title: miRNA, placebo, D1 [HGJFJDSXY_104077-002-044_TATAATAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D3 [HGJFJDSXY_104077-002-045_TCATTCAT-GTTCAGAG_L003]

status: Public on Dec 09 2023

type: SRA

city: Leiden

first: Eleonora

last: Vianello

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

description: miRNA-seq

library_source: transcriptomic

data_processing:
Adapters and indexes have been removed by using cutadapt v2.10.
Reads were aligned to GRCh38 by using bowtie2 v2.3.5.1.
Alignments were processed using samtools v1.9 to obtain a sorted bam-file which was used as input in HTSeq.count v0.13.0.
Counts were normalized by sequencing depth, dividing each sample with the column sums and multiplying them by 1 M. Baseline adjustment was performed individually by dividing the normalized data at each time point (day 1, 2, 3, and 7) by day 0 (e.g. day 1/day 0). All values were Log2-transfomed before further analyses. The R software v4.0.1 was used to perform normalization and baseline adjustment.
Assembly: GRCh38
Supplementary files format and content: csv file with normalized and log2 transformed counts

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
WB-RNAs, including miRNAs, were isolated by using the PAXgene blood miRNA kit (PreAnalytiX). This kit guarantees the extraction of intracellular RNA and miRNA upon cell lysis and stabilization of intracellular RNA during whole blood collection in PAXgene blood RNA tubes (PreAnalytiX). The elutes were quantified with a Qubit fluorometer (ThermoFisher Scientific) by using the RNA Broad Range assay kit (ThermoFisher Scientific). RNA quality was assessed by using Agilent RNA (15nt) fragment analysis (Agilent).
Libraries were prepared using the NEBNextâ Multiplex Small RNA Library Prep Kit for Illumina (New England BioLabs) (Index Primers 1-48, #7560S). Their quality and yield were measured by Agilent HS NGS fragment analysis (Agilent). The final products have approximate size of 150 bp. The 1.1 nM libraries, derived from the WB RNAs, were sequenced using the NovaSeq 6000 sequencer with a 150 bp paired-end protocol. Between 9 and 41 million reads were obtained for each sample (average of 17 million reads per sample).

tag: tissue

value: whole blood

tag: treatment

value: placebo

tag: time


title: miRNA, placebo, D1 [HGJFJDSXY_104077-002-044_TATAATAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D7 [HGJFJDSXY_104077-002-042_TAATCGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D1 [HGKVFDSXY_104077-002-044_TATAATAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D7 [HGKVFDSXY_104077-002-042_TAATCGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D7 [HGJFJDSXY_104077-002-042_TAATCGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D3 [HGJFJDSXY_104077-002-040_CTCAGAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D2 [HGJFJDSXY_104077-002-041_GACGACAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D3 [HGJFJDSXY_104077-002-036_CCAACAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D7 [HGJFJDSXY_104077-002-037_CGGAATAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D1 [HGJFJDSXY_104077-002-039_CTATACAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D1 [HGHTFDSXY_104077-002-034_CATGGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D7 [HGJFJDSXY_104077-002-032_CACTCAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D3 [HGJFJDSXY_104077-002-031_CACGATAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D1 [HGJFJDSXY_104077-002-029_CAACTAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D2 [HGJFJDSXY_104077-002-030_CACCGGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D1 [HGKVFDSXY_104077-002-027_ATTCCTAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D1 [HGJFJDSXY_104077-002-027_ATTCCTAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D0 [HGHTFDSXY_104077-002-028_CAAAAGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D1 [HGJFJDSXY_104077-002-027_ATTCCTAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D0 [HGHTFDSXY_104077-002-026_ATGAGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D0 [HGJFJDSXY_104077-002-043_TACAGCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D7 [HGHTFDSXY_104077-002-025_ACTGATAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D2 [HGJFJDSXY_104077-002-041_GACGACAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D2 [HGKVFDSXY_104077-002-041_GACGACAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D2 [HGJFJDSXY_104077-002-023_GAGTGGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGJFJDSXY_104077-002-021_GTTTCGAT-GTTCAGAG_L002]

description: miRNA-seq

value: rVSV{delta}G-ZEBOV-GP vaccine, dose 2*10^7


title: miRNA, placebo, D3 [HGJFJDSXY_104077-002-024_GGTAGCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGJFJDSXY_104077-002-019_GTGAAAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGKVFDSXY_104077-002-019_GTGAAAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D0 [HGJFJDSXY_104077-002-038_CTAGCTAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGJFJDSXY_104077-002-019_GTGAAAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGJFJDSXY_104077-002-021_GTTTCGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGJFJDSXY_104077-002-022_CGTACGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGKVFDSXY_104077-002-021_GTTTCGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHTFDSXY_104077-002-020_GTGGCCAT-GTTCAGAG_L002]

description: miRNA-seq


title: S16

city: Chicago

first: Shashwat

last: Tripathi

state: Illinois

address: 302 e Huron St

department: Neurosurgery

country: USA

institute: Northwestern

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger
Seurat
Assembly: hg38
Supplementary files format and content: Tab seperated and matrix

source_name: Brain

extract_protocol:
Patient tumors were graded pathologically by the study neuropathologists (CMH, NW) according to the World Health Organization classification [14]. At least 500 mg of the viable tumor was required to obtain enough for analysis and was processed within 30 min-1hour after resection. The normal brain was obtained from subjects as part of the planned surgical approach to gain access to a low-grade non-infiltrating glioma or during a planned super-total resection of adjacent regions that lacked T2/Flair abnormality on MRI imaging. The normal brain was sent for analysis separately from the tumor. The freshly resected tissue was processed in parallel both for a single cell suspension and formalin-fixed paraffin embedded (FFPE) analysis. For the former, the tissue was minced into small pieces using a scalpel, dissociated, and suspended using a Pasteur pipette in 10ml Iscove’s DMEM (IMDM; Iscove’s Modification of DMEM) 1X (Corning) containing 2% inactivated Fetal Bovine Serum (FBS; Sigma Aldrich) and Collagenase and DNase enzymes at final concentrations of 100μg/ml and 20units/ml, respectively. The prepared mixture was incubated for 35-40mins at 37°C with agitation. After tissue filtration using a 70-μm nylon cell strainer (BD Biosciences) and a brief centrifugation at 4°C, the pellet was resuspended in 20ml mix of 5.4ml of Percoll™ Plus (GE Healthcare) overlaid with 12ml of 1X Phosphate Buffered Saline (PBS) and 0.6ml of 10X PBS (Corning). The tube was centrifuged at 800gfor 10min at 4°C, with 9 acceleration and 0 deceleration. After centrifugation, the immune enriched cell pellet was collected, washed, stained with Trypan blue dye (Sigma-Aldrich), and counted using Countess II FL automated cell counter in a Countess cell counting chamber (Invitrogen). The FFPE slides were collected from the Neurological Surgery Tumor Bank (NSTB) of Northwestern University. Slides of tissue of 4 µm thickness were prepared, mounted on positively charged glass slides (Super Frost Plus microscope slides, ThermoFisher), and stored at room temperature for subsequent staining analysis. For each case, 1 H&E slide was reviewed, and tissue was segmented by a certified neuropathologist (CMH).
Single-cell sequencing was carried out using the chromium Next GEM Single Cell protocol (10x genomics). Post-library preparation cells were sequenced using the Illumina Novaseq

value: Brain

tag: disease

value: LGG


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGJFJDSXY_104077-002-015_ATGTCAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D2 [HGJFJDSXY_104077-002-035_CATTTTAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGJFJDSXY_104077-002-013_AGTCAAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGJFJDSXY_104077-002-011_GGCTACAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGHTFDSXY_104077-002-018_GTCCGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHTFDSXY_104077-002-010_TAGCTTAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGHTFDSXY_104077-002-017_GTAGAGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D0 [HGHTFDSXY_104077-002-033_CAGGCGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGJFJDSXY_104077-002-016_CCGTCCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGJFJDSXY_104077-002-016_CCGTCCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGJFJDSXY_104077-002-008_ACTTGAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGJFJDSXY_104077-002-006_GCCAATAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGKVFDSXY_104077-002-007_CAGATCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGJFJDSXY_104077-002-007_CAGATCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGKVFDSXY_104077-002-016_CCGTCCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGKVFDSXY_104077-002-014_AGTTCCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGHTFDSXY_104077-002-012_CTTGTAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGJFJDSXY_104077-002-005_ACAGTGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGJFJDSXY_104077-002-007_CAGATCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGJFJDSXY_104077-002-014_AGTTCCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGHTFDSXY_104077-002-009R_GATCAGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGJFJDSXY_104077-002-004_TGACCAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGJFJDSXY_104077-002-004_TGACCAAT-GTTCAGAG_L003]

description: miRNA-seq


title: ADU-S100+combo-5

type: RNA

city: Pittsburgh

first: Jessica

last: Filderman

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing: NanoString

organism: Mus musculus

source_name: BPR (BRAFV600E Pten-/-) murine melanoma

extract_protocol: Resected tumors were enzymatically dissociated into single-cell suspensions and then frozen in RLT buffer at -80C. RNA was isolated from the cell lysates using the RNEasy Micro Plus Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Female C57Bl/6J mice (6-8 weeks old) were purchased from Jackson Laboratory (Bar Harbor, Maine, USA). Mice were injected subcutaneously (s.c.) in the right flank with either 10^5 B16.F10 or 3.5 x 10^5 BPR20 melanoma cells in 100 uL of PBS and allowed to establish solid tumors. After ~10 days (as indicated in text), palpable tumors were measured with calipers and mice were randomized into treatment groups with comparable mean tumor sizes. Mice were then injected intratumorally (i.t.) with sterile phosphate-buffered saline (PBS) or 5 ug of endotoxin-free ADU-S100 (Cat. No: HY-12885B, MedChemExpress) resuspended in 50 ul of sterile PBS. Repeat injections were administered 4 days later.

