title: AGM_3_run3_NB06

description: Library name: AGM_3_run3_NB06_GL34_078_GL_SC_1_plate1_H9_S78


title: JJ-13-332

status: Public on Sep 29 2025

type: SRA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

description: colon content rDNA was sequenced

library_source: other

data_processing:
Raw demultiplexed fastq files were imported into R and processed using the DADA2 package from Bioconductor
Reads were inspected for quality, filtered, truncated at 220 bp, the paired reads were merged, a sequence table of amplicon sequence variants (ASVs) was constructed, and chimeras were removed.
The taxonomic classification of the ASVs was generated by a q2-feature-classifiervia classify-sklearn plugin
The operational taxonomic unit (OTU) database was mapped on the Silva reference database v132 with 99% taxonomy reference to curate taxa4
Supplementary files format and content: 16s radiation data file contains the abundance of Taxonomic classifications of ASVs
Library strategy: 16S

molecule: other

organism: Mus musculus

source_name: Descending colon

extract_protocol:
PowerSoil DNA Isolation Kit
Illumina 16S Metagenomics Library Preparation

tag: tissue

value: Descending colon

tag: radiation dose

tag: timepoint

value: 3 Days


title: 4C_mRNA_C

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

library_source: transcriptomic

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

molecule: polyA RNA

source_name: oocyte or embryo

extract_protocol:
Ten equal fractions were recovered and subjected to RNA isolation by Trizol reagent (Sigma).
The RNA-seq libraries were generated from individual fractions by using the Smart-seq2 v4 kit with minor modification from manufacturer’s instructions. Briefly, individual cells were lysed, and mRNA was captured and amplified with the Smart-seq2 v4 kit (Clontech). After AMPure XP beads purification, amplified RNAs were quality checked by using Agilent High Sensitivity D5000 kit (Agilent Technologies). High-quality amplified RNAs were subject to library preparation (Nextera XT DNA Library Preparation Kit; Illumina) and multiplexed by Nextera XT Indexes (Illumina). The concentration of sequencing libraries was determined by using Qubit dsDNA HS Assay Kit (Life Technologies) and KAPA Library Quantification Kits (KAPA Biosystems). The size of sequencing libraries was determined by means of High Sensitivity D5000 Assay in at Tapestation 4200 system (Agilent). Pooled indexed libraries were then sequenced on the Illumina HiSeq X platform with 150-bp paired-end reads.

treatment_protocol: Approximately 100 oocytes (GV or MII oocyte) or embryos at different developmental stages (zygote, 2-, 4-, 8-cell, morula, and blastocyst) were combined with lysis buffer containing 10 mM HEPES (pH 7.5), 5 mM KCL, 5 mM MgCL2, 2 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide, complete EDTA-free protease inhibitor (Roche), and 40 U/ml RNase inhibitor. Oocytes and embryos were disrupted by zirconium silica beads (Sigma) in the mixer mill apparatus MM301 (shake frequency 30, total time 45s, Retsch). Lysates were cleaned by centrifugation in 10,000 x g for 5 min at 4°C and the supernatants were loaded into 10-40 % linear sucrose gradients containing 10 mM HEPES (pH7.5), 100 mM KCL, 5 mM MgCl2, 2mM DTT, 100 μg/ml cycloheximide, complete EDTA-free protease inhibitor, and 5 U/ml RNase inhibitor. Ultracentrifugation was carried out with a SW55Ti rotor and Optima L-90 Ultracentrifuge (Beckman Coulter). Ribosome profiles were recorded by ISCO UV absorbance reader. The overall quality of particular ribosome fractionation experiment was monitored by analysis of a parallel Hek293 cells sample.

value: oocyte or embryo

tag: treatment


title: 8C_mRNA_C


title: JJ-13-315

description: colon content rDNA was sequenced

value: 1 Day


title: 2C_mRNA_C


title: OS774_IgG_NONE_1

city: San Francisco

first: Alex

middle: G

last: Lee

state: CA

address: 1550 4th Street

institute: UCSF

description: Library name: OS774_IgG_NONE_1

library_source: genomic

data_processing:
CUT&Run samples were processed using a custom pipeline scripted with CGPipe. FastQ files were paired, trimmed, and aligned to both human (hg38) and yeast (sac3) genomes using Bowtie2 with the ‘--dovetail’ setting. Reads were classified as human or yeast using the NGSUtilsJ bam-best function, and yeast-aligned reads were removed. Peak calling was performed with MACS3
Assembly: hg38
Supplementary files format and content: bedGraph pileups generated using MACS2
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: All cell lines were routinely tested for mycoplasma and STR tested to confirm identify.  Cells were cultured in standard DMEM media (Corning) supplemented with 10% bovine growth serum (Hyclone SH30541.03) and 1% penicillin–streptomycin–glutamine

extract_protocol:
Cells were harvested using trypsine and used as input for CUT&RUN libraries.
Briefly, cells were harvested, washed, and bound to activated Concanavalin A-coated magnetic beads (Cell Signaling Technology #93569S) and permeabilized. The bead-cell complex was incubated overnight with either an Acetyl-Histone H3 (Lys27) antibody (Cell Signaling Technology #8173, RRID:AB_10949503), Mono-Methyl-Histone H3 (Lys4) antibody (Cell Signaling Technology #5326, RRID:AB_10695148), Tri-Methyl-Histone H3 (Lys4) antibody (Cell Signaling Technology #9751, RRID:AB_2616028) or an IgG antibody control (Cell Signaling Technology #66362, RRID:AB_2924329) at 4°C. Cells were then washed with digitonin buffer (Cell Signaling Technology #16359S), resuspended in 50 μl of pAG/Mnase (Cell Signaling Technology #57813S) and incubated for 1hr at 4°C. Spike-In DNA (5ng, Cell Signaling Technology #36598S) was added to each reaction. DNA from enriched chromatin samples was purified using the DNA Purification Buffers and Spin Columns kit (Cell Signaling Technology #14209). DNA libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645L) and NEBNext® Multiplex Oligos for Illumina® (NEB #E7600S). Fragment size and quality of the libraries were evaluated by Tapestation (4200 system, Agilent, RRID:SCR_018435). Libraries were sequenced in a NextSeq500 system (Illumina).

tag: cell line

tag: cell type

value: OS PDX-derived

tag: epitope

value: IgG


title: AGM_3_run2_NB72

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: Library name: AGM_3_run2_NB72_GL43_200_plate1_C11_Gfi_HE_S8

data_processing:
Nanopore sequencing data were basecalled using Dorado (v0.9.1) using the high-accuracy model (dna_r10.4.1_e8.2_400bps_hac@v5.0.0). Raw reads were trimmed for SMARTseq adapters using bbduk.sh (v39.08). Chimeric reads were filtered from the data using YACRD (v1.0.0) and porechop (v0.2.4). Cleaned reads were aligned to GENCODE transcripts (Release 37) using Minimap2 (v2.26), retaining a maximum of 10 alignments per read. Alignments were quantified using Nanocount (v1.0.0.post6). Abundance files were read into R (v4.3.0) filtered for low library size samples using findOutliers (scuttle v1.10.3; type = "lower", nmads = 1) and normalised using DESeq2 (v1.40.2). Estimated and normalised counts were subject to analysis using IsoformSwitchAnalyzeR and SplicingFactory as previously described.
Assembly: GENCODE transcripts (Release 37)
Supplementary files format and content: nanoCount_trans_Estcount.txt; nanoCount Estimated counts as TSV
Supplementary files format and content: nanoCount_trans_tpm.txt; nanoCount TPM as TSV

source_name: mouse embryo AGM-region

growth_protocol: fresh samples (AGM and Yolksac) were harvested from mouse embryos and directly processed for sequencing

extract_protocol:
Single cells were FACS sorted into wells of a 384-well plate containing lysis buffer and snap-frozen.
10ng full-length purified amplified cDNA from a miniaturised Smart-seq2 cDNA was purified using a 0.7x volume of AMPure XP reagent (Beckman Coulter). Purified amplification product was quantified by Qubit (ThermoFisher) and sized / quality checked by Fragment Analyzer (Agilent). 200fmol was used as input for the Ligation sequencing amplicons - Native Barcoding Kit 24 V14 (SQK-NBD114.24) protocol (revision H) (Oxford Nanopore). Sequencing was performed on a PromethION P2 Solo (Oxford Nanopore) using flow cell FLO-PRO114M

treatment_protocol: No treatments were performed. Cells were directly harvested from Embryos and FACS sorted into lyses buffer for sequence library preparation.

value: mouse embryo AGM-region

value: primary material

value: HE-AGM (early)


title: OS766_K27Ac_NONE_2

description: Library name: OS766_K27Ac_NONE_2


title: JJ-13-313

description: colon content rDNA was sequenced


title: AGM_3_run2_NB46

description: Library name: AGM_3_run2_NB46_GL34_074_GL_SC_1_plate1_G10_S74


title: JJ-13-312

description: colon content rDNA was sequenced


title: Zygote_mRNA_C


title: OS766_K27Ac_NONE_1

description: Library name: OS766_K27Ac_NONE_1


title: AGM_3_run2_NB35

description: Library name: AGM_3_run2_NB35_GL34_044_GL_SC_1_plate1_G21_S44


title: MII_mRNA_C


title: OS766_IgG_NONE_2

description: Library name: OS766_IgG_NONE_2


title: GV_mRNA_C


title: Morula_mRNA_C


title: OS766_IgG_NONE_1

description: Library name: OS766_IgG_NONE_1


title: JJ-13-311

description: colon content rDNA was sequenced


title: AGM_3_run2_NB34

description: Library name: AGM_3_run2_NB34_GL34_065_GL_SC_1_plate1_G14_S65


title: AGM_3_run2_NB27

description: Library name: AGM_3_run2_NB27_GL34_212_GL_SC_3_plate1_F1_S212


title: JJ-12-193

description: colon content rDNA was sequenced

value: 9 Days


title: Blastocyst_mRNA_B


title: OS742_ZNF148_NONE_2

description: Library name: OS742_ZNF148_NONE_2


title: JJ-12-192

description: colon content rDNA was sequenced


title: Morula_mRNA_B


title: OS742_ZNF148_NONE_1

description: Library name: OS742_ZNF148_NONE_1


title: JJ-12-191

description: colon content rDNA was sequenced


title: AGM_3_run2_NB21

description: Library name: AGM_3_run2_NB21_GL34_068_GL_SC_1_plate1_E24_S68


title: 8C_mRNA_B


title: OS742_SP7_NONE_2

description: Library name: OS742_SP7_NONE_2


title: JJ-12-194

description: colon content rDNA was sequenced


title: AGM_3_run2_NB19

description: Library name: AGM_3_run2_NB19_GL34_076_GL_SC_1_plate1_G3_S76


title: 4C_mRNA_B


title: OS742_SP7_NONE_1

description: Library name: OS742_SP7_NONE_1


title: AGM_3_run2_NB13

description: Library name: AGM_3_run2_NB13_GL34_071_GL_SC_1_plate1_E13_S71


title: JJ-12-134

description: colon content rDNA was sequenced


title: JJ-12-133

description: colon content rDNA was sequenced


title: AGM_3_run2_NB15

description: Library name: AGM_3_run2_NB15_GL43_197_plate1_C08_Gfi_HE_S5


title: 2C_mRNA_B


title: AGM_3_run2_NB04

description: Library name: AGM_3_run2_NB04_GL34_048_GL_SC_1_plate1_G1_S48


title: OS742_SATB2_NONE_2

description: Library name: OS742_SATB2_NONE_2


title: Zygote_mRNA_B


title: JJ-12-132

description: colon content rDNA was sequenced


title: OS742_SATB2_NONE_1

description: Library name: OS742_SATB2_NONE_1


title: AGM_3_run1_NB61

description: Library name: AGM_3_run1_NB61_GL34_053_GL_SC_1_plate1_H8_S53


title: MII_mRNA_B


title: JJ-12-131

description: colon content rDNA was sequenced


title: AGM_3_run1_NB47

description: Library name: AGM_3_run1_NB47_GL36_262_GL_SC_7_C04_E10-5_het_pos_S166


