title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 3_12h

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
4-thiouridine incorporation events were analyzed using the SlamDunk software  (v0.3.4) for SLAMseq analysis
SLAMseq reads were first reverse complemented to match the hard-coded assumed SlamDunk orientation using fastx_reverse_complement from the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit) with default settings.
The resulting fastq files were mapped to the reference genome with slamdunk map and parameters: -5 0  -ss q
The mapped reads were filtered to only retain intragenic mappings according to the reference transcriptome with a high identity using slamdunk filter and parameters: -mi 0.9
SNP variants in the samples were called with slamdunk snp with parameters: -c 1 -f 0.2
The SNP variants from all samples were combined in a single master vcf file. Indexing of the individual vcf file was done using tabix of the htslib package (https://github.com/samtools/htslib) and  merging using vcf-merge from the VCFtools package (Danecek et. Al 2011)  The SNP variants from all samples were combined in a single master vcf file. This involved indexing of the individual vcf file using tabix of the htslib package  (https://github.com/samtools/htslib) and subsequently merging using vcf-merge from the VCFtools package (Danecek et. Al 2011).  The SNP variants from all samples were combined in a single master vcf file. This involved indexing of the individual vcf file using tabix of the htslib package  (https://github.com/samtools/htslib) and subsequently merging using vcf-merge from the VCFtools package (Danecek et. Al 2011).
4-thiouridine incorporation events  and conversion rates were calculated separately for exonic gene segments of the reference transcriptome using slamdunk count with default parameters and the master SNP vcf file for SNP filtering
Assembly: GENCODE GRCh38 primary assembly
Supplementary files format and content: Tab separated value files listing 4-thiouridine incorporation events and conversion rates for exonic segments.

source_name: HeLa 11ht

growth_protocol: HeLa 11ht cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using the Absolutely RNA miniprep kit (Agilent) with on-column DNase digestion.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit according to the manufacturer's instructions.

treatment_protocol: HeLa 11ht cells were treated with 12µM 4-thiouridine for 24hr (media exchange every 3 hr), treatment was stopped with 1.2 mM uridine, and timepoints were collected (0, 3, 6, 9, 12hr after uridine quench).

value: HeLa 11ht

value: cervical cancer cells

value: LARP1 KO

value: 24h S4U labeling, wash-out

tag: time after_wash-out


title: FaDu-1

status: Public on Jan 15 2024

type: SRA

city: Shanghai

first: Lixiao

last: Chen

address: No.85 Wujin road, Hongkou district, Shnaghai,200080, China

department: Otorhinolaryngology head and neck surgery

country: China

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: FaDu cell line

extract_protocol:
Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: hypopharyngeal tumor cell

tag: cell line

value: FaDu

tag: shRNA


title: Islet_147, SAMN20923891, 24 Hr Thapsigargin

city: Farmington

first: Eishani

middle: Kumar

last: Sokolowski

state: CT

address: 263 Farmington Avenue

country: USA

institute: University of Connecticut Health Center

library_source: genomic

data_processing:
The paired-end (2x150 bp) ATAC-seq FASTQ files for each islet were trimmed using Trimmomatic.
Alignment was performed against the human genome (GRCh38/hg38) using BWA-MEM.
Duplicate reads were removed and the remaining reads were shifted by 9bp to account for the binding site of Tn5.
Technical replicates were merged using SAMtools.
Peaks were called using MACS2.
Separate consensus peaksets for ER stress (ERS) and pro-inflammatory cytokine (CYT) samples were generated by considering peaks that were present in at least 2 samples, and those peaks that mapped to ENCODE Exclusion List regions were excluded using DiffBind.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file (ERS_ATAC-seq_Consensus_Peakset_Raw_Counts.txt) that includes the raw counts for the consensus peakset generated using all the 24 Hr DMSO and 24 Hr Thapsigargin treated samples.
Supplementary files format and content: Tab-delimited text file (CYT_ATAC-seq_Consensus_Peakset_Raw_Counts.txt) that includes the raw counts for the consensus peakset generated using all the 24 Hr Untreated and 24 Hr Cytokines treated samples.

molecule: genomic DNA

source_name: Pancreatic Islets

growth_protocol: Fresh human cadaveric pancreatic islets were procured from Prodo Labs or the Integrated Islet Distribution Program (IIDP). Upon arrival, cells were transferred into PIM(S) media (Prodo Labs) supplemented with PIM(ABS) (Prodo Labs) and PIM(G) (Prodo Labs) and incubated in a T-150 non-tissue culture treated flask (VWR) for recovery at 37°C and 5% CO2 overnight.

extract_protocol:
50 islet equivalents (50,000 cells) per sample were transposed in triplicate using 2.5 μL Transposase (Illumina). Sample purification was then performed using the Qiagen Minelute kit.
Human islet ATAC-seq libraries were prepared following the Active motif ATAC prep kit (Active motif catalog# 53150).

treatment_protocol: The media was changed to CMRL (10% FBS, 1% Glutamax) supplemented with either 0.025%v DMSO, 250nM thapsigargin or 25 U/mL of IL1β + 1000 U/mL of IFNγ (R&D Systems) for 24-hr incubation at 37°C and 5% CO2.

value: Pancreatic Islets

tag: treatment

value: 24 Hr Thapsigargin

tag: unos id


title: Islet_146, SAMN20821183, 24 Hr Thapsigargin


title: Islet_106, SAMN15314807, 24 Hr Untreated

value: 24 Hr Untreated


title: p003-bdf1_009_rna

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description:
progenitor-1
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz

data_processing:
RNA reads were mapped to mm10 transcriptome reference using hisat2.
Gene expression were quantified using RSEM.
Hi-C reads were processed and analysed using Dip-C and hickit package.
We generated three replicate structures (_1.3dg.gz, _2.3dg.gz and _3.3dg.gz) per cell reconstructed with different random seeds (1-3).
We pooled Hi-C samples for each group.
Assembly: mm10
Supplementary files format and content: .hic
Supplementary files format and content: .3dg
Supplementary files format and content: .allValidPairs.txt.gz

molecule: polyA RNA

organism: Mus musculus

source_name: mouse olfactory epithelium

extract_protocol:
The main olfactory epithelium was dissected and minced to small pieces, then was dissociated into single cell suspension with the Papain Dissociation System (Worthington Biochemical, Cat. #LK003150) at 37°C for 15 min, during incubation, titration every 5 min with wide-bore pipette tip according to previously described2. Then filtered with 30 μm strainer (MACS), then wash twice with ice-cold 1 x PBS.
simultaneous 3D genome and gene expression by LiMCA
Smart-seq2 for LiMCA RNA library; Dip-C protocol for LiMCA Hi-C library

tag: tissue

value: mouse olfactory epithelium

tag: age

value: postnatal day 3

tag: strain

tag: genotype

value: WT


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 3_12h


title: 812RNAHPBCD4POS

city: Seoul

first: Seul

last: Lee

address: 50-1, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

country: South Korea

institute: Yonsei University

data_processing:
FastQC v0.11.7
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic 0.38
Trimmed sequence reads were mapped using HISAT2 version 2.1.0
assembled using StringTie version 2.1.3b
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: CD4 T cell

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 SureSelect RNA Direct_Human Library Prep Kit following manufacturer's protocols.

value: CD4 T cell

value: lymphocytes

value: high

tag: time

value: Day 5


title: 812RNAHPBCD8POS

source_name: CD8 T cell

value: CD8 T cell


title: 812RNAHPBCD8NEG

value: low

value: Day 0


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 3_12h

value: HeLa 11ht

value: cervical cancer cells


title: Islet_144, SAMN20523746, 24 Hr Thapsigargin


title: Islet_153, SAMN22818629, 24 Hr Thapsigargin


title: 812RNAHPBCD4NEG


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.4, biol rep 3

data_processing:
Sequenced reads were aligned against the human genome using R version 4.1.1 with Bioconductor version 3.13 to execute the qAlign tool (QuasR package, version 1.32.0), with default parameters except for aligner = "Rhisat2", splicedAlignment = "TRUE", allowing only uniquely mapping reads.
Raw gene counts were obtained using the qCount tool (QuasR) with a TxDb generated from gencode.v38.primary_assembly.annotation.gtf as query, with default parameters counting only alignments on the opposite strand as the query region.
The count table was filtered to only keep genes which had at least 1 cpm in at least 3 samples.
Differential gene expression was calculated with the Bioconductor package edgeR (version 3.34.0, ref 2) using the quasi-likelihood F-test after applying the calcNormFactors function, obtaining the dispersion estimates and fitting the negative binomial generalized linear models.
Genes with log2 CPM <1 were filtered out to remove low confidence hits, and significant differences in gene expression were detected by applying the following thresholds of abs log2 FC >0.5 and -log10 p-value >5.
Assembly: GENCODE GRCh38 primary assembly
Supplementary files format and content: tab-delimited text file listing transcript counts (raw, CPM) and differential gene expression analysis results

extract_protocol:
RNA was harvested using the Absolutely RNA miniprep kit (Agilent) with on-column DNase digestion.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA reagents according to the manufacturer's protocol

value: LARP1 KO


title: Islet_153, SAMN22818629, 24 Hr DMSO

value: 24 Hr DMSO


title: p003-bdf1_008_rna

description:
iOSN
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: p003-bdf1_007_rna

description:
progenitor-2
LiMCA_olfactory_rna_gene_counts.tsv.gz
LiMCA_olfactory_rna_gene_fpkm.tsv.gz


title: p003-bdf1_006_rna


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 2_12h

value: 24h S4U labeling, wash-out


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.4, biol rep 1


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.4, biol rep 2


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 2_12h


title: p003-bdf1_005_rna


title: p003-bdf1_010_rna


title: p003-bdf1_004_rna


title: Islet_148, SAMN20926064, 24 Hr DMSO

value: Pancreatic Islets


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.3, biol rep 3


title: Islet_147, SAMN20923891, 24 Hr DMSO


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 2_12h


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.3, biol rep 2


title: p003-bdf1_003_rna


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 2_12h


title: Islet_146, SAMN20821183, 24 Hr DMSO


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 3_12h


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 1_12h


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.3, biol rep 1


title: p003-bdf1_002_rna


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 1_12h


title: p003-bdf1_001_rna


title: Islet_144, SAMN20523746, 24 Hr DMSO


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.2, biol rep 3


title: Islet_151, SAMN21855451, 24 Hr DMSO


title: MOE_METATAC_210315-P28-Plate10

description: MOE_METATAC_peak files

library_source: genomic single cell

data_processing:
Cell barcodes and META sequences were identified for each pair of reads using a custom script. Reads from each cell were split according to their barcodes. Adapters were then trimmed using cutadapt (v4.0) with parameters “-e 0.22 -a CTGTCTCTTATACACATCT” followed by parameters “-e 0.22 -g AGATGTGTATAAGAGACAG”. Cleaned reads were then mapped to mm10 (GRCm38) reference genome using bowtie2 (v2.3.4.3) with parameters “-X 2000 --local --mm --no-discordant --no-mixed”. Duplicated reads were removed using custom script according to both their mapped location on the genome and META tags. Mapped paired reads were transformed into fragments, and a bias of “+4” or “-5” was added to each end of each fragment to center the Tn5 insertion sites.
10X scRNA-seq reads were processed and mapped to mm10 genome using Cell Ranger (v 5.0.1).
Assembly: mm10
Supplementary files format and content: count matrix (scRNA-seq)
Supplementary files format and content: bed (scATAC-seq)

