title: 7512551022_R02C02


title: 7512551038_R04C01

status: Public on Apr 20 2018

type: genomic

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

country: China

institute: Fudan University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: minfi, R

label: not applicable

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions

tag: disease status

value: MS case

tag: gender

value: female

tag: age

tag: smoking status

value: never smoker

tag: tissue

value: peripheral blood


title: 7512551022_R03C02

value: Healthy control

value: ever smoker


title: 7512551022_R06C02


title: 7512551022_R01C02


title: 7512551022_R04C02

value: male


title: cl.413-transduced T cells treated with SGC0946, rep 1

type: RNA

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

description: A2/MART1 low-affinity TCR (cl.413)-transduced CD8+ T cells were cultured in the presence of SGC0946 and stimulated by the cognate antigen, rep 1

hyb_protocol: Samples were hybridized with Affymetrix Human Gene 2.0 ST array for 16-18 hr at 45°C.

scan_protocol: Affymetrix GeneChip Scanner 3000 (Scanner #4)

data_processing: Raw intensity files were processed using Affymetrix Expression Console (version 1.4.1). Processed using RMA algorithm.

label: biotin

molecule: total RNA

source_name: cl.413 TCR-transduced human CD8+ T cells treated with SGC0946, biological replicate #1

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate.

growth_protocol: Human CD8+ T cells were cultured in vitro (RPMI supplemented with 10% human AB serum, 100 IU/ml IL-2 and 10 ng/ml IL-15).

extract_protocol: RNA was collected from the stimulated T cells 24 hours later using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: CD8+ T cells were individually transduced with A2-MART127-35-specific high-affinity (DMF5) or low-affinity (cl.413) T cell receptor (TCR). TCR-transduced T cells were treated with SGC0946 or DMSO and further cultured for 7 days. After resting overnight in cytokine-free media, they were stimulated by artificial antigen presenting cells that express HLA-A2, CD80 and CD83 loaded with MART127-35 peptide.

tag: cell type

value: CD8+ T cells

tag: tcr gene

tag: chemical probe

tag: donor


title: DMF5-transduced T cells treated with SGC0946, rep 2

description: A2/MART1 high-affinity TCR (DMF5)-transduced CD8+ T cells were cultured in the presence of SGC0946 and stimulated by the cognate antigen, rep 2

source_name: DMF5 TCR-transduced human CD8+ T cells treated with SGC0946, biological replicate #2


title: DMF5-transduced T cells treated with SGC0946, rep 1

description: A2/MART1 high-affinity TCR (DMF5)-transduced CD8+ T cells were cultured in the presence of SGC0946 and stimulated by the cognate antigen, rep 1

source_name: DMF5 TCR-transduced human CD8+ T cells treated with SGC0946, biological replicate #1


title: 7512551022_R06C01


title: 7512551022_R05C02


title: DMF5-transduced T cells treated with DMSO, rep 1

description: A2/MART1 high-affinity TCR (DMF5)-transduced CD8+ T cells were cultured in the presence of control DMSO and stimulated by the cognate antigen, rep 1

source_name: DMF5 TCR-transduced human CD8+ T cells treated with DMSO, biological replicate #1

value: DMSO


title: DMF5-transduced T cells treated with DMSO, rep 2

description: A2/MART1 high-affinity TCR (DMF5)-transduced CD8+ T cells were cultured in the presence of control DMSO and stimulated by the cognate antigen, rep 2

source_name: DMF5 TCR-transduced human CD8+ T cells treated with DMSO, biological replicate #2


title: 7512551022_R05C01


title: DMF5-transduced T cells treated with DMSO, rep 3

description: A2/MART1 high-affinity TCR (DMF5)-transduced CD8+ T cells were cultured in the presence of control DMSO and stimulated by the cognate antigen, rep 3

source_name: DMF5 TCR-transduced human CD8+ T cells treated with DMSO, biological replicate #3


title: Day42naive_blood_rep4

city: York

first: Paul

last: Kaye

address: Wentworth way

country: United Kingdom

institute: University of York

hyb_protocol: Amplified RNA was then assayed using the SurePrint G3 mouse 8x60k microarray chip

scan_protocol: Samples were scanned using the agilent c surescan high resolution scanner

data_processing: Data was normalised using a 75th percentile shift method using GeneSpring software, version 9, agilent

organism: Mus musculus

source_name: Blood uninfected mouse at the same time point as 42 days post infection of other mice

label_protocol: standard Agilent protocol

extract_protocol: RNA was isolated from tissues and blood using the agilent low input quick amp labelling kit

treatment_protocol: 6-8 week old BALB/c mice were infected with 2 x10^7 amastigotes of LV9 strain

tag: strain

value: BALB/c

value: 6-8 weeks

tag: infected with

value: none (uninfected, naïve)

tag: time point

value: blood


title: Day42naive_blood_rep5

value: at the same time point as 42 days post infection of other mice


title: 7512551044_R05C01


title: Day42naive_blood_rep3


title: Day42naive_blood_rep1


title: 7512551022_R04C01


title: 7497398128_R06C01


title: Day42naive_blood_rep2


title: Day42infected_blood_rep5

source_name: Blood infected mouse 42 days post infection

value: 2 x10^7 amastigotes of LV9 strain

value: 42 days post infection


title: Day42infected_blood_rep4


title: 7497398128_R05C01


title: 7512551022_R01C01


title: 7512551022_R03C01


title: 7497398128_R01C01


title: Day42infected_blood_rep3


title: 7497398127_R05C02


title: 7497398128_R02C02


title: 7497398128_R04C01


title: Day42infected_blood_rep2


title: 7497398128_R02C01


title: 7497398127_R06C02


title: Day42infected_blood_rep1


title: 7497398128_R01C02


title: 7497398127_R03C02


title: 7497398128_R03C02


title: 7497398128_R03C01


title: Day36naive_blood_rep5

source_name: Blood uninfected mouse at the same time point as 36 days post infection of other mice


title: 7497398127_R01C02


title: 7497398127_R05C01


title: 7497398127_R06C01


title: 7497398127_R01C01


title: 7497398127_R02C02


title: 7497398127_R03C01


title: 7512551038_R01C01


title: 7497398127_R04C01


title: 7497398127_R04C02


title: 7497398123_R05C02


title: 7512551022_R02C01


title: 7497398127_R02C01


title: Day36naive_blood_rep4

value: at the same time point as 36 days post infection of other mice


title: Day36naive_blood_rep1


title: 7497398123_R04C02

value: MS case


title: Day36infected_blood_rep2

source_name: Blood infected mouse 36 days post infection

value: 36 days post infection


title: 7497398123_R06C02

value: female

value: never smoker


title: Day36infected_blood_rep4


title: 7497398123_R05C01

value: peripheral blood


title: Day36naive_blood_rep3


title: Day36infected_blood_rep5


title: Day36infected_blood_rep1


title: 7497398123_R04C01

value: ever smoker


title: Day36infected_blood_rep3


title: 7497398123_R03C01


title: 7497398123_R02C02


title: Day21infected_blood_rep3

source_name: Blood infected mouse 21 days post infection

value: 21 days post infection


title: Day21infected_blood_rep4


title: 7497398119_R04C02

value: Healthy control


title: 7497398119_R06C02


title: 7497398123_R01C01


title: 7497398123_R02C01


title: Day21infected_blood_rep2


title: 7497398123_R06C01


title: 7497398119_R01C02


title: 7497398123_R01C02

value: male


title: 7497398119_R02C02


title: 7497398119_R06C01


title: Day21infected_blood_rep1

value: BALB/c


title: 7497398119_R05C02


title: 7497398119_R05C01


title: Day17infected_blood_rep5

value: 6-8 weeks


title: Day17infected_blood_rep4

source_name: Blood infected mouse 17 days post infection

value: 17 days post infection


title: 7497398119_R03C01


title: Day17infected_blood_rep3

value: blood


title: Day17infected_blood_rep2


title: 7497398101_R06C02


title: 7497398101_R04C02


title: Day15infected_blood_rep5

source_name: Blood infected mouse 15 days post infection

value: 15 days post infection


title: 7497398119_R01C01


title: 7497398101_R01C02


title: Day17infected_blood_rep1

value: 2 x10^7 amastigotes of LV9 strain


title: 7497398101_R06C01


title: 7497398101_R05C02


title: Day15infected_blood_rep3


title: 7497398119_R02C01


title: 7497398101_R02C02


title: 7497398101_R04C01


title: 7497398101_R03C01


title: 7497398119_R03C02


title: 7497398101_R05C01


title: 7497398098_R02C02


title: Day15infected_blood_rep2


title: 3D-ATAC

type: SRA

city: los angeles

first: Matteo

last: Pellegrini

state: CA

address: 675 Charles E Young Drive S

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

library_source: genomic

data_processing:
For RNA-Seq, Tophat is used map all the reads back to genome with default parameters. Uniquely mapped reads were kept.
For RNA-Seq, Htseq-count software is used to calculate the number of reads falling into reference genes.
For ATAC-Seq, bowtie is used map all the reads back to genome, allowing no more than 2 mismatches. Uniquely mapped reads were kept.
For ATAC-Seq, MACS2 software is used to perform the data normalization and peak calling.
Not applicable
Genome_build: mm10
Supplementary_files_format_and_content: txt and bedgraph

source_name: cardiac fibroblasts

growth_protocol: Freshly isolated cardiac fibroblasts from mice 8-12 weeks old were seeded onto 2D, 3D or other topological states.

extract_protocol:
RNA was isolated using the Bio-Rad(CAT#732-6820),  nuclei was isolated using lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630)
RNA libraries were prepared for sequencing using standard Illumina protocols, DNA Librariesthe were amplified and purified using a Qiagen PCR cleanup kit

treatment_protocol: Not applicable

tag: protocol

value: heart fibroblasts


title: 2D-ATAC


title: 7497398101_R01C01


title: 7497398101_R02C01


title: 7497398098_R01C02


title: 2D-64kPa-3

library_source: transcriptomic


title: 7497398098_R06C01


title: 2D-64kPa-2


title: Day15infected_blood_rep4


title: 7497398098_R06C02


title: 7497398098_R04C02


title: 2D-64kPa-1


title: Day0naive_blood_rep4

source_name: Blood uninfected mouse

value: none (uninfected, naïve)


title: 2D-8kPa-3


title: 7497398098_R03C02


title: Day0naive_blood_rep3


title: Day0naive_blood_rep2


title: 7497398087_R06C02

value: MS case


title: 7497398123_R03C02


title: Day42naive_liver_rep4

source_name: Liver uninfected mouse at the same time point as 42 days post infection of other mice

value: liver


title: 7497398098_R05C01

source_name: peripheral blood


title: 7497398098_R03C01


title: Day0naive_blood_rep1


title: 2D-0.5kPa-3


title: 7497398098_R02C01

value: female


title: Day15infected_blood_rep1


title: 7497398098_R04C01


title: 2D-0.5kPa-2


title: 7497398119_R04C01


title: 2D-0.5kPa-1


title: Day42naive_liver_rep1

value: at the same time point as 42 days post infection of other mice


title: 7497398087_R03C02

value: peripheral blood


title: 3D-5days-2


title: 7497398087_R04C02

value: never smoker


title: 3D-5days-3


title: 7497398087_R05C02

value: ever smoker


title: Day42naive_liver_rep2


title: 3D-5days-1


title: Day42infected_liver_rep4

source_name: Liver infected mouse 42 days post infection

value: 42 days post infection


title: 7497398087_R02C02


title: Day42infected_liver_rep3


title: 7497398101_R03C02


title: Day42infected_liver_rep2


title: 2D-5days-3


title: Day42infected_liver_rep5


title: 7497398087_R05C01


title: Day42infected_liver_rep1


title: 2D-8kPa-2


title: 7497398098_R05C02

value: Healthy control


title: 7497398087_R04C01

value: male


title: 2D-5days-1


title: 3D-2D-2D-3


title: Day36naive_liver_rep5

source_name: Liver uninfected mouse at the same time point as 36 days post infection of other mice

