title: BCR sequences from T-antigen-specific and B cells of unknown specificity from Merkel cell carcinoma patient tumors

city: Seattle

first: Haroldo

middle: Jose

last: Rodriguez

state: WA

address: 850 Republican St

department: Medicine

institute: University of Washington

description: Library name: MCC_BCR_sequences

data_processing:
Raw sequencing reads were aligned to the hg38 genome using Cell Ranger v.8.0.1. Filtered counts matrices of transcripts and feature barcoding counts were loaded into a SingleCellExperiment object for further analyses in R (v.4.1.2). Sample hash deconvolution was performed using DropletUtils (v.1.14.2). Doublets were detected using scds (v.1.10.0) and hash deconvolution and subsequently removed. Cells from different runs were then integrated using the mutual nearest neighbor method though the batchelor package (v1.10.0). UMAP dimensionality reduction was performed using the integrated values. Clustering was performed using the integrated transcript values reads through the walktrap algorithm on a nearest neighbor graph (scran v.1.22.1). Numbers of clusters was varied by scaling the number of nearest neighbors (k) during graph construction followed by analysis via clustree (v.0.5.0). Clusters were then labeled as major cell lineages of T cells, B cells, myeloid cells, epithelial cells, dendritic cells, and tumor cells through expression of key genes including CD79A, CLEC4C, COL3A1, NCAM1, CD14, and CD3E. Cluster labels were then validated by investigating the portion of cluster with productive BCR or TCR rearrangements. Cell lineages were then isolated in silico and dimensionality reduction and B cells and CD4+ T cells re-clustered as above. Clusters were labeled based on expression of lineage markers. To identify T-Ag-specific B cells in tumors, we analyzed T-Ag oligo reads and control antigen oligo reads in B cells. T-Ag-specific CD19+ B cells were defined as cells with T-Ag oligo reads at least one log higher than background and fewer than 20 reads from GST or RSV F control antigens. Additionally, eight B cell families in which fewer than 50% of clones met this threshold were classified as non-specific.
Raw output files were demultiplexed and processed using CellRanger v.8.0.1 software (10X Genomics). For each donor, publicly available reference sequences from the IMGT/V-QUEST reference directory at https://www.imgt.org/ were used to identify V, D, and J gene segments. Next, data were processed and analyzed using the Immcantation Framework (http://immcantation.org) with Change-O v.1.0.2. For each 10X dataset, the filtered_contig.fasta file was annotated using IgBlast v.1.16 with the related donor-specific VJ genes database. To generate adaptive immune receptor repertoire (AIRR) rearrangement data, the filtered_contig_annotations.csv file was used, and only productive sequences were kept. The heavy and light chain sequences were separated in two files. The threshold for trimming the hierarchical clustering of B cell clones was determined by the SHazaM module for determining distance to nearest neighbor. With the Change-O DefineClones function, clones were assigned based on IGHV genes, IGHJ gene and junction distance calculated by SHazaM (distance 0.14). The generated clone-pass file was verified and corrected using the Change-O light_cluster function, based on the analysis of the light chain partners associated with the heavy chain clone. Independent clone-pass files were generated for each 10X run. For downstream analysis, all clone-pass files from were combined and re-clustered all together. Germlines were reconstructed using the Change-O CreateGermlines function. To obtain the final AIRR format file containing paired information on the same row, we used a Java script to process and filter the sequences. Only the heavy chains paired with one κ and/or one λ were filtered in for downstream analysis. Number and frequency of IgH mutations for each B cell were obtained using the SHazaM observedMutations function. Clonal families were visualized using the R package ggalluvial.

source_name: Merkel cell carcinoma tumor

extract_protocol:
Tumor samples from MCC patients were collected with informed consent for research use and were approved by the Fred Hutchinson Cancer Center (FHCC) institutional review board, in accordance with the Declaration of Helsinki (2013) as part of observational registry studies focusing on Merkel cell carcinoma (IRB protocol 6585). Additionally, tumor samples for single cell experiments were selected based on availability of frozen viable tumor digests, number of cells available in sample (>10 million), and included only MCPyV-positive cases. Briefly, tumors were processed into single-cell digests by mincing them into small pieces with sterile forceps and scissors, followed by incubation in 20 mL of digestion medium composed of RPMI plus 0.002 g DNase, 0.008 g collagenase, and 0.002 g hyaluronidase in a 10-cm dish at 37°C with frequent, gentle swirling. After 3 hours of digestion, cells were strained through a 70 μm filter, centrifuged, resuspended in freezing medium and stored in liquid nitrogen. Frozen cells were thawed at 37°C, followed by dropwise addition of 1 mL complete media (RPMI, 10% Fetal bovine serum, 100 U/mL penicillin, 100 mg/mL streptomycin). Four equivolume additions of complete media was added dropwise with gentle mixing in between additions  for a total volume of 32 mL. Thawed cells were washed twice with 4°C 1xDPBS and transferred to 5 mL FACS tubes. Live/dead stain was added, followed by a blocking buffer to bring samples to 0.5% BSA, 5% TruStain FcX buffer, 100 nM dasatinib, and control tetramers (oligo-PE-GSTDL594 and APCDL755-GST). Samples were then incubated on ice for 10 min followed by the following reagents in order: tetramers (T-Ag PE-oligo tetramer, T-Ag APC tetramer, RSV F PE-oligo tetramer, and RSV F APC tetramer), oligo-hashtag antibodies to identify sample origin in subsequent pooling steps, fluorochrome-labeled antibodies, and oligo-labeled antibodies. Cells were then incubated on ice for 30 min and washed three times with sorting buffer. Cells were then sorted on an Aria II Cell sorter. After exclusion of cell debris, dead cells, PE/APC tetramer-binding CD19+ CD3– CD56– PE594– APC755– B cells, tetramer-negative B cells CD19+ CD3– CD56– PE594– APC755– B cells, CD3+ CD19– CD56– T cells, and CD56+ CD3– CD19– cells were sorted into cold complete media, pooled and immediately prepared for sequencing. For most experiments, tetramer+ CD19+ B cells were sorted into a tube with CD3+ T cells and kept separate from Tetramer– CD19+ B cells that were sorted into a tube with CD56+ MCC cells.
Single cell suspensions sorted from tumors and brought to a concentration of 700-1,200 cells/mL, loaded into microfluidic chip G (10X Genomics), and run through a Chromium controller to obtain Gel Beads-in-Emulsion (10X Genomics). Resulting cell suspensions then went through a library preparation process for single-cell RNA-sequencing along with paired V(D)J-seq for BCR and TCR receptor clonotypes using the 5’ transcriptome kit with feature barcoding (V2; 10X Genomics) per manufacturer guidelines. The cDNA library was enriched for 1056 human immunology panel genes (10X Genomics) and sequenced using a NovaSeq instrument (Illumina) with 2 x 92 base pair paired-end reads aiming for an average of 20,000 reads/cell.

value: Merkel cell carcinoma tumor

value: B cells


title: BSLN, 68-1 RhCMV/SIV, orally, Non-protected, 28724

status: Public on Aug 01 2025

type: SRA

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

description:
Library name: G001_ABL01_28724_BSLN
!0x Genomics

library_source: transcriptomic single cell

data_processing:
demuliplexed and aligned data using CellRanger v6.0.1 to the Rhesus Macaque genome (Mmul10, Ensembl v100)
Aligned reads from samples collected only during post SIV challenge time points to SIV genome SIV239_M33262_1 using scPathoQuant
Assembly: Rhesus Macaque genome (Mmul10, Ensembl v100)
Supplementary files format and content: Barcodes.tsv, feature.tsv, and matrix.mtx files

molecule: total RNA

organism: Macaca mulatta

source_name: PBMCs

extract_protocol:
10x extraction protocol
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 ; 10X Genomics

treatment_protocol: Adminstration of 68-1 or 68-1.2 RhCMV/SIV vector in  prime and boost regimine

tag: tissue

value: PBMCs

tag: treatment

value: 68-1 RhCMV/SIV, orally

tag: treatment outcome

value: Non-protected

tag: animal id

tag: Sex

value: Male

tag: time

value: BSLN


title: GF-Folate1-ip

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
*library strategy: meRIP-seq
Adaptors and raw reads containing low-quality bases were first removed by applying trim_galore (version 0.6.6) to all RNA-seq raw data including the MeRIP-seq input libraries. The resulting reads of at least 35 bp were mapped to the reference genome (mm39, dm6-FLYBASE).
The obtained comparison results were removed and sorted using samtools (version 1.3.1) for PCR duplicates.
The featureCounts program (43) in the Subread package (version 2.0.1) at SourceForge was used to count the reads that mapped to genes. The genes that showed an average read count of less than 10 in any group or lacked read count in any replicate were primarily filtered.
The R package DESeq2 (version 1.36.0) was used for the identification of differentially expressed genes (DEGs) by setting a false discovery rate-corrected P value < 0.05 and fold change >= 0.5 as the thresholds for significance.
We first processed the raw data of MeRIP-seq IP libraries with the same upstream pipeline employed for RNA-seq. The mapping results of both MeRIP-seq IP and input libraries were used for calling m6A peaks. Differential m6A peaks of the single-factor comparisons between groups were analyzed using the R package exomePeak2 (version 1.8.1) (45), with Poisson's generalized linear model (GLM) used as a quantitative method to call the m6A peaks of individual groups as well as the m6A peaks of single-factor comparative differences between groups. To reduce false positives, the called m6A peaks from each biological replicate were considered significant and retained for subsequent analyses according to the following thresholds: peak width <= 1500 bp, log2FC > 1, FDR < 0.05, Input.RPM>=0.1, IP.RPM>=0.1. Similarly, the called differential m6A peaks between groups were considered significant under the following thresholds: peak width <= 1500 bp, |diff.log2FC|>1, FDR < 0.05, Input.Control.RPM>0.1, IP.Control.RPM>0.1, Input.Treated.RPM>0.1, IP.Treated.RPM>0.1. HOMER (version 3.12) (46) was used for de novo motif searching around peak summit-centered (mouse, peak 300 bp region; Drosophila, peak 250 bp) regions. The R packages ChIPseeker (version 1.32.0) (47) and Guitar (version 2.12.0) (48) were used for annotation and representation of the distribution characteristics of the significant/differential m6A peaks. The bamCoverage script in deeptools (version 3.5.1) was used to perform read-coverage trajectory calculations on the results of mapping IP libraries and Input libraries to the genome. Integrative Genomics Viewer (IGV) software (version 2.14.0) (49) was used to display read coverage tracks of target genes.
Assembly: mm39,dm6-FLYBASE
Supplementary files format and content: bed
Supplementary files format and content: csv

molecule: polyA RNA

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were cultured at 28℃ in SIM-SF(Gibco) insect cell medium with 10% fetal calf serum, and the cells were resuspended and sub-cultured every three days.

extract_protocol:
Total RNAs were extracted with Trizol and NanoDrop 2000 spectrophotometer (ThermoFisher) was used to quantify the concentration of total RNA at a wavelength of 260 nm.
About 1.5 µg of purified poly(A)-RNA was fragmented into ~100 nt fragments using RNA fragmentation buffer (AM8740, Thermo Scientific). One-tenth of fragmented RNAs were used for the construction of RNA-seq libraries (Input) and the left RNAs were used for the construction of m6A MeRIP-seq libraries (IP). m6A IP was conducted using an EpiMark® N6-Methyladenosine Enrichment Kit (#E1610S, NEB) following the product manual. The resultant m6A-enriched and untreated poly(A)-RNA fragments were used to construct strand-specific IP and Input libraries, respectively. A VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (NR604-02, Vazyme Biotech. Co., Ltd.) and VAHTS® RNA Adapters set3 for Illumina (N809, Vazyme Biotech. Co., Ltd.) provided the necessary reagents for first- and second-strand cDNA synthesis, adaptor ligation, and library amplification. RNA-seq and MeRIP-seq of the prepared libraries were performed in Berry Genomics on the NovaSeq 6000 platform (Illumina, CA, USA) to obtain paired-end reads of 150 bp. Library quality was assessed on an Agilent Bioanalyzer 4200 TapeStation before loading onto the sequencer, ~8G of raw reads was obtained for each library.

