title: Input-Donor24-aMDM

data_processing:
ChIP-seq data processing and quality controls have been performed with the Institut Curie ChIP-seq Nextflow pipeline (1.0.6) available at https://github.com/bioinfo-pf-curie/ChIP-seq.
Briefly, reads were trimmed for adapter content, and aligned on the Human reference genome (hg38) with BWA-mem.
Low quality mapped reads, reads aligned on ENCODE blacklist regions, reads aligned on the spike-in genome and reads marked as duplicates were discarded from the analysis.
Bigwig tracks were then generated with deeptools and normalized to 1 million reads to account for differences in sequencing depth.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: blood

growth_protocol: Cells were grown and treated as described. Cells were centrifuged at 1500 × g for 5 min at room temperature. The pelleted cells were resuspended in medium, counted and crosslinked with 1% formaldehyde for 10 min at room temperature. Then, 2.5 M glycine was added to a final concentration of 0.125 M and incubated for 5 min at room temperature followed by centrifugation at 1500 × g for 5 min at 4 °C. The pelleted cells were washed twice with ice-cold 1× PBS and collected by centrifugation at 1500 × g for 5 min at 4 °C. Pellets were resuspended in lysis buffer A (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, cOmplete) and incubated for 30 min on a rotating wheel at 4 °C. Next, lysates were centrifuged at 1500 × g for 15 min at 8 °C to prevent SDS precipitation, and the supernatants were discarded. Pellets were then sheared in buffer B (25 mM Tris-HCl pH 8, 3 mM EDTA, 0.1% SDS, 1% Triton X-100, 150 mM NaCl, cOmplete) to approximately 200–600 base-pair average size using a Bioruptor Pico (Diagenode). After centrifugation at 20000 × g at 4 ºC for 15 min, supernatants containing sheared chromatin were used for immunoprecipitation. 25 μL (10%) of sheared chromatin was used as input DNA to normalize sequencing data. As an additional control for normalization, spike-in chromatin from Drosophila and a spike-in antibody were used. Chromatin immunoprecipitation (1 million cells per ChIP condition) was carried out using sheared chromatin and antibodies against specific histone marks, which were subsequently complexed to either Dynabeads Protein G-coated magnetic beads (ThermoFisher Scientific, 10003D) for H3K27ac, H3K14ac, H3K9ac, H3K27me3 and H3K9me2. Briefly, each antibody was mixed with 1 μg of spike-in antibody. Then, 22 μL magnetic beads were washed three times in ice-cold buffer C (20 mM Tris-HCl pH 8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 150 mM NaCl, cOmplete) and incubated with the mixture of antibodies for 4 h, at room temperature on a rotating wheel in buffer C (494 μL). After spinning and removal of supernatants, beads were resuspended in 50 μL buffer C. This suspension was subsequently incubated with 250 μL sheared chromatin previously mixed with 50 ng of spike-in chromatin from Drosophila (250 μL chromatin of interest: 2.5 μL spike -in chromatin) at 4 °C on a rotating wheel overnight (16 h). After a spinning, supernatants were discarded and beads were successively washed in buffer C (twice), buffer D (20 mM Tris-HCl pH 8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 500 mM NaCl), buffer E (10 mM Tris-HCl pH 8, 0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA) and once in buffer F (10 mM Tris-HCl pH 8, 1 mM EDTA, 50 mM NaCl). Finally, input and immunoprecipitated chromatin samples were resuspended in a solution containing TE buffer/1% SDS, de-crosslinked by heating at 65 °C overnight and subjected to both RNase A (ThermoFisher Scientific, 12091-039, 1 mg/mL) and Proteinase K (ThermoFisher Scientific, E00491, 20 mg/mL) treatments.

extract_protocol:
After reverse crosslinking, input and immunoprecipitated chromatin samples were treated with RNase A and proteinase K, and glycogen (ThermoFisher Scientific, R0561, 20 mg/mL) was added. Samples were incubated at 37 ºC for 2 h. DNA precipitation was carried out using 8 M LiCl (final concentration 0.44 M) and phenol:chloroform:isoamyl alcohol. Samples were vortexed and centrifuged at 20000 × g for 15 min at 4 ºC. The upper phase was mixed with chloroform by vortexing. After centrifugation at 20000 × g for 15 min at 4 ºC, the upper phase was mixed with –20 ºC absolute ethanol by vortexing and stored at –80 ºC for 2 h. Next, samples were pelleted at 20000 × g for 20 min at 4 ºC. The pellets were washed with ice-cold 70% ethanol and centrifuged at 20000 × g for 15 min at 4 ºC. The supernatants were discarded and pellets were dried at room temperature, dissolved in nuclease-free water and quantified using a Qubit fluorimetric assay (ThermoFisher Scientific) according to the manufacturer’s protocol.
Illumina compatible libraries were prepared from input and immunoprecipitated DNAs using the Illumina TruSeq ChIP library preparation kit according to the manufacturer’s protocol (IP-202-1012). Briefly, 4 to 10 ng of DNA were subjected to end-repair, dA-tailing and ligation of TruSeq indexed Illumina adapters. After a final PCR amplification step (with 15 cycles), the resulting barcoded libraries were equimolarly pooled and quantified by qPCR using the KAPA library quantification kit (Roche, 07960336001). Sequencing was performed on the NovaSeq 6000 (Illumina), targeting 75 M clusters per sample and using paired-end 2 x 100 bp.

tag: tissue

value: blood

value: pan monocyte

value: activated

tag: donor

tag: chip antibody


title: HG3 Control Input, rep1

status: Public on Mar 03 2023

type: SRA

city: Monrovia

first: Lili

last: Wang

state: CALIFORNIA

address: 1218 South Fifth Ave.

department: Systems biology

country: USA

institute: City of Hope

library_source: transcriptomic

data_processing:
Reads were aligned to the human reference genome (GRCh38/hg38) using STAR with default parameters. m6A peak calling, quantification, annotation and differential m6A sites analysis were performed using R package exomePeak.
Assembly: hg38
Supplementary files format and content: Peak track file (tdf)

molecule: total RNA

organism: Homo sapiens

source_name: B cells

extract_protocol:
Methylated RNA immunoprecipitation was processed by using EpiMark® N6-Methyladenosine Enrichment Kit (#E1610S, NEB).
Purified RNA fragments were used for library construction using Stranded Total RNA Prep with Ribo-Zero Plus Kit (#20040529, Illumina)

tag: cell line

tag: cell type

value: chronic lymphocytic leukemia cell line

tag: genotype

value: WT

tag: rip antibody


title: BSR133-Ep-123

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

data_processing:
Sequencing and base calling: RNA-seq libraries were sequenced on an Illumina HiSeq 2500 equipment (Illumina, San Diego, CA, USA) with base calling by CASAVA software (version 1.8.2, Illumina, San Diego, CA, USA).
Read alignment: Raw data were processed by TrimGalore package (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to trim the adapters, in following the RNA-seq library reads processed by FastQC tool (Andrews, 2010) and MultiQC (Ewels et al., 2016) and performed analysis of detection of differential expression in EPN using processed reads aligned with the reference genome (Genome Reference Consortium Human GRCh38) through STAR package (Dobin and Gingeras, 2015). Alignment performance was assessed with Picard and Qualimap tools.
Gene specific read counts: Gene specific read counts were determined with to FastQC tool (Andrews, 2010) and MultiQC (Ewels et al., 2016). DESeq2 (v1.26.0) (Love et al., 2014) was used to estimate the change in feature expression between conditions.
Genome_build: Reads are in .fastq.gz format and contain the raw base calls from sequencing. Alignment files are in .bam format and contain mapped reads.
Supplementary_files_format_and_content: Normalized abundance measurements are in .txt format as the output from DESeq2.

source_name: Frozen ependymal tumor tissue

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA/Protein Mini kit (QIAGEN, Hilden, Germany) and RNA integrity was evaluated by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) following manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Frozen ependymal tumor tissue

tag: primary/relapse

value: primary

tag: brain location

value: posterior fossa

tag: age at diagnosis years

tag: histological grade

value: II

tag: gender

value: female

tag: molecular subgroup


title: HG3 Control RNAseq, rep1

data_processing:
RNAseq:Reads were aligned to the human reference genome (GRCh38/hg38) using STAR with default parameters. Differentially expression of mRNA analysis was performed using DESeq2 R package. Genes with more than 2-fold change and FDR less than 0.05 were used as significance cutoff.
Assembly: hg38
Supplementary files format and content: Hg3_METTL3KO_diff.txt

extract_protocol:
Stranded Total RNA Prep
Ribo-Zero Plus Kit (Illumina)

tag: treatment


title: BSR137-Ep-45-15

value: supratentorial

value: III


title: bam mutant, Mei-P26 OE rep2

city: Cambridge

first: Tamsin

middle: Joy

last: Samuels

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description:
gene_exp.diff_bam_KD_meiP26_vs_bam_OE_meiP26.txt
gene_exp.diff_bam_vs_bam_OE_meiP26.txt

data_processing:
RNA- sequencing data was first aligned to ribosomal RNA using Bowtie2 (Langmead & Salzberg, 2012)
Non-rRNA reads were mapped to the Drosophila melanogaster genome (dm6) using STAR (Dobin et al., 2013)
transcript abundance was quantified and differentially expressed genes were identified using Cufflinks (Trapnell et al., 2010)
Assembly: dm6
Supplementary files format and content: genes_fpkm.txt files are output off cuflinks, showing fpkm per gene for each sample
Supplementary files format and content: gene_exp.diff are .txt files output of cufflinks, showing differential expression test between two samples for each gene