source_name: mouse olfactory epithelium (P150)

extract_protocol:
The main olfactory epithelium was dissected and minced to small pieces, then was dissociated into single cell suspension with the Papain Dissociation System (Worthington Biochemical, Cat. #LK003150) at 37°C for 15 min, during incubation, titration every 5 min with wide-bore pipette tip according to previously described2. Then filtered with 30 μm strainer (MACS), then wash twice with ice-cold 1 x PBS.
10X Genomics scRNA-seq and METATAC scATAC-seq

value: mouse olfactory epithelium (P150)

value: postnatal day 28


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 1_12h


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 1_12h


title: MOE_METATAC_210315-P28-Plate9

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P149)

value: mouse olfactory epithelium (P149)

value: mouse olfactory epithelium


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.2, biol rep 2


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.2, biol rep 1


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 3_9h


title: Post-treatment, RNAseq, patient DB08

city: Bethesda

first: Luis

middle: A

last: Fernandez de Castro Diaz

state: Maryland

address: 30 Convent Drive

department: SDMHS

institute: NIDCR/NIH

data_processing:
base-called demultiplexed (fastq) read qualities were determined using FastQC (v0.11.2)
Sequenced reads were mapped to GENCODE v32 human genome (GRCh38.v32).
Gene counts were generated with STAR (v2.7.3a) built-in counting option
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression between groups was performed using DESeq2.
Assembly: GRCh38.v32
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized counts per million, using edgeR built-in cpm() function, tab-delimited txt format.

source_name: FD Bone biopsy

extract_protocol:
Samples were snap-frozen, pulverized and immediately transferred to Trizol. Phenol-chloroform RNA extraction was carried out. cDNA synthesis, library construction and sequencing were performed by Novogene
mRNA libraries were prepared using the polyA TruSeq method (Illumina) and sequenced on an Illumina NovaSeq 6000 sequencer using 150 x 150 paired-end mode.

value: FD Bone biopsy

tag: age (y)

value: skeletal tissue

value: GNAS, p.R201C

value: Denosumab


title: Post-treatment, RNAseq, patient DB09

value: GNAS, p.R201H


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.1, biol rep 3


title: Pre-treatment, RNAseq, patient DB08

value: not applicable


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.1, biol rep 2


title: MOE_METATAC_210315-P28-Plate7

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P147)

value: mouse olfactory epithelium (P147)

value: WT


title: Post-treatment, RNAseq, patient DB07


title: MOE_METATAC_210315-P28-Plate6

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P146)

value: mouse olfactory epithelium (P146)


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 3_9h

value: HeLa 11ht

value: cervical cancer cells


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO s.c.1, biol rep 1

value: LARP1 KO


title: Pre-treatment, RNAseq, patient DB09


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 3_9h

value: 24h S4U labeling, wash-out


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 3


title: MOE_METATAC_210315-P28-Plate5

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P145)

value: mouse olfactory epithelium (P145)


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 2


title: Pre-treatment, RNAseq, patient DB07


title: MOE_METATAC_210315-P28-Plate4

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P144)

value: mouse olfactory epithelium (P144)

value: postnatal day 28


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 1


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 2_9h


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 2_9h


title: MOE_METATAC_210315-P28-Plate2

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P142)

value: mouse olfactory epithelium (P142)

value: mouse olfactory epithelium


title: MOE_METATAC_210315-P28-Plate3

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P143)

value: mouse olfactory epithelium (P143)


title: MOE_METATAC_210315-P28-Plate8

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P148)

value: mouse olfactory epithelium (P148)


title: Pre-treatment, RNAseq, patient DB04

value: FD Bone biopsy

value: skeletal tissue

value: GNAS, p.R201C


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.4, biol rep 3


title: Post-treatment, RNAseq, patient DB04

value: Denosumab


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 3_9h


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 2_9h

value: WT


title: MOE_METATAC_210315-P28-Plate1

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P141)

value: mouse olfactory epithelium (P141)


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.4, biol rep 2

source_name: HeLa 11ht

value: HeLa 11ht


title: Pre-treatment, RNAseq, patient DB05

value: GNAS, p.R201H

value: not applicable


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 2_9h

value: cervical cancer cells

value: 24h S4U labeling, wash-out


title: Post-treatment, RNAseq, patient DB02


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 1_9h

value: LARP1 KO


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.4, biol rep 1


title: Post-treatment, RNAseq, patient DB05


title: Pre-treatment, RNAseq, patient DB02


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 1_9h


title: MOE_METATAC_210311-P28-Plate19

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P139)

value: mouse olfactory epithelium (P139)

value: postnatal day 28


title: KYSE30 cells, OE_circ-PDE5A 3

city: Guangzhou

first: kai

last: lei

address: 107 Yan Jiang West Road

department: Department of Thoracic Surgery

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

data_processing:
preliminary quantification was performed using a Qubit 2.0 Fluorometer to dilute the library to 1.5 ng/ul. The library insert size was then determined using an Agilent 2100 bioanalyzer, and experimental RT-qPCR was performed to accurately quantify the effective concentration of the library (the effective concentration of the library was above 2nM) to ensure the quality of the library. After the libraries passed the quality control, different libraries were pooled according to the effective concentration and target downstream data volume for Illumina sequencing.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: KYSE30 cells

extract_protocol:
Total RNA was extracted from circ-PDE5A overexpressing or control ESCC cells using the TRIzol Total RNA Isolation Kit (Takara, USA), followed by strict quality control of the RNA samples.
Ribosomal RNA was removed from total RNA to enrich for mRNA, and RNA was reverse transcribed to cDNA using random primers. Purified double-stranded cDNA was subjected to end repair, A-tailed, and ligated to sequencing connectors. The cDNAs of around 250-300 bp were sieved on AMPure XP beads and amplified by PCR. The PCR products were purified again using AMPure XP beads to obtain the final library.

value: KYSE30 cells

value: Esophageal squamous carcinoma cells


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.3, biol rep 3


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 1_9h


title: MOE_METATAC_210311-P28-Plate18

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P138)

value: mouse olfactory epithelium (P138)

value: mouse olfactory epithelium


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.3, biol rep 2


title: KYSE30 cells, OE_circ-PDE5A 2


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 1_9h


title: MOE_METATAC_210311-P28-Plate20

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P140)

value: mouse olfactory epithelium (P140)


title: KYSE30 cells, OE_circ-PDE5A 1


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.3, biol rep 1


title: MOE_METATAC_210311-P28-Plate16

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P136)

value: mouse olfactory epithelium (P136)


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 3_6h


title: KYSE30 cells, vector 3

value: vector


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.2, biol rep 3


title: KYSE30 cells, vector 2


title: MOE_METATAC_210311-P28-Plate14

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P134)

value: mouse olfactory epithelium (P134)

value: WT


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.2, biol rep 2

value: HeLa 11ht


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 3_6h


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.2, biol rep 1


title: KYSE30 cells, vector 1


title: MOE_METATAC_210311-P28-Plate13

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P133)

value: mouse olfactory epithelium (P133)


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 3_6h


title: MOE_METATAC_210311-P28-Plate12

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P132)

value: mouse olfactory epithelium (P132)


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 2_6h

value: cervical cancer cells


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.1, biol rep 2


title: MOE_METATAC_210311-P28-Plate17

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P137)

value: mouse olfactory epithelium (P137)


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 2_6h

value: LARP1 KO

value: 24h S4U labeling, wash-out


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.1, biol rep 1


title: MOE_METATAC_220503-P14-Plate16

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P131)

value: mouse olfactory epithelium (P131)

value: postnatal day 14


title: Meso34-Monos-MV-neg [67_Meso34-P31-2333-Monos-MV-neg]

city: Nantes

first: Jean-Francois

last: Fonteneau

address: 8 quai Moncousu BP70721

country: France

institute: INSERM

description:
condition 3
67_Meso34-P31-2333-Monos-MV-neg

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1)
Assembly: Hg38
Supplementary files format and content: Matrix table of raw gene counts for all genes in all samples

growth_protocol: Mesothelioma cells were grown in RPMI+10% SVF+ 2 mM L-Glutamine + 100IU/mL Penicillin , 100µg/mL Streptomycin. Blood monocytes were isolated via negative magnetic sorting (EasySep Human Monocyte Enrichment Kit, StemCell) from PBMC of healthy donors. M2 macrophages were differentiated from monocytes over 4 days, seeded at 1.106 cells/mL in a 12-well plate with culture medium composed of RPMI 1640 supplemented as previously described. At seeding and the day after, 5000U/mL of M-CSF (Miltenyi) was added and macrophages were harvested after 4 days for experiments.

extract_protocol:
RNA were extracted with Kit Nucleospin RNAPlus MachereyNagel with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Libraries were prepared according to NovaSeq 6000 Sequencing Sytem's instructions accompanying the NovaSeq 6000 SP Reagent Kit (Ref# 20028401). Libraries were sequenced on the NovaSeq 6000 following the manufacturer's protocols.
3' SRP

treatment_protocol: Monocytes or macrophages were cocultured with MPM cells at a ratio of one myeloid cell for two tumor cells, in 50% fresh RPMI supplemented and 50% of tumor cells conditioned medium. After 24h, cells were infected with a multiplicity of infection of one viral particle per tumor cells. After 72h, cells were harvested using TryPLE. CD45 positive cells were sorted using human CD45 (TIL) MicroBeads (Miltenyi). An additional 4mL wash step was added to the manufacturer’s protocol. RNA were extracted immediately from CD45 positive (myeloid cells) and negative cells (tumor cells).

