title: RA1790_Skin-Non-Rash [A0154_S31_L001]

description:
A0154_S31_L001
Rhesus monkey

value: infected with Ebola virus


title: P352-N-RNAseq

status: Public on Mar 03 2023

type: SRA

city: CHICACO

first: Feng

last: Yue

state: ILLINOIS

address: 303 E. Superior Simpson Querrey

country: USA

institute: Northwestern University Feinberg School of Medicine

description: Tissue

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to hg38 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM.
ChIP-seq and ATAC-seq reads were aligned to hg38 genome assembly using Bowtie2;H3K27ac ChIP-Seq peaks were called using MACS2.
Hi-C raw FASTQ files and then mapped the trimmed files against hg38 human reference genome using runHiC pipeline. Hi-C matrix was generated using cooler.
WGS raw FASTQ files were first trimmed for adapter and then mapped against hg38 human reference genome using BWA-MEM algorithm (0.7.17-r1188). Duplicate reads were removed using Picard Tools.
Nanopore raw FASTQ files were mapped against the hg38 reference genome using the minimap2. The structure variations were identified using Sniffles.
Assembly: hg38 (GRCh38)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample; the bigwig files included sequencing reads enrichment signal for each Sample; The .cool file were the multi-resolution matrix of Hi-C for each Sample; the .vcf files included the structure variation information.

molecule: polyA RNA

organism: Homo sapiens

source_name: Tissue; Patient P352 normal control; Liposarcoma

extract_protocol:
20 mg of ground patient samples or 1.5 million liposarcoma cells were used for RNA-seq. The total RNA was extracted from Trizol according to the manufacturer’s protocol (Invitrogen). PolyA RNA was purified from 1,000 ng of total RNA using oligo (dT) beads (Invitrogen).
Extracted RNA was first fragmented, then followed by reverse transcription, end-repair, adenylation, adaptor ligation, and subsequent PCR amplification. The final product was checked by size distribution and concentration using a BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems).

treatment_protocol: Patient liposarcoma samples were ground in liquid nitrogen, transferred to dounce homogenizer and lyzed in cold lysis buffer (20mM Tris-HCl, pH 8.0, 15 mM NaCl, 60 mM KCl, 320 mM sucrose, 1 mM DTT, 0.1% triton X-100, 0.1 mM PMSF, 1x proteinase inhibitor cocktail) with douncing around 20 times using pestle B on the ice. Then the supernatant containing the nuclei was transferred to a 15 ml tube avoiding pipetting tissue debris. Nuclei were pelleted by spinning 6 min at 600 g in a swing-bucket centrifuge and were resuspended in lysis buffer. The same volume of 1.4 M sucrose buffer (20mM Tris-HCl, pH 8.0, 15 mM NaCl, 60 mM KCl, 1.4 M sucrose, 1 mM DTT, 0.1 mM PMSF, 1x proteinase inhibitor cocktail) was carefully added to the bottom of 15 ml tube underneath of nuclei solution. Then, the nuclei were purified by spinning 30 min at 2500 g in swing-bucket centrifuge and resuspended in 200 ul of 320 mM sucrose buffer (20mM Tris-HCl, pH 8.0, 15 mM NaCl, 60 mM KCl, 320 mM sucrose, 1 mM DTT, 0.1 mM PMSF, 1x proteinase inhibitor cocktail).

tag: tissue

value: Patient P352 normal control

tag: disease state

value: Liposarcoma


title: RA1790_Skin-Rash [A0153_S32_L001]

city: Cambridge

first: Siddharth

last: Raju

state: Massachusetts

address: 415 Main Street

institute: Broad Institute

description:
A0153_S32_L001
Rhesus monkey

data_processing:
Host transcriptomics data was processed using the umiRNAseq custom pipeline for Bulk RNA-seq Processing with UMI correction (https://github.com/broadinstitute/sabeti-host-txnomics-internal/blob/master/bulk-rna-seq/umiRNASeq.wdl).
Briefly, raw Fastq files were merged and tagged with their corresponding UMI barcode, then they were mapped using STAR to the Rhesus monkey (M. mulatta) reference genome and annotation (Mmul_10).
Resulting BAM files were filtered for multiple mapped reads, sorted and indexed using samtools. Then, PCR duplicates were removed by UMI-tools using the UMI barcodes of each transcript.
Furthermore, featureCounts were used to quantify expression from the aligned and processed RNA-Seq BAM files. Additionally, The BioMart R package was used to annotate the gene type, gene name, and gene function using the Ensembl M. mulatta database “mmulatta_gene_ensembl”.
Quality control over the sample was performed removing samples with low sequencing quality and mismatch sex assignment.
Assembly: Mmul_10
Supplementary files format and content: 20230121_counts_submission.txt: Tab-delimited format, raw counts.

molecule: total RNA

organism: Macaca mulatta

extract_protocol:
Total RNA was extracted from tissue homogenates inactivated in TRIzol using the MagMAX MirVana total RNA kit (ThermoFisher) on a KingFisher FLEX instrument.
Ribosomal RNA was depleted using an RNase H-based method, RNA was then heat-fragmented, reverse transcription was performed, and strand-specific double-stranded cDNA was generated. xGen UDI-UMI (IDT) adapters were ligated and libraries were amplified.

tag: monkey id

tag: treatment

tag: time


title: P347-T-RNAseq

description: Tissue

source_name: Tissue; Patient P347 tumor; Liposarcoma

value: Patient P347 tumor


title: Control_6_12

city: Durham

first: Weichun

last: Huang

state: NC

address: 109 TW Alexander Dr

department: ORD

institute: US EPA

data_processing:
Base calling was done with Illumina Real Time Analysis software v1.17.21.3 and output was converted to FASTQ format with Illumina Bcl2fastq v1.8.4.
Bowtie2 (ver. 2.3.5) was used to map RNA-seq sequencing reads to the full transcriptome of the fathead minnow genome.. RSEM (ver. 1.3.1) was employed to obtain estimated read count matrices for all samples
Genome_build: FHM2.0 EPA internal version with the same genome sequences of GCF_016745375.1. Annotations are publicly available through the UCSC browser hub track data at https://data.cyverse.org/dav-anon/iplant/home/myepa/FHM/FHM2assembly_hub.txt
Supplementary_files_format_and_content: Matrix table with estimated raw gene counts by RSEM for every transcript and every sample

organism: Pimephales promelas

source_name: male liver

extract_protocol:
Total RNA was isolated using Tri-Reagent (Molecular Research Center, Inc.) following manufacturer’s protocol and quantified using a Nanodrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE). RNA quality was checked using RNA ScreenTape Analysis on an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep for 48 samples (Illumina, San Diego, CA) according to the manufacturer’s protocol with an epMotion 5075 automated liquid handling platform

value: liver

tag: developmental stage

value: adult

tag: Sex

value: male

value: Control group at 6h


title: PHH_2

city: Valencia

first: Roque

last: Bort

address: Campanar 21

department: Unidad Hepatologia Experimental

country: Spain

institute: IIS La Fe

data_processing:
RNA expression levels were extracted from the RNA-seq data using featureCounts function available in Bioconductor R package Rsubread (Liao et al., 2014), after alignment on GRCh38 with STAR (Dobin et al., 2013) of trimmed reads by Trim Galore! (Krueger F, 2012).
Previously, these trimmed reads had been processed to remove ribosomal RNA contamination sequences using BWA (Li and Durbin, 2009). The last GENCODE database that contains RNA information of was used with featureCounts function.
Assembly: GRCh38
Supplementary files format and content: Excel (.xlsx) file containing total counts per sample for each gene as obtained after featureCounts function.

source_name: 24hr cultured hepatocytes

extract_protocol:
Total RNA was extracted using MicroElute Total RNA Kit (Omega Bio-Tek R6831). Bioanalyzer’s RQN values were at least 9.9 for all RNAs
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E

tag: cell type

value: hepatocytes

tag: cell line

value: 24hr cultured hepatocytes


title: P369-T-RNAseq

description: Tissue

source_name: Tissue; Patient P369 tumor; Liposarcoma

value: Patient P369 tumor


title: Control_6_11


title: RA1790_LN-MES [A0150_S156_L002]

description:
A0150_S156_L002
Rhesus monkey

source_name: Lymph node:LN-MES

value: Lymph node:LN-MES


title: PHH_1


title: Control_6_10


title: P347-N-RNAseq

description: Tissue

source_name: Tissue; Patient P347 normal control; Liposarcoma

value: Patient P347 normal control


title: P330-T-RNAseq

description: Tissue

source_name: Tissue; Patient P330 tumor; Liposarcoma

value: Patient P330 tumor


title: RA1818_Brain-Gr [A0160_S79_L002]

description:
A0160_S79_L002
Rhesus monkey


title: RA1790_LN-ING-L [A0149_S157_L002]

description:
A0149_S157_L002
Rhesus monkey

source_name: Lymph node:LN-ING-L

value: Lymph node:LN-ING-L


title: Control_6_9


title: PDlow diHLC-T_2

source_name: diHLC-T

value: hepatocyte-like cells

value: diHLC-T


title: P330-N-RNAseq

description: Tissue

source_name: Tissue; Patient P330 normal control; Liposarcoma

value: Patient P330 normal control


title: RA1790_LN-AX-R [A0148_S158_L002]

description:
A0148_S158_L002
Rhesus monkey

source_name: Lymph node:LN-AX-R

value: Lymph node:LN-AX-R

value: infected with Ebola virus


title: PDlow diHLC-T_3


title: P352-T-RNAseq

description: Tissue

source_name: Tissue; Patient P352 tumor; Liposarcoma

value: Patient P352 tumor

value: Liposarcoma


title: RA1790_Ovary [A0147_S3_L001]

description:
A0147_S3_L001
Rhesus monkey

source_name: Sex Organ:Ovary

value: Sex Organ:Ovary


title: PDlow diHLC-T_1


title: Control_6_7

value: liver

value: adult

value: male


title: RA1790_Brain-Gr [A0146_S80_L002]

description:
A0146_S80_L002
Rhesus monkey


title: PDhigh diHLC-T_3


title: Control_6_8

value: Control group at 6h


title: P303-N-RNAseq

description: Tissue

source_name: Tissue; Patient P303 normal control; Liposarcoma

value: Patient P303 normal control


title: NPp53T

city: Washington

first: Maho

last: Shibata

state: DC

address: 800 22nd Street, NW SEH 8430

institute: The George Washington University

data_processing:
Bioinformatics analysis on raw sequence data was conducted using the 10X Genomics cellranger pipeline (v5.0.1), starting with mkfastq for demultiplexing, count for alignment and featurecounting for each of the two samples.
The 10X Genomics mouse reference database was used (mm10 July 2020-A version) for the count feature.
The Yellow Fluorescent Protein (YFP) gene (JAX Strain #007903) was manually added to the reference database and reindexed with Cell Ranger’s mkref command before using the count command.
Assembly: Mouse: UCSC/mm10
Supplementary files format and content: filtered feature bc matrix h5 file

organism: Mus musculus

source_name: Whole prostate

extract_protocol:
Prostate tissue was dissected in PBS, minced with scissors, enzymatically digested with papain and filtered through a 20-mm cell strainer (PluriSelect). Cell suspensions of approximately 6000 cells with >90% viability were loaded onto a 10X Genomics Chromium Controller (10x Genomics) using a Chromium Next GEM Single Cell 3ʹ Kit v3.1 (PN-1000269) and prepared for next-generation sequencing following the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) User Guide.
Libraries were sequenced using a NextSeq High-Output 150 cycle kit (Illumina Inc.) following the 10x Genomics User Guide recommendations.  Each library produced approximately 200 million paired-end reads.