title: JJ-12-114

description: colon content rDNA was sequenced


title: GV_mRNA_B


title: AGM_3_run1_NB43

description: Library name: AGM_3_run1_NB43_GL34_056_GL_SC_1_plate1_E15_S56


title: Blastocyst_mRNA_A


title: OS742_RUNX2_NONE_1

description: Library name: OS742_RUNX2_NONE_1


title: JJ-12-113

description: colon content rDNA was sequenced


title: AGM_3_run1_NB40

description: Library name: AGM_3_run1_NB40_GL34_225_GL_SC_3_plate1_G4_S225


title: AGM_3_run1_NB38

description: Library name: AGM_3_run1_NB38_GL34_231_GL_SC_3_plate1_A4_S231


title: 8C_mRNA_A


title: JJ-10-394

description: colon content rDNA was sequenced

value: 11 Gy


title: OS742_K27Ac_NONE_5

description: Library name: OS742_K27Ac_NONE_5


title: JJ-10-393

description: colon content rDNA was sequenced


title: Morula_mRNA_A


title: AGM_3_run1_NB35

description: Library name: AGM_3_run1_NB35_GL34_243_GL_SC_3_plate1_D3_S243


title: AGM_3_run1_NB26

description: Library name: AGM_3_run1_NB26_GL43_286_plate2_D03_Gfi_HE_S94


title: OS742_K27Ac_NONE_4

description: Library name: OS742_K27Ac_NONE_4


title: OS742_K27Ac_NONE_1

description: Library name: OS742_K27Ac_NONE_1


title: 4C_mRNA_A


title: 2C_mRNA_A


title: JJ-10-392

description: colon content rDNA was sequenced


title: AGM_3_run1_NB22

description: Library name: AGM_3_run1_NB22_GL34_077_GL_SC_1_plate1_F9_S77


title: OS742_RUNX2_NONE_2

description: Library name: OS742_RUNX2_NONE_2


title: JJ-10-391

description: colon content rDNA was sequenced


title: OS742_IgG_NONE_3

description: Library name: OS742_IgG_NONE_3


title: AGM_3_run1_NB12

description: Library name: AGM_3_run1_NB12_GL34_045_GL_SC_1_plate1_F23_S45


title: MII_mRNA_A


title: JJ-10-335

description: colon content rDNA was sequenced


title: OS742_IgG_NONE_2

description: Library name: OS742_IgG_NONE_2


title: JJ-12-111

description: colon content rDNA was sequenced


title: AGM_3_run1_NB06

description: Library name: AGM_3_run1_NB06_GL34_233_GL_SC_3_plate1_A2_S233


title: GV_mRNA_A


title: OS742_K27Ac_NONE_3

description: Library name: OS742_K27Ac_NONE_3


title: end-stage heart failure, patient HF380

city: Evanston

first: Timothy

last: Pan

state: IL

address: 633 Clark St

institute: Northwestern University

description:
Library name: HF380
snNanoRNA-seq

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, and gene counting were performed by scNanoGPS (v1.0) with default parameters to generate the gene expression matrix.
Sequence alignment files output by scNanoGPS were merged and used to run IsoQuant (v3.4.2) with the nanopore datatype setting to generate the isoform expression matrix.
Assembly: GRCh38 (GENCODE v44/Ensembl110 annotations)
Supplementary files format and content: "matrix_gene_*.tsv" contains the single cell gene expression for individual samples and was output by the scNanoGPS pipelines
Supplementary files format and content: "matrix_isoform_all_Samples.tsv" contains the single cell isoform expression for all samples and was output by IsoQuant v3.4.2.
Supplementary files format and content: "gtf_isoform_all_Samples.gtf" is the GTF file that was output by IsoQuant v3.4.2 and holds the necessary structural information for both annotated and novel transcripts.

molecule: total RNA

source_name: Heart, left ventricle

extract_protocol:
Single nuclei suspensions were prepared from approximately 50-100 mg frozen heart left ventricle tissues. Tissues were first cut into tiny pieces using scissors in ice-cold nuclei extraction buffer (Miltenyi Biotec) and dissociated in a gentleMACS Octo Dissociator. The resulting suspensions were centrifuged at 300 x g, strained in 70 µm MACS SmartStrainers, and washed in additional nuclei extraction buffer. Nuclei were then pelleted at 300 x g and gently resuspended in 1 mL ice-cold resuspension buffer (PBS, 0.1% BSA, 0.2 U/µL RNAse inhibitor).
Initial cDNA libraries were prepared according to the 10X Genomics Chromium Single Cell 3' v3.1 protocol with a target of 3,000 nuclei per sample. The cDNA PCR amplification elongation step was extended to 3 minutes and fragmentation and subsequent steps were not performed. Full-length Nanopore cDNA libraries were prepared according to the Oxford Nanopore Technologies SQK-LSK114 kit.

value: Heart, left ventricle


title: OS742_K27Ac_NONE_2

description: Library name: OS742_K27Ac_NONE_2


title: OS742_IgG_NONE_1

description: Library name: OS742_IgG_NONE_1


title: JJ-10-334

description: colon content rDNA was sequenced


title: JJ-10-333

description: colon content rDNA was sequenced


title: SPN_C

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore (version 0.6.7) (-q 25 --length 20 --max_n 3 --stringency 3). The filtered reads were passed quality control using FastQC3 (v0.11.5), followed by alignment to the mouse genome (GRCm39) by HISAT2 (version 2.2.1) with default parameters. The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14). Read counts of all samples were quantified using Feature Count (Version 2.0.1) with the mouse genome as a reference and were adjusted to provide CPM (counts per million mapped reads). Clustering analysis was performed using R (version 3.3.3), PCA analysis was used to visualize the clustering results. Differential gene expression analysis was performed using R package edgeR with default parameters. The genes were deemed differentially expressed if they provided a false discovery rate of <0.01 and fold change >2. Biological pathways (denoted as Gene Ontology terms) over-represented among up- and down-regulated genes were identified using R package ClusterProfiler. A P-value cutoff of 0.05 was used in selecting significant pathways.
Assembly: GRCm39
Supplementary files format and content: csv, normalized read counts

source_name: Embryo

extract_protocol:
RNA isolation from cultured cells was used Trizol reagent.
The RNA-seq libraries were generated using the Smart-seq2 v4 kit following the manufacturer’s instructions. Briefly, embryos were lysed, and mRNA was captured and amplified with the Smart-seq2 v4 kit (Clontech). After AMPure XP beads purification, the high-quality amplified RNAs were subject to library preparation using Nextera XT DNA Library Preparation Kit (Illumina) and multiplexed by Nextera XT Indexes (Illumina). The concentration of sequencing libraries was determined using Qubit dsDNA HS Assay Kit (Life Technologies). The size of sequencing libraries was determined using the Agilent D5000 ScreenTape with Tapestation 4200 system (Agilent). Pooled indexed libraries were then sequenced on the Illumina NovaSeq 6000 platform with 150-bp paired-end reads.

treatment_protocol: Hormonal stimulation and oocyte isolation: Female B6D2F1 mice, age 8-12 weeks, were injected by 7-8IU of pregnant mare serum gonadotropin (PMSG; Bioveta, Czech Republic) and were sacrificed by cervical dislocation approximately 44h later. Ovaries were isolated and transferred to EmbryoMax M2 manipulation media supplemented with 2.5µM Milrinone to suppress the germinal vesicle breakdown (GVBD). Cumulus oocyte complexes (COCs) were retrieved from follicles by 27G needles and then transferred to culture media (Eagle´s Alpha MEM supplemented as described previously (3). The oocytes were kept in a 5%CO2 incubator at 37°C. High quality oocytes were selected based on the criteria described in (4) and used further. To obtain metaphase II eggs, the B6D2F1 mice were first injected by 7-8IU PMSG, followed by 5IU human choriogonadotropin (hCG). After 14-16h, the animals were sacrificed by cervical dislocation and the oviducts were placed in EmbryoMax M2 media supplemented with hyaluronidase. The COCs were freed from the ampullae and transferred to EmbryoMax KSOM and kept till later use. Selective enucleation: To prepare cytoplasts with highly abnormal parameters, the germinal vesicle (GV) stage oocytes were subjected to selective enucleation.

value: Embryo

tag: condition

value: SPN


title: end-stage heart failure, patient HF379

description:
Library name: HF379
snNanoRNA-seq


title: OS526_TEAD1_NONE_2

description: Library name: OS526_TEAD1_NONE_2


title: SPN_B


title: JJ-10-331

description: colon content rDNA was sequenced


title: SPN_A


title: JJ-10-314

description: colon content rDNA was sequenced


title: OS526_RUNX2_NONE_3

description: Library name: OS526_RUNX2_NONE_3


title: end-stage heart failure, patient HF378

description:
Library name: HF378
snNanoRNA-seq


title: Zygote_mRNA_A


title: LPN_C

value: LPN


title: end-stage heart failure, patient HF375

description:
Library name: HF375
snNanoRNA-seq


title: OS526_RUNX2_NONE_2

description: Library name: OS526_RUNX2_NONE_2


title: JJ-10-313

description: colon content rDNA was sequenced


title: OS526_TEAD1_NONE_1

description: Library name: OS526_TEAD1_NONE_1


title: LPN_B


title: JJ-10-311

description: colon content rDNA was sequenced


title: OS526_RUNX2_NONE_1

description: Library name: OS526_RUNX2_NONE_1


title: end-stage heart failure, patient HF373

description:
Library name: HF373
snNanoRNA-seq


title: LP06029

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

description:
Library name: Sample21
Column name in raw_counts_All_Samples.tsv: LP06029

data_processing:
Reads in FASTQ format were generated using the Illumina bcl2fastq command-line tool (v2.19.1.403) and the Lexogen idemux tool for optimal demultiplexing of long, unique, dual indices. Reads were trimmed and filtered using cutadapt version 2.8 to trim polyA tails, remove reads with N's, and trim bases with a quality of less than 30 from the 3' ends of the reads. On average, 5 million reads were left after this procedure. Trimmed reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using the STAR aligner version 2.6.1a in 2-pass mode. STAR counted raw reads per gene. Differential gene expression was calculated using DESeq2 version 1.22.2.
Assembly: Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode.
Supplementary files format and content: raw_counts_All_Samples.tsv contains a matrix with raw gene counts, gene symbols, and gene types for each sample.

source_name: gingiva

growth_protocol: Gingival fibroblasts were isolated and expanded in DMEM supplemented with 10% fetal calf serum (FCS) and 1% antibiotics (Invitrogen Corporation, Carlsbad, CA).

extract_protocol:
Total RNA was isolated with the GeneMATRIX Universal RNA purification kit with DNAse digestion (EURX, Gdańsk, Poland).
Sequencing libraries from total RNA were prepared at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq 3' FWD protocol version 2 with unique dual indices (Lexogen GmbH, Vienna, Austria). Fifteen PCR cycles were used for library preparation, as determined by quantitative PCR (qPCR) according to the library preparation manual.

treatment_protocol: Gingival fibroblasts were seeded at 30.000 cells/cm2 onto Mucoderm®, Collafleece® and Jason® membranes that were coated with HA and underwent lyophilization (all botiss biomaterials GmbH, Zossen, Germany). Since this is a confidential procedure, no details on the source and concentration of the HA, as well as the lyophilization procedure can be provided.

value: gingiva

value: gingival fibroblast

value: treated with Jason®


title: LPN_A


title: OS526_K27Ac_NONE_3

description: Library name: OS526_K27Ac_NONE_3


title: non-diseased, patient ND248

description:
Library name: ND248
snNanoRNA-seq


title: LP06018

description:
Library name: Sample20
Column name in raw_counts_All_Samples.tsv: LP06018


title: non-diseased, patient ND245

description:
Library name: ND245
snNanoRNA-seq


title: EPN_B

value: EPN


title: OS526_K27Ac_NONE_2

description: Library name: OS526_K27Ac_NONE_2


title: EPN_C


title: OS526_K27Ac_NONE_1

description: Library name: OS526_K27Ac_NONE_1


title: LP06028

description:
Library name: Sample18
Column name in raw_counts_All_Samples.tsv: LP06028

value: treated with Collafleece®


title: OS526_JUN_NONE_2

description: Library name: OS526_JUN_NONE_2

value: JUN


title: non-diseased, patient ND236

description:
Library name: ND236
snNanoRNA-seq


title: LP06017

description:
Library name: Sample17
Column name in raw_counts_All_Samples.tsv: LP06017


title: end-stage heart failure, patient HF374

description:
Library name: HF374
snNanoRNA-seq


title: G534_TP186_HP40_LR_E5

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

description: Library name: G534_TP186_HP40_LR_E5

data_processing:
Raw reads were aligned to Mmul_10 using the STAR aligner (version 2.7.0e)
Assembly: Mmul_10
Supplementary files format and content: comma-seperated file containing the raw couts of all samples

organism: Macaca mulatta

source_name: Inguinal lymph node

extract_protocol:
RNA was extracted from inguinal lymph node mononuclear cells . The quality of the recovered RNA was determined using a Bioanalyzer/TapeStation.
Sequencing libraries were generating following Illumina protocol.