tag: infection

value: schwarz attenuated measles virus

tag: cell population sorted

value: mesothelioma

tag: donor

tag: cocultured cecll type

value: Monocytes

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso34


title: Meso13-Monos-NI-neg [79_Meso13-P18-4119-Monos-NI-neg]

description:
condition 1
79_Meso13-P18-4119-Monos-NI-neg

value: uninfected

value: Human pleural mesothelioma cell line Meso13


title: MOE_METATAC_210311-P28-Plate15

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P135)

value: mouse olfactory epithelium (P135)

value: mouse olfactory epithelium

value: postnatal day 28


title: Meso34-Monos-MV-neg [8_Meso34-P32-7677-Monos-MV-neg]

description:
condition 3
8_Meso34-P32-7677-Monos-MV-neg


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 3

value: HeLa 11ht

value: WT


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 2_6h

value: cervical cancer cells

tag: time after_wash-out


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 3_6h

tag: cell type


title: Meso34-M2-MV-neg [40_Meso34-P36-3649-M2-MV-neg]

description:
condition 7
40_Meso34-P36-3649-M2-MV-neg


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 1

tag: cell line


title: MOE_METATAC_220503-P14-Plate15

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P130)

value: mouse olfactory epithelium (P130)


title: Meso34-M2-MV-pos [55_Meso34-P36-5300-M2-MV-pos]

description:
condition 8
55_Meso34-P36-5300-M2-MV-pos

value: myeloid


title: Meso34-Monos-NI-pos [66_Meso34-P31-2333-Monos-NI-pos]

description:
condition 2
66_Meso34-P31-2333-Monos-NI-pos

source_name: Monocytes


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 2_6h

value: 24h S4U labeling, wash-out


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 1_6h

value: LARP1 KO


title: MOE_METATAC_220503-P14-Plate14

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P129)

value: mouse olfactory epithelium (P129)

value: postnatal day 14


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 1_6h


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 2


title: siSOX9-TGFB Rep 3

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

data_processing:
De-multiplexed read sequences were aligned to the reference genome using STAR_2.5.0b.
Assembly and differential expression was estimated using Cufflinks 2.2.1 through bioinformatics apps available on Illumina Sequence Hub.
Assembly: hg19/GRCh37
Supplementary files format and content: Differentially expressed genes data tables

growth_protocol: A549 Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted from cells using TRIzol (Thermo Fisher Scientific).
NEBnext Ultra ii Stranded mRNA (New England Biolabs)

value: Lung adenocarcinoma

value: transfection siSOX9 and TGFB1 treatment


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO s.c.1, biol rep 3


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 1_6h


title: Meso13-Monos-NI-pos [32_Meso13-P19-3649-Monos-NI-pos]

description:
condition 2
32_Meso13-P19-3649-Monos-NI-pos

value: Monocytes


title: MOE_METATAC_220503-P14-Plate13

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P128)

value: mouse olfactory epithelium (P128)


title: MOE_METATAC_220503-P14-Plate12

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P127)

value: mouse olfactory epithelium (P127)


title: MOE_METATAC_210311-P28-Plate11

description: MOE_METATAC_peak files

value: mouse olfactory epithelium (P131)


title: siSOX9-TGFB Rep 2


title: Meso34-M2-NI-pos [72_Meso34-P31-2333-M2-NI-pos]

description:
condition 6
72_Meso34-P31-2333-M2-NI-pos

value: uninfected

value: Human pleural mesothelioma cell line Meso34


title: MOE_METATAC_220503-P14-Plate11

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P126)

value: mouse olfactory epithelium (P126)

value: mouse olfactory epithelium


title: siSOX9-TGFB Rep 1


title: MOE_METATAC_220503-P14-Plate10

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P125)

value: mouse olfactory epithelium (P125)

value: WT


title: Meso34-M2-NI-neg [27_Meso34-P33-7677-M2-NI-neg]

description:
condition 5
27_Meso34-P33-7677-M2-NI-neg

value: mesothelioma


title: Meso34-M2-MV-neg [62_Meso34-P30-1159-M2-MV-neg]

description:
condition 7
62_Meso34-P30-1159-M2-MV-neg

value: schwarz attenuated measles virus


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 3_4h

source_name: HeLa 11ht

value: HeLa 11ht

value: cervical cancer cells

value: LARP1 KO

value: 24h S4U labeling, wash-out


title: MOE_METATAC_220503-P14-Plate9

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P124)

value: mouse olfactory epithelium (P124)

value: postnatal day 14


title: siSOX9 Rep 2

value: Lung adenocarcinoma

value: transfection siSOX9


title: siSOX9 Rep 1


title: siCtrl-TGFB Rep 3

value: transfection siCtrl and TGFB1 treatment


title: Meso34-Monos-NI-neg [50_Meso34-P35-5300-Monos-NI-neg]

description:
condition 1
50_Meso34-P35-5300-Monos-NI-neg

value: uninfected

value: Monocytes


title: MOE_METATAC_220503-P14-Plate8

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P123)

value: mouse olfactory epithelium (P123)


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 3_4h


title: Meso34-M2-MV-neg [90_Meso34-P31-4119-M2-MV-neg]

description:
condition 7
90_Meso34-P31-4119-M2-MV-neg

value: Human pleural mesothelioma cell line Meso34


title: Meso34-M2-NI-neg [52_Meso34-P36-3649-M2-NI-neg]

description:
condition 5
52_Meso34-P36-3649-M2-NI-neg


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 3_4h


title: siCtrl-TGFB Rep 2


title: MOE_METATAC_220503-P14-Plate5

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P120)

value: mouse olfactory epithelium (P120)

value: mouse olfactory epithelium


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 2_4h


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 2_4h


title: MOE_METATAC_220503-P14-Plate6

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P121)

value: mouse olfactory epithelium (P121)

value: WT


title: siCtrl-TGFB Rep 1


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 1_6h

value: HeLa 11ht


title: Meso13-M2-NI-pos [9_Meso13-P17-6864-M2-NI-pos]

description:
condition 6
9_Meso13-P17-6864-M2-NI-pos

value: myeloid

value: Human pleural mesothelioma cell line Meso13


title: Meso34-M2-NI-neg [54_Meso34-P36-5300-M2-NI-neg]

description:
condition 5
54_Meso34-P36-5300-M2-NI-neg

value: mesothelioma


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 2_4h

value: cervical cancer cells

value: 24h S4U labeling, wash-out


title: siCtrl Rep 3

value: Lung adenocarcinoma

value: transfection siCtrl


title: Meso34-Monos-NI-neg [49_Meso34-P35-3649-Monos-NI-neg]

description:
condition 1
49_Meso34-P35-3649-Monos-NI-neg


title: MOE_METATAC_220503-P14-Plate3

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P118)

value: mouse olfactory epithelium (P118)

value: postnatal day 14


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 2_4h


title: siCtrl Rep 2


title: MOE_METATAC_220503-P14-Plate7

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P122)

value: mouse olfactory epithelium (P122)


title: siSOX9 Rep 3

value: transfection siSOX9


title: Meso13-M2-MV-neg [4_Meso13-P15-6532-M2-MV-neg]

description:
condition 7
4_Meso13-P15-6532-M2-MV-neg

value: schwarz attenuated measles virus


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 1_4h

value: LARP1 KO


title: siCtrl Rep 1


title: MOE_METATAC_220503-P14-Plate2

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P117)

value: mouse olfactory epithelium (P117)

value: mouse olfactory epithelium


title: Meso34-M2-MV-neg [42_Meso34-P36-5300-M2-MV-neg]

description:
condition 7
42_Meso34-P36-5300-M2-MV-neg

value: Human pleural mesothelioma cell line Meso34


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 3_4h

value: HeLa 11ht

value: WT


title: Zebrafish_batch2_male2

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

description: CH ATAC-seq

data_processing:
For each sequenced CHATAC-seq library, we obtained two FASTQ files, one of which contained combinatorial index for HY(768 indices) and Tn5 (384 indices) in specific base positions. We filtered reads with more than one mismatch in each index and trimmed adaptor sequences using trimmomatic(version 0.3.8). After that, reads from zebrafish were aligned to D. rerio danRer11 genome(UCSC) using BWA (version 0.7.15). Taking the 9-bp duplication caused by Tn5 transposase into account, we shifted aligned reads + 4bp and -5bp for each positive and negative strand using alignmentSieve(deeptools 3.5.1).Then we used snaptools(version 1.4.8) to keep nonduplicate fragments with high mapping quality (MAPQ > 30) and proper length(<1000 bp) and extracted fragment files from the snap files. Subsequent analysis was performed by ArchR (version 1.0.2). We created arrow files from fragment files by ‘createArrowFiles function’ and constructed customized genome using ‘createGenomeAnnotation’ and ‘createGeneAnnotation function’.
Assembly: D. rerio danRer11 genome(UCSC)
Supplementary files format and content: BED files recording coordinates of fragments captured by scATAC-seq

organism: Danio rerio

source_name: Whole body, wild-type strain AB, 4 month-old

extract_protocol:
Samples were subjected to manual pulverization via grinded in liquid nitrogen. The pulverized tissues were aliquoted into 1.5 ml lysis buffer [10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sangon Biotech), 0.1% IGEPAL-CA630 (Sigma Aldrich) and 0.01% Digitonin (Thermo Scientific) in water], and followed by incubation for 3 minutes on ice for nuclei extraction.
Library preparations were performed with the CH ATAC-seq protocol

treatment_protocol: Hypothermal shocked

value: whole body

value: strain AB

value: wild-type

value: 4 months

tag: Sex

value: male


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 1_4h

value: cervical cancer cells

tag: treatment

value: 24h S4U labeling, wash-out


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 1_4h


title: Meso13-M2-MV-neg [71_Meso13-P19-4119-M2-MV-neg]

description:
condition 7
71_Meso13-P19-4119-M2-MV-neg

value: mesothelioma

value: Human pleural mesothelioma cell line Meso13


title: Meso13-Monos-MV-neg [33_Meso13-P19-3649-Monos-MV-neg]

description:
condition 3
33_Meso13-P19-3649-Monos-MV-neg

value: Monocytes


title: MOE_METATAC_210315-P14-Plate19

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P114)

value: mouse olfactory epithelium (P114)

value: postnatal day 14


title: Meso13-Monos-NI-pos [63_Meso13-P18-2333-Monos-NI-pos]

description:
condition 2
63_Meso13-P18-2333-Monos-NI-pos

value: uninfected

value: myeloid


title: Zebrafish_batch2_male1

description: CH ATAC-seq


title: MOE_METATAC_210315-P14-Plate20

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P115)

value: mouse olfactory epithelium (P115)

value: mouse olfactory epithelium


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 3_2h

value: HeLa 11ht

value: LARP1 KO


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 1_4h

value: WT


title: MOE_METATAC_220503-P14-Plate4

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P119)

value: mouse olfactory epithelium (P119)


title: MOE_METATAC_210315-P14-Plate18

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P113)

value: mouse olfactory epithelium (P113)


title: Zebrafish_batch2_female1

description: CH ATAC-seq

value: whole body

value: strain AB

value: wild-type

value: 4 months

value: Female


title: Meso34-Monos-NI-neg [29_Meso34-P34-8225-Monos-NI-neg]

description:
condition 1
29_Meso34-P34-8225-Monos-NI-neg

value: mesothelioma

value: Monocytes

value: Human pleural mesothelioma cell line Meso34


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 3_2h

value: cervical cancer cells

value: 24h S4U labeling, wash-out


title: MOE_METATAC_210315-P14-Plate17

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P112)

value: mouse olfactory epithelium (P112)

value: postnatal day 14


title: Zebrafish_batch1_male2

description: CH ATAC-seq

value: male


title: MOE_METATAC_210315-P14-Plate16

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P111)

value: mouse olfactory epithelium (P111)

value: mouse olfactory epithelium


title: Meso13-Monos-NI-pos [5_Meso13-P16-6864-Monos-NI-pos]

description:
condition 2
5_Meso13-P16-6864-Monos-NI-pos

source_name: Monocytes

value: uninfected

value: myeloid

value: Human pleural mesothelioma cell line Meso13


title: Zebrafish_batch1_male1

description: CH ATAC-seq

value: whole body

value: strain AB


title: MOE_METATAC_220503-P14-Plate1

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P116)

value: mouse olfactory epithelium (P116)

value: WT


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 3_2h

source_name: HeLa 11ht

value: HeLa 11ht


title: MOE_METATAC_210315-P14-Plate15

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P110)

