title: HIKHOM4-1, d60 oligo differentiation

city: Aurora

first: Kevin

last: Ess

state: Co

address: 12700 East 19th Avenue

department: Pediatrics

institute: University Colorado Denver

description: Library name: HIKHOM4-1_d60

data_processing:
Raw paired-end RNA-seq reads in FASTQ format were first assessed for overall quality using FastQC
Low-quality bases and adapter sequences were then removed using Trimmomatic
High-quality trimmed reads were subsequently aligned to the human reference genome (GRCh38) using HISAT2
Gene-level quantification was performed using featureCounts from the Subread package guided by GTF annotation files from Ensembl (release 106)
Assembly: GRCh38
Supplementary files format and content: csv files containing gene IDs and gene count matrix

source_name: Mixed neural culture

growth_protocol: patient-derived iPSCs were differentiated into oligodendrocytes using Douvaras (2015) 90 day differentiation protocol

extract_protocol:
RNA was extracted from cells using the Qiagen RNAeasy Plus Kit (Qiagen 74134)
Stranded mRNA (polyA-selected) library preparation kit

treatment_protocol: Samples were collected at listed time points

value: Mixed neural culture

tag: treatment

value: Collected at d60


title: HIKHOM4-1, d8 oligo differentiation

status: Public on Mar 12 2026

type: SRA

country: USA

description: Library name: HIKHOM4-1_d8

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type

tag: genotype

value: Collected at d8


title: HIKHOM4-1, d90 oligo differentiation

description: Library name: HIKHOM4-1_d90

value: Collected at d90


title: HIKHOM4-1, d30 oligo differentiation

description: Library name: HIKHOM4-1_d30

value: Collected at d30


title: HS6

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on a DNBSEQ-G400 platform in 2 x 100 bp paired-end mode.
The DNBSEQ control software operated base calling analysis software and delivered raw sequencing data.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat, version 2.0.13, in combination with Bowtie2, version 2.2.3, and SAMtools, version 0.1.19.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.

molecule: total RNA

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA isolation was performed using the PAXgene Blood RNA System (BD Bioscience, San Jose, CA, USA).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: peripheral blood mononuclear cells

tag: disease state

value: heat stroke

tag: time

value: on admission


title: HIKHOM3-4, d8 oligo differentiation

description: Library name: HIKHOM3-4_d8


title: CM3

value: healthy donor

value: while climbing a mountain


title: HIKHOM3-4, d60 oligo differentiation

description: Library name: HIKHOM3-4_d60


title: HIKHOM3-4, d90 oligo differentiation

description: Library name: HIKHOM3-4_d90


title: HIKHOM3-4, d30 oligo differentiation

description: Library name: HIKHOM3-4_d30


title: HS3


title: HIKHOM1-3, d8 oligo differentiation

description: Library name: HIKHOM1-3_d8


title: HS4


title: HIKHOM1-3, d30 oligo differentiation

description: Library name: HIKHOM1-3_d30


title: HIKHet4-5, d90 oligo differentiation

description: Library name: HIKHet4-5_d90


title: HIKHOM1-3, d90 oligo differentiation

description: Library name: HIKHOM1-3_d90


title: HIKHet4-5, d30 oligo differentiation

description: Library name: HIKHet4-5_d30


title: HIKHet2-8, d30 oligo differentiation

description: Library name: HIKHet2-8_d30


title: HIKHet4-5, d8 oligo differentiation

description: Library name: HIKHet4-5_d8


title: HIKHet4-5, d60 oligo differentiation

description: Library name: HIKHet4-5_d60


title: HIKHet1-12, d8 oligo differentiation

description: Library name: HIKHet1-12_d8


title: HIKHet2-8, d8 oligo differentiation

description: Library name: HIKHet2-8_d8


title: HIKHet1-12, d90 oligo differentiation

description: Library name: HIKHet1-12_d90


title: HIKHOM1-3, d60 oligo differentiation

description: Library name: HIKHOM1-3_d60


title: HIKHet2-8, d90 oligo differentiation

description: Library name: HIKHet2-8_d90


title: HIKHet1-12, d30 oligo differentiation

description: Library name: HIKHet1-12_d30


title: HIKHet2-8, d60 oligo differentiation

description: Library name: HIKHet2-8_d60


title: Untreated HUVEC biological replicate 1

city: New Taipei City

first: VIJESH

middle: KUMAR

last: YADAV

address: No. 301號, Yuantong Rd, Zhonghe District, New Taipei City, 235

department: Department of Medical Research and Education, Taipei Medical University - Shuang Ho Hospital, New Taipei City, Taiwan

country: Taiwan

institute: SHH-TMU Taiwan

description:
Library name: Normal_Rep1
Untreated HUVEC replicate 1; reads quality-filtered using Trimmomatic v0.38, aligned to GRCh38 using HISAT2, quantified by featureCounts v2.0.0; differential expression analyzed with DESeq2

data_processing:
Raw FASTQ files were quality assessed using FastQC and summarized with MultiQC.
Assembly: GRCh38 (Homo sapiens reference genome)
Supplementary files format and content: The processed data file “Original_read_count.txt” contains gene-level raw read counts generated using featureCounts. Rows represent genes (Ensembl gene ID and gene symbol), and columns represent individual biological samples.

source_name: endothelium

extract_protocol:
Total RNA was extracted from HUVEC samples using a commercial RNA isolation kit according to the manufacturer’s instructions. RNA integrity and concentration were assessed prior to library preparation. Only high-quality RNA samples were used for sequencing.
RNA libraries were constructed using standard Illumina-compatible library preparation protocols. Briefly, mRNA was enriched from total RNA, fragmented, reverse transcribed into cDNA, end-repaired, adapter-ligated, and PCR amplified. Libraries were sequenced using Illumina paired-end sequencing technology.

tag: tissue

value: endothelium

tag: cell line

value: HUVEC

value: endothelial cells

value: wild type

value: untreated

tag: batch


title: HFPF-treated HUVEC biological replicate 2

description:
Library name: HFPF_Rep2
HUVEC treated with heart failure-associated pleural fluid replicate 2; reads quality-filtered using Trimmomatic v0.38, aligned to GRCh38 using HISAT2, quantified by featureCounts v2.0.0; differential expression analyzed with DESeq2

value: HFPF exposure


title: Untreated HUVEC biological replicate 2

description:
Library name: Normal_Rep2
Untreated HUVEC replicate 2; reads quality-filtered using Trimmomatic v0.38, aligned to GRCh38 using HISAT2, quantified by featureCounts v2.0.0; differential expression analyzed with DESeq2


title: Untreated HUVEC biological replicate 3

description:
Library name: Normal_Rep3
Untreated HUVEC replicate 3; reads quality-filtered using Trimmomatic v0.38, aligned to GRCh38 using HISAT2, quantified by featureCounts v2.0.0; differential expression analyzed with DESeq2


title: RPS4X1

city: Shenyang

first: Wensu

last: Liu

address: 77 Puhe Road, Shenbei District

country: China

institute: China Medical University

description: Library name: shRPS4X-1

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads The clean reads were mapped to GRCh38 using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count Assembly: The clean reads were mapped to GRCh38 using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: .txt file containing expression of genes on each samples
Supplementary files format and content: processed_file name: FPKM.gene.txt

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

value: prostate cancer


title: HFPF-treated HUVEC biological replicate 3

description:
Library name: HFPF_Rep3
HUVEC treated with heart failure-associated pleural fluid replicate 3; reads quality-filtered using Trimmomatic v0.38, aligned to GRCh38 using HISAT2, quantified by featureCounts v2.0.0; differential expression analyzed with DESeq2


title: shNC1

description: Library name: shNC-1


title: RPSA1

description: Library name: shRPSA-1


title: shNC2

description: Library name: shNC-2


title: RPL112

description: Library name: shRPL11-2


title: RPL281

description: Library name: shRPL28-1


title: RPS4X2

description: Library name: shRPS4X-2


title: RPL111

description: Library name: shRPL11-1


title: HIKHet1-12, d60 oligo differentiation

description: Library name: HIKHet1-12_d60

value: Mixed neural culture


title: HFPF-treated HUVEC biological replicate 1

description:
Library name: HFPF_Rep1
HUVEC treated with heart failure-associated pleural fluid replicate 1; reads quality-filtered using Trimmomatic v0.38, aligned to GRCh38 using HISAT2, quantified by featureCounts v2.0.0; differential expression analyzed with DESeq2


title: RPL282

description: Library name: shRPL28-2


title: RPL23A2

description: Library name: shRPL23A-2


title: RPL23A1

description: Library name: shRPL23A-1


title: THUMPD2KO_siLARP7 - THUMPD2 knockout with LARP7 knockdown si1 - Replicate 1

city: Göttingen

first: Katherine

last: Bohnsack

address: Humboldtallee 23

country: Germany

institute: University Medical Centre Göttingen

description: Library name: THUMPD2KO_siLARP7_1_rep1

data_processing:
Reads were trimmed for remaining sequencing adaptors using cutadapt.
High data quality was confirmed running the tool FastQC/0.11.9.
For mapping, the aligner STAR v2.7.11b with the following settings was used: --outFilterMultimapNmax 10 --outSAMattributes All --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --chimSegmentMin 20 --chimOutType WithinBAM Junctions --quantMode TranscriptomeSAM GeneCounts --outWigType bedGraph --outWigNorm RPM --outWigStrand Unstranded --outFilterMismatchNmax 2 (Li et al., 2009; Quinlan and Hall, 2010).
UCSC Genome Browser tools bedSort and bedGraphToBigWig were used to convert from bedgraph format to bigwig format for visualization of the data in the IGV genome browser (Kent et al., 2010; Thorvaldsdóttir et al., 2013).
Assembly: GRCh38.p14
Supplementary files format and content: BigWig

growth_protocol: HCT116 cells  were cultured in McCoys 5A medium supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 μg/mL streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRI-Reagent (Sigma-Aldrich) according to the manufacturer’s instructions. After treatment with TURBO DNase, RNAs were re-purified using the RNA clean and concentrator kit (Zymo) according to the manufacturer's instructions.
PolyA RNA enrichment was performed and libraries were constructed by TruSeq total RNA library preparation (Illumina) according to the maufacturer's instructions

treatment_protocol: WT and THUMPD2 KO cells were transfected with 40 nM non-target siRNAs or those targeting LARP7 using Lipofectamine RNAiMAX reagent according to the manufacturer's instructions. Cells were harvested 72 h after transfection.

