title: PDX derived 48396 #346, DMSO treated, 24 hours, rep3

description:
Library name: 48396_346_DMSO_3
J3
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_346_DMSO_1, 48396_346_DMSO_2, 48396_346_DMSO_3
MCC_counts.csv
treated_vs_untreated_counts.csv

value: DMSO


title: PDB_POD30

status: Public on Apr 03 2026

type: SRA

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

country: USA

institute: University of Arizona

description:
Library name: PDB_POD30
10x Genomics

library_source: transcriptomic single cell

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq
Then aligned against the mm10 (mouse) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis
Assembly: mm10 (mouse)
Supplementary files format and content: Tab seperated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: freshly isolated cells from wound tissue

growth_protocol: Freshly isolated murine cells from murine skin or wounds.

extract_protocol:
Tissue was enzymatically digested, cells were collected and washed. These cellular suspensions were then submitted for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA).
cDNA was fragmented followed by end repair and A-tailing at 65°C for 30min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.

treatment_protocol: Murine wounds were created using our excisional wounding protocol, in either leptin-receptor knockout, wildtype mice, or wildtype mice fed with a high-fat diet, then submitted for scRNA-seq analysis.

tag: tissue

tag: genotype

value: wildtype

tag: diet

value: High-fat diet

tag: strain


title: RBM25_MUT_2

city: Cleveland

first: Soon Yeul

last: Yi

state: OH

address: CWRU Wood Research Building W127A, 2109 Adelbert Rd,

department: Biochemistry

institute: Case Western Reserve University

description:
Library name: JL4460_RBM25_MUT_2
V5-RBM25-MUT-Rep2

library_source: transcriptomic

data_processing:
Raw fastq files were used as an input for CLIPittyClip processing pipeline (PMID: 38658162)
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file containing peak coordinates

organism: Homo sapiens

growth_protocol: HEK293 cell lines were grown and maintained at 37°C in DMEM media containing 5% FBS and 1% NEAA.

extract_protocol:
Cell pellets were lysed with PBS lysis buffer (1x PBS, 0.1% SDS, 0.5% NaDoc, 0.5% NP-40, 1 protease inhibitor tablet (Roche)) for 10 minutes on ice. Lysate was then treated with RQ1 DNase (Promega) for 5 minutes at 37°C with shaking at 1100RPM. The lysates were then briefly treated with RNase I at 1:100 or 1:1000 dilutions at the same condition as DNase treatment. Lysates were clarified by centrifuging on tabletop 4°C centrifuge for 10 minutes. For V5-tagged protein samples, V5 antibody (Addgene, cat. #218107-rAB) was used. For endogenous HNRNPC IP in competition CLIP samples, anti-HNRNPC antibody (Invitrogen, cat. #PA5-22280) was used. Immunoprecipitated samples were labeled with radioactivity (gamma-32P-ATP (Revvity)) and ran on SDS-PAGE in non-reducing conditions. The gels were transferred to a nitrocellulose membrane, and bands 10-30kDa above hnRNPC (32kDa) were excised. The excised membranes were treated with proteinase K (Roche) to release the protein-bound RNAs from the membrane.
CLIP footprints were reverse-transcribed using the BrdU incorporation and bead-capture strategy described previously (PMID: 24613350).

treatment_protocol: Expression of the exogenous V5-tagged HNRNPC/RBM25 was induced by treating the cells with 1ug/mL doxycycline for 48 hours. For competition CLIP conditions, wildtype or mutant RBM25 (harboring the HNRNPC RRM) was overexpressed and RNA-bound HNRNPC was immunoprecipitated. For knockdown conditions, siRNA targeting endogenous HNRNPC was transfected prior to doxycycline induction, such that doxycycline simultaneously induced expression of the exogenous V5-tagged HNRNPC construct and depletion of endogenous HNRNPC. Cellular media was replaced with ice-cold PBS for crosslinking using 254nm UV light, on ice, for a dose of 400mJ/cm^2 and a dose of 200mJ/cm^2. Samples were scraped into tubes, centrifuged and cell pellets stored at -80°C until use.

tag: cell line

tag: cell type

value: Human embryonic Kidney

tag: treatment

value: Doxycycline


title: PDX derived 48396 #325, DMSO treated, 24 hours, rep3

status: Public on Apr 02 2026

city: Boston

first: Andrew

last: Cherniack

state: Mass

address: 450 Brookline Ave

department: Molecular Oncology

institute: Dana Farber Cancer Institute

description:
Library name: 48396_325_DMSO_3
I3
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_325_DMSO_1, 48396_325_DMSO_2, 48396_325_DMSO_3
MCC_counts.csv
treated_vs_untreated_counts.csv

data_processing:
Reads containing adapters, containing N > 10% or with a Qscore <= 5 were removed by Novogene.
Reads were mapped to hg38 using STAR with GENCODE v47 for gene annotation. STAR was run with quantMode GeneCounts to retrieve raw read counts per gene.
Only genes with counts of 10 or higher in at least 3 samples were kept for further analysis. DESeq2 v1.42.1 was used to derive normalized counts.
Assembly: hg38
Supplementary files format and content: treated_vs_untreated_counts csv file contains normalized counts from running DESeq only on samples treated with DMSO and KTX-049. Additionally, MKL-1 is excluded from this file.
Supplementary files format and content: WaGa_counts csv file contains normalized counts from running DESeq on KTX and DMSO treated MCC / PDX 48396 samples
Supplementary files format and content: WaGa_counts csv file contains normalized counts from running DESeq on KTX and DMSO treated WaGa and WaGa CDX samples only
Supplementary files format and content: WaGa_parental_counts csv file contains normalized counts form running DESeq on WaGa parental samples only but all treatments
Supplementary files format and content: MKL_counts csv file contains normalized counts from running DESeq on MKL samples only but all treatments

molecule: polyA RNA

source_name: PDX derived cell line 48396 #325

growth_protocol: MKL-1, WaGa and WaGa CDX derived  cell lines were cultured in RPMI medium supplemented with 10% FBS, 1% Penicillin and Streptomycin and 1% GlutaMAX. MCC-301 and PDX derived cell lines were cultured in NeuroCult NS-A medium with 10% proliferation supplement, 1% Penicillin and Streptomycin, EGF, FGF (10mL of 100mg/mL stock solutions in 50 mL medium) and 0.02% Heparin. The cells were grown in an 37˚C incubator with 5% CO2.

extract_protocol:
Cells were collected by centrifugation, resuspended in TRIzol LS reagent followed by incubation at room temperature for five minutes. The homogenized samples were incubated with chloroform followed by centrifugation. The aqueous layer was transferred to an RNAeasy spin column and the Qiagen kit protocol for RNA extraction was followed (Qiagen # 74134). RNA QC analysis, mRNA library preparation (poly A enrichment) and sequencing (PE150, 15G raw data per sample) using NovaSeq X plus Series was carried out by Novogene Corporation.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. (cited from Novogene sequencing report)

treatment_protocol: Cells were seeded in the appropriate media and treated with DMSO, KTX-049 or DS-3032 for 24 hours.

value: PDX derived cell line 48396 #325

value: Merkel cell carcinoma cells

tag: time

value: 24 hours


title: Ctrl_IVM_OOCYTE_10

city: Baton Rouge

first: Hao

last: Ming

state: Louisiana

address: 39 Forestry Ln

department: School of Animal Science

institute: Louisiana State University

description:
Library name: sample20
colname in express_tpm.csv: O20

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore (version 0.6.7) (-q 25 --length 20 --max_n 3 --stringency 3). The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (GRCm39) by HISAT2 (version 2.2.1) with default parameters. The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14). Read counts of all samples were quantified by using FeatureCount (Version 2.0.1) with mouse genome as a reference and were adjusted to provide tpm (Counts per million mapped reads). Principal component analysis (PCA) and cluster analysis were performed by using R (a free software environment for statistical computing and graphics). Differentially expressed genes (DEGs) was identified by using edgeR in R. The genes were considered differentially expressed if they provided a false discovery rate of <0.05 and fold change >2. ClusterProfiler was used to reveal the Gene Ontology (GO) and KEGG pathways in R.
Assembly: UCD1.3
Supplementary files format and content: csv, normalized read counts

organism: Bos taurus

source_name: OOCYTE

growth_protocol: Immature COCs were recovered and transferred to either conventional or modified maturation systems. Maturation was performed using Tissue Culture Medium 199 (TCM199) supplemented with 10% fetal bovine serum, 2 mM glutamine, 0.2 mM sodium pyruvate, 1% penicillin-streptomycin, 50 ng/mL epidermal growth factor (EGF), and 5 µg/mL FSH. The pre-maturation medium used the same formulation excluding EGF and was supplemented with 200 nM CNP (Sigma 05-23-0310) for the 6-hour treatment period. Oocytes were divided between conventional and CNP maturation systems and incubated under 5% CO2 at 38.5°C. Conventional maturation lasted 22 hours while the modified system included a 6-hour pre-maturation CNP culture followed by 22 hours of maturation. After maturation, COCs were denuded in hyaluronidase and nuclear maturation was verified by the presence of a polar body. Individual GV and MII oocytes were collected for subsequent analyses.

extract_protocol:
Individual oocytes were washed three times in Dulbecco’s phosphate buffered saline (DPBS) and transferred to a 1.5 mL tube with 1 µL of media. Once in the 1.5 mL, individual oocytes were snap-frozen and stored at -80°C until RNA extraction and library preparation. RNA extraction was performed using the SMART-Seq® v4 Ultra® Low Input RNA Kit for sequencing (Takara Bio USA, Inc., San Jose, CA, USA) according to the manufacturer’s protocol.
The RNA-seq libraries were generated from oocytes by using the Smart-seq2 v4 kit with minor modification from manufacturer’s instructions. Briefly, individual cells were lysed, and mRNA was captured and amplified with the Smart-seq2 v4 kit (Clontech). After AMPure XP beads purification, amplified RNAs were quality checked by using Agilent High Sensitivity D5000 kit (Agilent Technologies). High-quality amplified RNAs were subject to library preparation (Nextera XT DNA Library Preparation Kit; Illumina) and multiplexed by Nextera XT Indexes (Illumina). The concentration of sequencing libraries was determined by using Qubit dsDNA HS Assay Kit (Life Technologies) and KAPA Library Quantification Kits (KAPA Biosystems). The size of sequencing libraries was determined by means of High Sensitivity D5000 Assay in at Tapestation 4200 system (Agilent). Pooled indexed libraries were then sequenced on the Illumina HiSeq X platform with 150-bp paired-end reads.