value: BALB/c

value: 6-8 weeks


title: 2D-8kPa-1


title: Day36naive_liver_rep3

value: at the same time point as 36 days post infection of other mice


title: 3D-2D-2D-1


title: 2D-5days-2


title: Day36naive_liver_rep4


title: 7497398087_R01C02


title: 3D-2D-3D-3


title: 3D-2D-3D-2


title: 7497398081_R06C02


title: Day42naive_liver_rep3


title: Day36naive_liver_rep1


title: 7497398087_R01C01


title: Day36infected_liver_rep5

source_name: Liver infected mouse 36 days post infection

value: 36 days post infection


title: Day36infected_liver_rep4

value: 2 x10^7 amastigotes of LV9 strain


title: 3D-2D-3D-1

value: heart fibroblasts


title: 7497398087_R03C01


title: 3D-2D-2


title: 3D-2D-1


title: Day36infected_liver_rep2


title: 7497398098_R01C01


title: 7497398081_R04C02


title: 7497398081_R03C02


title: 7497398087_R02C01


title: 3D-3


title: 3D-2


title: Day36infected_liver_rep1


title: 3D-1


title: 7497398081_R01C02


title: 2D-3


title: Day21infected_liver_rep5

source_name: Liver infected mouse 21 days post infection

value: 21 days post infection


title: 7497398087_R06C01

value: MS case


title: 2D-2


title: 7497398081_R02C02


title: Day21infected_liver_rep4

value: liver


title: Day21infected_liver_rep3


title: Day36naive_liver_rep2

value: none (uninfected, naïve)


title: Day21infected_liver_rep2


title: 7497398081_R06C01


title: SGC0946_3 RNA-seq

description:
Human CD8+ T cells were cultured in the presence of SGC0946 for two weeks, biological replicate 3
SGC0946_3

data_processing:
Illumina Hiseq 2500 was used for base calling.
Sequenced reads were trimmed with fastq_quality_trimmer from the FASTX toolkit.  Read lengths less than 30 nucleotides and a PHRED Quality Score of less than 20 were removed.
The trimmed reads were mapped to the GRCh37 human reference genome using TopHat (version 2.0.14) and Bowtie2 (version 2.2.9).
Read counts and FPKM values for each gene were calculated using Cufflinks (v2.1.1).
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw read counts and FPKM values for each samples were included in a tab-delimited text file.

source_name: Human CD8+ T cells treated with SGC0946

growth_protocol: Human CD8+ T cells were stimulated with artificial antigen presenting cells expressing membranous form of anti-CD3 mAb (clone OKT3), CD80 and CD83 (aAPC/mOKT3), and cultured in vitro for two weeks (RPMI supplemented with 10% human AB serum, 100 IU/ml IL-2 and 10 ng/ml IL-15).

extract_protocol:
RNA was collected from the T cells cultured for 2 weeks using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
Stranded, paired-end libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CD8+ T cells were treated with SGC0946 (0.5 µM) or DMSO.

value: CD8+ T cells

tag: treatment


title: 7497398081_R04C01

value: peripheral blood


title: SGC0946_2 RNA-seq

description:
Human CD8+ T cells were cultured in the presence of SGC0946 for two weeks, biological replicate 2
SGC0946_2


title: Day36infected_liver_rep3


title: 3D-2D-2D-2


title: Day17infected_liver_rep5


title: 2D-1


title: SGC0946_1 RNA-seq

description:
Human CD8+ T cells were cultured in the presence of SGC0946 for two weeks, biological replicate 1
SGC0946_1


title: 7497398081_R05C01

value: female

value: never smoker


title: Day21infected_liver_rep1


title: 7497398081_R02C01


title: Day17infected_liver_rep4

source_name: Liver infected mouse 17 days post infection

value: 17 days post infection


title: Day17infected_liver_rep2


title: DMSO_3 RNA-seq

description:
Human CD8+ T cells were cultured in the presence of control DMSO for two weeks, biological replicate 3
DMSO_3

source_name: Human CD8+ T cells treated with DMSO

value: DMSO


title: DMSO_2 RNA-seq

description:
Human CD8+ T cells were cultured in the presence of control DMSO for two weeks, biological replicate 2
DMSO_2


title: Day17infected_liver_rep3


title: Day17infected_liver_rep1


title: Liver_Wy_M_60ppm_28d_rep4

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: 3μg fragmented ssDNA was  hybridized for 16 h at 45°C. The microarrays were washed and stained with streptavidin-phycoerythrin (SAPE, Molecular Probes) on the Affymetrix Fluidics Station 450 according to the manufacturer’s instructions.

scan_protocol: The fluorescent images of the GeneChips were captured with the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data has been processed with the R/Bioconductor package “affy” version 1.44.1 modified by Brainarray lab for Gene ST support. Brainarray Custom CDF ragene20st version 19.0.0 was used for summarization. Raw data was normalized using RMA as implemented in the “affy” package.

organism: Rattus norvegicus

source_name: liver, Wy-14643, 60 mg/kg/day, 28 days

label_protocol: Starting from 300ng total RNA, Biotin-labeled cRNA samples for hybridization on Affymetrix RaGene_2.0_ST arrays were prepared according to the protocol supplied with the GeneChip ® WT PLUS Reagent Kit for Affymetrix GeneChip Whole Transcript (WT) Expression Arrays (P/N 703174 Rev.2, Affymetrix Inc., Santa Clara, CA) .

growth_protocol: Male Han Wistar rats from appropriate suppliers, e.g. Charles River Laboratories, were kept according to relevant SOPs at the performing laboratories.

extract_protocol: Frozen liver sections were grinded in a Mixer Mill MM 200 (Retsch GmbH and Co. KG, Haan, Germany) using precooled stainless steel balls. After adjusting the volume to 1ml with RLT lysis buffer, total RNA was isolated using Qiagen RNAeasy spin column kits, including a DNase digestion step according to the manufacturer’s instructions. A volume of lysate corresponding to 7mg of tissue was loaded per RNeasy spin column. The final product was quality controlled by gel analysis using RNA 6000 Nano chips on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). All samples had a RIN of 9-10. RNA concentrations were determined using a Nanodrop spectrophotometer.

treatment_protocol: Adults animals were assigned to dose groups (five to six rats/group) by randomization acc. to performing Laboratory SOPs. Substances or corresponding vehicle controls were administered by daily gastric gavage for up to 14, 28 or 90 days, and animals were sacrificed one day after the last application.

tag: compound abbreviation

value: Wy

tag: cpound full name

tag: compound cas no

tag: compound dose [mg/kg]

tag: timepoint [days]

tag: treatment group

tag: corresponding control

tag: tisue

tag: replicate

tag: quality ok?

value: Yes


title: Liver_Wy_M_60ppm_28d_rep5


title: Liver_Wy_M_60ppm_28d_rep3


title: 7512560119_R05C02

tag: disease status

value: Healthy control

tag: gender

tag: age

tag: smoking status

tag: tissue


title: Day15infected_liver_rep5

source_name: Liver infected mouse 15 days post infection

tag: strain

value: BALB/c

value: 6-8 weeks

tag: infected with

tag: time point

value: 15 days post infection


title: DMSO_1 RNA-seq

description:
Human CD8+ T cells were cultured in the presence of control DMSO for two weeks, biological replicate 1
DMSO_1

tag: cell type

tag: treatment

tag: donor


title: 7512560119_R04C02

value: ever smoker


title: 7497398081_R01C01


title: 7512560119_R03C02


title: 7497398081_R03C01


title: 7512560119_R06C02


title: Liver_Wy_M_60ppm_28d_rep2

tag: compound abbreviation

tag: cpound full name

tag: compound cas no

tag: compound dose [mg/kg]

tag: timepoint [days]


title: 7497398081_R05C02


title: 7512560119_R05C01


title: G2_62

city: Phoenix

first: Matthew

last: Huentelman

state: AZ

address: 445 N 5th St

department: Neurogenomics

institute: TGen

data_processing:
BCL files were converted to FASTQs and demultiplexed (bcl2fastq, 1.8).
FASTQ files were trimmed of adapter sequences (AlienTrimmer, 0.3.2).
Trimmed FASTQ files were aligned to the rn5 reference genome (STAR, 2.4.0a).
Reads were summarized as gene-level counts (featureCounts, 1.4.4).
Genome_build: rn5
Supplementary_files_format_and_content: Raw counts were normalized with the R package DESeq2.

source_name: CA1/CA2 region of hippocampus

growth_protocol: Animals were maintained on a 12 hour light/dark cycle and had access to food and water ad libitum.

extract_protocol:
Immediately after the probe trial on day 3 of testing, animals were anesthetized with isofluorane gas and decapitated using a guillotine, and brains were rapidly dissected and frozen. Dissected tissues were stored in pre-weighed microcentrifuge tubes at -70°C until analysis. Dissection of the CA1/CA2 region of the hippocampus (plates 39-42) was according to plate designations in Paxinos and Watson (1998). The brain was cut in the coronal plane to obtain access to the ventral CA1/CA2 region of the hippocampus. The dentate gyrus and the alveus were excluded. RNA was isolated from the left hippocampal region of each animal using TRIzol® Reagent (Invitrogen) and then purified with the RNeasy Kit (Qiagen) using a modified version of the RNeasy Trizol procedure. Rather than precipitating with 0.5mL isopropanol per 1mL Trizol, 1 volume of 70% ethanol was used. After precipitation, the RNeasy protocol was used. However, rather than using 700ul of RW1, half the volume was used, and DNase was used after this step. After the DNase step, another 350ul of RW1 was used, and the rest of the protocol was followed as originally written.
Each sample was prepared for sequencing using the TruSeq RNA Sample Preparation Kit (Illumina Inc), following the manufacturers protocol.

treatment_protocol: Rats were randomly divided into two treatment groups, receiving either vehicle (n=10) or ENZ (n=8). Rats received either daily subcutaneous injections of ENZ (25mg/kg; 0.4mL) (Selleck Chemicals, Houston, TX) suspended in polyethylene glycol (PEG, Sigma-Aldrich, St. Louis, MO) or vehicle (100% PEG) for three days concurrent to behavioral testing. Injections started the first day of behavioral testing.

value: ENZ (25mg/kg; 0.4mL)

value: 12 months


title: G2_26


title: HIEG clamp Muscle GSK subject #10 before TZD treatment

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description:
Simple annotation: Diabetes, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70035.gif
Compound Based Treatment: no

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 960, 5640; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Model = axon 4000B; Performer: Karine,,Clement

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

label_protocol: Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine3; Parameter Date performed = 2006-05-03; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Channel 1 reference name = Muscle GSK subject #10 before TZD treatment after HIEG clamp; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Date performed = 2006-02-01; Performer: Karine,,Clement
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round  amplification-Ambion; Parameter Date performed = 2006-04-27; Performer: Karine,,Clement

tag: Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Age = 53 years; Parameter Species = human; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie after HIEG clamp; Parameter Sex/Mating type = male; Performer

value: Karine,,Clement

label_protocol: Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 10microg; Parameter Type of label = Reverse transcription with aminoallyl dUTP and indirect labelling; Parameter Tube label = cyanine5; Parameter Date performed = 2006-05-03; Performer: Karine,,Clement

extract_protocol:
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Extraction method = guanidinium thiocyanate method; Parameter Extraction method reference = Laville, M. et al J. Clin. Invest. 98, 43-49; Parameter Extracted molecule = total RNA; Parameter Channel 2 reference name = Muscle GSK subject #10 before TZD treatment before HIEG clamp; Parameter Date performed = 2006-02-01; Performer: Karine,,Clement
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Type of amplification = one round amplification-Ambion; Parameter Date performed = 2006-04-27; Performer: Karine,,Clement

tag: Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Age = 53 years; Parameter Species = h; Parameter Disease State = Type 2 Diabetic before TZD treatment; Parameter Cell Type = skeletal muscle biopsie before HIEG clamp; Parameter Sex/Mating type = male; Performer


title: Liver_Wy_M_60ppm_28d_rep1

tag: treatment group

tag: corresponding control

tag: tisue

value: liver

tag: replicate

tag: quality ok?


