: bifenthrin_0.593ugL_brain_72hr_251959710454_2_2_X.txt


title: bifenthrin_0.3ugL_larvae_48hr_253657410226_1_3_14.txt


title: bifenthrin_0.3ugL_larvae_48hr_253657410222_1_1_14.txt


title: bifenthrin_0.593ugL_brain_72hr_251959710452_2_3_X.txt


title: bifenthrin_0.593ugL_brain_72hr_251959710450_1_2_X.txt


title: bifenthrin_0.593ugL_brain_72hr_251959710453_1_1_X.txt


title: bifenthrin_0.593ugL_brain_72hr_251959710326_2_1_X.txt


title: bifenthrin_0.148ugL_larva_48hr_251959710462_2_3_X.txt


title: bifenthrin_0.3ugL_larvae_48hr_253657410221_2_4_14.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410233_1_1_14.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410231_2_3_14.txt


title: bifenthrin_0.593ugL_brain_72hr_251959710461_1_1_X.txt


title: bifenthrin_0.593ugL_brain_72hr_251959710325_1_3_X.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410225_2_4_14.txt


title: bifenthrin_0.3ugL_larvae_48hr_253657410220_1_3_14.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410234_1_2_14.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410233_2_1_14.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410232_1_4_14.txt


title: bifenthrin_0.148ugL_larva_48hr_251959710461_2_1_X.txt


title: bifenthrin_0.148ugL_larva_48hr_251959710458_2_1_X.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410223_2_3_14.txt


title: bifenthrin_0.593ugL_brain_72hr_251959710449_1_4_X.txt


title: bifenthrin_0.148ugL_larva_48hr_251959710456_2_2_X.txt


title: bifenthrin_0.148ugL_larva_48hr_251959710454_2_1_X.txt


title: bifenthrin_0.148ugL_larva_48hr_251959710326_1_1_X.txt


title: cypermethrin_0.5ugL_larvae_48hr_253657410227_1_1_15.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410221_2_1_14.txt


title: bifenthrin_0.148ugL_larva_48hr_251959710325_2_3_X.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410222_1_2_14.txt


title: permethrin_0.4ugL_larvae_48hr_253657410219_1_3_23.txt


title: permethrin_0.4ugL_larvae_48hr_253657410219_1_2_23.txt


title: permethrin_0.4ugL_larvae_48hr_253657410217_1_2_23.txt


title: bifenthrin_0.148ugL_brain_72hr_251959710455_1_1_X.txt


title: bifenthrin_0.148ugL_brain_72hr_251959710458_2_2_X.txt


title: permethrin_0.4ugL_larvae_48hr_253657410218_2_1_23.txt


title: bifenthrin_0.148ugL_brain_72hr_251959710459_1_3_X.txt


title: bifenthrin_0.148ugL_brain_72hr_251959710453_2_4_X.txt


title: bifenthrin_0.148ugL_brain_72hr_251959710451_1_2_X.txt


title: bifenthrin_0.148ugL_brain_72hr_251959710449_2_4_X.txt


title: bifenthrin_0.148ugL_larva_48hr_251959710448_1_2_X.txt


title: bifenthrin_0.148ugL_brain_72hr_251959710327_2_3_X.txt


title: bifenthrin_0.148ugL_larva_48hr_251959710450_1_4_X.txt


title: permethrin_0.4ugL_larvae_48hr_253657410212_2_2_23.txt


title: permethrin_0.4ugL_larvae_48hr_253657410214_1_4_23.txt


title: permethrin_0.4ugL_larvae_48hr_253657410213_1_1_23.txt


title: cypermethrin_1ugL_larvae_48hr_253657410229_2_3_15.txt


title: permethrin_0.4ugL_larvae_48hr_253657410216_2_3_23.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410219_2_3_23.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410220_1_2_14.txt


title: bifenthrin_0.148ugL_brain_72hr_251959710326_2_2_X.txt


title: permethrin_0.4ugL_larvae_48hr_253657410212_2_4_23.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410218_2_2_23.txt


title: permethrin_0.4ugL_larvae_48hr_253657410215_2_4_23.txt


title: Patient 122 primary tumor

city: Barcelona

first: Juan

middle: Miguel

last: Cejalvo

state: Barcelona

address: Carrer Villaroel 170

department: Oncology

institute: Hospital Clinic Barcelona

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protcol. Detection probres were provided by the manufacturer and were labeled with a propierty flourescent barcode system

scan_protocol: Scaning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions

data_processing: Data were collected as NanoString RCC files. The data were normalized using 5 HK genes. Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detecction probe and counted by a confocal system

source_name: Breast cancer

label_protocol: RNA was not labeled; instead, RNA (100 ng/ul) was pre-processed following the NanoString manufacturer's protocol by VHIO's Translational Genomics Group

