title: 293T_control_FLAG_IP_VSV_rep1

description: Library name: EV124_IP


title: Sros_ChIP_input

status: Public on Mar 11 2025

type: SRA

city: Barcelona

first: Arnau

last: Sebé-Pedrós

address: C/ Dr. Aiguader, 88

department: Systems and Synthetic Biology

country: Spain

institute: Centre for Genomic Regulation (CRG)

library_source: genomic

data_processing:
Raw reads were filtered and trimmed with Trimmomtic (version 0.39) before mapping to the genome with bwa mem (version 0.7.17).
Duplicated reads were marked with bamsormadup from biobambam2 (https://github.com/gt1/biobambam2)
ATAC peaks were called with MACS2.
Assembly: Cladtertia collaboinventa genome assembly HoiH23_v2, Hormiphora californensis genome assembly GCA_020137815.1; Nematostella vectensis genome assembly GCA_932526225.1; Sphaeroforma arctica genome assembly Sarc_v2, Salpingoeca rosetta genome assembly Sros_v2
Supplementary files format and content: BigWig

molecule: genomic DNA

organism: Salpingoeca rosetta

source_name: Salpingoeca rosetta

growth_protocol: Sphaeroforma arctica culture was grown in Marine Broth (37.4 g/L) at 12 ºC. Salpingoeca rosetta culture was kept in artificial sea water with salinity 33 ppt supplemented with 4 % CGM3 and 4 % SWC at 23 ºC. Nematostella vectensis specimens were grown in 1/3 artificial sea water with salinity 14 ppt at 25 ºC. Cladtertia collaboinventa colonies were grown in artificial sea water (Red Sea, R11055) with salinity 33 ppt at 21 ºC.

extract_protocol:
S. arctica and S. rosetta cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392). H.californensis specimens were flash-frozen in liquid nitrogen. Frozen tissues were then pulverized, cells and nuclei were collected by centrifugation for 15 min at 2,000 g. Collected cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. N. vectensis 1.5-2 month old specimens were crosslinked with 1 % formaldehyde under vacuum. Crosslinked tissues were dissociated into single cells in Ca2+/Mg2+-free artificial sea water in the presence of Protease XIV (Sigma-Aldrich, P5147). Dissociated cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate mOrange-positive neuronal cells. FACS-sorted cells were additionally crosslinked with 3 mM DSG. C. collaboinventa specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Chromatin immunoprecipitation was performed as previously described by Lara-Astiaso et al. (PMID: 25103404) with following modifications. For each species, 100 ng chromatin was used for immunoprecipitation.

treatment_protocol: To synchronize cells in G1/early S phase, S. arctica cells were treated with 200 mM hydroxyurea (Sigma-Aldrich, H8627) for 18 hours, S. rosetta culture was treated with 0.05 mM aphidicolin for 18 hours.

tag: genotype

value: wild type

tag: treatment

value: 0.05 mM aphidicolin for 18 hours

tag: chip antibody


title: MDA-MB-231 Indisulam treated replica 3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

library_source: transcriptomic

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.7.5a
Assembly: hg38
Supplementary files format and content: deseq2_norm_with_annotations.txt: Gene expression values normalized by DESeq2 unsing FAST DB v2021_3 annotations

molecule: total RNA

organism: Homo sapiens

growth_protocol: MDA-MB-231 cells were grown in RPMI medium (Euroclone), supplemented with 10% fetal bovine serum, Sodium Pyruvate, HEPES, penicillin and streptomycin (GIBCO, Life Technologies) and glucose (Thermo Fisher)

extract_protocol:
total RNA was extracted and DNAse treated using the RNEasy mini kit (Qiagen) according to manufacturer’s instruction
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand).

treatment_protocol: 24hrs post-seeding MDA-MB-231 cells were treated with Pladienolide B (10nM, 6hrs), Indisulam (3.3µM, 12hrs) or DMSO, as control.

tag: cell line

tag: cell type

value: triple negative breast cancer cell line

value: Indisulam 3.3uM

tag: time

value: 12 hrs


title: 293T_control_HA_input_VSV_rep1

city: Houston

first: Eric

last: Van Nostrand

state: Tx

address: 1 Baylor Plaza

department: Biochemistry and Molecular Pharmacology

country: USA

institute: Baylor College of Medicine

description: Library name: EV123_input

library_source: other

data_processing:
Standard processing of eCLIP data was performed as previously described (Blue SB, et al. Nature Protocols 2022), with mapping performed to a custom genome index that included both the VSV genome and either hg19 (for 293T experiments) or mm10 (for MEF experiments) as described below.
UMI removal and cut adapt:  umi_tools extract   --random-seed 1   --bc-pattern NNNNNNNNNN   --stdin 23145FL-08-01-37_S37_L001_R1_001.fastq.gz   --log /dev/null | cutadapt   -j 8   --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 1   -   --report minimal   2> EV225_IP.cut.adapt.log | cutadapt   -j 8  --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 5   -   -o EV225_IP.trim.gz   --report minimal   >>EV225_IP.cut.adapt.log
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping:     STAR     --runMode alignReads     --runThreadN 8     --alignEndsType EndToEnd     --genomeDir  [mus_musculus_repbase_v2 or homo_sapiens_repbase_v2]   --genomeLoad NoSharedMemory     --outBAMcompression 10     --outFileNamePrefix EV225_IP.repeat.map     --outFilterMultimapNmax 100     --outFilterMultimapScoreRange 1     --outFilterScoreMin 10     --outFilterType BySJout     --outReadsUnmapped Fastx    --outSAMattrRGline ID:foo     --outSAMattributes All     --outSAMmode Full     --outSAMtype BAM Unsorted     --outSAMunmapped None     --outStd Log     --readFilesCommand zcat     --readFilesIn EV225_IP.trim.gz
Unique genomic mapping (takes repeat-removed reads and maps to the reference genome: STAR   --runMode alignReads   --runThreadN 8   --alignEndsType EndToEnd   --genomeDir [hg19+VSV or mm10+VSV] --genomeLoad NoSharedMemory   --outBAMcompression 10   --outFileNamePrefix EV225_IP.genome.map   --outFilterMultimapNmax 1   --outFilterMultimapScoreRange 1   --outFilterScoreMin 10   --outFilterType BySJout   --outReadsUnmapped Fastx   --outSAMattrRGline ID:foo   --outSAMattributes All   --outSAMmode Full   --outSAMtype BAM Unsorted   --outSAMunmapped None   --outStd Log   --readFilesIn EV225_IP.repeat.mapUnmapped.out.mate1
Sort mapped reads: samtools sort -@ 8 -m 2G -o EV225_IP.genome.map.bam *Aligned.out.bam
Remove PCR duplicate reads: samtools index EV225_IP.genome.map.bam umi_tools dedup   --random-seed 1   --stdin EV225_IP.genome.map.bam   --method unique   --stdout EV225_IP.bam
Make bigwigs: samtools index EV225_IP.bam b2bw EV225_IP.bam  --cpus 1
Isolate VSV-mapped reads only: bigWigToWig EV225.pos.bw -chrom=chrVSV EV225.pos.bw.chrVSV.wig
wigToBigWig EV225.pos.bw.chrVSV.wig /path/to/hg19_and_vsv.chrom.sizes EV242.pos.bw.chrVSV.wig.bw
Assembly: hg19 (for 293T) or mm10 (for MEF) with the addition of VSV (using accession NC_001560.1 with GFP was inserted between G and L as described in PMID 10400792)
Supplementary files format and content: bw files contain read density (in bigwig format) for the VSV genome (positive or negative strand as indicated in filename). Bigwig files are not included for datasets with zero reads

molecule: other

growth_protocol: HEK293T cells were obtained from ATCC (catalog # CRL-3216) and grown in complete medium containing DMEM (Gibco, Carlsbad, CA), 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco, Carlsbad, CA). For transient transfections, HEK293T cells were seeded the day prior to transfection in a 24-well plate (Genesee, El Cajon, CA) with 500 μL of complete media. Cells were transiently transfected with 500 ng of total DNA and 1.5 μL of TransIT-X2 (Mirus Bio, Madison, WI) following the manufacturer’s protocol.  For generation of inducible cell lines, sequences for mCherry, IFIT2, IFIT3, or IFIT2 and IFIT3 separated by a P2A site were cloned into the Flp-In vector pcDNA5/FRT/TO. Flp-In T-REx HEK293 cells (Invitrogen) maintained in 5 μg/mL of blasticidin were transfected at 70% confluency with mCherry or IFIT constructs and the vector containing the Flp recombinase pOG44 in a 1:10 molar ratio using TransIT-X2 (Mirus Bio). After one day, cells were transferred to new dishes, and on the following day, hygromycin (100 μg/mL) was added to cells. Following selection, cells were maintained in 5 μg/mL of blasticidin and 100 μg/mL of hygromycin. For induction of mCherry or IFIT proteins, cells were treated with 500 ng/mL of doxycycline for 24 h.   MEFs from Ifit2-/- and ΔIfit3a/b mice were prepared from day 13.5-14.5 embryos according to published protocols. Isolated MEFs were maintained in DMEM supplemented with 10% heat-inactivated, fetal bovine serum (FBS) (Cytiva), 100 U/mL penicillin-streptomycin (Invitrogen), non-essential amino acids (Cellgro), and Glutamax (Gibco). Passage 0 (P0 MEFs were frozen or split 1:4 when approximately 80% confluent (around 3 days). To generate transformed MEFs, 5x106 P1 primary MEFs were transfected with 10 μg of a plasmid (SV2) encoding the SV40 T antigen under control of a CMV promoter, using FuGene reagent (Promega) (3:1 μL FuGene to μg DNA ratio). Upon achieving confluence, MEF cultures were split 1:10. This process was repeated for approximately ten passages, at which time the transformed MEFs were frozen or used for experiments.

extract_protocol:
eCLIP was performed as previously described (Blue SB, et al. Nature Protocols 2022). Briefly, 10 million 293T or MEF cells were UV crosslinked (254 nM, 400 mJ/cm2), snap frozen, and lysed as previously described.
RNA fragmentation was performed, 2% of the sample was removed for size-matched input, and the remainder was subjected to immunoprecipitation of IFIT-bound RNA with antibodies against FLAG (M2 / F1804, Sigma) and HA (HA.11 / 901502, Biolegend) for 293T experiments, and IFIT2 (PA3-845, ThermoFisher) and IFIT3 (ABF1048, Millipore) for MEF experiments. Dephosphorylation, RNA adapter ligation, SDS-PAGE electrophoresis and nitrocellulose membrane transfer, RNA isolation, reverse transcription, and PCR amplification were performed as previously described (Blue, SM. et al, Nat Protocols 2022). Libraries are as previously described for eCLIP (Blue, SM. et al, Nat Protocols 2022), based on the Illumina RNA TruSeq HT adapter strategy.

treatment_protocol: Flp-In T-REx HEK293 cells expressing mCherry, IFIT2, IFIT3, or IFIT2 and IFIT3 in 10 cm culture dishes were induced with doxycycline for 24 h. Cells were then infected with VSV at an MOI of 3.0, and dishes were crosslinked using a UV cross-linker (254 nm; CL-1000 from UVP/Analytik Jena) at 400 mJ/cm2. Downstream sample processing and eCLIP were performed as previously described, using antibodies against FLAG (M2 / F1804, Sigma) and HA (HA.11 / 901502, Biolegend) for 293T experiments, and IFIT2 (PA3-845, ThermoFisher) and IFIT3 (ABF1048, Millipore) for MEF experiments. Most experiments were performed in biological duplicate, excepting the uninfected 293T samples (which were single replicates).

