title: Mouse541_17 B- Estradiol_Lever

description: Quality Control: Approved

source_name: Mouse541 Liver cells

value: 17 B- Estradiol


title: Dengue Patient Timepoint1 49

status: Public on Apr 01 2014

type: RNA

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analysed in Genespring GX11.5 software. Measurements less than 0.01 was set to 0.01. Data was then normalised at the 80th percentile.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human whole blood

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep -96 RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA was extracted from whole blood drawn in pax-gene vacutainer tubes by PAX-gene RNA kit (Qiagen). Quality control was performed with NanoDrop 1000 instrument

tag: sample type

value: blood

tag: collection time

value: Less than 72 hour after symptoms

tag: igg

value: Pos


title: Mouse554_Reserpine_Lever

city: Leiden

first: Joost

last: Melis

address: Postbus 9600

department: Toxicogenetics

country: Netherlands

institute: Leiden University Medical Center

description: Quality Control: Approved

hyb_protocol: Amplified materials were hybridized to Mouse Genome 430 2.0 Array for 16 hours at 45°C, subsequently washed and stained with the EukGE-WS2v5_450 protocol

scan_protocol: Samples were finally scanned using the GeneChip Scanner 3000-7G (Affymetrix Inc., Santa Clara, CA, USA). Image generation and feature extraction were performed using Affymetrix GCOS Software v1.4.0.036.

data_processing: Quality control and correction (correcting significant hybridization and experimental blocking effects), annotation, RMA normalization and subsequent data analysis was performed as previously described (Schaap et al. 2012). Only the annotated Entrez genes were used for further analysis. Functional genomics analyses, using the top 1000 FDR-ranked genes, were performed using Metacore (version 6.11 build 41105, GeneGo Inc. St. Joseph, MI, USA) to assess the biological response upon each chemical exposure

organism: Mus musculus

source_name: Mouse554 Liver cells

label_protocol: MRNA was amplified and labeled with the GeneChip Expression 3'-Amplification One-Cycle cDNA Synthesis Kit and GeneChip Expression 3'-Amplification Reagents For IVT Labeling according to the manufacturer’s instructions  (Eukaryotic Sample and Array Processing 701025 Rev.5; Affymetrix Inc., Santa Clara, CA, USA).

growth_protocol: Six-week-old male WT mice (C57BL/6J, n=4 per group) were acclimated for 2 weeks and subsequently treated for 7 days with a GTXC, NGTXC or NC through feed, gavage or i.p. injection. From the day of weaning, the health status of the mice was monitored daily and mice were weighed weekly starting at acclimation. Animals were kept in the same stringently controlled (specific pathogen-free, spf) environment, fed ad libitum and kept under a normal day/night rhythm. After 7 days of exposure, mice were sacrificed at a fixed time of the day. During autopsy, several organs (including the liver), were isolated and stored according to protocol using RNAlater (Qiagen, Valencia, CA, USA).

extract_protocol: Hepatic total RNA was isolated using the miRNeasy kit (Qiagen, Valencia, CA, USA) and the QIAcube (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. All samples passed RNA quality control using capillary gel electrophoresis (RIN > 7.6) (Bioanalyzer 2100; Agilent Technologies, Amstelveen, the Netherlands). The same total RNA isolates as used for mRNA were used for isolation of microRNAs. MicroRNA profiling was performed as previously described (Pothof et al. 2009).

treatment_protocol: For the chemicals used in this study, appropriate dosages were derived from previously performed dose range finding (DRF) studies (2-AAF, Phe, CsA, DEHP, DES, E2, PBB, Res, WY, D-man (van Kreijl et al. 2001; de Vries et al. 1997)) or if not known yet, identified by performing additional 28-day DRF studies prior to the short-term exposure studies (see supplemental information 1 for DRF studies using AFB1, CPPD, BPA, DIDP, SD and TBTO). In short, eight to ten weeks old male C57BL/6J mice (n = 10 per group) were exposed to chemicals, using multiple dosages based on literature or expert advice. Body weight dynamics during the first week and over the full 28-day exposure were monitored to extract suitable (non- or slightly cytotoxic) doses (Supplemental information 1). If body weight dynamics were not conclusive, the liver was studied macroscopically (data not shown). Exposure through feed was continuously during the experiment, application using i.p. injection occurred at day 0, 3 and 6 (autopsy on day 7) and exposure using gavage at day 0, 2, 4 and 6 (autopsy on day 7). Body weights were recorded during this 7-day exposure period (Supplemental information 2). Comparison of different control groups (gavage, i.p. injection or feed) showed no significant differential effect on transcriptional levels (Luijten et al. in preparation), hence only food administrated control samples were implemented in this study

tag: strain

tag: gender

value: male

tag: age

value: six-weeks-old

tag: treatment

value: Reserpine

tag: classification

value: NGTXC

tag: mouse number

tag: tissue

value: liver


title: Mouse539_17 B- Estradiol_Lever

description: Quality Control: Approved

source_name: Mouse539 Liver cells


title: Mouse535_Diethylstillbestrol_Lever

description: Quality Control: Approved

source_name: Mouse535 Liver cells

value: Diethylstillbestrol


title: Dengue Patient Timepoint1 47

value: Neg


title: Mouse522_Phenacetine_Lever

description: Quality Control: Approved

source_name: Mouse522 Liver cells

value: Phenacetine

value: GTXC


title: Dengue Patient Timepoint1 48


title: Mouse536_Diethylstillbestrol_Lever

description: Quality Control: Approved

source_name: Mouse536 Liver cells


title: Dengue Patient Timepoint2 47

value: 3 to 7 dys after symptoms


title: Mouse521_Phenacetine_Lever

description: Quality Control: Approved

source_name: Mouse521 Liver cells


title: Dry root time course 3H/0H Replicate 4

city: Tsukuba

first: Shingo

last: Nakamura

state: Ibaraki

address: Kannondai 2-1-18

country: Japan

institute: National Institute of Crop Science

description: Biological replicate 4 of 4.

hyb_protocol: The hybridization and washing were performed according to the Agilent manufacturer’s instructions.

scan_protocol: Scanned on an Agilent MicroarrayScanner. Images were quantified using Agilent Feature Extraction Software. (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

organism: Hordeum vulgare

source_name: NT root 0H

label_protocol: TotalRNA (400 ng) was labeled with Cy3 or Cy5 using an Agilent Quick Amp Labeling kit .

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that, the 3 germinated seeds were transferred on paper towels and incubated at 23˚C for indicated hours, then we harvested the shoot and root, separately.

extract_protocol: Total RNA was extracted from the harvested shoot and root from the 3 germinated seeds using Trizol following manufacture's instructions. The yield and RNA purity were determined spectrophotometrically. Integrity was verified using an Agilent 2100 Bioanalyzer.

treatment_protocol: Dry-treatment. The germinated seeds were transferred on paper towels. They were incubated at 23˚C for the indicated hours.

value: root

tag: incubation time (hours)

source_name: Dry root 3H


title: Dry shoot time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: NT shoot 0H

value: shoot

source_name: Dry shoot 6H


title: Dengue Patient Timepoint3 47

value: 2 to 5 weeks after symptoms


title: Dengue Patient Timepoint2 46


title: Dengue Patient Timepoint1 46


title: Dry shoot time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: Dry shoot 3H


title: Dry shoot time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Mouse504_control_Lever

description: Quality Control: Approved

source_name: Mouse504 Liver cells

value: control


title: Dengue Patient Timepoint3 45

value: blood


title: Dry root time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: Dry root 6H


title: Dry shoot time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Dry root time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Dry shoot time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Dengue Patient Timepoint2 45


title: Dengue Patient Timepoint3 46


title: Dry shoot time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Dry root time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Dry root time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Dry root time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Non-Treatment (NT) root time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9 cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that, the 3 germinated seeds were transferred to other Petri dishes and incubated for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: Non-treatment. The germinated seeds were transferred to Petri dishes with 2 layers of No.2 filter paper and 4.5ml disilled water. They were incubated for the indicated hours.

source_name: NT root 6H


title: Non-Treatment (NT) root time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.

source_name: NT root 3H


title: Non-Treatment (NT) shoot time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: NT shoot 6H


title: Non-Treatment (NT) shoot time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: NT shoot 3H


title: Dengue Patient Timepoint1 45

source_name: Human whole blood

value: Less than 72 hour after symptoms


title: Dengue Patient Timepoint3 44

value: Pos


title: Non-Treatment (NT) root time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.


title: Non-Treatment (NT) root time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Non-Treatment (NT) shoot time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Dengue Patient Timepoint1 44


title: Dengue Patient Timepoint2 44


title: Non-Treatment (NT) root time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Dengue Patient Timepoint2 43


title: Dengue Patient Timepoint3 43


title: Non-Treatment (NT) shoot time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Dengue Patient Timepoint3 42


title: Non-Treatment (NT) root time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Non-Treatment (NT) shoot time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Non-Treatment (NT) shoot time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: MeJA root time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that, the 3 germinated seeds were transferred to other Petri dishes and incubated with 4.5ml of 100mM methyl jasmonate(MeJA) for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: MeJA-treatment. The germinated seeds were transferred to Petri dishes with 2 layers of No.2 filter paper and 4.5ml of 100mM MeJA. They were incubated for the indicated hours.

source_name: MeJA root 6H


title: MeJA shoot time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: MeJA shoot 3H


title: MeJA shoot time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.