treatment_protocol: Folic acid supplementation in Drosophila：The conventional Drosophila melanogaster strain w1118 was reared on yeast-glucose medium (1 L water, 100 g yeast, 100 g glucose, 1.2% agar, 0.1% potassium sorbate) at 25°C, 70% relative humidity, and a photoperiod of 12L: 12D. Folic acid supplementation in mice：Three-week-old C57BL/6J SPF mice (six mice for male and female, respectively) were purchased, and each gender of mice was randomly divided into two groups with three mice in each group. All mice had free access to a sterilized diet and water, and the corn bedding was changed regularly. Each mouse was fed with folic acid via gavage at a volume of 0.1 mL/day and a concentration of 500 μg/kg/day for 14 days. After 14 days, mice organs were dissected and collected, including the brain, heart, liver, kidney, spleen, muscle, thymus, and testis. Mice organ samples were immediately frozen in liquid nitrogen and stored at -80℃ until use. The protocol for an animal experiment in this study was reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) of South China Normal University (protocol code SCNU-SLS-2022-009).

tag: strain


title: S2-Control1

source_name: S2 (Schneider 2)

tag: cell line

value: S2 (Schneider 2)

tag: cell type

value: Drosophila embryo s2 cell


title: MCPyV T-antigen reads for B cells derived from Merkel cell carcinoma patient tumors

description: Library name: MCC_Bcells_T-Ag_reads

library_source: other

data_processing:
Raw sequencing reads were aligned to the hg38 genome using Cell Ranger v.8.0.1. Filtered counts matrices of transcripts and feature barcoding counts were loaded into a SingleCellExperiment object for further analyses in R (v.4.1.2). Sample hash deconvolution was performed using DropletUtils (v.1.14.2). Doublets were detected using scds (v.1.10.0) and hash deconvolution and subsequently removed. Cells from different runs were then integrated using the mutual nearest neighbor method though the batchelor package (v1.10.0). UMAP dimensionality reduction was performed using the integrated values. Clustering was performed using the integrated transcript values reads through the walktrap algorithm on a nearest neighbor graph (scran v.1.22.1). Numbers of clusters was varied by scaling the number of nearest neighbors (k) during graph construction followed by analysis via clustree (v.0.5.0). Clusters were then labeled as major cell lineages of T cells, B cells, myeloid cells, epithelial cells, dendritic cells, and tumor cells through expression of key genes including CD79A, CLEC4C, COL3A1, NCAM1, CD14, and CD3E. Cluster labels were then validated by investigating the portion of cluster with productive BCR or TCR rearrangements. Cell lineages were then isolated in silico and dimensionality reduction and B cells and CD4+ T cells re-clustered as above. Clusters were labeled based on expression of lineage markers. To identify T-Ag-specific B cells in tumors, we analyzed T-Ag oligo reads and control antigen oligo reads in B cells. T-Ag-specific CD19+ B cells were defined as cells with T-Ag oligo reads at least one log higher than background and fewer than 20 reads from GST or RSV F control antigens. Additionally, eight B cell families in which fewer than 50% of clones met this threshold were classified as non-specific.
Raw output files were demultiplexed and processed using CellRanger v.8.0.1 software (10X Genomics). For each donor, publicly available reference sequences from the IMGT/V-QUEST reference directory at https://www.imgt.org/ were used to identify V, D, and J gene segments. Next, data were processed and analyzed using the Immcantation Framework (http://immcantation.org) with Change-O v.1.0.2. For each 10X dataset, the filtered_contig.fasta file was annotated using IgBlast v.1.16 with the related donor-specific VJ genes database. To generate adaptive immune receptor repertoire (AIRR) rearrangement data, the filtered_contig_annotations.csv file was used, and only productive sequences were kept. The heavy and light chain sequences were separated in two files. The threshold for trimming the hierarchical clustering of B cell clones was determined by the SHazaM module for determining distance to nearest neighbor. With the Change-O DefineClones function, clones were assigned based on IGHV genes, IGHJ gene and junction distance calculated by SHazaM (distance 0.14). The generated clone-pass file was verified and corrected using the Change-O light_cluster function, based on the analysis of the light chain partners associated with the heavy chain clone. Independent clone-pass files were generated for each 10X run. For downstream analysis, all clone-pass files from were combined and re-clustered all together. Germlines were reconstructed using the Change-O CreateGermlines function. To obtain the final AIRR format file containing paired information on the same row, we used a Java script to process and filter the sequences. Only the heavy chains paired with one κ and/or one λ were filtered in for downstream analysis. Number and frequency of IgH mutations for each B cell were obtained using the SHazaM observedMutations function. Clonal families were visualized using the R package ggalluvial.
Library strategy: CITE-seq

molecule: protein

organism: Homo sapiens


title: PBMCs, IL15, 6hr, 38142, 1

description: Library name: G022_O19_38142_IL15_6hr_1

data_processing:
Trimgalorev0.6.10 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.4
Aligned reads with STARv2.7.10b to both rhesus macaque and cynomolgus macaque genomes
Assembly: Macaca fascicularis version 6 Ensembl annoation v110 and Macaca mulatta version 10 Ensembl annoation v110
Supplementary files format and content: Two count matricies one the macaca fascicularis and macaca mulatta

organism: Macaca fascicularis

extract_protocol:
Isolation of RNA using Qiagen RNeasy Mini Kit
mRNA Library Prep Using KAPA mRNA HyperPrep Kit

treatment_protocol: Ex-vivo PBMCs from cynomolgus macaques were treated with IL-15/IL-15Ra (40ng/ml)

value: Female

tag: replicate

tag: dose

value: 40 ng/ml


title: PBMCs, Control, 48hr, 38142, 3

description: Library name: G018_O19_38142_C_48hr_3

value: Control

value: 0 ng/ml


title: CD4+ T cells derived from Merkel cell carcinoma patient tumors

description: Library name: MCC_CD4Tcells

value: CD4+ T cells


title: PBMCs, IL15, 12hr, 38142, 1

description: Library name: G025_O19_38142_IL15_12hr_1


title: PBMCs, IL15, 2hr, 38142, 3

description: Library name: G021_O19_38142_IL15_2hr_3


title: p24240.s031_1E9.CZ36.D18

city: Boston

first: Dan

last: Barouch

state: MA

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

description: Library name: p24240.s031_1E9.CZ36.D18

data_processing:
Alignment was performed using STAR version 2.7.9a to a composite of the Rhesus Mmul10 reference assembly sequence (Ensembl v104 annotation) and the NCBI H5N1 reference assembly (GCF_000864105.1). Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count. DESeq2 was used for normalization, producing a both raw and normalized read count tables and for differential gene expression analysis.
Assembly: Rhesus mmul10
Supplementary files format and content: raw-counts-H5N1.csv, raw read counts
Supplementary files format and content: normalized-counts-H5N1.csv, normalized read counts

source_name: Whole blood

extract_protocol:
Blood was collected into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (ThermoFisher Scientific).
RNA quality was assessed using a Fragment Analyzer (Agilent) and then one microgram of total RNA was subjected to globin transcript depletion using the GLOBINclear Kit, human (ThermoFisher Scientific). Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~30 million reads per sample on average.

value: Whole blood

tag: route

value: IN+IT

tag: dose (tcid50_h5n1)

tag: timepoint


title: T-antigen-specific and B cells of unknown specificity from Merkel cell carcinoma patient tumors

description: Library name: MCC_Bcells


title: p24240.s027_1E9.CZ29.D7

description: Library name: p24240.s027_1E9.CZ29.D7


title: PBMCs, IL15, 2hr, 38142, 1

description: Library name: G019_O19_38142_IL15_2hr_1


title: PBMCs, IL15, 2hr, 38142, 2

description: Library name: G020_O19_38142_IL15_2hr_2


title: p24240.s030_1E7.7102.D7

description: Library name: p24240.s030_1E7.7102.D7


title: mtscATAC-seq of MSK-143 sorted mGAMs

city: New York

first: Kenny

last: Yu

state: NY

address: 1275 York Ave

department: Neurosurgery

institute: Memorial Sloan Kettering Cancer Center

description:
10x Genomics
MSK143_fragments.tsv.gz

library_source: genomic single cell

data_processing:
Mitochondrial genotyping was performed with mgatk 60 in `tenx` mode using the barcodes identified as cells by CellRanger-ATAC
Assembly: hg38
Supplementary files format and content: Accessible chromatin fragments per ATAC library

molecule: genomic DNA

source_name: Brain Tumor (Glioma)

extract_protocol:
Immune cells were first isolated from dissociated glioma samples via CD45+ MACS followed by FACS purification for mGAM and non-mGAM populations. Peripheral blood from the same patient was collected and PBMCs isolated using gradient separation (Ficoll-Paque PLUS, Cytiva, USA) followed by CD14 MACS sorting to obtain monocytes.
Purified viable cells were used as input to the mtscATAC-seq protocol, and libraries were prepared using the Chromium Next GEM single-cell ATAC reagent kit v2.0 following the manufacturer’s instructions with the modifications described in the mtscATAC-seq protocol: https://www.nature.com/articles/s41587-020-0645-6

value: Brain Tumor (Glioma)

value: Leukocytes


title: PBMCs, Control, 24hr, 38142, 3

description: Library name: G015_O19_38142_C_24hr_3


title: mtscATAC-seq of MSK-156 PBMC-derived monocytes

description:
10x Genomics
MSK156_fragments.tsv.gz

source_name: Blood

value: Blood

value: Monocytes


title: p24240.s025_1E9.7442.D7

description: Library name: p24240.s025_1E9.7442.D7


title: GF-Control2-ip


title: WT-8weeks-male-rep1

city: Beijing

first: Wenhui

last: Li

address: 7 Science Park Road ZGC Life Science Park

data_processing:
Clean mRNA-seq reads were aligned to the mouse reference genome (GRCm38) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene-level read count for each Sample

organism: Mus musculus

source_name: Liver

growth_protocol: All animals were housed and maintained under specific pathogen-free conditions in a temperature- and humidity-controlled animal facility with food and water ad libitum, under a 12-hour light/12-hour dark cycle at the National Institute of Biological Sciences (NIBS), Beijing.

extract_protocol:
Freshly isolated livers were immediately frozen and stored in liquid nitrogen until use. mRNA was extracted using Trizol regent (Invitrogen) following the manufacturer’s instructions. For mRNA-seq analysis, mRNA was isolated with Dynabeads® mRNA Purification Kits (Invitrogen), fragmented in 5x first strand buffer(Invitrogen) at 95°C for 5 min, and reverse-transcribed using SuperScript® II Reverse Transcriptase (Invitrogen). After the first strand was synthesized, Second Strand Buffer (Invitrogen), RNase H (New England Biolabs), dNTPs, and DNA polymerase I (TaKaRa) were added to the second-strand synthesis reaction for 2.5 h at 16°C, and cDNA was purified with Agencourt AMPure XP beads (Beckman). Libraries were constructed with a NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs), PCR products were purified using AMPure XP beads. RNA libraries were quantified by Qubit 1.0 (Invitrogen) and analyzed with an Agilent 2100 bioanalyzer(Agilent) for size distribution, and were sequenced with the Illumina Hiseq-2500 platform.
Libraries were constructed with a NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs), PCR products were purified using AMPure XP beads. RNA libraries were quantified by Qubit 1.0 (Invitrogen) and analyzed with an Agilent 2100 bioanalyzer(Agilent) for size distribution.

tag: gender

value: male

tag: age

value: 8 weeks

tag: genotype

value: wild type

value: liver


title: Tumor, B cells, and T cells derived from Merkel cell carcinoma patient tumors

description: Library name: MCC_AllCells

tag: tissue

value: Merkel cell carcinoma tumor

value: B cells, T cells, and tumor cells


title: GF-Folate3-ip


title: GF-Folate3


title: p24240.s029_1E7.CS04.D7

description: Library name: p24240.s029_1E7.CS04.D7


title: GF-Folate2


title: mtscATAC-seq of MSK-156 sorted non-mGAMs

description:
10x Genomics
MSK156_fragments.tsv.gz


title: mtscATAC-seq of MSK-143 PBMC-derived monocytes

description:
10x Genomics
MSK143_fragments.tsv.gz


title: p24240.s028_1E7.CZ36.D7

description: Library name: p24240.s028_1E7.CZ36.D7


title: GF-Folate1


title: PBMCs, Control, 48hr, 38142, 2

description: Library name: G017_O19_38142_C_48hr_2

value: PBMCs

tag: treatment

value: Female


title: p24240.s023_1E7.CS04.D4

description: Library name: p24240.s023_1E7.CS04.D4


title: PBMCs, Control, 12hr, 38142, 3

description: Library name: G012_O19_38142_C_12hr_3

value: Control


title: mtscATAC-seq of MSK-143 sorted non-mGAMs

description:
10x Genomics
MSK143_fragments.tsv.gz


title: GF-Control3-ip


title: GF-Control2


title: p24240.s026_1E9.BN18.D7

description: Library name: p24240.s026_1E9.BN18.D7


title: GFP_cJL220_rep2

city: Cambridge

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

department: Biology

institute: Whitehead Institute

description: Library name: GFP_cJL220_rep2

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Reads were aligned using STAR v2.7.1.a with options ---runThreadN 6 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate for RIP-seq; --runThreadN 2 --limitBAMsortRAM 10000000000 --runMode alignReads --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 1000 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate for rRNA analysis.
Transcript counts were quantified using Htseq-count
Dfferential expression analysis was performed using DEseq2
Assembly: Human genome: hg38 (gencode v25) and Mouse genome: m38 (gencode v24)
Supplementary files format and content: Transcript counts are stored in tab-delimited files with one row per transcript, quantification done using Htseq-count.

