title: DENV_CX_UV_rep2

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

description: Dengue 1 crosslink +UV replicate 2

data_processing:
illumina adapter removal using cutadapt
alignment with bowtie2 'very-sensitive-local' preset
calculation of SPMR from raw read counts
Genome_build: EU081177; KU497555
Supplementary_files_format_and_content: csv: nucleotide_coodinate, singal_per_million_reads (SPMR)

organism: dengue virus type 1

source_name: Dengue 1 crosslink +UV

growth_protocol: Following previous procedures,[16] DENV and ZIKV C proteins were expressed in Escherichia coli cells C43 (DE3) and C41 (DE3), transformed with the DENV 2 C protein gene and with the ZIKV Brazil C protein gene, respectively, cloned into a pET21a plasmid (ampicillin resistance). 6 mL LB medium with 100 μg/mL ampicillin were inoculated with a single E. coli colony, containing the pET21a, from LB-agar plates with 100 μg/mL ampicillin, and incubated overnight at 220 rpm, 37 °C. The overnight culture was used to inoculate LB with 100 μg/mL ampicillin, to a final dilution of 1:50. The main culture was incubated at 220 rpm and 37 °C, until the optical density at 600 nm (OD600) reaches 0.8. Protein expression was induced with 0.5 mM isopropyl β-D-1-thiogalactopyranoside (IPTG), at 25 °C overnight and with 220 rpm agitation. The overnight culture was centrifuged at 7000 × g for 40 min at 4 °C. Supernatants were discarded and the cell pellets were resuspended in 1/10 of the volume of the initial culture, in a buffer with 25 mM HEPES, pH 7.4, 0.2 M NaCl, 1 mM EDTA, 5% (v/v) glycerol (Buffer 0.2 M NaCl) and 10 μM protease inhibitor cocktail (Sigma). Cells were lysed by sonication, keeping the suspension on ice, with 5 to 7 pulses (1.5 min) and pauses of 2 min. Sodium chloride was added to the cell lysate to achieve a final concentration of 2 M NaCl, and incubated for at least 1 h, with agitation, at 4 °C. The suspension was centrifuged at 16100 × g for 30 min at 4 °C, and supernatants were collected. Before the first chromatography step, these supernatants were diluted fourfold with Buffer 0.2 M NaCl. The diluted supernatants were applied to a 5 mL HiTrap heparin column (HiTrapTM Heparin HP, GE Healthcare) coupled to an ÄKTA purifier system (ÄKTA explorer, GE Healthcare). The C protein was then eluted performing a NaCl gradient from 0.2 to 2 M NaCl. The fractions corresponding to the C protein were collected and injected in a size exclusion column (S200). C proteins were purified in a buffer with 55 mM KH2PO4 and 550 mM KCl, pH 6.0. DENV C protein purified fractions were concentrated with a Centriprep Centrifugal Filter (Millipore; 3 kDa cutoff) and stored at -80 °C. ZIKV C protein purified fractions were centrifuged at 13,400 × g to remove protein aggregates and the supernatants were stored at -80 °C. The purity of the purified recombinant C protein samples was assessed by 15% SDS-PAGE. Protein concentrations were determined from the sample absorbance at 280 nm, with extinction coefficients calculated from their primary structures (GenBank database: AAC59275.1 and KU497555.1, for DENV and ZIKV, respectively). Matrix-assisted laser desorption/ionization, time-of-flight mass spectrometry (MALDI-TOF MS) analysis showed one peak, with the expected mass of the protein monomer and much lower peaks corresponding to a very low degradation.

extract_protocol: 2 µl of 10× T4 polynucleotide kinase (PNK) buffer and 2 µL of T4 PNK were added to 14 µL of each vRNA sample. Reaction mixtures were incubated for 4 h at 37 °C. Then, additional 0.5 µL of T4 PNK and 2 µL of 10 mM ATP were added, and the mixture reactions were incubated for 1 h at 37 °C. The final volume of the mixtures was adjusted to 50 µL by adding nuclease-free water. Following, high-quality vRNA samples were prepared with an RNA Clean & Concentrator kit (RNA Clean & Concentrator-5, Zymo Research). Briefly, 100 μL of RNA binding buffer were added to each 50 μL of vRNA sample. Then, an equal volume of ethanol 100% was added and mixed. Samples were transferred to a column in a collection tube and centrifuged for 30 s at 12,000 × g. The flow-through was discarded and 400 μL of the second RNA buffer were added. Viral RNA bound to the columns were washed twice. A dry spin was made to completely remove the washing buffer. Columns were transferred into RNA-free tubes and the vRNA was eluted by adding 8 μL of RNase-free water to the column matrix. After 1 min incubation, columns were centrifuged for 30 s at 12,000 × g. The recovered vRNA was double eluted and samples were storage at -80 °C. Library preparation was made with a NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (New England Biolabs), with small modifications to the protocol. 1 μL of 3’ SR Adaptor was added to 6 μL of the high-quality vRNA samples prepared, in nuclease-free PCR tubes. Reaction mixtures were incubated in a preheated thermal cycler for 2 min at 70 °C, and then transferred to ice. 10 μL of 3’ Ligation Reaction Buffer and 3 μL of 3’ Ligation Enzyme Mix were added to each reaction mixture. Samples were incubated in a thermal cycler for 1 h at 25°C. To prevent the formation of dimers of the remaining 3’ SR Adaptor, 4.5 μL of nuclease-free water and 1 μL of SR reverse transcription (RT) Primer for Illumina were added, and samples were incubated for 5 min at 75 °C, 15 min at 37 °C and 15 min at 25 °C. For the ligation of the 5’ SR Adaptor, an adaptor mix was prepared. For that, 5’ SR Adaptor was incubated in a thermal cycler at 70 °C for 2 min, and then immediately transferred to ice. Following, 1 μL of the denatured 5’ SR Adaptor was mixed with 1 μL of 5’ Ligation Reaction Buffer and 2.5 μL of 5’ Ligation Enzyme Mix. The adaptor mix was added to the samples with 3’ SR Adaptor and incubated in a thermal cycler for 1 h at 25 °C. To perform the RT of the adaptor ligated vRNA samples, 30 μL of these samples were mixed in nuclease-free tube with 8 μL of First Strand Synthesis Reaction Buffer, 1 μL of Murine RNase Inhibitor and 1 μL of ProtoScript II Reverse Transcriptase. Reaction mixtures were incubated at 50 °C for 60 min. Then, RT reactions were inactivated at 70 °C for 15 min and stored at -20 °C. A large-scale PCR amplification was performed using 12 PCR cycles, the number of cycles identified as enough to construct a library. For that, 10 μL of the cDNA were mixed, on ice, with 2.5 μL of F-primer (SR primer), 2.5 μL of R-primer (with different barcodes for each sample), 5 μL of nuclease-free water and 20 μL of 2X Q5 Master Mix. The barcoded cDNA samples were normalized to 1000 ng/mL and sent to next generation sequencing on the Illumina platform.

treatment_protocol: Eight reactions, four for DENV and four for ZIKV experiment, with 1 µg of vRNA in nuclease-free water were prepared in 0.2-ml PCR tubes. To renature the viral RNA, tubes were heated at 90 °C, for 2 min, in a thermal cycler with heated lid on and then transferred to ice for 2 min. 5 μL of 10× RNA structure buffer were added to the vRNA and gently homogenized by pipetting up and down. Then, tubes were placed into the thermal cycler and temperature increased from 4 °C to 37 °C over 35 min. DENV or ZIKV C proteins were added to the four reactions in increasing concentrations, to achieve different final ratios of C protein monomers to one molecule of vRNA (1:20, 1:100, 1:250 and 1:500). Samples were incubated at 37 °C for 30 min, to allow the interaction of the C protein with vRNA. 5 μl of RNase A/T1 Mix (RNase A 500 U/mL and RNase T1 20000 U/mL; Ambion AM2286) diluted 100 times were added to each tube, and incubated at 37 °C for 30 min. The dilution of RNase A/T1 Mix was previously determined with four serial 10 times dilutions of RNase A/T1 Mix from the stock solution. 45 µL of nuclease-free water were added to each sample to adjust the final volume of the reaction mixtures to 100 µL, and then transferred to 1.5 microfuge tubes with the same volume of phenol–chloroform–isoamyl alcohol. After mixing, tubes were centrifuged at 13,200 × g for 10 min at 4 °C. The aqueous phase of each sample was transferred to a new tube containing 10 µL sodium acetate 3 M and 1 µL glycogen 20 mg/mL. 300 µL of ethanol 100% were mixed with each aqueous solution and, to precipitate the vRNA, samples were stored at -20 °C overnight. To collect the vRNA, samples were spin at 13,200 × g for 30 min at 4 °C. Supernatants were discarded and 800 µL of ethanol 70% were added to the pellet. Samples were spin at 13,200 × g for 15 min at 4 °C and the supernatants removed. A dry spin at 13,200 × g for 1 min at 4 °C was made to completely remove ethanol. vRNA pellets were resuspend in 15 µL of nuclease-free water and stored at -80 °C.

value: viral RNA


title: mycelium, VOC-exposed, 72hrs, rep 2

status: Public on Dec 31 2022

type: SRA

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

country: China

institute: Jiangsu Academy of Agricultural Sciences

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic (Bolger et al., 2014) and the low-quality reads were removed to obtain the clean reads.
Then, about 48 M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the P. myriotylum SWQ7 reference genome JAAS_PmSWQ7_1_0_assembly.fsa (PRJNA692555) (Daly et al., 2022) using HISAT2 (Kim et al., 2015) and > 90% of the reads mapped to the genome from all the samples.
FPKM (Roberts et al., 2011) of each gene was calculated using Cufflinks (Trapnell et al., 2010) , and the read counts of each gene were obtained by HTSeq-count (Anders et al., 2015).
The GFF file "JAAS_PmSWQ7_1.0_assembly_augustus_MU_annots_exclud_t_posons_alt_ts.gff" available from another GEO submission (GSE174557) was used.
Assembly: JAAS_PmSWQ7_1_0_assembly.fsa (PRJNA692555)
Supplementary files format and content: tab-delimited text file of read counts for all samples
Supplementary files format and content: tab-delimited text file of FPKM values for all samples

molecule: total RNA

organism: Pythium myriotylum

source_name: mycelium

growth_protocol: The antimicrobial activity of the P. oligandrum strain GAQ1 was evaluated against P. myriotylum by using a bipartite plate technique. An actively growing fresh 5 mm diameter mycelial plug of P. oligandrum was inoculated on one side and P. myriotylum on the other side of the plate containing clarified V8 agar media (5% V8 juice and 1.5% agar) whereas the plates without either P. myriotylum or P. oligandrum served as control. Each treatment was applied to three replicate plates and was repeated at least three times (a polycarbonate membrane with a 0.1 µm pore size (GVS filter technology, USA) was placed on the agar). Plates were firmly sealed (at least nine times) with parafilm (PARAFILM M, Bemis, USA) to avoid the leakage of VOCs and incubated at 25°C in the dark. The entire P. myriotylum mycelia, except for the plug, was collected for RNA extraction from 48 h, 60 h, and 72 h after inoculation of the bi-partite plates in triplicate. The collected mycelia were flash-frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantity were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA) and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions.

treatment_protocol: See the growth protocol for the description of treatments.

tag: tissue

value: mycelium

tag: time

tag: strain

tag: treatment

value: VOC-exposed


title: crizotinib treated SUPM2 cell line

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Adapters were trimmed using skewer embedded in docker4seq package (https://pubmed.ncbi.nlm.nih.gov/29069297/)
Reads were mapped with STAR  embedded in docker4seq package
Counts were generated using RSEM  embedded in docker4seq package
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited, raw counts

organism: Homo sapiens

source_name: lymphoma

growth_protocol: RPMI with 10% FBS or RPMI with 10% FBS containing 0.5-1 μM crizotinib

extract_protocol:
RNA was purified from wild type and crizotinib resistant cell lines using RNeasy mini kit (Qiagen).
libraries generated using TruSeq RNA Access library prep kit (Illumina) following manufacturer’s instructions and starting from 40 ng of DNA-free RNA

treatment_protocol: crizotinib to the medium at a starting concentration of 10 nmol/L. Medium was replaced with fresh RPMI-1640 supplemented with crizotinib every 48 or 72 hours, and cell viability was assessed by flow cytometry after staining with 200 nM tetramethylrhodamine methyl ester (TMRM). After 2-3 passages at the same crizotinib concentration, a higher dose of crizotinib was added to the medium until a final concentration of 1 μM was achieved.