value: Inguinal lymph node

value: Mononuclear cells

value: DNA+gp120 protein

tag: animal id

tag: vaccine route

value: Both legs, SubQ

tag: number of_challenges_to_infection

tag: inoculated leg

value: LR


title: LP06006

description:
Library name: Sample16
Column name in raw_counts_All_Samples.tsv: LP06006


title: non-diseased, patient ND178

description:
Library name: ND178
snNanoRNA-seq


title: G533_TP186_HP40_LL_E5

description: Library name: G533_TP186_HP40_LL_E5

value: LL


title: G532_TP186_GM62_LR_E5

description: Library name: G532_TP186_GM62_LR_E5

value: Separate legs, SubQ


title: LP06027

description:
Library name: Sample15
Column name in raw_counts_All_Samples.tsv: LP06027

value: treated with Collafleece® + HA


title: G531_TP186_GM62_LL_E5

description: Library name: G531_TP186_GM62_LL_E5


title: OS526_IgG_NONE_2

description: Library name: OS526_IgG_NONE_2

value: OS PDX-derived

value: IgG


title: G530_TP186_HE88_LR_E5

description: Library name: G530_TP186_HE88_LR_E5


title: OS526_IgG_NONE_1

description: Library name: OS526_IgG_NONE_1


title: LP06007

description:
Library name: Sample19
Column name in raw_counts_All_Samples.tsv: LP06007


title: LP06005

description:
Library name: Sample13
Column name in raw_counts_All_Samples.tsv: LP06005


title: OS526_FOSL2_NONE_2

description: Library name: OS526_FOSL2_NONE_2


title: G528_TP186_JE14_LR_E5

description: Library name: G528_TP186_JE14_LR_E5

value: ND


title: LP06026

description:
Library name: Sample12
Column name in raw_counts_All_Samples.tsv: LP06026

value: gingiva

value: treated with Jason® + HA


title: OS526_FOSL2_NONE_1

description: Library name: OS526_FOSL2_NONE_1


title: EPN_A

value: Embryo


title: non-diseased, patient ND202

description:
Library name: ND202
snNanoRNA-seq

value: Heart, left ventricle


title: G527_TP186_JE14_LL_E5

description: Library name: G527_TP186_JE14_LL_E5


title: LP06015

description:
Library name: Sample11
Column name in raw_counts_All_Samples.tsv: LP06015

value: gingival fibroblast


title: OS526_JUN_NONE_1

description: Library name: OS526_JUN_NONE_1

value: JUN


title: OS526_FOSL1_NONE_2

description: Library name: OS526_FOSL1_NONE_2


title: Intestinal epithelial cells from the ileum C57BL/6J mouse 11

city: Lisbon

first: Eric

last: de Sousa

address: Champalimaud Centre for the Unknown, Avenida Brasília

department: Champalimaud Research

country: Portugal

institute: Champalimaud Foundation

description: Library name: I11

data_processing:
STAR version 2.7.11b was used to align reads to the reference and to count the number of reads per gene
Assembly: GRCm9
Supplementary files format and content: Tab-delimited text files contain raw counts for each sample

source_name: Ileum

extract_protocol:
RNA was isolated using RNeasy Plus Mini Kit (Qiagen)
RNA-Seq library construction via SMART-SeqII  protocol combined with transposase-based library construction technique

value: Ileum

tag: strain

tag: age

value: 8-10 weeks

tag: genotype

value: WT


title: Intestinal epithelial cells from the ileum C57BL/6J mouse 12

description: Library name: I12


title: G526_TP186_GM16_LR_E5

description: Library name: G526_TP186_GM16_LR_E5

value: Inguinal lymph node

value: Mononuclear cells

value: DNA+gp120 protein

value: Both legs, SubQ


title: Intestinal epithelial cells from the duodenum C57BL/6J mouse 12

description: Library name: D12

source_name: Duodenum

value: Duodenum


title: Intestinal epithelial cells from the ileum C57BL/6J mouse 10

description: Library name: I10


title: Intestinal epithelial cells from the ileum C57BL/6J mouse 9

description: Library name: I9


title: Intestinal epithelial cells from the duodenum C57BL/6J mouse 11

description: Library name: D11


title: G519_TP186_GK91_LL_E5

description: Library name: G519_TP186_GK91_LL_E5

value: Separate legs, SubQ

value: LL


title: LP06025

description:
Library name: Sample9
Column name in raw_counts_All_Samples.tsv: LP06025

value: treated with Mucoderm® + HA


title: OS526_FOSL1_NONE_1

description: Library name: OS526_FOSL1_NONE_1

value: OS PDX-derived


title: OS526_IgG_NONE_3

description: Library name: OS526_IgG_NONE_3

value: IgG


title: LP06016

description:
Library name: Sample14
Column name in raw_counts_All_Samples.tsv: LP06016

value: gingiva

value: treated with Collafleece® + HA


title: OS525_K27Ac_NONE_2

description: Library name: OS525_K27Ac_NONE_2


title: G517_TP186_EE71_LL_E5

description: Library name: G517_TP186_EE71_LL_E5


title: Intestinal epithelial cells from the duodenum C57BL/6J mouse 10

description: Library name: D10


title: OS525_K27Ac_NONE_1

description: Library name: OS525_K27Ac_NONE_1


title: Intestinal epithelial cells from the duodenum C57BL/6J mouse 9

description: Library name: D9


title: LP06014

description:
Library name: Sample8
Column name in raw_counts_All_Samples.tsv: LP06014

value: gingival fibroblast


title: G516_TP186_GN03_LR_E4

description: Library name: G516_TP186_GN03_LR_E4

value: LR


title: G515_TP186_JC12_LR_E4

description: Library name: G515_TP186_JC12_LR_E4


title: LP06003

description:
Library name: Sample7
Column name in raw_counts_All_Samples.tsv: LP06003


title: OS525_IgG_NONE_2

description: Library name: OS525_IgG_NONE_2


title: OS525_IgG_NONE_1

description: Library name: OS525_IgG_NONE_1


title: LP06024

description:
Library name: Sample6
Column name in raw_counts_All_Samples.tsv: LP06024

value: treated with Mucoderm®


title: G514_TP186_IJ26_LL_E4

description: Library name: G514_TP186_IJ26_LL_E4


title: LP06013

description:
Library name: Sample5
Column name in raw_counts_All_Samples.tsv: LP06013


title: LP06002

description:
Library name: Sample4
Column name in raw_counts_All_Samples.tsv: LP06002


title: G513_TP186_JF94_LR_E4

description: Library name: G513_TP186_JF94_LR_E4


title: G512_TP186_JF94_LL_E4

description: Library name: G512_TP186_JF94_LL_E4


title: LP06004

description:
Library name: Sample10
Column name in raw_counts_All_Samples.tsv: LP06004

value: treated with Jason® + HA


title: Control13

type: RNA

city: Basel

first: Judith

last: Zaugg

address: Hebelstrasse 20

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

hyb_protocol: Hybridized according to manufacturer protocol.

scan_protocol: Scanned according to manufacturer protocol.

data_processing: nSolver software package and nSolver Advanced Analysis module (NanoString Technologies) were used to evaluate the determined transcript counts. Quality-checked raw data was normalized utilizing the geometric mean of the housekeeping reference genes and the code sets’ internal positive controls were used to exclude samples that are outliers

label: NanoString Oligonucleotide Probe

source_name: Whole bone marrow aspirate

label_protocol: Labeled according to manufacturer protocols.

extract_protocol: Total mRNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen) following the manufacturer’s instructions. 150-300 ng RNA was extracted per sample.

value: Control


title: OS457_K27Ac_NONE_2

description: Library name: OS457_K27Ac_NONE_2


title: LP06023

description:
Library name: Sample3
Column name in raw_counts_All_Samples.tsv: LP06023

value: Tissue culture surface (TCS)


title: OS457_IgG_NONE_2

description: Library name: OS457_IgG_NONE_2


title: OS457_K27Ac_NONE_1

description: Library name: OS457_K27Ac_NONE_1


title: LP06012

description:
Library name: Sample2
Column name in raw_counts_All_Samples.tsv: LP06012


title: CHIP15

value: CHIP


title: Control16


title: G510_TP186_GI29_LL_E4

description: Library name: G510_TP186_GI29_LL_E4

value: Inguinal lymph node

value: Mononuclear cells

value: DNA+gp120 protein


title: Control22


title: Control2


title: OS457_IgG_NONE_1

description: Library name: OS457_IgG_NONE_1


title: LP06001

description:
Library name: Sample1
Column name in raw_counts_All_Samples.tsv: LP06001


title: OS384_K27Ac_NONE_2

description: Library name: OS384_K27Ac_NONE_2


title: PDO131 Patient-derived tumor organoids, RM-044, replicate2

city: Barcelona

first: Adria-Jaume

last: Roura

address: Carrer de Baldiri Reixac, 10

country: Spain

institute: IRB Barcelona

description:
Library name: Sample 8
Column name in raw_counts_All_samples.txt: 1143_2025_S16

data_processing:
Trim Galore (v0.0.6) was utilized for quality control and adapter trimming of FASTQ files
Single-end reads were aligned to the hg38 mouse genome using STAR (v2.7.10a)
The count matrix was generated with Rsubread’s featureCounts function, using the GENCODE (v34) primary assembly GTF annotation
Differential expression analysis was performed with DESeq2 (v1.42.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Patient-derived tumor organoids (PDO)

extract_protocol:
RNA was extracted using the PureLinkTM RNA Mini Kit (Life Technologies, 12183025) and PureLinkTM DNAse (Life Technologies, 12185010) following the manufacturer’s specifications. RNA was eluted using distilled water (Invitrogen, 10977-035) and the concentration was determined using the Nanodrop 1000 spectrophotometer (ThermoFisher)
Libraries were prepared using RNA-seq Stranded mRNA Library Illumina and sequenced with Illumina NextSeq 2000 P3. Trim Galore (v0.0.6) was utilized for quality control and adapter trimming of FASTQ files

value: Patient-derived tumor organoids (PDO)

value: Epithelial malignant cells

value: AKT mutant

value: RM-044 KRASi


title: OS384_K27Ac_NONE_1

description: Library name: OS384_K27Ac_NONE_1

value: OS PDX-derived


title: G508_TP186_JE99_LL_E4

description: Library name: G508_TP186_JE99_LL_E4

value: Both legs, SubQ

value: LL


title: PDO131 Patient-derived tumor organoids, RM-044, replicate1

description:
Library name: Sample 7
Column name in raw_counts_All_samples.txt: 1142_2025_S15


title: CHIP16


title: OS384_IgG_NONE_2

description: Library name: OS384_IgG_NONE_2

value: IgG


title: CHIP9


title: PDO131 Patient-derived tumor organoids, vehicle control, replicate2

description:
Library name: Sample 6
Column name in raw_counts_All_samples.txt: 1141_2025_S14


title: G511_TP186_GM52_LR_E4

description: Library name: G511_TP186_GM52_LR_E4

value: Separate legs, SubQ

value: ND

value: LR


title: G507_TP186_IA36_LR_E4

description: Library name: G507_TP186_IA36_LR_E4


title: PDO131 Patient-derived tumor organoids, vehicle control, replicate1

description:
Library name: Sample 5
Column name in raw_counts_All_samples.txt: 1140_2025_S13


title: G506_TP186_IA36_LL_E4

description: Library name: G506_TP186_IA36_LL_E4


title: OS186_K27Ac_NONE_2

description: Library name: OS186_K27Ac_NONE_2


title: OS186_K27Ac_NONE_1

description: Library name: OS186_K27Ac_NONE_1


title: MDS22

value: MDS


title: MDS16


title: MDS17


title: C31M Patient-derived tumor organoids, RM-044, replicate1

description:
Library name: Sample 3
Column name in raw_counts_All_samples.txt: 1134_2025_S7


title: CHIP5


title: G503_TP186_GI36_LR_E4

description: Library name: G503_TP186_GI36_LR_E4


title: OS186_IgG_NONE_1

description: Library name: OS186_IgG_NONE_1


title: C31M Patient-derived tumor organoids, vehicle control, replicate2

description:
Library name: Sample 2
Column name in raw_counts_All_samples.txt: 1133_2025_S6