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole ovary

extract_protocol:
120 pairs of ovaries were dissected for each sample and immediately stored at -80°C after dissection. Frozen samples were homogenized in TRIzol Reagent (Invitrogen) using an electrical pestle and further disrupted by passing 15 times through a 26-gauge syringe. Total RNA was isolated using TRIzol Reagent (Invitrogen) following the manufacturer9s protocol.
Poly(A)-selected RNA-sequencing (RNA- seq) libraries were generated using 2.5 μg of purified RNA with the NEBNext® Poly(A) mRNA Magnetic Isolation Module and the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina®. Libraries were multiplexed using the NEBNext® Multiplex Oligos for Illumina® and sequenced in single-end, 50-nt-long reads on an Illumina HiSeq 2500.

value: whole ovary

tag: age

value: adult

tag: Sex


title: bam mutant rep2

description:
gene_exp.diff_bam_vs_bam_KD_meiP26.txt
gene_exp.diff_bam_vs_bam_OE_meiP26.txt


title: bam mutant, Mei-P26 OE rep1


title: RA1834_WholeBlood-BL [A0330_S26_L001]

first: Siddharth

last: Raju

state: Massachusetts

address: 415 Main Street

institute: Broad Institute

description:
A0330_S26_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.

organism: Macaca mulatta

source_name: Whole blood

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: Whole blood

tag: monkey id

value: infected with Ebola virus

tag: time


title: RA1834_WholeBlood-BL [A0331_S96_L001]

description:
A0331_S96_L001
Rhesus monkey

tag: tissue


title: RA1834_WholeBlood-D3 [A0333_S94_L001]

description:
A0333_S94_L001
Rhesus monkey


title: bam mutant rep1


title: Input-Donor24-aMDM+LCC-12

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

library_source: genomic

molecule: genomic DNA

tag: donor

tag: chip antibody


title: Input-Donor24-naMDM

tag: cell type

value: non-activated


title: bam mutant Mei-P26 RNAi rep1

description:
gene_exp.diff_bam_KD_meiP26_vs_bam_OE_meiP26.txt
gene_exp.diff_bam_vs_bam_KD_meiP26.txt

tag: genotype

value: nosgal4/UAS-Mei-P26 RNAi;bam86


title: Input-Donor20-aMDM+LCC-12

value: blood

value: pan monocyte


title: LYS-2

city: Shanghai

first: Congcong

last: Zhu

address: 1278 Baode Road

country: China

institute: Shanghai Skin Disease Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited txt file includes Count and  FPKM values for each sample

organism: Mus musculus

source_name: skin

growth_protocol: Male BALB/c mice (22 ± 2 g) aged 6-8 weeks and were offered free access to food and water within a specific pathogen-free environment.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The mice were subjected to adaptive feeding for 7 days prior to the initiation of the experiments.  The backs of all the mice were shaved and depilated using depilatory cream to expose the back skin.Three groups except the control group received the application of 62.5 mg IMQ cream (5% w/w) daily on their back skins for five consecutive days. On day 13, back skin tissues were collected.

value: skin

tag: strain

value: BALB/c

value: Male

tag: condition

value: imiquimod-induced psoriasis-like mouse model

value: BALB/c mouse

value: Longkui Yinxiao soup


title: LYS-1


title: IMQ-3

value: imiquimod


title: RA0449_WholeBlood-D1 [A0328_S28_L001]

description:
A0328_S28_L001
Rhesus monkey


title: RA0449_WholeBlood-BL [A0327_S29_L001]

description:
A0327_S29_L001
Rhesus monkey


title: IMQ-2


title: IMQ-1


title: Control-1

value: control

value: blank


title: Control-2


title: Control-3


title: RA0449_WholeBlood-BL [A0326_S30_L001]

description:
A0326_S30_L001
Rhesus monkey


title: LYS-3


title: M4C

city: Bronx

first: Jiahn

last: Choi

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
output Illumina base call files were converted to FASTQ files (bcl2fastq), these from each mouse aligned to the mouse mm10 genome v1.2.0 and converted to count matrices (Cell Ranger software v3.0.2).
Assembly: mm10
Supplementary files format and content: HDF5 Feature Barcode Matrix Format

source_name: Small intestine

growth_protocol: CB6F1 hybrid male mice originally obtained at either 2 months or 21 months of age from NIA aging colony and maintained under standard condition

extract_protocol:
Mice were sacrificed, excised intestines opened longitudinally, rinsed with cold saline, single cell suspensions prepared, re-suspended in antibody staining buffer, blocked with FcR Blocking Reagent, washed and pelleted, then incubated for 20 minutes at 4°C with, EpCAM-APC and CD45-PerCP. Cells were sorted by FACs on a MoFlo instrument and Epcam positive, CD45 negative total epithelial cells collected.
scRNAseq libraries were constructed by the Albert Einstein Genomics Core using the 3’ kit protocols of 10X Genomics with approximately 10,000 single FACS collected epithelial cells from each mouse processed on a Chromium Chip B microfluidic apparatus (10X Genomics). Library quality was verified by size analysis of transcripts (BioAnalyzer; Agilent, Santa Clara, CA) and after passing quality control assays, multiple libraries were multiplexed and sequenced by HiSeq PE150 using pair-end sequencing, with a readout length of 150 bases (Novogene; Sacramento, California), and the data assigned to individual cells using the sample indexes.

treatment_protocol: On arrival young mice were immediately switched to a purified control diet and old mice were randomized to either the same control diet, or a diet in which either 0.1% metformin or microencapsulated rapamycin at a concentration of 42 ppm was incorporated into the formulation. Eudragit was also included into the control and metformin diets (429ppm) in order to match the rapamycin formulation. All mice were group housed and fed these diets for 3 months

value: Small intestine

value: 5 months old

value: epithelial cells


title: M4B

description: 10x Genomics


title: RA0223_WholeBlood-D3 [A0325_S31_L001]

description:
A0325_S31_L001
Rhesus monkey

value: Whole blood

value: infected with Ebola virus


title: H3K9me2-Donor24-aMDM+LCC-12


title: H3K9me2-Donor24-aMDM

value: activated


title: RA0223_WholeBlood-BL [A0323_S33_L001]

description:
A0323_S33_L001
Rhesus monkey


title: RA0223_WholeBlood-D1 [A0324_S32_L001]

description:
A0324_S32_L001
Rhesus monkey


title: RA0449_WholeBlood-D3 [A0329_S27_L001]

description:
A0329_S27_L001
Rhesus monkey


title: M3A

description: 10x Genomics

value: 24 months old

value: microencapsulated Rapamycin (42 ppm)


title: M3C

description: 10x Genomics


title: Input-Donor20-aMDM

value: blood

value: pan monocyte


title: RA0223_WholeBlood-BL [A0322_S34_L001]

description:
A0322_S34_L001
Rhesus monkey


title: H3K9me2-Donor24-naMDM

value: non-activated


title: H3K9me2-Donor20-aMDM+LCC-12


title: H3K9me2-Donor20-aMDM


title: Input-Donor20-naMDM


title: M2B

description: 10x Genomics

value: Male

value: Metformin (0.1%)


title: M2C

description: 10x Genomics


title: H3K9me2-Donor20-naMDM


title: RA1423_WholeBlood-D8-NEC [A0321_S35_L001]

description:
A0321_S35_L001
Rhesus monkey


title: M2A

description: 10x Genomics


title: RA1423_WholeBlood-BL [A0320_S36_L001]

description:
A0320_S36_L001
Rhesus monkey


title: M1C

description: 10x Genomics


title: M4A

description: 10x Genomics


title: RA1639_WholeBlood-D3 [A0347_S80_L001]

description:
A0347_S80_L001
Rhesus monkey


title: H3K9me2-Donor88-aMDM+LCC-12


title: M1A

description: 10x Genomics


title: H3K9me2-Donor88-aMDM


title: RA1423_WholeBlood-BL [A0319_S37_L001]

description:
A0319_S37_L001
Rhesus monkey


title: M3B

description: 10x Genomics


title: MET41_GU100_96_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

value: male

value: Group exposed to a mixture (41 ug/Lmetformin + 100 ug/Lguanylurea) at 96h


title: MET41_GU100_96_11


title: MET41_GU100_96_10


title: H3K9me2-Donor88-naMDM


title: MET41_GU100_96_9


title: RA0917_WholeBlood-D6-NEC [A0318_S38_L001]

description:
A0318_S38_L001
Rhesus monkey


title: MET41_GU100_96_8


title: MET41_GU100_96_7


title: RA0917_WholeBlood-BL [A0317_S39_L001]

description:
A0317_S39_L001
Rhesus monkey


title: MET41_GU100_96_5


title: RA0917_WholeBlood-BL [A0316_S40_L001]

description:
A0316_S40_L001
Rhesus monkey


title: MET41_GU100_96_6


title: M1B

description: 10x Genomics

value: Small intestine


title: RA1790_WholeBlood-D8-NEC [A0315_S41_L001]

description:
A0315_S41_L001
Rhesus monkey


title: RA1790_WholeBlood-BL [A0314_S42_L001]

description:
A0314_S42_L001
Rhesus monkey


title: MET41_GU100_96_4


title: H3K27me3-Donor90-aMDM


title: MET41_GU100_96_1


title: MET41_GU100_96_2


title: MET41_GU100_96_3


title: H3K27me3-Donor90-aMDM+LCC-12


title: MET41_GU100_48_12

value: Group exposed to a mixture (41 ug/Lmetformin + 100 ug/Lguanylurea) at 48h


title: H3K27me3-Donor90-naMDM


title: H3K9me2-Donor90-aMDM+LCC-12


title: H3K9me2-Donor90-aMDM


title: RA1790_WholeBlood-BL [A0313_S43_L001]

description:
A0313_S43_L001
Rhesus monkey


title: MET41_GU100_48_10


title: RA1779_WholeBlood-D8-NEC [A0312_S44_L001]

description:
A0312_S44_L001
Rhesus monkey


title: MET41_GU100_48_11


title: RA1779_WholeBlood-BL [A0311_S45_L001]

