title: miRNA, placebo, D4 263_S65_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D3 268_S70_L002

status: Public on Dec 18 2023

type: SRA

city: Göteborg

first: Björn

last: Andersson

address: Sahlgrenska akademin, Core Facilities, Box 413

department: Boinformatics and Data center

country: Sweden

institute: Univeristy of Gothenburg

description:
miRNA, placebo, D3
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: txt file with normalized and log2 transformed counts

molecule: total RNA

organism: Homo sapiens

source_name: serum-derived extracellular vesicles

extract_protocol:
extracellular vesicles (EV)-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: serum-derived extracellular vesicles

tag: treatment

value: placebo

tag: time


title: miRNA, placebo, D4 263_S65_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D1 260_S62_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D3 262_S64_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D0 265_S67_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D7 258_S60_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D2 261_S63_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D2 261_S63_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D3 262_S64_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D7 258_S60_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D0 259_S61_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D0 259_S61_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D3 256_S58_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D4 257_S59_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D2 255_S57_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D2 267_S69_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D4 257_S59_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D3 256_S58_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D1 260_S62_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D2 255_S57_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D0 253_S55_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D0 253_S55_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D7 246_S54_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D4 245_S53_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D7 246_S54_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D4 245_S53_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D2 243_S51_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D1 242_S50_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D0 241_S49_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D3 244_S52_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D1 242_S50_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D0 241_S49_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 240_S48_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: miRNA, rVSVΔG-ZEBOV-GP, D4 239_S47_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 238_S46_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 239_S47_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 238_S46_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 237_S45_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 240_S48_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 236_S44_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 237_S45_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, placebo, D7 234_S42_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 235_S43_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 236_S44_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, placebo, D1 254_S56_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 235_S43_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, placebo, D1 254_S56_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D4 233_S41_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D4 233_S41_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D3 232_S40_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D3 232_S40_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D2 243_S51_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D3 244_S52_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D1 230_S38_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D1 230_S38_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D0 229_S37_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D2 231_S39_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D2 231_S39_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D0 229_S37_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D7 228_S36_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D7 228_S36_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D2 225_S33_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D2 225_S33_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D3 226_S34_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D3 226_S34_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D7 234_S42_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D0 223_S31_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D1 224_S32_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D4 221_S29_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D0 223_S31_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D4 221_S29_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D3 220_S28_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D3 220_S28_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D7 222_S30_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D2 219_S27_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D2 219_S27_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D1 218_S26_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D1 218_S26_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D0 217_S25_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D0 217_S25_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D7 216_S24_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D4 227_S35_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D7 216_S24_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D3 214_S22_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D1 224_S32_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D4 227_S35_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D3 214_S22_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D4 215_S23_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D4 215_S23_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D2 213_S21_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D0 211_S19_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D1 212_S20_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D1 212_S20_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 210_S18_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, placebo, D0 211_S19_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 209_S17_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 210_S18_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 208_S16_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 209_S17_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 207_S15_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 207_S15_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, placebo, D7 222_S30_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 205_S13_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 206_S14_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 206_S14_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 204_S12_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 203_S11_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 203_S11_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 202_S10_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 200_S8_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 205_S13_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 202_S10_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 199_S7_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 204_S12_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 200_S8_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, placebo, D2 213_S21_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 201_S9_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 201_S9_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 208_S16_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 199_S7_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 197_S5_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 196_S4_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 198_S6_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 197_S5_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 198_S6_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 196_S4_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 195_S3_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 194_S2_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 194_S2_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 193_S1_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 195_S3_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 193_S1_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 96_S96_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 95_S95_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 96_S96_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 95_S95_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 94_S94_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 94_S94_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 92_S92_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 93_S93_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 92_S92_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 90_S90_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 9_S9_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 91_S91_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 89_S89_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 90_S90_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 9_S9_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 91_S91_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 88_S88_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 88_S88_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 87_S87_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 86_S86_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 87_S87_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 85_S85_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 85_S85_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 86_S86_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 84_S84_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 84_S84_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 83_S83_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 82_S82_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 81_S81_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 82_S82_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 83_S83_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 93_S93_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 80_S80_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 79_S79_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 8_S8_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 8_S8_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 89_S89_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 78_S78_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 78_S78_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 79_S79_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 77_S77_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 76_S76_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 75_S75_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 77_S77_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 76_S76_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 74_S74_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 74_S74_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 72_S72_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 72_S72_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 73_S73_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 81_S81_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 71_S71_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 80_S80_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 69_S69_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 7_S7_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 70_S70_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 7_S7_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 75_S75_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 73_S73_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 69_S69_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 71_S71_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 68_S68_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 70_S70_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 67_S67_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 68_S68_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 67_S67_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 66_S66_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 66_S66_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 65_S65_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 64_S64_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 63_S63_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 64_S64_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 63_S63_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 62_S62_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 60_S60_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 62_S62_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 6_S6_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 60_S60_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 6_S6_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 61_S61_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 57_S57_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 65_S65_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 56_S56_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 59_S59_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 57_S57_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 56_S56_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 59_S59_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 55_S55_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 55_S55_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, placebo, D7 54_S54_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D4 53_S53_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D4 53_S53_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D7 54_S54_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D3 52_S52_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 58_S58_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 58_S58_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, placebo, D3 52_S52_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D2 51_S51_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D1 50_S50_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 5_S5_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 5_S5_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, placebo, D2 51_S51_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 48_S48_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, placebo, D0 49_S49_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 48_S48_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, placebo, D1 50_S50_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 61_S61_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 45_S45_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 47_S47_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 47_S47_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 46_S46_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 44_S44_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 45_S45_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 44_S44_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 42_S42_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 43_S43_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: 2_siSTAU1_0hr

city: Bethesda

first: Ashish

last: Lal

state: Maryland

address: 37 Convent Drive, Room 6134

department: NCI

country: USA

institute: NIH

data_processing:
RTA 3.10.30 software used for basecalling.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt
Reads were aligned with the reference genome (hg38) and the annotated transcripts using STAR 2.7
Gene expression was quantified using RSEM 1.3.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files including output from RSEM for genes (expected counts, TPM and FPKM)

molecule: polyA RNA

extract_protocol:
Samples had their RNA extracted with RNeasy Plus Mini Kit.
RNA libraries were prepared using Illumina® Stranded mRNA Prep

tag: cell line

tag: cell type

value: Colorectal cancer cell line

value: 72 hours + 72 hours siSTAU1


title: miRNA, rVSVΔG-ZEBOV-GP, D0 43_S43_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: 1_siSTAU1_0hr


title: 2_siCTRL_0hr

value: 72 hours + 72 hours siCTRL


title: miRNA, rVSVΔG-ZEBOV-GP, D4 41_S41_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, placebo, D0 49_S49_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 46_S46_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 40_S40_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: 1_siCTRL_0hr


title: Ovariectomized + Angiotensin II (Sample 69)

city: Quebec

first: Jacques

last: Couet

state: QC

address: 2725 Chemin Sainte-Foy

department: Medicine

country: Canada

institute: Université Laval

data_processing:
Illumina BaseSpace Sequence Hub
RNA-Seq Alignment application (Illumina) was used to perform: Read mapping using the STAR aligner, Quantification of transcripts using salmon and QC metrics. Mus musculus UCSC mm10 (RefSeq gene annotation).
Assembly: mm10
Supplementary files format and content: Excel file reports normalized counts for each gene studied for each sample.

organism: Mus musculus

source_name: Left atrium

extract_protocol:
RNA was isolated from the entire left atrial tissue by the TRIzol reagent according to the manufacturer's instructions and dissolved in DEPC-treated H2O. The quality and concentration of the purified total RNA were confirmed by spectroscopy.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Library Prep Kit  following manufacturer's protocols.

