title: RpoN-V5_pBAD_overexpression_rep1

value: Anti-V5 Agarose Affinity Gel (Sigma A 7345)


title: aorta adventitia Cd45+ at steady state

status: Public on Aug 04 2020

type: SRA

city: Munich

first: Dena

last: Esfandyari

state: Bavaria

address: Haus 607, Biedersteiner Str. 29, IPT

department: Institute of Pharmacology and Toxicology

country: Germany

institute: Technical University of Munich

description: single cell 3' mRNA library (10x Genomics)

library_source: transcriptomic

data_processing:
RTA1.18.66.3, bcl2fastq for basecalling and fastq conversion
Je-demultiplex-illu (v1.2) to demultiplex fastq files
cellranger count (v3.1.0, 10x Genomics) for alignment, filtering, barcode counting, and UMI counting
Genome_build: NCBI Mouse Build 38 patch release 6 (GRCm38.p6), Gencode annotation M24, modified to include eYFP transgene
Supplementary_files_format_and_content: Feature-Barcode Matrices from cellranger (10x Genomics)

molecule: polyA RNA

organism: Mus musculus

source_name: adventitia

growth_protocol: Animals were approximately 16 weeks old

extract_protocol:
After sorting CD45-positive immune cells from whole aortas, viable cells were proceeded for single cell capture using the Chromium Controller (10X Genomics).
Barcoding and library preparation was done using Chromium Next GEM single cell 3’ (v3.1, 10x Genomics). The resulting 3‘ Gene Expression libraries were sequenced on an Illumina HiSeq 1500 (Illumina, San Diego, USA) in paired-end mode with asymmetric read length of 28+91 bp and a single indexing read of 8bp, to reach approximately 50.000 reads per single-cell.
Single cell RNA sequencing

treatment_protocol: no treatment or treatment with Angiotensin II (1.8 µg AngII/kg/min )

tag: condition

value: steady state

tag: cell type

value: Advenitital immune cells

tag: strain

tag: tissue

value: adventitia

tag: age

value: 16 weeks


title: Spt5-pThr806_rep1

city: Bronx

first: PABITRA

middle: K

last: PARUA

state: NY

address: 1300 Morris Park Avenue, Forchheimer 236, Molecular Pharmacology

department: Molecular Pharmacology

country: USA

institute: Albert Einstein College of Medicine

library_source: genomic

data_processing:
ChIP-seq: Single-end (75-nt reads) or paired-end (40-nt reads) sequencing was performed on an Illumina NextSeq 500.
ChIP-seq: ‘FastQC Read Quality Reports’ (Galaxy Version 0.72) and ‘Trimmomatic Flexible Read Trimming Tool’ (Galaxy Version 0.36.6) were used to check quality of the sequencing reads and for barcode trimming, respectively.
ChIP-seq: Trimmed sequencing reads were aligned to the human genome (version b37, hg19) using Bowtie2 in Galaxy (Galaxy Version 2.3.4.2). Normalization of the aligned reads was done using ‘bamCoverage’ (Galaxy Version 3.1.2.0.0) by 1) computing and applying scaling factor obtained using aligned sequencing reads of the spike-in reference genome (Saccharomyces cerevisiae, for spike-in samples) and 2) by computing RPKM (reads per kilobase per million) (for the samples without spike-in control).
ChIP-seq: Aligned sequences of each biological replicate were processed separately to identify enriched binding sites using MACS2 callpeak program (Galaxy Version 2.1.1.20160309.6). The resulting bedgraph files were converted to bigwig using ‘Wig/BedGraph-to-bigWig converter’ (Galaxy Version 1.1.1), replicates were combined using ‘Concatenate datasets’ (Galaxy Version 1.0.0).
ChIP-seq: Matrix was computed using ‘computeMatrix’ (Galaxy v.2.3.6.0) in DeepTools to prepare data for plotting heat maps and/or profiles of given regions. The genome-wide distributions, heat maps and metagene plots were created using ‘plotHeatmap’ (Galaxy Version 3.1.2.0.1) and ‘plotProfile’ (Galaxy Version 3.1.2.0.0) tools, respectively. The phospho-over-total signal ratios (log2-ratio) were calculated using ‘bigwigCompare’ (Galaxy Version 3.1.2.0.0). To generate principal component analysis (PCA) plots ‘plotPCA’ (Galaxy Version 3.1.2.0.0) was used.
Genome_build: ChIP-seq: Feb 2009 GRCh37/hg19
Genome_build: ChIP-seq: Skip-in control Saccharomyces cerevisiae (April 2011, sacCer3)
Supplementary_files_format_and_content: ChIP-seq: processed files are in bigWig format (n = 2 biological replicates combined). There are 15-bigWig files in total. .

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: ChIP-seq: HCT116 cells cultured in McCoy’s 5A medium with L-glutamine (10-050-CV, Corning) supplemented with 10% Fetal Bovine Serum (FBS, 10437-028, Gibco) and 1x Penicillin-Streptomycin (30-002-Cl, Corning). Drug treatments were performed at 50-60% confluence by substituting the growth medium with fresh medium containing either DMSO, 250 nM (except where noted) NVP-2 (provided by N.S. Gray), 10 μM RO-3306 (S7747, Selleckchem) and 5 μM nutlin-3 (10004372, Cayman Chemical Company).

extract_protocol:
ChIP-seq: HCT116 cells grown to 50-60% confluence were crosslinked with 1% formaldehyde (BP-531, Fisher Scientific) for 10 min at 25°C. Crosslinking was quenched with 125 mM glycine for 5 min at 25°C. Cells were washed twice with ice-cold PBS and collected into 1 ml of RIPA buffer supplemented with protease and phosphatase inhibitors for each 150-mm dish. Cells were lysed and chromatin sheared by sonication in a Bioruptor at high power, for 5 x 10 min with cycles of 30 sec ON and 30 sec OFF. Lysates were clarified by centrifugation at 20,000 x gav for 20 min at 4°C. Before immunoprecipitation, lysates (~5 x 106 cells per experiment) were pre-cleared with PierceTM Protein A Agarose (20333, Thermo Scientific) for 2 hr at 4°C. Beads were separated by centrifugation at 4000 x gav for 1 min at 4°C. The resulting supernatant was incubated with antibodies for 4 hr at 4°C with constant nutation. In spike-in control experiments, 10% (w/w) of the crosslinked Saccharomyces cerevisiae chromatin was added to the immunoprecipitation reaction.
ChIP-seq: Preparation of multiplexed ChIP-seq libraries from purified immunoprecipitated chromatin and sequencing were performed as described. In brief, the NEBNext Ultra II DNA Library Preparation kit (E7103S) was used to generate libraries using 5-10 ng of input or immunoprecipitated DNA and barcode adaptors (NEBNext Multiplex Oligos for Illumina (Set 1, E7335 and Set 2, E7500)).

treatment_protocol: ChIP-seq: Drug treatment was performed at 50-60% confluence by substituting the growth medium with fresh medium containing either DMSO or 5 μM nutlin-3 (10004372, Cayman Chemical Company) for 2 hour.

tag: cell line

tag: temperature

tag: drug treatiment

tag: drug dose

tag: time of treatiment (hour)

tag: antibody

value: rabbit anti-Spt5-pThr806 (21st Century Biochemicals)

tag: assay

value: ChIP-seq


title: Spt5-pSer666

value: rabbit anti-Spt5-pSer666 (21st Century Biochemicals)


title: pat 14 tumor [HDV_14A_S39]

city: BALTIMORE

first: Luigi

last: Ferrucci

state: MD

address: 251 BAYVIEW BLVD.

department: Translational Gerontology Branch

institute: National Institute on Aging, National Institutes of Health

data_processing:
140 RNA-seq samples from 70 HCC tumors and matched nontumor tissue were pooled and sequenced on NovaSeq using Illumina TruSeq Stranded Total RNA Kit RS-122-2201 and paired-end sequencing.
The sequencing quality of the reads was assessed using FastQC (version 0.11.5), Preseq (version 2.0.3)32, Picard tools (version 1.119), and RSeQC (version 2.6.4).
Reads were trimmed using Cutadapt (version 1.14)33 to remove sequencing adapters, prior to mapping to the human reference genome hg38 using STAR (version 2.5.2b) in two-pass mode34.
Across the samples, the median percentage of mapped reads was 95.4%.  Expression levels were quantified using RSEM version 1.3.035 with GENCODE annotation version 2136.
The RSEM counts were then normalized using the voom algorithm37 from the Limma R package (version 3.40.6)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text data matrices with genes as rows and samples as columns: RSEM_GeneCounts.txt is an integer matrix of transcript counts, voom_GeneExpression.txt is the voom-normalized gene expression.

molecule: total RNA

source_name: liver tissue

extract_protocol:
Frozen liver samples were homogenized using 2.8mm ceramic beads (Mo Bio cat.no.13114-50) and RNA was extracted using Trizol reagent, treated with DNase, quality control was checked using Agilent Nano chip.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: subject status

value: hepatocellular carcinoma patient

tag: tumor/non-tumor

value: tumor


title: PC-3 Transfected rep3

city: Villanova

first: Jacob

last: Elmer

state: PA

address: 800 E Lancaster Ave

department: Chemical & Biological Engineering

institute: Villanova University

data_processing:
Data processed using Excel, raw data normalized for FPKM and synthesized using vLookup function.
Supplementary_files_format_and_content: FPKM, DEG

source_name: Prostate Cancer Cells

growth_protocol: PC-3 cells were grown using RPMI 1640 media supplemented with 10% FBS and 1% P/S and passaged every 2-5 days (PC-3).

extract_protocol:
Small sample of cells evaluated using flow cytometry for transfection efficiency at 24 hours post-transfection, and then the remaining sample was lysed and extracted according to the Qiagen RNeasy kit instructions.
Samples sent off for sequencing with BGI for mRNA sequencing. (polyA capture)

treatment_protocol: PC-3 cells were seeded in T-75 well plates and grown in RPMI-1640 media. Transfections with Lipofectamine® LTX were performed according to the manufacturer’s protocol using Lipofectamine LTX, Plus Reagent, and pEF-GFP.

tag: treatment

value: pEF-GFP


title: aorta adventitia Cd45+ AngiotensinII

value: AnII-induced inflammation


title: Spt5_rep2

value: rabbit anti-Spt5 (A300-868A, Bethyl Laboratories)


title: pat 13 non-tumor [HDV_13B_S1]

value: non-tumor


title: subcutaneous adipose tissue of control mice, rep 3

type: RNA

city: Xuzhou

first: Wei

last: Pan

state: Jiangsu

address: 209 Tongshan Road

country: China

institute: Xuzhou Medical University

description: Gene expression of subcutaneous adipose tissues from control mice

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

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software version 10.7.1.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

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

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion, cat.AM1561) according to the manufacturer’s protocol. The kit can isolate total RNA containing small RNAs from 10^2-10^7 cultured cells/samples or 0.5-250 mg of tissue/samples. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Female C57BL/6J mice were intraperitoneally injected with a 200 μl suspension containing 2000 live EgPSC in 0.9% NaCl, and were sacrificed at the 16th week post infection. The lncRNA and mRNA expression patterns in subcutaneous adipose tissues of three EgPSC infected mice and three control mice were detected.

value: subcutaneous adipose tissue

tag: Sex

value: female

value: 7 months


title: PC-3 Transfected rep2


title: subcutaneous adipose tissue of EgPSC infected mice, rep 3

description: Gene expression of subcutaneous adipose tissues from EgPSC infected mice


title: subcutaneous adipose tissue of control mice, rep 2


title: subcutaneous adipose tissue of EgPSC infected mice, rep 2


title: subcutaneous adipose tissue of EgPSC infected mice, rep 1


title: subcutaneous adipose tissue of control mice, rep 1


title: PC-3 Transfected rep1


title: pat 12 non-tumor [HDV_12B_S46]


title: pat 13 tumor [HDV_13A_S56]


title: PC-3 Untransfected + 1 uM iCRT14 rep3

value: 1 uM Icrt14


title: pat 11 non-tumor [HDV_11B_S6]


title: pat 12 tumor [HDV_12A_S54]


title: PC-3 Untransfected + 1 uM iCRT14 rep1


title: Spt5_rep1


title: PC-3 Untransfected + 1 uM iCRT14 rep2


title: Pol II-pSer2_rep2

value: rabbit anti-Rpb1 CTD pSer2 (ab5095, Abcam)


title: Pol II-pSer2_rep1


title: Pol II_rep1

value: rabbit anti- Rpb1 (sc-899; Santa Cruz Biotechnology)


title: PC-3 Untransfected rep3

value: No plasmid


title: Pol II_rep2


title: pat 10 non-tumor [HDV_10B_S37]


title: Input rep2


title: PC-3 Untransfected rep2


title: DP2

city: Silver Spring

first: Frederick

middle: C

last: Mills

address: Building 52, Room 2108

department: CDER, OPQ, OBP, Division IV

institute: FDA

description: Gene expression

hyb_protocol: On completion of the fragmentation reaction, 55 ul of 2x Agilent hi-RPM Hyb buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v2 8x60K Microarrays (Design ID: 039484) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Agilent Wash Buffer 1 and 1 minute with 37°C Agilent Wash buffer 2, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%). -> Cy3 channel

data_processing: Microarray raw data files were loaded into R version 2.12.1 to process data analysis. Foreground values were imported from each raw data txt file, and quantile normailzation was then performed on each file.

source_name: tonsil

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug RNA using the Agilent Low Input Quick Amp Labeling Kit (#5190-2305, Agilent) according to the manufacturer's. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 15 minutes in a reaction volume of 25 ul containing 2x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions.

extract_protocol: RNA was extracted from sort-purified B cell subsets using RNeasy Micro kit (Qiagen, Germantown, MD). RNA quality and integrity were determined using an Agilent 2100 Bioanalyzer.