tag: cell line

value: crizotinib treated


title: DENV_CX_UV_rep1

description: Dengue 1 crosslink +UV replicate 1


title: crizotinib treated COST cell line

value: COST


title: mycelium, VOC-exposed, 60hrs, rep 3


title: 4hr_contralateral

city: Los Angeles

first: Weihong

last: Ge

state: CA

address: 635 Charles E Young Dr South 355

country: USA

institute: UCLA

data_processing:
Demux, Cell Ranger 2.2.0, 10X genomics
Alignment/counts, Cell ranger 2.2.0, 10XGenomics
Clustering, Seurat V3
Genome_build: mm10
Supplementary_files_format_and_content: filtered_gene_bc-matrices generated from Cell ranger 2.2.0

organism: Mus musculus

source_name: brain

extract_protocol:
Single cell suspensions of adult cortices were prepared as described previously (Wu et al., 2017, Detecting activated cell populations using single-cell RNA-seq. Neuron 96, 313-329). Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (10X Genomics, PN-120237) and the Chromium Single Cell A Chip Kit (10X Genomics, PN-120236) as per the manufacturer ʼs protocol.
10XGenomics Single Cell 3' Droplet-based single cell approach

treatment_protocol: C57BL/6 mice weighing 24-28g were anesthetized with isoflurane. The body temperature of animals was maintained with a heating pad at 37C during surgery and 60 mins ischemia period. MCAO mice were sacrified at 4 different time points after MCAO, otgheter with 2 uninjured wild type controls

tag: age

value: 6 wks

tag: Sex

value: male

tag: brain region

value: cortical coresponding to ipsilateral perilesional area


title: DENV_CX_BACKGROUND_rep1

description: Dengue 1 crosslink background replicate 1

source_name: Dengue 1 crosslink background


title: untreated TS cell line

description: TS

value: TS

value: untreated


title: untreated SUPM2 cell line


title: untreated SR786 cell line


title: mycelium, VOC-exposed, 60hrs, rep 1


title: DENV_CX_CONTROL_rep2

description: Dengue 1 crosslink control replicate 2

source_name: Dengue 1 crosslink control


title: mycelium, VOC-exposed, 72hrs, rep 1


title: DENV_CX_CONTROL_rep1

description: Dengue 1 crosslink control replicate 1


title: heart_MI_7d_WT2_rep1

type: RNA

city: Shanghai

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

description: Gene expression in heart tissues after  7 days myocardial infarction

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

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

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: LV_MI_7 day

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: myocardial infarction

value: heart

value: myocardial infarction

tag: genotype/variation

value: WT

tag: time point

value: 7 days after myocardial infarction

tag: gender


title: heart_MI_7d_WT3_rep1


title: mycelium, VOC-exposed, 48hrs, rep 3


title: heart_MI_7d_KO2_rep1

value: KDM5B knock-out


title: untreated KARPAS cell line

description: KARPAS

value: KARPAS


title: DENV_1to500_rep2

description: Dengue 1 footprinting 1:500 replicate 2

source_name: Dengue 1 footprinting 1:500


title: mycelium, VOC-exposed, 48hrs, rep 2


title: DENV_CX_BACKGROUND_rep2

description: Dengue 1 crosslink background replicate 2


title: DENV_1to500_rep1

description: Dengue 1 footprinting 1:500 replicate 1


title: mycelium, VOC-exposed, 48hrs, rep 1


title: mycelium, VOC-exposed, 60hrs, rep 2


title: untreated DEL cell line

description: DEL

value: DEL


title: untreated COST cell line

description: COST


title: mycelium, non-exposed, 72hrs, rep 3

value: non-exposed


title: DENV_1to250_rep1

description: Dengue 1 footprinting 1:250 replicate 1

source_name: Dengue 1 footprinting 1:250

value: viral RNA


title: DENV_1to250_rep2

description: Dengue 1 footprinting 1:250 replicate 2


title: mycelium, non-exposed, 72hrs, rep 2

value: mycelium


title: mycelium, non-exposed, 60hrs, rep 3


title: untreated JB6 cell line


title: DENV_1to100_rep2

description: Dengue 1 footprinting 1:100 replicate 2

source_name: Dengue 1 footprinting 1:100


title: DENV_1to100_rep1

description: Dengue 1 footprinting 1:100 replicate 1


title: LEC_VEGFC_rep3

city: Liège

first: Bernard

last: Staumont

address: Avenue de l'Hôpital 11

country: Belgium

institute: University of Liège

data_processing:
Raw reads were demultiplexed and adapter-trimmed using Illumina bcl2fastq conversion software v2.17
After removal of reads aligning to rRNA, tRNA or mitochondrial sequences through Bowtie2 alignments, the remaining reads were aligned to the human UCSC hg19 reference genome (downloaded with annotations from Illumina iGenomes website) using STAR v2.5.2b
Quality of the sequencing data was successfully controlled using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Picard tools (http://broadinstitute.github.io/picard/) along with MultiQC
For the differential expression analysis at the gene level, raw gene counts were generated using STAR for all annotated transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including raw gene counts for each sample
Supplementary_files_format_and_content: Matrix table (text file) with raw gene counts for every gene and every sample

source_name: Lymphatic endothelial cells

growth_protocol: Lymphatic endothelial cells (HMVEC-dLyAd, CC-2810, Lonza, Verviers, Belgium) were cultured in EGM2-MV medium (CC-3202, Lonza) until confluence. All cells used were negative for mycoplasma contamination.

extract_protocol:
RNA was extracted using High Pure RNA Isolation Kit (11828665001, Roche). RNA quality was evaluated using the Agilent 2100 Bioanalyzer System and associated RNA 6000 Nano assay (Agilent Technologies). Samples with an RNA integrity number of less than 8 (RIN < 8) were discarded.
cDNA libraries were generated from 500 ng total RNA of each sample using Truseq® stranded mRNA Sample Preparation Kits (Illumina, CA, USA) following manufacturer’s instructions. Libraries were validated on a Bioanalyzer DNA 6000 nano chip and quantified by qPCR using the KAPA Library Quantification Universal kit (Roche)

treatment_protocol: Three replicates (controls) were treated with conditioned medium of LEC for 24 hours, four replicates were treated with conditioned medium of HaCaT-II-4 cells for 24 hours and four replicates were treated with VEGF-C (at 400 ng/ml) for 24 hours. Preparation of conditioned mediums (CMs): subconfluent tumor cells and LEC were incubated in serum-free DMEM medium (10938-025, Thermofisher, MA) and serum-free EBM2 medium (Lonza), respectively; after 48 hours for tumor cells and 24 hours for LEC, CM was harvested, centrifuged at 1000 × g for 10 min; CM aliquots were stored at −20 °C until use.

value: HMVEC-dLyAd (Human Dermal Lymphatic Microvascular Endothelial Cells)

value: treated with VEGF-C (400 ng/ml) for 24 hours


title: mycelium, non-exposed, 60hrs, rep 2


title: LEC_VEGFC_rep1


title: mycelium, non-exposed, 60hrs, rep 1


title: mycelium, non-exposed, 72hrs, rep 1


title: DENV_1to20_rep1

description: Dengue 1 footprinting 1:20 replicate 1

source_name: Dengue 1 footprinting 1:20


title: DENV_1to20_rep2

description: Dengue 1 footprinting 1:20 replicate 2


title: LEC_VEGFC_rep4


title: LEC_II4_rep4

value: treated with conditioned medium of HaCaT-II-4 cells for 24 hours


title: mycelium, non-exposed, 48hrs, rep 3


title: DENV_CONTROL_rep2

description: Dengue 1 control replicate 2

source_name: Dengue 1 control


title: LEC_VEGFC_rep2


title: LEC_II4_rep3


title: mycelium, non-exposed, 48hrs, rep 2


title: LEC_II4_rep2


title: high glucose treated HK-2 cells derived exosomes from third batch of cells

city: chandigarh

first: sanjeev

last: puri

department: uiet, biotechnology branch

country: India

institute: panjab university

description: Experimental

data_processing:
The amplification efficiency was calculated using algorithms similar to the LinReg software. All assays were inspected for distinct melting curves and the Tm was checked to be within known specifications for the assay. Furthermore assays must be detected with 5 Cqs less than the negative control, and with Cq < 37 to be included in the data analysis. Data that did not pass these criteria were omitted from any further analysis. Cq was calculated as the 2nd derivative.
Using NormFinder the best normalizer was found to be the average of the assays detected in all samples. The formula used to calculate the normalized Cq values are: Normalized Cq = average Cq (n=6) – assay Cq (sample)

label: SYBR Green

source_name: kidney proximal tubular cells

label_protocol: PCR assays were performed using the miRCURY LNA™ Universal RT microRNA PCR (Exiqon, Denmark) following the manufacturer’s instructions.19 μl RNA was reverse transcribed in 95 μl reactions using the miRCURY LNA™ Universal RT microRNA PCR, Polyadenylation and cDNA synthesis kit (Exiqon) with UniSp6 as cDNA synthesis control. cDNA was diluted 50 x and assayed in 10 ul PCR reactions according to the protocol for miRCURY LNA™ Universal RT microRNA PCR; each microRNA was assayed once by qPCR on the microRNA Ready-to-Use PCR, Human panel I+II using ExiLENT SYBR® Green master mix. The amplification was performed in a LightCycler® 480 Real-Time PCR System  (Roche) in 384 well plates.

growth_protocol: HK-2 cells were cultivated in Keratinocyte Serum Free Media (K-SFM) (GIBCO, USA) supplemented with epidermal growth factor (EGF, 5 ng/ml) (GIBCO, USA) and bovine pituitary extract (BPE, 0.05 mg/ml) (GIBCO, USA) as growth factors followed by 1% penicillin-streptomycin (MP Biomedicals, USA).

extract_protocol: Total RNA was extracted with mirVana™ miRNA Isolation Kit (Invitrogen™, USA)

treatment_protocol: HK-2 cells were treated with low glucose (5mM) and high glucose (30mM) for 96 hours. Exosomes were isolated from the supernatant of these cells.

tag: cell type

value: human kidney proximal tubular cells

tag: activation agent

value: high glucose

value: 96 hours


title: mycelium, non-exposed, 48hrs, rep 1


title: LEC_CTRL_rep3

value: untreated (only with condtioned medium of LEC)


title: DENV_CONTROL_rep1

description: Dengue 1 control replicate 1


title: high glucose treated HK-2 cells derived exosomes from one batch of cells

description: Experimental


title: low glucose treated HK-2 cells derived exosomes from third batch of cells

description: Control

value: low glucose


title: high glucose treated HK-2 cells derived exosomes from second batch of cells

description: Experimental


title: Nematostella vectensis MHC::mCherry Adult mesentery_20955

city: Vienna

first: Alison

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

description:
NemVecMesenteryBULK.txt
20955

data_processing:
adapter trimming (cutadapt)
rRNA removal (SorMeRna)
read mapping (tophat)
counting (HTSeqq)
Genome_build: Reads were mapped to a customized transcriptome (David Fredman 2013)
Supplementary_files_format_and_content: NemVecMesenteryBULK.txt

organism: Nematostella vectensis

source_name: Adult mesentery

extract_protocol:
Mesenteries from eight Nematostella vectensis::MHC::mCherry adults were isolated, and the distal-most tissue removed. Tissue pieces were dissociated into single-cell suspensions in a papain (Sigma-P-4762) / collagenase (Sigma-CC9407) solution, cell suspensions were washed, and then FACS sorted into TRIZOL (ThermoFisher Scientific) as mCherry+ or mCherry- populations.
NEB polyA

value: mesentery muscle


title: Nematostella vectensis MHC::mCherry Adult mesentery_20954

description:
NemVecMesenteryBULK.txt
20954

value: mesentery non muscle


title: Nematostella vectensis MHC::mCherry Adult mesentery_20956

description:
NemVecMesenteryBULK.txt
20956


title: LEC_CTRL_rep2


title: low glucose treated HK-2 cells derived exosomes from second batch of cells

description: Control


title: LEC_CTRL_rep1


title: Nematostella vectensis MHC::mCherry Adult mesentery_20953

description:
NemVecMesenteryBULK.txt
20953


title: HEK293_NC (PacBio Sequel II)

status: Public on Dec 30 2022

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

description: HEK293 cell line is a permanent line established from primary embryonic human kidney