value: ADU-S100 + ARG2i/COX2i/NOS2i

tag: genotype

value: BPR

value: melanoma


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGKVFDSXY_104077-002-002_CGATGTAT-GTTCAGAG_L003]

description: miRNA-seq


title: ADU-S100+combo-4


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGJFJDSXY_104077-002-002_CGATGTAT-GTTCAGAG_L002]

description: miRNA-seq


title: ADU-S100+combo-6


title: ADU-S100+combo-3


title: ADU-S100-6


title: ADU-S100+combo-1


title: ADU-S100-5


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGHTFDSXY_104077-002-001_ATCACGAT-GTTCAGAG_L002]

description: miRNA-seq


title: ADU-S100-3


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGKVFDSXY_104077-002-004_TGACCAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGJFJDSXY_104077-002-014_AGTTCCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-095_TCGAAGAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGJFJDSXY_104077-002-003_TTAGGCAT-GTTCAGAG_L003]

description: miRNA-seq


title: Th2_USP7_WT

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation for scRNA-seq were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 according to manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina).

value: Spleen

value: Control

tag: cell type

value: Wild-type


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGJFJDSXY_104077-002-002_CGATGTAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-096_TCGGCAAT-GTTCAGAG_L001]

description: miRNA-seq


title: ADU-S100-4


title: ADU-S100-2


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-096_TCGGCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: Th2_USP7_KO

description: 10x Genomics

value: USP7 KO


title: ADU-S100-1


title: WT, myc Input, replicate 2

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

country: China

institute: The Second Affiliated Hospital of Xinjiang Medical University

description: Wild type CD4+T cells, isolated from littermate control mice.

library_source: genomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software(version 0.20.1). Clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The clean reads were mapped to the genome using bowtie2(version 2.4.2). MACS2(version 2.2.7.1) was used to call peaks.
Called peaks were then annotated using R package ChIPseeker.
HOMER (http://homer.ucsd.edu/homer/download.html，v4.11.1) were used to find de novo and known motif.
ifferential peaks analysis was performed using R package  Diffbind for experimental design with replication.
Assembly: GRCm38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: primary cells

growth_protocol: Splenic CD4+T cells were magnitic sorted, and treated with RPMI 1640 culture medium supplemented with 10% Fetal bovine serum (FBS, Gibco)

extract_protocol:
Add final concentration of 1% Formaldehyde solution for Cross-Linking of DNA and Protein. Then stoped the cross-linking reaction by adding final concentration of 125mM glycine. Extract chromatin from cross-linked cells by adding Lysis Buffer
The sequencing libraries of immunoprecipitated chromatin DNA were generated with varied index label by NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA, cat. E7645L). Add End Repair Reaction Buffer (10X)和End Prep Enzyme Mix for end repair by the following condition: 20°C for 30min, 65°C for 30min.  And then NEBNext Adaptor and Blunt/TA Ligase Master Mix was added to ligate adaptor at 20°C for 15min. USER Enzyme was added to remove base U of adaptor at 37°C for 5min. After purification with beads, products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 10 sec; denaturation at 98℃ for 10 sec, annealing at 65℃ for 30 sec, and extension at 72℃ for 30 sec. The library size was selected and then purified with AMPure XP Beads.

treatment_protocol: Cells were stimulated with anti-CD3 (1 μg/mL) and anti-CD28 (2μg/mL)  in a 6-well plate, at the concentration of 10^7 cells/per plate, and cultured for 48 hrs.

tag: cell line

value: primary cells

value: mouse CD4+T cell

tag: chip antibody

value: Wild type


title: WT, myc IP, replicate 1


title: ADU-S100+combo-2


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-001-093_TCATTCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HNNTGDRXX_104077-001-093_TCATTCAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-001-092_TATAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-091_TACAGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: KO, myc Input, replicate 3

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HNNTGDRXX_104077-001-094_TCCCGAAT-GTTCAGAG_L001]

description: miRNA-seq


title: WT, myc Input, replicate 3


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-090_TAATCGAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-001-094_TCCCGAAT-GTTCAGAG_L004]

description: miRNA-seq


title: KO, myc IP, replicate 2

description: KAT6A-deficient CD4+T cells


title: KO, myc IP, replicate 1

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-095_TCGAAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: KO, myc Input, replicate 2

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HNNTGDRXX_104077-001-092_TATAATAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-090_TAATCGAT-GTTCAGAG_L004]

description: miRNA-seq


title: WT, myc IP, replicate 2


title: KO, myc IP, replicate 3

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HNNTGDRXX_104077-001-089_GACGACAT-GTTCAGAG_L001]

description: miRNA-seq


title: KO, myc Input, replicate 1

description: KAT6A-deficient CD4+T cells


title: WT, hif1a IP, replicate 3


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HNNTGDRXX_104077-001-088R_CTCAGAAT-GTTCAGAG_L001]

description: miRNA-seq


title: WT, hif1a IP, replicate 2


title: WT, hif1a Input, replicate 3


title: WT, myc Input, replicate 1


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-087R_CTATACAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-001-088R_CTCAGAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-091_TACAGCAT-GTTCAGAG_L001]

description: miRNA-seq


title: WT, hif1a Input, replicate 2


title: WT, hif1a IP, replicate 1


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-087R_CTATACAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-086_CTAGCTAT-GTTCAGAG_L001]

description: miRNA-seq


title: WT, hif1a Input, replicate 1


title: KO, hif1a Input, replicate 3

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HNNTGDRXX_104077-001-085_CGGAATAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-001-085_CGGAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-086_CTAGCTAT-GTTCAGAG_L004]

description: miRNA-seq


title: KO, hif1a IP, replicate 3

description: KAT6A-deficient CD4+T cells


title: KO, hif1a IP, replicate 2

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HNNTGDRXX_104077-001-083_CATTTTAT-GTTCAGAG_L001]

description: miRNA-seq


title: KO, hif1a IP, replicate 1

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-001-084_CCAACAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-001-089_GACGACAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-001-083_CATTTTAT-GTTCAGAG_L004]

description: miRNA-seq


title: KO, hif1a Input, replicate 1

description: KAT6A-deficient CD4+T cells


title: KO, hif1a Input, replicate 2

description: KAT6A-deficient CD4+T cells


title: WT, H3K27ac and H3K9ac Input, replicate 3


title: WT, myc IP, replicate 3


title: WT,H3K27ac and H3K9ac Input, replicate 2


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-082_CATGGCAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-082_CATGGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: WT, H3K9ac IP, replicate3


title: WT,H3K27ac and H3K9ac Input, replicate 1


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-081_CAGGCGAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-081_CAGGCGAT-GTTCAGAG_L004]

description: miRNA-seq


title: WT, H3K9ac IP, replicate2


title: WT, H3K9ac IP, replicate1


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HNNTGDRXX_104077-001-080_CACTCAAT-GTTCAGAG_L001]

description: miRNA-seq


title: WT, H3K27ac IP, replicate3


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HNNTGDRXX_104077-001-084_CCAACAAT-GTTCAGAG_L001]

description: miRNA-seq


title: WT, H3K27ac IP, replicate1


title: KO,H3K27ac and H3K9ac Input, replicate 3

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HNNTGDRXX_104077-001-079_CACGATAT-GTTCAGAG_L001]

description: miRNA-seq


title: WT, H3K27ac IP, replicate2


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-001-079_CACGATAT-GTTCAGAG_L004]

description: miRNA-seq


title: KO, H3K9ac IP, replicate2

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-076_CAAAAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-001-078_CACCGGAT-GTTCAGAG_L004]

description: miRNA-seq


title: KO, H3K27ac IP, replicate3

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HNNTGDRXX_104077-001-074_ATGAGCAT-GTTCAGAG_L001]

description: miRNA-seq


title: 20900X31 HU mKO 14b

city: Salt Lake City

first: Micah

last: Drummond

state: UT

institute: University of Utah

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 108 and reference database was created using STAR version 2.7.9a
Optical duplicates were removed using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.34.0
Assembly: mm39
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: AMPKalpha1 alpha2 muscle specific double KO that were unloaded for 4 weeks

extract_protocol:
Total RNA was isolated by homogenizing myotubes in Qiazol Lysis Reagent (Qiagen, cat# 79306). The RNA was separated and precipitated using chloroform and isopropanol. Extracted RNA was washed with ethanol then suspended in nuclease-free water.
Libraries were prepared with Illumina Stranded Total RNA Library Prep NEB Ultra II directional and RNA was sequenced using Illumina NovaSeq S4 Reagent Kit v1.5 150x150 bp Sequencing

treatment_protocol: Individuals were given placebo or metformin at 500 mg for the first four days. On days five through 9, participants took one capsule with breakfast and 2 with dinner (1.5 g total). From days ten to fourteen, and throughout bed rest participants took two capsules with breakfast and 2 with dinner (2g total). After bed rest, participants stopped treatments, i.e. no treatment was taken throughout the seven day recovery period.