value: Heart

value: Left atrium

tag: Sex

value: Female

tag: age

value: 24 months

tag: gonadectomy

value: 12 months

value: AngiotensinII


title: Ovariectomized + Angiotensin II (Sample 70)


title: miRNA, rVSVΔG-ZEBOV-GP, D3 4_S4_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 39_S39_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 40_S40_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 39_S39_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: Ovariectomized (Sample 66)


title: miRNA, rVSVΔG-ZEBOV-GP, D3 4_S4_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 38_S38_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: Ovariectomized (Sample 65)


title: miRNA, rVSVΔG-ZEBOV-GP, D4 41_S41_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 38_S38_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: Ovariectomized + Angiotensin II (Sample 68)


title: miRNA, rVSVΔG-ZEBOV-GP, D0 37_S37_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 42_S42_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: J774_cells_UAL3

city: Medellin

first: alejandro

last: mejia garcia

state: antioquia

country: Colombia

institute: Universidad de Antioquia

data_processing:
quality control with FASTQC
Trimming of adapters and bad quality nucleotides with trimmomatic
Trimmed sequences were aligned to the reference human genome (hg19) or mm38 mouse genome using STAR
Raw counts were obtained using FeatureCounts
Normalization and gene expression analysis was performed using Deseq2 R package
Assembly: GRCh38 for human and GRCm39 for mouse
Supplementary files format and content: space-delimited text file with raw counts per sample

growth_protocol: J774A.1 (TIB-67™) mouse monocyte; macrophage cells and U-937 were cultured and maintained at 37°C and 5% CO2. J774A.1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS),1% penicillin/streptomycin (P/S) (Sigma- Aldrich, St. Louis, MO, USA), and 5.5 mM glucose (Growth medium – GM1). The U-937 cells were cultured in RPMI culture medium with 10% FBS, 1% P/S, and 11 mM glucose (Growth medium – GM2). At 80% confluence.

extract_protocol:
total RNA was extracted from cells with the RNeasy kit (QIAGEN, Valencia, CA, USA).
RNA quality control, library construction, and RNA sequencing using the DNBseq platform were performed by BGI Americas Corporation (Cambridge, MA, USA).

treatment_protocol:
U937 monocyte cells were differentiated into macrophages by adding 100 nM phorbolmyristate acetate (PMA) to the growth medium for 72 h.J774A.1 and U937 cells were incubated in GM1 medium containing 1 mg/ml LPS and 20 ng/ml IFNγ for 24h.
In the last 6h of activation, different treatments were added:  OBE100 100 µg/ml, M1 78 µg/ml (UA+OA+UAL mix), UA 47.7 µg/ml, OA 14 µg/ml, and UAL 16.3 µg/ml.

value: Monocytes

tag: genotype

value: WT

value: UAL


title: miRNA, placebo, D7 36_S36_L001

description:
miRNA, placebo, D7
miRNA-seq


title: Ovariectomized (Sample 64)


title: miRNA, placebo, D7 36_S36_L002

description:
miRNA, placebo, D7
miRNA-seq


title: J774_cells_OA3

value: OA


title: AngiotensinII (Sample 62)


title: miRNA, rVSVΔG-ZEBOV-GP, D0 37_S37_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: AngiotensinII (Sample 61)


title: Ovariectomized + Angiotensin II (Sample 67)


title: miRNA, placebo, D3 34_S34_L002

description:
miRNA, placebo, D3
miRNA-seq


title: AngiotensinII (Sample 60)


title: miRNA, placebo, D4 35_S35_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D4 35_S35_L001

description:
miRNA, placebo, D4
miRNA-seq


title: Ovariectomized (Sample 63)


title: J774_cells_UA3

value: UA


title: J774_cells_M13


title: miRNA, placebo, D3 34_S34_L001

description:
miRNA, placebo, D3
miRNA-seq

value: serum-derived extracellular vesicles


title: J774_cells_OBE3

value: OBE


title: miRNA, placebo, D1 32_S32_L002

description:
miRNA, placebo, D1
miRNA-seq

value: placebo


title: miRNA, placebo, D2 33_S33_L001

description:
miRNA, placebo, D2
miRNA-seq


title: Control (Sample 58)


title: J774_cells_CONTROL ACTIVADO3

value: Macrophage differentiation


title: miRNA, placebo, D1 32_S32_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D0 31_S31_L002

description:
miRNA, placebo, D0
miRNA-seq


title: Control (Sample 56)


title: Control (Sample 57)


title: miRNA, placebo, D0 31_S31_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 30_S30_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: J774_cells_UAL2


title: miRNA, rVSVΔG-ZEBOV-GP, D2 3_S3_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: Control (Sample 55)


title: miRNA, rVSVΔG-ZEBOV-GP, D2 3_S3_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 29_S29_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: J774_cells_UA2


title: J774_cells_OA2


title: Female, Gx, AngII (Sample 54)

source_name: Left ventricle

extract_protocol:
RNA was isolated from the free wall LV by the TRIzol reagent according to the manufacturer's instructions and dissolved in DEPC-treated H2O. The quality and concentration of the purified total RNA were confirmed by spectroscopy.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Library Prep Kit  following manufacturer's protocols.

value: Left ventricle

value: AngII


title: J774_cells_M12


title: miRNA, rVSVΔG-ZEBOV-GP, D4 29_S29_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 28_S28_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: AngiotensinII (Sample 59)

value: Heart

value: Left atrium


title: miRNA, rVSVΔG-ZEBOV-GP, D3 28_S28_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, placebo, D2 33_S33_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 27_S27_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: Female, Gx, AngII (Sample 47)

value: Female

value: 24 months


title: J774_cells_OBE2


title: miRNA, rVSVΔG-ZEBOV-GP, D2 27_S27_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: Female, Gx, AngII (Sample 46)

value: 12 months


title: J774_cells_CONTROL3

value: Monocytes

value: control


title: Female, Control, AngII (Sample 52)


title: J774_cells_CONTROL ACTIVADO2

value: WT


title: miRNA, rVSVΔG-ZEBOV-GP, D7 30_S30_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 26_S26_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 26_S26_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 25_S25_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: Female, Control, AngII (Sample 42)


title: J774_cells_CONTROL2


title: Female, Control, AngII (Sample 41)


title: miRNA, placebo, D7 24_S24_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D4 23_S23_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 25_S25_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, placebo, D7 24_S24_L001

description:
miRNA, placebo, D7
miRNA-seq


title: Female, Control, AngII (Sample 40)


title: J774_cells_M11


title: J774_cells_UA1


title: miRNA, placebo, D4 23_S23_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D3 22_S22_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D3 22_S22_L002

description:
miRNA, placebo, D3
miRNA-seq


title: Female, Gx (Sample 53)


title: miRNA, placebo, D2 21_S21_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D2 21_S21_L002

description:
miRNA, placebo, D2
miRNA-seq


title: J774_cells_OBE1


title: miRNA, placebo, D1 20_S20_L002

description:
miRNA, placebo, D1
miRNA-seq


title: Female, Gx (Sample 45)


title: J774_cells_CONTROL ACTIVADO1


title: Female, Gx (Sample 44)


title: miRNA, rVSVΔG-ZEBOV-GP, D1 2_S2_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 2_S2_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: Female, Gx (Sample 43)


title: J774_cells_UAL1

value: UAL


title: Female, Control (Sample 51)


title: Esophagus, EoE33, rep4

city: Scottsdale

first: Alfred

last: Doyle

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic

description:
raw gene hit counts
Column I

data_processing:
Sequencing reads were trimmed using Trimmomatic v.0.36
Trimmed reads were mapped to the Mus musculus GRCm38 reference genome using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated using featureCounts in Subread package v.1.5.2
Raw gene hit counts for all samples are presented in raw_counts.csv
Assembly: GRCm38
Supplementary files format and content: comma seperated value file containing raw counts for each sample

source_name: esophagus

growth_protocol: To assess transcriptional changes associated with esophageal overexpression of IL-33, bulk RNA sequencing was performed on whole esophageal tissue biopsies from eight week old male transgenic EoE33 mice and wild-type C57BL/6J littermates.

extract_protocol:
Whole esophagi were collected in RNeasy, immediately flash frozen in liquid nitrogen, and shipped on dry ice to GENEWIZ for bulk RNA extraction. Total RNA was extracted from fresh frozen cell pellets using the Qiagen RNeasy Plus Universal mini kit.
mRNA was enriched with polyA selection and sequenced using the Illumina HiSeq platform with a 2x150 paired end configuration.