title: G2_161

tag: strain

tag: age


title: 7512560119_R03C01

tag: disease status

value: MS case

tag: gender

tag: smoking status

tag: tissue


title: Liver_Rosi_M_10ppm_28d_rep4

source_name: liver, Rosiglitazone, 10 mg/kg/day, 28 days

tag: compound abbreviation

value: Rosi

tag: cpound full name

value: Rosiglitazone


title: G2_71

tag: treatment


title: Day15infected_liver_rep4

tag: infected with

value: 2 x10^7 amastigotes of LV9 strain

tag: time point


title: 7512560119_R02C01

value: female

value: peripheral blood


title: Day15infected_liver_rep3


title: Day15infected_liver_rep2


title: Liver_Rosi_M_10ppm_28d_rep3

tag: compound cas no

tag: compound dose [mg/kg]

tag: timepoint [days]

value: No


title: Day15infected_liver_rep1


title: 7512560119_R04C01

value: never smoker


title: G2_152


title: 7512560119_R01C01

value: Healthy control

value: male


title: Day0naive_liver_rep4

source_name: Liver uninfected mouse

value: BALB/c

value: 6-8 weeks

value: none (uninfected, naïve)


title: G2_125

value: ENZ (25mg/kg; 0.4mL)


title: G2_116

value: 12 months


title: G1_98

value: vehicle


title: Liver_Rosi_M_10ppm_28d_rep2

tag: treatment group

tag: corresponding control

tag: tisue

value: liver

value: Yes


title: 7512560105_R05C02

value: MS case


title: G1_89

tag: strain


title: 7512560105_R06C02

tag: age


title: 7512560105_R02C02

tag: disease status


title: G1_80


title: 7512560105_R04C02

tag: gender

value: ever smoker


title: Liver_Pio_M_63ppm_28d_rep5

source_name: liver, Pioglitazone, 63 mg/kg/day, 28 days

value: Pio

value: Pioglitazone

tag: replicate

tag: quality ok?


title: Liver_Rosi_M_10ppm_28d_rep1

tag: compound abbreviation

value: Rosi

value: Rosiglitazone


title: Day0naive_liver_rep3

tag: tissue


title: Liver_Rosi_M_10ppm_28d_rep5

tag: cpound full name

value: No


title: Day0naive_liver_rep2

tag: infected with


title: Day0naive_liver_rep1

tag: time point


title: Liver_Pio_M_63ppm_28d_rep4

tag: compound cas no


title: Day42naive_spleen_rep4

source_name: Spleen uninfected mouse at the same time point as 42 days post infection of other mice

value: spleen


title: Liver_Pio_M_63ppm_28d_rep3

tag: compound dose [mg/kg]


title: Liver_Pio_M_63ppm_28d_rep2

tag: timepoint [days]


title: G1_44

tag: treatment


title: G1_8


title: 7512560105_R01C02

value: female

tag: smoking status

value: peripheral blood


title: G1_53


title: Day42naive_spleen_rep2

value: BALB/c

value: 6-8 weeks

value: at the same time point as 42 days post infection of other mice


title: Day42naive_spleen_rep3

value: none (uninfected, naïve)


title: Liver_Pio_M_63ppm_28d_rep1

tag: treatment group

tag: corresponding control

tag: tisue


title: G1_18

value: vehicle

tag: strain

tag: age

value: 12 months


title: Day42naive_spleen_rep5


title: 7512560105_R03C02

tag: disease status

value: Healthy control

tag: gender


title: Day42naive_spleen_rep1


title: G1_143


title: Liver_Pio_M_16ppm_28d_rep4

source_name: liver, Pioglitazone, 16 mg/kg/day, 28 days

tag: compound abbreviation

value: liver

tag: replicate

tag: quality ok?


title: Liver_Pio_M_16ppm_28d_rep3

tag: cpound full name

value: Yes


title: Day42infected_spleen_rep4

source_name: Spleen infected mouse 42 days post infection

tag: infected with

value: 2 x10^7 amastigotes of LV9 strain

tag: time point

value: 42 days post infection

tag: tissue


title: Day42infected_spleen_rep3


title: G1_107


title: G1_134


title: 7512560105_R06C01

source_name: peripheral blood

value: MS case

value: male

value: never smoker


title: Liver_Pio_M_16ppm_28d_rep1

value: Pio

value: Pioglitazone

tag: compound cas no

tag: compound dose [mg/kg]

tag: timepoint [days]


title: Liver_Pio_M_16ppm_28d_rep2

tag: treatment group


title: Day36naive_spleen_rep5

source_name: Spleen uninfected mouse at the same time point as 36 days post infection of other mice

value: spleen


title: Day42infected_spleen_rep1

value: BALB/c


title: Day42infected_spleen_rep2

value: 6-8 weeks


title: Liver_PBO_M_600ppm_28d_rep2

source_name: liver, Piperonyl-butoxide, 600 mg/kg/day, 28 days

value: PBO

value: Piperonyl-butoxide

tag: corresponding control


title: Day36naive_spleen_rep4

value: none (uninfected, naïve)

value: at the same time point as 36 days post infection of other mice


title: 7512560105_R05C01

tag: smoking status

value: peripheral blood


title: Liver_PBO_M_600ppm_28d_rep3

tag: tisue

value: liver


title: 7512560095_R05C02

value: Healthy control

value: female

tag: age


title: 7512560105_R04C01

tag: disease status

value: ever smoker


title: 7512560105_R02C01

value: MS case

tag: gender


title: 7512560105_R03C01

value: male


title: Liver_PBO_M_600ppm_14d_rep3

source_name: liver, Piperonyl-butoxide, 600 mg/kg/day, 14 days

tag: compound abbreviation

value: Yes


title: 7512560095_R06C02

value: never smoker


title: Liver_PBO_M_600ppm_14d_rep2

tag: replicate


title: Liver_PBO_M_600ppm_14d_rep1

tag: quality ok?


title: 7512560105_R01C01


title: Day36naive_spleen_rep3

tag: strain


title: 7512560095_R03C02


title: 7512560095_R04C02


title: Liver_PB_M_80ppm_90d_rep4

source_name: liver, Phenobarbital, 80 mg/kg/day, 90 days

value: PB

tag: cpound full name

value: Phenobarbital


title: Day36naive_spleen_rep2

value: BALB/c

tag: infected with

tag: time point

value: spleen


title: Day36naive_spleen_rep1

value: 6-8 weeks

tag: tissue


title: Liver_PB_M_80ppm_90d_rep5

tag: compound cas no

tag: compound dose [mg/kg]


title: Day36infected_spleen_rep2

source_name: Spleen infected mouse 36 days post infection

value: 2 x10^7 amastigotes of LV9 strain

value: 36 days post infection


title: Day36infected_spleen_rep5


title: Liver_PB_M_80ppm_90d_rep2

tag: timepoint [days]

tag: treatment group


title: Day36infected_spleen_rep3


title: Day36infected_spleen_rep4


title: 7512560095_R01C02

tag: smoking status


title: Liver_PB_M_80ppm_28d_rep5

source_name: liver, Phenobarbital, 80 mg/kg/day, 28 days

tag: corresponding control

tag: tisue


title: Day36infected_spleen_rep1

tag: age


title: Liver_PB_M_80ppm_90d_rep1

value: No


title: Liver_PB_M_80ppm_90d_rep3


title: Liver_PBO_M_600ppm_28d_rep1

value: PBO

value: Piperonyl-butoxide


title: 7512560095_R03C01

tag: disease status

tag: gender

value: peripheral blood


title: 7512560095_R02C02

value: Healthy control


title: 7512560095_R05C01

value: female

value: ever smoker


title: 7512578084_R06C02

value: MS case

value: male


title: Day21infected_spleen_rep4

source_name: Spleen infected mouse 21 days post infection

value: 21 days post infection


title: 7512560095_R01C01


title: 7512560095_R04C01

value: never smoker


title: 7512560095_R02C01


title: Liver_PB_M_80ppm_28d_rep4

tag: compound abbreviation

value: PB

value: Phenobarbital

value: liver

tag: replicate

value: Yes


title: Day21infected_spleen_rep2

tag: strain

value: BALB/c

value: 6-8 weeks

value: 2 x10^7 amastigotes of LV9 strain

value: spleen


title: 7512560095_R06C01


title: 7512578084_R05C02


title: Liver_PB_M_80ppm_28d_rep2

tag: cpound full name

tag: quality ok?


title: skeletal muscle biopsy of constitutive thin subject in a basal state, biological rep6

hyb_protocol: samples were hybridized on  Affymetrix Human Exon 1.0 ST arrays  according to the manufacturer's instructions.

scan_protocol: microarrays were scanned with GeneChip® Scanner 30007G (Affymetrix)

data_processing: Data were processed with Affymetrix Expression console. Expression values were summarized and normalized using RMA expression summary algorithms. Core probesets only were selected and a gene-level summary analysis was conducted. Data analysis and statistical evaluations were performed with limma (bioconductor)

source_name: skeletal muscle biopsy_constitutive thin subject_basal state

label_protocol: 100ng of total RNA was submitted to WT expression kit (Ambion ) for sample processing

extract_protocol: total RNA was extracted with mirVana miRNA Isolation Kit Ambion

tag: subject group

value: constitutive thin patient

value: skeletal muscle


title: skeletal muscle biopsy of constitutive thin subject in a basal state, biological rep8

tag: tissue


title: Liver_PB_M_80ppm_14d_rep5

source_name: liver, Phenobarbital, 80 mg/kg/day, 14 days

tag: compound cas no


title: Liver_PB_M_80ppm_28d_rep1

tag: compound dose [mg/kg]


title: Liver_PB_M_80ppm_28d_rep3

tag: timepoint [days]


title: 7512578084_R04C02

value: peripheral blood


title: Day21infected_spleen_rep1

tag: infected with

tag: time point


title: Day21infected_spleen_rep5


title: Day17infected_spleen_rep5


title: 7512578084_R02C02

value: female

tag: smoking status


title: Liver_PB_M_80ppm_14d_rep3

tag: treatment group

tag: corresponding control

tag: tisue


title: 7512578084_R06C01

tag: disease status

tag: gender

tag: age


title: 7512578084_R05C01

value: ever smoker


title: Day17infected_spleen_rep2

source_name: Spleen infected mouse 17 days post infection

tag: strain

value: 17 days post infection


title: Day17infected_spleen_rep4


title: Liver_PB_M_80ppm_14d_rep4

tag: compound abbreviation

tag: cpound full name

tag: replicate

value: No


title: skeletal muscle biopsy of constitutive thin subject in a basal state, biological rep4

tag: subject group

tag: tissue


title: 7512578084_R03C02

value: MS case

value: male


title: 7512578084_R01C02

value: never smoker


title: skeletal muscle biopsy of constitutive thin subject in a basal state, biological rep1


title: skeletal muscle biopsy of constitutive thin subject in a basal state, biological rep7


title: skeletal muscle biopsy of constitutive thin subject in a basal state, biological rep3


title: skeletal muscle biopsy of constitutive thin subject in a basal state, biological rep2


title: Day17infected_spleen_rep1


title: Liver_PB_M_80ppm_14d_rep2

value: PB

value: Phenobarbital

tag: compound cas no

tag: compound dose [mg/kg]

tag: quality ok?


