title: SRSF1-non-targeting scramble siRNA-2

description: A549 transfected with scramble siRNA Experiment 2


title: SRSF1-non-targeting scramble siRNA-1

status: Public on Dec 18 2013

type: RNA

city: San Sebastian

first: Ravi

middle: Datta

last: Sharma

state: Gipuzkoa

address: Parque Tecnológico de San Sebastián, Paseo Mikeletegi, Nº 48,

department: Biomedical Engineering

country: Spain

institute: CEIT

description: A549 transfected with scramble siRNA Experiment 1

hyb_protocol: Hybridization was performed by the Proteomics, Genomics and Bioinformatics Core Facility of the Center for Applied Medical Research (CIMA) following manufacturer’s instructions.

scan_protocol: Affymetrix GeneChip 3000  Affymetrix® GeneChip® 3000  GeneChip® 3000

data_processing:
Background correction was processed with maximum likelihood estimation (mle). Quantile normalization was performed to adjust the experimental condition of the arrays. Summarized data by probesets.
probe group file: hjay.r1.pgf
meta-probeset file: hjay.r1.mps

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: A549 lung cancer cell line

label_protocol: Labeling was performed by the Proteomics, Genomics and Bioinformatics Core Facility of the Center for Applied Medical Research (CIMA) following manufacturer’s instructions.

growth_protocol: Cells were grown in RPMI supplemented with 2 mM glutamine, 10% Fetalclone, 100 U/ml of penicillin and 100 µg/ml of streptomycin

extract_protocol: Total RNA was extracted using the RNA/DNA Mini Kit (Qiagen)

treatment_protocol: Cells were transfected with a 30 nM solution of a non-targeting scramble siRNA (5´-ACGACACGCAGGTCGTCATtt-3´) or an SRSF1 siRNA (5´-TGAAGCAGGTGATGTATGTtt-3´) using lipofectamine

tag: transfection

value: scramble siRNA


title: Obese-FB-4

city: NEW YORK

first: Xiaoyuan

last: Xu

state: NY

address: 1150 St Nicholas Ave.

department: Medicine

country: USA

institute: Columbia University

description: Gene expression data from sorted FB ( F4/80+, CD11b+, CD11c-) macrophages.

hyb_protocol: Hybridization in AFFY Gene Chip HYB Oven 640 from AFFY for 16 hr at 45ºC and used EUKGE-WS2v5 wash protocol.

scan_protocol: GeneChips were scanned using the AFFY Gene Chip Scanner 3000 7G.

data_processing: Analyze on Expression Console

label: biotin

organism: Mus musculus

source_name: Adipose tissue macrophages from obese mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.  (GeneChip® Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: Lean (C57BL/6J Lep +/+) and obese leptin-deficient (C57BL/6J Lep ob/ob) mice were obtained from the Jackson Laboratory.

extract_protocol: For whole AT samples, total RNA was extracted from the PGAT of individual mice. RNA was isolated from sorted FBC (F4/80+, CD11b+, and CD11c+) cells and FB (F4/80+, CD11b+, and CD11c−) cells with RNeasy micro kits (Qiagen) with a PicoPure RNA isolation kit and amplified for two rounds

treatment_protocol: Isolation stromal vascular cells: Adipose tissue was isolated from mice immediately after CO2 asphyxiation. Tissues were minced into fine (<10-mg) pieces and centrifuged at 500 g for 5 minutes to remove connective tissue debris. Minced samples were placed in a digestion solution of DMEM containing Liberase3 TM (0.14 units/ml) (Roche Applied Science), BSA 20 mg/ml, DNaseI, 50 U/ml (Sigma-Aldrich). The samples were then incubated at 37°C on an orbital shaker (185 rpm) for 30-45 minutes. Once digestion was complete, samples were passed through a sterile 250-μm nylon mesh (Sefar Filtration Inc.). The suspension was centrifuged at 500 g for 5 minutes. The pelleted cells were collected as the SVCs.The SVCs were resuspendedin erythrocyte lysisbuffer (BD Biosciences) and incubated at room temperature for 3 minutes. The erythrocyte-depleted SVCs were centrifuged at 500 g for 5 minutes and the pellet cells resuspendedin FACS buffer (PBS, 0.2%, fatty acid depleted-BSA, 5 mM EDTA) at a concentration of 7 x 106cells/ml for fluorescence activated cell sorting

tag: tissue

value: Perigonadal

tag: genotype

tag: age

value: 12~14 weeks of age

tag: cell type

value: Macrophage of F4/80+, CD11b+, CD11c-


title: Obese-FB-2

value: obese leptin-deficient (C57BL/6J Lep ob/ob)


title: SRSF1-control-2

description: A549 transfected with lipofectamine alone Experiment 2

value: lipofectamine alone


title: SRSF1-control-3

description: A549 transfected with lipofectamine alone Experiment 3


title: SRSF1-control-1

description: A549 transfected with lipofectamine alone


title: Obese-FB-3


title: CHC1217T

type: genomic

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

description: Hepatocellular adenoma

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol. Log R Ratios exported from the Beadstudio software.

label: C-Bio and A-DNP

molecule: genomic DNA

label_protocol: standard Illumina protocol

extract_protocol: DNA was extracted from 3 mm3 frozen tumor samples using high salt precipitation (as described in PMID: 3344216).

tag: Sex

value: F

tag: pathological diagnosis


title: Nor AF-MSCs vs. Hypo AF-MSCs 2

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

country: South Korea

institute: Korea University

description:
2-1 vs. 2-2
20% O2 and 5% CO2 vs 1% O2 and 20% CO2  at 37°C for 72 h.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.
The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: AF-MSCs were cultured in growth medium containing low-glucose DMEM medium (Gibco), 10% fetal bovine serum (FBS, Hyclone) and 4 ng/ml human basic fibroblast growth factor (bFGF, R&D Systems), and incubated in incubator (20% O2 and 5% CO2)  at 37°C.

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

treatment_protocol: AF-MSCs were cultured in growth medium and incubated in incubator (1% O2 and 20% CO2) at 37°C for 72 h.

value: amniotic fluid-derived mesenchymal stem cells (AF-MSCs)

tag: growth condition

value: normal; 20% O2 and 5% CO2 at 37°C for 72h

value: hypoxia; 1% O2 and 20% CO2 at 37°C for 72 h


title: 22_DAP_14C_Rep1

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Five Medicago truncatula plants were grown at controlled light/temperature conditions: 14/11°C, 16h light/dark from the stage of flowering to the end of seed maturation. Seeds were collected at different maturation stages, from 22 DAP to Abscission. Dry seeds (DS) was the last analysed stage of development, after abscission seeds were let in the same environmental conditions for one week.

extract_protocol: For each data point of seed development and for each repetition, 50 seeds were collected and the total RNA was extracted with Macherey-Nagel's Nucleospin Plant II Kit according manufacturer's recommendations

treatment_protocol: Medicago truncatula seeds developed at 14/11°C, 16h light/darkf rom 1 DAP to DS stage

tag: tissus

value: seed

tag: genetic background

tag: developmental stage

value: 22_DAP maturation

tag: phenotype

value: Wild-type

tag: treatment

value: Seeds developed at 15-13°C 16h

value: 22 days after flowering

tag: harvest date


title: Lean-FBC-4

description: Gene expression data from sorted FBC ( F4/80+, CD11b+, CD11c+) macrophages

source_name: Adipose tissue macrophages from lean mice

value: lean (C57BL/6J Lep +/+)

value: Macrophage of F4/80+, CD11b+, CD11c-+


title: Lean-FB-4


title: Nor AF-MSCs vs. Hypo AF-MSCs 1

description:
1-1 vs. 1-2
20% O2 and 5% CO2 vs 1% O2 and 20% CO2  at 37°C for 72 h.


title: SRSF1-targeting scramble siRNA-2

description: A549 transfected with SRSF1 siRNA Experiment 2

value: SRSF1 siRNA


title: Lean-FBC-3

value: Perigonadal


title: Lean-FBC-2

value: 12~14 weeks of age


title: Lean-FB-3

value: Macrophage of F4/80+, CD11b+, CD11c-


title: Obese-FB-1

value: obese leptin-deficient (C57BL/6J Lep ob/ob)


title: Lean-FBC-1


status: Public on Dec 17 2013

city: Manchester

first: Pedro

last: Mendes

address: 131 Princess Street

department: Manchester Institute of Biotechnology

country: United Kingdom

institute: University of Manchester

description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast S98 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 640.