value: esophagus

tag: strain

value: male

value: 8 weeks


title: miRNA, rVSVΔG-ZEBOV-GP, D7 18_S18_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq

value: serum-derived extracellular vesicles


title: miRNA, rVSVΔG-ZEBOV-GP, D7 18_S18_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 17_S17_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: Esophagus, EoE33, rep1

description:
raw gene hit counts
Column F


title: Female, Gx, AngII (Sample 48)


title: Female, Control (Sample 39)


title: Female, Control (Sample 38)


title: miRNA, rVSVΔG-ZEBOV-GP, D3 16_S16_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: Esophagus, EoE33, rep2

description:
raw gene hit counts
Column G


title: miRNA, rVSVΔG-ZEBOV-GP, D4 17_S17_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: Female, Control (Sample 37)


title: miRNA, rVSVΔG-ZEBOV-GP, D3 16_S16_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: Esophagus, wild type, rep4

description:
raw gene hit counts
Column E

value: wild type


title: miRNA, rVSVΔG-ZEBOV-GP, D1 14_S14_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: miRNA, rVSVΔG-ZEBOV-GP, D2 15_S15_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: Male, Gx (Sample 50)

value: Left ventricle

value: Male


title: miRNA, placebo, D1 20_S20_L001

description:
miRNA, placebo, D1
miRNA-seq

value: placebo


title: Esophagus, wild type, rep3

description:
raw gene hit counts
Column D


title: miRNA, rVSVΔG-ZEBOV-GP, D1 14_S14_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 15_S15_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: J774_cells_CONTROL1


title: miRNA, placebo, D0 19_S19_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D0 19_S19_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 13_S13_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: Male, Gx (Sample 36)

value: Heart


title: miRNA, rVSVΔG-ZEBOV-GP, D0 13_S13_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: Male, Gx (Sample 35)


title: Esophagus, EoE33, rep3

description:
raw gene hit counts
Column H


title: Esophagus, wild type, rep1

description:
raw gene hit counts
Column B


title: Male, Gx (Sample 34)


title: Male, Control (Sample 49)


title: Male, Control (Sample 33)


title: Round Spermatids RNAseq rep1

city: Boston

first: Emily

last: Kaye

state: MA

address: 45 Shattuck Street

institute: Harvard Medical School

description:
mm10_rs_rnaseq_n3spike_F.bw
mm10_rs_rnaseq_n3spike_R.bw

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 100 nt.
Reads were first mapped to the ERCC genome using STAR 2.7.3a. Reads not mapping to spike were used for alignment to mm10 using parameters --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 42949672960 --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --outFilterMismatchNmax 4 --alignSJoverhangMin 8 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outWigType bedGraph --outWigNorm None --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0. Duplicates were also removed using STAR.
Stranded coverage bedGraph files were generated from deduplicated BAM files using STAR.  For each cell type, bedGraphs were normalized using normalize_bedGraph based on spike reads/mm10 read factors, correcting Round Spermatid factors by dividing by 2.
BedGraph files were converted to the bigWig format, and merged bedGraphs for each experimental condition were generated using bigWigMerge (UCSC tools).
Assembly: mm10
Supplementary files format and content: bigWigs represent 3 merged, normalized replicates for each cell type

source_name: testis

extract_protocol:
ERCC RNA spike-ins were added to 1M cells resuspended in Trizol, RNA was then extracted and purified.
Libraries were generated with the llumina TruSeq Stranded Total RNA kit using standard protocols.

value: testis

value: Round Spermatids


title: Round Spermatids RNAseq rep3


title: Round Spermatids RNAseq rep2


title: Male, Control (Sample 32)

value: 24 months


title: Spermatocytes RNAseq rep3

description:
mm10_sc_rnaseq_n3spike_F.bw
mm10_sc_rnaseq_n3spike_R.bw

value: Spermatocytes


title: miRNA, rVSVΔG-ZEBOV-GP, D3 10_S10_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 11_S11_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 1_S1_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 1_S1_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 12_S12_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 11_S11_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: Male, Control (Sample 31)


title: miRNA, placebo, D1 98_S2_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D2 99_S3_L001

description:
miRNA, placebo, D2
miRNA-seq


title: Spermatocytes RNAseq rep2


title: miRNA, placebo, D1 98_S2_L001

description:
miRNA, placebo, D1
miRNA-seq


title: Esophagus, wild type, rep2

description:
raw gene hit counts
Column C


title: miRNA, placebo, D7 192_S96_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D0 97_S1_L001

description:
miRNA, placebo, D0
miRNA-seq


title: Spermatocytes RNAseq rep1


title: miRNA, placebo, D0 97_S1_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 12_S12_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: Spermatogonia RNAseq rep3

description:
mm10_sg_rnaseq_n3spike_F.bw
mm10_sg_rnaseq_n3spike_R.bw

value: Spermatogonia


title: Female, MHS + RR, Day 56 (FAH562)

data_processing:
Illumina BaseSpace Sequence Hub
RNA-Seq Alignment application (Illumina) was used to perform: Read mapping using the STAR aligner, Quantification of transcripts using salmon and QC metrics. Mus musculus UCSC mm9 (RefSeq gene annotation)
Supplementary files format and content: Normalized gene expression (TPM).xlsx

source_name: Heart

tag: tissue region

value: Female

value: 56 days

value: AngII + HFD

tag: group

value: MHS + RR


title: Female, MHS + RR, Day 56 (FAH563)


title: miRNA, placebo, D7 192_S96_L001

description:
miRNA, placebo, D7
miRNA-seq


title: Female, MHS + RR, Day 56 (FAH561)


title: miRNA, placebo, D2 99_S3_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 10_S10_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, placebo, D4 191_S95_L002

description:
miRNA, placebo, D4
miRNA-seq


title: Female, Control, Day 56 (FC563)

value: 28 days

value: Control


title: Spermatogonia RNAseq rep2

value: wild type


title: miRNA, placebo, D4 191_S95_L001

description:
miRNA, placebo, D4
miRNA-seq

value: serum-derived extracellular vesicles


title: Spermatogonia RNAseq rep1


title: Female, Control, Day 56 (FC561)

value: Left ventricle


title: Female, MHS, Day 28 (FAH283)

value: MHS


title: miRNA, placebo, D2 189_S93_L001

description:
miRNA, placebo, D2
miRNA-seq

value: placebo


title: miRNA, placebo, D1 188_S92_L001

description:
miRNA, placebo, D1
miRNA-seq


title: WT_CutTag_Diff_H3K27me3_rep1

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

institute: UC Davis

data_processing:
For CUT&RUN/Tag data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html).
Raw paired-end reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) .
Trimmed reads were aligned mouse (GRCm38/mm10) genome using Bowtie2 (version 2.4.2) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. E. coli DNA carried along with bacterially-produced pAG-MNase protein brings along a fixed amount of E. coli DNA and can be used as spike-in DNA for CUT&RUN.  D. melanogaster DNA delivered by Drosophila S2 cells was used as spike-in DNA for CUT&Tag. For mapping E.coli or D. melanogaster spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates were removed from low-cell-number data using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/ ).
Biological replicates were pooled for the visualization and other analyses after validation of the reproducibility (Pearson correlation coefficient > 0.85). Spike-in normalization was implemented using the exogenous scaling factor computed from the E.coli or dm6 mapping files (the formula used for calculation of scale factors = 100,000 or 1,000,000 / spike-in reads).
For visualization using the Integrative Genomics Viewer55 (version 2.5.3), spike-in normalized genome coverage tracks were generated using the genomecov function of bedtools (version 2.29.2) with the ‘-bg -scale $scale_factor’ parameter.
SEACR (https://seacr.fredhutch.org/ ) was used for peak calling and HOMER (version 4.11) was used for peak annotation.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: nuclear RNA

extract_protocol:
CUT&Tag libraries were prepared as previously described (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ). CUT&RUN libraries of PRC1ctrl, PRC1cKO, and WT spermatogonia were conducted as previously described (a step-by-step protocol https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-14egnr4ql5dy/v3 ).
CUT&Tag libraries were prepared using NEBNext HiFi 2x PCR Master mix (NEB, M0541L) according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ). CUT&RUN libraries were constructed using NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).

value: WT

value: primary cells

value: Differentiating Spermatogonia

tag: chip antibody

tag: cell compartment

value: nuclei


title: WT_CutTag_Diff_H3K27me3_rep2

value: testis


title: Female, Control, Day 56 (FC562)

value: Heart


title: miRNA, placebo, D0 187_S91_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D0 187_S91_L001

description:
miRNA, placebo, D0
miRNA-seq


title: Female, MHS, Day 28 (FAH282)

value: Female


title: miRNA, rVSVΔG-ZEBOV-GP, D7 186_S90_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: WT_CutTag_Undiff_H3K27me3_rep2

value: Undifferentiated Spermatogonia


title: WT_CutTag_Undiff_H3K27me3_rep1


title: miRNA, rVSVΔG-ZEBOV-GP, D7 186_S90_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: Female, MHS, Day 28 (FAH281)

value: 56 days


title: miRNA, placebo, D3 190_S94_L002

description:
miRNA, placebo, D3
miRNA-seq


title: WT_CutTag_Diff_H2AK119ub_rep2


title: miRNA, placebo, D2 189_S93_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 184_S88_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 185_S89_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: Female, Control, Day 28 (FC282)

value: 28 days


title: WT_CutTag_Undiff_H2AK119ub_rep2


title: Female, Control, Day 28 (FC283)

value: Control


title: miRNA, rVSVΔG-ZEBOV-GP, D4 185_S89_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: WT_CutTag_Diff_H2AK119ub_rep1


title: 10x3V31_TRPI_tumor

city: Houston

first: Dawei

last: Zou

state: TX

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw Illumina sequencing reads were aligned to the reference mouse genome mm10 (Ensembl 93) using Cell Ranger v7.0.0 with default parameters, resulting in the generation of Fastq datasets.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: from tumor

extract_protocol:
Single-cell suspensions from tumors and draining lymph nodes were staining with fluorochrome-conjugated antibodies and were then sorted by a cell sorter
Single-Cell Gene Expression Libraries were created following the protocol outlined in the Chromium Next GEM Single Cell 3' Reagent Kits v3 (10x Genomics). In summary, a single-cell suspension, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were introduced to a Chromium controller (10x Genomics) to produce single-cell GEMs (Gel Beads-In-Emulsions). In these GEMs, full-length cDNA was synthesized and barcoded for each individual cell. Subsequently, the GEMs were broken, and cDNA from each single cell was combined. After cleanup using Dynabeads MyOne Silane Beads, the cDNA underwent PCR amplification. The amplified product was then fragmented to an optimal size before undergoing end-repair, A-tailing, and adaptor ligation. The final library was generated through amplification.