title: Liver_PB_M_80ppm_14d_rep1

tag: timepoint [days]

value: liver

value: Yes


title: Liver_MPY_M_30ppm_28d_rep3

source_name: liver, Methapyrilene HCl, 30 mg/kg/day, 28 days

value: MPY

value: Methapyrilene HCl


title: Day15infected_spleen_rep5

source_name: Spleen infected mouse 15 days post infection

value: BALB/c

value: 6-8 weeks

tag: infected with

value: 2 x10^7 amastigotes of LV9 strain

tag: time point

value: 15 days post infection

value: spleen


title: skeletal muscle biopsy of control subject in a basal state, biological rep8

source_name: skeletal muscle biopsy_control subject_basal state

value: female

value: control

value: skeletal muscle


title: 7512578084_R03C01

value: Healthy control

tag: smoking status

value: peripheral blood


title: 7512578084_R02C01

value: never smoker


title: Day17infected_spleen_rep3

value: 17 days post infection


title: 7512578084_R01C01

value: MS case

value: ever smoker


title: Liver_MPY_M_30ppm_28d_rep2

tag: treatment group

tag: corresponding control

tag: tisue

value: liver

value: Yes


title: Day15infected_spleen_rep3

tag: age


title: Day15infected_spleen_rep4

tag: strain


title: Liver_MPY_M_30ppm_28d_rep1

tag: compound abbreviation

value: MPY

value: Methapyrilene HCl


title: 7512578084_R04C01

tag: disease status

tag: gender


title: 7512560083_R06C02


title: skeletal muscle biopsy of control subject in a basal state, biological rep7

tag: subject group


title: skeletal muscle biopsy of constitutive thin subject in a basal state, biological rep5

value: constitutive thin patient

tag: tissue


title: Day15infected_spleen_rep1

value: BALB/c

value: 6-8 weeks

value: 2 x10^7 amastigotes of LV9 strain


title: Day15infected_spleen_rep2

value: 15 days post infection

value: spleen


title: 7512560083_R04C02

value: male


title: Liver_MPY_M_30ppm_14d_rep2

source_name: liver, Methapyrilene HCl, 30 mg/kg/day, 14 days

tag: cpound full name

tag: compound cas no

tag: replicate


title: Liver_MPY_M_30ppm_14d_rep1

tag: compound dose [mg/kg]

tag: timepoint [days]

tag: quality ok?


title: Day0naive_spleen_rep4

source_name: Spleen uninfected mouse

tag: infected with

value: none (uninfected, naïve)

tag: time point


title: Liver_MPY_M_30ppm_14d_rep3

tag: treatment group

tag: corresponding control


title: skeletal muscle biopsy of control subject in a basal state, biological rep3

value: female

value: control

value: skeletal muscle


title: Liver_MPY_M_100ppm_14d_rep3

source_name: liver, Methapyrilene HCl, 100 mg/kg/day, 14 days

tag: tisue


title: skeletal muscle biopsy of control subject in a basal state, biological rep4


title: Day0naive_spleen_rep3

tag: strain

tag: age


title: skeletal muscle biopsy of control subject in a basal state, biological rep2


title: 7512560083_R02C02

source_name: peripheral blood

tag: disease status

value: Healthy control

tag: smoking status

value: never smoker

value: peripheral blood


title: Day0naive_spleen_rep2


title: Liver_MPY_M_100ppm_14d_rep2

tag: compound abbreviation

value: liver

value: Yes


title: Day0naive_spleen_rep1

tag: tissue


title: 7512560083_R03C02

tag: gender

value: ever smoker


title: skeletal muscle biopsy of control subject in a basal state, biological rep1

tag: subject group


title: Liver_MPY_M_100ppm_14d_rep1

value: MPY

tag: cpound full name

value: Methapyrilene HCl

tag: compound cas no

tag: replicate


title: 7512560083_R05C02


title: Liver_H2O_E_28d_rep5

source_name: liver, Water, 0 mg/kg/day, 28 days

value: Water

tag: compound dose [mg/kg]

tag: timepoint [days]

tag: quality ok?


title: 7512560083_R06C01


title: 7512560083_R05C01


title: Liver_H2O_E_28d_rep4

tag: treatment group


title: 030353

description:
Adipose Tissue of Type 2 Diabetic subject 2 #A before insulin clamp vs Adipose tissue of Type 2 Diabetic subject 2 #B after insulin clamp
Date:2007/01/26

hyb_protocol: Agilent : 3000.0 ng at 62 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Lowess method followed by block median normalization

label_protocol: Fluorescent probes were synthesized by chemical coupling of 5µgaminoallyl aRNA with cyanine 3 (Cy3) or Cy5 dyes and purified using Rneasy Mini Kit (Qiagen)

extract_protocol: Trizol


title: 030252

description:
Adipose Tissue of Type 2 Diabetic subject 7 #A before insulin clamp vs Adipose tissue of Type 2 Diabetic subject 7 #B after insulin clamp
Date:2007/01/20


title: 030254

description:
Adipose Tissue of Type 2 Diabetic subject 9 #B after insulin clamp vs Adipose tissue of Type 2 Diabetic subject 9 #A before insulin clamp
Date:2007/01/20


title: Liver_H2O_E_28d_rep3


title: Subject #20, DETEMIR treatment, biological replicate 4

hyb_protocol: Hybridization on Agilent microarray 4x44k following the manufacturer’s instructions.

scan_protocol: Scanned with an Axon 4000B scanner and quantified with GenePix 6.0.

data_processing: Raw data were normalized using the limma library in Bioconductor in R, following this procedure: background subtraction Normexp with offset=50, lowess + Aquantile normalizations. Flagged spots were removed. Only spots present in all ten subjects (28,889) were analyzed.

source_name: skeletal biopsy taken after DETEMIR treatment

label_protocol: Five hundred ng of total RNA were submitted to the Quick Amp Labeling Kit (two colors) following a dye-switch procedure.

extract_protocol: Total RNA was isolated from frozen muscle samples using the mirVanaTM miRNA Isolation Kit (Applied Biosystems).

tag: disease state

value: type 2 diabetes

tag: treatment

value: detemir insulin

source_name: skeletal biopsy taken before DETEMIR treatment


title: 030253

description:
Adipose Tissue of Type 2 Diabetic subject 7 #C before insulin clamp vs Adipose tissue of Type 2 Diabetic subject 7 #D after insulin clamp
Date:2007/01/20


title: Liver_H2O_E_28d_rep2

tag: tisue


title: Subject #23, NPH treatment, biological replicate 5

source_name: skeletal biopsy taken after NPH treatment

value: NPH insulin

source_name: skeletal biopsy taken before NPH treatment


title: 7512560083_R01C01

value: MS case

tag: age


title: Subject #21, DETEMIR treatment, biological replicate 5


title: Subject #22, NPH treatment, biological replicate 4


title: Liver_H2O_E_28d_rep1


title: Subject #15, NPH treatment, biological replicate 3


title: 7512560077_R06C02

tag: disease status


title: 7512560083_R04C01

tag: smoking status


title: 030314

description:
Adipose Tissue of Type 2 Diabetic subject 6 #B after insulin clamp vs Adipose tissue of Type 2 Diabetic subject 6 #A before insulin clamp
Date:2007/01/24


title: 7512560083_R01C02


title: 7512560083_R02C01


title: skeletal muscle biopsy of control subject in a basal state, biological rep6


title: Liver_DCB_M_600ppm_28d_rep4

source_name: liver, 1,4-Dichlorobenzene, 600 mg/kg/day, 28 days

tag: compound abbreviation

value: DCB

tag: corresponding control

value: No


title: Liver_DCB_M_600ppm_28d_rep5


title: 030149

description:
Adipose Tissue of Type 2 Diabetic subject 4 #D after insulin clamp vs Adipose tissue of Type 2 Diabetic subject 4 #C before insulin clamp
Date:2007/01/24


title: 030148

description:
Adipose Tissue of Type 2 Diabetic subject 4 #B after insulin clamp vs Adipose tissue of Type 2 Diabetic subject 4 #A before insulin clamp
Date:2007/01/24


title: 030257

description:
Adipose Tissue of Type 2 Diabetic subject 6 #D after insulin clamp vs Adipose tissue of Type 2 Diabetic subject 6 #C before insulin clamp
Date:2007/01/24


title: Subject #13, DETEMIR treatment, biological replicate 3

tag: tissue


title: 7512560077_R05C02

tag: gender

value: female


title: Subject #12, NPH treatment, biological replicate 2

value: skeletal muscle


title: Liver_DCB_M_600ppm_28d_rep3

tag: cpound full name


title: 030150

description:
Adipose Tissue of Type 2 Diabetic subject 5 #A before insulin clamp vs Adipose Tissue of Type 2 Diabetic subject 5 #B after insulin clamp
Date:2007/01/24


title: Subject #11, DETEMIR treatment, biological replicate 2


title: Subject #1, NPH treatment, biological replicate 1


title: Liver_DCB_M_600ppm_28d_rep1

tag: compound cas no


title: Liver_DCB_M_600ppm_28d_rep2

tag: replicate


title: 030130

description:
Adipose Tissue of Type 2 Diabetic subject 8 #D after insulin clamp vs Adipose Tissue of Type 2 Diabetic subject 8 #C before insulin clamp
Date:2007/01/18


title: 7512560077_R02C02


title: 030202

description:
Adipose Tissue of Type 2 Diabetic subject 9 #D after insulin clamp vs Adipose tissue of Type 2 Diabetic subject 9 #C before insulin clamp
Date:2007/01/20


title: 7512560077_R03C02

value: Healthy control


title: 030201

description:
Adipose Tissue of Type 2 Diabetic subject 5 #C before insulin clamp vs Adipose tissue of Type 2 Diabetic subject 5 #D after insulin clamp
Date:2007/01/24


title: Liver_CPA_M_100ppm_28d_rep4

source_name: liver, Cyproterone acetate, 100 mg/kg/day, 28 days

value: CPA

value: Cyproterone acetate

tag: compound dose [mg/kg]


title: 7512560077_R01C02

value: male

value: never smoker

value: peripheral blood


title: skeletal muscle biopsy of control subject in a basal state, biological rep5

tag: subject group

value: control


title: HFC_MU_A7 versus HFR_MU_pool

description: Biological replicate 5 with dye switch.

hyb_protocol: 1µg of labelled nucleic acid was hybridized in 2X Agilent Hybridation Buffer at 67 degree_C during 17 hours.

scan_protocol: Scanned on Axon Genepix 4000B scanner. Images were quantified using Genepix pro 6.0.

data_processing: Lowess normalization. Only spots with SNR > 2 were considered.

label_protocol: One microgram of total RNA from muscle or 500ng of total RNA from adipose tissue was amplified with the Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer’s instructions. Fluorescent probes were synthesized by chemical coupling of 5 µg of aminoallyl aRNA with cyanine (Cy)3 or Cy5 dyes, following a dye switch experimental plan. Fluorescent probes were purified using Rneasy minikit (Qiagen).

