title: DI318 cells, WNK1 sh920, biological replicate 3

city: Cleveland

first: Erin

last: Mulkearns-Hubert

state: OH

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic

data_processing:
Contamination removal was performed usingBowtie2(v2.5.1)
The paired-end reads were aligned to the reference Human genome Feb.2009 release downloaded from UCSC database (GRCh37/hg19) using STAR (v2.7.3a).
The aligned reads were used for estimating expression of the genes. The raw read counts were estimated usingHTSeq(v0.11.2).Read count data were normalized using DESeq2. Additionally the aligned reads are used for estimating expression of the genes using cufflinks (v2.2.1). The expression values are reported in FPKM (Fragments per kilobase per million) units for each gene.
Differential expression analysis was performed usingDESeq2
Assembly: GRCh37/hg19
Supplementary files format and content: Excel file contains FPKM values for all samples

growth_protocol: DI318 cells were maintained in were cultured in suspension in Petri dishes in Neurobasal medium without phenol red supplemented with 1% penicillin/streptomycin, 2% B27 without vitamin A, 20 ng/mL EGF, 20 ng/mL FGF, 1 mM sodium pyruvate, and 2 mM L-glutamine in a humidified atmosphere at 37 degrees C with 5% CO2.

extract_protocol:
RNA was harvested using Qiagen Rneasy kit.
Libraries were constructed by MedGenome.

treatment_protocol: Cells were adhered to dishes using Geltrex and transduced with lentivirus (Sigma MISSION system). Two days after transduction, cells were treated with 2 ug/ml puromycin for 2 days.

value: glioblastoma patient-derived xenograft

value: WNK1 sh920


title: 9727_Total_Kidney

status: Public on Aug 11 2025

type: SRA

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

country: USA

institute: Albany Medical College

description: Library name: Sample_16

library_source: transcriptomic

data_processing:
Sequencing adapters and low-quality bases were trimmed using Trim Galore (v0.6.10). Reads were aligned to the human genome (hg38) using STAR (v2.7.10a). Gene-level counts were quantified with featureCounts (Subread v2.0.3). Differential expression was analyzed using the limma-voom pipeline in R (v4.3.2), with genes filtered by CPM >1 in at least 3 samples and adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: kidney

extract_protocol:
Trizol and Rneasy columns
RNA-seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), including polyA enrichment for mRNA. Libraries were barcoded, quantified by qPCR, and sequenced on an Illumina NovaSeq 6000 using 150 bp paired-end reads.

tag: tissue

value: kidney

tag: strain

tag: cell type

value: endothelial cells

tag: genotype

tag: treatment

value: saline


title: WTE105-20TALL

type: RNA

city: Perugia

first: Roberta

last: La Starza

address: Piazzale Menghini 9

department: Department of Medicine and Surgery

country: Italy

institute: University of Perugia

hyb_protocol: Hybridization of the microarrays was performed in a GeneChip® Hybridization Oven 645 (Affymetrix/Thermo Fisher Scientific). GeneChips were washed and stained

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy)

data_processing: Primary data analysis was performed with Transcriptome Analysis Console software version 4.0 (TAC 4.0.2.15). Differentially expressed RNA were estimated by fold-change filtering combined with Student’s t-test. Transcripts with fold change in expression > ±2.0 and FDR<0.05 were considered significantly differentially expressed. Hierarchical clustering was performed to show the distinguishing genes expression pattern among samples

label: biotin

organism: Homo sapiens

source_name: BONE MARROW

label_protocol: GeneChip® WT PLUS Reagent Kit (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy) was used to generates amplified and biotinylated sense-strand DNA targets from total RNA; it uses a reverse transcription priming method that primes the entire length of RNA. Amplified cDNA was quantified, fragmented, marked, and prepared for hybridization from the GeneChip® Clariom S Human Array (Thermo Fisher Scientific) for expression level measurement

extract_protocol: RNA was extracted from bone marrow or peripheral blood samples using a QIAamp RNA Blood Mini Kit (Qiagen) at a QIAcube automated station

value: BONE MARROW


title: DI318 cells, WNK1 sh920, biological replicate 2

tag: cell line


title: WTE112-20TALL


title: 9726_Total_Kidney

description: Library name: Sample_14

value: wt

value: lps


title: DI318 cells, WNK1 sh491, biological replicate 3

value: WNK1 sh491


title: Mouse uterus aged group2 rep2 H3K4me3

city: Cambridge

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description: Library name: H3K4me3_42wk_MH231(2D1)

library_source: genomic

data_processing:
Reads were aligned to the mouse genome assembly GRCm38 using bowtie2. We assessed the data quality using ChIPQC (v1.34.0). Peaks were identified using MACS2 (v2.2.9.1) with q < 0.01. The DiffBind R package (v3.8.0) was used to find consensus peaks in different sample groups and perform differential binding analysis [Stark & Brown, 2011]. Consensus peaks were defined as those present in more than 66% of samples within each group. A binding matrix was generated using read counts from consensus peaks overlapping within each group (summit width = 200 bp), followed by normalization. This matrix was then used to identify differentially accessible regions between age groups using DESeq2 (as implemented by default in DiffBind), applying a false discovery rate (FDR) threshold of ≤ 0.05. Peaks were assigned to genes or nearby genes using ChIPpeakAnno (v3.32.0). In addition to gene assignment, peaks were annotated for genomic feature overlap—whether located in TSS, exon, 5′ UTR, 3′ UTR, intronic, or intergenic regions using ChIPseeker (v1.34.1). deepTools (v3.5.1) was used to visualize the average profiles of histone modifications across gene regions ±5 kb in different groups.
To identify super-enhancers, H3K27ac peaks called with MACS2 (with parameter --- broad) and used as input for the ROSE (Rank Ordering of Super-Enhancers) software, which stitches together enhancer peaks located within 12.5 kb of each other (Whyte et al., 2013).
Assembly: Grcm38
Supplementary files format and content: Processed data files are in .txt format. Data contained are Log2RPKM quantitation of 1. consensus H3K4me3 peaks for H3K4me3 ChIp-seq samples (H3K4me3_AllPeaks_Log2RPKM.txt) and 2. consensus H3K27ac peaks for H3K27ac ChIP-seq samples (H3K27ac_AllPeaks_Log2RPKM.txt).

molecule: genomic DNA

source_name: uterus

extract_protocol:
Ultra-low input native ChIP-seq was performed on pieces of snap frozen endometrial tissue as previously described [ref]. Briefly, tissue was thawed on ice in 100μL nuclear isolation buffer (NIB, Sigma) and diced using a blade. An aliquot of 20,000 nuclei in 10μL NIB was then taken forward for Mnase (NEB) digestion at 21 °C for 7.5 minutes. Digested chromatin was then suspended in Complete IP buffer (20mM Tris-HCl (pH8), 2mM EDTA, 150mM NaCl, 0.1%Triton-X100, 1x Protease inhibitor cocktail,1mM PMSF). Following pre-clearing the chromatin on a mix of protein A/protein G beads (Thermo Fisher Scientific), and after 10% was set aside for input, the chromatin was divided for immunioprecipitation overnight rotating at 30 rpm, at 4 °C. IP was performed using 250ng antibodies for H3K4me3 (Diagenode, C15410003) and H3K27ac (Abcam, ab4729). DNA was washed in low then high salt washes, before eluting in ChIP elution buffer (100mM NaHCO3, 1% SDS). DNA was then SPRI purified before continuing to library preparation
Libraries were prepred using the MicroPlex Library Preparation kit (Diagenode, C05010001). Libraries were quantitated using the Agilent Bioanalyzer High Sensitivity DNA assay before pooling for sequencing. Libraries were sequenced on the Illumina NextSeq500, 75 bp paired end.

value: uterus


title: Mouse uterus aged group2 rep3 H3K4me3

description: Library name: H3K4me3_48wk_MH236(3D1)


title: 9726_Kidney_Endo

description: Library name: Sample_13


title: DI318 cells, WNK1 sh491, biological replicate 2


title: 9727_Kidney_Endo

description: Library name: Sample_15


title: Mouse uterus aged group2 rep4 H3K4me3

description: Library name: H3K4me3_42wk_MH234(4A1)


title: DI318 cells, WNK1 sh920, biological replicate 1


title: Mouse uterus aged group2 rep1 H3K4me3

description: Library name: H3K4me3_48wk_MH240(1B1)


title: WTE011-21TALL

source_name: PERIPHERAL BLOOD

value: PERIPHERAL BLOOD


title: 9725_Total_Kidney

description: Library name: Sample_12


title: DI318 cells, WNK1 sh491, biological replicate 1


title: WTE113-20TALL


title: Mouse uterus aged group1 rep4 H3K4me3

description: Library name: H3K4me3_36wk_MH228(4D1)


title: DI318 cells, Cx43 sh77, biological replicate 3

value: Cx43 sh77


title: 9725_Kidney_Endo

description: Library name: Sample_11


title: Mouse uterus aged group1 rep3 H3K4me3

description: Library name: H3K4me3_36wk_MH227(3A1)


title: 9724_Total_Kidney

description: Library name: Sample_10


title: DI318 cells, Cx43 sh77, biological replicate 2


title: Mouse uterus aged group1 rep2 H3K4me3

description: Library name: H3K4me3_28wk_MH225(2B1)


title: DI318 cells, Cx43 sh77, biological replicate 1


title: 9724_Kidney_Endo

description: Library name: Sample_9


title: WTE097-20TALL


title: WTE014-21TALL


title: WTE074-21TALL


title: 9723_Total_Kidney

description: Library name: Sample_8


title: DI318 cells, Cx43 sh73, biological replicate 3

value: Cx43 sh73


title: Mouse uterus aged group1 rep1 H3K4me3

description: Library name: H3K4me3_28wk_MH223(1D1)


title: 9723_Kidney_Endo

description: Library name: Sample_7


title: DI318 cells, Cx43 sh73, biological replicate 2


title: WTE009-21TALL


title: Mouse uterus young rep6 H3K4me3

description: Library name: H3K4me3_11wk_MH59(7C1)


title: Mouse uterus young rep5 H3K4me3

description: Library name: H3K4me3_10wk_MH54(7B1)


title: 9722_Total_Kidney

description: Library name: Sample_6


title: 9722_Kidney_Endo

description: Library name: Sample_5


title: DI318 cells, Cx43 sh73, biological replicate 1


title: DI318 cells, non-target shControl, biological replicate 3

value: non-target shControl


title: Mouse uterus young rep4 H3K4me3

description: Library name: H3K4me3_10wk_MH53(5C1)


title: 9721_Total_Kidney

description: Library name: Sample_4


title: Mouse uterus young rep3 H3K4me3

description: Library name: H3K4me3_10wk_MH52(4C1)


title: DI318 cells, non-target shControl, biological replicate 2


title: 9721_Kidney_Endo

description: Library name: Sample_3


title: Mouse uterus young rep2 H3K4me3

description: Library name: H3K4me3_9wk_MH270(3B1)


title: 9720_Total_Kidney

description: Library name: Sample_2


title: DI318 cells, non-target shControl, biological replicate 1


title: Mouse uterus young rep7 H3K4me3

description: Library name: H3K4me3_11wk_MH55(7D1)


title: WTE015-21TALL


title: WTE045-21TALL


title: 9720_Kidney_Endo

description: Library name: Sample_1


title: human iPSC-derived motor neurons, C9 NRE+ cytoplasmic ASO captured, MN307

city: New Haven

first: Suzhou

last: Yang

state: CT

address: 100 College Street, Room 225

department: Neuroscience

institute: Yale University

data_processing:
Fastq sequences were aligned to human genome assembly GRCh38/hg38 using STAR 2.7, with the following parameters: --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterMismatchNmax 2.
After alignment, read deduplication was performed by using the markdup function from SAMtools.
Assembly: GRCh38/hg38
Supplementary files format and content: csv files include raw counts of detected splice junctions in C9ORF72 RNAs.