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin/streptomycin

extract_protocol:
Cells in 6 well plates were washed once with 1x PBS then lysed in 400uL Trizol on plate. To the TRI Reagent lysate, 120 µL of chloroform was added, followed by shaking and centrifugation at 21,000 x g for 15 minutes at 4°C to achieve phase separation. The upper aqueous phase, was carefully transferred to a new tube, mixed with an equal volume of chloroform, and centrifuged again at 21,000 x g for 1 minute at 4°C. RNA was then precipitated by adding 300 mM NaCl and 30 µg of GlycoBlue (AM9516), along with an equal volume of isopropanol, and incubating the mixture overnight at -20°C. The RNA pellet was centrifuged at 21,000 x g for 15 minutes at 4°C, washed with 70% ethanol, and resuspended in RNase-free water. For the last replicate of SRSF12 overexpression analysis, we used Phasemaker tubes to extract RNA.
With one exeption (below), all RNA was prepped with the Watchmaker genomics kit with rRNA depletion according to manufacturer's instructions. For the third replicate of SRSF12 overexpression transcriptome analysis, rRNA depletion and library preparation were carried out with the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche KK8560) according to manufacturer’s instructions.

treatment_protocol: GFP transgene expression was induced with 1 ug/mL doxycycline for 2 days and cells were harvested for RNA-sequencing

value: HeLa

value: GFP

value: doxycycline


title: PBMCs, Control, 6hr, 38142, 3

description: Library name: G009_O19_38142_C_6hr_3

value: 0 ng/ml


title: p24240.s024_1E7.7102.D4

description: Library name: p24240.s024_1E7.7102.D4

value: Whole blood

value: IN+IT


title: GF-Control1-ip


title: PBMCs, Control, 48hr, 38142, 1

description: Library name: G016_O19_38142_C_48hr_1


title: dsGFP-2-ip

value: S2 (Schneider 2)

value: Drosophila embryo s2 cell


title: PBMCs, Control, 6hr, 38142, 2

description: Library name: G008_O19_38142_C_6hr_2


title: PBMCs, Control, 24hr, 38142, 1

description: Library name: G013_O19_38142_C_24hr_1


title: GF-Control3


title: p24240.s019_1E9.7442.D4

description: Library name: p24240.s019_1E9.7442.D4


title: SRSF12_GFP_cJL310_rep2

description: Library name: SRSF12_GFP_cJL310_rep2


title: PBMCs, Control, 24hr, 38142, 2

description: Library name: G014_O19_38142_C_24hr_2


title: p24240.s022_1E7.CZ36.D4

description: Library name: p24240.s022_1E7.CZ36.D4


title: p24240.s021_1E9.CZ29.D4

description: Library name: p24240.s021_1E9.CZ29.D4


title: PBMCs, Control, 12hr, 38142, 2

description: Library name: G011_O19_38142_C_12hr_2


title: SRSF12_GFP_cJL310_rep1

description: Library name: SRSF12_GFP_cJL310_rep1


title: GF-Control1


title: PBMCs, Control, 12hr, 38142, 1

description: Library name: G010_O19_38142_C_12hr_1


title: dsGFP-3-ip


title: WT (KQ ctrl)-H2O2-3

first: Douglas

last: Barrows

address: 1230 York Ave

institute: Rockefeller University

description:
Library name: RNA_KQ_9
rep 3

data_processing:
Combined Drosophila biarmipes and hg38 fasta and GTF files were derived from the BSgenome.Hsapiens.UCSC.hg38 and TxDb.Hsapiens.UCSC.hg38.knownGene R Bioconductor packages paired with the files from the RU_DBia_V1.1 genome assembly (RefSeq assembly number GCF_025231255.1). Fastq files were aligned to the combined reference with STAR (v2.5.2b) using default settings except the ‘outSAMmultNmax’ argument was set to 1. The reads that preferentially aligned to the hg38 chromosomes were extracted from the BAM file using the ‘view’ function from Samtools (v1.10), and gene level counts were obtained using the ‘summarizeOverlaps’ function from the GenomicAlignments R Bioconductor package (v1.28.0). The Drosophila biarmipes genes were used to estimate size factors during differential expression with the DESeq2 R Bioconductor package (v1.32.0).
Assembly: hg38 with Drosophila biarmipes spike in
Supplementary files format and content: raw counts from DESeq2

source_name: MCF7 WT MED1

extract_protocol:
Cells were harvested, washed with PBS, and flash frozen in liquid nitrogen. RNA was isolated using QIAGEN RNeasy kit.
Libraries were generated using mRNA TruSeq stranded 350bp

value: MCF7 WT MED1

value: breast cancer cell line

value: ectopic WT MED1 (with Drosophila biarmipes spike-in)

value: H2O2 (0.5mM) 6 hours


title: dsDhfr-3-ip


title: p24240.s015_1E9.CZ29.D2

description: Library name: p24240.s015_1E9.CZ29.D2


title: PBMCs, Control, 2hr, 38142, 1

description: Library name: G004_O19_38142_C_2hr_1


title: GFP_cJL220_rep1

description: Library name: GFP_cJL220_rep1


title: dsGFP-1-ip


title: mtscATAC-seq of MSK-156 sorted mGAMs

description:
10x Genomics
MSK156_fragments.tsv.gz

value: Brain Tumor (Glioma)

value: Leukocytes


title: 6KQ-H2O2-3

description:
Library name: RNA_KQ_12
rep 3

source_name: MCF7 6KQ MED1

value: MCF7 6KQ MED1

value: ectopic 6KQ MED1 (with Drosophila biarmipes spike-in)


title: 6KQ-H2O2-2

description:
Library name: RNA_KQ_11
rep 2


title: dsGFP-3


title: p24240.s018_1E7.7102.D2

description: Library name: p24240.s018_1E7.7102.D2


title: p24240.s017_1E7.CS04.D2

description: Library name: p24240.s017_1E7.CS04.D2


title: PBMCs, Control, 2hr, 38142, 3

description: Library name: G006_O19_38142_C_2hr_3

value: PBMCs

value: Control

value: Female


title: p24240.s020_1E9.BN18.D4

description: Library name: p24240.s020_1E9.BN18.D4


title: 6KQ-H2O2-1

description:
Library name: RNA_KQ_10
rep 1


title: dsDhfr-2-ip


title: PBMCs, Control, 0hr, 38142, 2

description: Library name: G002_O19_38142_C_0hr_2


title: dsGFP-2


title: PBMCs, Control, 2hr, 38142, 2

description: Library name: G005_O19_38142_C_2hr_2


title: WT (KQ ctrl)-H2O2-2

description:
Library name: RNA_KQ_8
rep 2


title: p24240.s012_1E7.7102.D1

description: Library name: p24240.s012_1E7.7102.D1


title: dsGFP-1


title: p24240.s016_1E7.CZ36.D2

description: Library name: p24240.s016_1E7.CZ36.D2


title: PBMCs, Control, 6hr, 38142, 1

description: Library name: G007_O19_38142_C_6hr_1


title: p24240.s065_VII.DT902.Necropsy

description: Library name: p24240.s065_VII.DT902.Necropsy

value: Necropsy


title: p24240.s011_1E7.CS04.D1

description: Library name: p24240.s011_1E7.CS04.D1


title: p24240.s014_1E9.BN18.D2

description: Library name: p24240.s014_1E9.BN18.D2


title: WT (KQ ctrl)-ctrl-3

description:
Library name: RNA_KQ_3
rep 3

value: control


title: p24240.s010_1E7.CZ36.D1

description: Library name: p24240.s010_1E7.CZ36.D1

value: Whole blood


title: p24240.s064_VII.DVS31.Necropsy

description: Library name: p24240.s064_VII.DVS31.Necropsy


title: 6KQ-ctrl-1

description:
Library name: RNA_KQ_4
rep 1


title: p24240.s063_V.DV832.Necropsy

description: Library name: p24240.s063_V.DV832.Necropsy

value: V (IN+IT)


title: WT (KQ ctrl)-H2O2-1

description:
Library name: RNA_KQ_7
rep 1


title: PBMCs, Control, 0hr, 38142, 3

description: Library name: G003_O19_38142_C_0hr_3

value: 0 ng/ml


title: dsDhfr-1

value: S2 (Schneider 2)

value: Drosophila embryo s2 cell


title: p24240.s013_1E9.7442.D2

description: Library name: p24240.s013_1E9.7442.D2

value: IN+IT


title: 6KQ-ctrl-3

description:
Library name: RNA_KQ_6
rep 3

value: breast cancer cell line


title: dsDhfr-1-ip


title: WT (KQ ctrl)-ctrl-2

description:
Library name: RNA_KQ_2
rep 2

value: MCF7 WT MED1

value: ectopic WT MED1 (with Drosophila biarmipes spike-in)


title: PBMCs, Control, 0hr, 38142, 1

description: Library name: G001_O19_38142_C_0hr_1


title: dsDhfr-3


title: dsDhfr-2


title: p24240.s009_1E9.CZ29.D1

description: Library name: p24240.s009_1E9.CZ29.D1


title: p24240.s061_VII.DV531.Necropsy

description: Library name: p24240.s061_VII.DV531.Necropsy


title: p24240.s008_1E9.BN18.D1

description: Library name: p24240.s008_1E9.BN18.D1


title: WT (KQ ctrl)-ctrl-1

description:
Library name: RNA_KQ_1
rep 1


title: EC09, scRNA-seq

city: Seodaemun-gu

first: Insuk

last: Lee

state: Seoul

address: 50 Yonsei-ro

department: Biotechnology

country: South Korea

institute: Yonsei University

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: h5 format for gene expression matrix

source_name: Esophagus

extract_protocol:
We collected fresh tumor tissues which was mechanically and enzymatically dissociated using a gentleMACS dissociator (Miltenyi Biotec, Gladbach Bergisch, Germany, Cat#130-093-235) and the Human Tumor Dissociation Kit (Miltenyi Biotec, Cat#130-095-929) following the manufacturer's instructions. After incubation for 1 h at 37℃, the resuspended samples were filtered through a 70-µm MACS SmartStrainer (Miltenyi Biotec, Cat# 130-098-462) into RPMI-1640 medium (Corning, Inc. Corning, NY, USA) supplemented with 10% fetal bovine serum (Biowest, Riverside, MO, USA) and centrifuged at 300 ×g for 10 min.
Libraries were prepared using the Chromium controller according to the 10x Chromium Next GEM Single Cell 5-v2_CellSurfaceProtein_UserGuide (CG000330). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 5′ Gel Beads and Partitioning Oil into a Next GEM Chip K. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and enriched with PCR. The amplified cDNA are separated by size selection for 5ʹ Gene Expression libraries, V(D)J Enriched Libraries and Cell Surface Protein libraries

