title: UNCseq1550 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI2 ARID1A Pos


title: GBe8s3_cordBlood-GFP_K27ac-1

status: Public on Apr 22 2026

type: SRA

city: Seattle

first: Jay

last: Sarthy

state: WA

address: 1920 Terry Ave

department: Ben Towne Center for Childhood Cancer Research

country: USA

institute: Seattle Children's Research Institute

description: Library name: Sample 2

library_source: genomic

data_processing:
CUT&Tag reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project's unified GRCh38 blacklist  bed file were removed using bedtools v2.30.0. The data was then processed by merging technical replicates using SAMtools merge. Peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility and binding was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
Assembly: GRCh38
Supplementary files format and content: CUT&Tag bigWig files give the normalized coverage of histone modifications and transcription factor binding across the genome (deepTools bamCoverage --binSize 40 --normalizeUsing CPM --exactScaling).
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

growth_protocol: Human umbilical cord blood CD34+ HSCs were isolated, sorted, and cultured as described in Le et al. (2022; J Clin Invest 132:e157101). Briefly, fresh CB was processed with red blood cell lysis, CD34+ enriched by CliniMACS, and HSCs sorted as DAPI⁻CD34+Lin⁻CD38⁻CD90loCD45RA⁻EPCR+ by FACS on a BD FACSAria II. Cells were cultured in endothelial co-culture conditions.

extract_protocol:
Transduced cord blood cells were harvested, washed, and processed for CUT&Tag as described for cell lines. Nuclei were incubated with antibodies targeting SMARCA4 (BRG1), H3K27ac, H3K4me3, or IgG control, followed by secondary antibody and pA-Tn5 incubation. Tagmentation was activated by MgCl₂ at 37°C and resulting DNA fragments were purified.
CUT&Tag libraries were prepared in-house using the CUT&Tag protocol (Kaya-Okur et al., 2019) and sequenced in-house at the Seattle Children's Research Institute Genomics Core. Paired-end sequencing was performed on an Illumina instrument.

treatment_protocol: CD34+ cord blood HSCs were transduced overnight with concentrated lentivirus encoding CBFA2T3::GLIS2 or GFP control as described in Le et al. (2022). Fresh media was added the following morning. Biological replicate experiments were completed for CBFA2T3::GLIS2 and single experiments for GFP control as indicated.

tag: tissue

value: Blood

tag: cell type

value: CD34+ Cord Blood Cells

tag: chip antibody

value: H3K27ac (EMD Millipore, MABE647)

tag: treatment

value: GFP transduced


title: UNCseq2101 ROI3 ARID1A Positive_Mutated

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description: Library name: UNCseq2101 ROI3 ARID1A Pos

library_source: transcriptomic

data_processing:
The .dcc files generated by the NanoString GeoMx Digital Spatial Profiler represent ROI digital counts derived from spatially resolved transcriptomic profiling.
The Hs_R_NGS_WTA_v1.0.pkc file is the probe annotation (PKC) file for the GeoMx Human RNA Whole Transcriptome Atlas (NGS-based) panel, used to map probe-level counts in .dcc files to gene targets and associated control probes during downstream processing.
Assembly: FASTQ files process into DCC files by geomxngspipline build 2.3.3.10
Supplementary files format and content: Nanostring genome assembly
Supplementary files format and content: DCC file format
Library strategy: Spatial Transcriptomics

molecule: total RNA

source_name: Endometrium

growth_protocol: No growth protocol

extract_protocol:
Nanostring antigen retrieval protocol
Nanostring library construction protocol

treatment_protocol: No treatment protocol

value: Endometrium

tag: genotype

value: ARID1A Mutated

tag: batch

value: total RNA


title: UNCseq2101 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq2101 ROI1 ARID1A Pos


title: UNCseq1550 ROI5 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI5 ARID1A Pos


title: UNCseq2171 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq2171 ROI3 ARID1A Pos


title: Tonsil, 3 DPI, replicate B

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description: Library name: sample083