description:
A0311_S45_L001
Rhesus monkey


title: MET41_GU100_48_7


title: MET41_GU100_48_8


title: MET41_GU100_48_6


title: H3K27me3-Donor88-aMDM


title: H3K9me2-Donor90-naMDM


title: RA1779_WholeBlood-BL [A0310_S46_L001]

description:
A0310_S46_L001
Rhesus monkey


title: MET41_GU100_48_5


title: H3K27me3-Donor88-naMDM


title: MET41_GU100_48_3


title: MET41_GU100_48_2


title: MET41_GU100_48_9


title: MET41_GU100_48_1


title: RA1818_WholeBlood-BL [A0307_S48_L001]

description:
A0307_S48_L001
Rhesus monkey


title: MET41_GU100_24_11

value: Group exposed to a mixture (41 ug/Lmetformin + 100 ug/Lguanylurea) at 24h


title: RA0700_WholeBlood-Dm04 [A0305_S12_L001]

description:
A0305_S12_L001
Rhesus monkey

value: Whole blood


title: MET41_GU100_24_10


title: RA0700_WholeBlood-D7-NEC [A0306_S11_L001]

description:
A0306_S11_L001
Rhesus monkey

value: infected with Ebola virus


title: RA1818_WholeBlood-BL [A0308_S47_L001]

description:
A0308_S47_L001
Rhesus monkey


title: MET41_GU100_24_8


title: MET41_GU100_24_6


title: MET41_GU100_24_9


title: MET41_GU100_24_7


title: H3K14ac-Donor90-aMDM

value: activated


title: MET41_GU100_48_4


title: H3K14ac-Donor90-aMDM+LCC-12


title: MET41_GU100_24_5


title: RA1856_WholeBlood-D0 [A0303_S187_L002]

description:
A0303_S187_L002
Rhesus monkey


title: RA1818_WholeBlood-D6-NEC [A0309_S10_L001]

description:
A0309_S10_L001
Rhesus monkey


title: H3K14ac-Donor90-naMDM


title: RA0700_WholeBlood-Dm30 [A0304_S13_L001]

description:
A0304_S13_L001
Rhesus monkey


title: MET41_GU100_24_4


title: MET41_GU100_24_3


title: H3K27ac-Donor90-aMDM


title: MET41_GU100_24_12


title: H3K27ac-Donor90-aMDM+LCC-12


title: H3K9ac-Donor90-aMDM+LCC-12


title: H3K27ac-Donor90-naMDM


title: H3K27me3-Donor88-aMDM+LCC-12


title: MET41_GU100_24_2


title: RA1856_WholeBlood-BL [A0302_S188_L002]

description:
A0302_S188_L002
Rhesus monkey


title: MET41_GU100_24_1


title: MET41_GU100_6_12

value: Group exposed to a mixture (41 ug/Lmetformin + 100 ug/Lguanylurea) at 6h


title: H3K9ac-Donor90-aMDM


title: RA1856_WholeBlood-BL [A0301_S189_L002]

description:
A0301_S189_L002
Rhesus monkey


title: MET41_GU100_6_11


title: MET41_GU100_6_10


title: RA1819_WholeBlood-D0 [A0300_S190_L002]

description:
A0300_S190_L002
Rhesus monkey


title: H3K9ac-Donor90-naMDM


title: MET41_GU100_6_9


title: MET41_GU100_6_8


title: MET41_GU100_6_7


title: RA1819_WholeBlood-BL [A0298_S192_L002]

description:
A0298_S192_L002
Rhesus monkey


title: Input-Donor90-aMDM+LCC-12


title: Input-Donor90-aMDM


title: MET41_GU100_6_6


title: MET41_GU100_6_5


title: RA1819_WholeBlood-BL [A0299_S191_L002]

description:
A0299_S191_L002
Rhesus monkey


title: MET41_GU100_6_4


title: Input-Donor90-naMDM


title: RA1082_WholeBlood-D0 [A0297_S14_L001]

description:
A0297_S14_L001
Rhesus monkey


title: RA1082_WholeBlood-Dm30b [A0295_S16_L001]

description:
A0295_S16_L001
Rhesus monkey


title: H3K27ac-Donor88-aMDM


title: H3K27ac-Donor88-aMDM+LCC-12


title: MET41_96_12

value: Group exposed to 41 ug/Lmetformin at 96h


title: MET41_GU100_6_2


title: RA1819_Skin-Non-Rash [A0294_S18_L001]

description:
A0294_S18_L001
Rhesus monkey


title: MET41_GU100_6_1


title: MET41_96_11


title: MET41_96_10


title: H3K27ac-Donor88-naMDM

value: blood


title: MET41_96_9


title: MET41_96_8


title: RA1819_Sex-Organ [A0292_S102_L002]

description:
A0292_S102_L002
Rhesus monkey

source_name: Sex Organ:Sex-Organ

value: Sex Organ:Sex-Organ


title: H3K14ac-Donor88-aMDM+LCC-12

value: pan monocyte


title: H3K14ac-Donor88-aMDM


title: RA1819_LN-ING-L [A0289_S125_L002]

description:
A0289_S125_L002
Rhesus monkey

source_name: Lymph node:LN-ING-L

value: Lymph node:LN-ING-L


title: MET41_GU100_6_3


title: MET41_96_1


title: MET41_96_2


title: MET41_48_12

value: Group exposed to 41 ug/Lmetformin at 48h


title: MET41_96_4

value: liver


title: MET41_96_5

value: adult


title: H3K9ac-Donor88-aMDM+LCC-12


title: H3K14ac-Donor88-naMDM

value: non-activated


title: RA1819_LN-AX-R [A0288_S126_L002]

description:
A0288_S126_L002
Rhesus monkey

source_name: Lymph node:LN-AX-R

value: Lymph node:LN-AX-R


title: MET41_96_3

value: male


title: RA1819_Brain-Gr [A0286_S70_L002]

description:
A0286_S70_L002
Rhesus monkey


title: RA1819_LN-MES [A0290_S124_L002]

description:
A0290_S124_L002
Rhesus monkey

source_name: Lymph node:LN-MES

value: Lymph node:LN-MES


title: H3K9ac-Donor88-naMDM


title: MET41_48_11


title: MET41_48_10


title: RA1819_Adrenal [A0284]

description:
A0284
Rhesus monkey

source_name: Adrenal Gland

value: Adrenal Gland


title: MET41_48_9


title: A0283 [A0283]

description:
A0283
Rhesus monkey

source_name: Liver

value: Liver


title: MET41_96_7


title: MET41_48_7


title: Input-Donor88-aMDM+LCC-12


title: Input-Donor88-aMDM


title: MET41_48_8


title: RA1819_Kidney [A0282_S91_L002]

description:
A0282_S91_L002
Rhesus monkey

source_name: Kidney

value: Kidney

value: infected with Ebola virus


title: MET41_96_6


title: MET41_48_6


title: MET41_48_5


title: RA1819_Ovary [A0287_S103_L002]

description:
A0287_S103_L002
Rhesus monkey

source_name: Sex Organ:Ovary

value: Sex Organ:Ovary


title: H3K9ac-Donor88-aMDM

value: activated


title: RA1074_Skin-Non-Rash [A0280_S20_L001]

description:
A0280_S20_L001
Rhesus monkey


title: Input-Donor88-naMDM

value: blood


title: MET41_24_9

value: Group exposed to 41 ug/Lmetformin at 24h


title: MET41_24_8


title: RA1819_Spleen [A0281_S10_L001]

description:
A0281_S10_L001
Rhesus monkey

source_name: Spleen

value: Spleen


title: RA1074_Sex-Organ [A0278_S104_L002]

description:
A0278_S104_L002
Rhesus monkey

value: Sex Organ:Sex-Organ


title: RA1074_Skin-Rash [A0279_S21_L001]

description:
A0279_S21_L001
Rhesus monkey


title: aMDM CD44 ko-Donor117

data_processing:
Trimmed reads were then aligned on the human hg38  reference genome using the STAR mapper (2.6.1b), up to the generation of a raw count table per gene (GENCODE annotation v29).
The bioinformatics pipelines used for these tasks are available online (rawqc v2.1.0: https://github.com/bioinfo-pf-curie/raw-qc, RNA-seq v3.1.4: https://github.com/bioinfo-pf-curie/RNA-seq).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: sorted CD44 ko aMDM

growth_protocol: Human primary monocytes were transfected with Human Monocyte Nucleofector kit (Lonza, VPA-1007). 5 × 10e^6 monocytes were resuspended in 100 µL of nucleofector solution with a 100 pmol CAS9 (Dharmacon, CAS12206)/ 200 pmol CD44 (Dharmacon, SQ-009999-01-0010) sgRNA mix. The CAS9/CD44 mix was incubated for 10 min at 37 °C before nucleofection with Nucleofector II (Lonza). Cells were then immediately removed and incubated overnight with 5 mL of prewarmed complete RPMI medium (ThermoFisher Scientific) and the following day, GM-CSF was added to the medium. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours. At the end of the experiment CD44 ko aMDM and CD44 wt aMDM  were sorted.