value: Esophagus

value: Total

tag: tumor type

value: ESCC


title: p24240.s006_1E7.7102.D0

description: Library name: p24240.s006_1E7.7102.D0


title: EC11, scRNA-seq

description: 10x Genomics


title: p24240.s007_1E9.7442.D1

description: Library name: p24240.s007_1E9.7442.D1


title: p24240.s060_V.DV832.Necropsy

description: Library name: p24240.s060_V.DV832.Necropsy


title: EC08, scRNA-seq

description: 10x Genomics


title: v2_h3k27ac, ChIP

city: Qingdao

first: Li-Xia

last: Lv

address: Ao Shanwei 72

institute: Shandong University

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseg output.
Assembly: hg38
Supplementary files format and content: bigWVig

organism: Penaeus japonicus

source_name: Hemocytes

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes.After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris)
ChlP-seg libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientifc.10 ng of DNA was used as starting material for input and ip samples.Libraries were amplifed using 13 cycles on the thermocycler. Post amplification libranries were size selected at 250-450bp in length using Agencout AlMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Hemocytes

value: Shrimp hemocytes

tag: chip antibody

value: UV-WSSV-trained


title: p24240.s059_VII.DS249.Necropsy

description: Library name: p24240.s059_VII.DS249.Necropsy

value: Necropsy


title: v2_input, Input


title: 6KQ-ctrl-2

description:
Library name: RNA_KQ_5
rep 2

value: MCF7 6KQ MED1

value: ectopic 6KQ MED1 (with Drosophila biarmipes spike-in)

value: control


title: p2_h3k27ac, ChIP

value: PBS-trained


title: p24240.s003_1E9.CZ29.D0

description: Library name: p24240.s003_1E9.CZ29.D0

value: Whole blood


title: EC06, scRNA-seq

description: 10x Genomics


title: p24240.s005_1E7.CS04.D0

description: Library name: p24240.s005_1E7.CS04.D0


title: p2_input, Input


title: EC07, scRNA-seq

description: 10x Genomics


title: EC12, scRNA-seq

description: 10x Genomics

value: EAC


title: p24240.s056_VII.DS249.D4

description: Library name: p24240.s056_VII.DS249.D4


title: EC04, scRNA-seq

description: 10x Genomics


title: p24240.s058_V.DV70B.Necropsy

description: Library name: p24240.s058_V.DV70B.Necropsy

value: V (IN+IT)


title: p24240.s062_VII.DT902.Necropsy

description: Library name: p24240.s062_VII.DT902.Necropsy


title: p24240.s057_VII.DT902.D4

description: Library name: p24240.s057_VII.DT902.D4


title: EC03, scRNA-seq

description: 10x Genomics


title: R_3

city: guiyang

first: Xilun

last: Huang

state: guizhou

address: 180 North Baoshan District Road, Yunyan District

institute: Guizhou Normal University

description: Parallel sample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Panax japonicus
Supplementary files format and content: tab-delimited text file includes TPM for each sample
Supplementary files format and content: tab-delimited text file includes annotation

organism: Panax japonicus

source_name: fruit

growth_protocol: Distributed in the high mountain areas of Guizhou, China, prefer fertilizer and moisture, avoiding strong direct light, cold and fear of high temperature, suitable for neutral or acidic (pH = 5.5-6.5) soil growth.

extract_protocol:
Total RNA was extracted from 15 samples of Panax japonicus pericarp (5 different fruit colour traits, 3 biological replicates) using Tiangen Kit, RNAprep Pure. The integrity and quality of RNA was assessed by agarose gel (Agarose horizontal electrophoresis machine model DYCP-32C) and Agilent Agilent 2100 Bioanalyzer.
The first strand of cDNA was synthesised in M-MuLV reverse transcriptase system using fragmented mRNA as template and random oligonucleotides as primers, and the second strand of cDNA was synthesised using dNTPs as raw material. The double-stranded cDNA was purified and subjected to PCR amplification to finally obtain the library. Qubit2.0 Fluorometer was used for preliminary quantification, and the library was diluted to 1.5 ng/ul. Agilent2100 bioanalyzer was used to insertsize the library to ensure the quality of the library.

treatment_protocol: The fruit was washed with pure water, the excess water on the pericarp was sucked up by filter paper, and the seeds and pericarp were removed with a scalpel; the pericarp was frozen in liquid nitrogen for 15 min, and then the pericarp was grinded in a mortar and pestle, and then stored in a refrigerator at -80℃ for later use.

value: fruit

value: R period


title: Y_3

description: Parallel sample 3

value: Y period


title: R_2

description: Parallel sample 2


title: EC01, scRNA-seq

description: 10x Genomics

value: Esophagus


title: p24240.s002_1E9.BN18.D0

description: Library name: p24240.s002_1E9.BN18.D0

value: IN+IT


title: EC05, scRNA-seq

description: 10x Genomics

value: Total

value: ESCC


title: Y_2

description: Parallel sample 2


title: p24240.s001_1E9.7442.D0

description: Library name: p24240.s001_1E9.7442.D0


title: TF3_3

city: Dalian City

first: xue

last: li

state: Liaoning Province

address: No. 1 Light Industry Court, Ganjingzi District

department: School of food science and technology

institute: Dalian Polytechnic University

data_processing:
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: NCBI accession number SDAR00000000
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Hafnia alvei

extract_protocol:
The culture solution was centrifuged and the supernatant was discarded. After freezing in liquid nitrogen, it was stored in a -80 degree refrigerator to prepare for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type


title: p24240.s055_VII.DV531.D4

description: Library name: p24240.s055_VII.DV531.D4


title: Y_1

description: Parallel sample 1


title: p24240.s053_V.DV832.D4

description: Library name: p24240.s053_V.DV832.D4


title: p24240.s054_V.DV428.D4

description: Library name: p24240.s054_V.DV428.D4


title: EC02, scRNA-seq

description: 10x Genomics


title: p24240.s004_1E7.CZ36.D0

description: Library name: p24240.s004_1E7.CZ36.D0


title: TF3_2


title: YFP_RNAi_i3

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the Caenorhabditis elegans transcriptome and genome version WBcel235 with annotations from Ensembl release 106 using TopHat v2.1.1 (ref 2). Counts per gene quantification was done with htseq-count v2.01 (ref. 3). Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0 (ref 4.). The normalized counts were further batch corrected for the effect of the 3 repeats of the biological procedure.
Assembly: WBcel235
Supplementary files format and content: Tayir_counts_DESeq2_normc.xlsx
Supplementary files format and content: excel table with raw counts and DESeq2 normalized counts per gene (rows) per sample(column)

organism: Caenorhabditis elegans

source_name: pool of whole worms

growth_protocol: Synchronized AM140 worms were grown from hatching on EV bacteria or on bacteria that express YFP RNAi at 20C. The worms were washed and transferred onto new plates every day to remove progeny.

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (MACHEREY-NAGEL; 740955) according to the manufacturer instructions.
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000 (Illumina), using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles

treatment_protocol: At day 5 of adulthood, half of the worms of each group were exposed to isoflurane while the other half was not. All four worm groups were harvested 3 hours after the treatment

value: pool of whole worms

tag: harvest time

value: day 5 of adulthood

value: grown on yfp RNAi and expose to isoflurane


title: LINE-1a mice replicate-3

city: New Haven

first: Takehiro

last: Takahashi

state: Connecticut

address: 300 Cedar Street TAC S630

institute: Yale University

description:
LINE1a_3
LINE1a_mice_cerebellum_normalized_counts.xlsx

data_processing:
Sequenced reads were aligned using STAR (STAR/2.5.3a-foss-2016b, mm10 assembly) with parameters: --runThreadN 20 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 35129075129 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 for mapping host genes.
For endogenous retroelements, ERVMAP (Tokuyama et al., 2018; Treger et al., 2019) and RepEnrich2 (Criscione et al., 2014) were used using modules, Python/2.7.13-foss-2016b, Bowtie2/2.2.9-foss-2016b, BEDTools/2.27.1-foss-2016b and SAMtools/1.9-foss-2016b using repeatmasker mm10 assembly.
Counts were counted using BEDTools (BEDTools/2.27.1-foss-2016b) (Quinlan and Hall, 2010), coverageBed function, and normalized using DESeq2 (Love et al., 2014).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: LINE1a_mice_cerebellum_normalized_counts.xlsx: Matrix table of normalized counts for cellular genes, uniquely mappable endogenous retrovirus (ERVs), and endogenous retroelements from Repenrich.

source_name: mouse cerebellar vermis

extract_protocol:
Total RNA was extracted from mouse cerebellar vermis using RNeasy Fibrous Tissue Kit (Qiagen).
Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770).

value: cerebellar vermis

value: 8 wk

value: LINE-1a mice


title: dCas mice replicate-3

description:
dCas_3
LINE1a_mice_cerebellum_normalized_counts.xlsx

value: dCas mice


title: TF3_1


title: YFP_RNAi_i2


title: p24240.s050_VII.DS249.D2

description: Library name: p24240.s050_VII.DS249.D2

value: Whole blood


title: p24240.s047_V.DV832.D2

description: Library name: p24240.s047_V.DV832.D2

value: V (IN+IT)


title: R_1

description: Parallel sample 1

value: fruit


title: p24240.s052_V.DV708.D4

description: Library name: p24240.s052_V.DV708.D4


title: Con_3

value: untreated


title: Con_1


title: P_2

description: Parallel sample 2

value: P period


title: dCas mice replicate-1

description:
dCas_1
LINE1a_mice_cerebellum_normalized_counts.xlsx


title: p24240.s051_VII.DT902.D2

description: Library name: p24240.s051_VII.DT902.D2


title: G_3

description: Parallel sample 3

value: G period


title: YFP_RNAi_i1


title: p24240.s046_V.DV708.D2

description: Library name: p24240.s046_V.DV708.D2


title: LINE-1a mice replicate-2

description:
LINE1a_2
LINE1a_mice_cerebellum_normalized_counts.xlsx


title: G_1

description: Parallel sample 1


title: EV_isoflurane3

value: grown on ev and expose to isoflurane


title: G_2

description: Parallel sample 2


title: LINE-1a mice replicate-1

description:
LINE1a_1
LINE1a_mice_cerebellum_normalized_counts.xlsx


title: dCas mice replicate-2

description:
dCas_2
LINE1a_mice_cerebellum_normalized_counts.xlsx


title: p24240.s049_VII.DVS31.D2

description: Library name: p24240.s049_VII.DVS31.D2


title: p24240.s048_V.DV428.D2

description: Library name: p24240.s048_V.DV428.D2


title: P_3

description: Parallel sample3


title: Con_2


title: B_1

description: Parallel sample 1

value: B period


title: p24240.s043_VII.DV531.D1

description: Library name: p24240.s043_VII.DV531.D1


title: YFP_RNAi_c3

value: grown on yfp RNAi


title: p24240.s042_V.DV428.D1

description: Library name: p24240.s042_V.DV428.D1


title: YFP_RNAi_c2


title: p24240.s045_VII.DT902.D1

description: Library name: p24240.s045_VII.DT902.D1


title: B_3

description: Parallel sample 3


title: YFP_RNAi_c1


title: EV_isoflurane2


title: p24240.s044_VII.DS249.D1

description: Library name: p24240.s044_VII.DS249.D1


title: B_2

description: Parallel sample 2


title: EV_isoflurane1


title: P_1

description: Parallel sample 1


title: SHR Endothelial Cells rep1

city: Hung Hom, Kowloon

first: Lanlan

last: Zhang

address: 11 Yuk Choi Road

country: Hong Kong

institute: The Hong Kong Polytechnic University

description: Library name: SHR_EC_3m_A

data_processing:
Reads of low quality, with adaptor sequences, or high levels of N base were filtered with SOAPnuke (v1.5.6).
Bowtie2 (v2.4.4) was employed to align the clean reads to the reference genes.
Gene expression was quantified using RSEM (v1.2.28) .
Normalization of gene expression was performed with DESeq2 (v1.42.1).
Assembly: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: countdata.csv: Raw read counts are provided for each sample.
Supplementary files format and content: processed_data.csv: Normalized read counts for each sample

organism: Rattus norvegicus

source_name: aorta

growth_protocol: Endothelial cells were cultured in Endothelial Cell Medium (ECM, ScienCell) supplemented with 10% FBS (v/v), 1% P/S (v/v), and 1% Endothelial Cell Growth Supplement (ECGS) (v/v)