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference human genome using Tophat.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq functions estimate Size Factors and nbinomTest. P value < 0.05 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: human genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each samples

source_name: HEK293 cells transfected with empty vector (NC) for 48 hours

growth_protocol: The human HEK293 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
For PacBio-Seq, Total RNA samples with RIN value≥8 were used for constructing the cDNA libraries in PacBio sequencing.
Using the Clontech SMARTer PCR cDNA Synthesis Kit (Takara Biotechnology, Dalian, China), 4μg RNA is synthesized to cDNA and subsequently amplified to generate double-stranded cDNA. The cDNA was then size selected for <4kb, >4 kb fractions using the BluePippin™ Size Selection System (Sage Science, Beverly, MA，USA). Each SMRTbell library was constructed using 1μg size-selected cDNA with the Pacific Biosciences SMRTbell template prep kit. The binding of SMRT bell templates to polymerases was conducted using the Sequel II Binding Kit, and then primer annealing was performed.
Sequencing was carried out on the PacBio Sequel II platform by Annoroad Gene Technology Company (Bejing, China).

treatment_protocol: HEK293 cells were transfected with either GFP-EBV EBNA2 vector or empty vector (NC)  for 48 hours.

value: embryonic human kidney

value: transfected with empty vector (NC)


title: HEK293_E2 (PacBio Sequel II)

source_name: HEK293 cells transfected with GFP-EBV EBNA2 vector for 48 hours

value: transfected with GFP-EBV EBNA2 vector


title: low glucose treated HK-2 cells derived exosomes from one batch of cells

description: Control


title: PD-005_MG1655-del-fhuA_Fed-batch_6h__2

city: La Jolla

first: Cameron

last: Lamoureux

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

data_processing:
Raw read trimming was performed with Trim Galore using the default options, followed by FastQC on the trimmed reads.
Reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using bowtie with the following optional arguments: -X 1000, -3 3, -n 2
Read direction was inferred with RSEQC.
Read counts were generated with featureCounts with the following optional arguments: -p -B -C -P --fracOverlap 0.5
Quality control metrics were assembled with MultiQC and the final expression was reported in units of log2-transformed transcripts per million for each gene.
Assembly: NC_000913.3
Supplementary files format and content: ddb_log_tpm.csv contains log2[TPM] values for all samples and genes.
Supplementary files format and content: ddb_counts.csv contains raw read counts as computed by featureCounts for all samples and genes.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: MG1655 del_fhuA

extract_protocol:
3 ml of cell broth (at an A600 ≈ 0.6) was immediately added to two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m. The supernatant was decanted, and the cell pellet was stored at −80 °C. Cell pellets were thawed and incubated with Ready-Lyse Lysozyme, SuperaseIn, protease K and 20% SDS for 20 min at 37 °C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase treatment was performed for 30 min at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA nano chip on a bioanalyser. The ribosomal RNA was removed using an Illumina Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around 300 bp

value: MG1655 del_fhuA

tag: culture type

value: fed-batch

value: 6 hour


title: PD-005_MG1655-del-fhuA_Batch_6h__3

value: batch


title: PD-005_MG1655-del-fhuA_Fed-batch_15h__1

value: 15 hour


title: PD-005_MG1655-del-fhuA_Batch_6h__2


title: PD-005_MG1655-del-fhuA_Fed-batch_15h__2


title: PD-005_MG1655-del-fhuA_Batch_6h__1


title: PD-005_MG1655-del-fhuA_Fed-batch_6h__1


title: HCT116, NVP-2, Rep 2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

data_processing:
Reads were mapped against the human genome (GRCh38) and rRNA sequences using ContextMap v2.7.9 and BWA as short read aligner.
Number of read fragments per gene were determined using featureCounts and gene annotations from Gencode version 25.
Assembly: GRCh38
Supplementary files format and content: gene read counts

molecule: polyA RNA

growth_protocol: HCT116 cells were cultured in McCoy’s 5A Medium supplemented with 10% FBS and 100 U/ml penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA isolation and on-column digestion of genomic DNA was performed using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was assessed by TapeStation 4200 and samples with a RIN value of 10 were used for library preparation and sequencing.
PolyA-selected libraries were made using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. The libraries were pooled and sequenced on one lane of an Illumina NextSeq500 (High Output 1 x 75 bp; single-end).

treatment_protocol: The cells were treated for 8 hours with the indicated compounds prior to extraction of total RNA.

value: colorectal carcnoma, epithelial

tag: genotype

value: WT


title: HCT116, NVP-2, Rep 3


title: HCT116, NVP-2, Rep 1


title: HCT116, Nutlin-3a+NVP-2, Rep 2

value: Nutlin-3a (10 uM)+NVP-2 (20 nM), 8 hr


title: HCT116, Nutlin-3a+NVP-2, Rep 3


title: NCC-2

type: genomic

city: Badalona

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

molecule: genomic DNA

source_name: DRG-derived neural crest cells

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: DRG-derived neural crest cells


title: 12-215-LN

description: Melanoma patient-derived short term culture

extract_protocol: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner.


title: 12-126 BM


title: 12-019-LN


title: H9

source_name: Embryonic stem cells

value: Embryonic stem cells


title: NCC-4

source_name: Facial ganglia-derived neural crest cells


title: LEC_II4_rep1

value: HMVEC-dLyAd (Human Dermal Lymphatic Microvascular Endothelial Cells)

value: treated with conditioned medium of HaCaT-II-4 cells for 24 hours


title: NCC-3


title: NM-B

source_name: Human Epidermal Melanocytes-medium (Sciencell, Cat. No. 2210)


title: 4L

source_name: WM239-derived 113/6-4L melanoma cell line


title: 501MEL

description: Melanoma cell line


title: HCT116, Nutlin-3a+NVP-2, Rep 1


title: HCT116, DMSO, Rep 3

value: DMSO, 8 hr


title: HCT116, Nutlin-3a, Rep 3

value: Nutlin-3a (10uM), 8 hr


title: 11-161-BM


title: 10-230-P


title: 12-273-BM


title: NCC-1


title: 11-103-BM


title: NM-A

source_name: Human Epidermal Melanocytes-light (Sciencell, Cat. No. 2200)


title: HRV15-024, Day2, PM1

city: ANN ARBOR

first: ALFRED

middle: Olivier

last: HERO

state: MI

address: 1301 BEAL AVE

institute: UNIVERSITY OF MICHIGAN

data_processing:
395 processed samples are included in this repository, each processed from paired end FASTQ files, with file names listed in columns K (Processed), L and M (paired end FASTQ) in the SAMPLES list above.
Assembly: The read counts in each pair of paired end FASTQ file were aligned and mapped to the reference genome Homo_sapiens.GRCh38.84 using HISAT2 2.0.4 software.
Supplementary files format and content: Processed samples were obtained by applying TPM (transcripts per million) normalization to the aligned and mapped counts.
Supplementary files format and content: The processed samples are given in two csv formats:
Supplementary files format and content: 1) A data matrix (genematrix_TPM.csv) of TPM normalized counts whose first column and first row are respectively  annotated with gene names and sample names;
Supplementary files format and content: 2) a zipped file (gene_TPM.zip) containing 395 files of TPM normalized counts, where each file is annotated by the sample name.

source_name: Whole blood

extract_protocol:
Whole blood was collected in PAXgene™ Blood RNA tubes (PreAnalytiX), and total RNA extracted using the PAXgene™ Blood miRNA Kit (QIAGEN) using the manufacturer’s recommended protocol.
RNA quantity and quality were assessed using Nanodrop 2000 spectrophotometer (Thermo-Fisher) and Bioanalyzer 2100 with RNA 6000 Nano Chips (Agilent).
RNA sequencing libraries were prepared using Illumina TruSeq mRNA Library Kit with RiboZero Globin depletion, and sequenced on an Illumina NextSeq sequencer with 50bp paired-end reads (target 40M reads per sample)

treatment_protocol:
Rhinovirus (RV39) inoculation was administered via intranasal drops of diluted virus after blood draw on the morning of day zero (4th day of challenge study)
The inoculation dose was 100 TCID50 in 1 mL Lactated Ringer’s Solution. The IND number for the RV-39 challenge pool was 12934

