title: transwell,DMSO treated 1

description:
Library name: sample4
DMSO_1


title: WT_FSK_Rep2

status: Public on Jul 03 2026

type: SRA

city: Seattle

first: Meagan

middle: Nicole

last: Esbin

state: WA

address: 850 Republican St. S280

department: Obstetrics & Gynecology

country: USA

institute: University of Washington School of Medicine

description: Library name: Sample 6

library_source: transcriptomic

data_processing:
Raw data were assessed using FastQC
FASTQ files were pseudoaligned to the hg38 transcriptome using Salmon to quantify transcripts in mapping-based mode (salmon quant -i) using decoy-aware mapping with gencode.v39. transcripts.fa.
Differential gene expression analysis was performed with EdgeR in Jupyter Notebook. Raw counts were filtered to remove genes with fewer than 10 reads per sample or fewer than 15 reads summed across all samples. Counts per million reads (CPM) was calculated for the filtered count data using the EdgeR function cpm. Statistical comparisons between individual sample conditions were made using EdgeR makeContrasts and then glmQLFit. The reported P-values and FDR values were corrected with adjust.method = “BH,” and differentially expressed genes are reported with an adjusted FDR of <0.05.
For visualization, the STAR program was used to map .fastq reads onto the hg38 genome to generate .bam files for each sample. These .bam files were converted to .bigWig files using bedtools and merged (summed) across the three replicates of each sample type.
Assembly: hg38
Supplementary files format and content: Comma separated values file containing CPM-normalized count data for each Sample by NCBI Gene ID and ifferential gene expression analysis output from EdgeR with the Log2 Fold-Change (FC)  and Benjamini-Hochberg (BH) corrected False Discovery Rate (FDR) for each gene comparing Forskolin-treated ZBTB10 KO vs. Forskolin-treated WT cells. Comparisons are noted as (FSK_KOvsWT) where positive FC values indicates higher gene expression in Forskolin-treated ZBTB10 KO cells.
Supplementary files format and content: Bigwig files to be used for Genome track visualization (i.e. IGV viewer) of binned reads mapped across the human genome merged (summed) across the 3 replicates for each sample type.

molecule: total RNA

organism: Homo sapiens

source_name: BeWo

growth_protocol: BeWo cells (ATCC CCL-98) were cultured at 37°C and 5% CO2 in F-12K medium (Corning or ATCC) supplemented with 10% fetal bovine serum and 10 U/mL penicillin–streptomycin. Cells were passaged by trypsinization every 2–4 days and split at a ratio of 1:3–1:5. Media was changed completely every 24–36 h.

extract_protocol:
RNA was extracted from each well using 500 µL of Trizol followed by two sequential chloroform extractions followed by ethanol precipitation per the Trizol user guide (Thermo Fisher MAN0001271).
Total RNA was depleted of rRNA using the Illumina rRNA depletion kit (NEB E6310) and then prepared for Illumina sequencing using the NEBNext Ultra II directional RNA library preparation kit for Illumina (E7760) per the manufacturer's protocol. Sequencing was performed by MedGenome on an Illumina NovaSeq with paired-end 150 bp reads.

treatment_protocol: BeWo cells were plated at 300,000 cells per well into a 6 well plate and allowed to settle 6 h to overnight. Cells were then treated with 0.1% DMSO or 20 μM Forskolin for 48 h. Media for all treatments was changed at 24 h.

tag: cell line

value: BeWo

tag: cell type

value: choriocarcinoma

tag: genotype

value: wild-type

tag: treatment

value: 20uM FSK, 48hr


title: transplantations_chromatin_p2

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description:
Library name: transplantations_chromatin_p2
Chromatin part of the plate

library_source: genomic

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: fragment files (chromatin)
Supplementary files format and content: full-length and umi-only count matrices (rna)
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: mammary gland

growth_protocol: Mammary cell preparation for transplantation. Mammary glands from K14cre/RosaYFP34,35 adult female mice were dissected and the lymph nodes removed before processing. Tissues were washed in HBSS, and chopped into pieces of 1 mm3. The tissues were placed in HBSS plus 300 U/ml collagenase (Sigma) plus 300 mg/ml hyaluronidase (Sigma) and digested for 2 h at 37°C under shaking. EDTA at a final concentration of 5mM was added for 10 min to the resultant organoid suspension, followed by 0.25% Trypsin-EGTA for 2 min before filtration through a 40-mm mesh, two successive washes in 2% FBS/PBS and labelling. Unisuspension of cells were incubated in 250 ml (per 5 millions cells) of 2% FBS/PBS with primary antibodies for 30 min, with shaking every 10 min. Primary antibodies were washed with 2% FBS/PBS cells were resuspended in 2.5 mg/ml DAPI (Invitrogen) before analysis. Primary antibodies used were: APC-Cy7-conjugated anti-Epcam (1/100, clone G8.8, Biolegend), AF700-conjugated anti-CD29 (1/100, clone HMB1-1, Biolegend), APC-conjugated anti-CD45 (1/100, clone 30-F11, eBiosciences), APC-conjugated anti-CD31(1/100, clone 390, eBiosciences), APC-conjugated anti-CD140a (1/100, clone APA5, eBiosciences). Data analysis and cell sorting was performed on a FACSAria III sorter using the FACS DiVa software (BD Biosciences). Dead cells were excluded with DAPI; CD45+, CD31+ and CD140a+ cells were excluded (Lin-) before analysis of the YFP+ cells. Basal cells were defined as Lin-YFP+Epcam+CD29high population while luminal cells were defined as Lin-YFP+Epcam+CD29low. Sorted basal cells were collected in 300 ul DMEM 50%/FBS 50%.  Mammary fat-pad transplantation. 10.000 sorted basal YFP+ cells were resuspended in 10 ul DMEM 25%/FBS 25%/Matrigel 50% and injected into the number 4 glands of 4-week-old NOD/SCID female mice that had been cleared of endogenous epithelium, using a 26g Hamilton syringe. Transplanted glands were harvested 4.5 days after grafting and processed as described in the 2 previous sections for sorting of YFP+ cells.

extract_protocol:
The plate was subjected to the multiome OneCell CUT&Tag protocol, as described in Schwager & Moutaux et. al 2026.
Combination of OneCell CUT&Tag with single-cell full-length transcriptomics, as described in (Schwager, Moutaux et al., 2026)

tag: tissue

value: mammary gland

value: fresh tissue

value: epithelial

value: no

tag: library type

value: DNA


title: CD4_PBMCs_Calbicans_Th17targets_nonTh17targets_HTO

status: Public on Jul 04 2026

city: Kiel

first: Philipp

last: Hofmann

address: Michaelisstraße 5

department: Institute of Medical Immunology

country: Germany

institute: Christian-Albrecht-University of Kiel

description:
Library name: CD4_blood_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: transcriptomic single cell

data_processing:
Raw sequencing base calls were converted to FASTQ files using cellranger mkfastq. The resulting FASTQ files were then processed with Cell Ranger (v7.1.0) and aligned to the GRCh38 human reference genome (Cell Ranger 2020-A release). Paired single-cell RNA and single-cell TCR data were processed using cellranger multi, utilizing the Cell Ranger VDJ reference 7.1.0 for TCR read alignment. Sample-specific demultiplexing for single cell experiments involving hashtag antibodies was achieved by employing a modified Cell Ranger workflow, adapting the 3’ CellPlex pipleline for 5’ chemistry as described in the 10X Genomics online protocol (https://www.10xgenomics.com/analysis-guides/demultiplexing-and-analyzing-5’-immune-profiling-libraries-pooled-with-hashtags). Briefly, a customized cell multiplexing oligo reference was created, specifying each hashtag antibody sequence and incorporating an updated sequence pattern “^NNNNNNNNNN(BC)NNNNNNNNN” to define the barcode position within the hashtag antibody FASTQ files. An initial run of cellranger multi was performed using FASTQ files for the gene expression and hashtag antibody libraries along with the customized cell multiplexing oligo reference to enable sample demultiplexing. The resulting sample-specific BAM files were converted to FASTQ format using 10X Genomics bamtofastq (v1.4.1) and utilized in a second cellranger multi run to allow fully demultiplexed processing of paired single-cell RNA and TCR data.
Assembly: GRCh38
Supplementary files format and content: CellRanger count pipeline output: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger vdj pipeline output: filtered_contig_annotations.csv

source_name: PBMCs

extract_protocol:
C. albicans-reactive CD154+ Tmem from peripheral blood or CD3+CD4+CD45RO+ cells from tissues were sorted with FACS and labeled with barcoded hashtag antibodies for sample multiplexing. In brief, PBMCs were stimulated with C. albicans, Th17 targets and Non-Th17 Targets for 6 h in the presence of 1 μg ml−1 of CD40 and 1 μg ml−1 of CD28 pure antibody. Cells were labeled with CD154-Biotin, followed by anti-biotin MicroBeads, and magnetically enriched by MS Columns (all from Miltenyi Biotec). Cells were stained on the column with TotalSeq-C anti-human hashtag antibodies (LNH-94, 1:50) in the presence of Human TruStain FcX (1:20) in 50 μl of staining volume. Columns were washed twice, and cells were eluted with 1000 μl of sterile filtered 1x PBS supplemented with 0.5% (v/v) human AB-serum. Subsequently, cells were sorted via FACS into precoated, low-bind collection tubes, containing sterile, filtered 1xPBS supplemented with 0.5% (v/v) human AB-serum. For intestinal tissue, up to four biopsies were pooled, whereas single biopsies were used  for oral samples (from the roof of the mouth, 4mm). Intestinal and oral biopsies were processed by mincing the tissue with scalpels and enzymatically digesting in 1mL of HBSS Ca2+Mg+ (Gibco) supplemented with 0.5% (v/v) human AB-serum (GemCell), 100 IU/mL penicillin, 100 mg/mL streptomycin, 0.25 mg/mL amphotericin B (Antibiotic Antimycotic Solution, Sigma Aldrich), 20uL/mL DNAseI (CellSystems), 1mg/mL collagenase type CLS IV (Biochrom). Tissue digestion was performed at 37°C while shaking for 30 minutes. Cells were passed through a sterile filter and stained with fluorochrome-conjugated antibodies to CD4-Vioblue or CD4-FITC, CD3-PE or CD3-VioGreen, CD45-AlexaFlour700, CD8/CD14/CD20-PerCP (Dump channel), CD45RO-APC, CLA-BV605 and Integrin-b7-PE-Vio770. Oral samples were stained with TotalSeq-C anti-human hashtag antibodies (LNH-94, 1:50) in the presence of Human TruStain FcX (1:20) in 50 μl of staining volume. Cells were sorted via FACS into precoated, low-bind collection tubes, containing sterile, filtered 1xPBS supplemented with 0.5% (v/v) human AB-serum.  After sorting, cells reactive for each antigen or oral cells derived from multiple donors were combined for sample multiplexing. FACS-enriched cells fractions from intestinal samples were processed individually.
FACS-enriched cells were loaded on a Chromium Next GEM Chip K (10X Genomics) for processing with the Chromium Next GEM Single Cell 5′ Kit v2 according to the manufacturer’s instructions. Sequencing libraries were generated as detailed in the manufacturer’s user guide (CG000511 Rev D).