treatment_protocol: Tonsils of anonymous donors were obtained from the Mid-Atlantic CHTN following institutionally approved protocols. Lymphocytes were isolated by manual disruption and Ficoll purification, using standard procedures. Lymphocytes were either used fresh or were frozen for later use in liquid nitrogen in 10% DMSO, 50% FBS in RPMI. For sorting, B cells were isolated from ~400x106 tonsil cells using the Pan B cell isolation kit (StemCell Tecnologies, Cambridge, MA), then stained with CD19-APC-Cy7, IgD-FITC, CD38-BV421, FCRL4-APC and FCRL5-PE (all from Biolegend, San Diego, CA), and sorted on FACSAria Fusion in buffer containing 7-AAD (BD Bioscience, San Jose, CA).

tag: sample type

value: Anonymous


title: DN3

description: Gene expression


title: pat 10 tumor [HDV_10A_S33]


title: DP3

description: Gene expression


title: DN2

description: Gene expression


title: DP1

description: Gene expression


title: pat 11 tumor [HDV_11A_S34]


title: HD5_TSCM

status: Public on Aug 03 2020

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

data_processing:
Basecalls performed using RTA v2 version 2.4.11
Reads were trimmed using Trimmomatic
RNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.5.1b
Differential Gene Expression analysis was performed using EdgeR 3.20.9 R version 3.4.4
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was extracted from T cell subsets FACS-sorted from the peripheral blood ex vivo. 20-50,000 cells were washed twice in PBS–/– and RNA was immediately extracted using Direct-Zol RNA Microprep Kit (Zymo Research) according to manufacturer’s instructions, and stored at -80°C. RNA quality control was performed with the Agilent 4200 Tape Station system using the High Sensitivity RNA ScreenTape analysis kit (Agilent, Santa Clara, CA, USA).
Total-RNA-sequencing library preparation was performed starting from 1 ng of total-RNA with the SMART-Seq Stranded Kit (Clontech-Takara). Libraries were qualitatively assessed by using TapeStation 4200 and quantified by Qubit Fluorimeter. Afterwards, libraries were multiplexed in an equimolar pool and sequenced on a NextSeq-500 Illumina Platform.

tag: donor

value: healthy donor 5

value: TSCM PD1-TIGIT-


title: HD4_TCM

value: healthy donor 4

tag: cell type

value: TCM PD1-TIGIT


title: HD3_TCM

value: healthy donor 3


title: HD5_TEM

value: TEM


title: HD3_TPEX

value: TPEX


title: DN1

description: Gene expression


title: PC-3 Untransfected rep1


title: F51

description: Gene expression


title: F52

description: Gene expression


title: HD4_TPEX


title: Input rep1

value: ChIP-seq


title: F53

description: Gene expression


title: HD2_TEM

value: healthy donor 2


title: HD5_TCM


title: HD3_TEM


title: HD5_TPEX


title: HD2_TPEX


title: HD3_TSCM


title: HD1_TSCM

value: healthy donor 1


title: 2D_C-2_RNA-seq

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
STAR was applied to tissue samples for mapping and to quantify reads to the Arabodipsis reference genome (TAIR10).
The read counts per
million fragments mapped (CPM) of each sample were used to estimate the expression level of each gene. The CPM data were normalized by the quantile method and log2 transformation.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text format with CPM values of transcripts

organism: Arabidopsis thaliana

source_name: Arabidopsis ecotype Columbia (Col-0)

extract_protocol:
Total RNA was isolated from Arabidopsis roots using RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. The quality and integrity of total RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by a visual examination of RNA under ultraviolet light.
RNA-seq library was prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

value: Non-treatment

tag: agent

value: Columbia (Col-0)

tag: drenched pathogen

value: Ralstonia solanacearum

tag: time after pathogen drench


title: HD4_TSCM


title: HD2_TCM


title: HD1_TPEX


title: 2D_C-4_RNA-seq


title: 2D_C-3_RNA-seq


title: HD1_TCM


title: 2D_B-1_RNA-seq

value: benzothiadiazole


title: HD2_TSCM


title: 2D_10-4_RNA-seq

value: Sound wave (10KHz)


title: 2D_C-1_RNA-seq


title: 2D_10-1_RNA-seq


title: 1D_C-2_RNA-seq


title: 2D_10-3_RNA-seq


title: 1D_10-1_RNA-seq


title: 1D_10-4_RNA-seq


title: 0D_C-2_RNA-seq


title: 1D_C-4_RNA-seq


title: 1D_10-2_RNA-seq


title: 1D_C-1_RNA-seq


title: 2D_B-4_RNA-seq


title: 1D_B-4_RNA-seq


title: 1D_B-3_RNA-seq


title: 1D_10-3_RNA-seq


title: 0D_B-2_RNA-seq


title: 1D_B-1_RNA-seq


title: 0D_C-1_RNA-seq


title: 2D_B-3_RNA-seq


title: 0D_B-4_RNA-seq


title: 0D_10-3_RNA-seq


title: 0D_10-2_RNA-seq


title: 0D_B-1_RNA-seq


title: 0D_10-4_RNA-seq


title: H3k27me3_M-1D-C2

data_processing:
The sequencing reads were aligned to the reference sequence (TAIR10) using the Bowtie2 (v.2.2.2) software.
Finding, estimation and annotation of ChIP-seq peaks were carried out by the Homer (v.4.8.2) platform.
ChIP-fragment density at each position in the genome was estimated by starting with each tag and extending it by the estimated fragment length determined by autocorrelation.
The ChIP-fragment density is then defined as the total number of overlapping fragments at each position in the genome.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph files were generated by makeUCSCfile module in the Hommer software. Scores represent ChIP-seq density value as described in data processing step.

extract_protocol:
Standard DNA extraction protocol using Qiagen prep kit.
Libraries were prepared according to Illumina's instructions.

tag: ecotype


title: H3k27me3_M-1D-C1


title: H3k27me3_M-1D-10k-2


title: H3k27me3_M-1D-10k-3


title: H3k27me3_M-1D-10k-1


title: H3k27me3_M-0D-C3


title: H3k27me3_M-0D-C2


title: 0D_C-4_RNA-seq


title: Input_i-1D-C3


title: H3k27me3_M-0D-10k-1


title: H3k27me3_M-0D-C1


title: H3k27me3_M-0D-10k-3


title: Input_i-0D-C3


title: Input_i-1D-10k-3


title: Input_i-1D-10k-1


title: Input_i-0D-10k-3


title: Input_i-1D-C1


title: Input_i-1D-C2


title: Input_i-1D-10k-2


title: Input_i-0D-10k-1


title: Input_i-0D-C2


title: Input_i-0D-10k-2


title: H3k36ac_A-1D-C3


title: H3k36ac_A-1D-C2


title: Input_i-0D-C1


title: H3k36ac_A-1D-C1


title: H3k27me3_M-1D-C3


title: H3k36ac_A-1D-10k-1


title: H3k36ac_A-1D-10k-3


title: H3k36ac_A-0D-C3


title: H3k36ac_A-1D-10k-2


title: H3k36ac_A-0D-C2


title: H3k36ac_A-0D-10k-3


title: H3k36ac_A-0D-C1


title: H3k27me3_M-0D-10k-2


title: H3k36ac_A-0D-10k-1


title: Hep3B-Control

city: Shapingba district, Chongqing

first: Ling

last: Ling

address: NO. 55 South Rd, University town

institute: chongqing university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each Sample

source_name: HCC

extract_protocol:
Medium were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Hepatocellular Carcinoma cell line (HCC)

tag: genotype/variation

value: control


title: Hep3B-SIRT7-KO


title: H3k36ac_A-0D-10k-2


title: Nox2KO_LPS_1

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

institute: University Hospital of Bonn

description: processed data file: Raw_gene_counts_matrix.csv

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for demultiplexing and base call file conversion.
Sequenced reads were corrected for low-quality sequence, then mapped to mm10 whole genome with the Ensembl gene annotation version 98 using STAR v2.7.3a with standard parameters and --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3.
Read count generation was performed using featureCounts/Subread v2.0.0 ignoring multimapping reads.
Differential expression analysis was performed with R v3.6.1 in RStudio v1.2.1335 using the DESeq2 package v1.26.0 with the contrasts either WT versus NOX-2 KO (factor genotypes) or PBS versus LPS (factor treatment). The log2-fold change (log2FC) shrinkage was performed using apeglm to preserve large effects of true positives [v1.8.0 (Zhu, Ibrahim, and Love 2019)].
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw_gene_counts_matrix.csv: Comma-separated matrix table with raw gene counts for every gene and every sample.

source_name: Brain

extract_protocol:
Brains were collected and divided into two halves. Left hemispheres were immediately homogenized in 1 ml QIAzol (QIAGEN) and RNA was isolated according to standard chloroform/isopropanol method.
Library preparation was performed using QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) with an input of 100 ng total RNA according to manufacturer's instructions.

treatment_protocol: Mice were intraperitoneally injected daily, and repeatedly over 4 consecutive days, with either 100 µl lipopolysaccharides (LPS) (1 µg/gbw/day, Enzo Life Science, Salmonella abortus equi S-form, Cat # ALX-581-009-002) or 100 µl PBS/day as vehicle control.

tag: strain

tag: genotype

value: Nox2 knockout

tag: age

value: 3 months

tag: tissue

value: Brain

value: LPS injection


title: Nox2KO_PBS_6

value: PBS injection


title: Nox2KO_LPS_2


title: Nox2KO_LPS_5


title: Nox2KO_LPS_6


title: Nox2KO_PBS_4


title: Nox2KO_PBS_5


title: Hep3B-USP39-KO


title: Nox2KO_LPS_3


title: WT_LPS_5

value: wild type


title: WT_LPS_6


title: Nox2KO_PBS_2


title: Nox2KO_PBS_3


title: Nox2KO_PBS_1


title: Nox2KO_LPS_4


title: WT_LPS_3


title: WT_PBS_6


title: WT_LPS_4


title: WT_PBS_4


title: WT_LPS_2


title: WT_LPS_1


title: WT_PBS_5


title: WT_PBS_2


title: TGF_10_1

city: Boston

first: Daniel

last: Dwyer

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

data_processing:
Data for each lane was separated by barcode and concatinated. Transcripts were alligned to GRCm38 (mm10) genome assembly with STAR (Dobin et al 2013) with the following parameter settings: --outSAMstrandField intronMotif --outSJfilterReads Unique --outSJfilterCountUniqueMin 100 1 1 1 --limitSjdbInsertNsj 10000000 --chimSegmentMin 10. Transcripts were quantified with HTseq (Anders et al, 2014).
Data analysis was conducted using Bioconductor for R. Count normalization and differential was conducted using the DESeq2 software package (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: raw count matrix

source_name: Bone marrow-derived cultured mast cells grown in 10 ng/mL IL-3

growth_protocol: BMMC cultures were maintained in IL-3 (5 ng/mL) for 6-8 weeks prior to stimulus.

extract_protocol:
Samples were lysed in TCL buffer (Qiagen)
SmartSeq2 libraries were prepared according to the SmartSeq2 protocol described by Trombetta et al, 2014. Briefly, total RNA was purified using RNA-SPRI beads. cDNA was generated from full-length mRNA transcripts using reverse transcriptase with terminal transferase activity. Combined with a second "template switch" primer, the cDNA was constructed to have two universal priming sequences. Following preamplification, the Nextera XT library construction kit was used to prepare 96 unique indexes specific to each sample. Barcoded cDNA fragments were then pooled prior to sequencing. Sequencing was carried out using an Illumina NextSeq500 as paired- end 2x38bp to a coverage of approximately ~4 million reads per well.

treatment_protocol: Samples were stimulated for 72h with the indicated treatments.

value: Bone marrow-derived cultured mast cells (BMMCs)

value: 6-8 weeks

value: 10 ng/mL TGF-b, 72h


title: TGF_1_2

value: 1 ng/mL TGF-b, 72h


title: WT_PBS_3


title: Liver cells_knockout_#4

city: Tucson

first: Dawn

last: Coletta

state: AZ

address: 1501 N. Campbell Ave

department: Medicine

institute: UNIVERSITY OF ARIZONA

hyb_protocol: The biotin labeled RNAs were hybridized to Affymetrix Mouse Gene 2.0 ST Array as per Affymetrix manufacturer's instructions.

scan_protocol: The arrays were read using the Agilent/Affymetrix 2500A scanner according to manufacturer's protocols.

data_processing: CEL files were imported into the open source R package. The Affymetric package and Linear Models for Microarray Data version 3.22.0 were used for analysis. The data were background corrected using normal exponent, quantile normalized , and an unweighted linear model was performed.

label: biotin

source_name: AML12 liver cells with deletion of VWA8

label_protocol: The isolated total RNAs were used to produce biotin labeled RNAs according to Affymetrix manufacturer's instructions.

growth_protocol: AML12 mouse hepatocytes purchased from ATCC (ATCC CRL-2254) were cultured in DMEM/F12 with 10% FBS, 1% Penicillin/Streptomycin, and 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone.

extract_protocol: Total RNA was isolated from AML12 cells using RNAStat solution (Tel-Test Inc., Friendswood, TX) and the total RNA was purified with RNeasy and DNase I treatment (Qiagen, Valencia, CA).

treatment_protocol: VWA8 gene was targeted and deleted from the AML12 cells using CRISPR/Cas9.  Wildtype VWA8 cells were used as a comaprison to the knockout cells.

value: liver


title: Liver cells_wildtype_#2

source_name: AML12 liver cells wildtype

value: Wild type


title: Liver cells_knockout_#1


title: Liver cells_knockout_#3


title: Liver cells_wildtype_#1


title: Liver cells_wildtype_#4


title: Liver cells_knockout_#2


title: Liver cells_wildtype_#3


title: SCF_TGF_1_2

value: SCF plus 1 ng/mL TGF-b, 72h


title: SCF_TGF_10_1

value: SCF plus 10 ng/mL TGF-b, 72h


title: SCF_TGF_10_2


title: SCF_TGF_1_1


title: SCF_2

value: 100 ng/mL SCF, 72h


title: IL3_2

value: IL3 alone


title: KO_RPF_2

city: SHANGHAI

first: HONGHUI

last: MA

address: Jimo Road 150

institute: Tongji University School of Medicine

description:
RiboZero mRNA
KO_RPF_2

data_processing:
Library strategy: Ribo-Seq
After adapter-trimming and quality-filtering, the sequences were further filtered to exclude rRNA and tRNA reads by aligning to mouse rRNA and tRNA sequences, respectively. The cleaned ribosome-protected fragments (RPFs) were aligned to the mouse reference gneome (UCSC, mm10) using Bowtie with a maximum one mismatch allowed (Langmead et al., 2009). The translation efficiency (TE) was calculated by dividing RPF abundancy on CDS by its mRNA abundancy.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx with abundance values and translation efficiency (TE) for each sample.