value: HU

value: mKO

tag: strain

tag: age

value: Soleus

tag: Sex

value: F


title: KO,H3K27ac and H3K9ac Input, replicate 2

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-077_CAACTAAT-GTTCAGAG_L001]

description: miRNA-seq

value: whole blood

value: rVSV{delta}G-ZEBOV-GP vaccine, dose 2*10^7


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-076_CAAAAGAT-GTTCAGAG_L001]

description: miRNA-seq


title: KO, H3K9ac IP, replicate3

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-077_CAACTAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HNNTGDRXX_104077-001-073_ACTGATAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-001-073_ACTGATAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-001-075_ATTCCTAT-GTTCAGAG_L004]

description: miRNA-seq


title: KO, H3K9ac IP, replicate1

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-072_GGTAGCAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-001-074_ATGAGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: 20900X28 HU mKO 49a

value: M


title: 20900X26 HU mKO 24c


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-072_GGTAGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-001-080_CACTCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: KO, H3K27ac and H3K9ac Input, replicate 1

description: KAT6A-deficient CD4+T cells


title: KO, H3K27ac IP, replicate2

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HNNTGDRXX_104077-001-075_ATTCCTAT-GTTCAGAG_L001]

description: miRNA-seq


title: 20900X30 HU mKO 13b


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-071_GAGTGGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HNNTGDRXX_104077-001-070_CGTACGAT-GTTCAGAG_L001]

description: miRNA-seq


title: KO, H3K27ac IP, replicate1

description: KAT6A-deficient CD4+T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HNNTGDRXX_104077-001-078_CACCGGAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HNNTGDRXX_104077-001-069_GTTTCGAT-GTTCAGAG_L001]

description: miRNA-seq


title: 20900X24 HU mKO 26c


title: 20900X29 HU mKO 5b


title: 20900X25 HU mKO 34c


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-001-070_CGTACGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-001-069_GTTTCGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-071_GAGTGGAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HNNTGDRXX_104077-001-068_GTGGCCAT-GTTCAGAG_L001]

description: miRNA-seq


title: 20900X27 HU mKO 44a


title: 20900X20 HU Ctrl 46a

source_name: AMPKalpha1 alpha2 double floxed - no Cre controls that were unloaded for 4 weeks

value: Ctrl


title: 20900X22 HU Ctrl 4b


title: 20900X21 HU Ctrl 47a


title: 20900X19 HU Ctrl 17c


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-001-068_GTGGCCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-067_GTGAAAAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-066_GTCCGCAT-GTTCAGAG_L001]

description: miRNA-seq


title: 20900X18 HU Ctrl 35c


title: 20900X17 HU Ctrl 19c


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-067_GTGAAAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-066_GTCCGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HNNTGDRXX_104077-001-065_GTAGAGAT-GTTCAGAG_L001]

description: miRNA-seq


title: 20900X14 AMB mKO 43a

source_name: AMPKalpha1 alpha2 muscle specific double KO that were ambulatory for 4 weeks

value: AMB


title: 20900X15 AMB mKO 2b


title: 20900X13 AMB mKO 40a


title: 20900X11 AMB mKO 29c


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-001-065_GTAGAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: 20900X23 HU Ctrl 7b


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGKVFDSXY_104077-001-064_CCGTCCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HNNTGDRXX_104077-001-063_ATGTCAAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-062_AGTTCCAT-GTTCAGAG_L004]

description: miRNA-seq


title: 20900X10 AMB mKO 32c


title: 20900X5 AMB Ctrl 41a

source_name: AMPKalpha1 alpha2 double floxed - no Cre controls that were ambulatory for 4 weeks


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-001-063_ATGTCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: 20900X16 AMB mKO 3b


title: 20900X7 AMB Ctrl 1b


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-061_AGTCAAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HNNTGDRXX_104077-001-060_CTTGTAAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-062_AGTTCCAT-GTTCAGAG_L001]

description: miRNA-seq


title: 20900X6 AMB Ctrl 28a


title: 20900X3 AMB Ctrl 23c


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-061_AGTCAAAT-GTTCAGAG_L001]

description: miRNA-seq


title: 20900X8 AMB Ctrl 20b


title: 20900X9 AMB mKO 11b


title: 20900X2 AMB Ctrl 33c


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-001-060_CTTGTAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HNNTGDRXX_104077-001-058_TAGCTTAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HNNTGDRXX_104077-001-059_GGCTACAT-GTTCAGAG_L001]

description: miRNA-seq


title: 20900X1 AMB Ctrl 15c


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-001-059_GGCTACAT-GTTCAGAG_L004]

description: miRNA-seq


title: Contralateral Control [TAR349]

city: Gainesville

first: Mark

middle: Robert

last: Viggars

state: Alachua

address: University of Florida, M531

department: Physiology & Aging

institute: University of Florida

data_processing:
Partek Flow
Quality score trimmed for Phred <20, 3-prime right end, min-read length 25,
Trimmed sequence reads were mapped to RN7 for rat and mm10 for mouse, GRCm39. Annotated to genomes. Star alignment 2.7.8a
CPM values used in processed data file. Deseq2 median of ratios and Deseq2 differential expression analysis used.
Assembly: mm10 (GRCm39) /rn7
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Tibialis Anterior Muscle

extract_protocol:
Trizol with Qiagen, RNEasy Kit
Illumina library kit.

value: Tibialis Anterior Muscle

value: WT

value: Contralateral Control


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-001-058_TAGCTTAT-GTTCAGAG_L004]

description: miRNA-seq


title: Contralateral Control [TAR348]


title: >17 Days [TAL349]

value: >17 Days Training

value: 1-Hour Post Exercise


title: Contralateral Control [TAR345]


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-056_ACTTGAAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-057_GATCAGAT-GTTCAGAG_L001]

description: miRNA-seq


title: 2 Days [TAL345]

value: 2 Days Training


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-057_GATCAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: 20900X4 AMB Ctrl 27a


title: 2 Days [TAL344]


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-056_ACTTGAAT-GTTCAGAG_L004]

description: miRNA-seq


title: Contralateral Control [TAR343]


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-055_CAGATCAT-GTTCAGAG_L001]

description: miRNA-seq


title: Contralateral Control [TAR344]


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-055_CAGATCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-054_GCCAATAT-GTTCAGAG_L001]

description: miRNA-seq


title: >17 Days [TAL343]


title: Contralateral Control [TAR342]


title: Contralateral Control [TAR341]


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-001-053_ACAGTGAT-GTTCAGAG_L004]

description: miRNA-seq


title: 10 Days [TAL341]

value: 10 Days Training


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HNNTGDRXX_104077-001-053_ACAGTGAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-054_GCCAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-001-052_TGACCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HNNTGDRXX_104077-001-051_TTAGGCAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HNNTGDRXX_104077-001-052_TGACCAAT-GTTCAGAG_L001]

description: miRNA-seq


title: Contralateral Control [TAR340]


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HNNTGDRXX_104077-001-050_CGATGTAT-GTTCAGAG_L001]

description: miRNA-seq


title: 10 Days [TAL340]


title: >17 Days [TAL337]


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-001-050_CGATGTAT-GTTCAGAG_L004]

description: miRNA-seq


title: Contralateral Control [TAR337]


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-001-049_ATCACGAT-GTTCAGAG_L004]

description: miRNA-seq


title: MUPATF4KO_2

city: Shanghai

first: Feng

last: He

address: 1200 Cailun Road

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
Illumina Casava1.6 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters. Then clean reads were separately aligned to mm9 with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method to identify the DEGs and RSEM was used to quantify gene abundances.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: liver

growth_protocol: regular chow fed mice

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was extracted from liver tissue  using TRIzol® Reagent (Life technologies, cat#15596-018).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: overnight fasting

value: liver

value: liver specific Atf4 deficient MUP-uPA mice (MUP-uPA/Atf4Delta_hep)

value: overnight (15 hrs) fasting before harvesting sample


title: MUPATF4KO_3


title: MUPATF4KO_1


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HNNTGDRXX_104077-001-049_ATCACGAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGKVFDSXY_104077-001-048_TCGGCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGHY2DSXY_104077-001-048_TCGGCAAT-GTTCAGAG_L003]

description: miRNA-seq


title: MUPATF4FF_3

value: liver specific MUP-uPA mice (MUP-uPA/Atf4F/F)


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGKVFDSXY_104077-001-047R_TCGAAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: 10 Days [TAL342]


title: MUPATF4FF_2


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHY2DSXY_104077-001-047R_TCGAAGAT-GTTCAGAG_L003]

description: miRNA-seq


title: ATF4KO_3

value: liver specific Atf4 deficient mice


title: ATF4KO_2


title: MUPATF4FF_1


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGHY2DSXY_104077-001-046_TCCCGAAT-GTTCAGAG_L003]

description: miRNA-seq

value: whole blood


title: ATF4KO_1


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGKVFDSXY_104077-001-046_TCCCGAAT-GTTCAGAG_L004]

description: miRNA-seq

value: rVSV{delta}G-ZEBOV-GP vaccine, dose 2*10^7


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-001-051_TTAGGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: AT4FF_2

value: Wild type Atf4F/F mice


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGJFJDSXY_104077-001-045_TCATTCAT-GTTCAGAG_L004]

description: miRNA-seq


title: AT4FF_3


title: AT4FF_1


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGHCYDSXY_104077-001-044_TATAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGJFJDSXY_104077-001-043_TACAGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGJFJDSXY_104077-001-044_TATAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: Vehicle-FAPs

city: Chengdu

first: Xia

last: Kang

address: Rongdu Avenue, #270

institute: General Hospital of Western Theater Command

data_processing:
all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8)
The expression level of each transcript was calculated using the fragments per kilobase of transcript per million mapped reads (FPKM) method
StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples)
Assembly: The mapped reads of each sample were assembled using StringTie.
Supplementary files format and content: Matrix table with raw gene counts for differentially expressed genes

source_name: muscle

growth_protocol: Freshly sorted FAPs were cultured in growth medium (GM) consisting of DMEM supplemented with 20% FBS, 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted from Musclin- or vehicle-treated FAPs using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 µM mouse recombinant Musclin or an equal amount of vehicle was added to the medium treating for 24 hours.

value: muscle

value: primary cells

value: vehicle


title: Musclin-FAPs

value: WT

value: Musclin


title: P40-3-6h

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: isolated monocytes, milk fat globule membrane shake, 6h after consumption

data_processing:
Sequencing reads that contained adapters and/or had low quality, aligned to rRNA were filtered off before mapping.
The tool Salmon (version 1.4.0) was used to map the cleaned reads to the GRCh38.p13 human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium (release 37). Salmon parameters used: -i ./salmon_index_H37  --libType A --seqBias --numBiasSamples 10000000 --gcBias --biasSpeedSamp 5 --validateMappings --numGibbsSamples 100
The Salmon-obtained transcript abundance estimates and lengths were imported in R using the package tximport to estimate gene level counts.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table (TxImport.GeneLevel.counts.GEO.txt) with raw gene counts for every gene and every sample (gene level counts were calculated from the Salmon-obtained transcript abundance estimates)
Supplementary files format and content: R-object (txi.counts.annotated.Rdata; exported tximport object) containing gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was not transformed nor scaled (i.e. countsFromAbundance = "no"), and can be used for subsequent analysis in edgeR or DESeq2.
Supplementary files format and content: R object (txi.lengthScaledTPM.annotated.Rdata; exported tximport object) containing scaled gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was scaled using library size and transcript gene length (i.e. countsFromAbundance = "lengthScaledTPM"), and these scaled counts can be used for subsequent analysis in limma (voom function).