treatment_protocol: Tamoxifen (200mg/kg body weight) was administered by oral gavage at 2 months of age for 4 days to induce deletion of floxed alleles

tag: strain

value: C57BL/6 mixed

value: Prostate

tag: age

value: 3 months

tag: tumor timepoint

value: 1 month after tamoxifen treatment

tag: genotype

value: Tamoxifen at 2 months of age


title: RA1790_Brain-Wh [A0145]

description:
A0145
Rhesus monkey


title: RA1790_Adrenal [A0144]

description:
A0144
Rhesus monkey

source_name: Adrenal Gland

value: Adrenal Gland


title: PDhigh diHLC-T_2

value: hepatocyte-like cells

value: diHLC-T


title: P300.3-N-RNAseq

description: Tissue

source_name: Tissue; Patient P300.3 normal control; Liposarcoma

value: Patient P300.3 normal control


title: PDhigh diHLC-T_1


title: Control_6_4


title: P300.3-T-RNAseq

description: Tissue

source_name: Tissue; Patient P300.3 tumor; Liposarcoma

value: Patient P300.3 tumor


title: Control_6_5

source_name: male liver


title: RA1790_Kidney [A0142_S105_L002]

description:
A0142_S105_L002
Rhesus monkey

source_name: Kidney

value: Kidney

value: infected with Ebola virus


title: RA1790_Spleen [A0141_S111_L002]

description:
A0141_S111_L002
Rhesus monkey

source_name: Spleen

value: Spleen


title: Control_6_3

value: liver

value: adult


title: P298-T-RNAseq

description: Tissue

source_name: Tissue; Patient P298 tumor; Liposarcoma

value: Patient P298 tumor

value: Liposarcoma


title: PDlow iHDF-T_2

source_name: iHDF-T

value: human dermal fibroblast

value: iHDF-T


title: Control_6_2

value: male

value: Control group at 6h


title: RA0452_Skin-Non-Rash [A0140_S33_L001]

description:
A0140_S33_L001
Rhesus monkey


title: P298-N-RNAseq

description: Tissue

source_name: Tissue; Patient P298 normal control; Liposarcoma

value: Patient P298 normal control


title: PDlow iHDF-T_3


title: P288-T-RNAseq

description: Tissue

source_name: Tissue; Patient P288 tumor; Liposarcoma

value: Patient P288 tumor


title: P303-T-RNAseq

description: Tissue

source_name: Tissue; Patient P303 tumor; Liposarcoma

value: Patient P303 tumor


title: Control_6_1


title: PDlow iHDF-T_1


title: PDhigh iHDF-T_3


title: RA0452_Skin-Rash [A0139_S34_L001]

description:
A0139_S34_L001
Rhesus monkey


title: A0137 [A0137]

description:
A0137
Rhesus monkey

source_name: Lung

value: Lung


title: PDhigh iHDF-T_2


title: Control_6_6


title: P252.2-T-RNAseq

description: Tissue

source_name: Tissue; Patient P252.2 tumor; Liposarcoma

value: Patient P252.2 tumor


title: PDhigh iHDF-T_1


title: P241-T-RNAseq

description: Tissue

source_name: Tissue; Patient P241 tumor; Liposarcoma

value: Patient P241 tumor


title: P252.2-N-RNAseq

description: Tissue

source_name: Tissue; Patient P252.2 normal control; Liposarcoma

value: Patient P252.2 normal control


title: Input DNA (Replicate 2)

city: New York

first: Claudio

last: Gouveia Roque

state: NY

address: 650 West 168th Street

department: The Taub Institute for Research on Alzheimer's disease and the Aging Brain

institute: Columbia University

description: Replicate 2

library_source: genomic

data_processing:
ChIP-seq sequencing data were processed and analyzed within the Galaxy web platform. First, library adapters and low quality reads were removed using Trim Galore (version 0.6.3) with the following settings: phred quality score threshold = 20, overlap with adapter sequence required to trim a sequence = 2, maximum allowed error rate = 0.1. Also during this step, reads shorter than 36 bp were discarded.
Second, reads were mapped to the hg38 reference genome with Bowtie 2 v2.3.4.1.
Third, unmapped and low quality (MAPQ < 20) reads were excluded with samtools v1.8.
Forth, files were converted to bigWig format using bamCoverage v3.3.0 and signals visualized in UCSC genome browser after conversion to bigWig format. Bin sizes = 25 bases, Scaling/normalization method = 1X, Effective genome size = 2701495761,  Extend reads to the given average fragment size = 150.
Genome_build: Human genome hg38 assembly
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage v.3.3.0 function in Galaxy.

molecule: genomic DNA

source_name: HEK293 cells

growth_protocol: HEK293T cells (#CRL-3216, ATCC), plated in 150 mm dishes (CLS430599, Corning), were maintained in DMEM supplemented with 10% fetal bovine serum plus antibiotics (50 U/ml penicillin-streptomycin).

extract_protocol:
Twenty-four hours post-transfection, we proceeded by crosslinking protein-DNA contacts with 1% (v/v) formaldehyde (#28908, Thermo Fisher) for 10 minutes at room temperature. After quenching cross-linking reaction with glycine, cells were washed twice with ice-cold PBS, harvested by scrapping in PBS with protease inhibitors, and centrifuged at 2,000 g and 4ºC, as per manufacturer’s instructions (SimpleChIP Plus Kit [#9005], Cell Signaling Technology). Chromatin fragments (mainly 1-3 nucleosomes in size) were obtained by incubation with micrococcal nuclease (3.5 ul [equivalent to 7,000 gel units] in 200 ul; M0247S, NEB) for 45 minutes in a 37ºC-water bath. Nuclear membranes were subsequently broken up by three rounds of 20-second, 15% amplitude pulses using a Sonic Dismembrator Model 500 (Fisher Scientific), and lysates clarified by centrifugation. Adequate digestion was assessed by agarose gel electrophoresis. For each condition, digested chromatin was split into two tubes and immunoprecipitated overnight at 4ºC with end-over-end rotation using pre-washed magnetic beads conjugated with anti-HA- or anti-V5 antibodies (anti-HA beads: PI88836, Thermo Fisher; anti-V5 beads: NC0777490, MBL International); 35 ul of anti-HA beads and 25 ul of anti-V5 beads were utilized per immunoprecipitation. Beads were captured on a magnetic stand and washed with low- and high-salt buffers, as directed. Elution was performed at 65ºC and 1,200 rpm for 30 minutes using a thermomixer, protein-DNA cross-links reversed by treatment with Proteinase K for 2 hours at 65ºC, and DNA column-purified. A representative 2% input sample was prepared by combining chromatin from the different backgrounds.
ChIP-seq library preparation and sequencing reactions were conducted at GENEWIZ, Inc., as described above. A total of 24 samples were submitted for analysis, comprising parallel HA and V5 immunoprecipitations, from 2 independent replicates. The sequencing libraries were multiplexed and clustered on two lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was performed using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.

treatment_protocol: DNA constructs were transiently transfected using Lipofectamine 3000 (Thermo Fisher) and amounts of DNA delivery were optimized to achieve comparable expression levels between the different homodimer and heterodimer configurations. While lipofectamine complexes were incubating, a complete media change was performed, and A/C heterodimerizer (Takara) was added at 500 nM at this point. ChIPmera system was incubated for 24 hours.

value: human embryonic kidney cells

tag: dna transfection

value: A single representative 2% input sample was prepared by combining chromatin from the different homodimer/heterodimer backgrounds.

tag: ChIP

value: Not applicable

tag: chip antibody-conjugated beads


title: RA0452_LN-AX-R [A0134_S161_L002]

description:
A0134_S161_L002
Rhesus monkey

source_name: Lymph node:LN-AX-R

value: Lymph node:LN-AX-R

value: infected with Ebola virus


title: RA0452_LN-ING-L [A0135_S160_L002]

description:
A0135_S160_L002
Rhesus monkey

source_name: Lymph node:LN-ING-L

value: Lymph node:LN-ING-L


title: KD_2

city: Houston

first: Shengzhe

last: Zhang

state: TX

address: 6565 MD Anderson Blvd

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

data_processing:
Illumina Casava 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
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: Breast cancer cells

extract_protocol:
RNA was harvested usingGIAGEN Rneasy Plus Mini Kit. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: TMEM9 KD


title: RA0452_LN-MES [A0136_S159_L002]

description:
A0136_S159_L002
Rhesus monkey

source_name: Lymph node:LN-MES

tag: tissue

value: Lymph node:LN-MES


title: Mock transfection - ChIP background control HA immunoprecipitation

description: Replicate 2 only

value: Mock transfection

value: HA immunoprecipitation

value: #PI88836, Thermo Fisher - magnetic beads pre-conjugated with anti-HA antibody


title: Mock transfection - ChIP background control V5 immunoprecipitation

description: Replicate 2 only

value: V5 immunoprecipitation

value: NC0777490, MBL International - magnetic beads pre-conjugated with anti-V5 antibody


title: LUC-LUC homodimers (Replicate 2) V5 immunoprecipitation

description: Replicate 2

value: HA-LUC-FRB + V5-LUC-FKBP


title: P241-N-RNAseq

description: Tissue

source_name: Tissue; Patient P241 normal control; Liposarcoma

value: Patient P241 normal control

tag: disease state

value: Liposarcoma


title: LUC-LUC homodimers (Replicate 2) HA immunoprecipitation

description: Replicate 2


title: RA0452_Ovary [A0133_S4_L001]

description:
A0133_S4_L001
Rhesus monkey

source_name: Sex Organ:Ovary

value: Sex Organ:Ovary

tag: monkey id


title: P209-T-RNAseq

description: Tissue

source_name: Tissue; Patient P209 tumor; Liposarcoma

value: Patient P209 tumor


title: WT_2

value: wild type


title: ATF4-CREB3L2 heterodimers (Replicate 2) V5 immunoprecipitation

description: Replicate 2

value: human embryonic kidney cells

value: HA-ATF4-FRB + V5-CREB3L2-FKBP


title: P288-N-RNAseq

description: Tissue

source_name: Tissue; Patient P288 normal control; Liposarcoma

value: Patient P288 normal control


title: WT_1


title: RA0452_Brain-Wh [A0131_S58_L001]

description:
A0131_S58_L001
Rhesus monkey

tag: treatment

value: infected with Ebola virus


title: A0129 [A0129]

description:
A0129
Rhesus monkey

source_name: Liver

value: Liver

tag: time


title: CREB3L2-ATF4 heterodimers (Replicate 2) V5 immunoprecipitation

description: Replicate 2

value: HA-CREB3L2-FRB + V5-ATF4-FKBP


title: ATF4-CREB3L2 heterodimers (Replicate 2) HA immunoprecipitation

description: Replicate 2


title: RA0452_Kidney [A0128_S55_L001]

description:
A0128_S55_L001
Rhesus monkey

source_name: Kidney

value: Kidney


title: WT_biol_rep_3_DOX

city: Montreal

first: Harvey

middle: Wilmore

last: Smith

state: Quebec

address: Life Sciences Complex, Room 602, 1160 Pine Avenue West

department: Goodman Cancer Research Centre

country: Canada

institute: McGill University

description:
Mammary epithelial organoids from wild-type MIC mice, treated with doxycycline for 12 days
Processed data file column P

data_processing:
Adaptor sequences and low quality score bases (Phred score < 30) were trimmed using Trimmomatic (Bolger et al., 2014)
Reads were aligned to the GRCm38 mouse reference genome assembly using STAR (Dobin et al., 2012)
Read counts were obtained using HTSeq (Anders et al., 2015) with parameters -m intersection-nonempty -stranded=no
Raw counts were normalized using edgeR’s TMM algorithm (Robinson et al., 2010) and were then transformed to log2-counts per million (logCPM) using the voom function implemented in the limma R package (Ritchie et al., 2015)
To assess differences in gene expression levels between the different conditions, we fitted a linear model using limma’s lmfit function (method="robust" parameter was applied for end-stage tumor dataset)
Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method
Distinct patterns of gene expression changes were identified using unsupervised hierarchical clustering method (R function hclust with Euclidean distance and complete linkage metrics)
Assembly: GrCM38/mm10
Supplementary files format and content: A tab-delimited text files includes RPKM values for all samples.

source_name: Mammary epithelium

growth_protocol:
Primary mammary epithelial cells were grown as 3D organoids in a medium consisting of Epicult-B (Stem Cell Technologies, 05610), with 1% (vol/vol) knockout serum replacement (Gibco, 10828010), 50µg/ml Penicillin/Streptomycin (Wisent, 450-200-EL), 10 ng/mL EGF, 25 μg/mL insulin, 1 μg/mL hydrocorticone and 2% Geltrex (ThermoFisher Scientific, A1413202)
Each organoid preparation (pooled cells from 5 mice) was divded into two separate samples, one of which was treated with doxycycline (2 μg/mL) for 12 days to induce expression of the PyV mT-IRES-Cre transgene.

extract_protocol:
Qiagen RNEasy Mini kit was used according to the manufacturer's instructions
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Library Prep Kit following manufacturer's protocols.