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

treatment_protocol: High fat diet containing refined salmon oil for 28 days.

tag: diet

value: refined salmon oil

treatment_protocol: High fat diet containing crude salmon oil for 28 days.

value: crude salmon oil


title: Liver_CPA_M_100ppm_28d_rep3

tag: timepoint [days]

tag: treatment group

value: liver

tag: quality ok?

value: Yes


title: HFC_MU_A3 versus HFR_MU_pool

description: Biological replicate 4 with dye switch.


title: HFC_MU_A8 versus HFR_MU_pool

description: Biological replicate 2.


title: HFC_MU_A6 versus HFR_MU_pool

description: Biological replicate 3.


title: Liver_CPA_M_100ppm_28d_rep2

tag: tisue


title: Liver_CPA_M_100ppm_28d_rep1


title: 7512560077_R04C01

tag: age


title: 7512560083_R03C01

tag: disease status

value: ever smoker


title: HFC_MU_A2 versus HFR_MU_pool

description: Biological replicate 1.


title: Subject #10, DETEMIR treatment, biological replicate 1

tag: disease state

value: type 2 diabetes

tag: treatment

value: detemir insulin


title: 7512560077_R03C01

tag: smoking status


title: Liver_CPA_M_100ppm_14d_rep3

source_name: liver, Cyproterone acetate, 100 mg/kg/day, 14 days

tag: compound abbreviation

tag: corresponding control


title: 030354

description:
Adipose Tissue of Type 2 Diabetic subject 2 #C before insulin clamp vs Adipose tissue of Type 2 Diabetic subject 2 #D after insulin clamp
Date:2007/01/26


title: HFC_WAT_A3 versus HFR_WAT_pool

description: Biological replicate 4 with dye switch.

tag: tissue

value: adipose tissue


title: 7512560077_R05C01

value: MS case

tag: gender


title: 7512560077_R06C01

value: female


title: HFC_WAT_A7 versus HFR_WAT_pool

description: Biological replicate 3 with dye switch.


title: HFC_WAT_A5 versus HFR_WAT_pool

description: Biological replicate 5 with dye switch.


title: 030135

description:
Adipose Tissue of Type 2 Diabetic subject #8C after TZD treatment vs Adipose Tissue of Type 2 Diabetic subject #8A before TZD treatment
Date:2007/02/09

hyb_protocol: Agilent : 3000.0 ng labelled nucleic acids hybridized at 62 degree_C during 17 hours


title: Liver_CPA_M_100ppm_14d_rep4

tag: cpound full name

tag: compound cas no

tag: replicate


title: HFC_WAT_A6 versus HFR_WAT_pool

description: Biological replicate 2.

tag: diet


title: 7512560063_R06C02

value: Healthy control


title: Liver_CPA_M_100ppm_14d_rep2

value: CPA

tag: compound dose [mg/kg]

tag: timepoint [days]


title: 030127

description:
Adipose Tissue of Type 2 Diabetic subject #7A before TZD treatment vs Adipose Tissue of Type 2 Diabetic subject #7C after TZD treatment
Date:2007/02/09


title: 030355

description:
Adipose Tissue of Type 2 Diabetic subject #2A before TZD treatment vs Adipose Tissue of Type 2 Diabetic subject #2C after TZD treatment
Date:2007/01/26


title: 030326

description:
Adipose Tissue of Type 2 Diabetic subject #5A before TZD treatment vs Adipose Tissue of Type 2 Diabetic subject #5C after TZD treatment
Date:2007/01/26


title: 030126

description:
Adipose tissue of Type 2 Diabetic subject 6C after TZD treatment vs Adipose tissue of Type 2 Diabetic subject 6A before TZD treatment
Date:2007/02/09


title: 7512560077_R01C01


title: Liver_CPA_F_100ppm_28d_rep4

value: Cyproterone acetate

tag: treatment group

tag: quality ok?


title: 7512560063_R05C02

tag: age


title: 7512560063_R04C02

tag: disease status


title: 7512560077_R04C02


title: 7512560077_R02C01


title: Liver_CPA_F_100ppm_28d_rep2

tag: tisue


title: Liver_CPA_F_100ppm_28d_rep3


title: 030128

description:
Adipose Tissue of Type 2 Diabetic subject 8 #B after insulin clamp vs Adipose Tissue of Type 2 Diabetic subject 8 #A before insulin clamp
Date:2007/01/18


title: Liver_CPA_F_100ppm_28d_rep1


title: HFC_WAT_A1 versus HFR_WAT_pool

description: Biological replicate 1.


title: 7512560063_R02C02


title: NCIH510_VEHICLE_24_H510V24B

city: Collegeville

first: Satyajit

last: Rajapurkar

state: PA

address: 1250S. Collegeville Rd.

institute: GlaxoSmithKline LLC

hyb_protocol: Hybridization was performed by Q2 Solutions (formerly Expression Analysis), following their standard protocols.

scan_protocol: Scanning was performed by Q2 Solutions (formerly Expression Analysis), following their standard protocols.

data_processing: CEL files were RMA normalized using the Affy package in Bioconductor and log2 transformed.  For each gene, the corresponding probeset with the maximal mean expression across the sample set was selected for quantification18. For differential expression analysis, the normalized data were fit to the appropriate linear model and pairwise contrasts were performed by applying an empirical Bayes moderated t-statistic using the limma Bioconductor package21. The resulting p-values were adjusted for multiple comparisons by applying the false discovery rate (FDR) correction

source_name: NCIH510 cell line at 24hrs

label_protocol: Sample processing was performed by Q2 Solutions (formerly Expression Analysis), following their standard protocols.

extract_protocol: RNA was isolated using the Qiagen RNeasy mini kit, following the manufacturer's protocol.

tag: treatment

value: VEHICLE

tag: time

tag: cell line

tag: concentration bet(nm)

tag: concentration mek(nm)

tag: tumor type

value: Small Cell Lung Carcinoma

tag: replicate info


title: Liver_CPA_F_100ppm_14d_rep4

tag: compound abbreviation

tag: cpound full name

tag: compound cas no

tag: corresponding control


title: 7512560063_R03C02

tag: gender

tag: smoking status

value: never smoker

tag: tissue

value: peripheral blood


title: NCIH510_VEHICLE_24_H510V24A


title: Liver_CPA_F_100ppm_14d_rep3

tag: compound dose [mg/kg]

tag: timepoint [days]

tag: treatment group

tag: replicate

tag: quality ok?


title: NCIH510_BET_24_H510B24A

tag: treatment

value: BET

tag: time

tag: cell line


title: NCIH510_VEHICLE_96_H510V96B

source_name: NCIH510 cell line at 96hrs

tag: concentration bet(nm)

tag: concentration mek(nm)

tag: tumor type


title: NCIH510_BET_24_H510B24B

tag: replicate info


title: NCIH510_VEHICLE_96_H510V96A


title: 7512560063_R01C02

tag: disease status

value: male

tag: age


title: Liver_CPA_F_100ppm_14d_rep2

tag: compound abbreviation

tag: cpound full name

tag: compound cas no

tag: corresponding control

tag: tisue

value: liver


title: Liver_CO_D_F_28d_rep4

source_name: liver, Corn oil, 0 mg/kg/day, 28 days

value: CO

value: Corn oil

tag: compound dose [mg/kg]

tag: timepoint [days]

tag: treatment group

value: Yes


title: Liver_CPA_F_100ppm_14d_rep1

tag: replicate

tag: quality ok?


title: NCIH510_BET_96_H510B96B

tag: treatment

tag: time

tag: cell line


title: 7512560063_R05C01

tag: gender

tag: smoking status

tag: tissue


title: 7512560063_R06C01

tag: disease status

tag: age

value: ever smoker


title: Liver_CPA_M_100ppm_14d_rep1

tag: compound abbreviation

tag: cpound full name


title: COLO201_BETMEK_96_crc_2

source_name: COLO201 cell line at 96hrs

value: BETMEK

tag: concentration bet(nm)

tag: concentration mek(nm)

tag: tumor type

value: Colorectal Carcinoma

tag: replicate info


title: NCIH510_BET_96_H510B96A


title: Liver_CO_D_F_28d_rep1

tag: compound dose [mg/kg]

tag: timepoint [days]

tag: treatment group

tag: tisue


title: Liver_CO_D_F_28d_rep3

tag: replicate

tag: quality ok?


title: COLO201_BETMEK_96_crc_1

tag: treatment

tag: time

tag: cell line


title: Liver_CO_D_F_28d_rep2


title: 7512560063_R02C01

tag: disease status

tag: gender

tag: smoking status

tag: tissue


title: RKO_BETMEK_96_crc_2

source_name: RKO cell line at 96hrs

value: RKO

tag: concentration bet(nm)


title: 030260

description:
Adipose Tissue of Type 2 Diabetic subject #4C after TZD treatment vs Adipose Tissue of Type 2 Diabetic subject #4A before TZD treatment
Date:2007/01/26


title: 7512560063_R04C01

value: Healthy control

tag: age


title: RKO_MEK_96_crc_2

value: MEK

tag: concentration mek(nm)

tag: tumor type


title: 7512560055_R06C02


title: 7512560063_R01C01

value: female


title: RKO_BET_96_crc_2

tag: replicate info


title: Liver_CO_D_F_14d_rep3

source_name: liver, Corn oil, 0 mg/kg/day, 14 days

tag: compound abbreviation

tag: cpound full name

tag: compound dose [mg/kg]

tag: timepoint [days]


title: Liver_CO_D_F_14d_rep2

tag: treatment group

tag: tisue

tag: replicate

tag: quality ok?


title: Liver_CO_D_F_14d_rep1


title: COLO201_MEK_96_crc_2

tag: treatment

tag: time

tag: cell line


title: Liver_CO_D_28d_rep2


title: COLO201_BET_96_crc_2


title: COLO201_MEK_96_crc_1


title: Liver_CO_D_28d_rep3


title: RKO_VEHICLE_96_crc_2

value: VEHICLE


title: 7512560063_R03C01

tag: disease status

tag: gender

tag: smoking status

tag: tissue


title: 7512560055_R04C02

tag: age


title: 7512560055_R05C02


title: Liver_CO_D_F_14d_rep4


title: Liver_CO_D_14d_rep4


title: RKO_BETMEK_24_crc_2

source_name: RKO cell line at 24hrs

tag: concentration bet(nm)

tag: concentration mek(nm)

tag: tumor type

tag: replicate info


title: Liver_CO_D_28d_rep1

tag: compound abbreviation

tag: cpound full name

tag: compound dose [mg/kg]

tag: timepoint [days]


title: 7512560055_R01C02

value: MS case


title: 7512560055_R02C02


title: 7512560055_R03C02


title: Liver_CO_D_14d_rep3

tag: treatment group

tag: tisue

tag: replicate

tag: quality ok?


title: 7512560055_R06C01

tag: disease status


title: 7512560055_R04C01

tag: gender


title: Liver_CO_D_14d_rep1


title: Liver_CO_D_14d_rep2


title: COLO201_VEHICLE_96_crc_2

tag: treatment

tag: time

tag: cell line


title: Liver_CO_B_28d_rep5


title: RKO_BET_24_crc_2

tag: concentration bet(nm)


title: COLO201_VEHICLE_96_crc_1

tag: concentration mek(nm)


title: Liver_CO_B_28d_rep4


title: Liver_CO_B_28d_rep2


title: Liver_CO_B_28d_rep3

value: No


title: RKO_BET_96_crc_1

tag: tumor type


title: Liver_CO_B_28d_rep1


title: RKO_MEK_96_crc_1

tag: replicate info


title: 7512560055_R02C01

tag: age

tag: smoking status

tag: tissue

value: peripheral blood


title: 7512560055_R03C01


title: RKO_VEHICLE_24_crc_2


title: RKO_VEHICLE_96_crc_1


title: Liver_CMC_C_28d_rep3

source_name: liver, Carboxymethylcellulose, 0 mg/kg/day, 28 days

tag: compound abbreviation

value: CMC

tag: cpound full name

value: Carboxymethylcellulose

tag: compound dose [mg/kg]

tag: timepoint [days]


title: 7512560055_R05C01

source_name: peripheral blood

value: never smoker


title: 7512560055_R01C01

value: male


title: Liver_CMC_C_28d_rep2

tag: treatment group

tag: tisue

value: liver

tag: replicate

tag: quality ok?


title: Liver_CMC_C_28d_rep1

value: Yes


title: BXPC3_BETMEK_96_panc_2

source_name: BXPC3 cell line at 96hrs

tag: treatment

tag: time

value: Pancreatic Carcinoma


title: BXPC3_BETMEK_96_panc_1

value: BETMEK

tag: cell line

tag: concentration bet(nm)


title: RKO_BETMEK_96_crc_1

tag: concentration mek(nm)

tag: tumor type

value: Colorectal Carcinoma


title: Liver_CMC_B_28d_rep5


title: Astrocyte medium, bio rep 2

city: Bronx

first: Dongsheng

last: Cai

state: NY

address: 1300 Morris Park Avenue, 1300 MORRIS PARK AVENUE

institute: ALBERT EINSTEIN COLLEGE OF MEDICINE

description: Exosomal total RNA purified from conditioned medium

hyb_protocol: Samples were hybridized using Affymetrix miRNA Array hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes. • Use 130μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16-18 hours at 48°C at 60rpm• Fluidics washing protocol is FS450_0002

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
CEL files were processed through Expression Console 1.4.1 using RMA-DABG. Only mouse miRNA signals were analyzed. The chip data of these samples were processed via RMA quantile normalization and presented as log2(x) values.
Mouse miRNA values were generated from Expression Console 1.4.1. The data are log2(x) values based on the same amount of exosomal RNA input for each sample. Additional analyses such as calculations according to cell numbers are not included.