value: Whole blood

tag: subject

tag: day


title: HRV15-024, Day2, PM2

tag: tissue


title: HRV15-024, Day0, PM1

tag: time


title: HRV15-024, Day3, PM1


title: HRV15-024, DayMinus1, PM1


title: 09-203-LN


title: 10-040-LN


title: HRV15-024, Day4, PM1


title: HRV15-024, DayMinus3, AM

value: AM


title: 11-001-BM


title: HRV15-024, DayMinus2, PM1


title: HRV15-024, DayMinus3, PM2


title: HRV15-024, DayMinus3, PM1


title: HRV15-024, Day1, AM


title: HRV15-024, Day2, AM


title: HRV15-024, DayMinus1, PM2


title: HRV15-024, DayMinus1, AM


title: HRV15-023, FollowUpDay21_28,


title: HRV15-023, Day1, PM2


title: HRV15-023, DayMinus1, PM1


title: HRV15-023, Day2, AM


title: HRV15-023, Day0, AM


title: HRV15-023, DayMinus1, PM2


title: HRV15-024, DayMinus2, AM


title: HRV15-024, Day0, AM


title: HRV15-023, Day2, PM2


title: HRV15-023, Day1, PM1


title: HRV15-023, Day2, PM1


title: HRV15-023, Day4, AM


title: HRV15-024, FollowUpDay21_28,


title: HRV15-023, DayMinus2, PM1


title: HRV15-023, Day1, AM


title: HRV15-023, DayMinus3, PM1


title: HRV15-023, DayMinus2, AM


title: HRV15-023, Day4, PM1


title: HRV15-023, Day0, PM1


title: HRV15-023, DayMinus3, PM2


title: HRV15-023, DayMinus1, AM


title: HRV15-023, DayMinus3, AM


title: HRV15-023, Day3, PM1


title: HRV15-023, Day3, AM


title: HRV15-022, Day0, AM


title: HRV15-023, DayMinus2, PM2


title: HRV15-022, Day1, PM1


title: HRV15-022, Day2, PM1


title: HRV15-022, DayMinus1, AM


title: HRV15-022, Day2, PM2


title: HRV15-022, Day1, PM2


title: HRV15-022, DayMinus1, PM2


title: HRV15-022, DayMinus3, PM2


title: HRV15-022, DayMinus2, AM


title: HRV15-022, Day0, PM1


title: HCT116, Nutlin-3a, Rep 2


title: HRV15-022, DayMinus2, PM2


title: HRV15-022, Day4, AM


title: HRV15-024, Day4, AM


title: HRV15-022, DayMinus1, PM1


title: HCT116, Nutlin-3a, Rep 1


title: HRV15-022, Day1, AM


title: HCT116, DMSO, Rep 2


title: HRV15-022, Day3, AM


title: HCT116, DMSO, Rep 1


title: HRV15-022, Day4, PM1


title: HRV15-022, FollowUpDay21_28,


title: HRV15-022, Day2, AM


title: HRV15-021, FollowUpDay21_28,


title: HRV15-022, Day3, PM1


title: HRV15-022, DayMinus2, PM1


title: HRV15-022, DayMinus3, AM


title: HRV15-024, Day1, PM1


title: HRV15-021, Day1, PM1


title: HRV15-021, DayMinus1, AM


title: HRV15-021, Day0, AM


title: HRV15-021, Day1, PM2


title: HRV15-021, DayMinus1, PM2


title: HRV15-021, Day1, AM


title: HRV15-021, Day2, PM1


title: HRV15-021, Day2, PM2


title: HRV15-021, Day3, AM


title: HRV15-021, DayMinus1, PM1


title: HRV15-021, Day2, AM


title: HRV15-021, DayMinus2, PM1


title: HRV15-021, DayMinus2, AM


title: HRV15-021, Day4, AM


title: HRV15-021, Day3, PM1


title: HRV15-024, DayMinus2, PM2


title: HRV15-021, DayMinus3, PM1


title: HRV15-021, Day0, PM1


title: HRV15-024, Day3, AM


title: HRV15-021, DayMinus3, AM


title: HRV15-021, DayMinus3, PM2


title: HRV15-020, DayMinus1, PM1


title: HRV15-021, Day4, PM1


title: HRV15-020, Day1, AM


title: HRV15-020, Day0, AM


title: HRV15-024, Day1, PM2


title: HRV15-020, Day1, PM1


title: HRV15-020, Day2, PM2


title: HRV15-020, DayMinus1, AM


title: HRV15-020, Day3, AM


title: HRV15-020, Day1, PM2


title: HRV15-020, DayMinus1, PM2


title: HRV15-020, Day2, AM


title: HRV15-020, FollowUpDay21_28,


title: HRV15-020, DayMinus3, PM1


title: HRV15-020, Day4, AM


title: HRV15-020, DayMinus2, PM1


title: HRV15-020, DayMinus3, PM2


title: HRV15-020, DayMinus2, PM2


title: HRV15-020, DayMinus3, AM


title: HRV15-020, Day0, PM1


title: HRV15-020, Day4, PM1


title: HRV15-021, DayMinus2, PM2


title: HRV15-020, Day3, PM1


title: HRV15-019, Day2, AM


title: HRV15-019, DayMinus1, PM1


title: HRV15-019, Day4, AM


title: HRV15-019, Day0, AM


title: HRV15-019, FollowUpDay21_28,


title: HRV15-019, Day2, PM1


title: HRV15-019, Day1, AM


title: HRV15-019, Day2, PM2


title: HRV15-020, Day2, PM1


title: HRV15-019, Day3, AM


title: HRV15-019, DayMinus1, PM2


title: HRV15-019, Day1, PM2


title: HRV15-020, DayMinus2, AM


title: HRV15-019, DayMinus1, AM


title: HRV15-019, DayMinus2, PM2


title: HRV15-019, Day1, PM1


title: HRV15-019, DayMinus2, AM


title: HRV15-019, DayMinus3, PM1


title: HRV15-019, Day4, PM1


title: HRV15-019, DayMinus3, AM


title: HRV15-019, DayMinus2, PM1


title: HRV15-019, Day0, PM1


title: HRV15-019, Day3, PM1


title: HRV15-019, DayMinus3, PM2


title: HRV15-018, FollowUpDay21_28,


title: HRV15-018, Day2, AM


title: HRV15-022, DayMinus3, PM1


title: HRV15-018, DayMinus1, AM


title: HRV15-018, Day1, PM1


title: HRV15-018, Day2, PM1


title: HRV15-018, Day0, AM


title: HRV15-018, Day3, AM


title: HRV15-018, Day1, AM


title: HRV15-018, Day1, PM2


title: HRV15-018, DayMinus1, PM1


title: HRV15-018, Day4, AM


title: HRV15-018, DayMinus1, PM2


title: HRV15-018, DayMinus2, PM2


title: HRV15-018, Day4, PM1


title: HRV15-018, DayMinus3, PM2


title: HRV15-018, DayMinus3, PM1


title: HRV15-018, Day2, PM2


title: HRV15-018, DayMinus2, AM


title: HRV15-018, DayMinus3, AM


title: HRV15-018, DayMinus2, PM1


title: HRV15-017, Day2, AM


title: HRV15-018, Day0, PM1


title: HRV15-018, Day3, PM1


title: HRV15-017, DayMinus1, PM1


title: HRV15-017, FollowUpDay21_28,


title: HRV15-017, Day0, AM


title: HRV15-017, Day1, AM


title: HRV15-017, DayMinus1, AM


title: HRV15-017, Day2, PM2


title: HRV15-017, Day3, AM


title: HRV15-017, Day1, PM2


title: HRV15-017, Day4, AM


title: HRV15-017, Day2, PM1


title: HRV15-017, DayMinus3, PM1


title: HRV15-017, DayMinus2, PM1


title: HRV15-017, Day3, PM1


title: HRV15-017, DayMinus3, PM2


title: HRV15-013, Day1, AM


title: HRV15-017, DayMinus2, AM


title: HRV15-017, DayMinus2, PM2


title: HRV15-013, Day0, AM


title: HRV15-017, Day0, PM1


title: HRV15-017, DayMinus1, PM2


title: HRV15-017, Day4, PM1


title: HRV15-013, Day2, PM2


title: HRV15-013, Day3, AM


title: HRV15-013, Day2, PM1


title: HRV15-013, Day1, PM2


title: HRV15-013, Day1, PM1


title: HRV15-013, DayMinus1, PM1


title: HRV15-013, Day2, AM


title: HRV15-017, Day1, PM1


title: HRV15-013, Day4, PM1


title: HRV15-017, DayMinus3, AM


title: HRV15-013, Day4, AM


title: HRV15-013, DayMinus1, AM


title: HRV15-013, DayMinus1, PM2


title: HRV15-013, Day3, PM1


title: HRV15-013, DayMinus3, PM1


title: HRV15-013, DayMinus2, AM


title: HRV15-013, DayMinus2, PM1


title: HRV15-013, DayMinus2, PM2


title: HRV15-013, DayMinus3, AM


title: HRV15-013, DayMinus3, PM2


title: HRV15-013, Day0, PM1


title: HRV15-012, DayMinus1, AM


title: HRV15-012, Day1, PM1


title: HRV15-012, Day1, PM2


title: HRV15-012, Day2, AM


title: HRV15-012, DayMinus1, PM2


title: HRV15-012, Day1, AM


title: HRV15-012, Day3, AM


title: HRV15-012, FollowUpDay21_28,


title: HRV15-012, DayMinus2, PM2


title: HRV15-012, Day2, PM1


title: HRV15-012, Day4, AM


title: HRV15-012, Day0, AM


title: HRV15-012, DayMinus2, PM1


title: HRV15-012, Day4, PM1


title: HRV15-013, FollowUpDay21_28,


title: HRV15-012, DayMinus3, PM2


title: HRV15-012, Day0, PM1


title: HRV15-012, Day3, PM1


title: HRV15-012, Day2, PM2


title: HRV15-012, DayMinus3, PM1


title: HRV15-012, DayMinus3, AM


title: HRV15-011, FollowUpDay21_28,


title: HRV15-011, DayMinus1, PM2


title: HRV15-011, Day1, AM


title: HRV15-011, DayMinus1, PM1


title: HRV15-011, DayMinus1, AM


title: HRV15-011, Day1, PM1


title: HRV15-011, Day2, AM


title: HRV15-011, Day2, PM1


title: HRV15-011, Day3, AM


title: HRV15-011, Day4, AM


title: HRV15-011, DayMinus3, AM


title: HRV15-011, Day4, PM1


title: HRV15-011, DayMinus2, PM1


title: HRV15-011, DayMinus3, PM2


title: HRV15-011, DayMinus2, AM


title: HRV15-012, DayMinus2, AM


title: HRV15-011, Day2, PM2


title: HRV15-009, DayMinus2, PM1


title: HRV15-009, Day2, AM


title: HRV15-012, DayMinus1, PM1


title: HRV15-011, Day3, PM1


title: HRV15-011, Day1, PM2


title: HRV15-009, FollowUpDay21_28,


title: HRV15-009, Day1, PM1


title: HRV15-009, Day4, AM


title: HRV15-009, Day0, AM


title: HRV15-009, DayMinus1, PM1


title: HRV15-009, Day2, PM2


title: HRV15-011, Day0, AM


title: HRV15-009, Day2, PM1


title: HRV15-009, DayMinus1, AM


title: HRV15-009, Day1, PM2


title: HRV15-009, DayMinus3, AM


title: HRV15-009, Day0, PM1


title: HRV15-011, DayMinus2, PM2


title: HRV15-011, DayMinus3, PM1


title: HRV15-009, Day4, PM1


title: HRV15-009, Day1, AM


title: HRV15-011, Day0, PM1


title: HRV15-009, DayMinus2, AM


title: HRV15-009, Day3, PM1


title: HRV15-009, DayMinus2, PM2


title: HRV15-009, DayMinus3, PM2


title: HRV15-008, DayMinus1, PM1


title: HRV15-008, DayMinus1, AM


title: HRV15-008, Day0, AM


title: HRV15-008, Day2, AM


title: HRV15-009, DayMinus1, PM2


title: HRV15-008, Day1, PM2


title: HRV15-008, Day3, AM


title: HRV15-008, Day2, PM1


title: HRV15-008, Day2, PM2


title: HRV15-008, Day4, AM


title: HRV15-009, Day3, AM


title: HRV15-008, DayMinus1, PM2


title: HRV15-008, Day1, AM


title: HRV15-008, DayMinus2, AM


title: HRV15-008, FollowUpDay21_28,


title: HRV15-008, Day3, PM1


title: HRV15-008, DayMinus3, PM1


title: HRV15-008, DayMinus2, PM2


title: HRV15-008, DayMinus2, PM1


title: HRV15-008, Day4, PM1