extract_protocol:
Total RNA was extracted with E.Z.N.A.® Total RNA Kit (Omega Biotek)
Library preparation and sequencing were outsourced to BGI Genomics. Samples were sequenced using DNBSEQ platform with a paired-end read length of 100 bp (PE100)

value: aorta

value: endothelial cells

value: spontaneously hypertensive

tag: batch


title: SHR Endothelial Cells rep3

description: Library name: SHR_EC_3m_C


title: EV_c3

value: pool of whole worms

tag: strain

value: day 5 of adulthood

value: grown on ev


title: EV_c2


title: p24240.s041_V.DV832.D1

description: Library name: p24240.s041_V.DV832.D1


title: EV_c1


title: p24240.s040_V.DV708.D1

description: Library name: p24240.s040_V.DV708.D1


title: SHR Endothelial Cells rep2

description: Library name: SHR_EC_3m_B


title: p24240.s039_VII.DT902.D0

description: Library name: p24240.s039_VII.DT902.D0


title: WKY Endothelial Cells rep3

description: Library name: WKY_EC_3m_C

value: Wistar Kyoto


title: p24240.s038_VII.DS249.D0

description: Library name: p24240.s038_VII.DS249.D0


title: WKY Endothelial Cells rep2

description: Library name: WKY_EC_3m_B


title: Firefighter-ID-30 Blood serum [2-030]

type: RNA

city: Oklahoma City

first: Chao

last: Xu

state: Oklahoma

address: 801 N. E. 13th Street

department: Biostatistics and Epidemiology

institute: University of Oklahoma Health Sciences Center

hyb_protocol: The quantity and quality of miRNA were assessed using the NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The expression levels of miRNA were ligated with bridge oligos and miRNA tags, making them long enough to hybridize to the probes using the nCounter Human v3 miRNA Expression panel with 800 endogenous human-associated miRNAs (NanoString Technologies, Seattle, WA). Prepared miRNA samples were then hybridized with the capture and reporter probes for 16 hours at 65C.

scan_protocol: Immediately after hybridization, the samples were loaded onto the NanoString nCounter Max Analysis System for clean-up and detection. Each run contained miRNA from six skin samples and six serum samples.

data_processing: The raw data were logarithm 2-transformed and then normalized as the manufacturer suggests.30,31 The RCC and RLF files were imported into NanoString’s nSolver Advanced Analysis Software v 4.0. Analysis of the normalized data was performed with the background correction threshold count value set to 30, no positive control correction, and normalization by geometric mean set at the top 100 genes. The normalization file was then imported into ROSALIND and processed through the miRNA nSolver normalized counts pipeline.

label: mirna

source_name: Blood serum

label_protocol: The RNA yield for both sample types was too low to quantify using Qubit RNA HS Assay Kits or Agilent Bioanalyzer RNA system. Therefore, the maximum 3 µL of RNA was deposited into the nCounter miRNA Expression Assay Kit provided with the panels.

extract_protocol: RNeasy Micro Kits (Qiagen, Chatsworth, CA) were used to isolate RNA from the STS and serum samples according to the manufacturer’s protocol. RNA was isolated using Qiagen’s miRNeasy Serum/Plasma Advanced Kit and established protocols. Upon completion, the samples were then concentrated using RNA Clean & Concentrator-5 (DNase Included) (Zymo Research, Irvine, CA).

tag: fire exposure

value: Post

tag: firefighter type

value: Career

tag: firefighter years served

value: Male

tag: height (m)

tag: weight (kg)

tag: race

value: Non_Hispanic White/European


title: Firefighter-ID-31 Dermal tape wrist [2-031-W]

source_name: Dermal tape wrist


title: Firefighter-ID-30 Dermal tape wrist [2-030-W]


title: WKY Endothelial Cells rep1

description: Library name: WKY_EC_3m_A

tag: cell type


title: p24240.s037_VII.DVS31.D0

description: Library name: p24240.s037_VII.DVS31.D0

value: Whole blood

tag: route

tag: dose (tcid50_h5n1)

tag: timepoint


title: p24240.s034_V.DV708.D0

description: Library name: p24240.s034_V.DV708.D0

tag: tissue

value: V (IN+IT)


title: p24240.s036_V.DV428.D0

description: Library name: p24240.s036_V.DV428.D0


title: BM-AG-6dpi-3

city: Daejeon

first: Dongbin

last: Park

address: 55, Expo-ro

institute: Institute for Basic Science

description:
Library name: 68_S10_L003
10x Genomics

data_processing:
Cellranger (v5.1.2)
Assembly: MuSPutFur1.0 and SFTSV (CB1)
Supplementary files format and content: matrix files

organism: Mustela putorius furo

source_name: BM

extract_protocol:
young-adult (20–24 months; YG, n = 26) and aged (36–40months; AG, n = 26) ferrets were inoculated intramuscularly with 0.5 ml of SFTSV CB1/2014 (10^6.0 TCID50/ml) and spleen, PBMC, and BM were collected from three ferrets per group at 2, 4, and 6 dpi, using separate tools to avoid cross-contamination
10x Genomics Chromium Single Cell 3′ GEM, Library & Gel Bead kit v3.1 (PN-1000121; 10X Genomics)

value: BM


title: Firefighter-ID-29 Blood serum [2-029]

tag: gender

tag: age


title: Firefighter-ID-29 Dermal tape wrist [2-029-W]


title: Firefighter-ID-20 Dermal tape wrist [2-020-W]


title: Candida albicans zcf31Δ rep1 (zcf31-delta-0801)

city: Taipei

first: Ching-Hsuan

last: Lin

state: Taiwan

address: National Taiwan University, 1 Roosevelt Rd. Sec. 4

department: Department of Biochemical Science and Technology

country: Taiwan

institute: National Taiwan University

data_processing:
Low quality bases(<QV20) and adapters were removed by Trimmomatic v0.36
whole transcriptome was reference-based assembled by Trinity v2.8.4
use cd-hit-est v4.7 to generate uni-transcript with 95﹪clustering cutoff
each sample paired-end reads were aligned to transcript fasta using Bowtie2 v2.3.4.3
calculating gene expression count by RSEM v1.2.28, differentially expressed genes(DEGs) were calculated by edgeR v3.24.1. Transcripts were downstreaming with ORF predicition by Transdecoder v5.3.0, the function analysis using Trinotate v3.1.1, transcript nucleotide fasta was annotated by BLASTX v2.5.0, predicted amino acid fasta was annotated by BLASTP v2.5.0
Genome_build: not provided

organism: Candida albicans

source_name: Fugus

growth_protocol: Overnight cultures of the SC5314 wild-type and zcf31Δ were refreshed in 10 ml YPD liquid medium at 30℃ for 4 hr. Samples were centrifuged and resuspended with 3 ml RPMI 1640 for 20 min

extract_protocol:
Total cells were collected by 6,000 rpm centrifugation for 10 mins, and washed by sterile distilled water for 3 times. Total cells of the SC5314 wild-type and zcf31Δ were collected and total RNA was extracted following MasterPureTM Yeast RNA Purification Kit protocol (Eicentre, Madison, WI, USA) and treated with DNase I (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA. Sample quality was validated on Agilent 2100 Bio-analyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation


title: p24240.s035_V.DV832.D0

description: Library name: p24240.s035_V.DV832.D0

source_name: Whole blood


title: BM-AG-6dpi-2

description:
Library name: 65_S7_L003
10x Genomics


title: BM-AG-4dpi-2

description:
Library name: 33_S3_L002
10x Genomics


title: BM-AG-4dpi-1

description:
Library name: 25_S1_L002
10x Genomics


title: Firefighter-ID-20 Blood serum [2-020]

tag: batch


title: BM-AG-6dpi-1

description:
Library name: 62_S4_L003
10x Genomics


title: Candida albicans zcf31Δ rep2 (zcf31-delta-0808)


title: BM-AG-4dpi-3

description:
Library name: 29_S8_L002
10x Genomics


title: Candida albicans WT rep2 (SC5314-0808)

value: wild-type (WT)


title: Firefighter-ID-31 Blood serum [2-031]


title: Firefighter-ID-28 Dermal tape wrist [2-028-W]


title: BM-AG-2dpi-2

description:
Library name: 44_S3_L004
10x Genomics


title: PC condition, replicate 2b

city: Los Angeles

first: Jesse

last: Kreger

state: CA

address: 1050 Childs Way

institute: University of Southern California

description:
Library name: PC2b
10x Genomics

data_processing:
Paired-end reads were processed using CellRanger v4.0.0 and mapped to the mm10 transcriptome v3.0.0 by 10× Genomics with default settings.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung metastasis

extract_protocol:
Lung metastases from NeuN mice (NT2.5-LM) under six different treatment conditions (V, E, EP, EC, EPC, PC) were dissected from lungs using fine-tipped scissors under sterile conditions inside a biosafety level 2 cabinet and digested using the Miltenyi mouse tumor dissociation kit (Miltenyi, cat. # 130-096-730) in combination with the Miltenyi Octo dissociator, following the manufacturer’s directions.
For library preparation, 10× Genomics Chromium Single-Cell 3′ RNA-seq kits v3 were used. Gene expression libraries were prepared according to the manufacturer's protocol.   Each batch had an approximately equal assortment of samples from each treatment group to reduce technical biases. Illumina HiSeqX Ten or NovaSeq was used to generate approximately 6.5 billion total reads.

value: lung metastasis

tag: cell line

tag: treatment

value: PC


title: EC condition, replicate 4c

description:
Library name: EC4c
10x Genomics

value: EC


title: EPC condition, replicate 3b

description:
Library name: EPC3b
10x Genomics

value: EPC


title: PC condition, replicate 2a

description:
Library name: PC2a
10x Genomics


title: EPC condition, replicate 4a

description:
Library name: EPC4a
10x Genomics


title: PC condition, replicate 1

description:
Library name: PC1
10x Genomics


title: PC condition, replicate 4a

description:
Library name: PC4a
10x Genomics


title: EC condition, replicate 4b

description:
Library name: EC4b
10x Genomics


title: EPC condition, replicate 1

description:
Library name: EPC1
10x Genomics


title: Candida albicans WT rep1 (SC5314-0801)


title: Firefighter-ID-19 Blood serum [2-019]

tag: fire exposure

tag: firefighter type


title: mouse Morula embryo，TMZ1

city: 温州

first: kefan

last: zheng

address: 瓯海区茶山街道温州医科大学

institute: wenzhou medical university

description:
Library name: Sample7
Column name in FPKM_Morula.txt:TMZ-Morula-cell-rep1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v 0.23.4
Trimmed sequence reads were mapped to GrCM39/mm39 using STAR v 2.7.9a
Read count extraction and normalization were performed using featureCounts v 2.0.6
Assembly: GRCm39
Supplementary files format and content: txt files include FPKM values for each Sample

source_name: mouse Morula embryo

growth_protocol: mouse embryos were maintained in KsOM and cultured in an incubator at 37°C with 5% CO₂

extract_protocol:
RNA was harvested using Single Cell Full Length mRNA-Amplification Kit(N712)    was used for the construction of sequencing libraries
The sequencing libraries were constructed using the TruePrep™ DNA Library Prep Kit V2 for Illumina (Vazyme #TD503)

treatment_protocol: At the 2-cell stage,embryos were treated with 100uM TMZ(Merck)

value: mouse Morula embryo

tag: genotype

value: TMZ inhibitor


title: BM-AG-2dpi-3

description:
Library name: 47_S2_L004
10x Genomics


title: mouse Morula embryo，TMZ2

address: 瓯海区茶山街道温州医科大学

description:
Library name: Sample8
Column name in FPKM_Morula.txt:TMZ-Morula-cell-rep2


title: BM-AG-2dpi-1

description:
Library name: 38_S1_L002
10x Genomics


title: EC condition, replicate 3a

description:
Library name: EC3a
10x Genomics


title: mouse Morula embryo，Control2

address: 瓯海区茶山街道温州医科大学

description:
Library name: Sample6
Column name in FPKM_Morula.txt:Control-Morula-cell-rep2

value: WT


title: Firefighter-ID-33 Blood serum [2-033]