value: WT

value: VSV infected


title: MDA-MB-231 Indisulam treated replica 2


title: 293T_control_HA_IP_VSV_rep1

description: Library name: EV123_IP


title: HoiH23_ChIP_H3K4me2

organism: Cladtertia collaboinventa

source_name: Cladtertia collaboinventa

tag: tissue

value: Whole-organism

value: H3K4me2, Abcam ab32356


title: MDA-MB-231 DMSO treated replica 3

value: DMSO


title: MDA-MB-231 Indisulam treated replica 1


title: MDA-MB-231 DMSO treated replica 2


title: HoiH23_ChIP_input


title: PP026

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description:
mRNA
InfantAdult_Tcells.scrnaseq.cts.txt

data_processing:
For scRNA-seq, we aligned the reads corresponding to each sample index to the GRCh38 genome / GENCODE v.24 transcriptome annotation with STAR v2.5.0 (23104886) after removing 3’ poly(A) tails from read 2 (anything >7 A’s) and discarding any resulting fragments < 25 nts in length.
We then constructed an address for each read with a unique, strand-specific, exonic alignment comprised of the cell-identifying barcode, unique molecular identifier (UMI) barcode, and gene identifier.
Next, we applied the algorithm described by Griffiths et al. to correct of index swapping between clusters on the Illumina flow cell (29991676). Finally, we collapsed PCR duplicates using UMIs and corrected errors in both the cell-identifying and UMI barcodes to generate an initial molecular count matrix.
To identify cell barcodes associated with cells, we used the EmptyDrops algorithm (Lun et al., Genome Biol, 2019) and then further filtered the resulting count matrix to remove cells above of the 95% confidence interval for the fraction of molecules aligned to the mitochondrial genome (possible dead cells), the fraction of molecules aligned to introns (possible nuclei), and the number of molecules per gene (filters red blood cells and other artifacts). We also pre-emptively removed cells with sufficiently low coverage that they would interfere with unsupervised clustering. To identify highly variable genes for clustering, we use the drop-out curve method previously described (Levitin et al., Mol Sys Bio, 2019), removing all cells in which fewer than three highly variable genes were detected.
For bulk RNA-seq, adapter-trimmed paired-end reads were aligned to the GRCh38 reference genome with ENSEMBL transcriptome annotation using the STAR aligner v.2.5.2b. Read quantification was performed using the featureCounts program in the Subread v.1.5.2 package.
Genome_build: GRCh38
Supplementary_files_format_and_content: InfantAdult_Tcells.scrnaseq.cts.txt: For scRNA-seq, the processed data are in a single, tab-delimited text file that contains the gene expression counts for each individual cell.
Supplementary_files_format_and_content: *.counts.txt: For each bulk RNA-seq sample, there is a tab-delimited text file containing the output of featureCounts.

source_name: Blood

extract_protocol:
For single-cell RNA-seq, RNA was extracted and poly(A) mRNA was converted into barcoded cDNA using the 10x Genomics Chromium platform. For bulk RNA-seq, RNA was extracted using the Qiagen RNeasy Micro Kit.
Single-cell RNA-seq libraries were constructed using the 10x Genomics Single Cell Gene Expression 3' v2 chemistry for donors D363, D370, Adult Donor A, Adult Donor B, HDL049, HDL055, D381 and the 10x Genomics Single Cell Gene Expression 3' v3 chemistry for donors D457, D471, HDL082. For bulk RNA-seq, library preparation was done using the SMART-Seq® ultra-low input RNA kit (Takara bio).

treatment_protocol: For both bulk and single-cell RNA-seq, cells were dissociated from each tissue. Organ donor samples (whole lungs, intestinal blocks, spleen, blood) in saline or University of Wisconsin solution were placed on ice, transported to the laboratory, and processed within 24-36 hours of procurement. Single cell suspensions were obtained from spleen, lung, intestine, and lymph node samples using mechanical and enzymatic digestion as previously described (Thome et al., Nature Med, 2016; Sathaliyawala et al., Immunity, 2013; Granot et al, Immunity, 2017). Lymph nodes were isolated by dissection from the mesentery of intestinal blocks and the tracheobronchial tree of the lung. Isolated lymph nodes and spleen samples were placed in complete media (IMDM (Gibco, ref #12440-053) +1% PSQ (100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, GeminiBio, cat #c400-110) + 10% FBS (GeminiBio, cat #100-106)) and mechanically disrupted with scissors and double filtered through 100μm strainers. Suspensions were washed with wash buffer (PBS (Corning, cat #20-030-CV) + 2mM EDTA (Corning, cat #46-034-CI) + 5% FBS) followed by red blood cell lysis (ACK lysing buffer, Gibco, ref A10492-01), then resuspended in complete media. Lung parenchyma were separated from the large airways (trachea) using scissors then placed into digestion media (IMDM + Collagenase D 1mg/mL (Millipore Sigma cat# 11088882001) and + DNase 0.1mg/mL (Millipore Sigma cat# DN25-5G) on a shaker at 37⁰ for 30 minutes. Intestinal tissue was washed with sterile PBS to remove luminal contents, chopped into pieces using scissors, then placed into digestion media on a shaker at 37⁰ degrees for 30 minutes. Following incubation, lung and intestinal samples were strained and washed with wash buffer. Samples were centrifuged with resultant cell pellet diluted for mononuclear cells isolation by density gradient centrifugation (Lymphocyte Separation Medium, Corning, cat #25-072-CI) followed by resuspension in complete media. Peripheral blood mononuclear cells were isolated from blood samples by density centrifugation. For bulk RNA-seq, CD4 and CD8 TEM cells were isolated by FACS. For scRNA-seq, pan T cells were isolated by negative selection using the EasySep Human T cell Enrichment Kit (STEMCELL Technologies) and dead cells were removed using a column-based Dead Cell Removal Kit (Miltenyi). T cells were rested overnight at 37C for 16 hours in complete medium or activated with Human CD3/CD28 T cell Activator (STEMCELL) 16 37C for 16 hours prior to scRNA-seq.

value: Blood

value: T cells

tag: age (years)

tag: Sex

value: Male

tag: stimulation

tag: donor id

tag: cell isolation

value: T cells by negative selection

tag: assay type

value: scRNA-seq


title: MDA-MB-231 DMSO treated replica 1


title: MDA-MB-231 Pladienolide B treated replica 2

value: Pladienolide B 10 nM

value: 6 hrs


title: PP024

source_name: Tonsil

value: Tonsil


title: PP023

value: Anti-CD3/Anti-CD28 Stimulated


title: Neurons-UT-2

city: Milan

first: Monah

last: Abou Alezz

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description: Neurons-UT biol rep 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore (options: "--quality 20 --length 25")
Trimmed reads were mapped to GRCh38 whole genome using STAR v2.7.6a (options: "--outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10")
Gene counts of mapped reads were obtained with the Subread package ("featureCounts" function with options: "-g gene_name -s 0")
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include counts of mapped reads for each Sample

molecule: polyA RNA

source_name: iPSC-derived neurons

growth_protocol: Healthy donor  human iPSCs (hiPSCs) were maintained in mTESR plus medium (Stemcell Techologies). For the generation of astrocytes and neurons, hiPSC were firstly differentiated into Neural Stem Cells  (NSCs), according to the published Dual Smad inhibition protocol (Chambers et al, 2009). Astrocyte differentiations from NSCs were performed as previously described (Giordano et al, 2023; Santos et al, 2017). At the end of the differentiation and maturation protocol on day 34, cells were passed at least twice before performing transduction experiments to deplete neurons and oligodendrocytes from mixed cultures and enrich for astrocytes. Transductions were performed in astrocyte maturation medium consisting of to DMEM/F-12 Glutamax (Thermo Fisher Scientific) supplemented with N2 and B27 (both from Thermo Fisher Scientific), 10% FBS and 10 ng/ml leukemia inhibitory factor (LIF). For the generation of neurons, NSCs obtained through the Dual Smad inhibition protocol were further differentiated with the STEMdiff Neuron Differentiation Kit and maintained in culture with the STEMdiff Neuron Maturation kit following manufacturer’s instructions. Cells were used for transduction experiments after 21 days in maturation medium.

extract_protocol:
Total mRNA was extracted from hiPSC-derived neurons or astrocytes in biological triplicates for each condition with ReliaPrep RNA miniprep system (Promega). RNA integrity was analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were prepared starting from 100ng of total RNA per sample.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).  The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions

treatment_protocol: Mature astrocytes and neurons were transduced with AAV vectors for 48h by adding the vectors into the culture media. After 48h cells were detached for RNA extraction.

value: iPSC-derived neurons

value: Wild type

value: Untreated


title: Neurons-UT-1

description: Neurons-UT biol rep 1


title: multiome, E15.5 back skin from 3 Prmt5;cKO embryos (pooled), ATAC, pool 4

city: Iowa City

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

description:
Library name: PRMT5cKO_E15.5_SKIN_ATAC_4
ATAC

library_source: genomic single cell

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using the Illumina bcl2fastq software. scRNA and scATAC-seq reads were processed and aligned to the mm10 reference genome using the Cell Ranger Count function. Further analysis and visualization was performed using Seurat (v4.3) (Hao et al., 2021) and Signac (v1.9) (Stuart et al., 2021). Briefly, peaks were unified between conditions and filtered based on length (20-10,000). EnsDb.Mmusculus.v79 was used for gene annotations. Cells underwent manual filtering to ensure cells used were between nCount_ATAC (100-50,000), nCount_RNA (100-25,000), nucleosome_signal <4, and TSS_enrichment >1. scRNA-seq separately underwent an additional SCTransform analysis. scATAC-seq underwent FindTopFeatures, RunTFIDF, and RunSVD. Datasets were then intersected using FindIntegrationAnchors (1:30, k.anchors=5) and IntegrateData (1:30). SCTransform, RunTFIDF, FindTopReatures, and RunSVD were rerun after integration. FindMultiModal neighbors using PCA (1:50) and LSI (2:50) was performed prior to FindClusters to generate the final UMAP. Trajectory analysis was performed with Monocle3 (Trapnell et al., 2014). Gene signature scoring was performed with UCell (Andreatta and Carmona, 2021). Cell cycle analysis was performed using CellCycleScoring with the cc.genes.updated.2019 converted to mouse format by Gprofiler2 (Kolberg et al., 2020). GO ontology analysis was performed using GO Biological Process and plotted using ShinyGO 0.8 (Ge et al., 2020).
For BigWig files, clusters were parsed into epidermis (2,3,5,7,8,10), dermis (0,1,4,6,9,18), and other (11,12,13,14,15,16,17,19,20,21,22) groups based on the cluster identities within Recka et al. 2025 supplemental figures 6-8. Epidermal or hair follicle related lineages were further subset into basal (2/5), spinous (3/10), differentiated (7), hair follicle (8), and dermal condensate (18). Reads originating from cells belonging to the described cell identities (clusters) were extracted via barcodes to create pseudobulk alignments. RNAseq and ATACseq were normalized using RPKM and read count, respectively, and tile size of 25 bp was used to generate final tracks.
Assembly: mm10
Supplementary files format and content: Cell Ranger Output Files: filtered_feature_bc_matrix.h5, raw_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: bigwig files of mRNA expression or ATAC-seq peaks in individual clusters

organism: Mus musculus

source_name: back skin

extract_protocol:
For single cell multiome-sequencing experiments, embryos were collected at E15.5 from multiple litters. Yolk-sac tissue was lysed quickly using the Extract-N-Amp Tissue PCR Kit (Sigma-Aldrich) and embryos quickly genotyped using Phusion High-Fidelity DNA Polymerase (New England Biolabs) and shortened PCR cycling parameters. During genotyping, the back skin from all E15.5 mouse embryos was dissected and immediately transferred to ice cold DEPC-PBS (Millipore Sigma). Samples were incubated in 0.25% Trypsin (ThermoFisher) for 30-45 mins at 37°C with frequent pipette mixing. Once cells reached a single cell suspension, the reaction was quenched with 10% FBS (ThermoFisher), passed through a 40 µM cell strainer (Flomi Cell Strainers, SP Bel-Art), and triplicates of each genotype (CRE-negative controls or Prmt5 cKOs, based on quick-genotyping results) pooled. 500,000 cells from each pooled sample were incubated with lysis buffer (10mM Tris HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40) for 5 mins on ice, nuclei extracted and quantified using trypan blue.
scRNA-Seq and scATAC-Seq sequencing libraries were prepared by the University of Iowa’s Iowa Institute of Human Genetics Genomics Division Laboratory. Briefly, 10,000 nuclei were targeted for bulk transposition before individual nuclei were encapsulated in oil droplets along with the 10X GEM code beads in the Chip J cartridge (P/N: 1000234) using the 10X Genomics Single Cell iX Chromium Controller. Generation of gel beads in emulsion (GEMs), barcoding, pre-amplification PCR, and ATAC library construction were all performed as recommended by the manufacturer (10X Genomics, Chromium Next GEM Single Cell Multiome + ATAC Reagent Kit, Rev F, P/N:1000283). The gene expression libraries were pooled and sequenced on a NovaSeq 6000 to give at least 20,000 reads per nuclei. The ATAC-Seq libraries were pooled and sequenced on a NovaSeq 6000 to give at least 25,000 reads per nuclei.