data_processing:
Raw FASTQ files were aligned to the combined AGM (ChlSab1, Ensembl v112) and NiV Bangladesh (GCA_003147825.1) genomes using STAR v2.7.11b.
samtools BAM; contains read alignments
PCR duplicates were removed with samtools v1.20
Count matrices were generated with featureCounts (Rsubread v2.20.0)
Assembly: ChlSab1 (Ensembl v112) and NiV Bangladesh (NCBI GCA_003147825.1)
Supplementary files format and content: TSV; contains featureCounts raw counts

molecule: polyA RNA

organism: Chlorocebus aethiops

source_name: Tonsil

extract_protocol:
Approximately 100 mg of each sample was stored in 1 mL RNAlater (Qiagen) for 7 days for stabilization. RNAlater was removed, and tissues were homogenized in 600 μL RLT buffer (Qiagen) in a 2 mL cryovial using a TissueLyser (Qiagen) and ceramic beads. RNA was isolated using the RNeasy MiniKit (Qiagen), according to the vendor's instructions. Residual genomic DNA was digested and RNA cleaned via the Zymo Clean and Concentrator-5 kit according to the manufacturer's instructions.
Libraries were constructed by poly-A selection and sequenced via Illumina NextSeq 550 to a target depth of 50 million reads.

value: Tonsil

tag: timepoint

value: 3 DPI


title: UNCseq1550 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI3 ARID1A Pos


title: JFS2435_WSUAML_IgG_rep2

description: Library name: Sample 16

data_processing:
CUT&RUN reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project's unified GRCh38 blacklist  bed file were removed using bedtools v2.30.0[14]. ATAC-seq data was processed by merging technical replicates using SAMtools merge. Peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility and binding was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
Assembly: GRCh38
Supplementary files format and content: CUT&RUN bigWig files give the normalized coverage of protein-DNA interactions across the genome (deepTools bamCoverage --binSize 40 --normalizeUsing CPM --exactScaling).
Library strategy: CUT&RUN

source_name: WSU-AML

growth_protocol: M-07e cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS, 1X GlutaMAX (Gibco), and 10 ng/mL recombinant human IL-3 (STEMCELL Technologies). WSU-AML cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS and 1X GlutaMAX (Gibco). K562 cells were seeded at 0.2 ×10⁶ cells/mL and cultured in IMDM (Gibco) supplemented with 10% FBS and 1% Penstrep. All cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Cells were harvested, washed in cold PBS, and nuclei were isolated according to the AutoCUT&RUN protocol (Janssens et al., 2018; Epigenetics Chromatin 11:74). Nuclei were incubated overnight at 4°C with primary antibodies targeting mSWI/SNF complex subunits (SMARCC1, SMARCB1, SMARCA4), the CBFA2T3::GLIS2 fusion protein components (CBFA2T3, GLIS2), or histone modifications (H3K27me3, H3K4me1, H3K4me3, H3K27ac), or IgG isotype control. Following primary antibody incubation, nuclei were incubated with protein A-MNase fusion (pA-MNase). Chromatin cleavage was initiated by addition of CaCl₂ at 0°C. Released DNA fragments were purified for library preparation.
CUT&RUN libraries were prepared at the Fred Hutchinson Cancer Center Genomics Core using the AutoCUT&RUN protocol. Paired-end 150 bp sequencing was performed on an Illumina instrument.

treatment_protocol: Cells were maintained under standard culture conditions without drug treatment prior to harvesting for chromatin profiling.

tag: cell line

value: WSU-AML

value: IgG (Abcam, AB172730)


title: UNCseq2101 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq2101 ROI3 ARID1A Neg


title: JFS2434_WSUAML_IgG_rep1

description: Library name: Sample 15


title: UNCseq2171 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq2171 ROI1 ARID1A Pos


title: Lung, 5 DPI, replicate A

description: Library name: sample072

source_name: Lung

value: Lung

value: 5 DPI


title: Lung, 5 DPI, replicate D

description: Library name: sample075


title: Tonsil, baseline, replicate A

description: Library name: sample076

value: Baseline


title: GBe8s5_cordBlood-GFP_K4me3-1

description: Library name: Sample 3

value: H3K4me3 (Active Motif, 39159)


title: UNCseq1550 ROI4 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI4 ARID1A Pos


title: UNCseq2101 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq2101 ROI2 ARID1A Neg