extract_protocol: A section of FFPE breast tissue was firs examined with a hematoxylin and eosin staining to confirm the diagnosis and determine the tumor surface area. For RNA purification, three 10um FFPE slides were cut for each tumor, and macrodissection was performed, when needed, to avoid normal breast contamination. A minimum of 100 ng of total RNA was used to measure the expression of 105 breast cancer-related genes and 5 house-keeping genes (ACTB, MRPL19, PSMC4, RLP0 and SF3A1)

tag: individual

value: Patient 122

value: Primary tumor

tag: age_dx primary tumor

tag: time to recurrence

tag: overall survival metastatic (months)

tag: intrinsic subtype breast cancer

value: LumB


title: Patient 123 metastatic tumor

value: Patient 123

tag: tissue

value: Metastatic tumor

tag: age_dx metastatic tumor

tag: metastatic site

value: Liver


title: Patient 121 primary tumor

value: Patient 121

value: Normal


title: Patient 122 metastatic tumor

value: Lymph nodes


title: Patient 123 primary tumor


title: Patient 121 metastatic tumor


title: esfenvalerate_0.15ugL_larvae_48hr_253657410212_1_3_23.txt

value: 48h post hatch


title: Patient 120 primary tumor

value: Patient 120


title: esfenvalerate_0.15ugL_larvae_48hr_253657410215_1_1_23.txt

value: larvae


title: esfenvalerate_0.15ugL_larvae_48hr_253657410214_2_4_23.txt


title: bifenthrin_Control_brain_72hr_251959710449_1_2_X.txt

value: Control

value: brain

value: 5-7 month


title: Patient 119 primary tumor

value: Patient 119


title: dmso_ControlugL_larvae_48hr_253657410219_2_1_23.txt

value: dmso

value: ControlugL


title: esfenvalerate_0.15ugL_larvae_48hr_253657410214_2_1_23.txt

value: esfenvalerate


title: Patient 120 metastatic tumor

value: LumB


title: dmso_ControlugL_larvae_48hr_253657410219_1_4_23.txt


title: Patient 119 metastatic tumor

value: LumA


title: esfenvalerate_0.15ugL_larvae_48hr_253657410215_1_4_23.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410218_1_2_23.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410213_2_2_23.txt


title: Patient 118 primary tumor

value: Patient 118

value: Primary tumor

value: Basal


title: dmso_ControlugL_larvae_48hr_253657410218_1_3_23.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410217_2_2_23.txt


title: dmso_ControlugL_larvae_48hr_253657410217_1_3_23.txt


title: dmso_ControlugL_larvae_48hr_253657410216_2_4_23.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410216_1_4_23.txt


title: dmso_ControlugL_larvae_48hr_253657410216_2_2_23.txt


title: dmso_ControlugL_larvae_48hr_253657410219_2_4_23.txt


title: Patient 118 metastatic tumor

value: Metastatic tumor


title: Patient 117 primary tumor

value: Patient 117


title: Patient 115 primary tumor

value: Patient 115


title: Patient 116 primary tumor

value: Patient 116


title: bifenthrin_0.15ugL_larvae_48hr_253657410224_1_4_14.txt

value: bifenthrin

value: larvae

value: 48h post hatch


title: Patient 115 metastatic tumor

value: Lymph nodes


title: Patient 116 metastatic tumor


title: Patient 117 metastatic tumor


title: dmso_ControlugL_larvae_48hr_253657410218_1_1_23.txt


title: Patient 114 primary tumor

value: Patient 114


title: Patient 114 metastatic tumor

value: Lung


title: Patient 112 primary tumor

value: Patient 112


title: Patient 113 metastatic tumor

value: Patient 113

value: Normal

value: Skin


title: Patient 112 metastatic tumor


title: dmso_ControlugL_larvae_48hr_253657410215_1_2_23.txt

value: dmso

value: ControlugL


title: dmso_ControlugL_larvae_48hr_253657410213_1_3_23.txt


title: dmso_ControlugL_larvae_48hr_253657410215_2_3_23.txt


title: Patient 111 primary tumor

value: Patient 111

value: Primary tumor

value: LumA


title: dmso_ControlugL_larvae_48hr_253657410212_2_1_23.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410219_1_1_23.txt

value: cypermethrin


title: dmso_ControlugL_larvae_48hr_253657410214_2_2_23.txt


title: dmso_ControlugL_larvae_48hr_253657410214_2_3_23.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410218_1_4_23.txt


