title: snRNASeq, human brain section, frontal lobe, control, rep2

city: Bethesda

first: Mark

middle: R

last: Cookson

state: MD

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

description: Library name: HBS1_UNT2

data_processing:
Paired‑end sequencing was performed on Illumina NextSeq 2000. Samples were processed using the Cell Ranger count pipeline (v7.2.0, May 2025) for gene expression data, including intronic reads, with the reference genome refdata‑gex‑GRCh38‑2024‑A.
Assembly: GRCh38
Supplementary files format and content: Rdata file with cell type annotations

source_name: frontal lobe

extract_protocol:
Sections were frozen and processed using the 10x Genomics single-cell nuclei isolation kit (PN-1000494)
~10,000 nuclei per sample per treatment were isolated and processed using the 10x Genomics Single Cell 3’ Gene Expression kit (cat #1000128)

treatment_protocol: Human cortical brain tissue from epilepsy surgery patients (a 27-year-old female, frontal lobe; and a 36-year-old male, anterior temporal cortex) was sectioned into 300 μm slices, halved, and incubated with or without 25 ng/mL IFN-γ in aCSF for 6 hours.

value: frontal lobe

value: untreated


title: REI_POWR167

status: Public on Mar 26 2026

type: genomic

city: Atlanta

first: Alicia

middle: K

last: Smith

state: GA

address: 101 Woodruff Circle NE

country: USA

institute: Emory University

hyb_protocol: Bisulfite conveted DNA was fragmented and hybridized according to MethylationEPICv2 (Illumina) standard protocol

scan_protocol: Array was imaged with HiScan and standard Illumina settings

data_processing:
Enmix package
*processed value definition: Average betas

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from blood using QiaQuick (Qiagen) kit using standard protocol

tag: tissue

value: Blood

tag: Sex

value: Female

tag: subject group

value: Fertile


title: snRNASeq, human brain section, frontal lobe, control, rep1

type: SRA

description: Library name: HBS1_UNT1

library_source: transcriptomic single cell

molecule: total RNA

source_name: temporal lobe

value: temporal lobe

tag: treatment


title: REI_POWR358


title: REI_POWR162


title: DNMT1_KO_h3k9me3_chip_rep_2_chip_seq

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description:
Library name: DNMT1_KO_h3k9me3_chip_rep_2_chip_seq
DNMT1_KO_h3k9me3_rep_2_chip_seq.bigWig

library_source: genomic

data_processing:
Fastq files were quality checked using FastQC (v0.11.4) and reads trimmed using TrimGalore (v0.4.1). Reads were then mapped to the genome (hg38) using bowtie2 (v2.3.1 with settings: -N 1 -L 20 --no-unal) (Langmead & Salzberg, 2012) for paired end data. Low mapping quality reads or fragments were removed using samtools (v1.6 with settings -bq 10). Duplicate reads were removed using sambamba markdup (v0.5.9, for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 ChIP-seq) or using UMI tools dedup function (v1.0.0 and setting: --paired, DNMT3A/B and H3K36me2 ChIP-seq). The number of reads pre- and post- alignment as well as the reads after deduplication and low mapping was then extracted and counted. Bed counts for 10 kb genomic windows and domains were generated from the bam files using bedtools coverage (seetings: -counts, v2.27.1). For paired-end data, the BAM file was first converted to a BED file of fragment locations using BEDtools bamtobed function. Coverage counts were scaled to counts per 10 million based on total number of mapped reads per sample and divided by the input read count to obtain a normalised read count. An offset of 0.5 was added to all windows prior to scaling and input normalisation to prevent intervals with zero reads in the input sample generating a normalised count of infinity. Regions where coverage was 0 in all samples were removed from the analysis. BigWig files for visualisation in the genome browser were generated, by calculating counts per million mapped reads using bamCoverage from deeptools (v3.2.0). Normalisation over inputs and means between replicas were then performed using bigwigCompare ratio and mean respectively. For a summary of ChIP-seq alignment statistics, see Supplementary Tables 4-9.
Assembly: hg38
Supplementary files format and content: Processed data files are bigWig files generated by normalisation over input as described under data processing.

source_name: HCT116 DNMT1 KO

growth_protocol: HCT116 and DNMT1 KO cells were gifts from B. Vogelstein (Rhee et al., 2000). Cells were cultured in McCoy’s 5A (Gibco) supplemented with 10% Fetal Calf Serum (Life Technologies) and penicillin–streptomycin antibiotics at 140 and 400 μg/ml, respectively at 37°C with 5% CO2. Cell lines were routinely tested for mycoplasma contamination. DNMT1 KO genotype was confirmed by western blot and sequencing.

extract_protocol:
ChIP-seq was performed as previously described (Masalmeh et al., 2021; Taglini et al., 2024). For T7-DNMT3B and T7-DNMT3A ChIP-seq experiments, 1×107 cells were harvested, washed and crosslinked with 1% methanol-free formaldehyde in PBS for 8 min at room temperature. Crosslinked cells were lysed for 10 min on ice in 50 μl of lysis buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 1 mM EDTA, 1% SDS) freshly supplemented with proteinase inhibitor (Sigma-Aldrich). IP dilution buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 1 mM EDTA, 0.1% Triton X-100) freshly supplemented with proteinase inhibitor, DTT and PMSF was added to the samples to reach a final volume of 500 μl. Chromatin was fragmented using Benzonase (Pchelintsev et al, 2016): samples were sonicated on ice with Soniprep 150 twice for 30 s to break up nuclei; then 200 U of Benzonase Nuclease (Sigma) and MgCl2 (final concentration 2.5 mM) were added and samples were incubated on ice for 15 min. The reaction was blocked by adding 10 μl of 0.5 M EDTA pH 8. Following centrifugation for 30 min at 18,407 g at 4 °C, supernatants were collected and supplemented with Triton X-100 (final concentration 1%) and 5% input aliquots were retained for later use. Protein A Dynabeads (Invitrogen) previously coupled with 10 μl of T7-Tag antibody per 1×107 cells in blocking solution (1x PBS, 0.5% BSA) were added and the samples incubated overnight under rotation at 4 °C. Beads were then washed for 10 min at 4 °C with the following buffers: IP dilution buffer 1% Triton X-100 (20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), buffer A (50mM HEPES pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), buffer B (20 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate), TE buffer (1mM EDTA pH 8, 10 mM Tris pH 8). Chromatin was eluted by incubating the beads in extraction buffer (0.1 M NaHCO3, 1% SDS) for 15 min at 37 °C. To reverse the cross-linking Tris-HCl pH 6.8 and NaCl were added to final concentrations of 130 mM and 300 mM respectively, and immunoprecipitations were incubated at 65 °C overnight. Samples were then incubated at 37 °C for 1 h after addition of 2 μl of RNase Cocktail Enzyme Mix (Ambion). Then 40 μg of Proteinase K (Roche) were added, followed by 2 h incubation at 55 °C. Input material was similarly de-crosslinked. Samples were purified with the MinElute PCR purification kit (QIAGEN). For ChIP-Rx-seq of ectopic T7-DNMT3B and T7-DNMT3A 20 μg of Spike-in chromatin (ActiveMotif 53083) was added to each sample after sonication. 2 μl of spike-in antibody per sample (ActiveMotif 61686) was also added in a ratio 1:5 versus the T7 antibody. A similar protocol was used for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 ChIP-seq experiments, except: 0.5×107 cells were harvested and crosslinked with 1% methanol-free formaldehyde in PBS for 5 min at room temperature. For H3K36me3 ChIP-Rx-seq crosslinked Drosophila S2 cells were spiked into samples before sonication at a ratio of 20:1 human to Drosophila cells. Following nuclei rupture by sonication on ice with Soniprep 150, chromatin was fragmented using Bioruptor Plus sonicator (Diagenode) for 40 cycles (30 s on/30 s off on high setting at 4 °C). 2 μl /1×106 cells of the following antibodies were used for immunoprecipitations: H3K4me3 (EpiCypher 13-00041), H3K9me3 (Active Motif 39161), H3K27me3 (Cell Signaling Technology C36B11) and H3K36me3 (Abcam ab9050).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) barcode adapters according to the manufacturer instructions. were used. Specifically, Illumina Index Primers Set 1 (E7335) for H3K36me3, and Unique Dual Index UMI Adaptors DNA Set 1 (E7395) for the other libraries. For histone modifications ChIP-seq, adapter-ligated DNA was size selected for an insert size of 150 bp using Agencourt AMPure XP beads. Libraries were quantified using the Qubit dsDNA HS or BR assay kit and assessed for size and quality using the Agilent Bioanalyser. H3K36me3 ChIP-Rx-seq libraries were sequenced using the NextSeq 500/550 high-output version 2.5 kit (75 bp single end reads). The other ChIP-seq libraries were sequenced using the NextSeq 2000 P3 (50 bp paired end reads). Libraries were combined into equimolar pools to run within individual flow cells. Sequencing was performed at the Edinburgh Clinical Research Facility.

tag: cell line

value: HCT116 DNMT1 KO

tag: cell type

value: colorectal cancer cell line

tag: genotype

value: DNMT1 KO

tag: chip antibody

value: H3K9me3 (Active Motif 39161)


title: Blood, HTP_II, RNA-seq, S30

city: Madrid

first: Ana I

last: Fernandez-Avila

state: Madrid

address: C/ Doctor Esquerdo, 46

department: Cardiology

country: Spain

institute: Hospital GU Gregorio Marañon

description:
Library name: 1A-038
column_name_in_FPKM_allSamples: 1A-038

library_source: transcriptomic

data_processing:
Sequencing was conducted in four randomized batches. FASTQ files from sequencing were aligned to the reference genome (hg38) with and transcript quantification was conducted with Salmon
FPKM were extracted with DESeq2 in a generalized linear modeling, adjusting for age, sex, body surface area, and sequencing batch
Assembly: hg38
Supplementary files format and content: FPKM in a csv file, samples (columns) and genes (rows)

source_name: whole blood

extract_protocol:
Tempus collection tube_Tempus RNA isolation kit
TruSeq Stranded Total RNA Library Prep Globin Kit , following guide

value: whole blood

tag: sample group

value: HTP

tag: batch


title: DNMT1_KO_h3k27me3_chip_rep_2_chip_seq

description:
Library name: DNMT1_KO_h3k27me3_chip_rep_2_chip_seq
DNMT1_KO_h3k27me3_rep_2_chip_seq.bigWig

value: H3K27me3 (Cell Signaling Technology C36B11)


description:
Library name: DNMT1_KO_h3k9me3_h3K27me3_in_rep_2_chip_seq
DNMT1_KO_h3k9me3_rep_2_chip_seq.bigWig
DNMT1_KO_h3k27me3_rep_1_chip_seq.bigWig

value: none (input)


title: DNMT1_KO_h3k27me3_chip_rep_1_chip_seq

description:
Library name: DNMT1_KO_h3k27me3_chip_rep_1_chip_seq
DNMT1_KO_h3k27me3_rep_1_chip_seq.bigWig


title: Blood, HTP_II, RNA-seq, S39

description:
Library name: 1A-047
column_name_in_FPKM_allSamples: 1A-047

value: Male


description:
Library name: DNMT1_KO_h3k9me3_h3K27me3_in_rep_1_chip_seq
DNMT1_KO_h3k9me3_rep_1_chip_seq.bigWig
DNMT1_KO_h3k27me3_rep_1_chip_seq.bigWig


title: DNMT1_KO_h3k4me3_in_rep_2_chip_seq

description:
Library name: DNMT1_KO_h3k4me3_in_rep_2_chip_seq
DNMT1_KO_h3k4me3_rep_2_chip_seq.bigWig


title: Blood, HTP_II, RNA-seq, S26

description:
Library name: 1A-031
column_name_in_FPKM_allSamples: 1A-031


title: snRNASeq, human brain section, frontal lobe, IFN-γ treatment, rep1

description: Library name: HBS2_IFN1

value: IFN-γ treated


title: DNMT1_KO_h3k9me3_chip_rep_1_chip_seq

description:
Library name: DNMT1_KO_h3k9me3_chip_rep_1_chip_seq
DNMT1_KO_h3k9me3_rep_1_chip_seq.bigWig