title: GBe8s1_cordBlood-GFP_BRG1-1

description: Library name: Sample 1

value: SMARCA4 (Abcam, ab110641)


title: Lung, 5 DPI, replicate B

description: Library name: sample073


title: UNCseq2101  ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq2101  ROI2 ARID1A Pos


title: UNCseq1550 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI1 ARID1A Pos


title: UNCseq1945 ROI6  ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI6  ARID1A Pos

value: ARID1A Wild-Type


title: Lung, 4 DPI, replicate D

description: Library name: sample071

value: 4 DPI


title: UNCseq2101 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq2101 ROI1 ARID1A Neg


title: UNCseq1945 ROI4  ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI4  ARID1A Pos


title: UNCseq1945 ROI5 ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI5 ARID1A Pos


title: Lung, 4 DPI, replicate B

description: Library name: sample069


title: Lung, 4 DPI, replicate C

description: Library name: sample070


title: JFS2432_WSUAML_GLIS2_rep2

description: Library name: Sample 14

value: GLIS2 (Invitrogen, PA5-72849)


title: UNCseq0468 ROI5 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI5 ARID1A Pos


title: UNCseq0468 ROI6 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI6 ARID1A Pos


title: JFS2429_WSUAML_H3K27me3_rep2

description: Library name: Sample 12

value: H3K27me3 (Cell Signaling Technology, 9733S)


title: Lung, 4 DPI, replicate A

description: Library name: sample068


title: JFS2430_WSUAML_CBFA2T3-ab1_rep2

description: Library name: Sample 13

value: CBFA2T3 (Sigma-Aldrich, AV33993-100UL)


title: JFS2423_WSUAML_H3K27me3_rep1

description: Library name: Sample 9


title: UNCseq0468 ROI4 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI4 ARID1A Pos

value: Endometrium


title: JFS2424_WSUAML_CBFA2T3-ab1_rep1

description: Library name: Sample 10


title: UNCseq1945 ROI3  ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI3  ARID1A Pos


title: UNCseq0468 ROI3 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI3 ARID1A Pos


title: Lung, 3 DPI, replicate B

description: Library name: sample065


title: Lung, 3 DPI, replicate C

description: Library name: sample066


title: JFS2421_M07e_IgG_rep2

description: Library name: Sample 8


title: UNCseq0591 ROI5 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI5 ARID1A Pos


title: Lung, 3 DPI, replicate D

description: Library name: sample067


title: JFS2426_WSUAML_GLIS2_rep1

description: Library name: Sample 11


title: UNCseq0591 ROI6 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI6 ARID1A Pos


title: UNCseq1945 ROI1  ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI1  ARID1A Pos


title: Lung, 3 DPI, replicate A

description: Library name: sample064


title: UNCseq0468 ROI2 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI2 ARID1A Pos


title: UNCseq1945 ROI2  ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI2  ARID1A Pos


title: UNCseq0468 ROI1 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI1 ARID1A Pos


title: UNCseq0591 ROI4 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI4 ARID1A Pos


title: Lung, baseline, replicate E

description: Library name: sample063


title: UNCseq0591 ROI2 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI2 ARID1A Pos


title: UNCseq0591 ROI3 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI3 ARID1A Pos


title: Lung, baseline, replicate D

description: Library name: sample062


title: No Template Control

description: Library name: No Template Control

value: No Template Control


title: JFS2420_M07e_IgG_rep1

description: Library name: Sample 7


title: UNCseq0590 ROI1 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI1 ARID1A Pos

value: total RNA


title: Lung, baseline, replicate B

description: Library name: sample060


title: JFS2416_M07e_CBFA2T3-ab1_rep2

description: Library name: Sample 5


title: Lung, baseline, replicate C

description: Library name: sample061


title: Lung, baseline, replicate A

description: Library name: sample059


title: MpHY5 DAP-seq

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

description: Library name: MpHY5 DAP-seq

data_processing:
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Assembly: Arabidopsis TAIR10 genome (Ensemble Release 42)
Assembly: Marchantia polymnorpha MpTak1 5.1 version
Supplementary files format and content: Significant peaks of protein-DNA interactions in BED fromat generated by GEMv3.4

organism: Marchantia polymorpha

source_name: 21-d-old gemmalings

growth_protocol: Arabidopsis: 10 days-old seedlings grown in MS medium. Marchantia polymorpha: 21-d-old gemmalings grown in 0.5x GB5 medium

extract_protocol:
Genomic DNA extracted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a double i5/i7 index.