value: FVB/N

value: Female

value: Mammary epithelium

value: Primary mammary epithelial cells

value: MIC/wild-type

value: Doxycyline (2ug/ml) for 12 days


title: SRC_biol_rep_3_DOX

description:
Mammary epithelial organoids from MIC mice with conditional Src alleles, treated with doxycycline for 12 days
Processed data file column S

value: MIC/conditional c-Src KO


title: SRC_biol_rep_2_DOX

description:
Mammary epithelial organoids from MIC mice with conditional Src alleles, treated with doxycycline for 12 days
Processed data file column R


title: SRC_biol_rep_1_DOX

description:
Mammary epithelial organoids from MIC mice with conditional Src alleles, treated with doxycycline for 12 days
Processed data file column Q


title: RA0452_Spleen [A0127_S112_L002]

description:
A0127_S112_L002
Rhesus monkey

source_name: Spleen

value: Spleen


title: RA0552_Skin-Non-Rash [A0126_S35_L001]

description:
A0126_S35_L001
Rhesus monkey


title: P19.3-T-RNAseq

description: Tissue

source_name: Tissue; Patient P19.3 tumor; Liposarcoma

value: Patient P19.3 tumor

value: Liposarcoma


title: P19.3-N-RNAseq

description: Tissue

source_name: Tissue; Patient P19.3 normal control; Liposarcoma

value: Patient P19.3 normal control


title: P209-N-RNAseq

description: Tissue

source_name: Tissue; Patient P209 normal control; Liposarcoma

value: Patient P209 normal control


title: LPS12-T-RNAseq

description: Tissue

source_name: Tissue; Patient LPS12 tumor; Liposarcoma

value: Patient LPS12 tumor


title: ATF4-ATF4 homodimers (Replicate 2) V5 immunoprecipitation

description: Replicate 2

source_name: HEK293 cells

value: human embryonic kidney cells

value: HA-ATF4-FRB + V5-ATF4-FKBP

value: V5 immunoprecipitation

value: NC0777490, MBL International - magnetic beads pre-conjugated with anti-V5 antibody


title: CREB3L2-ATF4 heterodimers (Replicate 2) HA immunoprecipitation

description: Replicate 2

value: HA-CREB3L2-FRB + V5-ATF4-FKBP

value: HA immunoprecipitation

value: #PI88836, Thermo Fisher - magnetic beads pre-conjugated with anti-HA antibody


title: ATF4-ATF4 homodimers (Replicate 2) HA immunoprecipitation

description: Replicate 2


title: RA0452_Brain-Gr [A0132_S81_L002]

description:
A0132_S81_L002
Rhesus monkey

value: infected with Ebola virus


title: WT_biol_rep_2_DOX

description:
Mammary epithelial organoids from wild-type MIC mice, treated with doxycycline for 12 days
Processed data file column O

value: FVB/N

value: Female

value: Mammary epithelium

value: Primary mammary epithelial cells

value: MIC/wild-type


title: RA0552_Skin-Rash [A0125_S36_L001]

description:
A0125_S36_L001
Rhesus monkey


title: KD_1

value: TMEM9 KD


title: A0123_L2 [A0123_L2]

description:
A0123_L2
Rhesus monkey

source_name: Lung

value: Lung


title: P15-T-RNAseq

description: Tissue

source_name: Tissue; Patient P15 tumor; Liposarcoma

value: Patient P15 tumor

value: Liposarcoma


title: CREB3L2-CREB3L2 homodimers (Replicate 2) V5 immunoprecipitation

description: Replicate 2

value: human embryonic kidney cells

value: HA-CREB3L2-FRB + V5-CREB3L2-FKBP


title: SRC_biol_rep_3_control

description:
Mammary epithelial organoids from MIC mice with conditional Src alleles, grown without doxycycline
Processed data file column M

value: MIC/conditional c-Src KO


title: SRC_biol_rep_2_control

description:
Mammary epithelial organoids from MIC mice with conditional Src alleles, grown without doxycycline
Processed data file column L


title: RA0552_LN-AX-R [A0120_S164_L002]

description:
A0120_S164_L002
Rhesus monkey

source_name: Lymph node:LN-AX-R

value: Lymph node:LN-AX-R


title: Input DNA

description: Replicate 1

value: A single representative 2% input sample was prepared by combining chromatin from the different homodimer/heterodimer backgrounds.

value: Not applicable


title: WT_biol_rep_1_DOX

description:
Mammary epithelial organoids from wild-type MIC mice, treated with doxycycline for 12 days
Processed data file column N

value: Doxycyline (2ug/ml) for 12 days


title: RA0552_Brain-Gr [A0118_S28_L001]

description:
A0118_S28_L001
Rhesus monkey

value: infected with Ebola virus


title: NONO eCLIP IN - SKBG-1(S) treated - rep2

city: LA JOLLA

first: Hsuan-Lin

last: Her

address: 9500 Gilman Dr,

institute: UCSD

description: NONO_10S_CLIP_rep2.peaks.normed.compressed.filtered.annotate.bed

data_processing:
Processed Using https://github.com/YeoLab/eclip 0.7.0
After standard HiSeq demultiplexing, eCLIP libraries with distinct in-line barcodes were demultiplexed using custom scripts, and the random-mer was appended to the read name for later usage. Reads were then adapter trimmed (cutadapt v1.9.dev1) and reads less than 18 bp were discarded
Mapping was then first performed against human elements in RepBase (v18.05) with STAR (v2.4.0i), repeat-mapping reads were segregated for separate analysis, and all others were then mapped against the full human genome (hg19) including a database of splice junctions with STAR (v 2.4.0i) (Dobin et al., 2013). Uniquely mapping reads were then run through a custom-built PCR duplicate removal script, removing duplicate reads based on sharing identical Read1 start position, Read2 start position, and random-mer sequence to leave 'Usable' reads.
eCLIP data sets with multiple in-line barcodes were merged at the usable read stage, and cluster identification was performed on usable reads using CLIPper (Yeo et al., 2009) (available at https://github.com/YeoLab/clipper/releases/tag/1.0) with options –s GRCh38 –o –bonferroni –superlocal–threshold-method binomial–save-pickle
data are further downsampled to roughly equal number per replicate
Assembly: hg38
Supplementary files format and content: wig files represent read covergae for plus and minus strands
Supplementary files format and content: peak files

source_name: 22Rv1 human prostate cancer cell line

growth_protocol: 2–3 × 10^6 22Rv1 cells (ATCC) were seeded into a 10 cm plate and grown for 40h. Media: RPMI-1640 with Glutamax and 10% fetal bovine serum (Life Technologies). 2-3 plates per treatment condition

extract_protocol:
22rv1 replicates were treated with 400mJ of UV using the CL-1000 UV Crosslinker, harvested in ice cold PBS and pelleted by centrifugation. Cell pellets were flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with NONO antibody-bound Dynabeads. Subsequent protocol was followed as detailed in Van Nostrand et al, Methods Mol Biol 2017. Sequencing was performed on Illumina Novaseq 6000 single-end reads and data processed through Dr. Yeo's seCLIP pipeline.
Libraries were constructed as per the (s)eCLIP protocol using Illumina 50x forward and 70x reverse primers.

treatment_protocol: Cells were treated with 0.04% DMSO or 20uM compound in 0.04% DMSO for 4h

value: human prostate cancer cell line

tag: chip antibody


title: Lipo863B-rep2-RNAseq

description: Cell Line

source_name: Cell Line; Lipo863B; Liposarcoma

growth_protocol: Liposarcoma cell lines were cultured in Dulbecco's Modified Eagle's Medium supplemented with 15% FBS and additional 1 mM GlutaMax supplement (ThermoFisher, 35050061).


title: SRC_biol_rep_1_control

description:
Mammary epithelial organoids from MIC mice with conditional Src alleles, grown without doxycycline
Processed data file column K

value: FVB/N

tag: Sex

value: Female


title: Lipo863B-rep1-RNAseq

description: Cell Line


title: LPS12-N-RNAseq

description: Tissue

source_name: Tissue; Patient LPS12 normal control; Liposarcoma

value: Patient LPS12 normal control


title: NONO eCLIP IN - SKBG-1(S) treated - rep1

description: NONO_10S_CLIP.peaks.normed.compressed.filtered.annotate.bed

tag: cell type


title: LUC-LUC homodimers HA immunoprecipitation

description: Replicate 1

value: HA-LUC-FRB + V5-LUC-FKBP

value: HA immunoprecipitation

value: #PI88836, Thermo Fisher - magnetic beads pre-conjugated with anti-HA antibody


title: RA0552_LN-ING-L [A0121_S163_L002]

description:
A0121_S163_L002
Rhesus monkey

source_name: Lymph node:LN-ING-L

value: Lymph node:LN-ING-L


title: WT_biol_rep_3_control

description:
Mammary epithelial organoids from wild-type MIC mice, grown without doxycycline
Processed data file column J

value: Mammary epithelium

tag: cell line

value: Primary mammary epithelial cells

value: MIC/wild-type


title: LUC-LUC homodimers V5 immunoprecipitation

description: Replicate 1

value: human embryonic kidney cells

value: V5 immunoprecipitation

value: NC0777490, MBL International - magnetic beads pre-conjugated with anti-V5 antibody


title: NONO eCLIP IP - SKBG-1(S) treated - rep1

value: Rabbit anti- NONO (Bethyl Laboratories, Cat#:A300-587A)


title: CREB3L2-CREB3L2 homodimers (Replicate 2) HA immunoprecipitation

description: Replicate 2

value: HA-CREB3L2-FRB + V5-CREB3L2-FKBP


title: RA0552_Ovary [A0119_S5_L001]

description:
A0119_S5_L001
Rhesus monkey

source_name: Sex Organ:Ovary

value: Sex Organ:Ovary

value: infected with Ebola virus


title: NONO eCLIP IP - SKBG-1(S) treated - rep2

value: human prostate cancer cell line


title: RA0552_LN-MES [A0122_S162_L002]

description:
A0122_S162_L002
Rhesus monkey

source_name: Lymph node:LN-MES

value: Lymph node:LN-MES


title: RA0552_Brain-Wh [A0117_S115_L002]

description:
A0117_S115_L002
Rhesus monkey


title: WT_biol_rep_1_control

description:
Mammary epithelial organoids from wild-type MIC mice, grown without doxycycline
Processed data file column H

tag: strain

value: FVB/N

value: Female


title: ATF4-CREB3L2 heterodimers HA immunoprecipitation

description: Replicate 1

value: HA-ATF4-FRB + V5-CREB3L2-FKBP

value: HA immunoprecipitation


title: NONO eCLIP IN - SKBG-1(R) treated - rep2

description: NONO_10R_CLIP_rep2.peaks.normed.compressed.filtered.annotate.bed


title: ATF4-CREB3L2 heterodimers V5 immunoprecipitation

description: Replicate 1


title: CREB3L2-ATF4 heterodimers HA immunoprecipitation

description: Replicate 1

value: HA-CREB3L2-FRB + V5-ATF4-FKBP

value: #PI88836, Thermo Fisher - magnetic beads pre-conjugated with anti-HA antibody


title: CREB3L2-ATF4 heterodimers V5 immunoprecipitation

description: Replicate 1


title: NONO eCLIP IN - SKBG-1(R) treated - rep1

description: NONO_10R_CLIP.peaks.normed.compressed.filtered.annotate.bed


title: NONO eCLIP IP - SKBG-1(R) treated - rep2


title: RA0552_Spleen [A0113_S113_L002]

description:
A0113_S113_L002
Rhesus monkey

value: Spleen


title: RA0552_Kidney [A0114_S112_L002]

description:
A0114_S112_L002
Rhesus monkey

source_name: Kidney

value: Kidney


title: ATF4-ATF4 homodimers V5 immunoprecipitation

description: Replicate 1

value: human embryonic kidney cells

value: HA-ATF4-FRB + V5-ATF4-FKBP


title: NONO eCLIP IP - SKBG-1(R) treated - rep1


title: NONO eCLIP IN - DMSO treated - rep2

description: NONO_DMSO_CLIP_rep2.peaks.normed.compressed.filtered.annotate.bed

value: DMSO


title: CREB3L2-CREB3L2 homodimers HA immunoprecipitation

description: Replicate 1


title: ATF4-ATF4 homodimers HA immunoprecipitation

description: Replicate 1


title: CREB3L2-CREB3L2 homodimers V5 immunoprecipitation

description: Replicate 1

value: V5 immunoprecipitation

value: NC0777490, MBL International - magnetic beads pre-conjugated with anti-V5 antibody


title: Organoid_p9

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
To assess the quality of raw data, FastQC (v.0.11.9) and MultiQC (v.1.9) were used prior to processing the data.
The first 11 bases were trimmed from each read and low-quality bases (Phred score < 20) were removed using Cutadapt (v1.18).
To align the sequences STAR (v.2.7.4.a) was applied.
The reference genome used in this step was mRatBN7.2.  Finally, the number of counts per gene was obtained by STAR.
Assembly: mRatBN7.2
Supplementary files format and content: Excel file containing raw count data for all samples

organism: Rattus norvegicus

source_name: WAG/Rij rats

growth_protocol: The CC-531 cell line are colon carcinoma cells derived from WAG/Rij rats. This cell line was cultured in RPMI1640 medium (Gibco) containing 25 mM HEPES and supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin/glutamine (Gibco). Cells were maintained at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol:
RNA was extracted from CC-531 cells, CC-531 organoids and CC-531 ex vivo tumor tissue grown in the peritoneum of WAG/Rij rats using the RNA isolation kit (Bioke). Three different passages per sample type were used resulting in a total of 9 samples.
Library preparation was constructed using KAPA mRNA Hyperprep following by RNAseq performed on an Illumina HiSeq 4000.