source_name: MeJA shoot 6H


title: Dengue Patient Timepoint1 42


title: Dengue Patient Timepoint2 42


title: MeJA root time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.

source_name: MeJA root 3H


title: MeJA root time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.


title: MeJA shoot time course 6H/0H Replicate4

description: Biological replicate 4 of 4.


title: Dengue Patient Timepoint1 43


title: MeJA shoot time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: MeJA shoot time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: MeJA root time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.


title: MeJA root time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: MeJA shoot time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Cold root time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that, the 3 germinated seeds were transferred to other Petri dishes and incubated at 4˚C for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: Cold-treatment. The germinated seeds were transferred to Petri dishes with 2 layers of No.2 filter paper and 4.5ml of distilled water. They were incubated at 4˚C for the indicated hours.

source_name: Cold root 3H


title: Dengue Patient Timepoint2 41


title: Cold root time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: NT root 0H

source_name: Cold root 6H


title: Dengue Patient Timepoint3 40


title: Dengue Patient Timepoint3 41


title: Dengue Patient Timepoint1 41


title: Dengue Patient Timepoint2 40


title: Cold shoot time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: NT shoot 0H

source_name: Cold shoot 6H


title: MeJA root time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Dengue Patient Timepoint1 40


title: Cold root time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Cold root time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Cold shoot time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Cold shoot time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: Cold shoot 3H


title: NaCl root time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that, the 3 germinated seeds were transferred to other Petri dishes and incubated with 4.5ml of 0.2M NaCl for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: NaCl-treatment. The germinated seeds were transferred to Petri dishes with 2 layers of No.2 filter paper and 4.5ml of 0.2M NaCl. They were incubated for the indicated hours.

source_name: NaCl root 6H


title: Dengue Patient Timepoint2 39


title: Dengue Patient Timepoint1 39


title: Cold shoot time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Cold root time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Cold shoot time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Cold shoot time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: NaCl root time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: NaCl root 3H


title: NaCl root time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: NaCl shoot time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: NaCl shoot 3H


title: Cold root time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: NaCl root time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Dengue Patient Timepoint1 38


title: NaCl shoot time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: NaCl shoot 6H


title: Dengue Patient Timepoint3 38


title: Dengue Patient Timepoint1 37


title: NaCl shoot time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: NaCl shoot time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.


title: aluminum root time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that, the 3 germinated seeds were transferred to other Petri dishes and incubated with 4.5ml of 10mM AlCl3 for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: Aluminum-treatment. The germinated seeds were transferred to Petri dishes with 2 layers of No.2 filter paper and 4.5ml of 10mM AlCl3. They were incubated for the indicated hours.

source_name: aluminum root 6H


title: Dengue Patient Timepoint1 36


title: aluminum root time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: aluminum root 3H


title: NaCl shoot time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: NaCl root time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Dengue Patient Timepoint3 36

source_name: Human whole blood


title: Dengue Patient Timepoint2 36


title: NaCl root time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: aluminum root time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: NaCl shoot time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Dengue Patient Timepoint3 35


title: Dengue Patient Timepoint3 33


title: aluminum shoot time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.

source_name: aluminum shoot 3H


title: aluminum root time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Dengue Patient Timepoint1 35


title: aluminum shoot time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.

source_name: aluminum shoot 6H


title: ABA root time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that, the 3 germinated seeds were transferred to other Petri dishes and incubated with 4.5ml of 50mM abscisic acid (ABA) for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: ABA-treatment. The germinated seeds were transferred to Petri dishes with 2 layers of No.2 filter paper and 4.5ml of 50mM ABA. They were incubated for the indicated hours.

source_name: ABA root 6H


title: Dengue Patient Timepoint2 34


title: aluminum root time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.


title: ABA shoot time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: ABA shoot 3H


title: aluminum shoot time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Dengue Patient Timepoint3 34


title: aluminum shoot time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.


title: Dengue Patient Timepoint3 32


title: Dengue Patient Timepoint2 33


title: Dengue Patient Timepoint1 34


title: aluminum shoot time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.


title: aluminum shoot time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: ABA root time course 3H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: ABA root 3H


title: ABA root time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: NT root 0H


title: aluminum root time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: ABA shoot time course 6H/0H Replicate 4

description: Biological replicate 4 of 4.

source_name: ABA shoot 6H


title: ABA shoot time course 6H/0H Replicate 3

description: Biological replicate 3 of 4.

source_name: NT shoot 0H


title: Dengue Patient Timepoint1 33


title: ABA root time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: ABA root time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: Dengue Patient Timepoint2 32


title: Dengue Patient Timepoint3 30


title: NaCl root time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT  root 0H

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that,  the 3 germinated seeds were transferred to other Petri dishes and incubated with 4.5ml of 0.2M NaCl for indicated hours, then we harvested the shoot and root, separately.

extract_protocol: Total RNA was extracted from the harvested shoot and root from the 3 germinated seeds using Trizol following manufacture's instructions.   The yield and RNA purity were determined spectrophotometrically. Integrity was verified using an Agilent 2100 Bioanalyzer.

treatment_protocol: NaCl-treatment. The germinated seeds were transferred  to Petri dishes  with 2 layers of No.2 filter paper and  4.5ml of 0.2M NaCl. They were incubated for the indicated hours.

tag: time (h)

tag: cultivar

value: Haruna Nijo

value: 0.2 M NaCl


title: Dengue Patient Timepoint1 30


title: Non-Treatment (NT) root time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9 cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that,  the 3 germinated seeds were transferred to other Petri dishes and incubated for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: Non-treatment. The germinated seeds were transferred  to Petri dishes  with 2 layers of No.2 filter paper and  4.5ml disilled water. They were incubated for the indicated hours.

source_name: NT root 6H


title: Non-Treatment (NT) shoot time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT shoot 6H


title: Dengue Patient Timepoint1 29


title: NaCl shoot time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT  shoot 0H


title: Dengue Patient Timepoint2 30


title: NaCl shoot time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NaCl shoot 3H


title: Non-Treatment (NT) root time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT root 24H


title: NaCl shoot time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NaCl shoot 24H


title: ABA root time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: MeJA root time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that,  the 3 germinated seeds were transferred to other Petri dishes and incubated with 4.5ml of 100mM methyl jasmonate(MeJA)  for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: MeJA-treatment. The germinated seeds were transferred  to Petri dishes  with 2 layers of No.2 filter paper and  4.5ml of 100mM MeJA. They were incubated for the indicated hours.

source_name: MeJA  root 24H

value: Methyl Jasmonate


title: MeJA root time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: MeJA  root 6H


title: ABA shoot time course 6H/0H Replicate 2

description: Biological replicate 2 of 4.


title: ABA shoot time course 3H/0H Replicate 3

description: Biological replicate 3 of 4.


title: Dengue Patient Timepoint3 28

source_name: Human whole blood


title: MeJA root time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: MeJA  root 3H


title: ABA shoot time course 3H/0H Replicate 2

description: Biological replicate 2 of 4.


title: NaCl root time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NaCl root 24H


title: Dengue Patient Timepoint2 31


title: Dengue Patient Timepoint1 31


title: NaCl root time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NaCl root 3H


title: Dengue Patient Timepoint1 32


title: Dengue Patient Timepoint1 28


title: Non-Treatment (NT) shoot time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT shoot 24H


title: Dengue Patient Timepoint1 27


title: MeJA shoot time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: MeJA  shoot 24H


title: Dry shoot time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that,  the 3 germinated seeds were transferred onto filter papers and incubated for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: Dry-treatment. The germinated seeds were transferred on paper towels. They were incubated at 23C for the indicated hours.

source_name: Dry shoot 6H

value: dessication


title: Dry shoot time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT shoot 0H

source_name: Dry shoot 24H


title: Dry root time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT  root 0H

source_name: Dry root 6H


title: Dry root time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: Dry root 24H


title: Cold root time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that,  the 3 germinated seeds were transferred to other Petri dishes and incubated at 4˚C for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: Cold-treatment. The germinated seeds were transferred  to Petri dishes  with 2 layers of No.2 filter paper and  4.5ml of distilled water. They were incubated at 4˚C for the indicated hours.

source_name: Cold root 6H


title: Non-Treatment (NT) root time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT root 0H

source_name: NT root 3H


title: Dengue Patient Timepoint2 28


title: Cold root time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: Cold root 24H


title: Non-Treatment (NT) shoot time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT shoot 3H


title: Dry root time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: Dry root 3H


title: Dengue Patient Timepoint2 26

source_name: Human whole blood


title: Cold shoot time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: Cold shoot 24H


title: Dengue Patient Timepoint1 26


title: Dengue Patient Timepoint3 24


title: Cold shoot time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT  shoot 0H

source_name: Cold shoot 6H


title: Dengue Patient Timepoint3 26


title: Dengue Patient Timepoint3 25


title: aluminum root time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that,  the 3 germinated seeds were transferred to other Petri dishes and incubated with 4.5ml of 10mM AlCl3  for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: Aluminum-treatment. The germinated seeds were transferred  to Petri dishes  with 2 layers of No.2 filter paper and  4.5ml of 10mM AlCl3. They were incubated for the indicated hours.