title: dmso_ControlugL_larvae_48hr_253657410216_1_3_23.txt


title: Patient 111 metastatic tumor

value: Metastatic tumor

value: LumB


title: dmso_ControlugL_larvae_48hr_253657410214_1_1_23.txt

value: larvae


title: dmso_ControlugL_larvae_48hr_253657410212_2_3_23.txt

value: 48h post hatch


title: dmso_ControlugL_larvae_48hr_253657410212_1_4_23.txt


title: dmso_ControlugL_larvae_48hr_253657410213_1_2_23.txt


title: Patient 110 primary tumor

value: Patient 110

value: Basal


title: Patient 110 metastatic tumor


title: Patient 109 primary tumor

value: Patient 109


title: Patient 113 primary tumor


title: Patient 109 metastatic tumor


title: cypermethrin_0.2ugL_larvae_48hr_253657410217_1_1_23.txt


title: Patient 108 primary tumor

value: Patient 108


title: Patient 107 primary tumor

value: Patient 107


title: Patient 108 metastatic tumor


title: cypermethrin_0.2ugL_larvae_48hr_253657410217_2_1_23.txt


title: Patient 107 metastatic tumor

value: Liver


title: Patient 106 primary tumor

value: Patient 106


title: cypermethrin_0.2ugL_larvae_48hr_253657410214_1_3_23.txt


title: Patient 106 metastatic tumor


title: Patient 105 primary tumor

value: Patient 105


title: cypermethrin_0.2ugL_larvae_48hr_253657410213_2_1_23.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410217_2_4_23.txt


title: Patient 105 metastatic tumor


title: Patient 104 primary tumor

value: Patient 104


title: cypermethrin_0.2ugL_larvae_48hr_253657410216_1_2_23.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410213_2_3_23.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410212_1_1_23.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410218_2_4_23.txt

value: bifenthrin


title: bifenthrin_0.15ugL_larvae_48hr_253657410218_2_3_23.txt


title: Patient 103 primary tumor

value: Patient 103

value: Primary tumor

value: Normal


title: bifenthrin_0.15ugL_larvae_48hr_253657410219_2_2_23.txt


title: Patient 103 metastatic tumor

value: Metastatic tumor


title: bifenthrin_0.15ugL_larvae_48hr_253657410217_2_3_23.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410215_2_2_23.txt

value: cypermethrin


title: Patient 102 primary tumor

value: Patient 102

value: LumA


title: Patient 101 primary tumor

value: Patient 101


title: Patient 104 metastatic tumor


title: Patient 101 metastatic tumor

value: Basal

value: Skin


title: bifenthrin_0.15ugL_larvae_48hr_253657410214_1_2_23.txt

value: larvae

value: 48h post hatch


title: Patient 99 metastatic tumor

value: Patient 99


title: Patient 100 metastatic tumor

value: Patient 100


title: Patient 99 primary tumor


title: Patient 102 metastatic tumor


title: bifenthrin_0.15ugL_larvae_48hr_253657410215_1_3_23.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410215_2_1_23.txt