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).

value: pan monocyte

value: CD44 KO


title: MET41_48_2

value: liver

value: adult

value: Group exposed to 41 ug/Lmetformin at 48h


title: aMDM wt-Donor117

source_name: sorted CD44 wt aMDM

value: WT


title: aMDM wt-Donor116


title: aMDM CD44 ko-Donor116


title: MET41_24_10

value: male


title: MET41_24_12


title: MET41_24_6


title: aMDM CD44 ko-Donor114


title: MET41_24_5


title: MET41_48_4


title: RA1074_LN-ING-L [A0275_S128_L002]

description:
A0275_S128_L002
Rhesus monkey

value: Lymph node:LN-ING-L


title: MET41_48_1


title: RA1074_LN-AX-R [A0274_S129_L002]

description:
A0274_S129_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: MET41_48_3


title: MET41_24_4


title: MET41_24_11


title: MET41_24_3


title: aMDM wt-Donor113


title: MET41_24_7


title: MET41_24_2


title: RA1074_LN-MES [A0276_S127_L002]

description:
A0276_S127_L002
Rhesus monkey

value: Lymph node:LN-MES


title: RA1074_Brain-Gr [A0272_S71_L002]

description:
A0272_S71_L002
Rhesus monkey


title: MET41_24_1


title: MET41_6_11

value: Group exposed to 41 ug/Lmetformin at 6h


title: RA1074_Adrenal [A0270]

description:
A0270
Rhesus monkey

value: Adrenal Gland


title: MET41_6_12


title: aMDM wt-Donor114

value: activated


title: aMDM CD44 ko-Donor113


title: MET41_6_9


title: IL-4, Z-DON(Z006), rep3

city: Nagoya

first: Hideki

last: Tatsukawa

state: AICHI

address: Furo-cho, Chikusa

country: Japan

institute: Nagoya University

description: Human macrophages treated with IL-4 + TG2 inhibitor

data_processing:
Raw reads were aligned to the human genome (hg38) using the RNA-Seq Alignment App on Basespace (Illumina, CA).
Assembly: hg38
Supplementary files format and content: Gene name, Length, EffectiveLength, TPM, NumReads

source_name: macrophage

growth_protocol: Human monocytic leukemia cell line (THP-1) was differentiated into macrophages by incubation with 150 nM phorbol 12-myristate-13-acetate (PMA; AdipoGen Life Sciences) for 24 h.

extract_protocol:
Total RNA from THP-1 cells was lysed extracted using tissue total RNA mini kit according to manufacturer’s instructions.
mRNA is enriched using oligo(dT) beads and rRNA is removed. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: M2 macrophage polarization was induced by 20 ng/ml recombinant human IL-4 (PeproTech) in 5% FBS containing RPMI after starvation in the presence or absence of TG2 inhibitor (Z-DON, Z006).

value: macrophage

tag: cell line

value: THP-1 (PMA-treated)

value: Monocytes

value: differentiated into macrophages


title: MET41_6_8


title: IL-4, Z-DON(Z006), rep2


title: RA1074_Spleen [A0267_S11_L001]

description:
A0267_S11_L001
Rhesus monkey

value: Spleen


title: MET41_6_6


title: IL-4, Z-DON(Z006), rep1


title: IL-4, DMSO, rep2

description: Human macrophages treated with IL-4

value: IL-4, DMSO


title: MET41_6_4

value: liver


title: MET41_6_5

value: adult


title: IL-4, DMSO, rep3

description: Human macrophages treated with IL-4


title: RA1082_Sex-Organ [A0264_S49_L001]

description:
A0264_S49_L001
Rhesus monkey

value: Sex Organ:Sex-Organ


title: MET41_6_2


title: RA1082_Skin-Rash [A0265_S23_L001]

description:
A0265_S23_L001
Rhesus monkey


title: MET41_6_1


title: MET41_6_7


title: RA1082_Skin-Non-Rash [A0266_S22_L001]

description:
A0266_S22_L001
Rhesus monkey


title: MET41_6_3


title: GU100_96_12

value: Group exposed to 100 ug/Lguanylurea at 96h


title: IL-4, DMSO, rep1

description: Human macrophages treated with IL-4


title: RA1074_Kidney [A0268_S92_L002]

description:
A0268_S92_L002
Rhesus monkey

value: Kidney


title: RA1082_LN-MES [A0262_S130_L002]

description:
A0262_S130_L002
Rhesus monkey


title: MET41_6_10

value: male


title: PBS, Z-DON(Z006), rep3

description: Human macrophages treated with TG2 inhibitor

value: PBS, Z-DON(Z006)


title: GU100_96_10


title: GU100_96_9


title: RA1082_LN-ING-L [A0261_S131_L002]

description:
A0261_S131_L002
Rhesus monkey

value: Lymph node:LN-ING-L


title: GU100_96_8


title: RA1082_LN-AX-R [A0260_S132_L002]

description:
A0260_S132_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: GU100_96_7


title: PBS, Z-DON(Z006), rep1


title: PBS, Z-DON(Z006), rep2


title: RA1082_Ovary [A0259_S50_L001]

description:
A0259_S50_L001
Rhesus monkey

value: Sex Organ:Ovary


title: GU100_96_5


title: PBS, DMSO, rep3

description: Human macrophages treated with vehicle

value: PBS, DMSO


title: GU100_96_4


title: RA1082_Brain-Gr [A0258_S72_L002]

description:
A0258_S72_L002
Rhesus monkey


title: GU100_96_2


title: GU100_48_12

value: Group exposed to 100 ug/Lguanylurea at 48h


title: GU100_96_3


title: GU100_96_1


title: GU100_48_11


title: PBS, DMSO, rep2

description: Human macrophages treated with vehicle

value: macrophage

value: THP-1 (PMA-treated)


title: GU100_96_6


title: A0256 [A0256]

description:
A0256
Rhesus monkey

value: Adrenal Gland


title: RA1082_Kidney [A0254_S93_L002]

description:
A0254_S93_L002
Rhesus monkey


title: PBS, DMSO, rep1

description: Human macrophages treated with vehicle

value: Monocytes

value: differentiated into macrophages


title: LVCFB, M39

city: Madison

first: Fathima

last: Shabnam

state: WI

address: 1415 Engineering Hall

institute: University of Wisconsin-Madison

data_processing:
FASTQ files were aligned using STAR v2.5.3a
Transcript abundances were calculated using featureCounts v2.0.3
Assembly: hg38
Supplementary files format and content: counts file and TPM

source_name: heart

extract_protocol:
Cells were lysed using Buffer RLT and β-mercaptoethanol and total mRNA was isolated following manufacturer’s instructions of the Qiagen RNeasy mini kit and treated with DNase (Qiagen). Quantity and quality of RNA samples were analyzed for the presence of 18S and 28S ribosomal RNA with appropriate A260/A280 and A260/A230 ratios using the NanoDrop 2000.
First-strand cDNA synthesis (after ribosomal RNA was removed) and library preparation was performed using the Takara SMARTer Stranded Total RNA- HI Mammalian Library Prep Kit (Takara Bio).

value: heart

value: left ventricular cardiac fibroblast


title: GU100_96_11

value: liver

value: adult


title: GU100_48_10


title: LVCFB, F34

value: female


title: GU100_48_9

value: male


title: GU100_48_7


title: RA1082_Spleen [A0253_S22_L001]

description:
A0253_S22_L001
Rhesus monkey

value: Spleen


title: GU100_48_8


title: LVCFB, F33


title: GU100_48_5


title: GU100_48_6


title: VIC, M39

value: valvular interstitial cell


title: GU100_48_4


title: RA1856_LN-MES [A0248_S133_L002]

description:
A0248_S133_L002
Rhesus monkey

value: Lymph node:LN-MES


title: Parthenote PA2

city: Columbus

first: Jinsoo

last: Ahn

state: OH

address: 2029 Fyffe Rd

institute: The Ohio State University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low quality reads were eliminated.
The cleaned reads were aligned to the reference genome (Sscrofa11.1) using Bismark (v0.22.3) with default parameters.
After deduplication using the deduplicate_bismark command, the Bismark methylation extractor was used to calculate methylation percentage of every cytosine in CpG context.
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-delimited files in bedGraph format containing methylation rates

organism: Sus scrofa

source_name: embryo

growth_protocol: After electric stimulation of oocytes followed by 2 h of stabilization period, parthenogenetic embryos were placed into oviducts of each of the two LYD surrogate gilts aged 12 months at onset of estrus to produce developed parthenogenetic embryos.

extract_protocol:
From the whole collected embryos of CN and PA (n = 3 for each), genomic DNA was isolated and fragmented.
For optimization of bisulfite conversion of genomic DNA, Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Inc. Ann Arbor, MI, USA) was used according to the manufacturer`s instructions.

treatment_protocol: In a fusion chamber with 250 µm diameter wire electrodes, selected oocytes were placed and fusion was achieved by two DC pulses (1 sec interval) of 1.2 kV/cm for 30 µs using an LF101 Electro Cell Fusion Generator.

value: Landrace x Yorkshire x Duroc (LYD)

value: whole embryo

value: embryonic day 21

value: parthenogenesis


title: RA1856_Skin-Non-Rash [A0252_S24_L001]

description:
A0252_S24_L001
Rhesus monkey


title: RA1856_LN-ING-L [A0247_S134_L002]

description:
A0247_S134_L002
Rhesus monkey

value: Lymph node:LN-ING-L


title: GU100_48_3

value: Group exposed to 100 ug/Lguanylurea at 48h


title: VIC, F34


title: RA1856_LN-AX-R [A0246_S135_L002]

description:
A0246_S135_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: GU100_48_2


title: Parthenote PA1


title: Control CN2

value: untreated


title: TBI 3, scRNAseq

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

description:
10x Genomics
tbi_TE_raw_matrix.csv
tbi_TE_norm_cluster_size_matrix.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

value: tbi

value: M

tag: time post_injury


title: VIC, F33

value: heart


title: Control CN1


title: RA1856_Adrenal [A0242]