value: from tumor

value: CD45+ cells

value: Trp1 CD4+ T cells


title: miRNA, rVSVΔG-ZEBOV-GP, D3 184_S88_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq

value: serum-derived extracellular vesicles


title: WT_CutTag_Undiff_H2AK119ub_rep1


title: Female, Control, Day 28 (FC281)

value: Left ventricle


title: miRNA, rVSVΔG-ZEBOV-GP, D2 183_S87_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 182_S86_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: 10x3V31_NT_tumor

description: 10x Genomics

value: PBS


title: miRNA, rVSVΔG-ZEBOV-GP, D2 183_S87_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: 10x3V31_TRPI_LN

description: 10x Genomics

source_name: from draining lymph node

value: from draining lymph node


title: U937_cells_UAL3

value: Monocytes

value: WT

value: UAL


title: Male, MHS + RR, Day 56 (MAH563)

value: Heart

value: Male

value: AngII + HFD

value: MHS + RR


title: Male, MHS + RR, Day 56 (MAH562)

value: 56 days


title: Myeloid cells, TMAO_3, 24h

city: Wuhan

first: Junhao

last: Wan

state: Hubei

address: Jiefang Road

country: China

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
The data generated from Illumina/BGI platform were used for bioinformatics analysis. All of the analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology. The major software and parameters are as follows.
Assembly: GRCm39
Supplementary files format and content: table-delimited text files include raw counts for each sample

source_name: primary cells

extract_protocol:
Total RNA was extracted using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, sequencing was performed with an Illumina Novaseq 6000 /MGISEQ-T7 instrument.

value: TMAO

value: myeloid cells

value: primary cells


title: Myeloid cells, TMAO_2, 24h


title: U937_cells_OA3

value: OA


title: miRNA, rVSVΔG-ZEBOV-GP, D1 182_S86_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: Male, MHS + RR, Day 56 (MAH561)


title: U937_cells_UA3

value: UA


title: Myeloid cells, TMAO_1, 24h


title: Male, Control, Day 56 (MC563)

value: Left ventricle

value: 28 days

value: Control


title: miRNA, placebo, D3 190_S94_L001

description:
miRNA, placebo, D3
miRNA-seq

value: serum-derived extracellular vesicles

value: placebo


title: miRNA, rVSVΔG-ZEBOV-GP, D0 181_S85_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: U937_cells_M13

value: Monocytes

value: WT


title: U937_cells_OBE3

value: OBE


title: miRNA, rVSVΔG-ZEBOV-GP, D0 181_S85_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: Myeloid cells, Control_3, 24h


title: Myeloid cells, Control_2, 24h


title: Male, Control, Day 56 (MC561)

value: Heart

value: Male

value: AngII + HFD


title: U937_cells_CA3

value: Macrophage differentiation


title: miRNA, rVSVΔG-ZEBOV-GP, D7 180_S84_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: miRNA, placebo, D1 188_S92_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 180_S84_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: Male, MHS, Day 28 (MAH283)

value: 56 days

value: MHS


title: Male, MHS, Day 28 (MAH282)


title: miRNA, rVSVΔG-ZEBOV-GP, D4 179_S83_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: Myeloid cells, Control_1, 24h

value: myeloid cells

value: primary cells


title: U937_cells_CONTROL3

value: control


title: U937_cells_OA2

value: OA


title: miRNA, rVSVΔG-ZEBOV-GP, D4 179_S83_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: U937_cells_UA2

value: UA


title: miRNA, rVSVΔG-ZEBOV-GP, D3 178_S82_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq

value: serum-derived extracellular vesicles


title: Male, MHS, Day 28 (MAH281)

value: Left ventricle


title: Male, Control, Day 28 (MC283)

value: 28 days

value: Control


title: Male, Control, Day 28 (MC282)


title: Tumor, sgTrp53+MYC,04

city: Montpellier

first: Damien

middle: J

last: Grégoire

address: 1919, route de Mende

country: France

institute: CNRS

data_processing:
Base calling is performed by the software RTA provided by Illumina. This step allows for the correction of intensities and the conversion of intensity into nucleotide bases.
Demultiplexing and the generation of fastq files are then carried out using the Illumina software bcl2fastq (v2.20.0.422).
Sequences were aligned using HISAT2 using the mm39 genome.
Assembly: mm39
Supplementary files format and content: Tab delimited text file with raw counts for each samples.

source_name: Tumoral liver

extract_protocol:
Total RNA was harvested using the Qiagen Rneasy kit.
Library construction was made using the Illumina TruSeq Stranded mRNA kit following manufacturer's instruction

value: Tumoral liver


title: Tumor, sgTrp53+MYC,03


title: Tumor, sgTrp53+MYC,02


title: U937_cells_M12

value: Monocytes

value: WT


title: Male, Control, Day 56 (MC562)

value: Heart

value: Male

value: AngII + HFD


title: miRNA, rVSVΔG-ZEBOV-GP, D3 178_S82_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: Tumor, sgTrp53+MYC,01


title: miRNA, rVSVΔG-ZEBOV-GP, D2 177_S81_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: U937_cells_OBE2

value: OBE


title: Male, Control, Day 28 (MC281)


title: Tumor, sgTrp53+MYC,05


title: miRNA, rVSVΔG-ZEBOV-GP, D2 177_S81_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: U937_cells_CA2

value: Macrophage differentiation


title: Human primary keratinocytes, treated 1µM S1P 24 h, rep4

city: Toulouse

first: Nathalie

last: ANDRIEU-ABADIE

address: 2 Avenue Hubert Curien

institute: INSERM

data_processing:
Illumina Truseq adapter, polyA and polyT sequences were trimmed with cutadapt v2.3
Trimmed sequences were aligned to human genome version 38 (hg38) using bowtie2 aligner with parameters according to ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline)
Gene expression levels were quantified using RSEM v1.3.1
Ensembl gene annotation version 93 was used in the alignment and quantification steps
RNA-seq sequence, alignment and quantification quality was assessed using FastQC v0.11.7 (https://www. bioinformatics.babraham.ac.uk/projects/fastqc/).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Expected counts values for each Sample

source_name: epidermis

growth_protocol: HPK were grown in Dermalife K medium (Cellsystems) supplemented with 100 UI/ml penicillin and 100 µg/ml streptomycin, with medium changes thrice a week. Experiments were performed on low passage (≤ 3) keratinocytes.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Truseq Stranded mRNA Kit and IDT for Illumina Truseq RNA UD Indexes from Illumina, following manufacturer's protocols.

treatment_protocol: HPK were treated, or not, with S1P (1 μM) for 24 h

value: epidermis

value: cultured primary cells

value: keratinocyte

value: S1P 1uM


title: U937_cells_UAL2

value: UAL


title: Human primary keratinocytes, treated 1µM S1P 24 h, rep5


title: miRNA, rVSVΔG-ZEBOV-GP, D1 176_S80_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq

value: serum-derived extracellular vesicles

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: U937_cells_UAL1


title: WT_Li_4

city: Ulm

first: Valentin

last: Ioannidis

address: Albert-Einstein-Allee 11

department: Institut for Anatomy and Cell Biology

country: Germany

institute: Ulm University

data_processing:
Raw data (raw reads) of fastq format were cleaned by removing reads containing adapter, ploy-N and low-quality reads. Reference genome index was built and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. Read counts were calculated with featureCounts v1.5.0-p3.
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: excel files containing matrix of read counts, one file for each batch

source_name: hippocampus

extract_protocol:
Qiagen RNeasy Mini kit was used to isolate total RNA according to the manufacturer’s description including all purification steps. RNA was eluted in 40 μl RNAse-free water.
Library construction was performed by Novogen UK. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations  Libraries were quality checked with Qubit and pooled for sequencing on Illumina platform.