source_name: aluminum root 6H


title: MeJA shoot time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: MeJA shoot 3H


title: aluminum root time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: aluminum root 24H


title: Dry shoot time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT shoot 0H

source_name: Dry shoot 3H


title: Dengue Patient Timepoint1 25


title: Cold root time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT  root 0H

source_name: Cold root 3H


title: aluminum shoot time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: aluminum shoot 24H


title: Cold shoot time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: Cold shoot 3H


title: Dengue Patient Timepoint3 23


title: Dengue Patient Timepoint1 24


title: Dengue Patient Timepoint1 23


title: aluminum shoot time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: aluminum shoot 6H


title: ABA root time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT root 0H

growth_protocol: Seven Barley (Hordeum vulgare, cultivar: 'Haruna Nijo') seeds were incubated on 2 layers of No.2 filter paper with 4.5ml disilled water in 9cm Petri dishes at 24˚C for 4 days with 8 hour day length. After that, the 3 germinated seeds were transferred to other Petri dishes and incubated with 4.5ml of 50mM abscisic acid (ABA)  for indicated hours, then we harvested the shoot and root, separately.

treatment_protocol: ABA-treatment. The germinated seeds were transferred  to Petri dishes  with 2 layers of No.2 filter paper and  4.5ml of 50mM ABA. They were incubated for the indicated hours.

source_name: ABA root 24H

value: ABA


title: ABA root time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: ABA root 6H


title: Dengue Patient Timepoint2 23

source_name: Human whole blood


title: Dengue Patient Timepoint2 21


title: aluminum root time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: aluminum root 3H


title: aluminum shoot time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: aluminum shoot 3H


title: ABA root time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: ABA root 3H


title: Dengue Patient Timepoint1 20


title: ABA shoot time course 24H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: ABA shoot 24H


title: Dengue Patient Timepoint3 19


title: ABA shoot time course 3H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: ABA shoot 3H


title: Dengue Patient Timepoint1 21


title: Dengue Patient Timepoint1 22


title: Dengue Patient Timepoint3 20


title: Dengue Patient Timepoint3 21


title: Dengue Patient Timepoint2 19


title: ABA shoot time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: ABA shoot 6H


title: Dengue Patient Timepoint2 20


title: Dengue Patient Timepoint1 19


title: Dengue Patient Timepoint2 17


title: Dengue Patient Timepoint1 17


title: Dengue Patient Timepoint2 18


title: Dengue Patient Timepoint2 16


title: Dengue Patient Timepoint3 17


title: CRC3b_serum_exo_14_after

city: Chuo-ku

first: Naoto

last: Tsuchiya

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center Reasearch Institute

description: MicroRNA profile in serum exosomes of colorectal cancer patients after sergical resection of primary tumor

hyb_protocol: Cy3-labelled miRNA was incubated at 100°C for 5 minutes in a reaction volume of 45uL containing Hyb Spike-In, 2x Hi-RPM Hybridization Buffer and 10x Gene Expression blocking agent following the manufacturers instructions and cooled down in ice-cold water for 5 min. Reaction mixture hybridized to Agilent Human miRNA V3 Microarray (G4470C) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green ).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09) and Grid: 021827_D_F_20081129) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IIIb, serum, exosomes,14

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from total RNA using the miRNA Complete Labeling and Hyb Kit (Agilent)and MicroRNA Spike-In Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Exosome fraction was mixed with Trizol-LS reagent (Invitrogen), and aqueous phase was collected by adding chloroform. After addition of ethanol to the aqueous phase, it was placed on to an RNeasy mini spin column (Qiagen) for the purification of total RNAs.

treatment_protocol: Peripheral blood sera from colorectal cancer patients were diluted 1:7 with PBS.  Exosomes fraction  were prepared by step-wise centrifugation-ultracentrifugation method.

tag: microrna source

value: exosomes

tag: biological source of exosomes

value: serum

value: male

tag: disease state

value: Colorectal cancer

tag: tnm stages

value: IIIb

tag: time

value: after surgical resection of primary tumor


title: CRC4_serum_exo_7_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IV, serum, exosomes,7

value: IV


title: Dengue Patient Timepoint1 18

tag: sample type

tag: collection time

value: Neg


title: Vibrio cholerae rep2

city: Corvallis

first: Claudia

last: Hase

address: 105 Magruder Hall

country: USA

institute: Oregon State University

description: This sample is of wild-type Vibrio cholerae O395N1. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package.

organism: Vibrio cholerae

source_name: Vibrio cholerae O395N1

label_protocol: Labeling was performed by NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Vibrio cholerae O395N1 was grown to early-log phase (O.D.600nm 0.2) aerobically at 30°C in LB (pH6.5).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by TURBO DNA-free™ Kit (Ambion). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Center for Genome Research and Biocomputing (Oregon State University, Corvallis, OR USA).

tag: genotype/variation

value: Wild-type


title: CRC3b_serum_exo_9_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IIIb, serum, exosomes,9

tag: gender


title: CRC4_serum_exo_2_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IV, serum, exosomes,2

tag: age


title: CRC3b_serum_exo_3_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IIIb, serum, exosomes,3


title: CRC3b_serum_exo_6_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IIIb, serum, exosomes,6


title: Dengue Patient Timepoint1 16

value: blood

tag: igg


title: CRC4_serum_exo_11_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IV, serum, exosomes,11

value: female


title: CRC3b_serum_exo_1_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IIIb, serum, exosomes,1


title: CRC3a_serum_exo_13_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IIIa, serum, exosomes,13

value: IIIa


title: Vibrio cholerae rep1

description: This sample is of wild-type Vibrio cholerae O395N1. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: CRC3a_serum_exo_12_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IIIa, serum, exosomes,12


title: Dengue Patient Timepoint2 15

source_name: Human whole blood

value: 3 to 7 dys after symptoms

value: Pos


title: Dengue Patient Timepoint1 15

value: Less than 72 hour after symptoms


title: Vibrio cholerae nqr rep2

description: This sample is of Vibrio cholerae O395N1 delta-nqrA-F mutant.

source_name: Vibrio cholerae O395N1 dellta-nqrA-F

value: nqrA-F mutant


title: Dengue Patient Timepoint3 14

value: 2 to 5 weeks after symptoms


title: Dengue Patient Timepoint3 15


title: CRC3a_serum_exo_8_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IIIa, serum, exosomes,8

value: exosomes


title: Dengue Patient Timepoint2 14


title: CRC3a_serum_exo_3_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IIIa, serum, exosomes,3

value: serum


title: Dengue Patient Timepoint1 14


title: CRC3a_serum_exo_2_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage IIIa, serum, exosomes,2


title: CRC1_serum_exo_12_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage I, serum, exosomes,12

value: I


title: MeJA shoot time course 6H/0H Replicate 1

description: Biological replicate 1 of 4.

source_name: NT  shoot 0H

value: Haruna Nijo

value: shoot

tag: treatment

source_name: MeJA  shoot 6H

value: Methyl Jasmonate


title: CRC2_serum_exo_6_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage II, serum, exosomes,6

value: male

value: Colorectal cancer

value: II

value: after surgical resection of primary tumor


title: Dengue Patient Timepoint3 16

value: blood


title: Dengue Patient Timepoint2 13


title: CRC2_serum_exo_8_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage II, serum, exosomes,8


title: CRC2_serum_exo_10_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage II, serum, exosomes,10


title: Dengue Patient Timepoint1 12

value: Neg


title: Dengue Patient Timepoint2 12

value: 3 to 7 dys after symptoms


title: CRC2_serum_exo_2_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage II, serum, exosomes,2


title: Dengue Patient Timepoint3 12


title: Dengue Patient Timepoint1 11


title: CRC1_serum_exo_4_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage I, serum, exosomes,4


title: Dengue Patient Timepoint2 11


title: Dengue Patient Timepoint2 10

value: Pos


title: CRC1_serum_exo_5_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage I, serum, exosomes,5

value: female


title: CRC2_serum_exo_1_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage II, serum, exosomes,1


title: CRC1_serum_exo_8_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage I, serum, exosomes,8


title: Dengue Patient Timepoint1 10

value: Less than 72 hour after symptoms


title: Dengue Patient Timepoint3 11

value: 2 to 5 weeks after symptoms


title: CRC1_serum_exo_2_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage I, serum, exosomes,2

value: exosomes


title: Dengue Patient Timepoint1 13

source_name: Human whole blood


title: CRC4_serum_exo_12

description: MicroRNA profile in serum exosomes of colorectal cancer patients with TNM stage IV

hyb_protocol: Cy3-labelled miRNA was incubated at 100°C for 5 minutes in a reaction volume of 45uL containing 2x Hi-RPM Hybridization Buffer and 10x Gene Expression blocking agent following the manufacturers instructions and cooled down in ice-cold water for 5 min. Reaction mixture hybridized to Agilent Human miRNA V3 Microarray (G4470C) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_105_Jan(09) and Grid: 021827_D_F_20081129) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,12

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from total RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.

treatment_protocol: Peripheral blood sera from healthy volunteers and colorectal cancer patients were diluted 1:7 with PBS.  Exosomes fraction  were prepared by step-wise centrifugation-ultracentrifugation method.