title: Blood, HTP_II, RNA-seq, S29

description:
Library name: 1A-036
column_name_in_FPKM_allSamples: 1A-036


title: REI_POWR511


title: DNMT1_KO_h3k4me3_chip_rep_2_chip_seq

description:
Library name: DNMT1_KO_h3k4me3_chip_rep_2_chip_seq
DNMT1_KO_h3k4me3_rep_2_chip_seq.bigWig

value: H3K4me3 (EpiCypher 13-00041)


title: Blood, HTP_II, RNA-seq, S25

description:
Library name: 1A-021
column_name_in_FPKM_allSamples: 1A-021


title: Blood, HTP_II, RNA-seq, S27

description:
Library name: 1A-032
column_name_in_FPKM_allSamples: 1A-032


title: DNMT1_KO_h3k4me3_in_rep_1_chip_seq

description:
Library name: DNMT1_KO_h3k4me3_in_rep_1_chip_seq
DNMT1_KO_h3k4me3_rep_1_chip_seq.bigWig


title: snRNASeq, human brain section, frontal lobe, IFN-γ treatment, rep2

description: Library name: HBS2_IFN2

value: frontal lobe


title: DNMT1_KO_h3k4me3_chip_rep_1_chip_seq

description:
Library name: DNMT1_KO_h3k4me3_chip_rep_1_chip_seq
DNMT1_KO_h3k4me3_rep_1_chip_seq.bigWig


title: Blood, HTP_II, RNA-seq, S28

description:
Library name: 1A-033
column_name_in_FPKM_allSamples: 1A-033


title: DNMT1_KO_h3k36me2_in_rep_2_chip_seq

description:
Library name: DNMT1_KO_h3k36me2_in_rep_2_chip_seq
DNMT1_KO_h3k36me2_rep_2_chip_seq.bigWig

extract_protocol:
For H3K36me2, native ChIP-seq was performed adapting ultra-low-input (ULI) ChIP (Brind'Amour & Lorincz, 2022) as follows. Nuclei were isolated from 1x106 unfixed cells using PBS 0.1% NP-40 and resuspended in 75 μl of Nuclear Isolation buffer (10mM Tris HCl, 0.1% NaDeOx, 0.1% Triton-100) and 75 μl of 2X MNase digestion Buffer (NEB). Chromatin was digested using MNase (NEB) for 6 min at 37 °C. Enzyme concentration was determined experimentally to obtain a majority of mononucleosomes and reaction stopped adding 5 μl of 0.5 M EDTA pH 8. Nuclei were lysed as follows: 30 μl of 5X Nuclear Lysis Buffer (5% NaDeOx, 5% Triton X-100) were added and samples vortexed, then 160 μl of ChIP Dilution buffer (0.1% Triton X-100, 20 mM Tris-HCl (pH 8.1), 150mM NaCl) were added and samples sonicated using Bioruptor Plus sonicator (Diagenode) for two cycles (30 sec on/30 sec off on high setting at 4 °C). Following centrifugation for 30 min at maximum speed at 4 °C, supernatants were collected and 350 μl of ChIP Dilution buffer added. Half the sample was retained to check chromatin fragmentation and half processed for immunoprecipitation as previously described. 10% of input retained and antibody-bound-beads added for overnight incubation at 4 °C. 3 μl of anti-H3K36me2 (Invitrogen, T.571.7, MA5-14867) were used per sample. Beads were then washed for 10 min at 4 °C with the following buffers: IP dilution buffer 1% Triton X-100 (20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), buffer A (50mM HEPES pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), buffer B (20 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate), TE buffer (1mM EDTA pH 8, 10 mM Tris pH 8). Chromatin was eluted by incubating the beads in extraction buffer (0.1 M NaHCO3, 1% SDS) for 15 min at 37 °C. To reverse the cross-linking Tris-HCl pH 6.8 and NaCl were added to final concentrations of 130 mM and 300 mM respectively, and immunoprecipitations were incubated at 65 °C overnight. Samples were then incubated at 37 °C for 1 h after addition of 2 μl of RNase Cocktail Enzyme Mix (Ambion). Then 40 μg of Proteinase K (Roche) were added, followed by 2 h incubation at 55 °C. Input material was similarly de-crosslinked. Samples were purified with the MinElute PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) barcode adapters according to the manufacturer instructions. were used. Specifically, Illumina Index Primers Set 1 (E7335) for H3K36me3, and Unique Dual Index UMI Adaptors DNA Set 1 (E7395) for the other libraries. For histone modifications ChIP-seq, adapter-ligated DNA was size selected for an insert size of 150 bp using Agencourt AMPure XP beads. Libraries were quantified using the Qubit dsDNA HS or BR assay kit and assessed for size and quality using the Agilent Bioanalyser. H3K36me3 ChIP-Rx-seq libraries were sequenced using the NextSeq 500/550 high-output version 2.5 kit (75 bp single end reads). The other ChIP-seq libraries were sequenced using the NextSeq 2000 P3 (50 bp paired end reads). Libraries were combined into equimolar pools to run within individual flow cells. Sequencing was performed at the Edinburgh Clinical Research Facility.


title: Mouse, AAV-cTnT-uORF-TBX18-GFP, bio rep 5

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: Library name: Sample 9

data_processing:
Libraries were sequenced on NovaSeq X Plus using paired-end 150 bp
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Assembly: mm10
Supplementary files format and content: Excel file with differential expression analysis (DESeq2)
Supplementary files format and content: RNA-seq_Wang_2025_Mouse.xlsx

molecule: polyA RNA

organism: Mus musculus

source_name: Adult mouse left ventricular tissues

extract_protocol:
RNA was harvested using NucleoSpin RNA kit (Macherey-Nagel). 1.25 ug of total RNA was used for construction of sequencign libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep (mRNA Capture) following manufacturer's protocol.

value: Adult mouse left ventricular tissues


title: REI_POWR390

value: Blood


title: REI_POWR357

value: Female


title: Blood, HTP_II, RNA-seq, S24

description:
Library name: 1A-020
column_name_in_FPKM_allSamples: 1A-020


title: REI_POWR148

value: Fertile


title: DNMT1_KO_h3k36me2_chip_rep_2_chip_seq

description:
Library name: DNMT1_KO_h3k36me2_chip_rep_2_chip_seq
DNMT1_KO_h3k36me2_rep_2_chip_seq.bigWig


title: Blood, HTP_II, RNA-seq, S23

description:
Library name: 1A-019
column_name_in_FPKM_allSamples: 1A-019


title: Mouse, AAV-cTnT-uORF-TBX18-GFP, bio rep 4

description: Library name: Sample 8


title: DNMT1_KO_h3k36me2_in_rep_1_chip_seq

description:
Library name: DNMT1_KO_h3k36me2_in_rep_1_chip_seq
DNMT1_KO_h3k36me2_rep_1_chip_seq.bigWig


title: Mouse, AAV-cTnT-uORF-TBX18-GFP, bio rep 3

description: Library name: Sample 7


title: DNMT1_KO_h3k36me2_chip_rep_1_chip_seq

description:
Library name: DNMT1_KO_h3k36me2_chip_rep_1_chip_seq
DNMT1_KO_h3k36me2_rep_1_chip_seq.bigWig


title: HCT116_h3k36me2_chip_rep_2_chip_seq

description:
Library name: HCT116_h3k36me2_chip_rep_2_chip_seq
HCT116_h3k36me2_rep_2_chip_seq.bigWig

value: WT


title: Mouse, AAV-cTnT-uORF-TBX18-GFP, bio rep 2

description: Library name: Sample 6


title: HCT116_h3k36me2_in_rep_2_chip_seq

description:
Library name: HCT116_h3k36me2_in_rep_2_chip_seq
HCT116_h3k36me2_rep_2_chip_seq.bigWig


title: Blood, HTP_II, RNA-seq, S21

description:
Library name: 1A-017
column_name_in_FPKM_allSamples: 1A-017


title: HCT116_h3k36me2_in_rep_1_chip_seq

description:
Library name: HCT116_h3k36me2_in_rep_1_chip_seq
HCT116_h3k36me2_rep_1_chip_seq.bigWig


title: Mix

city: Guangzhou

first: Liu

state: GuangDong

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

description:
Library name: Mix
M20 Genomics platform

data_processing:
Raw reads were aligned to the reference genome and counted using STARsolo
downstream analyses performed in Annotated Data Format. Further processing was conducted in Seurat
Assembly: Prevotella intermedia ：https://www.ncbi.nlm.nih.gov/datasets/taxonomy/1122984/； Fusobacterium animalis：https://www.ncbi.nlm.nih.gov/datasets/taxonomy/76859/

organism: Fusobacterium nucleatum

source_name: strain

extract_protocol:
500,000 bacterial cells were pelleted by centrifugation at 4 °C. The pellet was resuspended in 2 mL of ice-cold 4% formaldehyde (Sigma, #47608), followed by an overnight fixation with shaking at 4 °C. After centrifugation at 4000 rpm for 5 min at 4 °C, the fixative was removed. The pellet was washed twice with 1 mL of PBS-TRI (1× PBS containing 0.1% Tween-20 and 0.1 U/mL Murine RNase Inhibitor (Vazyme, #R301), and then resuspended in 200 μL of PBS-TRI (1× PBS with 0.1% Tween-20 and 0.2 U/mL Murine RNase Inhibitor (Vazyme, #R301). The cell concentration was determined using a MoxiTM Z cell counter, and the suspension was diluted according to the manufacturer’s protocol to achieve a single-cell suspension.
Libraries were prepared from bacterial cells using the VITAPilote® kit (M20 Genomics, #R20114124) according to the manufacturer’s protocol.

value: strain

value: Fusobacterium nucleatum

value: coculture


title: HCT116_h3k36me2_chip_rep_1_chip_seq

description:
Library name: HCT116_h3k36me2_chip_rep_1_chip_seq
HCT116_h3k36me2_rep_1_chip_seq.bigWig

value: colorectal cancer cell line


title: Blood, HTP_II, RNA-seq, S20

description:
Library name: 1A-016
column_name_in_FPKM_allSamples: 1A-016

value: whole blood


title: Mouse, AAV-cTnT-uORF-TBX18-GFP, bio rep 1

description: Library name: Sample 5


title: Mouse, AAV-cTnT-uORF-Nluc-GFP, bio rep 4

description: Library name: Sample 4


title: Blood, HTP_II, RNA-seq, S19

description:
Library name: 1A-015
column_name_in_FPKM_allSamples: 1A-015

value: HTP


title: coculture of Mix_1

description:
Library name: Mix_1
Mix1
Fn and Pi coculture

data_processing:
RNA-Seq reads were adaptor trimmed and the data quality was assessed with the fastp (v 0.23.2) software.
Cleaned data were aligned to human reference genome (GRCh38 release 106 version) by STAR software (v 2.7.10).
RNA expression quantification with RSEM (v 1.3.3) for further quantification were calculated by rsem-calculate-expression.
Assembly: Prevotella intermedia ：https://www.ncbi.nlm.nih.gov/datasets/taxonomy/1122984/； Fusobacterium animalis：https://www.ncbi.nlm.nih.gov/datasets/taxonomy/76859/
Supplementary files format and content: count.csv is a CSV file that records the count for each sample.

source_name: bacterial cell

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (QIAGEN, #74104)
Sequencing libraries were constructed using ALFA-SEQ RNA Library Prep Kit II (FINOROP, #NRI002E) following the manufacturer’s recommendations.