value: back skin

value: Mixed - epidermis/dermis

value: Prmt5 cKO

tag: batch


title: PP020

value: Adult

value: Adult Donor B


title: PP021

source_name: Bone Marrow

value: Bone Marrow


title: multiome, E15.5 back skin from 3 control embryos (pooled), ATAC, pool 4

description:
Library name: CTRL_E15.5_SKIN_ATAC_4
ATAC

value: control


title: Neurons-Spk-3

description: Neurons-Spk biol rep 3

value: AAV Spk100-CAG-GFP


title: multiome, E15.5 back skin from 3 Prmt5;cKO embryos (pooled), ATAC, pool 2

description:
Library name: PRMT5cKO_E15.5_SKIN_ATAC_2
ATAC


title: Neurons-Spk-2

description: Neurons-Spk biol rep 2


title: multiome, E15.5 back skin from 3 Prmt5;cKO embryos (pooled), ATAC, pool 3

description:
Library name: PRMT5cKO_E15.5_SKIN_ATAC_3
ATAC


title: multiome, E15.5 back skin from 3 Prmt5;cKO embryos (pooled), ATAC, pool 1

description:
Library name: PRMT5cKO_E15.5_SKIN_ATAC_1
ATAC


title: PP019

value: Blood

value: T cells

value: Male

value: T cells by negative selection


title: multiome, E15.5 back skin from 3 Prmt5;cKO embryos (pooled), GEX

description:
Library name: PRMT5cKO_E15.5_SKIN_RNA
3' mRNA (v3 10x Genomics)

library_source: transcriptomic single cell


title: PP018

value: Adult Donor A

value: scRNA-seq


title: multiome, E15.5 back skin from 3 control embryos (pooled), ATAC, pool 3

description:
Library name: CTRL_E15.5_SKIN_ATAC_3
ATAC


title: multiome, E15.5 back skin from 3 control embryos (pooled), ATAC, pool 2

description:
Library name: CTRL_E15.5_SKIN_ATAC_2
ATAC


title: Neurons-Spk-1

description: Neurons-Spk biol rep 1

value: iPSC-derived neurons


title: Neurons-Empty-3

description: Neurons-Empty biol rep 3

value: Wild type

value: Empty AAV9 capsid


title: PP017

value: Anti-CD3/Anti-CD28 Stimulated


title: PP016

source_name: Spleen

value: Spleen


title: Neurons-Empty-2

description: Neurons-Empty biol rep 2


title: PP025


title: Neurons-Empty-1

description: Neurons-Empty biol rep 1


title: multiome, E15.5 back skin from 3 control embryos (pooled), GEX

description:
Library name: CTRL_E15.5_SKIN_RNA
3' mRNA (v3 10x Genomics)

value: back skin

value: Mixed - epidermis/dermis


title: Neurons-UT-3

description: Neurons-UT biol rep 3

value: Untreated


title: PBS 1hr treated BMDM, IgG CUT&Run (Input)

city: Seoul

first: Su Min

last: Kim

state: Gangnam-gu

address: Dogok-ro 237

country: South Korea

institute: Severance Hospital

description: Library name: UT_IgG

data_processing:
CUT&Run : The prepared CUT&RUN libraries were pre-processed with the nf-core CUT&RUN pipeline (v3.1), executed via Nextflow (v23.04.5) to ensure reproducible and standardized data analysis. The GRCm38 mouse genome assembly was used as the reference. Raw sequencing reads were trimmed, quality controlled, and aligned to the reference genome using Bowtie2 (v2.4.4). To remove potential artifacts, regions overlapping a pre-defined blacklist (mm10-blacklist.v2) were excluded. Peaks were identified using MACS2 (v2.2.7.1) with a genome size of 1.87 × 10⁹ bp. Normalization of coverage was performed using counts per million (CPM) with a bin size of 1.
Assembly: mm10 (GRCm38)
Supplementary files format and content: CUT&Run : BigWig, Narrowpeak (except for input)
Library strategy: CUT&Run

source_name: Bone Marrow Derived Macrophages

growth_protocol: BMs were extracted from the femur and tibia of mice. To generate BMDMs, BM cells were cultured in Dulbecco’s Modified Eagle’s Medium (HyClone, SH30243.01) supplemented with 10% fetal bovine serum (FBS; Gibco, 10099141) and 20% L929-conditioned media. After 6 d in culture, cells were seeded and treated under the indicated conditions.

extract_protocol:
CUT&Run : We performed Cleavage Under Targets & Release Using Nuclease (CUT&RUN) on bone marrow-derived macrophages (BMDMs) using the CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, 14-1048) following the manufacturer’s protocol. Briefly, 1 × 10⁵ cells were immobilized on Concanavalin A-coated magnetic beads and incubated with H3K4me1 (EpiCypher, 13-0057) and H3K27ac (EpiCypher, 13-0045) antibodies. After antibody binding, the cells were treated with pAG-MNase for targeted chromatin cleavage at 37°C. The cleaved chromatin fragments were purified and used for downstream library preparation.
CUT&Run : CUT&RUN libraries were prepared using the CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, 14-1001) following the manufacturer’s instructions. Approximately 5 ng of purified DNA was used for library preparation. The process included end repair, A-tailing, adapter ligation, and uracil excision, followed by dual-indexed PCR amplification using i5 and i7 primers. Libraries were purified and size-selected using AMPure XP beads to remove contaminants and enrich for fragments of the desired size. The final libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end (2 × 150 bp) reads, ensuring high coverage for downstream analysis.

value: Bone Marrow Derived Macrophages

value: PBS


title: Neurons-AAV9-3

description: Neurons-AAV9 biol rep 3


title: PP022

value: Bone Marrow


title: PP014

source_name: Lung Lymph Node

value: Lung Lymph Node


title: PBS 1hr treated BMDM, H3K4me1 CUT&Run (ChIP)

description: Library name: UT_me1


title: Neurons-AAV9-2

description: Neurons-AAV9 biol rep 2


title: PP012

value: T cells


title: Neurons-AAV6-3

description: Neurons-AAV6 biol rep 3


title: Neurons-AAV6-2

description: Neurons-AAV6 biol rep 2


title: PP013

value: Male


title: LPS 1hr treated BMDM, IgG CUT&Run (Input)

description: Library name: LPS_IgG

value: LPS


title: Neurons-AAV6-1

description: Neurons-AAV6 biol rep 1


title: PP011

value: T cells by negative selection


title: PP009

source_name: Lung

value: Lung

value: scRNA-seq


title: Neurons-AAV5-3

description: Neurons-AAV5 biol rep 3

value: iPSC-derived neurons

value: Wild type


title: PP006

value: Anti-CD3/Anti-CD28 Stimulated


title: MI_NAV5

city: Guangzhou

first: Jun

last: Lin

address: 107 Yanjiang West Road, Yuexiu District

department: Cardiovascular Surgery

country: China

institute: Sun Yat-sen Memorial Hospital

description:
Library name: Sample 10
MI_NAV5

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: xlsx files include FPKM values for each sample

source_name: heart

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: heart

value: WT

value: myocardial infartion+NAV


title: PBS 1hr treated BMDM, H3K27Ac CUT&Run (ChIP)

description: Library name: UT_27ac


title: LPS 1hr treated BMDM, H3K4me1 CUT&Run (ChIP)

description: Library name: LPS_me1


title: PP010


title: MI_NAV4

description:
Library name: Sample 9
MI_NAV4


title: Neurons-AAV5-2

description: Neurons-AAV5 biol rep 2


title: MI_NAV3

description:
Library name: Sample 8
MI_NAV3


title: Neurons-AAV5-1

description: Neurons-AAV5 biol rep 1


title: PP015

value: Spleen


title: MI_NAV2

description:
Library name: Sample 7
MI_NAV2


title: PP004


title: PP005


title: Neurons-AAV2-3

description: Neurons-AAV2 biol rep 3


title: PP003


title: MI_NAV1

description:
Library name: Sample 6
MI_NAV1


title: Neurons-AAV2-2

description: Neurons-AAV2 biol rep 2


title: PP002


title: Neurons-AAV9-1

description: Neurons-AAV9 biol rep 1


title: MI_5

description:
Library name: Sample 5
MI_5

value: myocardial infartion

value: MI


title: LPS 1hr treated BMDM, H3K27Ac CUT&Run (ChIP)

description: Library name: LPS_27ac

value: Bone Marrow Derived Macrophages


title: PP001


title: Neurons-AAV2-1

description: Neurons-AAV2 biol rep 1


title: MI_4

description:
Library name: Sample 4
MI_4


title: Neurons-AAV1-3

description: Neurons-AAV1 biol rep 3


title: MI_3

description:
Library name: Sample 3
MI_3


title: MI_2

description:
Library name: Sample 2
MI_2


title: Neurons-AAV1-2

description: Neurons-AAV1 biol rep 2


title: S48stm2 stm1Cd

city: Nanjing

first: cheng

last: gao

state: Jiangsu

address: Nanjing Agricultural University

institute: Nanjing Agricultural University

description: Library name: Sample-48

data_processing:
Reads with an average mass fraction lower than Q20 were removed, and the filtered Reads were compared to the reference genome TAIR10.fas using the upgraded HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml ) software of TopHat2.
Assembly: TAIR10.fas
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Shoots

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols

value: Shoots

value: stm2 stm1

value: Cd


title: MI_1

description:
Library name: Sample 1
MI_1


title: S47stm2 stm1Cd

description: Library name: Sample-47


title: S46stm2 stm1Cd

description: Library name: Sample-46


title: S45stm2 stm1Con

description: Library name: Sample-45

value: Con


title: Astrocytes-UT-4

description: Astrocytes-UT biol rep 4

source_name: iPSC-derived astrocytes

value: iPSC-derived astrocytes

value: Untreated


title: Neurons-AAV1-1

description: Neurons-AAV1 biol rep 1


title: Astrocytes-UT-3

description: Astrocytes-UT biol rep 3


title: Astrocytes-UT-2

description: Astrocytes-UT biol rep 2


title: S44stm2 stm1Con

description: Library name: Sample-44


title: Astrocytes-UT-1

description: Astrocytes-UT biol rep 1


title: S43stm2 stm1Con

description: Library name: Sample-43


title: S42stm2_2Cd

description: Library name: Sample-42


title: Bulk RNAseq, E15.5 back skin from 1 control embryo, SAMPLE 3

description:
Library name: CTRL_E15.5_SKIN_RNA_bulk_3
E4(ctrl)

data_processing:
Following demultiplexing, reads were mapped to the Mm10 genome using STAR (Dobin et al., 2013), transcript and read counts conducted using Stringtie (Pertea et al., 2015), and differential gene expression analysis carried out using DeSeq2 (Love et al., 2014). This approach identified 1,454 differentially expressed genes (DEGs) (p adj < 0.01, log2FC > 1), although this list was skewed by the reduction in total ectoderm of Prmt5 cKOs, compared to CTRLs, as bulk samples contained both epidermis and dermis. As a result of reduced epidermis tissue in the overall Prmt5 cKO sample (relative to CTRLs), a large portion of epidermis-associated genes were correspondingly significantly down-regulated.
Assembly: mm10
Supplementary files format and content: xlsx file includes expression values for each sample using 2 pipelines

extract_protocol:
Back skin from E15.5 mouse embryos (3 control and 3 Prmt5 cKO embryos) was dissected and immediately transferred to ice cold DEPC-PBS (Millipore Sigma, D5758). RNA was isolated using the RNeasy Fibrous Mini Kit (Qiagen, 74704) following manufacturer’s instructions.
cDNA libraries were generated using the Illumina TruSeq Stranded mRNA kit and samples sequenced using the NovaSeq6000 platform (~30 million, 200 bp, paired-end reads/sample).