value: hippocampus

value: primary hippocampal cells DIV27

value: Li

tag: batch


title: WT_Veh_4

value: primary hippocampal cells DIV26

value: Veh


title: KO_Veh_4

value: primary hippocampal cells DIV28

value: KO


title: Human primary keratinocytes, treated 1µM S1P 24 h, rep3


title: Human primary keratinocytes, treated 1µM S1P 24 h, rep2


title: miRNA, rVSVΔG-ZEBOV-GP, D0 175_S79_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: U937_cells_OA1

value: Monocytes

value: WT

value: OA


title: KO_Li_3

value: primary hippocampal cells DIV25


title: Human primary keratinocytes, not treated, 24 h, rep5

value: epidermis

value: cultured primary cells

value: not treated


title: Human primary keratinocytes, treated 1µM S1P 24 h, rep1

value: keratinocyte

value: S1P 1uM


title: KO_Veh_3

value: primary hippocampal cells DIV24


title: miRNA, rVSVΔG-ZEBOV-GP, D0 175_S79_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq

value: serum-derived extracellular vesicles

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: miRNA, rVSVΔG-ZEBOV-GP, D7 174_S78_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: U937_cells_M11


title: Human primary keratinocytes, not treated, 24 h, rep4


title: WT_Li_3

value: hippocampus

value: primary hippocampal cells DIV23

value: Li


title: miRNA, rVSVΔG-ZEBOV-GP, D7 174_S78_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: KO_Li_4

value: primary hippocampal cells DIV29


title: WT_Veh_3

value: primary hippocampal cells DIV22

value: Veh


title: U937_cells_CONTROL2

value: Monocytes

value: WT

value: control


title: KO_Li_2

value: primary hippocampal cells DIV21

value: KO


title: Human primary keratinocytes, not treated, 24 h, rep2

value: epidermis

value: cultured primary cells

value: not treated


title: miRNA, rVSVΔG-ZEBOV-GP, D1 176_S80_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D4 173_S77_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: U937_cells_CA1

value: Macrophage differentiation


title: Human primary keratinocytes, not treated, 24 h, rep3

value: keratinocyte


title: miRNA, rVSVΔG-ZEBOV-GP, D4 173_S77_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq

value: serum-derived extracellular vesicles

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: U937_cells_CONTROL1


title: Human primary keratinocytes, not treated, 24 h, rep1


title: miRNA, rVSVΔG-ZEBOV-GP, D3 172_S76_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: KO_Veh_2

value: hippocampus

value: primary hippocampal cells DIV20


title: U937_cells_UA1

value: UA


title: RPE_37_ctrl_rep2

city: Lausanne

first: Gioele

last: La Manno

state: Vaud

address: Station 19

department: BMI

country: Switzerland

institute: EPFL

data_processing:
Raw fastq files were processed with CellRanger using the default human reference transcriptome to obtain count matrices. To obtain unspliced and spliced count matrices, we used velocyto version 0.17.17.
Assembly: GRCh38
Supplementary files format and content: Processed data files include the CellRanger output filtered_bc_matrix folders as well as a loom file corresponding to the output from running velocyto version 0.17.17 with default parameters.

molecule: cytoplasmic RNA

extract_protocol:
FUCCI-RPE-1 cells (see Fig. 4), a gift from Battich et al64, were cultured at 37°C and 5% CO2 in DMEM/F12 medium (Gibco 11320033) supplemented with 1% NEAA (Gibco 11140-035), 1% Penicillin/Streptomycin (Sigma Aldrich G6784) and 10% FBS (Gibco 10437-028). Additional RPE-1 cells (see Fig. 5) were obtained from ATCC and cultured at 37°C, 20% O2, and 5% CO2 in DMEM/F12 medium (Gibco 21331-020) supplemented with 1% MEM NEAA (Sartorius 01-340-1B), 0.5% sodium pyruvate 1% penicillin/streptomycin/glutamine, and 10% FBS. Media was replaced daily and cells were passaged twice a week. RPE-1 cells were maintained in culture for at least two passages and confirmed to be free of mycoplasma.
For the preparation of scRNA-seq libraries, an experimental setup was designed to mimic the conditions used for live-cell imaging. FUCCI-RPE-1 cells were seeded (7000 cells/cm²) in duplicate 2 days before collection.  On collection day, cells were detached with trypsin, washed with PBS, counted and diluted to a cell concentration of 1000 cells/uL. Barcoded cDNA libraries were generated from single cell suspensions using the 10x Genomics Chromium v3.1 dual-index system. The procedure was done in accordance with the manufacturer's instructions, with a goal of 4,000 cells per library. Samples were individually indexed and evenly pooled together. After quality control, libraries were sequenced on an Illumina HiSeq4000 platform, with a depth of approximately 300 million reads per sample, by the EPFL Gene Expression Core Facility (GECF). Similarly, RPE-1 cells were detached using Trypsin–EDTA solution A 0.25% (Biological Industries; 030501B) for 5 min at 37°C. Trypsin was neutralized with medium including 10% FBS and cells were centrifuged at 250 rcf for 5 min, followed by washing and resuspension in PBS with 0.04% BSA. The cell suspension was filtered with a 40-μm cell strainer to remove cell clumps. A cell viability percentage higher than 90% was determined by trypan blue staining. Cells were diluted to a final concentration of 700 cells per μl. scRNA-seq libraries were generated using the 10x Genomics Chromium v3.1 dual-index system. The procedure was done in accordance with the manufacturer's instructions, with a goal of 3,000 cells per library. Samples were then indexed and sequenced on an Illumina NovaSeq 6000 platform by the EPFL Gene Expression Core Facility (GECF).


title: WT_Li_2

value: primary hippocampal cells DIV19

value: Li


title: RPE_37_ctrl_rep1


title: KO_Li_1

value: primary hippocampal cells DIV17


title: miRNA, rVSVΔG-ZEBOV-GP, D3 172_S76_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: U937_cells_OBE1

value: Monocytes

value: WT

value: OBE


title: WT_Veh_2

value: primary hippocampal cells DIV18

value: Veh


title: miRNA, rVSVΔG-ZEBOV-GP, D2 171_S75_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 171_S75_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: KO_Veh_1

value: primary hippocampal cells DIV16

value: KO


title: miRNA, rVSVΔG-ZEBOV-GP, D1 170_S74_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: WT_Li_1

value: primary hippocampal cells DIV15


title: miRNA, rVSVΔG-ZEBOV-GP, D1 170_S74_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 169_S73_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: miRNA, placebo, D7 168_S72_L002

description:
miRNA, placebo, D7
miRNA-seq

value: placebo


title: miRNA, placebo, D7 168_S72_L001

description:
miRNA, placebo, D7
miRNA-seq

value: serum-derived extracellular vesicles


title: NAI_rep2_CiANKRD52_DNAtemplate

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
Library strategy: SHAPE-MaP
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Analyses by Shapemapper V2.1.3.
Genome_build: Target RNA sequence
Supplementary_files_format_and_content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.

extract_protocol:
RNAs in the reactions were extracted by TRIZOL according to the manufacturer’s protocol, followed by DNase I digestion and phenol/chloroform extraction.
Next, recovered RNAs were used for reverse transcription using SuperScript II (Invitrogen) and specific primers for circular or linear ankrd52 RNAs. Finally, nest PCRs were done to amplify circular or linear ankrd52 DNAs using primers for library preparation and deep sequencing.

treatment_protocol: In vitro synthesized circular or linear ankrd52 RNAs were incubated with or without an equal amount of DNA template respectively, heated for 5 min at 65 ℃ in PA buffer (10 mM Tris pH 7.5, 10 mM MgCl2, 100 mM NH4Cl) and slowly cooled down to room temperature in vitro. The mixture was then treated with DMSO or SHAPE reagent NAI at a final concentration of 200 mM respectively and incubated at 37 ℃ for 15 min. Meanwhile, in vitro synthesized circular or linear ankrd52 RNAs were heated for 1 min at 95 ℃ with denaturing buffer (60% formamide, 20 mM HEPES PH 8.0, 1.6 mM EDTA PH 8.0), and instantly cooled down to denature RNAs. The denatured RNAs were labeled with NAI at a final concentration of 200 mM at 95 ℃ for 1 min as denaturing control (DC).