value: 21-d-old gemmalings

tag: protein


title: JFS2410_M07e_CBFA2T3-ab1_rep1

description: Library name: Sample 2


title: Chronic lung disease 11

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: Pennsylvania

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

description:
Library name: HL011
10x Genomics Visium v2 FFPE

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequencing were aligned to hg38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: .h5ad file contains gene expression count data; image of tiisue and spots; list of spatial barcodes and the coordinates specifying spots; and hi-res image of tissue
Library strategy: Spatial Transcriptomics

extract_protocol:
Samples were assessed for RNA quality, and all FFPE samples had a DV200 score above the minimum threshold of ≥30%.
Spatial transcriptomic libraries were generated with the Visium v2 Human Transcriptome gene expression kit (10x Genomics: 1000443). Five-micron FFPE sections were placed on Superfrost Plus slides (FisherScientific) and processed through the 10x Visium v2 for FFPE protocol according to the manufacturer’s instructions (CG000518, CG000520, CG000495). H&E images were taken at 20x magnification using a Leica Aperio CS2 slide scanner (Leica Biosystems). Library QC was completed with an Agilent TapeStation 4150. Libraries were normalized and pooled to 2nM prior to loading on an Illumina NextSeq 2000, using a P4 100 flow cell with a target of a minimum of 120 million reads per sample for transcriptomic libraries.


title: Normal kidney tissue 1

description:
Library name: HK008
10x Genomics Visium v2 FFPE

source_name: Kidney

value: Kidney


title: JFS2415_M07e_H3K27me3_rep2

description: Library name: Sample 4


title: MpInput

description: Library name: MpInput

value: Marchantia Input sample


title: JFS2409_M07e_H3K27me3_rep1

description: Library name: Sample 1


title: Visium CytAssist Spatial Gene and Protein Expression, GEX,PBC_PR_6837

description:
Library name: PBC_PR_6837_mRNA
Gene expression from malignant mesothelioma patient

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: The .h5ad file is an AnnData object generated using the Scanpy toolkit based on the Space Ranger output from Visium CytAssist Spatial Gene and Protein Expression for FFPE platform by 10x Genomics, which captures both gene expression and protein (ADT) information. The dataset has been pre-processed by removing low-quality spots and lowly expressed genes, followed by log-normalization and standard scaling.
Library strategy: Spatial Transcriptomics

source_name: Mesothelium/pleura

extract_protocol:
Two formalin-fixed & paraffin-embedded (FFPE) malignant mesothelioma tissue blocks were obtained from National Meosthelioma Virtual Bank. Malignant mesothelioma samples were assessed for RNA quality, and all samples had a DV200 score above the minimum threshold ≥30%.
Spatial transcriptomic and proteomic libraries were generated with Visium CytAssist for FFPE v2 gene expression kit (10x Genomics: 1000520) with the Human Immune Cell Profiling Panel (10x Genomics: PN-1000607). 5 micron FFPE sections were placed on Schott Nexterion Hydrogel Coated Slides (Schott North America: 1800434) or Fisherbrand Superfrost Plus Slides (Fisher: 22-037-246) and processed through the 10x CytAssist for FFPE v2 protocol according to the manufacturer’s instructions. H&E images were taken at 10x magnification using an EVOS 7000 Imaging System (Thermo Fisher Scientific).

value: Mesothelium/pleura


title: Visium CytAssist Spatial Gene and Protein Expression, ADT, PBC-PR_6835-5A

description:
Library name: PBC-PR_6835-5A_adt
Antibody-derived tags from malignant mesothelioma

library_source: other

molecule: protein


title: Chronic kidney disease 3

description:
Library name: HK003
10x Genomics Visium v2 FFPE


title: JFS2418_M07e_GLIS2_rep2

description: Library name: Sample 6


title: JFS2412_M07e_GLIS2_rep1

description: Library name: Sample 3


title: Chronic lung disease 1

description:
Library name: HL001
10x Genomics Visium v2 FFPE

value: Lung


title: Visium CytAssist Spatial Gene and Protein Expression, GEX, PBC-PR_6835-5A

description:
Library name: PBC-PR_6835-5A_mRNA
Gene expression from malignant mesothelioma patient