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

data_processing: The data were normalized with RMA (RMAExpress version 0.5).

organism: Saccharomyces cerevisiae

source_name: Yeast, Yap1 mutant, CHP treated, t=3 min, biological replicate 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Yeast cultures were grown in controlled batch conditions, in 1 L fermentors at 30C, pH 6.0, 500 rpm, and dO2> 80%.

extract_protocol: RNA was extracted with a procedure modified from the hot phenol protocol, as described (Martins, A. et al (2007) Yeast 24, 181-188)

treatment_protocol: In mid-exponential phase (OD600 ~ 1.5), three replicate cultures were treated with 0.19 mM CHP, while three untreated cultures were used as controls.

tag: agent

value: CHP

tag: time point

value: t=3 min

tag: strain

value: yap1 mutant

tag: growth phase

value: Mid-exponental phase


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 3

source_name: Yeast, Yap1 mutant, CHP treated, t=12 min, biological replicate 3

value: t=12 min


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 3

source_name: Yeast, Yap1 mutant, CHP treated, t=6 min, biological replicate 3

value: t=6 min


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 2

source_name: Yeast, Yap1 mutant, CHP treated, t=3 min, biological replicate 2


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 2

source_name: Yeast, Yap1 mutant, CHP treated, t=0 min, biological replicate 2

value: t=0 min


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 3

source_name: Yeast, Yap1 mutant, CHP treated, t=0 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 2

source_name: Yeast, Yap1 mutant, CHP treated, t=6 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 2

source_name: Yeast, Yap1 mutant, CHP treated, t=12 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 3

source_name: Yeast, Yap1 mutant, CHP treated, t=3 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 2

source_name: Yeast, Yap1 mutant, CHP treated, t=20 min, biological replicate 2

value: t=20 min


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 3

source_name: Yeast, Yap1 mutant, CHP treated, t=20 min, biological replicate 3


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Yap1 mutant, Control, t=6 min, biological replicate 3

value: Control


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 1

source_name: Yeast, Yap1 mutant, CHP treated, t=0 min, biological replicate 1


title: Lean-FB-1

description: Gene expression data from sorted FB ( F4/80+, CD11b+, CD11c-) macrophages.

tag: tissue


title: Lean-FB-2

tag: genotype


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Yap1 mutant, Control, t=12 min, biological replicate 3


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Yap1 mutant, Control, t=3 min, biological replicate 3


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Yap1 mutant, Control, t=0 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 1

source_name: Yeast, Yap1 mutant, CHP treated, t=6 min, biological replicate 1


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Yap1 mutant, Control, t=20 min, biological replicate 3


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Yap1 mutant, Control, t=12 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 1

source_name: Yeast, Yap1 mutant, CHP treated, t=20 min, biological replicate 1


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Yap1 mutant, Control, t=20 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 1

source_name: Yeast, Yap1 mutant, CHP treated, t=12 min, biological replicate 1


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Yap1 mutant, Control, t=6 min, biological replicate 2


title: 52_DAP_14C_Rep2

value: seed

value: 52_DAP maturation

value: Wild-type

value: Seeds developed at 15-13°C 16h

tag: age

value: 52 days after flowering


title: ChIP-chip of Zip3-Flag from cells at 4 hr in meiosis

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

institute: Institut Curie

description: Zip3-Flag ChIP chip in meiotic cells (4 hr)

hyb_protocol: 16 hours at 65°C in the 1X hybridization buffer supplied by Agilent

scan_protocol: Axon 4000B scanner. GenePix6.0 software

data_processing: Ratios of background-corrected intensities were normalized such that the median of all ratios equals one. Then we computed a weighted average from the ratios from replicate #1 and replicate #2, wih the standard deviation of the chip as the weight. The resulting mean ratios were divided by the mean of the lowest 10% ratio probes of the array (decile normalization, as described in Panizza et al, Cell, 2011)

source_name: ChIP of Zip3-Flag

label_protocol:
ch1:two-thirds of the immunoprecipitated DNA was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling
ch2:1/70 of the DNA from the whole-cell extract was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 4 hr in meiosis

extract_protocol: 10ml (2*108 cells) were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold PBS, and then chromatin immunoprecipitation was performed as described (Robine et al., 2007), using 2 µg of mouse monoclonal M2 anti-FLAG (Sigma) and 30 µl protein G magnetic beads suspension (New England Biolabs)

value: at 4 hr in meiosis

source_name: Whole cell extract


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 3

source_name: Yeast, wild type, CHP treated, t=0 min, biological replicate 3

value: wild type


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 3

source_name: Yeast, wild type, CHP treated, t=3 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 2

source_name: Yeast, wild type, CHP treated, t=20 min, biological replicate 2


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Yap1 mutant, Control, t=0 min, biological replicate 1


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Yap1 mutant, Control, t=3 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 3

source_name: Yeast, wild type, CHP treated, t=20 min, biological replicate 3


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Yap1 mutant, Control, t=6 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 3

source_name: Yeast, wild type, CHP treated, t=6 min, biological replicate 3


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 2

source_name: Yeast, wild type, CHP treated, t=0 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 2

source_name: Yeast, wild type, CHP treated, t=12 min, biological replicate 2


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Yap1 mutant, Control, t=20 min, biological replicate 1


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Yap1 mutant, Control, t=0 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 1

source_name: Yeast, wild type, CHP treated, t=3 min, biological replicate 1


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 1

source_name: Yeast, wild type, CHP treated, t=0 min, biological replicate 1


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, wild type, Control, t=12 min, biological replicate 3


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Yap1 mutant, Control, t=3 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 2

source_name: Yeast, wild type, CHP treated, t=3 min, biological replicate 2


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, wild type, Control, t=3 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 1

source_name: Yeast, wild type, CHP treated, t=6 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 3

source_name: Yeast, wild type, CHP treated, t=12 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 1

source_name: Yeast, wild type, CHP treated, t=12 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 1

source_name: Yeast, wild type, CHP treated, t=20 min, biological replicate 1


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, wild type, Control, t=20 min, biological replicate 3


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, wild type, Control, t=6 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 2

source_name: Yeast, wild type, CHP treated, t=6 min, biological replicate 2


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, wild type, Control, t=20 min, biological replicate 2


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, wild type, Control, t=0 min, biological replicate 3


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, wild type, Control, t=12 min, biological replicate 2


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, wild type, Control, t=6 min, biological replicate 1


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, wild type, Control, t=3 min, biological replicate 1


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 2

source_name: Yeast, Grx2 mutant, CHP treated, t=0 min, biological replicate 2

value: grx2 mutant


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, wild type, Control, t=12 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 3

source_name: Yeast, Grx2 mutant, CHP treated, t=20 min, biological replicate 3

value: CHP


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, wild type, Control, t=6 min, biological replicate 2


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, wild type, Control, t=0 min, biological replicate 1


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, wild type, Control, t=20 min, biological replicate 1


source_name: Yeast, Grx2 mutant, CHP treated, t=20 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 1

source_name: Yeast, Grx2 mutant, CHP treated, t=3 min, biological replicate 1

value: t=3 min


source_name: Yeast, Grx2 mutant, Control, t=6 min, biological replicate 3


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Grx2 mutant, Control, t=12 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 3

source_name: Yeast, Grx2 mutant, CHP treated, t=12 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 2

source_name: Yeast, Grx2 mutant, CHP treated, t=12 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 2

source_name: Yeast, Grx2 mutant, CHP treated, t=20 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 2

source_name: Yeast, Grx2 mutant, CHP treated, t=6 min, biological replicate 2


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Grx2 mutant, Control, t=3 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 2

source_name: Yeast, Grx2 mutant, CHP treated, t=3 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 3

source_name: Yeast, Grx2 mutant, CHP treated, t=6 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 1

source_name: Yeast, Grx2 mutant, CHP treated, t=6 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 1

source_name: Yeast, Grx2 mutant, CHP treated, t=12 min, biological replicate 1


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, wild type, Control, t=0 min, biological replicate 2


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 3

source_name: Yeast, Grx2 mutant, CHP treated, t=0 min, biological replicate 3


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, wild type, Control, t=3 min, biological replicate 2


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Grx2 mutant, Control, t=20 min, biological replicate 3


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Grx2 mutant, Control, t=0 min, biological replicate 3


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 1

source_name: Yeast, Grx2 mutant, CHP treated, t=0 min, biological replicate 1


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Grx2 mutant, Control, t=20 min, biological replicate 2