description:
A0242
Rhesus monkey

value: Adrenal Gland


title: ASAP4_PD_P74

description: PacBio Isoseq

data_processing:
Single cell/nuclei: Raw base calls were demultiplexed to obtained sample specific FastQ files using mkfastq in default parameters (10x Genomics), and reads were aligned to GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics, Cellranger count v6) with default parameters (--include-introns was used for nuclei mapping)
Bulk RNAseq: Raw base calls were demultiplexed to obtain sample specific FastQ files using bcl2fastq (Illumina). Reads were aligned using STAR aligner (version 2.6.0c) in default parameters to quantify gene expression, but using unique mapping (outFilterMultimapNmax 1, outFilterMismatchNoverLmax 0.03) for quantification of TEs. For mapping and quantification of individual TEs, we split BAM files per strand. Genes and TEs were quantified using featureCounts (subread package version 1.6.3). Genes were quantified using gencode annotation for hg38 version 36. TEs were quantified using a manually curated GTF file derived from repeatmasker (hg38) to avoid simple repeats, small RNAs and low-complexity regions; this GTF was retrieved from the authors of TEtranscripts (Jin et al., 2015). To quantify TE subfamilies, we mapped reads using STAR aligner (version 2.6.0c) with a multi-mapping approach (outFilterMultimapNmax 100, winAnchorMultimapNmax 200) and quantified using TEcounts from TEtoolkit (Jin et al., 2015).
Bulk RNAseq (pacbio): SMRTLink pipeline was ran using the default settings
Assembly: GRCh38
Supplementary files format and content: Single cell/nuclei: Cellranger count output matrices
Supplementary files format and content: Bulk RNAseq (truseq): Gene, TEs, and TE subfamilies read count matrices

source_name: prefrontal cortex

extract_protocol:
The nuclei isolation from the brain tissue was performed according to Jönsson et al., 2021. In brief, the tissue was thawed and dissociated in ice-cold lysis buffer (0.32 M 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 tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose cushion (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl, pH 8.0, and 1 mM DTT) before centrifugation at 30,000 × g for 2 hours and 15 min. Pelleted nuclei were softened for 10 min in 100 ml of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) before being resuspended in 300 ml of dilution buffer (10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) and run through a cell strainer (70 mm). Cells were run through the FACS (FACS Aria, BD Biosciences) at 4°C at a low flow rate using a 100 mm nozzle (reanalysis showed >99% purity).
Single cell/nuclei: Nuclei/cells were directly loaded onto the Chromium Next GEM Chip G or Chromium Next GEM Chip K Single Cell Kit along with the reverse transcription mastermix following the manufacturer’s protocol for the Chromium Next GEM Single Cell 5’ Kit (10x Genomics, PN-1000263) to generate single-cell gel beads in emulsion. cDNA amplification was done as per the guidelines from 10x Genomics using 15 cycles of amplification.
Bulk RNAseq (truseq): Total RNA was isolated from nuclei using the RNeasy Mini Kit (Qiagen).
Bulk RNAseq (pacbio)Total RNA was obtained from tissue samples using miRNA Easy Mini Kit (Qiagen). RNA samples were subsequently put on dry ice and shipped to the National Genomics Infrastructure of Sweden. There, input QC of samples was performed on the Agilent Bioanalyzer instrument, using the Eukaryote Total RNA Nano kit to evaluate RIN and concentration. The sample libraries were prepared as described in "Procedure & Checklist – Iso-Seq™ Express Template Preparation for Sequel® and Sequel II Systems" (PN 101-763-800 Version 02 (October 2019)) using the NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads (Promega) and the SMRTbell Express Template Prep Kit 2.0. 300 ng of total RNA was used for cDNA Synthesis followed by 12 + 3 cycles of cDNA Amplification. In the purification step of amplified cDNA the standard workflow was applied (sample is composed primarily of transcripts centered around 2 kb).
Single cell/nuclei: Sequencing libraries were generated with unique dual indices (TT set A) and pooled for sequencing on a Novaseq6000 using a 100-cycle kit and 28-10-10-90 reads.
Bulk RNAseq (truseq): Libraries were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection) and sequenced on a NextSeq500 (PE 2×150bp).
Bulk RNAseq (pacbio): After purification the amplified cDNA went into the SMRTbell library construction. Quality control of the SMRTbell libraries was performed with the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. Primer annealing and polymerase binding was performed using the Sequel II binding kit 2.0. Finally, the samples were sequenced on Sequel II and Sequel IIe System using Sequel® II Sequencing Plate 2.0, with an On-Plate Loading Concentration of 110 pM, movie time 24 hours and pre-extension time 2 hours.

value: prefrontal cortex

tag: type

value: Bulk

value: male


title: GU100_48_1

source_name: male liver

value: liver

value: adult


title: GU100_24_11

value: Group exposed to 100 ug/Lguanylurea at 24h


title: TBI 2, scRNAseq


title: GU100_24_10


title: GU100_24_9


title: RA1856_Kidney [A0240_S95_L002]

description:
A0240_S95_L002
Rhesus monkey

value: Kidney


title: TBI 1, scRNAseq


title: TBI 20, scRNAseq

value: F


title: TBI 21, scRNAseq


title: NFO190_159-VeroE6

city: Copenhagen

last: Fossat

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

description:
Paired-end 2 x 75 bp
Table S15.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)

organism: Chlorocebus sabaeus

source_name: Monkey kidney VeroE6 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: No

tag: sars-cov-2 genotype

tag: moi

tag: duration of infection

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: NFO190_99-VeroE6

description:
Paired-end 2 x 75 bp
Table S15.txt


title: RA1856_Brain-Wh [A0243_S106_L002]

description:
A0243_S106_L002
Rhesus monkey

tag: tissue

tag: monkey id

tag: treatment

tag: time


title: RA1325_Skin-Non-Rash [A0238_S25_L001]

description:
A0238_S25_L001
Rhesus monkey

value: infected with Ebola virus


title: GU100_24_8

tag: Sex


title: RA1856_Brain-Gr [A0244_S73_L002]

description:
A0244_S73_L002
Rhesus monkey


title: A0235 [A0235]

description:
A0235
Rhesus monkey

source_name: Lung

value: Lung


title: GU100_24_6

tag: developmental stage


title: NFO190_141-VeroE6-SARSCoV2

description:
Paired-end 2 x 75 bp
Table S15.txt

value: Yes

value: Wild-type

value: 48 hours


title: RA1325_LN-MES [A0234_S136_L002]

description:
A0234_S136_L002
Rhesus monkey

value: Lymph node:LN-MES


title: NFO190_39-VeroE6

description:
Paired-end 2 x 75 bp
Table S15.txt


title: GU100_24_7


title: TBI 16, scRNAseq

value: brain

tag: condition

value: tbi

tag: age

value: M


title: TBI 11, scRNAseq

tag: time post_injury


title: GU100_24_5

value: liver

value: male


title: RA1325_LN-AX-R [A0232_S138_L002]

description:
A0232_S138_L002
Rhesus monkey

source_name: Lymph node:LN-AX-R

value: Lymph node:LN-AX-R


title: RA1325_LN-ING-L [A0233_S137_L002]

description:
A0233_S137_L002
Rhesus monkey

source_name: Lymph node:LN-ING-L

value: Lymph node:LN-ING-L


title: NFO190_21-VeroE6-SARSCoV2

description:
Paired-end 2 x 75 bp
Table S15.txt

tag: infected


title: RA1856_Spleen [A0239_S23_L001]

description:
A0239_S23_L001
Rhesus monkey

value: Spleen


title: TBI 8, scRNAseq


title: TBI 10, scRNAseq


title: RA1325_Brain-Gr [A0230_S74_L002]

description:
A0230_S74_L002
Rhesus monkey


title: GU100_24_3

value: adult

value: Group exposed to 100 ug/Lguanylurea at 24h


title: TBI 19, scRNAseq

value: F


title: s5__6_dpl_

city: Dresden

first: Fabian

last: Rost

address: Pfotenhauerstraße 108

country: Germany

institute: MPI-CBG

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Data from individual samples was aggregated to one count matrix using cellranger aggr v3.1.0
Assembly: GRCz11_GFP_mCherry
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format. Barcodes ending with "-1" are from sample s1__Uninjured_Ch__, "-2" from s2__44_hpl_, etc