value: bacterial cell


title: Fn

description:
Library name: Fn
M20 Genomics platform

value: monoculture


title: coculture of Mix_3

description:
Library name: Mix_3
Mix3
Fn and Pi coculture


title: Blood, HTP_II, RNA-seq, S18

description:
Library name: 1A-013
column_name_in_FPKM_allSamples: 1A-013


title: Mouse, AAV-cTnT-uORF-Nluc-GFP, bio rep 3

description: Library name: Sample 3


title: monoculture of Fn_2

description:
Library name: Fn_2
Fa2
Fn monoculture


title: Blood, HTP_II, RNA-seq, S17

description:
Library name: 1A-012
column_name_in_FPKM_allSamples: 1A-012

value: Male


title: coculture of Mix_2

description:
Library name: Mix_2
Mix2
Fn and Pi coculture


title: Mouse, AAV-cTnT-uORF-Nluc-GFP, bio rep 2

description: Library name: Sample 2


title: monoculture of Fn_1

description:
Library name: Fn_1
Fa1
Fn monoculture


title: Cut&Tag-seq H3K4me1 in D5  with GSKJ4

city: hefei

first: wenxian

last: wang

address: No. 81, Meishan Road, Shushan District, Hefei City, Anhui Province

institute: Anhui Medical University

description: Library name: Sample4

data_processing:
Fastp was conducted for trimming raw fastq files to remove adaptors and low-quality bases.
The trimmed fastq files were then mapped to the mm10 reference genome utilizing Bowtie2.
Then uniquely mapped reads were obtained using SAMtools.
Picard was used to remove duplicates and For visualization, deepTools was utilized with the “bamCoverage” function to generate normalized RPM bigWig files. Then MACS2 was utilized for peak calling.
Assembly: mm10
Supplementary files format and content: Bigwig files for Cut&Run-seq and Cut&Tag-seq.
Library strategy: CUT&Tag

source_name: Differentiated motor neuron

growth_protocol: C57BL/6 mouse embryonic stem cells (mESCs) were cultured on a monolayer of Mitomycin-C–treated mouse embryonic fibroblasts in Knockout DMEM medium supplemented with 10% fetal bovine serum, 5% Knockout serum replacement , 100 U/ml penicillin-streptomycin solution, 2 mM L-glutamax, 1X MEM non-essential amino acid solution, 0.1 mM β-mercaptoethanol and 1000 U/ml leukemia inhibitory factor.

extract_protocol:
Cells were harvested at indicated stages for Cut&Run assay using Hyperactive pG-MNase Cut&Run Assay Kit for Illumina (Vazyme HD102), for Cut&Tag assay using Hyperactive Universal Cut&Tag Assay Kit for Illumina Pro (Vazyme TD904) according to manufacture's protocols.
Regarding Cut&Run-seq,  VAHTS multiplex Oligos Set 5 (Vazyme N322) was used for library construction. As for Cut&Tag-seq, Trueprep Index Kit V2 for Illumina (Vazyme TD202) was employed for library construction. For RNA-seq, First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Prime and lastly PCR products were purified.

treatment_protocol: mESCs were dissociated with 0.25% trypsin into single cell suspension at 2.5x104 cells/ml in ADFNK medium (Advanced DMEM/F12:Neurobasal (1:1) medium, 10% Knockout Serum Replacement, 100 U/ml penicillin-streptomycin solution, 2 mM L-glutamax, 1X MEM non-essential amino acid solution and 0.1 mM β-mercaptoethanol). Then 20μl of cell mixture (500 cells) was seeded onto the cover of petri dish to initiate formation of embryoid bodies (EBs) (D0: day 0). Two days later (D2: day 2), EBs were harvested and plated into differentiation medium (ADFNK medium supplemented with 1 μM all-trans retinoic acid (RA, Sigma) and 0.5μM Sonic Hedgehog Agonist (SAG, Selleck) for caudalization and ventralization. Culture Medium was then changed at D3 (day 3).  For directed hypaxial motor column (HMC) differentiation, 5 μM DAPT was added to the differentiation medium at D4 (day 4) and ADFNK medium at D5 (day 5).  GSKJ4 was added at D4 and cells were harvested at D5.

value: Differentiated motor neuron

tag: differentiation stage

tag: antibody


title: Blood, HTP_II, RNA-seq, S15

description:
Library name: 1A-007
column_name_in_FPKM_allSamples: 1A-007


title: TZELEP, Negative pgRNA_4

city: ALEAXNDROUPOLIS

first: AIKATERINI

last: SKEVA

state: EVROS

address: DRAGANA 1

department: MEDICINE

country: Greece

institute: DEMOCRITUS UNIVERSITY OF THRACE

description:
Library name: Sample 12
Column names: Gene, counts

data_processing:
All samples were trimmed with Trim Galore software.
Alignment was performed with Hisat on GRCh38p14 human genome.
Assembly: GRCh38p14
Supplementary files format and content: Each tab-delimited text file contains raw counts for one Sample.

source_name: Plasma

extract_protocol:
RNA was extracted based on Trizol, Invitrogen protocol and 1ug of RNA was processed for library preparation.
For the library preparation we used TruSeq RNA Library Prep Kit v2, Illumina following manufacturer's instructions.

value: Plasma

value: Cell free

value: Negative pgRNA

value: Nucleoside analogs


title: Blood, HTP_II, RNA-seq, S22

description:
Library name: 1A-018
column_name_in_FPKM_allSamples: 1A-018

value: Female


title: Blood, HTP_II, RNA-seq, S16

description:
Library name: 1A-011
column_name_in_FPKM_allSamples: 1A-011


title: DODI, Negative pgRNA_3

description:
Library name: Sample 11
Column names: Gene, counts


title: monoculture of Fn_3

description:
Library name: Fn_3
Fa3
Fn monoculture


title: Cut&Tag-seq H3K27ac in D5 with GSKJ4

description: Library name: Sample3

value: H3K27ac (Abcam, #ab4729)


title: MPLO, Positive pgRNA_3

description:
Library name: Sample 7
Column names: Gene, counts

value: Positive pgRNA


title: Cut&Tag-seq H3K27me3 in D5 with GSKJ4

description: Library name: Sample2

value: WT


title: XANA, Positive pgRNA_4

description:
Library name: Sample 8
Column names: Gene, counts


title: Mouse, AAV-cTnT-uORF-Nluc-GFP, bio rep 1

description: Library name: Sample 1

value: Adult mouse left ventricular tissues


title: Blood, HTP_II, RNA-seq, S14

description:
Library name: 1A-006
column_name_in_FPKM_allSamples: 1A-006


title: KEAMSE, Positive pgRNA_1

description:
Library name: Sample 5
Column names: Gene, counts


title: OMEL. Negative pgRNA_2

description:
Library name: Sample 10
Column names: Gene, counts


title: MOAP, Negative pgRNA_1

description:
Library name: Sample 9
Column names: Gene, counts


title: IND61_F, Healthy, female_2

description:
Library name: Sample 4
Column names: Gene, counts

value: Healthy individual


title: Cut&Run-seq Kdm6b in D4H8 with Olig2-KD

description: Library name: Sample1

data_processing:
Fastp was conducted for trimming raw fastq files to remove adaptors and low-quality bases.
The trimmed fastq files were then mapped to the mm10 reference genome utilizing Bowtie2.
Then uniquely mapped reads were obtained using SAMtools.
Picard was used to remove duplicates and For visualization, deepTools was utilized with the “bamCoverage” function to generate normalized RPM bigWig files. Then MACS2 was utilized for peak calling.
Assembly: mm10
Supplementary files format and content: Bigwig files for Cut&Run-seq and Cut&Tag-seq.
Library strategy: CUT&Run

value: Kdm6b (this study)


title: liver wt tunicamycin 6

city: Saint Louis

first: Paul

last: Cliften

state: MO

address: 4444 Forest Park Avenue

department: Genetics

institute: Washington University School of Medicine

description:
Library name: dz_tunica_1686
sample.DZ_Tunica_1686

data_processing:
BATCH1: Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read
BATCH2: Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software
BATCH1&2: RNA-seq reads were aligned with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
BATCH1&2: Differential expression analysis was performed with EdgeR
Assembly: Ensembl release 101 top-level assembly (GRCm38)
Supplementary files format and content: SR003713-all.gene_moderated_log2cpm_samples.tsv: moderated log2cpm counts
Supplementary files format and content: mgi3302-all.gene_moderated_log2cpm_samples.tsv: moderated log2cpm counts

source_name: liver

growth_protocol: Three month old male mice were maintained on 12-hour dark/light cycles with ad libitum access to standard rodent chow and water

extract_protocol:
Described in Kulkarni et al., PPAR Research, 2021
Described in Kulkarni et al., PPAR Research, 2021

treatment_protocol: Mice were treated with intraperitoneal injection of sterile PBS, TNFa (2 hours), DMSO or tunicamycin (24-hours).

value: liver

value: wildtype

value: tunicamycin


title: Blood, HTP_II, RNA-seq, S12

description:
Library name: 1A-003
column_name_in_FPKM_allSamples: 1A-003

value: whole blood

value: HTP


title: IND47_M, Healthy, male_2

description:
Library name: Sample 3
Column names: Gene, counts


title: IND27_F, Healthy, female_1

description:
Library name: Sample 1
Column names: Gene, counts


title: liver wt tunicamycin 5

description:
Library name: dz_tunica_1674
sample.DZ_Tunica_1674


title: Blood, HTP_II, RNA-seq, S11

description:
Library name: 1A-001
column_name_in_FPKM_allSamples: 1A-001


title: Blood, HTP_II, RNA-seq, S10

description:
Library name: 19A-003
column_name_in_FPKM_allSamples: 19A-003


title: hiPSC, siScr DNKASH, LMNB1 rep3

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: siScr DNK C_R LMNB1 rep3

data_processing:
Cut&Run: Adapters were trimmed from fastq files using TrimGalore with default parameters (ver 0.6.4 using Cutadapt 4.2, (Krueger, 2023). The resulting reads were mapped to the hg38 assembly with bowtie2 (Langmead and Salzberg, 2012) with the parameters -X 2000 -N 1 --local --dovetail. Duplicates were marked using Picard MarkDuplicates (Broad Institute) and removed for downstream analysis. LADs were called using the Enriched Domain Detector (Lund et al., 2014) with parameters required_fraction_of_informative_bins=0.98, p_hat_CI_method=agresti_coull, log_ratio_bin_size=10, fdr=0.05, and gap parameter 4, using LMNB1 as the signal file and matched IgG file as background. Genome-wide LMNB1 signal was calculated for visualization and downstream analysis by counting reads detected in each 1kb or 10kb genomic bin using deeptools multiBigwigSummary (Ramirez et al., 2016), z-scores were calculated excluding any bin with no reads from any sample mapped, and then were smoothed using a rolling mean of the flanking 5 windows to each side.
RNAseq: Adapters were trimmed as described above in Cut&Tag analysis section. Reads were mapped to the hg38 genome with STAR v2.7.10a (Dobin et al., 2013) with the parameters --genomeSAindexNbases 14 --outFilterScoreMinOverLread 0.9 --outFilterMatchNmin 16 --outFilterMatchNoverLmax 0.05 --alignIntronMax 100000, with the additional parameter --peOverlapNbasesMin 5 for paired-end reads. Duplicates were marked with Picard as described above and excluded from count and differential expression analysis. Counts on exons of genes from the NCBI RefSeq Select hg38 annotation (Goldfarb et al., 2025)  were calculated using an in-house R script utilizing summarizeOverlaps from the GenomicRanges package (Lawrence et al., 2013).
Assembly: hg38
Supplementary files format and content: zscore bws: bigwig signal files containing zscores called in 10kb window and smoothed using a rolling mean of the flanking 5 windows to each side
Supplementary files format and content: RNA.counts.txt: number of reads mapped to exons of each gene from RNA-seq samples
Library strategy: CUT&Run

source_name: NCardia

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS (16000044; Gibco), 1% Penicillin-Streptomycin (15140122; Gibco), and 2% B-27 (17504044; Gibco).