source_name: Astrocyte culture medium

label_protocol: Samples were labeled using Affimetrix FlashTag™ Biotin HSR RNA Labeling Kit

growth_protocol: Primary htNSC, hippoNSC and astrocytes were cultured in an exosome-free culture medium under standard conditions for 2 days and media were collected for exosome isolation.

extract_protocol: Each sample was centrifuged and filtered to remove debris and large particles, then exosomes were isolated by differential centrifugation and processed for RNA extraction. The same amount of RNA (800 ng) for each sample (based on about 1.4-fold more hippoNSC and about 2.6-fold more astrocytes compared to htNSC) was provided for Affymetrix miRNA Array assay.

treatment_protocol: not applicable

tag: strain

tag: age

value: new-born

tag: cell type

value: astrocytes

tag: cell compartment

value: exosome


title: BXPC3_MEK_96_panc_1

value: MEK

tag: replicate info


title: Liver_CMC_B_28d_rep4

tag: compound abbreviation

tag: cpound full name

tag: compound dose [mg/kg]


title: BXPC3_VEHICLE_96_panc_1

value: VEHICLE


title: Liver_CMC_B_28d_rep1

tag: timepoint [days]

tag: treatment group

tag: tisue


title: BXPC3_MEK_96_panc_2

tag: treatment


title: Liver_CMC_C_14d_rep3

source_name: liver, Carboxymethylcellulose, 0 mg/kg/day, 14 days

tag: replicate

tag: quality ok?


title: BXPC3_BET_96_panc_1

value: BET

tag: time

tag: cell line

tag: concentration bet(nm)


title: Liver_CMC_B_28d_rep3


title: Liver_CMC_C_14d_rep1


title: HPAFII_BETMEK_96_panc_1

source_name: HPAFII cell line at 96hrs

value: HPAFII

tag: concentration mek(nm)

tag: tumor type


title: BXPC3_BET_96_panc_2


title: BXPC3_VEHICLE_96_panc_2


title: Liver_CMC_C_14d_rep2


title: Astrocyte medium, bio rep 1

tag: strain

tag: age

tag: cell type


title: Liver_CO_D_28d_rep4

tag: compound abbreviation

value: CO

value: Corn oil


title: COLO201_BET_96_crc_1

tag: replicate info


title: HPAFII_BETMEK_96_panc_2


title: hippoNSC medium, bio rep 1

source_name: hippoNSC culture medium

value: hippocampal NSC (hippoNSC)

tag: cell compartment


title: HPAFII_MEK_96_panc_2


title: OXR1A_F_1

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

data_processing:
Sequencing: The library products are ready for sequencing via SE50 instrument.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.   The clean reads were mapped to human reference sequences and/or reference gene set using TopHat2(Kim et al, 2013). FPKM(Fragments Per Kilo bases per Million reads) is used to estimate gene expression level. Readcount was adjusted by TMM, then differential expression analysis was performed by using the DEGseq R package.
The software GOseq (Young et al., 2010) was used for Gene Ontology (OG) enrichment analysis.
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Genome_build: standard reference of mouse genome mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

source_name: OXR1A-/- liver, female

extract_protocol:
The total RNA was isolated from mice liver using a RNeasy kit from Qiagen.
The mRNA was separated from total RNA by Oligo(dT) magnetic beads, and cDNA synthesized by reverse transcription with N6 primer. Adaptors were ligated to the sticky 3' end of the cDNA. Two specific primers were used in PCR to amplify the ligation products. Denature the PCR product by heating and the single strand DNA is cyclized by splint oligo and DNA ligase.

tag: tissue

value: 12 months

tag: genotype

tag: Sex

value: female


title: hippoNSC medium, bio rep 2


title: RKO_MEK_24_crc_2

tag: treatment

value: RKO


title: OXR1A_F_2

value: liver


title: OXR1A_F_3


title: OXR1A_M_3

source_name: OXR1A-/- liver, male

value: male


title: Cells grown in Titan-like promoting medium for 24 h, replicate 2

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

description:
Titan-like_Cells_24h_rep2
Annotated Probe Report All 24h
Annotated Probe Report DESeq2 24h_p005
OZ-021_S21

data_processing:
Reads were filtered for length>= 50 nt and average quality Q>= 30). For each sample, two fastq files were combined and subjected to the alignment step
Alignment was made with Bowtie2 2-1.0 (sensitive, local mode) and SAM files generated
SAM files were loaded into Seqmonk v1.39.0 (Brabaham Institute) and two replicate sets were created ("Small" [3 samples] and "Titan-like"  [2 samples]). The RNA-Seq  pipeline was used (CDS probes, same strand specific, merge transcript isoforms, raw counts) yielding 6974 probes. Both sets were analyzed for differential expression using the Bioconductor DESeq2 algorithm (p<0.05). Reads for selected probes were then quantitated as reads per million.
Genome_build: CNA3 (Gene Bank  assembly accession:  GCA_000149245.3)
Supplementary_files_format_and_content: Four .txt files. Two of them contain reads for all probes at 7 or 24 h and the other two include only probes that are differentially expressed according to DESeq2 (p <0.05)

organism: Cryptococcus neoformans H99

source_name: cultured yeast cells

growth_protocol: Cells were grown in titan-like cell medium (TCM) inoculated with C. neoformans at low density (10^4 cell/mL, that induces titan-like cells) and high density(10^6 cells/mL, that produces cells of regular size).  Cells were incubated at 37oC with 5% CO2, and RNA was extracted after 7 and 18 h of incubation.

extract_protocol:
RNA extraction was performed using Trizol (TRI Reagent, Sigma Aldrich) with some modifications. Cells of regular size were broken during 5 minutes with FastPrepR -24 (MP), alternating 20 seconds beating with 1 minute on ice. Titan-like cells were disrupted for 10 minutes following the same procedure. The RNAs concentration and quality was determined with a Nanodrop 8000 Spectrophotometer (Thermo Scientific). Then RNA samples were purified using RNeasy® Mini Kit (Qiagen) and RiboZero kit (EpiCentre, Illumina).
The total RNA samples (0.5-1 µg) were treated to remove rRNA using Ribo-Zero Magnetic Kit (Epicentre, Illumina, San Diego, CA) according to the manufacturer´s instructions. Then, mRNA was processed for Library preparation using the strand-specific ScriptSeq™ v2 RNA-Seq Library Preparation KIT (Epicentre, Illumina, San Diego, CA). Libraries were quantified using the QuantiFluor® RNA System (Promega) and the quality and average size was determined using an Agilent 2100 Bioanalyzer.

tag: growth condition

value: Titan-like promoting medium


title: Liver_CMC_B_28d_rep2

value: CMC

tag: cpound full name

value: Carboxymethylcellulose

tag: compound dose [mg/kg]

tag: timepoint [days]

tag: treatment group

tag: tisue

tag: replicate

tag: quality ok?

value: Yes


title: HPAFII_MEK_96_panc_1

tag: time

tag: cell line

tag: concentration bet(nm)

tag: concentration mek(nm)

tag: tumor type

value: Pancreatic Carcinoma


title: Liver_CMC_A_90d_rep5

source_name: liver, Carboxymethylcellulose, 0 mg/kg/day, 90 days

tag: compound abbreviation

value: No


title: htNSC medium, bio rep 2

source_name: htNSC culture medium

tag: strain

tag: age

value: new-born

tag: cell type

value: hypothalamic stem/progenitor cells (htNSC)

tag: cell compartment

value: exosome


title: Liver_CMC_A_90d_rep4

tag: cpound full name


title: Liver_CMC_A_90d_rep3

tag: compound dose [mg/kg]


title: HPAFII_BET_96_panc_1

tag: treatment

value: BET

value: HPAFII

tag: replicate info


title: Liver_CMC_A_28d_rep5

tag: timepoint [days]

tag: treatment group

tag: tisue


title: Cells grown in Titan-like promoting medium for 24 h, replicate 1

description:
Titan-like_Cells_24h_rep1
Annotated Probe Report All 24h
Annotated Probe Report DESeq2 24h_p005
OZ-017_S17

tag: growth condition

tag: time


title: RKO_BETMEK_24_crc_1

value: BETMEK

tag: cell line

tag: concentration bet(nm)

value: Colorectal Carcinoma


title: Liver_CMC_A_90d_rep1

tag: replicate

tag: quality ok?


title: HPAFII_BET_96_panc_2

tag: concentration mek(nm)

tag: tumor type


title: HPAFII_VEHICLE_96_panc_2

value: VEHICLE


title: Cells grown in standard medium for 24 h, replicate 3

description:
Control_Small_Cells_24h_rep3
Annotated Probe Report All 24h
Annotated Probe Report DESeq2 24h_p005
OZ-020_S20

value: standard medium


title: Liver_CMC_A_90d_rep2

tag: compound abbreviation

value: liver


title: Liver_CMC_A_28d_rep4


title: RKO_MEK_24_crc_1

value: MEK

value: RKO


title: RKO_BET_24_crc_1


title: OXR1A_M_2

tag: tissue

tag: age

value: 12 months

tag: genotype

tag: Sex

value: male


title: Liver_CMC_A_28d_rep3

value: CMC

tag: cpound full name

value: Carboxymethylcellulose

tag: compound dose [mg/kg]

value: Yes


title: Cells grown in standard medium for 24 h, replicate 2

description:
Control_Small_Cells_24h_rep2
Annotated Probe Report All 24h
Annotated Probe Report DESeq2 24h_p005
OZ-018_S18


title: OXR1A_M_1


title: WT_F_3

source_name: wild type liver, female

value: WT

value: female


title: HPAFII_VEHICLE_96_panc_1

tag: treatment

value: Pancreatic Carcinoma

tag: replicate info


title: WT_F_2


title: WT_F_1


title: Cells grown in Titan-like promoting medium for 7 h, replicate 1

description:
Titan-like_Cells_7h_rep1
Annotated Probe Report All 7h
Annotated Probe Report DESeq2 7h_p005
OZ-008_S8

tag: growth condition

value: Titan-like promoting medium

value: 7 h


title: WT_M_3

source_name: wild type liver, male


title: Cells grown in standard medium for 24 h, replicate 1

description:
Control_Small_Cells_24h_rep1
Annotated Probe Report All 24h
Annotated Probe Report DESeq2 24h_p005
OZ-016_S16

tag: time


title: Cells grown in standard medium for 7 h, replicate 3

description:
Control_Small_Cells_7h_rep3
Annotated Probe Report All 7h
Annotated Probe Report DESeq2 7h_p005
OZ-011_S11


title: Liver_CMC_A_14d_rep5

tag: timepoint [days]

tag: treatment group

tag: tisue


title: Cells grown in standard medium for 7 h, replicate 2

description:
Control_Small_Cells_7h_rep2
Annotated Probe Report All 7h
Annotated Probe Report DESeq2 7h_p005
OZ-009_S9


title: WT_M_2


title: Liver_CMC_A_14d_rep4

tag: replicate

tag: quality ok?


title: RKO_VEHICLE_24_crc_1

tag: cell line

tag: concentration bet(nm)

tag: concentration mek(nm)

tag: tumor type


title: Liver_CMC_A_28d_rep1

tag: compound abbreviation


title: Cells grown in standard medium for 7 h, replicate 1

description:
Control_Small_Cells_7h_rep1
Annotated Probe Report All 7h
Annotated Probe Report DESeq2 7h_p005
OZ-007_S7


title: WT_M_1

tag: tissue

tag: age

tag: genotype

tag: Sex


title: GFP_negative_Endothelial_Cells

status: Public on Apr 19 2018

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: mapped reads per kilobase transcript per million mapped reads per sample