molecule: cytoplasmic RNA

growth_protocol: iPSCs were grown in six-well plates coated with matrigel (Corning, 354277) in mTeSR Plus media (Stem Cell Technologies, 100-0276). Upon reaching 90% confluence, iPSCs were either differentiated or passaged using Accutase (Sigma-Aldrich, A6964) and resuspended in media containing Y27632 (10 µM, Tocris, 1254). Upon reaching 90% confluency (day 0), iPSCs were dissociated using Accutase (Sigma-Aldrich, A6964) for 5 min at 37°C. The cells were then centrifuged at 200 rcf for 5 min and resuspended at a density of 2x105 cells/ml in ultra-low attachment 6-well plates (Sigma, CLS3471) using N2B27 medium (50% Advanced DMEM/F12 (ThermoFisher, 12634010), 50% Neurobasal Medium (ThermoFisher, 21103049), supplemented with 1% Pen/Strep (ThermoFisher, 15140122), Glutamax (ThermoFisher, 35050061), and 0.1mM 2-mercaptoethanol (ThermoFisher, 31350010), B27 (ThermoFisher, 17504044), and N2 (ThermoFisher, 17502048)) supplemented with Y27632 (10 µM, Tocris, 1254), FGF2 (10 ng/ml; ThermoFisher, 13256029), SB431542 (20 µM; Tocris, 1614/10), LDN193189 (0.1 µM; Tocris, 6053/10), CHIR 99021 (3 µM; Tocris, 4423/10), and ascorbic acid (10 µM, Tocris, 4055/50). At days 2 and 4, embryoid bodies were visible, and cells were centrifuged at 200 rcf for 5 min and resuspended in N2B27 with the same supplements as on day 0 except for the removal of Y27632 and addition of all-trans retinoic acid (100 nM; Tocris, 0695/50) and SAG (500 nM; EMD Calbiochem, 566660). At day 7, the embryoid bodies were centrifuged at 200 rcf for 5 min and resuspended in N2B27 supplemented with BDNF (10 µg/ml; PeproTech, 450-02), ascorbic acid, all-trans retinoic acid, and SAG. Media were changed on days 9 and 11 with N2B27 with the same supplements as day 7 but with the addition of DAPT (10 mM; Tocris, 2634/10). At day 14, the cells were resuspended in the same media as day 9, but with the addition of GDNF (10 µg/ml; PeproTech, 450-10). On day 16, the embryoid bodies were dissociated in 3 mL of pre-warmed 0.05% Trypsin-EDTA (ThermoFisher, 25300062) and DNase I (Fisher, NC9199796) for 1 hour at 37 °C. After adding an equal volume of FBS (ATCC, SCRR-30-2020) and DNase I, the cells were centrifuged at 200 rcf for 5 min. After collecting the supernatant, 1 ml cold PBS (Thermo Fisher, 20012027) was added to the pellet, which was then triturated gently 15 times and let to rest for 5 min. The supernatant was collected, and this process was repeated three times with 2 mL of PBS. The pooled collected supernatant was filtered through a 40 µm cell strainer (Fisher, 08-771-1) into a tube containing 2 ml cold PBS. The cells were centrifuged at 200 rcf for 5 min, resuspended in 1 ml cold PBS, and counted. iMNs were resuspended in NDM medium (Neurobasal Medium supplemented with Glutamax, 0.1mM 2-mercaptoethanol, N2, Pen/Strep, MEM NEAA, ThermoFisher, 11140050), supplemented with GDNF (10 µg/ml), CNTF (10 µg/ml; PeproTech, 450-13), BDNF (10 µg/ml), IGF-1 (10 µg/ml, PeproTech, 100-11), retinoic acid (100 nM), ascorbic Acid (10 µM), and plated in six-well plates pre-coated with PDL (Corning, 354413) coated with laminin (10 µg/mL; Invitrogen, 23017-015) at a density of 2 x 106 cells/ml. NDM media with supplements was replaced every 2-3 days.

extract_protocol:
iPSC-derived motor neurons were first subcellular fractionated. Total RNAs were extracted from each fraction by using TRIzol LS reagent (ThermoFisher) according to the manufacturer’s instructions. Residual DNA in both fractions was removed from RNA extracts by using TURBO DNA-free (ThermoFisher). NRE-RAP was performed similarly as the previously described RAP method (Engreitz, J. M. et al., 2014) with 5ʹ biotinylated (CCCCGG)3 ASO. The final RNA samples were cleaned up by using Monarch RNA Cleanup Kit (New England Biolabs).
After ribosomal RNA depletion (Takara, 634846), RNA libraries were prepared using SMARTer Pico-Input stranded RNA-seq kit (Takara, 634836). For input RNA samples, RNA-seq libraries were constructed using a KAPA RNA HyperPrep Kit with RiboErase (Roche).

value: human iPSC-derived motor neurons

value: C9ORF72 (GGGGCC)n expansion


title: human iPSC-derived motor neurons, C9 NRE- cytoplasmic ASO captured, MN920

value: WT


title: WTE087-20TALL


title: WTE012-21TALL


title: MEF, H3K27me3, Rep2

city: Rochester

first: Patrick

middle: J

last: Murphy

state: New York

address: 601 Elmwood Avenue

department: Biomedical Genetics and Genomics

institute: University of Rochester

description: Library name: H3K27me3_rep2

data_processing:
cutAdapt was used on all raw fastq files, and then each was mapped with bowtie2 using mm10.
PICARD MergeSamFiles was used to convert files to BAM files, and PICARD MarkDuplicates was used to remove duplicate reads.
bigWig files were made with deeptools BAMcoverage  --normalizeUsing RPKM --binSize 10 --extendReads 100.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: mouse embyronic fibroblast

growth_protocol: Primary MEFs were obtained from embryonic day 13.5 mouse embryos and grown in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.  Cells were cultured at 37°C.

extract_protocol:
Nuclei were extracted from MEFs using the standard CUT&Tag (Kaya-Okur et al. Nat. Comm. 2019. and https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) protocol (Nuclear Extraction Buffer).
Libraries were prepared for sequencing using standard CUT&Tag (Kaya-Okur et al. Nat. Comm. 2019. and https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) protocols. i5 and i7 sequencing adaptors were added to isolated DNA via PCR.
CUT&Tag with H2A.Z, H3K27ac, H3K27me3 and H3K9me3 antibodies

value: mouse embyronic fibroblast


title: Mouse uterus young rep1 H3K4me3

description: Library name: H3K4me3_10wk_MH60(2C1)


title: patient-derived fibroblasts, C9 NRE+ cytoplasmic ASO captured, FB506

description: NRE+_Cyto_ASO_captured_C9orf72_SJ_counts.csv

source_name: NINDS Fibroblast IDs: ND42506

growth_protocol: Fibroblasts were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% heat-inactivated fetal bovine serum (FBS) and 1x non-essential amino acids (NEAA) (ThermoFisher).

extract_protocol:
Fibroblasts were first subcellular fractionated. Total RNAs were extracted from each fraction by using TRIzol LS reagent (ThermoFisher) according to the manufacturer’s instructions. Residual DNA in both fractions was removed from RNA extracts by using TURBO DNA-free (ThermoFisher). NRE-RAP was performed similarly as the previously described RAP method (Engreitz, J. M. et al., 2014) with 5ʹ biotinylated (CCCCGG)3 ASO. The final RNA samples were cleaned up by using Monarch RNA Cleanup Kit (New England Biolabs).
After ribosomal RNA depletion (Takara, 634846), RNA libraries were prepared using SMARTer Pico-Input stranded RNA-seq kit (Takara, 634836). For input RNA samples, RNA-seq libraries were constructed using a KAPA RNA HyperPrep Kit with RiboErase (Roche).

value: NINDS Fibroblast IDs:ND42506

value: patient-derived skin fibroblasts


title: WTE010-21TALL


title: WTE039-20TALL


title: Endo_Tamoxifen_LPS8

data_processing:
The gene counts were normalized by rlog transformation and analyzed by the DeSeq2 pipeline. The analyzed DeSeq2 results were uploaded on the web-based application called iPathway Guide and significantly upregulated and downregulated genes and pathways were identified. The log2fold change threshold was >0.6 and the p-value threshold was <0.05 was applied.
Assembly: mm10
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

extract_protocol:
Endothelial enrichment and RNA isolation was performed following established protocols (Bossardi Ramos et al PMID 37667913).
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

treatment_protocol: Mice were challenged with 250 micrograms of LPS (E coli 0111:B4) in 250 microlitters of saline. Sham were injected with saline alone. Mice were euthanized 15 hours later.

value: kidney

value: Kidney endothelium

value: STINGiEKO

value: LPS


title: MEF, H3K27me3, Rep1

description: Library name: H3K27me3_rep1


title: WTE061-21TALL


title: patient-derived fibroblasts, C9 NRE+ cytoplasmic input, FB506


title: WTE051-21TALL

value: BONE MARROW


title: MEF, H3K27ac, Rep2

description: Library name: H3K27ac_rep2


title: WTE055-20 TALL


title: Total_Tamoxifen_LPS7

value: Whole kidney


title: WTE026-20TALL


title: WTE044-21TALL


title: patient-derived fibroblasts, C9 NRE+ nuclear ASO captured, FB506

description: NRE+_Nuc_ASO_captured_C9orf72_SJ_counts.csv

molecule: nuclear RNA


title: patient-derived fibroblasts, C9 NRE+ nuclear input, FB506


title: Endo_Tamoxifen_LPS7


title: Total_Tamoxifen_LPS8


title: patient-derived fibroblasts, C9 NRE+ cytoplasmic ASO captured, FB504

source_name: NINDS Fibroblast IDs: ND42504

value: NINDS Fibroblast IDs:ND42504


title: Endo_Tamoxifen_LPS6


title: WTE059-21TALL


title: patient-derived fibroblasts, C9 NRE+ cytoplasmic input, FB504


title: MEF, H2AZ, Rep2

description: Library name: H2AZ_rep2


title: MEF, H3K27ac, Rep1

description: Library name: H3K27ac_rep1


title: Total_Oil_LPS6


title: patient-derived fibroblasts, C9 NRE+ nuclear ASO captured, FB504


title: Total_Tamoxifen_LPS6


title: WTE043-20TALL


title: Endo_Oil_LPS6


title: MEF, Supernatant3, Rep2

description: Library name: supernatant3_rep2

data_processing:
cutAdapt was used on all raw fastq files, and then each was mapped with bowtie2 using mm10.
PICARD MergeSamFiles was used to convert files to BAM files, and PICARD MarkDuplicates was used to remove duplicate reads.
bigWig files were made with deeptools BAMcoverage  --normalizeUsing RPKM --binSize 10 --extendReads 100.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: chromatin fractionation and sequencing

extract_protocol:
5 µL of Proteinase K + 20 mM EDTA was added to each supernatant sample, and each pellet was resuspended in 500 µL of 1% SDS Lysis Buffer + 5 µL of Proteinase K + 20 mM EDTA.  Pellet samples were then broken up with a 20-gauge syringe.  All supernatant and pellet samples incubated for 1 hour at 50°C.  1% SDS was added to each sample, and the pellet samples were again broken up with a 20-gauge syringe.  All samples were incubated overnight at 65°C.  DNA was purified via chloroform extraction and ethanol precipitation.
i5 and i7 sequencing adaptors were directly added to DNA isolated from all supernatant samples with an NEBNext Multiplex Oligos for Illumina kit. DNA isolated from all pellet samples was digested with 1 uL of Tn5 protein at 37°C for 30 minutes at 1000 RPM, and i5 and i7 sequencing adaptors were added via PCR.

treatment_protocol: Cells were treated with 1% paraformaldehyde in PBS for 10 minutes at room temperature.  To stop crosslinking, 125 mM glycine was added to each plate. Samples were sonicated for 1 or 3 cycles (pulse = 10s; rest = 20s; amplitude = 30%; 5 min on). Samples were centrifuged at 3,000xg for 10 minutes at room temperature and then separated into supernatant and pellet fractions.