title: HRV15-008, DayMinus3, AM


title: HRV15-008, DayMinus3, PM2


title: HRV15-007, Day1, PM1


title: HRV15-007, DayMinus1, PM1


title: HRV15-007, FollowUpDay21_28,


title: HRV15-007, Day4, AM


title: HRV15-007, Day2, PM1


title: HRV15-007, Day3, AM


title: HRV15-008, Day1, PM1


title: HRV15-007, Day0, AM


title: HRV15-008, Day0, PM1


title: HRV15-007, Day0, PM1


title: HRV15-007, Day1, AM


title: HRV15-007, Day2, AM


title: HRV15-007, Day1, PM2


title: HRV15-007, Day2, PM2


title: HRV15-007, DayMinus1, AM


title: HRV15-007, DayMinus3, AM


title: HRV15-007, DayMinus3, PM1


title: HRV15-007, DayMinus2, AM


title: HRV15-007, Day4, PM1


title: HRV15-007, DayMinus3, PM2


title: HRV15-007, Day3, PM1


title: HRV15-007, DayMinus1, PM2


title: HRV15-007, DayMinus2, PM2


title: HRV15-007, DayMinus2, PM1


title: HRV15-006, Day0, AM


title: HRV15-006, Day1, AM


title: HRV15-006, DayMinus1, AM


title: HRV15-006, Day2, AM


title: HRV15-006, Day1, PM2


title: HRV15-006, FollowUpDay21_28,


title: HRV15-006, Day1, PM1


title: HRV15-006, DayMinus1, PM2


title: HRV15-006, DayMinus1, PM1


title: HRV15-006, Day4, AM


title: HRV15-006, DayMinus3, PM1


title: HRV15-006, DayMinus2, PM2


title: HRV15-006, DayMinus2, AM


title: HRV15-006, Day3, AM


title: HRV15-006, Day2, PM1


title: HRV15-005, Day1, PM1


title: HRV15-006, DayMinus2, PM1


title: HRV15-005, Day1, PM2


title: HRV15-006, Day4, PM1


title: HRV15-006, DayMinus3, PM2


title: HRV15-005, Day0, AM


title: HRV15-005, DayMinus1, PM2


title: HRV15-005, FollowUpDay21_28,


title: HRV15-005, Day3, AM


title: HRV15-005, Day2, PM1


title: HRV15-005, Day1, AM


title: HRV15-006, Day2, PM2


title: HRV15-005, DayMinus2, PM1


title: HRV15-005, Day2, PM2


title: HRV15-005, DayMinus1, AM


title: HRV15-005, DayMinus2, PM2


title: HRV15-006, Day0, PM1


title: HRV15-005, DayMinus3, PM1


title: HRV15-005, DayMinus3, AM


title: HRV15-005, Day3, PM1


title: HRV15-006, Day3, PM1


title: HRV15-005, DayMinus2, AM


title: HRV15-005, Day0, PM1


title: HRV15-004, Day1, PM2


title: HRV15-005, Day4, PM1


title: HRV15-006, DayMinus3, AM


title: HRV15-004, Day0, AM


title: HRV15-004, Day1, AM


title: HRV15-004, Day2, AM


title: HRV15-004, Day2, PM1


title: HRV15-005, DayMinus1, PM1


title: HRV15-004, DayMinus1, PM2


title: HRV15-004, Day1, PM1


title: HRV15-004, Day4, AM


title: HRV15-005, Day4, AM


title: HRV15-004, Day3, AM


title: HRV15-004, FollowUpDay21_28,


title: HRV15-005, DayMinus3, PM2


title: HRV15-004, DayMinus2, AM


title: HRV15-005, Day2, AM


title: HRV15-004, DayMinus3, PM2


title: HRV15-004, Day3, PM1


title: HRV15-004, DayMinus2, PM1


title: HRV15-004, DayMinus3, PM1


title: HRV15-004, Day4, PM1


title: HRV15-004, DayMinus1, PM1


title: HRV15-002, FollowUpDay21_28,


title: HRV15-002, DayMinus1, AM


title: HRV15-004, DayMinus2, PM2


title: HRV15-004, Day0, PM1


title: HRV15-002, Day1, AM


title: HRV15-004, DayMinus3, AM


title: HRV15-002, Day3, AM


title: HRV15-002, Day4, AM


title: HRV15-004, DayMinus1, AM


title: HRV15-002, Day2, PM1


title: HRV15-002, Day2, PM2


title: HRV15-002, Day0, AM


title: HRV15-002, DayMinus1, PM2


title: HRV15-002, Day1, PM2


title: HRV15-002, DayMinus1, PM1


title: HRV15-002, Day2, AM


title: HRV15-002, Day4, PM1


title: HRV15-004, Day2, PM2


title: HRV15-002, DayMinus3, PM1


title: HRV15-002, DayMinus3, AM


title: HRV15-002, DayMinus2, PM2


title: HRV15-002, Day3, PM1


title: HRV15-002, Day0, PM1


title: HRV15-002, DayMinus2, AM


title: HRV15-002, DayMinus2, PM1


title: HRV15-002, DayMinus3, PM2


title: MDA-MB-231-Control-2

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
BaseCall performed with CASAVA
Reads were aligned to the hg38 version of the human genome as reference using STAR v2.7.3a after removal of contaminants  (rDNA, tRNA, mtrDNA) were removed using Bowtie2 (version 2.2.5)
Reads aligned to STAR were quantified to the hg38-Ref Seq Transcripts 96 (released- 2020-11-02), normalized by TMM and transfromed by log2
Normalized counts were used to determine differential gene expression between DMSO controls and NSC33353 cells
All analyses were corrected for multiple comparisons at false discovery rate (FDR) 0.05 (at least)
Assembly: hg38
Supplementary files format and content: txt files contain raw and normalized counts

source_name: MDA-MB-231 treated with vehicle (DMSO)_replicate 1

growth_protocol: Cells were grown and maintained in Dulbecco's modified Eagle medium/F12 medium (GIBCO) supplemented with fetal bovine serum (FBS;10%) and penicillin-streptomycin (100 units/mL).

extract_protocol:
RNA was isolated from NSC33353 treated and DMSO treated MDA-MB-231 cells using the Universal RNA/DNA Isolation kit (Qiagen, Germantown, MD) following the manufacturer's protocol
Single-end libraries (1 x 75) were prepared (100ng per sample) using the Illumina's RNA Exome Library Prep kit

treatment_protocol: MDA-MB-231 cells treated with 2.5 uM of the NSC33353 for 24 h

value: Breast Cancer cel line


title: MDA-MB-231-Control-1


title: MDA-MB-231-2.5uM-1

source_name: MDA-MB-231 treated with 5uM of NSC33353_replicate 1


title: HRV15-002, Day1, PM1


title: DO_Mouse_High Fat_Muscle-148

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description:
RNA sequencing using MiSeq
Muscle-148

data_processing:
FastQC was run on all samples to ensure adequate per base sequence quality, per base N content, and adapter content. FastQC analysis detected adapter content at the end of the reads. Trim Galore version 0.4.4 was used to trim Illumina adapter sequence from the end of the reads. Any reads that were trimmed to less than 50 bp were removed.
FASTQ files of trimmed Illumina Tru-Seq RNA-Seq reads were aligned to the pooled transcriptome of all 8 DO founder strains (ftp://churchill-lab.jax.org/software/GBRS/) using Bowtie version 1.2.2  with the following parameters: -a -v 3 --best --strata. This configuration allows up to 3 mismatches and reports all alignments. After alignment, the total sequenced reads, total aligned reads, and alignment rate were calculated for each sample.
Genome_build: The Expectation Maximization algorithm for allele-specific expression (EMASE) was used to resolve the probable origin of multireads and estimate the gene abundance. This was implemented through the GBRS software using the EMASE model M4, which apportions multi-reads equally among genes, isoforms, and alleles. Multiway allele specificity was quantified for each sample using the “quantify” function in GBRS. Then the sample’s genome was reconstructed based upon gene-level transcripts per million signals in the 8 DO founder strains using GBRS “reconstruct” function and recommended settings. For each sample, the computationally reconstructed genome was then used (“quantify” function) to estimate the expression signal resulting in normalized diploid expression for each gene for each sample. Each gene was assigned a sample-specific founder genotype signifying the two founder strains for the diploid call.
Supplementary_files_format_and_content: total counts

source_name: Muscle

growth_protocol: Male Diversity Outbred mice (Jackson Laboratory, Bar Harbor, ME) at 6 weeks of age were housed individually in polycarbonate cages with hardwood bedding (Northeastern Products Corporation, Warrensburg, NY) and a cotton fiber nestlet. Cages were maintained at a temperature between 20 and 25 ± 3 degrees C, relative humidity of 30-70%, and a 12-hour light-dark cycle. Animals were fed control diet (10 kcal % fat, D12450J/D12450JN; Research Diets, New Brunswick, NJ) ad libitum until start of the study. Reverse-osmosis treated tap water (City of Durham, NC) was provided to animals ad libitum throughout the study.

extract_protocol:
RNA was extracted from liver, muscle, and adipose samples collected from each animal at necropsy. Tissues (10 mg liver; 20 mg muscle; 60 mg adipose) were homogenized in the FastPrep 24-5G Homogenizer (MP Biomedicals, Irvine, CA) using Lysing Matrix D tubes. The RNA extractions were completed using the Maxwell RSC simplyRNA Tissue kit (Promega, Madison, WI).  Lysate pre-processing and cartridge preparation was done on the Promega Maxprep liquid handler and extractions were performed using the Promega Maxwell RSC48 instrument.  Sample concentrations were quantified  using the NanoDrop 8000 (Thermo Fisher Scientific) and RNA quality was checked on the Agilent 5200 Fragment Analyzer System (Agilent Technologies, Santa Clara, CA) using the Standard Sensitivity RNA kit (15NT). Samples with RQN ≥ 8 (muscle and liver) and RQN ≥ 7 (adipose) were used for sequencing.
RNA libraries were prepared using TrueSeq Stranded Total RNA LP kit (Illumina, San Diego, CA) using manufacturer protocols and 100 ng of RNA. Sequencing was conducted using the MiSeq system  (Illumina, San Diego, CA).

treatment_protocol: At study start animals were randomized and half of the mice (N=75) were placed on the High Fat diet (60 kcal %, D12492/D12492N; Research Diets, New Brunswick, NJ) for 14 weeks while the other half (N=75) continued receiving control diet ad libitum, except during designated fasting periods for measuring resting state glucose levels.