value: mouse olfactory epithelium (P110)


title: Zebrafish_batch2_female2

description: CH ATAC-seq

value: wild-type

value: 4 months

value: Female


title: MOE_METATAC_210315-P14-Plate14

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P109)

value: mouse olfactory epithelium (P109)


title: Meso34-Monos-NI-pos [34_Meso34-P35-3649-Monos-NI-pos]

description:
condition 2
34_Meso34-P35-3649-Monos-NI-pos

value: Monocytes

value: Human pleural mesothelioma cell line Meso34


title: Zebrafish_batch1_female2

description: CH ATAC-seq


title: MOE_METATAC_210315-P14-Plate13

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P108)

value: mouse olfactory epithelium (P108)

value: postnatal day 14


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 2_2h

value: cervical cancer cells

value: LARP1 KO

value: 24h S4U labeling, wash-out


title: Zebrafish_batch1_female1

description: CH ATAC-seq

value: whole body


title: Earthworm_whole body, 4 month-old, 2

description: CH ATAC-seq

data_processing:
For each sequenced CHATAC-seq library, we obtained two FASTQ files, one of which contained combinatorial index for HY(768 indices) and Tn5 (384 indices) in specific base positions. We filtered reads with more than one mismatch in each index and trimmed adaptor sequences using trimmomatic(version 0.3.8). After that, reads from earthworm were aligned to earthworm GWHACBE00000000 genome(downloaded from Genome Warehouse) using BWA (version 0.7.15).  Taking the 9-bp duplication caused by Tn5 transposase into account, we shifted aligned reads + 4bp and -5bp for each positive and negative strand using alignmentSieve(deeptools 3.5.1).Then we used snaptools(version 1.4.8) to keep nonduplicate fragments with high mapping quality (MAPQ > 30) and proper length(<1000 bp) and extracted fragment files from the snap files. Subsequent analysis was performed by ArchR (version 1.0.2). We created arrow files from fragment files by ‘createArrowFiles function’ and constructed customized genome using ‘createGenomeAnnotation’ and ‘createGeneAnnotation function’.
Assembly: earthworm GWHACBE00000000 genome(downloaded from Genome Warehouse)
Supplementary files format and content: BED files recording coordinates of fragments captured by scATAC-seq

organism: Eisenia andrei

source_name: whole body

extract_protocol:
Samples were  subjected to manual pulverization via grinded in liquid nitrogen. The pulverized tissues were aliquoted into  1.5 ml lysis buffer  [10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sangon Biotech), 0.1% IGEPAL-CA630 (Sigma Aldrich) and 0.01% Digitonin (Thermo Scientific) in water], and followed by incubation for 3 minutes on ice for nuclei extraction.
Library preparations were performed with the CH ATAC-seq protocol


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 2_2h


title: MOE_METATAC_210315-P14-Plate11

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P106)

value: mouse olfactory epithelium (P106)

value: mouse olfactory epithelium


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 2_2h

value: WT


title: Whole body, wild-type Eisenia andrei , 4 month-old

description: 10x Genomics

data_processing:
We run cellranger-atac (v2.0.0) to pre-process 10X scATAC-seq data of earthworm with default parameters. Then we used fragment files from cellranger-atac outputs for downstream analysis using ArchR.
Assembly: earthworm GWHACBE00000000 genome(downloaded from Genome Warehouse)
Supplementary files format and content: BED files recording coordinates of fragments captured by scATAC-seq

extract_protocol:
Sample preparations were performed with the 10X Genomics sc-ATAC protocol
Library preparations were performed with the 10X Genomics sc-ATAC protocol


title: MOE_METATAC_210315-P14-Plate12

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P107)

value: mouse olfactory epithelium (P107)


title: Earthworm_whole body, 4 month-old, 1

description: CH ATAC-seq


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 3_2h

value: HeLa 11ht


title: MOE_METATAC_210311-P14-Plate10

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P105)

value: mouse olfactory epithelium (P105)


title: Meso34-Monos-MV-neg [35_Meso34-P35-3649-Monos-MV-neg]

description:
condition 3
35_Meso34-P35-3649-Monos-MV-neg

value: schwarz attenuated measles virus

value: mesothelioma


title: MOE_METATAC_210311-P14-Plate9

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P104)

value: mouse olfactory epithelium (P104)


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 1_2h


title: Meso13-M2-NI-neg [81_Meso13-P19-2333-M2-NI-neg]

description:
condition 5
81_Meso13-P19-2333-M2-NI-neg

value: uninfected

value: Human pleural mesothelioma cell line Meso13


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 1_2h


title: Meso13-M2-NI-pos [68_Meso13-P19-2333-M2-NI-pos]

description:
condition 6
68_Meso13-P19-2333-M2-NI-pos

value: myeloid


title: MOE_METATAC_210311-P14-Plate8

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P103)

value: mouse olfactory epithelium (P103)

value: postnatal day 14


title: Meso13-Monos-NI-neg [21_Meso13-P16-6864-Monos-NI-neg]

description:
condition 1
21_Meso13-P16-6864-Monos-NI-neg

value: Monocytes


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 2_2h

value: cervical cancer cells

value: LARP1 KO

value: 24h S4U labeling, wash-out


title: Meso34-M2-NI-pos [11_Meso34-P33-7677-M2-NI-pos]

description:
condition 6
11_Meso34-P33-7677-M2-NI-pos

value: Human pleural mesothelioma cell line Meso34


title: MOE_METATAC_210311-P14-Plate6

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P101)

value: mouse olfactory epithelium (P101)

value: mouse olfactory epithelium

value: WT


title: MOE_METATAC_210311-P14-Plate7

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P102)

value: mouse olfactory epithelium (P102)


title: Meso13-Monos-NI-neg [56_Meso13-P17-1382-Monos-NI-neg]

description:
condition 1
56_Meso13-P17-1382-Monos-NI-neg


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 1_2h

value: HeLa 11ht


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 3_0h


title: Meso13-M2-MV-pos [20_Meso13-P15-6532-M2-MV-pos]

description:
condition 8
20_Meso13-P15-6532-M2-MV-pos

value: schwarz attenuated measles virus


title: Meso13-M2-MV-pos [82_Meso13-P19-2333-M2-MV-pos]

description:
condition 8
82_Meso13-P19-2333-M2-MV-pos


title: Meso13-Monos-MV-pos [18_Meso13-P15-6532-Monos-MV-pos]

description:
condition 4
18_Meso13-P15-6532-Monos-MV-pos


title: MOE_METATAC_210311-P14-Plate5

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P100)

value: mouse olfactory epithelium (P100)


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 3_0h


title: Meso34-Monos-MV-pos [96_Meso34-P31-2333-Monos-MV-pos]

description:
condition 4
96_Meso34-P31-2333-Monos-MV-pos


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 3_0h


title: MOE_METATAC_210311-P14-Plate4

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P99)

value: mouse olfactory epithelium (P99)


title: Meso34-M2-MV-pos [28_Meso34-P33-7677-M2-MV-pos]

description:
condition 8
28_Meso34-P33-7677-M2-MV-pos


title: Meso34-M2-MV-pos [53_Meso34-P36-3649-M2-MV-pos]

description:
condition 8
53_Meso34-P36-3649-M2-MV-pos


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 3_0h


title: MOE_METATAC_210311-P14-Plate3

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P98)

value: mouse olfactory epithelium (P98)


title: IK23_ASC52_DED_5

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were processed and normalised using RMA with Transcriptome analysis Console software

label: biotin

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Thermo Fisher Scientific).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: cell line background

value: ASC52htert adipocyte derived mesenchymal stem cells

value: Dedifferentiated adipocytes


title: IK19_ASC52_DED_2


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 2_0h


title: IK20_ASC52_DED_3


title: Meso13-Monos-NI-neg [78_Meso13-P18-2333-Monos-NI-neg]

description:
condition 1
78_Meso13-P18-2333-Monos-NI-neg

value: uninfected

value: mesothelioma

value: Human pleural mesothelioma cell line Meso13


title: MOE_METATAC_210311-P14-Plate2

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P97)

tag: tissue

value: mouse olfactory epithelium (P97)

value: postnatal day 14


title: IK22_ASC52_DED_4


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 2_0h

value: cervical cancer cells

value: 24h S4U labeling, wash-out


title: IK17_ASC52_MA_5

value: Mature adipocytes


title: MOE_METATAC_210311-P14-Plate1

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P96)

value: mouse olfactory epithelium (P96)

value: mouse olfactory epithelium

value: WT

tag: age


title: Meso13-Monos-MV-neg [44_Meso13-P17-1382-Monos-MV-neg]

description:
condition 3
44_Meso13-P17-1382-Monos-MV-neg

value: schwarz attenuated measles virus

value: Monocytes


title: Meso34-Monos-NI-neg [80_Meso34-P31-2333-Monos-NI-neg]

description:
condition 1
80_Meso34-P31-2333-Monos-NI-neg

value: Human pleural mesothelioma cell line Meso34


title: MOE_METATAC_220503-P7-Plate20

description: MOE_METATAC_peak files

value: postnatal day 7


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 2_0h

source_name: HeLa 11ht

value: HeLa 11ht


title: Meso34-Monos-NI-neg [23_Meso34-P32-7677-Monos-NI-neg]

description:
condition 1
23_Meso34-P32-7677-Monos-NI-neg


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 KO, biol rep 1_0h

value: LARP1 KO


title: IK16_ASC52_MA_4

value: ASC52htert adipocyte derived mesenchymal stem cells


title: Meso13-Monos-NI-pos [1_Meso13-P15-6532-Monos-NI-pos]

description:
condition 2
1_Meso13-P15-6532-Monos-NI-pos

source_name: Monocytes

value: uninfected

value: myeloid


title: MOE_METATAC_220503-P7-Plate19

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P95)

value: mouse olfactory epithelium (P95)


title: IK18_ASC52_DED_1

value: Dedifferentiated adipocytes


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 1_2h

value: cervical cancer cells


title: MOE_METATAC_220503-P7-Plate18

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P94)

value: mouse olfactory epithelium (P94)


title: IK12_ASC52_MA_1

value: Mature adipocytes


title: Meso13-M2-NI-neg [74_Meso13-P17-1382-M2-NI-neg]

description:
condition 5
74_Meso13-P17-1382-M2-NI-neg

value: mesothelioma

value: Human pleural mesothelioma cell line Meso13


title: IK13_ASC52_MA_2


title: IK11_ASC52_MSC_5

value: mesenchymal stem cells


title: MOE_METATAC_220503-P7-Plate17

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P93)

value: mouse olfactory epithelium (P93)

value: mouse olfactory epithelium

value: WT


title: Meso13-Monos-NI-neg [94_Meso13-P18-4288-Monos-NI-neg-]

description:
condition 1
94_Meso13-P18-4288-Monos-NI-neg-

value: Monocytes


title: HeLa 11ht cells, Canonical mRNA, LARP1 KO, biol rep 1_0h

value: HeLa 11ht

value: 24h S4U labeling, wash-out


title: MOE_METATAC_220503-P7-Plate16

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P92)

value: mouse olfactory epithelium (P92)

value: postnatal day 7


title: HeLa 11ht cells, Canonical mRNA, LARP1 WT, biol rep 1_0h


title: Meso13-Monos-MV-neg [64_Meso13-P18-2333-Monos-MV-neg]

description:
condition 3
64_Meso13-P18-2333-Monos-MV-neg

value: schwarz attenuated measles virus


title: MOE_METATAC_220503-P7-Plate15

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P91)

value: mouse olfactory epithelium (P91)


title: MOE_METATAC_220503-P7-Plate13

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P89)

value: mouse olfactory epithelium (P89)


title: HUVEC_3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: counts.matrix.norm