tag: firefighter years served

value: Female

tag: height (m)

tag: weight (kg)


title: Firefighter-ID-33 Dermal tape wrist [2-033-W]

tag: race


title: BM-AG-CTRL-3

description:
Library name: 71_S7_L003
10x Genomics


title: EC condition, replicate 1

description:
Library name: EC1
10x Genomics


title: mouse Morula embryo，Control1

address: 瓯海区茶山街道温州医科大学

description:
Library name: Sample5
Column name in FPKM_Morula.txt:Control-Morula-cell-rep1


title: mouse 8-Cell embryo，TMZ1

address: 瓯海区茶山街道温州医科大学

description:
Library name: Sample3
Column name in FPKM_8-cell.txt:TMZ-8-cell-rep1

source_name: mouse 8-Cell embryo

value: mouse 8-Cell embryo


title: EP condition, replicate 3b

description:
Library name: EP3b
10x Genomics

value: EP


title: mouse 8-Cell embryo，TMZ2

address: 瓯海区茶山街道温州医科大学

description:
Library name: Sample4
Column name in FPKM_8-cell.txt:TMZ-8-cell-rep2


title: EP condition, replicate 2b

description:
Library name: EP2b
10x Genomics


title: BM-AG-CTRL-2

description:
Library name: 41_S5_L003
10x Genomics


title: mouse 8-Cell embryo，Control2

address: 瓯海区茶山街道温州医科大学

description:
Library name: Sample2
Column name in FPKM_8-cell.txt:Control-8-cell-rep2


title: BM-AG-CTRL-1

description:
Library name: 59_S4_L004
10x Genomics


title: BM-YG-6dpi-2

description:
Library name: 95_S3_L002
10x Genomics


title: Firefighter-ID-17 Dermal tape wrist [2-017-W]

value: Post

value: Career


title: EP condition, replicate 1

description:
Library name: EP1
10x Genomics


title: mouse 8-Cell embryo，Control1

address: 瓯海区茶山街道温州医科大学

description:
Library name: Sample1
Column name in FPKM_8-cell.txt:Control-8-cell-rep1


title: Firefighter-ID-13 Dermal tape wrist [2-013-W]

value: Male

value: Non_Hispanic White/European


title: Firefighter-ID-13 Blood serum [2-013]


title: BM-YG-6dpi-1

description:
Library name: 92_S7_L004
10x Genomics


title: E condition, replicate 4a

description:
Library name: E4a
10x Genomics

value: E


title: BM-YG-6dpi-3

description:
Library name: 98_S2_L002
10x Genomics

value: BM


title: LysoDCs from GPR31 KO mouse 3, infected

city: Shizuoka

first: Katsuhiro

last: Nakanishi

address: 52-1 Yada, Suruga-ku

country: Japan

institute: University of Shizuoka

description:
Library name: LysoDC KO infected 3
column name in raw_counts_All_samples.txt: KOinfect_3

data_processing:
Raw RNA-seq reads were trimmed and filtered for quality control using fastp. The clean reads were then mapped to the GRCm39 reference genome using HISAT2, and read counts for each sample were obtained using featureCounts.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Peyer's patches

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
The cDNA library was constructed using a SMART-Seq HT PLUS Kit (TaKaRa Bio) following the manufacturer’s protocol.

treatment_protocol: Wild-type and Gpr31b-deficient mice were orally administered 1 × 109 CFU of L. monocytogenes EGDe strain. Two days after infection, PP cells were prepared by collagenase D (Roche)/DNase I buffer. LysoDCs were sorted using the BD FACSAria™ II Cell Sorter.

value: Peyer's patches

value: GPR31 knockout

value: oral L. monocytogenes infection


title: EP condition, replicate 2a

description:
Library name: EP2a
10x Genomics

value: lung metastasis


title: Firefighter-ID-12 Dermal tape wrist [2-012-W]

value: Volunteer


title: BM-YG-4dpi-3

description:
Library name: 89_S2_L004
10x Genomics


title: LysoDCs from GPR31 KO mouse 2, infected

description:
Library name: LysoDC KO infected 2
column name in raw_counts_All_samples.txt: KOinfect_2


title: E condition, replicate 3b

description:
Library name: E3b
10x Genomics


title: Firefighter-ID-32 Dermal tape wrist [2-032-W]


title: LysoDCs from GPR31 KO mouse 1, infected

description:
Library name: LysoDC KO infected 1
column name in raw_counts_All_samples.txt: KOinfect_1


title: BM-YG-4dpi-1

description:
Library name: 83_S5_L004
10x Genomics


title: Firefighter-ID-15 Dermal tape wrist [2-015-W]


title: BM-YG-4dpi-2

description:
Library name: 86_S8_L004
10x Genomics


title: Firefighter-ID-19 Dermal tape wrist [2-019-W]


title: Firefighter-ID-17 Blood serum [2-017]


title: Firefighter-ID-14 Dermal tape wrist [2-014-W]


title: Firefighter-ID-15 Blood serum [2-015]


title: Firefighter-ID-32 Blood serum [2-032]


title: Firefighter-ID-14 Blood serum [2-014]


title: Firefighter-ID-12 Blood serum [2-012]


title: Firefighter-ID-11 Blood serum [2-011]


title: E condition, replicate 3a

description:
Library name: E3a
10x Genomics


title: LysoDCs from WT mouse 3, infected

description:
Library name: LysoDC WT infected 3
column name in raw_counts_All_samples.txt: WTinfect_3


title: Firefighter-ID-11 Dermal tape wrist [2-011-W]


title: BM-YG-2dpi-3

description:
Library name: 74_S2_L004
10x Genomics


title: E condition, replicate 2

description:
Library name: E2
10x Genomics


title: Firefighter-ID-9 Blood serum [2-009]


title: V condition, replicate 4a

description:
Library name: V4a
10x Genomics

value: V


title: LysoDCs from WT mouse 2, infected

description:
Library name: LysoDC WT infected 2
column name in raw_counts_All_samples.txt: WTinfect_2


title: LysoDCs from WT mouse 1, infected

description:
Library name: LysoDC WT infected 1
column name in raw_counts_All_samples.txt: WTinfect_1


title: BM-YG-2dpi-2

description:
Library name: 6_S5_L004
10x Genomics


title: Firefighter-ID-9 Dermal tape wrist [2-009-W]


title: BM-YG-2dpi-1

description:
Library name: 8_S9_L004
10x Genomics


title: LysoDCs from GPR31 KO mouse 2, uninfected

description:
Library name: LysoDC KO uninfected 2
column name in raw_counts_All_samples.txt: KOuninfect_2


title: V condition, replicate 2c

description:
Library name: V2c
10x Genomics


title: LysoDCs from GPR31 KO mouse 1, uninfected

description:
Library name: LysoDC KO uninfected 1
column name in raw_counts_All_samples.txt: KOuninfect_1


title: Firefighter-ID-7 Blood serum [2-007]


title: 6KO_sh1A_DS_rep2

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

description: Library name: 6KO_sh1A_DS_rep2

data_processing:
Trim adapter and low quality reads using Trim_galore
Map reads on mouse genome and transcripts by Tophat2
Calculate gene and TE texpression by Tetranscript
Assembly: mm10
Supplementary files format and content: tab-deliminated text file includes row counts in each sample

source_name: 6KO iMEFs

growth_protocol: We used previously established Setdb1, Suv39h1/2, Ehmt1, Ehmt2, Ring1b KO iMEFs to analysis the role of uH2A in heterochromatin maintenance (Fukuda et al., 2023). Mouse embryonic fibroblasts were maintained in Dulbecco's modified Eagle's medium (Nacalai tesque, 08458-16) containing 10% fetal bovine serum (Biosera, FB1061), MEM Non-Essential medium and 2-Mercaptoethanol (Nacalai tesque, 21417-52).

extract_protocol:
RNA was extracted by Rneasy plus mini kit (QIAGEN)
500 ng of total RNA was used for RNA-seq library construction. RNA-seq library was constructed by KAPA mRNA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit (Roche) according to manufacturer instructions. The concentration of the RNA-seq library was quantified by KAPA Library quantification kit (KAPA BIOSYSTEMS).

treatment_protocol: To inhibit EZH1/2 catalytic activity, iMEFs were cultured for seven days with 1 uM DS3201. To knockdown Ring1a, we produced a lentiviral vector expressing shRNA targeting Ring1a by transfecting 293FT cells with shRNA vector, psPax2, and pMD2.G using PEI. Two days later, we collected the culture supernatant and then used it to transduce 5KO-Ring1b KO iMEFs at MOI=2. Following selection with 7 μg/ml BSD for 3 days, we collected the cells.

value: 6KO iMEFs

tag: cell type

value: MEF

value: RIng1a shRNA + DS3201


title: V condition, replicate 2b

description:
Library name: V2b
10x Genomics


title: LysoDCs from WT mouse 3, uninfected

description:
Library name: LysoDC WT uninfected 3
column name in raw_counts_All_samples.txt: WTuninfect_3

value: WT


title: Firefighter-ID-6 Dermal tape wrist [2-006-W]


title: Firefighter-ID-7 Dermal tape wrist [2-007-W]


title: BM-YG-CTRL-3

description:
Library name: 80_S7_L004
10x Genomics


title: V condition, replicate 2a

description:
Library name: V2a
10x Genomics


title: BM-YG-CTRL-2

description:
Library name: 26_S3_L001
10x Genomics


title: V condition, replicate 1

description:
Library name: V1
10x Genomics


title: LysoDCs from GPR31 KO mouse 3, uninfected

description:
Library name: LysoDC KO uninfected 3
column name in raw_counts_All_samples.txt: KOuninfect_3


title: Firefighter-ID-6 Blood serum [2-006]


title: PBMC-AG-6dpi-3

description:
Library name: 67_S9_L003
10x Genomics

source_name: PBMC

value: PBMC


title: Firefighter-ID-44 Blood serum [1-044]

value: Pre


title: BM-YG-CTRL-1

description:
Library name: 11_S2_L004
10x Genomics


title: mLPS-NICD Knockout-p39

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

data_processing:
Salmon Index
DESeq2
Assembly: mm39
Supplementary files format and content: Results tables are generated using the function results, which extracts a results table with log2 fold changes, p values and adjusted p values.

source_name: mLPS1 NICD Knockout

extract_protocol:
TRI Reagent extracted total RNA followed by chloroform extraction and isopropanol precipitation of RNA.
Fragmentation, size selection, end repair and A-tailing, adaptor ligation, PCR amplification, and splint circularization

value: mLPS1 NICD Knockout

value: dedifferentiated liposarcoma cells

value: NICD Knockout


title: Firefighter-ID-44 Dermal tape wrist [1-044-W]

value: Male

value: Non_Hispanic White/European


title: LysoDCs from WT mouse 2, uninfected

description:
Library name: LysoDC WT uninfected 2
column name in raw_counts_All_samples.txt: WTuninfect_2

value: Peyer's patches


title: 6KO_sh1A_DS_rep1

description: Library name: 6KO_sh1A_DS_rep1


title: PBMC-AG-6dpi-2

description:
Library name: 64_S6_L003
10x Genomics


title: 6KO_scr_DS_rep2

description: Library name: 6KO_scr_DS_rep2

value: ctr shRNA + DS3201


title: PBMC-AG-4dpi-3

description:
Library name: 27_S2_L002
10x Genomics


title: 6KO_sh1A_rep1

description: Library name: 6KO_sh1A_rep1

value: Ring1a shRNA


title: PBMC-AG-4dpi-1

description:
Library name: 36_S6_L002
10x Genomics


title: Input CATCH-seq in 5KO+DS iMEFs rep2

description: Library name: Input_5KO_DS_rep2

data_processing:
Trim adapter and low quality reads using Trim_galore
Map reads on mouse genome by Bowtie2
Remove PCR duplicates by Picard
Assembly: mm10
Supplementary files format and content: bigWig