extract_protocol:
RNA was isolated from hiPSC-CMs 48 hours after treatment with either scramble control or LMNA siRNA (+mChery control) using TRIzol reagent, following manufacturer’s protocol (15596018, Invitrogen).
CUT&RUN was performed using ~150,000 hiPSC-CMs and LMNB1 antibody or control IgG antibody as described in Skene & Henikoff 2018.
RNA libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) to enrich for poly-A tailed RNA molecules. RNA-seq library quality was analyzed by TapeStation (Agilent Genomics) and quantified using qPCR (Kapa Biosystems).
CUT&RUN DNA concentrations were quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit (NEB). Samples were indexed for multiplex sequencing. Library quality was analyzed by TapeStation (Agilent Genomics) and quantified using qPCR (Kapa Biosystems).

treatment_protocol: On day 0, cells were treated with siRNAs, against either a non-targeting scramble control (D-001210-05-20; Horizon) or LMNA (SMARTPool, L-004978-00-0005; Horizon) at a concentration of 5nM using Lipofectamine RNAiMax (13778150; ThermoFisher) transfection reagent diluted in Opti-MEM (31985062; Gibco).  Cells were treated with either control mCherry AdV (1767; VectorBiolabs) or dominant-negative KASH AdV (VectorBiolabs) at a concentration of ~500 PFU/mL.

value: NCardia

value: hiPSC-cardiomyocyte

value: siScr + DNKASH


title: Blood, HTP_II, RNA-seq, S13

description:
Library name: 1A-005
column_name_in_FPKM_allSamples: 1A-005

value: Male


title: MIEG, Positive pgRNA_2

description:
Library name: Sample 6
Column names: Gene, counts

value: Plasma

value: Cell free

value: Nucleoside analogs


title: liver wt tunicamycin 4

description:
Library name: dz_tunica_1667
sample.DZ_Tunica_1643


title: hiPSC, siScr DNKASH, LMNB1 rep1

description: Library name: siScr DNK C_R LMNB1 rep1


title: IND44_M, Healthy, male_1

description:
Library name: Sample 2
Column names: Gene, counts


title: Blood, HTP_II, RNA-seq, S9

description:
Library name: 19A-002
column_name_in_FPKM_allSamples: 19A-002

value: Female


title: hiPSC, siLMNA DNKASH, LMNB1, rep3

description: Library name: siLMNA DNK C_R LMNB1 rep3

value: siLMNA + DNKASH


title: liver wt tunicamycin 3

description:
Library name: dz_tunica_1647
sample.DZ_Tunica_1667


title: liver wt tunicamycin 2

description:
Library name: dz_tunica_1643
sample.DZ_Tunica_1647


title: hiPSC, siLMNA DNKASH, LMNB1, rep2

description: Library name: siLMNA DNK C_R LMNB1 rep2


title: hiPSC, siScr DNKASH, IgG

description: Library name: siScr DNK C_R IgG


title: hiPSC, siLMNA DNKASH, LMNB1, rep1

description: Library name: siLMNA DNK C_R LMNB1 rep1


title: Blood, HTP_II, RNA-seq, S8

description:
Library name: 19A-001
column_name_in_FPKM_allSamples: 19A-001


title: hiPSC, siLMNA DNKASH, IgG

description: Library name: siLMNA DNK C_R IgG


title: liver wt tunicamycin 1

description:
Library name: dz_tunica_1564
sample.DZ_Tunica_1564


title: Pi

description:
Library name: Pi
M20 Genomics platform

organism: Prevotella intermedia

value: strain

value: Prevotella intermedia

value: monoculture


title: liver wt vehicle 6

description:
Library name: dz_dmso_1685
sample.DZ_DMSO_1685

value: liver

value: vehicle (DMSO)


title: monoculture of Pi_3

description:
Library name: Pi_3
Pi3
Pi monoculture

value: bacterial cell


title: hiPSC, siLMNA mCh, LMNB1, rep3

description: Library name: siLMNA mCh C_R LMNB1 rep3

value: siLMNA + mCh


title: liver wt vehicle 5

description:
Library name: dz_dmso_1665
sample.DZ_DMSO_1665

value: wildtype


title: Blood, HTP_II, RNA-seq, S5

description:
Library name: 11A-08R
column_name_in_FPKM_allSamples: 11A-08R

value: whole blood

value: HTP


title: hiPSC, siLMNA mCh, LMNB1, rep1

description: Library name: siLMNA mCh C_R LMNB1 rep1

value: NCardia

value: hiPSC-cardiomyocyte


title: hiPSC, siLMNA mCh, LMNB1, rep2

description: Library name: siLMNA mCh C_R LMNB1 rep2


title: Blood, HTP_II, RNA-seq, S4

description:
Library name: 11A-006
column_name_in_FPKM_allSamples: 11A-006


title: hiPSC, siScr DNKASH, LMNB1 rep2

description: Library name: siScr DNK C_R LMNB1 rep2

value: siScr + DNKASH


title: monoculture of Pi_1

description:
Library name: Pi_1
Pi1
Pi monoculture


title: liver wt vehicle 4

description:
Library name: dz_dmso_1664
sample.DZ_DMSO_1664


title: Blood, HTP_II, RNA-seq, S6

description:
Library name: 11S-003
column_name_in_FPKM_allSamples: 11S-003

value: Male


title: monoculture of Pi_2

description:
Library name: Pi_2
Pi2
Pi monoculture


title: Blood, HTP_II, RNA-seq, S3

description:
Library name: 10A-015
column_name_in_FPKM_allSamples: 10A-015


title: hiPSC, siLMNA mCh, IgG

description: Library name: siLMNA mCh C_R IgG


title: NDV_3

city: Harbin

first: Shi

last: Qiankai

address: No.678 Haping Road

institute: The Chinese Academy of Agricultural Sciences

description:
Library name: NDV_3
HD11 cells, infected with Newcastle disease virus, biological replicate 3

data_processing:
Raw reads were filtered to remove adapter sequences, reads containing excessive ambiguous bases, and low-quality reads.
Clean reads were mapped to the Gallus gallus reference genome.
Assembly: Gallus gallus GRCg6a
Supplementary files format and content: Processed data files include a gene-level raw count matrix and a normalized expression matrix (TPM or FPKM) for all samples. Rows represent genes and columns represent libraries listed in the SAMPLES section.

organism: Gallus gallus

growth_protocol: HD11 cells were maintained in complete culture medium under standard cell culture conditions at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from HD11 cells using a standard RNA isolation protocol according to the manufacturer's instructions. RNA quality and quantity were assessed prior to library preparation.
RNA-seq libraries were constructed from total RNA according to the manufacturer's standard protocol and sequenced on a high-throughput sequencing platform to generate paired-end reads.

treatment_protocol: HD11 cells were assigned to two experimental groups: Mock and NDV. Cells in the NDV group were infected with Newcastle disease virus, and cells in the Mock group received mock treatment. Each condition included three biological replicates.

value: chicken macrophage-like cell line

value: NDV


title: liver wt vehicle 3

description:
Library name: dz_dmso_1662
sample.DZ_DMSO_1662


title: liver wt vehicle 2

description:
Library name: dz_dmso_1639
sample.DZ_DMSO_1639


title: hiPSC, siScr mCh, LMNB1, rep3

description: Library name: siScr mCh C_R LMNB1 rep3

value: siScr + mCh


title: Blood, HTP_II, RNA-seq, S2

description:
Library name: 10A-012
column_name_in_FPKM_allSamples: 10A-012

value: Female


title: Blood, HTP_II, RNA-seq, S1

description:
Library name: 10A-002
column_name_in_FPKM_allSamples: 10A-002


title: NDV_1

description:
Library name: NDV_1
HD11 cells, infected with Newcastle disease virus, biological replicate 1


title: NDV_2

description:
Library name: NDV_2
HD11 cells, infected with Newcastle disease virus, biological replicate 2


title: Blood, HTP_II, RNA-seq, S7

description:
Library name: 14A-001
column_name_in_FPKM_allSamples: 14A-001


title: liver wt vehicle 1

description:
Library name: dz_dmso_1563
sample.DZ_DMSO_1563


title: RPMI8226 p300 ChIP-seq control replicate 3

city: Singapore

first: Phyllis SY

last: Chong

address: 14 Medical Drive

country: Singapore

institute: NUS Medicine/CSI Singapore

description:
Library name: p300_3
Nil

data_processing:
The library was constructed by Novogene Corporation (Beijing, China)
Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA)
Library quality was assessed on the Agilent Bioanalyzer 2100 system.
Clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets.
Assembly: The reference genome ID used was ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: hg38
Supplementary files format and content: bigWig

source_name: Multiple Myeloma

growth_protocol: Cells were cultured in RPMI-1640 (Cytiva) supplemented with heat-inactivated 10% fetal bovine serum (FBS, Gibco) and maintained in a 37oC incubator with 5% CO2

extract_protocol:
20 million cells per sample were fixed with 1% paraformaldehyde, quenched with glycine and lysed following the SimpleChIP® protocol (Cell Signaling Technology)
Chromatin was sheared by sonication, and the mixture was centrifuged to isolate DNA. The DNA was then incubated overnight with antibodies, and antibody-DNA complexes were captured using beads (Active Motif), followed by elution and decrosslinking with proteinase K. The immunoprecipitated DNA was purified with a MinElute PCR Purification Kit (Qiagen) and used for library preparation at NovogeneAIT Genomics (Singapore). Quality control included agarose gel electrophoresis, NanoPhotometer® spectrophotometer (IMPLEN) for DNA purity, and Qubit® 3.0 Fluorometer for measuring concentration. Pair-end sequencing was performed on an Illumina platform, with libraries assessed via Agilent Bioanalyzer 2100.

value: Multiple Myeloma

value: Plasma cells

value: MAF

value: Knockdown


title: hiPSC, siScr mCh, LMNB1, rep2

description: Library name: siScr mCh C_R LMNB1 rep2


title: hiPSC, siScr mCh, IgG

description: Library name: siScr mCh C_R IgG


title: Mock_3

description:
Library name: Mock_3
HD11 cells, mock-infected, biological replicate 3

value: mock


title: MGS1 orthotopic model pooled replicate 1 (8803)

city: Chicago

last: Youngblood

state: IL

address: 676 N. St. Clair Street; Suite 2210

department: Department of Neurological Surgery

institute: Northwestern University

description: Library name: Sample S5

data_processing:
SoupX was used to remove ambient RNA and scDblFinder to remove doublets. Following which, cells were filtered using a percent mitochondrial DNA threshold of 10% and a UMI range of 100 to 4000. Cells were then subject to Log Normalize, Scale Data, and PCA functions.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Whole Brain

extract_protocol:
Whole brains were grossly dissected and digested into single cell suspension using collagenase (20µl/ml; Roche) and DNase (1µl/ml; Roche) in RPMI 1640 medium (Roswell Park Memorial Institute; Corning) supplemented with 2% fetal bovine serum (FBS). The CD45+ population was isolated using Percoll and spiked 1:1 with CD45- before sequencing to obtain sufficient immune cells for profiling.
scRNAseq library was constructed with the Chromium GEM-X Single Cell kit for a sequencing depth of 20,000 reads per cell. 20,000 cells were targeted for each sample

value: Whole Brain

value: Murine Meningioma

tag: strain

value: FVB/N

value: 8803 STING Agonist


title: RPMI8226 p300 ChIP-seq control Input

description:
Library name: p300_Input
Nil


title: hiPSC, siScr mCh, LMNB1, rep1

description: Library name: siScr mCh C_R LMNB1 rep1

value: NCardia


title: Mock_2

description:
Library name: Mock_2
HD11 cells, mock-infected, biological replicate 2


title: MGS1 orthotopic model pooled replicate 2 (Control)

description: Library name: Sample C7

value: Control PBS


title: MGS1 orthotopic model pooled replicate 2 (8803)

description: Library name: Sample S7

value: 8804 STING Agonist


title: RPMI8226 p300 ChIP-seq control replicate 1

description:
Library name: p300_1
Nil


title: RPMI8226 p300 ChIP-seq control replicate 2

description:
Library name: p300_2
Nil


title: MGS1 orthotopic model pooled replicate 1 (Control)

description: Library name: Sample C6


title: DNMT1_KO_rep_2_early_repli_seq

description: Library name: DNMT1_KO_rep_2_early_repli_seq

data_processing:
Repli-seq fastq files were quality checked using FastQC (v0.11.4) and reads were trimmed using TrimGalore (v0.4.1) using default settings. Reads were then mapped to the genome (hg38) using bowtie2 for paired end data (version settings: -N1 -L 20 --no-unal -- no-mixed -- no-discordant -X 1000) (Langmead & Salzberg, 2012). Low mapping quality reads were removed using samtools (v1.6, settings: -bq10). Repli-seq data were analysed as previously described (Ryba et al, 2011). Briefly, read counts were generated for 10kb genomic windows using bedtools coverage (v2.27.1, settings: -counts) and normalised to reads per million (RPM). Replication timing was then calculated as the ratio between the early and late fraction RPM counts. Quantile normalisation of counts was then performed across samples and Loess smoothing was performed throughout all chromosomes using R (expect for the Y chromosome and mitochondrial DNA). The RPM counts over 10kb windows for early, middle, and late samples as well as the Loess smoothed replication timing counts were converted into BigWigs using bedGraphToBigWig from UCSC tools. For a summary of Repli-seq alignment statistics, see Supplementary Table 3.
Assembly: hg38
Supplementary files format and content: Bigwig files of Loess smoothed replication timing in 10Kb windows calculated from the early and late read depth.