source_name: mESC

growth_protocol: The mESCs were cultured in 2i/lif medium. The 2i/lif medium contained N2B27 medium with 2i (PD0325901:1µM, Selleck; CHIR99021: 3µM, Selleck) and leukemia inhibitory factor lif (1,000U/ml, Millipore). N2B27 medium consisted of 50% DMEM/F12(GIBCO, #10565-018),50%Neurobasal medium (GIBCO, #21103-049) supplemented with 1xN2 (GIBCO, #17502048), 1xB27 (GIBCO, #17504044), 1xGlutamax (GIBCO, #35050061),1mM NEAA (GIBCO, #11140050),1xSodium Pyruvate (GIBCO, #11360070) and 0.1mM 2-mercaptoethanol (Sigma-Aldrich, #M3148).

extract_protocol:
Cells were treated by cyclohexamide to pause translation and lyzed in Mammalian Polysome Buffer. Input mRNAs and RPFs were isolated, ribosomal RNAs were depleted and cDNA libraries were prepared using NEBNext® Small RNA Library Prep Set for Illumina® as described before(Han,D et al, Nature 2019).
NEBNext® Small RNA Library Prep Set for Illumina®

treatment_protocol: Mettl5 knockout mESC cells were generated by CRISPR/Cas9-mediated gene editing

value: mESC

tag: strain background

value: 129Sv females mated with C57BL/6 BVSC males

value: Mettl5 KO

value: RPF


title: KO_RPF_1

description:
RiboZero mRNA
KO_RPF_1


title: SCF_1


title: KO_input_1

description:
RiboZero mRNA
KO_input_1

value: Input


title: WT_input_1

description:
RiboZero mRNA
WT_input_1

value: WT


title: WT_PBS_1

value: wild type

value: 3 months

value: Brain

value: PBS injection


title: IL3_1

value: Bone marrow-derived cultured mast cells (BMMCs)

value: 6-8 weeks


title: WT_RPF_1

description:
RiboZero mRNA
WT_RPF_1


title: WT_RPF_2

description:
RiboZero mRNA
WT_RPF_2


title: Non-cancer 2 [SH66Y18_Cell3]

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

description:
miRNA
NB13032603

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: serum

value: M

tag: cstage

tag: child-pugh

tag: afp

value: unknown


title: Non-cancer 2 [SH67429_Cell2]

description:
miRNA
NB13041704

tag: Sex


title: Non-cancer 2 [SH66Y21_Cell4]

description:
miRNA
NB13040101


title: Non-cancer 2 [SH67431_Cell3]

description:
miRNA
NB13042202


title: Non-cancer 2 [SH66Y17_Cell2]

description:
miRNA
NB13032504

value: F


title: Non-cancer 2 [SH66X53_Cell1]

description:
miRNA
NB13021403


title: Non-cancer 2 [SH66Y09_Cell3]

description:
miRNA
NB13031303


title: Non-cancer 2 [SH67433_Cell4]

description:
miRNA
NB13042301


title: Non-cancer 2 [SH66Y14_Cell2]

description:
miRNA
NB13031806


title: Non-cancer 2 [SH66Y23_Cell1]

description:
miRNA
NB13040102


title: Non-cancer 2 [SH67450_Cell4]

description:
miRNA
NB13052102


title: Non-cancer 2 [SH67440_Cell3]

description:
miRNA
NB13050703


title: Non-cancer 2 [SH67440_Cell2]

description:
miRNA
NB13050702


title: Non-cancer 2 [SH67451_Cell1]

description:
miRNA
NB13052201


title: Non-cancer 2 [SH66X43_Cell4]

description:
miRNA
NB13012905


title: Non-cancer 2 [SH66X36_Cell1]

description:
miRNA
NB13011604


title: Non-cancer 2 [SH66X47_Cell3]

description:
miRNA
NB13020602


title: Non-cancer 2 [SH66X39_Cell3]

description:
miRNA
NB13012107


title: Non-cancer 2 [SH66X35_Cell1]

description:
miRNA
NB13011505


title: Non-cancer 2 [SH66X32_Cell4]

description:
miRNA
NB13011103


title: Non-cancer 2 [SH66X32_Cell2]

description:
miRNA
NB13011002


title: Non-cancer 2 [SH66X28_Cell1]

description:
miRNA
NB12122601


title: Non-cancer 2 [SH66X24_Cell4]

description:
miRNA
NB12122001


title: Non-cancer 2 [SH67422_Cell1]

description:
miRNA
NB13040802


title: Non-cancer 2 [SH66X27_Cell1]

description:
miRNA
NB12122501


title: Non-cancer 2 [SH66X50_Cell3]

description:
miRNA
NB13021202


title: Non-cancer 2 [SH66Y23_Cell3]

description:
miRNA
NB13040202


title: Non-cancer 2 [SH66X30_Cell2]

description:
miRNA
NB12122803


title: Non-cancer 2 [SH66X22_Cell1]

description:
miRNA
NB12121404


title: Non-cancer 2 [SH64630_Cell3]

description:
miRNA
NB12121402


title: Non-cancer 2 [SH66X17_Cell4]

description:
miRNA
NB12120601


title: Non-cancer 2 [SH66P52_Cell1]

description:
miRNA
NB12081002


title: Non-cancer 2 [SH66X14_Cell4]

description:
miRNA
NB12120302


title: Non-cancer 2 [SH66X05_Cell3]

description:
miRNA
NB12111405


title: Non-cancer 2 [SH66P48_Cell4]

description:
miRNA
NB12080304


title: Non-cancer 2 [SH66X09_Cell1]

description:
miRNA
NB12111905


title: Non-cancer 2 [SH66W20_Cell3]

description:
miRNA
NB12101202


title: Non-cancer 2 [SH66W21_Cell3]

description:
miRNA
NB12101502


title: Non-cancer 2 [SH66W17_Cell4]

description:
miRNA
NB12100902


title: Non-cancer 2 [SH66T05_Cell2]

description:
miRNA
NB12091004


title: Non-cancer 2 [SH66W32_Cell3]

description:
miRNA
NB12110201


title: Non-cancer 2 [SH66T16_Cell1]

description:
miRNA
NB12092701


title: Non-cancer 2 [SH66T17_Cell2]

description:
miRNA
NB12092801


title: Non-cancer 2 [SH66P42_Cell4]

description:
miRNA
NB12072403


title: Non-cancer 2 [SH66W01_Cell3]

description:
miRNA
NB12062802


title: Non-cancer 2 [SH66W25_Cell2]

description:
miRNA
NB12102402


title: Non-cancer 2 [SH66T19_Cell3]

description:
miRNA
NB12100204


title: Non-cancer 2 [SH66P59_Cell2]

description:
miRNA
NB12082203


title: Non-cancer 2 [SH66P43_Cell2]

description:
miRNA
NB12072502


title: Non-cancer 2 [SH64629_Cell1]

description:
miRNA
NB12071103


title: Non-cancer 2 [SH66P30_Cell3]

description:
miRNA
NB12061503


title: Non-cancer 2 [SH66W02_Cell4]

description:
miRNA
NB12070302


title: Non-cancer 2 [SH66T17_Cell3]

description:
miRNA
NB12100101


title: Non-cancer 2 [SH66T26_Cell4]

description:
miRNA
NB12062604


title: Non-cancer 2 [SH66T21_Cell2]

description:
miRNA
NB12061804


title: Non-cancer 2 [SH66T23_Cell4]

description:
miRNA
NB12062103


title: Non-cancer 2 [SH66P26_Cell2]

description:
miRNA
NB12060803


title: Non-cancer 2 [SH66P26_Cell4]

description:
miRNA
NB12060805


title: Non-cancer 2 [SH66P12_Cell1]

description:
miRNA
NB12051801


title: Non-cancer 2 [SH66P15_Cell3]

description:
miRNA
NB12052501


title: Non-cancer 2 [SH66P24_Cell4]

description:
miRNA
NB12060701


title: Non-cancer 2 [SH66P11_Cell3]

description:
miRNA
NB12051703


title: Non-cancer 2 [SH66N42_Cell3]

description:
miRNA
NB12031605


title: Non-cancer 2 [SH66N27_Cell2]

description:
miRNA
NB12022104


title: Non-cancer 2 [SH66N54_Cell4]

description:
miRNA
NB12041203


title: Non-cancer 2 [SH66N19_Cell2]

description:
miRNA
NB12021001


title: Non-cancer 2 [SH66N02_Cell3]

description:
miRNA
M12011201


title: Non-cancer 2 [SH64601_Cell3]

description:
miRNA
M12012306


title: Non-cancer 2 [SH66N14_Cell3]

description:
miRNA
M12013104


title: Non-cancer 2 [SH66N51_Cell2]

description:
miRNA
NB12040404


title: Non-cancer 2 [SH66P02_Cell4]

description:
miRNA
NB12050702


title: Non-cancer 2 [SH66P06_Cell3]

description:
miRNA
NB12051402


title: Non-cancer 2 [SH66N29_Cell2]

description:
miRNA
NB12022701


title: Non-cancer 2 [SH66N58_Cell4]

description:
miRNA
NB12042005


title: Non-cancer 2 [SH66N06_Cell4]

description:
miRNA
M12011901


title: Non-cancer 2 [SH66N57_Cell3]

description:
miRNA
NB12041902


title: Non-cancer 2 [SH66N35_Cell2]

description:
miRNA
NB12030902


title: Non-cancer 2 [SH66N05_Cell1]

description:
miRNA
M12011702


title: Non-cancer 2 [SH66N13_Cell2]

description:
miRNA
M12013003


title: Non-cancer 2 [SH66N02_Cell2]

description:
miRNA
M12011102


title: Non-cancer 2 [SH66N19_Cell4]

description:
miRNA
NB12021003


title: Non-cancer 2 [SH66M59_Cell2]

description:
miRNA
M11122201


title: Non-cancer 2 [SH66M49_Cell3]

description:
miRNA
M11120703


title: Non-cancer 2 [SH63Z51_Cell1]

description:
miRNA
M11112101


title: Non-cancer 2 [SH66M42_Cell4]

description:
miRNA
M11112203


title: Non-cancer 2 [SH66N01_Cell1]

description:
miRNA
M12010603


title: Non-cancer 2 [SH66N29_Cell3]

description:
miRNA
NB12022704


title: Non-cancer 2 [SH66N31_Cell1]

description:
miRNA
NB12022903


title: Non-cancer 2 [SH66M50_Cell3]

description:
miRNA
M11120901


title: Non-cancer 2 [SH64604_Cell1]

description:
miRNA
M12013005


title: Non-cancer 2 [SH66M16_Cell4]

description:
miRNA
M11111001


title: Non-cancer 2 [SH66M18_Cell4]

description:
miRNA
M11111701


title: Non-cancer 2 [SH66M17_Cell2]

description:
miRNA
M11111101


title: Non-cancer 2 [SH66M06_Cell3]

description:
miRNA
M11102102


title: Non-cancer 2 [SH63Z46_Cell3]

description:
miRNA
M11103103


title: Non-cancer 2 [SH66L32_Cell3]

description:
miRNA
M11072802


title: Non-cancer 2 [SH66M02_Cell2]

description:
miRNA
M11101103


title: Non-cancer 2 [SH66L55_Cell3]

description:
miRNA
M11091403


title: Non-cancer 2 [SH66L49_Cell4]

description:
miRNA
M11090201


title: Non-cancer 2 [SH66L37_Cell2]

description:
miRNA
M11080502


title: Non-cancer 2 [SH66L48_Cell2]

description:
miRNA
M11083001


title: Non-cancer 2 [SH66L31_Cell3]

description:
miRNA
M11072603


title: Non-cancer 2 [SH66L29_Cell3]

description:
miRNA
M11072202


title: Non-cancer 2 [SH66L27_Cell1]

description:
miRNA
M11072001


title: Non-cancer 2 [SH66E25_Cell1]

description:
miRNA
M11071503


title: Non-cancer 2 [SH66L44_Cell2]

description:
miRNA
M11082201


title: Non-cancer 2 [SH66L25_Cell3]

description:
miRNA
M11071502


title: Non-cancer 2 [SH66E24_Cell4]

description:
miRNA
M11071303


title: Non-cancer 2 [SH63Z47_Cell2]

description:
miRNA
M11110206


title: Non-cancer 2 [SH64L43_Cell2]

description:
miRNA
M11070808


title: Non-cancer 2 [SH64L39_Cell3]

description:
miRNA
M11070806


title: Non-cancer 2 [SH64721_Cell3]

description:
miRNA
M11051303


title: Non-cancer 2 [SH66L16_Cell3]

description:
miRNA
M11051307


title: Non-cancer 2 [SH64740_Cell1]

description:
miRNA
M11061602


title: Non-cancer 2 [SH64736_Cell2]

description:
miRNA
M11060702


title: Non-cancer 2 [SH64L49_Cell1]

description:
miRNA
M11052705


title: Non-cancer 2 [SH66E35_Cell3]

description:
miRNA
M11041502


title: Non-cancer 2 [SH66F14_Cell4]

description:
miRNA
M11041303


title: Non-cancer 2 [SH66F20_Cell3]

description:
miRNA
M11032502


title: Non-cancer 2 [SH66L07_Cell4]

description:
miRNA
M11032902


title: Non-cancer 2 [SH66L18_Cell1]

description:
miRNA
M11041306


title: Non-cancer 2 [SH66L15_Cell2]

description:
miRNA
M11030808


title: Non-cancer 2 [SH66E30_Cell2]

description:
miRNA
M11031105


title: Non-cancer 2 [SH64L57_Cell2]

description:
miRNA
M10122001


title: Non-cancer 2 [SH66F16_Cell4]

description:
miRNA
M11030205


title: Non-cancer 2 [SH66E09_Cell3]