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (Davis et al., Kraken: A set of tools for quality control and analysis of high-throughput sequence data). Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl human genome version hg19 (GRCh37.p5) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.62 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Only genes with a minimum fold change of +- 2 (log2 +-1), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: hg19
Supplementary_files_format_and_content: library size normalized counts per sample

source_name: Endothelial cells

extract_protocol:
RNA was isolated from cultured endothelial cells using the miRNeasy micro Kit (Qiagen) combined with on-column Dnase digestion (DNase-Free DNase Set, Qiagen)
4µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in minimum of 37M reads per library with 1x75bp single end setup.

value: human umbilical vein endothelial cells


title: Meso13-M2-NI-neg [51_Meso13-P20-3649-M2-NI-neg]

description:
condition 5
51_Meso13-P20-3649-M2-NI-neg

value: uninfected


title: HUVEC_2

description: counts.matrix.norm


title: HUVEC_1

description: counts.matrix.norm


title: HeLa 11ht cells, 5′TOP mRNA, LARP1 WT, biol rep 1_0h

value: cervical cancer cells


title: Meso13-M2-MV-neg [60_Meso13-P17-1382-M2-MV-neg]

description:
condition 7
60_Meso13-P17-1382-M2-MV-neg

value: mesothelioma


title: Meso34-Monos-NI-neg [86_Meso34-P31-4119-Monos-NI-neg]

description:
condition 1
86_Meso34-P31-4119-Monos-NI-neg

value: Human pleural mesothelioma cell line Meso34


title: IK14_ASC52_MA_3

value: ASC52htert adipocyte derived mesenchymal stem cells

value: Mature adipocytes


title: Meso34-Monos-NI-pos [36_Meso34-P35-5300-Monos-NI-pos]

description:
condition 2
36_Meso34-P35-5300-Monos-NI-pos

value: myeloid


title: HMVEC_2

description: counts.matrix.norm

value: human micro-vascular endothelial cells


title: IK08_ASC52_MSC_3

value: mesenchymal stem cells


title: MOE_METATAC_220503-P7-Plate12

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P88)

value: mouse olfactory epithelium (P88)

value: mouse olfactory epithelium

value: WT


title: Meso13-M2-NI-pos [3_Meso13-P15-6532-M2-NI-pos]

description:
condition 6
3_Meso13-P15-6532-M2-NI-pos

value: Human pleural mesothelioma cell line Meso13


title: HMVEC_1

description: counts.matrix.norm


title: MOE_METATAC_220503-P7-Plate11

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P87)

value: mouse olfactory epithelium (P87)

value: postnatal day 7


title: IK07_ASC52_MSC_2


title: JU72_AT_adjacent_Pz60

extract_protocol: RNA was extracted with QIAGEN RNeasy Lipid Tissue Mini kit in accordance with the prescribed protocol provided with the kit.

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: lymphnode positivity

value: neg

tag: hystotype

value: Ductal

tag: tumor grade

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos

value: IHC 3+):neg

tag: tumor ki67 positivity (pos

value: Adipose tissues (AT)


title: IK06_ASC52_MSC_1

tag: cell type


title: IK10_ASC52_MSC_4


title: MOE_METATAC_220503-P7-Plate10

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P86)

value: mouse olfactory epithelium (P86)

tag: genotype


title: JU73_AT_distant_Pz61

value: pos

value: Lobular


title: HAEC_3

description: counts.matrix.norm

value: human aortic endothelial cells


title: HMVEC_3

description: counts.matrix.norm

value: human micro-vascular endothelial cells


title: MOE_METATAC_220503-P7-Plate14

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P90)

value: mouse olfactory epithelium (P90)


title: JU74_AT_adjacent_Pz61


title: MOE_METATAC_220503-P7-Plate8

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P84)

value: mouse olfactory epithelium (P84)


title: MOE_METATAC_220503-P7-Plate9

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P85)

value: mouse olfactory epithelium (P85)

value: mouse olfactory epithelium


title: Meso34-M2-MV-neg [16_Meso34-P34-8225-M2-MV-neg]

description:
condition 7
16_Meso34-P34-8225-M2-MV-neg

tag: infection

value: schwarz attenuated measles virus

tag: cell population sorted

value: mesothelioma

tag: donor

tag: cocultured cecll type

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso34


title: HAEC_2

description: counts.matrix.norm


title: Meso34-Monos-MV-neg [92_Meso34-P30-7306-Monos-MV-neg-]

description:
condition 3
92_Meso34-P30-7306-Monos-MV-neg-

value: Monocytes


title: JU71_AT_distant_Pz60

tag: subject status

value: patients subjected to mastectomy

tag: age

value: neg

tag: tissue


title: HAEC_1

description: counts.matrix.norm


title: MOE_METATAC_220503-P7-Plate7

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P83)

value: mouse olfactory epithelium (P83)

value: WT

tag: treatment

value: postnatal day 7


title: Meso13-M2-MV-neg [69_Meso13-P19-2333-M2-MV-neg]

description:
condition 7
69_Meso13-P19-2333-M2-MV-neg

value: Human pleural mesothelioma cell line Meso13


title: HLEC_3

description: counts.matrix.norm

value: human lymphatic endothelial cells


title: JU69_AT_distant_Pz59

tag: bmi

tag: lymphnode positivity

tag: hystotype

value: Ductal

tag: tumor grade

value: IHC 3+):pos

value: Adipose tissues (AT)


title: MOE_METATAC_220503-P7-Plate6

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P82)

value: mouse olfactory epithelium (P82)


title: HLEC_2

description: counts.matrix.norm


title: Meso13-Monos-MV-pos [22_Meso13-P16-6864-Monos-MV-pos]

description:
condition 4
22_Meso13-P16-6864-Monos-MV-pos

value: myeloid


title: JU70_AT_adjacent_Pz59

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos


title: JU64_AT_adjacent_Pz55

value: IHC 3+):neg

tag: tumor ki67 positivity (pos


title: JU63_AT_distant_Pz55


title: Meso13-M2-MV-pos [26_Meso13-P17-6864-M2-MV-pos]

description:
condition 8
26_Meso13-P17-6864-M2-MV-pos

tag: infection

value: schwarz attenuated measles virus

tag: cell population sorted


title: Meso13-M2-NI-pos [70_Meso13-P19-4119-M2-NI-pos]

description:
condition 6
70_Meso13-P19-4119-M2-NI-pos

value: uninfected

tag: donor

tag: cocultured cecll type


title: MOE_METATAC_220503-P7-Plate4

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P80)

value: mouse olfactory epithelium (P80)

tag: cell type

value: mouse olfactory epithelium

tag: genotype


title: HLEC_1

description: counts.matrix.norm


title: Meso34-Monos-NI-pos [93_Meso34-P30-7306-Monos-NI-pos-]

description:
condition 2
93_Meso34-P30-7306-Monos-NI-pos-

source_name: Monocytes

value: Monocytes

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso34


title: Brain, 46E_G90_L40463_500

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

description: Glyphosate_0024_1_BR_Whole_C1_ISRRZ_L40463

data_processing:
Raw reads were aligned to the reference genome GrCm38 using STAR v2.7.5b , and summarization of counts at the gene level was conducted by means of featureCounts, as implemented in the R-package Rsubread . Quality controls to assess reads amount and mapping were conducted using MultiQC v1.12. Then, raw counts were imported into DESeq2 v1.34.0 and transformed by variance stabilizing transformation (VST) to conduct principal component analysis (PCA) for further quality controls. Sex-check was carried out using the counts mapping on X and Y chromosomes using a custom R script [39]. Normalization and differential expression were conducted by means of DESeq2, using a Likelihood Ratio Test (LRT) to assess the relationship between different dosages and gene expression, including sex as a covariate. P-values were adjusted for multiple testing using the False Discovery Rate method (FDR)
Assembly: GrCm38
Supplementary files format and content: tab delimited file including unfiltered raw counts (genes in rows, samples in column)

source_name: brain (bulk tissue)

extract_protocol:
RNA was isolated from half-brain samples using the RNeasy Kit (Qiagen)
Sequencing libraries were prepared with 250 ng of total RNA using Illumina Stranded Total RNA with Ribo-Zero Plus library preparation (Illumina Inc). PCR-enriched fragments were validated on a 2200 TapeStation (Agilent Technologies) and quantitated via qPCR. The final library was sequenced by 100 bp paired-end sequencing on a HiSeq 2500 (Illumina) at the Collaborative Sequencing Center (Translational Genomics Research Institute, Phoenix, AZ)

treatment_protocol: Chemically pure glyphosate (N-(Phosphonomethyl)glycine; C3H8NO5P) was purchased from Sigma-Aldrich (product number P9556) and prepared at 0.107 g/L in 1.89 M sodium hydroxide (NaOH). The solution was adjusted to a pH of 7 and serially diluted using RO water to achieve the lower concentrations. This solution with no glyphosate served as the vehicle. Mice were randomly assigned to receive one of three dosages starting at 4 months of age: vehicle (control) 125 mg/kg, 250 mg/kg, 500 mg/kg of body weight. Dosages were administered daily via oral gavage for a total of 14 days

tag: tissue

value: brain (bulk tissue)

tag: treatment

value: glyphosate 500 mg/Kg

tag: Sex

value: male


title: JU61_AT_distant_Pz54

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: age

tag: lymphnode positivity

value: neg

tag: hystotype

value: Lobular


title: MOE_METATAC_220503-P7-Plate3

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P79)

value: mouse olfactory epithelium (P79)

value: WT

value: postnatal day 7


title: JU60_AT_adjacent_Pz53

value: pos

value: Ductal

tag: tumor grade

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos

value: Adipose tissues (AT)


title: Meso34-M2-NI-neg [88_Meso34-P31-4119-M2-NI-neg]

description:
condition 5
88_Meso34-P31-4119-M2-NI-neg

tag: infection

value: uninfected

tag: cell population sorted

value: mesothelioma

tag: donor

tag: cocultured cecll type


title: Meso34-M2-NI-neg [85_Meso34-P31-2333-M2-NI-neg]

description:
condition 5
85_Meso34-P31-2333-M2-NI-neg

tag: tumor cell line


title: MOE_METATAC_220503-P7-Plate5

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P81)

tag: tissue

value: mouse olfactory epithelium (P81)

tag: cell type

value: mouse olfactory epithelium

tag: genotype

tag: treatment


title: MOE_METATAC_220503-P7-Plate1

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P77)

value: mouse olfactory epithelium (P77)

tag: age


title: Meso34-M2-MV-pos [31_Meso34-P34-8225-M2-MV-pos]