title: G509_TP186_JE99_LR_E4

description: Library name: G509_TP186_JE99_LR_E4


title: MDS23


title: OS152_RUNX2_NONE_1

description: Library name: OS152_RUNX2_NONE_1


title: Control5

value: Control


title: G502_TP186_GI36_LL_E4

description: Library name: G502_TP186_GI36_LL_E4


title: OS152_K27Ac_NONE_3

description: Library name: OS152_K27Ac_NONE_3


title: G501_TP186_GM41_LR_E3

description: Library name: G501_TP186_GM41_LR_E3


title: OS384_IgG_NONE_1

description: Library name: OS384_IgG_NONE_1


title: BeWo b30 Ctrl 3

city: Moscow

first: Ivan

last: Antipenko

address: 11 Pokrovksy Bulvar, Moscow, 109028, Russia

country: Russia

institute: HSE University

description:
Library name: Sample 9
Column name in counts.tsv and fpkm.tsv: BeWo-Ctrl-3

data_processing:
FASTQ quality was assessed with FastQC v0.11.9.
Adapters were trimmed with cutadapt v2.10.
Trimmed mRNA-seq reads were aligned to the human reference genome (GENCODE GRCh38.p13) with STAR v2.7.5b using GENCODE annotation release 34.
Gene-level counts were generated with STAR (‘--quantMode GeneCounts’) using the same GENCODE r34 GTF.
Library sizes were normalized with the trimmed mean of M-values (TMM) method in edgeR v3.30.3; low-expression features were filtered with edgeR default settings.
FPKM values were computed in edgeR using GENCODE gene lengths; values used in downstream analyses were log2-transformed.
For downstream analyses, genes in the lower 25% by median FPKM within each experimental condition were excluded.
Assembly: GRCh38.p13 (hg38), GENCODE release 34 (primary assembly; GCA_000001405.28)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: placental choriocarcinoma

growth_protocol: BeWo b30 cells were cultured in T25 flasks with ventilated caps (Costar, Corning) at 37 °C and 5% CO₂. The culture medium was DMEM (4.5 g/L glucose) supplemented with 10% FBS, 1% MEM Non-Essential Amino Acids (100X), 2 mM L-glutamine, and 1% Penicillin-Streptomycin solution (10,000 U/mL) (all reagents from Gibco, Thermo Fisher Scientific, USA). Cells were passaged every 2–3 days using 0.25% trypsin-EDTA solution (PanEco, Cat. P034).

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (QIAGEN, Germany). RNA concentration was determined with a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, USA), and quality control was performed using the Experion automated electrophoresis system (Bio-Rad, USA). The RNA Quality Indicator (RQI) was at least 9 for all analyzed samples.
Libraries for next-generation sequencing (NGS) were prepared using the Illumina Stranded mRNA Library Prep Kit (Illumina, USA). Sequencing was performed on a NextSeq 500 system (Illumina, USA).

treatment_protocol: Upon reaching 80% confluence, the culture medium was replaced either with fresh medium with 0,05% DMSO or with medium containing 0,05% DMSO and 300 μM cobalt (II) chloride (Sigma-Aldrich, USA) or 0,05% DMSO and 5 μM oxyquinoline derivative 4896-3212 (ChemRar, Russia). After 24 h of incubation, the cells were lysed in 700 μL of QIAzol Lysis Reagent (QIAGEN).

value: placental choriocarcinoma

value: BeWo b30

value: placental choriocarcinoma cell line

value: WT


title: G500_TP186_GB06_LR_E3

description: Library name: G500_TP186_GB06_LR_E3

value: Inguinal lymph node

value: Mononuclear cells

value: DNA+gp120 protein


title: OS152_K27Ac_NONE_2

description: Library name: OS152_K27Ac_NONE_2


title: BeWo b30 Ctrl 2

description:
Library name: Sample 8
Column name in counts.tsv and fpkm.tsv: BeWo-Ctrl-2


title: Control12


title: OS152_K27Ac_NONE_1

description: Library name: OS152_K27Ac_NONE_1


title: C31M Patient-derived tumor organoids, RM-044, replicate2

description:
Library name: Sample 4
Column name in raw_counts_All_samples.txt: 1135_2025_S8

value: Patient-derived tumor organoids (PDO)

value: Epithelial malignant cells

value: AKT mutant

value: RM-044 KRASi


title: G505_TP186_IA21_LR_E4

description: Library name: G505_TP186_IA21_LR_E4

value: Both legs, SubQ


title: G504_TP186_IA21_LL_E4

description: Library name: G504_TP186_IA21_LL_E4

value: LL


title: G499_TP186_JC52_LR_E3

description: Library name: G499_TP186_JC52_LR_E3

value: Separate legs, SubQ


title: OS152_IgG_NONE_3

description: Library name: OS152_IgG_NONE_3

value: OS PDX-derived

value: IgG


title: Control14

value: Control


title: BeWo b30 Oxy 3

description:
Library name: Sample 6
Column name in counts.tsv and fpkm.tsv: BeWo-Oxy-3

value: placental choriocarcinoma

value: 0,05% DMSO + oxyquinoline derivative (4896-3212) 5 μM


title: BeWo b30 Ctrl 1

description:
Library name: Sample 7
Column name in counts.tsv and fpkm.tsv: BeWo-Ctrl-1

value: BeWo b30

value: placental choriocarcinoma cell line


title: OS152_IgG_NONE_1

description: Library name: OS152_IgG_NONE_1


title: OS152_IgG_NONE_2

description: Library name: OS152_IgG_NONE_2


title: BeWo b30 Oxy 2

description:
Library name: Sample 5
Column name in counts.tsv and fpkm.tsv: BeWo-Oxy-2

value: WT


title: G498_TP186_JC52_LL_E3

description: Library name: G498_TP186_JC52_LL_E3

value: Inguinal lymph node

value: Mononuclear cells


title: Control1


title: BeWo b30 Oxy 1

description:
Library name: Sample 4
Column name in counts.tsv and fpkm.tsv: BeWo-Oxy-1


title: CHIP2

value: CHIP


title: CHIP3


title: OS052_K27Ac_NONE_2

description: Library name: OS052_K27Ac_NONE_2


title: G495_TP186_GH35_LR_E3

description: Library name: G495_TP186_GH35_LR_E3

value: DNA+gp120 protein

value: LR


title: C31M Patient-derived tumor organoids, vehicle control, replicate1

description:
Library name: Sample 1
Column name in raw_counts_All_samples.txt: 1132_2025_S5

value: Patient-derived tumor organoids (PDO)

value: Epithelial malignant cells

value: AKT mutant


title: BeWo b30 CoCl2 3

description:
Library name: Sample 3
Column name in counts.tsv and fpkm.tsv: BeWo-CoCl2-3

value: 0,05% DMSO + 300 μM cobalt (II) chloride


title: MDS11

value: MDS


title: OS052_K27Ac_NONE_1

description: Library name: OS052_K27Ac_NONE_1

value: OS PDX-derived


title: OS052_IgG_NONE_2

description: Library name: OS052_IgG_NONE_2

value: IgG


title: BeWo b30 CoCl2 2

description:
Library name: Sample 2
Column name in counts.tsv and fpkm.tsv: BeWo-CoCl2-2

value: placental choriocarcinoma


title: G494_TP186_GH35_LL_E3

description: Library name: G494_TP186_GH35_LL_E3

value: Separate legs, SubQ

value: LL


title: G493_TP186_GC03_LR_E3

description: Library name: G493_TP186_GC03_LR_E3


title: G497_TP186_GJ04_LR_E3

description: Library name: G497_TP186_GJ04_LR_E3


title: MDS14


title: BeWo b30 CoCl2 1

description:
Library name: Sample 1
Column name in counts.tsv and fpkm.tsv: BeWo-CoCl2-1

value: BeWo b30

value: placental choriocarcinoma cell line


title: OS052_IgG_NONE_1

description: Library name: OS052_IgG_NONE_1


title: CHIP14


title: MDS15


title: CHIP1


title: G492_TP186_GC03_LL_E3

description: Library name: G492_TP186_GC03_LL_E3

value: Inguinal lymph node


title: OS833_H3K27Ac_3

data_processing:
*library strategy: CUT&Run
CUT&Run samples were processed using a custom pipeline scripted with CGPipe. FastQ files were paired, trimmed, and aligned to both human (hg38) and yeast (sac3) genomes using Bowtie2 with the ‘--dovetail’ setting. Reads were classified as human or yeast using the NGSUtilsJ bam-best function, and yeast-aligned reads were removed. Peak calling was performed with MACS3
Assembly: hg38
Supplementary files format and content: bedGraph pileups generated using MACS2

source_name: From PDX

extract_protocol:
Cells were harvested using trypsine and used as input for CUT&RUN libraries.
DNA from enriched chromatin samples was purified using the DNA Purification Buffers and Spin Columns kit (#14209, CST). DNA libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (#E7645L, NEB) and NEBNext® Multiplex Oligos for Illumina® (#E7600S, NEB).
CUT&Run was performed using the CUT&RUN Assay Kit (#86652, CST) according to manufacturer’s protocol. 1.0x105 cells were used per antibody. Briefly, cells were harvested, washed, and bound to activated Concanavalin A-coated magnetic beads and permeabilized. The bead-cell complex was incubated overnight with either an Acetyl-Histone H3 (Lys27) antibody (#8173, CST), Mono-Methyl-Histone H3 (Lys4) antibody (#5326, CST), Tri-Methyl-Histone H3 (Lys4) antibody (#9751, CST) or an IgG antibody control (#66362, CST) at 4°C. Cells were then washed with digitonin buffer, resuspended in 50 μl of pAG/Mnase and incubated for 1h at 4°C. Spike-In DNA (5ng) was added to each reaction.

value: From PDX

value: Osteosarcoma PDX-cell line


title: G491_TP186_JC25_LR_E3

description: Library name: G491_TP186_JC25_LR_E3

value: Mononuclear cells

value: DNA+gp120 protein

value: Both legs, SubQ


title: G496_TP186_GJ04_LL_E3

description: Library name: G496_TP186_GJ04_LL_E3


title: OS742_siSP7_3

description: Library name: B09

data_processing:
Reads were trimmed using NGSUtils. Trimmed reads were aligned to the GRCh38.p5 human genome assembly with Bowtie2 using the ‘--very-sensitive’ parameter. Duplicates and mitochondrial reads were removed using NGSUtils, and reads with high mapping quality (>q30) were retained using Samtools. Peak calling was performed with MACS2, using default options and flags ‘-nomodel –keep-dup all’. Peaks overlapping ENCODE blacklisted features were discarded, and only peaks with FDR q ≤ 0.01 were retained
Assembly: hg38
Supplementary files format and content: bedGraph pileups generated using MACS2

extract_protocol:
Cell lines were harvested using trypsin and used as input in ATAC-seq libraries.
ATAC-seq libraries were prepared with minor modifications as previously described. Briefly, 1x10^5 cells were lysed on ice to isolate nuclei, which were then incubated with Tn5 transposase (Illumina) at 37 °C for 30 minutes with shaking. Libraries were amplified by PCR for 6-11 cycles, purified using SPRI beads, and sequenced at the UCSF CAT facility using HiSeq 4000 with 100-bp paired-end reads. Fresh/frozen PDXs or patient samples followed the same preparation method.