description:
miRNA
M10121701


title: Non-cancer 2 [SH64R04_Cell2]

description:
miRNA
M10121504


title: Non-cancer 2 [SH66E11_Cell1]

description:
miRNA
M10122403


title: Non-cancer 2 [SH66F05_Cell1]

description:
miRNA
M11020302


title: Non-cancer 2 [SH66L12_Cell1]

description:
miRNA
M11020904


title: Non-cancer 2 [SH66E29_Cell1]

description:
miRNA
M11030401


title: Non-cancer 2 [SH66E13_Cell2]

description:
miRNA
M11011403


title: Non-cancer 2 [SH66F16_Cell1]

description:
miRNA
M11031803


title: Non-cancer 2 [SH64L58_Cell3]

description:
miRNA
M10102504


title: Non-cancer 2 [SH66E57_Cell2]

description:
miRNA
M11011104


title: Non-cancer 2 [SH64R01_Cell3]

description:
miRNA
M11010506


title: Non-cancer 2 [SH64R02_Cell3]

description:
miRNA
M10111702


title: Non-cancer 2 [SH66D63_Cell4]

description:
miRNA
M10112902


title: Non-cancer 2 [SH66E36_Cell3]

description:
miRNA
M10110503


title: Non-cancer 2 [SH64L53_Cell2]

description:
miRNA
M10121402


title: HCC [SH5X537_Cell1]

description:
miRNA
HC0356

value: III

value: A


title: Non-cancer 2 [SH64R02_Cell4]

description:
miRNA
M10111803


title: HCC [SH5X535_Cell4]

description:
miRNA
HC0355

value: II


title: HCC [SH5X535_Cell3]

description:
miRNA
HC0354

value: I


title: HCC [SH5X535_Cell2]

description:
miRNA
HC0353


title: HCC [SH5X534_Cell2]

description:
miRNA
HC0349


title: HCC [SH5X535_Cell1]

description:
miRNA
HC0352


title: HCC [SH5X534_Cell3]

description:
miRNA
HC0350


title: Non-cancer 2 [SH66E39_Cell3]

description:
miRNA
M11010603


title: HCC [SH5X534_Cell4]

description:
miRNA
HC0351


title: Non-cancer 2 [SH66E42_Cell2]

description:
miRNA
M10121001


title: Non-cancer 2 [SH66E41_Cell2]

description:
miRNA
M10112402


title: HCC [SH5X533_Cell4]

description:
miRNA
HC0347


title: HCC [SH5X532_Cell4]

description:
miRNA
HC0343


title: HCC [SH5X532_Cell2]

description:
miRNA
HC0341


title: HCC [SH5X533_Cell3]

description:
miRNA
HC0346


title: HCC [SH5X532_Cell1]

description:
miRNA
HC0340


title: HCC [SH5X533_Cell2]

description:
miRNA
HC0345


title: HCC [SH5X532_Cell3]

description:
miRNA
HC0342


title: HCC [SH5X533_Cell1]

description:
miRNA
HC0344


title: HCC [SH5X530_Cell1]

description:
miRNA
HC0332

value: X


title: HCC [SH5X528_Cell4]

description:
miRNA
HC0327


title: HCC [SH5X529_Cell3]

description:
miRNA
HC0330


title: HCC [SH5X529_Cell2]

description:
miRNA
HC0329


title: HCC [SH5X530_Cell4]

description:
miRNA
HC0335


title: HCC [SH5X531_Cell3]

description:
miRNA
HC0338


title: HCC [SH5X530_Cell2]

description:
miRNA
HC0333


title: HCC [SH5X530_Cell3]

description:
miRNA
HC0334


title: HCC [SH5X529_Cell4]

description:
miRNA
HC0331


title: HCC [SH5X528_Cell2]

description:
miRNA
HC0325


title: HCC [SH5X528_Cell3]

description:
miRNA
HC0326


title: HCC [SH5X528_Cell1]

description:
miRNA
HC0324


title: HCC [SH5X527_Cell4]

description:
miRNA
HC0323


title: HCC [SH5X527_Cell1]

description:
miRNA
HC0320


title: HCC [SH5X526_Cell4]

description:
miRNA
HC0319


title: HCC [SH5X526_Cell3]

description:
miRNA
HC0318


title: HCC [SH5X526_Cell1]

description:
miRNA
HC0316


title: HCC [SH5X534_Cell1]

description:
miRNA
HC0348


title: HCC [SH5X526_Cell2]

description:
miRNA
HC0317


title: HCC [SH5X527_Cell3]

description:
miRNA
HC0322


title: HCC [SH5X524_Cell2]

description:
miRNA
HC0309


title: HCC [SH5X524_Cell3]

description:
miRNA
HC0310


title: HCC [SH5X531_Cell4]

description:
miRNA
HC0339


title: HCC [SH5X525_Cell4]

description:
miRNA
HC0315


title: HCC [SH5X524_Cell1]

description:
miRNA
HC0308

value: B


title: HCC [SH5X524_Cell4]

description:
miRNA
HC0311


title: HCC [SH5X523_Cell2]

description:
miRNA
HC0305


title: HCC [SH5X525_Cell2]

description:
miRNA
HC0313


title: HCC [SH5X523_Cell3]

description:
miRNA
HC0306


title: HCC [SH5X527_Cell2]

description:
miRNA
HC0321


title: HCC [SH5X523_Cell1]

description:
miRNA
HC0304


title: HCC [SH5X522_Cell2]

description:
miRNA
HC0301


title: HCC [SH5X522_Cell4]

description:
miRNA
HC0303


title: HCC [SH5X520_Cell3]

description:
miRNA
HC0298


title: HCC [SH5X520_Cell4]

description:
miRNA
HC0299


title: HCC [SH5X520_Cell2]

description:
miRNA
HC0297


title: HCC [SH5X520_Cell1]

description:
miRNA
HC0296


title: HCC [SH5X519_Cell3]

description:
miRNA
HC0294


title: HCC [SH5X519_Cell4]

description:
miRNA
HC0295


title: HCC [SH5X519_Cell2]

description:
miRNA
HC0293


title: HCC [SH5X518_Cell3]

description:
miRNA
HC0290


title: HCC [SH5X518_Cell1]

description:
miRNA
HC0288


title: HCC [SH5X518_Cell4]

description:
miRNA
HC0291


title: HCC [SH5X519_Cell1]

description:
miRNA
HC0292


title: HCC [SH5YL20_Cell2]

description:
miRNA
HC0287


title: HCC [SH5X517_Cell3]

description:
miRNA
HC0286


title: HCC [SH5X517_Cell1]

description:
miRNA
HC0284


title: HCC [SH5X516_Cell4]

description:
miRNA
HC0283


title: HCC [SH5X517_Cell2]

description:
miRNA
HC0285


title: HCC [SH5X522_Cell1]

description:
miRNA
HC0300


title: HCC [SH5X513_Cell1]

description:
miRNA
HC0272


title: HCC [SH5X516_Cell1]

description:
miRNA
HC0280


title: HCC [SH5X513_Cell4]

description:
miRNA
HC0275


title: HCC [SH5X514_Cell3]

description:
miRNA
HC0278


title: HCC [SH5X516_Cell2]

description:
miRNA
HC0281


title: HCC [SH5X512_Cell1]

description:
miRNA
HC0268


title: HCC [SH5X511_Cell4]

description:
miRNA
HC0267


title: HCC [SH5X512_Cell4]

description:
miRNA
HC0271


title: HCC [SH5X512_Cell3]

description:
miRNA
HC0270


title: HCC [SH5X511_Cell1]

description:
miRNA
HC0264


title: HCC [SH5X511_Cell2]

description:
miRNA
HC0265


title: HCC [SH5X514_Cell4]

description:
miRNA
HC0279


title: HCC [SH5X510_Cell3]

description:
miRNA
HC0262


title: HCC [SH5X510_Cell2]

description:
miRNA
HC0261


title: HCC [SH5X510_Cell1]

description:
miRNA
HC0260


title: HCC [SH5X507_Cell3]

description:
miRNA
HC0254


title: HCC [SH5X516_Cell3]

description:
miRNA
HC0282


title: HCC [SH5X509_Cell3]

description:
miRNA
HC0258


title: HCC [SH5YL20_Cell1]

description:
miRNA
HC0256


title: HCC [SH5X513_Cell2]

description:
miRNA
HC0273


title: HCC [SH5YL19_Cell4]

description:
miRNA
HC0255


title: HCC [SH5X507_Cell1]

description:
miRNA
HC0252


title: HCC [SH5X507_Cell2]

description:
miRNA
HC0253


title: HCC [SH5X509_Cell2]

description:
miRNA
HC0257


title: HCC [SH5X506_Cell1]

description:
miRNA
HC0248


title: HCC [SH5X506_Cell3]

description:
miRNA
HC0250


title: HCC [SH5X506_Cell4]

description:
miRNA
HC0251


title: HCC [SH5X506_Cell2]

description:
miRNA
HC0249


title: HCC [SH5X504_Cell4]

description:
miRNA
HC0247


title: HCC [SH5X501_Cell1]

description:
miRNA
HC0240


title: HCC [SH5X156_Cell3]

description:
miRNA
HC0238


title: HCC [SH5X504_Cell3]

description:
miRNA
HC0246


title: HCC [SH5X501_Cell3]

description:
miRNA
HC0242


title: HCC [SH5X155_Cell4]

description:
miRNA
HC0235


title: HCC [SH5X155_Cell3]

description:
miRNA
HC0234


title: HCC [SH5X501_Cell2]

description:
miRNA
HC0241


title: HCC [SH5X155_Cell1]

description:
miRNA
HC0232


title: HCC [SH5X156_Cell2]

description:
miRNA
HC0237


title: HCC [SH5X155_Cell2]

description:
miRNA
HC0233


title: HCC [SH5X154_Cell3]

description:
miRNA
HC0230


title: HCC [SH5X156_Cell1]

description:
miRNA
HC0236


title: HCC [SH5X153_Cell2]

description:
miRNA
HC0225


title: HCC [SH5X156_Cell4]

description:
miRNA
HC0239


title: HCC [SH5X154_Cell2]

description:
miRNA
HC0229


title: HCC [SH5X153_Cell4]

description:
miRNA
HC0227


title: HCC [SH5X153_Cell3]

description:
miRNA
HC0226


title: HCC [SH5X154_Cell1]

description:
miRNA
HC0228


title: HCC [SH5X511_Cell3]

description:
miRNA
HC0266


title: HCC [SH5X153_Cell1]

description:
miRNA
HC0224

value: IV


title: HCC [SH5X151_Cell1]

description:
miRNA
HC0216


title: HCC [SH5X148_Cell3]

description:
miRNA
HC0214


title: HCC [SH5X151_Cell2]

description:
miRNA
HC0217


title: HCC [SH5X152_Cell4]

description:
miRNA
HC0223


title: HCC [SH5X154_Cell4]

description:
miRNA
HC0231


title: HCC [SH5X152_Cell3]

description:
miRNA
HC0222


title: HCC [SH5X147_Cell2]

description:
miRNA
HC0209


title: HCC [SH5X151_Cell3]

description:
miRNA
HC0218


title: HCC [SH5YL19_Cell3]

description:
miRNA
HC0219


title: HCC [SH5X152_Cell2]

description:
miRNA
HC0221


title: HCC [SH55T64_Cell1]

description:
miRNA
HC0201


title: HCC [SH5X145_Cell1]

description:
miRNA
HC0205


title: HCC [SH5X145_Cell2]

description:
miRNA
HC0206


title: HCC [SH5X148_Cell1]

description:
miRNA
HC0212


title: HCC [SH56968_Cell4]

description:
miRNA
HC0195


title: HCC [SH5YL19_Cell2]

description:
miRNA
HC0210


title: HCC [SH55T62_Cell2]

description:
miRNA
HC0194


title: HCC [SH5X144_Cell4]

description:
miRNA
HC0204


title: HCC [SH55T62_Cell1]

description:
miRNA
HC0193


title: HCC [SH5X144_Cell3]

description:
miRNA
HC0203


title: HCC [SH5X148_Cell4]

description:
miRNA
HC0215


title: HCC [SH55T63_Cell4]

description:
miRNA
HC0200


title: HCC [SH56968_Cell3]

description:
miRNA
HC0192


title: HCC [SH55T63_Cell1]

description:
miRNA
HC0197


title: HCC [SH55T62_Cell4]

description:
miRNA
HC0196


title: HCC [SH5X148_Cell2]

description:
miRNA
HC0213


title: HCC [SH55T58_Cell1]

description:
miRNA
HC0189


title: HCC [SH55T58_Cell3]

description:
miRNA
HC0191


title: HCC [SH55T58_Cell2]

description:
miRNA
HC0190


title: HCC [SH5X144_Cell2]

description:
miRNA
HC0202


title: HCC [SH55T63_Cell3]

description:
miRNA
HC0199


title: HCC [SH56967_Cell3]

description:
miRNA
HC0181


title: HCC [SH56967_Cell2]

description:
miRNA
HC0180


title: HCC [SH55T55_Cell2]

description:
miRNA
HC0182


title: HCC [SH56967_Cell4]

description:
miRNA
HC0183


title: HCC [SH55T57_Cell2]

description:
miRNA
HC0186


title: HCC [SH56968_Cell1]

description:
miRNA
HC0187


title: HCC [SH55T55_Cell4]

description:
miRNA
HC0184


title: HCC [SH55T53_Cell1]

description:
miRNA
HC0177


title: HCC [SH56966_Cell4]

description:
miRNA
HC0175


title: HCC [SH56966_Cell3]

description:
miRNA
HC0174


title: HCC [SH56968_Cell2]

description:
miRNA
HC0188


title: HCC [SH56965_Cell3]

description:
miRNA
HC0168


title: HCC [SH56965_Cell2]

description:
miRNA
HC0167


title: HCC [SH56965_Cell1]

description:
miRNA
HC0166


title: HCC [SH55T50_Cell4]

description:
miRNA
HC0176


title: HCC [SH56965_Cell4]

description:
miRNA
HC0169


title: HCC [SH55T43_Cell4]

description:
miRNA
HC0164


title: HCC [SH55T43_Cell3]