value: serum

tag: fraction

value: IV

tag: presence of data after operation (1=present, 0=not tested)


title: CRC4_serum_exo_11

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,11

tag: tissue


title: Dengue Patient Timepoint3 9


title: CRC4_serum_exo_10

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,10


title: CRC1_serum_exo_1_after

source_name: Colorectal cancer patient, after surgical resection, TNM Stage I, serum, exosomes,1

value: I


title: Dengue Patient Timepoint1 9


title: Dengue Patient Timepoint2 9


title: Dengue Patient Timepoint1 8


title: Dengue Patient Timepoint3 8


title: Dengue Patient Timepoint2 8


title: CRC4_serum_exo_8

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,8


title: CRC4_serum_exo_7

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,7


title: Dengue Patient Timepoint3 7


title: CRC4_serum_exo_5

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,5


title: CRC4_serum_exo_9

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,9


title: CRC4_serum_exo_4

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,4


title: CRC4_serum_exo_2

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,2


title: Dengue Patient Timepoint3 6


title: Dengue Patient Timepoint1 7


title: Dengue Patient Timepoint2 7


title: CRC4_serum_exo_3

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,3


title: Dengue Patient Timepoint1 6


title: Dengue Patient Timepoint1 5


title: CRC4_serum_exo_6

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,6


title: CRC4_serum_exo_1

source_name: Colorectal cancer patient, TNM Stage IV, serum, exosomes,1


title: Dengue Patient Timepoint3 4


title: Dengue Patient Timepoint2 4


title: Patient_Timepoint2 11

value: 4-7 days afer symptoms


title: Dengue Patient Timepoint2 6


title: Patient_Timepoint3 11

value: 15-25 days after symptoms


title: Patient_Timepoint1 11


title: Patient_Timepoint3 10


title: Dengue Patient Timepoint1 4


title: CRC3b_serum_exo_14

description: MicroRNA profile in serum exosomes of colorectal cancer patients with TNM stage IIIb

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,14

value: male

value: IIIb


title: Dengue Patient Timepoint3 3


title: CRC3b_serum_exo_16

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,16


title: CRC3b_serum_exo_12

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,12


title: CRC3b_serum_exo_15

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,15


title: Patient_Timepoint2 10

source_name: Human whole blood


title: Patient_Timepoint1 8


title: Dengue Patient Timepoint3 2


title: CRC3b_serum_exo_11

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,11


title: Patient_Timepoint1 10


title: Dengue Patient Timepoint1 3


title: Patient_Timepoint2 9


title: Dengue Patient Timepoint2 2


title: Dengue Patient Timepoint3 18


title: Dengue Patient Timepoint3 1


title: Dengue Patient Timepoint2 3


title: CRC3b_serum_exo_13

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,13


title: Dengue Patient Timepoint2 1


title: Patient_Timepoint3 9


title: CRC3b_serum_exo_9

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,9


title: CRC3b_serum_exo_8

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,8


title: Patient_Timepoint3 8


title: CRC3b_serum_exo_7

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,7


title: Dengue Patient Timepoint1 2


title: Patient_Timepoint1 9


title: CRC3b_serum_exo_10

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,10


title: CRC3b_serum_exo_4

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,4


title: CRC3b_serum_exo_5

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,5


title: In Vitro Infection_68B_2010

source_name: Cell line

extract_protocol: Total RNA was extracted from U937 cells by Rneasy Mini kit (Qiagen). Quality control was performed with NanoDrop 1000 instrument

value: Dengue-infected 48h add VP-16 1ug/ml treated 72hr

tag: cell line

value: Test


title: Patient_Timepoint3 7

value: blood


title: CRC3b_serum_exo_2

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,2


title: In Vitro Infection_68A_2010


title: Patient_Timepoint2 7


title: In Vitro Infection_67C_2010

value: Dengue-infected 48h add VP-16 0.1ug/ml treated 72hr


title: CRC3b_serum_exo_3

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,3


title: Patient_Timepoint1 7


title: Dengue Patient Timepoint1 1

value: Neg


title: Patient_Timepoint2 6


title: Dengue Patient Timepoint3 13

value: Pos


title: CRC3b_serum_exo_6

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,6


title: CRC3a_serum_exo_20

description: MicroRNA profile in serum exosomes of colorectal cancer patients with TNM stage IIIa

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,20

value: IIIa


title: Patient_Timepoint2 8


title: In Vitro Infection_68C_2010


title: CRC3b_serum_exo_1

source_name: Colorectal cancer patient, TNM Stage IIIb, serum, exosomes,1


title: CRC3a_serum_exo_19

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,19

value: female


title: In Vitro Infection_67A_2010


title: Patient_Timepoint3 6


title: Patient_Timepoint2 5


title: Patient_Timepoint1 6

value: Less than 72 hour after symptoms


title: Patient_Timepoint3 4


title: CRC3a_serum_exo_18

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,18

value: exosomes


title: Patient_Timepoint3 5

source_name: Human whole blood


title: In Vitro Infection_66C_2010

value: Dengue-infected 48h add VP-16 0.01ug/ml treated 72hr


title: CRC3a_serum_exo_13

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,13

value: serum


title: Patient_Timepoint1 5


title: Patient_Timepoint2 4


title: Patient_Timepoint1 4


title: In Vitro Infection_65C_2010

value: Dengue-infected 48h add Ros 10uM treated 72hr


title: In Vitro Infection_66B_2010


title: In Vitro Infection_65A_2010


title: In Vitro Infection_65B_2010


title: CRC3a_serum_exo_15

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,15


title: CRC3a_serum_exo_17

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,17


title: CRC3a_serum_exo_14

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,14


title: CRC3a_serum_exo_12

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,12


title: In Vitro Infection_64B_2010

value: Dengue-infected VP-16 1ug/ml treated 72hr


title: CRC3a_serum_exo_16

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,16


title: Patient_Timepoint2 3

value: 4-7 days afer symptoms


title: In Vitro Infection_66A_2010


title: CRC3a_serum_exo_10

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,10

value: male


title: CRC3a_serum_exo_9

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,9


title: Patient_Timepoint3 2

value: 15-25 days after symptoms


title: CRC3a_serum_exo_8

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,8


title: Patient_Timepoint3 3


title: Patient_Timepoint3 1


title: CRC3a_serum_exo_5

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,5


title: In Vitro Infection_63C_2010

source_name: Cell line

value: Dengue-infected VP-16 0.1ug/ml treated 72hr


title: In Vitro Infection_63B_2010

value: Test


title: In Vitro Infection_64C_2010


title: Patient_Timepoint1 2

value: blood


title: CRC3a_serum_exo_6

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,6


title: CRC3a_serum_exo_4

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,4


title: In Vitro Infection_67B_2010

value: Dengue-infected 48h add VP-16 0.1ug/ml treated 72hr


title: In Vitro Infection_63A_2010


title: Patient_Timepoint1 3


title: Patient_Timepoint2 2


title: In Vitro Infection_62B_2010

value: Dengue-infected VP-16 0.01ug/ml treated 72hr


title: Patient_Timepoint2 1


title: CRC3a_serum_exo_3

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,3


title: In Vitro Infection_64A_2010


title: CRC3a_serum_exo_7

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,7


title: Patient_Timepoint1 1


title: In Vitro Infection_62C_2010


title: In Vitro Infection_61A_2010

value: Dengue-infected Ros 10uM treated 72hr


title: In Vitro Infection_62A_2010


title: In Vitro Infection_54C_2010

value: Dengue-infected 24h add VP-16 1ug/ml treated 48hr


title: In Vitro Infection_61B_2010


title: CRC3a_serum_exo_11

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,11

value: female

value: IIIa


title: In Vitro Infection_61C_2010


title: Primary CRC tumor non responder to Cetuximab in ex vivo platform 4

city: Bangalore

first: Pradip

middle: K

last: Majumder

address: Suite 202, Narayana Nethralaya, Narayana Hrudayalaya Health City, Hosur Main Road, Bangalore 99, Karnataka State.

country: India

institute: Mitra Biotech Pvt Ltd.

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner  using one color scan setting for 8*60k array slides

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity for entities with fold change >2.0

source_name: Primart Colorectal Tumor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Fresh biposy or surgical samples stored in RNA later were used for the study

extract_protocol: RNA was extracted using Qiagen's micro kit according to manufacturer's instructions

treatment_protocol: Tumors were tested in ex vivo platform for sensitivity to Cetuximab for 72 hours, post which samples were segregated as responders and non responders and subjected to microarray analysis

tag: response

value: Colorectal Cancer Tumor Sample


title: In Vitro Infection_54B_2010


title: CRC3a_serum_exo_1

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,1

value: exosomes


title: CRC3a_serum_exo_2

source_name: Colorectal cancer patient, TNM Stage IIIa, serum, exosomes,2

value: serum


title: In Vitro Infection_53A_2010

value: Dengue-infected 24h add VP-16 0.1ug/ml treated 48hr


title: CRC2_serum_exo_19

description: MicroRNA profile in serum exosomes of colorectal cancer patients with TNM stage II