value: Muscle

value: male

tag: feed type

value: High fat diet

tag: duration

tag: duration unit

value: weeks


title: DO_Mouse_High Fat_Muscle-145

description:
RNA sequencing using MiSeq
Muscle-145


title: DO_Mouse_High Fat_Muscle-146

description:
RNA sequencing using MiSeq
Muscle-146


title: DO_Mouse_High Fat_Muscle-147

description:
RNA sequencing using MiSeq
Muscle-147


title: DO_Mouse_High Fat_Muscle-150

description:
RNA sequencing using MiSeq
Muscle-150


title: DO_Mouse_High Fat_Muscle-144

description:
RNA sequencing using MiSeq
Muscle-144


title: DO_Mouse_High Fat_Muscle-143

description:
RNA sequencing using MiSeq
Muscle-143


title: DO_Mouse_High Fat_Muscle-142

description:
RNA sequencing using MiSeq
Muscle-142


title: DO_Mouse_High Fat_Muscle-140

description:
RNA sequencing using MiSeq
Muscle-140


title: DO_Mouse_High Fat_Muscle-139

description:
RNA sequencing using MiSeq
Muscle-139


title: DO_Mouse_High Fat_Muscle-141

description:
RNA sequencing using MiSeq
Muscle-141


title: DO_Mouse_High Fat_Muscle-137

description:
RNA sequencing using MiSeq
Muscle-137


title: DO_Mouse_High Fat_Muscle-136

description:
RNA sequencing using MiSeq
Muscle-136


title: MDA-MB-231-2.5uM-2

source_name: MDA-MB-231 treated with 5uM of NSC33353_replicate 2


title: DO_Mouse_High Fat_Muscle-131

description:
RNA sequencing using MiSeq
Muscle-131


title: DO_Mouse_High Fat_Muscle-133

description:
RNA sequencing using MiSeq
Muscle-133


title: DO_Mouse_High Fat_Muscle-132

description:
RNA sequencing using MiSeq
Muscle-132


title: DO_Mouse_High Fat_Muscle-135

description:
RNA sequencing using MiSeq
Muscle-135


title: DO_Mouse_High Fat_Muscle-134

description:
RNA sequencing using MiSeq
Muscle-134


title: DO_Mouse_High Fat_Muscle-130

description:
RNA sequencing using MiSeq
Muscle-130


title: DO_Mouse_High Fat_Muscle-149

description:
RNA sequencing using MiSeq
Muscle-149


title: DO_Mouse_High Fat_Muscle-127

description:
RNA sequencing using MiSeq
Muscle-127


title: DO_Mouse_High Fat_Muscle-126

description:
RNA sequencing using MiSeq
Muscle-126


title: DO_Mouse_High Fat_Muscle-125

description:
RNA sequencing using MiSeq
Muscle-125


title: DO_Mouse_High Fat_Muscle-128

description:
RNA sequencing using MiSeq
Muscle-128


title: DO_Mouse_High Fat_Muscle-129

description:
RNA sequencing using MiSeq
Muscle-129


title: DO_Mouse_High Fat_Muscle-123

description:
RNA sequencing using MiSeq
Muscle-123


title: DO_Mouse_High Fat_Muscle-120

description:
RNA sequencing using MiSeq
Muscle-120


title: DO_Mouse_High Fat_Muscle-116

description:
RNA sequencing using MiSeq
Muscle-116


title: DO_Mouse_High Fat_Muscle-119

description:
RNA sequencing using MiSeq
Muscle-119


title: DO_Mouse_High Fat_Muscle-115

description:
RNA sequencing using MiSeq
Muscle-115


title: DO_Mouse_High Fat_Muscle-118

description:
RNA sequencing using MiSeq
Muscle-118


title: DO_Mouse_High Fat_Muscle-122

description:
RNA sequencing using MiSeq
Muscle-122


title: DO_Mouse_High Fat_Muscle-114

description:
RNA sequencing using MiSeq
Muscle-114


title: DO_Mouse_High Fat_Muscle-117

description:
RNA sequencing using MiSeq
Muscle-117


title: DO_Mouse_High Fat_Muscle-138

description:
RNA sequencing using MiSeq
Muscle-138


title: DO_Mouse_High Fat_Muscle-112

description:
RNA sequencing using MiSeq
Muscle-112


title: DO_Mouse_High Fat_Muscle-113

description:
RNA sequencing using MiSeq
Muscle-113


title: DO_Mouse_High Fat_Muscle-111

description:
RNA sequencing using MiSeq
Muscle-111


title: DO_Mouse_High Fat_Muscle-110

description:
RNA sequencing using MiSeq
Muscle-110


title: DO_Mouse_High Fat_Muscle-109

description:
RNA sequencing using MiSeq
Muscle-109


title: DO_Mouse_High Fat_Muscle-107

description:
RNA sequencing using MiSeq
Muscle-107


title: DO_Mouse_High Fat_Muscle-103

description:
RNA sequencing using MiSeq
Muscle-103


title: DO_Mouse_High Fat_Muscle-108

description:
RNA sequencing using MiSeq
Muscle-108


title: DO_Mouse_High Fat_Muscle-105

description:
RNA sequencing using MiSeq
Muscle-105


title: DO_Mouse_High Fat_Muscle-101

description:
RNA sequencing using MiSeq
Muscle-101


title: DO_Mouse_High Fat_Muscle-102

description:
RNA sequencing using MiSeq
Muscle-102


title: DO_Mouse_High Fat_Muscle-96

description:
RNA sequencing using MiSeq
Muscle-96


title: DO_Mouse_High Fat_Muscle-104

description:
RNA sequencing using MiSeq
Muscle-104


title: DO_Mouse_High Fat_Muscle-106

description:
RNA sequencing using MiSeq
Muscle-106


title: DO_Mouse_High Fat_Muscle-95

description:
RNA sequencing using MiSeq
Muscle-95


title: DO_Mouse_High Fat_Muscle-124

description:
RNA sequencing using MiSeq
Muscle-124


title: DO_Mouse_High Fat_Muscle-97

description:
RNA sequencing using MiSeq
Muscle-97


title: DO_Mouse_High Fat_Muscle-121

description:
RNA sequencing using MiSeq
Muscle-121


title: DO_Mouse_High Fat_Muscle-100

description:
RNA sequencing using MiSeq
Muscle-100


title: DO_Mouse_High Fat_Muscle-99

description:
RNA sequencing using MiSeq
Muscle-99


title: DO_Mouse_High Fat_Muscle-98

description:
RNA sequencing using MiSeq
Muscle-98


title: DO_Mouse_High Fat_Muscle-94

description:
RNA sequencing using MiSeq
Muscle-94


title: DO_Mouse_High Fat_Muscle-93

description:
RNA sequencing using MiSeq
Muscle-93


title: DO_Mouse_High Fat_Muscle-92

description:
RNA sequencing using MiSeq
Muscle-92


title: DO_Mouse_High Fat_Muscle-91

description:
RNA sequencing using MiSeq
Muscle-91


title: DO_Mouse_High Fat_Muscle-90

description:
RNA sequencing using MiSeq
Muscle-90


title: DO_Mouse_High Fat_Muscle-89

description:
RNA sequencing using MiSeq
Muscle-89


title: DO_Mouse_High Fat_Muscle-88

description:
RNA sequencing using MiSeq
Muscle-88


title: DO_Mouse_High Fat_Muscle-82

description:
RNA sequencing using MiSeq
Muscle-82


title: DO_Mouse_High Fat_Muscle-87

description:
RNA sequencing using MiSeq
Muscle-87


title: DO_Mouse_High Fat_Muscle-85

description:
RNA sequencing using MiSeq
Muscle-85


title: DO_Mouse_High Fat_Muscle-84

description:
RNA sequencing using MiSeq
Muscle-84


title: HT22 cells, siNCOA4+DFO biol rep 3

city: Seoul

first: Moon-Suhn

last: Ryu

address: 50 Yonsei-ro, Seodaemun-gu

department: Food and Nutrition

country: South Korea

institute: Yonsei University

data_processing:
2 x 75bp FastQ paired-end reads for 12 samples (n=13.4 Million reads average per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC. Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (mm10) as reference.
Gene quantification was done via Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: HT22 mouse hippocampal neuron cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using Direct-zol RNA Miniprep Kit (Zymo Research)
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq – Pico Mammalian Kit v2 (Takara) following manufacturer's protocols.

treatment_protocol: Gene knockdown was accomplished via liposome-mediated delivery of siRNA into cells, and iron deficiency was induced by treatment of DFO at 100 µM for 24 h

tag: cell line

value: hippocampal neuron cells

value: NCOA4 knockdown

tag: treatment

value: Low iron (DFO)


title: DO_Mouse_High Fat_Muscle-83

description:
RNA sequencing using MiSeq
Muscle-83

tag: Sex


title: DO_Mouse_High Fat_Muscle-86

description:
RNA sequencing using MiSeq
Muscle-86


title: HT22 cells, siNCOA4+DFO biol rep 2


title: HT22 cells, siNCOA4+DFO biol rep 1


title: HT22 cells, siControl+DFO biol rep 3

value: control


title: HT22 cells, siControl+DFO biol rep 1


title: DO_Mouse_High Fat_Muscle-80

description:
RNA sequencing using MiSeq
Muscle-80


title: HT22 cells, siNCOA4 biol rep 1

value: Normal iron


title: DO_Mouse_High Fat_Muscle-76

description:
RNA sequencing using MiSeq
Muscle-76


title: HT22 cells, siNCOA4 biol rep 3


title: HT22 cells, siControl+DFO biol rep 2


title: DO_Mouse_High Fat_Muscle-81

description:
RNA sequencing using MiSeq
Muscle-81


title: DO_Mouse_High Fat_Muscle-79

description:
RNA sequencing using MiSeq
Muscle-79


title: DO_Mouse_High Fat_Muscle-77

description:
RNA sequencing using MiSeq
Muscle-77


title: HT22 cells, siControl biol rep 3


title: DO_Mouse_High Fat_Muscle-78

description:
RNA sequencing using MiSeq
Muscle-78


title: DO_Mouse_Control_Muscle-75

description:
RNA sequencing using MiSeq
Muscle-75

value: Control


title: HT22 cells, siNCOA4 biol rep 2


title: DO_Mouse_Control_Muscle-74

description:
RNA sequencing using MiSeq
Muscle-74


title: DO_Mouse_Control_Muscle-73

description:
RNA sequencing using MiSeq
Muscle-73


title: HT22 cells, siControl biol rep 2


title: DO_Mouse_Control_Muscle-72

description:
RNA sequencing using MiSeq
Muscle-72


title: DO_Mouse_Control_Muscle-71

description:
RNA sequencing using MiSeq
Muscle-71


title: EV-F-Post-D7

city: Atlanta

first: Michael

middle: E.

last: Davis

address: 2015 Uppergate Dr NE

institute: Emory University

data_processing:
Base calling was conducted with RTA v3.4.4 and demultiplexing was performed with bcl2fastq v2.20.0.422
Fastq files were aligned to the human genome using the Qiagen GeneGlobe primary analysis tool
Assembly: Sample reads aligned with hg19 reference genome.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Ovis aries

source_name: EVs isolated from serum

extract_protocol:
Serum samples were centrifuged first at 300 xg to remove debris and then loaded onto Izon qEV single column to isolate 70 – 1000 nm particle fractions. The EVs were eluted in 700 µl PBS for particle characterization and downstream processing.
RNA were isolated by using Qiagen RNeasy mini kit following manufacturer's protocol.
1 ng of RNA was used as input for library preparation with the Qiagen QIAseq miRNA Library Prep Kit

treatment_protocol: Adolescent sheep with otherwise normal biventricular cardiac anatomy underwent a single-stage Fontan.

value: Fontan surgery


title: EV-E-Post-D7


title: DO_Mouse_Control_Muscle-70

description:
RNA sequencing using MiSeq
Muscle-70


title: DO_Mouse_Control_Muscle-68

description:
RNA sequencing using MiSeq
Muscle-68


title: DO_Mouse_Control_Muscle-67

description:
RNA sequencing using MiSeq
Muscle-67


title: EV-D-Pre


title: DO_Mouse_Control_Muscle-66

description:
RNA sequencing using MiSeq
Muscle-66


title: EV-C-Pre


title: DO_Mouse_Control_Muscle-65

description:
RNA sequencing using MiSeq
Muscle-65


title: DO_Mouse_Control_Muscle-64

description:
RNA sequencing using MiSeq
Muscle-64


title: EV-B-Pre


title: EV-A-Pre


title: Serum-E-Post-D7

source_name: Serum


title: DO_Mouse_Control_Muscle-62

description:
RNA sequencing using MiSeq
Muscle-62


title: Serum-D-Post-D6


title: DO_Mouse_Control_Muscle-69

description:
RNA sequencing using MiSeq
Muscle-69


title: DO_Mouse_Control_Muscle-61

description:
RNA sequencing using MiSeq
Muscle-61


title: DO_Mouse_Control_Muscle-63

description:
RNA sequencing using MiSeq
Muscle-63


title: DO_Mouse_Control_Muscle-58

description:
RNA sequencing using MiSeq
Muscle-58


title: Serum-E-Pre


title: Serum-C-Pre


title: HT22 cells, siControl biol rep 1


title: DO_Mouse_Control_Muscle-59

description:
RNA sequencing using MiSeq
Muscle-59


title: Serum-F-Post-D7


title: DO_Mouse_Control_Muscle-57

description:
RNA sequencing using MiSeq
Muscle-57


title: DO_Mouse_Control_Muscle-60

description:
RNA sequencing using MiSeq
Muscle-60


title: DO_Mouse_Control_Muscle-56

description:
RNA sequencing using MiSeq
Muscle-56


title: EV-D-Post-D6


title: EV-E-Pre


title: Serum-B-Pre


title: Serum-A-Pre


title: DO_Mouse_Control_Muscle-55

description:
RNA sequencing using MiSeq
Muscle-55


title: DO_Mouse_Control_Muscle-45

description:
RNA sequencing using MiSeq
Muscle-45


title: DO_Mouse_Control_Muscle-53

description:
RNA sequencing using MiSeq
Muscle-53


title: DO_Mouse_Control_Muscle-52

description:
RNA sequencing using MiSeq
Muscle-52


title: DO_Mouse_Control_Muscle-44

description:
RNA sequencing using MiSeq
Muscle-44


title: DO_Mouse_Control_Muscle-49

description:
RNA sequencing using MiSeq
Muscle-49


title: DO_Mouse_Control_Muscle-51

description:
RNA sequencing using MiSeq
Muscle-51


title: DO_Mouse_Control_Muscle-54

description:
RNA sequencing using MiSeq
Muscle-54


title: DO_Mouse_Control_Muscle-47

description:
RNA sequencing using MiSeq
Muscle-47


title: Serum-D-Pre


title: DO_Mouse_Control_Muscle-50

description:
RNA sequencing using MiSeq
Muscle-50


title: DO_Mouse_Control_Muscle-46

description:
RNA sequencing using MiSeq
Muscle-46


title: DO_Mouse_Control_Muscle-42

description:
RNA sequencing using MiSeq
Muscle-42


title: DO_Mouse_Control_Muscle-43

description:
RNA sequencing using MiSeq
Muscle-43


title: DO_Mouse_Control_Muscle-48

description:
RNA sequencing using MiSeq
Muscle-48


title: DO_Mouse_Control_Muscle-40

description:
RNA sequencing using MiSeq
Muscle-40


title: DO_Mouse_Control_Muscle-36

description:
RNA sequencing using MiSeq
Muscle-36


title: DO_Mouse_Control_Muscle-34

description:
RNA sequencing using MiSeq
Muscle-34


title: DO_Mouse_Control_Muscle-38

description:
RNA sequencing using MiSeq
Muscle-38


title: DO_Mouse_Control_Muscle-41

description:
RNA sequencing using MiSeq
Muscle-41


title: DO_Mouse_Control_Muscle-35

description:
RNA sequencing using MiSeq
Muscle-35


title: #25 T

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

hyb_protocol: Biotinylated cRNAs were hybridized to Human HT-12 v3 BeadChips (code BD-103-020, Illumina®) and stained with streptavidin-Cy3  according to manufacturer’s instructions.

scan_protocol: scanned with Illumina® BeadArray Reader according to manufacturer’s instructions.

data_processing: Raw data were summarized and cubic-spline normalized with the GenomeStudio software (Illumina). Expression filtering, log(2) ratio transformation, correlation analyses, statistics, and other data analysis procedures were carried out with Excel (Microsoft).

label: Biotin

source_name: Colorectal Cancer patient_Neoplastic Tissue

label_protocol: For microarray analysis, 500 ng of total RNA were reverse-transcribed and converted into biotinylated complementary RNA (cRNA) with the Illumina® TotalPrep RNA Amplification Kit, (Ambion) according to manufacturer’s instructions. Quality controls were performed with Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA was extracted using the TRIzol reagent and purified with the Pure Link Micro-to-Midi Kit (Invitrogen, Carlsbad, CA.), according to manufacturer’s instructions.

treatment_protocol: Fresh specimens of the surgically resected colorectal cancer tissue and adjacent noncancerous mucosa were collected in RNAlater (Ambion,) and frozen  at -80° prior to RNA  extraction.