value: OOCYTE

value: WT

value: in vitro maturation


title: HEK293T_Mix_S7E_sp_2rep

city: Austin

first: Yan Jessie

last: Zhang

state: TX

address: 100 E 24th St

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Library name: Mix_S7E_sp_2rep

library_source: genomic

data_processing:
Reads were trimmed and filtered using cutadapt v.4.6.
Reads were aligned to the hg38 human genome (Ensembl) with Bowtie2 v.2.4.5 for Chip.
Alignment files were converted to Bam files with Samtools (version 1.14) for downstream analysis.
bamCompare v.3.5.5 was used to generate bigWig files normalized to Input (control) for each sample using the log2 ratio of mapped reads (MAPQ > 10).
Data matrices were generated using the computeMatrix function in Deeptools v3.5.1, from which metagene plots and heatmaps were derived.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Human embryonic kidney

growth_protocol: HEK293T were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin and incubated at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature, followed by quenching with 0.125 M glycine for 5 min. Cells were sequentially lysed in 1 mL LB1 buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and 1×protease and phosphatase inhibitor (1×PPI)) at 4°C for 10 min. After centrifugation and supernatant removal, the pellet was washed with 1 mL LB2 buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1×PPI) at 4°C for 5 min. The pellet was collected by centrifugation and resuspended in 300 μL LB3 buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1×PPI). Chromatin was sonicated to an average fragment size of approximately 200–500 bp using a Q800R3 Sonicator (30 s ON, 30 s OFF, for 20 min). For immunoprecipitation, 5 μg of GFP antibody (Proteintech, 50430-2-AP), pre-incubated with 50 μL Dynabeads Protein A (Invitrogen), was added to the chromatin samples along with 1% Triton X-100 and incubated overnight at 4°C. Beads were washed twice with low-salt wash buffer (0.1% Na-deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 150 mM NaCl), once with high-salt wash buffer (0.1% Na-deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), once with LiCl wash buffer (250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.0), and twice with TE buffer. Chromatin was reverse crosslinked overnight at 65°C with shaking at 800 rpm in reverse crosslinking buffer (1% SDS and 0.1 M NaHCO₃). DNA was purified using phenol-chloroform extraction and resuspended in 10 mM Tris-HCl pH 8.0.
ChIP-seq libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: Cells transfected with an engineered RPB1 containing an modified CTD

value: Human embryonic kidney

value: Transfected with engineered RPB1 containing half wildtype and half S7E CTD repeats


title: Ctrl_IVM_OOCYTE_9

description:
Library name: sample19
colname in express_tpm.csv: O19


title: CDX derived WaGa #E51, DMSO treated, 24 hours, rep3

description:
Library name: WaGa_E51_DMSO_3
G3
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E51_DMSO_1, WaGa_E51_DMSO_2, WaGa_E51_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

source_name: CDX derived cell line WaGa #E51

value: CDX derived cell line WaGa #E51


title: HEK293T_Mix_T4E_sp_1rep

description: Library name: Mix_T4E_sp_1rep

value: Transfected with engineered RPB1 containing half wildtype and half T4E CTD repeats


title: CDX derived WaGa #E38, KTX-049 treated, 24 hours, rep3

description:
Library name: WaGa_E38_KTX-049_3
F6
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E38_KTX_049_1, WaGa_E38_KTX_049_2, WaGa_E38_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

source_name: CDX derived cell line WaGa #E38

value: CDX derived cell line WaGa #E38

value: 1nM KTX-049


title: HEK293T_Mix_T4E_sp_2rep

description: Library name: Mix_T4E_sp_2rep


title: HEK293T_CTD17_2rep

description: Library name: CTD17_2rep

value: Transfected with engineered RPB1 containing 17 CTD repeats


title: HEK293T_Mix_S7E_sp_1rep

description: Library name: Mix_S7E_sp_1rep


title: CDX derived WaGa #E34, KTX-049 treated, 24 hours, rep3

description:
Library name: WaGa_E34_KTX-049_3
E6
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E34_KTX_049_1, WaGa_E34_KTX_049_2, WaGa_E34_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

source_name: CDX derived cell line WaGa #E34

value: CDX derived cell line WaGa #E34


title: CDX derived WaGa #E38, DMSO treated, 24 hours, rep3

description:
Library name: WaGa_E38_DMSO_3
F3
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E38_DMSO_1, WaGa_E38_DMSO_2, WaGa_E38_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: DMSO


title: Patient derived MCC-301, DMSO treated, 24 hours, rep3

description:
Library name: MCC-301_DMSO_3
H3
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: MCC_301_DMSO_1, MCC_301_DMSO_2, MCC_301_DMSO_3
MCC_counts.csv
treated_vs_untreated_counts.csv

source_name: Patient derived cell line MCC-301

value: Patient derived cell line MCC-301


title: Ctrl_IVM_OOCYTE_7

description:
Library name: sample17
colname in express_tpm.csv: O17


title: CDX derived WaGa #E51, KTX-049 treated, 24 hours, rep3

description:
Library name: WaGa_E51_KTX-049_3
G6
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E51_KTX_049_1, WaGa_E51_KTX_049_2, WaGa_E51_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv


title: Ctrl_IVM_OOCYTE_6

description:
Library name: sample16
colname in express_tpm.csv: O16


title: CDX derived WaGa #E25, KTX-049 treated, 24 hours, rep3

description:
Library name: WaGa_E25_KTX-049_3
D6
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E25_KTX_049_1, WaGa_E25_KTX_049_2, WaGa_E25_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

source_name: CDX derived cell line WaGa #E25

value: CDX derived cell line WaGa #E25


title: CDX derived WaGa #E34, DMSO treated, 24 hours, rep3

description:
Library name: WaGa_E34_DMSO_3
E4
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E34_DMSO_1, WaGa_E34_DMSO_2, WaGa_E34_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv


title: HEK293T_CTD17_1rep

description: Library name: CTD17_1rep


title: CDX derived WaGa #E25, DMSO treated, 24 hours, rep3

description:
Library name: WaGa_E25_DMSO_3
D3
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E25_DMSO_1, WaGa_E25_DMSO_2, WaGa_E25_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv


title: CDX derived WaGa #E9 cells, KTX-049 treated, 24 hours, rep3

description:
Library name: WaGa_E9_KTX-049_3
C6
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E9_KTX_049_1, WaGa_E9_KTX_049_2, WaGa_E9_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

source_name: CDX derived cell line WaGa #E9

value: CDX derived cell line WaGa #E9


title: Ctrl_IVM_OOCYTE_5

description:
Library name: sample15
colname in express_tpm.csv: O15


title: WaGa cells, KTX-049 treated, 24 hours, rep3

description:
Library name: WaGa_KTX-049_3
B6
3 replicates (rep1, rep2, rep3), with column names in WaGa_parental_counts.csv, WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_KTX_049_1, WaGa_KTX_049_2, WaGa_KTX_049_3
WaGa_counts.csv
WaGa_parental_counts.csv
treated_vs_untreated_counts.csv

source_name: WaGa

value: WaGa

value: Merkel cell carcinoma cells


title: hNPCs, WNV NY99, 48h, rep3

city: Atlanta

first: Emilio

middle: E.

last: Espínola

state: Georgia

address: 145 Piedmont Ave SE

department: Biology

institute: Georgia State University

description:
Library name: Sample 45
Column name in Table_S3_DEGs_48h.xlsx, sheet WNV-NY_48h: Infected_FPKM

data_processing:
Paired-end RNA-seq reads were first aligned to human transcriptome annotations and genome assembly (hg38) using TopHat v2.1.1.
Fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks v2.2.1.
Pairwise comparisons between infected and mock conditions were performed to detect differentially expressed (DE) genes using Cuffdiff.
DE genes were defined as the ones with a False Discovery Rate (FDR) less than 0.05.
Assembly: hg38
Supplementary files format and content: xlsx files include FPKM values for each sample

source_name: Neural progenitor cells

growth_protocol: Human iPS cell colonies were detached from the feeder layer with 1 mg/ml of collagenase Type IV treatment (Gibco, Cat# 17104-019) for 1 h and suspended in embryoid body (EB) media, consisting of DMEM/F12 (Life Tech, Cat# 11330057) supplemented with 20% KOSR (Life Tech, Cat# 10828028), 2 mM Glutamax (Life Tech, Cat# 35050079), 0.1 mM NEAA (Life Tech, Cat# 11140076), 0.1 mM 2-ME (Life Tech, Cat# 21985023), 2 uM dorsomorphin (Tocris Bio, Cat# 3093) and 2 uM A-83 (Tocris Bio, Cat# 2939), in non-treated polystyrene plates for 4 days with a daily media change. On day 6, the floating EBs were then transferred to Matrigel-coated 6-well plates at day 7 to form neural tube-like rosettes. EB media was replaced by neural induction media (hNPC media) consisting of 1:1 DMEM/F12 (Life Tech, Cat# 11330057) and NeuroBasal Medium (Life Tech, Cat# 21103049), 2 mM Glutamax (Life Tech, Cat# 35050079), 0.1 mM NEAA (Life Tech, Cat# 11140076), B27 (Life Tech, Cat# 17504044), N2 supplement (Life Tech, Cat# 17502-048), and 1 uM Cyclopamine (CellagenTech, Cat# C2925-50). The attached rosettes were kept for 16 days with an hNPC media change every other day. On day 22, the rosettes were picked mechanically and transferred to low attachment plates in hNPC media. On day 24, hNPC aggregates were observed to form spherical structures. hNPC spheres were dissociated into single cells using Collagenase IV, followed by seeding onto Matrigel-coated plates.

extract_protocol:
After the cells were gently washed 3X with PBS, cell lysates were harvested at 12, 24, or 48 h, after addition of 1 ml ice-cold TRI-reagent (Invitrogen Cat# AM9738) and total RNA was extracted following the manufacturer’s protocol.
RNA-seq libraries were constructed using 1 µg of total RNA obtained from each of the samples per condition, after employing ribosomal RNA depletion and poly(A) selection methods using the TruSeq Stranded mRNA Library Prep Kit (Illumina Cat# 20020595).

treatment_protocol: hNPCs were infected with one of the four viruses at a multiplicity of infection (MOI) of 1 in 100 µl/well of media for 1 h at 37°C with rocking every 15 min. Fresh media was then added and the plates were incubated at 37°C until harvest.

value: Neural progenitor cells

value: WNV NY99

tag: batch

value: Batch 1


title: Ctrl_IVM_OOCYTE_3

description:
Library name: sample13
colname in express_tpm.csv: O13

value: OOCYTE

value: WT

value: in vitro maturation


title: hNPCs, WNV NY99, 48h, rep1

description:
Library name: Sample 43
Column name in Table_S3_DEGs_48h.xlsx, sheet WNV-NY_48h: Infected_FPKM


title: CDX derived WaGa #E9 cells, DMSO treated, 24 hours, rep3

description:
Library name: WaGa_E9_DMSO_3
C3
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E9_DMSO_1, WaGa_E9_DMSO_2, WaGa_E9_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: 24 hours


title: MKL-1 cells, DMSO control, 24 hours, rep3

description:
Library name: MKL-1_DMSO_3
A3
3 replicates (rep1, rep2, rep3), column name in MKL_counts.csv: MKL_1_DMSO_1, MKL_1_DMSO_2, MKL_1_DMSO_3
MKL_counts.csv


title: HEK293T_CTD0_1rep

description: Library name: CTD0_1rep

value: Human embryonic kidney

value: Transfected with engineered RPB1 containing 0 CTD repeats


title: Ctrl_IVM_OOCYTE_2

description: Library name: sample12


title: HEK293T_CTD0_2rep

description: Library name: CTD0_2rep


title: Ctrl_IVM_OOCYTE_4

description: Library name: sample14


title: MKL-1 cells, KTX-049 treated, 24 hours, rep3

description:
Library name: MKL-1_KTX-049_3
A6
3 replicates (rep1, rep2, rep3), with column name in MKL_counts.csv: MKL_1_KTX_049_1,MKL_1_KTX_049_2, MKL_1_KTX_049_3
MKL_counts.csv

value: 1nM KTX-049


title: hNPCs, WNV NY99, 48h, rep2

description:
Library name: Sample 44
Column name in Table_S3_DEGs_48h.xlsx, sheet WNV-NY_48h: Infected_FPKM


title: PDX derived 48396 #346, KTX-049 treated, 24 hours, rep2

description:
Library name: 48396_346_KTX-049_2
J5
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_346_KTX_049_1, 48396_346_KTX_049_2, 48396_346_KTX_049_3
MCC_counts.csv
treated_vs_untreated_counts.csv

source_name: PDX derived cell line 48396 #346

value: PDX derived cell line 48396 #346


title: WaGa cells, DMSO control, 24 hours, rep3

description:
Library name: WaGa_DMSO_3
B3
3 replicates (rep1, rep2, rep3), with column names in WaGa_parental_counts.csv, WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_DMSO_1, WaGa_DMSO_2, WaGa_DMSO_3
WaGa_counts.csv
WaGa_parental_counts.csv
treated_vs_untreated_counts.csv