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Grx2 mutant, Control, t=12 min, biological replicate 2


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Grx2 mutant, Control, t=20 min, biological replicate 1


source_name: Yeast, Grx2 mutant, Control, t=3 min, biological replicate 2


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Grx2 mutant, Control, t=12 min, biological replicate 1


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Grx2 mutant, Control, t=3 min, biological replicate 1


source_name: Yeast, Grx2 mutant, Control, t=0 min, biological replicate 2


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Grx2 mutant, Control, t=0 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 3

source_name: Yeast, Grx1 mutant, CHP treated, t=3 min, biological replicate 3

value: grx1 mutant


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Grx2 mutant, Control, t=6 min, biological replicate 2

value: Mid-exponental phase


source_name: Yeast, Grx1 mutant, CHP treated, t=0 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 2

source_name: Yeast, Grx1 mutant, CHP treated, t=3 min, biological replicate 2


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 2

source_name: Yeast, Grx1 mutant, CHP treated, t=0 min, biological replicate 2


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Grx2 mutant, Control, t=6 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 2

source_name: Yeast, Grx1 mutant, CHP treated, t=6 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 3

source_name: Yeast, Grx1 mutant, CHP treated, t=6 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 1

source_name: Yeast, Grx1 mutant, CHP treated, t=20 min, biological replicate 1


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Grx1 mutant, Control, t=20 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 1

source_name: Yeast, Grx1 mutant, CHP treated, t=12 min, biological replicate 1

value: t=12 min


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 1

source_name: Yeast, Grx1 mutant, CHP treated, t=0 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 1

source_name: Yeast, Grx1 mutant, CHP treated, t=6 min, biological replicate 1

value: t=6 min


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 2

source_name: Yeast, Grx1 mutant, CHP treated, t=12 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 1

source_name: Yeast, Grx1 mutant, CHP treated, t=3 min, biological replicate 1


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Grx1 mutant, Control, t=12 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 3

source_name: Yeast, Grx1 mutant, CHP treated, t=12 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 3

source_name: Yeast, Grx1 mutant, CHP treated, t=20 min, biological replicate 3


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Grx1 mutant, Control, t=6 min, biological replicate 3


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Grx1 mutant, Control, t=3 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 2

source_name: Yeast, Grx1 mutant, CHP treated, t=20 min, biological replicate 2


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Grx1 mutant, Control, t=12 min, biological replicate 2


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Grx1 mutant, Control, t=20 min, biological replicate 1


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Grx1 mutant, Control, t=0 min, biological replicate 2

value: t=0 min


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Grx1 mutant, Control, t=0 min, biological replicate 3


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Grx1 mutant, Control, t=12 min, biological replicate 1


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Grx1 mutant, Control, t=3 min, biological replicate 2


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Grx1 mutant, Control, t=6 min, biological replicate 2


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Grx1 mutant, Control, t=20 min, biological replicate 2

value: t=20 min


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 3

source_name: Yeast, Gpx2 mutant, CHP treated, t=6 min, biological replicate 3

value: gpx2 mutant


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 2

source_name: Yeast, Gpx2 mutant, CHP treated, t=6 min, biological replicate 2


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 3

source_name: Yeast, Gpx2 mutant, CHP treated, t=0 min, biological replicate 3


source_name: Yeast, Gpx2 mutant, CHP treated, t=12 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 2

source_name: Yeast, Gpx2 mutant, CHP treated, t=12 min, biological replicate 2


source_name: Yeast, Gpx2 mutant, CHP treated, t=20 min, biological replicate 2


source_name: Yeast, Gpx2 mutant, CHP treated, t=20 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 1

source_name: Yeast, Gpx2 mutant, CHP treated, t=12 min, biological replicate 1


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Grx1 mutant, Control, t=0 min, biological replicate 1

value: Control


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 1

source_name: Yeast, Gpx2 mutant, CHP treated, t=3 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 1

source_name: Yeast, Gpx2 mutant, CHP treated, t=20 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 1

source_name: Yeast, Gpx2 mutant, CHP treated, t=6 min, biological replicate 1


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 2

source_name: Yeast, Gpx2 mutant, CHP treated, t=0 min, biological replicate 2


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Grx1 mutant, Control, t=6 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 3

source_name: Yeast, Gpx2 mutant, CHP treated, t=3 min, biological replicate 3


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Grx1 mutant, Control, t=3 min, biological replicate 1


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Gpx2 mutant, Control, t=3 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 2

source_name: Yeast, Gpx2 mutant, CHP treated, t=3 min, biological replicate 2


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Gpx2 mutant, Control, t=0 min, biological replicate 3


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Gpx2 mutant, Control, t=6 min, biological replicate 3


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 1

source_name: Yeast, Gpx2 mutant, CHP treated, t=0 min, biological replicate 1


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Gpx2 mutant, Control, t=20 min, biological replicate 2


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Yap1 mutant, Control, t=12 min, biological replicate 1

value: yap1 mutant


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Gpx2 mutant, Control, t=6 min, biological replicate 2


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Gpx2 mutant, Control, t=3 min, biological replicate 2


source_name: Yeast, Gpx2 mutant, Control, t=12 min, biological replicate 1


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Gpx2 mutant, Control, t=12 min, biological replicate 3


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Gpx2 mutant, Control, t=20 min, biological replicate 3


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Gpx2 mutant, Control, t=12 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 3

source_name: Yeast, Gpx1 mutant, CHP treated, t=12 min, biological replicate 3

value: gpx1 mutant


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 3

source_name: Yeast, Gpx1 mutant, CHP treated, t=6 min, biological replicate 3


source_name: Yeast, Grx2 mutant, CHP treated, t=3 min, biological replicate 3


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Gpx2 mutant, Control, t=0 min, biological replicate 2


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Gpx2 mutant, Control, t=6 min, biological replicate 1


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Gpx2 mutant, Control, t=20 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 3

source_name: Yeast, Gpx1 mutant, CHP treated, t=3 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 3

source_name: Yeast, Gpx1 mutant, CHP treated, t=20 min, biological replicate 3


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 3

source_name: Yeast, Gpx1 mutant, CHP treated, t=0 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 2

source_name: Yeast, Gpx1 mutant, CHP treated, t=20 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 2

source_name: Yeast, Gpx1 mutant, CHP treated, t=3 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 2

source_name: Yeast, Gpx1 mutant, CHP treated, t=6 min, biological replicate 2


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Gpx2 mutant, Control, t=3 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 2

source_name: Yeast, Gpx1 mutant, CHP treated, t=12 min, biological replicate 2


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 2

source_name: Yeast, Gpx1 mutant, CHP treated, t=0 min, biological replicate 2


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 1

source_name: Yeast, Gpx1 mutant, CHP treated, t=20 min, biological replicate 1


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Gpx2 mutant, Control, t=0 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 1

source_name: Yeast, Gpx1 mutant, CHP treated, t=12 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 1

source_name: Yeast, Gpx1 mutant, CHP treated, t=6 min, biological replicate 1


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 1

source_name: Yeast, Gpx1 mutant, CHP treated, t=0 min, biological replicate 1


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Gpx1 mutant, Control, t=12 min, biological replicate 3


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Gpx1 mutant, Control, t=20 min, biological replicate 3


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 1

source_name: Yeast, Gpx1 mutant, CHP treated, t=3 min, biological replicate 1


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Gpx1 mutant, Control, t=20 min, biological replicate 2


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Gpx1 mutant, Control, t=12 min, biological replicate 2


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Gpx1 mutant, Control, t=0 min, biological replicate 2


title: Stamen of stage 4-rep 2

city: Beijing

first: Rui

last: Chen

address: 5 Yiheyuan Road, Haidian District

department: College of Life Sciences

country: China

institute: Peking University

description: Dissected from spikelets

hyb_protocol: The resulting cRNA was used for hybridization in the Affymetrix® Hybridization Oven 640 according to manufacturer’s instruction. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000. GeneChip Operating software (GCOS 1.4) were adopted for transforming pixels to intensities .

data_processing: Raw data was processed by an adjustment method to remove the bias raising from the two-cycle RNA linear amplification at probe level(Wang F, Chen R, Ji D, Bai S, Qian M, Deng M. 2013. Adjustment method for microarray data generated using two-cycle RNA labeling protocol. BMC Genomics 14(1): 31.), and then RMA was used for background correction, normalization and summary in Bioconductor.