value: PBMCs

value: CD4+ T cells

tag: condition

value: Crohn's disease patient

tag: Sex

value: male

value: mixed sample (Calbicans-reactive, Th17-targets-reactive, nonTh17-targets-reactive)

value: HTO

tag: hto

value: TotalSeq-C0253 anti-human Hashtag 3 (Calbicans-reactive), TotalSeq-C0254 anti-human Hashtag 4 (nonTh17-target-reactive), TotalSeq-C0256 anti-human Hashtag 6 (Th17-target-reactive)


title: ZBTB10KO_FSK_Rep1

description: Library name: Sample 4

value: ZBTB10 KO


title: Sample21_Tumor, PEO, rep3

city: Shanghai, China

first: Shengnan

last: She

state: Shanghai, China

address: Shanghai, China

country: China

institute: Fudan University, China

description:
Library name: Sample21
Column name in Tumor_count.csv: PEO_3

data_processing:
Sequence reads were trimmed for adapters and low-quaity sequence using Trimmomatic v0.39
Trimmed sequence reads were mapped to hg38/mm39 using Hisat2 v2.2.1
Read count extraction and normalization were performed using FeatureCounts v2.0.6 (parameters- Q: 10 -p --countReadPairs -B -C)
Assembly: hg38, mm39
Supplementary files format and content: tab-delimited text file includes raw counts for samples (for Sample1 to Sample15)
Supplementary files format and content: tab-delimited text file includes raw counts for samples (for Sample16 to Sample21)

molecule: polyA RNA

source_name: tumor

extract_protocol:
RNA was harvested using Quick-RNA™ Microprep Kit (Zymo). 1.3 ug of total RNA was used for the construction of sequencing libraries.
mRNA was enriched by Oligo(dT) beads, and fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530,New England Biolabs, Ipswich, MA, USA).

value: tumor

value: single cell suspension obtained by percoll of tumor

value: PEO


title: Male,FR,Saline,P0,rep5

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

description:
Library name: 16B.1_Male_FR_Saline_PFC_P0
16B.1_Male_FR_Saline_PFC_P0
P0_mPFC_counts.txt

data_processing:
Reads were aligned to the rat genome with STAR
Read counts per gene were computed with STAR
Assembly: Rnor_6.0
Supplementary files format and content: Ensembl gene Ids and read counts, tab delimited
Supplementary files format and content: Differential expression data, tab delimited

organism: Rattus norvegicus

source_name: Medial prefrontal cortex

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Medial prefrontal cortex


title: Male,FR,Insulin,Adult,rep6

description:
Library name: 2A.4_Male_FR_Insulin_mPFC_Adult
2A.4_Male_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: CD9_PBMCs_Calbicans_Th17targets_nonTh17targets_HTO

description:
Library name: CD9_blood_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: TotalSeq-C0252 anti-human Hashtag 2 (Calbicans-reactive), TotalSeq-C0254 anti-human Hashtag 4 (nonTh17-target-reactive), TotalSeq-C0256 anti-human Hashtag 6 (Th17-target-reactive)


title: ZBTB10KO_DMSO_Rep1

description: Library name: Sample 3

value: BeWo

value: choriocarcinoma


title: zygotes_onecell_multiome_h3k4me1_batch1

description:
Library name: zygotes_onecell_multiome_h3k4me1_batch1
L548_Zygote_rH3K4me1.fragments.tsv.gz
L548_Zygote_rH3K4me1.bigwig

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: fragment files (chromatin)
Supplementary files format and content: full-length and umi-only count matrices (rna)
Supplementary files format and content: Chromatin pseudobulk bigwig
Supplementary files format and content: Example single-cell chromatin and RNA bigwigs for same single cells
Library strategy: CUT&Tag

source_name: zygote

extract_protocol:
Zygotes were manually dispensed in 2µl of M2 medium with 0.2µl Dynabeads Myone Carboxylic (Fisher, 10563775) and kept on ice. After a 5 min centrifugation at 800g at 4°C, the supernatant was removed using the magnetic plate and replaced by 2µl of lysis buffer. Plates were then frozen at -80°C. Multiome OneCell CUT&Tag experiment was performed in two biological replicates, each corresponding to zygotes from one mouse.
Combination of OneCell CUT&Tag with single-cell full-length transcriptomics, as described in (Moutaux, Schwager et al., 2025)

value: zygote

value: mouse zygote

value: no


title: Sample20_Tumor, PEO, rep2

description:
Library name: Sample20
Column name in Tumor_count.csv: PEO_2


title: Male,Adlib,Insulin,Adult,rep7

description:
Library name: 25B.4_Male_Adlib_Insulin_mPFC_Adult
25B.4_Male_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: ZBTB10KO_DMSO_Rep3

description: Library name: Sample 11


title: mammary_gland_rna_mouse1

description:
Library name: mammary_gland_rna_mouse1
RNA part of the plate

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: fagment files for chromatin
Supplementary files format and content: full length and umi-only count matrices for rna

growth_protocol: Mice were sacrificed by cervical dislocation. Six mammary glands (numbers 2, 3, and 4 from each side) were collected and pooled. The pooled tissues were roughly chopped using dissecting scissors, followed by finer mincing with two scalpels. Single-cell dissociation was achieved through enzymatic digestion using 3 mg ml–1 collagenase I (Roche, 11088793001) and 100 U m–1 hyaluronidase (Sigma-Aldrich, H3506) in complete media (HBSS 24020117; 5% FBS) for 2 h under agitation (170 rpm) at 37°C. Cells were then treated with pre-warmed (37°C) PBS 0.25% trypsin-versen (Thermo Fisher Scientific, 15040-033) for 1 min 30s, with pipetting for 45s. Twas further processed with 5 mg ml–1 dispase (Sigma-Aldrich, D4693) and DNase 0.1 mg ml–1 (Roche, 11284932001) in complete media for 6 min at 37°C. Red blood cells were lysed using red blood cell lysis buffer (Thermo Fisher Scientific, 00-4333-57), and the suspension was filtered through a 40 µm cell strainer before cell counting and FACS staining. The cells were stained in the dark at 4°C for 20 min. Stained cells were resuspended at 10 million cells ml–1 in cytometry media (PBS with 1% BSA and 2 mM EDTA).  Three control mice were sorted with the following antibodies: anti-CD45-APC (1:50, BioLegend, 103112), anti-CD31-APC (1:50, BioLegend, 102510), anti-CD24-BV421 (1:50, BioLegend, 101826) and anti-CD49f-PE-Cy7 (1:50, BioLegend, 313622) to stain one million cells.  Sorting was performed using a SH800 sorter with a 100 µm chip, and epithelial cells (CD45-, CD31-, CD24 medium/high, CD49f medium/high) were collected in a 384-well plate, with one cell per well, using a custom single-cell sorting mode (60% mask). Two control mice were sorted with an expanded FACS panel comprising the following antibodies: anti-CD45-BV510 (1:500, BioLegend, 103138), CD31-BV510 (1:100, BD Biosciences, 563089); anti-CD29-PE-Dazzle594 (1:500, BioLegend, 102245), EpCAM-PE-Cy7 (1:500, BioLegend, 118215), Tspan8-BUV395 (1:100, BD Biosciences, 748043). Dead cells were excluded using Zombie NIR Fixable Viability Dye (1:5000, BioLegend, 423106); according to the manufacturer’s instructions. When the expanded panel was applied, 10 million cells were stained to enable capture of the rare Tspan8+ cell population. Cell sorting was performed on a BD Aria Fusion cell sorter. Epithelial cells (CD45-, CD31-, EpCAM medium/high, CD29 medium/high) were index-sorted into 384-well plates at one cell per well. Wells were allocated as follows: 50% luminal cells (CD45-, CD31-, EpCAM high, CD29 medium), 25% Tspan8⁺ basal cells (CD45-, CD31, EpCAM low, CD29 high, Tspan8+), and 25% Tspan8- basal cells (CD45-, CD31-, EpCAM low, CD29 high, Tspan8-).

value: mammary gland

value: epithelial

value: mRNA


title: WT_FSK_Rep1

description: Library name: Sample 2

value: wild-type

value: 20uM FSK, 48hr


title: ZBTB10_FSK_biol rep 2

description:
Library name: Sample 5
ZBTB10 immunoprecipitation

data_processing:
Raw sequencing reads were assessed for quality using FastQC (v0.11.9)
Adapter sequences and low-quality bases were trimmed using Trim Galore (v0.6.7) with default parameters.
Trimmed reads were aligned to the reference genome (hg38) using BWA (v0.7.17), and alignments were converted to BAM format with SAMtools (v1.17).
BAM files were subsequently filtered to remove duplicate reads (Picard, v3.0.0), non-primary alignments, unmapped reads, and reads mapping to blacklisted regions.
Signal-enriched regions were identified using MACS2 (v2.2.7.1) with a q-value threshold of 0.1, using the corresponding input sample as background. Broad signal-enriched regions were identified using epic2 (v0.0.52) with a q-value threshold of 0.05, using the corresponding input sample as background.
Peaks were annotated to the nearest gene and genomic feature using HOMER (v4.11). Known and de novo motif enrichment analyses were performed with HOMER (v4.11) on peak sets to identify enriched DNA-binding protein motifs.
Fraction of reads in peaks (FRiP) was calculated as a quality control metric. Filtered BAM files were converted to bigWig format using deepTools (v3.5.1)91 and normalized as counts per million (CPM) for visualization.
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak (for Forskolin IP samples, all consensus peaks in both replicates compared to input control for each sample)

extract_protocol:
Samples were sent to Active Motif (Carlsbad, CA) for ChIP-Seq. Active Motif prepared chromatin, performed ChIP reactions, generated libraries, sequenced the libraries, and performed basic analysis. Cells were fixed by adding formaldehyde to a final concentration of 1% in the existing medium and incubating for 15 min and then quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 200-500 bp with Active Motif’s PIXUL® Multi-Sample Sonicator, catalog 53130. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Qubit (Thermofisher). Extrapolation to the original chromatin volume allowed determination of the total chromatin yield. An aliquot of 30ug chromatin was precleared with protein G agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4ug of antibody against ZBTB10 (Abcam, cat number ab117786, lot number 1036026-8). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Takara PrepX DNA Library Kit). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 2000 (PE50, 30 million reads).

treatment_protocol: Two biological replicates each of human BeWo choriocarcinoma cells stably overexpressing N-terminally tagged Halo-3XFlag-ZBTB10 (integrated via Piggybac under an L30 promoter and Puro selection) were grown to ~50% confluence then treated for 48 hours with 0.1% DMSO or 20uM Forskolin with media changed at 24 hours.