extract_protocol:
Repli-seq data was generated from cells at approximately 70% confluency to ensure most of the cells were actively cycling. To label DNA, cells were given fresh media supplemented with 100μM 5-Ethynyl-2'-deoxyuridine (EdU) and incubated at 37°C for 30 minutes. Cells were then collected by trypsinization along with media and a PBS wash of the flask to ensure non-adherent mitotic cells were not lost. The cell suspension was then centrifuged at 200g for 5 minutes and washed with 10ml PBS before being resuspended in 2.5ml PBS supplemented with 1% FCS. Cells were fixed by gently adding 7.5ml of 100% ethanol to a final concentration of 70% with gentle vortexing followed by incubation on ice for 30 mins and storage at –20°C. Fixed cells were washed with 5ml ice cold PBS, and then resuspended in 5ml 100mM HCl and 0.015% pepsin (0.75mgr) in H2O before being incubated at 37°C for 30 minutes while rotating. Following centrifugation at 600g for 10 minutes, pellets were washed with 5 ml ice cold PBS and then resuspended in 1ml PBS along with 50μl Propidium Iodide (PI) and 20μl RNase A and incubated at room temperature for 30 minutes while protected from light. Extracted Nuclei were counted using a hematocytometer and suspended to approximately 3x106 nuclei/ml to ensure optimal flow during FACS sorting. Nuclei were sorted on a FACSAria flow cytometer (BD Biosciences) in PBS supplemented with 0.25% BSA based on their DNA content using PI staining, into three fractions: Early, Middle and Late S-Phase (defined by equally splitting the window between the G1 and G2 peaks into three equal portions). DNA was then extracted from sorted nuclei as described above except they were sonicated on a Bioruptor following proteinase K digestion (15 cycles of 30 seconds on – 30 seconds off, on high at 4°C). Precipitation of extracted DNA was then performed with linear acrylamide (LPA) carrier and isopropanol and resuspended in TE. DNA was then quantified using Qubit High Sensitivity reagents and sonicated on a Covaris E220 sonicator to yield 100-300bp fragments which were quality controlled on a Bioanalyser. Re-precipitation of DNA was was then performed with LPA carrier and ethanol before being resuspended in water. A click reaction was then performed to conjugate biotin to the EdU by adding 3ul 2M TAB (0.4M), 30ul DMSO, 6ul 5mM Ascorbic Acid (2mM), 1.2ul 10mM Biotin Azide (0.8mM), 3ul 10mM CuTBTA (2mM) and 1.8ul H2O. Samples were then incubated overnight at room temperature while covered from light and cleaned up by ethanol precipitation with LPA carrier. EdU containing DNA was then enriched using Myone C1 Streptavidin Dynabeads (Invitrogen) and a magnetic rack overnight at 4°C with rotation. Following this, the samples were washed at 4°C with: TSE-I (20 mM Tris-HCl, pH 8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton, 0.1% (v/v) SDS) x2, TSE-II (20 mM Tris-HCl pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton, 0.1%(v/v) SDS) x1 and TE x1. Samples were eluted by adding water at 95°C and incubation with vortexing at 95°C for 10 mins. Successful enrichment of early and late replicating DNA was then validated by qPCR of early (BMP1, TEK, MELK, RTTN) and late replicating (NETO1, CDH8, DPPA2 and PTPRD) loci, based on a published protocol and HCT116 WT repli-seq data (Du et al., 2021; Marchal et al, 2018). Primer sequences used in this validation are included in Supplementary Table 2.
Repli-seq libraries were then prepapred using the Acel-NGS 1a Plus DNA library kit along with the 1A Plus Set A Indexing Kit following the manufacturer’s instruction (Swift Biosciences). However, as our DNA template contain Uracil due to the EdU incorporation, the kit’s polymerase, and subsequent buffer (Reagent W2, Buffer W3 and Enzyme W4) were replaced with KAPA HiFi HotStart Uracil+ Ready Mix Kit (Roche), which included an uracil tolerant polymerase. Libraries were assessed for size distribution on the Agilent Bioanalyser (Agilent Technologies) and quantified using the Qubit 2.0 Fluorometer. Repli-seq libraries were sent for whole genome sequencing at the Wellcome Trust Clinical Research Facility (WTCRF). The libraries were sequenced using the Illumina NextSeq 500/550 High-Output v2.5 (75 cycles) Kit on the Illumina NextSeq 550 platform over 2 flow cells to give 75bp single-end reads.

value: HCT116 DNMT1 KO

value: colorectal cancer cell line

value: DNMT1 KO


title: Mock_1

description:
Library name: Mock_1
HD11 cells, mock-infected, biological replicate 1

value: chicken macrophage-like cell line


title: VDD_2

city: shanghai

first: MINGHUI

last: YU

address: wanyuan road 399

institute: Children’s Hospital of Fudan University

description: Library name: sample4

data_processing:
Raw reads were filtered and mapped to mouse genom GRCm39 using bowtie2 (version 2.2.9). Peaks were called using SEACR (version 1.3) and annotated using ChIPseeker (version 1.12.1).
Assembly: mm39
Supplementary files format and content: Peaks of H3K4me3 Enrichment at the Genomic Level
Library strategy: CUT&Tag

source_name: E12.5d embryoic kidnye

extract_protocol:
E12.5 embryonic kidney tissue was extracted and dissociated into a single-cell suspension. After passing the cell counting and viability tests, libraries were constructed using the Vazyme (TD904) kit protocol. The samples were then sent to Novogene for quality control, sequencing, and analysis.
E12.5 embryonic kidney tissue was extracted and dissociated into a single-cell suspension. After passing the cell counting and viability tests, libraries were constructed using the Vazyme (TD904) kit protocol. The samples were then sent to Novogene for quality control, sequencing, and analysis.

value: E12.5d embryoic kidnye

value: Ureteric Bud and Metanephric Mesenchyme cells

value: Ureteric Bud and Metanephric Mesenchyme

value: WT

value: Vitamin D-free feed


title: 23366-64_ATAC

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

description:
Library name: 23366-64_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 32 HAI

library_source: other

data_processing:
The nf-core/atacseq pipeline (https://nf-co.re/atacseq/2.1.2/) was used to process ATAC-Seq data (Ewels et al., 2020). Following the initial analysis with the nf-core/atacseq pipeline, further explorations into the data were carried out using customized bioinformatics tools including differential analysis and motif analysis. First, FastQC (Andrews, 2010) was used to produce quality metrics. Then adapter trimming was performed with Trim Galore, a comprehensive wrapper combining Cutadapt and FastQC, for the refinement of FastQ files (Andrews, 2010; Martin, 2011). We used default settings to identify and remove adapter sequences to streamline preprocessing steps without manual intervention.
Hisat2 was used to align sequencing data (Kim et al., 2015). Trimmed ATAC-Seq reads were aligned against the MorexV3 reference genome with the addition of Bln1 (Bln1 was not annotated in the original MorexV3 release) (Mascher et al., 2021). The output was transmitted into Samtools (Li and Durbin, 2009), which was then converted into a compressed BAM file, filtering out secondary alignments, and leveraging multiple threads for efficiency. After alignment, reads were filtered using a combination of SAMtools, BEDTools, BAMTools, and Pysam (https://github.com/pysam-developers/pysam) to ensure high-quality alignments for downstream analysis (Li and Durbin, 2009; Quinlan and Hall, 2010; Barnett et al., 2011). SAMtools and BEDTools were used to remove reads mapping to blacklisted genomic regions, as well as reads marked as duplicates, non-primary alignments, unmapped reads, and those mapping to multiple genomic locations. BAMTools handled the exclusion of reads with excessive mismatches (more than four), soft-clipped alignments, large insert sizes (>2 kb), and provided additional quality control. Pysam was employed to filter out inter-chromosomal paired-end reads, those with improper FR orientation, and to remove both reads from any pair where a single read failed the criteria.
MACS2 was applied to identify regions with narrow peaks or broad peaks (Zhang et al., 2008). Then, deepTools (Ramírez et al., 2014) was used to convert filtered BAM files into BigWig format, employing Counts Per Million (CPM) as the default normalization method to prepare the data for such comparative analyses and further bioinformatics processing.
After obtaining the count matrix where each row is a consensus peak region and each column is a sample, we implemented a differential analysis to compute statistically significant differential peaks between pairwise comparisons through DESeq2 (Love et al., 2014). A minimal pre-filtering step was performed to keep only rows that had at least 10 reads total. After differential tests were been applied to each peak, p-values were calculated and adjusted to control false positives via  multiple testing. This filtering threshold was automatically determined to maximize detection power (i.e., maximize the number of differential peaks detected) at a specified false discovery rate (FDR). Tables were generated to report the peak annotation, and statistics and p adjusted and fold change for each pairwise comparison.
Assembly: Barley (Mascher 2021) and Blumeria (Ensembl Fungi Assembly EF 2) (Spanu 2018).
Supplementary files format and content: Aligned Next-Generation Sequencing reads in BAM format

molecule: other

organism: Hordeum vulgare

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: The wild-type progenitor, CI 16151 (Mla6, Bln1), was developed by the introgression of Mla6 into the Manchuria background (Moseman 1972) [10.2135/cropsci1972.0011183X001200050038x] and maintained by single seed descent. CI 16151 derived mutants [m18982 (mla6, Bln1); m19089 (Mla6, bln1); m19028 (mla6, bln1)] were generated via fast-neutrons (4 Gy Nf) as described in Meng et al. (2009) [10.1104/pp.108.129031] and Xi et al. (2009) [https://doi.org/10.1105/tpc.109.066167] and further characterized by  Chapman et al. 2021 [10.1093/genetics/iyaa026] and Velásquez-Zapata et al. (2024) [https://doi.org/10.1016/j.isci.2024.111013]. Seven-day old barley (Hordeum vulgare) first leaves were grown in 20 × 30-cm trays using sterilized potting mix (Sunshine Mix #1, Sungrow) in a climate-controlled greenhouse (16 h supplemental light, 20-22 C).