value: CiANKRD52 with DNA template NAI samples modified by NAI in DMSO


title: NAI_rep2_pre_ANKRD52_DNAtemplate

value: pre-ANKRD52 with DNA template NAI samples modified by NAI in DMSO


title: NAI_rep2_pre_ANKRD52

value: pre-ANKRD52 NAI samples modified by NAI in DMSO


title: miRNA, placebo, D4 167_S71_L002

description:
miRNA, placebo, D4
miRNA-seq


title: NAI_rep1_pre_ANKRD52


title: NAI_rep2_CiANKRD52

value: CiANKRD52 NAI samples modified by NAI in DMSO


title: NAI_rep1_pre_ANKRD52_DNAtemplate


title: NAI_rep1_CiANKRD52


title: miRNA, rVSVΔG-ZEBOV-GP, D0 169_S73_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: DMSO_pre_ANKRD52

value: pre-ANKRD52 DMSO samples only treated with DMSO


title: NAI_rep1_CiANKRD52_DNAtemplate


title: WT_Veh_1

value: hippocampus

value: primary hippocampal cells DIV14


title: DMSO_CiANKRD52

value: CiANKRD52 DMSO samples only treated with DMSO


title: miRNA, placebo, D4 167_S71_L001

description:
miRNA, placebo, D4
miRNA-seq


title: DMSO_pre_ANKRD52_DNAtemplate

value: pre-ANKRD52 with DNA template DMSO samples only treated with DMSO


title: miRNA, placebo, D3 166_S70_L001

description:
miRNA, placebo, D3
miRNA-seq


title: DC_pre_ANKRD52

value: pre_ANKRD52 DC samples denatured by formamide at 95C


title: miRNA, placebo, D3 166_S70_L002

description:
miRNA, placebo, D3
miRNA-seq


title: DMSO_CiANKRD52_DNAtemplate

value: CiANKRD52 with DNA template DMSO samples only treated with DMSO


title: H2-O WT CD4 Tcell, Replicate 2

city: Baltimore

first: Scheherazade

last: Sadegh Nasseri

state: MD

address: 720 Rutland Ave, Ross Building Rm 664C

department: Pathology

institute: Johns Hopkins University

description: 10x Genomics

data_processing:
Cellranger mkfastq (v6.1.2) was used to convert BCL files to FASTQ files. Cellranger count (v6.1.2) was used to align the reads and generate feature-barcode matrices
Assembly: mm10
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: Spleen

extract_protocol:
Total splenocytes were isolated from H2-O WT and H2-O KO spleens using manual tissue disruption and 70 um filtration. Red blook cells (RBCs) were lysed using ACK (4mL, 3mins on ice). Cells were washed 2 times with RPMI + 10% FBS to remove ACK buffer. Recovered cells were surface stained with anti-CD3, -CD4,-B220, and -Nk1.1 for 30mins at 4 degree. PI was added right before sorting for dead cell exclusion. Sorted cells were collected into HBSS + 10% FBS and submitted for scRNA-Seq analysis.
The samples were prepared using the 10x Genomics Chromium Next GEM Single Cell 5' Library and Gel Bead Kit v1.1, Chromium Next GEM Chip and Dual Index Kit TN Set A. They were run on the Illumina NovaSeq6000 with a run configuration of 28bp x 10bp x 10bp x 91bp.

value: Spleen

value: 8 Week Old

value: CD3+ CD4+ B220- NK1.1- T cells

value: H2-O Wildtype

value: Naive


title: miRNA, placebo, D2 165_S69_L002

description:
miRNA, placebo, D2
miRNA-seq

value: serum-derived extracellular vesicles

value: placebo


title: H2-O WT CD4 Tcell, Replicate 3

description: 10x Genomics


title: H2-O WT CD4 Tcell, Replicate 1

description: 10x Genomics


title: DC_pre_ANKRD52_DNAtemplate

value: pre_ANKRD52 with DNA template DC samples denatured by formamide at 95C


title: DC_CiANKRD52

value: CiANKRD52 DC samples denatured by formamide at 95C


title: miRNA, placebo, D2 165_S69_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D1 164_S68_L002

description:
miRNA, placebo, D1
miRNA-seq


title: RNAseq_K562_61_IGHMBP2_Rep2

city: San Francisco

first: Jesslyn

last: Park

address: 513 Parnassus Ave

department: Cell and Tissue Biology

institute: University of California, San Francisco

data_processing:
FASTQ files were converted to FASTA format. Adapter sequences from Ribo-seq FASTQ files were removed with cutadapt. Using cutadapt, adapter sequences were removed from RNA-seq and Ribo-seq sample reads, and reads were filtered to a minimum length of 22 nt. Reads were collapsed by UMI, which were then removed. Ribosomal RNAs, repeat RNAs and other non-coding RNAs were aligned against and removed with repeatmasker using bowtie2 2.4.1. Index files were generated using STAR 2.7.5a, GRCh38 primary assembly genome.fa file, and a GENCODE v25 .gtf annotation file with --sjdbOverhang set to 64 or 29 for RNA-seq and Ribo-seq indices, respectively. Filtered reads were then mapped to corresponding indices, generating annotated .bam files for analysis.
To determine localized read mapping coverage for specific genes, bamCoverage from deeptools was used to convert RNA-seq and Ribo-seq pre-processed .bam files to .bigwig files, where reads were normalized to counts per million (CPM).
Assembly: hg38
Supplementary files format and content: Processed data are bw

growth_protocol: RPMI 1640 (Gibco) containing L-glutamine and 25 mM HEPES, supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Refer to manuscript for RNA-seq and Ribo-seq RNA extraction protocols
Refer to manuscript for RNA-seq and Ribo-seq library construction protocols

treatment_protocol: Cells were seeded in fresh media 16 hr prior to harvest. Cell count was measured near 0.3E6 cells/mL per cell line at time of harvest, reflecting active growth conditions.

value: lymphoblast cells

value: IGHMBP2 KO; expression is fully deleted in K-562 expressing CRISPRi machinery (doi:10.1016/j.cell.2014.09.029)


title: RNAseq_K562_WT_IGHMBP2_Rep2

value: Parental K-562 expressing CRISPRi machinery (doi:10.1016/j.cell.2014.09.029)


title: Riboseq_K562_WT_IGHMBP2_Rep2

description: Ribosomal footprint RNA

library_source: other

data_processing:
FASTQ files were converted to FASTA format. Adapter sequences from Ribo-seq FASTQ files were removed with cutadapt. Using cutadapt, adapter sequences were removed from RNA-seq and Ribo-seq sample reads, and reads were filtered to a minimum length of 22 nt. Reads were collapsed by UMI, which were then removed. Ribosomal RNAs, repeat RNAs and other non-coding RNAs were aligned against and removed with repeatmasker using bowtie2 2.4.1. Index files were generated using STAR 2.7.5a, GRCh38 primary assembly genome.fa file, and a GENCODE v25 .gtf annotation file with --sjdbOverhang set to 64 or 29 for RNA-seq and Ribo-seq indices, respectively. Filtered reads were then mapped to corresponding indices, generating annotated .bam files for analysis.
To determine localized read mapping coverage for specific genes, bamCoverage from deeptools was used to convert RNA-seq and Ribo-seq pre-processed .bam files to .bigwig files, where reads were normalized to counts per million (CPM).
Assembly: hg38
Supplementary files format and content: Processed data are .bam
Library strategy: Ribo-Seq

molecule: other


title: Riboseq_K562_33_IGHMBP2_Rep2

description: Ribosomal footprint RNA

value: IGHMBP2 HET; expression is partially deleted in K-562 expressing CRISPRi machinery (doi:10.1016/j.cell.2014.09.029)


title: Riboseq_K562_33_IGHMBP2_Rep1

description: Ribosomal footprint RNA


title: RNAseq_K562_33_IGHMBP2_Rep2


title: RNAseq_K562_115_IGHMBP2_Rep1


title: RNAseq_K562_WT_IGHMBP2_Rep1


title: RNAseq_K562_118_IGHMBP2_Rep1


title: Riboseq_K562_WT_IGHMBP2_Rep1

description: Ribosomal footprint RNA


title: RNAseq_K562_61_IGHMBP2_Rep1


title: RNAseq_K562_118_IGHMBP2_Rep2


title: RNAseq_K562_115_IGHMBP2_Rep2


title: RNAseq_K562_33_IGHMBP2_Rep1


title: H2-O KO CD4 Tcell, Replicate 3

description: 10x Genomics

value: H2-O Knockout


title: Riboseq_K562_61_IGHMBP2_Rep2

description: Ribosomal footprint RNA


title: DC_CiANKRD52_DNAtemplate

value: CiANKRD52 with DNA template DC samples denatured by formamide at 95C


title: H2-O KO CD4 Tcell, Replicate 2

description: 10x Genomics


title: Suc 3

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

data_processing:
RTA performs image analysis and base calling during the sequencing run. The NextSeq  500 uses  RTA 2.0
Reads were aligned to the ASM746v reference genome using BBMap.
Differential gene expression analysis was performed using DeSeq2
Assembly: ASM746v2
Supplementary files format and content: counts