title: MDS2


title: OS833_H3K27Ac_2


title: OS833_H3K27Ac_1


title: G490_TP186_JC25_LL_E3

description: Library name: G490_TP186_JC25_LL_E3


title: OS742_siSP7_1

description: Library name: B07


title: Control31

value: Control


title: Control32


title: G489_TP186_GI46_LR_E3

description: Library name: G489_TP186_GI46_LR_E3

value: LR


title: OS742_siSP7_2

description: Library name: B08


title: G488_TP186_GI46_LL_E3

description: Library name: G488_TP186_GI46_LL_E3


title: G487_TP186_GH90_LR_E3

description: Library name: G487_TP186_GH90_LR_E3


title: OS742_siRUNX2_2

description: Library name: B05


title: OS833_IgG_1


title: OS774_H3K27Ac_1


title: CHIP10

value: CHIP


title: G486_TP186_GH90_LL_E3

description: Library name: G486_TP186_GH90_LL_E3


title: G485_TP186_FG06_LR_E3

description: Library name: G485_TP186_FG06_LR_E3

value: ND


title: OS742_siRUNX2_1

description: Library name: B04

value: OS PDX-derived


title: OS774_IgG_3


title: OS742_siNeg_3

description: Library name: B03

value: siNeg


title: OS742_siNeg_2

description: Library name: B02


title: Control10


title: CHIP11


title: Control30


title: OS742_siNeg_1

description: Library name: B01


title: CHIP13


title: CHIP12


title: G483_TP186_GI26_LR_E2

description: Library name: G483_TP186_GI26_LR_E2


title: OS774_IgG_1


title: G484_TP186_FG06_LL_E3

description: Library name: G484_TP186_FG06_LL_E3


title: OS742_siRUNX2_3

description: Library name: B06


title: MDS6

value: MDS


title: G482_TP186_GI26_LL_E2

description: Library name: G482_TP186_GI26_LL_E2


title: os833_siSP7_3

description: Library name: A09


title: OS766_H3K27Ac_2


title: os833_siSP7_2

description: Library name: A08


title: MDS1


title: G481_TP186_GH91_LR_E2

description: Library name: G481_TP186_GH91_LR_E2

value: Separate legs, SubQ


title: OS766_H3K27Ac_1


title: MDS4


title: G480_TP186_GH91_LL_E2

description: Library name: G480_TP186_GH91_LL_E2

value: LL


title: os833_siSP7_1

description: Library name: A07


title: OS774_IgG_2


title: G479_TP186_IV92_LR_E2

description: Library name: G479_TP186_IV92_LR_E2


title: OS766_IgG_1


title: os833_siRUNX2_3

description: Library name: A06


title: OS766_IgG_2


title: os833_siRUNX2_1

description: Library name: A04


title: G477_TP186_HV65_LR_E2

description: Library name: G477_TP186_HV65_LR_E2


title: MDS3


title: G476_TP186_HV65_LL_E2

description: Library name: G476_TP186_HV65_LL_E2


title: G478_TP186_IV92_LL_E2

description: Library name: G478_TP186_IV92_LL_E2


title: os833_siRUNX2_2

description: Library name: A05


title: os833_siNeg_3

description: Library name: A03


title: OS742_H3K27Ac_4


title: os833_siNeg_2

description: Library name: A02


title: OS742_H3K27Ac_5


title: os833_siNeg_1

description: Library name: A01


title: OS742_H3K27Ac_3


title: G474_TP186_IC95_LL_E2

description: Library name: G474_TP186_IC95_LL_E2


title: G475_TP186_IC95_LR_E2

description: Library name: G475_TP186_IC95_LR_E2


title: G473_TP186_EE32_LR_E2

description: Library name: G473_TP186_EE32_LR_E2


title: OS384 ATACseq Portion

description:
Library name: PDX_OS384_ATAC
Expression

data_processing:
Raw sequencing data from the single-cell multiome experiment were processed using the Cell Ranger ARC pipeline (10x Genomics, version 2.0.0) to generate gene expression and chromatin accessibility matrices. The cellranger-arc count command was used with a pre-built human reference genome (10x Genomics, GRCh38-2020-A-2.0.0).
Assembly: hg38
Supplementary files format and content: h5 for gene experssion matrix and data matrix for atacseq

molecule: nuclear RNA

source_name: PDX

growth_protocol: The xenografts were grown in subcutaneous model in NSG mice

extract_protocol:
We used protocol CG000505 from 10X genomics for nuclei isolation from tissue.
We used the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000285) as instructed by the manufacturer.

value: PDX


title: OS833_IgG_2


title: OS384 Expression Portion

description:
Library name: PDX_OS384_GEX
ATACseq

library_source: genomic single cell


title: OS742_IgG_5


title: G472_TP186_EE32_LL_E2

description: Library name: G472_TP186_EE32_LL_E2


title: OS742_IgG_4


title: OS833 Expression Portion

description:
Library name: PDX_OS833_GEX
Expression


title: G471_TP186_GM22_LR_E2

description: Library name: G471_TP186_GM22_LR_E2


title: OS833 ATACseq Portion

description:
Library name: PDX_OS833_ATAC
ATACseq


title: OS742_IgG_3


title: G470_TP186_GM22_LL_E2

description: Library name: G470_TP186_GM22_LL_E2


title: OS742_IgG_2


title: G469_TP186_GM40_LR_E2

description: Library name: G469_TP186_GM40_LR_E2


title: OS774 Expression Portion

description:
Library name: PDX_OS774_GEX
Expression


title: OS742_IgG_1


title: G468_TP186_IN66_LR_E2

description: Library name: G468_TP186_IN66_LR_E2


title: OS742_H3K27Ac_2


title: OS526 Expression Portion

description:
Library name: PDX_OS526_GEX
Expression


title: OS774 ATACseq Portion

description:
Library name: PDX_OS774_ATAC
ATACseq


title: OS526_H3K27Ac_3


title: G467_TP186_IN66_LL_E2

description: Library name: G467_TP186_IN66_LL_E2


title: OS526 ATACseq Portion

description:
Library name: PDX_OS526_ATAC
ATACseq


title: OS742_H3K27Ac_1


title: OS526_H3K27Ac_2


title: GIC from tumor 4 channel C

type: genomic

city: Badalona

first: Mar

last: Mallo

address: Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC

institute: Josep Carreras Leukaemia Research Institute

description:
8_(OncoScan_CNV).OSCHP
Hybridized to OncoScan CNV

hyb_protocol: As per manufacturer (ThermoFisher)

scan_protocol: As per manufacturer (ThermoFisher)

data_processing:
The array image was acquired using ThermoFihser GeneChip® Operating Software. Copy number and SNP study was performed with the Chromosome Analysis Suite (ThermoFisher, versión 4.2).
Copy number and SNP data (OSCHP file). One OSCHP per two CEL files

label: Biotin

source_name: GIC from tumor

label_protocol: As per manufacturer (ThermoFisher)

extract_protocol: The genomic DNA was extracted from primary cultures by using the Blood and Cell Culture DNA Mini kit (Qiagen 13323, Hilden, Germany) and from tumor tissues by using the QIAamp DNA FFPE Tissue Kit.

value: GIC from tumor


title: AKTP MTO mouse tumor organoids, vehicle control, replicate 2

description:
Library name: Sample 14
Column name in counts.txt: 326123_Organoid_DMSO
Column name in tcCounts.txt: 326123_Organoid_DMSO

data_processing:
Gene and 3' UTR annotations were assembled as described in Muhar et. al. Here, annotations were obtained from the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables, June 2016). 3’ UTR annotations were assigned to Entrez GeneIDs and collapsed on a per-gene basis using bedtools’ merge command. For genes lacking an annotated 3' UTR, Ensembl v84 3' UTRs were added if available. Adapters were trimmed from raw reads using cutadapt through the trim_galore (v0.3.7) wrapper tool with adapter overlaps set to 3bp for trimming.
Trimmed reads were further processed using SlamDunk v0.2.4 (http://github.com/t-neumann/slamdunk), running the full analysis procedure (slamdunk all) and aligning against the mouse genome (mm10), trimming 12bp from the 5’ end, reporting up to 100 alignments for multi-mappers and activating the multi-mapper retention strategy, filtering for variants with a variant fraction of 0.2 and filtering for base-quality cutoff of ≥27. Unless indicated otherwise, reads were filtered for having ≥2 T>C conversions. Remaining parameters were left to their defaults. Genes with total counts of 5 or greater across all samples were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text includes total raw counts for total RNA and for T>C counts

source_name: Mouse Tumor Organoids (MTO)

extract_protocol:
RNA was extracted using TRIzol reagent followed by chloroform phase separation. Total RNA was subjected to alkylation by iodoacetamide (Sigma, 10mM) for 15 min and RNA was repurified by ethanol precipitation.
500ng alkylated RNA were used as input for generating 3’-end mRNA sequencing libraries using a commercially available kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina and PCR Add-on Kit for Illumina, Lexogen). Deep sequencing was performed using NovaSeqX platforms (Illumina).

value: Mouse Tumor Organoids (MTO)

value: Epithelial malignant cells

value: AKTP mutant


title: GIC from tumor 4 channel A


title: AKTP MTO mouse tumor organoids, vehicle control, replicate 1

description:
Library name: Sample 13
Column name in counts.txt: 326122_Organoid_DMSO
Column name in tcCounts.txt: 326122_Organoid_DMSO


title: OS526_H3K27Ac_1

value: From PDX

value: Osteosarcoma PDX-cell line


title: OS526_IgG_3


title: OS107 Expression Portion

description:
Library name: PDX_OS107_GEX
Expression


title: AKTP MTO mouse tumor organoids, vehicle control, replicate 3

description:
Library name: Sample 15
Column name in counts.txt: 326124_Organoid_DMSO
Column name in tcCounts.txt: 326124_Organoid_DMSO


title: OS107 ATACseq Portion

description:
Library name: PDX_OS107_ATAC
ATACseq


title: Tumor 4 channel C

description:
7_(OncoScan_CNV).FFPE.OSCHP
Hybridized to OncoScan CNV

source_name: Tumor

value: Tumor


title: AKTP MTO mouse tumor organoids, RM-044 14h, replicate 3

description:
Library name: Sample 12
Column name in counts.txt: 326121_Organoid_12h
Column name in tcCounts.txt: 326121_Organoid_12h

value: RM-044 KRASi


title: Tumor 4 channel A


title: MV4-11, LAA+ATRA, ATAC-seq, rep3

city: Miami

first: Luisa

last: Cimmino

state: Florida

address: 1501 NW 10th Ave, BRB 711

institute: University of Miami

description: Library name: mv4_com3

data_processing:
Reads were trimmed and filtered using cutadapt and Trim Galore
Reads were aligned to hg38 with Bowtie2(v2.3.5)
Duplicates discarded with Picard(v2.18.27)
MACS2(v2.1.0.20150731) was used to call peaks.
Assembly: hg38
Supplementary files format and content: .bigwig files containing indexed binary format alignment data for viewing on a genome browser
Supplementary files format and content: narrowPeak.gz files containing compressed peak data in bed format

growth_protocol: MV4-11 cells were cultured in vitro with RPMI 1640, 10% fetal bovine serum, and 10 units/mL penicillin and 10µg/mL streptomycin in a humidified incubator at 37˚C and 5% CO2.

extract_protocol:
Nuclei were extracted from 50,000 cells per sample, using the Diagenode ATAC-seq kit (C01080002).
Diagenode ATAC-seq kit (C01080002) also used for library construction along with unique dual-indexing primers for tagmented libraries (C01011034)

treatment_protocol: Cells were treated for 72hr with 250µM L-ascorbic acid (LAA; Sigma A4544; dissolved in PBS), 1µM all-trans retinoic acid (ATRA; Sigma R2625; dissolved in DMSO), the combination thereof, or vehicle controls (PBS+DMSO).

value: macrophage

value: LAA + ATRA


title: AKTP MTO mouse tumor organoids, RM-044 14h, replicate 2

description:
Library name: Sample 11
Column name in counts.txt: 326120_Organoid_12h
Column name in tcCounts.txt: 326120_Organoid_12h


title: OS526_IgG_1


title: OS526_IgG_2


title: MV4-11, LAA+ATRA, ATAC-seq, rep2

description: Library name: mv4_com2


title: AKTP MTO mouse tumor organoids, RM-044 14h, replicate 1

description:
Library name: Sample 10
Column name in counts.txt: 326119_Organoid_12h
Column name in tcCounts.txt: 326119_Organoid_12h


title: OS525_H3K27Ac_2


title: MV4-11, LAA+ATRA, ATAC-seq, rep1

description: Library name: mv4_com1


title: GIC from tumor 3 channel A

description:
6_(OncoScan_CNV).OSCHP
Hybridized to OncoScan CNV


title: GIC from tumor 3 channel C


title: AKTP MTO mouse tumor organoids, RM-044 10h, replicate 3

description:
Library name: Sample 9
Column name in counts.txt: 326118_Organoid_8h
Column name in tcCounts.txt: 326118_Organoid_8h


title: Tumor 3 channel C

description:
5_(OncoScan_CNV).FFPE.OSCHP
Hybridized to OncoScan CNV


title: MV4-11, ATRA, ATAC-seq, rep3

description: Library name: mv4_atra3

value: All-trans retinoic acid (ATRA, 1µM)


title: OS525_IgG_2


title: MV4-11, ATRA, ATAC-seq, rep2

description: Library name: mv4_atra2


title: AKTP MTO mouse tumor organoids, RM-044 10h, replicate 1

description:
Library name: Sample 7
Column name in counts.txt: 326116_Organoid_8h
Column name in tcCounts.txt: 326116_Organoid_8h


title: OS525_IgG_1


title: MV4-11, ATRA, ATAC-seq, rep1

description: Library name: mv4_atra1


title: GIC from tumor 2 channel A

description:
4_(OncoScan_CNV).OSCHP
Hybridized to OncoScan CNV


title: OS457_H3K27Ac_2


title: AKTP MTO mouse tumor organoids, RM-044 6h, replicate 2

description:
Library name: Sample 5
Column name in counts.txt: 326114_Organoid_4h
Column name in tcCounts.txt: 326114_Organoid_4h