value: DMSO


title: Ctrl_IVM_OOCYTE_1

description:
Library name: sample11
colname in express_tpm.csv: O11


title: hNPCs, WNV MAD78, 48h, rep3

description:
Library name: Sample 42
Column name in Table_S3_DEGs_48h.xlsx, sheet WNV-MA_48h: Infected_FPKM

value: WNV MAD78


title: MKL-1 cells, DS-3032 treated, 24 hours, rep3

description:
Library name: MKL-1_DS-3032_3
A9
3 replicates (rep1, rep2, rep3), with column name in MKL_counts.csv: MKL_1_DS_3032_1, MKL_1_DS_3032_2, MKL_1_DS_3032_3
MKL_counts.csv


title: PDX derived 48396 #325, DMSO treated, 24 hours, rep2

description:
Library name: 48396_325_DMSO_2
I2
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_325_DMSO_1, 48396_325_DMSO_2, 48396_325_DMSO_3
MCC_counts.csv
treated_vs_untreated_counts.csv

value: PDX derived cell line 48396 #325


title: PDX derived 48396 #346, DMSO treated, 24 hours, rep2

description:
Library name: 48396_346_DMSO_2
J2
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_346_DMSO_1, 48396_346_DMSO_2, 48396_346_DMSO_3
MCC_counts.csv
treated_vs_untreated_counts.csv


title: WaGa cells, DS-3032 treated, 24 hours, rep3

description:
Library name: WaGa_DS-3032_3
B9
3 replicates (rep1, rep2, rep3), with column names in WaGa_parental_counts.csv, WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_DS_3032_1, WaGa_DS_3032_2, WaGa_DS_3032_3
WaGa_counts.csv
WaGa_parental_counts.csv
treated_vs_untreated_counts.csv


title: GV_OOCYTE_8

description: Library name: sample8

value: pre maturation


title: Patient derived MCC-301, KTX-049 treated, 24 hours, rep2

description:
Library name: MCC-301_KTX-049_2
H5
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: MCC_301_KTX_049_1, MCC_301_KTX_049_2, MCC_301_KTX_049_3
MCC_counts.csv
treated_vs_untreated_counts.csv

value: Patient derived cell line MCC-301


title: hNPCs, WNV MAD78, 48h, rep2

description:
Library name: Sample 41
Column name in Table_S3_DEGs_48h.xlsx, sheet WNV-MA_48h: Infected_FPKM


title: PDX derived 48396 #325, KTX-049 treated, 24 hours, rep2

description:
Library name: 48396_325_KTX-049_2
I5
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_325_KTX_049_1, 48396_325_KTX_049_2, 48396_325_KTX_049_3
MCC_counts.csv
treated_vs_untreated_counts.csv

value: Merkel cell carcinoma cells


title: Atherosclerotic plaques, late fibroatheroma (LFA), rep3

city: Shanghai

first: Yuanyuan

last: Wei

address: No. 130, Dong'an Road

country: China

institute: Fudan University

data_processing:
The fastx_clipper software was used to remove splice sequences from the 3' end and low-quality fragments.
FastQC is used to evaluate the quality of the sequence after quality control.
Bowtie software was used to align the sequences to the reference genome, Rfam database, RepBase database, and miRBase database.
DESeq software was used for statistical differences.
Miranda is used for target prediction
Assembly: hg38
Supplementary files format and content: Raw counts of all miRNAs in the 13 samples

source_name: Carotid artery

extract_protocol:
Total RNAs were extracted using miRNeasy Mini Kit (Qiagen), followed by subsequent treatment with the RNase-Free DNase Set (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QIAseq miRNA Library Kit (Qiagen, 331502, Germany) following manufacturer's protocols.

value: Carotid artery

tag: condition

value: late fibroatheroma (LFA)


title: CDX derived WaGa #E51, KTX-049 treated, 24 hours, rep2

description:
Library name: WaGa_E51_KTX-049_2
G5
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E51_KTX_049_1, WaGa_E51_KTX_049_2, WaGa_E51_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E51


title: hNPCs, WNV MAD78, 48h, rep1

description:
Library name: Sample 40
Column name in Table_S3_DEGs_48h.xlsx, sheet WNV-MA_48h: Infected_FPKM

value: Neural progenitor cells

value: Batch 1


title: CDX derived WaGa #E51, DMSO treated, 24 hours, rep2

description:
Library name: WaGa_E51_DMSO_2
G2
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E51_DMSO_1, WaGa_E51_DMSO_2, WaGa_E51_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv


title: GV_OOCYTE_7

description:
Library name: sample7
colname in express_tpm.csv: O7

value: OOCYTE

value: WT


title: GV_OOCYTE_9

description:
Library name: sample10
colname in express_tpm.csv: O10

value: in vitro maturation


title: GV_OOCYTE_6

description:
Library name: sample6
colname in express_tpm.csv: O6


title: hNPCs, POWV, 48h, rep3

description:
Library name: Sample 39
Column name in Table_S3_DEGs_48h.xlsx, sheet POWV_48h: Infected_FPKM

value: POWV


title: GV_OOCYTE_5

description: Library name: sample5


title: CDX derived WaGa #E38, KTX-049 treated, 24 hours, rep2

description:
Library name: WaGa_E38_KTX-049_2
F5
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E38_KTX_049_1, WaGa_E38_KTX_049_2, WaGa_E38_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E38

value: 1nM KTX-049

value: 24 hours


title: Patient derived MCC-301, DMSO treated, 24 hours, rep2

description:
Library name: MCC-301_DMSO_2
H2
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: MCC_301_DMSO_1, MCC_301_DMSO_2, MCC_301_DMSO_3
MCC_counts.csv
treated_vs_untreated_counts.csv

value: DMSO


title: CDX derived WaGa #E34, KTX-049 treated, 24 hours, rep2

description:
Library name: WaGa_E34_KTX-049_2
E5
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E34_KTX_049_1, WaGa_E34_KTX_049_2, WaGa_E34_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E34


title: CDX derived WaGa #E9 cells, DMSO treated, 24 hours, rep2

description:
Library name: WaGa_E9_DMSO_2
C2
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E9_DMSO_1, WaGa_E9_DMSO_2, WaGa_E9_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E9


title: CDX derived WaGa #E38, DMSO treated, 24 hours, rep2

description:
Library name: WaGa_E38_DMSO_2
F2
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E38_DMSO_1, WaGa_E38_DMSO_2, WaGa_E38_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv


title: hNPCs, POWV, 48h, rep2

description:
Library name: Sample 38
Column name in Table_S3_DEGs_48h.xlsx, sheet POWV_48h: Infected_FPKM


title: CDX derived WaGa #E34, DMSO treated, 24 hours, rep2

description:
Library name: WaGa_E34_DMSO_2
E2
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E34_DMSO_1, WaGa_E34_DMSO_2, WaGa_E34_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv


title: WaGa cells, KTX-049 treated, 24 hours, rep2

description:
Library name: WaGa_KTX-049_2
B5
3 replicates (rep1, rep2, rep3), with column names in WaGa_parental_counts.csv, WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_KTX_049_1, WaGa_KTX_049_2, WaGa_KTX_049_3
WaGa_counts.csv
WaGa_parental_counts.csv
treated_vs_untreated_counts.csv

value: WaGa


title: hNPCs, ZIKV, 48h, rep3

description:
Library name: Sample 36
Column name in Table_S3_DEGs_48h.xlsx, sheet ZIKV_48h: Infected_FPKM

value: ZIKV


title: hNPCs, ZIKV, 48h, rep2

description:
Library name: Sample 35
Column name in Table_S3_DEGs_48h.xlsx, sheet ZIKV_48h: Infected_FPKM


title: GV_OOCYTE_4

description:
Library name: sample4
colname in express_tpm.csv: O4

value: pre maturation


title: GV_OOCYTE_2

description:
Library name: sample2
colname in express_tpm.csv: O2


title: CDX derived WaGa #E25, KTX-049 treated, 24 hours, rep2

description:
Library name: WaGa_E25_KTX-049_2
D5
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E25_KTX_049_1, WaGa_E25_KTX_049_2, WaGa_E25_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E25

value: Merkel cell carcinoma cells


title: GV_OOCYTE_3

description:
Library name: sample3
colname in express_tpm.csv: O3


title: WaGa cells, DS-3032 treated, 24 hours, rep2

description:
Library name: WaGa_DS-3032_2
B8
3 replicates (rep1, rep2, rep3), with column names in WaGa_parental_counts.csv, WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_DS_3032_1, WaGa_DS_3032_2, WaGa_DS_3032_3
WaGa_counts.csv
WaGa_parental_counts.csv
treated_vs_untreated_counts.csv


title: CDX derived WaGa #E25, DMSO treated, 24 hours, rep2

description:
Library name: WaGa_E25_DMSO_2
D2
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E25_DMSO_1, WaGa_E25_DMSO_2, WaGa_E25_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv


title: hNPCs, POWV, 48h, rep1

description:
Library name: Sample 37
Column name in Table_S3_DEGs_48h.xlsx, sheet POWV_48h: Infected_FPKM

value: Neural progenitor cells


title: GV_OOCYTE_1

description:
Library name: sample1
colname in express_tpm.csv: O1


title: CDX derived WaGa #E9 cells, KTX-049 treated, 24 hours, rep2

description:
Library name: WaGa_E9_KTX-049_2
C5
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E9_KTX_049_1, WaGa_E9_KTX_049_2, WaGa_E9_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv


title: hNPCs, ZIKV, 48h, rep1

description:
Library name: Sample 34
Column name in Table_S3_DEGs_48h.xlsx, sheet ZIKV_48h: Infected_FPKM

value: Batch 1


title: MKL-1 cells, DS-3032 treated, 24 hours, rep2

description:
Library name: MKL-1_DS-3032_2
A8
3 replicates (rep1, rep2, rep3), with column name in MKL_counts.csv: MKL_1_DS_3032_1, MKL_1_DS_3032_2, MKL_1_DS_3032_3
MKL_counts.csv


title: MEG-01 MELK knockdown (sh2-MELK) rep3

city: Suzhou

first: Jiaqian

last: Qi

state: Jiangsu

address: No.188 Shizi Road

institute: The First Affiliated Hospital of Soochow University

description:
Library name: F5_meg01_sh2_MELK_3
MEG-01 cells transduced with MELK-targeting shRNA (sh2-MELK); biological replicate 3.

data_processing:
Raw paired-end FASTQ files were subjected to quality control FastQC. Adapter sequences and low-quality bases were removed fastp. Clean reads were aligned to the human reference genome GRCh38/hg38 using STAR. Gene-level read counts were generated using HTSeq-count to produce a complete count matrix for all genes and all samples, exported as expr_count.tsv. Differential expression and downstream pathway analyses were performed using DESeq2 in R 4.3.3.
Assembly: h38
Supplementary files format and content: Tab-separated valued files

extract_protocol:
Total RNA was extracted from MEG-01 cells for each biological replicate using TRIzol reagent according to the manufacturer’s instructions. Residual genomic DNA was removed with DNase I treatment. RNA quantity and purity were assessed by NanoDrop, and RNA integrity was assessed by Bioanalyzer. High-quality RNA was used for library preparation.
RNA-seq libraries were prepared from [~1 µg] total RNA per sample using an Illumina-compatible library preparation workflow. Briefly, RNA was enriched poly(A) selection fragmented, and reverse-transcribed to cDNA, followed by end repair, adapter ligation with unique dual indexes, and PCR amplification. Library size distribution and concentration were evaluated by Bioanalyzer, pooled, and sequenced in paired-end mode on Illumina instrument model.