description:
condition 8
31_Meso34-P34-8225-M2-MV-pos

value: schwarz attenuated measles virus

value: myeloid

value: Human pleural mesothelioma cell line Meso34


title: MOE_METATAC_210315-P7-Plate20

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P76)

value: mouse olfactory epithelium (P76)


title: Meso13-Monos-NI-neg [17_Meso13-P15-6532-Monos-NI-neg]

description:
condition 1
17_Meso13-P15-6532-Monos-NI-neg

value: Monocytes

value: Human pleural mesothelioma cell line Meso13


title: Brain, 45F_G66_L40457_250

description: Glyphosate_0018_1_BR_Whole_C1_ISRRZ_L40457

value: brain (bulk tissue)

value: glyphosate 250 mg/kg

tag: Sex

value: male


title: Meso13-Monos-MV-pos [48_Meso13-P19-3649-Monos-MV-pos]

description:
condition 4
48_Meso13-P19-3649-Monos-MV-pos


title: MOE_METATAC_210315-P7-Plate19

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P75)

value: mouse olfactory epithelium (P75)

value: WT

value: postnatal day 7


title: MOE_METATAC_210315-P7-Plate18

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P74)

value: mouse olfactory epithelium (P74)


title: JU56_AT_adjacent_Pz49

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: lymphnode positivity

value: pos

tag: hystotype

value: Ductal

value: IHC 3+):neg

tag: tumor ki67 positivity (pos

value: Adipose tissues (AT)


title: Brain, 44C_G79_L40460_500

description: Glyphosate_0021_1_BR_Whole_C1_ISRRZ_L40460

value: glyphosate 500 mg/Kg

value: female


title: Brain, 46D_G87_L40462_500

description: Glyphosate_0023_1_BR_Whole_C1_ISRRZ_L40462


title: Brain, 45G_G64_L40456_250

description: Glyphosate_0017_1_BR_Whole_C1_ISRRZ_L40456


title: Meso13-M2-NI-neg [83_Meso13-P19-4119-M2-NI-neg]

description:
condition 5
83_Meso13-P19-4119-M2-NI-neg

value: uninfected

value: mesothelioma


title: JU55_AT_distant_Pz49

tag: tumor grade

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos


title: MOE_METATAC_210315-P7-Plate17

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P73)

value: mouse olfactory epithelium (P73)

value: mouse olfactory epithelium


title: JU59_AT_distant_Pz53


title: MOE_METATAC_220503-P7-Plate2

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P78)

value: mouse olfactory epithelium (P78)


title: Meso13-Monos-MV-neg [95_Meso13-P18-4288-Monos-MV-neg-]

description:
condition 3
95_Meso13-P18-4288-Monos-MV-neg-

tag: infection

value: schwarz attenuated measles virus

tag: cell population sorted

tag: donor

tag: cocultured cecll type

value: Monocytes

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso13


title: Brain, 43E_G45_L40452_125

description: Glyphosate_0013_1_BR_Whole_C1_ISRRZ_L40452

tag: tissue

value: brain (bulk tissue)

tag: genotype

value: WT

tag: treatment

value: glyphosate 125 mg/kg

value: male


title: JU52_AT_adjacent_Pz47

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: age

value: neg

value: Ductal


title: JU62_AT_adjacent_Pz54

tag: lymphnode positivity

tag: hystotype

value: Lobular

value: IHC 3+):neg

tag: tumor ki67 positivity (pos

value: Adipose tissues (AT)


title: JU54_AT_adjacent_Pz48

value: pos

tag: tumor grade

tag: tumor size (t)

tag: tumor er positivity (pos


title: JU51_AT_distant_Pz47

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos


title: Meso13-M2-NI-neg [25_Meso13-P17-6864-M2-NI-neg]

description:
condition 5
25_Meso13-P17-6864-M2-NI-neg

tag: infection

value: uninfected

tag: cell population sorted

value: mesothelioma

tag: donor


title: Brain, 43D_G40_L40450_125

description: Glyphosate_0011_1_BR_Whole_C1_ISRRZ_L40450

tag: tissue

tag: Sex


title: Brain, 45H_G71_L40458_250

description: Glyphosate_0019_1_BR_Whole_C1_ISRRZ_L40458

tag: genotype

tag: treatment

value: glyphosate 250 mg/kg


title: MOE_METATAC_210315-P7-Plate16

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P72)

value: mouse olfactory epithelium (P72)

tag: cell type

value: mouse olfactory epithelium

value: postnatal day 7


title: Brain, 43C_G34_L40449_125

description: Glyphosate_0010_1_BR_Whole_C1_ISRRZ_L40449

value: brain (bulk tissue)


title: MOE_METATAC_210315-P7-Plate13

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P69)

value: mouse olfactory epithelium (P69)

value: WT

tag: age


title: MOE_METATAC_210315-P7-Plate14

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P70)

value: mouse olfactory epithelium (P70)


title: Brain, 45A_G49_L40453_250

description: Glyphosate_0014_1_BR_Whole_C1_ISRRZ_L40453

value: female


title: Meso13-Monos-MV-neg [6_Meso13-P16-6864-Monos-MV-neg]

description:
condition 3
6_Meso13-P16-6864-Monos-MV-neg

value: schwarz attenuated measles virus

tag: cocultured cecll type

value: Monocytes

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso13


title: Brain, 42A_G25_L40447_125

description: Glyphosate_0008_1_BR_Whole_C1_ISRRZ_L40447

value: glyphosate 125 mg/kg


title: Meso34-M2-NI-neg [76_Meso34-P30-1159-M2-NI-neg]

description:
condition 5
76_Meso34-P30-1159-M2-NI-neg

value: Human pleural mesothelioma cell line Meso34


title: JU48_AT_adjacent_Pz44

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: lymphnode positivity

value: neg

tag: hystotype

value: Lobular

value: IHC 3+):neg

tag: tumor ki67 positivity (pos

value: Adipose tissues (AT)


title: Meso13-M2-MV-neg [39_Meso13-P20-3649-M2-MV-neg]

description:
condition 7
39_Meso13-P20-3649-M2-MV-neg

value: mesothelioma


title: Brain, 43B_G18_L40445_Control

description: Glyphosate_0006_1_BR_Whole_C1_ISRRZ_L40445

value: Control


title: Meso13-M2-NI-neg [19_Meso13-P15-6532-M2-NI-neg]

description:
condition 5
19_Meso13-P15-6532-M2-NI-neg

value: uninfected


title: MOE_METATAC_210315-P7-Plate11

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P67)

value: mouse olfactory epithelium (P67)

value: mouse olfactory epithelium

value: postnatal day 7


title: JU53_AT_distant_Pz48

value: pos

value: Ductal

tag: tumor grade

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos


title: JU47_AT_distant_Pz44

tag: tissue


title: JU49_AT_distant_Pz46

value: IHC 3+):pos


title: JU46_AT_adjacent_Pz43s


title: Brain, 46B_G15_L40444_Control

description: Glyphosate_0005_1_BR_Whole_C1_ISRRZ_L40444

value: brain (bulk tissue)

tag: genotype

value: WT

tag: Sex

value: female


title: Brain, 42B_G29_L40448_125

description: Glyphosate_0009_1_BR_Whole_C1_ISRRZ_L40448

tag: treatment

value: glyphosate 125 mg/kg


title: MOE_METATAC_210315-P7-Plate10

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P66)

value: mouse olfactory epithelium (P66)

tag: cell type

tag: age


title: JU50_AT_adjacent_Pz46

value: patients subjected to mastectomy

value: neg


title: Brain, 46A_G9_L40443_Control

description: Glyphosate_0004_1_BR_Whole_C1_ISRRZ_L40443


title: Meso34-M2-MV-neg [12_Meso34-P33-7677-M2-MV-neg]

description:
condition 7
12_Meso34-P33-7677-M2-MV-neg

tag: infection

value: schwarz attenuated measles virus

tag: cell population sorted

tag: donor

tag: cocultured cecll type

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso34


title: JU44_AT_adjacent_Pz43d

tag: subject status

tag: bmi

tag: lymphnode positivity

tag: hystotype

value: IHC 3+):neg

tag: tumor ki67 positivity (pos

value: Adipose tissues (AT)


title: Meso34-Monos-MV-neg [37_Meso34-P35-5300-Monos-MV-neg]

description:
condition 3
37_Meso34-P35-5300-Monos-MV-neg

value: mesothelioma

value: Monocytes


title: Brain, 41F_G5_L40442_Control

description: Glyphosate_0003_1_BR_Whole_C1_ISRRZ_L40442

value: Control

value: male


title: MOE_METATAC_210315-P7-Plate12

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P68)

value: mouse olfactory epithelium (P68)

value: mouse olfactory epithelium

value: postnatal day 7


title: MOE_METATAC_210315-P7-Plate8

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P64)

value: mouse olfactory epithelium (P64)

value: WT


title: MOE_METATAC_210315-P7-Plate9

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P65)

value: mouse olfactory epithelium (P65)


title: JU45_AT_distant_Pz43s

value: pos

value: Ductal

tag: tumor grade

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos


title: Meso13-Monos-MV-neg [2_Meso13-P15-6532-Monos-MV-neg]

description:
condition 3
2_Meso13-P15-6532-Monos-MV-neg

value: Human pleural mesothelioma cell line Meso13


title: Meso34-M2-NI-neg [30_Meso34-P34-8225-M2-NI-neg]

description:
condition 5
30_Meso34-P34-8225-M2-NI-neg

value: uninfected


title: JU40_AT_adjacent_Pz41

value: patients subjected to mastectomy

value: IHC 3+):pos

tag: tissue


title: MOE_METATAC_210315-P7-Plate7

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P63)

value: mouse olfactory epithelium (P63)

tag: cell type

tag: genotype

tag: treatment

tag: age


title: Meso13-M2-MV-pos [84_Meso13-P19-4119-M2-MV-pos]

description:
condition 8
84_Meso13-P19-4119-M2-MV-pos

tag: infection

value: schwarz attenuated measles virus

tag: cell population sorted

value: myeloid

tag: donor

tag: cocultured cecll type


title: MOE_METATAC_210315-P7-Plate6

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P62)

value: mouse olfactory epithelium (P62)


title: Brain, 41E_G1_L40440_Control

description: Glyphosate_0001_1_BR_Whole_C1_ISRRZ_L40440

source_name: brain (bulk tissue)

value: brain (bulk tissue)

value: Control

tag: Sex

value: male


title: Meso34-M2-NI-pos [41_Meso34-P36-5300-M2-NI-pos]

description:
condition 6
41_Meso34-P36-5300-M2-NI-pos

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso34


title: 3T3-H-OE3

description: 3T3wt_vs_3T3 HNF4a OE72h.gene_exp.diff.xlsx

data_processing:
De-multiplexed read sequences were aligned to the reference genome using STAR_2.5.0b.
Assembly and differential expression was estimated using Cufflinks 2.2.1 through bioinformatics apps available on Illumina Sequence Hub.
Assembly: mm10
Supplementary files format and content: Differentially expressed genes data table.