title: GIC from tumor 2 channel C


title: AKTP MTO mouse tumor organoids, RM-044 6h, replicate 3

description:
Library name: Sample 6
Column name in counts.txt: 326115_Organoid_4h
Column name in tcCounts.txt: 326115_Organoid_4h


title: MV4-11, LAA, ATAC-seq, rep3

description: Library name: mv4_laa3

value: L-ascorbic acid (LAA, 250µM)


title: OS457_H3K27Ac_1


title: MV4-11, LAA, ATAC-seq, rep2

description: Library name: mv4_laa2


title: Tumor 2 channel C

description:
3_(OncoScan_CNV).FFPE.OSCHP
Hybridized to OncoScan CNV


title: OS457_IgG_2


title: AKTP MTO mouse tumor organoids, RM-044 6h, replicate 1

description:
Library name: Sample 4
Column name in counts.txt: 326113_Organoid_4h
Column name in tcCounts.txt: 326113_Organoid_4h


title: Tumor 2 channel A


title: OS525_H3K27Ac_1


title: AKTP MTO mouse tumor organoids, RM-044 2.5h, replicate 3

description:
Library name: Sample 3
Column name in counts.txt: 326112_Organoid_30min
Column name in tcCounts.txt: 326112_Organoid_30min


title: MV4-11, vehicle, ATAC-seq, rep3

description: Library name: mv4_veh3

value: Vehicle


title: AKTP MTO mouse tumor organoids, RM-044 10h, replicate 2

description:
Library name: Sample 8
Column name in counts.txt: 326117_Organoid_8h
Column name in tcCounts.txt: 326117_Organoid_8h


title: GIC from tumor 1 channel C

description:
2_(OncoScan_CNV).OSCHP
Hybridized to OncoScan CNV


title: AKTP MTO mouse tumor organoids, RM-044 2.5h, replicate 2

description:
Library name: Sample 2
Column name in counts.txt: 326111_Organoid_30min
Column name in tcCounts.txt: 326111_Organoid_30min


title: MV4-11, vehicle, ATAC-seq, rep2

description: Library name: mv4_veh2


title: OS384_H3K27Ac_2


title: GIC from tumor 1 channel A


title: MV4-11, vehicle, ATAC-seq, rep1

description: Library name: mv4_veh1


title: AKTP MTO mouse tumor organoids, RM-044 2.5h, replicate 1

description:
Library name: Sample 1
Column name in counts.txt: 326110_Organoid_30min
Column name in tcCounts.txt: 326110_Organoid_30min


title: OS384_H3K27Ac_1


title: Tumor 3 channel A


title: Tumor 1 channel A

description:
1_(OncoScan_CNV).FFPE.OSCHP
Hybridized to OncoScan CNV


title: Tumor 1 channel C


title: OS384_IgG_1


title: OS384_IgG_2


title: OS186_H3K27Ac_2


title: U-937, LAA+ATRA, rep1

data_processing:
FASTQ files were trimmed with cutadapt (v1.18) to remove adaptor sequences, with additional 2 bases
Trimmed reads were aligned to GRCh38.p12 with Bismark (v0.22.1)
CpG sites were destranded with bsseq (v4.2.3)
methylSig (v4.2.2) was used to call signifcantly differential hmCs with adjusted p-value < 0.05, absolute hmC difference > 10%, and coverage between 10 and 400
Assembly: GRCh38.p12
Supplementary files format and content: Bismark methylation reports consisting of the following columns: chromosome, position, strand, count hydroxymethylated, cound unmethylated, C-context, trinucleotide context
Library strategy: Enzymatic 5hmC-seq (reduced representation)

growth_protocol: U-937 cells were cultured in vitro with RPMI 1640, 10% fetal bovine serum, and 10 units/mL penicillin and 10µg/mL streptomycin in a humidified incubator at 37˚C and 5% CO2.

extract_protocol:
Cells were collected and pelleted after treatment, digested with RNase in a 10% SDS buffer for 30minutes, followed by overnight proteinase K digestion at 55°C. Lysate was phenol-chloroform extracted, ethanol-salt precipitated, and resuspended in buffer EB.
Genomic DNA was MspI digested to enrich for CpGs. Libraries were prepared using the NEBNext® Enzymatic 5hmC-seq Kit (NEB, E3350)

value: pro-monocytic


title: OS186_H3K27Ac_1


title: P7SH_7DPS

city: Beijing

first: Yifan

last: Xie

address: Mentougou District

country: China

institute: Fuwai Hospital

data_processing:
CellRanger (version: 4.0.0), Seurat (version: 3.2.2)
Sequencing read alignment, cell barcode/UMI counting of the single cell transcriptomic data were performed separately for each library using the 10× Genomics official tool kit CellRanger with FASTQ files as inputs.
A combined dataset consisting of 69,303 single cells and encompassing 30,905 genes was generated for single cell sequencing.
Gene-barcode matrix extraction and performed using Seurat.
Assembly: refdata-cellranger-mm10-3.0.0
Supplementary files format and content: tab-delimited text file includeds barcodes, gene name, and raw counts for each sample
Supplementary files format and content: tab-delimited text file includeds origin identity, number of count, number of gene, and group information, etc

source_name: heart

extract_protocol:
Heart tissue from the apical region of the ventricular was collected and pooled from 4 to 6 hearts. The study included six different time points, namely P1+(1dpr, 1dps, 4dpr, 4dps, 7dpr, 7dps) and P7+(1dpr, 1dps, 4dpr, 4dps, 7dpr, 7dps). Subsequently, the collected tissue underwent enzymatic digestion using the Neonatal Heart Dissociation Kit (Miltenyi Biotec) to obtain single cells.
The single cells were utilized for single cell RNA sequencing, specifically for the generation of single cell RNA-seq libraries. The Single Cell 3′ Reagent Kits v2 (10×Genomics) were employed in accordance with the manufacturer's instructions. After completing the capture and lysis procedures, cDNA synthesis and amplification were carried out according to the guidelines provided by the manufacturer (10X Genomics). The amplified cDNA obtained from each channel of the Chromium System was utilized for the construction of a sequencing library.

value: heart

value: Sham


title: U-937, LAA+ATRA, rep2


title: P1SH_1DPS_b


title: U-937, LAA+ATRA, rep3


title: U-937, ATRA, rep1

value: All-trans retinoic acid (ATRA, 1uM)


title: P7AR_7DPR

value: Apex resection


title: OS186_IgG_2


title: U-937, LAA, rep3

value: L-ascorbic acid (LAA, 250uM)


title: OS457_IgG_1


title: OS186_IgG_1


title: P1AR_1DPR_b


title: U-937, ATRA, rep2


title: P7SH_4DPS


title: OS152_H3K27Ac_3


title: OS774_H3K27Ac_2


title: U-937, ATRA, rep3


title: P7AR_4DPR


title: U-937, LAA, rep1


title: U-937, LAA, rep2


title: OS152_H3K27Ac_1


title: CTLASO p20

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

country: Canada

institute: UOHI

hyb_protocol: Samples were hybridized to a Clariom_S array (Affymetrix) and scanned at the Centre for Applied Genomics (TCAG), Toronto

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Relative expression changes assessed by Expression Console

source_name: HepG2 cells

label_protocol: Standard Affymetrix protocol

growth_protocol: Low glucose (Gibco) medium supplemented with 10% FBS and Pen/Strep

extract_protocol: High Pure RNA isolation using Trizol and cartridges

treatment_protocol: Cells were transfected with a total of 30 nM ASO (15 nM per ZFAS1 ASO or 30 nM of CTLASO) with 1 ul of RNAiMax in 24-well plates for 48 h

value: Hepatoblastoma culture


title: CTLASO p12


title: ASOs 7 and 8 p13


title: ASOs 7 and 8 p19


title: CTLASO p19


title: P7SH_1DPS


title: CTLASO p13


title: ASOs 7 and 8 p20


title: U-937, vehicle, rep2


title: OS152_IgG_3


title: P1SH_7DPS


title: P7AR_1DPR


title: OS152_IgG_2


title: U-937, vehicle, rep1


title: P1AR_7DPR


title: ASOs 5 and 6 p20


title: OS152_IgG_1


title: ASOs 5 and 6 p19


title: 833 Expression portion

description:
cell_833_GEX
Expression

source_name: From osteosarcoma PDX

extract_protocol:
We used protocol CG000365 from 10X genomics for the PDX-cell lines. Cells were harvested using accutase (Innovative Cell Technologies, Inc. AT 104-500). 500,000 cells were harvested at ~70-80 confluent and followed the nuclei isolation protocol. OS384 was incubated 5 min in lysis buffer ([NP40]f=0.05%) and OS833 was incubated 3 min in lysis buffer ([NP40]f=0.045%).
single-nucleus  (snRNAseq + snATACseq)
We used the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000285) as instructed by the manufacturer. 500,000 cells were harvested at ~70-80 confluent and followed the nuclei isolation protocol.

value: From osteosarcoma PDX


title: P1SH_4DPS


title: OS152_H3K27Ac_2

value: From PDX


title: OS052_H3K27Ac_2

value: Osteosarcoma PDX-cell line


title: U-937, vehicle, rep3


title: 833 ATACseq portion

description:
cell_833_ATAC
ATACseq


title: ASOs 5 and 6 p12


title: ASOs 5 and 6 p13


title: P1AR_4DPR


title: OS052_H3K27Ac_1


title: 384 Expression portion

description:
cell_384_GEX
Expression


title: ASOs 7 and 8 p12


title: 384 ATACseq portion

description:
cell_384_ATAC
ATACseq


title: P1AR_1DPR_a


title: ASOs 3 and 4 p20


title: OS052_IgG_1


title: P1D8

status: Public on Sep 28 2025

first: Mei

last: He

address: 2033 Mowry Rd, Cancer and Genetics Research Complex

department: Pharmaceutics

description: Library name: Plasma_7

data_processing:
FREYA
Sequence reads were trimmed for adaptor sequence/low quality sequence using fastp
Trimmed sequence reads were mapped to hg38 using Salmon
Read count extraction and processing was performed using FeatureCounts
Assembly: GRCh38.109
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Plasma

extract_protocol:
Total RNA was extracted from PMN samples using the RNeasy Plus Universal Mini Kit (Qiagen, Germantown, MD) according to the manufacturer’s protocol.
). Sequencing libraries were prepared using the Illumina RNA-Seq Library Prep Set for low-input RNA, following the manufacturer’s guidelines. Libraries were quantified using qPCR and assessed for fragment size distribution using the Agilent Bioanalyzer before pooling.

value: Plasma

tag: disease state

value: NMIBC


title: P1D6

description: Library name: Plasma_6


title: P1D5

description: Library name: Plasma_5

value: MIBC


title: P1D3

description: Library name: Plasma_3

value: Healthy


title: P1D4

description: Library name: Plasma_4


title: P1D2

description: Library name: Plasma_2


title: ASOs 3 and 4 p12


title: P1D1

description: Library name: Plasma_1


title: B009

description: Library name: Urine_16

source_name: Urine

value: Urine


title: B007

description: Library name: Urine_15


title: B003

description: Library name: Urine_12


title: B004

description: Library name: Urine_13


title: B005

description: Library name: Urine_14


title: P1SH_1DPS_a


title: B001

description: Library name: Urine_10


title: B002

description: Library name: Urine_11


title: A0015

description: Library name: Urine_8


title: A008

description: Library name: Urine_7


title: OS052_IgG_2


title: A006

description: Library name: Urine_5


title: A001

description: Library name: Urine_2


title: A004

description: Library name: Urine_3


title: A007

description: Library name: Urine_6


title: ASOs 3 and 4 p19


title: A00L

description: Library name: Urine_1


title: A005

description: Library name: Urine_4


title: A0016

description: Library name: Urine_9


title: Aggressive Periodontitis, 3, Patients

city: Seoul

first: Byeongsoo

last: Eom

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

description: Library name: AP187666

data_processing:
Single cell gene expression data was analyzed using Cell Ranger v6.1.2 (10x Genomics, USA).
Raw BCL files from Illumina HiSeq X were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’.
Raw FASTQ files were analyzed using ‘cellranger count’.
The ‘cellranger count’ step includes mapping to the human reference genome (GRCh38), measuring gene expression with unique molecular identifier (UMI) and cell barcode, determining cell clusters, and conducting differential gene expression analysis.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger Feature Barcode Matrices (MEX Format)

source_name: gingiva

extract_protocol:
Gingival tissues subjected for single-cell RNA sequencing were first dissociated using multi tissue dissociation kit 2 according to the manufacturer’s instruction (#130-110-203, Miltenyi Biotec, Germany)
Library preparation was carried out following the guidelines of the 10X Chromium Next GEM Single Cell Library kit v3.1 (#1000121, 10X Genomics, USA)

value: gingiva

value: total RNA

tag: batch

value: paired-end


title: scRNA Uri-S93

city: chongqing

first: Ye

last: qian

address: No. 1 Youyi Road, Yuzhong District, Chongqing

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 20%;  Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Peripheral blood

extract_protocol:
Peripheral blood samples were collected and gently rotated to mix thoroughly. Whole blood was first diluted by adding an equal amount of sterile phosphate-buffered saline (PBS), the diluted whole blood was layered onto Ficoll PAQUE, after horizontally centrifuged, the middle mononuclear cell layer was transferred to a new tube, ACK lysis buffer (Miltenyi Biotec) was added to lyse red blood cells. After the last wash, pipet off the supernatant and loosen the pellet by adding PBS with 0.04% BSA.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3.1 and prepared for sequencing using standard Illumina protocols

tag: tissue

value: Peripheral blood

value: PBMCs

value: Immune cells

tag: gender

value: Female

tag: sample collection_site

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

tag: group

value: Adult Sepsis

tag: sepsis infection_source

value: Urinary

tag: ethnicity

value: East Asian


title: scRNA Uri-S88

tag: cell line

tag: cell type


title: scRNA Uri-S157


title: scRNA Uri-S20


title: ASOs 3 and 4 p13

value: Hepatoblastoma culture


title: scRNA Uri-S147


title: scRNA Uri-S116


title: scRNA Skin-S74

value: Male

value: Skin


title: scRNA Uri-S112


title: scRNA Skin-S46


title: scRNA Skin-S43


title: scRNA Skin-S142


title: scRNA Skin-S38


title: scRNA Skin-152

value: Chongqing Emergency Medical Center, Chongqing, China.