source_name: isolated human monocytes, 6h after consumption of a milk fat globule membrane shake

growth_protocol: The human study was a randomized, double-blind crossover intervention trial and aimed at comparing the postprandial effects (6h) of formula vegetable fat (VEGE), anhydrous milk fat (AMF), and anhydrous milk fat plus milk fat globule membranes (CREAM) on the immune response. Participants, males and females, were aged 40–70 years, and had a BMI of 22–27 kg/m2. The study was conducted at Wageningen University, the Netherlands, from 07-01-2020 until 10-03-2020. The experimental protocol and procedures were approved by the Medical Ethical Committee of Wageningen University and were in accordance with the Helsinki Declaration of 1975 as revised in 1983. The study was registered at ClinicalTrials.gov with identifier NCT04178681.

extract_protocol:
At least 500,000 cells were collected from each subject for every intervention and both time points and used for total RNA isolation using a RNeasy Micro Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. RNA concentration was measured with a Nanodrop 1000 spectrometer and RNA integrity was determined using an Agilent 2100 Bioanalyzer with RNA 6000 microchips (Agilent Technologies).
Library construction and RNA sequencing on BGISEQ-500 were conducted at Beijing Genomics Institute (BGI) for pair-end 150bp runs. At BGI, Genomic DNA was removed with two digestions using Amplification grade DNAse I (Invitrogen). The RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction. The library quality was determined by using Bioanalyzer 2100 (Agilent Technologies). Then, the library was used for sequencing with the sequencing platform BGISEQ-500 (BGI).

treatment_protocol: The three intervention fat shakes were supplied by FrieslandCampina. Shake VEGE (vegetable-sourced lipids) is based on the vegetable lipid formula used in infant formula. To form the VEGE and anhydrous milk fat (AMF) shakes, 118g of the respective powdered formulas were mixed with 500mL skim milk, whereas for the CREAM shake 461mL skim milk plus 39mL water were added. Except for the presence of milk fat globule membranes (MFGM), shake AMF and shake CREAM contained the same milk-sourced lipids. All shakes contained 95g of fat, 21g of protein, and 42g of carbohydrates and provided slighly over 4600kJ. Forty participants were given three different shakes on three different days. There was at least one week for washout between interventions. On the test day, subjects arrived fasted, and the concentration of C-reactive protein (CRP) in the blood was determined via a finger prick using a QuickRead CRP test (Orion Diagnostica Oy) before any blood was collected. When the CRP concentration was below 10.0 mg/L, participants were qualified for the study, and a catheter cannula was inserted in an antecubital vein. After a 30-minute rest, fasted blood was drawn into EDTA-containing tubes to obtain a baseline (t=0h) sample. Subjects were then asked to consume a shake within 10 min. Blood was drawn again 6h post-shake consumption. Each subject consumed all three shakes in a randomized order. Whole blood was collected in CPT tubes, mixed by inverting, and centrifuged at room temperature for 20m at 1800RCF. The white cloudy cell layer was collected for PBMC purification. Cells were washed with cold PBS three times, and monocytes were isolated by MojoSort CD14 negative selection kits (Biolegend, California, United States) and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany).

value: isolated monocytes

tag: subjectid

tag: shakeid

tag: shake description

value: CREAM

tag: sampling time (h)

value: female

tag: age (yrs)

tag: bmi (kg/m2)


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGHCYDSXY_104077-001-043_TACAGCAT-GTTCAGAG_L004]

description: miRNA-seq

tag: tissue


title: Sham [TAL300]

organism: Rattus norvegicus

value: Tibialis Anterior Muscle

tag: treatment

value: Sham

value: Sham surgery


title: P40-3-0h

description: isolated monocytes, milk fat globule membrane shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a milk fat globule membrane shake


title: Contralateral Control [TAR300]

value: Contralateral Control

tag: time


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HTHCLDMXX_104077-001-042_TAATCGAT-GTTCAGAG_L002]

description: miRNA-seq


title: Contralateral Control [TAR299]


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGJFJDSXY_104077-001-040_CTCAGAAT-GTTCAGAG_L004]

description: miRNA-seq


title: Contralateral Control [TAR298]


title: P40-2-0h

description: isolated monocytes, anhydrous milk fat shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a anhydrous milk fat shake

value: AMF


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HTHCLDMXX_104077-001-041_GACGACAT-GTTCAGAG_L002]

description: miRNA-seq


title: P40-1-6h

description: isolated monocytes, vegetable fat shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a vegetable fat shake

value: VEGE


title: Every 3 Days 30 Days [TAL298]

value: Every 3 Days 30 Days

value: 1-Hour Post Exercise


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGKVFDSXY_104077-001-039_CTATACAT-GTTCAGAG_L004]

description: miRNA-seq

value: whole blood

value: rVSV{delta}G-ZEBOV-GP vaccine, dose 2*10^7


title: Contralateral Control [TAR297]


title: P40-1-0h

description: isolated monocytes, vegetable fat shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a vegetable fat shake


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGHY2DSXY_104077-001-039_CTATACAT-GTTCAGAG_L003]

description: miRNA-seq

source_name: whole blood


title: Contralateral Control [TAR296]


title: P37-3-6h


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HTHCLDMXX_104077-001-038_CTAGCTAT-GTTCAGAG_L002]

description: miRNA-seq


title: Sham [TAL297]


title: SKO n2

city: Chongqing

first: Ran

last: Ren

address: Shazheng Street

institute: Chongqing University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Human hepatocarcinoma cell

value: STIM2 KO


title: SKO n3

value: STIM3 KO


title: Sham  [TAL296]

value: WT


title: SKO n1

value: STIM1 KO


title: P37-3-0h

value: isolated monocytes

value: CREAM


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGJFJDSXY_104077-001-037_CGGAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: Contralateral Control [TAR295]

value: Tibialis Anterior Muscle


title: P37-1-6h

value: female


title: CN n3


title: P40-2-6h

description: isolated monocytes, anhydrous milk fat shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a anhydrous milk fat shake


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HTHCLDMXX_104077-001-036_CCAACAAT-GTTCAGAG_L002]

description: miRNA-seq


title: CN n2


title: Every 3 Days 30 Days [TAL295]


title: Every 3 Days 30 Days [TAL299]


title: CN n1


title: P36-2-6h


title: P37-1-0h


title: Daily Training 30 Days [TAL294]

value: Daily Training 30 Days


title: Contralateral Control [TAR294]

value: Contralateral Control


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGHCYDSXY_104077-001-035_CATTTTAT-GTTCAGAG_L004]

description: miRNA-seq


title: DR n3

value: DR

tag: sample group

value: sorafenib acquired resistance cells


title: DR n2

tag: genotype


title: P36-1-6h

tag: cell type

value: VEGE


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHCYDSXY_104077-001-034_CATGGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: Contralateral Control [TAR292]


title: Daily Training 30 Days [TAL292]

value: 1-Hour Post Exercise


title: P36-1-0h


title: DR n1

tag: cell line


title: P34-3-6h


title: CONTROL n3

value: Con

value: parental cells


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HTHCLDMXX_104077-001-033_CAGGCGAT-GTTCAGAG_L002]

description: miRNA-seq

value: whole blood

value: rVSV{delta}G-ZEBOV-GP vaccine, dose 2*10^7


title: P34-3-0h


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGJFJDSXY_104077-001-035_CATTTTAT-GTTCAGAG_L004]

description: miRNA-seq


title: CONTROL n2

value: Human hepatocarcinoma cell


title: P34-2-6h

value: AMF


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGJFJDSXY_104077-001-032R_CACTCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGJFJDSXY_104077-001-031R_CACGATAT-GTTCAGAG_L004]

description: miRNA-seq


title: P36-2-0h


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGJFJDSXY_104077-001-034_CATGGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGKVFDSXY_104077-001-030_CACCGGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGHY2DSXY_104077-001-030_CACCGGAT-GTTCAGAG_L003]

description: miRNA-seq


title: Newly diagnosed multiple myeloma [M_7]

city: changsha

first: XIN

last: CHEN

state: None Selected

address: Department of Hematology, the Third Xiangya Hospital of Central South University, Changsha, China

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8
Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed adaptor bases by cutadapt ) are aligned
The trimmed reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2
The abundance of miRNA are evaluated using their sequencing counts with miRDeep2
Assembly: miRBase mature.fa
Supplementary files format and content: Tab-delimited text files include raw counts for total sample

source_name: Bone marrow

extract_protocol:
Total RNA and Exosomal RNA were isolated using Trizol reagent. The RNA concentration and purity were confifirmed using absorbance measurements with a NanoDrop 2000 (Thermo Scientifific, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for miRNA-seq were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina

value: Bone marrow

tag: disease state

value: Newly diagnosed multiple myeloma


title: CONTROL n1


title: P34-2-0h

value: isolated monocytes


title: P34-1-6h


title: Newly diagnosed multiple myeloma [M_6]

institute: the Third Xiangya Hospital of Central South University


title: Newly diagnosed multiple myeloma [M_5]


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGJFJDSXY_104077-001-028_CAAAAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: Newly diagnosed multiple myeloma [M_4]


title: SIG_CTRL_1

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_2_1.txt
Gene expression after 24 h exposure to 0 ug/ml of SIG

hyb_protocol: Labeled cRNA samples were hybridised onto the Agilent 2-colour 8x60k arrays according to the manufacturer's recommendations and hybridized for 17 hours at 65°C. After hybridization, slides were washed following the manufacturer's recommendations (Agilent).