organism: Oryza sativa Japonica Group

source_name: Stamen of stage 4-rep 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by amplifying and labeling 50-300ng total RNA with Two-Cycle Eukaryotic Target Labeling Assay kit.

growth_protocol: Rice (O. sativa L. ssp. japonica cv. Zhonghua 15) seeds were soaked in water at 30oC for about a week. Then seedlings were transplanted in plastic pots and cultured at 30±2oC under 11 hours day/13 hours night cycle in growth chamber, or transplanted into the experimental field in growing season.

extract_protocol: Total RNA was isolated with TRIzol Reagent from Invitrogen Life Technologies.

tag: cultivar

value: Zhonghua 15

tag: organ

value: stamen


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Gpx1 mutant, Control, t=0 min, biological replicate 3


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Gpx1 mutant, Control, t=3 min, biological replicate 3


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Gpx1 mutant, Control, t=6 min, biological replicate 3


title: Stamen of stage 6-rep 1

description: Dissected from spikelets

source_name: Stamen of stage 6-rep 1


title: Stamen of stage 5-rep 2

description: Dissected from spikelets

source_name: Stamen of stage 5-rep 2


title: Stamen of stage 6-rep 3

description: Dissected from spikelets

source_name: Stamen of stage 6-rep 3


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Gpx1 mutant, Control, t=3 min, biological replicate 2


title: Stamen of stage 3-rep 3

description: Dissected from spikelets

source_name: Stamen of stage 3-rep 3


title: Stamen of stage 4-rep 1

description: Dissected from spikelets

source_name: Stamen of stage 4-rep 1


title: Stamen of stage 5-rep 1

description: Dissected from spikelets

source_name: Stamen of stage 5-rep 1


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Gpx1 mutant, Control, t=6 min, biological replicate 2


title: Stamen of stage 4-rep 3

description: Dissected from spikelets

source_name: Stamen of stage 4-rep 3


title: Stamen of stage 5-rep 3

description: Dissected from spikelets

source_name: Stamen of stage 5-rep 3


title: Stamen of stage 3-rep 1

description: Dissected from spikelets

source_name: Stamen of stage 3-rep 1


title: Stamen of stage 3-rep 2

description: Dissected from spikelets

source_name: Stamen of stage 3-rep 2


title: Stamen of stage 6-rep 2

description: Dissected from spikelets

source_name: Stamen of stage 6-rep 2


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Gpx1 mutant, Control, t=20 min, biological replicate 1


source_name: Yeast, Gpx1 mutant, Control, t=0 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 3

source_name: Yeast, Glr1 mutant, CHP treated, t=20 min, biological replicate 3

value: glr1 mutant


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Gpx1 mutant, Control, t=3 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 3

source_name: Yeast, Glr1 mutant, CHP treated, t=12 min, biological replicate 3


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Gpx1 mutant, Control, t=6 min, biological replicate 1


title: Stamen of stage 2-rep 3

description: Dissected from spikelets

source_name: Stamen of stage 2-rep 3


title: Stamen of stage 2-rep 2

description: Dissected from spikelets

source_name: Stamen of stage 2-rep 2


title: The just-expanded leaf-rep 3

description: The third just-expanded leaf

source_name: The just-expanded leaf-rep 3

value: leaf


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Gpx1 mutant, Control, t=12 min, biological replicate 1


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 3

source_name: Yeast, Glr1 mutant, CHP treated, t=6 min, biological replicate 3


title: The just-expanded leaf-rep 1

description: The third just-expanded leaf

source_name: The just-expanded leaf-rep 1


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 2

source_name: Yeast, Glr1 mutant, CHP treated, t=6 min, biological replicate 2


title: Neuroblastoma patient tissue-20

city: Taipei

first: Pei-Yi

last: Wu

address: 1 Roosevelt Rd., Sec. 4

country: Taiwan

institute: National Taiwan University

hyb_protocol: 2 μg of Cy-labeled cRNA was fragmented to an average size of approximately 50–100 nucleotides by incubation with a fragmentation buffer at 60°C for 30 min. Correspondingly fragmented labeled cRNA was then pooled and hybridized to Human 1A (version 2) oligo microarray (Agilent Technologies) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Scanned images were analyzed using Feature extraction 8.1 software (Agilent Technologies), image analysis and normalization software was used to quantify signal and background intensity for each feature, substantially normalizing the data by rank-consistency-filtering LOWESS method.

source_name: Neuroblastoma patient tissue

label_protocol: Total RNA (0.5 μg) was amplified by a low RNA input fluor linear amp kit (Agilent Technologies, USA), and labeled with Cy3 or Cy5 (CyDye, PerkinElmer) during the in vitro transcription process. Tumor RNA was labeled by Cy5 and RNA from Universal Human Reference RNA was labeled by Cy3.

value: Neuroblastoma tissue

tag: mycn status

value: Amplified

source_name: Universal Human Reference RNA

tag: sample type

value: Universal Human Reference RNA


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 3

source_name: Yeast, Glr1 mutant, CHP treated, t=3 min, biological replicate 3

value: CHP

value: t=3 min


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 3

source_name: Yeast, Glr1 mutant, CHP treated, t=0 min, biological replicate 3

value: Mid-exponental phase


title: The just-expanded leaf-rep 2

description: The third just-expanded leaf

source_name: The just-expanded leaf-rep 2


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 2

source_name: Yeast, Glr1 mutant, CHP treated, t=12 min, biological replicate 2

value: t=12 min


title: Neuroblastoma patient tissue-13


title: Neuroblastoma patient tissue-18


title: Neuroblastoma patient tissue-14


title: Neuroblastoma patient tissue-17


title: Neuroblastoma patient tissue-12


title: Neuroblastoma patient tissue-16


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 2

source_name: Yeast, Glr1 mutant, CHP treated, t=20 min, biological replicate 2


title: Neuroblastoma patient tissue-19


title: Neuroblastoma patient tissue-15


title: Neuroblastoma patient tissue-10

value: Normal


description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 1

source_name: Yeast, Glr1 mutant, CHP treated, t=12 min, biological replicate 1


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Glr1 mutant, Control, t=20 min, biological replicate 3

value: t=20 min


description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 1

source_name: Yeast, Glr1 mutant, CHP treated, t=20 min, biological replicate 1


title: Neuroblastoma patient tissue-11


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 1

source_name: Yeast, Glr1 mutant, CHP treated, t=0 min, biological replicate 1

value: t=0 min


description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 1

source_name: Yeast, Glr1 mutant, CHP treated, t=6 min, biological replicate 1

value: t=6 min


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Glr1 mutant, Control, t=12 min, biological replicate 3

value: Control


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 2

source_name: Yeast, Glr1 mutant, CHP treated, t=3 min, biological replicate 2


description: Culture to be treated with CHP 0.19mM, collected at t=0 min (immediately before adding CHP), biological replicate 2

source_name: Yeast, Glr1 mutant, CHP treated, t=0 min, biological replicate 2


title: Neuroblastoma patient tissue-8


title: Neuroblastoma patient tissue-3


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Glr1 mutant, Control, t=6 min, biological replicate 3


title: Neuroblastoma patient tissue-4


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Glr1 mutant, Control, t=3 min, biological replicate 3


title: Neuroblastoma patient tissue-9

source_name: Neuroblastoma patient tissue


title: Neuroblastoma patient tissue-5

source_name: Universal Human Reference RNA


title: Neuroblastoma patient tissue-6


title: Neuroblastoma patient tissue-1


title: Neuroblastoma patient tissue-7


description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 1

source_name: Yeast, Glr1 mutant, CHP treated, t=3 min, biological replicate 1


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 3

source_name: Yeast, Glr1 mutant, Control, t=0 min, biological replicate 3


title: Neuroblastoma patient tissue-2


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Glr1 mutant, Control, t=20 min, biological replicate 2


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Glr1 mutant, Control, t=12 min, biological replicate 2


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Glr1 mutant, Control, t=6 min, biological replicate 2


description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Glr1 mutant, Control, t=6 min, biological replicate 1


title: FA_E3

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description: Exp3: 6297001018_B

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with JMP/Genomics after dropping probes with detection p-value greater than 0.1 in all arrays.

source_name: FA

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

growth_protocol: Murine peritoneal macrophages, harvested 4 or 5 days after injecting 1.0 ml 3% Brewer’s thioglycollate (Beckton Dickenson/BBL) i.p., were allowed to adhere to plastic wells for 4-6 hours in complete RPMI (52).   The cells were then washed twice with PBS and cultured further in DMEM without phenol red (Sigma D5030)  that contained 0.5% low endotoxin fetal bovine serum (Hyclone), 1 g/L (5.5 mM) glucose, 44 mM NaHCO3, 1 mM sodium pyruvate, 2 mM L-glutamine, 100 U/ml penicillin G, and 100 µg/ml streptomycin (“cDMEM”).