title: MEF, Supernatant3, Rep1

description: Library name: supernatant3_rep1


title: WTE052-21TALL


title: WTE070-20TALL


title: WTE030-20TALL


title: patient-derived fibroblasts, C9 NRE- cytoplasmic ASO captured, FB503

description: NRE-_Cyto_ASO_captured_C9orf72_SJ_counts.csv

source_name: NINDS Fibroblast IDs: ND42503

value: NINDS Fibroblast IDs:ND42503


title: MEF, Supernatant1, Rep3

description: Library name: supernatant1_rep3


title: Endo_Oil_LPS5


title: WTE048-20TALL


title: MEF, H2AZ, Rep1

description: Library name: H2AZ_rep1


title: WTE054-20 TALL


title: Total_Tamoxifen_Saline5

value: Saline


title: patient-derived fibroblasts, C9 NRE- cytoplasmic input, FB503


title: MEF, Supernatant1, Rep2

description: Library name: supernatant1_rep2


title: MEF, Supernatant3, Rep3

description: Library name: supernatant3_rep3


title: Endo_Tamoxifen_Saline5


title: WTE069-20TALL


title: MEF, Supernatant1, Rep1

description: Library name: supernatant1_rep1


title: Total_Oil_LPS5


title: patient-derived fibroblasts, C9 NRE+ nuclear input, FB504


title: patient-derived fibroblasts, C9 NRE- nuclear input, FB503


title: WTE078-21TALL


title: Total_Oil_LPS4


title: Endo_Oil_LPS4


title: WTE004-19TALL


title: patient-derived fibroblasts, C9 NRE- cytoplasmic ASO captured, FB485

source_name: NINDS Fibroblast IDs: ND42485

value: NINDS Fibroblast IDs:ND42485

value: MAPT P301L


title: MEF, Pellet1, Rep3

description: Library name: pellet1_rep3


title: patient-derived fibroblasts, C9 NRE- cytoplasmic input, FB485


title: Total_Oil_Saline4


title: MEF, Pellet1, Rep1

description: Library name: pellet1_rep1


title: patient-derived fibroblasts, C9 NRE- nuclear ASO captured, FB503

description: NRE-_Nuc_ASO_captured_C9orf72_SJ_counts.csv


title: WTE069-21TALL


title: patient-derived fibroblasts, C9 NRE- nuclear ASO captured, FB485


title: Endo_Oil_Saline4


title: patient-derived fibroblasts, C9 NRE- nuclear input, FB485


title: WTE065-20TALL


title: H3.1/H3.2/BMAL1 ChIP input (all CTs pooled)_replicate1

city: Lyon

first: Kiran

last: Padmanabhan

address: 32-34 Av. Tony Garnier

country: France

institute: IGFL - ENS Lyon

description: Library name: Input-Complexe-WT-Rep1

data_processing:
Reads were filtered out to remove the Illumina adaptaters, the bad quality reads (Phred < 20) and the short length reads (<75b).
Reads were aligned to mm39 genome assembly using Bowtie2 : --very-sensitive –phred33 –no-mixed –no-discordant --dovetail
The reads unmapped, mate unmapped, not primary alignment, reads failing platform, duplicates were removed using Samtools view (-F 1804)/Picard MarkDuplicates.
The blacklisted regions were also removed using Bedtools intersect and the ENCODE list for mm39 : https://doi-org.insb.bib.cnrs.fr/10.1038/s41598-019-45839-z .
Peaks were called using MACS with a -q 0.01 for the Impact Factor and -q 0,05 for Marked Histone.
Assembly: mm39
Supplementary files format and content: Bigwig (genome-wide signal, MACS output)

source_name: liver

growth_protocol: Mice were housed under a temperature-controlled, 12h:12h light-dark cycles, and were fed ad libitum. Aged-matched male littermates were randomly assigned to experimental groups. Prior tissue collection, mice were entrained to a 12h:12h light-dark cycle in temperature and humidity-controlled ventilated cabinets for 2 weeks and then kept in constant darkness. Tissues were collected every 4hrs over 24hrs.

extract_protocol:
Liver nuclei isolation and generation of MNase-digested soluble chromatin extracts (according to Lichtsteiner et al. 1987 and Khan et al. 2020).
The libraries were prepared with NEBNext UltraII DNA Library Prep Kit for Illumina sequencing, enriching for fragments from 100-150bp with the 0.9X beads. PE-150 sequencing was performed on Illumina NovaSeq6000 system using NovaSeqS4 flow cell. Approximately 30,000,000+ 150 bases paired-end reads were obtained for each replicate.

value: liver

tag: Sex

value: male


title: WTE016-21TALL


title: H3.1/H3.2/BMAL1 ChIP input (all CTs pooled)_replicate3

description: Library name: Input-Complexe-WT-Rep3


title: Total_Tamoxifen_Saline4


title: sRNA_83 knockout, 2mM H2O2, biol rep 3

city: Baltimore

first: Emma

last: Dallon

state: Maryland

address: 3400 N Charles St Levi 235

department: Biology

institute: Johns Hopkins University

description: Library name: 83C_RNA

data_processing:
Adapters were trimmed using Trim Galore (0.6.4_dev using Cutadapt 1.18)
Trimmed reads were aligned to the Haloferax volcanii DS2 NCBI RefSeq genome (GCF 000025685.1, ASM2568v1) using Bowtie (1.2.3 64-bit) allowing 2 mismatches
Read counts were calculated using featureCounts (v2.0.6)
Assembly: Hv NCBI RefSeq genome (taxonomy identification 2246, GCF 000025685.1, ASM2568v1)
Supplementary files format and content: sample_readcount.txt files are tab delimited text files with raw gene counts for each sample
Supplementary files format and content: Hfx_smORFs.gff is an annotation file with appended sRNAs and smORFs
Supplementary files format and content: Hfx_smORFs.gtf is an annotation file with appended sRNAs and smORFs

organism: Haloferax volcanii

growth_protocol: Haloferax volcanii DS2 strain H98 was grown in liquid Hv-YPC supplemented with 40 mg/mL thymidine at 42°C, with shaking, to OD >0.5. Cultures were diluted into fresh media to an OD of 0.01 and grown to OD 0.4-0.6.

extract_protocol:
RNA extraction was performed using a Quick-RNA Miniprep kit (Zymo).
rRNA was depleted using 2.5 µg of DNase-treated RNA and the Ribo-Zero rRNA removal kit for bacteria (Illumina, discontinued). The SMARTer Stranded RNA-Seq kit (Takara Bio) was used to prepare the libraries with 100 ng RNA, dual-index primers, and 12 PCR cycles. For knockout strains, library preparation and sequencing were performed by SeqCenter in Pittsburgh, PA using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and custom probes.

treatment_protocol: For oxidative stress treatment, cultures were incubated with 2mM H2O2 for one hour at 42°C with shaking

value: sRNA_83 knockout

value: 2mM H2O2


title: Endo_Tamoxifen_Saline4


title: Total_Oil_Saline3

value: WT


title: H3.1/H3.2/BMAL1 ChIP PerKO CT20 input_replicate3

description: Library name: Input-Complexe-CT20-PerKO-Rep3

value: FLAG-FLAG-HA-H3.3A Per1, Per2 double-knockout


title: sRNA_83 knockout, 2mM H2O2, biol rep 2

description: Library name: 83B_RNA


title: MEF, Pellet1, Rep2

description: Library name: pellet1_rep2

value: mouse embyronic fibroblast


title: H3.1/H3.2/BMAL1 ChIP PerKO CT20 input_replicate1

description: Library name: Input-Complexe-CT20-PerKO-Rep1


title: sRNA_83 knockout, 2mM H2O2, biol rep 1

description: Library name: 83A_RNA


title: Endo_Oil_Saline3

value: kidney

value: Kidney endothelium


title: WTE075-21TALL

source_name: PLEURAL EFFUSION

value: PLEURAL EFFUSION


title: sRNA_24 knockout, 2mM H2O2, biol rep 3

description: Library name: 24C_RNA

value: sRNA_24 knockout


title: WTE047-21TALL

value: BONE MARROW


title: BMAL1 ChIP (PerKO, CT20_replicate3)

description: Library name: Bmal1-CT20-PerKO-Rep3

tag: chip antibody

value: BMAL1 (Bethyl Laboratories, A302-616A)


title: WTE099-20TALL


title: WTE049-20TALL


title: WTE043-21TALL


title: BMAL1 ChIP (PerKO, CT20_replicate2)

description: Library name: Bmal1-CT20-PerKO-Rep2


title: sRNA_24 knockout, 2mM H2O2, biol rep 2

description: Library name: 24B_RNA


title: BMAL1 ChIP (PerKO, CT20_replicate1)

description: Library name: Bmal1-CT20-PerKO-Rep1


title: Total_Tamoxifen_Saline3

value: Whole kidney

value: STINGiEKO


title: BMAL1 ChIP (wild-type, CT20_replicate3)

description: Library name: Bmal1-CT20-WT-Rep3


title: Endo_Tamoxifen_Saline3

value: Saline


title: sRNA_24 knockout, 2mM H2O2, biol rep 1

description: Library name: 24A_RNA


title: sRNA_20 knockout, 2mM H2O2, biol rep 3

description: Library name: 20C_RNA

value: sRNA_20 knockout


title: Endo_Tamoxifen_LPS3

value: LPS


title: BMAL1 ChIP (wild-type, CT20_replicate1)

description: Library name: Bmal1-CT20-WT-Rep1

value: liver

value: male


title: Total_Tamoxifen_LPS3


title: Total_Oil_LPS2


title: sRNA_20 knockout, 2mM H2O2, biol rep 2

description: Library name: 20B_RNA

value: 2mM H2O2


title: WT RNA-seq, 2mM H2O2, biol rep 3

description: Library name: WTC_oxi_RNA

value: WT


title: BMAL1 ChIP (wild-type, CT20_replicate2)

description: Library name: Bmal1-CT20-WT-Rep2


title: Endo_Oil_LPS2


title: BMAL1 ChIP (wild-type, CT8_replicate2)

description: Library name: Bmal1-CT8-WT-Rep2


title: sRNA_20 knockout, 2mM H2O2, biol rep 1

description: Library name: 20A_RNA


title: BMAL1 ChIP (wild-type, CT8_replicate3)

description: Library name: Bmal1-CT8-WT-Rep3


title: WTE005-19TALL


title: WTE096-20TALL


title: WTE001-20TALL


title: WTE090-20TALL


title: WTE055-21TALL

value: PERIPHERAL BLOOD


title: WTE057-21TALL


title: WTE011-19TALL


title: Endo_Oil_LPS1


title: Total_Oil_LPS1


title: WT RNA-seq, 2mM H2O2, biol rep 1

description: Library name: WTA_oxi_RNA


title: H3.1/H3.2 ChIP (PerKO, CT20_replicate3)

description: Library name: H3-12-CT20-PerKO-Rep3

value: FLAG-FLAG-HA-H3.3A Per1, Per2 double-knockout

value: Histone H3.1/3.2 (1D4F2) (Active Motif, 61629)


title: BMAL1 ChIP (wild-type, CT8_replicate1)

description: Library name: Bmal1-CT8-WT-Rep1


title: H3.1/H3.2 ChIP (PerKO, CT20_replicate1)

description: Library name: H3-12-CT20-PerKO-Rep1


title: Total_Tamoxifen_LPS2

value: kidney


title: WT RNA-seq, untreated, biol rep 1

description: Library name: WTA_control_RNA


title: Endo_Tamoxifen_LPS2

value: Kidney endothelium


title: WTE025-21TALL

value: PLEURAL EFFUSION


title: H3.1/H3.2 ChIP (wild-type, CT20_replicate3)

description: Library name: H3-12-CT20-WT-Rep3


title: WTE026-21TALL

value: BONE MARROW


title: H3.1/H3.2 ChIP (PerKO, CT20_replicate2)

description: Library name: H3-12-CT20-PerKO-Rep2


title: WT RNA-seq, 2mM H2O2, biol rep 2

description: Library name: WTB_oxi_RNA


title: hypoxic_Candida-albicans_Enterococcus-faecalis_3

city: San Francisco

first: Haley

middle: Elizabeth

last: Gause

state: CA

institute: UCSF

description: Library name: Candida-albicans_Enterococcus-faecalis_hypoxic_3

data_processing:
trimming/filtering: fastp (ver: 0.20.1), parameters: "--adapter_sequence='AGATCGGAAGAGCACACGTCTGAACTCCAGTCA' -x"
alignment: star (ver: 2.7.9a), parameters: "--outSAMmultNmax 10,  --alignIntronMax 4000 --alignIntronMin 4"
filter out reads less than 30bp in length:  samtools (ver:1.14), parameters: "view --expr 'length(seq)>30'  -O {outputfolder} -o {outputfilename} {inputfilename}"
extract gene counts: subread (ver: 2.0.1)
Assembly: CGD Candida albicans Assembly 22 (C_albicans_SC5314_version_A22-s07-m01-r105_chromosomes.fasta)
Assembly: Enterococcus_faecalis_og1rf.ASM17257v2.dna.chromosome.Chromosome.fa
Supplementary files format and content: CaSTAR_mRNA_counts_above30bp.txt, , EfSTAR_gene_counts_above30bp.txt: counts matrix with raw counts per gene. Columns are sample names, genes are column names
Supplementary files format and content: *_normcounts.csv: normalized count per gene using DESeq2 count normalization
Supplementary files format and content: *.bam: BAM files of alignment of reads to genome generated by STAR, then filtered to contain only reads that were greater than 30bp in length. These BAM files were used to generate the count files

organism:
Enterococcus faecalis
Candida albicans

source_name: whole cell

growth_protocol: All cell growth was done at 0.2% O2, 5% CO2, and 37C. For each strain, mid-log cells were backdiluted to OD=0.2 in BHI broth and at shaken at 800RPM for 4 hours. Cells were harvested via centrifugation (3500 RPM for 5 min) and flash frozen in liquid nitrogen before placed at -80C.

extract_protocol:
RNA extracted following the protocol found at dx.doi.org/10.17504/protocols.io.5jyl8jjx7g2w/v1, with the following modifications: only 1 phenol/chloroform precipitation.
rRNA depletion using siTOOLS riboPOOL probes: filamentous fungi, pan-bacteria, and Mus musculus (probes used when species is present). Followed manufacturer protocol for one-step depletion followed by NEB Monarch RNA Clean Up 10ug kit (NEB #T2030) per provided protocol. 5 ng of rRNA depleted RNA was used to prepare libraries using CORALL Total RNA-seq kit according to provided protocols.
RNA extracted following the protocol found at: dx.doi.org/10.17504/protocols.io.5jyl8jjx7g2w/v1

value: whole cell

tag: strain 1

tag: strain 2

tag: genotype 1

tag: genotype 2


title: WT RNA-seq, untreated, biol rep 3

description: Library name: WTC_control_RNA


title: Endo_Tamoxifen_Saline2


title: WTE021-19TALL


title: H3.1/H3.2 ChIP (wild-type, CT20_replicate2)

description: Library name: H3-12-CT20-WT-Rep2


title: Total_Tamoxifen_LPS1

value: Whole kidney


title: WT RNA-seq, untreated, biol rep 2

description: Library name: WTB_control_RNA


title: hypoxic_Candida-albicans_Enterococcus-faecalis_1

description: Library name: Candida-albicans_Enterococcus-faecalis_hypoxic_1


title: H3.1/H3.2 ChIP (wild-type, CT8_replicate3)

description: Library name: H3-12-CT8-WT-Rep3


title: H3.1/H3.2 ChIP (wild-type, CT20_replicate1)

description: Library name: H3-12-CT20-WT-Rep1


title: RNAi-wdr5a_RNAseq_rep3

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

description: single-end 50bp

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file includes normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C for 12 d.