value: megakaryoblast

value: MELK knockdown (sh2-MELK)

value: MELK shRNA


title: WaGa cells, DMSO control, 24 hours, rep2

description:
Library name: WaGa_DMSO_2
B2
3 replicates (rep1, rep2, rep3), with column names in WaGa_parental_counts.csv, WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_DMSO_1, WaGa_DMSO_2, WaGa_DMSO_3
WaGa_counts.csv
WaGa_parental_counts.csv
treated_vs_untreated_counts.csv


title: MEG-01 MELK knockdown (sh2-MELK) rep1

description:
Library name: F5_meg01_sh2_MELK_1
MEG-01 cells transduced with MELK-targeting shRNA (sh2-MELK); biological replicate 1.


title: hNPCs, Mock, 48h, rep1

description:
Library name: Sample 31
Column name in Table_S3_DEGs_48h.xlsx, sheet ZIKV_48h: Mock_FPKM

value: WT

value: Mock


title: MEG-01 control (pLKO.1) rep3

description:
Library name: F5_meg01_plko_3
MEG-01 cells transduced with control pLKO.1; biological replicate 3.

value: control (pLKO.1)

value: control vector


title: hNPCs, Mock, 48h, rep3

description:
Library name: Sample 33
Column name in Table_S3_DEGs_48h.xlsx, sheet ZIKV_48h: Mock_FPKM


title: MKL-1 cells, DMSO control, 24 hours, rep2

description:
Library name: MKL-1_DMSO_2
A2
3 replicates (rep1, rep2, rep3), column name in MKL_counts.csv: MKL_1_DMSO_1, MKL_1_DMSO_2, MKL_1_DMSO_3
MKL_counts.csv

value: DMSO

value: 24 hours


title: CDX derived WaGa #E38, KTX-049 treated, 24 hours, rep1

description:
Library name: WaGa_E38_KTX-049_1
F4
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E38_KTX_049_1, WaGa_E38_KTX_049_2, WaGa_E38_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E38

value: 1nM KTX-049


title: hNPCs, Mock, 48h, rep2

description:
Library name: Sample 32
Column name in Table_S3_DEGs_48h.xlsx, sheet ZIKV_48h: Mock_FPKM


title: MEG-01 MELK knockdown (sh2-MELK) rep2

description:
Library name: F5_meg01_sh2_MELK_2
MEG-01 cells transduced with MELK-targeting shRNA (sh2-MELK); biological replicate 2.


title: Patient derived MCC-301, DMSO treated, 24 hours, rep1

description:
Library name: MCC-301_DMSO_1
H1
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: MCC_301_DMSO_1, MCC_301_DMSO_2, MCC_301_DMSO_3
MCC_counts.csv
treated_vs_untreated_counts.csv

value: Patient derived cell line MCC-301


title: PDX derived 48396 #346, KTX-049 treated, 24 hours, rep1

description:
Library name: 48396_346_KTX-049_1
J4
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_346_KTX_049_1, 48396_346_KTX_049_2, 48396_346_KTX_049_3
MCC_counts.csv
treated_vs_untreated_counts.csv

value: PDX derived cell line 48396 #346


title: PDX derived 48396 #325, KTX-049 treated, 24 hours, rep1

description:
Library name: 48396_325_KTX-049_1
I4
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_325_KTX_049_1, 48396_325_KTX_049_2, 48396_325_KTX_049_3
MCC_counts.csv
treated_vs_untreated_counts.csv

value: PDX derived cell line 48396 #325


title: PDX derived 48396 #325, DMSO treated, 24 hours, rep1

description:
Library name: 48396_325_DMSO_1
I1
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_325_DMSO_1, 48396_325_DMSO_2, 48396_325_DMSO_3
MCC_counts.csv
treated_vs_untreated_counts.csv

value: Merkel cell carcinoma cells


title: hNPCs, WNV NY99, 24h, rep3

description:
Library name: Sample 30
Column name in Table_S2_DEGs_24h.xlsx, sheet WNV-NY_24h: Infected_FPKM

value: Neural progenitor cells

value: WNV NY99


title: MEG-01 control (pLKO.1) rep1

description:
Library name: F5_meg01_plko_1
MEG-01 cells transduced with control pLKO.1; biological replicate 1.

value: megakaryoblast


title: hNPCs, WNV NY99, 24h, rep2

description:
Library name: Sample 29
Column name in Table_S2_DEGs_24h.xlsx, sheet WNV-NY_24h: Infected_FPKM

value: Batch 1


title: MKL-1 cells, KTX-049 treated, 24 hours, rep2

description:
Library name: MKL-1_KTX-049_2
A5
3 replicates (rep1, rep2, rep3), with column name in MKL_counts.csv: MKL_1_KTX_049_1,MKL_1_KTX_049_2, MKL_1_KTX_049_3
MKL_counts.csv


title: CDX derived WaGa #E51, KTX-049 treated, 24 hours, rep1

description:
Library name: WaGa_E51_KTX-049_1
G4
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E51_KTX_049_1, WaGa_E51_KTX_049_2, WaGa_E51_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E51


title: CDX derived WaGa #E34, KTX-049 treated, 24 hours, rep1

description:
Library name: WaGa_E34_KTX-049_1
E3
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E34_KTX_049_1, WaGa_E34_KTX_049_2, WaGa_E34_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E34


title: Patient derived MCC-301, KTX-049 treated, 24 hours, rep1

description:
Library name: MCC-301_KTX-049_1
H4
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: MCC_301_KTX_049_1, MCC_301_KTX_049_2, MCC_301_KTX_049_3
MCC_counts.csv
treated_vs_untreated_counts.csv


title: MEG-01 control (pLKO.1) rep2

description:
Library name: F5_meg01_plko_2
MEG-01 cells transduced with control pLKO.1; biological replicate 2.


title: hNPCs, WNV NY99, 24h, rep1

description:
Library name: Sample 28
Column name in Table_S2_DEGs_24h.xlsx, sheet WNV-NY_24h: Infected_FPKM

value: WT


title: CDX derived WaGa #E51, DMSO treated, 24 hours, rep1

description:
Library name: WaGa_E51_DMSO_1
G1
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E51_DMSO_1, WaGa_E51_DMSO_2, WaGa_E51_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv


title: CDX derived WaGa #E38, DMSO treated, 24 hours, rep1

description:
Library name: WaGa_E38_DMSO_1
F1
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E38_DMSO_1, WaGa_E38_DMSO_2, WaGa_E38_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv


title: PDX derived 48396 #346, DMSO treated, 24 hours, rep1

description:
Library name: 48396_346_DMSO_1
J1
3 replicates (rep1, rep2, rep3), with column names in MCC_counts, treated_vs_untreated_counts.csv: 48396_346_DMSO_1, 48396_346_DMSO_2, 48396_346_DMSO_3
MCC_counts.csv
treated_vs_untreated_counts.csv


title: Mouse liver Visium spatial transcriptomics, LMS-K, sample Liv_S2-7

city: Gwangju

first: Wooje

last: Lee

address: 86, Kimchiro, Namgu

department: Kimchi Healthcare Research Group

country: South Korea

institute: World Institute of Kimchi

description:
Library name: Liv_S2-7
10x Genomics Visium spatial transcriptomics of mouse liver

data_processing:
Base call files were demultiplexed into FASTQ files.
Libraries were sequenced on an Illumina HiSeq X Ten platform using paired-end sequencing.
Read 1 corresponded to the 10X barcode read and Read 2 corresponded to the insert read. Read lengths were 28 bp for the barcode read and 50 bp for the insert read. Some samples were sequenced across multiple flowcells and lanes.
Reads were processed using the 10x Genomics Visium workflow with the Visium Mouse Transcriptome Probe Set.
Assembly: mm10
Supplementary files format and content: Processed data files include filtered gene-barcode count matrices in MEX format (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz), filtered feature-barcode HDF5 matrices, spatial coordinate files (tissue_positions_list.csv), scale factor files, tissue images (aligned fiducials, aligned tissue, detected tissue, hires and lowres images), metrics summary files, and web summary reports. The probe set reference version used in this dataset was 2020-A.
Library strategy: Spatial Transcriptomics

source_name: Mouse Liver

growth_protocol: Male C57BL/6J mice were maintained under standard laboratory conditions and assigned to dietary intervention groups.

extract_protocol:
Liver tissues were sectioned and mounted onto 10x Genomics Visium slides for spatial transcriptomics analysis according to the manufacturer's protocol.
Spatially barcoded libraries were prepared using the 10x Genomics Visium workflow with the Visium Mouse Transcriptome Probe Set according to the manufacturer's instructions.

treatment_protocol: Mice were assigned to normal diet (ND), high-fat diet (HFD), high-fat diet supplemented with spontaneously fermented kimchi (S-K), or high-fat diet supplemented with starter kimchi fermented with Leuconostoc mesenteroides KCKM0828 (LMS-K).

value: Mouse Liver

tag: Sex

value: male

value: HFD + LMS-K


title: CDX derived WaGa #E25, KTX-049 treated, 24 hours, rep1

description:
Library name: WaGa_E25_KTX-049_1
D4
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E25_KTX_049_1, WaGa_E25_KTX_049_2, WaGa_E25_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E25

value: 24 hours


title: hNPCs, WNV MAD78, 24h, rep2

description:
Library name: Sample 26
Column name in Table_S2_DEGs_24h.xlsx, sheet WNV-MA_24h: Infected_FPKM

value: WNV MAD78


title: CDX derived WaGa #E25, DMSO treated, 24 hours, rep1

description:
Library name: WaGa_E25_DMSO_1
D1
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E25_DMSO_1, WaGa_E25_DMSO_2, WaGa_E25_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: DMSO


title: CDX derived WaGa #E9 cells, KTX-049 treated, 24 hours, rep1

description:
Library name: WaGa_E9_KTX-049_1
C4
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E9_KTX_049_1, WaGa_E9_KTX_049_2, WaGa_E9_KTX_049_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E9

value: 1nM KTX-049


title: CDX derived WaGa #E34, DMSO treated, 24 hours, rep1

description:
Library name: WaGa_E34_DMSO_1
E1
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E34_DMSO_1, WaGa_E34_DMSO_2, WaGa_E34_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: Merkel cell carcinoma cells


title: hNPCs, WNV MAD78, 24h, rep3

description:
Library name: Sample 27
Column name in Table_S2_DEGs_24h.xlsx, sheet WNV-MA_24h: Infected_FPKM

value: Neural progenitor cells


title: hNPCs, WNV MAD78, 24h, rep1

description:
Library name: Sample 25
Column name in Table_S2_DEGs_24h.xlsx, sheet WNV-MA_24h: Infected_FPKM


title: Mouse liver Visium spatial transcriptomics, ND, sample Liv_N-3

description:
Library name: Liv_N-3
10x Genomics Visium spatial transcriptomics of mouse liver

value: ND


title: Mouse liver Visium spatial transcriptomics, S-K, sample Liv_K-4

description:
Library name: Liv_K-4
10x Genomics Visium spatial transcriptomics of mouse liver

value: HFD + S-K


title: hNPCs, POWV, 24h, rep3

description:
Library name: Sample 24
Column name in Table_S2_DEGs_24h.xlsx, sheet POWV_24h: Infected_FPKM

value: POWV

value: Batch 1


title: WaGa cells, KTX-049 treated, 24 hours, rep1

description:
Library name: WaGa_KTX-049_1
B4
3 replicates (rep1, rep2, rep3), with column names in WaGa_parental_counts.csv, WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_KTX_049_1, WaGa_KTX_049_2, WaGa_KTX_049_3
WaGa_counts.csv
WaGa_parental_counts.csv
treated_vs_untreated_counts.csv

value: WaGa


title: Mouse liver Visium spatial transcriptomics, HFD, sample Liv_H-4

description:
Library name: Liv_H-4
10x Genomics Visium spatial transcriptomics of mouse liver

value: HFD


title: KO 4, Zfp36l1 fl/fl Alb-Cre+

city: Durham

first: Rajesh Kumar

last: Dutta

state: NC

address: 1049 Umstead Grove Way

department: Medicine

institute: Duke University

description:
Library name: Sample8
ES843

data_processing:
Raw sequencing reads were assessed for quality, trimmed if needed, and aligned to the reference genome. Gene-level counts were generated using standard RNA-seq processing tools.
Assembly: mm10
Supplementary files format and content: Processed files are tab-delimited text files containing gene-level expression/count values for each sample.