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

treatment_protocol: Control and fatty acid-loaded macrophages (2 x 10e6/well) were treated with LPS  (10 ng/ml) or vehicle for 24 hrs prior to extraction of the RNA as described above.

tag: cell type

value: cultured peritoneal macrophages


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Glr1 mutant, Control, t=0 min, biological replicate 2


description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Glr1 mutant, Control, t=20 min, biological replicate 1


description: Control (untreated culture), collected at t=0 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Glr1 mutant, Control, t=0 min, biological replicate 1


title: FA+LPS_E3

description: Exp3: 6297001018_D

source_name: FA+LPS


description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Glr1 mutant, Control, t=12 min, biological replicate 1


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 1

source_name: Yeast, Glr1 mutant, Control, t=3 min, biological replicate 1


description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 2

source_name: Yeast, Glr1 mutant, Control, t=3 min, biological replicate 2


title: FA+LPS_E2

description: Exp2: 6297001015_F


title: Unstim_E3

description: Exp3: 6297001018_A

source_name: Unstim


title: LPS_E3

description: Exp3: 6297001018_C

source_name: LPS


title: FA_E2

description: Exp2: 6297001015_D


title: Unstim_E4

description: Exp4: 6297001018_E


title: LPS_E2

description: Exp2: 6297001015_E


title: FA_E4

description: Exp4: 6297001014_F


title: ear BALBc_PSG_48h_rep4

city: London

first: Emilie

middle: De La Llave

last: Giraud

address: Keppel Street

department: IID

institute: London School of Hygiene and Tropical Medicine

description: gene expression data from PSG48 ears

hyb_protocol: Affymetrix EukGE-WS2v5 Hybridization

scan_protocol: Standard Affymetrix protocol

data_processing: Data processing, background correction, normalization and signal quantification were carried out with Robust Multiarray Analysis (RMA) algorithm using all samples. Local pooled error (LPE) tests were performed to identify significant differences in gene expression between L. mexicana-inoculated ears and L. mexicana with PSG inoculated ears.  Benjamini-Hochberg (BH) multiple-test correction was applied to control for the number of false positives with an adjusted 5% statistical significance threshold.  We used RMA algorithm, LPE tests and BH multiple-test correction.

source_name: ear + M379 + PSG 48h

growth_protocol: Colony reared female Lu. longipalpis (Jacobina strain) were infected with L. mexicana (MNYC/BZ/62/M379) amastigotes freshly isolated from BALB/c rump lesions . PSG was dissected from 7 days old fly infections and sterilized through 0.22 µm pore syringe filters. Promastigote developmental forms of L. mexicana were grown until Log phase in supplemented M199 medium pH 7.2 and then passaged into Grace's insect culture medium pH 5.5 to reach stationary phase at 26°C. One thousand metacyclic promastigotes in Dulbecco’s phosphate buffered saline (PBS) were injected intradermally in ear dermis into 6–8-week old female BALB/c mice, with or without 1 µg L. mexicana PSG.

extract_protocol: Total RNA extraction directly from entire ears (RNeasy+ Mini-Kit, Qiagen), RNA quality control and concentration were determined using the NanoDrop ND-1000 microspectrophotometer. RNA integrity was assessed using the Agilent-2100 Bioanalyzer (RNA Integrity Numbers ≥ 9/10).

treatment_protocol: At t=0 Leismania mexicana and PSG were inoculated into mouse ears in a final volume of 190 nL (qsp PBS). At t=6h, 24h and 48h, ears were collected and processed for RNA extraction.

value: BALB/c

value: ear

tag: time post inoculation

value: PSG +


title: FA+LPS_E4

description: Exp4: 6297001015_B


title: ear BALBc_MT_48h_rep2

description: gene expression data from MT48 ears

value: PSG -


title: LPS_E4

description: Exp4: 6297001015_A


title: FA+LPS_E1

description: Exp1: 6297001014_D


title: ear BALBc_MT_48h_rep1

description: gene expression data from MT48 ears


title: ear BALBc_PSG_48h_rep2

description: gene expression data from PSG48 ears


title: ear BALBc_MT_24h_rep1

description: gene expression data from MT24 ears


title: ear BALBc_PSG_48h_rep3

description: gene expression data from PSG48 ears


title: Unstim_E1

description: Exp1: 6297001014_A


title: ear BALBc_PSG_24h_rep3

description: gene expression data from PSG24 ears

source_name: ear + M379 + PSG 24h


title: ear BALBc_MT_24h_rep2

description: gene expression data from MT24 ears


title: ear BALBc_MT_6h_rep2

description: gene expression data from MT6 ears

source_name: ear + M379 6h


title: LPS_E1

description: Exp1: 6297001014_C


title: ear BALBc_MT_24h_rep3

description: gene expression data from MT24 ears


title: ear BALBc_PSG_48h_rep1

description: gene expression data from PSG48 ears


title: ear BALBc_PSG_24h_rep2

description: gene expression data from PSG24 ears


title: Clone_Dog-3_DyeSwap

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

institute: Catholic University of Korea

hyb_protocol: Each dye-labeled DNA was purified and mixed with hybridization reagents, applied on the array and incubated for 48 hours at 42ºC in a MAUI hybridization machine (BioMicro). After hybridization, slides were washed sequentially.

scan_protocol: The arrays were scanned using GenePix 4000B scanner (Axon Instruments)

data_processing: Image separation, signal intensity extraction, and normalization were performed using the NimbleScan software version 2.5 (Roche)

organism: Canis lupus familiaris

source_name: Nuclear_Donor blood

label_protocol: 1 µg of genomic DNA were labeled with fluorescent dye at 37°C for 2 hours. BioPrime aCGH labeling system (Invitrogen) was used for labeling step.

extract_protocol: genomic DNA extracted using DNeasy Blood & Tissue Kit (Qiagen) following manufacturer's instructions.

tag: breed

value: Labrador Retriever

tag: gender

value: Male

source_name: Clone_Dog-3 blood


title: E. coli galT mutant with galactose

first: Andrei

middle: Nikolai

last: Trostel

state: Maryland

address: 9000 Rockville Pike, Building 37, Room 5138

department: Laboratory of Molecular Biology

institute: National Institutes of Health

hyb_protocol: Labeled cDNA fragments (3 ug) were hybridized at 45 °C at 60 rpm for 16 h to the tiling array chips (coli_Tab520346F) purchased from Affymetrix. The chips were then washed with wash buffer A: nonstringent wash buffer (6X SSPE, 0.01% Tween-20); wash buffer B: (100 mM Mes, 0.1M [Na+], 0.01% Tween-20) and stained with streptavidin phycoerythrin (Invitrogen, S-866) and antistreptavidin goat antibody biotinylated (Vector Laboratories, BA-0500) on a Genechip Fluidics Station 450 (Affymetrix) according to washing and staining protocol (ProkGE-WS2 450).

scan_protocol: Arrays were scanned on an GeneChip© Scanner 3000 per manufacturer’s protocol.

data_processing:
The program used to generate the bed/bar files is “Affymetrix Tiling Analysis Software.” Standardized signals, for each probe in the arrays, were generated using the MAT software (Johnson WE et al. 2006), which provides a model-based, sequence-specific, background correction for each sample. A gene-specific score was then calculated for each gene by averaging all MAT scores (natural log) for all probes under the annotated gene coordinates. Gene annotation was from the ASAP database (Glasner JD et al. 2003) at the University of Wisconsin-Madison, for E. coli K-12 MG1655 version m56. Differences of two log scale values in the absence or presence of D-galactose were calculated in galT mutant cells.  Finally, the transcriptome results (log scale values) with or without D-galactose were compared graphically [References: Johnson WE, et al. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 103:12457–12462; Glasner JD, et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 31:147–151]
The TAS software provides analysis capabilities specifically for the GeneChip® Tiling Arrays. TAS analyzes feature intensity data stored in GCOS output .CEL files and produces:
Signal and p-values for each genomic position interrogated.
Computation of genomic intervals based on computed signal and p-values
Computation of summary statistics
Visualizations for assessing the quality of the array data

organism: Escherichia coli

source_name: with D-galactose

label_protocol: Fragmented cDNA was then 3' termini biotin-labeled using the GeneChip DNA labeling reagent, 900542 (Affymetrix) and 60 U of terminal deoxynucleotidyl transferase, M1875 (Promega) at 37 °C for 1 h. The labeling reaction was then stopped by the addition of 0.5M EDTA.