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the transcriptome file with bwa v .0.5.9 with default parameters, converted to .bam format by samtools 0.1.19
Reads aligning to each transcript were counted with samtools v.0.1.19 idxstats,
Genome_build: transcripts as of March 2013, plus ERCC spike in probes and mitochondrial sequences.  File name included in submission is "mouse_refgu_ERCC.seq.fa"
Supplementary_files_format_and_content: the total number of mapped reads and the length of each transcript was used to convert the read counts for each transcript in each sample to RPKM

source_name: Mesenteric Endothelial Cells

extract_protocol:
Total RNA from sorted cells was isolated by TRIzol Reagent (Thermo Scientific) according to manufacturer’s instructions and purified by Qiagen RNeasy columns.
two nanograms of total RNA was used to make Illumina-compatible sequencing libraries with NuGen Ultra Low RNAseq librar prep kit, and the libraries were sequenced using 50 bp single reads on an Illumina HiSeq 1000

treatment_protocol: The Gpr68 eGFP reporter mice were sacrificed with CO2 and the bladders were dissected out and cut into small pieces with micro scissors in PBS. The tissues were digested with 12.5 mg/mL collagenase IV (Gibco) and 10 U/mL papain (Worthington) at 37 ºC for 1 h. The suspension was triturated with fire-polished glass pipettes and then spun down to collect the cell pellet. After washing the pellet twice with PBS, the cells were suspended in FACS buffer. The cells were stained with CD31-APC and CD45-APC-Cy7 (BD Biosciences) for 20 min at 4 ºC in the dark, and stained with PI before sorting. We sorted the cells that are CD31+ CD45- GFP+ and CD31+ CD45- GFP- into two 1.5 mL tubes each containing 1ml Trizol (Thermo Scientific)

tag: strain

value: FVB/N

value: Mesenteric Endothelial Cells

tag: treatment

value: untreated


title: Liver_CMC_A_14d_rep3_2

description: Technical replicate of sample CMC_A_14d_3

tag: cpound full name

tag: compound dose [mg/kg]

value: No


title: GFP_positive_Endothelial_Cells


title: atrial fibrillation patient, biological replicate2

description: Gene expression data from atrial fibrillation patient

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133 Plus 2,0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner GCS3000.

data_processing: The dataset was analyzed inside the R environment using packages from the BioConductor project. Normalization was performed with RMA algorithm

source_name: pulmonary vein from atrial fibrillation patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol adapted for small amounts of RNA from 100ng total RNA

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

tag: patient disease status

value: atrial fibrillation patient

value: pulmonary vein


title: P100+--2

city: paris

first: Jessica

last: Apulei

address: 11 place marcelin berthelot

institute: Collège de France

data_processing:
Reads were filtered and mapped with Bowtie using the following parameters -n 2 -l 28 -e 70 -k 2 –best.
Unmapped reads were removed and expression levels for Ensembl-annotated genes were estimated using htseq-count with the following parameters –m union –s yes –t exon.
Differentially expressed genes between ages and genotypes samples were obtained using DESeq package version 1.8.3.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing genes expression level

source_name: Layer IV of visual cortex

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Lipid Tissue Mini Kit
Layer IV were manually dissected, flash frozen on dry ice, and RNA was harvested using RNeasy Lipid Tissue Mini Kit (Qiagen) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

value: Layer IV visual cortex

value: post natal day 100


title: WT_3D

city: Tianjin

first: liangcai

last: lin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Neurospora crassa OR74A genome (version 12) using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM) and differential gene expression was determined by NOISeq package (v2.6.0).
Genome_build: Neurospora crassa OR74A
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample.

organism: Neurospora crassa

source_name: Mycelia

growth_protocol: Conidia of △gul-1 and wild-type (WT) strains were separately inoculated into Avicel medium (1×Vogel's salt, 2% w/v crystalline cellulose, 0.75% w/v yeast extract and 0.2% v/v Tween 80) and batch cultured for 3 days at 25 ℃ with constant light.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild type

value: Mycelia


title: Liver_CMC_A_14d_rep3

value: CMC

value: Carboxymethylcellulose

tag: timepoint [days]

tag: treatment group

tag: tisue

value: liver

tag: replicate


title: NCU01197_3D


title: control patient, biological replicate 2

description: Gene expression data from control patient

source_name: auricle from control patient

value: control patient

value: left auricle


title: atrial fibrillation patient, biological replicate4

source_name: auricle from atrial fibrillation patient


title: atrial fibrillation patient, biological replicate1


title: T98G Input, Replicate 1

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Reads were aligned to the human genome (hg38) using BWA and peaks were called using MACS2.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.final.dukefilt.peaks.bed9: BED9 files include peak calls.

growth_protocol: T98G cells (ATCC-CRL-1690 and ATCC-HTB14) were grown in EMEM with 10% FBS (Gibco). All cell lines were maintained at 37oC and 5% CO2.

extract_protocol:
Antibodies used were H3K4me3 (EMD Millipore, 07-473) and H3K27me3 (Millipore 07-449).
Libraries were prepared according to the New England Biolabs NEBNext library prep kit (E6240L). Ampure XP beads (A63881) were used for size-selection and clean-up steps.

tag: cell line

tag: cell type

value: Glioblastoma multiforme cell line

tag: chip antibody


title: T98G H3K27me3 ChIP-seq, Replicate 1


title: T98G H3K27me3 ChIP-seq, Replicate 2


title: T98G H3K4me3 ChIP-seq, Replicate 2


title: T98G H3K4me3 ChIP-seq, Replicate 1


title: Liver_CMC_A_14d_rep1

extract_protocol: Frozen liver sections were grinded in a Mixer Mill MM 200 (Retsch GmbH and Co. KG, Haan, Germany) using precooled stainless steel balls. After adjusting the volume to 1ml with RLT lysis buffer, total RNA was isolated using Qiagen RNAeasy spin column kits, including a DNase digestion step according to the manufacturer’s instructions. A volume of lysate corresponding to 7mg of tissue was loaded per RNeasy spin column. The final product was quality controlled by gel analysis using RNA 6000 Nano chips on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). All samples had a RIN of 9-10. RNA concentrations were determined using a Nanodrop spectrophotometer.

tag: compound abbreviation

tag: quality ok?

value: Yes


title: P100+--1

tag: tissue

tag: age


title: atrial fibrillation patient, biological replicate3

value: right auricle


title: Liver_CMC_A_14d_rep2


title: htNSC medium, bio rep 1

tag: strain

value: new-born

value: hypothalamic stem/progenitor cells (htNSC)

tag: cell compartment

value: exosome


title: control patient, biological replicate 1


title: BM-MSC_osteogenic differentiation_day10_rep3

city: Guangzhou

first: tang

last: su'an

state: Guangdong

address: 107# Yan Jiang Road West

department: Department of Orthopedics

institute: Sun Yat-sen Memorial Hospital

description: Gene expression in day 10 of osteogenic differentiation human bone marrow-derived MSCs

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with  Feature Extraction Software v10.7 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized and analyzed using GeneSpring software (Agilent).

source_name: bone marrow-derived MSC, osteogenic differentiation, day10

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

growth_protocol: MSCs were separated from bone marrow by density gradient centrifugation. Dulbecco’s modified Eagle’s medium (DMEM; Gibco) with 10% fetal bovine serum (FBS, Sijiqing Biological Engineering Material Company) was used to resuspend cells. And the cells were seeded into flasks and cultured in an incubator at a condition of 37℃, 5% CO2 and 100% relative humidity. After 48 hours, the fluid was changed to remove the suspended cells. Thereafter, the medium was changed every 3 days. When MSCs reached 80-90% confluence, 0.25% trypsin containing 0.53mM EDTA was used to digest the cells. And the cells would be evenly divided and reseeded into new flasks as passage 1.

extract_protocol: Total RNA was isolated using  TRIzol (Invitrogen) and purified using NucleoSpin RNA cleanup kits (Macherey-Nagel) following the manufacturer's recommendations.  RNA integrity was determined by formaldehyde denaturing gel electrophoresis. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For osteogenic differentiation, MSCs were cultured with osteogenic differentiation medium (OM), consisting of DMEM with 10% FBS, 100 IU/mL penicillin, 100 IU/mL streptomycin, 0.1 μM dexamethasone, 10mM β-glycerol phosphate, and 50μM ascorbic acid (Sigma-Aldrich). The medium was changed every 3 days. On day 10 of induction, total RNA was extracted from cells.

tag: Stage

value: osteogenic differentiation

tag: gender

value: male


title: BM-MSC_osteogenic differentiation_day10_rep1


title: HNE-1 TNFRSF19 KO

first: Chengcheng

last: Deng

address: No.2 lujing Road

institute: Dermatology Hospital, Southern Medical University

description: Gene expression data from WT and TNFRSF19 KO NPC cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HNE-1 TNFRSF19 KO cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: The cells were maintained in Dulbecco’s Modified Eagle’s Medium (Invitrogen) with 10% fetal bovine serum (Invitrogen) at 37 °C and 5% CO2.

extract_protocol: Total RNA of NPC cells was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Cells were rinsed with PBS and placed on ice in the Trizol solution.

value: NPC cells


title: HNE-1 TNFRSF19 WT

source_name: HNE-1 TNFRSF19 WT cells


title: BM-MSC_undifferentiation_day0_rep3

description: Gene expression in undifferentiation human bone marrow-derived MSCs

source_name: bone marrow-derived MSC, undifferentiation, day0

value: undifferentiation


title: BM-MSC_osteogenic differentiation_day10_rep2


title: Foliar nectary post-secretory control replicate2 (2)

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

description: FO P 2C Rep.2

data_processing:
Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn, normalized by upper-quartile count and reference length
Contigs aligned to cotton reference proteins
Cotton reference proteins annotated with closest Arabidopsis thaliana match
Genome_build: Cotton: https://www.ncbi.nlm.nih.gov/assembly/GCF_000987745.1/
Genome_build: Arabidopsis used Araport 11 build 201606
Supplementary_files_format_and_content: Cotton_protein_counts.txt - file with upper quartile and mRNA-length normalized counts

organism: Gossypium hirsutum

source_name: Foliar nectary post-secretory control

growth_protocol: Seeds for Gossipium hirsutum cv. TM1 were chipped and germinated in 8cm x 8cm x 10 cm pots filled with a soil mixture of 3-parts LC8 soil to 1-part sand. Plants were grown in Environmental Growth Chambers kept at 12h light 26 °C /12h dark 22 °C cycle. Seedlings were transplanted into two-gallon (2A) pots after reaching approximately 30 cm in height. Upon transplanting, 10 g of Osmocote Pro 19-5-8 was mixed into the previously described soil mixture per pot. Plants were water each day and once per week with a 10% fertilizer solution of Scotts Excel 21-5-20 all purpose water soluble fertilizer and Scotts Excel 15-5-15 Cal-Mag water soluble fertilizer. All tissues were collected from plants after the first flower bloomed, approximately ten weeks after sowing, between the times of 1000 and 1500.