description:
miRNA
HC0163


title: HCC [SH55T43_Cell2]

description:
miRNA
HC0162


title: HCC [SH56964_Cell3]

description:
miRNA
HC0161


title: HCC [SH56964_Cell1]

description:
miRNA
HC0156


title: HCC [SH55T41_Cell1]

description:
miRNA
HC0157


title: HCC [SH56963_Cell3]

description:
miRNA
HC0154


title: HCC [SH56964_Cell2]

description:
miRNA
HC0160


title: HCC [SH56963_Cell2]

description:
miRNA
HC0153


title: HCC [SH55T38_Cell4]

description:
miRNA
HC0152


title: HCC [SH55T38_Cell3]

description:
miRNA
HC0151


title: HCC [SH55T49_Cell4]

description:
miRNA
HC0172


title: HCC [SH55T49_Cell2]

description:
miRNA
HC0170


title: HCC [SH55T36_Cell3]

description:
miRNA
HC0143


title: HCC [SH55T37_Cell2]

description:
miRNA
HC0146


title: HCC [SH56964_Cell4]

description:
miRNA
HC0165


title: HCC [SH55T38_Cell2]

description:
miRNA
HC0150


title: HCC [SH55T37_Cell1]

description:
miRNA
HC0145


title: HCC [SH55T37_Cell4]

description:
miRNA
HC0148


title: HCC [SH55T36_Cell4]

description:
miRNA
HC0144


title: HCC [SH55T38_Cell1]

description:
miRNA
HC0149


title: HCC [SH55T36_Cell1]

description:
miRNA
HC0141


title: HCC [SH55T35_Cell1]

description:
miRNA
HC0137


title: HCC [SH55T33_Cell4]

description:
miRNA
HC0136


title: HCC [SH55T35_Cell3]

description:
miRNA
HC0139


title: HCC [SH55T33_Cell2]

description:
miRNA
HC0134


title: HCC [SH55T33_Cell3]

description:
miRNA
HC0135


title: HCC [SH55T31_Cell4]

description:
miRNA
HC0132


title: HCC [SH55T28_Cell4]

description:
miRNA
HC0128


title: HCC [SH55T28_Cell1]

description:
miRNA
HC0125


title: HCC [SH55T35_Cell4]

description:
miRNA
HC0140


title: HCC [SH55T31_Cell1]

description:
miRNA
HC0129


title: HCC [SH55T27_Cell3]

description:
miRNA
HC0123


title: HCC [SH55T27_Cell4]

description:
miRNA
HC0124


title: HCC [SH55T28_Cell2]

description:
miRNA
HC0126


title: HCC [SH55T27_Cell2]

description:
miRNA
HC0122


title: HCC [SH55T31_Cell3]

description:
miRNA
HC0131


title: HCC [SH55T26_Cell3]

description:
miRNA
HC0119


title: HCC [SH55T24_Cell2]

description:
miRNA
HC0110


title: HCC [SH55T27_Cell1]

description:
miRNA
HC0121


title: HCC [SH55T24_Cell1]

description:
miRNA
HC0109


title: HCC [SH55T26_Cell1]

description:
miRNA
HC0117


title: HCC [SH55T25_Cell3]

description:
miRNA
HC0115


title: HCC [SH55T25_Cell1]

description:
miRNA
HC0113


title: HCC [SH55T24_Cell3]

description:
miRNA
HC0111


title: HCC [SH55T25_Cell2]

description:
miRNA
HC0114


title: HCC [SH55T22_Cell4]

description:
miRNA
HC0104


title: HCC [SH55T23_Cell1]

description:
miRNA
HC0105


title: HCC [SH55T28_Cell3]

description:
miRNA
HC0127


title: HCC [SH54N58_Cell1]

description:
miRNA
HC0097


title: HCC [SH54N58_Cell3]

description:
miRNA
HC0099


title: HCC [SH54N58_Cell4]

description:
miRNA
HC0100


title: HCC [SH54N58_Cell2]

description:
miRNA
HC0098


title: HCC [SH55T25_Cell4]

description:
miRNA
HC0116


title: HCC [SH54N57_Cell3]

description:
miRNA
HC0095


title: HCC [SH54N57_Cell2]

description:
miRNA
HC0094


title: HCC [SH54N57_Cell1]

description:
miRNA
HC0093


title: HCC [SH55T23_Cell4]

description:
miRNA
HC0108


title: HCC [SH54N55_Cell4]

description:
miRNA
HC0088


title: HCC [SH54N55_Cell3]

description:
miRNA
HC0087


title: HCC [SH54N56_Cell3]

description:
miRNA
HC0091


title: HCC [SH55T22_Cell2]

description:
miRNA
HC0102


title: HCC [SH54N56_Cell2]

description:
miRNA
HC0090


title: HCC [SH54N55_Cell2]

description:
miRNA
HC0086


title: HCC [SH54N54_Cell2]

description:
miRNA
HC0082


title: HCC [SH54N53_Cell4]

description:
miRNA
HC0080


title: HCC [SH54N54_Cell1]

description:
miRNA
HC0081


title: HCC [SH54N55_Cell1]

description:
miRNA
HC0085


title: HCC [SH54N53_Cell3]

description:
miRNA
HC0079


title: HCC [SH54N53_Cell2]

description:
miRNA
HC0078


title: HCC [SH54N51_Cell3]

description:
miRNA
HC0075


title: HCC [SH54N53_Cell1]

description:
miRNA
HC0077


title: HCC [SH54N54_Cell3]

description:
miRNA
HC0083


title: HCC [SH54N51_Cell1]

description:
miRNA
HC0073


title: HCC [SH54N57_Cell4]

description:
miRNA
HC0096


title: HCC [SH54N51_Cell2]

description:
miRNA
HC0074


title: HCC [SH54N45_Cell4]

description:
miRNA
HC0072


title: HCC [SH54N45_Cell1]

description:
miRNA
HC0069


title: HCC [SH54N45_Cell3]

description:
miRNA
HC0071


title: HCC [SH54N44_Cell2]

description:
miRNA
HC0066


title: HCC [SH54N43_Cell2]

description:
miRNA
HC0062


title: HCC [SH54N44_Cell3]

description:
miRNA
HC0067


title: HCC [SH54N56_Cell1]

description:
miRNA
HC0089


title: HCC [SH54N43_Cell4]

description:
miRNA
HC0064


title: HCC [SH54N43_Cell3]

description:
miRNA
HC0063


title: HCC [SH54N41_Cell4]

description:
miRNA
HC0060


title: HCC [SH54N40_Cell1]

description:
miRNA
HC0053


title: HCC [SH54N40_Cell3]

description:
miRNA
HC0055


title: HCC [SH54N41_Cell3]

description:
miRNA
HC0059


title: HCC [SH54N41_Cell2]

description:
miRNA
HC0058


title: HCC [SH54N38_Cell4]

description:
miRNA
HC0052


title: HCC [SH54N38_Cell3]

description:
miRNA
HC0051


title: HCC [SH54N38_Cell2]

description:
miRNA
HC0050


title: HCC [SH54N38_Cell1]

description:
miRNA
HC0049


title: HCC [SH54N37_Cell4]

description:
miRNA
HC0048


title: HCC [SH54N37_Cell3]

description:
miRNA
HC0047


title: HCC [SH54N37_Cell1]

description:
miRNA
HC0045


title: HCC [SH54N36_Cell4]

description:
miRNA
HC0044


title: HCC [SH54N37_Cell2]

description:
miRNA
HC0046


title: HCC [SH54N36_Cell2]

description:
miRNA
HC0042


title: HCC [SH54N43_Cell1]

description:
miRNA
HC0061


title: HCC [SH54N34_Cell3]

description:
miRNA
HC0035


title: HCC [SH54N33_Cell3]

description:
miRNA
HC0031


title: HCC [SH54N40_Cell4]

description:
miRNA
HC0056


title: HCC [SH54N34_Cell2]

description:
miRNA
HC0034


title: HCC [SH54N33_Cell4]

description:
miRNA
HC0032


title: HCC [SH54N34_Cell1]

description:
miRNA
HC0033


title: HCC [SH54N33_Cell2]

description:
miRNA
HC0030


title: HCC [SH54N35_Cell4]

description:
miRNA
HC0040


title: HCC [SH54N35_Cell2]

description:
miRNA
HC0038


title: HCC [SH54N33_Cell1]

description:
miRNA
HC0029


title: HCC [SH54N35_Cell3]

description:
miRNA
HC0039


title: HCC [SH54N32_Cell4]

description:
miRNA
HC0028


title: HCC [SH54N36_Cell3]

description:
miRNA
HC0043


title: HCC [SH54N36_Cell1]

description:
miRNA
HC0041


title: HCC [SH54N30_Cell3]

description:
miRNA
HC0023


title: HCC [SH54N30_Cell2]

description:
miRNA
HC0022


title: HCC [SH54N35_Cell1]

description:
miRNA
HC0037


title: HCC [SH54N29_Cell4]

description:
miRNA
HC0020


title: HCC [SH54N32_Cell2]

description:
miRNA
HC0026


title: HCC [SH54N32_Cell1]

description:
miRNA
HC0025


title: HCC [SH54N30_Cell1]

description:
miRNA
HC0021


title: HCC [SH54N30_Cell4]

description:
miRNA
HC0024


title: HCC [SH54N29_Cell2]

description:
miRNA
HC0018


title: HCC [SH54N29_Cell3]

description:
miRNA
HC0019


title: HCC [SH54N28_Cell1]

description:
miRNA
HC0013


title: HCC [SH56963_Cell1]

description:
miRNA
HC0015


title: HCC [SH54N28_Cell4]

description:
miRNA
HC0016


title: HCC [SH54N28_Cell2]

description:
miRNA
HC0014


title: HCC [SH54N27_Cell3]

description:
miRNA
HC0011


title: HCC [SH54N27_Cell4]

description:
miRNA
HC0012


title: HCC [SH54N32_Cell3]

description:
miRNA
HC0027


title: HCC [SH54N27_Cell2]

description:
miRNA
HC0010


title: HCC [SH54N27_Cell1]

description:
miRNA
HC0009


title: HCC [SH54N26_Cell1]

description:
miRNA
HC0005


title: HCC [SH54N25_Cell2]

description:
miRNA
HC0002


title: HCC [SH54N26_Cell2]

description:
miRNA
HC0006


title: HCC [SH54N26_Cell4]

description:
miRNA
HC0008


title: HCC [SH54N25_Cell4]

description:
miRNA
HC0004


title: HCC [SH54N29_Cell1]

description:
miRNA
HC0017


title: Non-cancer 2 [SH6XQ21_Cell4]

description:
miRNA
CHC908


title: Non-cancer 2 [SH6XQ19_Cell4]

description:
miRNA
CHC899


title: HCC [SH54N25_Cell3]

description:
miRNA
HC0003


title: Non-cancer 2 [SH6XQ14_Cell2]

description:
miRNA
CHC873


title: Non-cancer 2 [SH69857_Cell3]

description:
miRNA
CHC776


title: Non-cancer 2 [SH64703_Cell4]

description:
miRNA
CHC814


title: Non-cancer 2 [SH6XQ14_Cell1]

description:
miRNA
CHC871


title: HCC [SH54N26_Cell3]

description:
miRNA
HC0007


title: Non-cancer 2 [SH6XQ11_Cell2]

description:
miRNA
CHC860


title: Non-cancer 2 [SH6XQ05_Cell1]

description:
miRNA
CHC829


title: Non-cancer 2 [SH6XQ08_Cell1]

description:
miRNA
CHC845


title: HCC [SH54N25_Cell1]

description:
miRNA
HC0001


title: Non-cancer 2 [SH69848_Cell3]

description:
miRNA
CHC740


title: Non-cancer 2 [SH69853_Cell2]

description:
miRNA
CHC757


title: Non-cancer 2 [SH69848_Cell1]

description:
miRNA
CHC737


title: Non-cancer 2 [SH69851_Cell3]

description:
miRNA
CHC748


title: Non-cancer 2 [SH69854_Cell3]

description:
miRNA
CHC760


title: Non-cancer 1 [SH4YM09_Cell4]

description:
miRNA
BC1461


title: Non-cancer 2 [SH69835_Cell1]

description:
miRNA
CHC684


title: Non-cancer 1 [SH4YL60_Cell3]

description:
miRNA
BC1433


title: Non-cancer 2 [SH69834_Cell3]

description:
miRNA
CHC681


title: Non-cancer 1 [SH4YL58_Cell2]

description:
miRNA
BC1348


title: Non-cancer 1 [SH4YE51_Cell2]

description:
miRNA
BC1347


title: Non-cancer 1 [SH4YL42_Cell3]

description:
miRNA
BC0973


title: Non-cancer 1 [SH4YL52_Cell4]

description:
miRNA
BC1284


title: Non-cancer 2 [SH6XQ09_Cell3]

description:
miRNA
CHC851


title: Chronic hepatitis [SH68Y62_Cell1]

description:
miRNA
4-SR-23


title: Liver Cirrhosis [SH68Y60_Cell4]

description:
miRNA
4-SL-46


title: Chronic hepatitis [SH68Y62_Cell4]

description:
miRNA
4-SR-103


title: Liver Cirrhosis [SH68Y61_Cell4]

description:
miRNA
4-SR-14


title: Liver Cirrhosis [SH68Y62_Cell3]

description:
miRNA
4-SR-80


title: Non-cancer 1 [SH4YD55_Cell4]

description:
miRNA
BC1269


title: Liver Cirrhosis [SH68Y61_Cell3]

description:
miRNA
4-SL-151


title: Chronic hepatitis [SH68Y60_Cell3]

description:
miRNA
4-SL-15


title: Liver Cirrhosis [SH68Y62_Cell2]

description:
miRNA
4-SR-53


title: Chronic hepatitis [SH68Y59_Cell2]

description:
miRNA
4-AD-57


title: Liver Cirrhosis [SH68Y59_Cell1]

description:
miRNA
4-AD-47


title: Chronic hepatitis [SH68Y61_Cell1]

description:
miRNA
4-SL-121


title: Liver Cirrhosis [SH68Y58_Cell4]