growth_protocol: E. coli galT mutant cells were cultivated in 125-mL corning flasks containing 30 mL of M63 minimal medium plus glycerol (final 0.3%) at 37 °C.

extract_protocol: Cells were then placed on ice and RNAprotect™ bacteria reagent (Qiagen) was added to stabilize the RNA. Total RNAs of cells were purified by RNeasy mini kit (Qiagen). Isolated RNA (10 ug) was used for random primer cDNA synthesis using SuperScript II reverse transcriptase, 18064–071 (Invitrogen). The reaction mixture was then subsequently treated with 1 N NaOH to degrade any remaining RNA and treated with 1 N HCl to neutralize the NaOH. Synthesized cDNA was then purified using MiniElute PCR purification columns, 28004 (Qiagen). Purified cDNA (3 ug) was fragmented to between 50 and 200 bps by 0.6 U/ g of DNase I, 27–0514-01 (Amersham Biosciences) for 10 min at 37 °C in 1  One-Phor-All buffer, 27–0901-02 (Amersham Biosciences). Heat inactivation of the DNase I enzyme was performed at 98 °C for 10 min.

treatment_protocol: At OD600 of 0.5, cell cultures were separated into two flasks. D-galactose (final 0.3%) was added to one and cells were grown for 1.5 h further.

tag: genotype/variation

value: galT mutant


title: Clone_Dog-6

source_name: Clone_Dog-6 blood


title: E. coli galT mutant without galactose

source_name: without D-galactose


title: Clone_Dog-7

source_name: Clone_Dog-7 blood


title: ear BALBc_PSG_6h_rep3

description: gene expression data from PSG6 ears

source_name: ear + M379 + PSG 6h

tag: treatment


title: FA_E1

description: Exp1: 6297001014_B

source_name: FA


title: ear BALBc_MT_6h_rep1

description: gene expression data from MT6 ears


title: ear BALBc_PSG_24h_rep1

description: gene expression data from PSG24 ears


title: Clone_Dog-4

source_name: Clone_Dog-4 blood


title: Clone_Dog-2

source_name: Clone_Dog-2 blood


title: Myostatin KO

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: tibialis anterior muscle, KO

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Mice were housed under SPF conditions

extract_protocol: RNA samples were extracted from tissues using miRNeasy Mini kit (Qiagen).

treatment_protocol: Muscles were surgically isolated from animals and frozen in liquied nitrogen. Frozen tissues were physically crushed, and used for total RNA  isolation.

value: male

value: Myostatin KO

value: tibialis anterior muscle


title: Gut.CD4+RO+TCRab+RH123-#1

city: Cambridge

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

description: FACS-sorted CD3+ CD4+ CD45RO+ Rh123- from gut

hyb_protocol: The labeled fragmented DNA was hybridized to the Gene Arrays 1.0ST for 16-18 hours in GeneChip Hybridization oven 640 at 45 °C with rotation (60 rpm).  The hybridized samples were washed and stained using Affymetrix fluidics station 450. The first stain with streptavidin-R-phycoerythrin (SAPE) was followed by signal amplification using a biotinilated goat anti-streptavidin antibody and another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix).

scan_protocol: Standard Affymetrix protocol on an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix).

data_processing: Samples were RMA normalized using Affymetrix Power Tools (gcbg background correction, quantile normalization, median polish) on the annotated set of probesets. Unannotated probesets were removed prior to normalization (see supplemental .mps file)

label_protocol: biotin

growth_protocol: all FACS-sorted cells were harvested directly ex vivo, and used for RNA isolation without further in vitro manipulation

extract_protocol: Total RNA was extracted using the Qiagen RNeasy with on-column DNase treatment method.


title: ear BALBc_PSG_6h_rep1

description: gene expression data from PSG6 ears


title: Gut.CD4+RO+TCRab+RH123+#1

description: FACS-sorted CD3+ CD4+ CD45RO+ Rh123+ from gut


title: Clone_Dog-3


title: B.CD4+RO+TCRab+RH123-#1

description: FACS-sorted CD3+ CD4+ CD45RO+ Rh123- from PBMC


title: Wild-Type

source_name: tibialis anterior muscle, WT

value: Wild-Type


title: B.CD4+RO+TCRab+RH123+#1

description: FACS-sorted CD3+ CD4+ CD45RO+ Rh123+ from PBMC


title: Clone_Dog-5

source_name: Clone_Dog-5 blood


title: ear BALBc_PSG_6h_rep2

description: gene expression data from PSG6 ears


title: Clone_Dog-1

source_name: Clone_Dog-1 blood


title: Clone_Dog-7

hyb_protocol: Each fragmented DNA was purified and mixed with hybridization reagents, applied on the BeadChip and incubated for 16 hours. After hybridization, single-base extension and allele-specific staining was performed on a Teflow chamber rack system sequentially.

scan_protocol: The BeadChip were scanned using Illumina BeadStation 500G array scanner

data_processing: Intensity files were processed by GenomeStudio V2011.1, GT module 1.9.4  with default analysis settings. Each SNP is analyzed independently to cluster and identify genotypes. Genotype calls are generated by comparing experimental data with those in the supplied cluster file.

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction. After incubation the amplified DNA was fragmented with fragmentation mix, precipitated with isopropanol and precipitation mix and resuspended in hybridization buffer.


title: Clone_Dog-2


title: Clone_Dog-3


title: THP-1 treated with PBS

city: Setagaya-ku

first: Kosuke

last: Tanegashima

state: Tokyo

address: 2-1-6 Kamikitazawa

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: 0.60 ug of Cy3-labelled 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, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression Microarray 8x60K Ver.2.0 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), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: THP-1, PBS treated 60 min

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling 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-2000 Spectrophotometer.

extract_protocol: Cells were dissoluved in TRIZOL, and total RNA were extracted with standerd protcol. RNA was further purified with Rnasy kit.

tag: cell line

value: PBS treated 60 min


title: Nuclear_Donor

source_name: Boxer blood

value: Boxer

value: Female


title: Leaf_jasmonate_rep3

status: Public on Dec 16 2013

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

hyb_protocol: Four micrograms of labeled aRNA was fragmented and hybridized to a Grape Array 1.2 (Combimatrix) in a hybridization cap (Combimatrix) in an oven containing the CombiMatrix 32 CustomArrayTM Rotisserie (Combimatrix) according to the manufacturer’s protocols.

scan_protocol: Microarrays were scanned using ScannArray 4000 XL (PerkinElmer Life Sciences) and image data were collected with the ScanArray Express software.

data_processing: Feature data were extracted with the Microarray Imager software (Combimatrix) and were normalized by the application of a global median normalization strategy.

organism: Vitis vinifera

source_name: Leaf, jasmonate, replicate 3

label_protocol: Labeled aRNA was produced from 1 µg of total RNA using AminoAllyl MessageAmpTM aRNA (Ambion).

growth_protocol: The Vitis vinifera cv Marselan plants, susceptible to Plasmopara viticola, were obtained from herbaceous cuttings placed in individual pots (8 x 8 cm) containing a mixture of peat, sand and perlite (4/0.5/1, v/v/v), and grown in a glasshouse at a temperature of 24/18°C (day/night) with a photoperiod of 16h light and at a relative humidity (RH) of around 50% until they developed 6 leaves. Plants were watered daily and fertilized once a week. Leaf material was taken from the 2nd and 3rd rank leaves.

extract_protocol: Total RNA extraction was performed as described previously by Reid K.E. et al. (2006) with a slight modification: RNA were selectively precipitate with 0.3 volume of 10 M LiCl.

treatment_protocol: PS3 and laminarin were provided by Goëmar SA and were prepared in 0.1% surfactant (confidential) in order to improve its penetration. Equal volume of 0.1% surfactant was used as control in  plant experiments. For plant treatments, solutions were applied to both upper and lower leaf surfaces until the point of run-off using a manual sprayer. All pharmacological compounds were purchased from Sigma-Aldrich. All of the chemicals were dissolved in dimethylsulfoxide (DMSO). Equivalent volumes of DMSO were added to control plants to ensure they did not interfere with the experiments. When used, final DMSO concentration did not exceed 0.25% (v/v).