tag: disease

value: colorectal cancer

tag: patient id

tag: tissue type

value: neoplastic tissue (T)


title: #29 N

source_name: Colorectal Cancer patient_Normal Adjacent mucosa

value: adjacent normal mucosa (N)


title: #26 T


title: #23 T


title: #33 N


title: #30 N


title: #29 T


title: #24 N


title: #21 T


title: DO_Mouse_Control_Muscle-39

description:
RNA sequencing using MiSeq
Muscle-39


title: #28 T


title: #26 N


title: #34 N


title: #24 T


title: #28 N


title: #31 N


title: #30 T


title: DO_Mouse_Control_Muscle-33

description:
RNA sequencing using MiSeq
Muscle-33


title: #33 T


title: #34 T


title: #31 T


title: DO_Mouse_Control_Muscle-32

description:
RNA sequencing using MiSeq
Muscle-32


title: #25 N


title: DO_Mouse_Control_Muscle-30

description:
RNA sequencing using MiSeq
Muscle-30


title: #21 N


title: #23 N


title: DO_Mouse_Control_Muscle-29

description:
RNA sequencing using MiSeq
Muscle-29


title: DO_Mouse_Control_Muscle-28

description:
RNA sequencing using MiSeq
Muscle-28


title: DO_Mouse_Control_Muscle-27

description:
RNA sequencing using MiSeq
Muscle-27


title: #19 N


title: #18 N


title: #19 T


title: DO_Mouse_Control_Muscle-22

description:
RNA sequencing using MiSeq
Muscle-22


title: #18 T


title: DO_Mouse_Control_Muscle-25

description:
RNA sequencing using MiSeq
Muscle-25


title: DO_Mouse_Control_Muscle-23

description:
RNA sequencing using MiSeq
Muscle-23


title: DO_Mouse_Control_Muscle-24

description:
RNA sequencing using MiSeq
Muscle-24


title: DO_Mouse_Control_Muscle-18

description:
RNA sequencing using MiSeq
Muscle-18


title: DO_Mouse_Control_Muscle-17

description:
RNA sequencing using MiSeq
Muscle-17


title: DO_Mouse_Control_Muscle-16

description:
RNA sequencing using MiSeq
Muscle-16


title: #17 N


title: DO_Mouse_Control_Muscle-20

description:
RNA sequencing using MiSeq
Muscle-20


title: DO_Mouse_Control_Muscle-26

description:
RNA sequencing using MiSeq
Muscle-26


title: DO_Mouse_Control_Muscle-15

description:
RNA sequencing using MiSeq
Muscle-15


title: DO_Mouse_Control_Muscle-21

description:
RNA sequencing using MiSeq
Muscle-21


title: DO_Mouse_Control_Muscle-19

description:
RNA sequencing using MiSeq
Muscle-19


title: DO_Mouse_Control_Muscle-12

description:
RNA sequencing using MiSeq
Muscle-12


title: DO_Mouse_Control_Muscle-14

description:
RNA sequencing using MiSeq
Muscle-14


title: DO_Mouse_Control_Muscle-13

description:
RNA sequencing using MiSeq
Muscle-13


title: DO_Mouse_Control_Muscle-11

description:
RNA sequencing using MiSeq
Muscle-11


title: #15 T


title: DO_Mouse_Control_Muscle-10

description:
RNA sequencing using MiSeq
Muscle-10


title: #07 N


title: DO_Mouse_Control_Muscle-9

description:
RNA sequencing using MiSeq
Muscle-9


title: DO_Mouse_Control_Muscle-8

description:
RNA sequencing using MiSeq
Muscle-8


title: #15 N


title: #17 T


title: #14 N


title: #14 T


title: #07 T


title: #06 N


title: DO_Mouse_Control_Muscle-7

description:
RNA sequencing using MiSeq
Muscle-7


title: #05 N


title: DO_Mouse_Control_Muscle-6

description:
RNA sequencing using MiSeq
Muscle-6


title: DO_Mouse_Control_Muscle-5

description:
RNA sequencing using MiSeq
Muscle-5


title: DO_Mouse_Control_Muscle-4

description:
RNA sequencing using MiSeq
Muscle-4


title: #06 T


title: #04 T


title: #04 N


title: #02 T


title: #05 T


title: #02 N


title: #01 N


title: #03 N


title: DO_Mouse_Control_Muscle-3

description:
RNA sequencing using MiSeq
Muscle-3


title: DO_Mouse_Control_Muscle-31

description:
RNA sequencing using MiSeq
Muscle-31


title: #03 T


title: DO_Mouse_High Fat_Liver-149

description:
RNA sequencing using MiSeq
Liver-149

source_name: Liver

value: Liver


title: DO_Mouse_High Fat_Liver-150

description:
RNA sequencing using MiSeq
Liver-150


title: DO_Mouse_Control_Muscle-2

description:
RNA sequencing using MiSeq
Muscle-2


title: DO_Mouse_Control_Muscle-1

description:
RNA sequencing using MiSeq
Muscle-1


title: DO_Mouse_High Fat_Liver-148

description:
RNA sequencing using MiSeq
Liver-148


title: DO_Mouse_High Fat_Liver-147

description:
RNA sequencing using MiSeq
Liver-147


title: #01 T


title: Patient V2-081

city: Annandale

first: Kathleen

last: Darcy

state: VA

address: 3289 Woodburn Road Suite 370

department: Gynecologic Cancer Center of Excellence

institute: Henry M Jackson Foundation for the Advancement of Military Medicine

description: Gene expression data from EEC patients

hyb_protocol: Approximately 5 microgram of total RNA from each sample was labeled using the high yield transcript labeling kit (ENZO) and labeled RNAs were hybridized to U133A Plus 2.0 microarrays (Affymetrix Inc).

scan_protocol: Hybridized U133A Plus 2.0 microarrays (Affymetrix Inc) were washed and scanned according to the manufacturers specifications (Affymetrix Inc., 2001).

data_processing: Affymetrix hybridization-based microarray data were normalized using the RMA algorithm implemented in ‘simpleaffy’ Bioconductor package applied on raw CEL files, and only those probesets detected with expression levels >0 in at least 2/3 samples were retained for further analysis, respectively.

label: biotin

source_name: Endometrial Cancer

label_protocol: One hundred ng of total RNA was amplified (Two-Cycle cDNA Synthesis Kit, Affymetrix Inc., Santa Clara, CA) from which biotinylated aRNA was prepared (Affymetrix Labeling Kit, Affymetrix Inc). Approximately 5 microgram of total RNA from each sample was labeled using the high yield transcript labeling kit (ENZO).

extract_protocol: Total RNA was isolated (RNeasy Micro Kit) and spectrophotometrically quantified (Nanodrop 1000, ThermoFischer Scientific, Inc., Wilmington, DE). The RNA Integrity Number (RIN, Bioanalyzer 2100, Agilent Technologies, Santa Clara, CA) was utilized as a surrogate of RNA (and tissue specimen) integrity. Only those cases with a RIN > 5 were included in the transcriptomic analysis.  Cases were excluded if they had poor quality RNA (RIN<5) or a high GAPDH 3’:5’ ratio (>10).

treatment_protocol: Frozen primary tumors were embedded in optimal cutting temperature (OCT) compound and thin sections (8 micrometer) were cut and mounted on glass slides for pathology review.  A board-certified pathologist centrally reviewed hematoxylin and eosin stained sections, to select cases with at least 10% tumor cellularity, endometrioid histotype, and <=50% necrosis. Malignant epithelial cells were harvested from tissue specimens using laser microdissection (LMD) or macrodissection/scraping. When LMD was required, tissue sections were prepared on PEN membrane slides, crosslinked for 30 min using a UV crosslinker (Spectronics Corporation, Westbury, NY), stained in Mayer’s hematoxylin, air dried for 24 h, and underwent laser microdissection (LMD 6500, Leica Microsystems, Wetzlar, Germany) Malignant epithelial cells were collected into RLT Buffer (Qiagen, Valencia, CA) plus 1% ?-mercaptoethanol and stored at -80 °C.