value: L30 Halo-3XFlag-ZBTB10 IRES Puro stable BeWo cell line

value: 20uM FSK for 48hrs

tag: chip antibody


title: Oral_Biopsy_HTO

description:
Library name: Oral_Experiment1_HTO
Hashtag-derived oligonucleotide
HTO (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

source_name: Oral tissue

value: Oral tissue

value: CD4+ T cells

value: Healthy Control and Crohn's disease patient

value: mixed sample (Oral CD4 +Tcells from HC1, HC2. HC3. HC4. CD1)

value: HTO

value: TotalSeq-C0251 anti-human Hashtag 1 (HC1), TotalSeq-C0252 anti-human Hashtag 2 (HC2), TotalSeq-C0253 anti-human Hashtag 3 (HC3), TotalSeq-C0254 anti-human Hashtag 4 (HC4), TotalSeq-C0255 anti-human Hashtag 5 (CD1)


title: transplantations_rna

description:
Library name: transplantations_rna
RNA part of the plate

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: fragment files (chromatin)
Supplementary files format and content: full-length and umi-only count matrices (rna)

value: fresh tissue


title: GLUT3 overexpressed Aged HUVECs RNAseq rep3

city: aaaaaaaa

first: Wanzhou

last: Wu

address: aaaaaaaaa

institute: aaaaaaa

description:
Library name: Sample 9
OEC-GLUT3-OE3
Expression_Transcript.xlsx

data_processing:
Raw sequencing reads were assessed using FastQC. Adapter sequences and low-quality bases were removed using Cutadapt.  For RNA-seq data, clean reads were aligned to the Mus musculus reference genome (GRCm38) using HISAT2. Transcript assembly and abundance estimation were performed using StringTie based on GENCODE gene annotations. Gene and transcript expression levels were quantified as FPKM values. Differential expression analysis was performed using Ballgown. Alternative splicing events were identified using rMATS, and coding potential of novel transcripts was evaluated using CPAT.  For Ribo-seq data, reads shorter than 22 nt or longer than 34 nt after trimming were discarded. Reads mapping to rRNA, tRNA, snRNA, and snoRNA were removed using Bowtie. Remaining reads were aligned to the Mus musculus reference genome (GRCm38) using STAR. Only uniquely mapped reads were retained for downstream analyses. Ribosome footprint quality control analyses were performed using RiboTish. Transcript-level ribosome occupancy was quantified using Plastid and normalized as RPKM values. Differential translation analysis was performed using edgeR, translational efficiency (TE) was analyzed using RiboDiff, and ORF prediction was performed using RiboCode.
Assembly: GRCh38
Supplementary files format and content: Processed data files are provided as .xlsx table files. RNA-seq outputs include raw gene count matrices. Ribo-seq outputs include raw ribosome-protected fragment (RPF) count matrices.

source_name: Vascular

extract_protocol:
Samples were collected and immediately frozen in liquid nitrogen and stored at −80°C until processing. For RNA-seq samples, total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer's instructions. RNA quality and concentration were assessed using agarose gel electrophoresis and a NanoDrop ND-1000 spectrophotometer. Poly(A)+ mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), while ribosomal RNA depletion was performed when necessary.  For ribosome profiling (Ribo-seq) samples, tissues were homogenized in polysome lysis buffer supplemented with cycloheximide and RNase inhibitors. Cell debris was removed by centrifugation and lysates were treated with RNase I to digest unprotected RNA. Ribosome-protected fragments (RPFs) were isolated and purified. RNA quantity and integrity were evaluated prior to library preparation.
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Prep Kit (Roche). Briefly, enriched mRNA or rRNA-depleted RNA was fragmented and reverse-transcribed into first-strand cDNA using random primers. Second-strand cDNA synthesis was performed with dUTP incorporation to preserve strand specificity. Double-stranded cDNA was end-repaired, A-tailed, ligated to Illumina-compatible adapters, PCR-amplified, and purified.  Ribo-seq libraries were prepared using the NEB Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs). Ribosome-protected fragments corresponding to 26–34 nt footprints were size-selected and ligated to 3′ and 5′ adapters. Reverse transcription was performed to generate cDNA, followed by PCR amplification. PCR products corresponding to 146–154 bp were purified by PAGE gel extraction.  Library quality and fragment size distributions were evaluated using an Agilent 2100 Bioanalyzer and quantified by qPCR. Sequencing was performed on the Illumina NovaSeq 6000 platform. RNA-seq libraries were sequenced in paired-end 150 bp mode, whereas Ribo-seq libraries were sequenced in single-end mode.

value: Vascular

value: Primary Cell

value: Human Umbilical Vein Endothelial Cells

value: GLUT3 overexpress

tag: age

value: Aged


title: Male,FR,Insulin,Adult,rep9

description:
Library name: 5B.4_Male_FR_Insulin_mPFC_Adult
5B.4_Male_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt

value: Medial prefrontal cortex


title: Female,FR,Insulin,Adult,rep9

description:
Library name: 5A.7_Female_FR_Insulin_mPFC_Adult
5A.7_Female_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: transwell,DMSO treated 2

city: shanghai

first: Yong

middle: hui

last: Chen

address: 160, Pujian Road

institute: Renji hospital

description:
Library name: sample5
DMSO_2

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: DMSO


title: Male,FR,Insulin,Adult,rep8

description:
Library name: 5A.6_Male_FR_Insulin_mPFC_Adult
5A.6_Male_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: ZBTB10KO_FSK_Rep2

description: Library name: Sample 8

value: BeWo

value: choriocarcinoma

value: ZBTB10 KO

value: 20uM FSK, 48hr


title: Female,FR,Insulin,Adult,rep8

description:
Library name: 24B.8_Female_FR_Insulin_mPFC_Adult
24B.8_Female_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample19_Tumor, PEO, rep1

description:
Library name: Sample19
Column name in Tumor_count.csv: PEO_1

value: tumor

value: single cell suspension obtained by percoll of tumor

value: PEO


title: transwell,bw723c86 treated 3

description:
Library name: sample3
BW3


title: transplantations_chromatin_p3

description:
Library name: transplantations_chromatin_p3
Chromatin part of the plate

value: mammary gland

value: epithelial

value: no

value: DNA


title: ZBTB10_FSK_biol rep 1

description:
Library name: Sample 4
ZBTB10 immunoprecipitation

value: L30 Halo-3XFlag-ZBTB10 IRES Puro stable BeWo cell line

value: 20uM FSK for 48hrs

value: Abcam, cat number ab117786, lot number 1036026-8


title: Sample18_Tumor, PBS, rep3

description:
Library name: Sample18
Column name in Tumor_count.csv: PBS_3

value: PBS


title: Female,FR,Insulin,Adult,rep7

description:
Library name: 24B.7_Female_FR_Insulin_mPFC_Adult
24B.7_Female_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt

value: Medial prefrontal cortex


title: Female,Adlib,Insulin,Adult,rep7

description:
Library name: 2B.7_Female_Adlib_Insulin_mPFC_Adult
2B.7_Female_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Human PBMC PCOS TCR

city: Beijing

first: Chenlei

last: Xu

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: PCOS_TCR
Single-cell TCR V(D)J library from human peripheral blood mononuclear cells in the PCOS group, paired with the corresponding GEX library.

data_processing:
Raw sequencing data from gene expression libraries were processed using Cell Ranger to generate gene-barcode expression matrices.
Raw sequencing data from TCR V(D)J libraries were processed using Cell Ranger with the human V(D)J reference.
Filtered feature-barcode matrices were used for downstream single-cell RNA-seq analysis.
Single-cell RNA-seq data were analyzed using Seurat. Cells were filtered based on quality control metrics, followed by normalization, feature selection, dimensionality reduction, clustering, and cell type annotation.
TCR clonotype information was obtained from Cell Ranger V(D)J output files and integrated with the corresponding single-cell gene expression data.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression data files include 10x Genomics feature-barcode matrices for each sample, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files containing cell barcodes, gene annotations, and raw UMI count matrices.
Supplementary files format and content: Processed TCR V(D)J data files include filtered_contig_annotations.csv and clonotypes.csv files containing TCR contig annotations and clonotype information for each sample.
Library strategy: TCR-seq

source_name: peripheral blood

growth_protocol: Peripheral blood samples were collected from participants according to approved institutional protocols.

extract_protocol:
Peripheral blood mononuclear cells were isolated from peripheral blood using density gradient centrifugation. Single-cell suspensions were prepared, filtered, and assessed for cell viability and concentration before single-cell library preparation.
Single-cell gene expression libraries were prepared using the 10x Genomics Chromium Single Cell 5' Gene Expression platform. Single-cell TCR V(D)J libraries were prepared from the same cell suspensions using the 10x Genomics Chromium Single Cell V(D)J enrichment workflow according to the manufacturer's instructions.

treatment_protocol: Participants were assigned to the healthy control group or PCOS group according to the study design. No in vitro treatment was applied before single-cell library preparation.

value: peripheral blood

value: peripheral blood mononuclear cells

value: PCOS

tag: batch

value: batch 1


title: Male,FR,Insulin,Adult,rep5

description:
Library name: 24B.3_Male_FR_Insulin_mPFC_Adult
24B.3_Male_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample17_Tumor, PBS, rep2

description:
Library name: Sample17
Column name in Tumor_count.csv: PBS_2


title: transwell,bw723c86 treated 2

description:
Library name: sample2
BW2


title: Human PBMC PCOS GEX

description:
Library name: PCOS_5
Single-cell gene expression library from human peripheral blood mononuclear cells in the PCOS group.

data_processing:
Raw sequencing data from gene expression libraries were processed using Cell Ranger to generate gene-barcode expression matrices.
Raw sequencing data from TCR V(D)J libraries were processed using Cell Ranger with the human V(D)J reference.
Filtered feature-barcode matrices were used for downstream single-cell RNA-seq analysis.
Single-cell RNA-seq data were analyzed using Seurat. Cells were filtered based on quality control metrics, followed by normalization, feature selection, dimensionality reduction, clustering, and cell type annotation.
TCR clonotype information was obtained from Cell Ranger V(D)J output files and integrated with the corresponding single-cell gene expression data.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression data files include 10x Genomics feature-barcode matrices for each sample, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files containing cell barcodes, gene annotations, and raw UMI count matrices.
Supplementary files format and content: Processed TCR V(D)J data files include filtered_contig_annotations.csv and clonotypes.csv files containing TCR contig annotations and clonotype information for each sample.


title: ZBTB10_DMSO_biol rep 2

description:
Library name: Sample 3
ZBTB10 immunoprecipitation

value: BeWo

value: choriocarcinoma

value: 0.1% DMSO for 48hrs


title: transplantations_chromatin_p1

description:
Library name: transplantations_chromatin_p1
Chromatin part of the plate

value: fresh tissue


title: WT_DMSO_Rep2

description: Library name: Sample 5

value: wild-type


title: Sample16_Tumor, PBS, rep1

description:
Library name: Sample16
Column name in Tumor_count.csv: PBS_1

value: tumor

value: single cell suspension obtained by percoll of tumor


title: ZBTB10_DMSO_biol rep 1

description:
Library name: Sample 2
ZBTB10 immunoprecipitation


title: Male,Adlib,Insulin,Adult,rep6

description:
Library name: 24A.4_Male_Adlib_Insulin_mPFC_Adult
24A.4_Male_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Human PBMC control TCR

description:
Library name: control_TCR
Single-cell TCR V(D)J library from human peripheral blood mononuclear cells in the healthy control group, paired with the corresponding GEX library.

value: healthy control


title: ZBTB10_Pooled_Input

description:
Library name: Sample 1
Input control

value: L30 Halo-3XFlag-ZBTB10 IRES Puro stable BeWo cell line


title: transwell,bw723c86 treated 1

description:
Library name: sample1
BW1


title: zygotes_h3k27me3_bulk_CUT&RUN_r2

description: Library name: zygotes_h3k27me3_bulk_CUT_RUN_r2

data_processing:
Raw reads were aligned to mm10 mouse reference genome using bowtie. The CPM-normalized bigwigs were produced using Deeptools bamCoverage --normalizeUsing CPM.
Assembly: mm10
Supplementary files format and content: Bigwig (CPM-normalized):D1535_D1480C05_mouse.bw, D1535_D1480C06_mouse.bw
Library strategy: CUT&Run

growth_protocol: Zygotes were obtained from 6-week-old B6D2F1/J females mated with C57BL6/J males (3–6 months old) after hormonal induction with pregnant mare serum gonadotropin (5 IU) and human chorionic gonadotropin (hCG, 5 IU) 46–48-h later.