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,19

value: II


title: In Vitro Infection_53C_2010


title: In Vitro Infection_54A_2010


title: Primary CRC tumor non responder to Cetuximab in ex vivo platform 2


title: CRC2_serum_exo_20

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,20


title: Primary CRC tumor non responder to Cetuximab in ex vivo platform 3


title: Primary CRC tumor responder to Cetuximab in ex vivo platform 3


title: CRC2_serum_exo_16

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,16


title: CRC2_serum_exo_18

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,18


title: CRC2_serum_exo_15

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,15


title: In Vitro Infection_53B_2010


title: Primary CRC tumor responder to Cetuximab in ex vivo platform 2


title: CRC2_serum_exo_17

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,17


title: CRC2_serum_exo_13

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,13


title: CRC2_serum_exo_14

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,14


title: Primary CRC tumor responder to Cetuximab in ex vivo platform 4


title: CRC2_serum_exo_11

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,11


title: Primary CRC tumor responder to Cetuximab in ex vivo platform 1


title: CRC2_serum_exo_12

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,12


title: In Vitro Infection_52B_2010

source_name: Cell line

value: Dengue-infected 24h add VP-16 0.01ug/ml treated 48hr


title: Primary CRC tumor non responder to Cetuximab in ex vivo platform 1

value: male


title: In Vitro Infection_51B_2010

value: Dengue-infected 24h add Ros 10uM treated 48hr


title: In Vitro Infection_52C_2010


title: CRC2_serum_exo_9

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,9


title: In Vitro Infection_51A_2010


title: In Vitro Infection_51C_2010


title: CRC2_serum_exo_7

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,7


title: CRC2_serum_exo_8

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,8


title: In Vitro Infection_52A_2010


title: In Vitro Infection_50B_2010

value: Dengue-infected VP-16 1ug/ml treated 48hr


title: In Vitro Infection_50A_2010

value: Test


title: CRC2_serum_exo_5

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,5


title: In Vitro Infection_48C_2010

value: Dengue-infected VP-16 0.01ug/ml treated 48hr


title: CRC1_serum_exo_20

description: MicroRNA profile in serum exosomes of colorectal cancer patients with TNM stage I

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,20

value: I


title: CRC2_serum_exo_4

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,4


title: CRC2_serum_exo_1

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,1


title: CRC2_serum_exo_2

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,2


title: In Vitro Infection_49C_2010

value: Dengue-infected VP-16 0.1ug/ml treated 48hr


title: CRC2_serum_exo_6

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,6


title: CRC1_serum_exo_18

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,18


title: CRC1_serum_exo_17

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,17


title: In Vitro Infection_48B_2010


title: In Vitro Infection_48A_2010


title: In Vitro Infection_49A_2010


title: In Vitro Infection_47C_2010

value: Dengue-infected Ros 10uM treated 48hr


title: In Vitro Infection_50C_2010


title: In Vitro Infection_49B_2010


title: In Vitro Infection_40B_2010

value: Dengue-infected VP-16 1ug/ml treated 24hr


title: CRC1_serum_exo_16

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,16

value: female


title: In Vitro Infection_40A_2010


title: In Vitro Infection_40C_2010


title: CRC1_serum_exo_19

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,19


title: In Vitro Infection_47B_2010


title: In Vitro Infection_47A_2010


title: CRC1_serum_exo_15

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,15


title: In Vitro Infection_39C_2010

value: Dengue-infected VP-16 0.1ug/ml treated 24hr


title: CRC1_serum_exo_10

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,10


title: CRC1_serum_exo_14

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,14


title: CRC1_serum_exo_13

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,13


title: CRC1_serum_exo_11

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,11


title: CRC1_serum_exo_12

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,12


title: CRC1_serum_exo_9

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,9


title: In Vitro Infection_38B_2010

source_name: Cell line

value: Dengue-infected VP-16 0.01ug/ml treated 24hr


title: CRC1_serum_exo_6

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,6

value: exosomes


title: In Vitro Infection_39A_2010


title: In Vitro Infection_39B_2010


title: CRC1_serum_exo_8

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,8

value: serum


title: In Vitro Infection_38C_2010


title: In Vitro Infection_37A_2010

value: Dengue-infected Ros 10uM treated 24hr


title: CRC1_serum_exo_7

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,7


title: In Vitro Infection_38A_2010


title: In Vitro Infection_30C_2010

value: Dengue-infected VP-16 1ug/ml treated 18hr


title: In Vitro Infection_37C_2010


title: CRC1_serum_exo_2

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,2


title: CRC1_serum_exo_5

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,5


title: CRC1_serum_exo_3

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,3


title: In Vitro Infection_29C_2010

value: Dengue-infected VP-16 0.1ug/ml treated 18hr


title: CRC1_serum_exo_4

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,4

value: male


title: In Vitro Infection_30A_2010


title: In Vitro Infection_37B_2010


title: In Vitro Infection_29B_2010


title: CRC1_serum_exo_1

source_name: Colorectal cancer patient, TNM Stage I, serum, exosomes,1


title: In Vitro Infection_30B_2010


title: HC_serum_exo_10

description: MicroRNA profile in serum exosomes of healthy control

source_name: Healthy Control, serum, exosomes, 10

value: normal


title: HC_serum_exo_8

source_name: Healthy Control, serum, exosomes, 8


title: HC_serum_exo_7

source_name: Healthy Control, serum, exosomes, 7


title: HC_serum_exo_11

source_name: Healthy Control, serum, exosomes, 11


title: In Vitro Infection_29A_2010


title: In Vitro Infection_28C_2010

value: Dengue-infected VP-16 0.01ug/ml treated 18hr


title: In Vitro Infection_27B_2010

value: Dengue-infected Ros 10uM treated 18hr

value: Test


title: In Vitro Infection_28A_2010


title: 526mel IFN-g

city: Chuo

first: Takashi

last: Inozume

state: Yamanashi

address: Shimokato 1110

department: Dermatology

institute: University of Yamanashi

description: Gene expression after 48h culture in the presense of IFN-γ

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocl using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Auburn, CA). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridzation bufer was hybridized for 17 hours at 65°C to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven. The microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 for 1 minute. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System Agilent Technologies, Auburn, CA).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intesities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Roseeta Resolver gene expression data analysis system (Rosetta Biosoftware)

source_name: human melanoma cell line

label_protocol: To produce Cy3-labeled cRNA, RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit     　(Agilent Technologies, Auburn, CA) following the manufacterer's protocol.     　Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer    　 (NanoDrop Technologies, Thermo Fisher Scientific, Waltham, MA).

growth_protocol: Culture in RPMI1640 supplemented with 10% FCS

extract_protocol: QIAGEN Rneasy Kit

treatment_protocol: untreated or treated with IFN-γ (1000IU/ml , 48h)

tag: phenotype

value: IFN-γ-susceptible cell line


title: 1833mel IFN-g


title: 2487mel IFN-g

value: IFN-γ-resistant cell line


title: HC_serum_exo_6

source_name: Healthy Control, serum, exosomes, 6


title: In Vitro Infection_28B_2010


title: In Vitro Infection_27C_2010


title: HC_serum_exo_9

source_name: Healthy Control, serum, exosomes, 9


title: 501Amel IFN-g


title: HC_serum_exo_5

source_name: Healthy Control, serum, exosomes, 5


title: 2487mel

description: Gene expression after 48h culture

value: No treatment


title: miR17_92_tKO2_13.5hr

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on the GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: FoB cells_miR17_92_tKO_stimulated

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200ng total RNA.

extract_protocol: Total RNA was extracted using RNeasy kit (QIAGEN).

tag: strain

value: C57BL/6 x 129 mixed background

tag: genotype

tag: cell type

value: Follicular B cells


title: 1833mel

description: Gene expression after 48h culture


title: 501Amel

description: Gene expression after 48h culture


title: miR17_92_tKO3_13.5hr


title: 526mel

description: Gene expression after 48h culture


title: HC_serum_exo_4

source_name: Healthy Control, serum, exosomes, 4

tag: tnm stages


title: In Vitro Infection_56C_2010

source_name: Cell line

value: Dengue-infected 72hr

tag: sample type


title: CRC2_serum_exo_3

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,3

value: female

value: II


title: In Vitro Infection_56B_2010

tag: collection time


title: HC_serum_exo_3

source_name: Healthy Control, serum, exosomes, 3

value: serum

value: exosomes


title: HC_serum_exo_1

source_name: Healthy Control, serum, exosomes, 1


title: HC_serum_exo_2

source_name: Healthy Control, serum, exosomes, 2


title: CRC2_serum_exo_10

source_name: Colorectal cancer patient, TNM Stage II, serum, exosomes,10


title: miR17_92_tKO1_13.5hr


title: RKO_endo_rep2

description: MicroRNA expression profile in endogenous RNA of cells

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_105_Dec08 and Grid: 021827_D_F_20081129) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: RKO cells, endogenous RNA, replicate-2

treatment_protocol: Conditioned medium from cell-cultured 100 mm dish (1x10^7 cells) were collected.  Exosomes fraction  were prepared by step-wise centrifugation-ultracentrifugation method.