value: Epithelial Cells


title: RPSA2

description: Library name: shRPSA-2


title: THUMPD2KO_siNT - THUMPD2 knockout  - Replicate 3

description: Library name: THUMPD2KO_siNT_rep3


title: 70-day-old forebrain organoids, isogenic control, replicate 1

city: Québec

first: Thiery

last: De Serres-Bérard

state: Québec

department: Medicine

country: Canada

institute: Université Laval

description:
Library name: Isogenic_control_70d_rep1
eCLIP
MBNL2_cDM1_isogenic_control.reproducible_enriched_windows.tsv

library_source: other

data_processing:
Libraries were sequenced to a minimum of 20 million SE100 reads per replicate using a NovaSeq X Plus (Illumina). eCLIP data were analyzed using Skipper (Boyle et al., Cell Genom, 2023). Reads were aligned to the hg38 reference genome and annotated with GENCODE v38.
Assembly: hg38
Supplementary files format and content: Tab-separated values files containing enriched eCLIP binding windows

molecule: other

source_name: forebrain organoid

growth_protocol: Forebrain organoids were differentiated from human induced pluripotent stem cells (hiPSCs) using a modified version of the protocol described by Lancaster et al. (Nature Protocols, 2014). Human iPSCs at 50-80% confluence were dissociated into single cells (day 0) with Accutase (Sigma-Aldrich) and seeded at 1000-2000 cells per well in poly-HEMA (Sigma-Aldrich)-coated 96-well round-bottom cell culture plates (Costar) in hESC medium (DMEM/F12 (Gibco), 20% KnockOut Serum Replacement (Invitrogen), 3% ESC-qualified FBS (Gibco), 1% GlutaMAX supplement (Gibco), 1% MEM Non-Essential Amino Acids (MEM-NEAA) Solution (Gibco), and 100 µM 2-mercaptoethanol (Gibco)) supplemented with 50 µM Y-27632 (RayBiotech) and 10 ng/mL thermostable human FGF-2 IS (Miltenyi Biotec). The medium was partially changed at day 3 with fresh hESC medium without Y-27632 and FGF-2. At day 5, the medium was switched to neural induction medium (NIM: DMEM/F12, 1% N2-supplement (Gibco), 1% GlutaMAX, 1% MEM-NEAA and 1 µg/mL heparin (Sigma-Aldrich)). At day 7, the embryoid bodies were embedded in 20 µL Matrigel droplets (Corning) and transferred to a 60-mm Petri dish for suspension culture (Sarstedt) in differentiation medium (1:1 DMEM/F12 and Neurobasal medium (Gibco), 1% B27 supplement without vitamin A (Gibco), 0.5% N2 supplement, 1% GlutaMAX supplement, 0.5% MEM-NEAA, 2.5 µg/mL insulin (Sigma-Aldrich), 1x penicillin-streptomycin (Gibco) and 50 µM 2-mercaptoethanol). After 4 days (day 11), the medium was switched to the same formula, but with B27 supplement containing vitamin A and 0.4 mM ascorbic acid (Sigma-Aldrich). At day 13 or when neuroepithelial buds were apparent, organoids were removed from the Matrigel by incubating in 0.5 mM EDTA/0.18% NaCl diluted in DPBS without Mg2+/Ca2+ (Wisent) at 4 C with gentle agitation for 45 minutes and were then placed back in the incubator on an orbital shaker (Celltron) set at 56 rpm with medium changes every 3-4 days. At day 40, when cortical tissue becomes visible as dark zones surrounding the ventricles, the medium was supplemented with 1% Matrigel. Organoids were cultured up to day 80 before processing.

extract_protocol:
70-day-old organoids were transferred into ice-cold HBSS (STEMCELL Technologies) in approximately tenfold the original tissue volume and triturated with a micropipette. Dissociated tissues were irradiated three times at 400 mJ/cm² in a Stratalinker 1800 UV crosslinker while keeping the suspension on ice and mixing between each irradiation, and then flash-frozen in liquid nitrogen. eCLIP was performed essentially as described by Van Nostrand et al. (Nature Methods, 2016). Briefly, organoids were lysed and treated with RNase I at a 1:1000 dilution. 2% of each lysate was reserved for preparation of a parallel size-matched input (SMInput) library, while the remaining material was subjected to immunoprecipitation using a mouse anti-MBNL2 antibody (Santa Cruz #sc-136167). Bound RNA fragments in the immunoprecipitates were dephosphorylated and 3'-end-ligated to an RNA adaptor. Protein-RNA complexes from SMInputs and immunoprecipitates were run on an SDS-polyacrylamide gel and transferred to a nitrocellulose membrane. Membrane regions corresponding to a molecular weight between 35 and 50 kDa above the expected size were excised, and RNA was released from the complexes using proteinase K.
SMInput samples were dephosphorylated and ligated at the 3' end to an RNA adaptor. All RNA samples (immunoprecipitates and SMInputs) were reverse transcribed using AffinityScript Reverse Transcriptase (Agilent). cDNAs were ligated at the 5' end to a DNA adaptor. cDNA yields were quantified by qPCR, and 100-500 fmol of library per sample were generated using Q5 High-Fidelity PCR Master Mix (New England Biolabs).

value: forebrain organoid

value: induced pluripotent stem cells

tag: disease

value: congenital myotonic dystrophy

tag: genetic modification

value: CTG repeat expansion removed from the DMPK gene

value: 70 days


title: THUMPD2KO_siLARP7 - THUMPD2 knockout with LARP7 knockdown si1 - Replicate 3

description: Library name: THUMPD2KO_siLARP7_1_rep3


title: THUMPD2KO_siNT - THUMPD2 knockout  - Replicate 1

description: Library name: THUMPD2KO_siNT_rep1


title: 70-day-old forebrain organoids, unaffected control, replicate 2, input

description:
Library name: Unaffected_control_70d_rep2_INPUT
eCLIP
MBNL2_cDM1_healthy.reproducible_enriched_windows.tsv

value: unaffected individual


title: 70-day-old forebrain organoids, isogenic control, replicate 1, input

description:
Library name: Isogenic_control_70d_rep1_INPUT
eCLIP
MBNL2_cDM1_isogenic_control.reproducible_enriched_windows.tsv


title: WT_siLARP7 - LARP7 knockdown si1- Replicate 3

description: Library name: WT_siLARP7_1_rep3


title: WT_siNT - Control - Replicate 2

description: Library name: WT_siNT_rep2


title: THUMPD2KO_siNT - THUMPD2 knockout  - Replicate 2

description: Library name: THUMPD2KO_siNT_rep2


title: 80-day-old forebrain organoids, isogenic control

description:
Library name: Isogenic_control_80d
10X Genomics

library_source: transcriptomic single cell

data_processing:
Through 10× Cell Ranger's pipeline, the raw base call (BCL) files were demultiplexed into FASTQ files with the 10x Genomics Cell Ranger pipeline. Raw sequencing data were processed using Cell Ranger v7.2.0 (10x Genomics) to perform alignment, filtering, barcode assignment and UMI counting, with intronic reads included in the counting matrix.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values and sparse matrix files corresponding to barcode, feature, and gene expression data

extract_protocol:
80-day-old forebrain organoids were washed with HBSS (STEMCELL Technologies) and incubated in dissociation solution (30 units/mL of activated papain (STEMCELL Technologies, prepared according to the manufacturer's instructions), 125 U/mL DNase I (New England Biolabs) in HBSS) at 37 °C on an orbital shaker at 90 rpm for 40 minutes with gentle mechanical dissociation using a micropipette every 10 minutes. Papain was then neutralized by the addition of 10 mg/mL ovomucoid protease inhibitor (Worthington) solution. Cells were washed with HBSS supplemented with 0.4% BSA (Proliant), passed through a 100 µm cell strainer (ThermoFisher) and resuspended at 1 x 10e6 cells/mL in HBSS 0.4% BSA. The concentration of the single-cell suspension as well as cell quality control were assessed with a Bio-Rad TC20 automated cell counter (Bio-Rad). An average of 3460 cells per sample was loaded onto the Chromium Controller (10x Genomics) to generate single-cell GEMs (gel beads in emulsion).
GEM reverse transcription, Dynabeads cleanup (ThermoFisher Scientific), PCR amplification and SPRIselect beads cleanup (Beckman Coulter) were performed using the Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) following the manufacturer's user guide. Indexed single-cell libraries were generated using the Chromium Next GEM Single Cell 3' Library and the Chromium Dual Index Kit. The quality of final indexed libraries was examined with a D1000 DNA Screentape on a TapeStation 2200 (Agilent Technologies) and the quantification was performed on the Qubit 3.0 fluorometer (ThermoFisher Scientific). The 10x Genomics libraries with unique indexes were pooled in equimolar ratios and sequenced for paired-end 100 bp reads on a NovaSeq 6000 (Illumina) at a depth of 82,500 read pairs per cell.

value: 80 days


title: 70-day-old forebrain organoids, isogenic control, replicate 2, input

description:
Library name: Isogenic_control_70d_rep2_INPUT
eCLIP
MBNL2_cDM1_isogenic_control.reproducible_enriched_windows.tsv


title: WT_siLARP7 - LARP7 knockdown si1 - Replicate 1

description: Library name: WT_siLARP7_1_rep1


title: 70-day-old forebrain organoids, congenital myotonic dystrophy, replicate 1

description:
Library name: CDM_70d_rep1
eCLIP
MBNL2_cDM1.reproducible_enriched_windows.tsv


title: 80-day-old forebrain organoids, congenital myotonic dystrophy

description:
Library name: CDM_80d
10X Genomics


title: 70-day-old forebrain organoids, unaffected control, replicate 1, input

description:
Library name: Unaffected_control_70d_rep1_INPUT
eCLIP
MBNL2_cDM1_healthy.reproducible_enriched_windows.tsv


title: 70-day-old forebrain organoids, congenital myotonic dystrophy, replicate 2

description:
Library name: CDM_70d_rep2
eCLIP
MBNL2_cDM1.reproducible_enriched_windows.tsv


title: 70-day-old forebrain organoids, congenital myotonic dystrophy, replicate 1, input

description:
Library name: CDM_70d_rep1_INPUT
eCLIP
MBNL2_cDM1.reproducible_enriched_windows.tsv


title: 70-day-old forebrain organoids, unaffected control, replicate 2

description:
Library name: Unaffected_control_70d_rep2
eCLIP
MBNL2_cDM1_healthy.reproducible_enriched_windows.tsv


title: 70-day-old forebrain organoids, unaffected control, replicate 1

description:
Library name: Unaffected_control_70d_rep1
eCLIP
MBNL2_cDM1_healthy.reproducible_enriched_windows.tsv


title: 70-day-old forebrain organoids, isogenic control, replicate 2

description:
Library name: Isogenic_control_70d_rep2
eCLIP
MBNL2_cDM1_isogenic_control.reproducible_enriched_windows.tsv


title: WT_siNT - Control - Replicate 3

description: Library name: WT_siNT_rep3


title: 70-day-old forebrain organoids, congenital myotonic dystrophy, replicate 2, input

description:
Library name: CDM_70d_rep2_INPUT
eCLIP
MBNL2_cDM1.reproducible_enriched_windows.tsv