description:
miRNA
4-AD-24


title: Liver Cirrhosis [SH68Y59_Cell3]

description:
miRNA
4-AD-75


title: Liver Cirrhosis [SH68Y57_Cell4]

description:
miRNA
3-SR-6


title: Chronic hepatitis [SH68Y58_Cell1]

description:
miRNA
3-SR-88


title: Liver Cirrhosis [SH68Y58_Cell3]

description:
miRNA
4-AD-22


title: Liver Cirrhosis [SH68Y51_Cell2]

description:
miRNA
3-SL20


title: Liver Cirrhosis [SH68Y60_Cell1]

description:
miRNA
4-AD-138


title: Liver Cirrhosis [SH68Y58_Cell2]

description:
miRNA
3-SR-158


title: Chronic hepatitis [SH68Y52_Cell2]

description:
miRNA
3-SL-87


title: Liver Cirrhosis [SH68Y52_Cell3]

description:
miRNA
3-SL-90


title: Liver Cirrhosis [SH68Y59_Cell4]

description:
miRNA
4-AD-106


title: Liver Cirrhosis [SH68Y60_Cell2]

description:
miRNA
4-AD-148


title: Liver Cirrhosis [SH68Y52_Cell1]

description:
miRNA
3-SL-82


title: Chronic hepatitis [SH68Y61_Cell2]

description:
miRNA
4-SL-137


title: Liver Cirrhosis [SH68Y51_Cell4]

description:
miRNA
3-SL-52


title: Chronic hepatitis [SH68Y51_Cell3]

description:
miRNA
3-SL-40


title: Liver Cirrhosis [SH68Y57_Cell3]

description:
miRNA
3-SL-294


title: Liver Cirrhosis [SH68Y57_Cell2]

description:
miRNA
3-SL-272


title: Chronic hepatitis [SH68Y56_Cell3]

description:
miRNA
3-SL-252


title: Liver Cirrhosis [SH68Y56_Cell4]

description:
miRNA
3-SL-257


title: Liver Cirrhosis [SH68Y57_Cell1]

description:
miRNA
3-SL-263


title: Chronic hepatitis [SH68Y56_Cell2]

description:
miRNA
3-SL-248


title: Liver Cirrhosis [SH68Y52_Cell4]

description:
miRNA
3-SL-92


title: Chronic hepatitis [SH68Y51_Cell1]

description:
miRNA
3-SL-6


title: Liver Cirrhosis [SH68Y55_Cell3]

description:
miRNA
3-SL-224


title: Liver Cirrhosis [SH68Y55_Cell2]

description:
miRNA
3-SL-205


title: Liver Cirrhosis [SH68Y56_Cell1]

description:
miRNA
3-SL-234


title: Chronic hepatitis [SH68Y54_Cell4]

description:
miRNA
3-SL-167


title: Chronic hepatitis [SH68Y55_Cell1]

description:
miRNA
3-SL-198


title: Liver Cirrhosis [SH68Y54_Cell2]

description:
miRNA
3-SL-158


title: Chronic hepatitis [SH68Y54_Cell1]

description:
miRNA
3-SL-152


title: Liver Cirrhosis [SH68Y53_Cell4]

description:
miRNA
3-SL-132


title: Liver Cirrhosis [SH68Y48_Cell4]

description:
miRNA
3-AD-92


title: Chronic hepatitis [SH68Y53_Cell2]

description:
miRNA
3-SL-106


title: Chronic hepatitis [SH68Y54_Cell3]

description:
miRNA
3-SL-161


title: Chronic hepatitis [SH68Y48_Cell3]

description:
miRNA
3-AD-67


title: Liver Cirrhosis [SH68Y53_Cell3]

description:
miRNA
3-SL-117


title: Chronic hepatitis [SH68Y53_Cell1]

description:
miRNA
3-SL-101


title: Liver Cirrhosis [SH68Y48_Cell1]

description:
miRNA
3-AD-53


title: Chronic hepatitis [SH68Y48_Cell2]

description:
miRNA
3-AD-54


title: Liver Cirrhosis [SH68Y47_Cell2]

description:
miRNA
3-AD-45


title: Liver Cirrhosis [SH68Y50_Cell3]

description:
miRNA
3-AD-151


title: Liver Cirrhosis [SH68Y50_Cell1]

description:
miRNA
3-AD-136


title: Chronic hepatitis [SH68Y47_Cell3]

description:
miRNA
3-AD-49


title: Liver Cirrhosis [SH68Y47_Cell1]

description:
miRNA
3-AD-44


title: Chronic hepatitis [SH68Y46_Cell4]

description:
miRNA
3-AD-40


title: Chronic hepatitis [SH68Y49_Cell4]

description:
miRNA
3-AD-120


title: Liver Cirrhosis [SH68Y50_Cell4]

description:
miRNA
3-SL-2


title: Liver Cirrhosis [SH68Y49_Cell3]

description:
miRNA
3-AD-117


title: Chronic hepatitis [SH68Y49_Cell2]

description:
miRNA
3-AD-111


title: Liver Cirrhosis [SH68Y49_Cell1]

description:
miRNA
3-AD-109


title: Chronic hepatitis [SH68Y47_Cell4]

description:
miRNA
3-AD-50


title: Chronic hepatitis [SH68Y50_Cell2]

description:
miRNA
3-AD-150


title: Chronic hepatitis [SH68Y45_Cell2]

description:
miRNA
2-SL-173


title: Liver Cirrhosis [SH68Y43_Cell4]

description:
miRNA
1-SR-81


title: Liver Cirrhosis [SH68Y46_Cell3]

description:
miRNA
3-AD-10


title: Chronic hepatitis [SH68Y45_Cell3]

description:
miRNA
2-SL-192


title: Chronic hepatitis [SH68Y46_Cell1]

description:
miRNA
2-SR-3


title: Liver Cirrhosis [SH68Y43_Cell3]

description:
miRNA
1-SR-59


title: Liver Cirrhosis [SH68Y45_Cell1]

description:
miRNA
2-SL-44


title: Chronic hepatitis [SH68Y44_Cell4]

description:
miRNA
2-SL-35


title: Chronic hepatitis [SH68Y44_Cell1]

description:
miRNA
2-AD-1


title: Chronic hepatitis [SH68Y46_Cell2]

description:
miRNA
2-SR-16


title: Liver Cirrhosis [SH68Y41_Cell1]

description:
miRNA
1-SL-65


title: Liver Cirrhosis [SH68Y43_Cell2]

description:
miRNA
1-SR-8


title: Liver Cirrhosis [SH68Y41_Cell2]

description:
miRNA
1-SL-99


title: Liver Cirrhosis [SH68Y43_Cell1]

description:
miRNA
1-SL-284


title: Liver Cirrhosis [SH68Y39_Cell4]

description:
miRNA
1-SL-49


title: Liver Cirrhosis [SH68Y44_Cell3]

description:
miRNA
2-AD-59


title: Liver Cirrhosis [SH68Y39_Cell3]

description:
miRNA
1-SL-27


title: Liver Cirrhosis [SH68Y42_Cell4]

description:
miRNA
1-SL-268


title: Liver Cirrhosis [SH68Y42_Cell3]

description:
miRNA
1-SL-226


title: Liver Cirrhosis [SH68Y42_Cell2]

description:
miRNA
1-SL-220


title: Chronic hepatitis [SH68Y45_Cell4]

description:
miRNA
2-SL-293


title: Liver Cirrhosis [SH68Y42_Cell1]

description:
miRNA
1-SL-208


title: Liver Cirrhosis [SH68Y41_Cell4]

description:
miRNA
1-SL-162


title: Liver Cirrhosis [SH68Y41_Cell3]

description:
miRNA
1-SL-108


title: Liver Cirrhosis [SH68J34_Cell2]

description:
miRNA
1-AD-97


title: Liver Cirrhosis [SH68Y44_Cell2]

description:
miRNA
2-AD-26


title: Liver Cirrhosis [SH68J34_Cell1]

description:
miRNA
1-AD-96


title: Liver Cirrhosis [SH68J29_Cell4]

description:
miRNA
1-AD-6


title: Liver Cirrhosis [SH68J33_Cell3]

description:
miRNA
1-AD-84


title: Liver Cirrhosis [SH68J32_Cell2]

description:
miRNA
1-AD-52


title: Liver Cirrhosis [SH68J33_Cell4]

description:
miRNA
1-AD-94


title: Liver Cirrhosis [SH68J30_Cell1]

description:
miRNA
1-AD-7


title: Liver Cirrhosis [SH68J33_Cell1]

description:
miRNA
1-AD-70


title: Liver Cirrhosis [SH68J33_Cell2]

description:
miRNA
1-AD-82


title: Liver Cirrhosis [SH68J29_Cell3]

description:
miRNA
1-AD-5


title: Liver Cirrhosis [SH68J32_Cell3]

description:
miRNA
1-AD-56


title: Liver Cirrhosis [SH68J31_Cell3]

description:
miRNA
1-AD-38


title: Liver Cirrhosis [SH68J30_Cell4]

description:
miRNA
1-AD-27


title: Liver Cirrhosis [SH68J32_Cell4]

description:
miRNA
1-AD-58


title: Liver Cirrhosis [SH68J31_Cell1]

description:
miRNA
1-AD-33


title: Liver Cirrhosis [SH68J31_Cell4]

description:
miRNA
1-AD-39


title: Liver Cirrhosis [SH68J31_Cell2]

description:
miRNA
1-AD-36


title: Liver Cirrhosis [SH68J29_Cell2]

description:
miRNA
1-AD-3


title: Liver Cirrhosis [SH68J29_Cell1]

description:
miRNA
1-AD-2


title: Liver Cirrhosis [SH68Y39_Cell2]

description:
miRNA
1-AD-154


title: Liver Cirrhosis [SH68Y37_Cell2]

description:
miRNA
1-AD-131


title: Liver Cirrhosis [SH68Y37_Cell4]

description:
miRNA
1-AD-137


title: Liver Cirrhosis [SH68J35_Cell4]

description:
miRNA
1-AD-123


title: Liver Cirrhosis [SH68Y39_Cell1]

description:
miRNA
1-AD-142


title: Liver Cirrhosis [SH68Y37_Cell3]

description:
miRNA
1-AD-132


title: Liver Cirrhosis [SH68Y37_Cell1]

description:
miRNA
1-AD-129


title: Liver Cirrhosis [SH68J32_Cell1]

description:
miRNA
1-AD-51


title: Liver Cirrhosis [SH68Y55_Cell4]

description:
miRNA
3-SL-228


title: Liver Cirrhosis [SH68J30_Cell3]

description:
miRNA
1-AD-12


title: Liver Cirrhosis [SH68J35_Cell1]

description:
miRNA
1-AD-113


title: Liver Cirrhosis [SH68J35_Cell2]

description:
miRNA
1-AD-116


title: Liver Cirrhosis [SH68J30_Cell2]

description:
miRNA
1-AD-11


title: Liver Cirrhosis [SH68J34_Cell4]

description:
miRNA
1-AD-105


title: Liver Cirrhosis [SH68J35_Cell3]

description:
miRNA
1-AD-122


title: Liver Cirrhosis [SH68J34_Cell3]

description:
miRNA
1-AD-104


title: Non-cancer 3 [SH53B23_Cell1]

description:
miRNA
XB0186


title: Non-cancer 3 [SH54119_Cell1]

description:
miRNA
XB0194


title: Non-cancer 3 [SH53B24_Cell2]

description:
miRNA
XB0191


title: Non-cancer 3 [SH54119_Cell3]

description:
miRNA
XB0197


title: Non-cancer 3 [SH53B24_Cell1]

description:
miRNA
XB0190


title: Non-cancer 3 [SH53B22_Cell4]

description:
miRNA
XB0185


title: Non-cancer 3 [SH55R13_Cell1]

description:
miRNA
XB0232


title: Non-cancer 3 [SH53B26_Cell1]

description:
miRNA
XB0198


title: Non-cancer 3 [SH53B22_Cell1]

description:
miRNA
XB0182


title: Non-cancer 3 [SH53A54_Cell2]

description:
miRNA
XB0219


title: Non-cancer 3 [SH53Z63_Cell4]

description:
miRNA
XB0203


title: Non-cancer 3 [SH53B22_Cell2]

description:
miRNA
XB0183


title: Non-cancer 3 [SH53B22_Cell3]

description:
miRNA
XB0184


title: Non-cancer 3 [SH53A49_Cell1]

description:
miRNA
XB0206


title: Non-cancer 3 [SH53B21_Cell4]

description:
miRNA
XB0181


title: Non-cancer 3 [SH53B23_Cell4]

description:
miRNA
XB0189


title: Non-cancer 3 [SH53252_Cell1]

description:
miRNA
XB0178


title: Non-cancer 3 [SH53251_Cell4]

description:
miRNA
XB0177


title: Non-cancer 3 [SH53B21_Cell3]

description:
miRNA
XB0180


title: Non-cancer 3 [SH53B23_Cell2]

description:
miRNA
XB0187


title: Non-cancer 3 [SH53B23_Cell3]

description:
miRNA
XB0188


title: Non-cancer 3 [SH53247_Cell3]

description:
miRNA
XB0172


title: Non-cancer 3 [SH53251_Cell3]

description:
miRNA
XB0176


title: Non-cancer 3 [SH53251_Cell2]

description:
miRNA
XB0175


title: Non-cancer 3 [SH53247_Cell4]

description:
miRNA
XB0173


title: Non-cancer 3 [SH53247_Cell1]

description:
miRNA
XB0170


title: Non-cancer 3 [SH53251_Cell1]

description:
miRNA
XB0174


title: Non-cancer 3 [SH53247_Cell2]

description:
miRNA
XB0171


title: Non-cancer 3 [SH53246_Cell4]

description:
miRNA
XB0169


title: Non-cancer 3 [SH53246_Cell3]

description:
miRNA
XB0168


title: Non-cancer 3 [SH53239_Cell1]

description:
miRNA
XB0154


title: Non-cancer 3 [SH53239_Cell2]

description:
miRNA
XB0155


title: CD8 T cells TGR cells [CD8_lo]