value: back skin

value: Mixed - epidermis/dermis

value: control


title: Bulk RNAseq, E15.5 back skin from 1 Prmt5;cKO embryo, SAMPLE 3

description:
Library name: PRMT5cKO_E15.5_SKIN_bulk_3
E9(mut)

value: Prmt5 cKO


title: Bulk RNAseq, E15.5 back skin from 1 Prmt5;cKO embryo, SAMPLE 2

description:
Library name: PRMT5cKO_E15.5_SKIN_bulk_2
E5(mut)


title: Bulk RNAseq, E15.5 back skin from 1 Prmt5;cKO embryo, SAMPLE 1

description:
Library name: PRMT5cKO_E15.5_SKIN_bulk_1
E1(mut)


title: Astrocytes-Empty-3

description: Astrocytes-Empty biol rep 3

value: Wild type

value: Empty AAV9 capsid


title: S41stm2_2Cd

description: Library name: Sample-41


title: Astrocytes-Empty-2

description: Astrocytes-Empty biol rep 2


title: Bulk RNAseq, E15.5 back skin from 1 control embryo, SAMPLE 1

description:
Library name: CTRL_E15.5_SKIN_RNA_bulk_1
E2(ctrl)


title: S40stm2_2Cd

description: Library name: Sample-40


title: Astrocytes-Empty-1

description: Astrocytes-Empty biol rep 1


title: S39stm2_2Con

description: Library name: Sample-39


title: Astrocytes-AAV9-3

description: Astrocytes-AAV9 biol rep 3


title: S38stm2_2Con

description: Library name: Sample-38


title: WT_4M_rep2

city: Morgantown

first: Gangqing

last: Hu

state: WV

address: 64 Medical Center Drive

institute: West Virginia University

description: Library name: WT_4M_rep2

data_processing:
The scRNA-seq datasets was processed by cellranger version 6.1.2. The reference genome was GRCm38. cellranger count was used to generated the gene feature for the libraries.
Assembly: GRCm38
Supplementary files format and content: *.filtered_feature_bc_matrix.h5 : Filtered feature barcode matrix stored as a Compressed Sparse Column (CSC) sparse matrix in hdf5 format. The rows consist of all the gene features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells.

source_name: retina

extract_protocol:
Single-cell suspensions were prepared with pooled retinas from one- and four-month-old male and female from each genotype according to the protocol by Fadl and colleagues to preserve cone viability (Fadl BR, Brodie SA, Malasky M, et al. An optimized protocol for retina single-cell RNA sequencing. Mol Vis. 2020;26:705-717.)
Single-cell libraries were prepared using the 10x Chromium Platform following the manufacturer’s instructions at the WVU Flow Cytometry & Single Cell Core Facility.

value: retina

value: WT

tag: age


title: WT_4M_rep1

description: Library name: WT_4M_rep1


title: Astrocytes-AAV9-2

description: Astrocytes-AAV9 biol rep 2


title: Astrocytes-AAV9-1

description: Astrocytes-AAV9 biol rep 1


title: WT_1M_rep1

description: Library name: WT_1M_rep1


title: S36stm1_1Cd

description: Library name: Sample-36


title: DKO_4M_rep2

description: Library name: DKO_4M_rep2

value: DKO


title: S35stm1_1Cd

description: Library name: Sample-35


title: Astrocytes-AAV5-2

description: Astrocytes-AAV5 biol rep 2


title: Astrocytes-AAV5-3

description: Astrocytes-AAV5 biol rep 3


title: DKO_4M_rep1

description: Library name: DKO_4M_rep1


title: S34stm1_1Cd

description: Library name: Sample-34


title: S33stm1_1Con

description: Library name: Sample-33


title: DKO_1M_rep2

description: Library name: DKO_1M_rep2


title: Astrocytes-AAV2-3

description: Astrocytes-AAV2 biol rep 3


title: Astrocytes-AAV2-2

description: Astrocytes-AAV2 biol rep 2


title: S32stm1_1Con

description: Library name: Sample-32


title: Bulk RNAseq, E15.5 back skin from 1 control embryo, SAMPLE 2

description:
Library name: CTRL_E15.5_SKIN_RNA_bulk_2
E3(ctrl)


title: Astrocytes-AAV5-1

description: Astrocytes-AAV5 biol rep 1


title: DKO_1M_rep1

description: Library name: DKO_1M_rep1


title: C198R_4M_rep2

description: Library name: C198R_4M_rep2


title: Astrocytes-AAV2-1

description: Astrocytes-AAV2 biol rep 1


title: S30Col_0Cd

description: Library name: Sample-30


title: Popliteal Lymph Node, VACV-gB injection, Spatial transcriptomics, 21dpi

city: Ithaca

first: Shaowen

last: Jiang

address: 237 Tower Rd

institute: Cornell University

description: Library name: D21_PLN_SR_21dpi

data_processing:
Raw sequencing reads from spatial transriptomics were aligned to the mouse genome (assembly: GRCm38) using the STARsolo (v2.7.10a) pipeline to generate a gene x bead barcode expression count matrix. By integrating the corresponding the BeadBarcodes coordinate file downloaded from Curio Bioscience website, slide-seq count matrix with spatial position information for each sample was generated and loaded into an AnnData object using Scanpy (v1.9.8).
Raw sequencing reads from long read were base called using the super accuracy model (SUP) of the GPU accelerated Guppy algorithm (v6.5.7, config file: dna_r10.4.1_e8.2_400bps_sup.cfg); Basecalled reads were then processed and demultiplexed into R2C2 consensus reads and their subreads using C3POa (v3). After that, BC1 commands were applied in the above reads to generate R2C2+UMI consensus reads. Custome scripts were used for demultiplexed and clonocalling via MiXCR (v4.6.0) to generate two tabula files; One contains adaptive immune receptor clonotype information and its corresponding spatial barcode and UMI for each read; the other is a bead x clonotype table.
Assembly: GRCm38
Supplementary files format and content: HDF5 file containing raw gene expression count matrix (UMI counts) per bead barcode and tablula files contain adaptive immune receptor clonotype information per spatial barcode
Library strategy: Spatial transcriptomics

source_name: Popliteal Lymph Node

extract_protocol:
Slide-seq Spatial Transcriptomics libraries for all tissue sections were prepared using the Curio Seeker Spatial Transcriptomics kit (Curio Biosciences), following the manufacturer's instructions. Briefly, fresh-frozen tissue was mounted on 3mm x 3mm Curio Seeker tiles, followed by RNA hybridization, reverse transcription, enzymatic digestion, and bead detachment from the glass tiles. This was followed by second strand cDNA synthesis and amplification.
The cDNA library from each sample was divided into two portions. For spatial transcriptomics, the cDNA ibraries were prepared with the Nextera XT DNA sample preparation kit following Curio instructions. The samples were then pooled and sequenced on an Illumina NextSeq 2K system with a P2 flow cell and a 100-cycle kit, with read configurations as follows: Read 1 = 50 bp, Read 2 = 72 bp, Index 1 = 8 bp, and Index 2 = 8 bp. For the Long read, the cDNA library was processed with hybridization-based target enrichment of TCR and BCR transcripts and rolling circle amplification to concatemeric consensus (R2C2). The processed libraries were prepared using Ligation Sequencing Kit V14 from the Oxford Nanopore before sequencing by MinION (R10.4.1) flowcell for at least 48 hours.

treatment_protocol: Mature adult male mice (3-month old; C57BL/6J) were injected with 1e5 PFU recombinant Vaccinia virus expressing the gB peptide (VACV-gB) in the left hind footpad via 30G needles. Equal volume of PBS were injected to the mice of the same age as controls.

value: Popliteal Lymph Node

tag: strain

value: Male

value: 10uL 1e5 PFU Vaccinia virus injection in the left hind and tissue collection 21dpi

value: 3 months


title: C198R_1M_rep2

description: Library name: C198R_1M_rep2


title: S29Col_0Cd

description: Library name: Sample-29

value: Shoots

value: Cd


title: WT_1M_rep2

description: Library name: WT_1M_rep2


title: Popliteal Lymph Node, VACV-gB injection, Spatial transcriptomics, 14dpi

description: Library name: D14_PLN_SR_14dpi

value: 10uL 1e5 PFU Vaccinia virus injection in the left hind and tissue collection 14dpi


title: DPT082

source_name: Jejunum Lymph Node

value: Jejunum Lymph Node

value: T cells

value: Anti-CD3/Anti-CD28 Stimulated

value: T cells by negative selection

value: scRNA-seq


title: C198R_4M_rep1

description: Library name: C198R_4M_rep1


title: C198R_1M_rep1

description: Library name: C198R_1M_rep1


title: DPT081

source_name: Colon

value: Colon


title: mCD8T:DFMO, H3K27me3, 3rep

city: Baltimore

first: Taekjip

last: Ha

state: Maryland

address: 3400 N. Charles Street

institute: Johns Hopkins University

description:
Library name: H3K27me3_Treat_3rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in

data_processing:
Reads were aligned on the reference genome by Bowtie2 and read counts were normalized by the spike-in. Assembly
genome build:  mm10 (Mouse)
Supplementary files format and content:  Normalized read counts with read positions mapped on the reference genome.

source_name: CD8+ T cell

extract_protocol:
Nuclei suspensions were sonicated to obtain ~ 300–500 bp fragments of chromatin.
Condense-seq

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 15 min at room temperature, and the reaction was quenched with glycine.

value: CD8+ T cell

value: Difluoromethylornithine (DFMO) treated


title: Popliteal Lymph Node, VACV-gB injection, Spatial transcriptomics, 7dpi

description: Library name: D7_PLN_SR_7dpi

value: 10uL 1e5 PFU Vaccinia virus injection in the left hind and tissue collection 7dpi


title: S28Col_0Cd

description: Library name: Sample-28


title: S27Col_0Con

description: Library name: Sample-27

value: Con


title: S37stm2_2Con

description: Library name: Sample-37


title: S26Col_0Con

description: Library name: Sample-26


title: S31stm1_1Con

description: Library name: Sample-31


title: DPT079

description:
mRNA
InfantAdult_Tcells.scrnaseq.cts.txt

source_name: Jejunum

value: Jejunum


title: mCD8T:DFMO, H3K27me3, 1rep

description:
Library name: H3K27me3_Treat_1rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in

value: WT


title: S25Col_0Con

description: Library name: Sample-25


title: Popliteal Lymph Node, VACV-gB injection, Spatial transcriptomics, 3dpi

description: Library name: D3_PLN_SR_3dpi

value: Popliteal Lymph Node

value: Male

value: 10uL 1e5 PFU Vaccinia virus injection in the left hind and tissue collection 3dpi


title: Popliteal Lymph Node, VACV-gB injection, Spatial transcriptomics, 10dpi

description: Library name: D10_PLN_SR_10dpi

value: 10uL 1e5 PFU Vaccinia virus injection in the left hind and tissue collection 10dpi

value: 3 months


title: mCD8T:DFMO, H3K27me3, 2rep

description:
Library name: H3K27me3_Treat_2rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in


title: Popliteal Lymph Node, PBS injection, Spatial transcriptomics, 3dpi

description: Library name: Mock_PLN_SR_3dpi

value: 10uL PBS injection in the left hind and tissue collection 3dpi


title: DPT078

value: Lung

value: T cells


title: mCD8T:WT, H3K27me3, 3rep

description:
Library name: H3K27me3_Ctrl_3rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in


title: DPT083

source_name: Colon Lymph Node

value: Colon Lymph Node

value: Anti-CD3/Anti-CD28 Stimulated

value: T cells by negative selection


title: treatment_rep2_ATAC

data_processing:
The scMultiome datasets was processed by cellranger-arc version 2.0.1. The reference genome was GRCm38. cellranger-arc count was used to generated the gene and peaks feature for the libraries.
Assembly: GRCm38
Supplementary files format and content: *.filtered_feature_bc_matrix.h5 : Filtered feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells.