title: Patient 98 metastatic tumor

value: Patient 98

value: Lymph nodes


title: bifenthrin_0.15ugL_larvae_48hr_253657410213_2_4_23.txt

value: bifenthrin


title: bifenthrin_0.15ugL_larvae_48hr_253657410217_1_4_23.txt


title: Patient 97 primary tumor

value: Patient 97


title: Patient 98 primary tumor

value: Primary tumor


title: bifenthrin_0.15ugL_larvae_48hr_253657410212_1_2_23.txt


title: Patient 97 metastatic tumor

value: Ovarian


title: Patient 100 primary tumor


title: permethrin_0.4ugL_larvae_48hr_253657410211_1_1_22.txt

value: permethrin


title: permethrin_0.4ugL_larvae_48hr_253657410209_2_2_22.txt


title: permethrin_0.4ugL_larvae_48hr_253657410209_2_3_22.txt


title: permethrin_0.4ugL_larvae_48hr_253657410210_1_4_22.txt


title: permethrin_0.4ugL_larvae_48hr_253657410208_2_1_22.txt


title: permethrin_0.4ugL_larvae_48hr_253657410207_1_2_22.txt


title: permethrin_0.4ugL_larvae_48hr_253657410206_2_4_22.txt


title: permethrin_0.4ugL_larvae_48hr_253657410211_1_3_22.txt


title: Patient 96 primary tumor

value: Patient 96


title: Patient 96 metastatic tumor

value: Patient 95

value: Metastatic tumor

value: LumB

value: Bone


title: Patient 95 primary tumor

value: LumA


title: Patient 94 primary tumor

value: Patient 94

value: Basal


title: Patient 95 metastatic tumor

value: Pleura


title: Patient 93 primary tumor

value: Patient 93


title: Patient 94 metastatic tumor

value: Skin


title: permethrin_0.4ugL_larvae_48hr_253657410205_1_3_22.txt

value: larvae

value: 48h post hatch


title: permethrin_0.4ugL_larvae_48hr_253657410204_2_2_22.txt


title: permethrin_0.4ugL_larvae_48hr_253657410204_2_1_22.txt


title: Patient 93 metastatic tumor


title: esfenvalerate_0.15ugL_larvae_48hr_253657410210_2_2_22.txt

value: esfenvalerate


title: Patient 92 primary tumor

value: Patient 92

value: Primary tumor


title: esfenvalerate_0.15ugL_larvae_48hr_253657410209_2_4_22.txt


title: dmso_ControlugL_larvae_48hr_253657410216_2_1_23.txt

value: dmso

value: ControlugL


title: Patient 92 metastatic tumor


title: esfenvalerate_0.15ugL_larvae_48hr_253657410211_2_1_22.txt


title: Patient 91 primary tumor

value: Patient 91


title: Patient 91 metastatic tumor

value: Metastatic tumor

value: Liver


title: Patient 90 primary tumor

value: Patient 90


title: Patient 90 metastatic tumor

value: LumA


title: esfenvalerate_0.15ugL_larvae_48hr_253657410207_2_4_22.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410209_1_3_22.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410206_2_2_22.txt


title: Patient 89 primary tumor

value: Patient 89


title: dmso_ControlugL_larvae_48hr_253657410211_2_2_22.txt


title: Patient 88 primary tumor

value: Patient 88


title: esfenvalerate_0.15ugL_larvae_48hr_253657410208_1_1_22.txt


title: dmso_ControlugL_larvae_48hr_253657410211_2_4_22.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410208_2_3_22.txt


title: Patient 88 metastatic tumor

value: Basal


title: Patient 87 primary tumor

value: Patient 87


title: Patient 87 metastatic tumor

value: Brain


title: esfenvalerate_0.15ugL_larvae_48hr_253657410205_1_2_22.txt

value: larvae


title: Patient 89 metastatic tumor

value: Skin


title: Patient 86 primary tumor

value: Patient 86


title: Patient 86 metastatic tumor


title: Patient 85 primary tumor

value: Patient 85

value: Normal


title: Patient 85 metastatic tumor

value: Breast


title: dmso_ControlugL_larvae_48hr_253657410210_2_1_22.txt

value: dmso

value: ControlugL

value: 48h post hatch


title: dmso_ControlugL_larvae_48hr_253657410209_1_4_22.txt


title: dmso_ControlugL_larvae_48hr_253657410208_2_4_22.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410204_1_4_22.txt

value: esfenvalerate


title: dmso_ControlugL_larvae_48hr_253657410207_2_2_22.txt


title: Patient 84 primary tumor

value: Patient 84

value: Primary tumor


title: dmso_ControlugL_larvae_48hr_253657410210_1_2_22.txt


title: dmso_ControlugL_larvae_48hr_253657410206_2_3_22.txt


title: dmso_ControlugL_larvae_48hr_253657410209_1_1_22.txt


title: dmso_ControlugL_larvae_48hr_253657410210_1_3_22.txt


title: Patient 83 primary tumor

value: Patient 83


title: Patient 84 metastatic tumor

value: Metastatic tumor

value: Lymph nodes


title: Patient 82 primary tumor

value: Patient 82


title: Patient 82 metastatic tumor


title: Patient 81 primary tumor

value: Patient 81


title: dmso_ControlugL_larvae_48hr_253657410205_1_1_22.txt

value: larvae


title: dmso_ControlugL_larvae_48hr_253657410204_2_3_22.txt


title: dmso_ControlugL_larvae_48hr_253657410206_1_4_22.txt


title: Patient 80 primary tumor

value: Patient 80


title: dmso_ControlugL_larvae_48hr_253657410205_2_4_22.txt


title: Patient 81 metastatic tumor

value: Skin


title: dmso_ControlugL_larvae_48hr_253657410204_1_3_22.txt


title: dmso_ControlugL_larvae_48hr_253657410208_1_3_22.txt


title: dmso_ControlugL_larvae_48hr_253657410207_1_4_22.txt


title: Patient 83 metastatic tumor

value: LumA

value: Pleura


title: Patient 80 metastatic tumor

value: Lung


title: dmso_ControlugL_larvae_48hr_253657410204_1_1_22.txt

value: dmso


title: cypermethrin_0.2ugL_larvae_48hr_253657410211_2_3_22.txt

value: cypermethrin


title: Patient 79 metastatic tumor

value: Patient 79


title: Patient 79 primary tumor

value: Normal


title: Patient 78 primary tumor

value: Patient 78


title: cypermethrin_0.2ugL_larvae_48hr_253657410209_1_2_22.txt

value: 48h post hatch


title: cypermethrin_0.2ugL_larvae_48hr_253657410210_2_3_22.txt


title: Patient 78 metastatic tumor

value: LumB

value: Liver


title: Patient 77 metastatic tumor

value: Patient 77

value: Metastatic tumor

value: Basal

value: Lymph nodes


title: cypermethrin_0.2ugL_larvae_48hr_253657410208_1_2_22.txt

value: larvae


title: cypermethrin_0.2ugL_larvae_48hr_253657410207_1_3_22.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410206_1_1_22.txt