title: ILC2, asthmatic, experiment 11

city: Braunschweig

first: Stefan

last: Floess

address: Inhoffenstr. 7

department: Experimental Immunology

institute: Helmholtz-Centre for Infection Research

description: Library name: AS3

library_source: genomic

data_processing:
Illumina RTA3 was used for basecalling. Sequencing data were processed using the nf-core/methylseq pipeline (version 2.2.0), using default parameters, genome assembly GRCh38. Briefly, the pipeline employs FASTQC (version 0.11.9), trimgalore (version 0.6.7) and bismark (version 0.24.0) (DOI:10.1093/bioinformatics/btr167) for read-level quality control, adapter trimming, bisulfite-aware alignment and cytosine-level DNA methylation quantification. Methylation calls were analyzed with the Bioconductor package BSseq (version bsseq_1.34.0 implemented in R 4.2.1) [Hansen KD et al. (2012) Genome Biology, 13(10), R83. doi:10.1186/gb-2012-13-10-r83.]. The detection of differentially methylated regions (DMRs) was based on Methylation profiles of CpGs with a minimum coverage of 2 mapped reads in at least two replicates of one condition. The t-statistics were computed and DMRs identified (quantile-based cutoff: 0.01 and 0.99, maximum distance of 200 bp between each CpG). DMRs were filtered (mean methylation difference (across the DMR) of at least 0.25 (25 %), incorporating at least three CpGs). Finally, DMRs were ranked by the sum of the t-statistics of each CpG associated (areaStat parameter) as suggested (bsseq documentation).
Assembly: GRCh38
Supplementary files format and content: PDF shows principal component analysis (PCA) plot of all ILC2 samples.
Supplementary files format and content: CSV files contain a table with identified DMRs from the pairwise ILC2 comparisons AT vs. HE, AS vs. HE, and AS vs. AT using the averaged methylation values of a sample group. Columns show numbering, DMR chromosomal location (chromosome (chr), start, end), CpG motif count (n), DMR size (width), area statistics representing the sum of t-statistics for all CpG motifs within the DMR (areaStat), mean methylation (meanDiff), sample group 1 mean methylation (group1.mean), sample group 2 mean methylation (group2.mean), methylation type (direction), transcript name of nearest transcriptional start site (tss) (nearest_tss), distance to nearest tss (distance_ to_nearest_tss), nearest gene id (nearest_gene_id), gene description of the nearest gene (nearest_gene_desc), the transcript of the preceding tss (preceding tss), the transcript of the following tss (following_tss), preceding_gene_id (preceding_gene_id), preceding gene name (preceding_gene_name), description of the preceding gene (preceding_gene_desc),  following_gene_id (following_gene_id), following gene name (following_gene_name), description of the following gene (following_gene_desc).
Library strategy: EM-seq

molecule: genomic DNA

source_name: blood

extract_protocol:
Genomic DNA was prepared from flow cytometrically sorted ILC2 by using the DNeasy Blood and Tissue Kit (Qiagen, manufacturer’s protocol).
The prepared genomic DNA was fragmented by sonication and served as input for library preparation using the NEBNext Enzymatic Methyl-seq Kit (New England Biolabs, manufacturer’s protocol).

treatment_protocol: Human peripheral blood mononuclear cells (PBMC) were used as a source to isolate ILC2. Lineage-positive cells were removed by using the Human Lineage Cell Depletion Kit (Miltenyi Biotec) and the autoMACS Pro (Miltenyi Biotec) according to the manufacturer’s protocol. The remaining cells were used to sort ILC2 (CD127+CD45+CD56-CRTH2+) by flow cytometry.

value: blood


title: WT_siLARP7 - LARP7 knockdown si1 - Replicate 2

description: Library name: WT_siLARP7_1_rep2


title: ILC2, asthmatic, experiment 12

description: Library name: AS4


title: WT_siNT - Control - Replicate 1

description: Library name: WT_siNT_rep1


title: 80-day-old forebrain organoids, unaffected control

description:
Library name: Unaffected_control_80d
10X Genomics


title: THUMPD2KO_siLARP7 - THUMPD2 knockout with LARP7 knockdown si1 - Replicate 2

description: Library name: THUMPD2KO_siLARP7_1_rep2


title: ILC2, atopic, experiment 5

description: Library name: AT1


title: ILC2, healthy, experiment 1

description: Library name: HE1


title: ILC2, healthy, experiment 4

description: Library name: HE4


title: NK cells, experiment 3

description: Library name: 20_NK-3

data_processing:
Illumina RTA3 was used for basecalling. Sequencing data were processed using the nf-core/methylseq pipeline (version 2.2.0), using default parameters, genome assembly GRCh38, except --accel=true (--clip_r2 15 and --three_prime_clip_r1 15) and the --relax_mismatches argument was used (DOI:10.5281/zenodo.1343417, DOI:10.1038/s41587-020-0439-x). Briefly, the pipeline employs FASTQC (version 0.11.9), trimgalore (version 0.6.7) and bismark (version 0.24.0) (DOI:10.1093/bioinformatics/btr167) for read-level quality control, adapter trimming, bisulfite-aware alignment and cytosine-level DNA methylation quantification. Methylation calls were analyzed with the Bioconductor package BSseq (version bsseq_1.34.0 implemented in R 4.2.1) [Hansen KD et al. (2012) Genome Biology, 13(10), R83. doi:10.1186/gb-2012-13-10-r83.]. The detection of differentially methylated regions (DMRs) was based on Methylation profiles of CpGs with a minimum coverage of 2 mapped reads in at least two replicates of one condition. The t-statistics were computed and DMRs identified (quantile-based cutoff: 0.01 and 0.99, maximum distance of 200 bp between each CpG). DMRs were filtered (mean methylation difference (across the DMR) of at least 0.25 (25 %), incorporating at least three CpGs). Finally, DMRs were ranked by the sum of the t-statistics of each CpG associated (areaStat parameter) as suggested (bsseq documentation).
Assembly: GRCh38
Supplementary files format and content: PDF shows principal component analysis (PCA) plot including samples from all ILC subsets.
Supplementary files format and content: CSV files contain a table with identified DMRs from the pairwise comparisons ILC2 vs. ILC1, ILC2 vs. ILC3, ILC2 vs. NK cells, ILC3 vs. ILC1, ILC3 vs. NK cells, and NK cells vs. ILC1 using the averaged methylation values of a sample group. Columns show numbering, DMR chromosomal location (chromosome (chr), start, end), CpG motif count (n), DMR size (width), area statistics representing the sum of t-statistics for all CpG motifs within the DMR (areaStat), mean methylation (meanDiff), sample group 1 mean methylation (group1.mean), sample group 2 mean methylation (group2.mean), methylation type (direction), transcript name of nearest transcriptional start site (tss) (nearest_tss), distance to nearest tss (distance_ to_nearest_tss), nearest gene id (nearest_gene_id), gene description of the nearest gene (nearest_gene_desc), the transcript of the preceding tss (preceding tss), the transcript of the following tss (following_tss), preceding_gene_id (preceding_gene_id), preceding gene name (preceding_gene_name), description of the preceding gene (preceding_gene_desc),  following_gene_id (following_gene_id), following gene name (following_gene_name), description of the following gene (following_gene_desc).

extract_protocol:
Genomic DNA was prepared from flow cytometrically sorted ILC1, ILC2, ILC3 and NK cells by using the DNeasy Blood and Tissue Kit (Qiagen, manufacturer’s protocol). The genomic DNA was then bisulfite converted using the EZ DNA Methylation Kit (Zymo Research,  manufacturer’s protocol) and subjected to library preparation.
The bisulfite converted DNA was fragmented by sonication and served as input for library preparation using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, manufacturer’s protocol).

treatment_protocol: Human peripheral blood mononuclear cells (PBMC) and uninfected, non-inflamed human tonsils were used as a source to isolate ILC subpopulations. Lineage-positive cells (CD1a+CD3+CD19+TCRαβ+TCRγδ+CD14+CD11c+FcεRIα+) were removed through two rounds of magnetic depletion by using the autoMACS Pro (Miltenyi Biotec). The remaining cells were separated into NK cells (CD127-CD45+ population expressing either CD56 or NKG2A, or both), ILC1 (CD127+CD45+CD56-CD117-CRTH2-), ILC2 (CD127+CD45+CD56-CRTH2+) and ILC3 (CD127+CD45+CD56-CD117+CRTH2-NKp44+) by using flow cytometry-based cell sorting.

value: NK cells


title: ILC2, healthy, experiment 2

description: Library name: HE2


title: NK cells, experiment 1

description: Library name: 19_Nk-1


title: S_2312_000139_PB

city: Seattle

first: Petter

last: Bjornstad

state: Washington

address: 750 Republican St

department: Division of Metabolism, Endocrinology and Nutrition

institute: University of Washington

description:
Library name: Sample 27
10x Genomics

data_processing:
Sample demultiplexing, barcode processing, and gene expression quantifications were performed with the cellranger v8+ (10x Genomics) pipeline.
SoupX was employed, as noted per sample in the methods section for this manuscript, using default parameters.
Integration was conducted with RunHarmony, embedded within Seurat.
Assembly: hg38, v. GRCh38-2020-A
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Matrix files

source_name: Kidney cortex

extract_protocol:
Cortical human kidney biopsies that had been stored in Cryostor were subjected to a cellular RNA extraction protocol from the Kidney Precision Medicine Project.
Library construction was performed according to the manufacturer's instructions (single cell 3' v4 protocol, 10x Genomics)

treatment_protocol: Where indicated, patients were prescribed and had been administered an SGLT2 inhibitor or placebo for 16 weeks.

value: Kidney cortex

value: Kidney and immune cells

value: Placebo

value: PRE


title: S_2310_001680_PB

description:
Library name: Sample 24
10x Genomics


title: ILC2, asthmatic, experiment 10

description: Library name: AS2


title: ILC2, asthmatic, experiment 9

description: Library name: AS1


title: ILC2, healthy, experiment 3

description: Library name: HE3


title: ILC2, atopic, experiment 7

description: Library name: AT5


title: NK cells, experiment 2

description: Library name: 36_Nk-2


title: ILC1, experiment 2

description: Library name: 8_ILC1-2

source_name: tonsil

value: tonsil


title: S_2307_009796_PB

description:
Library name: Sample 23
10x Genomics

value: Dapagliflozin

value: POST


title: S_2310_001743_PB

description:
Library name: Sample 26
10x Genomics


title: S_2310_001725_PB

description:
Library name: Sample 25
10x Genomics


title: ILC3, experiment 2

description: Library name: 14_ILC3-2


title: ILC3, experiment 1

description: Library name: 13_ILC3-1


title: S_2304_009134_PB

description:
Library name: Sample 16
10x Genomics


title: S_2307_009769_PB

description:
Library name: Sample 21
10x Genomics


title: ILC2, experiment 3

description: Library name: 12_ILC2-3


title: Sample 11_III-7

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

description: Library name: Sample 11

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and subsequently aligned to the reference genome hg38 applying STAR RNA-seq aligner (version 2.7.11b), Samtools (version 1.9) and Picard (version 2.9.2). Htseq (version 0.9.1) was applied to calculate raw read counts.
Assembly: hg38
Supplementary files format and content: raw read counts from RNA-seq samples

source_name: Buffy coat

growth_protocol: Total RNA-seq was done for human buffy coat.

extract_protocol:
Total RNA was extracted from the tissue from mice and purified with RNeasy Plus Mini Kit (Invitrogen, 12183018A). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a Nextseq 2000 (Illumina).
Libraries for sequencing were prepared using standard New England Biolabs's protocols.