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Single-end sequencing libraries were built for RNA-seq (DNBSEQ platform, 50bp), paired-end sequencing libraries were built for RNA-seq (Illumina Novaseq 6000 platform, 150bp).

treatment_protocol: 12d Col-0 seedlings from MS media were transferred to H2O (Col-H2O), liquid MS (Col-MS), or liquid MS with AZD8055 (Col-AZD) for 4d; 12d drmy1 and gtb123 from MS media were transferred to liquid MS (drmy1-MS and gtb123-MS) for 4d.

value: seedlings

value: wild type

tag: age

value: 12 days


title: Total_Tamoxifen_Saline1

value: STINGiEKO

value: Saline


title: Endo_Tamoxifen_LPS1

value: LPS


title: H3.1/H3.2 ChIP (wild-type, CT8_replicate2)

description: Library name: H3-12-CT8-WT-Rep2

value: liver

value: male


title: Endo_Tamoxifen_Saline1


title: total-WT Saline 5

extract_protocol:
TRAP RNA isolation was performed following established protocols (Heiman et al Nature protocols 2014 PMID 24810037).
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

treatment_protocol: Mice were challenged with 250 micrograms of LPS (E coli 0111:B4) in 200 microlitters of saline. Sham were injected with saline alone. Mice were euthanized 15 hours later.

value: whole kidney

value: WT


title: RNAi-wdr5a_RNAseq_rep2

description: single-end 50bp


title: WTE048-21TALL


title: WTE060-21TALL


title: WTE022-20TALL


title: WTE080-21TALL

value: PERIPHERAL BLOOD


title: WTE017-20TALL


title: WTE012-19TALL


title: H3.3A circadian input (all CTs pooled)_replicate3

description: Library name: Input-HA-WT-Rep3


title: total-WT Saline 3

value: kidney


title: total-WT Saline 4


title: hypoxic_Candida-albicans_Enterococcus-faecalis_2

description: Library name: Candida-albicans_Enterococcus-faecalis_hypoxic_2


title: RNAi-wdr5a_RNAseq_rep1

description: single-end 50bp


title: drmy1_RNAseq_rep3

description: single-end 50bp


title: total-WT LPS 7


title: drmy1_RNAseq_rep1

description: single-end 50bp


title: total-WT LPS 6


title: H3.3A PerKO CT20 input_replicate3

description: Library name: Input-HA-CT20-PerKO-Rep3

value: FLAG-FLAG-HA-H3.3A Per1, Per2 double-knockout


title: H3.3A PerKO CT20 input_replicate1

description: Library name: Input-HA-CT20-PerKO-Rep1


title: H3.3A circadian ChIP (PerKO, CT20_replicate 3)

description: Library name: HA-CT20-PerKO-Rep3

value: HA-Tag (C29F4) (Cell Signaling, #3724)


title: drmy1_RNAseq_rep2

description: single-end 50bp


title: total-WT LPS 5


title: gtb123_RNAseq_rep3

description: single-end 50bp


title: total-SOCS3iEKO Saline 4


title: H3.3A circadian ChIP (PerKO, CT20_replicate 2)

description: Library name: HA-CT20-PerKO-Rep2


title: WTE081-21TALL

value: BONE MARROW


title: H3.1/H3.2 ChIP (wild-type, CT8_replicate1)

description: Library name: H3-12-CT8-WT-Rep1

value: Histone H3.1/3.2 (1D4F2) (Active Motif, 61629)


title: gtb123_RNAseq_rep2

description: single-end 50bp


title: Total_Tamoxifen_Saline2

value: Whole kidney


title: WTE013-19TALL


title: WTE002-21TALL

source_name: LYMPH NODE

value: LYMPH NODE


title: gtb123_RNAseq_rep1

description: single-end 50bp

value: seedlings


title: WTE049-21TALL


title: WTE005-21TALL


title: H3.3A circadian input (all CTs pooled)_replicate1

description: Library name: Input-HA-WT-Rep1


title: total-WT LPS 4


title: gta123_RNAseq_rep3

description: single-end 50bp

value: 12 days


title: H3.3A circadian ChIP (wild-type, CT20_replicate 3)

description: Library name: HA-CT20-WT-Rep3


title: WTE022-19TALL


title: WTE042-20TALL


title: H3.3A circadian ChIP (wild-type, CT20_replicate 2)

description: Library name: HA-CT20-WT-Rep2


title: total-WT Saline 2


title: total-SOCS3iEKO LPS 5


title: gta123_RNAseq_rep2

description: single-end 50bp


title: total-SOCS3iEKO LPS 6


title: H3.3A circadian ChIP (wild-type, CT20_replicate 1)

description: Library name: HA-CT20-WT-Rep1


title: total-SOCS3iEKO LPS 3


title: WTE076-21TALL


title: H3.3A circadian ChIP (wild-type, CT16_replicate 2)

description: Library name: HA-CT16-WT-Rep2


title: gte16_RNAseq_rep2

description: single-end 50bp


title: gte16_RNAseq_rep3

description: single-end 50bp


title: H3.3A circadian ChIP (wild-type, CT16_replicate 3)

description: Library name: HA-CT16-WT-Rep3


title: total-SOCS3iEKO LPS 4


title: WTE082-21TALL


title: WTE007-19TALL


title: H3.3A circadian ChIP (PerKO, CT20_replicate 1)

description: Library name: HA-CT20-PerKO-Rep1


title: H3.3A circadian ChIP (wild-type, CT16_replicate 1)

description: Library name: HA-CT16-WT-Rep1


title: Col-0 RNAseq_rep3

description: single-end 50bp

value: wild type


title: gte16_RNAseq_rep1

description: single-end 50bp


title: total-WT LPS 3


title: gta123_RNAseq_rep1

description: single-end 50bp


title: WTE052-20TALL


title: H3.3A circadian ChIP (wild-type, CT12_replicate 3)

description: Library name: HA-CT12-WT-Rep3


title: WTE025-19TALL


title: WTE008-21TALL


title: Col-0 RNAseq_rep2

description: single-end 50bp


title: total-SOCS3iEKO LPS 2


title: H3.3A circadian ChIP (wild-type, CT12_replicate 2)

description: Library name: HA-CT12-WT-Rep2


title: total-SOCS3iEKO Saline 2

value: Saline


title: WTE019-20TALL


title: Col-0 RNAseq_rep1

description: single-end 50bp


title: WTE023-21TALL


title: H3.3A circadian ChIP (wild-type, CT12_replicate 1)

description: Library name: HA-CT12-WT-Rep1


title: H3.3A circadian ChIP (wild-type, CT8_replicate 3)

description: Library name: HA-CT8-WT-Rep3


title: total-WT LPS 2

value: LPS


title: total-SOCS3iEKO Saline


title: Rpp14-GFP_cJL477_rep1_IP

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

institute: Whitehead Institute

library_source: other

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

molecule: other

source_name: HeLa

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

extract_protocol:
After dox induction cells were harvested after incubation with 5 mM EDTA in 1X PBS for 5 minutes at 37 °C. Harvested cells were pelleted by centrifugation at 200 x g. Cells were washed once with 1X PBS and then once with 1x lysis buffer (25 mM HEPES pH 8.0, 2 mM MgCl2, 0.1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 300 mM KCl and 10% glycerol). Cells were pelleted between each wash step. Finally, the cells were resuspended in a 1:1 ratio in 1x lysis buffer and flash frozen in liquid nitrogen before being stored at -80 °C. Polysome lysis buffer (20 mM Hepes pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) supplemented with 1% CHAPS, 1 cOmplete EDTA-free protease inhibitor cocktail (Roche), and 0.02 U/μl of SUPERaseIn (Invitrogen) was added to each frozen cell pellet before thawing the cells in a 37 °C water bath. Cells were lysed by 10 cycles of sonication at high amplitude with a 30 second on time and 1 minute off time (Bioruptor, Diagenode). The lysate was clarified by centrifugation at 21,000 x g for 30 minutes at 4 °C. Clarified lysate was then incubated with Protein A beads (BioRad) coupled to a rabbit anti-GFP antibody at 4 °C for 2 hours on a rotating wheel.  Following incubation with the clarified lysate the beads were washed 4 times for 5 minutes with polysome lysis buffer supplemented with 1 mM DTT, 10 µg/ml leupeptin/pepstatin/chymostatin, and 0.02 U/ml of SUPERaseIn. RNA was eluted from the beads by addition of TRI reagent.
For RIP-seq library preparation, libraries were prepared with the Watchmaker library prep kit (Watchmaker Genomics) with a QiaFast Select rRNA kit (Qiagen) module for rRNA depletion and each step was performed according to the manufacturer’s instructions.

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

value: HeLa

value: doxycycline


title: H3.3A circadian ChIP (wild-type, CT8_replicate 2)

description: Library name: HA-CT8-WT-Rep2

value: liver

value: male


title: WTE054-21TALL


title: Rpp14-GFP_cJL477_rep2_input


title: WTE064-20TALL


title: total-SOCS3iEKO LPS 1

value: whole kidney


title: Rpp14-GFP_cJL477_rep1_input


title: total-SOCS3iEKO Saline 1

value: kidney


title: total-SOCS3iEKO Saline 3


title: H3.3A circadian ChIP (wild-type, CT8_replicate 1)

description: Library name: HA-CT8-WT-Rep1


title: WTE053-21TALL


title: Rpp21-GFP_cJL477_rep2_IP


title: H3.3A circadian ChIP (wild-type, CT4_replicate 3)

description: Library name: HA-CT4-WT-Rep3


title: total-WT LPS 1

value: WT


title: Rpp21-GFP_cJL477_rep1_IP


title: WTE015-20TALL


title: H3.3A circadian ChIP (wild-type, CT4_replicate 1)

description: Library name: HA-CT4-WT-Rep1

value: HA-Tag (C29F4) (Cell Signaling, #3724)


title: WTE035-20TALL

value: BONE MARROW


title: Rpp21-GFP_cJL477_rep2_input


title: Rpp14-GFP_cJL477_rep2_IP


title: WTE004-20TALL


title: H3.3A circadian ChIP (wild-type, CT0_replicate 3)

description: Library name: HA-CT0-WT-Rep3


title: Rpp21-GFP_cJL477_rep1_input


title: WTE077-21TALL


title: WTE050-21TALL


title: H3.3A circadian ChIP (wild-type, CT0_replicate 2)

description: Library name: HA-CT0-WT-Rep2


title: EC-WT LPS 7

value: endothelial cells


title: WTE106-20TALL


title: EC-WT Saline 4


title: H3.3A circadian ChIP (wild-type, CT0_replicate 1)

description: Library name: HA-CT0-WT-Rep1


title: C18orf21-GFP_cJL476_rep2_IP


title: C18orf21-GFP_cJL476_rep1_IP


title: WTE073-21TALL


title: EC-WT Saline 3


title: BRCAS1 sample 4

city: Columbus

first: Alessandro

last: Canella

address: 700 Children’s Drive

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description: 60-80M read pairs