source_name: Liver

extract_protocol:
Total RNA was extracted from liver using illustra QuickPrep mRNA Purification Kit from GE healthcare
libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina as per manufacturer protocol

value: Liver

value: Zf36l1 KO


title: WaGa cells, DS-3032 treated, 24 hours, rep1

description:
Library name: WaGa_DS-3032_1
B7
3 replicates (rep1, rep2, rep3), with column names in WaGa_parental_counts.csv, WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_DS_3032_1, WaGa_DS_3032_2, WaGa_DS_3032_3
WaGa_counts.csv
WaGa_parental_counts.csv
treated_vs_untreated_counts.csv


title: WaGa cells, DMSO control, 24 hours, rep1

description:
Library name: WaGa_DMSO_1
B1
3 replicates (rep1, rep2, rep3), with column names in WaGa_parental_counts.csv, WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_DMSO_1, WaGa_DMSO_2, WaGa_DMSO_3
WaGa_counts.csv
WaGa_parental_counts.csv
treated_vs_untreated_counts.csv


title: KO 3, Zfp36l1 fl/fl Alb-Cre+

description:
Library name: Sample7
ES842

value: male


title: MKL-1 cells, DS-3032 treated, 24 hours, rep1

description:
Library name: MKL-1_DS-3032_1
A7
3 replicates (rep1, rep2, rep3), with column name in MKL_counts.csv: MKL_1_DS_3032_1, MKL_1_DS_3032_2, MKL_1_DS_3032_3
MKL_counts.csv


title: TJP1iEC_C

first: Ying-Yu

last: Lin

address: 534 Research Drive

description: Library name: Sample1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2[2] as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCountsv 1.5.0-p3 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: xls files includes differential expression analysis of iECs and iRECs (iECs as control), FPKM values and raw counts for each sample.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and purified using the RNeasy Mini Kit (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP

value: hiPSC-derive endothelial cells

tag: sample group


title: hNPCs, POWV, 24h, rep2

description:
Library name: Sample 23
Column name in Table_S2_DEGs_24h.xlsx, sheet POWV_24h: Infected_FPKM

value: WT


title: hNPCs, ZIKV, 24h, rep1

description:
Library name: Sample 19
Column name in Table_S2_DEGs_24h.xlsx, sheet ZIKV_24h: Infected_FPKM

value: ZIKV


title: hNPCs, POWV, 24h, rep1

description:
Library name: Sample 22
Column name in Table_S2_DEGs_24h.xlsx, sheet POWV_24h: Infected_FPKM


title: MKL-1 cells, KTX-049 treated, 24 hours, rep1

description:
Library name: MKL-1_KTX-049_1
A4
3 replicates (rep1, rep2, rep3), with column name in MKL_counts.csv: MKL_1_KTX_049_1,MKL_1_KTX_049_2, MKL_1_KTX_049_3
MKL_counts.csv

value: 24 hours


title: hNPCs, ZIKV, 24h, rep3

description:
Library name: Sample 21
Column name in Table_S2_DEGs_24h.xlsx, sheet ZIKV_24h: Infected_FPKM


title: TJP1iEC_D

description: Library name: Sample2


title: hNPCs, ZIKV, 24h, rep2

description:
Library name: Sample 20
Column name in Table_S2_DEGs_24h.xlsx, sheet ZIKV_24h: Infected_FPKM


title: TJP1iREC_E

description: Library name: Sample7


title: Control 4, Zf36l1 fl/fl

description:
Library name: Sample4
ES839


title: KO 2, Zfp36l1 fl/fl Alb-Cre+

description:
Library name: Sample6
ES841


title: MKL-1 cells, DMSO control, 24 hours, rep1

description:
Library name: MKL-1_DMSO_1
A1
3 replicates (rep1, rep2, rep3), column name in MKL_counts.csv: MKL_1_DMSO_1, MKL_1_DMSO_2, MKL_1_DMSO_3
MKL_counts.csv

value: DMSO


title: KO 1, Zfp36l1 fl/fl Alb-Cre+

description:
Library name: Sample5
ES840


title: CDX derived WaGa #E9 cells, DMSO treated, 24 hours, rep1

description:
Library name: WaGa_E9_DMSO_1
C1
3 replicates (rep1, rep2, rep3), with column names in WaGa_counts.csv, treated_vs_untreated_counts.csv: WaGa_E9_DMSO_1, WaGa_E9_DMSO_2, WaGa_E9_DMSO_3
WaGa_counts.csv
treated_vs_untreated_counts.csv

value: CDX derived cell line WaGa #E9


title: TJP1iREC_F

description: Library name: Sample8


title: TJP1iREC_C

description: Library name: Sample5


title: TJP1iEC_F

description: Library name: Sample4


title: hNPCs, Mock, 24h, rep3

description:
Library name: Sample 18
Column name in Table_S2_DEGs_24h.xlsx, sheet ZIKV_24h: Mock_FPKM

value: Mock


title: TJP1iREC_D

description: Library name: Sample6


title: Control 2, Zf36l1 fl/fl

description:
Library name: Sample2
ES837


title: Spleen, L-type, S0377

city: Seoul

first: Suyeon

last: Wy

address: 20, Neungdong-ro, Gwangjin-gu

department: Department of Biomedical Science and Engineering

institute: Konkuk University

description: Library name: kmp_l_s0377_spleen

data_processing:
Raw RNA-seq reads were trimmed using Trimmomatic (v0.36) with the “keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36” options. Next, rRNA sequences were filtered employing SortMeRNA (v4.2.0).
The pre-processed RNA-seq reads were assembled using rnaSPAdes (v4.2.0) to build a transcriptome assembly. The transcripts from all samples with TPM values ≥1 were subsequently analyzed. To reduce redundancy, transcripts with ≥98% sequence identity were clustered with CD-HIT (v4.8.1) using the “-c 0.98 -p 1 -d 0 -b 3” options. Lastly, the transcriptome assemblies generated for all tissues were merged with the final de novo assembly using the “tr2aacds.pl” script from EvidentialGene (v23jul15).
Transcript expression profiles for each tissue sample were generated using the Korean minipig transcriptome assembly constructed in this study. Normalized transcript-level expression data (TPM values) were quantified with Salmon (v1.10.0) using RNA-seq reads from all samples .
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes TPM values for each sample
Supplementary files format and content: FASTA file includes transcript sequences for Korean minipig
Supplementary files format and content: tab-delimited text file includes functional annotation of transcripts

organism: Sus scrofa

source_name: Spleen

extract_protocol:
Total RNA was extracted using the TRIzol reagent.
Sequencing libraries were prepared with a TruSeq Stranded mRNA LT Sample Prep Kit.

value: Spleen


title: SCGS_3

first: baoying

last: xu

address: No. 333, Nan Chen Road, Baoshan District

department: School of Life Sciences

institute: Shanghai University

description:
Library name: SCGS_3
Cells pre-incubated with HCS@Se followed by H2O2 treatment, replicate biosample 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 hg38  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: hg38
Supplementary files format and content: tab-delimited text files include FPKM value and gene count for each Sample

extract_protocol:
RNA was extracted from cell using TRIzol reagent. Briefly, cell were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: cell culture


title: Spleen, L-type, S0349

description: Library name: kmp_l_s0349_spleen


title: hNPCs, WNV NY99, 12h, rep3

description:
Library name: Sample 15
Column name in Table_S1_DEGs_12h.xlsx, sheet WNV-NY_12h: Infected_FPKM

value: Neural progenitor cells

value: WNV NY99


title: Spleen, L-type, S0384

description: Library name: kmp_l_s0384_spleen


title: hNPCs, WNV NY99, 12h, rep2

description:
Library name: Sample 14
Column name in Table_S1_DEGs_12h.xlsx, sheet WNV-NY_12h: Infected_FPKM

value: Batch 1


title: TJP1iEC_E

description: Library name: Sample3


title: hNPCs, Mock, 24h, rep1

description:
Library name: Sample 16
Column name in Table_S2_DEGs_24h.xlsx, sheet ZIKV_24h: Mock_FPKM


title: Spleen, L-type, S0385

description: Library name: kmp_l_s0385_spleen


title: SCGS_1

description:
Library name: SCGS_1
Cells pre-incubated with HCS@Se followed by H2O2 treatment, replicate biosample 1


title: Control 3, Zf36l1 fl/fl

description:
Library name: Sample3
ES838


title: Lung, L-type, S0384

description: Library name: kmp_l_s0384_lung

source_name: Lung

value: Lung


title: Control 1, Zf36l1 fl/fl

description:
Library name: Sample1
ES836


title: Lung, L-type, S0385

description: Library name: kmp_l_s0385_lung


title: SCGS_2

description:
Library name: SCGS_2
Cells pre-incubated with HCS@Se followed by H2O2 treatment, replicate biosample 2


title: hNPCs, Mock, 24h, rep2

description:
Library name: Sample 17
Column name in Table_S2_DEGs_24h.xlsx, sheet ZIKV_24h: Mock_FPKM


title: Liver, L-type, S0385

description: Library name: kmp_l_s0385_liver


title: Spleen, L-type, S0355

description: Library name: kmp_l_s0355_spleen


title: H2O2_3

description:
Library name: H2O2_3
Cells treated with H2O2, replicate biosample 3

value: Cells treated with H2O2


title: Liver, L-type, S0384

description: Library name: kmp_l_s0384_liver

value: Liver


title: H2O2_2

description:
Library name: H2O2_2
Cells treated with H2O2, replicate biosample 2


title: H2O2_1

description:
Library name: H2O2_1
Cells treated with H2O2, replicate biosample 1


title: Lung, L-type, S0355

description: Library name: kmp_l_s0355_lung


title: Liver, L-type, S0377

description: Library name: kmp_l_s0377_liver


title: Kidney, L-type, S0384

description: Library name: kmp_l_s0384_kidney

source_name: Kidney

value: Kidney


title: CTRL_2

description:
Library name: CTRL_2
Untreated cells (normal growth, no treatment), replicate biosample 2


title: hNPCs, WNV NY99, 12h, rep1

description:
Library name: Sample 13
Column name in Table_S1_DEGs_12h.xlsx, sheet WNV-NY_12h: Infected_FPKM


title: hNPCs, POWV, 12h, rep3

description:
Library name: Sample 9
Column name in Table_S1_DEGs_12h.xlsx, sheet POWV_12h: Infected_FPKM

value: POWV


title: Lung, L-type, S0349

description: Library name: kmp_l_s0349_lung


title: hNPCs, WNV MAD78, 12h, rep3

description:
Library name: Sample 12
Column name in Table_S1_DEGs_12h.xlsx, sheet WNV-MA_12h: Infected_FPKM

value: WNV MAD78


title: CTRL_3

description:
Library name: CTRL_3
Untreated cells (normal growth, no treatment), replicate biosample 3