organism: Danio rerio

source_name: Retina

extract_protocol:
Uninjured and light-lesioned Tg(pcna:EGFP);Tg(gfap:nls-mCherry) fish were exposed to an overdose (0.2%) of MS-222 (Sigma) (Brand et al., 2002) until cessation of the operculum movement. Subsequently, each cornea was poked with a needle, and tweezers were gently pressured on each side of the eye to remove the lens. Then, tweezers were used to carefully isolate the retinae, which were put in a dissociation solution of papain (16 U/ml), dispase (0.2 U/ml) and DNAse (168 U/ml) dissolved in Earle's Balanced Salt Solution (EBSS, Worthington Biochemical Corporation). Up to 6 retinae were put in 1.7 ml of dissociation solution. Retinae were digested for 30 minutes at 28°C, and then calcein blue (final concentration: 1µM, Invitrogen) was added for 10 minutes to the digestion solution at 28°C to stain for living cells. At the end of the enzymatic digestion, mechanical trituration was applied using fire-polished glass pipettes of decreasing tip diameter to help tissue dissociation. Single cells were centrifuged (300 g) at 4°C, for 6 minutes. The cell pellet was re-suspended in EBSS supplemented with DNAse (100 U/ml) to eliminate residual, ambient DNA, and albumin ovomucoid inhibitor (1:10 of stock solution, Worthington Biochemical Corporation) to stop papain action. The single cell solution was eventually filtered (20 µm filters) to remove clumps and debris, and put on ice, ready for Fluorescent Activated Cell Sorting (FACS). Each single cell suspension was obtained by pooling 8 retinae (from 4 fish, 2 males and 2 females) of uninjured and light-lesioned Tg(pcna:EGFP);Tg(gfap:mCherry) animals. Uninjured WT AB, Tg(gfap:mCherry) and Tg(pcna:EGFP) fish were used to prepare single cell suspensions of dissected retinae for setting the single fluorophore gates in flow cytometry. Additionally, a calcein only stained single cell suspension was prepared from uninjured WT AB fish retinae for the setting of the calcein gate in the flow cytometry.
Flow cytometry and FACS
A BD FACSAria™ III cell sorter was used for flow cytometry and FACS. mCherry fluorophore was detected using a 561 nm excitation laser and a 610/20 nm band pass filter, EGFP using a 488 nm laser and a 530/30 nm band pass filter and calcein blue using a 405 nm laser and a 450/40 nm band pass filter. The gating strategy is shown in Figure 1-supplemental figure 3 for uninjured samples and was the same for all the light-lesioned samples. Forward and side scatters were used to gate cells among all the events in the single cell suspension and to gate singlets among those cells (Figure 1-figure supplement 3A). mCherry-positive only as well as EGFP-positive only gates were set in comparison to the unstained, WT control (Figure1-figure supplement 3B). Calcein blue positive, single cells were eventually gated as living cells (60.000 living cells from uninjured, 44 hpl and 4 dpl samples, 41.389 living cells from 6 dpl sample). 15.000 cells were sorted from each samples, put on ice and sent to the CMCB Deep Sequencing Facility for single cell RNA sequencing (scRNAseq).
Single cell transcriptome sequencing was performed based on the 10x Genomics Single cell transcriptome workflow (Zheng et al., 2017). Specifically, 15.000 FACS-sorted cells were recovered in BSA-coated tubes containing 5 ul PBS with 0.04% BSA. Cell samples were carefully mixed with Reverse Transcription Reagent (Chromium Single Cell 3’ Library Kit v3) and loaded onto a Chromium Single Cell B Chip to reach a recovery of 10.000 cells per sample.  The samples were processed further following the guidelines of the 10x Genomics user manual for single cell 3’ RNA-seq v3. In short, the droplets were directly subjected to reverse transcription, the emulsion was broken and cDNA was purified using silane beads (Chromium Single Cell 3’ Gel Bead Kit v2). After amplification of cDNA with 11 cycles, samples were purified with 0.6x volume of SPRI select beads to deplete DNA fragments smaller than 400 base pairs and cDNA quality was monitored using the Agilent FragmentAnalyzer 5200 (NGS Fragment Kit). 10 ul of the resulting cDNA were used to prepare single cell RNA seq libraries - involving fragmentation, dA-Tailing, adapter ligation and 11 cycles of indexing PCR following manufacturer’s guidelines. After quantification, both libraries were sequenced on an Illumina NextSeq500 in 75 base pair paired-end mode, generating 45-109 million  fragments per transcriptome library.

tag: cell type

value: mixed

value: Retina

tag: strain

value: pooled male and female

value: 6-12 months

value: 6 days post-light lesion


title: s4_Uninjured__whole_retina_ctrl_

description: 10x Genomics

value: Uninjured (control)


title: RA1325_Brain-Wh [A0229_S107_L002]

description:
A0229_S107_L002
Rhesus monkey

value: infected with Ebola virus


title: s3__4_dpl_

description: 10x Genomics

value: 4 days post-light lesion


title: GU100_24_1


title: GU100_24_2


title: RA1325_Liver-L [A0227_S51_L001]

description:
A0227_S51_L001
Rhesus monkey

source_name: Liver

value: Liver


title: NFO190_81-VeroE6-SARSCoV2

description:
Paired-end 2 x 75 bp
Table S15.txt

value: Yes

tag: sars-cov-2 genotype

value: Wild-type

tag: moi

tag: duration of infection

value: 48 hours

value: RNA-Seq from total RNA

value: Total RNA (minus rRNA)


title: TBI 7, scRNAseq

value: brain

value: tbi

value: M


title: TBI 6, scRNAseq


title: s2__44_hpl_

description: 10x Genomics

value: mixed

value: 44 hours post-light lesion


title: GU100_24_4

value: liver

value: adult

value: male

value: Group exposed to 100 ug/Lguanylurea at 24h


title: Control 502, temporal lobe, scRNAseq

description:
10x Genomics
control_TE_raw_matrix.csv
control_TE_norm_cluster_size_matrix.csv
TBI_HuBrainCTL_Nuclei502T_Hg38_TE_norm_cluster_size_matrix.csv

value: control


title: RA1325_Kidney [A0226_S96_L002]

description:
A0226_S96_L002
Rhesus monkey

source_name: Kidney

value: Kidney

value: infected with Ebola virus


title: GU100_6_11

value: Group exposed to 100 ug/Lguanylurea at 6h


title: GU100_6_12


title: Control 529, frontal lobe, scRNAseq

description:
10x Genomics
control_TE_raw_matrix.csv
control_TE_norm_cluster_size_matrix.csv
TBI_HuBrainCTL_Nuclei529F_Hg38_TE_norm_cluster_size_matrix.csv


title: Control 501, temporal lobe, scRNAseq

description:
10x Genomics
control_TE_raw_matrix.csv
control_TE_norm_cluster_size_matrix.csv
TBI_HuBrainCTL_Nuclei501T_Hg38_TE_norm_cluster_size_matrix.csv


title: GU100_6_10


title: Parthenote PA1

data_processing:
Sequenced reads were trimmed for adaptor sequence and low quality reads were eliminated.
Then, the cleaned reads were aligned to the reference genome (Sscrofa11.1) using STAR (v2.7.5) with default parameters.
Duplicated reads were removed using Picard MarkDuplicates and reads were filtered using SAMtools (-q 30).
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-delimited text files containing normalized read counts from Salmon (v1.3.0)

extract_protocol:
Total RNA from whole CN embryos (n = 3) and whole PA embryos (n = 3) samples was isolated with TRIzol reagent. DNase I was treated to the RNA samples to avoid genomic DNA contamination. One ug of total RNA was used to construct cDNA libraries with the TruSeq RNA Sample Prep Kit v.2.
RNA libraries were prepared for sequencing according to Illumina's instructions accompanying the TruSeq RNA Sample Prep Kit v.2.

value: Landrace x Yorkshire x Duroc (LYD)

value: whole embryo

value: embryonic day 21

value: parthenogenesis


title: RA1639_Skin-Non-Rash [A0224_S27_L001]

description:
A0224_S27_L001
Rhesus monkey


title: GU100_6_9


title: Control 501, frontal lobe, scRNAseq

description:
10x Genomics
control_TE_raw_matrix.csv
control_TE_norm_cluster_size_matrix.csv
TBI_HuBrainCTL_Nuclei501F_Hg38_TE_norm_cluster_size_matrix.csv

value: brain


title: Control CN2

value: untreated


title: RA1639_LN-MES [A0220_S141_L002]

description:
A0220_S141_L002
Rhesus monkey

source_name: Lymph node:LN-MES

value: Lymph node:LN-MES


title: A0221_A [A0221_A]

description:
A0221_A
Rhesus monkey

value: Lung


title: GU100_6_8


title: Lipo863B-ChIPseq-input

city: CHICACO

first: Feng

last: Yue

state: ILLINOIS

address: 303 E. Superior Simpson Querrey

institute: Northwestern University Feinberg School of Medicine

description: Cell Line

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.

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).

extract_protocol:
About 30,000 of nuclei or cells were used for one ChIP. Native nuclei or cells were taken out from -80°C freezer and resuspended in cold ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 1X proteinase inhibitor cocktail).
1 ug of H3K27ac antibody (Active Motif, 39133) was used per ChIP. After PCR amplification, libraries were size-selected by 0.6X/1.0X KAPA pure beads.

tag: disease state

value: Liposarcoma

tag: cell line


title: Control CN1

tag: tissue


title: RA1639_LN-ING-L [A0219_S142_L002]

description:
A0219_S142_L002
Rhesus monkey

value: Lymph node:LN-ING-L

tag: monkey id


title: GU100_6_7

value: liver

value: adult

tag: treatment


title: s1__Uninjured_Ch__

description:
10x Genomics
This sample contains 15.000 cells derived from the dissociation and FACS of 8 retinae pooled from  4, uninjured zebrafish. The sorting gate includes gfap:mCherry-positive cells.

value: mixed

value: Retina

value: pooled male and female

value: 6-12 months

value: Uninjured (control)


title: Lipo863B-ATAC-rep2

description: Cell Line

extract_protocol:
50,000 cells were washed with PBS, counted and kept on ice as a pellet. Pelleted cells were reconstituted in a freshly made lysis buffer to remove unwashed mitochondria DNA, spun down, and the buffer was discarded. Then, the pelleted nuclei were tagmented with Tn5 transposase (Illumina ref: 15027866 & 15027865) in 50 μl volume for 30 min at 37 °C and the DNA was subsequently purified using Qiagen MinElute kit (Qiagen).
The transposal DNA was purified with the Qiagen MinElute PCR Purification Kit (Qiagen, 28006) and then amplified with appropriate number of cycles.


title: GU100_6_6

value: male

value: Group exposed to 100 ug/Lguanylurea at 6h


title: RA1325_Spleen [A0225_S24_L001]

description:
A0225_S24_L001
Rhesus monkey

source_name: Spleen

value: Spleen

value: infected with Ebola virus

tag: time


title: BgnKO fracture, replicate 5, bulk RNAseq

city: Bethesda

first: Marian

last: Young

state: MD

address: Building 30, Room 5A509

institute: NIH

description:
BgnKO5_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.vM11 mouse genome using STAR v2.5.2a in  single-pass mode
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a custom GRCm38.vM11 genome annotation GTF which included select transgenes, ERCCs and SIRVs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCm38.vM11
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

source_name: femur bone

extract_protocol: Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on tow separate runs on a NextSeq 500 sequencer (Illumina) on 37x37 paired-end mode.