data_processing:
Low-quality reads (q<10), and adaptor sequences were eliminated from raw reads using bbduk version 37.64
Features were identified from the GFF file that came with the assembly from Gencode (V28).
Feature coverage counts were calculated using featureCounts
Normalized (TPM) quantification for each sample was done using salmon counts
GRCm38.p6 assembly of theMus musculus reference from NCBI
Assembly: comma separated file that includes the aggregated normalized salmon TPM counts for all samples
Supplementary files format and content: processed data file contain normalized counts of sequencing reads

growth_protocol: Cell were mantained in culture in DMEM + 10% FBS + 1% penicillin/streptomycin

extract_protocol:
Total RNA from tumor-infiltrating immune cells was isolated using the Qiagen miRNeasy Micro kit (Qiagen) and eluted with 20uL H2O. The quality and quantity of RNA was checked with Bioanalyzer.
Total RNA-seq by Illumina NovaSeq6000

value: HGG


title: WTE003-21TALL

value: LYMPH NODE


title: EC-WT LPS 6


title: BRCAS1 sample 3

description: 60-80M read pairs


title: total-WT Saline 1


title: C18orf21-GFP_cJL476_rep1_input


title: BRCAS1 sample 2

description: 60-80M read pairs


title: GFP_cJL259_rep2_IP


title: EC-SOCS3iEKO Saline 4


title: BRCAS1 sample 1

description: 60-80M read pairs


title: WTE102-20TALL


title: EC-WT LPS 5


title: EC-WT LPS 4


title: GFP_cJL259_rep2_input


title: CT2A sample 4

description: 60-80M read pairs


title: GFP_cJL259_rep1_IP


title: CT2A sample 3

description: 60-80M read pairs


title: EC-SOCS3iEKO LPS 6


title: H3.3A circadian ChIP (wild-type, CT4_replicate 2)

description: Library name: HA-CT4-WT-Rep2


title: C18orf21-GFP_cJL476_rep2_input


title: GFP_cJL259_rep1_input


title: EC-WT Saline 2


title: WTE006-19TALL


title: CT2A sample 2

description: 60-80M read pairs


title: WTE008-20TALL


title: leaf,Y-S,rep3

city: Changsha

first: Guo

last: Purui

address: No.498 Shaoshan South Road

institute: Central South University of Forestry and Technology

data_processing:
The Clean Data was sequence-assembled to obtain a Unigene library for this species.
After the sequencing data is taken off the machine, the bioinformatics analysis process provided by BMKCloud (www.biocloud.net) of the Bemak cloud platform is used for data analysis.
Assembly: The left files (read1 files) from all libraries/samples were pooled into one big left.fq.gz file, and right files (read2 files) into one big right.fq.gz file. Transcriptome assembly was accomplished based on the left.fq.gz and right.fq.gz using Trinity with min_kmer_cov set to 2 by default and all other parameters set default
Supplementary files format and content: count fpkm

organism: Sesbania grandiflora

source_name: leaf

extract_protocol:
The purity, concentration and integrity of RNA samples are tested using advanced molecular biology equipment to ensure the use of qualified samples for transcriptome sequencing.
Eukaryotic mRNA enrichment with magnetic beads with Oligo(dT). Add Fragmentation Buffer to randomly interrupt the mRNA. The first cDNA strand and the second strand were synthesized using mRNA as a template, and cDNA purification was carried out. The purified double-stranded cDNA is then repaired at the end, A-tailed and ligated with sequencing adapters, and then slipped with AMPure XP beads segment size selection. Finally, the cDNA library was obtained by PCR enrichment.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

value: leaf


title: CT2A sample 1

description: 60-80M read pairs


title: EC-SOCS3iEKO LPS 5


title: WTE004-21TALL


title: WTE014-19TALL


title: leaf,Y-S,rep2


title: WTE061-20TALL


title: leaf,Y-S,rep1


title: CD61_KO4

city: London

first: Huafu

last: Li

address: 237 Fulham Road, Fulham Road

institute: Institute of Cancer Research- Fulham Road (ICR)

data_processing:
Raw reads were quality checked Trimmomatic v.0.3635 before alignment.
Reads were mapped to the mouse transcriptome using the STAR aligner v.2.5.2b using GRCm38 (Ensembl release 102) as the annotation source.
Normalisation of raw count data was performed with the DESeq2 package (version 1.32.0).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file including normalised counts for each sample.

source_name: KPFV

growth_protocol: Organoids were cultured in advanced DMEM/F12 (Thermo Fisher Scientific) medium containing 100 µg/mL Primocin (InvivoGen), 1x B27 supplement (Thermo Fisher Scientific), 10 mM Nicotinamide (Sigma-Aldrich), 1.25 mM N-acetylcysteine (Sigma-Aldrich), 10 nM Gastrin (Sigma-Aldrich), 100 ng/mL hFGF-10 (Peprotech), 50 ng/mL EGF (Peprotech), 10% (v/v) R-Spondin-1 conditioned medium and 10% (v/v) mNoggin conditioned medium.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
cDNA libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina) following manufacturer's instructions.

value: KPFV

value: Pancreatic cancer organoids

value: CD61 knockout


title: EC-SOCS3iEKO LPS 4

source_name: kidney

value: LPS


title: CD61_KO5


title: WTE101-20TALL

source_name: BONE MARROW


title: EC-SOCS3iEKO LPS 3


title: WTE024-21TALL


title: CD61_KO3


title: EC-WT LPS 3


title: leaf,Y-L,rep2


title: CD61_KO2


title: H98 ribosome footprints, 2mM H2O2, biol rep 3

description: Library name: H98F_ribo

data_processing:
Adapters were trimmed using Trim Galore (0.6.4_dev using Cutadapt 1.18)
Trimmed reads were aligned to the Haloferax volcanii DS2 NCBI RefSeq genome (GCF 000025685.1, ASM2568v1) using Bowtie (1.2.3 64-bit) allowing 2 mismatches
Read counts were calculated using featureCounts (v2.0.6)
Assembly: Hv NCBI RefSeq genome (taxonomy identification 2246, GCF 000025685.1, ASM2568v1)
Supplementary files format and content: sample_readcount.txt files are tab delimited text files with raw gene counts for each sample
Supplementary files format and content: Hfx_smORFs.gff is an annotation file with appended sRNAs and smORFs
Supplementary files format and content: Hfx_smORFs.gtf is an annotation file with appended sRNAs and smORFs
Library strategy: Ribo-Seq

extract_protocol:
Cultures were flash frozen in liquid nitrogen and lysed by cryogenic mill, using 55 g of frozen culture and 100 µg/mL of anisomycin. Ribosomes were collected by ultracentrifugation on a 1 M sucrose cushion. Polysomes were digested using MNase and separated using a 10-50% sucrose gradient. RNA from monosome fractions was isolated with Trizol LS reagent.
Size selection (15-45 nt) of RNA extracted from monosome fractions was performed by polyacrylamide gel electrophoresis, followed by rRNA reduction using the Ribo-zero (Bacteria) kit (Illumina, discontinued). RNA fragments were ligated to a univeral cloning linker (NEB Universal miRNA Cloning Linker, #S13115S), and reverse transcribed using SuperScript III (Invitrogen, #18080044). DNA was then circularized using CircLigase (Epicentre, CL4115K), and PCR amplified.

value: 2mM H2O2


title: WTE024-19TALL

extract_protocol: RNA was extracted from bone marrow or peripheral blood samples using a QIAamp RNA Blood Mini Kit (Qiagen) at a QIAcube automated station


title: CD61_KO1


title: EC-SOCS3iEKO Saline 3

value: Saline


title: H98 ribosome footprints, 2mM H2O2, biol rep 4

description: Library name: H98H_ribo


title: EC-SOCS3iEKO LPS 2


title: leaf,DS-S,rep3


title: Con_5

value: Control


title: EC-SOCS3iEKO Saline 2


title: H98 ribosome footprints, 2mM H2O2, biol rep 2

description: Library name: H98D_ribo


title: H98 ribosome footprints, 2mM H2O2, biol rep 1

description: Library name: H98B_ribo


title: leaf,DS-S,rep2


title: EC-WT LPS 2


title: Con_4


title: H98 ribosome footprints, untreated, biol rep 4

description: Library name: H98G_ribo


title: H98 ribosome footprints, untreated, biol rep 3

description: Library name: H98E_ribo


title: leaf,DS-S,rep1


title: Con_3


title: EC-SOCS3iEKO Saline 1


title: EC-SOCS3iEKO LPS 1


title: leaf,DS-L,rep3


title: WTE005-20TALL


title: WTE037-21TALL

value: PERIPHERAL BLOOD


title: leaf,DS-L,rep2


title: Con_1


title: EC-WT LPS 1


title: H98 ribosome footprints, untreated, biol rep 1

description: Library name: H98A_ribo


title: EC-WT Saline 1


title: H98 ribosome footprints, untreated, biol rep 2

description: Library name: H98C_ribo


title: leaf,DS-L,rep1


title: ko82c22

value: Spp1 knockout


title: leaf,DS+Y-S,rep3


title: H98 RNA-seq, 2mM H2O2, biol rep 3

description: Library name: H98F_RNA


title: scRNA_JKPF3

city: Tokyo

first: Yu

last: Fujita

address: 3-25-8 Nishishinbashi

country: Japan

institute: The Jikei University School of Medicine

description:
Library name: scRNA_JKPF3
10x Genomics

library_source: transcriptomic single cell

data_processing:
(Spatial) Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.       (scRNA-seq) Raw sequencing data were processed using 10x Cell Ranger pipeline (version 6.1.2, 10X Genomics) to generate FASTQ files.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned_fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spot
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue

source_name: IPF lung

extract_protocol:
(Spatial )Fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat.     (scRNA-seq) The isolated lung tissue fragments were mechanically minced and dissociated using enzymes, according to the protocol of a lung dissociation kit (130-095-927; Miltenyi Biotec, Bergisch Gladbach, Germany). After dissociation, the viability of single cells was confirmed to be > 90% using trypan blue staining. The cells were then washed using phosphate-buffered saline (PBS) supplemented with 0.1% bovine serum albumin (BSA, Sigma-Aldrich), filtered using 70- and 40-μm filters, centrifuged at 300 × g for 10 min, and resuspended in PBS supplemented with 1% BSA.
(Spatial) Spatial transcriptome sequencing libraries were prepared with 10XGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.    (scRNA-seq) Cells were counted and resuspended in PBS supplemented with 0.1% BSA for the single-cell library construction using a 10X Genomics platform (10X Genomics). The target number of captured cells ranged from 3,000 to 8,000. The samples were tested using a Chromium single-cell 3’ GEM and library & gel bead kit v3.1. Briefly, the cells were loaded into each channel and then partitioned into gel beads in an emulsion in the Chromium Controller, where cell lysis and barcoded RNA RT occurred, followed by amplification, fragmentation, and 5′ adaptor and sample index attachment. Sequencing was performed using a HiSeq X instrument (Illumina, San Diego, CA, USA)

value: IPF lung


title: H98 RNA-seq, 2mM H2O2, biol rep 4

description: Library name: H98H_RNA

value: WT


title: leaf,DS+Y-S,rep2


title: scRNA_JKPF2

description:
Library name: scRNA_JKPF2
10x Genomics


title: H98 RNA-seq, 2mM H2O2, biol rep 2

description: Library name: H98D_RNA


title: ko46c12


title: Con_2


title: scRNA_JKPF1

description:
Library name: scRNA_JKPF1
10x Genomics


title: H98 RNA-seq, 2mM H2O2, biol rep 1

description: Library name: H98B_RNA


title: leaf,DS+Y-L,rep3


title: Drosophila S2 cells, shBrr2,rep3

city: Chongqing

first: jin

last: you

address: Huxi Campus

institute: Chongqing University

data_processing:
Trimmomatic  was used to remove adaptor sequences and low-quality reads. The cleaned reads were then mapped to the reference genome (the Drosophila melanogaster genome (BDGP6)) from Ensembl using TopHat2.
Assembly: dme6
Supplementary files format and content: gene_count.txt include raw counts of each sample

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were cultured in Schneider’s Drosophila Medium  containing 10% (v/v) fetal bovine serum  and 1% (v/v) penicillin-streptomycin  at 25℃.

extract_protocol:
RNA was isolated using RNAiso Plus reagent.
ribosomal RNA (rRNA) was removed by Illumina Ribo-Zero Gold kit and surplus RNA was purified and subjected to library construction using TruSeq Ribo Profile Library Prep Kit.

treatment_protocol: To KD the indicated Drosophila protein-coding gene, 1.5×106 S2 cells were incubated with 8 μg of corresponded dsRNA in 600 μL serum-free medium for 30 min, and then 400 μL of medium with 20% (v/v) FBS was added to maintain cell growth.