treatment_protocol:
To establish a 3D cell culture, CC-531 cells were cultured in matrigel in order to develop organoids.
Tumor lesions throughout the abdominal cavity were induced by intraperitoneal injections in the right lower part of the abdominal cavity with 1 mL 2 ×106 cells/mL cell suspension in culture medium in 8-10 week-old WAG/Rij rats. CC-531 cells were cultured for at least two passages after being thawed.

value: colon carcinoma

value: CC-531 organoids


title: RA0449_Skin-Rash [A0111_S38_L001]

description:
A0111_S38_L001
Rhesus monkey

value: infected with Ebola virus


title: RA0449_LN-ING-L [A0107_S166_L002]

description:
A0107_S166_L002
Rhesus monkey

value: Lymph node:LN-ING-L


title: NONO eCLIP IN - DMSO treated - rep1

description: NONO_DMSO_CLIP.peaks.normed.compressed.filtered.annotate.bed

value: human prostate cancer cell line


title: P15-N-RNAseq

description: Tissue

source_name: Tissue; Patient P15 normal control; Liposarcoma

value: Patient P15 normal control

value: Liposarcoma


title: A0115 [A0115]

description:
A0115
Rhesus monkey

source_name: Liver

value: Liver


title: SCC25, YBX1KO, DOXpos, rep 3 [RNA-seq]

city: Melbourne

first: Charbel

last: Darido

state: VIC

address: 305 Grattan street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Center

description:
labelled as SCC25.–YBX1.3 in processed data file 2
Normalized.Counts.RNAseq.YBX1.txt

data_processing:
Sequence reads were trimmed and aligned to hg38 genome using Cutadapt and HISAT2 packages. Gene counts were obtained from featureCounts. Expression normalisation and filtration were performed using Limma. All analysis packages were operated within the Galaxy suite environment (version 4.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

growth_protocol: The normal oral epithelial cell line OKF6 was purchased from the Harvard Skin Disease Research Centre (HSDRC, Boston MA). The oral cancer cell lines SCC15 (CRL-1623) and SCC25 (CRL-1628) were purchased from the American Type Culture Collection (ATCC, Manassas, VA). All cell lines were authenticated and validated by short tandem repeat (STR) profiling and tested negative for mycoplasma contamination (33). OKF6 and SCC25 were cultured in keratinocyte serum-free medium (K-SFM, GibcoTM) supplemented with growth factors (25 mg/mL BPE, 0.2 ng/mL EGF and 0.3 mM CaCl2) and 1% penicillin-streptomycin (P/S). SCC9, SCC15, and CAL27 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, GibcoTM) with 10% foetal bovine serum (FBS) and 1% P/S. All cell lines were cultured at 37°C in a 5% CO2 humidified incubator and maintained at less than 25 passages.

extract_protocol:
Cells were lysed and RNA was extracted using TRIzol (Thermo Fisher Scientific). The total RNA quantity was measured using Qubit RNA HS (Thermo Fisher Scientific).
500 ng of total RNA was used for library preparation according to standard protocols (QuantSeq 3’mRNA-seq FWD, Lexogen).
Indexed libraries were pooled and sequenced on a NextSeq500 (Illumina). 5-15 million single-end 75 bp reads were generated per sample.

treatment_protocol: Lentiviral expression constructs were mixed with the packaging plasmids pMDLgRRE, pRSV-Rev, pCMV-VSVG (Addgene) and transfected into lenti-X293T cells (Takara Bio, #632180) using Lipofectamine 2000 (Thermo Fisher Scientific) according to the manufacturer’s protocol. Virus-containing conditioned media was collected 48–72 hours after transfection and filtered using a 0.45-µm filter. Viral conditioned media was supplemented with polybrene and applied to sub-confluent cells. Conditioned media was replaced with fresh cell culture media 6 hours post transduction. Double-positive GFP and mCherry-expressing cells were sorted using a FACS Calibur cell sorter 72 hours post transduction and then expanded in culture. Doxycycline (Dox) Hyclate (Sigma Aldrich) was added (1µg/ml) to the culture media to induce CRISPR-Cas9-mediated gene deletion for downstream analysis.

value: Head and Neck Cancer Cells

value: YBX1 knockout

value: Doxcycline Treatment (1 ug/mL)

value: 3 Days


title: SCC25, YBX1KO, DOXpos, rep 2 [RNA-seq]

description:
labelled as SCC25.–YBX1.2 in processed data file 2
Normalized.Counts.RNAseq.YBX1.txt


title: SCC25, YBX1KO, DOXpos, rep 1 [RNA-seq]

description:
labelled as SCC25.–YBX1.1 in processed data file 2
Normalized.Counts.RNAseq.YBX1.txt


title: RA0449_LN-AX-R [A0106_S167_L002]

description:
A0106_S167_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: Organoid_p7


title: Exvivo_3

value: CC-531 ex vivo tumor tissue


title: RB_wt

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

description:
patient_counts.txt
patient_md.txt
patient_embeddings.txt

data_processing:
scRNAseq samples were de-multiplexed and aligned to human reference genome GRCh38 before being quantified using CellRanger version 3.0
Quality control filtering was applied to remove any cells where fewer than 1000 reads or 500 genes or greater than 15% mitochondrial reads.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression matrix, cell annotations and UMAP embeddings

source_name: Organoids

growth_protocol: adaped protocol based on Kuwahara et al., 2015

extract_protocol:
Retinal organoids (day114) were dissociated to single cells using the Neurosphere Dissociation kit (P) (Miltenyi Biotech) according to the manufacturer’s protocol
Chromium Single Cell 3′ Library & Gel Bead Kit, version 3 (10x Genomics)

tag: sample type

value: RB_wt (patient derived, iPSC)


title: SCC25, YBX1KO, DOXneg, rep 3 [RNA-seq]

description:
labelled as SCC25.3 in processed data file 1; labelled as SCC25.+YBX1.3 in processed data file 2
Normalized.Counts.RNAseq.cellline.txt
Normalized.Counts.RNAseq.YBX1.txt

value: Wild Type


title: NONO eCLIP IP - DMSO treated - rep1

value: Rabbit anti- NONO (Bethyl Laboratories, Cat#:A300-587A)

value: DMSO


title: RA0449_Ovary [A0105_S6_L001]

description:
A0105_S6_L001
Rhesus monkey

value: Sex Organ:Ovary


title: RA0449_Skin-Non-Rash [A0112_S37_L001]

description:
A0112_S37_L001
Rhesus monkey

value: infected with Ebola virus


title: RA0449_LN-MES [A0108_S165_L002]

description:
A0108_S165_L002
Rhesus monkey

value: Lymph node:LN-MES


title: SCC25, YBX1KO, DOXneg, rep 2 [RNA-seq]

description:
labelled as SCC25.2 in processed data file 1; labelled as SCC25.+YBX1.2 in processed data file 2
Normalized.Counts.RNAseq.cellline.txt
Normalized.Counts.RNAseq.YBX1.txt


title: RB_hetrozygous (c.2082delC)

value: RB_hetrozygous (patient derived, iPSC)


title: Organoid_p8

value: colon carcinoma

value: CC-531 organoids


title: RA0449_Brain-Wh [A0103]

description:
A0103
Rhesus monkey


title: NONO eCLIP IP - DMSO treated - rep2

value: human prostate cancer cell line


title: RB_homozygous (c.2082delC)

value: RB_homozygous (patient derived, iPSC)


title: Exvivo_1


title: RA0449_Brain-Gr [A0104_S29_L001]

description:
A0104_S29_L001
Rhesus monkey


title: RB1_null_ROs

description:
h9_counts.txt
h9_md.txt
h9_embeddings.txt

value: RB1_null_Ros (human ESC derived, H9)


title: Exvivo_2


title: SCC25, YBX1KO, DOXneg, rep 1 [RNA-seq]

description:
labelled as SCC25.1 in processed data file 1; labelled as SCC25.+YBX1.1 in processed data file 2
Normalized.Counts.RNAseq.cellline.txt
Normalized.Counts.RNAseq.YBX1.txt

value: Head and Neck Cancer Cells


title: SCC15, YBX1KO, DOXpos, rep 3 [RNA-seq]

description:
labelled as SCC15.–YBX1.3 in processed data file 2
Normalized.Counts.RNAseq.YBX1.txt

value: YBX1 knockout

value: Doxcycline Treatment (1 ug/mL)

value: 3 Days


title: Cells_p8

value: CC-531 cell line


title: Cells_p5


title: SCC15, YBX1KO, DOXpos, rep 2 [RNA-seq]

description:
labelled as SCC15.–YBX1.2 in processed data file 2
Normalized.Counts.RNAseq.YBX1.txt


title: Cells_p11


title: SCC15, YBX1KO, DOXpos, rep 1 [RNA-seq]

description:
labelled as SCC15.–YBX1.1 in processed data file 2
Normalized.Counts.RNAseq.YBX1.txt


title: RA0449_Spleen [A0099_S114_L002]

description:
A0099_S114_L002
Rhesus monkey

source_name: Spleen

value: Spleen


title: A0101 [A0101]

description:
A0101
Rhesus monkey

value: Liver


title: AD4_Thioridazine

description:
counts.txt
annotation.txt
embeddings.txt

source_name: retinal organoids

extract_protocol:
Retinal organoids (day 200) were dissociated to single cells using the Neurosphere Dissociation kit (P) (Miltenyi Biotech) according to the manufacturer’s protocol
Chromium Single Cell 3′ Library & Gel Bead Kit, version 3 (10x Genomics)

treatment_protocol: drug exposure for 24 hours (Sildenafil for 7 days)

value: retinal organoids

value: Thioridazine (135uM)


title: SCC15, YBX1KO, DOXneg, rep 3 [RNA-seq]

description:
labelled as SCC15.3 in processed data file 1; labelled as SCC15.+YBX1.3 in processed data file 2
Normalized.Counts.RNAseq.cellline.txt
Normalized.Counts.RNAseq.YBX1.txt

value: Wild Type


title: AD4_Sildenafil

value: Sildenafil (225uM)


title: SCC15, YBX1KO, DOXneg, rep 2 [RNA-seq]

description:
labelled as SCC15.2 in processed data file 1; labelled as SCC15.+YBX1.2 in processed data file 2
Normalized.Counts.RNAseq.cellline.txt
Normalized.Counts.RNAseq.YBX1.txt


title: RA1834_Skin-Non-Rash [A0098_S39_L001]

description:
A0098_S39_L001
Rhesus monkey

value: infected with Ebola virus


title: AD4_Methanol

value: Methanol (0.4%)


title: LUC-LUC rep4

data_processing:
RNA-seq sequencing data were processed and analyzed within the Galaxy web platform, using the public server at usegalaxy.org.
Library adapters and low-quality reads were removed using Trimmomatic (version 0.38) with the following settings: initial ILLUMINACLIP step to cut adapters and other Illumina-specific sequences from the reads, seedMismatches = 2, palindromeClipThreshold = 30, simpleClipThreshold = 10, minAdapterLength = 8, keepBothReads = True, AVGQUAL  ≥ 20, SLIDINGWINDOW: windowSize = 4 and requiredQuality = 20, and MINLEN = 50
Reads were mapped to the Rattus norvegicus (Rn) 6.0 reference genome and gene model (downloaded from Ensembl) with RNA STAR (version 2.7.5b) using default settings except: sjdbOverhang = 149, outFilterType = True, alignIntronMax = 1000000, alignMatesGapMax = 1000000, and alignSJoverhangMin = 8; additionally, unmapped reads, alignments that had junctions with inconsistent strands, alignments across unannotated non-canonical junctions and all alignments across non-canonical junctions were excluded from output.
featureCounts (version 1.6.4+galaxy2) was run to quantify reads mapping to exons with the following parameters: ‘create gene length file’ = True, ‘count fragments instead of reads’ = True, ‘only allow fragments with both reads aligned’ = True, ‘exclude chimeric fragments’ = True, ‘GFF feature type filter’ = exon, ‘GFF gene identifier’ = gene_id, ‘on feature level’ = False, ‘allow reads to map to multiple features’ = False, ‘minimum mapping quality per read’ = 10; otherwise default tool settings.
Genome_build: Rat Rn 6.0
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample

source_name: Primary hippocampal neurons

growth_protocol: Hippocampi were dissected from embryonic day (E) 17 rat embryos obtained from pregnant Sprague-Dawley dams. Cell dissociation was performed using TripLE Express. Neurons (250,000 per well) were plated on 0.1 mg ml-1 poly-D-lysine (Millipore Sigma) and 2 mg ml-1 laminin (Bio-Techne) coated 12-well plates and grown in Neurobasal supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 1 mM sodium pyruvate, and antibiotics (50 U ml -1 penicillin-streptomycin).