title: scRNA Skin-S140


title: scRNA Res-S56

value: Respiratory


title: scRNA Res-S41


title: scRNA Res-S21


title: scRNA Res-S40


title: scRNA Res-S183


title: scRNA Res-S3


title: scRNA Res-S22


title: scRNA Res-S32


title: scRNA Uri-S85


title: scRNA RES-S174


title: scRNA RES-S177


title: scRNA Res-S184


title: scRNA Res-S170


title: scRNA Uri-S134


title: scRNA Res-S167


title: scRNA RES-S176


title: scRNA Res-S166


title: scRNA RES-S164


title: scRNA Res-S168


title: scRNA Res-S15


title: scRNA Skin-S52


title: scRNA Res-S149


title: scRNA Res-S146


title: scRNA Res-S77


title: scRNA Res-S144


title: scRNA Res-S145


title: scRNA Res-S127


title: scRNA Res-S139


title: scRNA Res-S136


title: scRNA Res-S125


title: scRNA Res-S18


title: scRNA RES-S118


title: scRNA Res-S110


title: scRNA Res-S100


title: scRNA Res-S10


title: scRNA Res-PS16

value: Children's Hospital of Chongqing Medical University, Chongqing, China

value: Pediatric Sepsis


title: scRNA RES-PS26


title: scRNA Res-PS25


title: scRNA Res-PS03


title: scRNA Res-PS12


title: scRNA Res-S70


title: scRNA Res-PS22


title: scRNA PIC05

value: Pediatric ICU Control


title: scRNA Res-S26


title: scRNA Res-PS02


title: scRNA Res-S150


title: scRNA Res-S19


title: scRNA PIC01


title: scRNA PIC02


title: scRNA PHC05

value: Pediatric Healthy Control


title: scRNA PHC03

value: Peripheral blood


title: scRNA PHC02

value: PBMCs


title: scRNA PHC01

value: Immune cells


title: scRNA IC19

value: Adult ICU Control


title: scRNA IC22

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China


title: scRNA IC23

value: Female


title: scRNA IC16


title: scRNA IC15


title: scRNA Res-PS21


title: scRNA IC09


title: scRNA IC08


title: scRNA IC10


title: scRNA HC16

value: Adult Healthy Control


title: scRNA HC13

value: East Asian


title: scRNA HC07


title: scRNA HC09


title: scRNA CNS-S50

value: Adult Sepsis

value: Central Nervous System


title: scRNA HC12

value: Male


title: scRNA CNS-S61


title: scRNA HC05


title: scRNA Abd-S91

value: Chongqing Emergency Medical Center, Chongqing, China.

value: Abdominal


title: scRNA Abd-S98


title: scRNA CNS-S189


title: scRNA Res-S87

value: Respiratory


title: scRNA Abd-S9


title: scRNA PIC04

value: Children's Hospital of Chongqing Medical University, Chongqing, China


title: scRNA Abd-S83


title: scRNA Abd-S80


title: scRNA Abd-S79


title: scRNA Abd-S8


title: scRNA Abd-S75


title: scRNA Abd-S67


title: scRNA Abd-S66


title: scRNA Abd-S59


title: scRNA Abd-S58


title: scRNA Abd-S54


title: scRNA Abd-S57


title: scRNA Abd-S55


title: scRNA Abd-S53


title: scRNA Abd-S51


title: scRNA Abd-S49


title: scRNA Abd-S47


title: scRNA Abd-S156


title: scRNA Abd-S23


title: scRNA Abd-S81


title: scRNA HC01


title: scRNA Abd-S123


title: scRNA Abd-S45


title: scRNA Abd-S120


title: scRNA Abd-S42


title: scRNA Abd-S11


title: scRNA Abd-S13


title: scRNA Abd-S101


title: scRNA Abd-S12


title: scRNA Abd-S73


title: scRNA Abd-S111


title: scRNA Abd-S72


title: scRNA Abd-S103


title: scRNA Abd-PS27

value: Pediatric Sepsis


title: scRNA Abd-PS20


title: scRNA Abd-S102


title: scRNA Abd-PS18


title: scRNA Abd-PS23


title: scRNA Abd-PS19


title: scRNA Abd-S39


title: scRNA Abd-PS13


title: scRNA Abd-PS07


title: citeseq Uri-S88

data_processing:
Raw data scRNAseq and Multiome files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: GRCh38
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes
Library strategy: CITE-seq

extract_protocol:
Peripheral blood samples were collected and gently rotated to mix thoroughly. Whole blood was first diluted by adding an equal amount of sterile phosphate-buffered saline (PBS), the diluted whole blood was layered onto Ficoll PAQUE, after horizontally centrifuged, the middle mononuclear cell layer was transferred to a new tube, ACK lysis buffer (Miltenyi Biotec) was added to lyse red blood cells. After the last wash, pipet off the supernatant and loosen the pellet by adding PBS with 0.04% BSA.
The cells were stained with antibody panel containing oligo-conjugated antibodies and RNA and ADT libraries were prepared using the 10x Genomics platform.

value: Urinary


title: citeseq Uri-S85

value: Peripheral blood


title: citeseq Uri-S157

value: PBMCs


title: citeseq Uri-S134

value: Immune cells


title: citeseq Res-S19


title: citeseq Res-S183


title: citeseq Res-S41


title: citeseq Res-S40


title: citeseq Res-S22


title: citeseq Res-S149


title: citeseq Res-S166


title: citeseq Res-S118


title: citeseq Res-S146


title: citeseq IC23

value: Adult ICU Control


title: citeseq Res-S10

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China


title: citeseq Res-S100


title: citeseq IC19


title: citeseq IC09


title: citeseq IC08


title: citeseq IC10


title: scRNA Abd-PS05


title: citeseq HC05


title: citeseq HC13

value: Female


title: scRNA Abd-PS04


title: citeseq Abd-S91


title: citeseq Abd-S9


title: citeseq Res-S70


title: citeseq HC01

value: Adult Healthy Control


title: citeseq Abd-S81

value: East Asian


title: citeseq Res-S170

value: Adult Sepsis


title: citeseq Abd-S75


title: citeseq Abd-S55


title: citeseq Abd-S80


title: citeseq Res-S164


title: citeseq Abd-S66


title: citeseq Abd-S49


title: citeseq Abd-S67


title: citeseq Abd-S51


title: citeseq Abd-S42


title: citeseq Abd-S45


title: bulkRNA Uri-S94

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCh_38
Supplementary files format and content: TXT file contain counts for each sample

extract_protocol:
PBMCs RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: citeseq Abd-S23


title: bulkRNA Uri-S95


title: citeseq Abd-S111


title: bulkRNA Uri-S93


title: bulkRNA Uri-S48


title: bulkRNA Uri-S213


title: bulkRNA Uri-S217


title: bulkRNA Uri-S201


title: bulkRNA Uri-S200


title: bulkRNA Uri-S208


title: bulkRNA Uri-S20


title: bulkRNA Uri-S180


title: bulkRNA Uri-S157


title: bulkRNA Uri-S162


title: bulkRNA Uri-S155


title: bulkRNA Uri-S147


title: bulkRNA Uri-S143


title: bulkRNA Uri-S134


title: bulkRNA Uri-S124


title: bulkRNA Uri-S104


title: bulkRNA Skin-S52

value: Skin


title: bulkRNA Skin-S74

value: Male


title: bulkRNA Skin-S46


title: CA-Quin, C8

city: Detroit

first: Wanqing

last: Liu

state: MI

address: 6135 Woodward Ave

department: Eugene Applebaum School of Pharmaceutical Sciences

institute: Wayne State University

description: Library name: C8

data_processing:
FastQC
Trimmomatic
hisat/2-2.0.1
HTSeq map to GRCm38
Assembly: GRCm38
Supplementary files format and content: tab delimited file contains raw counts

source_name: Liver

extract_protocol:
Frozen liver samples stored in Qiagen RNAprotect Tissue Reagent were homogenized and RNA was extracted utilizing the Qiagen RNeasy Kit by following the manufacturer’s protocol. Additional flash frozen liver and ileum samples were homogenized in Ther-moFisher Scientific TriZol and extracted by following manufacturer’s protocol. Briefly, total RNA was extracted from frozen liver and ileum samples using TRIzol re-agent (Thermo Fisher Scientific) followed by purification steps as detailed by the man-ufacturer. RNA purity and quantity were assessed via spectrophotometer (NanoDrop 8000, Thermo-Fisher Scientific).
Single end RNA sequencing was performed by the Wayne State University Genome Sciences Core. The mRNA-seq library was prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen).

treatment_protocol: Male mice (n=8 per group) were be treated with a once daily dose of DMSO, 50 mg/kg CamSA or 50 mg/kg CA-Quin for 7 consecutive days. On day 7, all animals were eu-thanized with CO2 and organs were harvested as follows. Livers from each animal were harvested and weighted. A liver slice (not wider than 0.5 cm) was stored in cold RNAprotect Tissue Reagent.

value: Liver


title: bulkRNA Skin-S43


title: bulkRNA Skin-S38


title: CA-Quin, C6

description: Library name: C6


title: CA-Quin, C7

description: Library name: C7


title: bulkRNA Skin-S30


title: CA-Quin, C4

description: Library name: C4


title: bulkRNA Skin-S191


title: CA-Quin, C5

description: Library name: C5


title: bulkRNA Skin-S192


title: bulkRNA Skin-S152

value: Chongqing Emergency Medical Center, Chongqing, China.


title: CA-Quin, C3

description: Library name: C3


title: bulkRNA Skin-S142


title: CamSA, B7

description: Library name: B7


title: CamSA, B8

description: Library name: B8


title: bulkRNA Skin-S140


title: bulkRNA Skin-S117


title: bulkRNA Res-S89

value: Respiratory


title: bulkRNA Uri-S112


title: bulkRNA Res-S87


title: CamSA, B6

description: Library name: B6


title: CamSA, B5

description: Library name: B5


title: CamSA, B4

description: Library name: B4


title: bulkRNA Skin-S99


title: bulkRNA Res-S77


title: CamSA, B2

description: Library name: B2


title: CamSA, B3

description: Library name: B3


title: CamSA, B1

description: Library name: B1


title: bulkRNA Res-S64


title: bulkRNA Res-S40


title: bulkRNA Res-S34


title: DMSO, A7

description: Library name: A7


title: bulkRNA Res-S26


title: CA-Quin, C1

description: Library name: C1


title: DMSO, A6

description: Library name: A6


title: bulkRNA Res-S219


title: DMSO, A5

description: Library name: A5


title: DMSO, A4

description: Library name: A4


title: bulkRNA Res-S218


title: bulkRNA Res-S214


title: bulkRNA Res-S212


title: DMSO, A2

description: Library name: A2


title: DMSO, A3

description: Library name: A3


title: bulkRNA Res-S209


title: DMSO, A1

description: Library name: A1


title: bulkRNA Res-S207


title: bulkRNA Res-S206


title: bulkRNA Res-S205


title: bulkRNA Res-S78


title: HFD-Res-30

city: Kunming City

first: yifeng

last: qin

state: Yunnan Province

address: School of Life Science, Yunnan University, Chenggong District

institute: yunnan university

description: Library name: sample14

data_processing:
Trim Galore (v0.6.10)  Bowtie (v1.3.1)  STAR (v2.7.10b) featureCounts (v2.0.1)
Assembly: mm39
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: csv file include TPM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted using TRIzol-chloroform, and 5 μg of the isolated RNA was utilized for mRNA enrichment and subsequent library construction.
PolyA selection for mRNA species was employed for rRNA depletion (Vazyme, N401-01) and RNA library construction (Vazyme, NR605-02).