extract_protocol:
At 5 weeks post-vaccination, spleens were harvested from IL-27p28eGFP BCG-vaccinated mice. The spleens were then crushed through 40 µm mesh strainers and then pelleted by centrifugation at 350 x g for 5 min. Red blood cells were subsequently lysed using ACK lysis buffer (Gibco; Grand Island, NY) for 5 min and the lysis buffer was neutralized using DMEM supplemented with 10% FBS. The splenocytes were pelleted again and resuspended in buffer (1x PBS, 0.5% BSA, and 2 mM EDTA) for counting. All cells were mixed with 10 µL of FcR Blocking Reagent (Miltenyi Biotec) per 10^7 cells for 10 min at 4°C. Cells were labeled for 45 min at 4°C with 1:1500 dilution of fixable viability dye 780 (APC-Cy7) and the following antibodies (BD Biosciences; Franklin Lakes, NJ): 0.25 µg of CD3 (PE-CF594) and CD19 (PE-CF594). Live GFP+ CD3/CD19- cells were sorted with a FACSAria III Cell Sorter, collected into 10% BSA, and counted. Nuclei were then isolated from the GFP+ cells according to the 10X Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing protocol (CG000365). All steps were completed on ice.
Prepared per manufacturer's instructions (10X Genomics, 1000283; CG000338 Rev E)

value: Spleen

value: BCG Vaccinated


title: R24stm2 stm1Cd

description: Library name: Sample-24

source_name: Roots

value: Roots

value: stm2 stm1

value: Cd


title: R23stm2 stm1Cd

description: Library name: Sample-23


title: mCD8T:WT, H3K27me3 2rep

description:
Library name: H3K27me3_Ctrl_2rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in

value: CD8+ T cell

value: WT


title: treatment_rep1_ATAC


title: DPT076

source_name: Ileum

value: Ileum

value: Male

value: scRNA-seq


title: mCD8T:WT, H3K27me3, 1rep

description:
Library name: H3K27me3_Ctrl_1rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in


title: control_rep2_ATAC

value: Unvaccinated


title: R22stm2 stm1Cd

description: Library name: Sample-22


title: DPT080


title: R21stm2 stm1Con

description: Library name: Sample-21

value: Con


title: mCD8T:DFMO, H3K27ac, 3rep

description:
Library name: H3K27ac_Treat_3rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in

value: Difluoromethylornithine (DFMO) treated


title: control_rep1_ATAC


title: DPT074

value: Lung

value: T cells


title: mCD8T:DFMO, H3K27ac, 2rep

description:
Library name: H3K27ac_Treat_2rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in


title: treatment_rep2_GEX

molecule: nuclear RNA


title: R20stm2 stm1Con

description: Library name: Sample-20


title: DPT073

value: Lung Lymph Node

value: Anti-CD3/Anti-CD28 Stimulated


title: treatment_rep1_GEX

value: Spleen


title: DPT072

value: Colon Lymph Node

value: T cells by negative selection


title: mCD8T:WT, H3K27ac, 3rep

description:
Library name: H3K27ac_Ctrl_3rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in


title: control_rep2_GEX


title: R18stm2_2Cd

description: Library name: Sample-18

value: Roots


title: mCD8T:DFMO, H3K27ac, 1rep

description:
Library name: H3K27ac_Treat_1rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in


title: DPT071

value: Jejunum Lymph Node


title: DPT077

value: Colon


title: control_rep1_GEX


title: DPT070


title: R17stm2_2Cd

description: Library name: Sample-17

value: Cd


title: mCD8T:WT, H3K27ac, 2rep

description:
Library name: H3K27ac_Ctrl_2rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in

value: CD8+ T cell

value: WT


title: mCD8T:WT, H3K27ac, 1rep

description:
Library name: H3K27ac_Ctrl_1rep
Quantative Histone PTM ChIP-seq with Drosophila spike-in


title: R16stm2_2Cd

description: Library name: Sample-16


title: DPT075

value: Jejunum

value: Male

value: scRNA-seq


title: DP064

value: Female


title: E14,NCP,sp,9,2rep

description:
Library name: E14_NCP_sp_9_2rep
Native nucleosome sample, Spermine used as condensing agent

data_processing:
Bowtie2 alignment
Coverage and read counts were computed using custom python scripts
Nucleosome peak calling using custom python scripts
Condensabilities for each genomic bins and each nucleosomes were computed
Assembly: hg38 (Human), mm10 (Mouse)
Supplementary files format and content: Condensability scores for 10kb, 1kb genomic bins and individual nucleosome resolution
Library strategy: Condense-seq

source_name: E14 mESC

extract_protocol:
DNA library were prepared using NEBNext Ultra II kit
Condense-seq

treatment_protocol: Native nuclesomes were purified from cells using HAP (hydroxy apartite purification) protocol and genomic DNA were purified by phenol chloroform extraction

value: E14 mESC


title: DP063

source_name: Peyer's Patch

value: Peyer's Patch

value: T cells


title: R14stm2_2Con

description: Library name: Sample-14

value: Con


title: E14,NCP,sp,8,2rep

description:
Library name: E14_NCP_sp_8_2rep
Native nucleosome sample, Spermine used as condensing agent


title: R13stm2_2Con

description: Library name: Sample-13


title: DP062

value: Ileum

value: Anti-CD3/Anti-CD28 Stimulated


title: siBAZ2B BRACO19 Replicate 1

city: Boston

first: Tovah

middle: A.

last: Day

state: MA

address: 330 Huntington Avenue, Northeastern University Mugar Life Science Building, Room 134

department: Biology

institute: Northeastern University

description:
Library name: siBAZ2B BRACO19 Replicate 1
1bp locations of where the breaks are occuring.

data_processing:
Sequencing reads were processed as previously described. Briefly, read trimming was performed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptor sequences, followed by alignment to the human genome (hg19) using BWA-mem. Soft-clipped reads, low-quality alignments (MAPQ < 30), secondary alignments, optical duplicates and alignments mapping to the ENCODE blacklist or incomplete reference contigs were removed using samclip (https://github.com/tseemann/samclip), samtools, bedtools, and custom awk scripts. Break positions were assigned as the first 5’ nucleotide upstream of each read with respect to strand orientation to generate a BED file of every break at a single-nucleotide position. Bedtools merge was then utilized to generate a BED file of quantified single nucleotide break positions. Recurrent breaks were identified by using bedtools merge with parameter d0 and by subsequently filtering the data for locations containing more than three breaks.
Assembly: hg19
Supplementary files format and content: bed files (containing the breakends as assigned above)

source_name: lung

growth_protocol: A549 cells (ATCC, CCL-185) were cultured in DMEM (Corning, 10-013-CV) supplemented with 10% fetal bovine serum (FBS; Gibco, 10437028), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco, 15140163). All cells were cultured in a humidified incubator with  5% CO2 at 37°C.

extract_protocol:
Following the indicated transfections and optional 18 hr BRACO19 treatment, cells were harvested, resuspended in PBS, and plated at a density of 2 x 105 cells per well onto a poly-D-lysine 96-well plate. The plates were spun at 300 x g followed by incubation for 2 hr at 37°C and 5% CO2. Cells were then fixed by adding methanol-free formaldehyde at a 4% concentration and incubating for 10 min. After washing twice with PBS, the cells were stored in 200 μL PBS at 4°C until the INDUCE-seq was performed as previously described. Briefly, cells were permeabilized with Buffer 1 (1hr 4°C; 10 mM Tris-HCl, 10 mM NaCl, 1 mM EDTA, 0.2% Triton x-100) and Buffer 2 (1hr 37°C; 10 mM Tri-HCl, 150 mM NaCl, 1 mM EDTA, 0.3% SDS) with intervening PBS washes. Cells were washed with CutsmartTM buffer (NEB, B6004S) then DNA breaks were end-repaired (1 hr room temperature; Quick Blunting Kit (NEB, E1201L) plus 100 µg/mL BSA) and A- tailed (30 min 37°C; NEBNext® dA-Tailing Module; NEB, E6053L) with intervening CutsmartTM washes.
A modified p5 adapter was ligated onto A-tailed break-ends in-situ using T4 DNA ligase (16-20 hr 16°C; NEB, M0202M). Excess adapter was removed with 10 washes with wash buffer (10 mM Tris-HCl, 2 M NaCl, 2 mM EDTA, 0.5% Triton x-100), then cells were lysed in DNA extraction buffer (10 min, 37°C; 10 mM Tris-HCl, 100 mM NaCl, 50 mM EDTA, 1% SDS with addition of 1 mg/ml Proteinase K) and crosslinking was reversed (1 hr, 65°C). Genomic DNA was extracted and purified (ZR-96 Genomic Clean & Concentrator-5, Zymo), then sheared to a 300-500 bp (Covaris ME220) and size selected using CleanNGS beads (GC Biotech, CNGS-0050). DNA was end-repaired and A-tailed (NEBNext Ultra II End Repair/dA-Tailing Module, NEB E7546L) and a modified p7 adapter was ligated (NEBNext Ultra II Ligation Module, NEB E7595L) to repaired break-ends. Libraries were purified twice, and size selected using CleanNGS beads (GC Biotech, CNGS-0050). Purified libraries were quantified using qPCR (KAPA Library Quantification Kit for Illumina® Platforms (Roche, 07960255001) and 1 x 75 bp sequencing performed using a high output flow-cell on a NextSeq 550 (Illumina).

treatment_protocol: A549 cells were transfected with 71 nM siRNA using lipofectamine 3,000 transfection reagent (Fisher Scientific, L3000015) for 48 hours.

value: lung

value: epithelial cell

tag: drug


title: siBAZ2B BRACO19 Replicate 2

description:
Library name: siBAZ2B BRACO19 Replicate 2
1bp locations of where the breaks are occuring.


title: E14,NCP,sp,7,2rep

description:
Library name: E14_NCP_sp_7_2rep
Native nucleosome sample, Spermine used as condensing agent

tag: genotype


title: R19stm2 stm1Con

description: Library name: Sample-19

value: Roots

value: stm2 stm1

tag: treatment


title: siBAZ2B Vehicle Replicate 3

description:
Library name: siBAZ2B Vehicle Replicate 3
1bp locations of where the breaks are occuring.

value: Vehicle


title: DP061

description:
mRNA
InfantAdult_Tcells.scrnaseq.cts.txt

value: T cells by negative selection


title: DP060

value: Lung


title: E14,NCP,sp,6,2rep

description:
Library name: E14_NCP_sp_6_2rep
Native nucleosome sample, Spermine used as condensing agent

value: WT


title: siBAZ2B Vehicle Replicate 1

description:
Library name: siBAZ2B Vehicle Replicate 1
1bp locations of where the breaks are occuring.


title: E14,NCP,sp,5,2rep

description:
Library name: E14_NCP_sp_5_2rep
Native nucleosome sample, Spermine used as condensing agent


title: R12stm1_1Cd

description: Library name: Sample-12

value: Cd


title: siBAZ2B Vehicle Replicate 2

description:
Library name: siBAZ2B Vehicle Replicate 2
1bp locations of where the breaks are occuring.


title: R11stm1_1Cd

description: Library name: Sample-11


title: DP059

value: scRNA-seq


title: E14,NCP,sp,4,2rep

description:
Library name: E14_NCP_sp_4_2rep
Native nucleosome sample, Spermine used as condensing agent


title: DP058

value: Female


title: siBAZ2A BRACO19 Replicate 3

description:
Library name: siBAZ2A BRACO19 Replicate 3
1bp locations of where the breaks are occuring.


title: siBAZ2B BRACO19 Replicate 3

description:
Library name: siBAZ2B BRACO19 Replicate 3
1bp locations of where the breaks are occuring.