extract_protocol:
At the time of collection (DIV6), cells were washed with ice-cold Hank’s Balanced Salt Solution (HBSS; Thermo Fischer) and lysed with TRIzol reagent (#15596026, Thermo Fisher) by scrapping. The reaction was allowed to proceed on ice for 5 minutes, at which point samples were centrifuged at 12,000 g and 4ºC and supernatants transferred to new tubes before a 1:1 (v/v) dilution with molecular biology-grade 100% ethanol (Millipore Sigma). The RNA extraction protocol was continued using the Direct-zol RNA MicroPrep kit (Zymo Research), in accordance to manufacturer’s instructions, and included an on-column DNA digestion step with DNase I. RNA was typically eluted in 30 ul of water.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
RNA-seq. Samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS).

treatment_protocol: After 24 hours (i.e., DIV1), medium was changed to Neurobasal containing 1× B27 and 2 mM L-glutamine (growth medium). At the same time, transgenes were delivered by lentiviral infection. On DIV2, dimerizer A/C heterodimerizer (C-16-(S)-7-methylindolerapamycin [AP21967], purchased from Takara) was incubated at a concentration of 100 nM. On DIV4, cells were supplemented with additional growth medium containing heterodimerizer.

tag: dissection age

value: E17 pregnant rats. This is DIV0.

tag: infection protocol

value: DIV1. FK-tagged Renilla luciferase. Lentiviral delivery.

tag: dimerizer incubation

tag: time of collection

value: Sprague-Dawley


title: AD4_Ketorolac

value: Ketorolac (2.5mM)


title: Control_ROs

value: Control_Ros (human ESC derived, H9)


title: OKF6, rep 3 [RNA-seq]

description:
labelled as OKF6.3 in processed data file 1
Normalized.Counts.RNAseq.cellline.txt

value: Normal Oral Cells

tag: genotype


title: RA1834_Sex-Organ [A0096_S62_L001]

description:
A0096_S62_L001
Rhesus monkey

source_name: Sex Organ:Sex-Organ

value: Sex Organ:Sex-Organ


title: RA1834_LNG-CD-R [A0095]

description:
A0095
Rhesus monkey

source_name: Lung

value: Lung


title: RA0449_Kidney [A0100_S114_L002]

description:
A0100_S114_L002
Rhesus monkey

value: Kidney


title: RA1834_Skin-Rash [A0097_S40_L001]

description:
A0097_S40_L001
Rhesus monkey


title: LUC-LUC rep2


title: LUC-LUC rep3


title: OKF6, rep 2 [RNA-seq]

description:
labelled as OKF6.2 in processed data file 1
Normalized.Counts.RNAseq.cellline.txt

value: 3 Days


title: LUC-LUC rep5


title: AD4_Ethanol

value: Ethanol (500mM)


title: AD4_Digoxin

value: retinal organoids

value: Digoxin (40nM)


title: RA1834_LN-MES [A0094_S168_L002]

description:
A0094_S168_L002
Rhesus monkey

value: Lymph node:LN-MES


title: LUC-LUC rep1


title: OKF6, rep 1 [RNA-seq]

description:
labelled as OKF6.1 in processed data file 1
Normalized.Counts.RNAseq.cellline.txt

value: Wild Type


title: CREB3L2-ATF4 rep5

value: DIV1. FK-tagged CREB3L2 and ATF4. Lentiviral delivery.


title: RA1834_LN-ING-L [A0093_S169_L002]

description:
A0093_S169_L002
Rhesus monkey

value: Lymph node:LN-ING-L

value: infected with Ebola virus


title: CREB3L2-ATF4 rep4

value: E17 pregnant rats. This is DIV0.


title: RA1834_LN-AX-R [A0092_S170_L002]

description:
A0092_S170_L002
Rhesus monkey

source_name: Lymph node:LN-AX-R

value: Lymph node:LN-AX-R


title: WT_biol_rep_2_control

description:
Mammary epithelial organoids from wild-type MIC mice, grown without doxycycline
Processed data file column I

source_name: Mammary epithelium

value: FVB/N

value: Female

value: Mammary epithelium

value: Primary mammary epithelial cells

value: MIC/wild-type


title: CREB3L2-ATF4 rep3

value: Sprague-Dawley


title: SCC15, YBX1KO, DOXneg, rep 1 [RNA-seq]

description:
labelled as SCC15.1 in processed data file 1; labelled as SCC15.+YBX1.1 in processed data file 2
Normalized.Counts.RNAseq.cellline.txt
Normalized.Counts.RNAseq.YBX1.txt

value: Head and Neck Cancer Cells

value: 3 Days


title: Primary Myoepithelial cell_patient_2 (Sample_11_Patient2_ND)

city: London

first: Richard

last: Grose

address: Charterhouse Sq

institute: Queen Mary University of London

description:
Patient_Myoepithelial_Raw_counts.xlsx
Sample_11_Patient2_ND

data_processing:
Partek Flow Genomic Analysis Software
Data aligned to genome (Homo Sapiens Hg38) - Star version STAR 2.7.3A
Genes and transcripts analysed (hg38 - GENCODE Genes - release 34)
Supplementary files format and content: Excel file_Raw counts

source_name: breast

growth_protocol: 1089 myoepithelial cells were cultured in Ham’s F12 medium, supplemented with 10% FBS, 0.5 μg/mL hydrocortisone, 10 ng/mL Epidermal Growth Factor and 5 μg/mL Insulin. Primary myoepithelial cells were cultured on 0.08 mg/mL Collagen I-coated plates in HuMEC medium, supplemented with 0.4% bovine pituitary extract, 0.5 μg/mL hydrocortisone, 10 μg/mL apo-transferrin, 10 ng/mL EGF and 5 μg/mL insulin.

extract_protocol:
RNA was extracted using the Monarch Total RNA Miniprep Kit (NEB), following manufacturers instructions.
RNA libraries for RNAseq was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: Cells were treated with 1 µg/mL doxycycline to induce ITGB6 expression for 48 hr. 1089 cells were also treated with 10 µM of TGFBRi (SB431542) for 48 hr.

value: breast

value: N/A (primary cells)

value: myoepithelial cell

value: control


title: Primary Myoepithelial cell_patient_1 (Sample_10_Patient1_D)

description:
Patient_Myoepithelial_Raw_counts.xlsx
Sample_10_Patient1_D

value: ITGB6 overexpression

value: doxycycline induced


title: Primary Myoepithelial cell_patient_2 (Sample_12_Patient2_D)

description:
Patient_Myoepithelial_Raw_counts.xlsx
Sample_12_Patient2_D


title: Pik3caKI, Grhl3cKO C57BL/6 mouse, adjacent, rep 3

type: protein

description: SAMPLE 32

hyb_protocol: Sample lysates were run at the Host and Tumour Profiling Unit (HTPU, Cancer Research UK, Edinburgh, UK).

data_processing:
RPPA Relative Fluorescence Intensity (RFI) values were calculated by the Zeptoview software. A weighted linear regression through the dilution series was used to calculate the sample fluorescence intensity value which was then normalised to the reference BSA grid to account for intra-array spatial variation. Each intensity value was corrected to the background signal and the secondary antibody controls to validate the RFI value for each sample/antibody combination. ‘0’ accounted for RFI values where the primary antibody signal was lower than the signal emitted by the secondary antibody alone. 1e-9 was added to all RFI values for statistical analysis.
Please note that  PMR-125_NormToSec.RawData.xlsx is a direct output from ZeptoVision, which automatically normalises to the background.

label: biotin

molecule: protein

source_name: Mouse tongue epithelium

extract_protocol: Protein lysates from human HNC cells were extracted using the RPPA lysis buffer and quantified by the Pierce Coomassie Plus (Bradford) Assay Kit (ThermoFisher Scientific, Cat No. 23236).

value: Pik3ca variant knockin, Grhl3 knockout

tag: process center


title: RA1834_Testis [A0091_S7_L001]

description:
A0091_S7_L001
Rhesus monkey

tag: tissue

value: Sex Organ:Ovary

value: infected with Ebola virus


title: Pik3caKI, Grhl3cKO C57BL/6 mouse, tumour, rep 3

description: SAMPLE 31

scan_protocol: Sample lysates were run at the Host and Tumour Profiling Unit (HTPU, Cancer Research UK, Edinburgh, UK).


title: RA1834_Brain-Gr [A0090_S82_L002]

description:
A0090_S82_L002
Rhesus monkey


title: CREB3L2-ATF4 rep2

value: E17 pregnant rats. This is DIV0.

value: DIV1. FK-tagged CREB3L2 and ATF4. Lentiviral delivery.


title: Primary Myoepithelial cell_patient_1 (Sample_9_Patient1_ND)

description:
Patient_Myoepithelial_Raw_counts.xlsx
Sample_9_Patient1_ND


title: A0088 [A0088]

description:
A0088
Rhesus monkey

source_name: Adrenal Gland

value: Adrenal Gland


title: CREB3L2-ATF4 rep1


title: Pik3caKI, Grhl3cKO C57BL/6 mouse, adjacent, rep 2

description: SAMPLE 30

label_protocol: Sample lysates were run at the Host and Tumour Profiling Unit (HTPU, Cancer Research UK, Edinburgh, UK).


title: CREB3L2-CREB3L2 rep5

value: DIV1. FK-tagged CREB3L2. Lentiviral delivery.


title: RA1834_Spleen [A0085_S115_L002]

description:
A0085_S115_L002
Rhesus monkey

value: Spleen


title: CREB3L2-CREB3L2 rep4

value: Sprague-Dawley


title: Pik3caKI, Grhl3cKO C57BL/6 mouse, tumour, rep 2

description: SAMPLE 29

value: Host and Tumour Profiling Unit (HTPU, Cancer Research UK, Edinburgh, UK)


title: 1089 myoepithelial cell line (Sample_6_D2)

description:
1089_Myoepithelial_Raw_counts.xlsx
Sample_6_D2


title: RA1779_Skin-Non-Rash [A0084_S41_L001]

description:
A0084_S41_L001
Rhesus monkey


title: 1089 myoepithelial cell line (Sample_5_ND2)

description:
1089_Myoepithelial_Raw_counts.xlsx
Sample_5_ND2


title: Pik3caKI C57BL/6 mouse, rep 3

description: SAMPLE 26

value: Pik3ca variant knockin


title: RA1779_Skin-Rash [A0083_S42_L001]

description:
A0083_S42_L001
Rhesus monkey


title: CREB3L2-CREB3L2 rep2


title: 1089 myoepithelial cell line (Sample_4_DSB1)

description:
1089_Myoepithelial_Raw_counts.xlsx
Sample_4_DSB1

value: breast

value: doxycycline induced + TGFBRi


title: CREB3L2-CREB3L2 rep1


title: RA1779_LN-MES [A0080_S171_L002]

description:
A0080_S171_L002
Rhesus monkey

value: Lymph node:LN-MES


title: Pik3caKI C57BL/6 mouse, rep 2

description: SAMPLE 25


title: 1089 myoepithelial cell line (Sample_3_NDSB1)

description:
1089_Myoepithelial_Raw_counts.xlsx
Sample_3_NDSB1

value: myoepithelial cell

value: control

value: control + TGFBRi


title: RA1834_Kidney [A0086_S60_L001]

description:
A0086_S60_L001
Rhesus monkey

value: Kidney


title: Pik3caKI C57BL/6 mouse, rep 1

description: SAMPLE 24


title: 1089 myoepithelial cell line (Sample_8_DSB2)

description:
1089_Myoepithelial_Raw_counts.xlsx
Sample_8_DSB2

value: ITGB6 overexpression


title: RA1779_LN-ING-L [A0079_S172_L002]

description:
A0079_S172_L002
Rhesus monkey

source_name: Lymph node:LN-ING-L

value: Lymph node:LN-ING-L

value: infected with Ebola virus


title: 1089 myoepithelial cell line (Sample_7_NDSB2)

description:
1089_Myoepithelial_Raw_counts.xlsx
Sample_7_NDSB2


title: 1089 myoepithelial cell line (Sample 2_D1)

description:
1089_Myoepithelial_Raw_counts.xlsx
Sample_2_D1

value: doxycycline induced


title: Grhl3cKO C57BL/6 mouse, rep 3

description: SAMPLE 23

value: Grhl3 conditional knockout


title: Lipo863B-Nanopore

description: Cell Line

source_name: Cell Line; Lipo863B; Liposarcoma

extract_protocol: gDNA was isolated using BioNano Blood and Cell Culture DNA Isolation Kit (80004).