title: Kidney, L-type, S0385

description: Library name: kmp_l_s0385_kidney


title: Lung, L-type, S0377

description: Library name: kmp_l_s0377_lung


title: hNPCs, WNV MAD78, 12h, rep2

description:
Library name: Sample 11
Column name in Table_S1_DEGs_12h.xlsx, sheet WNV-MA_12h: Infected_FPKM

value: WT


title: Liver, L-type, S0355

description: Library name: kmp_l_s0355_liver


title: hNPCs, POWV, 12h, rep2

description:
Library name: Sample 8
Column name in Table_S1_DEGs_12h.xlsx, sheet POWV_12h: Infected_FPKM


title: Liver, L-type, S0349

description: Library name: kmp_l_s0349_liver


title: hNPCs, WNV MAD78, 12h, rep1

description:
Library name: Sample 10
Column name in Table_S1_DEGs_12h.xlsx, sheet WNV-MA_12h: Infected_FPKM


title: Kidney, L-type, S0355

description: Library name: kmp_l_s0355_kidney


title: CTRL_1

description:
Library name: CTRL_1
Untreated cells (normal growth, no treatment), replicate biosample 1


title: Kidney, L-type, S0349

description: Library name: kmp_l_s0349_kidney


title: Kidney, L-type, S0377

description: Library name: kmp_l_s0377_kidney


title: Heart, L-type, S0384

description: Library name: kmp_l_s0384_heart

source_name: Heart

value: Heart


title: hNPCs, ZIKV, 12h, rep3

description:
Library name: Sample 6
Column name in Table_S1_DEGs_12h.xlsx, sheet ZIKV_12h: Infected_FPKM

value: ZIKV


title: Heart, L-type, S0355

description: Library name: kmp_l_s0355_heart


title: Heart, L-type, S0377

description: Library name: kmp_l_s0377_heart


title: hNPCs, ZIKV, 12h, rep2

description:
Library name: Sample 5
Column name in Table_S1_DEGs_12h.xlsx, sheet ZIKV_12h: Infected_FPKM


title: Spleen, ET-type, S0235

description: Library name: kmp_et_s0235_spleen


title: IP91wk2_multiome_ATAC

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

description: Library name: IP91wk2_multiome

library_source: genomic single cell

data_processing:
Raw base call files were converted to FASTQ files.
Gene expression and chromatin accessibility data were processed using the Cell Ranger ARC pipeline (10x Genomics).
Reads were aligned to the mouse reference genome and gene expression and ATAC fragment matrices were generated.
Quality control filtering was performed to remove low-quality nuclei before downstream analysis.
ATAC fragments files were generated for each sample for downstream chromatin accessibility analysis.
Assembly: mm10
Supplementary files format and content: Processed data files include ATAC fragment files in gzipped TSV format (.tsv.gz).
Supplementary files format and content: Each processed file is accompanied by a tabix index file (.tsv.gz.tbi).

source_name: Mouse retina single-nucleus multiome (ATAC), aging sample (91 weeks)

growth_protocol: C57BL/6J mice were maintained under standard laboratory conditions on a 14 h light/10 h dark cycle. Retina and RPE tissues were collected from mice at multiple ages.

extract_protocol:
Retina and RPE tissues were dissected and nuclei were isolated for single-nucleus multiome profiling.
Single-nucleus multiome libraries were generated using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression platform following the manufacturer’s protocol.

treatment_protocol: No experimental treatment was applied. Samples represent natural aging mouse retina and RPE.

value: retina

value: aging


title: Spleen, ET-type, S0326

description: Library name: kmp_et_s0326_spleen


title: Heart, L-type, S0385

description: Library name: kmp_l_s0385_heart


title: IP106wk1_multiome_ATAC

description: Library name: IP106wk1_multiome

source_name: Mouse retina single-nucleus multiome (ATAC), aging sample (106 weeks)


title: hNPCs, ZIKV, 12h, rep1

description:
Library name: Sample 4
Column name in Table_S1_DEGs_12h.xlsx, sheet ZIKV_12h: Infected_FPKM


title: hNPCs, POWV, 12h, rep1

description:
Library name: Sample 7
Column name in Table_S1_DEGs_12h.xlsx, sheet POWV_12h: Infected_FPKM


title: Spleen, ET-type, S0309

description: Library name: kmp_et_s0309_spleen


title: IP5wk4_multiome_ATAC

description: Library name: IP5wk4_multiome

source_name: Mouse retina single-nucleus multiome (ATAC), aging sample (5 weeks)


title: IP91wk2_multiome_RNA

description: Library name: IP91wk2_multiome

data_processing:
Raw base call files were converted to FASTQ files.
Gene expression and chromatin accessibility data were processed using the Cell Ranger ARC pipeline (10x Genomics).
Reads were aligned to the mouse reference genome and gene expression and ATAC fragment matrices were generated.
Quality control filtering was performed to remove low-quality nuclei before downstream analysis.
RNA matrix were generated for each sample for downstream RNA expression analysis.
Assembly: mm10
Supplementary files format and content: Processed data files include RNA matrix files in h5 format (.h5).

source_name: Mouse retina single-nucleus multiome (RNA), aging sample (91 weeks)


title: Heart, L-type, S0349

description: Library name: kmp_l_s0349_heart


title: Spleen, ET-type, S0276

description: Library name: kmp_et_s0276_spleen


title: Spleen, ET-type, S0242

description: Library name: kmp_et_s0242_spleen


title: IP5wk3_multiome_ATAC

description: Library name: IP5wk3_multiome


title: hNPCs, Mock, 12h, rep3

description:
Library name: Sample 3
Column name in Table_S1_DEGs_12h.xlsx, sheet ZIKV_12h: Mock_FPKM

value: Mock


title: IP5wk3_multiome_RNA

description: Library name: IP5wk3_multiome

source_name: Mouse retina single-nucleus multiome (RNA), aging sample (5 weeks)


title: hNPCs, Mock, 12h, rep1

description:
Library name: Sample 1
Column name in Table_S1_DEGs_12h.xlsx, sheet ZIKV_12h: Mock_FPKM


title: Lung, ET-type, S0276

description: Library name: kmp_et_s0276_lung


title: Lung, ET-type, S0326

description: Library name: kmp_et_s0326_lung


title: Lung, ET-type, S0235

description: Library name: kmp_et_s0235_lung


title: GC B cell, mM-only TM4 pos, HTO

city: New York

first: Gabriela

middle: S

last: Silva Santos

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
Library name: mIgM_TM4_C_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

data_processing:
Single-cell BCR libraries were mapped to the Cell Ranger VDJ GRCm38 reference using Cell Ranger vdj v.8.1.0 (10x genomics). Contigs containing less than 50 reads and more than one heavy or light chain were removed. scRNA-seq and Hashtag-oligos unique molecular identifier quantification were performed with Cell Ranger counts v.8.0.1 using the Cell Ranger GEX reference mm10, and analyzed in R with Seurat v.5.1.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets or with mitochondrial content greater than 10 % and feature count less than 1,000 or greater than 6,500 were excluded. Cell cycle genes were regressed out. Sample batches were then merged, scaled and normalized with SCTransform.
Assembly: GRCm38
Supplementary files format and content: CellRanger output files: RNA_barcodes.tsv.gz, RNA_features.tsv.gz, RNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: airr_rearrangement.tsv
Supplementary files format and content: CellRanger output files:  HTO_barcodes.tsv.gz, HTO_features.tsv.gz, HTO_matrix.mtx.gz
Library strategy: CITE-Seq

source_name: Lymph node

extract_protocol:
Popliteal (draining) lymph nodes were isolated from the immunized mice and dissociated using a pestel. The resulting cell suspensions were incubated in FcBlock, followed by antibody incubation and hashtagged using the TotalSeqC antibodies (Biolegend). They were then sorted using the BD FACS Symphony S6 in tubes containing buffer before being charged on the Chromium.
RNA-seq libraries were prepared using the Chromium Single Cell 5' v.2 Reagent Kit (10x Genomics) according to the manufacturer's protocol. Libraries were then loaded on the Illumina NovaSeq for GEX (gene expression), VDJ (BCR) and HTO (hashtags) libraries at the Rockefeller University Genomics Resource Center.

treatment_protocol: Mice were immunised using 5µg of RBD, Spike, or different HIV CD4bs derived antigens in both footpad of the given mice with 33% alhydrogel (Invivogen). When indicated, boosts were perfomed using the same protocol.

value: Lymph node

value: GC B cells

value: mM-only

value: D96 4x CD4bs


title: hNPCs, Mock, 12h, rep2

description:
Library name: Sample 2
Column name in Table_S1_DEGs_12h.xlsx, sheet ZIKV_12h: Mock_FPKM

value: Neural progenitor cells

value: Batch 1


title: IP5wk4_multiome_RNA

description: Library name: IP5wk4_multiome


title: Lung, ET-type, S0309

description: Library name: kmp_et_s0309_lung

value: Lung


title: Liver, ET-type, S0242

description: Library name: kmp_et_s0242_liver

value: Liver


title: Liver, ET-type, S0235

description: Library name: kmp_et_s0235_liver


title: Liver, ET-type, S0326

description: Library name: kmp_et_s0326_liver


title: Lung, ET-type, S0242

description: Library name: kmp_et_s0242_lung


title: IP106wk1_multiome_RNA

description: Library name: IP106wk1_multiome

source_name: Mouse retina single-nucleus multiome (RNA), aging sample (106 weeks)


title: Liver, ET-type, S0276

description: Library name: kmp_et_s0276_liver


title: Liver, ET-type, S0309

description: Library name: kmp_et_s0309_liver


title: PBMC, CD45+, Pool1

city: Sao Paulo

first: Kenneth

last: Gollob

address: Albert Einstein Ave, 627/701

country: Brazil

institute: Hospital Israelita Albert Einstein

description:
Library name: Sample1
BD Rhapsody
Raw FASTQ files correspond to a pooled library of 6 multiplexed samples processed in one BD Rhapsody cartridge. Sample identity was resolved using BD Rhapsody Sample Tags. Processed gene expression matrix (MTX format) is provided for each patient individually. Patient 1 = ID13, patient 2 = ID32, patient 3 = ID67, patient 4 = ID70, patient 5 = ID95, patient 6 = ID106.

data_processing:
Raw FASTQ files correspond to a pooled library of 6 multiplexed samples processed in one BD Rhapsody cartridge. Sample identity was resolved using BD Rhapsody Sample Tags. Processed gene expression matrix (MTX format) is provided for this sample. Sample-tag demultiplexing and data processing in MTX format was conducted through the Seven Bridges Genomics platform, which incorporated the BD Rhapsody Sequence Analysis Pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
PBMC samples were thawed and previously sorted using BD FACS Aria Fusion for live leukocytes (calcein+DRAQ7-CD45+) and labeled with nucleotide-conjugated antibody sample tags (Human Single-Cell Multiplexing Kit, BD Rhapsody).
scRNASeq experiments were performed using the BD Rhapsody Express Single-cell Analysis System platform, according to the manufacturer’s instructions. Briefly, the cell suspension was applied to the cartridges at a suitable dilution and speed so that a single cell was distributed per well, where beads were distributed in sequence. Each bead had a specific barcode, in addition to a poly-T tail for capturing mRNA transcripts released after cell lysis. Then, reverse transcription, amplification and purification steps were performed to construct a cDNA library (Cartridge, Enhanced Cartridge Reagent, cDNA, WTA Amplification and TCR/BCR Amplification Kits, BD Rhapsody), which was submitted to deep sequencing in the NovaSeq 6000 equipment (Illumina).