tag: matastasis

value: Yes

tag: grade


title: Patient V2-080

description: Gene expression data from EEC patients


title: Patient V2-076

description: Gene expression data from EEC patients

value: No


title: Patient V2-075

description: Gene expression data from EEC patients


title: Patient V2-073

description: Gene expression data from EEC patients


title: Patient V2-072

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-143

description:
RNA sequencing using MiSeq
Liver-143


title: DO_Mouse_High Fat_Liver-144

description:
RNA sequencing using MiSeq
Liver-144


title: Patient V2-074

description: Gene expression data from EEC patients


title: Patient V2-070

description: Gene expression data from EEC patients


title: Patient V2-079

description: Gene expression data from EEC patients


title: Patient V2-071

description: Gene expression data from EEC patients


title: Patient V2-078

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-141

description:
RNA sequencing using MiSeq
Liver-141


title: DO_Mouse_High Fat_Liver-142

description:
RNA sequencing using MiSeq
Liver-142


title: DO_Mouse_High Fat_Liver-145

description:
RNA sequencing using MiSeq
Liver-145


title: Patient V2-069

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-146

description:
RNA sequencing using MiSeq
Liver-146


title: DO_Mouse_High Fat_Liver-139

description:
RNA sequencing using MiSeq
Liver-139


title: Patient V2-077

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-138

description:
RNA sequencing using MiSeq
Liver-138


title: Patient V2-068

description: Gene expression data from EEC patients


title: Patient V2-066

description: Gene expression data from EEC patients


title: Patient V2-063

description: Gene expression data from EEC patients


title: Patient V2-064

description: Gene expression data from EEC patients


title: Patient V2-067

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-136

description:
RNA sequencing using MiSeq
Liver-136


title: Patient V2-062

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-133

description:
RNA sequencing using MiSeq
Liver-133


title: Patient V2-065

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-132

description:
RNA sequencing using MiSeq
Liver-132


title: DO_Mouse_High Fat_Liver-134

description:
RNA sequencing using MiSeq
Liver-134


title: DO_Mouse_High Fat_Liver-129

description:
RNA sequencing using MiSeq
Liver-129


title: DO_Mouse_High Fat_Liver-137

description:
RNA sequencing using MiSeq
Liver-137


title: DO_Mouse_High Fat_Liver-135

description:
RNA sequencing using MiSeq
Liver-135


title: DO_Mouse_High Fat_Liver-128

description:
RNA sequencing using MiSeq
Liver-128


title: DO_Mouse_High Fat_Liver-127

description:
RNA sequencing using MiSeq
Liver-127


title: DO_Mouse_High Fat_Liver-131

description:
RNA sequencing using MiSeq
Liver-131


title: DO_Mouse_High Fat_Liver-126

description:
RNA sequencing using MiSeq
Liver-126


title: Patient V2-058

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-140

description:
RNA sequencing using MiSeq
Liver-140


title: Patient V2-060

description: Gene expression data from EEC patients


title: Patient V2-057

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-125

description:
RNA sequencing using MiSeq
Liver-125


title: DO_Mouse_High Fat_Liver-122

description:
RNA sequencing using MiSeq
Liver-122


title: DO_Mouse_High Fat_Liver-124

description:
RNA sequencing using MiSeq
Liver-124


title: Patient V2-051

description: Gene expression data from EEC patients


title: Patient V2-061

description: Gene expression data from EEC patients


title: Patient V2-049

description: Gene expression data from EEC patients


title: Patient V2-054

description: Gene expression data from EEC patients


title: Patient V2-056

description: Gene expression data from EEC patients


title: Patient V2-048

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-121

description:
RNA sequencing using MiSeq
Liver-121


title: Patient V2-059

description: Gene expression data from EEC patients


title: Patient V2-055

description: Gene expression data from EEC patients


title: Patient V2-050

description: Gene expression data from EEC patients


title: Patient V2-052

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-118

description:
RNA sequencing using MiSeq
Liver-118


title: DO_Mouse_High Fat_Liver-119

description:
RNA sequencing using MiSeq
Liver-119


title: Patient V2-053

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-120

description:
RNA sequencing using MiSeq
Liver-120


title: DO_Mouse_High Fat_Liver-117

description:
RNA sequencing using MiSeq
Liver-117


title: Patient V2-045

description: Gene expression data from EEC patients


title: Patient V2-047

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-115

description:
RNA sequencing using MiSeq
Liver-115


title: DO_Mouse_High Fat_Liver-116

description:
RNA sequencing using MiSeq
Liver-116


title: DO_Mouse_High Fat_Liver-114

description:
RNA sequencing using MiSeq
Liver-114


title: DO_Mouse_High Fat_Liver-113

description:
RNA sequencing using MiSeq
Liver-113


title: DO_Mouse_High Fat_Liver-111

description:
RNA sequencing using MiSeq
Liver-111


title: DO_Mouse_High Fat_Liver-112

description:
RNA sequencing using MiSeq
Liver-112


title: DO_Mouse_High Fat_Liver-130

description:
RNA sequencing using MiSeq
Liver-130


title: Patient V2-044

description: Gene expression data from EEC patients


title: Patient V2-046

description: Gene expression data from EEC patients


title: Patient V2-043

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-110

description:
RNA sequencing using MiSeq
Liver-110


title: Patient V2-040

description: Gene expression data from EEC patients


title: Patient V2-041

description: Gene expression data from EEC patients


title: Patient V2-042

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-109-2

description:
RNA sequencing using MiSeq
Liver-109-2


title: DO_Mouse_High Fat_Liver-106

description:
RNA sequencing using MiSeq
Liver-106


title: DO_Mouse_High Fat_Liver-108

description:
RNA sequencing using MiSeq
Liver-108


title: DO_Mouse_High Fat_Liver-107

description:
RNA sequencing using MiSeq
Liver-107


title: DO_Mouse_High Fat_Liver-105

description:
RNA sequencing using MiSeq
Liver-105


title: DO_Mouse_High Fat_Liver-104

description:
RNA sequencing using MiSeq
Liver-104


title: Patient V2-038

description: Gene expression data from EEC patients


title: Patient V2-036

description: Gene expression data from EEC patients


title: Patient V2-034

description: Gene expression data from EEC patients


title: Patient V2-032

description: Gene expression data from EEC patients


title: Patient V2-031

description: Gene expression data from EEC patients


title: Patient V2-039

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-102

description:
RNA sequencing using MiSeq
Liver-102


title: DO_Mouse_High Fat_Liver-101

description:
RNA sequencing using MiSeq
Liver-101


title: DO_Mouse_High Fat_Liver-100-2

description:
RNA sequencing using MiSeq
Liver-100-2


title: DO_Mouse_High Fat_Liver-103-2

description:
RNA sequencing using MiSeq
Liver-103-2


title: DO_Mouse_High Fat_Liver-99

description:
RNA sequencing using MiSeq
Liver-99


title: Patient V2-035

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-97-2

description:
RNA sequencing using MiSeq
Liver-97-2


title: DO_Mouse_High Fat_Liver-98

description:
RNA sequencing using MiSeq
Liver-98


title: DO_Mouse_High Fat_Liver-96

description:
RNA sequencing using MiSeq
Liver-96


title: Patient V2-037

description: Gene expression data from EEC patients


title: Patient V2-030

description: Gene expression data from EEC patients


title: Patient V2-029

description: Gene expression data from EEC patients


title: Patient V2-024

description: Gene expression data from EEC patients


title: Patient V2-023

description: Gene expression data from EEC patients


title: Patient V2-026

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-95

description:
RNA sequencing using MiSeq
Liver-95


title: DO_Mouse_High Fat_Liver-93

description:
RNA sequencing using MiSeq
Liver-93


title: DO_Mouse_High Fat_Liver-94-2

description:
RNA sequencing using MiSeq
Liver-94-2


title: Patient V2-028

description: Gene expression data from EEC patients


title: Patient V2-027

description: Gene expression data from EEC patients


title: Patient V2-033

description: Gene expression data from EEC patients


title: Patient V2-022

description: Gene expression data from EEC patients


title: Patient V2-019

description: Gene expression data from EEC patients


title: Patient V2-025

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-90

description:
RNA sequencing using MiSeq
Liver-90


title: DO_Mouse_High Fat_Liver-91

description:
RNA sequencing using MiSeq
Liver-91


title: DO_Mouse_High Fat_Liver-92-2

description:
RNA sequencing using MiSeq
Liver-92-2


title: DO_Mouse_High Fat_Liver-89

description:
RNA sequencing using MiSeq
Liver-89


title: DO_Mouse_High Fat_Liver-88

description:
RNA sequencing using MiSeq
Liver-88


title: DO_Mouse_High Fat_Liver-86

description:
RNA sequencing using MiSeq
Liver-86


title: DO_Mouse_High Fat_Liver-85

description:
RNA sequencing using MiSeq
Liver-85


title: DO_Mouse_High Fat_Liver-84

description:
RNA sequencing using MiSeq
Liver-84


title: DO_Mouse_High Fat_Liver-83-2

description:
RNA sequencing using MiSeq
Liver-83-2


title: Patient V2-014

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-81

description:
RNA sequencing using MiSeq
Liver-81


title: Patient V2-015

description: Gene expression data from EEC patients


title: Patient V2-021

description: Gene expression data from EEC patients


title: Patient V2-017

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-82

description:
RNA sequencing using MiSeq
Liver-82


title: Patient V2-016

description: Gene expression data from EEC patients


title: Patient V2-011

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-87

description:
RNA sequencing using MiSeq
Liver-87


title: Patient V2-018

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-80

description:
RNA sequencing using MiSeq
Liver-80


title: DO_Mouse_High Fat_Liver-79

description:
RNA sequencing using MiSeq
Liver-79


title: Patient V2-012

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-77

description:
RNA sequencing using MiSeq
Liver-77


title: Patient V2-009

description: Gene expression data from EEC patients


title: Patient V2-007

description: Gene expression data from EEC patients


title: Patient V2-020

description: Gene expression data from EEC patients


title: Patient V2-010

description: Gene expression data from EEC patients


title: Patient V2-005

description: Gene expression data from EEC patients


title: Patient V2-008

description: Gene expression data from EEC patients


title: Patient V2-002

description: Gene expression data from EEC patients


title: Patient V2-001

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-76

description:
RNA sequencing using MiSeq
Liver-76


title: Patient V2-006

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-74

description:
RNA sequencing using MiSeq
Liver-74


title: DO_Mouse_Control_Liver-73

description:
RNA sequencing using MiSeq
Liver-73


title: DO_Mouse_Control_Liver-75

description:
RNA sequencing using MiSeq
Liver-75


title: DO_Mouse_Control_Liver-72

description:
RNA sequencing using MiSeq
Liver-72


title: Patient V2-013

description: Gene expression data from EEC patients


title: DO_Mouse_High Fat_Liver-78

description:
RNA sequencing using MiSeq
Liver-78


title: DO_Mouse_Control_Liver-70

description:
RNA sequencing using MiSeq
Liver-70


title: Patient V2-004

description: Gene expression data from EEC patients


title: Patient T2-064

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-69

description:
RNA sequencing using MiSeq
Liver-69


title: DO_Mouse_Control_Liver-68

description:
RNA sequencing using MiSeq
Liver-68


title: Patient T2-062

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-67

description:
RNA sequencing using MiSeq
Liver-67


title: DO_Mouse_Control_Liver-65

description:
RNA sequencing using MiSeq
Liver-65


title: Patient T2-061

description: Gene expression data from EEC patients


title: Patient T2-059

description: Gene expression data from EEC patients


title: Patient T2-060

description: Gene expression data from EEC patients


title: Patient T2-058

description: Gene expression data from EEC patients


title: Patient V2-003

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-64

description:
RNA sequencing using MiSeq
Liver-64


title: DO_Mouse_Control_Liver-71

description:
RNA sequencing using MiSeq
Liver-71


title: Patient T2-063

description: Gene expression data from EEC patients


title: Patient T2-057

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-66

description:
RNA sequencing using MiSeq
Liver-66


title: DO_Mouse_Control_Liver-63

description:
RNA sequencing using MiSeq
Liver-63


title: DO_Mouse_Control_Liver-62

description:
RNA sequencing using MiSeq
Liver-62


title: DO_Mouse_Control_Liver-61

description:
RNA sequencing using MiSeq
Liver-61


title: Patient T2-056

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-59

description:
RNA sequencing using MiSeq
Liver-59


title: DO_Mouse_Control_Liver-60

description:
RNA sequencing using MiSeq
Liver-60


title: Patient T2-055

description: Gene expression data from EEC patients


title: Patient T2-053

description: Gene expression data from EEC patients


title: Patient T2-052

description: Gene expression data from EEC patients


title: Patient T2-051

description: Gene expression data from EEC patients


title: Patient T2-049

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-58

description:
RNA sequencing using MiSeq
Liver-58


title: DO_Mouse_Control_Liver-57

description:
RNA sequencing using MiSeq
Liver-57


title: Patient T2-054

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-54

description:
RNA sequencing using MiSeq
Liver-54


title: DO_Mouse_Control_Liver-56

description:
RNA sequencing using MiSeq
Liver-56


title: Patient T2-048

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-51

description:
RNA sequencing using MiSeq
Liver-51


title: DO_Mouse_Control_Liver-52

description:
RNA sequencing using MiSeq
Liver-52


title: DO_Mouse_Control_Liver-55

description:
RNA sequencing using MiSeq
Liver-55


title: DO_Mouse_Control_Liver-50

description:
RNA sequencing using MiSeq
Liver-50


title: DO_Mouse_Control_Liver-49-2

description:
RNA sequencing using MiSeq
Liver-49-2


title: DO_Mouse_Control_Liver-48

description:
RNA sequencing using MiSeq
Liver-48


title: DO_Mouse_Control_Liver-53

description:
RNA sequencing using MiSeq
Liver-53


title: DO_Mouse_Control_Liver-47

description:
RNA sequencing using MiSeq
Liver-47


title: DO_Mouse_Control_Liver-46

description:
RNA sequencing using MiSeq
Liver-46


title: Patient T2-047

description: Gene expression data from EEC patients


title: Patient T2-044

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-45-2

description:
RNA sequencing using MiSeq
Liver-45-2


title: Patient T2-042

description: Gene expression data from EEC patients


title: Patient T2-046

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-44

description:
RNA sequencing using MiSeq
Liver-44


title: DO_Mouse_Control_Liver-43

description:
RNA sequencing using MiSeq
Liver-43


title: Patient T2-041

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-42

description:
RNA sequencing using MiSeq
Liver-42


title: DO_Mouse_Control_Liver-41

description:
RNA sequencing using MiSeq
Liver-41


title: Patient T2-045

description: Gene expression data from EEC patients


title: Patient T2-039

description: Gene expression data from EEC patients


title: Patient T2-040

description: Gene expression data from EEC patients


title: Patient T2-038

description: Gene expression data from EEC patients


title: Patient T2-050

description: Gene expression data from EEC patients


title: Patient T2-033

description: Gene expression data from EEC patients


title: Patient T2-035

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-40

description:
RNA sequencing using MiSeq
Liver-40


title: Patient T2-029

description: Gene expression data from EEC patients


title: Patient T2-037

description: Gene expression data from EEC patients


title: Patient T2-043

description: Gene expression data from EEC patients


title: Patient T2-036

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-39

description:
RNA sequencing using MiSeq
Liver-39


title: Patient T2-032

description: Gene expression data from EEC patients


title: Patient T2-034

description: Gene expression data from EEC patients


title: Patient T2-028

description: Gene expression data from EEC patients


title: Patient T2-030

description: Gene expression data from EEC patients


title: Patient T2-031

description: Gene expression data from EEC patients


title: DO_Mouse_Control_Liver-36

description:
RNA sequencing using MiSeq
Liver-36


title: DO_Mouse_Control_Liver-35

description:
RNA sequencing using MiSeq
Liver-35


title: DO_Mouse_Control_Liver-38

description:
RNA sequencing using MiSeq
Liver-38


title: DO_Mouse_High Fat_Liver-123

description:
RNA sequencing using MiSeq
Liver-123


title: DO_Mouse_Control_Liver-34

description:
RNA sequencing using MiSeq
Liver-34


title: DO_Mouse_Control_Liver-33-2

description:
RNA sequencing using MiSeq
Liver-33-2


title: DO_Mouse_Control_Liver-32

description:
RNA sequencing using MiSeq
Liver-32