scan_protocol: Slides were scanned with Agilent microarray scanner G2505C and data were extracted using the Agilent Feature Extraction software (V12.02.2)

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and data were normalized with quantile normalization. This experiment was performed as a two-colour experiment, but data were analyzed as single-channel arrays. Raw data files are available as a tar archive on the series record.

source_name: THP-1 monocytes differentiated into macrophages, SIG 0 ug/ml unexposed control replicate 1

label_protocol: Samples were amplified using the T7 RNA polymerase method. cRNAs were labelled with Cy3 or Cy5 following the manufacturer's protocol (Agilent).

growth_protocol: THP-1 cells (ATCC TIB-202) were grown in culture flasks in  RPMI-1640 media ( supplemented with 10% FBS, Gibco). During culturing the cell density was kept below 1x10^6 cells/ml and they were seeded three times before culturing. Cells were PMA differentiated (25 nM) for 48 hours on 12-well plates (150 000 cells/well). After differentiation, media was replaced to RPMI supplemented with 1 % FBS and the cells rested for 24 hours before exposures.

extract_protocol: Cells were harvested and lysed with lysis buffer (Qiagen). Two samples of the same exposure and concentration were pooled together to increase the total amount of RNA. Total RNA was extracted and purified with the Rneasy Mini Kit by Qiagen following the kits' instructions.

treatment_protocol: Stock solution (1 mg /ml for BAY, CHT, MIT, SIG and SES, 0.5 mg/ml for NM400 and NM401) in 1 % FBS RPMI was sonicated in a bath sonicator at RT for 2 x 15 min (BAY, CHT, SIG, SES) or 3 x 15 min (MIT, NM400, NM401) and vortexed and diluted to final concentrations in 1 % FBS RPMI. Dilutions were further vortexed and sonicated for 5 minutes prior to exposure. Cells were exposed to rCNT for 24 hours. Untreated controls had the same treatment without the rCNTs. Exposures were performed as six replicates on two parallel plates for each exposure.

tag: differentiation

value: PMA differentiated macrophage

tag: dose

tag: dose unit

value: µg/ml

tag: exposure time

value: 24 hours

value: SIG

tag: samples prepared

tag: plate

tag: rin


title: SIG_CTRL_2

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_2_3.txt
Gene expression after 24 h exposure to 0 ug/ml of SIG

source_name: THP-1 monocytes differentiated into macrophages, SIG 0 ug/ml unexposed control replicate 2


title: SIG_C3_2

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_1_1.txt
Gene expression after 24 h exposure to 0.5 ug/ml of SIG

source_name: THP-1 monocytes differentiated into macrophages, SIG 0.5 ug/ml IC5 replicate 2


title: SIG_C3_3

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 0.5 ug/ml of SIG

source_name: THP-1 monocytes differentiated into macrophages, SIG 0.5 ug/ml IC5 replicate 3


title: Newly diagnosed multiple myeloma [M_3]


title: Newly diagnosed multiple myeloma [M_2]


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGHCYDSXY_104077-001-028_CAAAAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: P32-1-6h

tag: subjectid

tag: shakeid

tag: shake description

tag: sampling time (h)

tag: Sex

value: male

tag: age (yrs)


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGJFJDSXY_104077-001-027_ATTCCTAT-GTTCAGAG_L004]

description: miRNA-seq

tag: tissue

tag: treatment

tag: time


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGKVFDSXY_104077-001-029_CAACTAAT-GTTCAGAG_L004]

description: miRNA-seq


title: P32-1-0h

tag: cell type

tag: bmi (kg/m2)


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGHCYDSXY_104077-001-027_ATTCCTAT-GTTCAGAG_L004]

description: miRNA-seq


title: P26-2-6h

value: female


title: Newly diagnosed multiple myeloma [M_1]

tag: disease state


title: SIG_C2_1

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_1_4.txt
Gene expression after 24 h exposure to 1 ug/ml of SIG

source_name: THP-1 monocytes differentiated into macrophages, SIG 1 ug/ml IC10 replicate 1

tag: cell line

tag: differentiation

tag: dose

tag: dose unit


title: SIG_C2_3

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_1_3.txt
Gene expression after 24 h exposure to 1 ug/ml of SIG

source_name: THP-1 monocytes differentiated into macrophages, SIG 1 ug/ml IC10 replicate 3

tag: exposure time

tag: samples prepared

tag: plate

tag: rin


title: SIG_C2_2

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_2_3.txt
Gene expression after 24 h exposure to 1 ug/ml of SIG

source_name: THP-1 monocytes differentiated into macrophages, SIG 1 ug/ml IC10 replicate 2


title: P34-1-0h

tag: subjectid

tag: shakeid

tag: shake description

value: VEGE

tag: sampling time (h)


title: Healthy control [H_3]

tag: tissue

value: Healthy control


title: P32-3-6h

value: CREAM

tag: Sex

tag: age (yrs)


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHY2DSXY_104077-001-029_CAACTAAT-GTTCAGAG_L003]

description: miRNA-seq

tag: treatment

tag: time


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGHCYDSXY_104077-001-026_ATGAGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: SIG_C3_1

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_1_1.txt
Gene expression after 24 h exposure to 0.5 ug/ml of SIG

source_name: THP-1 monocytes differentiated into macrophages, SIG 0.5 ug/ml IC5 replicate 1

tag: cell line


title: P26-2-0h

tag: cell type

tag: bmi (kg/m2)


title: Healthy control [H_2]

tag: disease state


title: SIG_C1_2

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_2_2.txt
Gene expression after 24 h exposure to 2 ug/ml of SIG

source_name: THP-1 monocytes differentiated into macrophages, SIG 2 ug/ml IC20 replicate 2

tag: differentiation

tag: dose

tag: dose unit

tag: exposure time


title: P32-3-0h

tag: subjectid


title: SES_CTRL_2

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_2_1.txt
Gene expression after 24 h exposure to 0 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 0 ug/ml unexposed control replicate 2

value: SES

tag: samples prepared

tag: plate

tag: rin


title: SIG_C1_1

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_1_1.txt
Gene expression after 24 h exposure to 2 ug/ml of SIG

source_name: THP-1 monocytes differentiated into macrophages, SIG 2 ug/ml IC20 replicate 1


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HTHCLDMXX_104077-001-025_ACTGATAT-GTTCAGAG_L002]

description: miRNA-seq

tag: tissue

value: whole blood


title: Healthy control [H_1]


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGJFJDSXY_104077-001-024R_GGTAGCAT-GTTCAGAG_L004]

description: miRNA-seq

value: rVSV{delta}G-ZEBOV-GP vaccine, dose 2*10^7


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHCYDSXY_104077-001-024R_GGTAGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: P22-2-0h

source_name: isolated human monocytes, before consumption of a anhydrous milk fat shake

tag: shakeid

tag: shake description

tag: sampling time (h)

tag: Sex


title: P26-1-0h

tag: age (yrs)


title: P22-2-6h

tag: cell type


title: P22-1-6h

source_name: isolated human monocytes, 6h after consumption of a vegetable fat shake

tag: bmi (kg/m2)


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGHY2DSXY_104077-001-023R_GAGTGGAT-GTTCAGAG_L003]

description: miRNA-seq

tag: treatment

tag: time


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGKVFDSXY_104077-001-023R_GAGTGGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGKVFDSXY_104077-001-022_CGTACGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGHY2DSXY_104077-001-022_CGTACGAT-GTTCAGAG_L003]

description: miRNA-seq


title: P22-1-0h

source_name: isolated human monocytes, before consumption of a vegetable fat shake


title: SIG_C1_3

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_1_1.txt
Gene expression after 24 h exposure to 2 ug/ml of SIG

source_name: THP-1 monocytes differentiated into macrophages, SIG 2 ug/ml IC20 replicate 3

tag: cell line

tag: differentiation

tag: dose


title: SES_CTRL_1

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_1_4.txt
Gene expression after 24 h exposure to 0 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 0 ug/ml unexposed control replicate 1

tag: dose unit

tag: exposure time


title: P21-3-6h

description: isolated monocytes, milk fat globule membrane shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a milk fat globule membrane shake

tag: subjectid


title: P26-1-6h

description: isolated monocytes, vegetable fat shake, 6h after consumption


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGJFJDSXY_104077-001-021_GTTTCGAT-GTTCAGAG_L004]

description: miRNA-seq

source_name: whole blood


title: SES_C3_3

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_2_2.txt
Gene expression after 24 h exposure to 2 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 2 ug/ml IC5 replicate 3

tag: samples prepared

tag: plate

tag: rin


title: SES_C3_2

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_1_1.txt
Gene expression after 24 h exposure to 2 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 2 ug/ml IC5 replicate 2