value: Blood

tag: sorted cells

value: live CD45+

tag: id (patient_1)

tag: sex (patient_1)

value: M

tag: age (patient_1)

tag: response (patient_1)

value: responder, PR

tag: id (patient_2)

tag: sex (patient_2)

tag: age (patient_2)

tag: response (patient_2)

tag: id (patient_3)

tag: sex (patient_3)

value: F

tag: age (patient_3)

tag: response (patient_3)

value: non-responder, PD

tag: id (patient_4)

tag: sex (patient_4)

tag: age (patient_4)

tag: response (patient_4)

tag: id (patient_5)

tag: sex (patient_5)

tag: age (patient_5)

tag: response (patient_5)

tag: id (patient_6)

tag: sex (patient_6)

tag: age (patient_6)

tag: response (patient_6)

tag: sample-tag id_(patient_1)

tag: sample-tag sequence_(patient_1)

tag: sample-tag id_(patient_2)

tag: sample-tag sequence_(patient_2)

tag: sample-tag id_(patient_3)

tag: sample-tag sequence_(patient_3)

tag: sample-tag id_(patient_4)

tag: sample-tag sequence_(patient_4)

tag: sample-tag id_(patient_5)

tag: sample-tag sequence_(patient_5)

tag: sample-tag id_(patient_6)

tag: sample-tag sequence_(patient_6)


title: PBMC, CD45+, Pool2

description:
Library name: Sample2
BD Rhapsody
Raw FASTQ files correspond to a pooled library of 6 multiplexed samples processed in one BD Rhapsody cartridge. Sample identity was resolved using BD Rhapsody Sample Tags. Processed gene expression matrix (MTX format) is provided for each patient individually. Patient 1 = ID45, patient 2 = ID46, patient 3 = ID56, patient 4 = ID74, patient 5 = ID103, patient 6 = ID119.

tag: tissue

tag: sorted cells

tag: id (patient_1)

tag: sex (patient_1)

tag: age (patient_1)

tag: response (patient_1)

tag: id (patient_2)

tag: sex (patient_2)

tag: age (patient_2)

tag: response (patient_2)

tag: id (patient_3)

tag: sex (patient_3)

tag: age (patient_3)

tag: response (patient_3)

tag: id (patient_4)

tag: sex (patient_4)

tag: age (patient_4)

tag: response (patient_4)

tag: id (patient_5)

tag: sex (patient_5)

tag: age (patient_5)

tag: response (patient_5)


title: GC B cell, mM-only TM4 pos, BCR

description:
Library name: mIgM_TM4_C_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Single-cell BCR libraries were mapped to the Cell Ranger VDJ GRCm38 reference using Cell Ranger vdj v.8.1.0 (10x genomics). Contigs containing less than 50 reads and more than one heavy or light chain were removed. scRNA-seq and Hashtag-oligos unique molecular identifier quantification were performed with Cell Ranger counts v.8.0.1 using the Cell Ranger GEX reference mm10, and analyzed in R with Seurat v.5.1.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets or with mitochondrial content greater than 10 % and feature count less than 1,000 or greater than 6,500 were excluded. Cell cycle genes were regressed out. Sample batches were then merged, scaled and normalized with SCTransform.
Assembly: GRCm38
Supplementary files format and content: CellRanger output files: RNA_barcodes.tsv.gz, RNA_features.tsv.gz, RNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: airr_rearrangement.tsv
Supplementary files format and content: CellRanger output files:  HTO_barcodes.tsv.gz, HTO_features.tsv.gz, HTO_matrix.mtx.gz
Library strategy: BCR-Seq

tag: tissue

tag: cell type

tag: genotype

tag: treatment

tag: batch


title: Kidney, ET-type, S0326

description: Library name: kmp_et_s0326_kidney

value: Kidney


title: Kidney, ET-type, S0276

description: Library name: kmp_et_s0276_kidney


title: Kidney, ET-type, S0235

description: Library name: kmp_et_s0235_kidney


title: Kidney, ET-type, S0242

description: Library name: kmp_et_s0242_kidney


title: Kidney, ET-type, S0309

description: Library name: kmp_et_s0309_kidney


title: GC B cell, mM-only TM4 neg, BCR

description:
Library name: mIgM_TM4_C_1_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: GC B cell, M-only TM4 pos, BCR

description:
Library name: smIgM_TM4_B_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: M-only


title: GC B cell, M-only TM4 neg, BCR

description:
Library name: smIgM_TM4_B_1_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Heart, ET-type, S0242

description: Library name: kmp_et_s0242_heart

value: Heart


title: GC B cell, M-only TM4 pos, HTO

description:
Library name: smIgM_TM4_B_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: Lymph node


title: samp157_6hr

city: Washington,DC

first: Chen

last: Yi Wen

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

description:
Library name: 4_S7
10X Genomics

data_processing:
Pre-processing of the single-cell FASTQ samples, including demultiplexing, alignment, count, and quality visualization, was performed using Cell Ranger (version 6; 10X Genomics).
For the reference,reads were aligned to the the human reference genome GRCh38 – hg38
Next, we used the Seurat scRNA-seq pipeline for further downstream analysis on each sample individually. We filtered genes present in at least 10 cells, cells with low gene and transcript numbers (<200) and removed cells with greater than 15% mitochondrial content per sample.
Next, normalization was performed on each of the samples using SCTransform with 2000 variable genes, followed by doublet removal using DoubletFinder43. Principal component analysis (PCA) was then performed, followed by KNN graph using the first 30 PCAs, clustering using a resolution of 0.1, and Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) for visualization.
All the samples were then integrated, followed by creation of PCA, KNN graph (first 30 PCs), clustering (using a resolution of 0.1) and UMAP. Individual pairwise integration of different conditions was performed in the same fashion for differential expression analysis. Pseudo bulk analysis, using Wilcox t-test was performed between each condition with a significance level of p-value < 0.05 and log fold change > 0.25 or <0.25. Gene ontology was performed using the Hallmark genes dataset using the fgsea package in R.
Assembly: hg38
Supplementary files format and content: Tab seperated value files and matrix files.

source_name: Muscle

growth_protocol: Myoblasts from four separate individuals with FSHD, and from their healthy, first-degree relatives, were obtained from Dr. Woodring Erik Wright at UT Southwestern University (Texas, USA) and the Senator Paul Wellstone Muscular Dystrophy Cooperative Research Center at Boston Biomedical Research Institute (Boston, MA, USA). For all experiments, the cells were weaned from dexamethasone for 3 days by changing to media without dexamethasone (-DEX

extract_protocol:
We used a cell scraping approach to induce membrane injuries in thousands of cells simultaneously. cells were plated in 10 cm dishes, cultured in -DEX media for 3 days and scraped from the dish with a cell scraper (UltraCruz, Santa Cruz Biotechbology). The cells were collected, gently pelleted (130xg, 4 min), resuspended in 1 ml of -DEX media, and re-plated for 6- or 24-hrs for collection for single cell library generation
Single-cell RNA-seq libraries were generated using the Chromium Next GEM Single Cell v 3.1 (10x Genomics, US).

value: Muscle

tag: cell line

value: Immortalized Myoblast

value: FSHD

value: injured

value: I


title: samp234_6hr

description:
Library name: 234_6hr_S4
10X Genomics

value: Healthy

value: II


title: Tyknu, IgG IP, PBO control, 6hr, replicate 1

city: Washington

first: Reddick

middle: R

last: Walker

state: DC

address: 800 22nd St NW SEH 8960

department: MITM

institute: The George Washington University

description: Library name: Tyknu_IgG_PBO_6hr_rep1

data_processing:
Adaptors were trimmed using Cutadapt.
Sequences were aligned to hg38 using (mapq 30, very-sensitive-loca, soft-clipped-unmapped-tlen, dovetail, no-mixed,  no-discordant, I 10, X 1000)
Peaks were called against IgG control files using MACS2 (q-value: 0.05, BAMPE, nomodel, keep-dup, broad)
Assembly: hg38
Supplementary files format and content: bigwig format
Library strategy: CUT&Run

source_name: Tyknu

growth_protocol: DMEM, 10% FBS, 1% P/S

extract_protocol:
H3K9ac-targeted CUT&RUN-sequencing was performed according the the Cell Signaling Technologies CUT&RUN kit.
Libraries were prepared using the NEBNext Ultra II DNA library preparation kit.

treatment_protocol: 0.15mg/mL Prussian blue nanoparticles are introduced into 0.5mL suspension of cells with a final concentration of 10e6/mL. Suspensions treated with near infrared (808nm) light for 10 minutes at 1W laser intensity.

value: Tyknu

value: PBO control


title: Tyknu, IgG IP, 1W-treated, 6hr, replicate 1

description: Library name: Tyknu_IgG_1W_6hr_rep1

value: 1W photothermal therapy


title: samp227_6hr

description:
Library name: 227_6hr_S3
10X Genomics


title: samp234_baseline

description:
Library name: 234_baseline_S2
10X Genomics

value: un-injured


title: Tyknu, H3K9ac IP, PBO control, 6hr, replicate 2

description: Library name: Tyknu_H3K9ac_PBO_6hr_rep2


title: GC B cell, mM-only TM4 neg, HTO

description:
Library name: mIgM_TM4_C_1_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: GC B cells

value: mM-only

value: D96 4x CD4bs


title: samp161_baseline

description:
Library name: 2_S3
10X Genomics


title: Heart, ET-type, S0276

description: Library name: kmp_et_s0276_heart


title: Heart, ET-type, S0326

description: Library name: kmp_et_s0326_heart


title: GC B cell, M-only TM4 neg, HTO

description:
Library name: smIgM_TM4_B_1_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: M-only


title: samp161_6hr

description:
Library name: 3_S5
10X Genomics


title: Heart, ET-type, S0235

description: Library name: kmp_et_s0235_heart

value: Heart


title: samp227_baseline

description:
Library name: 227_baseline_S1
10X Genomics


title: Heart, ET-type, S0309

description: Library name: kmp_et_s0309_heart


title: GC B cell, WT TM4 pos, HTO

description:
Library name: CTRL_TM4_A_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: Lymph node

value: wildtype, C57BL/6J


title: HH23, H3K9ac IP, PBO control, 6hr, replicate 2

description: Library name: HH23_H3K9ac_PBO_6hr_rep2

source_name: HH23 - Hey CRISPR-modified (R175H)

value: HH23 - Hey CRISPR-modified (R175H)


title: HH23, H3K9ac IP, PBO control, 6hr, replicate 1

description: Library name: HH23_H3K9ac_PBO_6hr_rep1


title: MB18_S2_L002

first: Amanda

middle: D

last: Barreto

address: 1427 Fitzpatrick Center

description:
Library name: Sample 45
raw data file

data_processing:
RNA-seq reads were trimmed using Trim Galore v 0.6.4 and mapped to the human genome (GRCh38) with STAR (Spliced Transcripts Alignment to a Reference) 76 (v 2.6.1d, with parameters --twopassMode Basic and supplying the Ensembl GRCh38 annotation). Mapped reads were filtered by MAPQ (Mapping quality) (no smaller than 30) (Supplementary table 3) and counted using featureCounts 77 (v 1.6.4, with parameters -s 2). Bioconductor package DESeq2 78 (v 1.26.0) was used to analyze differential gene expression (Supplementary Table 4) . TPM (transcripts per million) values were quantified using Salmon 79 (v 0.14.1) and summarized using tximport 80 (v 1.14.2). To account for multiple testing, we applied the False Discovery Rate (FDR) correction, with an adjusted p-value threshold of < 0.05 to identify statistically significant differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: excel worksheet files with DESeq2.Salmon.diff for each disease model compared to control

source_name: kidney

extract_protocol:
RNA isolation was performed using a NucleoSpin RNA extraction kit (Takara Bio, 740955.25, CA, USA). Three samples of RNA per treatment condition were collected in three independent experiments.
RNA integrity was assessed using an Agilent 2100 Bioanalyzer. All samples used for sequencing had an RNA Integrity Number (RIN) of 8.0 or higher, ensuring high-quality RNA suitable for high-resolution transcriptomic analyses (Supplementary Table 5). RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 platform using three lanes of SP flow cells with 51 base pair paired-end (PE) reads. This setup provided high-throughput sequencing with robust data output per sample.