extract_protocol:
Zygotes were collected at 23 post-hCG treatment in M2 medium. Cumulus cells were removed using M2 media containing hyaluronidase (Merck-Millipore MR-051-F). The zona pellucida was removed with Pronase (SIGMA P8811), followed by two washes in M2 medium.
Bulk CUT&RUN as described in (Moutaux& Schwager et al., 2025)

value: zygote

value: no

value: DNA


title: Female,FR,Insulin,Adult,rep6

description:
Library name: 23B.8_Female_FR_Insulin_mPFC_Adult
23B.8_Female_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt

value: Medial prefrontal cortex


title: Human PBMC control GEX

description:
Library name: control_5
Single-cell gene expression library from human peripheral blood mononuclear cells in the healthy control group.

value: peripheral blood


title: zygotes_h3k27me3_bulk_CUT&RUN_r1

description: Library name: zygotes_h3k27me3_bulk_CUT_RUN_r1


title: Male,Adlib,Insulin,Adult,rep8

description:
Library name: 2B.4_Male_Adlib_Insulin_mPFC_Adult
2B.4_Male_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: HBL-1 cells, Ro 08-2750 biol rep 3, 24+5 hours

city: Münster

first: Lasse

last: Reichstein

state: NRW

address: Robert-Koch-Straße 31

department: Department of Radiation Oncology

institute: Münster University Hospital

description:
Library name: Sample 6
colname in RNAseqRo08-2750inHBL1_rawcounts.tsv: HBL06.RO3

data_processing:
quality control of FASTQ files with FASTQC(v.0.11.9) and fastp(v.0.23.2) with additional adapter removal (Illumina) and "CA" base trimming at the read start
Samtools(v.1.16.1) "markup" applied to balance in case of PCR duplicates
read alignment to human genome (flavour EMBL-EBI Ensenmbl v111) using STAR (v.2.7.11a) with secondary allignement using BOWtie2 (v2.5.3) as crosscheck
Quantification with Salmon version 1.6-1.7 according to the manual and program defaults.
Assembly: Current builds of the Human genome reference GRCh38.p14 from EBI in England, mirBase release 22.1.
Supplementary files format and content: tab delimited tsv file with raw counts for each sample

growth_protocol: HBL-1 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (PAN-Biotech), 25 mM Hepes (Roth), 1% Penicillin/Streptomycin, 1% sodium pyruvate and 0.1% beta-mercaptoethanol (all PAN-Biotech) in H20-saturated incubator at 37°C, 5% CO2

extract_protocol:
RNA was isolated using the RNeasy Mini kit (Qiagen). A DNAse digestion step was added according to manufacturer protocol using DNAse I and a DNAse reaction buffer (both New England Bio Labs).
RNA integrity number (RIN) values  were checked using the Agilent TapeStation 4200 with a standard-RNA tape
mRNA enrichment and DNA NGS library preparation was completed using a NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, UK).

treatment_protocol: Ro 08-2750/DMSO treatment was performed by adding 5 µM Ro 08-2750 or 0.05% DMSO to the cell medium twice, 24 hours and 5 hours prior to analysis

value: diffuse large B-cell lymphoma

value: WT

value: 5 µM Ro 08-2750 for 24+5 hours


description: Library name: zygotes_OneCell_multiome_h3k27me3_batch2

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: 10X-like UMI matrix of RNA counts :  zygotes_barcodes.tsv, zygotes_genes.tsv, zygotes_matrix.mtx
Supplementary files format and content: fragment files of DNA counts : Zygote_4_rH3K27me3_pA.fragments.tsv.gz,  Zygote_5_rH3K27me3_pA.fragments.tsv.gz
Supplementary files format and content: fragment file indexes: Zygote_5_rH3K27me3_pA.fragments.tsv.gz.tbi, Zygote_4_rH3K27me3_pA.fragments.tsv.gz.tbi,
Supplementary files format and content: single-cell bigwigs, H3K27me3 (CPM-normalized) L548_Zygote_4_rH3K27me3_pA_Cell2.bigwig L548_Zygote_4_rH3K27me3_pA_Cell3.bigwig L548_Zygote_4_rH3K27me3_pA_Cell4.bigwig L548_Zygote_5_rH3K27me3_pA_Cell1.bigwig L548_Zygote_5_rH3K27me3_pA_Cell2.bigwig L548_Zygote_5_rH3K27me3_pA_Cell3.bigwig L548_Zygote_5_rH3K27me3_pA_Cell4.bigwig L548_Zygote_5_rH3K27me3_pA_Cell5.bigwig L548_Zygote_5_rH3K27me3_pA_Cell6.bigwig L548_Zygote_5_rH3K27me3_pA_Cell7.bigwig L548_Zygote_5_rH3K27me3_pA_Cell8.bigwig
Supplementary files format and content: single-cell bigwigs, RNA (CPM-normalized) D1888T0578_Zygote_4_cell2_RNA.bw D1888T0579_Zygote_4_cell3_RNA.bw D1888T0580_Zygote_4_cell4_RNA.bw D1888T0588_Zygote_5_cell1_RNA.bw D1888T0589_Zygote_5_cell2_RNA.bw D1888T0590_Zygote_5_cell3_RNA.bw D1888T0591_Zygote_5_cell4_RNA.bw D1888T0592_Zygote_5_cell5_RNA.bw D1888T0593_Zygote_5_cell6_RNA.bw D1888T0594_Zygote_5_cell7_RNA.bw D1888T0595_Zygote_5_cell8_RNA.bw
Supplementary files format and content: pseudobulk bigwigs, RNA (CPM-normalized)
Library strategy: CUT&Tag

extract_protocol:
Zygotes were collected at 23 post-hCG treatment in M2 medium. Cumulus cells were removed using M2 media containing hyaluronidase (Merck-Millipore MR-051-F). The zona pellucida was removed with Pronase (SIGMA P8811), followed by two washes in M2 medium. Zygotes were then manually dispensed in 384-well plates filled with 2µl of M2 medium with 0.2µl Dynabeads Myone Carboxylic (Fisher, 10563775) and kept on ice. After centrifugation, M2 medium was replaced by 2µl of lysis buffer (0.2% Triton X-100, 1x Protease Inhibitor Cocktail, 1.2U/µl Recombinant RNAse Inhibitor, 9.2µM oligo-dT /5BiosG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN).
Combination of OneCell CUT&Tag with single-cell full-length transcriptomics, as described in (Moutaux& Schwager et al., 2025) using manual OneCell CUT&Tag


title: Male,FR,Insulin,Adult,rep4

description:
Library name: 23B.5_Male_FR_Insulin_mPFC_Adult
23B.5_Male_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: HBL-1 cells, DMSO control biol rep 3, 24+5 hours

description:
Library name: Sample 5
colname in RNAseqRo08-2750inHBL1_rawcounts.tsv: HBL05.Ctrl3

value: 0.05% DMSO for 24+5 hours


title: Insulin 4

city: Stockholm

first: Danai

last: Zareifi

address: Nobels väg 6

department: Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

description: Library name: P23101_1051

data_processing:
Library preparation and sequencing were conducted on an Illumina platform, generating reads with Phred scores consistently above Q30. Quality and adapter trimming of reads was performed using Cutadapt (v2.8). Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.7). Reads were aligned to the Ensembl GRCh38 reference genome using STAR (v2.7.9a). Counts for each gene were obtained using featureCounts (v1.5.1).
Assembly: Ensembl GRCh38
Supplementary files format and content: txt file contains raw counts for all samples

source_name: human adipocytes

extract_protocol:
RNA isolation, cDNA synthesis and quantitative real-time PCR (qPCR) were performed as previously described11. Briefly, total RNA was purified using the NucleoSpin RNA kit (Macherey-Nagel #740955) and quantified with a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific). Reverse transcription and qPCR were performed using iScript (Bio-Rad #1708891) and iQ SYBR Green Supermix (Bio-Rad #1708882), respectively. Relative mRNA levels were calculated using the comparative 2-DDct method. Where indicated, z-score analysis was applied using the formula: (observed value - mean) / standard deviation.
The library pool was prepared with Illumina mRNA stranded ligation protocol.

value: human adipocytes

value: male

value: insulin


title: Insulin 7

description: Library name: P23101_1052


title: HBL-1 cells, Ro 08-2750 biol rep 2, 24+5 hours

description:
Library name: Sample 4
colname in RNAseqRo08-2750inHBL1_rawcounts.tsv: HBL04.RO2


title: zygotes_OneCell_multiome_rna

description: Library name: zygotes_OneCell_multiome_rna

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: 10X-like UMI matrix of RNA counts :  zygotes_barcodes.tsv, zygotes_genes.tsv, zygotes_matrix.mtx
Supplementary files format and content: fragment files of DNA counts : Zygote_4_rH3K27me3_pA.fragments.tsv.gz,  Zygote_5_rH3K27me3_pA.fragments.tsv.gz
Supplementary files format and content: fragment file indexes: Zygote_5_rH3K27me3_pA.fragments.tsv.gz.tbi, Zygote_4_rH3K27me3_pA.fragments.tsv.gz.tbi,
Supplementary files format and content: single-cell bigwigs, H3K27me3 (CPM-normalized) L548_Zygote_4_rH3K27me3_pA_Cell2.bigwig L548_Zygote_4_rH3K27me3_pA_Cell3.bigwig L548_Zygote_4_rH3K27me3_pA_Cell4.bigwig L548_Zygote_5_rH3K27me3_pA_Cell1.bigwig L548_Zygote_5_rH3K27me3_pA_Cell2.bigwig L548_Zygote_5_rH3K27me3_pA_Cell3.bigwig L548_Zygote_5_rH3K27me3_pA_Cell4.bigwig L548_Zygote_5_rH3K27me3_pA_Cell5.bigwig L548_Zygote_5_rH3K27me3_pA_Cell6.bigwig L548_Zygote_5_rH3K27me3_pA_Cell7.bigwig L548_Zygote_5_rH3K27me3_pA_Cell8.bigwig
Supplementary files format and content: single-cell bigwigs, RNA (CPM-normalized) D1888T0578_Zygote_4_cell2_RNA.bw D1888T0579_Zygote_4_cell3_RNA.bw D1888T0580_Zygote_4_cell4_RNA.bw D1888T0588_Zygote_5_cell1_RNA.bw D1888T0589_Zygote_5_cell2_RNA.bw D1888T0590_Zygote_5_cell3_RNA.bw D1888T0591_Zygote_5_cell4_RNA.bw D1888T0592_Zygote_5_cell5_RNA.bw D1888T0593_Zygote_5_cell6_RNA.bw D1888T0594_Zygote_5_cell7_RNA.bw D1888T0595_Zygote_5_cell8_RNA.bw
Supplementary files format and content: pseudobulk bigwigs, RNA (CPM-normalized)

value: mRNA


title: Female,FR,Insulin,Adult,rep5

description:
Library name: 22B.8_Female_FR_Insulin_mPFC_Adult
22B.8_Female_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: AP d7, rep 2

city: Cambridge

first: Timotheus

last: Halim

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Initial mapping and counting of 10x Genomics scRNA-seq reads was performed using Cell Ranger v3.1.0.
Assembly: GRCm38.p6
Supplementary files format and content: Cell Ranger output containing barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files

source_name: Pancreas

extract_protocol:
Single-cell encapsulation was performed using the Chromium Single Cell B Chip Kit (10x Genomics, PN-1000073).
Library preparation was performed using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 (10x Genomics, PN-1000075).