organism: Streptococcus mutans

source_name: bacterial cells

growth_protocol: Growth in TSB medium, eventually supplemented with 0,5% (w/v) carbohydrate, for 6 hours at 37 °C with 5% CO2

extract_protocol:
Pellets were frozen in liquid nitrogen and mechanically crushed, RNA was harvested using Trizol reagent. Illumina ScriptSeq Complete Kit (Bacteria) was used  for the construction of sequencing libraries with input 2,5 ug of mRNA.
Illumina ScriptSeq Complete Kit (Bacteria) (BB1224) - firstly total RNA was depleted with Ribo-Zero rRNA Removal Reagents, following with the steps cDNA synthesis, 3'Terminal tagging and PCR and library purification within Script-Seq v2 RNA-Seq Library Preparation Kit

value: bacterial cells

value: sucrose


title: Riboseq_K562_61_IGHMBP2_Rep1

description: Ribosomal footprint RNA


title: miRNA, placebo, D1 164_S68_L001

city: Göteborg

first: Björn

last: Andersson

institute: Univeristy of Gothenburg

description:
miRNA, placebo, D1
miRNA-seq

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: txt file with normalized and log2 transformed counts

extract_protocol:
extracellular vesicles (EV)-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).


title: Suc 2


title: H2-O KO CD4 Tcell, Replicate 1

description: 10x Genomics

value: Spleen


title: H3K9me2_CUTRUN_WT1

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

library_source: genomic

data_processing:
Raw paired-end sequenced reads were first cut adaptors and trimmed using trim_galore (v0.6.6) with “-q 20, --stringency 1, --length 20 and -e 0.1”.
Then, these cleaned fastq data were mapped using bowtie2 (v2.4.2) to the mm10 reference genome with “--end-to-end, --very-sensitive, --no-mixed, --no-discordant, --phred33, -I 10 and -X 700” model
Next, Picard was used for marking and removing duplication. Samtools (v1.11) was used for converting and sorting the sam files to sort bam files
Finally, Homer was used for peak calling. Differential peaks between Tumor treg and spleen treg were calculated by homer mergePeaks and homer getDifferentialPeaks. Differential peaks between WT and KO were calculated by homer.Peaks were annotated by annotatePeaks.pl with mm10 genome and gencodeVM25 gtf files.
Parallelly, deeptools was used for normalizing signals from sort bam files via bamCoverage.ComputeMatrix was used for calculating the overall signal distribution around the peak center called by homer using “reference-point” model with “-b 2000, -a 2000, --missingDataAsZero, --referencePoint center, --skipZeros, --blackListFileName mm10.blacklist.bed (discarding weird regions)”. Data were visualized using plotProfile and plotHeatmap in deeptools.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: Tab-separated values peaks file

molecule: genomic DNA

source_name: tumor tissue

extract_protocol:
Tumor tissue was resected and digested with enzyme. Lymphocytes were purified using percoll. Treg cells were purified by magnetic-activated cell sorting (MACS) positive selection. Tumor infiltrated treg of the WT and jmjd1c tregcKO mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of fluorence signal. H3K9me2 modified genomic regions and Stat3 binding regions were harvested by anti-H3K9me2 antibody anti-Stat3 antibody and “HD102 Hyperactive pG-MNase CUT&RUN Assay Kit for Illumina”.
Libraries were constructing using “HD102 Hyperactive pG-MNase CUT&RUN Assay Kit for Illumina” and “TD202 TruePrep® Index Kit V2 for Illumina®” from Vazyme Biotech Co., Ltd.

value: tumor tissue

value: Treg cells

tag: antibody

value: 8-12 weeks old


title: H3K9me2_CUTRUN_KO1


title: H3K9me2_CUTRUN_KO3


title: H3K9me2_CUTRUN_WT3


title: H3K9me2_CUTRUN_WT2


title: Riboseq_K562_115_IGHMBP2_Rep2

description: Ribosomal footprint RNA


title: Riboseq_K562_118_IGHMBP2_Rep2

description: Ribosomal footprint RNA


title: Riboseq_K562_115_IGHMBP2_Rep1

description: Ribosomal footprint RNA


title: miRNA, placebo, D0 163_S67_L001

address: Sahlgrenska akademin, Core Facilities, Box 413

description:
miRNA, placebo, D0
miRNA-seq


title: H3K9me2_CUTRUN_KO2


title: miRNA, rVSVΔG-ZEBOV-GP, D7 162_S66_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: Riboseq_K562_118_IGHMBP2_Rep1

description: Ribosomal footprint RNA


title: miRNA, rVSVΔG-ZEBOV-GP, D4 161_S65_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq

value: serum-derived extracellular vesicles


title: Suc 1


title: Glu 3

value: glucose


title: Xyl 3

value: xylitol


title: miRNA, rVSVΔG-ZEBOV-GP, D7 162_S66_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: Liver, Non treated,05

source_name: Healthy liver

value: Healthy liver

value: Non treated


title: miRNA, rVSVΔG-ZEBOV-GP, D4 161_S65_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: Liver, Non treated,04


title: Liver, Non treated,03


title: Liver, Non treated,02


title: Xyl 2


title: miRNA, placebo, D0 163_S67_L002

description:
miRNA, placebo, D0
miRNA-seq

value: placebo


title: Liver, Non treated,01


title: Glu 2


title: Tumor, FGF19+MYC,05

value: Tumoral liver


title: Tumor, FGF19+MYC,03


title: miRNA, rVSVΔG-ZEBOV-GP, D3 160_S64_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: Tfap2a_CUT&RUN_24hpf_n2

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 5269B CBRC Newton Road

institute: University of Iowa

description: CUT&RUN

data_processing:
Reads trimmed using TrimGalore
Reads mapped using Biotie2
Peak called using MACS2
Peaks visualized using UCSC on bigWig-generated files.
DanRer10 called peaks lifted to danRer11 using UCSC
Assembly: DanRer10
Supplementary files format and content: Peak bed file
Library strategy: CUT&RUN

organism: Danio rerio

source_name: Whole embryo

growth_protocol: Wild-type zebrafish were crossed, and embryos were collected and maintained at 28 degrees celsius for 24 hours post-fertilization (hpf)

extract_protocol:
Ten zebrafish embryos at 24hpf were dissociated in calcium-free wash buffer, washed three times with PBS, and filtered through a 40μm gauze. Approximately 250k cells were attached to CoA beads per sample, incubated with a 1:100 ratio of anti-Tfap2a or IgG antibody, and cleaved with pAG-MNase for 30 minutes. The cut fragments were purified, and library preparation was conducted using KAPA kits. Sequencing was performed with 150PE reads at 20 million reads per sample
Library construction was performed using the KAPA Biosciences kit following the manufacturer's protocol.

treatment_protocol: Embryos were not subject to treatment

value: Whole embryo

value: wild type


title: Tumor, FGF19+MYC,04


title: Glu 1


title: Xyl 1


title: TSB 3

value: TSB


title: miRNA, rVSVΔG-ZEBOV-GP, D2 159_S63_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq

source_name: serum-derived extracellular vesicles


title: TSB 2

value: bacterial cells


title: HCI-002

first: Sourav

last: Bandyopadhyay

state: California

address: 1450 3rd Street

department: Helen Diller Family Comprehensive Cancer Center

description: 10x genomics

data_processing:
Data were processed according to the 10x Cell Ranger v1.1.0 pipeline following the standard pipeline listed in the 10x software manual with default parameters.
Assembly: hg19
Supplementary files format and content: *_barcodes.tsv: Cell barcodes. *_genes.tsv: Genes. *_matrix.mtx: 10x gene barcode matrix

growth_protocol: Breast cancer cell lines were grown according to published guidelines except for SKBR3 cells which were cultured using RPMI media supplemented with 10% fetal bovine serum (FBS) and 1% pen/strep. All cell lines tested negative for mycoplasma contamination.