value: Buffy coat

tag: Sex

value: Female

tag: age


title: S_2304_009089_PB

description:
Library name: Sample 15
10x Genomics


title: Sample 10_III-6

description: Library name: Sample 10


title: ILC2, experiment 2

description: Library name: 11_ILC2-2


title: S_2307_009688_PB

description:
Library name: Sample 19
10x Genomics


title: Sample 9_III-5

description: Library name: Sample 9

value: Male


title: ILC1, experiment 3

description: Library name: 9_ILC1-3


title: S_2307_009733_PB

description:
Library name: Sample 20
10x Genomics


title: S_2209_007581_PB

description:
Library name: Sample 12
10x Genomics


title: ILC2, atopic, experiment 6

description: Library name: AT2


title: ILC3, experiment 3

description: Library name: 15_ILC3-3


title: S_2209_007554_PB

description:
Library name: Sample 10
10x Genomics


title: S_2304_009161_PB

description:
Library name: Sample 18
10x Genomics


title: ILC2, atopic, experiment 8

description: Library name: AT6


title: ILC1, experiment 1

description: Library name: 7_ILC1-1


title: Sample 7_III-3

description: Library name: Sample 7


title: Sample 8_III-4

description: Library name: Sample 8


title: S_2302_015924_PB

description:
Library name: Sample 14
10x Genomics


title: S_2209_007500_PB

description:
Library name: Sample 9
10x Genomics


title: ILC2, experiment 1

description: Library name: 10_ILC2-1


title: S_2307_009778_PB

description:
Library name: Sample 22
10x Genomics


title: S_2304_009152_PB

description:
Library name: Sample 17
10x Genomics


title: Sample 5_II-6

description: Library name: Sample 5


title: Sample 13_III-9

description: Library name: Sample 13


title: S_2209_007572_PB

description:
Library name: Sample 11
10x Genomics


title: S_2203_000846_PB

description:
Library name: Sample 6
10x Genomics


title: S_2203_000892_PB

description:
Library name: Sample 7
10x Genomics


title: Visium_placenta_non_transmitter_1

city: Medellin

first: Sneider

middle: Alexander

last: Gutierrez Guarnizo

state: Antioquia

department: Biology

country: Colombia

institute: Universidad de Antioquia

description: Library name: 2

data_processing:
For RNAseq analysis, raw RNA-seq reads were assessed with FastQC and MultiQC, trimmed for adapters and low-quality bases using BBDuk (BBMap), and re-evaluated for quality. Clean paired-end reads were aligned to the human GRCh38 reference genome using HISAT2, followed by SAM sorting with samtools and duplicate marking with Picard. Alignment quality and gene body coverage were examined using Qualimap RNA-seq. Gene-level quantification was performed with featureCounts (Subread). Differential gene expression analysis was performed using DESeq2. Spatial transcriptomics data were processed in R using Seurat. Spaceranger output files were imported with Load10X_Spatial, retaining only tissue-associated spots. Quality metrics (e.g., spot UMI counts) were inspected by violin and spatial feature plots. Each sample was normalized using SCTransform to correct for sequencing depth and technical variation. Datasets were merged into a single Seurat object, and variable features were used for PCA, nearest-neighbor graph construction, Louvain clustering, and UMAP visualization. Batch effects between samples were corrected using Harmony. Spatial cluster identities were visualized with SpatialDimPlot, and cluster-specific marker genes were identified using FindMarkers after PrepSCTFindMarkers normalization. Region-level annotations (e.g., trophoblasts, secondary villi) were added to the metadata based on cluster membership. For differential expression, raw count matrices from the Spatial assay were used to construct DESeq2 objects with sample condition as the design variable. Differentially expressed genes were extracted, filtered by adjusted p-value and fold change, and exported for visualization and downstream interpretation.
Assembly: GRCh38.p14
Supplementary files format and content: Comma-separated values files include features count values for each sample
Supplementary files format and content: Robust Cell Type Decomposition files contains annotations for spatial transcriptome
Library strategy: Spatial Transcriptomics

source_name: Central chorionic villi

extract_protocol:
For RNA-seq in peripheral blood:
Peripheral blood treated with EDTA was collected from the mother immediately after delivery and resuspended in DNA/RNA Shield. RNA was purified using the Zymo R1057 protocol. Purified RNA was obtained following TURBO DNase treatment.
For RNA-seq in placenta tissue:
Placental tissue was collected within 1 hour after delivery. A ~30 mg biopsy was stored in RNAlater, followed by RNA purification using TRIzol reagent. Purified RNA was obtained following TURBO DNase treatment.
For spatial transcriptomics in placenta tissue:
Whole placental tissue was fixed in 10% neutral-buffered formalin for 24 hours. A perpendicular section of the central chorionic villi was embedded in paraffin. A 5 µm section was H&E-stained using a charged Superfrost Plus slide. Samples were processed with the Visium system using the 6.5 × 6.5 mm Cytassist run format.
Illumina Paired-end sequencing

value: Central chorionic villi


title: Sample 4_II-5

description: Library name: Sample 4


title: S_2107_023682_PB

description:
Library name: Sample 3
10x Genomics


title: S_2209_007599_PB

description:
Library name: Sample 13
10x Genomics


title: Placenta_Non.transmitter_mother_2

description: Library name: S298

data_processing:
For RNAseq analysis, raw RNA-seq reads were assessed with FastQC and MultiQC, trimmed for adapters and low-quality bases using BBDuk (BBMap), and re-evaluated for quality. Clean paired-end reads were aligned to the human GRCh38 reference genome using HISAT2, followed by SAM sorting with samtools and duplicate marking with Picard. Alignment quality and gene body coverage were examined using Qualimap RNA-seq. Gene-level quantification was performed with featureCounts (Subread). Differential gene expression analysis was performed using DESeq2. Spatial transcriptomics data were processed in R using Seurat. Spaceranger output files were imported with Load10X_Spatial, retaining only tissue-associated spots. Quality metrics (e.g., spot UMI counts) were inspected by violin and spatial feature plots. Each sample was normalized using SCTransform to correct for sequencing depth and technical variation. Datasets were merged into a single Seurat object, and variable features were used for PCA, nearest-neighbor graph construction, Louvain clustering, and UMAP visualization. Batch effects between samples were corrected using Harmony. Spatial cluster identities were visualized with SpatialDimPlot, and cluster-specific marker genes were identified using FindMarkers after PrepSCTFindMarkers normalization. Region-level annotations (e.g., trophoblasts, secondary villi) were added to the metadata based on cluster membership. For differential expression, raw count matrices from the Spatial assay were used to construct DESeq2 objects with sample condition as the design variable. Differentially expressed genes were extracted, filtered by adjusted p-value and fold change, and exported for visualization and downstream interpretation.
Assembly: GRCh38.p14
Supplementary files format and content: Comma-separated values files include features count values for each sample
Supplementary files format and content: Robust Cell Type Decomposition files contains annotations for spatial transcriptome

source_name: Central placenta feltal side

value: Central placenta feltal side


title: S_2203_000804_PB

description:
Library name: Sample 4
10x Genomics


title: S_2203_000916_PB

description:
Library name: Sample 8
10x Genomics


title: Sample 2_II-1

description: Library name: Sample 2


title: Placenta_Non.transmitter_mother_4

description: Library name: S206


title: Sample 1_I-1

description: Library name: Sample 1


title: S_2107_023637_PB

description:
Library name: Sample 2
10x Genomics


title: Sample 6_II-7

description: Library name: Sample 6


title: Sample 12_III-8

description: Library name: Sample 12


title: Sample 3_II-3

description: Library name: Sample 3


title: S_2203_000822_PB

description:
Library name: Sample 5
10x Genomics


title: Placenta_Non.transmitter_mother_3

description: Library name: S183


title: Visium_placenta_uninfected_1

description: Library name: 5


title: S_2107_023529_PB

description:
Library name: Sample 1
10x Genomics


title: Primed Replicate 2

city: Miami

first: Rodrigo

last: Lucena Borges

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: Sylvester Comprehensive Cancer Center

description: Library name: T47D_LTED_6M_44_sorted_REP2

data_processing:
Paired-end fastq files were processed using ENCODE ATAC-Seq pipeline v2.2.3 was used for read trimming, QC, alignment against hg19  and generation of bigwigs with default parameters except: atac.adapters_rep1_R1 :  TAAGGCGA, atac.adapters_rep1_R2 : TAAGGCGA, atac.adapters_rep2_R1 : GCTACGCT, atac.adapters_rep2_R2 : GCTACGCT. Consensus Peaks selected by Irreproducible Discovery Rate (IDR) DOI: 10.1214/11-AOAS466) were filtered by size<1000, score>=1000 and  qValue>=5 to be used in downstream analysis.
Assembly: hg19
Supplementary files format and content: Bigwig files (average signal between replicates)

source_name: Cell line

extract_protocol:
ATAC-seq experiments were performed as previously described (Corces et al., 2017) with minor modifications. 50,000 viable cells were used to perform the transposition reaction.The cleanup of the transposed fragments was performed using Zymo DNA Clean and Concentrator-5 Kit (Zymo catalog number D4014) and DNA was eluted in 21 µL of provided elution buffer
Library construction was performed as previously described (Corces et al, 2017). To determine the average fragment size of each library, samples were run through a high sensitivity DNA screentape (Agilent Technologies #5067–5584) following the manufacturer’s instructions on an Agilent Technologies 2200 TapeStation machine. Concentration of each library was measured using Qubit dsDNA high sensitivity reagents (Thermo Fisher Scientific #Q32851) following the manufacturer’s instructions on a Qubit 3 fluorometer. .

value: T47D ATCC HTB-113

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: 6 months after E2 depletion


title: Primed Replicate 1

description: Library name: T47D_LTED_6M_44_sorted_REP1


title: Placenta_Non.transmitter_mother_1

description: Library name: S205


title: Placenta_Transmitter_mother_7

description: Library name: S181


title: O. tipulae Mutant, Con_10kb_2L, Mixed worms, illumina

city: Knoxville

first: Jianbin

last: Wang

state: TN

address: 1311 Cumberland Avenue 309 Ken and Blaire Mossman Bldg

department: Biochemistry & Cellular and Molecular Biology

institute: The University of Tennessee Knoxville

description: Library name: Con_10kb_2L

data_processing:
Genomic reads from O. tipulae SFE mutants were aligned to the O. tipulae telomere-to-telomere reference genome using Bowtie2. The resulting SAM files were converted to BAM format and sorted using SAMtools. Read coverage across the genome was calculated using BEDTools to generate a BEDGRAPH file.
Assembly: Oscheius tipulae ASM1342590v1
Supplementary files format and content: .bw

organism: Oscheius tipulae

source_name: Mixed worms

extract_protocol:
O. tipulae mutants were grown on 150 mm rich agar plates seeded with E. coli strain NA22. When the bacterial lawn was nearly exhausted, worms were washed off the plates using M9 buffer and pelleted by centrifugation at 170 x g for 1 min. The worm pellets were washed multiple times with M9 buffer to remove microbial contaminants. High molecular weight genomic DNA was extracted using Genomic-tips (Qiagen, Cat# 10223) according to the manufacturer’s protocol.
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, Cat# E7645S) and sequenced on an Illumina NovaSeq 6000 platform.