tag: disease state

value: Liposarcoma


title: Bacillus subtilis 168, Stationary control, rep3

city: Newcastle upon Tyne

first: David

last: Markham

address: Devonshire Building

department: ICOS

data_processing:
Nextflow nf-core/rnaseq 3.8.1
Trimming and removal of unwanted sequences by the following tools in the workflow: UMI-tools,  Trim Galore 0.6.7, BBSplit, SortMeRNA
Alignment of reads performed by STAR 2.6.1d and quantified using Salmon 1.5.2
Additional FASTA file was included for alignment against ERCC spike-in controls, ERCC92
Assembly: eb2
Supplementary files format and content: tab-delimited text file containing a matrix of all gene-counts established by Salmon. Samples as columns, Features as rows.

organism: Bacillus subtilis

source_name: Bacillus subtilis

extract_protocol:
RNA was extracted using Total RNA Purification Kit (Norgen Biotek) according to maunfacturer's specifications for gram-positive bacteria
The rRNA depletion was performed using NEBNext rRNA Depletion Kit (Bacteria). RNA sequencing library preparation was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented according to manufacturer’s instruction. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).

value: strain 168

value: Bacillus subtilis

value: Exponential phase


title: 1089 myoepithelial cell line (Sample_1_ND1)

description:
1089_Myoepithelial_Raw_counts.xlsx
Sample_1_ND1


title: CREB3L2-CREB3L2 rep3

value: E17 pregnant rats. This is DIV0.

value: DIV1. FK-tagged CREB3L2. Lentiviral delivery.

value: Sprague-Dawley


title: Grhl3cKO C57BL/6 mouse, rep 2

description: SAMPLE 22

value: Host and Tumour Profiling Unit (HTPU, Cancer Research UK, Edinburgh, UK)


title: Pik3caKI, Grhl3cKO C57BL/6 mouse, adjacent, rep 1

description: SAMPLE 28

value: Pik3ca variant knockin, Grhl3 knockout


title: Bacillus subtilis 168, Stationary control, rep2


title: RA1779_Ovary [A0077_S8_L001]

description:
A0077_S8_L001
Rhesus monkey

source_name: Sex Organ:Testis

extract_protocol:
Total RNA was extracted from tissue homogenates inactivated in TRIzol using the MagMAX MirVana total RNA kit (ThermoFisher) on a KingFisher FLEX instrument.
Ribosomal RNA was depleted using an RNase H-based method, RNA was then heat-fragmented, reverse transcription was performed, and strand-specific double-stranded cDNA was generated. xGen UDI-UMI (IDT) adapters were ligated and libraries were amplified.

value: Sex Organ:Testis

tag: monkey id


title: Pik3caKI, Grhl3cKO C57BL/6 mouse, tumour, rep 1

description: SAMPLE 27


title: Bacillus subtilis 168, Stationary control, rep1

tag: treatment


title: NFO190_170-A549hACE2-SARSCoV2-72hpi

city: Copenhagen

first: Nicolas

last: Fossat

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

description:
Paired-end 2 x 75 bp
Table S16.txt

data_processing:
CLEAR-CLIP_Preprocessing: Removal of adaptors and  quality trimming using Trimmomatic with settings 'SLIDINGWINDOW:4:20'. Collapsing of PCR duplicates, read demultiplexing and barcode/index/linker removal was aided by the R package CLIPflexR v0.1.20.
CLEAR-CLIP_Singleton reads: Sequenced reads were aligned to hg38/chlSab2/SARS-CoV-2 reference genomes using Rbowtie2, through the CLIPflexR wrapper with default settings. BED files and bedgraphs were created using CLIPflexR, and normalized to RPM for downstream analyses and coverage plots. Peak calling of aligned reads was done using Homer through the CLIPflexR wrapper, and peaks where annotated using GenomicFeatures v1.38.2, GenomicRanges v1.38 and ChiPseeker v1.22.1. Prediction of miRNA seed sites from 7mer-m8 or 7mer-A1 seed matches was done using a combination of CLIPflexR and custom methods.
CLEAR-CLIP_Chimera reads: Reads that remained unmapped after singleton alignment, were treated as potential chimeras. Unmapped reads were thus reverse aligned to the sequences of mature microRNAs and forward aligned to possible target sequences in hg38/chlSab2/SARS-CoV-2 reference genomes using Rbowtie2 and CLIPflexR. Chimeras were analysed for differential miRNA abundance (infected vs. non-infected), using edgeR, to indirectly scan for putative viral miRNA sequestration, by analysing loss of cell-bound miRNAsusing the edgeR package. Relative abundances of miRNAs for non-infected cells, were calculated as the average fraction of the three non-infected samples for each cell line.
RNA-Seq: Demultiplexed files were lane-merged and aligned to the SARS-CoV-2 reference genome using STAR (v2.7.9a). RPKM normalized genome coverage was generated from BAM files using deeptools genomecov. Average coverage was plotted against colored backgrounds, according to SARS-CoV-2 annotation regions in R.
Assembly: Green monkey: chlSab2; Human: hg38; SARS-CoV-2: Strain DK-AHH1 (PMID: 33903110). For each mutant, strain DK-AHH1 was also used but modified to carry the corresponding engineered point mutations.
Supplementary files format and content: Table_S1.xlsx - Number of reads per sample for CLEAR-CLIP in VeroE6 cells
Supplementary files format and content: Table_S2.txt - Singleton reads for CLEAR-CLIP in VeroE6 cells
Supplementary files format and content: Table_S3.txt - Chimeric reads for CLEAR-CLIP in VeroE6 cells
Supplementary files format and content: Table_S4.xlsx - List of miRNAs binding SARS-CoV-2 RNA in VeroE6 cells
Supplementary files format and content: Table_S5.xlsx - Functional miRNAs expressed in VeroE6 cells
Supplementary files format and content: Table_S6.xlsx - Number of reads per sample for CLEAR-CLIP in A549hACE2 cells
Supplementary files format and content: Table_S7.txt - Singleton reads for CLEAR-CLIP in A549hACE2 cells
Supplementary files format and content: Table_S8.txt - Chimeric reads for CLEAR-CLIP in A549hACE2 cells
Supplementary files format and content: Table_S9.xlsx - List of miRNAs binding SARS-CoV-2 RNA in A549hACE2 cells
Supplementary files format and content: Table_S10.xlsx - Functional miRNAs expressed in A549hACE2 cells
Supplementary files format and content: Table_S11.xlsx - Differential expression of miRNAs in infected VeroE6 cells
Supplementary files format and content: Table_S12.xlsx - Differential expression of miRNAs in infected A549hACE2 cells
Supplementary files format and content: Table_S13.xlsx - Differential miRNA binding on cellular RNAs in infected VeroE6 cells
Supplementary files format and content: Table_S14.xlsx - Differential miRNA binding on cellular RNAs in infected A549hACE2 cells
Supplementary files format and content: Table S15.txt Differential gene expression in infected VeroE6 cells
Supplementary files format and content: Table S16.txt Differential gene expression in infected A549hACE2 cells (72 hpi)

source_name: Human lung A549hACE2 cells

growth_protocol: Cells were grown in standard conditions.

extract_protocol:
For CLEAR-CLIP, cells were washed twice with ice cold PBS, UV254 cross-linked or not, scrapped, collected, pelleted by centrifugation at 500 g for 5 min at 4C and snap frozen, before to be gently lysed and processed further as described in PMID: 26602609 with minor changes. For RNA-Seq, cells were washed twice with ice cold PBS, dissolved in ice-cold reagent and total RNA extracted using a RNA Clean & Concentrator-25 kit (Zymo Research Z1018) strictly following manufacturer instrcutions and adding a DNAse I step.
For CLEAR-CLIP, library was constructed following a custom-made protocol (see PMID: 26602609) and minor changes. For RNA-Seq, library was constructed strictly following the TruSeq Stranded Total RNA protocol from Illumina and using TruSeq RNA CD index plate (96 indexes, 96 samples).

treatment_protocol: Cells were infected or not with SARS-CoV-2 (Wild-type or engineered mutants) at MOI = 0.001 for 48 hours.

tag: infected

value: Yes

tag: sars-cov-2 genotype

value: Wild-type

tag: moi

tag: duration of infection

value: 72 hours

tag: experiment

value: RNA-Seq from total RNA

tag: cross-linked

tag: igg used for ip

tag: molecule subtype

value: Total RNA (minus rRNA)


title: RA1779_Brain-Gr [A0076_S83_L002]

description:
A0076_S83_L002
Rhesus monkey

value: infected with Ebola virus

tag: time


title: Wildtype C57BL/6 mouse, rep 2

description: SAMPLE 20

value: Wild Type


title: Grhl3cKO C57BL/6 mouse, rep 1

description: SAMPLE 21

value: Grhl3 conditional knockout


title: NFO190_110-A549hACE2-SARSCoV2-72hpi

description:
Paired-end 2 x 75 bp
Table S16.txt


title: RA1779_Adrenal [A0074_S61_L001]

description:
A0074_S61_L001
Rhesus monkey

value: Adrenal Gland


title: NFO190_50-A549hACE2-SARSCoV2-72hpi

description:
Paired-end 2 x 75 bp
Table S16.txt


title: Bacillus subtilis 168, Stationary, rep3

tag: strain

value: strain 168

tag: cell type

value: Bacillus subtilis

value: Stationary phase


title: Wildtype C57BL/6 mouse, rep 1

description: SAMPLE 19

tag: genotype


title: RA1779_LN-AX-R [A0078_S173_L002]

description:
A0078_S173_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: Bacillus subtilis 168, Stationary, rep2


title: SCC25, YBX1KO, DOXpos, EGFpos, rep 2

description: SAMPLE 18

source_name: Head and Neck Cancer Cells

tag: cell line

value: YBX1 knockout

value: Doxcycline Treatment (1 ug/mL), EGF Treatment (100ng/mL)

value: 3 Days, 30mins

tag: process center


title: NFO190_180-A549hACE2-72hpi

description:
Paired-end 2 x 75 bp
Table S16.txt

value: No


title: RA1779_Kidney [A0072_S119_L002]

description:
A0072_S119_L002
Rhesus monkey

source_name: Kidney

tag: tissue

value: Kidney


title: Bacillus subtilis 168, Stationary, rep1


title: RA1779_Spleen [A0071_S116_L002]

description:
A0071_S116_L002
Rhesus monkey

source_name: Spleen

value: Spleen

tag: monkey id


title: Bacillus subtilis 168, Competence control, rep3

tag: treatment

value: Competence control


title: SCC25, YBX1KO, DOXpos, EGFpos, rep 1

description: SAMPLE 17

value: 3 Days, 30 mins

value: Host and Tumour Profiling Unit (HTPU, Cancer Research UK, Edinburgh, UK)


title: NFO190_60-A549hACE2-72hpi

description:
Paired-end 2 x 75 bp
Table S16.txt

tag: infected

value: RNA-Seq from total RNA

value: Total RNA (minus rRNA)


title: RA0223_Skin-Non-Rash [A0070_S43_L001]

description:
A0070_S43_L001
Rhesus monkey

value: infected with Ebola virus


title: Bacillus subtilis 168, Competence control, rep2


title: NFO190_120-A549hACE2-72hpi

description:
Paired-end 2 x 75 bp
Table S16.txt

tag: sars-cov-2 genotype


title: SCC25, YBX1KO, DOXpos, EGFneg, rep 2

description: SAMPLE 16

value: Doxcycline Treatment (1 ug/mL)

value: 3 Days


title: RA0223_Skin-Rash [A0069_S44_L001]

description:
A0069_S44_L001
Rhesus monkey


title: Bacillus subtilis 168, Competence control, rep1

value: strain 168

value: Bacillus subtilis


title: SCC25, YBX1KO, DOXpos, EGFneg, rep 1

description: SAMPLE 15


title: NFO190_160-A549hACE2-48hpi

description: Paired-end 2 x 75 bp

tag: moi


title: NFO190_100-A549hACE2-48hpi

description: Paired-end 2 x 75 bp

tag: duration of infection


title: SCC25, YBX1KO, DOXneg, EGFpos, rep 1

description: SAMPLE 13

value: Wild Type

value: EGF Treatment (100ng/mL)

value: 30 mins


title: NFO190_40-A549hACE2-48hpi

description: Paired-end 2 x 75 bp

tag: experiment


title: SCC25, YBX1KO, DOXneg, EGFpos, rep 2

description: SAMPLE 14


title: RA0223_LN-MES [A0066_S174_L002]

description:
A0066_S174_L002
Rhesus monkey

source_name: Lymph node:LN-MES

value: Lymph node:LN-MES


title: Bacillus subtilis 168, Competence, rep2

value: Competence


title: RA0223_LN-AX-R [A0064_S176_L002]

description:
A0064_S176_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: BdEC KDM6A ChIP

city: İZMİR

first: Serap

last: Erkek Özhan

state: BALÇOVA

address: İzmir Biyotıp ve Genom Merkezi (IBG), Dokuz Eylül Üniversitesi Sağlık Yerleşkesi, Mithatpaşa Caddesi No:58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

data_processing:
ChIP-seq data was aligned to the human genome (hg38) using nf-core/chip-seq pipeline
KDM6A peak calling was done using MACS2 using the parameters:  p<10−5 and FDR < 0.1 filter with narrow option.
Assembly: hg38
Supplementary files format and content: narrowPeak  (except for Input samples)

source_name: BdEC

growth_protocol: T24 was grown in Dubacco’s Modified Eagle Medium (Gibco), SV-HUC-1 was grown in Roswell Park Memorial Institute (RPMI) 1640 Medium supplemented with 10% FBS and 1% Penicillin. BdEC was grown in Bladder Epithelial Cell Basal Medium (ATCC PCS-420-032) supplemented with Bladder Epithelial Growth Kit (ATCC PCS-420-042).