title: R15stm2_2Con

description: Library name: Sample-15


title: R9stm1_1Con

description: Library name: Sample-9


title: R10stm1_1Cd

description: Library name: Sample-10


title: E14,NCP,sp,3,2rep

description:
Library name: E14_NCP_sp_3_2rep
Native nucleosome sample, Spermine used as condensing agent

value: E14 mESC


title: DP057

value: Jejunum


title: siBAZ2A BRACO19 Replicate 2

description:
Library name: siBAZ2A BRACO19 Replicate 2
1bp locations of where the breaks are occuring.


title: R8stm1_1Con

description: Library name: Sample-8


title: E14,NCP,sp,2,2rep

description:
Library name: E14_NCP_sp_2_2rep
Native nucleosome sample, Spermine used as condensing agent


title: DP056

value: Jejunum Lymph Node

value: T cells


title: E14,NCP,sp,1,2rep

description:
Library name: E14_NCP_sp_1_2rep
Native nucleosome sample, Spermine used as condensing agent


title: DP055

source_name: Lung Lymph Node

value: Lung Lymph Node


title: R7stm1_1Con

description: Library name: Sample-7

value: Con


title: E14,NCP,sp,0,2rep

description:
Library name: E14_NCP_sp_0_2rep
Native nucleosome sample, Spermine used as condensing agent


title: R6Col_0Cd

description: Library name: Sample-6


title: siBAZ2A Vehicle Replicate 2

description:
Library name: siBAZ2A Vehicle Replicate 2
1bp locations of where the breaks are occuring.

value: lung


title: DP054

source_name: Blood

value: Blood

value: Anti-CD3/Anti-CD28 Stimulated


title: mCD8T:ODCKO,NCP,sp,9,2rep

description:
Library name: mCD8T:ODCKO_NCP_sp_9_2rep
Native nucleosome sample, Spermine used as condensing agent

value: CD8+ T cell

value: Ornithine decarboxylase (ODC) knockout


title: R4Col_0Cd

description: Library name: Sample-4

value: Roots


title: R5Col_0Cd

description: Library name: Sample-5


title: siControl BRACO19 Replicate 3

description:
Library name: siControl BRACO19 Replicate 3
1bp locations of where the breaks are occuring.

value: epithelial cell

value: siControl


title: mCD8T:ODCKO,NCP,sp,8,2rep

description:
Library name: mCD8T:ODCKO_NCP_sp_8_2rep
Native nucleosome sample, Spermine used as condensing agent


title: DP052

description:
mRNA
InfantAdult_Tcells.scrnaseq.cts.txt

value: T cells by negative selection


title: siBAZ2A Vehicle Replicate 1

description:
Library name: siBAZ2A Vehicle Replicate 1
1bp locations of where the breaks are occuring.

value: Vehicle


title: siControl BRACO19 Replicate 2

description:
Library name: siControl BRACO19 Replicate 2
1bp locations of where the breaks are occuring.


title: DP051

value: Female

value: scRNA-seq


title: R2Col_0Con

description: Library name: Sample-2


title: siControl BRACO19 Replicate 1

description:
Library name: siControl BRACO19 Replicate 1
1bp locations of where the breaks are occuring.


title: DP050


title: R1Col_0Con

description: Library name: Sample-1


title: siBAZ2A BRACO19 Replicate 1

description:
Library name: siBAZ2A BRACO19 Replicate 1
1bp locations of where the breaks are occuring.


title: mCD8T:ODCKO,NCP,sp,5,2rep

description:
Library name: mCD8T:ODCKO_NCP_sp_5_2rep
Native nucleosome sample, Spermine used as condensing agent


title: siControl Vehicle Replicate 3

description:
Library name: siControl Vehicle Replicate 3
1bp locations of where the breaks are occuring.


title: siBAZ2A Vehicle Replicate 3

description:
Library name: siBAZ2A Vehicle Replicate 3
1bp locations of where the breaks are occuring.


title: DP049

source_name: Spleen

value: Spleen


title: siControl Vehicle Replicate 2

description:
Library name: siControl Vehicle Replicate 2
1bp locations of where the breaks are occuring.


title: DH016


title: MEF_IP-3KO-VSV-INF-2-B

description: Library name: EV255_IP

source_name: Mouse Embryonic Fibroblast

value: Mouse Embryonic Fibroblast

value: VSV infected

value: Interferon treated


title: MEF_INPUT-3KO-VSV-INF-B

description: Library name: EV255_input


title: mCD8T:ODCKO,NCP,sp,3,2rep

description:
Library name: mCD8T:ODCKO_NCP_sp_3_2rep
Native nucleosome sample, Spermine used as condensing agent


title: siControl Vehicle Replicate 1

description:
Library name: siControl Vehicle Replicate 1
1bp locations of where the breaks are occuring.


title: DH015

value: T cells


title: DP053


title: mCD8T:ODCKO,NCP,sp,2,2rep

description:
Library name: mCD8T:ODCKO_NCP_sp_2_2rep
Native nucleosome sample, Spermine used as condensing agent


title: TAF1C_3

city: ropar

first: srivatsava

last: naidu

state: punjab

address: bhara phool

department: biomedical engineering

country: India

institute: indian institute of technology ropar

data_processing:
Adaptor trimming using Trimmomatic-0.36, Contamination removal using Bowtie2 (version 2.2.4)
Read alignment to hg19 genome using HISAT2, miRDeep2 for miRNA reads alignment and piRBase for piRNA alignment
Expression estimation using cufflinks (version 2.2.1) and Randfold
Differential expression using DESeq2
miRNA target prediction using Miranda with query identity percentage of 100
Assembly: hg19
Supplementary files format and content: .txt file, content : raw read counts

source_name: BEAS-2B cell line

growth_protocol: BEAS-2B cell line cultured in LHC9 media supplemented with 10% FBS, stable cells cultured with G418 selection media

extract_protocol:
mirVana RNA isolation kit for RNA isolation
NEBNext RNA Ultra for long RNA libraries with ribo depletion, NEBNext Multiplex small RNA library prep kit for small RNA libraries

treatment_protocol: BEAS-2B cell line treated with empty vector and TAF1C vector with pCMV6 promoter, stable cells generated and maintained in selection media

value: TAF1C overexpression


title: mCD8T:ODCKO,NCP,sp,1,2rep

description:
Library name: mCD8T:ODCKO_NCP_sp_1_2rep
Native nucleosome sample, Spermine used as condensing agent


title: TAF1C_2


title: MEF_IP-3KO-VSV-INF-3-A

description: Library name: EV252_IP


title: R3Col_0Con

description: Library name: Sample-3

value: Con


title: mCD8T:ODCKO,NCP,sp,6,2rep

description:
Library name: mCD8T:ODCKO_NCP_sp_6_2rep
Native nucleosome sample, Spermine used as condensing agent


title: DH013

value: Colon


title: mCD8T:ODCKO,NCP,sp,7,2rep

description:
Library name: mCD8T:ODCKO_NCP_sp_7_2rep
Native nucleosome sample, Spermine used as condensing agent

value: CD8+ T cell


title: mCD8T:ODCKO,NCP,sp,0,2rep

description:
Library name: mCD8T:ODCKO_NCP_sp_0_2rep
Native nucleosome sample, Spermine used as condensing agent

value: Ornithine decarboxylase (ODC) knockout


title: TAF1C_1


title: mCD8T:DFMO,NCP,sp,9,2rep

description:
Library name: mCD8T:DFMO_NCP_sp_9_2rep
Native nucleosome sample, Spermine used as condensing agent

value: WT

value: Difluoromethylornithine (DFMO) treated


title: eV_2

value: Empty vector


title: MEF_IP-3KO-INF-3-A

description: Library name: EV250_IP

value: uninfected


title: mCD8T:DFMO,NCP,sp,8,2rep

description:
Library name: mCD8T:DFMO_NCP_sp_8_2rep
Native nucleosome sample, Spermine used as condensing agent


title: mCD8T:ODCKO,NCP,sp,4,2rep

description:
Library name: mCD8T:ODCKO_NCP_sp_4_2rep
Native nucleosome sample, Spermine used as condensing agent


title: MEF_IP-3KO-VSV-INF-2-A

description: Library name: EV251_IP


title: DH012

description:
mRNA
InfantAdult_Tcells.scrnaseq.cts.txt

value: Jejunum Lymph Node

value: Anti-CD3/Anti-CD28 Stimulated

value: T cells by negative selection


title: MEF_INPUT-3KO-VSV-INF-A

description: Library name: EV251_input


title: DH008

value: Ileum

value: Female

value: scRNA-seq


title: MEF_IP-3KO-INF-2-A

description: Library name: EV249_IP

value: Mouse Embryonic Fibroblast

value: Interferon treated


title: mCD8T:DFMO,NCP,sp,7,2rep

description:
Library name: mCD8T:DFMO_NCP_sp_7_2rep
Native nucleosome sample, Spermine used as condensing agent


title: MEF_IP-3KO-INF-3-B

description: Library name: EV254_IP


title: Popliteal Lymph Node, VACV-gB injection, Long read, 21dpi

description: Library name: D21_PLN_LR_21dpi

value: Popliteal Lymph Node

value: Male

value: 10uL 1e5 PFU Vaccinia virus injection in the left hind and tissue collection 21dpi

value: 3 months


title: DH014

value: Colon

value: T cells


title: mCD8T:DFMO,NCP,sp,6,2rep

description:
Library name: mCD8T:DFMO_NCP_sp_6_2rep
Native nucleosome sample, Spermine used as condensing agent

value: CD8+ T cell

value: WT

value: Difluoromethylornithine (DFMO) treated


title: MEF_INPUT-3KO-INF-A

description: Library name: EV249_input

value: uninfected


title: DH006

value: Jejunum

value: Anti-CD3/Anti-CD28 Stimulated


title: MEF_IP-2KO-VSV-INF-3-B

description: Library name: EV248_IP

value: VSV infected


title: Popliteal Lymph Node, VACV-gB injection, Long read, 14dpi

description: Library name: D14_PLN_LR_14dpi

value: 10uL 1e5 PFU Vaccinia virus injection in the left hind and tissue collection 14dpi


title: mCD8T:DFMO,NCP,sp,5,2rep

description:
Library name: mCD8T:DFMO_NCP_sp_5_2rep
Native nucleosome sample, Spermine used as condensing agent


title: Popliteal Lymph Node, VACV-gB injection, Long read, 10dpi

description: Library name: D10_PLN_LR_10dpi

value: 10uL 1e5 PFU Vaccinia virus injection in the left hind and tissue collection 10dpi


title: DH005

value: Female

value: T cells by negative selection

value: scRNA-seq


title: mCD8T:DFMO,NCP,sp,4,2rep

description:
Library name: mCD8T:DFMO_NCP_sp_4_2rep
Native nucleosome sample, Spermine used as condensing agent


title: MEF_IP-2KO-VSV-INF-2-B

description: Library name: EV247_IP

value: Mouse Embryonic Fibroblast

value: Interferon treated


title: Popliteal Lymph Node, VACV-gB injection, Long read, 7dpi

description: Library name: D7_PLN_LR_7dpi

value: Popliteal Lymph Node

value: Male

value: 10uL 1e5 PFU Vaccinia virus injection in the left hind and tissue collection 7dpi

value: 3 months


title: DH004

source_name: Lung

value: Lung

value: T cells


title: MEF_INPUT-2KO-VSV-INF-B

description: Library name: EV247_input


title: DH011

value: Jejunum Lymph Node


title: mCD8T:DFMO,NCP,sp,3,2rep

description:
Library name: mCD8T:DFMO_NCP_sp_3_2rep
Native nucleosome sample, Spermine used as condensing agent

value: CD8+ T cell

value: WT

value: Difluoromethylornithine (DFMO) treated


title: Popliteal Lymph Node, VACV-gB injection, Long read, 3dpi

description: Library name: D3_PLN_LR_3dpi

source_name: Popliteal Lymph Node

value: 10uL 1e5 PFU Vaccinia virus injection in the left hind and tissue collection 3dpi