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGJFJDSXY_104077-001-020_GTGGCCAT-GTTCAGAG_L004]

description: miRNA-seq

tag: tissue


title: SES_C2_3

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_2_3.txt
Gene expression after 24 h exposure to 4.5 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 4.5 ug/ml IC10 replicate 3


title: P21-3-0h

description: isolated monocytes, milk fat globule membrane shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a milk fat globule membrane shake

tag: shakeid

tag: shake description

tag: sampling time (h)


title: P21-2-0h

description: isolated monocytes, anhydrous milk fat shake, baseline (t=0)

tag: cell type

tag: Sex

tag: age (yrs)


title: SES_C3_1

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_2_2.txt
Gene expression after 24 h exposure to 2 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 2 ug/ml IC5 replicate 1

tag: treatment


title: SES_C2_1

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_1_3.txt
Gene expression after 24 h exposure to 4.5 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 4.5 ug/ml IC10 replicate 1

tag: cell line


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHCYDSXY_104077-001-019_GTGAAAAT-GTTCAGAG_L004]

description: miRNA-seq

tag: time


title: SES_C2_2

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_1_3.txt
Gene expression after 24 h exposure to 4.5 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 4.5 ug/ml IC10 replicate 2

tag: differentiation

tag: dose


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGKVFDSXY_104077-001-018_GTCCGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: P20-2-6h

description: isolated monocytes, anhydrous milk fat shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a anhydrous milk fat shake

tag: bmi (kg/m2)


title: SES_C1_3

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_1_2.txt
Gene expression after 24 h exposure to 10 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 10 ug/ml IC20 replicate 3

tag: dose unit

tag: exposure time


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGKVFDSXY_104077-001-017_GTAGAGAT-GTTCAGAG_L003]

description: miRNA-seq


title: SES_C1_1

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_1_4.txt
Gene expression after 24 h exposure to 10 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 10 ug/ml IC20 replicate 1

tag: samples prepared

tag: plate


title: P20-2-0h

source_name: isolated human monocytes, before consumption of a anhydrous milk fat shake

tag: subjectid


title: SES_C1_2

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_1_2.txt
Gene expression after 24 h exposure to 10 ug/ml of SES

source_name: THP-1 monocytes differentiated into macrophages, SES 10 ug/ml IC20 replicate 2

tag: rin


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HTHCLDMXX_104077-001-017_GTAGAGAT-GTTCAGAG_L002]

description: miRNA-seq

tag: tissue


title: P17-3-6h

tag: shakeid

tag: shake description

tag: sampling time (h)


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGKVFDSXY_104077-001-016_CCGTCCAT-GTTCAGAG_L004]

description: miRNA-seq


title: P20-1-0h

description: isolated monocytes, vegetable fat shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a vegetable fat shake

tag: cell type

tag: Sex

tag: age (yrs)


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGHY2DSXY_104077-001-016_CCGTCCAT-GTTCAGAG_L003]

description: miRNA-seq

tag: treatment

tag: time


title: P21-2-6h


title: NM401_CTRL_1

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_2_1.txt
Gene expression after 24 h exposure to 0 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 0 ug/ml unexposed control replicate 1

tag: cell line

tag: differentiation

tag: dose


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGJFJDSXY_104077-001-019_GTGAAAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGKVFDSXY_104077-001-015R_ATGTCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HTHCLDMXX_104077-001-018_GTCCGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: P17-2-6h

tag: bmi (kg/m2)


title: P17-3-0h


title: P20-1-6h

source_name: isolated human monocytes, 6h after consumption of a vegetable fat shake


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGHY2DSXY_104077-001-015R_ATGTCAAT-GTTCAGAG_L003]

description: miRNA-seq


title: P17-2-0h


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGJFJDSXY_104077-001-014_AGTTCCAT-GTTCAGAG_L004]

description: miRNA-seq


title: NM401_CTRL_2

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_1_3.txt
Gene expression after 24 h exposure to 0 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 0 ug/ml unexposed control replicate 2

tag: dose unit

tag: exposure time

tag: samples prepared


title: NM401_C3_2

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 0.5 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 0.5 ug/ml IC5 replicate 2

tag: plate

tag: rin


title: P16-3-6h

description: isolated monocytes, milk fat globule membrane shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a milk fat globule membrane shake

tag: subjectid

tag: shakeid


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGJFJDSXY_104077-001-013_AGTCAAAT-GTTCAGAG_L004]

description: miRNA-seq

source_name: whole blood

tag: tissue


title: NM401_C3_3

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_1_4.txt
Gene expression after 24 h exposure to 0.5 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 0.5 ug/ml IC5 replicate 3


title: NM401_C2_3

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_2_1.txt
Gene expression after 24 h exposure to 1 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 1 ug/ml IC10 replicate 3


title: NM401_C3_1

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_1_3.txt
Gene expression after 24 h exposure to 0.5 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 0.5 ug/ml IC5 replicate 1


title: NM401_C2_2

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_1_3.txt
Gene expression after 24 h exposure to 1 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 1 ug/ml IC10 replicate 2


title: NM401_C2_1

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_2_2.txt
Gene expression after 24 h exposure to 1 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 1 ug/ml IC10 replicate 1


title: P16-2-6h

source_name: isolated human monocytes, 6h after consumption of a anhydrous milk fat shake

tag: cell type

tag: shake description

tag: sampling time (h)


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGJFJDSXY_104077-001-012_CTTGTAAT-GTTCAGAG_L004]

description: miRNA-seq

tag: treatment


title: P16-3-0h

description: isolated monocytes, milk fat globule membrane shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a milk fat globule membrane shake

tag: Sex

tag: age (yrs)


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGHCYDSXY_104077-001-012_CTTGTAAT-GTTCAGAG_L004]

description: miRNA-seq

tag: time


title: P16-1-6h

description: isolated monocytes, vegetable fat shake, 6h after consumption


title: P16-2-0h

description: isolated monocytes, anhydrous milk fat shake, baseline (t=0)


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGJFJDSXY_104077-001-011_GGCTACAT-GTTCAGAG_L004]

description: miRNA-seq


title: NM401_C1_2

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_2_3.txt
Gene expression after 24 h exposure to 2 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 2 ug/ml IC20 replicate 2

tag: cell line

tag: differentiation

tag: dose


title: NM401_C1_1

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_2_2.txt
Gene expression after 24 h exposure to 2 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 2 ug/ml IC20 replicate 1

tag: dose unit

tag: exposure time


title: NM401_C1_3

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_2_1.txt
Gene expression after 24 h exposure to 2 ug/ml of NM401

source_name: THP-1 monocytes differentiated into macrophages, NM401 2 ug/ml IC20 replicate 3

tag: samples prepared

tag: plate


title: P16-1-0h

source_name: isolated human monocytes, before consumption of a vegetable fat shake

tag: subjectid

tag: bmi (kg/m2)


title: P15-3-0h

tag: shakeid


title: P15-3-6h

tag: cell type


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGHY2DSXY_104077-001-010_TAGCTTAT-GTTCAGAG_L003]

description: miRNA-seq

tag: tissue


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGKVFDSXY_104077-001-010_TAGCTTAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGJFJDSXY_104077-001-009_GATCAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: P15-1-6h

tag: shake description

tag: sampling time (h)


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHCYDSXY_104077-001-009_GATCAGAT-GTTCAGAG_L004]

description: miRNA-seq

tag: treatment


title: P14-3-6h

tag: Sex

tag: age (yrs)


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGHY2DSXY_104077-001-008_ACTTGAAT-GTTCAGAG_L003]

description: miRNA-seq

tag: time


title: P15-1-0h


title: NM400_CTRL_2

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_2_3.txt
Gene expression after 24 h exposure to 0 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 0 ug/ml unexposed control replicate 2

tag: cell line

tag: differentiation

tag: rin


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGKVFDSXY_104077-001-008_ACTTGAAT-GTTCAGAG_L004]

description: miRNA-seq


title: NM400_C3_1

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_1_4.txt
Gene expression after 24 h exposure to 0.5 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 0.5 ug/ml IC5 replicate 1

tag: dose

tag: dose unit

tag: exposure time


title: NM400_CTRL_1

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_2_1.txt
Gene expression after 24 h exposure to 0 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 0 ug/ml unexposed control replicate 1

tag: samples prepared

tag: plate


title: NM400_C3_3

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 0.5 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 0.5 ug/ml IC5 replicate 3


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGJFJDSXY_104077-001-007_CAGATCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGHCYDSXY_104077-001-006_GCCAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: P14-2-6h

description: isolated monocytes, anhydrous milk fat shake, 6h after consumption

tag: subjectid

tag: shakeid

tag: bmi (kg/m2)


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGJFJDSXY_104077-001-006_GCCAATAT-GTTCAGAG_L004]

description: miRNA-seq

tag: tissue


title: P14-1-6h

source_name: isolated human monocytes, 6h after consumption of a vegetable fat shake

tag: cell type

tag: shake description

tag: sampling time (h)


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HTHCLDMXX_104077-001-005_ACAGTGAT-GTTCAGAG_L002]

description: miRNA-seq

source_name: whole blood

tag: treatment


title: NM400_C2_1

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 1 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 1 ug/ml IC10 replicate 1


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HTHCLDMXX_104077-001-004_TGACCAAT-GTTCAGAG_L002]

description: miRNA-seq

tag: time


title: P14-1-0h

description: isolated monocytes, vegetable fat shake, baseline (t=0)

tag: Sex

tag: age (yrs)


title: NM400_C2_3

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_2_2.txt
Gene expression after 24 h exposure to 1 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 1 ug/ml IC10 replicate 3

tag: cell line

tag: differentiation

tag: rin


title: NM400_C2_2

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_1_3.txt
Gene expression after 24 h exposure to 1 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 1 ug/ml IC10 replicate 2

tag: dose

tag: dose unit

tag: exposure time


title: NM400_C1_3_2

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 2 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 2 ug/ml IC20 replicate 3 technical replicate 2

tag: samples prepared

tag: plate


title: NM400_C1_3_1

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_1_1.txt
Gene expression after 24 h exposure to 2 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 2 ug/ml IC20 replicate 3 technical replicate 1


title: NM400_C1_2

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_1_2.txt
Gene expression after 24 h exposure to 2 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 2 ug/ml IC20 replicate 2


title: NM400_C3_2

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_1_3.txt
Gene expression after 24 h exposure to 0.5 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 0.5 ug/ml IC5 replicate 2


title: NM400_C1_1

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 2 ug/ml of NM400

source_name: THP-1 monocytes differentiated into macrophages, NM400 2 ug/ml IC20 replicate 1


title: MIT_CTRL_2

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 0 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 0 ug/ml unexposed control replicate 2

value: MIT


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HTHCLDMXX_104077-001-002_CGATGTAT-GTTCAGAG_L002]

description: miRNA-seq


title: P14-3-0h

description: isolated monocytes, milk fat globule membrane shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a milk fat globule membrane shake

tag: subjectid

tag: shakeid

tag: bmi (kg/m2)


title: MIT_CTRL_1

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_2_1.txt
Gene expression after 24 h exposure to 0 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 0 ug/ml unexposed control replicate 1


title: P14-2-0h

description: isolated monocytes, anhydrous milk fat shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a anhydrous milk fat shake

tag: cell type

tag: shake description

value: AMF


title: P13-1-6h

description: isolated monocytes, vegetable fat shake, 6h after consumption

tag: sampling time (h)