extract_protocol:
Chromatin extraction and chromatin immunoprecipitation was performed following Schubeler Lab Protocol (Weber et al. 2007).
ChIP-seq libraries were prepared using NEBNext DNA Ultra II kit in EMBL GeneCore Facility.

treatment_protocol: No specific treatments were applied.

tag: chip antibody

value: BdEC

value: Human Primary Bladder Epithelial Cells

value: Untreated


title: SCC25, YBX1KO, DOXneg, EGFneg, rep 2

description: SAMPLE 12

value: Host and Tumour Profiling Unit (HTPU, Cancer Research UK, Edinburgh, UK)


title: RA0223_LN-ING-L [A0065_S175_L002]

description:
A0065_S175_L002
Rhesus monkey

data_processing:
Host transcriptomics data was processed using the umiRNAseq custom pipeline for Bulk RNA-seq Processing with UMI correction (https://github.com/broadinstitute/sabeti-host-txnomics-internal/blob/master/bulk-rna-seq/umiRNASeq.wdl).
Briefly, raw Fastq files were merged and tagged with their corresponding UMI barcode, then they were mapped using STAR to the Rhesus monkey (M. mulatta) reference genome and annotation (Mmul_10).
Resulting BAM files were filtered for multiple mapped reads, sorted and indexed using samtools. Then, PCR duplicates were removed by UMI-tools using the UMI barcodes of each transcript.
Furthermore, featureCounts were used to quantify expression from the aligned and processed RNA-Seq BAM files. Additionally, The BioMart R package was used to annotate the gene type, gene name, and gene function using the Ensembl M. mulatta database “mmulatta_gene_ensembl”.
Quality control over the sample was performed removing samples with low sequencing quality and mismatch sex assignment.
Assembly: Mmul_10
Supplementary files format and content: 20230121_counts_submission.txt: Tab-delimited format, raw counts.

value: Lymph node:LN-ING-L


title: Bacillus subtilis 168, Competence, rep3


title: BdEC Input


title: SCC25, YBX1KO, DOXneg, EGFneg, rep 1

description: SAMPLE 11


title: RA0223_Brain-Gr [A0062_S84_L002]

description:
A0062_S84_L002
Rhesus monkey


title: Bacillus subtilis 168, Aerobic, rep3

value: Aerobic


title: RA0223_Ovary [A0063_S9_L001]

description:
A0063_S9_L001
Rhesus monkey

value: Sex Organ:Testis

value: infected with Ebola virus


title: SV-HUC-1 KDM6A ChIP

value: Human Immortalized Uroepithelium Cells


title: Bacillus subtilis 168, Competence, rep1

value: strain 168


title: SCC15, YBX1KO, DOXpos, EGFpos, rep 2

description: SAMPLE 10

value: YBX1 knockout

value: Doxcycline Treatment (1 ug/mL), EGF Treatment (100ng/mL)

value: 3 Days, 30 mins


title: Bacillus subtilis 168, Aerobic, rep2

value: Bacillus subtilis


title: RA0223_Kidney [A0058_S120_L002]

description:
A0058_S120_L002
Rhesus monkey

value: Kidney


title: RA0223_Spleen [A0057_S117_L002]

description:
A0057_S117_L002
Rhesus monkey

value: Spleen


title: Bacillus subtilis 168, Aerobic, rep1


title: Bacillus subtilis 168, Anaerobic, rep3

value: Anaerobic


title: SCC15, YBX1KO, DOXpos, EGFneg, rep 2

description: SAMPLE 8

value: Doxcycline Treatment (1 ug/mL)

value: 3 Days


title: T24 KDM6A ChIP

value: Human Urinary Bladder Cancer

value: Untreated


title: T24 Input


title: RA0700_Skin-Non-Rash [A0056_S45_L001]

description:
A0056_S45_L001
Rhesus monkey


title: Bacillus subtilis 168, Anaerobic, rep2


title: TBI 11, bulk RNAseq

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

description:
Illumina Truseq
ERV_count_matrix_2.csv

data_processing:
Single nuclei RNAseq: Raw base calls were demultiplexed to obtained sample specific FastQ files and reads were aligned to GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics, Cellranger count v5) with default parameters (--include-introns was used for nuclei mapping)
Single nuclei RNAseq: Downstream analyses was performed with Seurat. All samples were merged and batch effects were removed using the Harmony algorithm. Cells with at least 1000 detected genes were retained and the data was normalized to transcript copies per 10,000, and log-normalized to reduce sequencing depth variability.
Single nuclei RNAseq: For visualization and clustering, manifolds were calculated using UMAP methods (RunUMAP, Seurat) and 20 precomputed principal components and the shared nearest neighbor algorithm modularity optimization-based clustering algorithm (FindClusters, Seurat) with a resolution of 0.1.
Single nuclei RNAseq: trusTEr (https://github.com/raquelgarza/truster) was ran pooling cells within clusters per condition, and per sample per condition.
Bulk RNAseq: Unique mapping using STAR aligner (--outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.03)
Bulk RNAseq: ERV predictions from RetroTector (https://github.com/PatricJernLab/RetroTector) were quantified using featureCounts (Subread version 1.6.3), forcing matching strandness of the reads to the features being quantified (-s 2).
Bulk RNAseq: BAM files were indexed using samtools (version 1.12) and converted to bigwig files using deeptools bamCompare (version 2.5.4) (--normalizeUsingRPKM)
Assembly: GRCh38
Supplementary files format and content: Single nuclei RNAseq: Cellranger's filtered_feature_bc_matrix: barcodes, features and matrix files
Supplementary files format and content: Single nuclei RNAseq: csv files containing TE subfamily quantification per cluster per condition (tbi and control _TE_raw_matrix.csv). This is basically Tetranscripts output reformatted into csv
Supplementary files format and content: Single nuclei RNAseq: csv files containing TE subfamily quantification per cluster per sample ([sample] _TE_raw_matrix.csv). This is basically Tetranscripts output reformatted into csv
Supplementary files format and content: Single nuclei RNAseq: csv files containing TE subfamily quantification per cell in cluster (cluster expression / num cells in cluster), per condition (tbi and control _TE_norm_cluster_size_matrix.csv)
Supplementary files format and content: Single nuclei RNAseq: csv files containing TE subfamily quantification per cell in cluster (cluster expression / num cells in cluster), per sample ([sample] _TE_norm_cluster_size_matrix.csv)
Supplementary files format and content: Bulk RNAseq bigwigs for genome browser visualization
Supplementary files format and content: Bulk RNAseq ERV quantification read count matrix

source_name: brain

extract_protocol:
Surgically removed brain tissue was immediately placed in a sterile pre-labelled container and subsequently stored in -80_C freezer until analyzed. Half of the tissue was put in a routinely used fixative, 4% buffered formalin (Histo- Lab Products AB, Gothenburg, Sweden, catalogue no 02176). The samples were fixed for 24–72 h and then paraffin-embedded and processed by hardware Tissue tek VIP (Sakura, CA, USA). From the fresh frozen contused brain tissue, samples of ca 5mm2  were taken for scRNA sequencing.
Single nuclei RNAseq: Protocol based on published nuclei isolation protocol (Södersten et al., 2018). Around 20 μg of -80 C-conserved tissue were thawed and dissociated in ice-cold lysis buffer (0.32M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl pH 8.0, 1 mM DTT) using a 1 ml glass douncer (Wheaton). The homogenate was slowly and carefully layered in the centrifuge tubes on top of a sucrose layer (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl pH 8.0, 1 mM DTT) to create a gradient, and then centrifuged at 15500 rpm for 2 h 15 min. Following centrifugation, the supernatant was removed and the pellet softened for 10 minutes in 100 μl of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl pH 7.2, 70 mM KCl, 2 mM MgCl2) prior resuspension in 300 μl of dilution buffer (10 mM Tris-HCl pH 7.2, 70 mM KCl, 2 mM MgCl2, Draq7 1:1000). The suspension was then filtered (70 μm cell strainer) and sorted via FACS (FACS Aria III, BD Biosciences) at 4° C with low flowrate, using a 100 μm nozzle (Pipette tips and Eppendorf tubes for transferring nuclei were pre-coated with 1% BSA). Bulk RNAseq: Total RNA was isolated from nuclei using the RNeasy Mini Kit (Qiagen).
Single nuclei RNAseq: 8500 nuclei were sorted for single-nuclei RNA-sequencing and then loaded onto the Chromium Next GEM Single Cell 3’ Kit (10x Genomics). Sequencing libraries samples were multiplexed and sequenced on a Novaseq machine using a 150-cycle kit using the recommended read length from 10x Genomics. Bulk RNAseq: Libraries were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection) and were sequenced on an Illumina NextSeq500 machine (paired-end 2×150bp).

value: brain

tag: condition

value: tbi

tag: age

tag: Sex

value: M

tag: time post_injury


title: RA0700_LN-MES [A0052_S177_L002]

description:
A0052_S177_L002
Rhesus monkey

value: Lymph node:LN-MES

value: infected with Ebola virus

tag: time


title: SCC15, YBX1KO, DOXneg, EGFpos, rep 2

description: SAMPLE 6

tag: genotype

value: Wild Type

value: EGF Treatment (100ng/mL)

value: 30 mins

value: Host and Tumour Profiling Unit (HTPU, Cancer Research UK, Edinburgh, UK)


title: Bacillus subtilis 168, Anaerobic, rep1

tag: strain

value: strain 168

tag: cell type

value: Bacillus subtilis


title: TBI 3, bulk RNAseq

description:
Illumina Truseq
ERV_count_matrix_2.csv

tag: tissue


title: SCC15, YBX1KO, DOXneg, EGFpos, rep 1

description: SAMPLE 5

tag: cell line

tag: process center


title: RA0700_LN-ING-L [A0051_S178_L002]

description:
A0051_S178_L002
Rhesus monkey

value: Lymph node:LN-ING-L

tag: monkey id

tag: treatment


title: Bacillus subtilis 168, Low Temperature control (37°C), rep3

value: Control Temperature (37degreeC)


title: RA0700_LN-AX-R [A0050_S179_L002]

description:
A0050_S179_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: SCC15, YBX1KO, DOXpos, EGFpos, rep 1

description: SAMPLE 9

value: YBX1 knockout

value: Doxcycline Treatment (1 ug/mL), EGF Treatment (100ng/mL)

value: 3 Days, 30 mins


title: SCC15, YBX1KO, DOXneg, EGFneg, rep 2

description: SAMPLE 4


title: TBI 2, bulk RNAseq

description:
Illumina Truseq
ERV_count_matrix_2.csv

value: brain


title: SV-HUC-1 Input

value: Human Immortalized Uroepithelium Cells

value: Untreated


title: SCC15, YBX1KO, DOXneg, EGFneg, rep 1

description: SAMPLE 3


title: OKF6, rep 2

description: SAMPLE 2

source_name: Normal Oral Cells

value: 3 Days


title: RA0700_Ovary [A0049_S12_L001]

description:
A0049_S12_L001
Rhesus monkey

source_name: Sex Organ:Ovary

value: Sex Organ:Ovary

value: infected with Ebola virus


title: Bacillus subtilis 168, Low Temperature control (37°C), rep1


title: Control 529, frontal lobe, bulk RNAseq

description:
Illumina Truseq
ERV_count_matrix_2.csv

value: control

value: M


title: Bacillus subtilis 168, Low Temperature (16°C), rep3

value: Low Temperature (16degreeC)