value: liver


title: HFD-337-27

description: Library name: sample12


title: HFD-Res-29

description: Library name: sample13


title: HFD-337-26

description: Library name: sample11


title: bulkRNA Res-S204


title: HFD-Res-34

description: Library name: sample15


title: bulkRNA Res-S202


title: HFD-337-23

description: Library name: sample10


title: DMSO, A8

description: Library name: A8


title: bulkRNA Res-S199


title: bulkRNA Res-S196


title: HFD-338-17

description: Library name: sample7


title: bulkRNA Res-S194


title: HFD-NS-16

description: Library name: sample6


title: bulkRNA Res-S187


title: HFD-NS-13

description: Library name: sample5


title: bulkRNA Res-S195


title: bulkRNA Res-S184


title: bulkRNA Res-S186


title: bulkRNA Res-S182


title: bulkRNA Res-S181


title: colon tissue,TNBS 6

city: NANCHANG

first: yuchang

last: sun

address: Xinqizhou Dong Avenue, Ganjiang New

institute: Ganjiang Traditional Chinese Medicine Innovation Center

description: Library name: TNBS_6

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
Assembly: Ensembl_v112
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Colon tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Colon tissue

value: TNBS


title: SD–NS-8

description: Library name: sample3


title: SD–NS-6

description: Library name: sample1


title: SD–NS-7

description: Library name: sample2


title: bulkRNA Res-S203

value: Peripheral blood


title: HFD-338-19

description: Library name: sample9


title: HFD-NS-12

description: Library name: sample4


title: bulkRNA Res-S173

value: PBMCs


title: bulkRNA Res-S177

value: Immune cells


title: bulkRNA Res-S174


title: colon tissue,TNBS 3

description: Library name: TNBS_3


title: HFD-338-18

description: Library name: sample8


title: colon tissue,TNBS 4

description: Library name: TNBS_4


title: bulkRNA Res-S166


title: colon tissue,TNBS 2

description: Library name: TNBS_2


title: bulkRNA Res-S164


title: bulkRNA Res-S19


title: colon tissue,IBC 6

description: Library name: IBC_6

value: IBC


title: bulkRNA Res-S150

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China


title: colon tissue,TNBS 1

description: Library name: TNBS_1


title: colon tissue,IBC 5

description: Library name: IBC_5


title: bulkRNA Res-S149


title: bulkRNA Res-S146


title: colon tissue,IBC 4

description: Library name: IBC_4


title: colon tissue,IBC 2

description: Library name: IBC_2


title: colon tissue,IBC 3

description: Library name: IBC_3


title: bulkRNA Res-S136


title: colon tissue,IBC 1

description: Library name: IBC_1


title: bulkRNA Res-S130


title: bulkRNA Res-S127

value: Female


title: colon tissue,vector 5

description: Library name: control_5

value: vector


title: colon tissue,TNBS 5

description: Library name: TNBS_5


title: bulkRNA Res-S125

value: East Asian


title: bulkRNA Res-S105

value: Adult Sepsis


title: colon tissue,vector 4

description: Library name: control_4


title: bulkRNA Res-S10


title: colon tissue,vector 2

description: Library name: control_2


title: colon tissue,vector 1

description: Library name: control_1


title: bulkRNA Res-PS25

value: Children's Hospital of Chongqing Medical University, Chongqing, China

value: Pediatric Sepsis


title: bulkRNA Res-PS22

value: Male


title: ChIP_TCF4_Abcam_CTL_R8_rep1

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: Library name: ChIP_TCF4_Abcam_CTL_R8_rep1

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Version 2.3.4.1 of bowtie2 was employed to align reads to mouse assembly mm10 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0. For samples with Drosophila H2Av spike ins (Camta1 and Tcf4), reads were also aligned to the D. melanogaster assembly dm6.
Enriched regions were discovered using MACS2 with a p-value setting of 0.001 using the input control as background and then filtered for blacklisted regions.
The BEDTools suite was used to create normalized bigwig files. For histone modification data, the ChIP signal was normalized to the sequencing depth for uniquely mapped reads, while TF ChIP data were normalized to an external spike in by scaling the data inversely to the number of Drosophila H2Av reads.
Assembly: mm10
Supplementary files format and content: normalized bigwigs

source_name: Brain, ANT

extract_protocol:
Nuclear extraction. Animals were anesthetized with isoflurane within an hour of performing the task retrieval and perfused with PBS. ANT or ACC tissue was micro-dissected under a microscope and snap frozen on liquid nitrogen for later processing. Nuclei were isolated from mouse brain tissue based on a previously described method18 with slight modifications. Tissue from 8-9 mice were pooled for Camta1-knockout and Tcf4-knockout, and their respective controls, and tissue from 2-3 mice were pooled for each  biological replicate for Ash1l-knockout testing. Briefly, 0.3 ml fixative solution (1% (wt/vol) formaldehyde in DPBS) was added to the pooled sample (~60-80mg tissue) in a 1.5 ml tube. Tissue was gently homogenized in the fixative by gently breaking up with a P1000 pipette tip until no large visible pieces remained. For Ash1l samples, the 0.3 ml homogenate was added to a 4.7 ml fixative solution in a 15 ml tube using a P1000 tip, washing out the 1.5 ml tube to maximize homogenate transferred. Homogenate was rocked at 30 cycles/min, RT for 10 min. To quench the formaldehyde and prevent overfixation of the sample, 0.5 ml 2.5 M glycine, [final] = 0.125 M, was added to the homogenate and rocked at 30 cycles/min, RT for 5 min. (For Tcf4 and Camta1 samples, a double fixation protocol was used: homogenization of sample in 0.3 ml 2 mM DSG solution, followed by transfer to 4.7 ml 2 mM DSG, rocked at 30 cycles/minute, RT, 30 min. 37% (wt/vol) formaldehyde was added to the homogenate to create a 1% (wt/vol) formaldehyde solution, rocked for 10 min at RT. The sample was quenched with 0.125 glycine.) After fixation and quenching, the rest of the steps were the same. The homogenate was spun at 1,100g for 5 min, 4°C in a swing rotor bucket centrifuge with 15 ml adaptors. Supernatant was removed and pellet was suspended with 10 ml ice-cold NF1 buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 5 mM MgCl2, 0.1 M sucrose, and 0.5% (vol/vol) Triton X-100) for a first wash. This was repeated for a second wash and on the third (final) was, sample was re-suspended in 5 ml ice cold NF1 buffer. Homogenate was incubated on ice for 30 min, then transferred to a 7 ml glass dounce. A loose pestle was passed through the homogenate 20x, and then a tight pestle passed through 5x. The homogenate was passed through a 70µm strainer and collected into a 50 ml tube. Ann additional 15 ml NF1 buffer was passed through the strainer to collect a total volume of 20 ml. A 5 ml sucrose cushion (1.0 M sucrose cushion with  1.2 M sucrose solution with 10 mM Tris-HCl pH 8.0, 3 mM MgCl2, and 1 mM DTT) was laid underneath the homogenate by slowly pipetting to the bottom of the tube with a P1000, with care to maintain an interphase. The sucrose gradient was spun at 3,900g for 30 min at 4°C. After spinning, a white nuclei pellet was visible at the bottom, below the sucrose cushion. The upper, aqueous phase, interphase, and sucrose cushion were gently removed. The nuclei pellet was resuspended in 1 ml NF1 buffer and transferred to a 15 ml tube. 9 ml NF1 buffer was added to wash the nuclei pellet, followed by spinning at 1,600g for 5 min 4°C to pellet the nuclei. For antibody staining for nuclei sorting, the nuclei pellet was resuspended in 5 ml FANS buffer, spun at 1,600 g for 5 min, 4°C, and resuspended in 0.3 ml FANS buffer. 3µl was taken for an unstained control and the remaining nuclei were transferred to a FACS tube for staining overnight 4°C with NeuN-Ax488 antibody (Millipore, #MAB377X) at 1:2500 dilution with gentle rocking. The next day, 4 ml FANS buffer was added to the nuclei, then spun at 1,600g for 5 min, 4°C. The remaining 0.3 ml nuclei were passed through a 35 µm cap into a new tube for FACS, and counterstained with  0.5 µg ml−1 DAPI. Nuclei were sorted using a 100 µm nozzle. Nuclei were gated based on DAPI+, NeuN+ according to the original protocol. After sorting, nuclei samples were adjusted to 1% wt/vol BSA, then spun at 1,600g for 15 min 4°C to collect nuclei for further processing. FANS buffer was removed and samples were snap frozen on liquid N2.
Libraries were prepared for sequencing using standard Illumina protocols

value: Brain, ANT

value: Neurons (sorted)

tag: treatment

tag: antibody

value: Tcf4 (ProteinTech, #22337-1-AP)


title: colon tissue,vector 3

description: Library name: control_3

value: Colon tissue


title: bulkRNA Res-S108

value: Respiratory


title: ChIP_TCF4_Abcam_TCF4KO_R8_rep1

description: Library name: ChIP_TCF4_Abcam_TCF4KO_R8_rep1

value: C57Bl6/J + Tcf4 KO


title: bulkRNA Res-PS21

value: Peripheral blood

value: PBMCs


title: ChIP_H3K4me3_CTL_R8_rep2

description: Library name: ChIP_H3K4me3_CTL_R8_rep2

source_name: Brain, ACC

value: Brain, ACC

value: H3K4me3 (Epicypher, 13-0041)


title: ChIP_H3K4me3_CTL_R8_rep1

description: Library name: ChIP_H3K4me3_CTL_R8_rep1


title: bulkRNA Res-PS12

value: Immune cells

value: Female


title: bulkRNA Res-PS16

value: East Asian


title: ChIP_Input_CTL_R8_rep1

description: Library name: ChIP_Input_CTL_R8_rep1


title: bulkRNA Res-S139

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

value: Adult Sepsis


title: ChIP_H3K4me3_CTL_R20_rep2

description: Library name: ChIP_H3K4me3_CTL_R20_rep2


title: ChIP_H3K4me3_CTL_R20_rep1

description: Library name: ChIP_H3K4me3_CTL_R20_rep1


title: colon tissue,vector 6

description: Library name: control_6

value: vector


title: bulkRNA Res-PS03

value: Children's Hospital of Chongqing Medical University, Chongqing, China

value: Pediatric Sepsis


title: bulkRNA Res-PS02

value: Male


title: ChIP_H3K4me3_Ash1lKO_R8_rep1

description: Library name: ChIP_H3K4me3_Ash1lKO_R8_rep1

value: Neurons (sorted)

value: C57Bl6/J + Ash1l KO


title: bulkRNA PIC05

value: Pediatric ICU Control


title: ChIP_H3K4me3_Ash1lKO_R8_rep2

description: Library name: ChIP_H3K4me3_Ash1lKO_R8_rep2


title: bulkRNA PIC04


title: ChIP_H3K4me3_Ash1lKO_R20_rep2

description: Library name: ChIP_H3K4me3_Ash1lKO_R20_rep2


title: bulkRNA Res-PS26

value: Respiratory


title: bulkRNA PIC02

value: Peripheral blood


title: ChIP_H3K4me3_Ash1lKO_R20_rep1

description: Library name: ChIP_H3K4me3_Ash1lKO_R20_rep1


title: ChIP_CAMTA1_Milli_Camta1KO_R8_rep1

description: Library name: ChIP_CAMTA1_Milli_Camta1KO_R8_rep1

value: Brain, ANT

value: C57Bl6/J + Camta1 KO

value: Camta1 (Millipore, #SAB4301068)


title: bulkRNA PHC05

value: PBMCs

value: Immune cells

value: Pediatric Healthy Control


title: ChIP_CAMTA1_Milli_CTL_R8_rep1

description: Library name: ChIP_CAMTA1_Milli_CTL_R8_rep1