extract_protocol:
Nuclei were prepared by REquest Genomics (Athens, GA, USA). Barley tissue was chopped on ice using a razor blade for ~2 minutes in 600 μL of pre-chilled Nuclei Isolation Buffer (NIB) [https://doi.org/10.1186/1746-4811-9-31]. The chopped tissue was filtered through a 40-μm cell strainer and then subjected to centrifugation at 500 rcf for 5 minutes at 4C. The supernatant was removed and the pellet was resuspended in 500 μL of NIB. The sample was filtered again using a 20-μm cell strainer and then loaded onto the surface of 1 mL of a 35% Percoll buffer, prepared by mixing 35% Percoll with 65% NIB wash buffer. The nuclei centrifuged at 500 rcf for 10 minutes at 4C. The supernatant was carefully removed, and the pellets were washed in 100 μL of 1X TAPS buffer (5X TAPS buffer:  50mM TAPS-NaOH, pH8.0; 25mM MgCl2) [https://doi.org/10.1093/nar/gkw1179].
ATAC-seq libraries were prepared by REquest Genomics (Athens, GA, USA). Nuclei were reconstituted in 30 μL of 2.5X TAPS buffer. A total of 5 μL of nuclei were diluted tenfold and stained with DAPI (Sigma Cat. D9542) to evaluate the quality and abundance using a hemocytometer. A total of 50,000 nuclei were use for library preparation. The Tn5 assembly and library preparation procedures were conducted following previously established methods [https://doi.org/10.1093/nar/gkw1179].

treatment_protocol: Trays were blocked by biological replicate and plant genotype with seedling rows randomly assigned to one of four harvest timepoints (0, 16, 20, and 32 HAI). First leaf seedlings were inoculated with Blumeria hordei (Bh) isolate 5874 (AVRa6) and immediately transferred to a growth chamber (16 h light / 8 dark, 18 C). One gram of pooled tissue was collected for each timepoint and flash frozen in liquid nitrogen. Four biological replicates were collected for each genotype / timepoint combination; two replicates on August 25/26, 2023 and two replicates on September 29/30, 2023 and processed for ATAC-Seq protocols.

value: Barley infected first leaf (PO:0007094)

tag: plant genotype

tag: fungal isolate

value: Bh isolate 5874 (AVRa6)

tag: time point

value: 32 HAI

tag: replication

value: Rep # 4


title: DNMT1_KO_rep_1_late_repli_seq

description: Library name: DNMT1_KO_rep_1_late_repli_seq


title: 23366-63_ATAC

description:
Library name: 23366-63_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 20 HAI

tag: tissue

value: m18982 (susceptible mla6 mutant)

value: 20 HAI


title: RPMI8226 MAF ChIP-seq control Input [shscr]

description:
Library name: shscr_Input
Nil

value: Multiple Myeloma

value: Plasma cells

value: MAF

value: Knockdown


title: DNMT1_KO_rep_2_late_repli_seq

description: Library name: DNMT1_KO_rep_2_late_repli_seq

value: HCT116 DNMT1 KO

value: colorectal cancer cell line

value: DNMT1 KO


title: 23366-62_ATAC

description:
Library name: 23366-62_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 16 HAI

value: CI 16151 (resistant progenitor)

value: 16 HAI


title: DNMT1_KO_rep_1_early_repli_seq

description: Library name: DNMT1_KO_rep_1_early_repli_seq


title: VDD_1

description: Library name: sample3

value: E12.5d embryoic kidnye

value: Ureteric Bud and Metanephric Mesenchyme cells

value: Ureteric Bud and Metanephric Mesenchyme

value: WT


title: RPMI8226 MAF ChIP-seq control replicate 2 [shscr]

description:
Library name: shscr_IP_2
Nil


title: RPMI8226 MAF ChIP-seq control replicate 3 [shscr]

description:
Library name: shscr_IP_3
Nil


title: HCT116_rep_2_late_repli_seq

description: Library name: HCT116_rep_2_late_repli_seq


title: CON_2

description: Library name: sample2

value: normal Vitamin D feed


title: RPMI8226 MAF ChIP-seq control replicate 1 [shscr]

description:
Library name: shscr_IP_1
Nil


title: RPMI8226 H3K4me1 ChIP-seq control Input

description:
Library name: H3K4me1_Input
Nil


title: CON_1

description: Library name: sample1


title: 23366-61_ATAC

description:
Library name: 23366-61_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 16 HAI

value: Barley infected first leaf (PO:0007094)

value: m19089 (resistant bln1 mutant)

value: Bh isolate 5874 (AVRa6)

value: Rep # 4


title: HCT116_rep_2_early_repli_seq

description: Library name: HCT116_rep_2_early_repli_seq


title: TA-GelMA-implants

city: Shanghai

first: Tianle

last: Ma

address: 180 Fenglin Rd

institute: Zhongshan Hospital

description:
Library name: Sample2
femoral bone marrow samples and implant-adherent cells from osteoporotic fracture mice implanted with Mg-TAGelMA intramedullary nails.

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.


title: RPMI8226 H3K4me1 ChIP-seq control replicate 3

description:
Library name: H3K4me1_3
Nil

value: Multiple Myeloma

value: Plasma cells


title: 23366-60_ATAC

description:
Library name: 23366-60_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 32 HAI

value: 32 HAI


title: Mg-implants

description:
Library name: Sample1
femoral bone marrow samples and implant-adherent cells from osteoporotic fracture mice implanted with magnesium (Mg) intramedullary nails


title: HCT116_rep_1_early_repli_seq

description: Library name: HCT116_rep_1_early_repli_seq


title: 23366-58_ATAC

description:
Library name: 23366-58_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 0 HAI

value: 0 HAI


title: RPMI8226 H3K4me1 ChIP-seq control replicate 2

description:
Library name: H3K4me1_2
Nil

value: MAF

value: Knockdown


title: 23366-57_ATAC

description:
Library name: 23366-57_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 0 HAI

value: m18982 (susceptible mla6 mutant)


title: WY10

city: Los Angeles

first: Ophir

last: Klein

state: California

address: 8700 Beverly Blvd

department: Geurin Children's

institute: Cedars Sinai Medical Center

description: Library name: WY10

data_processing:
Data processing was done by Novogene as described below
Raw data (raw reads) of fastq format were firstly processed throughfastpsoftware. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-Nandlowquality reads from raw data. At the same time, Q20, Q30 and GCcontent the clean data were calculated. All the downstreamanalyses were basedon the clean data with high quality.
Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built 3 using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned tothereference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctionsbased on the gene model annotation file and thus a better mappingresult than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mappedto each gene. And then FPKM of each gene was calculated basedonthelength of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequenceper Millions base pairs sequenced, considers the effect of sequencingdepthand gene length for the reads count at the same time, and is currentlythe most commonly used method for estimating gene expressionlevels.
Assembly: mm39
Supplementary files format and content: xls file with the Fpkm values for each sample

source_name: Colon organoid

extract_protocol:
Organoids were harvested in RLT solution, and RNA was extracted using the RNeasy Qiagen kit following the manufacturer’s protocol (Cat. No. 74104).
The library was prepared by Novogene following their standard pipeline. Briefly, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.

treatment_protocol: Three days after passaging, organoids were treated with WY-14643 (100uM) or vehicle (ctrl) for two days.

value: Colon organoid


title: WY9

description: Library name: WY9


title: h1_ut_d20_rep2

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

description: Library name: h1_ut_d20_rep2

data_processing:
We used Trim Galore! (v0.6.5) to trim the adapter sequences with a quality threshold of 20. Alignment of reads to the human reference genome (GRCh38.p13/GENCODE release 36) was performed using Bowtie2 (v2.2.8). Duplicate reads were removed with PICARD v2.2.4.
Assembly: hg38
Supplementary files format and content: master_atac_peaks.narrowPeak

source_name: hematopoietic

growth_protocol: H1 hESCs were differentiated into HPCs.

extract_protocol:
50,000 hESC-HSPCs were processed as follows: nuclei were isolated by lysing with 50 ul of ATAC lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) and washing with 1 mL of ATAC wash buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20).
Cell lysates were spun to obtain nuclear pellets, which were subjected to transposase reaction for 45 minutes using the Illumina Nextera DNA Sample Preparation Kit according to the manufacturer’s instructions. The final libraries were quantified using the Agilent BioAnalyzer. Sequencing of 75 nucleotide-long paired-end reads was performed in a NextSeq-500 (Illumina).

value: hematopoietic

value: H1 hESC

value: hematopoietic progenitor cells

tag: time

value: UT


title: 23366-56_ATAC

description:
Library name: 23366-56_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 32 HAI


title: h1_ut_d20_rep3

description: Library name: h1_ut_d20_rep3


title: RPMI8226 H3K27ac ChIP-seq shMAF knockdown Input

description:
Library name: shMAF_In
Nil


title: RPMI8226 H3K4me1 ChIP-seq control replicate 1

description:
Library name: H3K4me1_1
Nil


title: WY8

description: Library name: WY8


title: 23366-59_ATAC

description:
Library name: 23366-59_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 20 HAI

value: 20 HAI


title: 23366-55_ATAC

description:
Library name: 23366-55_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 32 HAI

value: Barley infected first leaf (PO:0007094)

value: CI 16151 (resistant progenitor)


title: WY7

description: Library name: WY7


title: h1_ut_d18_rep2

description: Library name: h1_ut_d18_rep2


title: h1_ut_d16_rep3

description: Library name: h1_ut_d16_rep3


title: h1_ut_d18_rep3

description: Library name: h1_ut_d18_rep3


title: 23366-54_ATAC

description:
Library name: 23366-54_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 0 HAI

value: m19089 (resistant bln1 mutant)

value: Bh isolate 5874 (AVRa6)


title: RPMI8226 H3K27ac ChIP-seq shMAF knockdown replicate 2

description:
Library name: shMAF_2
Nil

value: Multiple Myeloma


title: 23366-53_ATAC

description:
Library name: 23366-53_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 0 HAI

value: Rep # 4


title: RPMI8226 H3K27ac ChIP-seq shMAF knockdown replicate 3

description:
Library name: shMAF_3
Nil

value: Plasma cells


title: WY6

description: Library name: WY6


title: h1_ut_d16_rep2

description: Library name: h1_ut_d16_rep2


title: CT5

description: Library name: CT5

value: Control


title: 23366-51_ATAC

description:
Library name: 23366-51_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 20 HAI


title: HCT116_rep_1_late_repli_seq

description: Library name: HCT116_rep_1_late_repli_seq

value: colorectal cancer cell line

value: WT


title: CT4

description: Library name: CT4


title: 23366-52_ATAC

description:
Library name: 23366-52_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 20 HAI


title: RPMI8226 H3K27ac ChIP-seq control Input

description:
Library name: R8226scr_In
Nil

value: MAF

value: Knockdown


title: h1_ut_d14_rep3

description: Library name: h1_ut_d14_rep3

value: hematopoietic


title: RPMI8226 H3K27ac ChIP-seq control replicate 3

description:
Library name: R8226scr_3
Nil


title: CT3

description: Library name: CT3

value: Colon organoid


title: 23366-50_ATAC

description:
Library name: 23366-50_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 16 HAI

value: 16 HAI


title: CT2

description: Library name: CT2


title: RPMI8226 H3K27ac ChIP-seq control replicate 2

description:
Library name: R8226scr_2
Nil


title: RPMI8226 H3K27ac ChIP-seq shMAF knockdown replicate 1

description:
Library name: shMAF_1
Nil


title: h1_ut_d14_rep2

description: Library name: h1_ut_d14_rep2

value: H1 hESC

value: hematopoietic progenitor cells

value: UT


title: h1_ut_d12_rep3

description: Library name: h1_ut_d12_rep3


title: RPMI8226 H3K27ac ChIP-seq control replicate 1

description:
Library name: R8226scr_1
Nil


title: h1_ut_d10_rep3

description: Library name: h1_ut_d10_rep3


title: 23366-49_ATAC

description:
Library name: 23366-49_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 16 HAI

value: Barley infected first leaf (PO:0007094)

value: m18982 (susceptible mla6 mutant)


title: h1_ut_d12_rep2

description: Library name: h1_ut_d12_rep2


title: CT1

description: Library name: CT1


title: 23366-48_ATAC

description:
Library name: 23366-48_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 32 HAI

value: CI 16151 (resistant progenitor)

value: Bh isolate 5874 (AVRa6)

value: 32 HAI

value: Rep # 3


title: scRNASeq_Mulitplexed_SubLibrary_JR8

description: Library name: JR8

data_processing:
Parse Bioscience Pipeline v1.6.0 was used for processing and demulitplexing cDNA samples
Colon and Cecum count data was subsetted for downstream analysis, where it was analyzed using Seurat, SCT transformed and then integrated with other datasets using Harmony
Assembly: mm39
Supplementary files format and content: all_genes.csv, count_matrix.mtx, cell_metadata.csv

source_name: Colon, Cecum

extract_protocol:
The colons were opened and washed with PBS. Epithelial cells were isolated by incubating the tissue in 15 mM EDTA for 45 minutes at 37°C, followed by manual shaking. Crypts were dissociated into single cells by incubation in a dissociation buffer containing Dispase II (2 U/mL) and DNase I (30 μg/mL) for 30 minutes at 37°C. Cells were pooled by condition and sorted at a 1:1 ratio of proliferative epithelial cells (EPCAM⁺, CD44⁺, CD45⁻) and differentiated epithelial cells (EPCAM⁺, CD44⁻, CD45⁻) using fluorescence-activated cell sorting (FACS).
The library was prepared using the Parse Biosciences Evercode WT Library Kit according to the manufacturer’s protocol.