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HTHCLDMXX_104077-001-001_ATCACGAT-GTTCAGAG_L002]

description: miRNA-seq

tag: tissue

tag: treatment

tag: time


title: XPO2 siRNA matched replicate 4, Nuclear fraction, sequencing round 1

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 (Illumina), CASAVA version 1.8+
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v2.1, using minimum-length 18, error-rate 0.2, overlap 5, paired-output options.
Trimmed reads were mapped against the GRChr37/hg19 human reference genome modified to include the circRNA spike vector sequence, using the STAR spliced alignment algorithm (version 2.6.1d with default parameters and --chimSegmentMin 20, --quantMode GeneCounts).
Quantification of circRNA abundance was conducted utilising the chimeric junction file produced by the STAR aligner and processed by the CIRCexplorer2 Parse and Annotate functions.
Assembly: GRChr37/hg19
Supplementary files format and content: Tab separated circRNA abundance estimations from CircExplorer2

molecule: nuclear RNA

source_name: Breast

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 10% (v/v) fetal bovine serum (Gibco) and 1% (v/v) penicillin-streptomycin (Thermo Fisher) at 37°C in a 5% CO2 incubator and routinely tested for mycoplasma contamination

extract_protocol:
Fractionation of cytoplasmic and nuclear RNA was performed using digitonin. cells were washed in ice cold PBS before permeabilised in digitonin solution (50 μg/mL digitonin (MP Biomedicals), 100 mM NaCl, 10 mM Tris, pH 8.0, 40 U/mL RNaseOUT (Invitrogen), 1 x Protease inhibitor cocktail (Roche)) for 15 min on ice. Nuclear and cytoplasmic fractions were separated by centrifugation for 3 min at 1000 g at 4°C. RNA in each fraction was then recovered using RNeasy Mini Kit (Qiagen) according to manufacturer instructions.
Samples were treated with RNase H for ribosomal RNA depletion then purified with RNA beads (Axygen Ampure) following the standard bead clean up protocol. Samples were then treated with RNase R for 15 min at 37°C (0.2 μl RNase R and 2μl 10X buffer, Lucigen) to enrich for circRNA, followed by RNA bead purification (Axygen Ampure). Stranded RNA libraries were made using the KAPA RNA HyperPrep Kit (Roche)

treatment_protocol: Depletions of different factors were induced by reverse transfection using small interfering RNA and DharmaFECT1 transfection reagent (Dharmacon). Cells were harvested 48 hour and 72 hour post-transfection.

value: Breast

tag: cell line

value: Epithelial-like, adherent, triple negative breast cancer cell line

value: XPO2 siRNA


title: MIT_C3_3

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_2_3.txt
Gene expression after 24 h exposure to 0.3 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 0.3 ug/ml IC5 replicate 3

tag: differentiation

value: PMA differentiated macrophage


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HFC7YDSXY_104042-001-010_TAGCTTAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGJFJDSXY_104077-001-003_TTAGGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HFC3KDSXY_104042-001-010_TAGCTTAT-GTTCAGAG_L004]

description: miRNA-seq


title: P12-3-6h

description: isolated monocytes, milk fat globule membrane shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a milk fat globule membrane shake

value: isolated monocytes

tag: Sex

tag: age (yrs)


title: P13-1-0h

source_name: isolated human monocytes, before consumption of a vegetable fat shake


title: P13-2-0h


title: P13-2-6h

description: isolated monocytes, anhydrous milk fat shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a anhydrous milk fat shake


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HFC7YDSXY_104042-001-009_GATCAGAT-GTTCAGAG_L004]

description: miRNA-seq

source_name: whole blood


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HFC3KDSXY_104042-001-009_GATCAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: P12-3-0h


title: MIT_C3_1_2

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 0.3 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 0.3 ug/ml IC5 replicate 1 technical replicate 2

tag: dose

tag: dose unit

value: µg/ml

value: 24 hours

tag: rin


title: MIT_C3_2

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_1_4.txt
Gene expression after 24 h exposure to 0.3 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 0.3 ug/ml IC5 replicate 2

tag: exposure time

tag: samples prepared

tag: plate


title: P12-2-0h

tag: subjectid

tag: shakeid

tag: bmi (kg/m2)


title: MIT_C2_3

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_1_4.txt
Gene expression after 24 h exposure to 0.5 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 0.5 ug/ml IC10 replicate 3


title: XPO2 siRNA matched replicate 4, Cytoplasmic fraction, sequencing round 1

molecule: cytoplasmic RNA

tag: cell type


title: XPO2 siRNAneg Cntrl matched replicate 4, Cytoplasmic fraction, sequencing round 1

tag: tissue

value: Cntrl siRNA


title: XPO2 siRNAneg Cntrl matched replicate 4, Nuclear fraction, sequencing round 1

tag: treatment


title: MIT_C3_1_1

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_2_3.txt
Gene expression after 24 h exposure to 0.3 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 0.3 ug/ml IC5 replicate 1 technical replicate 1


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HFC7YDSXY_104042-001-008_ACTTGAAT-GTTCAGAG_L004]

description: miRNA-seq

tag: time


title: P12-1-0h

description: isolated monocytes, vegetable fat shake, baseline (t=0)

tag: shake description

tag: sampling time (h)

value: female


title: XPO2 siRNA matched replicate 3, Nuclear fraction, sequencing round 1

tag: cell line


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HFC3KDSXY_104042-001-008_ACTTGAAT-GTTCAGAG_L004]

description: miRNA-seq


title: MIT_C2_1

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_1_2.txt
Gene expression after 24 h exposure to 0.5 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 0.5 ug/ml IC10 replicate 1

tag: differentiation


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HFC7YDSXY_104042-001-006_GCCAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: P10-3-0h

tag: Sex

tag: age (yrs)


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HFC3KDSXY_104042-001-006_GCCAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: XPO2 siRNA matched replicate 3, Cytoplasmic fraction, sequencing round 1


title: P10-2-6h


title: XPO2 siRNAneg Cntrl matched replicate 3, Cytoplasmic fraction, sequencing round 1


title: MIT_C1_3

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_2_3.txt
Gene expression after 24 h exposure to 1.5 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 1.5 ug/ml IC20 replicate 3

tag: dose

tag: dose unit

tag: rin


title: MIT_C2_2

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_1_2.txt
Gene expression after 24 h exposure to 0.5 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 0.5 ug/ml IC10 replicate 2

tag: exposure time

tag: samples prepared

tag: plate


title: XPO2 siRNA matched replicate 2, Nuclear fraction, sequencing round 2


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HFC3KDSXY_104042-001-005_ACAGTGAT-GTTCAGAG_L004]

description: miRNA-seq


title: MIT_C1_2

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_2_1.txt
Gene expression after 24 h exposure to 1.5 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 1.5 ug/ml IC20 replicate 2


title: MIT_C1_1

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_1_3.txt
Gene expression after 24 h exposure to 1.5 ug/ml of MIT

source_name: THP-1 monocytes differentiated into macrophages, MIT 1.5 ug/ml IC20 replicate 1


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HFC3KDSXY_104042-001-004_TGACCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: P12-2-6h

tag: subjectid

tag: shakeid

tag: bmi (kg/m2)


title: P10-2-0h

tag: cell type


title: P09-3-6h


title: P10-1-0h

value: VEGE


title: P09-3-0h

description: isolated monocytes, milk fat globule membrane shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a milk fat globule membrane shake


title: P10-1-6h

source_name: isolated human monocytes, 6h after consumption of a vegetable fat shake


title: XPO2 siRNAneg Cntrl matched replicate 2, Cytoplasmic fraction, sequencing round 3

source_name: Breast

tag: tissue

tag: treatment


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HFC7YDSXY_104042-001-004_TGACCAAT-GTTCAGAG_L004]

description: miRNA-seq

tag: time


title: XPO2 siRNA matched replicate 2, Cytoplasmic fraction, sequencing round 3

tag: cell line


title: CHT_CTRL_2

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 0 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 0 ug/ml unexposed control replicate 2

tag: differentiation

value: CHT


title: CHT_C3_3

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_2_4.txt
Gene expression after 24 h exposure to 3 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 3 ug/ml IC5 replicate 3


title: XPO2 siRNAneg Cntrl matched replicate 2, Nuclear fraction, sequencing round 2


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HFC3KDSXY_104042-001-007_CAGATCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HFC7YDSXY_104042-001-003_TTAGGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: P09-2-0h

description: isolated monocytes, anhydrous milk fat shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a anhydrous milk fat shake

tag: shake description

tag: sampling time (h)

tag: Sex


title: CHT_C3_2

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_2_2.txt
Gene expression after 24 h exposure to 3 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 3 ug/ml IC5 replicate 2

tag: dose

tag: dose unit


title: P09-2-6h

source_name: isolated human monocytes, 6h after consumption of a anhydrous milk fat shake

tag: age (yrs)


title: XPO2 siRNAneg Cntrl matched replicate 3, Nuclear fraction, sequencing round 1


title: CHT_CTRL_1

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_1_4.txt
Gene expression after 24 h exposure to 0 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 0 ug/ml unexposed control replicate 1

tag: exposure time

tag: samples prepared

tag: rin


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HFC7YDSXY_104042-001-002_CGATGTAT-GTTCAGAG_L004]

description: miRNA-seq

source_name: whole blood


title: P09-1-6h

description: isolated monocytes, vegetable fat shake, 6h after consumption

tag: subjectid

tag: shakeid


title: XPO2 siRNAneg Cntrl matched replicate 1, Nuclear fraction, sequencing round 2

tag: cell type


title: XPO2 siRNA matched replicate 1, Nuclear fraction, sequencing round 2

tag: tissue


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HFC3KDSXY_104042-001-003_TTAGGCAT-GTTCAGAG_L004]

description: miRNA-seq

tag: treatment


title: XPO2 siRNA matched replicate 1, Cytoplasmic fraction, sequencing round 3


title: P08-3-0h

value: CREAM

value: male

tag: bmi (kg/m2)