title: Patient 76 primary tumor

value: Patient 76

value: Primary tumor


title: Patient 75 metastatic tumor

value: Patient 75

value: Skin


title: cypermethrin_0.2ugL_larvae_48hr_253657410208_1_4_22.txt


title: Patient 75 primary tumor


title: Patient 74 primary tumor

value: Patient 74

value: LumA


title: Patient 76 metastatic tumor

value: Peritoneal


title: Patient 77 primary tumor


title: Patient 74 metastatic tumor


title: cypermethrin_0.2ugL_larvae_48hr_253657410207_2_1_22.txt

value: cypermethrin


title: Patient 73 primary tumor

value: Patient 73


title: cypermethrin_0.2ugL_larvae_48hr_253657410206_2_1_22.txt

value: 48h post hatch


title: Patient 72 metastatic tumor

value: Patient 72


title: bifenthrin_0.15ugL_larvae_48hr_253657410209_2_1_22.txt

value: bifenthrin


title: Patient 73 metastatic tumor

value: LumB

value: Ovarian


title: bifenthrin_0.15ugL_larvae_48hr_253657410208_2_2_22.txt


title: Patient 72 primary tumor


title: bifenthrin_0.15ugL_larvae_48hr_253657410211_1_4_22.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410210_2_4_22.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410205_2_2_22.txt


title: Patient 71 primary tumor

value: Patient 71


title: bifenthrin_0.15ugL_larvae_48hr_253657410207_1_1_22.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410216_1_1_23.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410206_1_3_22.txt


title: Patient 70 primary tumor

value: Patient 70


title: cypermethrin_0.2ugL_larvae_48hr_253657410204_2_4_22.txt

value: larvae


title: Patient 70 metastatic tumor

value: Metastatic tumor

value: Lymph nodes


title: bifenthrin_0.15ugL_larvae_48hr_253657410204_1_2_22.txt


title: Patient 69 primary tumor

value: Patient 69

value: Primary tumor


title: Patient 69 metastatic tumor

value: Normal

value: Skin


title: Patient 68 metastatic tumor

value: Patient 68


title: Patient 68 primary tumor


title: Patient 67 primary tumor

value: Patient 67


title: bifenthrin_0.15ugL_larvae_48hr_253657410205_1_4_22.txt


title: Patient 67 metastatic tumor


title: permethrin_0.4ugL_larvae_48hr_253657410200_2_3_21.txt

value: permethrin


title: permethrin_0.4ugL_larvae_48hr_253657410201_1_2_21.txt

value: 48h post hatch


title: Patient 66 primary tumor

value: Patient 66

value: LumA


title: permethrin_0.4ugL_larvae_48hr_253657410199_1_3_21.txt


title: permethrin_0.4ugL_larvae_48hr_253657410203_1_4_21.txt


title: permethrin_0.4ugL_larvae_48hr_253657410196_2_1_21.txt


title: Patient 66 metastatic tumor


title: permethrin_0.4ugL_larvae_48hr_253657410197_1_1_21.txt


title: Patient 65 primary tumor

value: Patient 65


title: cypermethrin_0.2ugL_larvae_48hr_253657410205_2_3_22.txt

value: cypermethrin


title: Patient 65 metastatic tumor

value: LumB


title: permethrin_0.4ugL_larvae_48hr_253657410195_1_2_21.txt


title: Patient 64 primary tumor

value: Patient 64

value: Basal


title: Patient 64 metastatic tumor

value: Metastatic tumor


title: esfenvalerate_0.15ugL_larvae_48hr_253657410203_2_1_21.txt

value: esfenvalerate

value: larvae


title: permethrin_0.4ugL_larvae_48hr_253657410195_1_4_21.txt


title: Patient 63 primary tumor

value: Patient 63

value: Primary tumor


title: Patient 63 metastatic tumor

value: Lymph nodes


title: esfenvalerate_0.15ugL_larvae_48hr_253657410203_2_3_21.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410201_2_1_21.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410200_1_4_21.txt


title: Patient 62 primary tumor

value: Patient 62


title: esfenvalerate_0.15ugL_larvae_48hr_253657410196_2_4_21.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410200_1_2_21.txt