extract_protocol:
Breast cancer cell lines were thawed and carried according to published culture methods as described. Viably frozen PDX cell suspensions were thawed, washed and stained for fluorescence-activated cell sorting (FACS) using fluorescently labeled antibodies for human antigen CD298 (PE; 341704, BioLegend) and mouse antigens CD45 (APC; 559864, BD Pharmingen), CD31 (APC; 551262, BD Pharmingen) and Ter119 (APC; 557909, BD Pharmingen). Flow sorting was done using a BD FACSAria II cell sorter (Becton Dickinson) where contaminating hematopoietic and endothelial cells were excluded by gating out Lin+ (CD45, Ter119, CD31) cells. Dead populations from both PDX samples and cell lines were eliminated by excluding Sytox positive (SYTOX Blue Dead Cell Stain, S34857, Life Technologies) cells with cells showing at least 80% viability proceeded with for single-cell sequencing. Single-cell data for the HCC38 cell line was provided by 10x Genomics.
Sorted cells were washed in PBS with 0.04% BSA and resuspended at a concentration of ~1000 cells/µl. Single-cell RNA sequencing was performed at the IHG Genomics Core (UCSF) using the Chromium Single Cell 3ʹ Reagents Kit (CG00026 Rev B., 10x Genomics), and libraries were prepared following the manufacturer’s protocol. Libraries were then sequenced using the Illumina HiSeq2500 platform to achieve an average depth of 50,000 reads per cell.

treatment_protocol: HCI-002 PDX tissue was harvested and processed into single-cell suspensions following established protocols. Briefly, PDX tissue was mechanically chopped with scalpels and placed in culture medium DMEM/F12 with 5% FBS, 5 µg ml−1 insulin (UCSF Cell Culture Facility), 50 ng ml−1 gentamycin (UCSF Cell Culture Facility) and supplemented with 2 mg ml−1 collagenase-1 (Sigma). Sample was then digested for 45 min at 37 °C. The resulting suspensions were resuspended in 2 U µl−1 DNase (D4263-5VL, Sigma Aldrich) for 3 min at room temperature, washed and dissociated with 2 ml of 0.05% trypsin/EDTA (25-052-CI, Corning) for 10 min at 37 °C. Cell suspensions were then filtered through a 70 µm filter, and frozen in DMEM/F12 with 50% serum, 10% DMSO, and stored in liquid nitrogen prior to study.

value: PDX


title: miRNA, rVSVΔG-ZEBOV-GP, D2 159_S63_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: MDA-MB-231

description: 10x genomics

value: cell line


title: Tumor, FGF19+MYC,01


title: Tumor, FGF19+MYC,02


title: Lac 3

value: lactate


title: SKBR3

description: 10x genomics


title: Lac 2


title: miRNA, rVSVΔG-ZEBOV-GP, D0 157_S61_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: TSB 1


title: Tumor, Aldafermin+MYC,05

value: Aldafermin+MYC


title: Tfap2a_CUT&RUN_24hpf_n1

description: CUT&RUN


title: miRNA, rVSVΔG-ZEBOV-GP, D0 157_S61_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D0
miRNA-seq


title: Tumor, Aldafermin+MYC,03


title: MCF7

description: 10x genomics


title: miRNA, rVSVΔG-ZEBOV-GP, D1 158_S62_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 160_S64_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 158_S62_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D1
miRNA-seq


title: Tumor, Aldafermin+MYC,02


title: miRNA, rVSVΔG-ZEBOV-GP, D7 156_S60_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: Tumor, Aldafermin+MYC,01


title: miRNA, rVSVΔG-ZEBOV-GP, D7 156_S60_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D7
miRNA-seq


title: HSCs, Control (4)

city: Kumamoto

first: Toshio

last: Suda

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description:
S16
raw_counts.csv

data_processing:
mRNA profile generated by deep sequencing using Illumina Next-Seq 500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm39 whole genome using Spliced Transcripts Alignment (STAR) pipeline (Dobin et al. Bioinformatics, 2013:29)
The generated BAM files were then merged using samtools and transcripts were counted using subread package.
Assembly: mm39
Supplementary files format and content: Tab-delimited csv file includes raw counts number for each Sample.

source_name: Bone marrow

extract_protocol:
After 100 cells were sorted, first strand cDNA were synthesized followed by generating 2nd strand by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) .
Using Nextera XT DNA sample Prep Kit (Illumina Inc., San Diego, CA), libraries were prepared by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) .

value: Bone marrow

value: hematopoietic stem cells

value: Control

value: 8-10 weeks


title: Tumor, Aldafermin+MYC,04


title: E3 cells, Usp17le OE, rep1

city: Tianjin

first: Linlin

last: Liu

address: Weijin Road 97

institute: Nankai university

data_processing:
Raw reads were processed using trim-galore and clean reads were mapped to mm10 from UCSC genome by Hisat2 with default parameters .
Uniquely mapped reads annotated in Gencode vM17 were calculated by Featurecounts , with default parameters.
Raw counts were normalized by library size via transcripts per kilobase of exon model per million mapped reads (CPM).
Assembly: mm10
Supplementary files format and content: Excel file includes CPM values for each Sample

growth_protocol: Cell lines were cultured normally

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols manufacturer's protocols.

value: mouse embryonic stem cells

value: Usp17le OE

value: 48h after overexpression


title: Lac 1


title: miRNA, rVSVΔG-ZEBOV-GP, D4 155_S59_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq

value: serum-derived extracellular vesicles

value: rVSV-delta-G-ZEBOV-GP vaccine, dose 2x10^7


title: HSCs, Control (1)

description:
S13
raw_counts.csv


title: HSCs, Control (2)

description:
S14
raw_counts.csv


title: Old, UA, 3

city: Madrid

first: Juan Ignacio

last: Jiménez-Loygorri

state: Madrid

address: Ramiro de Maeztu 9

department: Cellular and Molecular Biology

country: Spain

institute: Centro de Investigaciones Biológicas Margarita Salas

data_processing:
Resulting RNA-seq reads were processed and aligned using STAR at the Biostatistics and Bioinformatics Unit, IRB Barcelona.
Assembly: GRCm39
Supplementary files format and content: Normalized expression for each sample.

source_name: Neuroretina

growth_protocol: Animals were housed in an animal facility with food and water ad libitum and maintained in a 12h/12h light-dark cycle. Samples were collectec at 9am, one hour after light onset

extract_protocol:
Total RNA was extracted from a whole neuoretina using RNeasy Mini coupled to DNAse in-column treatment (Qiagen).
Total RNA extractions were quantified with a Nanodrop One (Thermo Fisher), and RNA integrity was assessed with the Bioanalyzer 2100 RNA Nano assay (Agilent). Libraries for RNA-seq were prepared at IRB Barcelona Functional Genomics Core Facility. Briefly, mRNA was isolated from 620 ng of total RNA using the kit NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The isolated mRNA was used to generate dual-indexed cDNA libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). Ten cycles of PCR amplification were applied to all libraries. Sequencing-ready libraries were quantified using the Qubit dsDNA HS assay (Invitrogen) and quality controlled with the Bioanalyzer 2100 DNA HS assay (Agilent). An equimolar pool was prepared with the eighteen libraries for SE75 sequencing on a NextSeq550 (Illumina). Sequencing output was 513.7 million 75-nt single-end reads and a minimum of 26 million reads was obtained for all samples.

treatment_protocol: Animals were injected daily with UA or vehicle, dosage was adjusted to each animal according to their weight.

value: Neuroretina

value: WT

value: M

value: Old

value: UA


title: Old, UA, 5


title: HSCs, Control (3)

description:
S15
raw_counts.csv


title: Old, UA, 4


title: E3 cells, Control, rep2

value: E3 transfected with the empty vector


title: HSCs, Mitol KO (4)

description:
S12
raw_counts.csv

value: Mitol knockout


title: Old, UA, 2

value: F


title: miRNA, rVSVΔG-ZEBOV-GP, D4 155_S59_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D4
miRNA-seq


title: E3 cells, Control, rep1


title: miRNA, rVSVΔG-ZEBOV-GP, D3 154_S58_L001

description:
miRNA, rVSVΔG-ZEBOV-GP, D3
miRNA-seq


title: HSCs, Mitol KO (2)

description:
S10
raw_counts.csv

value: Bone marrow


title: miRNA, rVSVΔG-ZEBOV-GP, D2 153_S57_L002

description:
miRNA, rVSVΔG-ZEBOV-GP, D2
miRNA-seq


title: Old, UA, 1


title: HSCs, Mitol KO (3)

description:
S11
raw_counts.csv

value: hematopoietic stem cells


title: E3 cells, Usp17le OE, rep2