value: S2 cells

value: Drosophila Schneider 2 (S2) cells

value: Brr2 knockdown

value: RNAi


title: H98 RNA-seq, untreated, biol rep 4

description: Library name: H98G_RNA


title: ko46c11


title: Con4


title: Drosophila S2 cells, shBrr2,rep2


title: leaf,DS+Y-L,rep2


title: Con3


title: ko82c21


title: EC-WT Saline 5

value: kidney

value: endothelial cells


title: Drosophila S2 cells, shBrr2,rep1


title: H98 RNA-seq, untreated, biol rep 3

description: Library name: H98E_RNA


title: leaf,DS+Y-L,rep1

value: leaf


title: Con2

value: KPFV

value: Pancreatic cancer organoids


title: H98 RNA-seq, untreated, biol rep 2

description: Library name: H98C_RNA


title: leaf,ck,rep3


title: leaf,ck,rep2


title: Con1


title: leaf,DS+Y-S,rep1


title: H98 RNA-seq, untreated, biol rep 1

description: Library name: H98A_RNA


title: Drosophila S2 cells, shControl,rep2


title: scRNA_HH6_TrunkGraft

city: Boston

first: Marcos

last: Simoes-Costa

address: 300 Longwood Ave

department: Pathology

institute: Boston Children's Hospital

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Alignment and cell calling, cellranger-atac 1.2.0 count
Assembly: GRCg6a
Supplementary files format and content: Tab-separated values files and matrix files

organism: Gallus gallus

source_name: Tissue grafted with HH6 Hensen's node

growth_protocol: Gastrula stage chicken embryos were obtained from fertilized eggs and dissected in Ringers solution

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: Tissue grafted with HH6 Hensen's node


title: Drosophila S2 cells, shControl.rep1


title: E73_pig_cortex, scRNAseq

first: Alex

last: Pollen

institute: University of California San Francisco

data_processing:
Genes were quantified using CellRanger v7.0.1, ambient RNA was removed using Cellbender v0.2.1, inhibitory neurons were isolated used conserved markers (DLX1/2/5/6, GAD1/2)
Assembly: Sscrofa11.1 (pig), MusPutFur1.0 (ferret), mm10 (mouse)
Supplementary files format and content: barcodes.csv contains cell metadata
Supplementary files format and content: genes.csv contains gene metadata
Supplementary files format and content: matrix.mtx contains raw cells by genes CellRanger and Cellbender matrix

molecule: polyA RNA

organism: Sus scrofa

source_name: cortex, LGE

extract_protocol:
Regions of interest were dissected and tissue was dissociated in papain. Whole cells  from pig and ferret were resuspended in PBS supplemented with 0.04% BSA for Chromium 10X processing, mouse cells were resuspended in PBS supplemented with 0.1% BSA and sorted for Nkx2.1-cre;Ai14 expression using BD FACSAria Fusion for Chromium 10X processing.
Library was constructed according to manufacturer's instructions (10X Genomics Chromimum Next GEM single Cell 3' HT  v3.1)

value: cortex, LGE

value: WT, E73

value: developing brain


title: E18_mouse_Nkx21_1, scRNAseq

source_name: striatum, LGE, MGE

value: striatum, LGE, MGE


title: scRNA_HH4

description: 10X Genomics

source_name: Hensen's node

extract_protocol:
N.A.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: Hensen's node

tag: developmental stage


title: leaf,ck,rep1


title: scRNA_HH6

description: 10X Genomics


title: E18_mouse_Nkx21_2, scRNAseq


title: E73_pig_striatum, scRNAseq

source_name: striatum

value: striatum


title: E17_mouse_Nkx21, scRNAseq


title: HT1080_8KO_4

status: Public on Aug 10 2025

city: New Orleans

first: Terry

last: Watt

state: LA

address: 1 Drexel Dr.

department: Chemistry

institute: Xavier University of Louisiana

description:
Library name: HT1080_8KO_4
HT1080_8KO_4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic v0.39 with default settings
Trimmed sequence reads were mapped to GrCh38.83 using bowtie2 v2.5.4 as implemented by RSEM v1.3.3, with default settings
Mapped sequences were annotated and counted using RSEM v1.3.3 with default settings
Read count extraction was performed using tximport v1.34.0
Read count statistical analysis was performed using DESeq2 v1.46.0
Assembly: Human NCBI genome build GrCH38 build 83
Supplementary files format and content: Expected counts from RSEM output and ENSEMBL entries, cross-referenced to gene names and UNIPROT entries

source_name: Connective tissue

growth_protocol: HT1080 cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
3x10^6 cells were pelleted, resuspended in MEM with 5% glycerol, and frozen at -80 °C. Cells were shipped on dry ice, and total RNA extracted by Creative Genomics using a commercially available kit. Quality of RNA was verified using RNA Screen Tape (Agilent). RNA was rRNA-depleted using the Ribo-Zero plus kit (Illumina).
Libraries were prepared using the PE150 platform (Illumina) following the manufacturer's instructions.

value: Connective tissue

value: fibrosarcoma

value: KDAC8 knockout


title: S0281 Single cell RNAseq on OS-17 lung metastasis PDX

first: Matt

last: Cannon

address: 700 Children's Dr.

department: Center for Childhood Cancer

description: Library name: S0281

data_processing:
Raw data and initial processing was performed using Cell Ranger (10X Genomics) with reads mapped to the mm10 version of the mouse genome (mouse tumor samples), the hg38 version of the human genome (human patient samples), or a mixed genome containing both (xenograft samples).
Assembly: mm10/hg38/mm10 and hg38
Supplementary files format and content: Compressed tar file containing output from cellranger count including: barcodes.tsv.gz, filtered_feature_bc_matrix.h5, metrics_summary.csv, web_summary.html, features.tsv.gz, matrix.mtx.gz, raw_feature_bc_matrix.h5

organism:
Homo sapiens
Mus musculus

source_name: Lung tumor

growth_protocol: All cell lines utilized herein were routinely authenticated with STR and mycoplasma testing through Laboratory Corporation of America. Cells utilized for experiments were within 20 passage doublings after reviving from liquid nitrogen storage. OS-17 cells, a human osteosarcoma cell line, were derived from an early passage of the OS-17 patient-derived xenograft, grown from a primary femur biopsy at St. Jude’s Children’s Research Hospital in Memphis and was a gift from Dr. Peter Houghton. Cells were maintained in RPMI (Corning, 10-040-CV) with 10% fetal bovine serum (FBS) (Atlanta Biologicals, S11150H). HBEC3-KT cells were obtained from American Type Culture Collection (ATCC, CRL-4051) and maintained in Airway Epithelial Cell Basal Medium (ATCC, PCS-300-030) with the Bronchial Epithelial Cell Growth Kit (ATCC, PCS-300-040). HBEC:OS-17 organotypic co-culture were established as follows: HBEC were grown to confluence on 0.4µm inserts (Corning, 353090) with HBEC media in upper and lower chambers. OS-17 cells (50,000), were plated into top chamber in DMEM/F12 (Corning, 10-090-CV) + 1% FBS with HBEC media in lower chamber. Cultures were maintained until 72 hours prior to processing for single-cell RNA-sequencing. All animal experiments were carried out in accordance with the Institutional Animal Care and Use Committee (IACUC, protocols AR15-00022 and AR14-00045) of the Research Institute at Nationwide Children’s Hospital (Columbus, OH) guidelines. The approved protocols aimed to minimize the number of mice used and to minimize any pain or distress. All manipulations occurred under sterile conditions in a laminar flow hood. Staff performed all surgical procedures under general anesthesia and aseptic conditions. Mice used were 6-8 weeks-old CB17SC scid-/- (RRID: IMSR_TAC:cb17sc) female mice for the OS-17 models. Mice were maintained under barrier conditions.

extract_protocol:
Lungs harvested from mice were processed using the human tumor dissociation kit (Miltenyi Biotec, 130-095-929) with a GentleMacs Octo Dissociator with Heaters (Miltenyi Biotec, 130-096-427). HBEC mono-cultures, OS-17 monocultures, or HBEC:OS-17 co-cultures (72 hours) were gently trypsinized and dissociated into single cell suspensions.
Following dissociation into single cell suspension, single-cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell 3′RNA-sequencing system (10X Genomics) with the Reagent Kit v3.1 (10X Genomics, PN-1000121) according to the manufacturer’s instructions. cDNA library quality and quantity were determined using an Agilent 2100 bioanalyzer using the High Sensitivity DNA Reagents kit (Agilent, 5607-4626) and then sequenced.

value: Lung tumor


title: FMLVY0

first: Zhaoqi

last: Zhang

state: Beijing

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

institute: University of Chinese Academy of Sciences

description: Library name: sample4

data_processing:
The RNA extraction, cDNA library preparation, and sequences were generated by CapitalBio Technology (Beijing, China)
Assembly: Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat
Supplementary files format and content: the expression level of each genes were extraced by String-tie

source_name: liver

extract_protocol:
Samples were sorted from YFP- and YFP+ KCs from 6-8 weeks old male and female Lyz2cre-RosaYFP reporter mice for 2×105 KCs each group.
Total RNA was dissolved by Trizol lysis buffer and then sent for RNA extraction and cDNA library preparation for RNA-sequencing analysis. .

value: liver

value: macrophage

value: YFP-


title: HT1080_8KO_2

description:
Library name: HT1080_8KO_2
HT1080_8KO_2


title: Drosophila S2 cells, shControl,rep3

value: S2 cells

value: Drosophila Schneider 2 (S2) cells

value: WT

value: RNAi


title: E15_mouse_Nkx21, scRNAseq


title: HT1080_8KO_3

description:
Library name: HT1080_8KO_3
HT1080_8KO_3


title: FMLVY1

description: Library name: sample3

value: YFP+


title: MLVY0

description: Library name: sample2


title: scRNA_HH3

description: 10X Genomics


title: MLVY1

description: Library name: sample1


title: HT1080_6KO_2

description:
Library name: HT1080_6KO_2
HT1080_6KO_2

value: KDAC6 knockout


title: HT1080_6KO_1

description:
Library name: HT1080_6KO_1
HT1080_6KO_1


title: HT1080_6KO_4

description:
Library name: HT1080_6KO_4
HT1080_6KO_4


title: HT1080_wt_4

description: Library name: HT1080_WT_4


title: HT1080_wt_1

description: Library name: HT1080_WT_1


title: HT1080_wt_2

description: Library name: HT1080_WT_2


title: si-LINC01547 2 RNA-seq

city: Yantai

first: Defang

address: No. 346 Guanhai, Laishan District

institute: Binzhou Medical University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
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 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: xenograft

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: xenograft

value: HCC


title: NC 1 RNA-seq

value: control


title: si-LINC01547 1 RNA-seq


title: si-LINC01547 3 RNA-seq


title: HT1080_8KO_1

description:
Library name: HT1080_8KO_1
HT1080_8KO_1


title: NC 2 RNA-seq


title: Bufotalin 3 miRNA

value: Bufotalin

tag: molecule type

value: small RNA


title: Control 2 miRNA

value: Control


title: Control 3 miRNA


title: Control 1 miRNA


title: Control 2-1 total RNA seq

description:
mRNA_Diff_gene.FPKM.txt
lncRNA_Diff_transcript.FPKM.txt


title: HT1080_6KO_3

description:
Library name: HT1080_6KO_3
HT1080_6KO_3

value: Connective tissue

value: fibrosarcoma


title: Control 1-1 total RNA seq


title: Bufotalin 3-1 total RNA seq


title: Bufotalin 1 miRNA


title: aorta control replicate 1

city: Leipzig

first: Olga

last: Bondareva

state: Saxony

address: Philipp-Rosenthal-Straße 27

department: HI-MAG

country: Germany

institute: Helmholtz Zentrum München

description: 10x Genomics

data_processing:
Raw data were de-multiplexed and mapped to the domesticated pig genome (build Sscrofa11) using CellRanger v5.0. Further analyses were performed using Seurat package v.5.0. Firstly, we performed data filtering steps by removing low expressed genes and low-quality nuclei from further analyses: (i) genes with 0 raw counts were removed; (ii) nuclei with <500 or >6000 uniquely expressed genes, or with >25000 UMIs were excluded; (iii) nuclei with high percentage of mitochondrial genes (>5%) were removed. Next, the data were corrected for ambient RNA with SoupX using automated contamination estimation method. Cell doublets were removed with DoubletFinder package.
Assembly: Sscrofa11
Supplementary files format and content: Cellranger output filtered_feature_bc_matrix

source_name: Ossabaw pig

extract_protocol:
Frozen tissues were processed for nuclei isolation followed by snRNA-seq protocol. Briefly, snap frozen aortic tissue was stored at -80°C until nuclei isolation took place. For each sample, a piece of frozen vessel tissue approximately 50 mm length was cut on dry ice to avoid thawing, and transferred directly into a gentleMACS C-tube (Miltenyi Biotec 130-096-334) containing nuclei isolation buffer (NIB) (5 mM CaCl2; 3 mM MgAc; 2 mM EDTA; 0.5 mM EGTA; 10 mM Tris-HCl, pH 8; cOmplete protease inhibitor cocktail, Roche; 1 mM dithiothreitol; RNAse OUTTM , Invitrogen). It was further dissociated with the gentleMACS™ Octo Dissociator system with heaters using the “protein_01” protocol at 4°C. The nuclei suspension was rinsed with NIB supplemented with 0.4% Triton X-100 to final 0.2% concentration, filtered through a 70 µm cell strainer and the cell strainer was rinsed once with 10 ml FACS buffer (2% FCS in PBS (Sigma D8537)). Nuclei were collected via centrifugation (4°C, 1000 g, for 5 min), resuspended in FACS buffer and passed through a 40 µm cell strainer into a FACS tube. All samples were stained with the DRAQ5 stain (1:100, Cell Signaling Technology) diluted in FACS buffer for 10 min on ice in a total volume of 1 ml. Intact single nuclei were sorted on the FACS Melody (BD Biosciences) and collected into low-binding 1.5 ml Eppendorf tubes pre-coated with 2% FCS-PBS to reduce nuclei clumping and aggregation. Next, nuclei were concentrated by centrifugation, and their quality and concentration were established manually with hemocytometer, and processed immediately to the single cell workflow.
Single nuclei RNA-seq was performed using 10x Next GEM Single Cell 3 GEM kit v3.1 according to the manufacturers protocol. Separate 10x genomics reactions were used for each sample. Generated libraries were sequenced on an Illumina NovaSeq configuration 30-8-0-100 with >27.5 x 10^3 reads per cell.