value: Colon, Cecum

value: Epithelium

value: multiple (Ctrl, Abx, GF)


title: h1_ut_d10_rep2

description: Library name: h1_ut_d10_rep2


title: scRNASeq_Mulitplexed_SubLibrary_JR6

description: Library name: JR6


title: doxee17_dox_d20_rep3

description: Library name: doxee17_dox_d20_rep3

value: DOX


title: JJ012-Melatonin

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

description: Library name: Sample 2

data_processing:
Raw reads were quality filtered using Cutadapt (v1.9.1) to remove adapter sequences and low-quality bases (Phred score <20); reads shorter than 75 bp after trimming were discarded.
Clean reads were aligned to the human reference genome (hg38) using HISAT2 (v2.2.1).
Gene and isoform expression levels were quantified from paired-end clean reads using HTSeq (v0.6.1).
Differential expression analysis was performed using DESeq2; genes with adjusted p-values were used for downstream analyses.
Assembly: hg38
Supplementary files format and content: Processed data files include gene-level raw counts, FPKM values, and differential expression analysis results in XLS/XLSX format. Additional processed outputs include GO enrichment, KEGG enrichment, and PCA results.

growth_protocol: The 143B cell line were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA), while the JJ012 cell line was kindly provided by Dr. Sean P. Scully (University of Miami School of Medicine, Miami, FL, USA).

extract_protocol:
Total RNA was harvested using TRIzol reagent according to the manufacturer’s instructions.
Poly(A) mRNA was isolated using Oligo(dT) beads, fragmented, and reverse-transcribed to synthesize first- and second-strand cDNA. The purified double-stranded cDNA was end-repaired, A-tailed, ligated to sequencing adapters, size-selected, and PCR-amplified. Libraries were multiplexed and sequenced on an Illumina NovaSeq 6000 platform using a 2×150 bp paired-end configuration.

treatment_protocol: Total RNA was extracted from JJ012 and 143B cells treated with or without melatonin (1 mM) under detachment conditions for RNA sequencing (RNA-Seq).

value: human chondrosarcoma

value: Melatonin (1 mM, 72 h)


title: 143B-Melatonin

description: Library name: Sample 4

value: human osteosarcoma


title: 143B-Control

description: Library name: Sample 3

value: Untreat


title: 23366-47_ATAC

description:
Library name: 23366-47_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 16 HAI

value: 16 HAI


title: 23366-46_ATAC

description:
Library name: 23366-46_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 32 HAI


title: JJ012-Control

description: Library name: Sample 1


title: scRNASeq_Mulitplexed_SubLibrary_JR5

description: Library name: JR5


title: 23366-45_ATAC

description:
Library name: 23366-45_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 20 HAI

value: m19089 (resistant bln1 mutant)

value: 20 HAI


title: HK1, Mix03

description:
Library name: Mix03
Fusobacterium nucleatum and Prevotella intermedia

data_processing:
RNA-Seq reads were adaptor trimmed and the data quality was assessed with the fastp (v 0.23.2) software.
Cleaned data were aligned to human reference genome (GRCh38 release 106 version) by STAR software (v 2.7.10).
RNA expression quantification with RSEM (v 1.3.3) for further quantification were calculated by rsem-calculate-expression.
Assembly: GRCh38 release 106 version
Supplementary files format and content: CellRNAseq_count.csv is a CSV file that records the count for each sample.
Supplementary files format and content: CellRNAseq_tpm.csv is a CSV file that records the tpm for each sample.

extract_protocol:
We extracted RNA from tissue samples using the AllPrep DNA/RNA Micro Kit (QIAGEN GmbH).
Sequencing libraries were constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations.


title: scRNASeq_Mulitplexed_SubLibrary_JR7

description: Library name: JR7


title: scRNASeq_Mulitplexed_SubLibrary_JR4

description: Library name: JR4


title: doxee17_dox_d18_rep3

description: Library name: doxee17_dox_d18_rep3

value: hematopoietic

value: H1 hESC

value: hematopoietic progenitor cells


title: HK1, Mix02

description:
Library name: Mix02
Fusobacterium nucleatum and Prevotella intermedia


title: 23366-43_ATAC

description:
Library name: 23366-43_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 16 HAI

value: Barley infected first leaf (PO:0007094)

value: m18982 (susceptible mla6 mutant)

value: Bh isolate 5874 (AVRa6)


title: scRNASeq_Mulitplexed_SubLibrary_JR3

description: Library name: JR3

value: Colon, Cecum


title: doxee17_dox_d18_rep2

description: Library name: doxee17_dox_d18_rep2


title: 23366-41_ATAC

description:
Library name: 23366-41_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 32 HAI

value: 32 HAI

value: Rep # 3


title: doxee17_dox_d16_rep2

description: Library name: doxee17_dox_d16_rep2

value: DOX


title: scRNASeq_Mulitplexed_SubLibrary_JR2

description: Library name: JR2

value: Epithelium

value: multiple (Ctrl, Abx, GF)


title: HK1, Pi03

description:
Library name: Pi03
Prevotella intermedia

value: Prevotella intermedia


title: 23366-44_ATAC

description:
Library name: 23366-44_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 0 HAI

value: 0 HAI


title: HK1, Mix01

description:
Library name: Mix01
Fusobacterium nucleatum and Prevotella intermedia


title: doxee17_dox_d20_rep2

description: Library name: doxee17_dox_d20_rep2


title: doxee17_dox_d14_rep3

description: Library name: doxee17_dox_d14_rep3


title: 23366-42_ATAC

description:
Library name: 23366-42_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 20 HAI


title: HK1, Pi02

description:
Library name: Pi02
Prevotella intermedia


title: doxee17_dox_d16_rep3

description: Library name: doxee17_dox_d16_rep3


title: scRNASeq_Mulitplexed_SubLibrary_JR1

description: Library name: JR1


title: KO PS low

first: jiayin

last: Peng

address: Yueyang Road

institute: Center for Excellence in Molecular Cell Science

description:
Library name: KO PS low
10×Genomics

data_processing:
The constructed library was sequenced using illumina NovaSeq™ X Plus platform. FASTQ files were imported into Cell Ranger for analysis. After trimming barcode and unique molecular identifier (UMI) tags, transcriptreads were aligned to STAR 2.7.3a. Reads mapping to duplicate UMIs were removed. Transcripts were quantified using the Ensembl database (mm10 - Ensembl Transcripts release).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PSlow CD8+ T cells

extract_protocol:
B16-F10 tumors were dissected from WT or KO mice and single-cell suspensions were obtained. PShigh and PSlow CD8+ T cells (approximately lowest and highest 1/3 staining, respectively) were enriched using FACS sorting.
The freshly prepared single-cell suspension was adjusted to 700-1200 cell/μl according to the 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (No. 1000268) Operation manual for computer and library construction. The constructed library was sequenced using Illumina Nova 6000 PE150 platform.

value: PSlow CD8+ T cells

value: CD300ld KO


title: 23366-38_ATAC

description:
Library name: 23366-38_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 20 HAI

value: 20 HAI


title: HK1, Pi01

description:
Library name: Pi01
Prevotella intermedia


title: 23366-40_ATAC

description:
Library name: 23366-40_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 32 HAI


title: doxee17_dox_d14_rep1

description: Library name: doxee17_dox_d14_rep1

value: hematopoietic


title: 23366-39_ATAC

description:
Library name: 23366-39_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 20 HAI

value: CI 16151 (resistant progenitor)


title: HK1, Fn03

description:
Library name: Fn03
Fusobacterium nucleatum

value: Fusobacterium nucleatum


title: KO PS high

description:
Library name: KO PS high
10×Genomics

source_name: PShigh CD8+ T cells

value: PShigh CD8+ T cells


title: WT PS low

description:
Library name: WT PS low
10×Genomics

value: WT


title: doxee17_dox_d12_rep3

description: Library name: doxee17_dox_d12_rep3

value: H1 hESC

value: hematopoietic progenitor cells


title: 23366-37_ATAC

description:
Library name: 23366-37_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 16 HAI

value: Barley infected first leaf (PO:0007094)

value: Bh isolate 5874 (AVRa6)

value: 16 HAI


title: WT PS high

description:
Library name: WT PS high
10×Genomics


title: 23366-36_ATAC

description:
Library name: 23366-36_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 0 HAI

value: Rep # 3


title: HK1, Fn01

description:
Library name: Fn01
Fusobacterium nucleatum


title: Supt6 KO mouse_1

first: Jingting

last: Li

address: No 1, Zhongshan 2 Road, 12th Floor

department: Institue of Precision Medicine

institute: The First Affiliated Hospital, Sun Yat-sen University

description:
Library name: Sample 2
10X Genomics

data_processing:
Reads were processed using the Cell Ranger (v7.1.0) pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome (version GRCm39), using the STAR algorithm. Gene-barcode matrices were generated for each sample by counting UMIs and filtering non-cell-associated barcodes. The resulting matrix, containing barcoded cells and gene expression counts, was imported into the Seurat R toolkit (v4.1.1) for quality control and downstream clustering analysis. Cells were clustered using graph-based principal component analysis (PCA) followed by modularity optimization. Cell types were annotated using SingleR and validated against established marker gene expression. We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE).
Assembly: GRCm39,mm39
Supplementary files format and content: Barcodes and matrix files

source_name: Dorsal skin

growth_protocol: The mice were housed in an SPF environment.

extract_protocol:
Following euthanasia, dorsal skin was aseptically excised and subcutaneous tissue was removed using a sterile scalpel. The skin was incubated in 0.3% Dispase solution (prepared in PBS) at 4°C overnight to separate the epidermis from the dermis. The epidermal layer was carefully dissected, minced into fine fragments, and digested in 0.05% Trypsin (diluted in PBS) at 37°C for 15 minutes. Trypsin activity was neutralized by adding 0.5% bovine serum albumin (BSA) solution. The cell suspension was filtered through a 40-μm cell strainer to remove debris and centrifuged at 300 × g for 10 minutes at 4°C. Pelleted cells were washed once with 0.04% BSA and finally resuspended in 0.04% BSA. Cells were stained with 0.4% Trypan blue (Thermo Fisher: 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher). The cell suspension was maintained on ice for subsequent experiments.
Single cells and 10x Chromium beads (with UMIs and cell barcodes) were co-encapsulated in GEMs at near-saturation loading. Following cell lysis, polyadenylated RNAs were captured on beads via hybridization. Beads from all GEMs were pooled for reverse transcription, generating cDNA molecules tagged at the 5’ end (corresponding to transcript 3’ ends) with cell-specific barcodes and UMIs. Beads were then subjected to second-strand cDNA synthesis, adaptor ligation, and universal amplification. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3.1). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The sequencing were sequenced on Illumina Novaseq Xplus using PE150 mode.