treatment_protocol: Mice were treated with PBS (n=3) or repeated hourly doses of 75ng/g body weight of caerulein for 6 hours, and taken down at day 1 (n=2), day 3 (n=3), or day 7 (n=2).

value: Pancreas

value: Caerulein


title: Male,FR,Insulin,Adult,rep3

description:
Library name: 22B.4_Male_FR_Insulin_mPFC_Adult
22B.4_Male_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Insulin 2

description: Library name: P23101_1050


title: AP d7, rep 1


title: HBL-1 cells, DMSO control biol rep 2, 24+5 hours

description:
Library name: Sample 3
colname in RNAseqRo08-2750inHBL1_rawcounts.tsv: HBL03.Ctrl2


title: Insulin 1

description: Library name: P23101_1049


title: Female,Adlib,Insulin,Adult,rep6

description:
Library name: 20A.8_Female_Adlib_Insulin_mPFC_Adult
20A.8_Female_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Male,Adlib,Insulin,Adult,rep5

description:
Library name: 20A.4_Male_Adlib_Insulin_mPFC_Adult
20A.4_Male_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Control 4

description: Library name: P23101_1048

value: control


title: Female,Adlib,Insulin,Adult,rep5

description:
Library name: 19A.8_Female_Adlib_Insulin_mPFC_Adult
19A.8_Female_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Control 3

description: Library name: P23101_1047


title: ZBTB10KO_STB_Rep3

description: Library name: Sample 22

data_processing:
Plasmidsaurus performed read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp
Plasmidsaurus aligned reads to the human hg38 reference genome using STAR aligner v2.7.1181 with non-canonical splice junction removal and output of unmapped reads.
Plasmidsaurus performed gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id.
Differential gene expression analysis was performed with EdgeR in Jupyter Notebook with filtering for low-expressed genes with edgeR::filterByExpr. Statistical comparisons between individual sample conditions were made using EdgeR makeContrasts and then glmQLFit. The reported P-values and FDR values were corrected with adjust.method = “BH,” and differentially expressed genes are reported with an adjusted FDR of <0.05.
Assembly: hg38
Supplementary files format and content: Comma separated values file containing CPM-normalized count data for each Sample by Ensembl Gene ID
Supplementary files format and content: Comma separated values file containing differential gene expression analysis output from EdgeR with the Log2 Fold-Change (logFC), p-value (pValue) and Benjamini-Hochberg (BH) corrected False Discovery Rate (FDR) comparing NEG (non-targeting sgRNA transfected) hTSCs to ZBTB10 KO hTSCs in Undifferentiated, STB-differentiated, and EVT-differentiated conditions. Comparisons are noted as (_KOvsWT) where positive FC values indicates higher gene expression in ZBTB10 KO cells compared to NEG control.

source_name: hTSC

growth_protocol: Naïve-derived human trophoblast stem cells were established previously and cultured in hypoxic conditions (37°C, 5% CO2, 5% O2) in TSC Media (DMEM/F12 supplemented with 0.1 mM β-mercaptoethanol, 0.2% FBS (Sigma, F4135), 0.5% Penicillin-Streptomycin (P/S; Gibco, 15140122), 0.3% BSA, 1% ITS-X (Gibco, 41400045), 1.5 μg/mL L-ascorbic acid, 50 ng/mL EGF, 2 μM CHIR99021, 0.5 μM A83-01, 1 μM SB431542, 0.8 mM VPA, and 5 μM Y-27632).51 Media was changed every other day and TSCs were passaged using TrypLE Express (Gibco, 12605010) when 80% confluent (approximately every 4 days) at a ratio of 1:4–6 on Cultrex-coated plates. Cells from passage 10-25 were used.

extract_protocol:
hTSC RNA was harvested using the RNeasy mini kit (Qiagen, 74104).
RNA-sequencing was performed by Plasmidsaurus using Illumina Sequencing Technology with custom analysis and annotation.

treatment_protocol: Human hTSCs were plated at a density of 1E5 cells/well in Cultrex-coated 6-well plates and differentiated for 6 days into EVT or STB and harvested at Day 7, or if undifferentiated were harvested when confluent at Day 4. For the induction of EVTs, Cells were allowed to adhere overnight in TSC medium, then differentiation was initiated by switching to EVT1 medium (DMEM/F12, 0.1 mM β-mercaptoethanol, 0.5% Pen/Strep, 0.3% BSA, 1% ITS-X, 100ng/mL NRG1, 7.5uM A83-01, 2.5 μM Y-27632, and 4% Knockout Serum Replacement) supplemented with 1% Geltrex (Day 1). On day 3, the medium was replaced with EVT2 medium (EVT1 medium without NRG1) supplemented with 0.5% Geltrex. On day 5, the medium was replaced with EVT2 medium. For the induction of STBs, TSCs were seeded identically as above. Cells were allowed to adhere overnight in TSC medium, then differentiation was initiated by switching to STB medium (DMEM/F12, 0.1 mM β-mercaptoethanol, 0.5% Pen/Strep, 0.3% BSA, 1% ITS-X, 2.5 μM forskolin, 2.5 μM Y-27632, and 4% Knockout Serum Replacement) on Day 1. The medium was replaced on day 4.

value: hTSC

value: naive pluripotent stem cell derived human trophoblast stem cells

value: polyclonal ZBTB10 KO

value: 6 day STB differentiation


title: HBL-1 cells, DMSO control biol rep 1, 24+5 hours

description:
Library name: Sample 1
colname in RNAseqRo08-2750inHBL1_rawcounts.tsv: HBL01.Ctrl.1


title: Male,Adlib,Insulin,Adult,rep4

description:
Library name: 19A.4_Male_Adlib_Insulin_mPFC_Adult
19A.4_Male_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt

value: Medial prefrontal cortex


title: NEG_STB_Rep3

description: Library name: Sample 21

value: NEG (polyclonal nucleofected with Cas9+non-targeting sgRNA)


title: AP d1, rep 2


title: Female,FR,Insulin,Adult,rep4

description:
Library name: 16B.8_Female_FR_Insulin_mPFC_Adult
16B.8_Female_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: AP d1, rep 1


title: ZBTB10KO_EVT_Rep4

description: Library name: Sample 20

value: 6 day EVT differentiation


title: Female,FR,Insulin,Adult,rep3

description:
Library name: 16B.7_Female_FR_Insulin_mPFC_Adult
16B.7_Female_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: mm468_onecell_multiome_rna

description: Library name: mm468_onecell_multiome_rna

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: hg38
Supplementary files format and content: fragment files (chromatin)
Supplementary files format and content: full-length and umi-only count matrices (rna)

growth_protocol: MDA-MB-468 cells (American Type Culture Collection (ATCC), HTB-132) were maintained in DMEM (Gibco-BRL, 11966025) supplemented with 10% heat-inactivated fetal bovine serum (Gibco, 10500064) and cultured in a humidified 5% CO2 atmosphere at 37 °C. MDA-MB-468 cells were sorted into plates using CellenONE dispenser (Scienion).

extract_protocol:
The plate was subjected to the multiome OneCell CUT&Tag protocol, as described in (Schwager, Moutaux et al., 2026)
Combination of OneCell CUT&Tag with single-cell full-length transcriptomics, as described in (Schwager, Moutaux et al., 2026)

value: mammary gland

value: epithelial

value: no


title: NEG_EVT_Rep4

description: Library name: Sample 19


title: PBS, rep 3

value: PBS


title: DMSO treated 4

description:
Library name: sample7
DMSO_4
D4

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: PBMC

value: PBMC

value: DMSO


title: Male,FR,Insulin,Adult,rep2

description:
Library name: 16B.4_Male_FR_Insulin_mPFC_Adult
16B.4_Male_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt

data_processing:
Reads were aligned to the rat genome with STAR
Read counts per gene were computed with STAR
Assembly: Rnor_6.0
Supplementary files format and content: Ensembl gene Ids and read counts, tab delimited
Supplementary files format and content: Differential expression data, tab delimited


title: DMSO treated 3

description:
Library name: sample6
DMSO_3
D3


title: ZBTB10KO_Undiff_Rep4

description: Library name: Sample 18

value: Untreated


title: PBS, rep 2

value: Pancreas


title: NEG_Undiff_Rep4

description: Library name: Sample 17


title: PBS, rep 1


title: Male,Adlib,Insulin,Adult,rep3

description:
Library name: 16A.4_Male_Adlib_Insulin_mPFC_Adult
16A.4_Male_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Female,Adlib,Insulin,Adult,rep3

description:
Library name: 15B.8_Female_Adlib_Insulin_mPFC_Adult
15B.8_Female_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: naive_ILC2_scRNAseq


title: DMSO treated 1

description:
Library name: sample4
DMSO_1
D1


title: NEG_STB_Rep2

description: Library name: Sample 15


title: Female,FR,Insulin,Adult,rep2

description:
Library name: 15A.8_Female_FR_Insulin_mPFC_Adult
15A.8_Female_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: bw723c86 treated 3

description:
Library name: sample3
BW3
E3


title: IL13KO_coculture_2

data_processing:
Quality of raw sequence data was assessed using FastQC (version 0.11.9)
Raw sequence was trimmed for adapter content using Trimmomatic (version 0.39)
Reads were aligned to the GRCm38.p6 genome using STAR (v 2.7.7a)
Alignment quality was assess using Picard’s CollectAlignmentMetrics, CollectRnaSeqMetrics, MarkDuplicates and CollectInsertSizeMetrics tools (v 2.27.3)
Quantification of gene expression was performed using Salmon (v 1.6.0) in mapping-based mode versus the Ensembl release 102 transcriptome
Assembly: GRCm38.p6
Supplementary files format and content: Raw and DESeq2-normalised counts matrix (as .csv file)

source_name: Fibroblast

extract_protocol:
RNA was extracted using RNeasy plus micro kit (Qiagen) and 5 to 15 ng used as input material for library preparation.
Libraries were generated with the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB) according to manufacturer's instructions. The pooled libraries were quantified with KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and sequenced (paired end 50nt) on an Illumina NovaSeq 6000 system (Illumina).

value: Fibroblast

value: IL13KO ILC2 coculture


title: ZBTB10KO_EVT_Rep3

description: Library name: Sample 14

value: hTSC


title: bw723c86 treated 2

description:
Library name: sample2
BW2
E2


title: Male,Adlib,Insulin,Adult,rep2

description:
Library name: 13B.5_Male_Adlib_Insulin_mPFC_Adult
13B.5_Male_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: AP d3, rep 2

value: Caerulein


title: IL13KO_coculture_1


title: Female,Adlib,Insulin,Adult,rep2

description:
Library name: 12A.8_Female_Adlib_Insulin_mPFC_Adult
12A.8_Female_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: bw723c86 treated 1

description:
Library name: sample1
BW1
E1


title: ZBTB10KO_Undiff_Rep3

description: Library name: Sample 12

value: naive pluripotent stem cell derived human trophoblast stem cells

value: polyclonal ZBTB10 KO


title: WT_coculture_3

value: WT ILC2 coculture


title: Male,Adlib,Insulin,Adult,rep1

description:
Library name: 12A.4_Male_Adlib_Insulin_mPFC_Adult
12A.4_Male_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt

value: Medial prefrontal cortex


title: LV-ATF7, rep3

city: Luoyang

first: Pengcheng

address: 24 Jinghua Road

institute: The First Affiliated Hospital of Henan University of Science and Technology

description: Library name: B3

data_processing:
mRNA-seq reads were processed using Fastp (version 0.23.1) for quality control, which included removing adapter contamination and low-quality reads to obtain clean data for subsequent analysis.
Assembly: GRCh38
Supplementary files format and content: CSV file indlude gene count for each sample
Supplementary files format and content: csv files include FPKM values for each Smaple

source_name: HaCaT cells

extract_protocol:
Total RNA from cells or tissues was isolated using TRIpure reagent (BioTeke, China).
After quality verification, mRNA was enriched using Oligo(dT) magnetic beads and fragmented in fragmentation buffer. First-strand cDNA was synthesized using random hexamers, followed by second-strand synthesis with DNA polymerase I and RNase H. The double-stranded cDNA was purified with AMPure XP beads, then end-repaired, A-tailed, and ligated to sequencing adapters. Size selection was performed using AMPure XP beads, and the final library was obtained after PCR amplification and bead purification.