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: Cells grwon for 3 days then acutely exposed to glucose restrictive conditions

data_processing:
Samples were demultiplexed and aligned using Cell Ranger 2.2 (10X genomics)
Samples were processed and analyzed in R (3.6.0) using Seurat (v3)
Genes from specific metabolic pathways were retrieved from KEGG
Differentially expressed genes, with greater than a 1.2 fold change and an adjusted p value of less than 0.1, were analyzed for pathway enrichment using STRING
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells. A list of cell barcodes and detected genes is also included for each sample.

source_name: Spleen

growth_protocol: CD8+ T cells were obtained from spleens and lymph nodes isolated from 8-12-week-old OT-I mice. Within experiments mice were age and sex matched. Single cell suspensions of splenocytes were incubated for 48 hr in IL-2 containing 1640 media (invitrogen) supplemented with 10% fetal calf serum (Gibco), 4mM L-glutamine, 1% penicillin/streptomycin, 100 U/ml hrIL-2 (Peprotech), 55mM beta- mercaptoethanol, in a humidified incubator at 37°C, atmospheric oxygen supplemented with 5% CO2. Media was supplemented with SIINFEKL peptide.

extract_protocol:
Single cell RNA sequencing was performed using a 10X Genomics Chromium Controller.
Single cells were processed with GemCode Single Cell Platform using GemCode Gel Beads, Chip and Library Kits (v2) following the manufacturer’s protocol. An estimated 5,000 cells were added to each channel with an average of 3,000 cells recovered.  Libraries were sequenced on HiSeq 3000 (Illumina)

treatment_protocol: 48 hours after activation, media was replaced with expansion media containing 11mM glucose and 100U/ml IL-2. Cells were then exposed to control or transient glucose restriction for 20 hours.

value: OT-I mice

value: Spleen

value: CD8 T cell

tag: treatment

value: TGR (1mM glucose)


title: Non-cancer 3 [SH53240_Cell2]

description:
miRNA
XB0159


title: Non-cancer 3 [SH53240_Cell1]

description:
miRNA
XB0158


title: Non-cancer 3 [SH53240_Cell3]

description:
miRNA
XB0160


title: CD8 T effector control cells [CD8_hi]

description: Cells grwon for 3 days then acutely exposed to normal conditions

tag: cell type

value: Control (11mM glucose)


title: Non-cancer 3 [SH53238_Cell2]

description:
miRNA
XB0151


title: Non-cancer 3 [SH53238_Cell4]

description:
miRNA
XB0153


title: Non-cancer 3 [SH53239_Cell3]

description:
miRNA
XB0156


title: Non-cancer 3 [SH53245_Cell2]

description:
miRNA
XB0163


title: Non-cancer 3 [SH53246_Cell1]

description:
miRNA
XB0166


title: Non-cancer 3 [SH53240_Cell4]

description:
miRNA
XB0161


title: Non-cancer 3 [SH53237_Cell3]

description:
miRNA
XB0148


title: Non-cancer 3 [SH53245_Cell1]

description:
miRNA
XB0162


title: Non-cancer 3 [SH53237_Cell2]

description:
miRNA
XB0147


title: Non-cancer 3 [SH53236_Cell2]

description:
miRNA
XB0143


title: Non-cancer 3 [SH53236_Cell4]

description:
miRNA
XB0145


title: Non-cancer 3 [SH53245_Cell4]

description:
miRNA
XB0165


title: Non-cancer 3 [SH53237_Cell4]

description:
miRNA
XB0149


title: BS.Pa.EVs

type: genomic

city: Lebanon

first: David

middle: Alan

last: Armstrong

state: NH

address: 1 Medical Center Dr., Borwell 508E

institute: Dartmouth Hitchcock Medical Center

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing:
Raw intensity data files (IDATs) from the MethylationEPIC BeadChips were processed by the minfi R/Bioconductor analysis pipeline (version 1.30) annotation file version ilm10b4.hg19
Cross reactive probes, probes on sex chromosomes, probes associated with known SNPs were excluded

label: cy3, cy5

label_protocol: Illumina

growth_protocol: Right upper lobe (RUL) lung macrophages were used in this study

extract_protocol:
Subjects underwent flexible bronchoscopy following local anesthesia with lidocaine to the posterior pharynx and intravenous sedation. A bronchoscope was inserted trans-orally and advanced through the vocal cords. BAL fluid was obtained from tertiary airways via rinses with 20 ml of sterile saline followed by 10 ml of air and repeated for a total of 5 times per airway.
Primary lung macrophages were isolated from BAL fluid via gravity filtration through 2 layers of gauze, followed by three sequential washes in normal saline with subsequent centrifugation to pellet cells (400 x g /5 minutes /20 oC).

treatment_protocol: Cells were plated in 6-well tissue culture dishes seeded at 1 x 106 cells per well. Cells were allowed to set down for 60 minutes followed by the addition of P.a. EVs at a ratio of 100:1 (EVs:cell)

tag: gender

tag: agent

value: EVs isolated from P. aeruginosa

tag: time point

value: 2 Day


title: BS.control

value: M


title: Non-cancer 3 [SH53235_Cell1]

description:
miRNA
XB0138

value: serum

value: unknown


title: Non-cancer 3 [SH53233_Cell1]

description:
miRNA
XB0130


title: CMK.Pa.EVs

value: F


title: CK.control


title: Non-cancer 3 [SH53234_Cell4]

description:
miRNA
XB0137


title: CLM.Pa.EVs


title: CMK.control


title: JS.control


title: CK.Pa.EVs


title: Non-cancer 3 [SH53236_Cell1]

description:
miRNA
XB0142


title: SH.Pa.EVs


title: JS.Pa.EVs


title: AH.Pa.EVs


title: CLM.control


title: AH.control


title: Non-cancer 3 [SH53232_Cell4]

description:
miRNA
XB0129


title: Non-cancer 3 [SH53232_Cell1]

description:
miRNA
XB0126


title: Non-cancer 3 [SH53235_Cell4]

description:
miRNA
XB0141


title: SH.control


title: JK.Pa.EVs


title: Non-cancer 3 [SH53230_Cell2]

description:
miRNA
XB0123


title: JK.control


title: Non-cancer 3 [SH53228_Cell4]

description:
miRNA
XB0121


title: 20190725_30102343970221-01_Sample07_07 (DHA : Saline)

city: Fort Collins

first: Tara

middle: M

last: Nordgren

state: CO

address: Colorado State University, Physiology 133

department: Environmental and Radiological Health Sciences

institute: Colorado State University

description: codeset and reporter probes for Nanostring platform GPL19964

scan_protocol: Chip was imaged and quantified by a nCounter Sprint profiler.

data_processing: Gene expression data analysis was performed using the nCounter Analysis System, nSolver 4.0 software. The expression data were normalized by using a geometric mean of 4 housekeeping genes: OAZ1, PPIA, RPL19, and EEF1G. Following normalization, 20 of the samples passed normalization and were viable to use for the subsequent analyses, including 4 Control Diet + saline, 6 Control diet + HDE, 3 DHA diet + saline, and 7 DHA + HDE samples.

source_name: RNA from lung tissue, single saline treatment

label_protocol: Assessment of transcript-level gene expression changes was performed using the NanoString mouse Immunology Panel (NanoString Technologies, Seattle, WA, USA), a codeset designed to target 561 genes related to inflammation and immune response. Fifty to 100 ng of total RNA was mixed with the codeset and reporter probes and hybridized for 16 hr to form a purified target-probe complex that was then imaged and quantified by a nCounter Sprint profiler.

growth_protocol: Male wildtype C57BL/6J mice 5–8 weeks of age were obtained from The Jackson Laboratory (Bar Harbor, ME) and housed in the University of Nebraska Medical Center (UNMC) Comparative Medicine Facilities. Mice were allowed free access to food and water and housed in micro-isolator cages (five per cage). The food was changed weekly by the investigators while the water was changed by UNMC animal care staff. Each mouse was weighed weekly (see Supplemental Figure 1 for initial and final weights) and examined for any signs of distress. All related experiments and procedures were approved by the UNMC Institutional Animal Care and Use Committee.

extract_protocol: The left lungs were collected and stored in RNA later (ThermoFisher, Waltham, MA). Randomly selected left lung tissues (n=24) out of the possible 40 mice, representing tissues collected across three unique experimental trials, were homogenized and RNA was extracted using the PureLink RNA Mini Kit (Invitrogen). RNA sample quality was quantified using NanoDrop ND-100 (NanoDrop Technologies, Inc, Wilmington, DE) and an Agilent 2100 Bioanalyzer (UC Riverside Core Facilities, Agilent Technologies, Santa Clara, CA).

treatment_protocol: We employed a previously established murine model that utilizes an intranasal exposure of HDE to induce airway inflammation for our in vivo investigations [30,31]. Studies were performed as 3 independent experimental sets, for total of 8 mice for saline-treated groups and 12 mice for HDE-treated groups. Mice were lightly anesthetized by isoflurane inhalation prior to receiving a single intranasal challenge of 50 μL sterile saline (PBS) or 12.5% HDE. Four weeks prior to receiving the intranasal instillation, mice were initiated on either a DHA-rich diet or control diet containing no DHA. The animal chow diets were prepared by Envigo (Madison, WI) using a base AIN-93G diet. The DHA diet preparation was the same as previously described [30,33]. Briefly, to prepare the DHA-rich diet, soybean oil from the AIN-93G base diet was replaced with DHASCO oil (DSM Nutritional Products, Kingstree, SC), a DHA-based oil containing 39.2% DHA and high-oleic safflower oil. The control diet, containing no DHA, modified the same AIN-93G diet by replacing soybean oil with high-oleic safflower oil. The newly formulated DHA-rich diet provides the mice with approximately 1.4% of total caloric intake strictly from DHA. Five hr following the single HDE intranasal challenge, mice were euthanized.

value: Male

tag: diet

value: DHA diet-fed

value: lung


title: 20190725_30102343970221-01_Sample06_06 (Control : HDE)

source_name: RNA from lung tissue, single HDE treatment

value: Control diet-fed


title: 20190725_30102343970221-01_Sample10_10 (DHA : HDE)


title: Non-cancer 3 [SH52802_Cell1]

description:
miRNA
XB0107


title: Non-cancer 3 [SH53228_Cell3]

description:
miRNA
XB0120


title: 20190725_30102343970221-01_Sample11_11 (DHA : HDE)


title: 20190725_30102343970221-01_Sample04_04 (Control : HDE)


title: 20190725_30102343970221-01_Sample05_05 (Control : HDE)


title: 20190725_30102343970221-01_Sample02_02 (Control : Saline)


title: 20180810_30102053701118-01_Sample10_10 (DHA : HDE)


title: 20180810_30102053701118-01_Sample11_11 (DHA : HDE)


title: 20190725_30102343970221-01_Sample03_03 (Control : HDE)


title: 20190725_30102343970221-01_Sample01_01 (Control : Saline)


title: 20180810_30102053701118-01_Sample12_12 (DHA : HDE)


title: Non-cancer 3 [SH53230_Cell4]

description:
miRNA
XB0125


title: Non-cancer 3 [SH52801_Cell4]

description:
miRNA
XB0106


title: Non-cancer 3 [SH52801_Cell1]

description:
miRNA
XB0103


title: Non-cancer 3 [SH53228_Cell1]

description:
miRNA
XB0118


title: Non-cancer 3 [SH52808_Cell1]

description:
miRNA
XB0115


title: Non-cancer 3 [SH52808_Cell3]

description:
miRNA
XB0117


title: 20190725_30102343970221-01_Sample12_12 (DHA : HDE)


title: 20180810_30102053701118-01_Sample09_09 (DHA : HDE)


title: Non-cancer 3 [SH53230_Cell3]

description:
miRNA
XB0124


title: 20180810_30102053701118-01_Sample08_08 (DHA : Saline)


title: Non-cancer 3 [SH52668_Cell1]

description:
miRNA
XB0099


title: Non-cancer 3 [SH52668_Cell2]

description:
miRNA
XB0100


title: Non-cancer 3 [SH52667_Cell3]

description:
miRNA
XB0097


title: Non-cancer 3 [SH52668_Cell3]

description:
miRNA
XB0101


title: 20180810_30102053701118-01_Sample07_07 (DHA : Saline)


title: 10µM Heme (Schn+Heme) Aag2 replicate 3

city: College Station

first: Zach

last: Adelman

state: TX

address: 370 Olsen Blvd

department: Entomology

institute: Texas A&M University

data_processing:
Aligning reads to reference genome: Reads were aligned to the Ae. aegypti reference genome AaegL5 (www.vectorbase.org) using HISAT2 v2.1.0
Cleaning up mapped files: SAMtools view and SAMtools sort commands v1.7 were used to sort the mapped files and remove low quality mapping scores
Counting number of reads per transcript: BEDtools suite v2.19.1 used to calculate the number of reads per mRNA transcript
Merging Count tables: Counts data was merged from all samples into one file
EdgeR analysis: The counts table was analyzed in EdgeR (Robinson et al, 2010)
Genome_build: AaegL5 (www.vectorbase.org)
Supplementary_files_format_and_content: tab delimited text file containing the raw counts data from each of the four cultured cell datasets examined

organism: Aedes aegypti

source_name: Aag2 cells incubated with serum deficient media + 10µM Heme (Schneider's Drosophila) for 72hrs

growth_protocol: Cultured cells were maintained at 28 degrees C in Schneider's Drosophila medium (Lonza BioWhittaker, Basel, Switzerland) supplemented with 10% FBS, 1% penicillin-streptomycin, and 1% L-glutamine or Leibovitz's L-15 medium (Invitrogen, Carlsbad, CA) supplemented with 10% FBS, and 1% penicillin-streptomycin