title: RA0700_Brain-Gr [A0048_S86_L002]

description:
A0048_S86_L002
Rhesus monkey


title: SCC15, YBX1KO, DOXpos, EGFneg, rep 1

description: SAMPLE 7

value: Doxcycline Treatment (1 ug/mL)

value: Host and Tumour Profiling Unit (HTPU, Cancer Research UK, Edinburgh, UK)


title: Control 502, frontal lobe, bulk RNAseq

description:
Illumina Truseq
ERV_count_matrix_2.csv


title: MNase-seq, HBV cccDNA, saturated nucleosomes,  In vitro Experiment3, Over digested

first: Andres

last: Mansisidor

address: 1230 York Ave Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: Rockefeller University

description: MNase-seq

data_processing:
UMI demultiplexing (custom script)
adapter trimming (custom script)
alignment to HBV genome (Bowtie2 v2.3.4.3)
nucleosome coverage mapping (nucleoATAC)
Bedgraphs from both RNA- and MNase-seq were plotted using Sushi package v1.30.0 in R v4.1.0
Assembly: NC_003977.2 (offset by 500 bp)
Supplementary files format and content: bedgraph files that include coverage of fragment centers (50 bp windows)

organism: Hepatitis B virus

source_name: in vitro

extract_protocol:
In vivo MNase-seq was performed on purified nuclei at different timepoints after transfection with HBV cccDNA or on in vitro reconstituted chromatin.
For MNase-seq on in vitro reconstituted chromatin, titration of MNase was performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested chromatin arrays. Chromatinized DNA (100 ng) was digested using MNase (NEB) in 25 µL reactions with 2.5–25 units of enzymes that was incubated for 5 minutes at 37C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37C. The reaction was stopped by adding 20 mM EDTA and 1% SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index Barcodes or Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out using only 5 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). For MNase-seq on cell cultured samples, HEK293T cells were transfected with recombinant cccDNA 4 or 24-hours prior to harvest for MNase-seq. The nuclei of HEK293 cells were purified by incubating cells in Nuclei isolation buffer for 10 minutes (0.1% Igepal, 0.1% Triton X -100, 1 mM DTT in 1 X PBS), mechanically lysing with 10 strokes of loose (A) pestle Dounce homogenizer, and washing nuclei twice in 10 mL of Wash Buffer with Tween (10 mM Tris-HCl pH 7.5, 2.5 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Titration of MNase was similarly performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested genomic DNA. MNase (NEB) was added to 2 x 106 nuclei in 50 µL reaction volume with 250–2000 units of enzyme that was incubated for 5 minutes at 37 C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37 C. The reaction was stopped by adding 20 mM EDTA and 1 % SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). Libraries were then pooled and enriched for HBV-containing reads using custom-designed xGen Lockdown probes (Integrated DNA Technology) of 60 bp each tiling the entire HBV genome and oligo capture protocol was followed per manufacture’s protocol. Enriched libraries were subsequently amplified using 11 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and purified using Ampure XP beads.

value: in vitro

value: not applicable

value: reconstituted nucleosomes


title: A0046 [A0046]

first: Siddharth

last: Raju

address: 415 Main Street

description:
A0046
Rhesus monkey

value: Adrenal Gland


title: OKF6, rep 1

description: SAMPLE 1

value: Wild Type


title: RA0700_Skin-Rash [A0055_S46_L001]

description:
A0055_S46_L001
Rhesus monkey


title: Bacillus subtilis 168, Low Temperature (16°C), rep2

value: strain 168

value: Bacillus subtilis


title: Control 501, frontal lobe, bulk RNAseq

description:
Illumina Truseq
ERV_count_matrix_2.csv

value: brain


title: Bacillus subtilis 168, Low Temperature (16°C), rep1


title: RA0700_Kidney [A0044_S121_L002]

description:
A0044_S121_L002
Rhesus monkey

value: Kidney


title: MNase-seq, HBV cccDNA, saturated nucleosomes,  In vitro Experiment3, Fully digested

description: MNase-seq


title: NFO190_150-A549hACE2-SARSCoV2-48hpi

description: Paired-end 2 x 75 bp

tag: infected

value: Yes

tag: sars-cov-2 genotype

value: Wild-type

tag: moi

value: 48 hours

value: RNA-Seq from total RNA

tag: cross-linked

tag: igg used for ip

tag: molecule subtype

value: Total RNA (minus rRNA)


title: TBI 16, bulk RNAseq

description:
Illumina Truseq
ERV_count_matrix_2.csv

tag: condition

value: tbi

tag: age

tag: Sex

value: M


title: Bacillus subtilis 168, Low Temperature control (37°C), rep2

value: Control Temperature (37degreeC)


title: MNase-seq, HBV cccDNA, intermediate nucleosomes,  In vitro Experiment3, Over digested

description: MNase-seq

value: in vitro

tag: genotype


title: RA0700_Spleen [A0043_S118_L002]

description:
A0043_S118_L002
Rhesus monkey

value: Spleen

value: infected with Ebola virus

tag: time


title: Bacillus subtilis 168, Nutrient shift (Malate to Glucose) control - No Glucose, rep3

tag: strain

tag: cell type

value: Malate


title: NFO190_90-A549hACE2-SARSCoV2-48hpi

description: Paired-end 2 x 75 bp

tag: duration of infection

tag: experiment


title: RA0717_Sex-Organ [A0040_S13_L001]

description:
A0040_S13_L001
Rhesus monkey

source_name: Sex Organ:Sex-Organ

tag: tissue

value: Sex Organ:Sex-Organ

tag: monkey id


title: MNase-seq, HBV cccDNA, intermediate nucleosomes,  In vitro Experiment3,  Fully digested

description: MNase-seq

value: not applicable

tag: treatment

value: reconstituted nucleosomes


title: NFO190_30-A549hACE2-SARSCoV2-48hpi

description: Paired-end 2 x 75 bp

tag: infected

tag: sars-cov-2 genotype


title: RA0717_LN-MES [A0038_S180_L002]

description:
A0038_S180_L002
Rhesus monkey

value: Lymph node:LN-MES


title: Bacillus subtilis 168, Nutrient shift (Malate to Glucose) control - No Glucose, rep2

value: strain 168

value: Bacillus subtilis


title: MNase-seq, HBV cccDNA, undersaturated nucleosomes,   In vitro Experiment3, Fully digested

description: MNase-seq


title: MNase-seq, HBV cccDNA, undersaturated nucleosomes,   In vitro Experiment3, Over digested

description: MNase-seq


title: Lung, COVID patient, sample 1 [RCL_extr1]

city: Boston

first: Megan

middle: M

last: Sperry

state: MA

address: 3 Blackfan Circle

institute: Wyss Institute at Harvard University

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Assembly: human (hg19)
Supplementary files format and content: Comma separated value (csv) matrix of raw read counts per gene for each sample

source_name: lung biopsy

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
TruSeq RNA Library Prep Kit v2

value: lung biopsy

tag: subject status

value: COVID-19 deceased patient


title: Bacillus subtilis 168, Nutrient shift (Malate to Glucose), rep3

value: Nutrient shift (Malate to Glucose)


title: Bacillus subtilis 168, Nutrient shift (Malate to Glucose) control - No Glucose, rep1


title: RA0717_LN-ING-L [A0037_S181_L002]

city: Cambridge

institute: Broad Institute

description:
A0037_S181_L002
Rhesus monkey

value: Lymph node:LN-ING-L


title: RA0717_Brain-Gr [A0034_S87_L002]

description:
A0034_S87_L002
Rhesus monkey


title: Bacillus subtilis 168, Nutrient shift (Malate to Glucose), rep1


title: Bacillus subtilis 168, Nutrient shift (Malate to Glucose), rep2


title: aMDM+LCC-12-Blood16

city: Paris Cedex 05

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Monocytes from blood 16 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were treated with IFN-gamma (20 ng/mL), LPS (100 ng/mL) and LCC-12 (10 µM) during 24 hours.
D440T19

data_processing:
Raw sequencing reads were aligned on the human hg38 reference genome using the STAR mapper [7] (2.5.3a), up to the generation of a raw count table per gene (Gencode annotation v26). Expressed genes (TPM>=1 in at least one sample) have then been selected for downstream analysis.The raw count table was then normalized using the TMM method from the edgeR R package [5] (v3,22,3), and the limma voom (v3.36.3) functions were applied to detect genes with differential expression between untreated and EGF samples. Genes with an adjusted pvalue < 0,05 were called significant.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: monocyte-derived macrophages treated with IFN-gamma, LPS and LCC-12

growth_protocol: Peripheral blood samples were collected from healthy donors. Pan monocytes were sorted using microbeads (negative sorting) according to the manufacturer's instructions (Miltenyi Biotec, Somerville, MA, USA), cultured in RPMI 1640 with glutamine (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum.

extract_protocol:
RNA extracted using the RNeasy mini kit (QIAGEN)
RNA sequencing libraries were prepared from 1 µg total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit, which allows strand specific sequencing to be performed. A first step of polyA selection using magnetic beads was performed to allow sequencing of polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. Sequencing was carried out on a NovaSeq 6000 instrument from Illumina based on a 2*100 cycle mode (paired-end reads, 100 bases).

treatment_protocol: Monocytes were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to generate their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) and co-treated with LCC-12 (10 μM) during 24 hours.

tag: individual

value: blood

value: pan monocyte


title: MNase-seq, HBV cccDNA, Empty,  In vitro Experiment3, Fully digested

description: MNase-seq


title: RA0717_LN-AX-R [A0036_S182_L002]

description:
A0036_S182_L002
Rhesus monkey

source_name: Lymph node:LN-AX-R

value: Lymph node:LN-AX-R


title: MNase-seq, HBV cccDNA, Empty,  In vitro Experiment3, Over digested

description: MNase-seq

value: in vitro


title: aMDM-Blood16

description:
Monocytes from blood 16 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
D440T18

source_name: monocyte-derived macrophages treated with IFN-gamma and LPS

value: Activated


title: Bacillus subtilis 168, Nutrient shift (Glucose to Malate) control - No Malate, rep3

source_name: Bacillus subtilis

value: Glucose


title: RA0717_Kidney [A0030_S122_L002]

description:
A0030_S122_L002
Rhesus monkey

value: Kidney

value: infected with Ebola virus


title: Lung, COVID patient, sample 2 [RCL_extr2]


title: naMDM-Blood16

description:
Monocytes from blood 16 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D440T17

source_name: monocyte-derived macrophages

value: Unactivated


title: Bacillus subtilis 168, Nutrient shift (Glucose to Malate) control - No Malate, rep2


title: MNase-seq,HBV cccDNA, intermediate nucleosomes,  In vitro Experiment 2

description: MNase-seq

value: not applicable

value: reconstituted nucleosomes


title: RA0717_Spleen [A0029_S119_L002]

description:
A0029_S119_L002
Rhesus monkey

value: Spleen


title: MNase-seq,HBV cccDNA, undersaturated nucleosomes,  In vitro Experiment 2

description: MNase-seq


title: aMDM+LCC-12-Blood14

description:
Monocytes from blood 14 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were treated with IFN-gamma (20 ng/mL), LPS (100 ng/mL) and LCC-12 (10 µM) during 24 hours.
D440T15


title: Bacillus subtilis 168, Nutrient shift (Glucose to Malate) control - No Malate, rep1

value: strain 168

value: Bacillus subtilis


title: MNase-seq,HBV cccDNA, Empty,  In vitro Experiment 2

description: MNase-seq


title: Bacillus subtilis 168, Nutrient shift (Glucose to Malate), rep3

value: Nutrient shift (Glucose to Malate)


title: A0025 [A0025]

description:
A0025
Rhesus monkey

source_name: Lung

value: Lung


title: MNase-seq,HBV cccDNA, saturated nucleosomes,  In vitro Experiment 2

description: MNase-seq


title: MNase-seq,HBV dslDNA loaded with reconstituted nucleosomes,  In vitro Experiment1

description: MNase-seq


title: aMDM+LCC-12-Blood13

description:
Monocytes from blood 13 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were treated with IFN-gamma (20 ng/mL), LPS (100 ng/mL) and LCC-12 (10 µM) during 24 hours.
D440T11


title: Bacillus subtilis 168, Nutrient shift (Glucose to Malate), rep2


title: RA0850_LN-MES [A0024_S183_L002]

description:
A0024_S183_L002
Rhesus monkey

value: Lymph node:LN-MES


title: RA0850_LN-ING-L [A0023_S184_L002]

description:
A0023_S184_L002
Rhesus monkey

source_name: Lymph node:LN-ING-L

value: Lymph node:LN-ING-L