value: Mixed worms


title: O. tipulae Mutant, Con_1kb_2L, Mixed worms, illumina

description: Library name: Con_1kb_2L


title: Placenta_Transmitter_mother_6

description: Library name: S202


title: O. tipulae Mutant, Con_X_middle, Mixed worms, illumina

description: Library name: Con_X_middle


title: Placenta_Transmitter_mother_4

description: Library name: S177


title: O. tipulae Mutant, Con_17_19_GGC_2L, Mixed worms, illumina

description: Library name: Con_17_19_GGC_2L


title: O. tipulae Mutant, Con_11_14_CGTG_2L, Mixed worms, illumina

description: Library name: Con_11_14_CGTG_2L


title: Placenta_Transmitter_mother_3

description: Library name: S200


title: O. tipulae Mutant, Con_13_16_TCAT_2L, Mixed worms, illumina

description: Library name: Con_13_16_TCAT_2L


title: Placenta_Transmitter_mother_5

description: Library name: S179


title: Placenta_Transmitter_mother_2

description: Library name: S297


title: O. tipulae Mutant, Con_7_10_TGTT_2L, Mixed worms, illumina

description: Library name: Con_7_10_TGTT_2L


title: Placenta_Transmitter_mother_1

description: Library name: S174


title: O. tipulae Mutant, Con_17_19_CCC_2L, Mixed worms, illumina

description: Library name: Con_17_19_CCC_2L


title: O. tipulae, Con_Swap_2L, Mixed worms, illumina

description: Library name: Con_Swap_2L


title: Placenta_Uninfected_mother_9

description: Library name: S199


title: Placenta_Uninfected_mother_7

description: Library name: S195


title: O. tipulae, WT_Con_2L, Mixed worms, illumina

description: Library name: WT_Con_2L


title: O. tipulae Mutant, Con_4_7_GATG_2L, Mixed worms, illumina

description: Library name: Con_4_7_GATG_2L


title: Placenta_Uninfected_mother_5

description: Library name: S192


title: Placenta_Uninfected_mother_8

description: Library name: S197


title: Placenta_Uninfected_mother_6

description: Library name: S194


title: Placenta_Uninfected_mother_4

description: Library name: S190


title: O. tipulae Mutant, L1, Hi-C

description: Library name: Con_X_middle_Hi-C

data_processing:
Paired-end Hi-C reads were aligned to the Oscheius reference genome using Bowtie2, and contact matrices were generated with HiC-Pro. AllValidPairs files were converted to .hic format using hicpro2juicebox from HiC-Pro for downstream analysis. Standard HiC-Pro quality control metrics were computed for all samples, including mapping rates, valid interaction percentages, and trans/cis interaction ratios. Contact heatmaps were generated at a resolution of 10 kb using custom python codes and ICE-normalized data. Datasets were normalized between each other using counts per million reads (cpm).
Assembly: Oscheius tipulae ASM1342590v1
Supplementary files format and content: .hic

extract_protocol:
Synchronous L1 larvae from the wild-type strain and the mutant strain harboring the SFE consensus sequence in the middle of the X chromosome (con-X-middle) were used to construct two Hi-C libraries using the Arima-Hi-C 2.0 kit (Arima, Cat# A410110), as per the manufacturer’s protocol. The larvae were fixed using the low input protocol, with the following modification: larval membranes were disrupted by forcing cells through a metal dounce in 5 mL of PBS + TC fixative buffer kept chilled on ice. After cross-linking and digestion, samples were fragmented using the Covaris M220 ultrasonicator with the following settings: temperature = 7°C, peak incident power = 75 W, duty factor = 5%, cycles per burst = 200, time = 70 s. Samples were sonicated to fragments of ~500 bp, confirmed using a TapeStation 4200 (Agilent). Size selection was performed using AMPure XP magnetic beads (Beckman Coulter, Cat# A63881).
Illumina libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit (NEB Cat# E7645S). Libraries were amplified using the KAPA Library Amplification kit (Roche Cat# KK2620) according to the manufacturer’s protocols. The libraries were sequenced with an Illumina NovaSeq 6000.


title: O. tipulae WT, L1, Hi-C

description: Library name: CEW1_L1_Hi-C


title: GF1-KO Imm NK cells, Exp2, Rep3

status: Public on Mar 13 2026

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

data_processing:
Read quality was assessed and low quality reads trimmed with fastp.
Reads were mapped to the mouse genome (mm10) using STAR v2.7.10
After mapping, reads were quantified with featureCounts v2.0.1
Assembly: mm10
Supplementary files format and content: Read counts following mapping to mm10 using featurecount

organism: Mus musculus

source_name: spleen

extract_protocol:
RNA was extracted from NK cells using RNeasy Plus Micro kit (Qiagen)
Libraries were prepared with TruSeq Stranded Total RNA kit (Illumina) or NEBNext Single Cell/low Input Library prep kit (New England Biolabs).

value: spleen

value: NK cells


title: O. tipulae Mutant, 2-32cells, End-Seq

description: Library name: GGC_2L_End_seq

data_processing:
END-seq reads (R1 file only) were first mapped to the O. tipulae reference genome or the corresponding mutant genomes with Bowtie2 and processed with SAMtools. The 5’ position of each read was mapped, and its strand was determined with genomecov in BEDTools. This analysis determines the DSB and its resected ends and confirms END-seq enriches DSBs and telomeres. Following that, telomere-unique reads were identified as sequences containing two or more sequential telomeric repeats (TTAGGCTTAGGC). All telomere-unique reads were converted to the G-rich strand (TTAGGC). Fastx_clipper was then used to trim the telomeric sequences. These trimmed reads were mapped to the genome, and the telomere-unique junctions were used to identify the telomere addition sites.
Assembly: Oscheius tipulae ASM1342590v1
Supplementary files format and content: .bw

extract_protocol:
Egg-laying worms were washed off plates and passed through a 70-µm mesh. This step allows existing eggs to fall through the mesh, leaving the mature worms on the top. These worms were then bleached with sodium hypochlorite solution (Sigma Cat# 425044-250ML, 0.5 M NaOH, 3% bleach) to collect embryos (largely 2-4 cell stage, Fig. S1). Early embryos were further developed in Virgin S Basal (VSB) medium (100 mM NaCl, 5.7 mM K2HPO4, 44.1 mM KH2PO4) at 25°C to reach to the desired embryonic stages An adapted END-seq protocol was used (Canela et al. 2016, Wong et al. 2021). Briefly, embryos were embedded in agarose plugs to protect the DNA from exogenous breaks. DSBs were blunted with exonuclease VII (NEB, catalog # R0630) and exonuclease T (NEB, catalog # M0625). Blunt ends were A-tailed and capped with END-seq adaptor 1, a biotinylated hairpin adaptor. DNA was liberated from the plugs and sheared to ~200-300 bp with a Covaris M220 focused-ultrasonicator (130 µL tube, peak power 50, duty 16, cycles/burst 200 for 420 seconds). DNA fragments containing END-seq adaptor 1 were isolated with Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen, catalog # 65001). The other ends broken by sonication were repaired and A-tailed with END-seq adaptor 2. Hairpins were digested with USER (NEB, catalog # M5505).
The DNA was amplified with Illumina TruSeq primers and barcodes. The libraries were sequenced with an Illumina NovaSeq 6000.


title: MIA_1

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

description:
Library name: MIA_1_PLA
10X Genomics

data_processing:
Nuclei from individual replicates underwent strict quality control filtering and were normalized using SCTransform. Cells with ≥ 5% mitochondrial genes, ≤ 200, and ≥ 2,500 unique feature counts were excluded from the datasets. To remove nuclei free mRNA contamination, SoupX was run on each sample. Replicates were integrated using Harmony. Seurat v5 (R v4.2.1) was used to perform data normalization, dimensional reduction using PCA, and graph-based clustering with UMAP
Assembly: mm10
Supplementary files format and content: tab-delimited matrix file and value files for each sample

molecule: nuclear RNA

source_name: Placenta

growth_protocol: 6 mouse placenta (n=3 control, n=3 MIA) were extracted from E13.5 pregnant mice.

extract_protocol:
For single-nucleus sequencing, placentas from saline-exposed and poly(I:C)mod-treated male mice (n = 3) were snap-frozen in liquid nitrogen. Frozen tissues were thawed in 1 ml of high sucrose buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl₂, 20 mM Tricine-KOH, pH 7.8, 0.15 mM spermine tetrahydrochloride, 0.5 mM spermidine trihydrochloride, 1 mM DTT) in presence of RNAse inhibitors. The samples were mechanically dissociated using a dounce homogenizer containing IGEPAL CA-630 (Sigma-Aldrich). Nuclei were collected from interface of 30% and 40% of iodixanol after 18 minutes of density gradient ultracentrifugation at 10,000 g. Purified nuclei were counted using a hemocytometer.
Nuclei were extracted from placenta samples and processed using the 10x Genomics Chromium System. Libraries were sequenced using the Nextseq platform at the Centre for Applied Genomics (TCAG; The Hospital for Sick Children) in Toronto, ON, Canada.

treatment_protocol: Pregnant mice are intraperitoneally administered 20 mg/kg of poly(I:C), a synthetic double stranded RNA that predominantly (but not exclusively) binds Toll-like receptor 3 (TLR3) to induce the same innate immune pathways as a viral infection21,22. Administration of poly(I:C) (or saline as control) occurs at E12.5, and embryos were collected for study 24 hr later.

value: Placenta

tag: developmental age

value: PolyIC


title: Placenta_Uninfected_mother_3

description: Library name: S188


title: O. tipulae, 4-16cells, H3K4me3

description: Library name: CEW1_4-16cells_H3K4me3

data_processing:
Chromatin profiling datasets, including CUT&RUN for H3K9me3, H3K4me3 were processed using a uniform alignment and peak calling process. For alignment, reads were first mapped to the reference genome using Bowtie2. The resulting SAM files were converted to BAM format and sorted using SAMtools. To reduce PCR amplification artifacts, duplicate reads were removed using Picard’s MarkDuplicates tool http://broadinstitute.github.io/picard/. For normalization across chromatin marks for different staged embryos, duplicate-free BAM files were down sampled to a fixed depth of 10 million uniquely mapped reads using SAMtools with a fixed random seed to ensure reproducibility.  Peak calling was performed on normalized BAM files using MACS3. Peaks were identified using a stringent q-value cutoff of 0.01, and both narrowPeak and summits.bed files were retained for each dataset.
Assembly: Oscheius tipulae ASM1342590v1
Supplementary files format and content: .bw
Library strategy: CUT&Run

extract_protocol:
O. tipulae embryos were homogenized with a metal dounce tissue grinder and larvae were ground to a fine powder using a mortar and pestle with liquid nitrogen. Each CUT&RUN reaction used ~50 μL of packed embryos or tissue powder. CUT&RUN was performed using the CUTANA ChIC-CUT&RUN kit (Epicypher Cat#14-1048) according to the manufacturer’s protocol. For each reaction, 0.5 μg of antibody against H3K9me3 (CMA318) or H3K4me3 (CMA304) was used.
Library preparation was done using a 2S Plus DNA Library Kit from Swift/IDT (Swift Cat# 21024). The libraries were sequenced with an Illumina NovaSeq 6000