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Invitrogen)
illumina TruSeq small RNA sample preparation kit (Aag2 incubated for 48hrs) or NEBNext Ultra RNA library preparation kit used (All other samples)

treatment_protocol: Cultured cells were either incubated with regular growth media, media containing heme or media difficient in heme, specific conditions depended on sample are are given in the sample discription

tag: cell line


title: Non-cancer 3 [SH52667_Cell2]

description:
miRNA
XB0096


title: Non-cancer 3 [SH52666_Cell4]

description:
miRNA
XB0094


title: Non-cancer 3 [SH52664_Cell4]

description:
miRNA
XB0090


title: 20180810_30102053701118-01_Sample05_05 (Control : HDE)


title: 0µM Heme (Schn) Aag2 replicate 1

source_name: Aag2 cells incubated with serum and heme deficient media (Schneider's Drosophila) for 72hrs


title: 10µM Heme (Schn+Heme) Aag2 replicate 2


title: Non-cancer 3 [SH52667_Cell4]

description:
miRNA
XB0098


title: 0µM Heme (Schn) Aag2 replicate 3


title: Untreated (Schn+FBS) Aag2 replicate 3

source_name: Aag2 cells incubated with normal growth conditions (Schneider's Drosophila) for 72hrs


title: 10µM Heme (Schn+Heme) Aag2 replicate 1


title: Untreated (Schn+FBS) Aag2 replicate 2


title: 20180810_30102053701118-01_Sample01_01 (Control : Saline)


title: Non-cancer 3 [SH52661_Cell2]

description:
miRNA
XB0079


title: Non-cancer 3 [SH52662_Cell1]

description:
miRNA
XB0083


title: 20180810_30102053701118-01_Sample04_04 (Control : HDE)


title: Non-cancer 3 [SH52662_Cell2]

description:
miRNA
XB0084


title: Non-cancer 3 [SH52664_Cell1]

description:
miRNA
XB0087


title: Untreated (Schn+FBS) Aag2 replicate 1


title: Non-cancer 3 [SH52661_Cell3]

description:
miRNA
XB0081


title: Non-cancer 3 [SH52633_Cell3]

description:
miRNA
XB0052


title: Non-cancer 3 [SH55R11_Cell4]

description:
miRNA
XB0080


title: Non-cancer 3 [SH52659_Cell2]

description:
miRNA
XB0075


title: Non-cancer 3 [SH52633_Cell2]

description:
miRNA
XB0051


title: 10µM Heme (L15+Heme) Aag2 replicate 3

source_name: Aag2 cells incubated with serum deficient media + 10µM Heme (L15) for 72hrs


title: 20180810_30102053701118-01_Sample02_02 (Control : Saline)


title: Non-cancer 3 [SH52615_Cell1]

description:
miRNA
XA0992


title: Non-cancer 3 [SH52664_Cell2]

description:
miRNA
XB0088


title: 0µM Heme (Schn) Aag2 replicate 2


title: Non-cancer 3 [SH52656_Cell2]

description:
miRNA
XA0981


title: 10µM Heme (L15+Heme) Aag2 replicate 1


title: 10µM Heme (L15+Heme) Aag2 replicate 2


title: 0µM Heme (L15) Aag2 replicate 1

source_name: Aag2 cells incubated with serum and heme deficient media (L15) for 72hrs


title: 0µM Heme (L15) Aag2 replicate 3


title: 0µM Heme (L15) Aag2 replicate 2


title: Non-cancer 3 [SH52P21_Cell2]

description:
miRNA
XA0964


title: Non-cancer 3 [SH52651_Cell4]

description:
miRNA
XA0979


title: Untreated (L15+FBS) Aag2 replicate 2

source_name: Aag2 cells incubated with normal growth conditions (L15) for 72hrs


title: Untreated (L15+FBS) Aag2 replicate 3


title: 10µM Heme (SF900II+Heme) A20 replicate 3

source_name: A20 cells incubated with serum deficient media (SF900II Gibco) +10µM heme for 72hrs


title: Untreated (L15+FBS) Aag2 replicate 1


title: 10µM Heme (SF900II+Heme) A20 replicate 2


title: 10µM Heme (SF900II+Heme) A20 replicate 1


title: 0µM Heme (SF900II) A20 replicate 3

source_name: A20 cells incubated with serum deficient media (SF900II Gibco) for 72hrs


title: 0µM Heme (SF900II) A20 replicate 2


title: Non-cancer 3 [SH52602_Cell2]

description:
miRNA
XA0917


title: Non-cancer 3 [SH52P21_Cell1]

description:
miRNA
XA0955


title: Non-cancer 3 [SH52602_Cell1]

description:
miRNA
XA0916


title: Non-cancer 3 [SH52643_Cell3]

description:
miRNA
XA0962


title: Non-cancer 3 [SH52606_Cell3]

description:
miRNA
XA0934


title: Non-cancer 3 [SH52606_Cell2]

description:
miRNA
XA0933


title: Non-cancer 3 [SH52234_Cell4]

description:
miRNA
XA0906


title: Non-cancer 3 [SH52233_Cell1]

description:
miRNA
XA0899


title: Non-cancer 3 [SH52230_Cell4]

description:
miRNA
XA0898


title: Non-cancer 3 [SH52P19_Cell3]

description:
miRNA
XA0953


title: Untreated (L15+FBS) A20 replicate 3

source_name: A20 cells incubated with normal growth conditions (L15) for 72hrs


title: Non-cancer 3 [SH52656_Cell1]

description:
miRNA
XA0980


title: Non-cancer 3 [SH52230_Cell3]

description:
miRNA
XA0897


title: Non-cancer 3 [SH51K52_Cell2]

description:
miRNA
XA0880


title: Untreated (L15+FBS) A20 replicate 2


title: Untreated (L15+FBS) A20 replicate 1


title: 20µM Heme replicate 2

source_name: Aag2 cells incubated with 10% FBS and 20µM heme (Schneider's Drosophila) for 48hrs


title: Non-cancer 3 [SH51K49_Cell4]

description:
miRNA
XA0878


title: Non-cancer 3 [SH51K37_Cell1]

description:
miRNA
XA0863


title: Non-cancer 3 [SH51K33_Cell3]

description:
miRNA
XA0861


title: 0µM Heme (SF900II) A20 replicate 1


title: Untreated  replicate 2

source_name: Aag2 cells incubated with normal growth conditions (Schneider's Drosophila) for 48hrs


title: Non-cancer 3 [SH51K29_Cell2]

description:
miRNA
XA0848


title: Untreated replicate 1


title: Non-cancer 3 [SH51G60_Cell2]

description:
miRNA
XA0804


title: Non-cancer 3 [SH51G56_Cell3]

description:
miRNA
XA0797


title: Non-cancer 3 [SH51G55_Cell3]

description:
miRNA
XA0793


title: 2D_C-2_1_miRNA-seq

data_processing:
After TruSeq small RNA adapters were eliminated among the sequenced reads by Trimommatic software (v.0.33), the remained sequence data were mapped to the Arabidopsis genome (TAIR10) using bowtie2 (v.2.2.2).
The quantification of each miRNA was estimated using HTSeq software package.
The read counts per
million fragments mapped (CPM) of each sample were used to estimate the expression level of each gene. The CPM data were normalized by the quantile method and log2 transformation.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text format with CPM values of miRNA

source_name: Arabidopsis ecotype Columbia (Col-0)

extract_protocol:
Total RNA was isolated using the mirVana miRNA isolation kit (Ambion).
Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified.

value: Non-treatment

tag: ecotype

value: Columbia (Col-0)

tag: drenched pathogen

value: Ralstonia solanacearum

tag: time after pathogen drench


title: 2D_C-4_1_miRNA-seq


title: 2D_10-4_1_miRNA-seq

value: Sound wave (10KHz)


title: 2D_C-1_1_miRNA-seq


title: 2D_C-3_1_miRNA-seq


title: 20µM Heme replicate 3


title: Non-cancer 3 [SH51G52_Cell1]

description:
miRNA
XA0787

tag: age


title: Non-cancer 3 [SH51G40_Cell2]

description:
miRNA
XA0760

tag: tissue


title: 20µM Heme replicate 1


title: 2D_10-1_1_miRNA-seq


title: Non-cancer 3 [SH51G32_Cell3]

description:
miRNA
XA0749


title: Non-cancer 3 [SH51G32_Cell1]

description:
miRNA
XA0747


title: 1D_C-2_1_miRNA-seq


title: Non-cancer 3 [SH51G31_Cell2]

description:
miRNA
XA0744


title: 1D_C-4_1_miRNA-seq


title: Non-cancer 3 [SH51E61_Cell2]

description:
miRNA
XA0724


title: 1D_C-1_1_miRNA-seq


title: Non-cancer 3 [SH51K27_Cell3]

description:
miRNA
XA0845


title: Non-cancer 3 [SH51E57_Cell3]

description:
miRNA
XA0717


title: Untreated  replicate 3


title: Non-cancer 3 [SH51E51_Cell2]

description:
miRNA
XA0708


title: 1D_10-3_1_miRNA-seq


title: 1D_10-2_1_miRNA-seq


title: 1D_10-1_1_miRNA-seq


title: Non-cancer 3 [SH51E47_Cell3]

description:
miRNA
XA0697


title: 0D_C-4_1_miRNA-seq


title: Non-cancer 3 [SH51E41_Cell3]

description:
miRNA
XA0681


title: Non-cancer 3 [SH51E32_Cell3]

description:
miRNA
XA0669


title: 0D_C-2_1_miRNA-seq


title: 0D_C-1_1_miRNA-seq


title: 0D_10-4_1_miRNA-seq


title: 0D_10-3_1_miRNA-seq


title: 0D_10-2_1_miRNA-seq


title: Non-cancer 3 [SH52809_Cell2]

description:
miRNA
XA0606


title: Non-cancer 3 [SH51D12_Cell2]

description:
miRNA
XA0543


title: Non-cancer 3 [SH51E28_Cell1]

description:
miRNA
XA0651


title: Non-cancer 3 [SH51D19_Cell2]

description:
miRNA
XA0559


title: Non-cancer 3 [SH51D45_Cell3]

description:
miRNA
XA0621


title: Non-cancer 3 [SH4ZR53_Cell1]

description:
miRNA
XA0506


title: Non-cancer 3 [SH4ZR57_Cell2]

description:
miRNA
XA0519


title: Non-cancer 3 [SH4ZR53_Cell3]

description:
miRNA
XA0508


title: Non-cancer 3 [SH51E30_Cell1]

description:
miRNA
XA0659


title: Non-cancer 3 [SH4ZR35_Cell2]

description:
miRNA
XA0483


title: Non-cancer 3 [SH4ZR05_Cell1]

description:
miRNA
XA0458


title: Non-cancer 3 [SH4ZR62_Cell1]

description:
miRNA
XA0534


title: edm2_RNA_Rep1

city: Riverside

first: Xueqing

middle: Maggie

last: Lu

state: CA

address: 3401 Watkins Drive, Genomics, Room 2126

department: Cell Biology

institute: University of California, Riverside

description: rRNA-depleted RNA

data_processing:
For  RNA-seq,the quality of raw reads was analyzed using FastQC. The first 13 bases and the last base were trimmed. Contaminating adaptor reads, reads that were unpaired, bases below 25 and Ns, and reads shorter than 18 bases are also filtered using Sickle.All trimmed reads were mapped to A. thaliana genome (TAIR 10) using HISAT2 v2.1.0 with a known splice site file, built from Araport annotation file v11, and strand information parameter, --rna-strandness RF. Coverage values for each transcript was calculated using BEDTools with –split, -D, and -S parameters.
For genome browser tracks, read coverage per nucleotide is calculated using BEDTools. Coverage values were then normalized per million mapped reads.
Genome_build: TAIR 10
Supplementary_files_format_and_content: normalized genome broswer tracks

source_name: Aerial parts of two-weeks old seedlings

growth_protocol: All Arabidopsis seedlings were grown on soil or half-strength Murashige and Skoog (1/2 MS) solid medium containing 1% (w/v) sucrose in a growth chamber (16-h day, 8-h night, 22 °C; 100 μE m-2s-1)

extract_protocol:
For ChIP-seq, chromatin was sonicated and immunoprecipitated with the respective antibody; For RNA-seq, total RNA were isolated using TRIzol reagent, DNA and ribosomal RNA were removed using the Ribo-Zero rRNA Removal Reagents (Plant Leaf)(Epicentre, USA).
ChIP-seq libraries and RNA-seq were prepared using NEBNext Ultra II DNA library prep kit for Illumina (E7645, New England Biolabs) and NEBNext Ultra Directional RNA library prep kit for Illumina (E7420, New England Biolabs) according to the manufacturer’s instruction respectively.

value: Aerial parts of two-weeks old seedlings


title: edm2_RNA_Rep2

description: rRNA-depleted RNA


title: WT_RNA_Rep1

description: rRNA-depleted RNA


title: WT_RNA_Rep3

description: rRNA-depleted RNA


title: WT_RNA_Rep2

description: rRNA-depleted RNA


title: edm2_RNA_Rep3

description: rRNA-depleted RNA


title: HA-EDM2_input_Rep1

data_processing:
For ChIP-seq, raw reads quality was first analyzed using FastQC, and any base with a quality score below 25 or N was trimmed using Sickle.  Trimmed reads were then mapped to the A. thaliana genome (TAIR 10) using BWA 0.7.15-r1140 with mem option default parameters. Uniquely mapped reads were further filtered for calculating H3K9me2 coverage in transcript, while unfiltered reads were used for calculating H3K9me2 coverage in transposable elements.
For both RNA-seq,the quality of raw reads was analyzed using FastQC. The first 10 bases and the last base were trimmed. Contaminating adaptor reads, reads that were unpaired, bases below 25 and Ns, and reads shorter than 18 bases are also filtered using Sickle.All trimmed reads were mapped to A. thaliana genome (TAIR 10) using HISAT2 v2.1.0 with a known splice site file, built from Araport annotation file v11, and strand information parameter, --rna-strandness RF. Coverage values for each transcript was calculated using BEDTools with –split, -D, and -S parameters.
For genome browser tracks, read coverage per nucleotide is calculated using BEDTools. Coverage values were then normalized per million mapped reads.
Genome_build: TAIR 10


title: HA-EDM2_input_Rep2


title: Col_input_Rep2


title: Non-cancer 3 [SH4ZR04_Cell4]

description:
miRNA
XA0457

source_name: Serum


title: Non-cancer 3 [SH4ZR03_Cell2]

description:
miRNA
XA0451


title: HA-EDM2_ChIP_Rep2


title: HA-EDM2_ChIP_Rep1