treatment_protocol: Castrate male Ossabaw pigs of 12-month age were put on HF/HFru or chow diet for 6 months. Abdominal aortae were dissected and snap-frozen.

value: Abdominal aorta

value: chow diet


title: Bufotalin 1-1total RNA seq


title: aorta control replicate 2

description: 10x Genomics


title: aorta obese replicate 3

description: 10x Genomics

value: HF/Hfru diet


title: HT1080_wt_3

description: Library name: HT1080_WT_3


title: aorta obese replicate 2

description: 10x Genomics


title: NC 3 RNA-seq


title: Bufotalin 2 miRNA


title: leaf,Y-L,rep3

value: leaf


title: PET, VPA, 20 uM, 2

city: Sagamihara

first: Hiromi

last: Hirata

state: Kanagawa

address: 5-10-1, Fuchinobe, Chuo-ku

institute: Aoyama Gakuin University

description:
Library name: Cell_334
mRNA from single larvae

data_processing:
The PCA was performed in R software using NormalizedDarta, ScaleData, FindVariable Fretures, and RunPCA functions in Seurat (version 5.1.0) (Hao et al., 2024) with default parameters except for “do.scale = F” for ScaleData.
Assembly: Danio_rerio.GRCz11.cdna.al.fa
Supplementary files format and content: csv-delimited text file includes rawcnt values for each sample

organism: Danio rerio

source_name: whole-mount

growth_protocol: Zebrafish (Danio rerio) were reared and maintained in 1.7 L tanks in a recirculating Meito System (Meito System) under a 14 h light and 10 h dark photoperiod according to the standard protocol.

extract_protocol:
RNA extraction from zebrafish larvae and RNA purification were described previously (Ujibe et al. 2021). The RNA concentration was determined using the Quantus Fluorometer with QuantiFluor RNA System Kit (Promega) according to the manufacturer’s manual. RNA was diluted to a final concentration of 2 ng/µl and used to prepare library for RNA-Seq.
Library preparation was conducted according to the Lasy-Seq ver 1.1 5 method (Kashima et al., 2021). In brief, reverse transcription was done using SuperScript IV reverse transcriptase (Thermo Fisher Scientific) and indexed reverse transcription primers. Following program was used for reverse transcription: 65 °C 10 min; 80 °C 15 min; 4 °C forever. Products of reverse transcription were pooled and then purified using an equal volume of AMpure XPKAPA Pure beads (Beckman CoulterRoche) according to the manufacturer’s manual. Second strand synthesis was conducted with RNase H (Enzymatics) and DNA polymerase I (Enzymatics) at 16 °C for 2 h. Synthetic double-strand DNA (dsDNA) were treated with RNase T1 (Thermo Fisher Scientific) at 37 °C for 5 min. Fragmentation was conducted using 5x WGS Fragmentation Mix (Enzymatics) at 32 °C for 5.5 min followed by heat inactivation at 65 °C for 30 min. Ligation was conducted using 5x Ligation Mix (Enzymatics) at 20 °C for 15 min. One cycle PCR was performed using a P7 primer containing a 5′ biotin modification ([BioON]CAAGCAGAAGACGGCATACGAGAT) to allow for selective purification of properly ligated molecules containing the original 3’-ends of the cDNAs. Biotin-labeled DNA was captured using Dynabeads M-280 Streptavidin (Thermo Fisher Scientific) in binding buffer (1M NaCl, 10 mM Tris-HCl pH 7.6), which were washed with TE-TW (10 mM Tris pH 7.6, 1 mM EDTA, 0.01% Tween20), twice. Subsequent amplification was performed with KAPA HiFi HotStart ReadyMix (Roche), and the optimal PCR cycle number was determined by EvaGreen (Biotium) -based qPCR using the following program: initial denaturation at 95 °C for 5 minutes; followed by cycles of 98 °C for 20 seconds, 60 °C for 15 seconds, and 72 °C for 40 seconds; a final extension at 72 °C for 3 minutes; and a hold at 4 °C indefinitely. The library was purified using an equal volume of KAPA Pure beads (Roche), and subjected to electrophoresis in Bioanalyzer 2,100 (Agilent Technologies) with the Agilent High Sensitivity DNA kit (Agilent Technologies). Library concentration was determined using Quantus Fluorometer (Promega) with the QuantiFluor ONE dsDNA System kit (Promega). Sequencing of 150-bp paired-end reads was conducted using NovaSeq X Plus (Illumina). Raw RNA-Seq reads were aligned to the Danio rerio genome assembly GRCz11 (Ensembl release 111), and gene-level quantification was conducted as previously described (Kashima et al. 2021).

treatment_protocol: To evaluate inter-strain variability in chemical susceptibility during zebrafish embryogenesis, we conducted malformation and embryo-fetal lethality (MEFL) testing, which is based on the established protocol of the OECD test guideline 236 (TG236), with minor procedural modifications tailored to our experimental needs (Figure 1). This assay enables the systematic assessment of developmental toxicity by tracking visible morphological outcomes and survival over early developmental stages. Fertilized eggs were obtained from adult zebrafish representing five distinct strains (AB, TU, RW, WIK, and PET), and were collected during 1–3 hours post-fertilization (hpf) to ensure early and synchronized developmental timing. Prior to chemical treatment, embryos were microscopically examined at 4–6 hpf to screen for and exclude those exhibiting any spontaneous developmental defects, such as irregular cleavage, abnormal yolk shape, or delayed development. This quality control step was essential to eliminate confounding variables and to ensure that subsequent observations would reflect chemical-specific effects rather than intrinsic developmental failure. Embryos that passed this screening were then allocated into experimental groups and exposed to test compounds from 5–6 hpf through 5 days post-fertilization (dpf) in a static exposure setup without medium replacement. At 5 dpf, embryos were individually inspected under a stereomicroscope, and their phenotypes were categorized into normal, malformed, or dead, enabling a quantitative comparison of teratogenic and lethal responses among strains.