tag: microrna source

value: cells

tag: biological source of exosomes or cells

value: colon cancer cells

value: epithelial

value: RKO

tag: disease state

value: colon carcinoma


title: RKO_exo_rep1

description: MicroRNA profile in exosomes of conditioned medium

source_name: RKO cells, exosomal RNA, replicate-1

value: conditioned medium  from colon cancer cells


title: In Vitro Infection_27A_2010

value: Dengue-infected Ros 10uM treated 18hr

value: Test


title: RKO_exo_rep2

source_name: RKO cells, exosomal RNA, replicate-2


title: Control_1_13.5hr

source_name: FoB cells_control_stimulated

value: Wild type


title: In Vitro Infection_55B_2010

value: Heat-inactivated

value: Control


title: Control_3_13.5hr

value: Follicular B cells


title: Control_2_13.5hr


title: In Vitro Infection_55A_2010


title: In Vitro Infection_55C_2010


title: miR17_92_tKO1

source_name: FoB cells_miR17_92_tKO

value: C57BL/6 x 129 mixed background


title: In Vitro Infection_41C_2010


title: In Vitro Infection_42B_2010

value: Dengue-infected 48hr


title: RKO_endo_rep1

source_name: RKO cells, endogenous RNA, replicate-1


title: SW48_exo_rep3

source_name: SW48 cells, exosomal RNA, replicate-3

value: colorectal adenocarcinoma


title: Control_3

source_name: FoB cells_control


title: In Vitro Infection_42A_2010


title: Control_2


title: SW48_exo_rep2

source_name: SW48 cells, exosomal RNA, replicate-2


title: miR17_92_tKO2


title: In Vitro Infection_41B_2010


title: In Vitro Infection_32C_2010

value: Dengue-infected 24hr


title: In Vitro Infection_42C_2010


title: In Vitro Infection_32B_2010


title: In Vitro Infection_41A_2010


title: Control_1


title: SW48_endo_rep2

source_name: SW48 cells, endogenous RNA, replicate-2


title: SW48_exo_rep1

source_name: SW48 cells, exosomal RNA, replicate-1

value: exosomes


title: DP_3

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

description: Gene expression analysis of CD4+ CD8+ thymocytes

hyb_protocol: RNA samples were amplified, labelled using Affymetrix's IVT labeling kit and hybridized according to the manufacturer's recommendations

data_processing: Expression data was obtained as Affymetrix CEL files, which were processed, background subtracted and normalized in R via the quantile normalization featured in the affy package for all microarray datasets, using the Mouse Gene 1.0 ST chip definition file (CDF) in the case of the microarrays described in this work, whereby probeset to gene annotation was carried out using the Affymetrix provided gene annotation

source_name: primary CD4+ CD8+ DP thymocytes

growth_protocol: Thymuses were extracted from 5-6-week-old C57BL/6 wild type mice and stored in RPMI medium. Cohorts of litter mates were used as biological replicates. To recover thymocytes, thymuses were subsequently passed twice through a 70m Falcon cell strainer and stored in PBS. Cells were crosslinked 10 min in 10% formaldehyde followed by 5 min quenching in 250 mM glycine. DP cells were subsequently sorted via AutoMACS using, in turn, a-CD8-PE antibody conjugated to a-PE beads, and anti-CD4 beads (Miltenyi). FACS profiles and cell purities were obtained for DP thymocytes via CD8-PE, CD4-FITC staining, respectively

extract_protocol: Trizol

treatment_protocol: total RNA was extracted using TRIzol (Invitrogen, USA) according to the manufacturers instructions with some modifications to ensure higher recovery rates of small RNAs. In brief, thymocytes were divided into 1x107 aliquots and 1ml of TRIzol was added. Cells were lysed with vigorous vortexing and pipetting. Homogenized samples were incubated at room temperature for 5 minutes and 0.2ml of chloroform was added. Samples were vigorously shaken and incubated at room temperature for an additional 5 minutes. Phase separation was carried out by centrifugation at 4C and 12,000g in a tabletop centrifuge for 15 minutes. The aqueous phase was transferred to fresh tubes and 1.5 volumes (approximately 1ml) of isopropanol together with 10ug of linear acrylamide (Ambion, USA) were added. Samples were vortexed and incubated at room temperature for 15 minutes. The precipitated RNA was pelleted by centrifugation at 4C and 12,000g in a tabletop centrifuge for 20 minutes. Pellets were washed with 80% ethanol, vortexed and centrifuged at 4C and 7,500g in a tabletop centrifuge for 10 minutes. Pellets were allowed to air dry and resuspended in nuclease-free water (Ambion, USA). DNA was digested using the rigorous Turbo DNase (Ambion, USA) treatment as per manufacturers instructions. RNA quantity was measured on a Nanodrop 1000 and the quality was verified using RNA Nano chips on a 2100 Bioanalyzer (Agilent, USA).

tag: genotype/variation

value: WT

tag: age

value: 5-6 weeks

value: primary CD4+ CD8+ DP thymocytes


title: HT-29_exo_rep2

source_name: HT-29 cells, exosomal RNA, replicate-2

value: epithelial


title: In Vitro Infection_56A_2010

source_name: Cell line

tag: treatment

value: Dengue-infected 72hr


title: SW48_endo_rep1

source_name: SW48 cells, endogenous RNA, replicate-1

value: cells

value: colon cancer cells


title: HT-29_exo_rep1

source_name: HT-29 cells, exosomal RNA, replicate-1

value: conditioned medium  from colon cancer cells


title: In Vitro Infection_32A_2010

value: Test


title: RKO_exo_rep3

source_name: RKO cells, exosomal RNA, replicate-3

value: RKO

value: colon carcinoma


title: miR17_92_tKO3

value: Follicular B cells


title: DP_2

scan_protocol: RNA samples were amplified, labelled using Affymetrix's IVT labeling kit and hybridized according to the manufacturer's recommendations


title: HT-29_exo_rep3

source_name: HT-29 cells, exosomal RNA, replicate-3


title: FK506/CsA-treated EB at D12, biological rep1

city: Stanford

first: Ahryon

last: Cho

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University School of Medicine

description: gene expression data from in vitro differentiation of mouse embryonic stem cells

hyb_protocol: Hybridization to the Affymetrix Mouse Gene 1.0 ST arrays was carried out by the Protein and Nucleic Acid Facility at Stanford University.

scan_protocol: Scanning was carried out by the Protein and Nucleic Acid Facility at Stanford University.

data_processing: After RMA normalization of the raw microarray images, gene expression values were determined by Gene Expression Console (Affymetrix).

source_name: FK506/CsA-treated mouse embryoid bodies (EB)

label_protocol: cDNA was prepared using the Ambion Expression Kit (Applied Biosystems) and labeled using Gene Chip Terminal Labeling kit (Affymetrix) following the manufacturers' instructions.

growth_protocol: ESC differentiation was started (day 1, d1) when undifferentiated ESCs were plated in gelatin-coated dishes containing ESC medium supplemented with LIF. On day 3 (d3), cells were seeded into ultra-low attachment dishes (Corning) in ESC medium. On day 7 (d7), EBs were plated onto tissue culture dishes in ESC medium. After 24 hours (d8), the ESC medium was replaced by serum-free ITS medium.

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

treatment_protocol: FK506(100ng/ml, A.G. Scientific) and Cyclosporin A (1ug/ml, Calbiochem) were treated during d3-d8 of in vitro differentiation.

tag: in vitro differentiation days

value: 46C embryonic stem cells


title: DP_1

label_protocol: RNA samples were amplified, labelled using Affymetrix's IVT labeling kit and hybridized according to the manufacturer's recommendations


title: HT-29_endo_rep2

source_name: HT-29 cells, endogenous RNA, replicate-2


title: HT-29_endo_rep1

source_name: HT-29 cells, endogenous RNA, replicate-1


title: FK506/CsA-treated EB at D12, biological rep2


title: FK506/CsA-treated EB at D12, biological rep3


title: Non-treated EB at D12, biological rep3

source_name: Non-treated mouse embryoid bodies (EB)

value: untreated


title: In Vitro Infection_31B_2010

value: Heat-inactivated

value: Control


title: In Vitro Infection_22A_2010

value: Dengue-infected 18hr


title: Non-treated EB at D12, biological rep2


title: In Vitro Infection_22B_2010


title: In Vitro Infection_31C_2010


title: In Vitro Infection_31A_2010


title: SW480_endo_rep2

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_v1_95_May07 and Grid: 021827_D_F_20081129) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: SW480 cells, endogenous RNA, replicate-2

value: colorectal adenocarcinoma


title: Non-treated EB at D12, biological rep1


title: HCT 116_exo_rep3

source_name: HCT116 cells, exosomal RNA, replicate-3

value: exosomes

value: HCT 116

value: colorectal carcinoma


title: In Vitro Infection_21B_2010


title: SW480_exo_rep1

source_name: SW480 cells, exosomal RNA, replicate-1

value: epithelial


title: In Vitro Infection_22C_2010


title: SW480_endo_rep1

source_name: SW480 cells, endogenous RNA, replicate-1

value: cells


title: FK506/CsA-treated EB at D8, biological rep3


title: SW480_exo_rep3

source_name: SW480 cells, exosomal RNA, replicate-3


title: Non-treated EB at D8, biological rep3


title: SW480_exo_rep2

source_name: SW480 cells, exosomal RNA, replicate-2


title: In Vitro Infection_21C_2010


title: FK506/CsA-treated EB at D8, biological rep1


title: FK506/CsA-treated EB at D8, biological rep2


title: In Vitro Infection_21A_2010


title: HCT 116_exo_rep2

source_name: HCT116 cells, exosomal RNA, replicate-2


title: Non-treated EB at D8, biological rep1


title: HCT 116_endo_rep2

source_name: HCT116 cells, endogenous RNA, replicate-2

value: colon cancer cells


title: HCT 116_exo_rep1

source_name: HCT116 cells, exosomal RNA, replicate-1

value: conditioned medium  from colon cancer cells


title: Non-treated EB at D8, biological rep2


title: 16HBE-RV16-T60-3-7

source_name: whole blood

value: Infected

value: 60 hr


title: FK506/CsA-treated EB at D6, biological rep3


title: 16HBE-RV16-T60-1-7


title: 16HBE-RV16-T60-2-7


title: 16HBE-RV16-T60-UV-1-7

value: Mock Infected


title: 16HBE-RV16-T48-UV-1-7

value: 48 hr


title: HCT 116_endo_rep1

source_name: HCT116 cells, endogenous RNA, replicate-1


title: FHC_exo_rep3

source_name: FHC cells, exosomal RNA, replicate-5

value: conditioned medium from fetal colon-derived cells

value: FHC

value: normal


title: FHC_exo_rep1

source_name: FHC cells, exosomal RNA, replicate-3


title: Non-treated EB at D6, biological rep2

value: untreated

value: 46C embryonic stem cells


title: Non-treated EB at D6, biological rep3


title: 16HBE-RV16-T36-UV-1-7

value: 36 hr


title: 16HBE-RV16-T48-3-7


title: FHC_exo_rep2

source_name: FHC cells, exosomal RNA, replicate-4

value: exosomes


title: FK506/CsA-treated EB at D6, biological rep1

source_name: FK506/CsA-treated mouse embryoid bodies (EB)