growth_protocol: NIH3T3 Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was harvested using Trizol reagent from Sigma

tag: cell line

value: Mousefibroblast cells

value: HNF4A ectopic expressed


title: MOE_METATAC_210315-P7-Plate5

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P61)

value: mouse olfactory epithelium (P61)

value: mouse olfactory epithelium

value: WT

value: postnatal day 7


title: Brain, 44A_G4_L40441_500

description: Glyphosate_0002_1_BR_Whole_C1_ISRRZ_L40441

value: glyphosate 500 mg/Kg

value: female


title: Meso13-M2-NI-pos [59_Meso13-P17-1382-M2-NI-pos]

description:
condition 6
59_Meso13-P17-1382-M2-NI-pos

value: uninfected

value: Human pleural mesothelioma cell line Meso13


title: JU39_AT_distant_Pz41

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: lymphnode positivity

value: pos

tag: hystotype

value: Ductal

tag: tumor grade

value: IHC 3+):pos

tag: tumor ki67 positivity (pos

value: Adipose tissues (AT)


title: 3T3-H-OE2

tag: cell type


title: JU38_AT_adjacent_Pz40

value: neg

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos

value: IHC 3+):neg

tag: tissue


title: MOE_METATAC_210315-P7-Plate4

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P60)

value: mouse olfactory epithelium (P60)

tag: genotype

tag: treatment

tag: age


title: 3T3-H-OE1

value: Mousefibroblast cells

value: HNF4A ectopic expressed


title: MOE_METATAC_210315-P7-Plate3

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P59)

value: mouse olfactory epithelium (P59)

value: mouse olfactory epithelium


title: Meso34-Monos-NI-pos [13_Meso34-P34-8225-Monos-NI-pos]

description:
condition 2
13_Meso34-P34-8225-Monos-NI-pos

source_name: Monocytes

tag: infection

tag: cell population sorted

value: myeloid

tag: donor

tag: cocultured cecll type

value: Monocytes

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso34


title: 3T3-WT3-RNA

tag: cell line

value: Empty Vector


title: 3T3-WT2-RNA


title: MOE_METATAC_210315-P7-Plate2

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P58)

value: mouse olfactory epithelium (P58)

value: WT

value: postnatal day 7


title: Meso34-Monos-MV-neg [87_Meso34-P31-4119-Monos-MV-neg]

description:
condition 3
87_Meso34-P31-4119-Monos-MV-neg

value: schwarz attenuated measles virus

value: mesothelioma


title: MOE_METATAC_210315-P7-Plate1

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P57)

value: mouse olfactory epithelium (P57)


title: JU37_AT_distant_Pz40

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: lymphnode positivity

value: neg

tag: hystotype

value: Ductal

tag: tumor grade

value: Adipose tissues (AT)


title: JU34_AT_adjacent_Pz37

value: pos

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

value: IHC 3+):neg

tag: tumor ki67 positivity (pos


title: JU43_AT_distant_Pz43d

tag: tumor her2 positivity (pos

tag: tissue


title: JU35_AT_distant_Pz39

tag: age


title: JU36_AT_adjacent_Pz39


title: Meso34-M2-NI-pos [61_Meso34-P30-1159-M2-NI-pos]

description:
condition 6
61_Meso34-P30-1159-M2-NI-pos

tag: infection

value: uninfected

tag: cell population sorted


title: 3T3-WT1-RNA

tag: cell type

value: Mousefibroblast cells

tag: genotype


title: MOE_METATAC_220503-P3-Plate24

description: MOE_METATAC_peak files

value: mouse olfactory epithelium

tag: treatment

value: postnatal day 3


title: Meso34-Monos-NI-pos [7_Meso34-P32-7677-Monos-NI-pos]

description:
condition 2
7_Meso34-P32-7677-Monos-NI-pos

value: myeloid

tag: donor

tag: cocultured cecll type

value: Monocytes

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso34


title: HNF4A-KO3-RNA

description: WTliver_vs_HNF4AKOliver.gene_exp.diff.xlsx

source_name: Liver cells

tag: cell line

value: Liver cells

value: Hepatocytes

value: HNF4A KO


title: MOE_METATAC_220503-P3-Plate23

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P56)

value: mouse olfactory epithelium (P56)

value: WT


title: HNF4A-KO2-RNA


title: JU33_AT_distant_Pz37

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: lymphnode positivity

tag: hystotype

tag: tumor grade


title: Meso34-M2-MV-neg [73_Meso34-P31-2333-M2-MV-neg]

description:
condition 7
73_Meso34-P31-2333-M2-MV-neg

value: schwarz attenuated measles virus

value: mesothelioma


title: MOE_METATAC_220503-P3-Plate22

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P55)

value: mouse olfactory epithelium (P55)


title: Meso34-M2-NI-pos [15_Meso34-P34-8225-M2-NI-pos]

description:
condition 6
15_Meso34-P34-8225-M2-NI-pos


title: HNF4A-KO1-RNA


title: MOE_METATAC_220503-P3-Plate21

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P54)

value: mouse olfactory epithelium (P54)


title: MOE_METATAC_220503-P3-Plate20

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P53)

value: mouse olfactory epithelium (P53)


title: Meso34-Monos-MV-neg [14_Meso34-P34-8225-Monos-MV-neg]

description:
condition 3
14_Meso34-P34-8225-Monos-MV-neg


title: Meso13-Monos-NI-pos [43_Meso13-P17-1382-Monos-NI-pos]

description:
condition 2
43_Meso13-P17-1382-Monos-NI-pos

value: uninfected

value: Human pleural mesothelioma cell line Meso13


title: Liver-WT2-RNA


title: Liver-WT3RNA


title: JU30_AT_adjacent_Pz34

value: neg

value: Ductal

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos

value: IHC 3+):neg

tag: tumor ki67 positivity (pos

value: Adipose tissues (AT)


title: MOE_METATAC_220503-P3-Plate18

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P51)

tag: tissue

value: mouse olfactory epithelium (P51)

tag: cell type

value: mouse olfactory epithelium

tag: age

value: postnatal day 3


title: Meso34-Monos-MV-pos [24_Meso34-P32-7677-Monos-MV-pos]

description:
condition 4
24_Meso34-P32-7677-Monos-MV-pos

tag: infection

tag: cell population sorted

value: myeloid

tag: donor

value: Monocytes

value: Human pleural mesothelioma cell line Meso34


title: Liver-WT1-RNA

tag: cell line

value: Liver cells

value: Hepatocytes

tag: genotype

value: WT


title: MOE_METATAC_220503-P3-Plate19

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P52)

value: mouse olfactory epithelium (P52)

tag: treatment


title: JU29_AT_distant_Pz34

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: lymphnode positivity


title: JU32_AT_adjacent_Pz35

value: pos

tag: hystotype

tag: tumor grade

tag: tumor size (t)


title: JU31_AT_distant_Pz35

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos


title: JU27_AT_distant_Pz33

tag: tumor ki67 positivity (pos

tag: tissue


title: MOE_METATAC_220503-P3-Plate17

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P50)

value: mouse olfactory epithelium (P50)

tag: cell type

tag: age


title: JU25_AT_distant_Pz32


title: Meso34-M2-NI-pos [89_Meso34-P31-4119-M2-NI-pos]

description:
condition 6
89_Meso34-P31-4119-M2-NI-pos

tag: infection

value: uninfected

tag: cell population sorted

tag: donor

tag: cocultured cecll type

tag: tumor cell line


title: JU26_AT_adjacent_Pz32

tag: subject status

tag: bmi

value: Ductal


title: MOE_METATAC_220503-P3-Plate16

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P49)

value: mouse olfactory epithelium (P49)

tag: genotype

tag: treatment


title: Meso34-Monos-NI-pos [45_Meso34-P30-1159-Monos-NI-pos]

description:
condition 2
45_Meso34-P30-1159-Monos-NI-pos


title: MOE_METATAC_220503-P3-Plate15

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P48)

value: mouse olfactory epithelium (P48)


title: IgG_control_for DDX6 RIPseq_1

city: Clayton

first: Partha

last: Das

state: VIC

address: 15 innovation walk

country: Australia

institute: Monash Biomedicine Discovery Institute, Monash University

description: Paired end 150bp

data_processing:
Low quality reads were filtered out using trim galore (v0.6.5)
The 150bp paired end reads were mapped to the mm10 mouse genome assembly using Bowtie 2 (v2.3.2) and For RNAseq data, Filtered reads were aligned to the mm10 mouse genome assembly and the GENCODE version M23 mouse transcriptome using STAR RNA-seq alignment v2.6.3b
BigWig tracks were generated using the ‘bamCoverage’ program from the DeepTools software suite (v2.5.3), with reads extended to 300bp and tracks normalized using the  RPKM (Reads Per Kilobase per Million mapped reads) algorithm.
Peak calling was done with the ExomePeak and MACS2 program (v2.1.1.20160309). For mostRIP-seq datasets default MACS2 settings were used.  MACS2 was run with the “--nomodel” option. ExomePeak was used for m6A-RIP peak calling with deafult conditions.
Heatmap and plotprofile plots were generated using the 'plotHeatmap' and 'plotProfile' program respectively from the DeepTools software suite (v2.5.3)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Embryonic Stem Cell

growth_protocol: Mouse ESCs (mESCs) were cultured in mouse ESC media that contains DMEM, supplemented with 15% fetal calf serum, 0.1mM b-mercaptoethanol, 2mM L-glutamine, 0.1mM NEAA, 1% of nucleoside mix , 1000 U/ml LIF/ESGRO, and 50U/ml Penicillin/Streptomycin. mESCs were cultured at 37ºC, 5% CO2.

extract_protocol:
Details of m6A-seq, Riboseq, RIPseq, RNAseq can be found in Methods section.
RNAseq, m6A-seq, RIPseq, Riboseq libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit and NEB NEXT Small RNA Library Prep Set for Illumina following the manufacturer’s instructions.