title: DH003


title: MEF_IP-2KO-INF-3B

description: Library name: EV246_IP

value: uninfected


title: eV_1

value: Empty vector


title: DH007

value: Ileum

value: Female

value: T cells by negative selection


title: MEF_IP-2KO-INF-2B

description: Library name: EV245_IP

value: Mouse Embryonic Fibroblast

value: Interferon treated


title: mCD8T:DFMO,NCP,sp,1,2rep

description:
Library name: mCD8T:DFMO_NCP_sp_1_2rep
Native nucleosome sample, Spermine used as condensing agent


title: mCD8T:DFMO,NCP,sp,2,2rep

description:
Library name: mCD8T:DFMO_NCP_sp_2_2rep
Native nucleosome sample, Spermine used as condensing agent


title: Popliteal Lymph Node, PBS injection, Long read, 3dpi

description: Library name: Mock_PLN_LR_3dpi

value: Popliteal Lymph Node

value: Male

value: 10uL PBS injection in the left hind and tissue collection 3dpi


title: DH001

value: Lung Lymph Node

value: scRNA-seq


title: MEF_INPUT-2KO-INF-B

description: Library name: EV245_input


title: 44

city: changsha

first: Zhaoyu

last: Yang

address: 87 of xiangya road

institute: xiangya hospital

data_processing:
Use the total RNA of each sample to prepare a miRNA sequencing library, including the following steps: 1) 3' connector connection; 2) 5' connector connection; 3) cDNA synthesis; 4) PCR amplification; 5) Select 135~155bp PCR amplified fragments.
The library was denatured into single-stranded DNA molecules, captured on an Illumina flow cell, amplified into clusters in situ, and performed 51 cycles of sequencing on the Illumina NextSeq 500 sequencer according to the supplier’s instructions.
The Illumina sequencer generates the original sequence in FASTQ format. To evaluate the quality of sequencing, the original sequence of each sample will be counted Q30:Q30=-10log10(P).
After sequencing quality control, the original data QC is preprocessed (using cutadapt to remove the 3' linker sequence and filtering out short fragments ≤ 15bp) to obtain trimmed reads, which are compared to the reference genome using bowtie.
Assembly: mm9
Supplementary files format and content: processed-1.xlsx: The Excel file contains the CPM value of gene in every sample.

source_name: hippocampus

extract_protocol:
Briefly, using TRIzol reagent to extract the total RNA from the hippocampus in accordance with the manufacturer’s instructions.
The NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, MA, USA) was used to establish an RNA library and assessed the RNA library quality and quantity via Agilent 2100 Bioanalyzer. The RNA library was used for sequence analysis. The sequence analysis was conducted by a NextSeq 500 platform (Illumina, CA, USA). The clean reads were filtered out from raw reads by FastQC and selected for further bioinformatics analysis.

value: hippocampus

value: post XFZYD treatment day 14

value: XFZYD


title: DP110

source_name: Colon

value: Colon

value: T cells

value: Anti-CD3/Anti-CD28 Stimulated


title: mCD8T:DFMO,NCP,sp,0,2rep

description:
Library name: mCD8T:DFMO_NCP_sp_0_2rep
Native nucleosome sample, Spermine used as condensing agent

source_name: CD8+ T cell

value: CD8+ T cell

value: WT

value: Difluoromethylornithine (DFMO) treated


title: MEF_IP-2KO-VSV-INF-3A

description: Library name: EV244_IP

value: VSV infected


title: mCD8T:WT,NCP,sp,9,2rep

description:
Library name: mCD8T:WT_NCP_sp_9_2rep
Native nucleosome sample, Spermine used as condensing agent


title: 43


title: 36

value: TBI


title: DP109

value: T cells by negative selection


title: MEF_IP-2KO-VSV-INF-2A

description: Library name: EV243_IP

value: Mouse Embryonic Fibroblast

value: Interferon treated


title: DP108

source_name: Jejunum

value: Jejunum

value: Male


title: 35


title: mCD8T:WT,NCP,sp,7,2rep

description:
Library name: mCD8T:WT_NCP_sp_7_2rep
Native nucleosome sample, Spermine used as condensing agent


title: MEF_INPUT-2KO-VSV-INF-A

description: Library name: EV243_input


title: 33


title: DP107

value: scRNA-seq


title: MEF_IP-2KO-INF-3A

description: Library name: EV242_IP

value: uninfected


title: mCD8T:WT,NCP,sp,6,2rep

description:
Library name: mCD8T:WT_NCP_sp_6_2rep
Native nucleosome sample, Spermine used as condensing agent


title: DH002

value: Lung Lymph Node

value: Female


title: 28

value: hippocampus

value: post XFZYD treatment day 14

value: XFZYD


title: DP106

source_name: Jejunum Lymph Node

value: Jejunum Lymph Node

value: T cells

value: Anti-CD3/Anti-CD28 Stimulated


title: MEF_IP-2KO-INF-2A

description: Library name: EV241_IP


title: 27


title: 26


title: mCD8T:WT,NCP,sp,4,2rep

description:
Library name: mCD8T:WT_NCP_sp_4_2rep
Native nucleosome sample, Spermine used as condensing agent

value: CD8+ T cell

value: WT


title: DP105

value: T cells by negative selection


title: MEF_IP-WT-VSV-INF-3B

description: Library name: EV240_IP

value: Mouse Embryonic Fibroblast

value: VSV infected


title: mCD8T:WT,NCP,sp,5,2rep

description:
Library name: mCD8T:WT_NCP_sp_5_2rep
Native nucleosome sample, Spermine used as condensing agent


title: DP104

value: Spleen


title: mCD8T:WT,NCP,sp,3,2rep

description:
Library name: mCD8T:WT_NCP_sp_3_2rep
Native nucleosome sample, Spermine used as condensing agent


title: MEF_INPUT-2KO-INF-A

description: Library name: EV241_input

value: Interferon treated


title: 21

value: TBI


title: mCD8T:WT,NCP,sp,2,2rep

description:
Library name: mCD8T:WT_NCP_sp_2_2rep
Native nucleosome sample, Spermine used as condensing agent


title: 20


title: DP102

value: Blood

value: Male

value: scRNA-seq


title: MEF_IP-WT-VSV-3-B

description: Library name: EV239_IP

value: untreated


title: mCD8T:WT,NCP,sp,8,2rep

description:
Library name: mCD8T:WT_NCP_sp_8_2rep
Native nucleosome sample, Spermine used as condensing agent


title: IgG_GV_2_Laceseq

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

description: RIP-Seq RNA

data_processing:
The analysis pipeline of LACE-seq data was also the same as described in the work by Su Ruibao et.al with a little adjusted. In brief, Cutadapt (v.1.18) was used to remove the adapter sequences, the polyA tail in the 3’-UTR and the two bases inserted between adapter and the reads with parameters as follow: -f fastq -q 30,0 -a ATCTCGTATGCCGTCTTCTGCTT -m 18 --max-n 0.25 --trim-n; -f fastq -a A{15} -m 18 -n 2; -f fastq -u 5. The trimmed reads were then mapped to the mouse pre-rRNA genome by Bowtie2 (v.2.3.5.1), and the remaining reads were finally mapped to mm10 genome by Bowtie2 with basic parameters. The output SAM files were transfered to BAM files with Samtools (v.1.0.0) and the duplicating reads were then removed by Sambamba (v.0.7.1). The remained clean reads were used for visualization, peak calling and calculating count of certain genes.
For visualization, the deeptools (v3.5.2) were used to transfer BAM files into BigWig format with parameters as follow: bamCoverage -bs 10, and the IGV software(v.2.14.0) were used to visualize the reads
For peakcalling and annotation, the reads overlapped to the repeat genome (https://www.repeatmasker.org/species/mm.html) were removed by using bedtools (v.2.26.0) because ~37% of the reads can be annotated into the repeat sequence in subsequent analysis (not mentioned in the article). Then macs2 (v2.2.8) were used with parameters: callpeak -f BED --keep-dup all --fe-cutoff 5 -p 0.001 --extsize 151 --nomodel -g mm, and ChIPseeker (v.1.5.1) were used to annotate the peaks.
For calculating count, the BAM files were used to quantified reads by using FeatureCounts (v2.0.2). The ration between the counts of WT and NC is considered to be the binding strength of ZAR1.
Assembly: mm10
Supplementary files format and content: Zar1-KO_IgG_merge.bin10.bw
Supplementary files format and content: Zar1-WT_merge.bin10.bw

source_name: Oocytes

extract_protocol:
2 μg per sample ZAR1 antibody was coupled to the activated protein A/G magnetic beads. Then 30 GV stage oocytes were harvested from WT and Zar1/2-/- female mice as described and were irradiated twice with UV-C light on ice at 400 mJ for RBP-RNA crosslinking. Afterwards, the cells were lysed on ice, and the antibody-coupled beads were added to the lysate, and the ZAR1 target RNA was then immunoprecipitated by beads and fragmented by MNase.
Then the RNA dephosphorylation and the first-strand synthesis of RT were both performed on beads, and the 3’ linker and biotin-carried T7-RT primer w be added to the RNA at this step. Then the first-strand cDNA was released and captured by streptavidin beads, and the followed polyA tailing and pre-amplification were both performed on beads, and the products were purified for further in vitro transcription (IVT). After IVT amplificating, the DNA template would be removed, and the remaining RNA was purified for further RT and PCR barcoding.

value: Oocytes


title: DP101

description:
mRNA
InfantAdult_Tcells.scrnaseq.cts.txt


title: mCD8T:WT,NCP,sp,0,2rep

description:
Library name: mCD8T:WT_NCP_sp_0_2rep
Native nucleosome sample, Spermine used as condensing agent


title: MEF_IP-WT-NO-INF-3-B

description: Library name: EV237_IP

data_processing:
Standard processing of eCLIP data was performed as previously described (Blue SB, et al. Nature Protocols 2022), with mapping performed to a custom genome index that included both the VSV genome and either hg19 (for 293T experiments) or mm10 (for MEF experiments) as described below.
UMI removal and cut adapt:  umi_tools extract   --random-seed 1   --bc-pattern NNNNNNNNNN   --stdin 23145FL-08-01-37_S37_L001_R1_001.fastq.gz   --log /dev/null | cutadapt   -j 8   --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 1   -   --report minimal   2> EV225_IP.cut.adapt.log | cutadapt   -j 8  --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 5   -   -o EV225_IP.trim.gz   --report minimal   >>EV225_IP.cut.adapt.log
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping:     STAR     --runMode alignReads     --runThreadN 8     --alignEndsType EndToEnd     --genomeDir  [mus_musculus_repbase_v2 or homo_sapiens_repbase_v2]   --genomeLoad NoSharedMemory     --outBAMcompression 10     --outFileNamePrefix EV225_IP.repeat.map     --outFilterMultimapNmax 100     --outFilterMultimapScoreRange 1     --outFilterScoreMin 10     --outFilterType BySJout     --outReadsUnmapped Fastx    --outSAMattrRGline ID:foo     --outSAMattributes All     --outSAMmode Full     --outSAMtype BAM Unsorted     --outSAMunmapped None     --outStd Log     --readFilesCommand zcat     --readFilesIn EV225_IP.trim.gz
Unique genomic mapping (takes repeat-removed reads and maps to the reference genome: STAR   --runMode alignReads   --runThreadN 8   --alignEndsType EndToEnd   --genomeDir [hg19+VSV or mm10+VSV] --genomeLoad NoSharedMemory   --outBAMcompression 10   --outFileNamePrefix EV225_IP.genome.map   --outFilterMultimapNmax 1   --outFilterMultimapScoreRange 1   --outFilterScoreMin 10   --outFilterType BySJout   --outReadsUnmapped Fastx   --outSAMattrRGline ID:foo   --outSAMattributes All   --outSAMmode Full   --outSAMtype BAM Unsorted   --outSAMunmapped None   --outStd Log   --readFilesIn EV225_IP.repeat.mapUnmapped.out.mate1
Sort mapped reads: samtools sort -@ 8 -m 2G -o EV225_IP.genome.map.bam *Aligned.out.bam
Remove PCR duplicate reads: samtools index EV225_IP.genome.map.bam umi_tools dedup   --random-seed 1   --stdin EV225_IP.genome.map.bam   --method unique   --stdout EV225_IP.bam
Make bigwigs: samtools index EV225_IP.bam b2bw EV225_IP.bam  --cpus 1
Isolate VSV-mapped reads only: bigWigToWig EV225.pos.bw -chrom=chrVSV EV225.pos.bw.chrVSV.wig
wigToBigWig EV225.pos.bw.chrVSV.wig /path/to/hg19_and_vsv.chrom.sizes EV242.pos.bw.chrVSV.wig.bw
Assembly: hg19 (for 293T) or mm10 (for MEF) with the addition of VSV (using accession NC_001560.1 with GFP was inserted between G and L as described in PMID 10400792)
Supplementary files format and content: bw files contain read density (in bigwig format) for the VSV genome (positive or negative strand as indicated in filename). Bigwig files are not included for datasets with zero reads