title: esfenvalerate_0.15ugL_larvae_48hr_253657410196_1_3_21.txt


title: dmso_ControlugL_larvae_48hr_253657410211_1_2_22.txt

value: dmso

value: ControlugL


title: Patient 61 metastatic tumor

value: Patient 61

value: Ovarian


title: Patient 60 metastatic tumor

value: Patient 60

value: LumA

value: Bone


title: Patient 61 primary tumor


title: Patient 60 primary tumor


title: Patient 59 primary tumor

value: Patient 59


title: Patient 59 metastatic tumor

value: Bowel


title: esfenvalerate_0.15ugL_larvae_48hr_253657410195_2_2_21.txt

value: 48h post hatch


title: Patient 58 metastatic tumor

value: Patient 58

value: Metastatic tumor

value: Basal

value: Breast


title: Patient 62 metastatic tumor

value: Skin


title: dmso_ControlugL_larvae_48hr_253657410201_2_3_21.txt

value: larvae


title: Patient 57 primary tumor

value: Patient 57

value: Primary tumor

value: LumB


title: dmso_ControlugL_larvae_48hr_253657410201_2_2_21.txt

value: dmso

value: ControlugL


title: Patient 57 metastatic tumor


title: Patient 58 primary tumor

value: Normal


title: dmso_ControlugL_larvae_48hr_253657410203_2_4_21.txt


title: dmso_ControlugL_larvae_48hr_253657410203_1_3_21.txt


title: dmso_ControlugL_larvae_48hr_253657410199_2_2_21.txt


title: dmso_ControlugL_larvae_48hr_253657410199_2_1_21.txt


title: dmso_ControlugL_larvae_48hr_253657410198_2_4_21.txt


title: dmso_ControlugL_larvae_48hr_253657410199_1_4_21.txt


title: dmso_ControlugL_larvae_48hr_253657410200_2_2_21.txt


title: Patient 55 primary tumor

value: Patient 55


title: Patient 56 metastatic tumor

value: Patient 56

value: Endometrial


title: Patient 55 metastatic tumor

value: Pericardial effusion


title: Patient 54 primary tumor

value: Patient 54


title: Patient 54 metastatic tumor


title: Patient 56 primary tumor

value: LumA


title: dmso_ControlugL_larvae_48hr_253657410198_2_3_21.txt

value: 48h post hatch


title: dmso_ControlugL_larvae_48hr_253657410198_1_3_21.txt


title: dmso_ControlugL_larvae_48hr_253657410197_2_1_21.txt


title: dmso_ControlugL_larvae_48hr_253657410197_1_3_21.txt


title: dmso_ControlugL_larvae_48hr_253657410197_1_4_21.txt


title: Patient 51 metastatic tumor

value: Patient 51

value: Metastatic tumor

value: Liver


title: dmso_ControlugL_larvae_48hr_253657410196_2_3_21.txt

value: larvae


title: Patient 53 primary tumor

value: Patient 53


title: dmso_ControlugL_larvae_48hr_253657410195_2_1_21.txt


title: dmso_ControlugL_larvae_48hr_253657410196_1_4_21.txt


title: Patient 50 primary tumor

value: Patient 50

value: Primary tumor

value: Basal


title: Patient 50 metastatic tumor

value: Lymph nodes


title: dmso_ControlugL_larvae_48hr_253657410197_1_2_21.txt

value: dmso

value: ControlugL


title: dmso_ControlugL_larvae_48hr_253657410195_2_4_21.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410203_1_1_21.txt

value: cypermethrin


title: cypermethrin_0.2ugL_larvae_48hr_253657410201_1_4_21.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410201_2_4_21.txt


title: Patient 52 primary tumor

value: Patient 52


title: Patient 52 metastatic tumor

value: Ovarian


title: Patient 51 primary tumor

value: LumB


title: Patient 49 metastatic tumor

value: Patient 49

value: Lung


title: cypermethrin_0.2ugL_larvae_48hr_253657410200_2_1_21.txt

value: 48h post hatch


title: Patient 48 primary tumor

value: Patient 48

value: LumA


title: Patient 48 metastatic tumor

value: Metastatic tumor

value: Skin


title: Patient 49 primary tumor


title: Patient 47 metastatic tumor

value: Patient 47


title: cypermethrin_0.2ugL_larvae_48hr_253657410200_1_3_21.txt

value: larvae


title: cypermethrin_0.2ugL_larvae_48hr_253657410199_2_3_21.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410199_1_1_21.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410197_2_2_21.txt


title: Patient 46 primary tumor

value: Patient 46

value: Primary tumor


title: permethrin_0.4ugL_larvae_48hr_253657410199_2_4_21.txt

value: permethrin


title: cypermethrin_0.2ugL_larvae_48hr_253657410196_1_2_21.txt


title: Patient 45 metastatic tumor

value: Patient 45

value: Basal


title: Patient 44 primary tumor

value: Patient 44


title: Patient 44 metastatic tumor

value: Ovarian


title: Patient 47 primary tumor

value: LumB


title: bifenthrin_0.15ugL_larvae_48hr_253657410203_2_2_21.txt

value: bifenthrin


title: Patient 71 metastatic tumor

value: Patient 71


title: cypermethrin_0.2ugL_larvae_48hr_253657410195_2_3_21.txt

value: cypermethrin

value: 48h post hatch


title: bifenthrin_0.15ugL_larvae_48hr_253657410200_2_4_21.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410201_1_3_21.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410198_2_1_21.txt