value: HaCaT cells

value: keratinocytes


title: NEG_Undiff_Rep3

description: Library name: Sample 11

value: NEG (polyclonal nucleofected with Cas9+non-targeting sgRNA)


title: WT_coculture_2


title: LV-ATF7, rep2

description: Library name: B2


title: Female,Adlib,Insulin,Adult,rep1

description:
Library name: 11B.8_Female_Adlib_Insulin_mPFC_Adult
11B.8_Female_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: WT_coculture_1


title: LV-ATF7, rep1

description: Library name: B1


title: NEG_STB_Rep1

description: Library name: Sample 9

value: 6 day STB differentiation


title: Female,FR,Insulin,Adult,rep1

description:
Library name: 11A.8_Female_FR_Insulin_mPFC_Adult
11A.8_Female_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: FB_monoculture_4

value: Monoculture


title: Male,FR,Insulin,Adult,rep1

description:
Library name: 11A.4_Male_FR_Insulin_mPFC_Adult
11A.4_Male_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: LV-NC, rep3

description: Library name: A4


title: FB_monoculture_3


title: ZBTB10KO_EVT_Rep2

description: Library name: Sample 8

value: 6 day EVT differentiation


title: LV-NC, rep2

description: Library name: A2


title: HBL-1 cells, Ro 08-2750 biol rep 1, 24+5 hours

description:
Library name: Sample 2
colname in RNAseqRo08-2750inHBL1_rawcounts.tsv: HBL02.RO1

value: diffuse large B-cell lymphoma

value: WT

value: 5 µM Ro 08-2750 for 24+5 hours


title: FB_monoculture_2

value: Fibroblast


title: LV-NC, rep1

description: Library name: A1


title: Male,Adlib,Saline,Adult,rep10

description:
Library name: 9B.3_Male_Adlib_Saline_mPFC_Adult
9B.3_Male_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: ZBTB10KO_Undiff_Rep2

description: Library name: Sample 6

value: Untreated


title: FB_monoculture_1


title: PMP CAF culture

city: Ghent

first: sandor

last: Dedeyne

address: C. Heymanslaan 10

country: Belgium

institute: University Ghent

description: Library name: Sample 1

data_processing:
Libraries were pooled and sequenced on a NovaSeq6000 (Illumina, San Diego, CA) using paired-end reads with 28/10/10/90 cycles for R1/i7/i5/R2 and 1% PhiX spike-in. Sequencing was performed at the VIB Nucleomics Core (VIB, Leuven, Belgium). Raw BCL files were demultiplexed using bcl2fastq. Raw sequencing data were processed with Cell Ranger count v6.0.0 (10x Genomics) using GRCh38-2020-A as reference genome. Downstream analyses were performed in R v4.2.2 with Seurat v5.3.0. Starting from the raw expression matrix, cells with less than 200 genes and genes expressed in less than 3 cells, were removed. After this initial quality control, HTO data was normalized using centered log-ratio (CLR) method. Hashtag demultiplexing was assessed using MultiSeqDemux and HTODemux and combined with SNP-based demultiplexing using freemuxlet (popscle). In a second round of quality control, outlier cells were removed based on library size, gene count, and mitochondrial percentages. Cells were flagged as outliers when they were five median absolute deviations (MAD) away from the median for each metric, or 15 MADs for the mitochondrial percentages. After quality control, data were log-normalized, variable genes identified, and expression values scaled. Dimensionality reduction was performed by principal component analysis (PCA), followed by UMAP embedding using the first seven corrected principal components (PCs). A shared nearest-neighbour (SNN) graph was constructed from these PCs, and clustering was performed with the Louvain algorithm at multiple resolutions.
Assembly: GRCh38-2020-A
Supplementary files format and content: matrix, barcodes, genes(tsv)

source_name: pseudomyxoma peritonei

extract_protocol:
CAFs at passage 6 were collected by trypsinization, cryopreserved, and processed for single-cell RNA sequencing (scRNAseq).
Amplified cDNA was used as input for gene expression library construction using the Chromium Next GEM Single Cell 3’ v3.1 library construction reagents (10x Genomics; catalog no. 1000352). Libraries were generated through enzymatic fragmentation, end repair, A-tailing, adapter ligation, and sample index PCR amplification (10 cycles) following the manufacturer’s protocol. Library quality and fragment size distribution were assessed using an Agilent Bioanalyzer, and library concentration was measured using a Qubit fluorometer. Hashtag oligonucleotide (HTO) libraries were generated from the amplified cDNA according to the 10x Genomics Feature Barcoding protocol for TotalSeq™-A antibodies. HTO fragments were selectively amplified by sample index PCR using 15 cycles. Library quality and fragment size distribution were assessed using an Agilent Bioanalyzer, and library concentrations were measured using a Qubit fluorometer.

value: pseudomyxoma peritonei

value: cancer-associated fibroblasts (CAFs)

tag: time

value: Passage 6


title: NEG_Undiff_Rep2

description: Library name: Sample 5

value: hTSC

value: naive pluripotent stem cell derived human trophoblast stem cells


title: CD8+ T cells, WMS-83-05

city: Oldenburg

first: Katharina

last: Hoffmann

address: Carl-von-Ossietzky-Straße 9-11,

institute: Carl von Ossietzky Universität

description:
Library name: CD8+ T cells_WMS-83-05
Column name in gene_count.xls: Tc1_WT2_83

data_processing:
RNA-seq was performed on an Illumina NovaSeq platform generating 150 bp paired-end reads with a minimum of 20 million read pairs per sample. Raw sequencing reads were filtered to remove adapters and low-quality reads using fastp.
Assembly: Clean reads were aligned to the reference genome using Hisat2 and the read numbers mapped to each gene were quantified using featureCounts.
Supplementary files format and content: data file gene_count.xls provides raw read counts per gene for each sample.

source_name: CD8+ T cells

growth_protocol: Polarization of mouse T cells was performed according to standard protocols (https://www.biolegend.com/en-gb/technical-protocols/polarization-activation-protocols)

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were performed using a poly(A) enrichment.

treatment_protocol: Purified T cells were treated with either vehicle DMSO or 0.1 µM of the respective KOR agonist WMS-200-01, WMS-64-07, WMS-75-13, WMS-76-04A and WMS-83-02.

value: CD8+ T cells


title: Nthy, EZH2 Q570R, RNA, rep3

city: Seoul

first: Hanbyeol

last: Kim

address: Daehak-ro 103

country: South Korea

institute: Seoul National University

description: Library name: Nthy_EZH2_Q570R_RNA_rep3

data_processing:
For data analysis, adapter sequences were trimmed using Trimmomatic, and reads were aligned to the human reference genome (hg38) using HISAT2. Transcript assembly was performed using StringTie. Differential gene expression analysis was carried out using DESeq2, with significance defined as a p-value < 0.05 and log2 |fold change| > 1. Normalized RNA expression values were derived from DESeq2. Pathway enrichment analysis and z-scores were calculated using the limma package.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Nthy-ori 3-1

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x antibiotics/antimycotics. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
Cells were resuspended in 1 mL of TRIzol and incubated for 5 min at room temperature. After incubation, 0.2 mL of chloroform was added, and the mixture was vortexed vigorously. The samples were centrifuged at 13,000 x g for 15 min at 4°C, and the upper aqueous phase was transferred to a fresh tube. RNA was precipitated with isopropanol and washed with ice-cold 70% ethanol. The RNA pellet was resuspended in DEPC-treated water, and the concentration was measured.
Sequencing libraries were prepared using TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit.

value: Nthy-ori 3-1

value: Thyroid follicular epithelial cell

value: EZH2 Q570R overexpression


title: Male,Adlib,Saline,Adult,rep9

description:
Library name: 8B.3_Male_Adlib_Saline_mPFC_Adult
8B.3_Male_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Medial prefrontal cortex


title: CD8+ T cells, WMS-76-04A

description:
Library name: CD8+ T cells_WMS-76-04A
Column name in gene_count.xls: Tc1_WT2_76


title: ZBTB10KO_EVT_Rep1

description: Library name: Sample 4

value: polyclonal ZBTB10 KO


title: Female,Adlib,Saline,Adult,rep8

description:
Library name: 6A.7_Female_Adlib_Saline_mPFC_Adult
6A.7_Female_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH2 Q570R, RNA, rep2

description: Library name: Nthy_EZH2_Q570R_RNA_rep2


title: ZBTB10KO_Undiff_Rep1

description: Library name: Sample 3


title: CD8+ T cells, WMS-75-16

description:
Library name: CD8+ T cells_WMS-75-16
Column name in gene_count.xls: Tc1_WT2_75


title: NEG_EVT_Rep1

description: Library name: Sample 2

value: NEG (polyclonal nucleofected with Cas9+non-targeting sgRNA)

value: 6 day EVT differentiation


title: Male,Adlib,Saline,Adult,rep8

description:
Library name: 6A.3_Male_Adlib_Saline_mPFC_Adult
6A.3_Male_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH2 Q570R, RNA, rep1

description: Library name: Nthy_EZH2_Q570R_RNA_rep1


title: Nthy, EZH2 WT, RNA, rep3

description: Library name: Nthy_EZH2_WT_RNA_rep3

value: EZH2 WT overexpression


title: NEG_Undiff_Rep1

description: Library name: Sample 1


title: CD8+ T cells, WMS-200-04

description:
Library name: CD8+ T cells_WMS-200-04
Column name in gene_count.xls: Tc1_WT2_200

value: WT


title: Male,FR,Saline,Adult,rep10

description:
Library name: 5B.3_Male_FR_Saline_mPFC_Adult
5B.3_Male_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH2 Q570R, CUT&Tag, H3K27me3, rep2

description: Library name: Nthy_EZH2_Q570R_CUT_Tag_H3K27me3_rep2

data_processing:
For data analysis, adapter sequences were trimmed using Cutadapt, and reads were aligned to the human (hg38) and Drosophila (dm6) reference genomes using Bowtie2. Potential PCR duplicates were removed using Picard tools. BAM files were initially normalized using CPM to account for sequencing depth. To correct for experimental variability, the data were further normalized using scaling factors derived from reads mapping to the Drosophila genome. Peak calling for H3K27me3 and H3K36me2 was performed using SICER2 with a window size of 1,000 bp and a gap size of 100,000 bp. Bigwig files and heatmaps were generated using deepTools.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed following the EpiCypher protocol. In brief, 50,000 nuclei were mixed with Drosophila melanogaster nuclei and incubated with ConA-conjugated magnetic beads in bead activation buffer (20 mM HEPES-NaCl [pH 7.9], 10 mM KCl, 1 mM CaCl2, and 1 mM MnCl2) for 10 min at room temperature. The nuclei-bound beads were incubated overnight at 4°C with primary antibodies against H3K27me3 or H3K36me2, alongside an anti-H2Av antibody, diluted in antibody buffer (20 mM HEPES-NaCl [pH 7.9], 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 2 mM EDTA, and protease inhibitors) on a nutator. The following day, the complexes were washed twice with Digitonin-150 buffer (20 mM HEPES-NaCl [pH 7.9], 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, and protease inhibitors) and incubated with secondary antibody diluted in Digitonin-150 buffer for 30 min at room temperature. After two washes, 2.5 µL pAG-Tn5 diluted in Digitonin-300 buffer (20 mM HEPES-NaCl [pH 7.9], 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, and protease inhibitors) was added and incubated for 1 h at room temperature. Complexes were washed twice with Digitonin-300 buffer and then incubated in Digitonin-300 buffer supplemented with 10 mM MgCl2 for 1 h at 37°C for tagmentation. The reaction was stopped by washing with TAPS buffer (10 mM TAPS [pH 8.5] and 0.2 mM EDTA). To release the tagmented DNA, SDS release buffer (10 mM TAPS [pH 8.5] and 0.1% SDS) was added, and the mixture was incubated at 58°C for 1 h. SDS was quenched by the addition of 0.67% Triton X-100.
Libraries were amplified by PCR using a non-hot start 2x PCR master mix with i5 and barcoded i7 primers. PCR products were purified using AMPure XP beads.