title: Blood_Non_transmitter_mother_7

description: Library name: 8652

source_name: Peripheral blood

value: Peripheral blood


title: O. tipulae, L1, H3K4me3

description: Library name: CEW1_L1_H3K4me3


title: O. tipulae, 36-250cells, H3K9me3

description: Library name: CEW1_36-250cells_H3K9me3


title: Blood_Uninfected_mother_11

description: Library name: 8591


title: O. tipulae, 2-8cells, H3K4me3

description: Library name: CEW1_2-8cells_H3K4me3


title: Blood_Non_transmitter_mother_6

description: Library name: 8541


title: Blood_Transmitter_mother_6

description: Library name: 8607


title: Placenta_Uninfected_mother_2

description: Library name: S171


title: Placenta_Uninfected_mother_1

description: Library name: S185


title: O. tipulae, L1, H3K9me3

description: Library name: CEW1_L1_H3K9me3


title: O. tipulae, 36-250cells, H3K4me3

description: Library name: CEW1_36-250cells_H3K4me3


title: Blood_Uninfected_mother_9

description: Library name: 8404


title: CNOT4_8h_rep2_ttseq

city: State College

first: Shardul

last: Kulkarni

state: PA

address: 463 North Frear Laboratory

institute: Penn State University

data_processing:
For libraries to caluculate changes in steadystate and RNA halflife  (Triptolide libraries), FASTQ files were further processed as per the Bulk RNA-seq Data Standards and Processing Pipeline (https://www.encodeproject.org/), using STAR [(Dobin et al. 2013), version - STAR_2.5.1b_modified] and RSEM (RNA-Seq by Expectation-Maximization) tool. The reads were mapped to hg38 (GRCh38) using Gencode-v29 comprehensive gene set, predicted tRNA genes, and the ERCC spike-in controls. Read-counts for each gene generated by RSEM were used for differential expression analysis using DESeq2 (Love et al., 2014, PMID: 25516281). Genes with a sum of ≥ 8 across both replicates and conditions were used in DESeq2. The expression data were normalized to ERCC spike in controls using estimateSizeFactors function in DESeq2.
TT-seq data was mapped to a human and S pombe concatenated genome reference sequence using STAR aligner. The alignments were filtered using samtools where alignments with a mapping quality < 7 were skipped and only proper pairs were selected. TT-Seq raw read counts were obtained for gene including exon and intron regions using featureCounts, Differential expression analysis was performed with DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw counts of each sample.
Supplementary files format and content: Excel files with DESeq2 output tables of differential expression analysis (TT-seq data). GSE308749_DESeq2_canonical_genes.xlsx: DESeq2 output tables for multiple comparisons (TT-seq [canonical genes]); GSE308749_DESeq2_IGRs.xlsx: DESeq2 output tables for multiple comparisons (TT-seq [Intergenic region windows]); GSE308749_DESeq2_rTEs.xlsx: DESeq2 output tables for multiple comparisons (TT-seq [retro-transposable elements]).

growth_protocol: Cells were maintained in complete media [Dulbecco's Modified Eagle Medium (DMEM) with 10% Fetal Bovine Serum, 1X glutamax and 1X Penicillin and Streptomycin] in 5% CO2 atmosphere at 37 °C in a humidified incubator.

extract_protocol:
To calculate changes in nascent RNA synthesis (TTseq): Parental (untagged), CNOT1AID and CNOT4AID cells were pretreated with 1mM auxin for 2 h, follwed by pulse labelling with 4-thiouridine (4SU) for 15 minutes, followed by total RNA extraction.
Total RNA was extracted from the cells using Trizol (Invitrogen#15596026) and cleaned up using PureLink RNA Mini kit (Invitrogen#12183018A)
For libraries to caluculate changes in steadystate and RNA halflife (Triptolide libraries), 500 ng of Turbo DNase digested RNA was mixed with 2 µl of 1:200 diluted ERCC Spike-in mix (Invitrogen#4456740) which was subjected to library preparation. TT-seq. libraries were prepared as described by Gregersen et al., 2020 (PMID: 31915390). Briefly, following depletion of desired protein, cells were treated with 4-thiouridine (4SU) for 15 minutes. The total RNA was extracted using Trizol and PureLink RNA Mini kit. RNA was mixed with that from S. pombe labelled with 4TU (as a spike in control). The labelled RNA was biotinylated using methanethiosulfonate (MTS)-biotin (Biotium#90065) and enriched using Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen#65001). 300 ng of RNA was subjected to library preparation. All the sequencing libraries were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina#20040525) according to manufacturer’s instructions. Sequencing was carried out at Genomics Research Incubator, Penn State University, USA using NextSeq™1000/2000 P2 Reagents(100Cycles) on NextSeq 2000.

treatment_protocol:
To calculate changes in steadystate RNA: Parental (untagged), CNOT1AID and CNOT4AID cells were treated with ± 1mM auxin for 8 h and 24 h, followed by total RNA extraction.
To calculate changes in RNA hallives: Parental (untagged), CNOT1AID and CNOT4AID cells were pretreated with 1mM auxin for 2 h, follwed by treatment with 1µM Triptlide for 0, 3, 6 and 12 h, followed by total RNA extraction.

value: Cells were treated with 1mM auxin for 8h; followed by 15' labelling with 4-thiouridine


title: CNOT4_8h_rep1_ttseq


title: Blood_Transmitter_mother_5

description: Library name: 8373


title: CNOT1_8h_rep2_ttseq


title: O. tipulae, 4-16cells, H3K9me3

description: Library name: CEW1_4-16cells_H3K9me3


title: O. tipulae, 2-8cells, H3K9me3

description: Library name: CEW1_2-8cells_H3K9me3


title: CNOT1_8h_rep1_ttseq


title: Mouse islets, 𝛂Glu, PA, S24

city: Lausanne

first: Cristina

last: Cosentino

address: Rue du Bugnon 9

department: Department of fundamental neurosciences

country: Switzerland

institute: Université de Lausanne

description: Library name: mi24_S24

data_processing:
Fastq files were submitted to QIAGEN RNA-seq Analysis Portal v 5.1 for annotation to the mouse genome reference (GRCm38.101) and normalization of counts.
Assembly: GRCm38.101
Supplementary files format and content: txt file containing normalized counts (RPKM, TPM, CPM) per samples

source_name: pancreatic islet cells

extract_protocol:
miRNeasy micro kit (Qiagen) was used to purified the total RNA
Illumina mRNA Stranded library kit was used following manifacturer instructions

value: pancreatic islet cells

value: Wild type

value: batch 2


title: Mouse islets, Ctr, PA, S23

description: Library name: mi23_S23


title: Blood_Uninfected_mother_8

description: Library name: 8308


title: WT_8h_rep2_ttseq

value: Parental


title: CNOT4_2h_rep2_ttseq

value: Cells were treated with 1mM auxin for 2h; followed by 15' labelling with 4-thiouridine


title: CNOT4_2h_rep1_ttseq


title: CNOT1_2h_rep2_ttseq


title: Blood_Non_transmitter_mother_3

description: Library name: 8268


title: Mouse islets, 𝛂Glu, BSA, S22

description: Library name: mi22_S22


title: CNOT1_2h_rep1_ttseq


title: Blood_Uninfected_mother_7

description: Library name: 8240


title: Blood_Non_transmitter_mother_4

description: Library name: 8306


title: Blood_Non_transmitter_mother_5

description: Library name: 8504


title: WT_2h_rep2_ttseq


title: Mouse islets, Ctr, BSA, S21

description: Library name: mi21_S21


title: WT_8h_rep1_ttseq


title: Mouse islets, 𝛂Glu, PA, S20

description: Library name: mi20_S20


title: Blood_Uninfected_mother_10

description: Library name: 8457


title: Mouse islets, Ctr, PA, S19

description: Library name: mi19_S19


title: Donor 4, LPS

city: CABA

first: Ignacio

middle: Gabriel

last: Mazzitelli

state: CABA

address: Paraguay 2155

country: Argentina

institute: INBIRS

description:
Library name: Sample 14
D4-LPS_S15

data_processing:
FastQ files were pseudoaligned to the human reference Ensembl transcriptome GRCh38 using Kallisto v.0.48.0,108 and raw count matrix was generated using tximport.118. Analysis was performed using Rstudio 2024.04.2+764, running R v. 4.4.0. DESeq2 R package was used for the analysis of differentially expressed genes
Assembly: GRCh38
Supplementary files format and content: comma separated values file includes raw counts for each sample
Supplementary files format and content: csv files includes raw counts for all samples

source_name: Neutrophils

growth_protocol: Human Neutrophils were cultered 4 h with 10% fetal bovine serum with 5% CO2 at 37

extract_protocol:
RNA was harvested using Monarch® RNA Purification Columns (New England Biolabs) 500 ug of RNA were used for library prep
mRNA was enriched via oligo-dT magnetic beads (KAPA mRNA HyperPrep Kit, Roche) from 300 ng of total RNA. Poly(A)+ RNA was fragmented (~250–300 bp) and reverse-transcribed to cDNA, followed by second-strand synthesis, A-tailing, and ligation of Illumina dual index adapters. Libraries were amplified (10 PCR cycles), purified with AMPure XP beads, quantified by qPCR, and sequenced as 150 bp paired-end reads on the Illumina NovaSeq platform.

treatment_protocol: Neutrophils were cultured with or without NaCl 50mM in the presence or absence of LPS 100 ng/ml

tag: donor id

value: Donor 4

value: Neutrophils

value: LPS 100 ng/ml


title: Donor 4, Control

description:
Library name: Sample 13
D4-CTL_S13

value: Control


title: Blood_Transmitter_mother_3

description: Library name: 8161


title: Blood_Transmitter_mother_4

description: Library name: 8166


title: Donor 4, NaCl

description:
Library name: Sample 15
D4-NA_S14

value: NaCl 50mM


title: Blood_Non_transmitter_mother_2

description: Library name: 8211


title: Donor 3, LPS

description:
Library name: Sample 10
D3-LPS_S11

value: Donor 3


title: Mouse islets, Ctr, BSA, S17

description: Library name: mi17_S17


title: Donor 4, Nacl+LPS

description:
Library name: Sample 16
D4-NA-LPS_S16

value: NaCl 50mM + LPS 100 ng/ml


title: Blood_Uninfected_mother_6

description: Library name: 8135


title: Mouse islets, 𝛂Glu, PA, S16

description: Library name: mi16_S16


title: Donor 3, Nacl+LPS

description:
Library name: Sample 12
D3-NA-LPS_S12


title: Donor 3, NaCl

description:
Library name: Sample 11
D3-NA_S10


title: Donor 3, Control

description:
Library name: Sample 9
D3-CTL_S9


title: Mouse islets, 𝛂Glu, BSA, S18

description: Library name: mi18_S18


title: Donor 2, NaCl

description:
Library name: Sample 7
D2-NA_S6

value: Donor 2


title: Blood_Uninfected_mother_5

description: Library name: 8042


title: WT_2h_rep1_ttseq


title: Donor 2, Nacl+LPS

description:
Library name: Sample 8
D2-NA-LPS_S8


title: Donor 2, Control

description:
Library name: Sample 5
D2-CTL_S5


title: Donor 2, LPS

description:
Library name: Sample 6
D2-LPS_S7


title: Mouse islets, 𝛂Glu, BSA, S14

description: Library name: mi14_S14


title: Mouse islets, Ctr, PA, S15

description: Library name: mi15_S15


title: Blood_Uninfected_mother_3

description: Library name: 7674


title: Blood_Transmitter_mother_2

description: Library name: 8036


title: Donor 1, Nacl+LPS

description:
Library name: Sample 4
D1-NA-LPS_S4

value: Donor 1


title: Donor 1, NaCl

description:
Library name: Sample 3
D1-NA_S2


title: Blood_Uninfected_mother_4

description: Library name: 7681


title: Mouse islets, Ctr, BSA, S13

description: Library name: mi13_S13


title: Blood_Non_transmitter_mother_1

description: Library name: 8118


title: NPC_ASVdTAG13_HiC_Rep1

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

description: Library name: 20250728_Sample29

data_processing:
Alignment (ChIP, HiC) was performed with Bowtie2
Alignment (RNA-Seq) was performed with STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from PCR-deduplicated .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM normalization. HiC contact maps were generated using Juicer and are usable in Juicebox.
Assembly: mm10
Supplementary files format and content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment, contact maps in .hic for HiC

source_name: ADNP-degron

growth_protocol: Mouse embryonic stem cells were grown in DMEM medium with 15% FBS, 25mM HEPES, 1x GlutaMAX, 1x non-essential amino acids, 100 U/mL penicillin-steptomycin, LIF, 3µM GSK inhibitor, 1µM MEK1/2 inhibitor at 37 ˚C.