title: cypermethrin_0.2ugL_larvae_48hr_253657410198_1_1_21.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410198_1_4_21.txt


title: Patient 45 primary tumor


title: Patient 46 metastatic tumor

value: LumA


title: bifenthrin_0.15ugL_larvae_48hr_253657410199_1_2_21.txt


title: Patient 43 metastatic tumor

value: Patient 43

value: Metastatic tumor

value: Liver


title: bifenthrin_0.15ugL_larvae_48hr_253657410207_2_3_22.txt

value: larvae


title: bifenthrin_0.15ugL_larvae_48hr_253657410196_2_2_21.txt


title: Patient 42 primary tumor

value: Patient 42


title: Patient 41 primary tumor

value: Patient 41

value: Primary tumor


title: Patient 43 primary tumor


title: Patient 41 metastatic tumor

value: Lymph nodes


title: Patient 42 metastatic tumor

value: Basal

value: Skin


title: Patient 40 primary tumor

value: Patient 40


title: bifenthrin_0.15ugL_larvae_48hr_253657410195_1_3_21.txt


title: Patient 40 metastatic tumor

value: LumB

value: Bone


title: bifenthrin_0.15ugL_larvae_48hr_253657410197_2_3_21.txt

value: bifenthrin


title: Patient 38 metastatic tumor

value: Patient 38


title: Patient 39 metastatic tumor

value: Patient 39


title: bifenthrin_0.15ugL_larvae_48hr_253657410195_1_1_21.txt

value: 48h post hatch


title: Patient 38 primary tumor

value: LumA


title: Patient 37 primary tumor

value: Patient 37


title: permethrin_0.4ugL_larvae_48hr_253657410198_2_2_21.txt

value: permethrin


title: EE2_25ngL_Liver_72h_253657410236_2_2_X.txt

value: Liver

value: 5-7 month

value: interlab


title: Patient 37 metastatic tumor

value: Metastatic tumor


title: EE2_25ngL_Liver_72h_253657410236_2_3_X.txt


title: EE2_25ngL_Liver_72h_253657410236_2_4_X.txt


title: EE2_25ngL_Liver_72h_253657410236_1_3_X.txt


title: bifenthrin_0.15ugL_larvae_48hr_253657410196_1_1_21.txt

value: larvae


title: EE2_25ngL_Liver_72h_253657410236_1_1_X.txt


title: Patient 36 primary tumor

value: Patient 36

value: Primary tumor

value: Normal


title: EE2_25ngL_Liver_72h_253657410235_2_1_X.txt


title: EE2_25ngL_Liver_72h_253657410236_1_2_X.txt


title: EE2_25ngL_Liver_72h_253657410235_1_4_X.txt


title: Patient 36 metastatic tumor

value: LumB


title: Patient 35 metastatic tumor

value: Patient 35

value: Bone


title: Patient 39 primary tumor


title: Patient 34 primary tumor

value: Patient 34


title: Patient 34 metastatic tumor

value: Skin


title: Control_0ngL_Liver_72h_253657410235_2_4_X.txt

value: Control


title: Patient 33 primary tumor

value: Patient 33

value: LumA


title: Patient 33 metastatic tumor

value: Lung


title: Control_0ngL_Liver_72h_253657410236_1_4_X.txt

value: Liver


title: Patient 35 primary tumor


title: Control_0ngL_Liver_72h_253657410235_2_3_X.txt

value: 5-7 month


title: Patient 31 primary tumor

value: Patient 31


title: Patient 32 metastatic tumor

value: Patient 32

value: Metastatic tumor


title: Control_0ngL_Liver_72h_253657410235_2_2_X.txt

value: interlab


title: Control_0ngL_Liver_72h_253657410236_2_1_X.txt


title: Control_0ngL_Liver_72h_253657410235_1_3_X.txt


title: Control_0ngL_Liver_72h_253657410235_1_1_X.txt


title: Patient 30 primary tumor

value: Patient 30

value: Primary tumor


title: EE2_1ngL_MaleBrain_96h_253657410279_2_2_X.txt

value: MaleBrain


title: Patient 31 metastatic tumor

value: LumB


title: Patient 30 metastatic tumor

value: Pleura


title: EE2_1ngL_MaleBrain_96h_253657410279_1_3_X.txt


title: Control_0ngL_Liver_72h_253657410235_1_2_X.txt


title: EE2_1ngL_MaleBrain_96h_253657410278_2_3_X.txt


title: Patient 29 primary tumor

value: Patient 29


title: EE2_1ngL_MaleBrain_96h_253657410258_1_1_X.txt


title: EE2_1ngL_MaleBrain_96h_253657410258_2_4_X.txt