source_name: 5KO+DS iMEFs

extract_protocol:
ChIP DNA was extracted by Native ChIP protocol
The ChIP DNA was fragmented by Picoruptor (Diagenode) for 10 cycles of 30 seconds on, 30 seconds off. Then, ChIP library was constructed by KAPA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit A (Roche) according to manufacturer instructions. The concentration of the ChIP-seq library was quantified by KAPA Library quantification kit (KAPA BIOSYSTEMS). ChIP sequencing was performed on a HiSeq X platform (Illumina). H2Aub CATCH-seq libraries were prepared as previously described (Zhu et al., 2021) with some modifications. Briefly, 2,000 MEFs per sample were used for library construction. Cells were permeabilized by Nuclei EZ lysis buffer supplemented with 0.1% Triton, 0.1% deoxycholate, complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride on ice. For each sample, 800 S2 Drosophila culture cells were added for a spike-in normalization purpose. Chromatin was fragmented in situ by 2 U/µl MNase (M0247S, NEB) at 37C for 7.5 min. The reaction was stopped by adding 1/10 volume of 100 mM EDTA and diluted in the freshly prepared immunoprecipitation buffer. As an input, 5% of the chromatin lysate was taken. Then, 30 ng of annealed I-SceI carrier DNA was added to each sample. The forward and reverse strands of the carrier DNA were as follows: /5AmMC6/Gtagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggat aacagggtaat*c/3AmMO/ and /5AmMC6/Gattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatcc cta*c/3AmMO/, respectively, where asterisks represent phosphorothioate bonds. The oligos were synthesized by Integrated DNA Technologies. For each immunoprecipitation reaction, 0.5 µl of rabbit monoclonal anti-H2AK119 monoubiquitylation antibody (Cell Signaling, #8240) conjugated to precleared Dynabeads Protein A and G mixture was used. After immunoprecipitation at 4C overnight, the chromatin-Dynabeads were washed by the low and high salt wash buffers, and the chromatin was eluted in the freshly prepared ChIP elution buffer at 65C for 1 hr. DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. Adaptor ligation was pre-formed by NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB) in a half scale of the manufacturer’s instruction, and the libraries were purified by 1.8x SPRIselect beads (B23318, Beckman Coulter). The DNA was amplified by KAPA Hifi 2X mater PCR mix (KK2605) for 14 PCR cycles with indexing primers. After purification with 0.9x SPRIselect beads, the samples were digested by I-SceI (5 U/µl, NEB, R0694) 37C for 2 hrs followed by heat inactivation at 65C for 20 min and purified by 0.9x SPRIselect beads. The second amplification was not performed. The libraries were sequenced on a HiSeq X.

value: 5KO+DS iMEFs

value: DS3201 treatment


title: LysoDCs from WT mouse 1, uninfected

description:
Library name: LysoDC WT uninfected 1
column name in raw_counts_All_samples.txt: WTuninfect_1


title: Firefighter-ID-42 Blood serum [1-042]

value: Volunteer


title: 6KO_scr_DS_rep1

description: Library name: 6KO_scr_DS_rep1

value: 6KO iMEFs


title: mLPS-NICD Knockout-p36


title: mLPS1-p35

source_name: mLPS1 wild type

value: mLPS1 wild type


title: 6KO_scr_rep1

description: Library name: 6KO_scr_rep1

value: MEF

value: ctr shRNA


title: PBMC-AG-2dpi-2

description:
Library name: 43_S3_L003
10x Genomics

value: PBMC


title: Firefighter-ID-38 Dermal tape wrist [1-038-W]

value: Pre


title: Firefighter-ID-42 Dermal tape wrist [1-042-W]


title: mLPS-NICD Knockout-p34

value: mLPS1 NICD Knockout


title: Firefighter-ID-38 Blood serum [1-038]


title: mLPS1-p37

value: dedifferentiated liposarcoma cells

value: WT


title: Firefighter-ID-34 Blood serum [1-034]

value: Male


title: PBMC-AG-4dpi-2

description:
Library name: 28_S5_L002
10x Genomics


title: Firefighter-ID-34 Dermal tape wrist [1-034-W]

value: Non_Hispanic White/European


title: Male-Folate3-ip

city: Guangzhou

first: Xiaoyun

last: Wang

address: 190 Kaiyuan Avenue, Huangpu

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
*library strategy: meRIP-seq
Adaptors and raw reads containing low-quality bases were first removed by applying trim_galore (version 0.6.6) to all RNA-seq raw data including the MeRIP-seq input libraries. The resulting reads of at least 35 bp were mapped to the reference genome (mm39, dm6-FLYBASE).
The obtained comparison results were removed and sorted using samtools (version 1.3.1) for PCR duplicates.
The featureCounts program (43) in the Subread package (version 2.0.1) at SourceForge was used to count the reads that mapped to genes. The genes that showed an average read count of less than 10 in any group or lacked read count in any replicate were primarily filtered.
The R package DESeq2 (version 1.36.0) was used for the identification of differentially expressed genes (DEGs) by setting a false discovery rate-corrected P value < 0.05 and fold change >= 0.5 as the thresholds for significance.
We first processed the raw data of MeRIP-seq IP libraries with the same upstream pipeline employed for RNA-seq. The mapping results of both MeRIP-seq IP and input libraries were used for calling m6A peaks. Differential m6A peaks of the single-factor comparisons between groups were analyzed using the R package exomePeak2 (version 1.8.1) (45), with Poisson's generalized linear model (GLM) used as a quantitative method to call the m6A peaks of individual groups as well as the m6A peaks of single-factor comparative differences between groups. To reduce false positives, the called m6A peaks from each biological replicate were considered significant and retained for subsequent analyses according to the following thresholds: peak width <= 1500 bp, log2FC > 1, FDR < 0.05, Input.RPM>=0.1, IP.RPM>=0.1. Similarly, the called differential m6A peaks between groups were considered significant under the following thresholds: peak width <= 1500 bp, |diff.log2FC|>1, FDR < 0.05, Input.Control.RPM>0.1, IP.Control.RPM>0.1, Input.Treated.RPM>0.1, IP.Treated.RPM>0.1. HOMER (version 3.12) (46) was used for de novo motif searching around peak summit-centered (mouse, peak 300 bp region; Drosophila, peak 250 bp) regions. The R packages ChIPseeker (version 1.32.0) (47) and Guitar (version 2.12.0) (48) were used for annotation and representation of the distribution characteristics of the significant/differential m6A peaks. The bamCoverage script in deeptools (version 3.5.1) was used to perform read-coverage trajectory calculations on the results of mapping IP libraries and Input libraries to the genome. Integrative Genomics Viewer (IGV) software (version 2.14.0) (49) was used to display read coverage tracks of target genes.
Assembly: mm39,dm6-FLYBASE
Supplementary files format and content: bed
Supplementary files format and content: csv

organism: Mus

source_name: brain

extract_protocol:
Total RNAs were extracted with Trizol and NanoDrop 2000 spectrophotometer (ThermoFisher) was used to quantify the concentration of total RNA at a wavelength of 260 nm.
About 1.5 µg of purified poly(A)-RNA was fragmented into ~100 nt fragments using RNA fragmentation buffer (AM8740, Thermo Scientific). One-tenth of fragmented RNAs were used for the construction of RNA-seq libraries (Input) and the left RNAs were used for the construction of m6A MeRIP-seq libraries (IP). m6A IP was conducted using an EpiMark® N6-Methyladenosine Enrichment Kit (#E1610S, NEB) following the product manual. The resultant m6A-enriched and untreated poly(A)-RNA fragments were used to construct strand-specific IP and Input libraries, respectively. A VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (NR604-02, Vazyme Biotech. Co., Ltd.) and VAHTS® RNA Adapters set3 for Illumina (N809, Vazyme Biotech. Co., Ltd.) provided the necessary reagents for first- and second-strand cDNA synthesis, adaptor ligation, and library amplification. RNA-seq and MeRIP-seq of the prepared libraries were performed in Berry Genomics on the NovaSeq 6000 platform (Illumina, CA, USA) to obtain paired-end reads of 150 bp. Library quality was assessed on an Agilent Bioanalyzer 4200 TapeStation before loading onto the sequencer, ~8G of raw reads was obtained for each library.

value: brain

tag: strain

value: C57BL/6J SPF


title: PBMC-AG-CTRL-3

description:
Library name: 70_S8_L003
10x Genomics

tag: tissue


title: Male-Folate2-ip


title: PBMC-AG-CTRL-2

description:
Library name: 40_S4_L003
10x Genomics


title: PBMC-AG-2dpi-1

description:
Library name: 37_S1_L003
10x Genomics


title: Male-Folate1-ip


title: Input CATCH-seq in WT+DS iMEFs rep2

description: Library name: Input_WT_DS_rep2

source_name: WT+DS iMEFs

value: WT+DS iMEFs


title: PBMC-YG-6dpi-3

description:
Library name: 97_S5_L002
10x Genomics


title: Male-Folate3


title: Input CATCH-seq in WT+DS iMEFs rep1

description: Library name: Input_WT_DS_rep1


title: Input CATCH-seq in 5KO+DS iMEFs rep1

description: Library name: Input_5KO_DS_rep1

value: 5KO+DS iMEFs


title: Firefighter-ID-32 Blood serum [1-032]

value: Career

tag: gender


title: Firefighter-ID-33 Dermal tape wrist [1-033-W]

value: Female

tag: age


title: PBMC-YG-6dpi-2

description:
Library name: 94_S4_L002
10x Genomics


title: Male-Folate2


title: Firefighter-ID-36 Blood serum [1-036]

value: Volunteer


title: mLPS1-p40

value: mLPS1 wild type


title: PBMC-AG-2dpi-3

description:
Library name: 46_S1_L004
10x Genomics


title: PBMC-AG-6dpi-1

description:
Library name: 61_S3_L003
10x Genomics


title: Input CATCH-seq in WT iMEFs rep2

description: Library name: Input_WT_rep2

source_name: WT iMEFs

value: WT iMEFs

value: MEF

value: No treatment


title: Male-Folate1


title: 6KO_sh1A_rep2

description: Library name: 6KO_sh1A_rep2

value: 6KO iMEFs

value: Ring1a shRNA


title: Input CATCH-seq in 5KO iMEFs rep2

description: Library name: Input_5KO_rep2

source_name: 5KO iMEFs

value: 5KO iMEFs


title: PBMC-YG-6dpi-1

description:
Library name: 91_S4_L004
10x Genomics

value: PBMC


title: Firefighter-ID-36 Dermal tape wrist [1-036-W]

source_name: Dermal tape wrist

value: Pre

value: Male


title: Firefighter-ID-32 Dermal tape wrist [1-032-W]

value: Non_Hispanic White/European


title: Firefighter-ID-31 Blood serum [1-031]

source_name: Blood serum


title: Firefighter-ID-33 Blood serum [1-033]


title: Input CATCH-seq in WT iMEFs rep1

description: Library name: Input_WT_rep1

value: WT


title: Firefighter-ID-31 Dermal tape wrist [1-031-W]


title: PBMC-YG-4dpi-3

description:
Library name: 88_S1_L004
10x Genomics


title: 6KO_scr_rep2

description: Library name: 6KO_scr_rep2

value: ctr shRNA


title: Male-Control3-ip

value: brain

value: C57BL/6J SPF


title: uH2A CATCH-seq in 5KO+DS iMEFs rep2

description: Library name: uH2A_5KO_DS_rep2

value: 5KO+DS iMEFs

value: DS3201 treatment


title: PBMC-YG-4dpi-2

description:
Library name: 85_S11_L004
10x Genomics


title: Male-Control1-ip


title: uH2A CATCH-seq in 5KO+DS iMEFs rep1

description: Library name: uH2A_5KO_DS_rep1


title: PBMC-AG-CTRL-1

description:
Library name: 58_S5_L004
10x Genomics


title: PBMC-YG-4dpi-1

description:
Library name: 82_S2_L003
10x Genomics


title: Firefighter-ID-30 Blood serum [1-030]

value: Career


title: Firefighter-ID-29 Blood serum [1-029]