title: FHC_endo_rep2

source_name: FHC cells, endogenous RNA, replicate-2

value: fetal colon-derived cells


title: 16HBE-RV16-T36-3-7


title: 16HBE-RV16-T48-2-7


title: FHC_endo_rep1

source_name: FHC cells, endogenous RNA, replicate-1


title: 16HBE-RV16-T48-1-7


title: FK506/CsA-treated EB at D6, biological rep2


title: FK506/CsA-treated EB at D4, biological rep3


title: NC_FBS_exo_rep3

description: MicroRNA profile in FBS exosomes

organism: Bos taurus

source_name: Fetal bovine serum, exosomal RNA, replicate-3

value: serum


title: FK506/CsA-treated EB at D4, biological rep2


title: FK506/CsA-treated EB at D4, biological rep1


title: NC_FBS_exo_rep2

description: MicroRNA profile in FBS exosomes

source_name: Fetal bovine serum, exosomal RNA, replicate-2


title: NC_FBS_exo_rep1

description: MicroRNA profile in FBS exosomes

source_name: Fetal bovine serum, exosomal RNA, replicate-1


title: 16HBE-RV16-T36-2-7


title: 16HBE-RV16-T24-UV-1-7

value: 24 hr


title: NC_FBS_exo_rep4

description: MicroRNA profile in FBS exosomes

source_name: Fetal bovine serum, exosomal RNA, replicate-4


title: Non-treated EB at D4, biological rep3

source_name: Non-treated mouse embryoid bodies (EB)


title: 16HBE-RV16-T24-3-7


title: 16HBE-RV16-T24-1-7


title: 16HBE-RV16-T16-UV-1-7

value: 16 hr


title: 16HBE-RV16-T16-3-7


title: Non-treated EB at D4, biological rep2


title: 16HBE-RV16-T24-2-7


title: 16HBE-RV16-T36-1-7


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 24 h after chitin oligosaccharide elicitor treatment rep 2

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 24 h after chitin oligosaccharide elicitor treatment replicate 2
Biological replicate 2 of 4.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2565

data_processing: Data was analyzed by Fearure Extraction software (Agilent)

organism: Oryza sativa

source_name: Chitin oligosaccharide elicitor-treated wild-type rice cells for 24 h

label_protocol: Low RNA input Linear Amplification/Labeling Kit (Agilent)

growth_protocol: Rice suspension cultured cells (Oryza sativa L. cv. Nipponnbare) used for total RNA extraction were maintained using N-6 medium and incubated on a rotary shaker at 25 C and 120 rpm in a dark. Cells were transferred to a fresh medium every week.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Rice cells 6 days after transfer to the new medium were used experiment and chitin oligosaccharide (1 ppm) was added to the culture medium.

tag: cultivar

value: Nipponnbare

value: wild type

tag: agent

value: Chitin oligosaccharide

tag: time

source_name: Chitin oligosaccharide elicitor-treated OsTGAP1-overexpressing rice cells for 24 h


title: 16HBE-RV16-T12-UV-1-7

tag: cell line

value: 12 hr


title: 16HBE-RV16-T16-1-7

value: Infected


title: 16HBE-RV16-T16-2-7


title: Non-treated EB at D4, biological rep1


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 24 h after chitin oligosaccharide elicitor treatment rep 3

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 24 h after chitin oligosaccharide elicitor treatment replicate 3
Biological replicate 3 of 4.


title: 16HBE-RV16-T12-3-7


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 24 h after chitin oligosaccharide elicitor treatment rep 4

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 24 h after chitin oligosaccharide elicitor treatment replicate 4
Biological replicate 4 of 4.


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 6 h after chitin oligosaccharide elicitor treatment rep 3

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 6 h after chitin oligosaccharide elicitor treatment replicate 3
Biological replicate 3 of 4.

source_name: Chitin oligosaccharide elicitor-treated wild-type rice cells for 6 h

value: 6 h

source_name: Chitin oligosaccharide elicitor-treated OsTGAP1-overexpressing rice cells for 6 h


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 6 h after chitin oligosaccharide elicitor treatment rep 4

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 6 h after chitin oligosaccharide elicitor treatment replicate 4
Biological replicate 4 of 4.


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 24 h after chitin oligosaccharide elicitor treatment rep 1

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 24 h after chitin oligosaccharide elicitor treatment replicate 1
Biological replicate 1 of 4.


title: B cells, time 24, technical replicate 2

city: Houston

first: Bruno

last: Di Stefano

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K arrays (G4851A-028004)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the LowInputQuick Amp Labeling kit (Agilent 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: ESCs and iPSCs were cultured on mitomycin C treated MEF feeder cells in KO-DMEM (Invitrogen) supplemented withL-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, 1,000 U/ml LIF (ESC medium) and 15% fetal bovine serum (FBS, Invitrogen). MEF cultures were established by trypsin digestion of mouse embryos (embryonic day 13.5) and the resulting cells cultured in DMEM supplemented with 10% FBS, L-glutamine and penicillin/streptomycin. CD19+ pro-B and pre-B cells were isolated from bone marrow using monoclonal antibodies to CD19 (1D3), obtained from BD Pharmingen, using MACS (Miltenyi Biotech). After isolation B cells were grown in RPMI medium supplemented with 10% FBS and IL-7. cell reprogramming experiments were conducted in gelatinized plates seeded with a feeder layer of the OP9 stromal cell line, using ESC medium supplemented with 2μg/ml of doxycycline and 15% FBS. For the reprogramming of B cells, IL-4 (10ng/ml), IL-7 (10ng/ml) and IL-15 (2ng/ml) were added to the medium.

extract_protocol: RNA isolation  was done with the miRNeasy Mini kit

treatment_protocol: Cells were trypsinized and FACS-sorted to remove feeder and dead cells.

tag: tissue

value: primary B cells

tag: time point

value: 24 hrs

value: B cells induced with OSKM for 24hrs


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 6 h after chitin oligosaccharide elicitor treatment rep 1

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 6 h after chitin oligosaccharide elicitor treatment replicate 1
Biological replicate 1 of 4.


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 6 h after chitin oligosaccharide elicitor treatment rep 2

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 6 h after chitin oligosaccharide elicitor treatment replicate 2
Biological replicate 2 of 4.


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 0 h after chitin oligosaccharide elicitor treatment rep 3

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 0 h after chitin oligosaccharide elicitor treatment replicate 3
Biological replicate 3 of 4.

source_name: Chitin oligosaccharide elicitor-treated wild-type rice cells for 0 h

value: 0 h

source_name: Chitin oligosaccharide elicitor-treated OsTGAP1-overexpressing rice cells for 0 h


title: 16HBE-RV16-T12-1-7

source_name: whole blood


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 0 h after chitin oligosaccharide elicitor treatment rep 2

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 0 h after chitin oligosaccharide elicitor treatment replicate 2
Biological replicate 2 of 4.


title: B cells, time 12, technical replicate 1

value: 12 hrs

value: B cells induced with OSKM for 12hrs


title: B cells, time 12, technical replicate 2


title: 16HBE-RV16-T8-UV-1-7

value: Mock Infected

value: 8 hr


title: 16HBE-RV16-T8-3-7


title: B cells, time 3, technical replicate 2

value: 3 hrs

value: B cells induced with OSKM for 3hrs


title: 16HBE-RV16-T12-2-7


title: B cells, time 6, technical replicate 2

value: 6 hrs

value: B cells induced with OSKM for 6hrs


title: B cells, time 3, technical replicate 1


title: B cells, time 6, technical replicate 1


title: 16HBE-RV16-T6-UV-1-7

value: 6 hr


title: B cells, time 24, technical replicate 1


title: 24h after chitin oligosaccharide treatment replicate 4

description: Biological replicate 4 of 4.

data_processing: Data was analyzed by Feature Extraction software (Agilent)

source_name: Untreated rice cells

value: Nipponnbare

value: Control (untreated)

source_name: Rice cells treated with chitin oligosaccharide for 24 h

value: Chitin oligosaccharide


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 0 h after chitin oligosaccharide elicitor treatment rep 1

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 0 h after chitin oligosaccharide elicitor treatment replicate 1
Biological replicate 1 of 4.