value: whole-mount

value: PET

value: valproic acid


title: PET, VPA, 20 uM, 6

description:
Library name: Cell_338
mRNA from single larvae


title: PET, VPA, 20 uM, 8

description:
Library name: Cell_340
mRNA from single larvae


title: Control 3-1 total RNA seq


title: Bufotalin 2-1 total RNA seq


title: PET, VPA, 20 uM, 4

description:
Library name: Cell_336
mRNA from single larvae


title: aorta obese replicate 1

description: 10x Genomics


title: PET, VPA, 20 uM, 3

description:
Library name: Cell_335
mRNA from single larvae


title: PET, VPA, 20 uM, 7

description:
Library name: Cell_339
mRNA from single larvae


title: PET, VPA, 20 uM, 1

description:
Library name: Cell_333
mRNA from single larvae


title: PET, VPA, 5 uM, 4

description:
Library name: Cell_328
mRNA from single larvae


title: PET, VPA, 5 uM, 7

description:
Library name: Cell_331
mRNA from single larvae


title: PET, VPA, 5 uM, 6

description:
Library name: Cell_330
mRNA from single larvae


title: PET, VPA, 5 uM, 8

description:
Library name: Cell_332
mRNA from single larvae


title: PET, VPA, 5 uM, 3

description:
Library name: Cell_327
mRNA from single larvae


title: PET, VPA, 5 uM, 5

description:
Library name: Cell_329
mRNA from single larvae


title: PET, VPA, 1 uM, 8

description:
Library name: Cell_324
mRNA from single larvae


title: PET, VPA, 1 uM, 7

description:
Library name: Cell_323
mRNA from single larvae


title: PET, VPA, 5 uM, 2

description:
Library name: Cell_326
mRNA from single larvae


title: PET, VPA, 1 uM, 5

description:
Library name: Cell_321
mRNA from single larvae


title: PET, VPA, 1 uM, 6

description:
Library name: Cell_322
mRNA from single larvae


title: PET, VPA, 1 uM, 4

description:
Library name: Cell_320
mRNA from single larvae


title: PET, VPA, 1 uM, 3

description:
Library name: Cell_319
mRNA from single larvae


title: PET, VPA, 1 uM, 2

description:
Library name: Cell_318
mRNA from single larvae


title: PET, VPA, 20 uM, 5

description:
Library name: Cell_337
mRNA from single larvae


title: PET, VPA, 0 uM, 3

description:
Library name: Cell_311
mRNA from single larvae


title: PET, VPA, 1 uM, 1

description:
Library name: Cell_317
mRNA from single larvae


title: PET, VPA, 0 uM, 7

description:
Library name: Cell_315
mRNA from single larvae


title: PET, VPA, 0 uM, 5

description:
Library name: Cell_313
mRNA from single larvae


title: PET, VPA, 0 uM, 4

description:
Library name: Cell_312
mRNA from single larvae


title: WIK, VPA, 20 uM, 8

description:
Library name: Cell_308
mRNA from single larvae

value: WIK


title: PET, VPA, 0 uM, 2

description:
Library name: Cell_310
mRNA from single larvae


title: PET, VPA, 0 uM, 6

description:
Library name: Cell_314
mRNA from single larvae


title: WIK, VPA, 20 uM, 5

description:
Library name: Cell_305
mRNA from single larvae


title: WIK, VPA, 20 uM, 3

description:
Library name: Cell_303
mRNA from single larvae


title: WIK, VPA, 20 uM, 7

description:
Library name: Cell_307
mRNA from single larvae


title: WIK, VPA, 20 uM, 6

description:
Library name: Cell_306
mRNA from single larvae


title: WIK, VPA, 5 uM, 8

description:
Library name: Cell_300
mRNA from single larvae


title: PET, VPA, 5 uM, 1

description:
Library name: Cell_325
mRNA from single larvae


title: WIK, VPA, 20 uM, 1

description:
Library name: Cell_301
mRNA from single larvae


title: WIK, VPA, 5 uM, 7

description:
Library name: Cell_299
mRNA from single larvae


title: WIK, VPA, 5 uM, 6

description:
Library name: Cell_298
mRNA from single larvae


title: WIK, VPA, 20 uM, 2

description:
Library name: Cell_302
mRNA from single larvae


title: WIK, VPA, 20 uM, 4

description:
Library name: Cell_304
mRNA from single larvae


title: WIK, VPA, 5 uM, 5

description:
Library name: Cell_297
mRNA from single larvae


title: WIK, VPA, 5 uM, 4

description:
Library name: Cell_296
mRNA from single larvae


title: WIK, VPA, 5 uM, 3

description:
Library name: Cell_295
mRNA from single larvae


title: WIK, VPA, 5 uM, 2

description:
Library name: Cell_294
mRNA from single larvae


title: WIK, VPA, 5 uM, 1

description:
Library name: Cell_293
mRNA from single larvae


title: WIK, VPA, 1 uM, 8

description:
Library name: Cell_292
mRNA from single larvae


title: PET, VPA, 0 uM, 8

description:
Library name: Cell_316
mRNA from single larvae


title: WIK, VPA, 1 uM, 7

description:
Library name: Cell_291
mRNA from single larvae


title: PET, VPA, 0 uM, 1

description:
Library name: Cell_309
mRNA from single larvae


title: WIK, VPA, 1 uM, 3

description:
Library name: Cell_287
mRNA from single larvae


title: WIK, VPA, 1 uM, 4

description:
Library name: Cell_288
mRNA from single larvae


title: WIK, VPA, 1 uM, 2

description:
Library name: Cell_286
mRNA from single larvae


title: WIK, VPA, 1 uM, 1

description:
Library name: Cell_285
mRNA from single larvae


title: WIK, VPA, 1 uM, 5

description:
Library name: Cell_289
mRNA from single larvae


title: WIK, VPA, 1 uM, 6

description:
Library name: Cell_290
mRNA from single larvae


title: WIK, VPA, 0 uM, 8

description:
Library name: Cell_284
mRNA from single larvae


title: WIK, VPA, 0 uM, 6

description:
Library name: Cell_282
mRNA from single larvae


title: WIK, VPA, 0 uM, 4

description:
Library name: Cell_280
mRNA from single larvae


title: WIK, VPA, 0 uM, 5

description:
Library name: Cell_281
mRNA from single larvae


title: WIK, VPA, 0 uM, 7

description:
Library name: Cell_283
mRNA from single larvae


title: RW, VPA, 20 uM, 6

description:
Library name: Cell_274
mRNA from single larvae

value: RW


title: RW, VPA, 20 uM, 4

description:
Library name: Cell_272
mRNA from single larvae


title: RW, VPA, 20 uM, 8

description:
Library name: Cell_276
mRNA from single larvae


title: WIK, VPA, 0 uM, 1

description:
Library name: Cell_277
mRNA from single larvae


title: RW, VPA, 20 uM, 2

description:
Library name: Cell_270
mRNA from single larvae


title: leaf,Y-L,rep1

source_name: leaf


title: RW, VPA, 20 uM, 5

description:
Library name: Cell_273
mRNA from single larvae


title: RW, VPA, 5 uM, 4

description:
Library name: Cell_264
mRNA from single larvae


title: RW, VPA, 5 uM, 6

description:
Library name: Cell_266
mRNA from single larvae


title: RW, VPA, 5 uM, 5

description:
Library name: Cell_265
mRNA from single larvae


title: E. faecium mutant strain S491L, replicate 4

city: PITTSBURGH

first: Daria

last: Van Tyne

state: PA

address: 200 Lothrop St

department: Department of Medicine

institute: University of Pittsburgh

description:
Library name: S491L_4
Column name in featureCounts_all_output.xlsx is the same as library name

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4)
Sequencing reads were processed using Trim galore v0.6.10. Reads passed quality control if the Phred score was >33 and the sequence length was >142 bp
Trimmed reads were then mapped to the annotated WT genome using STAR v2.7.11b
Reads mapping to coding sequences were counted using featureCounts v2.0.6 against the annotated WT sequence
Read counts extraction and normalization to library size was done using the DESeq2 package in Rstudio. Only genes with read counts of >10 were included in the analysis
Assembly: WT strain were sequenced and used as reference for read alignment
Supplementary files format and content: excel file includes counts for all samples

organism: Enterococcus faecium

source_name: Bacterial cell

growth_protocol: Overnight cultures were re-inoculated into 5 mL of fresh BHI and grown until mid-log phase. Then, 2x v/v of RNAprotect was added to each culture

extract_protocol:
RNA was extracted with the Rneasy Mini Kit (Qiagen) and DNAse treated
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI)

treatment_protocol: Pellet was treated with 10 µL of 2500 U/mL mutanolysin and 50 µL 50 mg/mL lysozyme at 37°C for 30 minutes prior to RNA extraction

value: Bacterial cell


title: RW, VPA, 5 uM, 1

description:
Library name: Cell_261
mRNA from single larvae


title: E. faecium mutant strain S491L, replicate 1

description:
Library name: S491L_1
Column name in featureCounts_all_output.xlsx is the same as library name


title: WIK, VPA, 0 uM, 2

description:
Library name: Cell_278
mRNA from single larvae


title: RW, VPA, 20 uM, 1

description:
Library name: Cell_269
mRNA from single larvae


title: RW, VPA, 5 uM, 2

description:
Library name: Cell_262
mRNA from single larvae


title: WIK, VPA, 0 uM, 3

description:
Library name: Cell_279
mRNA from single larvae


title: E. faecium mutant strain S491L, replicate 2

description:
Library name: S491L_2
Column name in featureCounts_all_output.xlsx is the same as library name


title: RW, VPA, 5 uM, 3

description:
Library name: Cell_263
mRNA from single larvae


title: RW, VPA, 1 uM, 8

description:
Library name: Cell_260
mRNA from single larvae


title: E. faecium mutant strain H486Y, replicate 3

description:
Library name: H486Y_3
Column name in featureCounts_all_output.xlsx is the same as library name


title: RW, VPA, 20 uM, 7

description:
Library name: Cell_275
mRNA from single larvae


title: RW, VPA, 20 uM, 3

description:
Library name: Cell_271
mRNA from single larvae


title: RW, VPA, 1 uM, 6

description:
Library name: Cell_258
mRNA from single larvae


title: RW, VPA, 1 uM, 7

description:
Library name: Cell_259
mRNA from single larvae


title: E. faecium mutant strain H486Y, replicate 4

description:
Library name: H486Y_4
Column name in featureCounts_all_output.xlsx is the same as library name


title: RW, VPA, 1 uM, 5

description:
Library name: Cell_257
mRNA from single larvae


title: RW, VPA, 1 uM, 4

description:
Library name: Cell_256
mRNA from single larvae


title: RW, VPA, 1 uM, 3

description:
Library name: Cell_255
mRNA from single larvae


title: RW, VPA, 5 uM, 8

description:
Library name: Cell_268
mRNA from single larvae


title: S0037 Single cell RNAseq on OS-17 tibial tumor PDX

description: Library name: S0037

source_name: Tibial tumor

value: Tibial tumor


title: E. faecium mutant strain H486Y, replicate 1

description:
Library name: H486Y_1
Column name in featureCounts_all_output.xlsx is the same as library name


title: RW, VPA, 5 uM, 7

description:
Library name: Cell_267
mRNA from single larvae


title: RW, VPA, 1 uM, 2

description:
Library name: Cell_254
mRNA from single larvae


title: E. faecium mutant strain S491L, replicate 3

description:
Library name: S491L_3
Column name in featureCounts_all_output.xlsx is the same as library name


title: RW, VPA, 1 uM, 1

description:
Library name: Cell_253
mRNA from single larvae


title: E. faecium mutant strain G482V, replicate 1

description:
Library name: G482V_1
Column name in featureCounts_all_output.xlsx is the same as library name


title: E. faecium mutant strain Q473K, replicate 4

description:
Library name: Q473K_4
Column name in featureCounts_all_output.xlsx is the same as library name


title: E. faecium mutant strain Q473K, replicate 2

description:
Library name: Q473K_2
Column name in featureCounts_all_output.xlsx is the same as library name


title: RW, VPA, 0 uM, 7

description:
Library name: Cell_251
mRNA from single larvae


title: RW, VPA, 0 uM, 8

description:
Library name: Cell_252
mRNA from single larvae


title: RW, VPA, 0 uM, 5

description:
Library name: Cell_249
mRNA from single larvae


title: E. faecium mutant strain Q473K, replicate 1

description:
Library name: Q473K_1
Column name in featureCounts_all_output.xlsx is the same as library name


title: E. faecium mutant strain Q473K, replicate 3

description:
Library name: Q473K_3
Column name in featureCounts_all_output.xlsx is the same as library name


title: RW, VPA, 0 uM, 6

description:
Library name: Cell_250
mRNA from single larvae


title: E. faecium wild type strain, replicate 3

description:
Library name: WT_3
Column name in featureCounts_all_output.xlsx is the same as library name

value: WT


title: E. faecium wild type strain, replicate 4

description:
Library name: WT_4
Column name in featureCounts_all_output.xlsx is the same as library name


title: E. faecium mutant strain G482V, replicate 4

description:
Library name: G482V_4
Column name in featureCounts_all_output.xlsx is the same as library name


title: E. faecium mutant strain H486Y, replicate 2

description:
Library name: H486Y_2
Column name in featureCounts_all_output.xlsx is the same as library name


title: E. faecium wild type strain, replicate 1

description:
Library name: WT_1
Column name in featureCounts_all_output.xlsx is the same as library name


title: RW, VPA, 0 uM, 2

description:
Library name: Cell_246
mRNA from single larvae


title: E. faecium wild type strain, replicate 2

description:
Library name: WT_2
Column name in featureCounts_all_output.xlsx is the same as library name


title: TU, VPA, 20 uM, 8

description:
Library name: Cell_244
mRNA from single larvae

value: TU


title: RW, VPA, 0 uM, 1

description:
Library name: Cell_245
mRNA from single larvae


title: TU, VPA, 20 uM, 7

description:
Library name: Cell_243
mRNA from single larvae


title: E. faecium mutant strain G482V, replicate 3

description:
Library name: G482V_3
Column name in featureCounts_all_output.xlsx is the same as library name


title: 3F2 FOLLOWERS BIO REP 4

city: Atlanta

first: Raaven

last: Goffe

state: GA

address: 100 Woodruff Circle

institute: Emory University School of Medicine

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_376

data_processing:
Read quality and contamination were assessed using FastQC v0.12.0 and Fastq-Screen v0.15.3 and reports generated with MultiQC v1.24.1
Reads were trimmed using fastp v0.23.4 and were then aligned to the human reference genome hg38 using STAR aligner v2.7.11b
HTSeq-Count v2.0.5 was used to generate raw count tables.
Assembly: Human reference genome hg38
Supplementary files format and content: Open XML Spreadsheet file includes raw counts for all samples

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen, Cat. No. 74104) followed by RNA quality and quantity assessments using Nanodrop (Thermo Fisher Scientific, USA) and Bioanalyzer (Agilent Technologies, USA).
Library preparation and sequencing were performed using the NEBNext® Ultra™ II DNA Library Prep kit for Illumina (New England Biolabs, Cat. No. E7465) and Novaseq X-Plus (Illumina Inc., USA).

value: lung carcinoma cells

value: MYO10 JAG1 WT


title: 3F2 FOLLOWERS BIO REP 3

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_375


title: TU, VPA, 20 uM, 6

description:
Library name: Cell_242
mRNA from single larvae


title: TU, VPA, 20 uM, 5

description:
Library name: Cell_241
mRNA from single larvae


title: 3F2 FOLLOWERS BIO REP 2

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_374


title: TU, VPA, 20 uM, 4

description:
Library name: Cell_240
mRNA from single larvae


title: RW, VPA, 0 uM, 4

description:
Library name: Cell_248
mRNA from single larvae


title: TU, VPA, 20 uM, 3

description:
Library name: Cell_239
mRNA from single larvae


title: TU, VPA, 20 uM, 1

description:
Library name: Cell_237
mRNA from single larvae


title: 3L2 LEADERS BIO REP 4

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_364


title: TU, VPA, 5 uM, 8

description:
Library name: Cell_236
mRNA from single larvae


title: TU, VPA, 20 uM, 2

description:
Library name: Cell_238
mRNA from single larvae


title: 3L2 LEADERS BIO REP 2

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_362


title: JAG1 KO CLONE 35 BIO REP 3

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_365

value: JAG1 KO

value: CRISPR-Cas9 edited


title: 3L2 LEADERS BIO REP 3

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_363


title: TU, VPA, 5 uM, 7

description:
Library name: Cell_235
mRNA from single larvae


title: 3L2 LEADERS BIO REP 1

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_361


title: TU, VPA, 5 uM, 6

description:
Library name: Cell_234
mRNA from single larvae


title: JAG1 KO CLONE 35 BIO REP 2

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_353


title: 3F2 FOLLOWERS BIO REP 1

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_373


title: JAG1 KO CLONE 35 BIO REP 4

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_377


title: H1299 PARENTALS BIO REP 3

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_351


title: TU, VPA, 5 uM, 3

description:
Library name: Cell_231
mRNA from single larvae


title: TU, VPA, 5 uM, 5

description:
Library name: Cell_233
mRNA from single larvae


title: TU, VPA, 5 uM, 1

description:
Library name: Cell_229
mRNA from single larvae


title: TU, VPA, 5 uM, 2

description:
Library name: Cell_230
mRNA from single larvae


title: H1299 PARENTALS BIO REP 1

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_349


title: H1299 PARENTALS BIO REP 2

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_350


title: TU, VPA, 1uM, 8

description:
Library name: Cell_228
mRNA from single larvae