value: jasmonate

value: Second and third fully expanded leaves from the apex


title: THP-1 treated with 100 nM CXCL14

source_name: THP-1, 100 nM CXCL14 treated 60 min

value: 100 nM CXCL14 treated 60 min


title: Clone_Dog-6


title: Clone_Dog-5


title: Leaf_salicylate_rep3

source_name: Leaf, salicylate, replicate 3

value: salicylate


title: Leaf_laminarin_rep2

source_name: Leaf, laminarin, replicate 2

value: laminarin


title: Nuclear_Donor

source_name: Nuclear_Donor blood


title: Leaf_dmso_rep3

source_name: Leaf, DMSO, replicate 3

value: DMSO


title: Leaf_laminarin_rep1

source_name: Leaf, laminarin, replicate 1


title: Leaf_dmso_rep1

source_name: Leaf, DMSO, replicate 1


title: Leaf_dmso_rep2

source_name: Leaf, DMSO, replicate 2


title: Leaf_ps3_rep3

source_name: Leaf, PS3, replicate 3


title: Clone_Dog-4

source_name: Clone_Dog-4 blood


title: Leaf_salicylate_rep1

source_name: Leaf, salicylate, replicate 1


title: Leaf_jasmonate_rep1

source_name: Leaf, jasmonate, replicate 1


title: Leaf_salicylate_rep2

source_name: Leaf, salicylate, replicate 2


title: Leaf_ps3_rep1

source_name: Leaf, PS3, replicate 1


title: Leaf_ps3_rep2

source_name: Leaf, PS3, replicate 2


title: Leaf_laminarin_rep3

source_name: Leaf, laminarin, replicate 3


title: Leaf_adjuvant_rep3

source_name: Leaf, adjuvant, replicate 3

value: adjuvant


title: Clone_Dog-1

source_name: Clone_Dog-1 blood

value: Labrador Retriever


title: MARC_Nsp11_rep1

city: Philidelphia

first: Yan

last: Sun

address: 380 South University Ave

department: Pathobiology

institute: University of Pennsylvania

description: kidney epithelial cells expressing viral Nsp11

hyb_protocol: Affymetrix P/N 702808 Revision 4 was followed to hybridize cocktail containing ~1.8 micrograms of labeled cDNA prepared with Affymetrix Hybridization Wash and Stain Kit P/N 900720 for 16 hours in oven model 640 or 645.

scan_protocol: Affymetrix protocol P/N 702731 Revision 3 was followed for washing, staining, and scanning utilizing Affymetrix GeneChip Command Console version 1.0, fluidics station 450/protocol FS450_0007 with reagent Kit P/N 900720 referenced above, and scanner model 3000 7G Plus.

data_processing: Data were processed in R (v 2.14.1) using the oligo package (v 1.18.1). Probe-level data were background corrected, normalized and summarized at the transcriptclusterid (gene) level using the RMA algorithm.

organism: Chlorocebus aethiops

label_protocol: Ambion P/N 4425209 Revison C Cycle 1 protocol was used to process 200 nanograms of total RNA with the Ambion Whole Transcript Expression Kit P/N 4411973 and Affymetrix Eukaryotic Poly-A RNA Control Kit P/N 900433.  15 micrograms of the resulting cRNA were then processed per Cycle 2.  Affymetrix protocol P/N 702808 Revision 4 was followed using Affymetrix WT Terminal Labeling Kit P/N 900670 to fragment 5.5 micrograms of the resulting cDNA, and a portion was biotin labeled.

growth_protocol: Maintained in Dulbecco’s modified Eagle’s medium (DMEM; Mediatech Inc, Manassas, VA) containing 10% heat-inactivated fetal bovine serum (FBS; Hyclone, Logan, UT) in a humidified incubator with 5% CO2 at 37 °C

extract_protocol: MARC-145 and MARC-Nsp11 cells were seeded one day prior to experiments and total cellular RNAs were extracted using Trizol (Invitrogen) and purified by RNeasy mini kit (Qiagen).

treatment_protocol: Used G418 in the DMEM for MARC-Nsp11 cells to select single  G418 resistant cell clone and then expanded this cell clone

value: expressing viral Nsp11

tag: batch

value: kidney epithelial cell line

tag: origin

value: subclone of MA-104


title: MARC_Nsp11_rep2

source_name: kidney epithelial cells expressing viral Nsp11


title: MARC_WT_rep4

description: wild-type kidney epithelial cells

source_name: wild-type kidney epithelial cells

value: wild-type


title: Leaf_adjuvant_rep1

source_name: Leaf, adjuvant, replicate 1


title: MARC_WT_rep1

description: wild-type kidney epithelial cells


title: MARC_WT_rep3

description: wild-type kidney epithelial cells


title: Leaf_adjuvant_rep2

source_name: Leaf, adjuvant, replicate 2


title: MARC_WT_rep2

description: wild-type kidney epithelial cells


title: lacZ positive, biological replicate 2

city: Epalinges

first: Werner

last: Held

address: Chemin des Boveresses 155

department: Ludwig Center for Cancer Research

country: Switzerland

institute: University of Lausanne

description:
P14 conductin LacZ
lacZpos571_7

hyb_protocol: Affymetrix mouse gene 1.0ST arrays (Affymetrix, Santa Clara, CA, USA) were hybridized with 2.3 μg of fragmented target at 45°C for 16 hours, washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: Expression data was background corrected, normalized and summarized on probe set level using the RMA algorithm implemented in Affymetrix Expression Console version 1.1.

source_name: Day 8 after LCMV WE infection

label_protocol: For each sample, 100 ng of total RNA was amplified using the Ambion® WT Expression Kit (4411973, Life Technologies) kit. 5.5 μg of the cDNA was fragmented and labeled with GeneChip® WT Terminal Labeling kit (901525, Affymetrix).

extract_protocol: Trizol (Invitrogen) extraction of total RNA and RNA clean up using Rneasy mini kit (Qiagen) were performed according to the manufacturers instructions.

treatment_protocol: P14 Conductin LacZ CD8 T cells (CD45.2) were transferred in CD45.1.2 recipient mice. The day after, recipients were infected with 200pfu LCMV WE. At day 8 after infection, cells from spleen and lymph nodes were harvested, magnetically enriched for CD8 T cells, loaded with a beta-galactosidase substrate (FDG) and sorted as 7AAD negative CD45.1 negative, beta-galactosidase positive or negative cells.

tag: strain

value: spleen + lymph nodes

value: effector CD8 T cells

value: lacZ positive (Wnt+)


title: lacZ negative, biological replicate 4

description:
P14 conductin LacZ
lacZneg651b_6

tag: tissue

value: lacZ negative (Wnt-)


title: lacZ negative, biological replicate 1

description:
P14 conductin LacZ
lacZneg543_2


title: lacZ positive, biological replicate 3

description:
P14 conductin LacZ
lacZpos648_3


title: lacZ positive, biological replicate 1

description:
P14 conductin LacZ
lacZpos543_1


title: lacZ negative, biological replicate 3

description:
P14 conductin LacZ
lacZneg648_4


title: lacZ positive, biological replicate 4

description:
P14 conductin LacZ
lacZpos651b_5


title: sar1a [TPB2006082917Aaa]

first: Carol

last: Shoulders

address: Charterhouse Square

department: Centre for Endocrinology

institute: QMUL

description: Gene expression data from McArdle RH7777 rat hepatoma cell line overexpressing human SAR1A

hyb_protocol: Following fragmentation, 15μg biotinylated cRNA was hybridized to GeneChip Rat Genome 230 2.0 arrays (Affymetrix) for 16 hr at 45°C in an Affymetrix Hybridization Oven 640. GeneChips were washed and stained in an Affymetrix Fluidics 450 Station according to standard Affymetrix protocols.

scan_protocol: Genechips were scanned with an Affymetrix Scanner 3000.

data_processing: Data analyses were performed through the Comprehensive R-based Microarray Analysis web service (CARMAweb: https:// CARMAweb.genome.tugraz.at /CARMA/). Raw intensity values were normalized using the Loess normalization, Affymetrix MAS 5 and summarization algorithms. Differences in probe-set values were determined on the normalized data using the Significance Analysis of Microarray (SAM) algorithm at specified False Discovery Rates. Cut-off values for significance determined by a tuning parameter, the delta value. The number of delta values was set at 50 and a Benjamini & Hochberg multiple testing correction was applied.