extract_protocol:
eCLIP was performed as previously described (Blue SB, et al. Nature Protocols 2022). Briefly, 10 million 293T or MEF cells were UV crosslinked (254 nM, 400 mJ/cm2), snap frozen, and lysed as previously described.
RNA fragmentation was performed, 2% of the sample was removed for size-matched input, and the remainder was subjected to immunoprecipitation of IFIT-bound RNA with antibodies against FLAG (M2 / F1804, Sigma) and HA (HA.11 / 901502, Biolegend) for 293T experiments, and IFIT2 (PA3-845, ThermoFisher) and IFIT3 (ABF1048, Millipore) for MEF experiments. Dephosphorylation, RNA adapter ligation, SDS-PAGE electrophoresis and nitrocellulose membrane transfer, RNA isolation, reverse transcription, and PCR amplification were performed as previously described (Blue, SM. et al, Nat Protocols 2022). Libraries are as previously described for eCLIP (Blue, SM. et al, Nat Protocols 2022), based on the Illumina RNA TruSeq HT adapter strategy.

value: uninfected


title: IgG_GV_1_Laceseq

description: RIP-Seq RNA


title: MEF_IP-WT-VSV-INF-2-B

description: Library name: EV236_IP


title: DF008

data_processing:
For scRNA-seq, we aligned the reads corresponding to each sample index to the GRCh38 genome / GENCODE v.24 transcriptome annotation with STAR v2.5.0 (23104886) after removing 3’ poly(A) tails from read 2 (anything >7 A’s) and discarding any resulting fragments < 25 nts in length.
We then constructed an address for each read with a unique, strand-specific, exonic alignment comprised of the cell-identifying barcode, unique molecular identifier (UMI) barcode, and gene identifier.
Next, we applied the algorithm described by Griffiths et al. to correct of index swapping between clusters on the Illumina flow cell (29991676). Finally, we collapsed PCR duplicates using UMIs and corrected errors in both the cell-identifying and UMI barcodes to generate an initial molecular count matrix.
To identify cell barcodes associated with cells, we used the EmptyDrops algorithm (Lun et al., Genome Biol, 2019) and then further filtered the resulting count matrix to remove cells above of the 95% confidence interval for the fraction of molecules aligned to the mitochondrial genome (possible dead cells), the fraction of molecules aligned to introns (possible nuclei), and the number of molecules per gene (filters red blood cells and other artifacts). We also pre-emptively removed cells with sufficiently low coverage that they would interfere with unsupervised clustering. To identify highly variable genes for clustering, we use the drop-out curve method previously described (Levitin et al., Mol Sys Bio, 2019), removing all cells in which fewer than three highly variable genes were detected.
For bulk RNA-seq, adapter-trimmed paired-end reads were aligned to the GRCh38 reference genome with ENSEMBL transcriptome annotation using the STAR aligner v.2.5.2b. Read quantification was performed using the featureCounts program in the Subread v.1.5.2 package.
Genome_build: GRCh38
Supplementary_files_format_and_content: InfantAdult_Tcells.scrnaseq.cts.txt: For scRNA-seq, the processed data are in a single, tab-delimited text file that contains the gene expression counts for each individual cell.
Supplementary_files_format_and_content: *.counts.txt: For each bulk RNA-seq sample, there is a tab-delimited text file containing the output of featureCounts.

extract_protocol:
For single-cell RNA-seq, RNA was extracted and poly(A) mRNA was converted into barcoded cDNA using the 10x Genomics Chromium platform. For bulk RNA-seq, RNA was extracted using the Qiagen RNeasy Micro Kit.
Single-cell RNA-seq libraries were constructed using the 10x Genomics Single Cell Gene Expression 3' v2 chemistry for donors D363, D370, Adult Donor A, Adult Donor B, HDL049, HDL055, D381 and the 10x Genomics Single Cell Gene Expression 3' v3 chemistry for donors D457, D471, HDL082. For bulk RNA-seq, library preparation was done using the SMART-Seq® ultra-low input RNA kit (Takara bio).

value: Colon


title: E14,NCP,sp,9,1rep

description:
Library name: E14_NCP_sp_9_1rep
Native nucleosome sample, Spermine used as condensing agent

value: E14 mESC


title: KO_GV_2_Laceseq

description: RIP-Seq RNA


title: KO_GV_1_Laceseq

description: RIP-Seq RNA


title: E14,NCP,sp,8,1rep

description:
Library name: E14_NCP_sp_8_1rep
Native nucleosome sample, Spermine used as condensing agent


title: DF005

value: Jejunum

value: T cells


title: MEF_INPUT-WT-VSV-INF-B

description: Library name: EV236_input

value: WT


title: WT_GV_4_Laceseq

description: RIP-Seq RNA


title: DF006

value: Anti-CD3/Anti-CD28 Stimulated

value: T cells by negative selection


title: E14,NCP,sp,7,1rep

description:
Library name: E14_NCP_sp_7_1rep
Native nucleosome sample, Spermine used as condensing agent


title: MEF_INPUT-WT-VSV-B

description: Library name: EV235_input

value: Mouse Embryonic Fibroblast

value: VSV infected


title: DP103

value: Spleen


title: WT_GV_2_Laceseq

description: RIP-Seq RNA


title: WT_GV_3_Laceseq

description: RIP-Seq RNA


title: DF002

value: Jejunum Lymph Node


title: MEF_IP-WT-VSV-2-B

description: Library name: EV235_IP


title: DF003

value: Blood


title: mCD8T:WT,NCP,sp,1,2rep

description:
Library name: mCD8T:WT_NCP_sp_1_2rep
Native nucleosome sample, Spermine used as condensing agent

value: CD8+ T cell


title: MEF_INPUT-WT-INF-B

description: Library name: EV234_input

value: Interferon treated


title: WT_GV_1_Laceseq

description: RIP-Seq RNA


title: MEF_IP-WT-INF-3-B

description: Library name: EV238_IP


title: E14,NCP,sp,5,1rep

description:
Library name: E14_NCP_sp_5_1rep
Native nucleosome sample, Spermine used as condensing agent


title: DF001

value: Male

value: scRNA-seq


title: DF004


title: MEF_IP-WT-INF-2-B

description: Library name: EV234_IP

value: uninfected


title: MEF_IP-WT-NO-INF-2-B

description: Library name: EV233_IP

value: untreated


title: E14,NCP,sp,3,1rep

description:
Library name: E14_NCP_sp_3_1rep
Native nucleosome sample, Spermine used as condensing agent

value: E14 mESC


title: MEF_INPUT-WT-NO-INF-B

description: Library name: EV233_input


title: E14,NCP,sp,6,1rep

description:
Library name: E14_NCP_sp_6_1rep
Native nucleosome sample, Spermine used as condensing agent


title: E14,NCP,sp,2,1rep

description:
Library name: E14_NCP_sp_2_1rep
Native nucleosome sample, Spermine used as condensing agent


title: Pat15.BL_1

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description: Library name: Sample 14

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.4 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.3 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Contrasts were created with DESeq2 based on the raw count matrix.
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: Right ventricular myocardial free wall biopsy

extract_protocol:
RNA isolation was performed with Qiagen miRNeasy micro Kit and Biozym bead bug 3 Homogenizer
100ng-1µg total RNA was used for Hi-Mammalian whole transcriptome preparation (Takara Bio). Sequencing was performed on Nextseq500 with 1x72bp single-end setup.

tag: esc risk_group

value: Intermediate

value: prePEA


title: Pat56.BL_1

description: Library name: Sample 13

value: Right ventricular myocardial free wall biopsy

value: Female


title: E14,NCP,sp,1,1rep

description:
Library name: E14_NCP_sp_1_1rep
Native nucleosome sample, Spermine used as condensing agent

source_name: E14 mESC

tag: cell line

value: WT


title: Pat9.BL_1

description: Library name: Sample 12


title: MEF_IP-WT-VSV-INF-3-A

description: Library name: EV232_IP

tag: cell type

value: Mouse Embryonic Fibroblast


title: E14,NCP,sp,4,1rep

description:
Library name: E14_NCP_sp_4_1rep
Native nucleosome sample, Spermine used as condensing agent


title: MEF_IP-WT-VSV-3-A

description: Library name: EV231_IP

value: VSV infected


title: E14,NCP,sp,0,1rep

description:
Library name: E14_NCP_sp_0_1rep
Native nucleosome sample, Spermine used as condensing agent


title: Pat69.BL_1

description: Library name: Sample 10


title: mCD8T:ODCKO,NCP,sp,9,1rep

description:
Library name: mCD8T:ODCKO_NCP_sp_9_1rep
Native nucleosome sample, Spermine used as condensing agent

value: Ornithine decarboxylase (ODC) knockout


title: Pat98.BL_1

description: Library name: Sample 11


title: MEF_IP-WT-NO-INF-3-A

description: Library name: EV229_IP


title: MEF_IP-WT-INF-3-A

description: Library name: EV230_IP


title: mCD8T:ODCKO,NCP,sp,8,1rep

description:
Library name: mCD8T:ODCKO_NCP_sp_8_1rep
Native nucleosome sample, Spermine used as condensing agent


title: PM381_strom

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

description:
Library name: M20219
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

data_processing:
Raw sequencing reads were trimmed to remove the UMI, Illumina TruSeq 3’ adapter sequence, and all nucleotides after the 3’ adapter. Pre-processed reads were aligned to the genome for seven small non-coding RNAs using the miRMaster2 online tool. Raw read counts were processed using R. Data was batch-corrected using COMBAT-seq. Low quality samples and sequences were removed, and data was normalized per sncRNA species separately using the Relative Log Expression (RLE) method and scaled by counts per million (CPM).
Assembly: hg38
Supplementary files format and content: Raw count matrix of all samples before quality control and normalization

source_name: placenta

extract_protocol:
Sorted cells were isolated from fresh chorionic villi using FACS as described in GSE159526. Sorted cells and chorionic villi samples were extracted using the ZYMO Quick-RNA MiniPrep kit according to manufacturer’s instructions or using TRIzol (ThermoFisher Scientific, USA).
5.8S rRNA was masked during adapter ligation by a complementary oligonucleotide, while miRNAs underwent 3′ adapter ligation, digestion of unligated adapters, and 5′ adapter ligation sequentially. The 5′ adapter contains a unique molecular identifier (UMI), followed by two nucleotides (CA) prior to the miRNA sequence. Upon conversion to cDNA by reverse transcription, the cDNA was amplified by PCR to include the sequences required for Illumina cluster generation and sample indexing developed by the GSC. The number of PCR cycles was dependent on the amount of input RNA; samples with low and high input were subjected to 20 and 15 cycles of PCR, respectively. Quality of libraries was assessed using the Agilent Bioanalyzer 2100 HS DNA chip Assay, (Agilent, USA)

treatment_protocol: All samples were stored in RNAlater (ThermoFisher Scientific, USA) upon sampling and prior to extraction

tag: case id

value: placenta

value: Stromal

tag: gestational age

tag: trimester

value: Term

tag: fetal sex

tag: plate

tag: extraction type

value: Sorted-cells:Zymo Quick-RNA Miniprep