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HFC3KDSXY_104042-001-001_ATCACGAT-GTTCAGAG_L004]

description: miRNA-seq

value: whole blood

tag: time


title: CHT_C2_3

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_2_1.txt
Gene expression after 24 h exposure to 6.5 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 6.5 ug/ml IC10 replicate 3

tag: cell line

tag: differentiation

tag: plate


title: IGF2BP1 siRNA matched replicate 3, Cytoplasmic fraction, sequencing round 1

value: IGF2BP1 siRNA


title: IGF2BP1 siRNA matched replicate 3, Nuclear fraction, sequencing round 1


title: P08-3-6h

description: isolated monocytes, milk fat globule membrane shake, 6h after consumption

source_name: isolated human monocytes, 6h after consumption of a milk fat globule membrane shake

tag: shake description

tag: sampling time (h)

tag: Sex


title: CHT_C1_3

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_1_4.txt
Gene expression after 24 h exposure to 15 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 15 ug/ml IC20 replicate 3

tag: dose

tag: dose unit


title: XPO2 siRNAneg Cntrl matched replicate 1, Cytoplasmic fraction, sequencing round 2


title: CHT_C2_2_2

description:
raw data file:
US11263921_257236348515_S01_GE2_1200_Jun14_1_1.txt
Gene expression after 24 h exposure to 6.5 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 6.5 ug/ml IC10 replicate 2 technical replicate 2

tag: exposure time

tag: samples prepared


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HFC3KDSXY_104042-001-002_CGATGTAT-GTTCAGAG_L004]

description: miRNA-seq

value: rVSV{delta}G-ZEBOV-GP vaccine, dose 2*10^7


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HFC7YDSXY_104042-001-001_ATCACGAT-GTTCAGAG_L004]

description: miRNA-seq


title: IGF2BP1 siRNAneg Cntrl matched replicate 3, Nuclear fraction, sequencing round 2


title: P08-2-6h

description: isolated monocytes, anhydrous milk fat shake, 6h after consumption

tag: subjectid

value: AMF

tag: age (yrs)


title: CHT_C3_1

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_1_1.txt
Gene expression after 24 h exposure to 3 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 3 ug/ml IC5 replicate 1

tag: rin


title: P08-1-6h

tag: cell type

tag: shakeid


title: P08-2-0h

tag: bmi (kg/m2)


title: CHT_C2_2_1

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_1_1.txt
Gene expression after 24 h exposure to 6.5 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 6.5 ug/ml IC10 replicate 2 technical replicate 1

tag: treatment


title: P08-1-0h

description: isolated monocytes, vegetable fat shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a vegetable fat shake


title: WCE_primary_met_TCCC-OS93-WCE

city: Bryan

first: Irtisha

last: Singh

state: Texas

address: 8447 Riverside Pkwy

department: Cell Biology and Genetics

institute: Texas A&M University Health Science Center

data_processing:
followed the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline, first by mapping the sequenced reads to the human reference genome hg38/GRCh38 using the Bowtie2
filtered low-quality, duplicate, multimapping, unmapped reads along with reads mapping to the mitochondrial genome and the blacklisted regions
performed peak calling using MACS2 with a P value threshold of 10^-5
determined the fraction of reads mapping within 2-kb of an annotated promoter as a quality control measure
The H3K27ac heatmaps and metaplots were generated using R Bioconductor package genomation
Assembly: hg38
Supplementary files format and content: bed files containing histone peak calls
Supplementary files format and content: ChiP-seq histone peaks were called using MACS2 with a threshold of p < 10-5

extract_protocol:
The chromatin was prepared by Diagenode ChIP-seq/ChIP-qPCR Profiling service using the iDeal ChIP- seq kit for Histones. Chromatin was sheared using Bioruptor® Pico sonication device  combined with the Bioruptor® Water cooler for 8 cycles using a 30’’ [ON] 30’’ [OFF] settings
Libraries were prepared using IP-Star® Compact Automated System from input and ChIP’d DNA using MicroPlex Library Preparation Kit v3.

value: osteosarcoma cells from patient-derived xenograft

tag: chip antibody

tag: diseased state


title: WCE_primary_met_TCCC-OS63-WCE


title: WCE_primary_met_TCCC-OS14-WCE


title: CHT_C2_1

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_1_1.txt
Gene expression after 24 h exposure to 6.5 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 6.5 ug/ml IC10 replicate 1

tag: cell line

tag: differentiation

tag: plate


title: CHT_C1_2

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_2_2.txt
Gene expression after 24 h exposure to 15 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 15 ug/ml IC20 replicate 2


title: P07-3-0h

description: isolated monocytes, milk fat globule membrane shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a milk fat globule membrane shake

tag: shake description

tag: sampling time (h)

tag: Sex


title: CHT_C1_1

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_2_2.txt
Gene expression after 24 h exposure to 15 ug/ml of CHT

source_name: THP-1 monocytes differentiated into macrophages, CHT 15 ug/ml IC20 replicate 1

tag: dose

tag: dose unit

tag: exposure time


title: WCE_primary_met_TCCC-OS54-WCE


title: BAY_CTRL_1

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_1_2.txt
Gene expression after 24 h exposure to 0 ug/ml of BAY

source_name: THP-1 monocytes differentiated into macrophages, BAY 0 ug/ml unexposed control replicate 1

value: BAY

tag: samples prepared


title: IGF2BP1 siRNA matched replicate 2, Cytoplasmic fraction, sequencing round 3

source_name: Breast

tag: tissue

value: Breast

value: Epithelial-like, adherent, triple negative breast cancer cell line


title: IGF2BP1 siRNA matched replicate 2, Nuclear fraction, sequencing round 2

tag: cell type


title: BAY_CTRL_2

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_1_2.txt
Gene expression after 24 h exposure to 0 ug/ml of BAY

source_name: THP-1 monocytes differentiated into macrophages, BAY 0 ug/ml unexposed control replicate 2

value: PMA differentiated macrophage

tag: rin


title: WCE_lung_met_TCCC-OS84-WCE


title: P07-2-6h

source_name: isolated human monocytes, 6h after consumption of a anhydrous milk fat shake

value: isolated monocytes

tag: subjectid

tag: shakeid

tag: age (yrs)

tag: bmi (kg/m2)


title: IGF2BP1 siRNAneg Cntrl matched replicate 2, Nuclear fraction, sequencing round 2

tag: cell line

tag: treatment


title: IGF2BP1 siRNAneg Cntrl matched replicate 2, Cytoplasmic fraction, sequencing round 3


title: P07-2-0h

description: isolated monocytes, anhydrous milk fat shake, baseline (t=0)

source_name: isolated human monocytes, before consumption of a anhydrous milk fat shake


title: WCE_localized_TCCC-OS94-WCE

tag: chip antibody

tag: diseased state

value: localized


title: WCE_localized_TCCC-OS75-WCE


title: IGF2BP1 siRNA matched replicate 1, Nuclear fraction, sequencing round 1


title: P07-1-6h

source_name: isolated human monocytes, 6h after consumption of a vegetable fat shake

tag: shake description

tag: sampling time (h)


title: WCE_lung_met_TCCC-OS45-WCE


title: IGF2BP1 siRNA matched replicate 1, Cytoplasmic fraction, sequencing round 1


title: BAY_C3_3

description:
raw data file:
US11263921_257236348514_S01_GE2_1200_Jun14_1_2.txt
Gene expression after 24 h exposure to 0.5 ug/ml of BAY

source_name: THP-1 monocytes differentiated into macrophages, BAY 0.5 ug/ml IC5 replicate 3

tag: differentiation

tag: dose

value: µg/ml

value: 24 hours

tag: plate


title: P06-3-6h

source_name: isolated human monocytes, 6h after consumption of a milk fat globule membrane shake

tag: Sex


title: P07-1-0h

value: VEGE


title: WCE_localized_TCCC-OS57-WCE


title: IGF2BP1 siRNAneg Cntrl matched replicate 1, Nuclear fraction, sequencing round 2

tag: tissue

value: Cntrl siRNA


title: IGF2BP1 siRNAneg Cntrl matched replicate 1, Cytoplasmic fraction, sequencing round 2

tag: cell type


title: WCE_local_control_TCCC-OS74-WCE


title: WCE_local_control_TCCC-OS73-WCE


title: P06-3-0h

value: CREAM


title: BAY_C3_2

description:
raw data file:
US11263921_257236348519_S01_GE2_1200_Jun14_1_2.txt
Gene expression after 24 h exposure to 0.5 ug/ml of BAY

source_name: THP-1 monocytes differentiated into macrophages, BAY 0.5 ug/ml IC5 replicate 2

tag: dose unit

tag: exposure time

tag: samples prepared

tag: rin


title: BAY_C2_3

description:
raw data file:
US11263921_257236348517_S01_GE2_1200_Jun14_2_3.txt
Gene expression after 24 h exposure to 1 ug/ml of BAY

source_name: THP-1 monocytes differentiated into macrophages, BAY 1 ug/ml IC10 replicate 3


title: BAY_C2_2

description:
raw data file:
US11263921_257236348518_S01_GE2_1200_Jun14_1_2.txt
Gene expression after 24 h exposure to 1 ug/ml of BAY

source_name: THP-1 monocytes differentiated into macrophages, BAY 1 ug/ml IC10 replicate 2


title: P06-2-6h

tag: subjectid

tag: shakeid

value: male

tag: age (yrs)

tag: bmi (kg/m2)