value: femur bone

value: 6-7 weeks

value: bone cells

tag: genotype

value: Bgn KO

value: fracture


title: Control 529, temporal lobe, scRNAseq

description:
10x Genomics
control_TE_raw_matrix.csv
control_TE_norm_cluster_size_matrix.csv
TBI_HuBrainCTL_Nuclei529T_Hg38_TE_norm_cluster_size_matrix.csv

value: brain

value: control

tag: Sex

value: M


title: RA1639_LN-AX-R [A0218_S143_L002]

description:
A0218_S143_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: Lipo863B-ATAC-rep1

description: Cell Line

value: Liposarcoma


title: GU100_6_5

value: liver

tag: developmental stage

value: adult


title: Parthenote PA2

value: Landrace x Yorkshire x Duroc (LYD)

value: whole embryo

tag: age

value: embryonic day 21

value: parthenogenesis


title: GU100_6_4

value: male

value: Group exposed to 100 ug/Lguanylurea at 6h


title: P69T_HiC

description: Tissue

source_name: Tissue; Patient P69 tumor; Liposarcoma

extract_protocol:
Hi-C was performed with 0.1 million-0.5 million isolated nuclei or 1 million liposarcoma cells. Briefly, 2% formaldehyde cross-linked nuclei were digested by endonuclease mix and then underwent biotin incorporation and proximity ligation. Next, the reverse crosslinked DNA was purified by 0.5X KAPA pure beads and was fragmented by sonication using Covaris E220 with the following parameters: 140 W, duty factor 10, 200 per burst, 50 seconds.
Size selection was performed by 0.55X/0.85X KAPA pure beads and DNA was dissolved in 1X TE buffer. Streptavidin beads included in the kit was used to pull down biotin-labeled DNA by rotation at room temperature for 15 min and then washed twice with 600 ul of wash buffer and one time with 10 mM Tris-HCl (pH 8.0). At last, washed beads were suspended in 40 ul of 10 mM Tris-HCl (pH 8.0) and amplified eight cycles by PCR.

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).

value: Patient P69 tumor


title: RA1639_Brain-Gr [A0216_S75_L002]

description:
A0216_S75_L002
Rhesus monkey

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: infected with Ebola virus


title: RA1639_Brain-Wh [A0215_S108_L002]

description:
A0215_S108_L002
Rhesus monkey


title: P69N_HiC

description: Tissue

source_name: Tissue; Patient P69 normal control; Liposarcoma

value: Patient P69 normal control


title: BgnKO fracture, replicate 3, bulk RNAseq

description:
BgnKO3_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: femur bone

value: 6-7 weeks

value: bone cells

value: Bgn KO

value: fracture


title: RA1639_Liver-L [A0213_S52_L001]

description:
A0213_S52_L001
Rhesus monkey

value: Liver


title: P298T_HiC

description: Tissue

source_name: Tissue; Patient P298 tumor; Liposarcoma

value: Patient P298 tumor

value: Liposarcoma


title: RA1639_Kidney [A0212_S97_L002]

description:
A0212_S97_L002
Rhesus monkey

value: Kidney


title: BgnKO fracture, replicate 2, bulk RNAseq

description:
BgnKO2_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt


title: GU100_6_3

value: liver

value: adult


title: BgnKO fracture, replicate 1, bulk RNAseq

description:
BgnKO1_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt


title: BgnKO fracture, replicate 6, bulk RNAseq

description:
BgnKO6_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt


title: GU100_6_2


title: BgnKO control, replicate 6, bulk RNAseq

description:
BgnKO6_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: control


title: RA1639_Spleen [A0211_S106_L002]

description:
A0211_S106_L002
Rhesus monkey

value: Spleen


title: GU100_6_1

value: male

value: Group exposed to 100 ug/Lguanylurea at 6h


title: BgnKO fracture, replicate 4, bulk RNAseq

description:
BgnKO4_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt


title: P298N_HiC

description: Tissue

source_name: Tissue; Patient P298 normal control; Liposarcoma

value: Patient P298 normal control


title: P241T_HiC

description: Tissue

source_name: Tissue; Patient P241 tumor; Liposarcoma

value: Patient P241 tumor


title: BgnKO control, replicate 5, bulk RNAseq

description:
BgnKO5_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: femur bone


title: RA1423_LN-MES [A0206_S144_L002]

description:
A0206_S144_L002
Rhesus monkey

value: Lymph node:LN-MES

value: infected with Ebola virus


title: Control_96_12

source_name: male liver

value: Control group at 96h


title: P241N_HiC

description: Tissue

source_name: Tissue; Patient P241 normal control; Liposarcoma

value: Patient P241 normal control


title: BgnKO control, replicate 4, bulk RNAseq

description:
BgnKO4_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: 6-7 weeks

value: bone cells

value: Bgn KO


title: RA1423_LN-AX-R [A0204_S146_L002]

description:
A0204_S146_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: Control_96_9

value: liver


title: RA1423_LN-ING-L [A0205_S145_L002]

description:
A0205_S145_L002
Rhesus monkey

value: Lymph node:LN-ING-L


title: RA1423_Brain-Gr [A0202_S76_L002]

description:
A0202_S76_L002
Rhesus monkey


title: P209N_HiC

description: Tissue

source_name: Tissue; Patient P209 normal control; Liposarcoma

value: Patient P209 normal control

value: Liposarcoma


title: Control_96_11

value: adult

value: male


title: P209T_HiC

description: Tissue

source_name: Tissue; Patient P209 tumor; Liposarcoma

value: Patient P209 tumor


title: BgnKO control, replicate 3, bulk RNAseq

description:
BgnKO3_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: control


title: Control_96_10


title: BgnKO control, replicate 2, bulk RNAseq

description:
BgnKO2_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: femur bone


title: Lipo863B_HiC

description: Cell Line


title: P69T_WGS

description: Tissue

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.
Library strategy: WGS

extract_protocol:
The genomic DNA from ground patient tissues or liposarcoma cell lines was extracted using DNeasy Blood & Tissue Kit (Qiagen, 69504).
Then, 500 ng of genomic DNA was used for DNA library preparation using the Illumina DNA PCR-free prep kit according to manufacturer’s protocol.

value: Patient P69 tumor


title: BgnKO control, replicate 1, bulk RNAseq

description:
BgnKO1_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: WT


title: RA1423_Liver-L [A0199_S53_L001]

description:
A0199_S53_L001
Rhesus monkey

value: Liver

value: infected with Ebola virus


title: WT fracture, replicate 6, bulk RNAseq

description:
WT6_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: 6-7 weeks

value: fracture


title: Control_96_7

value: Control group at 96h


title: WT fracture, replicate 5, bulk RNAseq

description:
WT5_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: bone cells


title: P298T_WGS

description: Tissue

value: Patient P298 tumor


title: P298N_WGS

description: Tissue

value: Patient P298 normal control


title: RA1423_Kidney [A0198_S98_L002]

description:
A0198_S98_L002
Rhesus monkey

value: Kidney


title: Control_96_4

value: liver


title: WT fracture, replicate 4, bulk RNAseq

description:
WT4_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt


title: Control_96_5

value: adult


title: RA0917_LN-MES [A0192_S147_L002]

description:
A0192_S147_L002
Rhesus monkey

value: Lymph node:LN-MES


title: RA0917_LN-ING-L [A0191_S148_L002]

description:
A0191_S148_L002
Rhesus monkey

source_name: Lymph node:LN-ING-L

value: Lymph node:LN-ING-L


title: RA1423_Brain-Wh [A0201_S109_L002]

description:
A0201_S109_L002
Rhesus monkey


title: RA0917_LN-AX-R [A0190_S149_L002]

description:
A0190_S149_L002
Rhesus monkey

source_name: Lymph node:LN-AX-R

value: Lymph node:LN-AX-R


title: P241T_WGS

description: Tissue

value: Patient P241 tumor

value: Liposarcoma


title: WT fracture, replicate 1, bulk RNAseq

description:
WT1_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: femur bone

value: WT


title: Control_96_2

value: male


title: Control_96_8


title: Control_96_1


title: Control_96_3


title: P209T_WGS

description: Tissue

value: Patient P209 tumor


title: RA0917_Ovary [A0189_S59_L001]

description:
A0189_S59_L001
Rhesus monkey

source_name: Sex Organ:Testis

value: Sex Organ:Testis

value: infected with Ebola virus


title: P69N_WGS

description: Tissue

value: Patient P69 normal control


title: Control_48_12

value: Control group at 48h


title: RA0917_Brain-Gr [A0188_S77_L002]

description:
A0188_S77_L002
Rhesus monkey


title: Control_96_6

value: Control group at 96h


title: WT control, replicate 6, bulk RNAseq

description:
WT6_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: 6-7 weeks

value: bone cells

value: control


title: WT control, replicate 5, bulk RNAseq

description:
WT5_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt


title: RA1423_Spleen [A0197_S107_L002]

description:
A0197_S107_L002
Rhesus monkey

value: Spleen


title: Lipo863B_WGS

description: Cell Line


title: WT fracture, replicate 3, bulk RNAseq

description:
WT3_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: fracture


title: Control_48_11

value: liver

value: adult


title: P241N_WGS

description: Tissue

value: Patient P241 normal control

value: Liposarcoma


title: RA0917_Liver-L [A0185_S54_L001]

description:
A0185_S54_L001
Rhesus monkey

source_name: Liver

value: Liver


title: Control_48_10

value: male


title: WT control, replicate 4, bulk RNAseq

description:
WT4_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: femur bone

value: WT


title: RA0917_Kidney [A0184_S99_L002]

description:
A0184_S99_L002
Rhesus monkey

source_name: Kidney

value: Kidney

value: infected with Ebola virus


title: Control_48_9

value: Control group at 48h


title: P69T_K27Ac

description: Tissue

tag: chip-antibody

value: Patient P69 tumor


title: WT fracture, replicate 2, bulk RNAseq

description:
WT2_Fract
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: 6-7 weeks


title: Control_48_8


title: WT control, replicate 3, bulk RNAseq

description:
WT3_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

value: bone cells


title: P298T_K27Ac

description: Tissue

value: Patient P298 tumor


title: P241T_K27Ac

description: Tissue

value: Patient P241 tumor


title: Control_48_6


title: P69N_K27Ac

description: Tissue

value: Patient P69 normal control


title: P209N_WGS

description: Tissue

value: Patient P209 normal control


title: Control_48_7

value: liver

value: adult


title: P298N_K27Ac

description: Tissue

value: Patient P298 normal control

value: Liposarcoma


title: RA0917_Spleen [A0183_S108_L002]

description:
A0183_S108_L002
Rhesus monkey

value: Spleen


title: A0179 [A0179]

description:
A0179
Rhesus monkey

source_name: Lung

value: Lung


title: RA1849_Sex-Organ [A0180_S116_L002]

description:
A0180_S116_L002
Rhesus monkey

source_name: Sex Organ:Sex-Organ

value: Sex Organ:Sex-Organ


title: NPp53

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

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

value: C57BL/6 mixed

value: Prostate

value: 3 months

tag: tumor timepoint

value: 1 month after tamoxifen treatment

value: Tamoxifen at 2 months of age


title: Control_48_5

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: male

value: Control group at 48h


title: WT control, replicate 2, bulk RNAseq

description:
WT2_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt

source_name: femur bone

value: femur bone

value: 6-7 weeks

tag: cell type

value: bone cells

value: WT

value: control


title: RA1849_LN-MES [A0178_S150_L002]

description:
A0178_S150_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.