title: CD8+ T cells, control

description:
Library name: CD8+ T cells_control
Column name in gene_count.xls: Tc1_WT2_DMSO

value: DMSO


title: Nthy, EZH2 WT, RNA, rep2

description: Library name: Nthy_EZH2_WT_RNA_rep2


title: Male,FR,Saline,Adult,rep9

description:
Library name: 5A.5_Male_FR_Saline_mPFC_Adult
5A.5_Male_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH2 Q570R, CUT&Tag, H3K27me3, rep1

description: Library name: Nthy_EZH2_Q570R_CUT_Tag_H3K27me3_rep1


title: WT_DMSO_Rep1

description: Library name: Sample 1

data_processing:
Raw data were assessed using FastQC
FASTQ files were pseudoaligned to the hg38 transcriptome using Salmon to quantify transcripts in mapping-based mode (salmon quant -i) using decoy-aware mapping with gencode.v39. transcripts.fa.
Differential gene expression analysis was performed with EdgeR in Jupyter Notebook. Raw counts were filtered to remove genes with fewer than 10 reads per sample or fewer than 15 reads summed across all samples. Counts per million reads (CPM) was calculated for the filtered count data using the EdgeR function cpm. Statistical comparisons between individual sample conditions were made using EdgeR makeContrasts and then glmQLFit. The reported P-values and FDR values were corrected with adjust.method = “BH,” and differentially expressed genes are reported with an adjusted FDR of <0.05.
For visualization, the STAR program was used to map .fastq reads onto the hg38 genome to generate .bam files for each sample. These .bam files were converted to .bigWig files using bedtools and merged (summed) across the three replicates of each sample type.
Assembly: hg38
Supplementary files format and content: Comma separated values file containing CPM-normalized count data for each Sample by NCBI Gene ID and ifferential gene expression analysis output from EdgeR with the Log2 Fold-Change (FC)  and Benjamini-Hochberg (BH) corrected False Discovery Rate (FDR) for each gene comparing Forskolin-treated ZBTB10 KO vs. Forskolin-treated WT cells. Comparisons are noted as (FSK_KOvsWT) where positive FC values indicates higher gene expression in Forskolin-treated ZBTB10 KO cells.
Supplementary files format and content: Bigwig files to be used for Genome track visualization (i.e. IGV viewer) of binned reads mapped across the human genome merged (summed) across the 3 replicates for each sample type.

source_name: BeWo

extract_protocol:
RNA was extracted from each well using 500 µL of Trizol followed by two sequential chloroform extractions followed by ethanol precipitation per the Trizol user guide (Thermo Fisher MAN0001271).
Total RNA was depleted of rRNA using the Illumina rRNA depletion kit (NEB E6310) and then prepared for Illumina sequencing using the NEBNext Ultra II directional RNA library preparation kit for Illumina (E7760) per the manufacturer's protocol. Sequencing was performed by MedGenome on an Illumina NovaSeq with paired-end 150 bp reads.

value: BeWo

value: choriocarcinoma

value: wild-type


title: Treg cells, WMS-83-04

description:
Library name: Treg cells_WMS-83-04
Column name in gene_count.xls: Treg_WT2_83

source_name: Treg cells

value: Treg cells


title: Male,FR,Saline,Adult,rep8

description:
Library name: 4B.5_Male_FR_Saline_mPFC_Adult
4B.5_Male_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nty, EZH1 Q571R;Y727D, RNA, rep3

description: Library name: Nthy_EZH1_Q571R;Y727D_RNA_rep3

value: EZH1 Q571R;Y727D overexpression


title: Treg cells, WMS-76-04A

description:
Library name: Treg cells_WMS-76-04A
Column name in gene_count.xls: Treg_WT2_76


title: Female,Adlib,Insulin,Adult,rep8

description:
Library name: 3B.8_Female_Adlib_Insulin_mPFC_Adult
3B.8_Female_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Female,Adlib,Saline,Adult,rep7

description:
Library name: 3B.7_Female_Adlib_Saline_mPFC_Adult
3B.7_Female_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH2 WT, CUT&Tag, H3K27me3, rep1

description: Library name: Nthy_EZH2_WT_CUT_Tag_H3K27me3_rep1


title: Nty, EZH1 Q571R;Y727D, RNA, rep2

description: Library name: Nthy_EZH1_Q571R;Y727D_RNA_rep2


title: Treg cells, WMS-75-15

description:
Library name: Treg cells_WMS-75-15
Column name in gene_count.xls: Treg_WT2_75


title: Male,Adlib,Saline,Adult,rep7

description:
Library name: 3B.3_Male_Adlib_Saline_mPFC_Adult
3B.3_Male_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nty, EZH1 Q571R;Y727D, RNA, rep1

description: Library name: Nthy_EZH1_Q571R;Y727D_RNA_rep1


title: Nthy, EZH1 Q571R;Y727D, CUT&Tag, H3K27me3, rep2

description: Library name: Nthy_EZH1_Q571R;Y727D_CUT_Tag_H3K27me3_rep2


title: Female,Adlib,Saline,Adult,rep6

description:
Library name: 2B.6_Female_Adlib_Saline_mPFC_Adult
2B.6_Female_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nty, EZH1 Y727D, RNA, rep3

description: Library name: Nthy_EZH1_Y727D_RNA_rep3

value: EZH1 Y727D overexpression


title: Nthy, EZH1 Q571R;Y727D, CUT&Tag, H3K27me3, rep1

description: Library name: Nthy_EZH1_Q571R;Y727D_CUT_Tag_H3K27me3_rep1


title: Treg cells, WMS-200-03

description:
Library name: Treg cells_WMS-200-03
Column name in gene_count.xls: Treg_WT3_200


title: Nty, EZH1 Y727D, RNA, rep2

description: Library name: Nthy_EZH1_Y727D_RNA_rep2


title: Treg cells, control

description:
Library name: Treg cells_control
Column name in gene_count.xls: Treg_WT3DMSO


title: Female,FR,Saline,Adult,rep9

description:
Library name: 2A.7_Female_FR_Saline_mPFC_Adult
2A.7_Female_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nty, EZH1 Y727D, RNA, rep1

description: Library name: Nthy_EZH1_Y727D_RNA_rep1


title: Male,FR,Insulin,Adult,rep7

description:
Library name: 4B.6_Male_FR_Insulin_mPFC_Adult
4B.6_Male_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH1 Y727D, CUT&Tag, H3K27me3, rep1

description: Library name: Nthy_EZH1_Y727D_CUT_Tag_H3K27me3_rep1


title: ZBTB10KO_DMSO_Rep2

description: Library name: Sample 7

value: ZBTB10 KO


title: Male,FR,Saline,Adult,rep7

description:
Library name: 2A.3_Male_FR_Saline_mPFC_Adult
2A.3_Male_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample15_PrimaryT, PEO, rep3

description:
Library name: Sample15
Column name in PrimaryT_count.csv: PEO_3

data_processing:
Sequence reads were trimmed for adapters and low-quaity sequence using Trimmomatic v0.39
Trimmed sequence reads were mapped to hg38/mm39 using Hisat2 v2.2.1
Read count extraction and normalization were performed using FeatureCounts v2.0.6 (parameters- Q: 10 -p --countReadPairs -B -C)
Assembly: hg38, mm39
Supplementary files format and content: tab-delimited text file includes raw counts for samples (for Sample1 to Sample15)
Supplementary files format and content: tab-delimited text file includes raw counts for samples (for Sample16 to Sample21)

source_name: lymphoid

extract_protocol:
RNA was harvested using Quick-RNA™ Microprep Kit (Zymo). 1.3 ug of total RNA was used for the construction of sequencing libraries.
mRNA was enriched by Oligo(dT) beads, and fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530,New England Biolabs, Ipswich, MA, USA).

value: lymphoid

value: Primary T cells

value: PEO


title: Nthy, EZH2 Q570R, ChIP, EZH2, rep2

description: Library name: Nthy_EZH2_Q570R_ChIP_EZH2_rep2

data_processing:
For data analysis, adapter sequences were trimmed using Cutadapt, and reads were aligned to the human reference genome (hg38) using Bowtie2. EZH1 peaks were called using MACS2 in narrow peak mode with a q-value threshold of 0.05. For downstream analysis, BAM files were normalized using CPM to account for differences in sequencing depth. BigWig files and heatmaps were generated with deepTools.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Approximately 5x10^6 cells were harvested and crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 35 min, followed by fixation with 1% formaldehyde for an additional 10 min. The crosslinking reaction was quenched with 125 mM glycine, and the cell pellet was washed with PBS. After fixation, nuclei were isolated using nuclei isolation buffer (20 mM HEPES-NaCl [pH 7.9], 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine, and protease inhibitors). The nuclei were resuspended in 130 μL of 1% SDS lysis buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% SDS, and protease inhibitors) and sonicated using a Covaris S220 focused-ultrasonicator (175 peak incident power, 10% duty factor, 200 cycles per burst) for 430 s. The sheared chromatin was diluted in ChIP dilution buffer (16.7 mM Tris-HCl [pH 8.0], 0.01% SDS, 1.1% Triton X-100, 16.7 mM NaCl, 1.2 mM EDTA, and protease inhibitors) and centrifuged at 13,000 x g for 15 min at 4°C to collect the soluble chromatin fraction. Chromatin was incubated overnight at 4°C with Dynabeads Protein A conjugated with an anti-EZH1 antibody. The following day, the beads were washed three times with Wash Buffer A (140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, and 10 mM Tris-HCl [pH 8.0]), twice with Wash Buffer B (300 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.2% SDS, 0.1% sodium deoxycholate, and 10 mM Tris-HCl [pH 8.0]), and once with Wash Buffer C (250 mM LiCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5% NP-40, and 0.5% sodium deoxycholate). The beads were resuspended in 10 mM Tris-HCl [pH 8.0] and incubated with 5 μg of RNase A for 30 min at 37°C, followed by incubation with 100 μg proteinase K overnight at 65°C for reverse crosslinking. The supernatant was transferred to new tubes, and DNA fragments around 200 bp were purified and size-selected using SPRIselect beads.
Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit. Libraries were sequenced on an Illumina NovaSeq 6000 (100 bp paired-end) or NovaSeq X Plus (150 bp paired-end) platform.