value: kidney

value: human induced pluripotent stem cell

value: WT

value: ADR

value: Round 3


title: Tyknu, H3K9ac IP, PBO control, 6hr, replicate 1

description: Library name: Tyknu_H3K9ac_PBO_6hr_rep1

value: Tyknu


title: HH23, IgG IP, 1W-treated, 6hr, replicate 1

description: Library name: HH23_IgG_1W_6hr_rep1


title: Hey, IgG IP, PBO control, 6hr, replicate 1

description: Library name: Hey_IgG_PBO_6hr_rep1

source_name: Hey

value: Hey

value: PBO control


title: GC B cell, mM-only prime boost, BCR

description:
Library name: mIgM_2_C_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: D98 3x spike


title: GC B cell, WT TM4 pos, BCR

description:
Library name: CTRL_TM4_A_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: GC B cells


title: GC B cell, WT TM4 neg, BCR

description:
Library name: CTRL_TM4_A_1_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Tyknu, H3K9ac IP, 1W-treated, 6hr, replicate 1

description: Library name: Tyknu_H3K9ac_1W_6hr_rep1

value: 1W photothermal therapy


title: Hey, IgG IP, 1W-treated, 6hr, replicate 1

description: Library name: Hey_IgG_1W_6hr_rep1


title: Hey, H3K9ac IP, PBO control, 6hr, replicate 2

description: Library name: Hey_H3K9ac_PBO_6hr_rep2


title: Tyknu, H3K9ac IP, 1W-treated, 6hr, replicate 2

description: Library name: Tyknu_H3K9ac_1W_6hr_rep2


title: HH23, IgG IP, PBO control, 6hr, replicate 1

description: Library name: HH23_IgG_PBO_6hr_rep1


title: samp157_baseline

description:
Library name: 1_S6
10X Genomics

value: Muscle

value: Immortalized Myoblast

value: FSHD

value: un-injured

value: I


title: MB17_S1_L001

description:
Library name: Sample 48
raw data file

value: CytoD


title: MB17_S1_L002

description:
Library name: Sample 47
raw data file

value: kidney


title: HH23, H3K9ac IP, 1W-treated, 6hr, replicate 2

description: Library name: HH23_H3K9ac_1W_6hr_rep2

value: HH23 - Hey CRISPR-modified (R175H)


title: MB18_S2_L001

description:
Library name: Sample 46
raw data file

value: human induced pluripotent stem cell

value: WT


title: MB19_S3_L001

description:
Library name: Sample 44
raw data file

value: LPS

value: Round 3


title: Hey, H3K9ac IP, 1W-treated, 6hr, replicate 2

description: Library name: Hey_H3K9ac_1W_6hr_rep2

value: Hey


title: Hey, H3K9ac IP, 1W-treated, 6hr, replicate 1

description: Library name: Hey_H3K9ac_1W_6hr_rep1


title: MB20_S4_L002

description:
Library name: Sample 41
raw data file

value: DMSO


title: A2780, IgG IP, 1W-treated, 6hr, replicate 1

description: Library name: A2780_IgG_1W_6hr_rep1


title: GC B cell, WT TM4 neg, HTO

description:
Library name: CTRL_TM4_A_1_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: Lymph node

value: wildtype, C57BL/6J

value: D96 4x CD4bs


title: MB19_S3_L002

description:
Library name: Sample 43
raw data file


title: GC B cell, M-only prime boost, BCR

description:
Library name: smIgM_2_B_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: GC B cells

value: M-only

value: D98 3x spike


title: GC B cell, WT prime boost, BCR

description:
Library name: CTRL_2_A_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: MB21_S5_L001

description:
Library name: Sample 40
raw data file

value: HG


title: HH23, H3K9ac IP, 1W-treated, 6hr, replicate 1

description: Library name: HH23_H3K9ac_1W_6hr_rep1

value: 1W photothermal therapy


title: Hey, H3K9ac IP, PBO control, 6hr, replicate 1

description: Library name: Hey_H3K9ac_PBO_6hr_rep1

value: PBO control


title: A2780, H3K9ac IP, PBO control, 6hr, replicate 1

description: Library name: A2780_H3K9ac_PBO_6hr_rep1


title: GC B cell, WT prime boost, HTO

description:
Library name: CTRL_2_A_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: MB21_S5_L002

description:
Library name: Sample 39
raw data file

value: kidney


title: MB20_S4_L001

description:
Library name: Sample 42
raw data file


title: GC B cell, M-only prime boost, HTO

description:
Library name: smIgM_2_B_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: MB22_S6_L001

description:
Library name: Sample 38
raw data file

value: NG


title: A2780, H3K9ac IP, 1W-treated, 6hr, replicate 1

description: Library name: A2780_H3K9ac_1W_6hr_rep1


title: Tyknu, IgG IP, 1W-treated, 10min, replicate 2

description: Library name: Tyknu_IgG_1W_10min_rep2

value: Tyknu


title: A2780, IgG IP, PBO control, 6hr, replicate 1

description: Library name: A2780_IgG_PBO_6hr_rep1


title: GC B cell, mM-only prime boost RBD neg, BCR

description:
Library name: mIgM_1_C_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mM-only


title: GC B cell, mM-only prime boost, HTO

description:
Library name: mIgM_2_C_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: A2780, H3K9ac IP, 1W-treated, 6hr, replicate 2

description: Library name: A2780_H3K9ac_1W_6hr_rep2


title: Tyknu, IgG IP, PBO control, 10min, replicate 1

description: Library name: Tyknu_IgG_PBO_10min_rep1


title: Tyknu, H3K9ac IP, 1W-treated, 10min, replicate 2

description: Library name: Tyknu_H3K9ac_1W_10min_rep2


title: Tyknu, H3K9ac IP, PBO control, 10min, replicate 1

description: Library name: Tyknu_H3K9ac_PBO_10min_rep1


title: Tyknu, IgG IP, PBO control, 10min, replicate 2

description: Library name: Tyknu_IgG_PBO_10min_rep2


title: GC B cell, WT prime boost RBD neg, BCR

description:
Library name: CTRL_1_A_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: HH23, IgG IP, PBO control, 10min, replicate 1

description: Library name: HH23_IgG_PBO_10min_rep1

value: HH23 - Hey CRISPR-modified (R175H)


title: GC B cell, M-only prime boost RBD neg, BCR

description:
Library name: smIgM_1_B_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: MB23_S7_L001

description:
Library name: Sample 36
raw data file

value: human induced pluripotent stem cell

value: WT

value: HG cytokines

value: Round 3


title: GC B cell, mM-only prime boost RBD neg, HTO

description:
Library name: mIgM_1_C_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: Lymph node


title: PC and GC B cells, mM-only prime, BCR

description:
Library name: 4_EXP_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: GC B cells + Plasma cells

value: D14 RBD prime


title: GC B cell, M-only prime boost RBD neg, HTO

description:
Library name: smIgM_1_B_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: GC B cells

value: M-only


title: MB24_S8_L001

description:
Library name: Sample 34
raw data file

value: UNT


title: MB23_S7_L002

description:
Library name: Sample 35
raw data file


title: HH23, H3K9ac IP, 1W-treated, 10min, replicate 2

description: Library name: HH23_H3K9ac_1W_10min_rep2

value: 1W photothermal therapy


title: HH23, IgG IP, 1W-treated, 10min, replicate 2

description: Library name: HH23_IgG_1W_10min_rep2


title: Tyknu, H3K9ac IP, PBO control, 10min, replicate 2

description: Library name: Tyknu_H3K9ac_PBO_10min_rep2

value: PBO control


title: MB22_S6_L002

description:
Library name: Sample 37
raw data file

value: kidney


title: Tyknu, H3K9ac IP, 1W-treated, 10min, replicate 1

description: Library name: Tyknu_H3K9ac_1W_10min_rep1


title: Tyknu, IgG IP, 1W-treated, 10min, replicate 1

description: Library name: Tyknu_IgG_1W_10min_rep1


title: HH23, H3K9ac IP, PBO control, 10min, replicate 1

description: Library name: HH23_H3K9ac_PBO_10min_rep1


title: MB24_S8_L002

description:
Library name: Sample 33
raw data file


title: HH23, IgG IP, PBO control, 10min, replicate 2

description: Library name: HH23_IgG_PBO_10min_rep2


title: MB25_S9_L001

description:
Library name: Sample 32
raw data file

value: CytoD

value: Round 2


title: HH23, H3K9ac IP, PBO control, 10min, replicate 2

description: Library name: HH23_H3K9ac_PBO_10min_rep2


title: PC and GC B cells, mM-only prime, HTO

description:
Library name: 4_EXP_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: mM-only


title: GC B cell, WT prime boost RBD neg, HTO

description:
Library name: CTRL_1_A_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: wildtype, C57BL/6J

value: D98 3x spike


title: MB25_S9_L002

description:
Library name: Sample 31
raw data file

value: human induced pluripotent stem cell

value: WT


title: A2780, H3K9ac IP, PBO control, 6hr, replicate 2

description: Library name: A2780_H3K9ac_PBO_6hr_rep2


title: MB26_S10_L001

description:
Library name: Sample 30
raw data file

value: ADR


title: Hey, IgG IP, 1W-treated, 10min, replicate 2

description: Library name: Hey_IgG_1W_10min_rep2

value: Hey


title: GC B cell, mM-only prime RBD pos, BCR

description:
Library name: 3_EXP_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Lymph node

value: GC B cells + CD8 T


title: MB26_S10_L002

description:
Library name: Sample 29
raw data file


title: HH23, IgG IP, 1W-treated, 10min, replicate 1

description: Library name: HH23_IgG_1W_10min_rep1

value: HH23 - Hey CRISPR-modified (R175H)


title: Hey, IgG IP, PBO control, 10min, replicate 1

description: Library name: Hey_IgG_PBO_10min_rep1


title: Hey, H3K9ac IP, 1W-treated, 10min, replicate 2

description: Library name: Hey_H3K9ac_1W_10min_rep2


title: GC B cell, mM-only prime RBD pos, GEX

description:
Library name: 3_EXP_2_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Single-cell BCR libraries were mapped to the Cell Ranger VDJ GRCm38 reference using Cell Ranger vdj v.8.1.0 (10x genomics). Contigs containing less than 50 reads and more than one heavy or light chain were removed. scRNA-seq and Hashtag-oligos unique molecular identifier quantification were performed with Cell Ranger counts v.8.0.1 using the Cell Ranger GEX reference mm10, and analyzed in R with Seurat v.5.1.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets or with mitochondrial content greater than 10 % and feature count less than 1,000 or greater than 6,500 were excluded. Cell cycle genes were regressed out. Sample batches were then merged, scaled and normalized with SCTransform.
Assembly: GRCm38
Supplementary files format and content: CellRanger output files: RNA_barcodes.tsv.gz, RNA_features.tsv.gz, RNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: airr_rearrangement.tsv
Supplementary files format and content: CellRanger output files:  HTO_barcodes.tsv.gz, HTO_features.tsv.gz, HTO_matrix.mtx.gz

value: D14 RBD prime


title: Hey, IgG IP, 1W-treated, 10min, replicate 1

description: Library name: Hey_IgG_1W_10min_rep1


title: Hey, H3K9ac IP, PBO control, 10min, replicate 1

description: Library name: Hey_H3K9ac_PBO_10min_rep1


title: MB27_S11_L001

description:
Library name: Sample 28
raw data file

value: LPS