extract_protocol:
RNA isolation: For a single biological replicate, approximately five nectaries were transferred with a clean forcep to a 2 ml Lysing matrix A tube (MP Biomedicals, Ref # 6910-500) containing a ceramic bead, resting in a liquid nitrogen bath. The tubes were quickly transferred to a QuickPrep adaptor (containing dry ice) and attached to the FastPrep 24™-5G  (MP Biomedicals) benchtop homogenizer. The tissue were subjected to 5 to 6 homogenizing runs of 40 seconds each at 6 m/sec, with each run interjected with a period of immersing the tubes in liquid nitrogen and refilling the adaptor with dry ice. Post-pulverization, 600µl of the RNA lysis buffer of the Quick-RNA™ MiniPrep kit (Zymo Research, Cat# R1054) was quickly added to the Lysing matrix tube and the tubes were vortexed. This was followed by addition of 50µl of the Plant RNA Isolation Aid (Thermo Fisher Scientific Cat#AM9690; erstwhile Ambion) and a quick vortex to aid removal of common plant contaminants such as polyphenolics and polysaccharides. Quick-RNA™ MiniPrep kit directions were followed for RNA isolation. Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for barcoded library creation and Illumina HiSeq 2500 sequencing. All libraries were pooled and sequenced across two and a half lanes, then sequencing was repeated for quality concerns. This generated ≥24 M reads for each sample and the average quality scores were above Q30.
Illumina's Truseq RNA Preparation v2 kit (RS-122-2001)

value: Near foliar nectary tissue

value: post-secretory control


title: Foliar nectary post-secretory control replicate1 (2)

description: FO P 1C Rep.2


title: Foliar nectary post-secretory replicate3 (2)

description: FO P 3 Rep.2

source_name: Foliar nectary post-secretory

value: Foliar nectary tissue

value: post-secretory


title: Foliar nectary post-secretory replicate1 (2)

description: FO P 1 Rep.2


title: Foliar nectary post-secretory replicate2 (2)

description: FO P 2 Rep.2


title: Foliar nectary post-secretory control replicate3 (2)

description: FO P 3C Rep.2


title: Foliar nectary presecretory replicate1 (2)

description: FO pre 1 Rep.2

source_name: Foliar nectary presecretory

value: presecretory


title: Foliar nectary presecretory control replicate1 (2)

description: FO pre 1C Rep.2

source_name: Foliar nectary presecretory control

value: presecretory control


title: Foliar nectary secretory replicate1 (2)

description: FO S 2 Rep.2

source_name: Foliar nectary secretory

value: secretory


title: Circumbracial nectary post-secretory control replicate2 (2)

description: C post 2C Rep.2

value: Near circumbracteal nectary tissue


title: Circumbracial nectary post-secretory control replicate1 (2)

description: C post 1C Rep.2


title: BM-MSC_undifferentiation_day0_rep1


title: Circumbracial nectary post-secretory replicate3 (2)

description: C post 3 Rep.2

source_name: Circumbracial nectary post-secretory

value: Circumbracteal nectary tissue


title: Circumbracial nectary post-secretory replicate2 (2)

description: C post 2 Rep.2


title: Circumbracial nectary post-secretory replicate1 (2)

description: C post 1 Rep.2


title: Foliar nectary presecretory control replicate2 (2)

description: FO pre 3C Rep.2


title: Circumbracteal nectary presecretory control replicate3 (2)

description: C pre 3C Rep.2


title: Circumbracteal nectary presecretory replicate3 (2)

description: C pre 3 Rep.2

source_name: Circumbracteal nectary presecretory


title: Circumbracteal nectary presecretory replicate1 (2)

description: C pre 1 Rep.2


title: Circumbracteal nectary presecretory control replicate1 (2)

description: C pre 1C Rep.2


title: Bracteal nectary post-secretory control replicate3 (2)

description: B post 3C Rep.2

source_name: Bracteal nectary post-secretory control

value: Near bracteal nectary tissue


title: Foliar nectary secretory control replicate1 (2)

description: FO S 2C Rep.2

source_name: Foliar nectary secretory control

value: secretory control


title: Foliar nectary presecretory replicate2 (2)

description: FO pre 2 Rep.2


title: BM-MSC_undifferentiation_day0_rep2


title: Bracteal nectary post-secretory control replicate2 (2)

description: B post 2C Rep.2


title: Bracteal nectary post-secretory control replicate1 (2)

description: B post 1C Rep.2


title: Bracteal nectary presecretory control replicate2 (2)

description: B pre 3C Rep.2

source_name: Bracteal nectary presecretory control


title: Bracteal nectary post-secretory replicate2 (2)

description: B post 2 Rep.2

source_name: Bracteal nectary post-secretory

value: Bracteal nectary tissue


title: Circumbracteal nectary presecretory control replicate2 (2)

description: C pre 2C Rep.2


title: Bracteal nectary post-secretory replicate1 (2)

description: B post 1 Rep.2


title: Bracteal nectary presecretory control replicate1 (2)

description: B pre 2C Rep.2


title: Bracteal nectary presecretory replicate1 (2)

description: B pre 2 Rep.2

source_name: Bracteal nectary presecretory


title: Circumbracteal nectary presecretory replicate2 (2)

description: C pre 2 Rep.2


title: Bracteal nectary post-secretory replicate3 (2)

description: B post 3 Rep.2


title: Bracteal nectary presecretory replicate2 (2)

description: B pre 3 Rep.2


title: Floral nectary post-secretory control replicate1 (2)

description: FL post 1C Rep.2

source_name: Floral nectary post-secretory control

value: Near floral nectary tissue


title: Floral nectary post-secretory replicate2 (2)

description: FL post 2 Rep.2

source_name: Floral nectary post-secretory

value: Floral nectary tissue


title: Floral nectary post-secretory replicate3 (2)

description: FL post 3 Rep.2


title: Floral nectary post-secretory replicate1 (2)

description: FL post 1 Rep.2


title: Floral nectary secretory control replicate2 (2)

description: FL sec 2C Rep.2

source_name: Floral nectary secretory control


title: Floral nectary secretory control replicate1 (2)

description: FL sec 1C Rep.2


title: Floral nectary secretory control replicate3 (2)

description: FL sec 3C Rep.2


title: Floral nectary secretory replicate2 (2)

description: FL sec 2 Rep.2

source_name: Floral nectary secretory


title: Floral nectary secretory replicate3 (2)

description: FL sec 3 Rep.2


title: Floral nectary presecretory control replicate3 (2)

description: FL pre 3C Rep.2

source_name: Floral nectary presecretory control


title: Floral nectary presecretory control replicate2 (2)

description: FL pre 2C Rep.2


title: Floral nectary secretory replicate1 (2)

description: FL sec 1 Rep.2


title: Liver_CMC_A_28d_rep2

data_processing: Microarray data has been processed with the R/Bioconductor package “affy” version 1.44.1 modified by Brainarray lab for Gene ST support. Brainarray Custom CDF ragene20st version 19.0.0 was used for summarization. Raw data was normalized using RMA as implemented in the “affy” package.

source_name: liver, Carboxymethylcellulose, 0 mg/kg/day, 28 days

value: CMC

tag: cpound full name

value: Carboxymethylcellulose

tag: compound dose [mg/kg]

value: liver

value: Yes


title: Floral nectary post-secretory control replicate2 (2)

description: FL post 2C Rep.2

value: post-secretory control


title: Floral nectary presecretory replicate1 (2)

description: FL pre 1 Rep.2

source_name: Floral nectary presecretory


title: Floral nectary presecretory replicate2 (2)

description: FL pre 2 Rep.2


title: Floral nectary presecretory control replicate1 (2)

description: FL pre 1C Rep.2


title: Foliar nectary post-secretory control replicate2 (1)

description: FO P 2C Rep.1

source_name: Foliar nectary post-secretory control

value: Near foliar nectary tissue


title: Floral nectary post-secretory control replicate3 (2)

description: FL post 3C Rep.2


title: Foliar nectary post-secretory replicate3 (1)

description: FO P 3 Rep.1

source_name: Foliar nectary post-secretory

value: Foliar nectary tissue

value: post-secretory


title: Foliar nectary post-secretory control replicate1 (1)

description: FO P 1C Rep.1


title: Foliar nectary presecretory control replicate2 (1)

description: FO pre 3C Rep.1

source_name: Foliar nectary presecretory control

value: presecretory control


title: Foliar nectary presecretory control replicate1 (1)

description: FO pre 1C Rep.1


title: Foliar nectary secretory replicate1 (1)

description: FO S 2 Rep.1

source_name: Foliar nectary secretory

value: secretory


title: Foliar nectary presecretory replicate1 (1)

description: FO pre 1 Rep.1

source_name: Foliar nectary presecretory

value: presecretory


title: Foliar nectary post-secretory control replicate3 (1)

description: FO P 3C Rep.1


title: Circumbracial nectary post-secretory control replicate2 (1)

description: C post 2C Rep.1

value: Near circumbracteal nectary tissue


title: Foliar nectary secretory control replicate1 (1)

description: FO S 2C Rep.1


title: Foliar nectary post-secretory replicate1 (1)

description: FO P 1 Rep.1


title: Foliar nectary post-secretory replicate2 (1)

description: FO P 2 Rep.1


title: Circumbracial nectary post-secretory control replicate3 (1)

description: C-post 3C Rep.1


title: Circumbracial nectary post-secretory control replicate1 (1)

description: C post 1C Rep.1


title: Circumbracial nectary post-secretory replicate3 (1)

description: C post 3 Rep.1

source_name: Circumbracial nectary post-secretory

value: Circumbracteal nectary tissue


title: Circumbracial nectary post-secretory replicate1 (1)

description: C post 1 Rep.1


title: Circumbracteal nectary presecretory control replicate2 (1)

description: C pre 2C Rep.1


title: Circumbracteal nectary presecretory control replicate1 (1)

description: C pre 1C Rep.1


title: Circumbracteal nectary presecretory replicate3 (1)

description: C pre 3 Rep.1

source_name: Circumbracteal nectary presecretory


title: Circumbracteal nectary presecretory replicate2 (1)

description: C pre 2 Rep.1


title: Circumbracteal nectary presecretory replicate1 (1)

description: C pre 1 Rep.1


title: Bracteal nectary post-secretory control replicate3 (1)

description: B post 3C Rep.1

source_name: Bracteal nectary post-secretory control

value: Near bracteal nectary tissue


title: Bracteal nectary post-secretory control replicate1 (1)

description: B post 1C Rep.1


title: Bracteal nectary post-secretory replicate3 (1)

description: B post 3 Rep.1

source_name: Bracteal nectary post-secretory

value: Bracteal nectary tissue


title: Bracteal nectary post-secretory replicate1 (1)

description: B post 1 Rep.1


title: Circumbracial nectary post-secretory control replicate3 (2)

description: C-post 3C Rep.2


title: Bracteal nectary presecretory control replicate1 (1)

description: B pre 2C Rep.1

source_name: Bracteal nectary presecretory control


title: Bracteal nectary presecretory replicate1 (1)

description: B pre 2 Rep.1

source_name: Bracteal nectary presecretory


title: Bracteal nectary post-secretory replicate2 (1)

description: B post 2 Rep.1


title: Bracteal nectary presecretory replicate2 (1)

description: B pre 3 Rep.1


title: Floral nectary post-secretory control replicate3 (1)

description: FL post 3C Rep.1

source_name: Floral nectary post-secretory control

value: Near floral nectary tissue


title: Cells grown in Titan-like promoting medium for 7 h, replicate 2

description:
Titan-like_Cells_7h_rep2
Annotated Probe Report All 7h
Annotated Probe Report DESeq2 7h_p005
OZ-010_S10

source_name: cultured yeast cells

tag: growth condition

value: Titan-like promoting medium

tag: time

value: 7 h


title: Circumbracial nectary post-secretory replicate2 (1)

description: C post 2 Rep.1


title: Floral nectary post-secretory control replicate2 (1)

description: FL post 2C Rep.1


title: Floral nectary post-secretory control replicate1 (1)

description: FL post 1C Rep.1


title: Floral nectary post-secretory replicate1 (1)

description: FL post 1 Rep.1

source_name: Floral nectary post-secretory

value: Floral nectary tissue


title: Floral nectary post-secretory replicate3 (1)

description: FL post 3 Rep.1


title: Circumbracteal nectary presecretory control replicate3 (1)

description: C pre 3C Rep.1


title: Floral nectary post-secretory replicate2 (1)

description: FL post 2 Rep.1


title: Floral nectary secretory control replicate2 (1)

description: FL sec 2C Rep.1

source_name: Floral nectary secretory control

value: secretory control


title: Floral nectary secretory control replicate1 (1)

description: FL sec 1C Rep.1


title: Floral nectary secretory replicate2 (1)

description: FL sec 2 Rep.1

source_name: Floral nectary secretory


title: Floral nectary secretory replicate3 (1)

description: FL sec 3 Rep.1


title: Floral nectary secretory replicate1 (1)

description: FL sec 1 Rep.1


title: Floral nectary presecretory control replicate3 (1)

description: FL pre 3C Rep.1

source_name: Floral nectary presecretory control


title: Floral nectary presecretory control replicate2 (1)

description: FL pre 2C Rep.1


title: Bracteal nectary post-secretory control replicate2 (1)

description: B post 2C Rep.1


title: Floral nectary presecretory control replicate1 (1)

description: FL pre 1C Rep.1


title: Floral nectary presecretory replicate2 (1)

description: FL pre 2 Rep.1

source_name: Floral nectary presecretory