organism: Rattus norvegicus

source_name: McArdle RH7777 cell line overexpressing Sar1A

label_protocol: cDNA was synthesized from total RNA using the One-Cycle Eukaryotic Target Labeling Assay Kit (Invitrogen) (Affymetrix https://www.affymetrix.com/support/downloads/manuals/expression_s21_manual.pdf). Double-stranded cDNA was purified with the kit GeneChip® Sample Cleanup Module (Affymetrix). Biotinlabelled cRNA was prepared using the BioArray High Yield RNA Transcript Labelling Kit (Enzo) and purified with the IVT cRNA GeneChip® Sample Cleanup Module.

growth_protocol: Cells were cultured in complete DMEM containing Blasticidin (10μg/ml; Sigma) and Zeocin (250μg/ml; Invitrogen). Twenty four hours prior to harvesting, 1μg/ml of tetracycline was added to the culture media.

extract_protocol: Total RNA was extracted with the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: transgene status

value: overexpressing human SAR1A


title: sar1bh79g 2 [TPB2006082913Aaa]

description: Gene expression data from McArdle RH7777 rat hepatoma cell line overexpressing consitutively active mutant human SAR1B

source_name: McArdle RH7777 cell line overexpressing Sar1B:H79G

value: overexpressing consitutively active mutant version of human SAR1B, Sar1B:H79G


title: sar1a [TPB2006082918Aaa]


title: sar1bh79g 2 [TPB2006082916Aaa]


title: sar1bh79g 2 [TPB2006082914Aaa]


title: sar1bh79g 1 [TPB2006082912Aaa]


title: Leaf_jasmonate_rep2

source_name: Leaf, jasmonate, replicate 2

value: jasmonate

value: Second and third fully expanded leaves from the apex


title: sar1a [TPB2006082920Aaa]


title: sar1a [TPB2006082919Aaa]


title: lacZ negative, biological replicate 2

description:
P14 conductin LacZ
lacZneg571_8


title: sar1bh79g 1 [TPB2006082911Aaa]


title: sar1bh79g 2 [TPB2006082915Aaa]


title: sar1bh79g 1 [TPB2006082910Aaa]


title: sar1b 2 [TPB2006082905Aaa]

description: Gene expression data from McArdle RH7777 rat hepatoma cell line overexpressing human SAR1B

source_name: McArdle RH7777 cell line overexpressing Sar1B

value: overexpressing human SAR1B


title: Murine HGSC, T5433

city: Boston

first: Sunita

middle: R

last: Setlur

address: 221 Longwood Avenue

institute: Brigham and Women's Hospital

description: Raw data file - " T5433_Tube_US85003610_252741410697_S01_CGH_105_Jan09",  linked to the processed FASST2 segmentation data file - "T5433_Tube_US85003610_252741410697_regions121012", from Nexus Software

hyb_protocol: Test and reference DNA were combined and hybridized to the Agilent 1M mouse catalog array for 40 hours at 65°C. The array slides were then washed and scanned.

scan_protocol: Arrays were scanned using the Agilent G2565AA scanner

data_processing: Probes signal intensities were obtained using the feature extraction software from Agilent for further analysis. In Feature Extraction software, for CGH data, linear normalization method is used.  Analysis was performed with Nexus software (BioDiscovery), for identification of copy number alterations. FASST2 segmentation algorithm was applied by setting the following parameters. A minimum number of 5 probes per segment were used to call a copy number aberration with significance threshold of 5x10-6. We used log ratio cut offs of ±0.3 to call one copy gain/loss and ±0.7 to call high gain/ homozygous loss.

source_name: Tumor

label_protocol: Briefly, reference and test DNA were first fragmented using a heat block at 95°C for 5 minutes and then labeled using Cyanine3 / Cyanine5 fluorescence labeled nucleotides respectively, according to the BioPrime Array CGH Genomic Labeling protocol (Invitrogen).Labeled DNA was purified using Amicon® Ultra-0.5 30k purification columns (Millipore).

extract_protocol: Mouse genomic DNA was isolated using Gentra Puregene Cell Kit (Qiagen) according to the manufacturer’s instructions

tag: genotype

source_name: Normal mouse fallopian tubes

tag: reference sample

value: Pooled DNA from normal fallopian tube of three mice


title: Murine HGSC, T5117

description: Raw data file - "T5117_US85003610_252741410609_S01_CGH_105_Jan09", linked to the processed FASST2 segmentation data file - "T5117_US85003610_252741410609_regions121012", from Nexus software


title: sar1b 2 [TPB2006082908Aaa]


title: control cell line 2 [ATB2006071815Aaa]

description: Gene expression data from McArdle RH7777 rat hepatoma cell line

source_name: McArdle RH7777 cell line

value: control


title: sar1b 2 [TPB2006082907Aaa]


title: sar1b 2 [TPB2006082906Aaa]


title: control cell line 2 [ATB2006071814Aaa]


title: sar1bh79g 1 [TPB2006082909Aaa]


title: Murine HGSC, T6096

description: Raw data file - "T6096_US85003610_252741410927_S01_CGH_105_Jan09", linked to the processed FASST2 segmentation data file - ""T6096_US85003610_252741410927_regions121012"  from Nexus software


title: sar1b 1 [TPB2006082902Aaa]


title: sar1b 1 [TPB2006082901Aaa]


title: sar1b 1 [TPB2006082904Aaa]


title: Spatial Aged-Unimpaired 8

city: Baltimore

first: Carlo

last: Colantuoni

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

hyb_protocol: as per manufacture's recommendation

scan_protocol: as per manufacture's recommendation

data_processing: Using the the R/Bioconductor system data were normalized and summarized using the affy and gcRMA packages. One array was dropped as an outlier. A known batch effect was removed by subtracting the average batch deviation from the mean on an individual probe basis. An empirical low expression cutoff of 5 units was used to remove noise from the data used here, leaving 16204 of the original 31099 probe sets in the analysis.

source_name: Spatial Aged-Unimpaired

label_protocol: as per manufacture's recommendation

growth_protocol: Aged rats, microdissected CA3 region of hippocampus

extract_protocol: Total RNA was extracted by homogenization in TRIzol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.

treatment_protocol: Spatial or Non-spatial task

value: CA3 Hippocampus


title: control cell line 1 [ATB2006071813Aaa]


title: Spatial Aged-Unimpaired 6


title: control cell line 2 [ATB2006071816Aaa]


title: control cell line 1 [ATB2006071812Aaa]


title: Spatial Aged-Unimpaired 7


title: Spatial Aged-Unimpaired 5


title: Spatial Aged-Impaired 7

source_name: Spatial Aged-Impaired


title: sar1b 1 [TPB2006082903Aaa]


title: Spatial Aged-Unimpaired 3


title: Non-spatial Aged-Unimpaired 8

source_name: Non-spatial Aged-Unimpaired


title: Non-spatial Aged-Unimpaired 6


title: Spatial Aged-Unimpaired 4


title: Non-spatial Aged-Unimpaired 7


title: Spatial Aged-Impaired 8


title: Spatial Aged-Impaired 4


title: Spatial Aged-Impaired 3


title: Spatial Aged-Unimpaired 2


title: Spatial Aged-Impaired 5


title: Spatial Aged-Unimpaired 1


title: Spatial Aged-Impaired 6


title: Non-spatial Aged-Unimpaired 4


title: Spatial Aged-Impaired 2


title: Non-spatial Aged-Unimpaired 3


title: Non-spatial Aged-Unimpaired 5


title: Spatial Aged-Impaired 1


title: Non-spatial Aged-Impaired 7

source_name: Non-spatial Aged-Impaired


title: Non-spatial Aged-Unimpaired 1


title: Non-spatial Aged-Impaired 4


title: Non-spatial Aged-Impaired 6


title: Non-spatial Aged-Unimpaired 2


title: Non-spatial Aged-Impaired 1


title: Patient W2 colon cancer tissue

city: suzhou

first: shouli

last: wang

address: renai road 199, suzhou industrial park

department: pathology

institute: soochow university school of medicine

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0)(Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal.

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: colon cancer tissue

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis. Please refer to “RNA_QC.pdf”

tag: patient id

value: Patient W2

tag: age

value: 64 years

value: Male

value: colon cancer

tag: tumor stage

value: III