value: Nthy-ori 3-1

value: Thyroid follicular epithelial cell

value: EZH2 Q570R overexpression


title: Th17 cells, WMS-76-04A

description:
Library name: Th17 cells_WMS-76-04A
Column name in gene_count.xls: Th17_WT1_76

source_name: Th17 cells

value: Th17 cells


title: Female,Adlib,Saline,Adult,rep5

description:
Library name: 25B.7_Female_Adlib_Saline_mPFC_Adult
25B.7_Female_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt

source_name: Medial prefrontal cortex

value: Medial prefrontal cortex


title: Nthy, EZH2 Q570R, ChIP, EZH2, rep1

description: Library name: Nthy_EZH2_Q570R_ChIP_EZH2_rep1


title: Th17 cells, WMS-75-14

description:
Library name: Th17 cells_WMS-75-14
Column name in gene_count.xls: Th17_WT1_75

value: WT


title: Female,FR,Saline,Adult,rep8

description:
Library name: 24B.6_Female_FR_Saline_mPFC_Adult
24B.6_Female_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH2 Q570R, ChIP, IgG, rep1

description: Library name: Nthy_EZH2_Q570R_ChIP_IgG_rep1


title: Th17 cells, WMS-64-08

description:
Library name: Th17 cells_WMS-64-08
Column name in gene_count.xls: Th17_WT1_64


title: Female,FR,Saline,Adult,rep7

description:
Library name: 24B.5_Female_FR_Saline_mPFC_Adult
24B.5_Female_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample12_PrimaryT, Twi-RNA, rep3

description:
Library name: Sample12
Column name in PrimaryT_count.csv: Twi-RNA_3

value: Twi-RNA


title: Nthy, EZH2 WT, ChIP, EZH2, rep2

description: Library name: Nthy_EZH2_WT_ChIP_EZH2_rep2

value: EZH2 WT overexpression


title: Th17 cells, WMS-200-02

description:
Library name: Th17 cells_WMS-200-02
Column name in gene_count.xls: Th17_WT1_200


title: Male,FR,Saline,Adult,rep6

description:
Library name: 23B.4_Male_FR_Saline_mPFC_Adult
23B.4_Male_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample11_PrimaryT, Twi-RNA, rep2

description:
Library name: Sample11
Column name in PrimaryT_count.csv: Twi-RNA_2


title: Nthy, EZH2 WT, ChIP, EZH2, rep1

description: Library name: Nthy_EZH2_WT_ChIP_EZH2_rep1


title: Th17 cells, control

description:
Library name: Th17 cells_control
Column name in gene_count.xls: Th17_WT2DMSO

value: DMSO


title: Male,FR,Saline,Adult,rep5

description:
Library name: 23B.3_Male_FR_Saline_mPFC_Adult
23B.3_Male_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample10_PrimaryT, Twi-RNA, rep1

description:
Library name: Sample10
Column name in PrimaryT_count.csv: Twi-RNA_1


title: Nthy, EZH2 WT, ChIP, IgG, rep1

description: Library name: Nthy_EZH2_WT_ChIP_IgG_rep1


title: Female,FR,Saline,Adult,rep6

description:
Library name: 22B.7_Female_FR_Saline_mPFC_Adult
22B.7_Female_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample9_PrimaryT, m1ψ-mRNA, rep3

description:
Library name: Sample9
Column name in PrimaryT_count.csv: m1ψ-mRNA_3


title: Nthy, EZH1 Q571R;Y727D, ChIP, EZH1, rep2

description: Library name: Nthy_EZH1_Q571R;Y727D_ChIP_EZH1_rep2


title: Female,FR,Saline,Adult,rep5

description:
Library name: 22B.6_Female_FR_Saline_mPFC_Adult
22B.6_Female_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample8_PrimaryT, m1ψ-mRNA, rep2

description:
Library name: Sample8
Column name in PrimaryT_count.csv: m1ψ-mRNA_2


title: Nthy, EZH1 Q571R;Y727D, ChIP, EZH1, rep1

description: Library name: Nthy_EZH1_Q571R;Y727D_ChIP_EZH1_rep1


title: Nthy, EZH2 WT, CUT&Tag, H3K27me3, rep2

description: Library name: Nthy_EZH2_WT_CUT_Tag_H3K27me3_rep2


title: Th17 cells, WMS-83-02

description:
Library name: Th17 cells_WMS-83-02
Column name in gene_count.xls: Th1_WT4_83

source_name: Th1 cells

value: Th1 cells


title: Male,FR,Saline,Adult,rep4

description:
Library name: 22B.3_Male_FR_Saline_mPFC_Adult
22B.3_Male_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Th1 cells, WMS-75-13

description:
Library name: Th1 cells_WMS-75-13
Column name in gene_count.xls: Th1_WT4_75


title: Sample7_PrimaryT, m1ψ-mRNA, rep1

description:
Library name: Sample7
Column name in PrimaryT_count.csv: m1ψ-mRNA_1


title: Treg cells, WMS-64-09

description:
Library name: Treg cells_WMS-64-09
Column name in gene_count.xls: Treg_WT2_64

value: Treg cells


title: Th1 cells, WMS-64-07

description:
Library name: Th1 cells_WMS-64-07
Column name in gene_count.xls: Th1_WT4_64


title: Th1 cells, WMS-76-04A

description:
Library name: Th1 cells_WMS-76-04A
Column name in gene_count.xls: Th1_WT4_76


title: HNSC-183X_H3K27ac_ChIPseq

city: Houston

first: Mahinur

last: Mattohti

state: TX

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

data_processing:
ChIPseq reads were aligned to hg19 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 and MACS2 using pvalue cutoff of 1e-5
bigwig files were generated by deeptools bamCoverage normalized by RPKM
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14 and MACS2

growth_protocol: All cell lines were expanded and maintained in specified growth medium from ATCC or MDACC.

extract_protocol:
Crosslinked samples were thawed on ice and resuspended in RIPA lysis buffer supplemented with protease inhibitor, lysed the cells on ice then sheared the chromatin by sonication. After centrifuge, the clean sonicated cell lysate mixed with protein G magnetic dynabeads (Invitrogen) coupled to antibodies described above and incubated over night at 4 degrees. Samples was washed 5 times with cold RIPA, twice with high salt RIPA, twice with LiCl buffer, twice with TE, and then eluted in elution buffer. The eluate was reverse crosslinked at 65C. Solid-phase reversible immobilization (SPRI) cleanup steps were performed. Beads were washed twice on the magnet with 70% ethanol and then air-dried. The DNA was eluted in EB buffer.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

value: Head & Neck cancer cell line


title: Male,Adlib,Saline,Adult,rep6

description:
Library name: 2B.2_Male_Adlib_Saline_mPFC_Adult
2B.2_Male_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample6_PrimaryT, Unmodified-mRNA, rep3

description:
Library name: Sample6
Column name in PrimaryT_count.csv: Unmodified-mRNA_3

value: Unmodified-mRNA


title: Male,Adlib,Saline,Adult,rep5

description:
Library name: 20A.3_Male_Adlib_Saline_mPFC_Adult
20A.3_Male_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: ZBTB10KO_FSK_Rep3

description: Library name: Sample 12

value: BeWo

value: choriocarcinoma

value: ZBTB10 KO

value: 20uM FSK, 48hr


title: Nthy, EZH1 Y727D, CUT&Tag, H3K27me3, rep2

description: Library name: Nthy_EZH1_Y727D_CUT_Tag_H3K27me3_rep2

value: Nthy-ori 3-1

value: EZH1 Y727D overexpression


title: Nthy, EZH1 Y727D, ChIP, EZH1, rep1

description: Library name: Nthy_EZH1_Y727D_ChIP_EZH1_rep1

value: Thyroid follicular epithelial cell


title: Female,FR,Saline,Adult,rep4

description:
Library name: 16B.6_Female_FR_Saline_mPFC_Adult
16B.6_Female_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample5_PrimaryT, Unmodified-mRNA, rep2

description:
Library name: Sample5
Column name in PrimaryT_count.csv: Unmodified-mRNA_2

value: lymphoid

value: Primary T cells


title: Th1 cells, control

description:
Library name: Th1 cells_control
Column name in gene_count.xls: Th1_WT4_DMSO

value: WT


title: Th1 cells, WMS-200-01

description:
Library name: Th1 cells_WMS-200-01
Column name in gene_count.xls: Th1_WT4_200


title: Nthy, EZH1 Q571R;Y727D, ATAC, rep2

description: Library name: Nthy_EZH1_Q571R;Y727D_ATAC_rep2

data_processing:
Adapter sequences were trimmed using fastp and reads were aligned to the human (hg38) and E. coli (k12) reference genomes using Bowtie2. Mitochondrial reads and reads mapping to the ENCODE black list were removed. BAM files were normalized using RPKM to account for differences in sequencing depth. Subsequently, these values were further adjusted using scaling factors derived from reads mapping to the E. coli genome (originating from residual DNA in the Tn5 transposase preparation) were used to calculate scaling factors. Bigwig files were generated using deepTools and visualized using the Integrative Genomics Viewer (IGV). Heatmaps were generated with deepTools to visualize chromatin accessibility patterns across conditions.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
ATAC-seq was performed as previously described. Briefly, 50,000 cells were harvested and washed with ice-cold PBS. The supernatant was removed, and the cell pellet was resuspended in 50 µL of lysis buffer (10 mM Tris-HCl [pH 7.4], 3 mM MgCl2, 10 mM NaCl, and 0.1% NP-40). Nuclei were collected and resuspended in 50 µL of transposition reaction buffer (10 mM TAPS [pH 8.5], 5 mM MgCl2, and 10% DMF) containing adaptor-loaded Tn5 transposase. The reaction was incubated at 37°C for 30 min in a thermomixer set to 1,000 rpm. To terminate tagmentation, 10 µL of clean-up buffer (900 mM NaCl and 300 mM EDTA [pH 8.0]) was added.
Tagmented DNA was purified using the MinElute PCR Purification Kit and quantified via qPCR. Libraries were amplified using the KAPA HiFi HotStart PCR Kit with index primers and purified using SPRIselect DNA Size Selection Reagent. Sequencing was performed on an Illumina NovaSeq X (100 bp paired-end) or NovaSeq X Plus (150 bp paired-end) platform.

value: EZH1 Q571R;Y727D overexpression


title: Th17 cells, WMS-83-03

description:
Library name: Th17 cells_WMS-83-03
Column name in gene_count.xls: Th17_WT3_83

value: Th17 cells


title: Sample4_PrimaryT, Unmodified-mRNA, rep1

description:
Library name: Sample4
Column name in PrimaryT_count.csv: Unmodified-mRNA_1


title: Female,FR,Saline,Adult,rep3

description:
Library name: 16B.5_Female_FR_Saline_mPFC_Adult
16B.5_Female_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt

value: Medial prefrontal cortex


title: Nthy, EZH1 Q571R;Y727D, ATAC, rep1

description: Library name: Nthy_EZH1_Q571R;Y727D_ATAC_rep1


title: Male,FR,Saline,Adult,rep3

description:
Library name: 16B.3_Male_FR_Saline_mPFC_Adult
16B.3_Male_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Sample3_PrimaryT, Untreated, rep3

description:
Library name: Sample3
Column name in PrimaryT_count.csv: Untreated_3

value: Untreated