value: wild type


title: OsTGAP1-overexpressing rice cells vs wild type rice cells 0 h after chitin oligosaccharide elicitor treatment rep 4

description:
Comparison of OsTGAP1-overexpressing rice cells with the wild type rice cells 0 h after chitin oligosaccharide elicitor treatment replicate 4
Biological replicate 4 of 4.


title: 24h after chitin oligosaccharide treatment replicate 3

description: Biological replicate 3 of 4.


title: 16HBE-RV16-T6-3-7

value: Infected


title: 16HBE-RV16-T8-1-7


title: 16HBE-RV16-T8-2-7


title: 18hrs pulse B cells, time 24, technical replicate 1

value: primary B cells

value: 24 hrs

value: B cells pulsed for 18hrs with C/EBPa, induced for 24 hrs with OSKM


title: 18hrs pulse B cells, time 24, technical replicate 2


title: 16HBE-RV16-T6-2-7


title: 18hrs pulse B cells, time 12, technical replicate 1

value: 12 hrs

value: B cells pulsed for 18hrs with C/EBPa, induced for 12 hrs with OSKM


title: 18hrs pulse B cells, time 12, technical replicate 2


title: 16HBE-RV16-T6-1-7


title: 18hrs pulse B cells, time 6, technical replicate 2

value: B cells pulsed for 18hrs with C/EBPa, induced for 6 hrs with OSKM


title: 6h after chitin oligosaccharide treatment replicate 4

description: Biological replicate 4 of 4.

source_name: Rice cells treated with chitin oligosaccharide for 6 h

value: 6 h


title: 24h after chitin oligosaccharide treatment replicate 2

description: Biological replicate 2 of 4.


title: 24h after chitin oligosaccharide treatment replicate 1

description: Biological replicate 1 of 4.


title: Non-treated EB at D6, biological rep1

value: untreated

value: 46C embryonic stem cells


title: 16HBE-RV16-T4-UV-1-7

value: Mock Infected

value: 4 hr


title: Gastric tumour GC0151

city: East Melbourne

first: Rita

middle: Ann

last: Busuttil

state: VIC

address: St Andrews Pl

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

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

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

data_processing: CEL files were produced using the Affymetrix ® GeneChip ® Command console ® Software (AGCC).

source_name: Primary gastric tumour

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 to 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

extract_protocol: Total RNA was extracted from primary tumors using Trizol extraction and RNeasy midi spin columns (Qiagen) according to the instructions of the manufacturer.

value: Primary gastric tumour


title: 18hrs pulse B cells, time 6, technical replicate 1

value: 6 hrs


title: Gastric tumour GC0149


title: 6h after chitin oligosaccharide treatment replicate 3

description: Biological replicate 3 of 4.

value: Nipponnbare

value: Control (untreated)


title: 6h after chitin oligosaccharide treatment replicate 2

description: Biological replicate 2 of 4.

value: Chitin oligosaccharide


title: Gastric tumour GC0146


title: 16HBE-RV16-T4-1-7

data_processing: The data were analysed in Genespring GX11.5 software. Measurements less than 0.01 was set to 0.01. Data was then normalised at the 80th percentile.

value: Infected


title: 16HBE-RV16-T4-3-7


title: 18hrs pulse B cells, time 3, technical replicate 2

value: primary B cells

value: 3 hrs

value: B cells pulsed for 18hrs with C/EBPa, induced for 3 hrs with OSKM


title: 16HBE-RV16-T4-2-7


title: 18hrs pulse B cells, time 3, technical replicate 1


title: 6h after chitin oligosaccharide treatment replicate 1

description: Biological replicate 1 of 4.


title: 16HBE-RV16-T3-3-7

value: 3 hr


title: Gastric tumour GC0145


title: Gastric tumour GC0144


title: Gastric tumour GC0147


title: DG Aged Impaired (5842733067_B)

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description:
replicate 2
DG Aged Impaired

data_processing: The data were normalized using average normalization

organism: Rattus norvegicus

source_name: Hippocampus

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

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

tag: strain

value: Fischer 344 x Brown Norway F1-hybrid (F344BN)

tag: age group

value: Aged Impaired (24M)

tag: tissue group

value: DG


title: 16HBE-RV16-T3-UV-1-7

tag: sample type

tag: collection time


title: DG Aged Impaired (5842733067_C)

description:
replicate 3
DG Aged Impaired


title: 16HBE-RV16-T3-1-7


title: Gastric tumour GC0142


title: 16HBE-RV16-T2-UV-1-7

value: 2 hr


title: 16HBE-RV16-T3-2-7


title: DG Aged Intact (5842733067_G)

description:
replicate 3
DG Aged Intact

value: Aged Intact (24M)


title: Gastric tumour GC0134


title: DG Aged Intact (5842733067_E)

description:
replicate 1
DG Aged Intact


title: DG Aged Impaired (5842733067_A)

description:
replicate 1
DG Aged Impaired


title: DG Aged Intact (5842733067_H)

description:
replicate 4
DG Aged Intact


title: Gastric tumour GC0140


title: 16HBE-RV16-T2-1-7


title: Gastric tumour GC0138


title: Gastric tumour GC0133


title: XH3

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Rattus rattus microarrays were manufactured with Agilent Sure Print Technology in Fall 2012.  RNA labeling, microarray hybridization, and microarray analysis were performed according to Agilent’s One-Color Microarray-Gene Based Expression Analysis protocol (May 2010) using an Agilent kit (Agilent, Mississauga, ON, CAN).  After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.

data_processing: Normalized signal intensity provided here is Quantile Normalization

organism: Rattus rattus

source_name: hair follicle

label_protocol: Agilent one color protocol for Cy3

extract_protocol: RNA was extracted using the E.Z.N.A total RNA kit (VWR International, Mississauga, ON, CA).  RNA quantity was measured using the NanoDrop ND2000 (Thermo Scientific) prior to DNase treatment for real-time PCR and RNA integrity was evaluated according to Agilent 2100 Bioanalyzer protocol (Agilent, Mississauga, ON, CAN).

tag: shock wave pressure

tag: gender

value: Male

value: Sprague-Dawley (SD)


title: Gastric tumour GC0136

value: Primary gastric tumour


title: DG Adult (5842733067_L)

description:
replicate 4
DG Adult

value: Adult (12M)


title: 16HBE-RV16-T2-3-7

extract_protocol: Total RNA was extracted from whole blood drawn in pax-gene vacutainer tubes by PAX-gene RNA kit (Qiagen). Quality control was performed with NanoDrop 1000 instrument


title: 16HBE-RV16-T1-UV-1-7

value: Mock Infected

value: 1 hr


title: DG Aged Intact (5842733067_F)

description:
replicate 2
DG Aged Intact


title: M3

scan_protocol: After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.


title: Gastric tumour GC0132


title: Gastric tumour GC0131


title: 16HBE-RV16-T1-3-7


title: DG Adult (5842733067_K)

description:
replicate 3
DG Adult


title: 16HBE-RV16-T1-2-7


title: 16HBE-RV16-T2-2-7


title: C3

value: 0 KPa (0 psi)


title: DG Adult (5842733067_J)

description:
replicate 2
DG Adult


title: Gastric tumour GC0130


title: DG Adult (5842733067_I)

description:
replicate 1
DG Adult


title: 16HBE-RV16-T1-1-7

value: Infected


title: C2


title: C1


title: Gastric tumour GC0127


title: Gastric tumour GC0128


title: 16HBE-RV16-T0 -3-7

value: 0 hr


title: H1


title: 16HBE-RV16-T0 -UV-1-7


title: Gastric tumour GC0125


title: CA1 Aged Impaired (5842733059_B)

description:
replicate 2
CA1 Aged Impaired


title: CA1 Aged Impaired (5842733059_D)

description:
replicate 4
CA1 Aged Impaired


title: CA1 Aged Impaired (5842733059_A)

description:
replicate 1
CA1 Aged Impaired


title: Gastric tumour GC0123


title: 16HBE-RV16-T0 -2-7


title: M2


title: CA1 Aged Intact (5842733059_H)

description:
replicate 4
CA1 Aged Intact


title: 16HBE-RV16-T0 -1-7


title: CA1 Aged Impaired (5842733059_C)

description:
replicate 3
CA1 Aged Impaired


title: Gastric tumour GC0129


title: Gastric tumour GC0126


title: 16HBE-RV16-T0 UNINFECT-UV-1-7

value: Mock Uninfected


title: Gastric tumour GC0122


title: 16HBE-RV16-T0 UNINFECT-3-7

value: Uninfected


title: CA1 Aged Intact (5842733059_E)

description:
replicate 1
CA1 Aged Intact


title: CA1 Aged Intact (5842733059_G)

description:
replicate 3
CA1 Aged Intact


title: CA1 Adult (5842733059_K)

description:
replicate 3
CA1 Adult


title: Gastric tumour GC0118


title: Gastric tumour GC0120


title: CA1 Aged Intact (5842733059_F)

description:
replicate 2
CA1 Aged Intact


title: Gastric tumour GC0117


title: CA1 Adult (5842733059_L)

description:
replicate 4
CA1 Adult


title: Gastric tumour GC0121


title: B2B-RV16-T36-2-7 (repeat)

value: 36 hr


title: CA1 Adult (5842733059_J)

description:
replicate 2
CA1 Adult

value: Fischer 344 x Brown Norway F1-hybrid (F344BN)


title: 16HBE-RV16-T0 UNINFECT-1-7


title: 16HBE-RV16-T0 UNINFECT-2-7