extract_protocol:
ChIP for ADNP and CTCF was performed on cells as previously described (Trizzino et al., Cell Rep. 2018).
Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen).
HiC was performed using the Arima Genomics Hi-C+ for High Coverage kit.
rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760).
ChIP samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute.
HiC samples were prepared using the NEBNext Ultra II DNA Library Prep Kit with modifications according to the Arima Genomics Hi-C kit.

value: ADNP-degron

value: NPC

value: ASV + dTAG-13


title: Blood_Transmitter_mother_1

description: Library name: 7594

value: Peripheral blood


title: Donor 1, LPS

description:
Library name: Sample 2
D1-LPS_S3


title: Mouse islets, 𝛂Glu, BSA, S10

description: Library name: mi10_S10

value: pancreatic islet cells

value: Wild type

value: batch 1


title: Mouse islets, Ctr, PA, S11

description: Library name: mi11_S11


title: Blood_Uninfected_mother_2

description: Library name: 7576


title: Mouse islets, 𝛂Glu, PA, S12

description: Library name: mi12_S12


title: NPC_ASVdTAG13_HiC_Rep2

description: Library name: 20250728_Sample30


title: Mouse islets, Ctr, BSA, S9

description: Library name: mi9_S9


title: Donor 1, Control

description:
Library name: Sample 1
D1-CTL_S1


title: NPC_ASVdTAG13_RNA_Rep3

description: Library name: 20250728_Sample26


title: NPC_ASVdTAG13_RNA_Rep2

description: Library name: 20250728_Sample25


title: mESC_ASVdTAG13_ADNP

description: Library name: 20250728_Sample31

value: mESC

tag: chip antibody

value: ADNP


title: NPC_Control_HiC_Rep1

description: Library name: 20250728_Sample27


title: Blood_Uninfected_mother_1

description: Library name: 7464


title: NPC_Control_HiC_Rep2

description: Library name: 20250728_Sample28


title: Mouse islets, Ctr, PA, S7

description: Library name: mi7_S7


title: SIRT7 knockdown in hiPSC-CM, biological replicate #3

city: Washington

first: Emilia

last: Entcheva

state: DC

address: 800 22nd Street NW SEH 5000

department: Biomedical Engineering

institute: George Washington University

description: Library name: S7.BR3

data_processing:
fastQC quality check, STAR alignment
FeatureCount for gene expression quantification, Deseq2 for differential gene expression
Assembly: GRCh38 reference genome
Supplementary files format and content: Processed data contains TPM counts for all samples. Zero-values have been removed. Ensembl gene accesssion numbers are provided in the first column.

source_name: hiPSC-CM

growth_protocol: Commercially differentiated human induced pluripotent stem cell derived cardiomycytes (Fujifilm) were thawed and plated according to manufacturers instructions at 150,000 cells/well 48-well format. Maintenance media was exchanged every two days.

extract_protocol:
On cell culture day 7, samples were lysed using TRIzol Reagent (Invitrogen), according to manufacturer's protocol.
RNA-seq library preperation

treatment_protocol: On cell culture day 5, cells were treated small interfering RNAs (siRNA) targeting each individual HDAC or SIRT gene (or scrambled negative control siRNA). Note that siRNAs targeting HDAC10 and SIRT1 were not available to us at the time, thus were not included in this study. Transfection media was replaced with normal maintenance media on cell culture day 7.

value: hiPSC-CM

value: stem cell derived cardiomyocytes

value: gene knockdown by short interfering RNA

value: B


title: NPC_Control_RNA_Rep3

description: Library name: 20250728_Sample23

value: Control


title: SIRT7 knockdown in hiPSC-CM, biological replicate #2

description: Library name: S7.BR2


title: Mouse islets, 𝛂Glu, PA, S8

description: Library name: mi8_S8


title: NPC_Control_RNA_Rep1

description: Library name: 20250728_Sample21


title: SIRT7 knockdown in hiPSC-CM, biological replicate #1

description: Library name: S7.BR1


title: Mouse islets, Ctr, BSA, S5

description: Library name: mi5_S5


title: mESC_Control_RNA_Rep3

description: Library name: 20250728_Sample20


title: Mouse islets, 𝛂Glu, PA, S4

description: Library name: mi4_S4


title: NPC_ASVdTAG13_Input

description: Library name: 20250728_Sample17

value: Input


title: mESC_Control_RNA_Rep1

description: Library name: 20250728_Sample18


title: NPC_ASVdTAG13_ADNP

description: Library name: 20250728_Sample16


title: mESC_Control_RNA_Rep2

description: Library name: 20250728_Sample19


title: SIRT6 knockdown in hiPSC-CM, biological replicate #3

description: Library name: S6.BR3


title: NPC_Control_RNA_Rep2

description: Library name: 20250728_Sample22


title: NPC_ASVdTAG13_CTCF_Rep2

description: Library name: 20250728_Sample15

value: CTCF


title: NPC_ASVdTAG13_RNA_Rep1

description: Library name: 20250728_Sample24


title: NPC_Control_Input

description: Library name: 20250728_Sample13


title: NPC_ASVdTAG13_CTCF_Rep1

description: Library name: 20250728_Sample14


title: SIRT6 knockdown in hiPSC-CM, biological replicate #2

description: Library name: S6.BR2


title: Mouse islets, Ctr, PA, S3

description: Library name: mi3_S3


title: SIRT6 knockdown in hiPSC-CM, biological replicate #1

description: Library name: S6.BR1


title: NPC_Control_ADNP_Rep2

description: Library name: 20250728_Sample12


title: Mouse islets, 𝛂Glu, BSA, S6

description: Library name: mi6_S6


title: Mouse islets, Ctr, BSA, S1

description: Library name: mi1_S1


title: SIRT5 knockdown in hiPSC-CM, biological replicate #3

description: Library name: S5.BR3


title: NPC_Control_ADNP_Rep1

description: Library name: 20250728_Sample11


title: NPC_Control_CTCF_Rep2

description: Library name: 20250728_Sample10


title: mESC_ASVdTAG13_Input

description: Library name: 20250728_Sample8


title: SIRT5 knockdown in hiPSC-CM, biological replicate #2

description: Library name: S5.BR2


title: Mouse islets, 𝛂Glu, BSA, S2

description: Library name: mi2_S2


title: Thymic_Carcinoma_2

city: Vienna

first: Martin

last: Direder

state: Vienna

address: Lazarettgasse 14

department: Orthopedic and Trauma Surgery

country: Austria

institute: Medical University Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome and counted using Cell Ranger (version 5.0.1; 10x Genomics).
Assembly: GrCh38
Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI counts for each sample

source_name: thymic carcinoma

extract_protocol:
Tissue samples dissociated using MACS Miltenyi Tumor  Dissociation Kit for mouse (Miltenyi)
libraries were prepared using Chromium Next GEM Single Cell 5´GEM, Library & Gel Bead Kit v5.2, Chromium Nexxt GEM Chip K Single Cell Kit and Single Index Kit TT Set A (all 10x Genomics, Pleasanton, CA, USA)

value: thymic carcinoma

value: Male


title: mESC_ASVdTAG13_CTCF_Rep2

description: Library name: 20250728_Sample7

value: ADNP-degron


title: SIRT4 knockdown in hiPSC-CM, biological replicate #3

description: Library name: S4.BR3


title: SIRT5 knockdown in hiPSC-CM, biological replicate #1

description: Library name: S5.BR1


title: mESC_Control_Input

description: Library name: 20250728_Sample5


title: TTH4

source_name: true thymic hyperplasia

value: true thymic hyperplasia

value: Female


title: SIRT3 knockdown in hiPSC-CM, biological replicate #3

description: Library name: S3.BR3


title: TTH3


title: mESC_Control_CTCF_Rep2

description: Library name: 20250728_Sample2


title: Thymic_Carcinoma_1


title: mESC_Control_CTCF_Rep1

description: Library name: 20250728_Sample1


title: Day_5_Limbal injury, rep1

city: Haifa

first: Shalini

last: Dimri-Wagh

state: Haifa

address: 1 Efron Street

department: Department of  Genetics and Developmental Biology

country: Israel

institute: Technion Israel Institute of Technology

description: Library name: Sample_3

data_processing:
Single-cell 3’ RNA-seq data were processed using Cell Ranger v4.0.0. Reads were aligned, filtered, and UMIs counted with the count function, mapping to the mm10 genome (GRCm38.84) supplemented with the eGFP sequence.
Assembly: mm10
Supplementary files format and content: Processed data are provided as  tab-delimited files (matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz) generated using the Cell Ranger pipeline from 10x Genomics. These include raw UMI counts for each gene in each cell across samples.

source_name: Cornea

extract_protocol:
Eyes were enucleated and cleaned to remove the lens and iris. The limbal region and underlying stroma, along with the adjoining conjunctival and peripheral corneal tissue (~0.5 mm), were dissected under a fluorescent binocular microscope. The collected tissue was incubated in Collagenase A (2 mg/ml) for 1 hour at 37°C, followed by a PBS wash and further incubation in Trypsin for 1 hour at 37°C. The resulting cell suspension was passed through a 40 µm cell strainer to obtain a single-cell suspension.
Single-cell RNA libraries were prepared using the 10x Genomics Chromium Next GEM 3’ Kit v3.1 with ~10,000 input cells per sample. Libraries were sequenced on an Illumina NextSeq 2000 (P3 100-cycle kit) with paired-end reads: 28 bp (Read 1), 90 bp (Read 2), and 10 bp indices.

treatment_protocol: Krt15-GFP transgenic mice with constitutive GFP expression were used. No induction of GFP expression was required.