title: uH2A CATCH-seq in 5KO iMEFs rep2

description: Library name: uH2A_5KO_rep2


title: PBMC-YG-2dpi-2

description:
Library name: 4_S4_L004
10x Genomics


title: uH2A CATCH-seq in WT+DS iMEFs rep2

description: Library name: uH2A_WT_DS_rep2

value: WT+DS iMEFs


title: uH2A CATCH-seq in 5KO iMEFs rep1

description: Library name: uH2A_5KO_rep1

value: MEF


title: Male-Control1


title: Male-Control3


title: Input CATCH-seq in 5KO iMEFs rep1

description: Library name: Input_5KO_rep1

value: No treatment


title: Male-Control2


title: Male-Control2-ip


title: PBMC-YG-2dpi-1

description:
Library name: 7_S7_L004
10x Genomics


title: Female-Folate3-ip


title: PBMC-YG-CTRL-3

description:
Library name: 79_S5_L001
10x Genomics


title: Firefighter-ID-29 Dermal tape wrist [1-029-W]


title: Firefighter-ID-27 Blood serum [1-027]

value: Volunteer

value: S. American Native


title: Firefighter-ID-30 Dermal tape wrist [1-030-W]


title: Firefighter-ID-28 Dermal tape wrist [1-028-W]


title: uH2A CATCH-seq in WT iMEFs rep2

description: Library name: uH2A_WT_rep2

value: WT iMEFs


title: uH2A CATCH-seq in WT+DS iMEFs rep1

description: Library name: uH2A_WT_DS_rep1


title: Female-Folate2-ip


title: PBMC-YG-CTRL-2

description:
Library name: 35_S6_L001
10x Genomics

value: PBMC


title: Firefighter-ID-27 Dermal tape wrist [1-027-W]

value: Pre


title: PBMC-YG-CTRL-1

description:
Library name: 10_S1_L001
10x Genomics


title: uH2A CATCH-seq in WT iMEFs rep1

description: Library name: uH2A_WT_rep1


title: Input in 6KO+sh1A iMEFs rep2

description: Library name: Input_6KO_sh1A_rep2

value: 6KO iMEFs

value: RIng1a shRNA


title: Female-Folate3


title: PBMC-YG-2dpi-3

description:
Library name: 73_S3_L004
10x Genomics


title: Spleen-AG-6dpi-3

description:
Library name: 69_S11_L003
10x Genomics

source_name: Spleen

value: Spleen


title: Input in 6KO+sh1A iMEFs rep1

description: Library name: Input_6KO_sh1A_rep1


title: Spleen-AG-6dpi-2

description:
Library name: 66_S8_L003
10x Genomics


title: Firefighter-ID-24 Dermal tape wrist [1-024-W]

value: Male

value: Non_Hispanic White/European


title: Female-Folate2

value: brain

value: C57BL/6J SPF


title: Spleen-AG-6dpi-1

description:
Library name: 63_S5_L003
10x Genomics


title: Female-Folate1


title: Firefighter-ID-23 Blood serum [1-023]


title: Spleen-AG-4dpi-3

description:
Library name: 31_S1_L003
10x Genomics


title: H3K27me3 ChIP-seq in 6KO+sh1A iMEFs rep1

description: Library name: H3K27me3_6KO_sh1A_rep1


title: Female-Control3-ip


title: Spleen-AG-4dpi-2

description:
Library name: 32_S4_L002
10x Genomics


title: Female-Control2-ip


title: Female-Folate1-ip


title: Hi-C in 6KO+sh1A+DS rep1

description:
Library name: Hi-C_6KO_sh1A_DS_rep1
Hi-C_6KO_sh1A_DS_rep1

data_processing:
4DN Hi-C pipeline (v43, https://github.com/4dn-dcic/docker-4dn-hic).
Assembly: mm10
Supplementary files format and content: .hic

extract_protocol:
2x10^6 fixed cells were sujected to Hi-C analysis
Hi-C experiments were performed as previously described (Ikeda et al., 2018; Kadota et al., 2020), based on DpnII enzyme (4-bps cutter) using 2×10^6 fixed cells. Hi-C libraries were subject to paired-end sequencing (150 base pair (bp) read length) using HiSeq X Ten. Detailed protocol for HiC-seq library preparation is available at Protocols.io (https://www.protocols.io/view/iconhi-c-protocol-ver-1-0-4mjgu4n).

value: Ring1a shRNA + DS3201


title: Firefighter-ID-24 Blood serum [1-024]


title: Hi-C in 6KO+sh1A+DS rep2

description:
Library name: Hi-C_6KO_sh1A_DS_rep2
Hi-C_6KO_sh1A_DS_rep2


title: Spleen-AG-4dpi-1

description:
Library name: 34_S7_L002
10x Genomics


title: Firefighter-ID-20 Blood serum [1-020]

value: Career


title: Hi-C in 6KO+scr+DS rep2

description:
Library name: Hi-C_6KO_scr_DS_rep2
Hi-C_6KO_scr_DS_rep2

value: scr shRNA + DS3201


title: Firefighter-ID-19 Blood serum [1-019]


title: Female-Control3


title: Spleen-AG-2dpi-3

description:
Library name: 48_S1_L003
10x Genomics


title: Hi-C in 6KO+scr+DS rep1

description:
Library name: Hi-C_6KO_scr_DS_rep1
Hi-C_6KO_scr_DS_rep1

value: MEF


title: H3K27me3 ChIP-seq in 6KO+sh1A iMEFs rep2

description: Library name: H3K27me3_6KO_sh1A_rep2


title: Hi-C in 6KO+sh1A reo2

description:
Library name: Hi-C_6KO_sh1A_rep2
Hi-C_6KO_sh1A_rep2


title: Firefighter-ID-23 Dermal tape wrist [1-023-W]


title: Spleen-AG-2dpi-2

description:
Library name: 45_S4_L004
10x Genomics


title: Female-Control1


title: Hi-C in 6KO+sh1A rep1

description:
Library name: Hi-C_6KO_sh1A_rep1
Hi-C_6KO_sh1A_rep1


title: Spleen-AG-2dpi-1

description:
Library name: 39_S1_L001
10x Genomics


title: Female-Control2


title: Firefighter-ID-19 Dermal tape wrist [1-019-W]


title: Spleen-AG-CTRL-3

description:
Library name: 72_S6_L003
10x Genomics


title: Firefighter-ID-15 Blood serum [1-015]


title: Firefighter-ID-17 Dermal tape wrist [1-017-W]


title: Firefighter-ID-17 Blood serum [1-017]


title: Hi-C in 6KO+scr rep2

description:
Library name: Hi-C_6KO_scr_rep2
Hi-C_6KO_scr_rep2

value: scr shRNA


title: Female-Control1-ip


title: Spleen-AG-CTRL-2

description:
Library name: 42_S2_L003
10x Genomics


title: Firefighter-ID-20 Dermal tape wrist [1-020-W]


title: MesenchymalPanel_6

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

country: Canada

institute: University of British Columbia

description: Mouse Mesenchymal gene panel

hyb_protocol: Sections were incubated in a probe solution for 22 hours at 50°C for hybridization. The probe solution contained a set of 347 or 480 gene-targeting probes (described in methods) in TE buffer (Fisher). The rest of the Xenium workflow for fresh frozen tissue (fixation, permeabilization, ligation, amplification, etc) was performed as recommended by 10x Genomics.

scan_protocol: Full sections were imaged and analyzed using the Xenium Analyzer, software v1.7.6.0.

data_processing: Output files (transcripts, cell boundaries, features, etc) were generated directly by the Xenium onboard analysis pipeline (analysis v1.7.1.0). **Important note on file names** File names have been pre-fixed with their associated sample to ensure they are unumbigious when contained in the upload folder (e.g. "BrainPanel1_" for BrainPanel_1). However, the experiment.xenium file will try to pull paths from non-prefixed files (e.g. "morphology.ome.tif", rather than "BrainPanel1_morphology.ome.tif"). Hence, data users should remove these pre-fixes prior to using the data. The probeset panel design file is listed as gene_panel.json, with the prefix either ‘Brain’ or ‘Mesenchymal’ to indicate which sample it’s associated with.  Remove the prefix before using the data.

label: Gene targeting probes

label_protocol: Single cell spatial transcriptomics was performed using a panel targeting 347 (Brain) or 480 (Mesenchymal)  mRNA transcripts. 247 of these probes were from the mouse brain panel designed by 10x Genomics (10xgenomics.com/products/xenium-panels) for the Brain Panel. An additional 100 custom probes were added which are documented in Ebert et al. supplementary table 9 and in the gene_panel.json raw data file attached. The mesenchymal panel consists of a fully custom 480 probe panel set also described in supplementary table 9

extract_protocol: Once dissected, brains were immediately embedded in O.C.T. compound (Tissue-Tek) on dry ice, stored at -70°C, and cryosectioned coronally onto Xenium slides (chemistry v1) to produce 10 μm sections.

value: F

value: brain, forebrain

value: adult


title: MesenchymalPanel_5

description: Mouse Mesenchymal gene panel

value: M


title: Hi-C in 6KO+scr rep1

description:
Library name: Hi-C_6KO_scr_rep1
Hi-C_6KO_scr_rep1


title: MesenchymalPanel_4

description: Mouse Mesenchymal gene panel


title: Spleen-AG-CTRL-1

description:
Library name: 60_S6_L004
10x Genomics


title: MesenchymalPanel_3

description: Mouse Mesenchymal gene panel


title: nphp1/nphp4 morphant embryos (48 hpf), treatment (Omarigliptin), sample 4

city: Freiburg im Breisgau

first: Toma

middle: Antonov

last: Yakulov

address: Hugstetter Str. 55

department: Department of Medicine

country: Germany

institute: University Freiburg Medical Center

description: Library name: Omarigliptin 4

data_processing:
Raw RNA sequencing reads were quality-controlled with FastQC (v0.11.8) and pre-processed with cutadapt (v4.0) to trim low-quality bases, adapter sequences, and remove low-quality reads. Processed reads were aligned against the zebrafish reference genome GRCz11 from Ensembl (v110) using STAR (v2.6.1e). Gene counts were obtained during alignment using the "--quantMode GeneCounts" option.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file containing raw counts (as generated by the STAR aligner)

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish were maintained according to standard protocols and in compliance with the guidelines of the local animal ethics committee at the Regierungspräsidium Freiburg (permit G-21/146).

extract_protocol:
Total RNA was extracted from 15-50 embryos at 48 hpf using the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.
Samples were sent for sequencing to Novogene (Cambridge, UK) on an Illumina platform.

treatment_protocol: Antisense morpholino oligonucleotides (MO) were diluted in 100mM KCL, 10mM 4- (2-hydroxyethyl)-1-piperazineethanesulfonic acid and 0.1% phenol red (Sigma-Aldrich). 4nl of this solution was microinjected into fertilized eggs at the one-cell stage (respectively 0.15mM nphp1 MO and 0.25mM nphp4 MO). All MO were co-injected with p53-MO to reduce off-target effects. At 24 hpf, embryos were dechorionated and incubated with DMSO or 25μM Omarigliptin. All embryos were additionally incubated in PTU (0.003% 1-phenyl-2-thiourea) to avoid skin pigmentation. Total RNA was extracted from 15-50 embryos at 48 hpf.

value: whole embryo

value: nphp1 & nphp4 MO, Omarigliptin


title: Firefighter-ID-15 Dermal tape wrist [1-015-W]

value: Pre


title: nphp1/nphp4 morphant embryos (48 hpf), treatment (Omarigliptin), sample 3

description: Library name: Omarigliptin 3


title: Firefighter-ID-14 Blood serum [1-014]


title: Spleen-YG-6dpi-2

description:
Library name: 96_S6_L002
10x Genomics

value: Spleen


title: MesenchymalPanel_2

description: Mouse Mesenchymal gene panel


title: MesenchymalPanel_1

description: Mouse Mesenchymal gene panel


title: nphp1/nphp4 morphant embryos (48 hpf), control (DMSO), sample 4

description: Library name: DMSO 4

value: nphp1 & nphp4 MO, DMSO


title: Spleen-YG-4dpi-3

description:
Library name: 90_S3_L004
10x Genomics


title: Spleen-YG-4dpi-2

description:
Library name: 87_S9_L004
10x Genomics


title: Firefighter-ID-12 Blood serum [1-012]

value: Volunteer

value: Male

value: Non_Hispanic White/European


title: nphp1/nphp4 morphant embryos (48 hpf), control (DMSO), sample 3

description: Library name: DMSO 3


title: nphp1/nphp4 morphant embryos (48 hpf), control (DMSO), sample 2

description: Library name: DMSO 2


title: BrainPanel_1

description: Mouse brain gene panel