treatment_protocol: Supt6 knockdown induced by tamoxifen injection

value: Dorsal skin

value: Supt6 knockdown


title: doxee17_dox_d10_rep1

description: Library name: doxee17_dox_d10_rep1

value: DOX


title: doxee17_dox_d12_rep1

description: Library name: doxee17_dox_d12_rep1


title: HK1, Fn02

description:
Library name: Fn02
Fusobacterium nucleatum


title: 23366-35_ATAC

description:
Library name: 23366-35_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 0 HAI

value: 0 HAI


title: HK1, Ctrl03

description:
Library name: Ctrl03
None


title: Wild-type mouse_1

description:
Library name: Sample 1
10X Genomics

value: Corn oil as a control


title: doxee17_ut_d20_rep3

description: Library name: doxee17_ut_d20_rep3

value: UT


title: 23366-33_ATAC

description:
Library name: 23366-33_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 0 HAI

value: m18982 (susceptible mla6 mutant)


title: doxee17_dox_d12_rep2

description: Library name: doxee17_dox_d12_rep2

value: hematopoietic


title: HK1, Ctrl02

description:
Library name: Ctrl02
None


title: HK1, Ctrl01

description:
Library name: Ctrl01
None


title: SHK-1 cells, control, replicate 3

city: Santiago

first: Veronica

last: Cambiazo

address: Av. El Libano 5524

country: Chile

institute: Instituto de Nutrición y Tecnología de los Alimentos (INTA)

data_processing:
Low quality reads and Illumina adapters were eliminated using BBduk software
Filtered reads were mapped using the STAR RNA-Seq alignment tool to P. salmonis CGR02 (NCBI accession N° GCF_001534725.1) assembly and S. salar (NCBI accession Nº GCA_905237065.2)
Reads that failed to map to any gene or mapped to multiple genes were removed before transcript analysis
Gene quantification was generated using the quantMode option available at STAR program
Assembly: S. salar GCA_905237065.2; P. salmonis CGR02 GCF_001534725.1
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Salmo salar

growth_protocol: P. salmonis strain CGR02 (GCA_001534725.1) was grown at 18 °C with agitation on Nutrient Piscirickettsia Broth (NPB; 30 gr/L Tryptic Soy Broth, 256.6 mM NaCl, 8.25 mM L-Cystein, 37µM FeCl3). SHK-1 cells were grown in Leibovitz's medium supplemented with 5% of fetal bovine serum (FBS) and without antibiotics. For infection experiments, bacteria were recovered from Nutrient Piscirickettsia Agar (NPA) plates and used to inoculate NPB. Cultures were incubated in a shaking incubator at 140 rpm and 18 °C for 3 days (exponentially growing bacteria) or 7 days (stationary state bacteria) before harvesting for infection experiments or RNA purification.

extract_protocol:
The pellets were suspended in 1.0 mL of TRIzol Reagent (Invitrogen), and total RNA was purified according to manufacturer`s instructions.
The libraries were generated using TruSeq Stranded Total RNA Library Prep (Illumina), with rRNA removal.

value: macrophage-like

value: control


title: 23366-34_ATAC

description:
Library name: 23366-34_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 16 HAI

value: m19089 (resistant bln1 mutant)


title: RNAseq of CUL_34R

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

description: Library name: CUL_34R

data_processing:
RNA-Seq reads were adaptor trimmed and the data quality was assessed with the fastp (v 0.23.2) software.
Cleaned data were aligned to human reference genome (GRCh38 release 106 version) by STAR software (v 2.7.10).
RNA expression quantification with RSEM (v 1.3.3) for further quantification were calculated by rsem-calculate-expression.
Assembly: GRCh38 release 106 version
Supplementary files format and content: TissueRNAseq_count.csv is a CSV file that records the count for each sample.
Supplementary files format and content: TissueRNAseq_tpm.csv is a CSV file that records the tpm for each sample.

source_name: NPC tumor tissue

value: NPC tumor tissue

tag: microbial subtype


title: doxee17_ut_d20_rep1

description: Library name: doxee17_ut_d20_rep1

value: H1 hESC

value: hematopoietic progenitor cells

tag: treatment


title: SHK-1 cells, control, replicate 1

tag: cell line


title: doxee17_ut_d18_rep1

description: Library name: doxee17_ut_d18_rep1

tag: cell type


title: 23366-32_ATAC

description:
Library name: 23366-32_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 16 HAI

value: Barley infected first leaf (PO:0007094)

value: Bh isolate 5874 (AVRa6)

value: Rep # 2


title: 23366-31_ATAC

description:
Library name: 23366-31_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 20 HAI

value: 20 HAI


title: RNAseq of CUL_33R

description: Library name: CUL_33R


title: SHK-1 cells infected with P. salmonis CGR02, replicate 3

value: infected with Piscirickettsia salmonis


title: doxee17_ut_d18_rep2

description: Library name: doxee17_ut_d18_rep2


title: RNAseq of CUL_32R

description: Library name: CUL_32R


title: doxee17_ut_d16_rep3

description: Library name: doxee17_ut_d16_rep3


title: SHK-1 cells, control, replicate 2


title: 23366-30_ATAC

description:
Library name: 23366-30_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 0 HAI

value: CI 16151 (resistant progenitor)


title: SHK-1 cells infected with P. salmonis CGR02, replicate 1


title: doxee17_ut_d16_rep2

description: Library name: doxee17_ut_d16_rep2


title: 23366-29_ATAC

description:
Library name: 23366-29_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 32 HAI

value: 32 HAI


title: SHK-1 cells infected with P. salmonis CGR02, replicate 2


title: RNAseq of CUL_31R

description: Library name: CUL_31R


title: RNAseq of CUL_30R

description: Library name: CUL_30R


title: 23366-28_ATAC

description:
Library name: 23366-28_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 20 HAI


title: 23366-27_ATAC

description:
Library name: 23366-27_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 32 HAI


title: liver piz p50 ko vehicle 5

description:
Library name: pftzz_pbs_60
sample.pftzz_pbs_60

data_processing:
BATCH1: Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read
BATCH2: Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software
BATCH1&2: RNA-seq reads were aligned with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
BATCH1&2: Differential expression analysis was performed with EdgeR
Assembly: Ensembl release 101 top-level assembly (GRCm38)
Supplementary files format and content: SR003713-all.gene_moderated_log2cpm_samples.tsv: moderated log2cpm counts
Supplementary files format and content: mgi3302-all.gene_moderated_log2cpm_samples.tsv: moderated log2cpm counts

extract_protocol:
Described in Kulkarni et al., PPAR Research, 2021
Described in Kulkarni et al., PPAR Research, 2021

value: liver

tag: genotype

value: vehicle (PBS)


title: RNAseq of CUL_35R

description: Library name: CUL_35R


title: liver piz p50 ko vehicle 4

description:
Library name: pftzz_pbs_59
sample.pftzz_pbs_59


title: doxee17_ut_d14_rep2

description: Library name: doxee17_ut_d14_rep2

value: UT


title: doxee17_ut_d14_rep1

description: Library name: doxee17_ut_d14_rep1

value: hematopoietic


title: liver piz p50 ko vehicle 3

description:
Library name: pftzz_pbs_55
sample.pftzz_pbs_55


title: RNAseq of CUL_29R

description: Library name: CUL_29R


title: doxee17_ut_d12_rep2

description: Library name: doxee17_ut_d12_rep2


title: RNAseq of CUL_28R

description: Library name: CUL_28R


title: RNAseq of CUL_27R

description: Library name: CUL_27R


title: doxee17_ut_d10_rep2

description: Library name: doxee17_ut_d10_rep2


title: liver piz p50 ko vehicle 1

description:
Library name: pftzz_pbs_53
sample.pftzz_pbs_53

value: PiZ p50-KO


title: doxee17_d20dox_Rep2

description: Library name: doxee17_d20dox_Rep2

data_processing:
Trim Galore! (v 0.6.5) was used to trim the adaptor sequences with a quality threshold of 20. Alignment was performed with STAR aligner . All samples passed the quality control requirements with > 50% of reads uniquely mapping (>20M uniquely mapped reads for each library). Gene level read counts were obtained using Salmon for all libraries.
Assembly: hg38
Supplementary files format and content: tab-delimited file with raw counts from all samples

extract_protocol:
200,000hESC-HPCs were collected and RNA extraction was performed with the RNeasy mini kit (QIAGEN).
PolyA-tailed mRNA was selected with beads from 300ng total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs)

value: DOX


title: 23366-23_ATAC

description:
Library name: 23366-23_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 20 HAI

value: m19089 (resistant bln1 mutant)


title: RNAseq of CUL_26R

description: Library name: CUL_26R

value: NPC tumor tissue


title: liver piz vehicle 4

description:
Library name: piz_pbs_16
sample.piz_pbs_16

value: PiZ


title: liver piz p50 ko vehicle 2

description:
Library name: pftzz_pbs_54
sample.pftzz_pbs_54


title: doxee17_ut_d12_rep1

description: Library name: doxee17_ut_d12_rep1

value: H1 hESC

value: hematopoietic progenitor cells


title: 23366-25_ATAC

description:
Library name: 23366-25_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 0 HAI

value: Barley infected first leaf (PO:0007094)

value: Bh isolate 5874 (AVRa6)

value: 0 HAI


title: liver piz vehicle 5

description:
Library name: piz_pbs_17
sample.piz_pbs_17


title: 23366-26_ATAC

description:
Library name: 23366-26_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 0 HAI

value: Rep # 2


title: 23366-22_ATAC

description:
Library name: 23366-22_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 32 HAI

value: CI 16151 (resistant progenitor)


title: doxee17_d20dox_Rep1

description: Library name: doxee17_d20dox_Rep1


title: RNAseq of CUL_24R

description: Library name: CUL_24R


title: doxee17_d18dox_Rep2

description: Library name: doxee17_d18dox_Rep2


title: 23366-19_ATAC

description:
Library name: 23366-19_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 16 HAI

value: 16 HAI


title: RNAseq of CUL_22R

description: Library name: CUL_22R


title: RNAseq of CUL_23R

description: Library name: CUL_23R


title: RNAseq of CUL_25R

description: Library name: CUL_25R


title: doxee17_d18dox_Rep1

description: Library name: doxee17_d18dox_Rep1


title: 23366-24_ATAC

description:
Library name: 23366-24_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 16 HAI

value: m18982 (susceptible mla6 mutant)


title: liver piz vehicle 2

description:
Library name: piz_pbs_14
sample.piz_pbs_14

value: liver

value: vehicle (PBS)


title: 23366-20_ATAC

description:
Library name: 23366-20_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 32 HAI

value: 32 HAI


title: liver piz vehicle 1

description:
Library name: piz_pbs_13
sample.piz_pbs_13


title: doxee17_d16dox_Rep2

description: Library name: doxee17_d16dox_Rep2

value: hematopoietic


title: 23366-21_ATAC

description:
Library name: 23366-21_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 20 HAI

value: 20 HAI


title: liver wildtype tnfa 5

description:
Library name: dz_tnfa_11
sample.dz_tnfa_11

value: wildtype

value: TNFa


title: doxee17_d14dox_Rep2

description: Library name: doxee17_d14dox_Rep2

value: DOX


title: RNAseq of CUL_20R

description: Library name: CUL_20R

value: NPC tumor tissue


title: 23366-17_ATAC

description:
Library name: 23366-17_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 0 HAI


title: RNAseq of CUL_21R

description: Library name: CUL_21R


title: liver wildtype tnfa 3

description:
Library name: dz_tnfa_9
sample.dz_tnfa_9


title: 23366-18_ATAC

description:
Library name: 23366-18_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 16 HAI


title: liver wildtype tnfa 6

description:
Library name: dz_tnfa_12
sample.dz_tnfa_12