value: Cornea

value: Limbal epithelial+ Stromal cells

value: Batch 1


title: mESC_Control_ADNP_Rep2

description: Library name: 20250728_Sample4

value: mESC


title: SIRT4 knockdown in hiPSC-CM, biological replicate #1

description: Library name: S4.BR1


title: Day_40_Limbal injury, rep1

description: Library name: Sample_5


title: B2_Thymoma

source_name: thymoma

value: thymoma


title: NPC_Control_CTCF_Rep1

description: Library name: 20250728_Sample9

value: NPC


title: mESC_Control_ADNP_Rep1

description: Library name: 20250728_Sample3

value: ADNP


title: SIRT2 knockdown in hiPSC-CM, biological replicate #3

description: Library name: S2.BR3

value: hiPSC-CM

value: stem cell derived cardiomyocytes

value: gene knockdown by short interfering RNA


title: P21TertCI_HFD_rep140

city: Marseille

first: Laura

last: BRAUD

address: 27 boulevard Leï Roure

country: France

institute: Institut Paoli Calmettes (IPC)

data_processing:
Sequenced libraries were then de-multiplexed and analysed using CellRanger v5.0.1 and bcl2fastq v2.20.0. Individual libraries were de-multiplexed with CellRanger mkfastq (allowing 1 mismatches) and the CellRanger count pipeline was used to align to the mouse genome (customized with mouse genotype alleles) and count UMIs.
Assembly: mm39
Supplementary files format and content: tab-separated values files and matrix files

source_name: Visceral White Adipose tissue

extract_protocol:
Single nucleus sequencing was carried out using visceral WAT (snap frozen and stored at -80C) in n=2 mice per group. WAT samples were processed in batches of n=2, randomizing the order, to minimize between condition batch effects. Frozen WAT (approx. 200mg) was cut into small pieces <0.2cm and homogenized with ice cold lysis buffer (Tris-HCL 10mM, NaCl 10mM, MgCl2 3mM, 0.1% NP40, 0.2U/µl RNase inhibitor) in a glass dounce homogenizer. Following homogenization, the sample was filtered through a 100µM cell strainer and centrifuged at 500 x g and 4oC for 5mins. After lipid layer and supernatant removal, the nuclei pellet was resuspended in wash buffer (PBS + 1% BSA and 0.2U/µl RNase inhibitor) and recentrifuged at 500 x g and 4°C for 5mins. Isolated nuclei were then resuspended in wash buffer with DAPI (0.1µg/ml) and filtered through 35µM cell strainer into a FACS tube. Stained nuclei were sorted by flow cytometry using the BD FACS Aria III (85-microm nozel) to remove excess lipid/debris and clumped nuclei, applying the following sequential gates: i. FSC-A and SSC-A; ii. FSC-H and FSC-A; iii. FSC-A and 450/40V-A. Nuclei were sorted into cold (4C) BSA and RNase-inhibitor rich collection buffer to prevent re-clumping and RNA degradation; final nuclei suspension post-FACS concentrations (BSA ~2% and RNase inhibitor ~0.3U/µl).
An estimated ~5-10K nuclei per sample were loaded onto Chromium Next GEM Single Cell 3’ Chips for GEM generation and barcoding, followed by clean up, cDNA amplification (10-12 cycles) and library construction, according to 10X manufacturer instructions. Single Cell 3ʹ Gene Expression libraries were quantified using the Agilent Bioanalyzer (High Sensitivity chip), and pooled for sequencing (Nextseq2000), aiming for a final sequencing depth of >20K reads/called-cell/sample.

value: Visceral White Adipose tissue

value: Primary cells

value: High Fat diet (HFD)


title: Uninjured_Control, rep1

description: Library name: Sample_1


title: SIRT4 knockdown in hiPSC-CM, biological replicate #2

description: Library name: S4.BR2

value: B


title: TTH2

value: Male


title: Day_10_Limbal injury, rep1

description: Library name: Sample_4


title: P21Tert_HFD_rep134


title: B2_B3_Thymoma


title: P21TertCI_HFD_rep138


title: SIRT3 knockdown in hiPSC-CM, biological replicate #1

description: Library name: S3.BR1


title: mESC_ASVdTAG13_CTCF_Rep1

description: Library name: 20250728_Sample6

value: ADNP-degron

value: ASV + dTAG-13

value: CTCF


title: Day_2_Limbal injury, rep1

description: Library name: Sample_2

value: Cornea

value: Limbal epithelial+ Stromal cells


title: SIRT3 knockdown in hiPSC-CM, biological replicate #2

description: Library name: S3.BR2


title: TTH1

value: true thymic hyperplasia


title: B1_Thymoma_2

value: thymoma


title: P21Tert_HFD_rep136


title: P21het_HFD_rep128


title: P21het_HFD_rep129


title: P21het_SD_rep144

value: Standard diet (SD)


title: SIRT2 knockdown in hiPSC-CM, biological replicate #1

description: Library name: S2.BR1


title: B1_Thymoma_1


title: P21het_SD_rep146


title: PGW9-2-5P-r1

type: RNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: Slices were placed on Merscope slides (Vizgen, #10500102) and processed according to the manufacturer’s user guides

scan_protocol: Cell boundary staining, gel embedding, clearing, and probe hybridization steps were performed without modification from the fresh-frozen sample preparation guide. Samples were imaged on the MERSCOPE instrument using the 300-plex imaging kit.

data_processing: Data processing was done using the in-instrument software MERLIN pipeline provided by Vizgen.

source_name: human fetus

extract_protocol: Fresh frozen 14 μm coronal samples, cryosectioned using a CM3050 Leica cryostat, from the fronto-nasal region.

tag: developmental stage

tag: side

value: posterior section


title: King nuclei, whole body

city: Sydney

first: Catherine

middle: Rose

last: Gatt

state: NSW

address: UNSW Sydney High St Kensington

department: School of Clinical Medicine

institute: University of New South Wales

description:
Library name: King
10X Genomics
features.tsv.gz

data_processing:
Raw fastq reads from each caste (queen, king, soldier, worker) were aligned to the Z. nevadensis reference genome. A custom reference genome of Z. nevadensis was generated using Cell Ranger mkref v8.0.0 37. A cell count matrix of all the castes was then generated using Cell Ranger count v8.0.0 37 with default parameters.
A combined cell count matrix of all the castes was then generated using Cell Ranger aggr v8.0.0 37 with default parameters.
The Cell Ranger aggr v8.0.0 37 barcode and matrix output files were separated by sample (caste; king, queen, soldier, worker).
Automated cell type labels were obtained using SATURN-xfer. Cell type annotations were cross-referenced with curated marker genes from the D. melanogaster single-cell atlas.
Assembly: Liu, C. et al. Unravelling the evolution of wood-feeding in termites with 47 high-resolution genome assemblies. Nat. Commun. 16, 11154 (2025)
Supplementary files format and content: Cell Ranger output files: tab separated values files and matrix files.
Supplementary files format and content: znev_all_castes.h5ad: gene expression count matrix of all castes and nuclei, with annotated cell types.

organism: Zootermopsis nevadensis

source_name: whole body

extract_protocol:
Dissociation and isolation of single nuclei from the whole body of each sample was performed using an adapted version of a protocol established for Drosophila 36. Briefly, 100 μl of homogenisation buffer was dispensed into an DNA LoBind 1.5 ml tube (Eppendorf 022431021) and placed on ice. The homogenisation buffer consisted of nuclease free water, 250 mM nuclease free sucrose (FUJIFILM Wako Pure Chemical Industries, Ltd. 19-0001), 10 mM Tris (pH 8.0) (Nippon Gene 312-90061), 25 mM KCl (Cayman Chemical Company 600213), 5 mM MgCl2 (Serva 39772), 0.1% Triton-x 100 (FUJIFILM Wako Pure Chemical Industries, Ltd. 168-11805), 0.5% RNasin Plus (Promega N261B), 1× protease inhibitor (Promega G6521), and 0.1 mM DTT (Formedium Ltd. DTT005). Samples were placed into the homogenisation buffer and nuclei were released by approximately 20 gentle strokes of a plastic pestle (Violamo 1-2955-01) and an additional 900 μl of homogenisation buffer was added to the tube. Each sample was centrifuged (Eppendorf 5424R) at 1000 g for 10 minutes at 4°C, the supernatant was discarded, and the nuclei were resuspended in a 1000 μl of resuspension buffer on ice. The resuspension buffer consisted of 1× PBS (pH 7.4) (Thermo Fisher 2669978), 0.5% BSA (Wako Pure Chemical Industries, Ltd. 017-21273), and 0.5% RNasin Plus (Promega N261B). Each sample was then passed twice through a 100 µm cell strainer (As One 100-98-5) and placed into a 5 ml FACS tube (Falcon 352235) with a 35 µm cap for FACS sorting. Following dissociation, nuclei were stained with 1 μl of DAPI and were isolated from remaining debris with Fluorescence Activated Cell Sorting (FACS) using a BD FACSAria III. The worker sample was sorted into a 1.5 ml tube containing 400 μl of resuspension buffer. The queen, soldier, and king samples were sorted into 1.5 ml tubes containing 200 μl of resuspension buffer. Immediately after FACS sorting, nuclei were centrifuged at 1000 g for 10 minutes at 4°C and the 700 μl of supernatant was discarded. Nuclei were resuspended in the remaining 50-60 μl of supernatant, and the concentration of nuclei was calculated using a Thoma cell counting plate (Watson 177312C) with a ZEISS Axio Scope A.1 microscope.
Sequencing was performed as per the 10x Genomics User Guide (CG000315 Rev E). Gel Beads-in-emulsion (GEMs) were generated using the Chromium X Instrument (10x Genomics, Pleasanton, CA, USA), and scRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (Dual Index). The worker sample was loaded in the Chromium Next GEM Chip G with a target output of 10,000 nuclei, and the queen, soldier, and king samples were loaded in the Chromium Next GEM Chip G with a target output of 5,000 nuclei. All reactions were performed in the Eppendorf Mastercycler X50s with a 96-Deep Well Reaction Module. For both cDNA amplification and sample index PCR, 14 cycles were used across all samples.Sequencing was performed in-house on the NovaSeq 6000 platform

value: whole body

tag: caste

value: King


title: SIRT2 knockdown in hiPSC-CM, biological replicate #2

description: Library name: S2.BR2

value: hiPSC-CM

tag: cell type

value: stem cell derived cardiomyocytes

tag: treatment

value: gene knockdown by short interfering RNA


title: PGW9-2-5P-r0


title: Queen nuclei, whole body

description:
Library name: Queen
10X Genomics
features.tsv.gz

value: Queen


title: Untreated hiPSC-CM, biological replicate #5

description: Library name: U2.BR1

value: B


title: Untreated hiPSC-CM, biological replicate #6

description: Library name: U2.BR2


title: PGW9-2-2A-r0

value: anterior section


title: Worker nuclei, whole body

description:
Library name: Worker
10X Genomics
features.tsv.gz

value: Worker


title: PGW9-2-2A-r1


title: Untreated hiPSC-CM, biological replicate #7

description: Library name: U2.BR3


title: Untreated hiPSC-CM, biological replicate #4

description: Library name: U1.BR4

value: A