source_name: Lymph node:LN-MES

value: Lymph node:LN-MES

value: infected with Ebola virus


title: WT control, replicate 1, bulk RNAseq

description:
WT1_Con
CPM_TMM_counts.txt
RawCountFile.txt
RawCountFile_filtered.txt


title: P209T_K27Ac

description: Tissue

value: Patient P209 tumor

value: Liposarcoma


title: P241N_K27Ac

description: Tissue

value: Patient P241 normal control


title: 120 hr Rep 2

city: Pullman

first: Michael

last: Griswold

state: WA

address: Biotechnology Life Sciences

department: School of Molecular Biosciences; Center for Reproductive Biology

institute: Washington State University

data_processing:
100,000 cells per replicate were collected and sent to Active Motif (Calsbad, CA, USA) for processing and data analysis
bcl2fastq (v2.20) used to process Illumina base-call data and demultiplex
bwa (v0.7.12) used for alignment of reads to reference genome
Samtools (v0.0.19)/BEDtools (v2.25.0) used for processing of BAM and BED files, respectively
MACS2 (v2.1.0) used for peak calling; narrow peaks
wigToBigWig (v4) used for generation of bigWIG files
Genome_build: mm10
Supplementary_files_format_and_content: compiled peak-calling with associated genes/regions and upload tracks for UCSC genome browser:
Supplementary_files_format_and_content: 01NNWSU_ATAC_seq_stats: alignment and peak calling statistics
Supplementary_files_format_and_content: 01NNWSU_ATAC_summary: additional statistics and comparisions between the samples
Supplementary_files_format_and_content: 01NNWSU_ATAC_intervals: annotation of all intervals (peak regions) with peak metrics and gene information
Supplementary_files_format_and_content: 01NNWSU_ATAC_genes: gene-centric presentation of intervals table
Supplementary_files_format_and_content: 01NNWSU_ATAC_mergedregs: comparison of peak region metrics between different samples
Supplementary_files_format_and_content: 01NNWSU_ATAC_ucsctracks: UCSC custom tracks bed file to see location of intervals and merged peak regions
Supplementary_files_format_and_content: 01NNWSU_ATAC_bigWig_URLs: UCSC custom tracks for browser to see peak shapes
Supplementary_files_format_and_content: 01NNWSU_ATAC_ucsctracks_bw: UCSC custom tracks file that loads both peak regions and bigWIG data in the correct order

source_name: Testis

growth_protocol: Germ cells were isolated from fresh testis via cell sorting of PIWIL2-eGFP positive cells.

treatment_protocol: Mice were treated with WIN 18,446 for 7 days then either collected (0 hours) or treated with retinoic acid (RA) and allowed to recover for 18, 48, or 120 hours post-injection.

tag: strain background

value: Derived from C57BL/6 x 129s4/SvJae

value: WIN 18,446 synchrony + RA + 120 hours

value: Testis


title: 120 hr Rep 1

extract_protocol: 100,000 cells per replicate were collected and sent to Active Motif (Calsbad, CA, USA) for processing and data analysis


title: RA1849_LN-AX-R [A0176_S152_L002]

description:
A0176_S152_L002
Rhesus monkey

value: Lymph node:LN-AX-R


title: Control_48_3

value: liver

value: adult


title: RA1849_Ovary [A0175_S1_L001]

description:
A0175_S1_L001
Rhesus monkey

value: Sex Organ:Testis


title: P209N_K27Ac

description: Tissue

value: Patient P209 normal control


title: Lipo863B_K27Ac

description: Cell Line

source_name: Cell Line; Lipo863B; Liposarcoma


title: 48 hr Rep 2

value: WIN 18,446 synchrony + RA + 48 hours


title: RA1849_Brain-Gr [A0174_S78_L002]

description:
A0174_S78_L002
Rhesus monkey


title: Control_48_2

value: male

value: Control group at 48h


title: Control_48_1


title: RA1849_Brain-Wh [A0173_S111_L002]

description:
A0173_S111_L002
Rhesus monkey


title: 18 hr Rep 2

value: WIN 18,446 synchrony + RA + 18 hours


title: P69-N-RNAseq

description: Tissue

source_name: Tissue; Patient P69 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).

value: Patient P69 normal control


title: 18 hr Rep 1


title: RA1849_Adrenal [A0172]

description:
A0172
Rhesus monkey

source_name: Adrenal Gland

value: Adrenal Gland

value: infected with Ebola virus


title: P413-T-RNAseq

description: Tissue

source_name: Tissue; Patient P413 tumor; Liposarcoma

value: Patient P413 tumor

value: Liposarcoma


title: Control_24_11

source_name: male liver

value: Control group at 24h


title: 0 hr Rep 2

value: Derived from C57BL/6 x 129s4/SvJae

value: WIN 18,446 synchrony


title: A0171 [A0171]

description:
A0171
Rhesus monkey

value: Liver


title: P413-N-RNAseq

description: Tissue

source_name: Tissue; Patient P413 normal control; Liposarcoma

value: Patient P413 normal control


title: RA1849_Spleen [A0169_S109_L002]

description:
A0169_S109_L002
Rhesus monkey

source_name: Spleen

value: Spleen


title: 0 hr Rep 1

value: Testis


title: Control_24_9

value: liver

value: adult


title: RA1818_Sex-Organ [A0166_S117_L002]

description:
A0166_S117_L002
Rhesus monkey

value: Sex Organ:Sex-Organ


title: P404-T-RNAseq

description: Tissue

source_name: Tissue; Patient P404 tumor; Liposarcoma

value: Patient P404 tumor


title: RA1818_LN-MES [A0164_S153_L002]

description:
A0164_S153_L002
Rhesus monkey

value: Lymph node:LN-MES


title: P381-T-RNAseq

description: Tissue

source_name: Tissue; Patient P381 tumor; Liposarcoma

value: Patient P381 tumor


title: P404-N-RNAseq

description: Tissue

source_name: Tissue; Patient P404 normal control; Liposarcoma

value: Patient P404 normal control


title: P69-T-RNAseq

description: Tissue

source_name: Tissue; Patient P69 tumor; Liposarcoma

value: Patient P69 tumor


title: Control_24_8

value: male


title: RA1818_LN-ING-L [A0163_S154_L002]

description:
A0163_S154_L002
Rhesus monkey

source_name: Lymph node:LN-ING-L

value: Lymph node:LN-ING-L

value: infected with Ebola virus


title: Control_24_7

value: Control group at 24h


title: P381-N-RNAseq

description: Tissue

source_name: Tissue; Patient P381 normal control; Liposarcoma

value: Patient P381 normal control

value: Liposarcoma


title: Control_48_4

value: Control group at 48h


title: 48 hr Rep 1

value: Derived from C57BL/6 x 129s4/SvJae

value: WIN 18,446 synchrony + RA + 48 hours


title: Control_24_12

value: liver


title: RA1849_LN-ING-L [A0177_S151_L002]

description:
A0177_S151_L002
Rhesus monkey


title: RA1818_LN-AX-R [A0162_S155_L002]

description:
A0162_S155_L002
Rhesus monkey

source_name: Lymph node:LN-AX-R

value: Lymph node:LN-AX-R


title: Control_24_5

value: adult


title: Control_24_6


title: RA1818_Ovary [A0161_S2_L001]

description:
A0161_S2_L001
Rhesus monkey

source_name: Sex Organ:Ovary

value: Sex Organ:Ovary


title: Control_24_10


title: P369-N-RNAseq

description: Tissue

source_name: Tissue; Patient P369 normal control; Liposarcoma

value: Patient P369 normal control


title: Control_24_4


title: RA1818_Liver-L [A0157_S56_L001]

description:
A0157_S56_L001
Rhesus monkey

source_name: Liver

value: Liver


title: Control_24_3


title: P365.2-T-RNAseq

description: Tissue

source_name: Tissue; Patient P365.2 tumor; Liposarcoma

value: Patient P365.2 tumor


title: P365.2-N-RNAseq

description: Tissue

source_name: Tissue; Patient P365.2 normal control; Liposarcoma

value: Patient P365.2 normal control


title: Control_24_2

value: male


title: Control_24_1


title: RA1818_Kidney [A0156_S101_L002]

description:
A0156_S101_L002
Rhesus monkey

source_name: Kidney

value: Kidney


title: PHH_3

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

value: hepatocytes

value: 24hr cultured hepatocytes