value: Wild-type

tag: strain

tag: antibody

value: Rabbit IgG:sc 2027 (Santa cruz)


title: IgG_control_for DDX6 RIPseq_2

description: Paired end 150bp


title: Meso34-Monos-NI-neg [57_Meso34-P30-1159-Monos-NI-neg]

description:
condition 1
57_Meso34-P30-1159-Monos-NI-neg

value: mesothelioma


title: Meso13-Monos-NI-neg [47_Meso13-P19-3649-Monos-NI-neg]

description:
condition 1
47_Meso13-P19-3649-Monos-NI-neg

value: Human pleural mesothelioma cell line Meso13


title: IgG_control_for MOV10 RIPseq_2

description: Paired end 150bp

value: Mouse IgG:sc 2025 (Santa cruz)


title: JU24_AT_adjacent_Pz30

tag: lymphnode positivity

value: neg

tag: hystotype

tag: tumor grade

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

value: IHC 3+):neg

value: Adipose tissues (AT)


title: Meso13-M2-MV-pos [75_Meso13-P17-1382-M2-MV-pos]

description:
condition 8
75_Meso13-P17-1382-M2-MV-pos

tag: infection

value: schwarz attenuated measles virus

value: myeloid


title: MOE_METATAC_220503-P3-Plate14

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P47)

tag: tissue

value: mouse olfactory epithelium (P47)

tag: cell type

value: mouse olfactory epithelium

value: WT

tag: age

value: postnatal day 3


title: Meso34-Monos-MV-pos [58_Meso34-P30-1159-Monos-MV-pos]

description:
condition 4
58_Meso34-P30-1159-Monos-MV-pos

tag: cell population sorted

tag: donor

tag: cocultured cecll type

value: Monocytes

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso34


title: JU28_AT_adjacent_Pz33

tag: subject status

value: patients subjected to mastectomy

tag: bmi

value: pos

value: Ductal

tag: tumor her2 positivity (pos

tag: tumor ki67 positivity (pos


title: MOV10_RIPseq_Wild-type_2

description: Paired end 150bp

tag: genotype

value: Wild-type

tag: strain

tag: antibody

value: MOV10:A301-571A (Bethyl Laboratories)


title: JU23_AT_distant_Pz30

tag: lymphnode positivity

tag: hystotype

tag: tumor grade

tag: tumor size (t)

tag: tumor er positivity (pos


title: MOE_METATAC_220503-P3-Plate13

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P46)

tag: tissue

value: mouse olfactory epithelium (P46)

tag: cell type

tag: treatment

tag: age


title: MOV10_RIPseq_Wild-type_1

description: Paired end 150bp


title: MOE_METATAC_220503-P3-Plate12

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P45)

value: mouse olfactory epithelium (P45)


title: IgG_control_for MOV10 RIPseq_1

description: Paired end 150bp

value: Mouse IgG:sc 2025 (Santa cruz)


title: DDX6-RIPseq_Wild-type_2

description: Paired end 150bp

value: DDX6:NB200-191 (Novus Biologicals)


title: JU22_AT_adjacent_Pz29

tag: tumor pgr positivity (pos

value: IHC 3+):neg

value: Adipose tissues (AT)


title: Meso13-M2-MV-neg [10_Meso13-P17-6864-M2-MV-neg]

description:
condition 7
10_Meso13-P17-6864-M2-MV-neg

tag: infection

value: schwarz attenuated measles virus

tag: cell population sorted

value: mesothelioma

tag: donor

tag: cocultured cecll type

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso13


title: MOE_METATAC_220503-P3-Plate11

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P44)

value: mouse olfactory epithelium (P44)

value: mouse olfactory epithelium

tag: genotype

value: WT

value: postnatal day 3


title: MOE_METATAC_220503-P3-Plate10

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P43)

value: mouse olfactory epithelium (P43)


title: Meso13-M2-NI-pos [38_Meso13-P20-3649-M2-NI-pos]

description:
condition 6
38_Meso13-P20-3649-M2-NI-pos

value: uninfected

value: myeloid


title: JU19_AT_distant_Pz28

tag: subject status

value: patients subjected to mastectomy

tag: bmi

value: neg

value: Ductal

tag: tumor her2 positivity (pos

tag: tumor ki67 positivity (pos


title: hSAP_MYCN_Late, scRNA-seq

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequenced libraries were quantified with Cell Ranger software (version 6.0.0) (Zheng et al., 2017) with default parameters.
The standard reference provided with Cell Ranger (v4.0.5) was used. This version was build on a GRCh38 human genome (bundle 3.0.0) and a filtered version of Gencode v32.
Assembly: GRCh38 human genome
Supplementary files format and content: Tab-separated barcodes, features and matrix files (representing 'Gene Expression' and 'Peaks' data)

extract_protocol:
Cells were treated with a digitonin lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.01% DIG and 2 U µl−1 of RNase inhibitor) for 5 min on ice, followed by adding 1 ml of chilled DIG wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2 and 1 U µl−1 of RNAse inhibitor) and inversion before centrifugation at 500g for 5 min at 4 °C. The supernatant was discarded, and cells were resuspended in DIG wash buffer, followed by counting using trypan blue and DAPI on a Countess II FL Automated Cell Counter.
Single Cell Multiome ATAC combined with Gene Expression was performed with 10X genomics system using Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog no. 1000282) and ATAC Kit A (catalog no. 1000280) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide with the difference that single cell suspension was prepared as described in Mimitou et al (DOGMA-seq protocol with Digitonin buffer).

value: iPSCs (J2)

tag: developmental stage

value: SAP developmental cells

tag: cell line

value: induced MYCN overexpression

tag: time

value: Late

tag: library type

value: 3’end gene expression


title: Mov10 KO_RNAseq stability_9hr_2

description: Paired end 150bp

value: Mov10 KO

tag: strain

tag: antibody


title: DDX6-RIPseq_Wild-type_1

description: Paired end 150bp

value: Wild-type

value: DDX6:NB200-191 (Novus Biologicals)


title: JU20_AT_adjacent_Pz28

tag: age

tag: lymphnode positivity

tag: hystotype

tag: tumor grade

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

value: IHC 3+):neg

tag: tissue

value: Adipose tissues (AT)


title: hSAP_MYCN_Early, scRNA-seq

description: 10x Genomics

tag: cell type

tag: treatment

value: Early


title: Mov10 KO_RNAseq stability_9hr_1

description: Paired end 150bp

tag: genotype


title: MOE_METATAC_220503-P3-Plate8

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P41)

value: mouse olfactory epithelium (P41)

value: mouse olfactory epithelium

value: WT

value: postnatal day 3


title: MOE_METATAC_220503-P3-Plate9

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P42)

value: mouse olfactory epithelium (P42)


title: Mov10 KO_RNAseq stability_3hr_2

description: Paired end 150bp


title: HeLa 11ht cells, 5′TOP mRNA, 4EBP1/2 KD, biol rep 3

source_name: HeLa 11ht

value: HeLa 11ht

value: cervical cancer cells

value: 4EBP1/2 KD


title: Meso13-Monos-MV-neg [65_Meso13-P18-4119-Monos-MV-neg]

description:
condition 3
65_Meso13-P18-4119-Monos-MV-neg

tag: infection

value: schwarz attenuated measles virus

tag: cell population sorted

value: mesothelioma

tag: donor

tag: cocultured cecll type

value: Monocytes

tag: tumor cell line

value: Human pleural mesothelioma cell line Meso13


title: JU17_AT_distant_Pz27

tag: subject status

value: patients subjected to mastectomy

tag: bmi

value: neg

value: Ductal

tag: tumor her2 positivity (pos

tag: tumor ki67 positivity (pos


title: MOE_METATAC_220503-P3-Plate7

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P40)

value: mouse olfactory epithelium (P40)

tag: age


title: JU18_AT_adjacent_Pz27

tag: lymphnode positivity

tag: hystotype

tag: tumor grade

tag: tumor size (t)

value: IHC 3+):neg

value: Adipose tissues (AT)


title: HeLa 11ht cells, 5′TOP mRNA, 4EBP1/2 KD, biol rep 2

tag: cell line

tag: cell type


title: JU21_AT_distant_Pz29

value: pos

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tissue


title: Mov10 KO_RNAseq stability_3hr_1

description: Paired end 150bp

tag: genotype

value: Mov10 KO

tag: strain

tag: antibody


title: HeLa 11ht cells, 5′TOP mRNA, 4EBP1/2 KD, biol rep 1


title: MOE_METATAC_220503-P3-Plate5

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P38)

value: mouse olfactory epithelium (P38)

value: mouse olfactory epithelium

value: WT

tag: treatment

value: postnatal day 3


title: Mov10 KO_RNAseq stability_0hr_2

description: Paired end 150bp


title: JU14_AT_adjacent_Pz25

tag: subject status

tag: bmi

value: Lobular


title: HeLa 11ht cells, 5′TOP mRNA, 4EBP1/2 WT, biol rep 3

value: HeLa 11ht

value: cervical cancer cells


title: Mov10 KO_RNAseq stability_0hr_1

description: Paired end 150bp


title: MOE_METATAC_220503-P3-Plate4

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P37)

value: mouse olfactory epithelium (P37)


title: HeLa 11ht cells, 5′TOP mRNA, 4EBP1/2 WT, biol rep 2


title: MOE_METATAC_210315-P7-Plate15

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P71)

value: mouse olfactory epithelium (P71)

value: postnatal day 7


title: Wild-type_RNAseq stability_9hr_2

description: Paired end 150bp

value: Wild-type


title: JU16_AT_adjacent_Pz26

value: patients subjected to mastectomy

value: neg

value: Ductal

tag: tumor her2 positivity (pos

tag: tumor ki67 positivity (pos


title: HeLa 11ht cells, 5′TOP mRNA, 4EBP1/2 WT, biol rep 1


title: JU10_AT_adjacent_Pz23

tag: age

tag: lymphnode positivity

value: IHC 3+):neg

value: Adipose tissues (AT)


title: MOE_METATAC_220503-P3-Plate3

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P36)

value: mouse olfactory epithelium (P36)


title: Wild-type_RNAseq stability_9hr_1

description: Paired end 150bp


title: HeLa 11ht cells, Canonical mRNA, 4EBP1/2 KD, biol rep 3

value: 4EBP1/2 KD


title: Wild-type_RNAseq stability_3hr_2

description: Paired end 150bp


title: MOE_METATAC_210607-P3-Plate20

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P33)

value: mouse olfactory epithelium (P33)

value: mouse olfactory epithelium


title: HeLa 11ht cells, Canonical mRNA, 4EBP1/2 KD, biol rep 2


title: Wild-type_RNAseq stability_3hr_1

description: Paired end 150bp


title: JU13_AT_distant_Pz25

tag: hystotype

tag: tumor grade


title: JU15_AT_distant_Pz26

tag: tumor size (t)


title: JU08_AT_adjacent_Pz22

value: pos


title: JU09_AT_distant_Pz23


title: HeLa 11ht cells, Canonical mRNA, 4EBP1/2 KD, biol rep 1

tag: cell line

tag: cell type


title: MOE_METATAC_220503-P3-Plate6

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P39)

value: mouse olfactory epithelium (P39)

value: WT

value: postnatal day 3


title: Wild-type_RNAseq stability_0hr_2

description: Paired end 150bp


title: MOE_METATAC_210607-P3-Plate19

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P32)

value: mouse olfactory epithelium (P32)


title: JU07_AT_distant_Pz22

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos


title: HeLa 11ht cells, Canonical mRNA, 4EBP1/2 WT, biol rep 3

value: HeLa 11ht

value: cervical cancer cells

tag: genotype


title: MOE_METATAC_210607-P3-Plate18

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P31)

tag: tissue

value: mouse olfactory epithelium (P31)


title: HeLa 11ht cells, Canonical mRNA, 4EBP1/2 WT, biol rep 2


title: Mov10 KO_RNAseq input for Riboseq_3

description: Paired end 150bp

source_name: Embryonic Stem Cell

value: Mov10 KO

tag: strain

tag: antibody


title: MOE_METATAC_210607-P3-Plate17

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P30)

value: mouse olfactory epithelium (P30)

tag: treatment


title: Wild-type_RNAseq stability_0hr_1

description: Paired end 150bp

value: Wild-type


title: JU04_AT_adjacent_Pz20

tag: subject status

value: patients subjected to mastectomy

tag: bmi

value: Ductal

value: IHC 3+):neg


title: HeLa 11ht cells, Canonical mRNA, 4EBP1/2 WT, biol rep 1


title: MOE_METATAC_210607-P3-Plate16

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P29)

value: mouse olfactory epithelium (P29)