title: EE2_1ngL_MaleBrain_96h_253657410257_1_4_X.txt


title: EE2_1ngL_MaleBrain_96h_253657410257_2_1_X.txt


title: Patient 32 primary tumor


title: Patient 28 primary tumor

value: Patient 28


title: EE2_1ngL_MaleBrain_96h_253657410278_1_1_X.txt


title: Patient 29 metastatic tumor

value: Lymph nodes


title: Patient 28 metastatic tumor

value: Breast


title: Patient 53 metastatic tumor

value: Patient 53


title: Patient 27 metastatic tumor

value: Patient 27

value: LumA

value: Bone


title: Patient 27 primary tumor


title: Patient 25 metastatic tumor

value: Patient 25


title: Patient 25 primary tumor

value: Normal


title: EE2_1ngL_MaleBrain_96h_253657410254_2_2_X.txt

value: 5-7 month


title: Patient 24 primary tumor

value: Patient 24


title: EE2_1ngL_MaleBrain_96h_253657410253_2_3_X.txt


title: Patient 26 primary tumor

value: Patient 26


title: Patient 23 metastatic tumor

value: Patient 23

value: Metastatic tumor


title: EE2_10ngL_MaleBrain_96h_253657410282_2_1_X.txt

value: MaleBrain


title: Patient 23 primary tumor

value: Primary tumor


title: EE2_1ngL_MaleBrain_96h_253657410254_1_4_X.txt


title: Patient 26 metastatic tumor

value: Liver


title: Patient 22 primary tumor

value: Patient 22


title: Patient 22 metastatic tumor


title: EE2_10ngL_MaleBrain_96h_253657410279_1_2_X.txt


title: EE2_10ngL_MaleBrain_96h_253657410278_2_1_X.txt


title: EE2_1ngL_MaleBrain_96h_253657410253_1_2_X.txt


title: EE2_10ngL_MaleBrain_96h_253657410258_1_4_X.txt


title: EE2_10ngL_MaleBrain_96h_253657410279_2_3_X.txt


title: Patient 21 metastatic tumor

value: Patient 21


title: Patient 21 primary tumor


title: EE2_10ngL_MaleBrain_96h_253657410278_1_3_X.txt


title: Patient 20 primary tumor

value: Patient 20

value: LumB


title: Patient 24 metastatic tumor


title: Patient 20 metastatic tumor


title: EE2_10ngL_MaleBrain_96h_253657410257_1_3_X.txt


title: EE2_10ngL_MaleBrain_96h_253657410254_2_3_X.txt


title: EE2_10ngL_MaleBrain_96h_253657410254_1_1_X.txt


title: EE2_10ngL_MaleBrain_96h_253657410257_2_2_X.txt


title: Patient 19 primary tumor

value: Patient 19


title: EE2_10ngL_MaleBrain_96h_253657410253_1_1_X.txt


title: Patient 18 primary tumor

value: Patient 18

value: LumA


title: Patient 19 metastatic tumor

value: Ovarian


title: EE2_0.1ngL_MaleBrain_96h_253657410279_2_4_X.txt


title: EE2_0.1ngL_MaleBrain_96h_253657410279_1_1_X.txt


title: Patient 18 metastatic tumor

value: Bone


title: Patient 16 metastatic tumor

value: Patient 16


title: Patient 16 primary tumor


title: Patient 17 primary tumor

value: Patient 17


title: Patient 15 primary tumor

value: Patient 15


title: Patient 15 metastatic tumor

value: Skin


title: EE2_0.1ngL_MaleBrain_96h_253657410258_2_2_X.txt

value: 5-7 month


title: EE2_0.1ngL_MaleBrain_96h_253657410278_1_2_X.txt

value: MaleBrain


title: Patient 17 metastatic tumor

value: Metastatic tumor


title: Patient 14 primary tumor

value: Patient 14

value: Primary tumor


title: Patient 14 metastatic tumor

value: Liver


title: EE2_0.1ngL_MaleBrain_96h_253657410257_2_3_X.txt


title: EE2_0.1ngL_MaleBrain_96h_253657410254_2_1_X.txt


title: Patient 13 primary tumor

value: Patient 13


title: EE2_10ngL_MaleBrain_96h_253657410253_2_4_X.txt


title: EE2_0.1ngL_MaleBrain_96h_253657410258_1_3_X.txt


title: EE2_0.1ngL_MaleBrain_96h_253657410278_2_4_X.txt


title: Control_0ngL_MaleBrain_96h_253657410282_1_2_X.txt

value: Control


title: Control_0ngL_MaleBrain_96h_253657410279_1_4_X.txt


title: EE2_0.1ngL_MaleBrain_96h_253657410253_2_1_X.txt


title: EE2_0.1ngL_MaleBrain_96h_253657410254_1_3_X.txt


title: Control_0ngL_MaleBrain_96h_253657410279_2_1_X.txt


title: Control_0ngL_MaleBrain_96h_253657410278_1_4_X.txt