title: Day 17 vasc. HOs-on-chip HF

city: Vancouver

first: Clement

last: Quintard

state: British Columbia

address: 3518 Wesbrook Mall

country: Canada

institute: University of British Columbia

description: Library name: Sample7

library_source: transcriptomic single cell

data_processing:
CellRanger (v.6.0 or v8.0, 10X Genomics) was used to extract unique molecular identifiers, cell barcodes and genomic reads from the sequencing results of 10X Chromium experiments. Next, count matrices, including both protein coding and non-coding transcripts, were constructed by aligning against the annotated human reference genome (GRCh38, v.3.0.0, 10X Genomics, https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz). The scRNA-seq data of each sample was merged and normalized using Seurat v. 5.0.0. Additional quality control steps included filtering out cells with more than 50,000 transcripts or fewer than 500 transcripts, as well as removing cells with over 15% mitochondrial transcripts.
Assembly: GRCh38
Supplementary files format and content: Count matrices

source_name: Organoids derived from pluripotent stem cells

extract_protocol:
For VNO single cell profiling, n = 3 independent microchannels were pooled together for each condition on-chip (low flow and high flow), and n = 3 wells of a 12-well plate, each containing about 50 VNOs, were used for the condition in well. For vasc. HOs-on-chip, n = 3 independent microchannels were pooled together. Organoids were dissociated enzymatically into single cells with 3 U/ml Dispase II (Gibco) and 2 U/ml Liberase (Roche) in PBS for 45 min at 37 °C. During incubation, organoids were mechanically disrupted every 10 min by vigorous pipetting with a P1000 tip. The dissociation reaction was stopped by adding 10 ml of inhibition medium containing DMEM/F12 with 10% FBS per ml of dissociation mixture. Next, the cell suspensions were centrifuged at 300 g for 8 min at 4 °C, resuspended in PBS containing 0.4% BSA, and filtered through a 70 µm cell strainer. Cell viability > 95% was assessed using a CellDrop FL cell counter (DeNovix), and final cell concentration was adjusted to 1,000 cells/µl.
Single Cell Suspensions were loaded onto the 10x Genomics Chromium X for capture in droplet emulsion. Libraries were prepared using the Chromium Next GEM Single Cell 3’ Kit v3.1, or the Chromium GEM-X Single Cell 3’ Kit v4, and the standard protocol was followed for all steps. Libraries were then sequenced on an Illumina NextSeq 2000.

value: WTC

value: iPSC

value: Day 17 vasc. HOs-on-chip HF


title: Chronic kidney disease 1

description:
Library name: HK001
10x Genomics Visium v2 FFPE


title: Chronic kidney disease 5

description:
Library name: HK005
10x Genomics Visium v2 FFPE


title: Visium CytAssist Spatial Gene and Protein Expression, ADT, PBC_PR_6837

description:
Library name: PBC_PR_6837_adt
Antibody-derived tags from malignant mesothelioma


title: ENZ-3

city: Tianjing

first: Wang

middle: Meng

last: meng

address: Haitang subdistrict

country: China

institute: Nankai University

description: Library name: ENZ-3

data_processing:
1. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. 2. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using HISAT2 v2.0.5 and paired-end clean reads were aligned to the human reference genome GRCh38/hg38 using HISAT2 v2.0.5. 3. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. 4. Differential expression analysis between two groups (three biological replicates per group) was performed using the DESeq2 R package v1.20.0. The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.05 and |log2 (fold change)| > 1 were considered significantly differentially expressed. 5. Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected P-value < 0.05 were considered significantly enriched. 6. KEGG pathway enrichment analysis was also performed using clusterProfiler R package.
Assembly: GRCh38/hg38
Supplementary files format and content: 1. Raw read counts matrix in tab-delimited text format (.txt), containing the number of reads mapped to each gene for all samples. 2. FPKM normalized expression matrix in tab-delimited text format (.txt).
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, Cat# 15596026) according to the manufacturer's instructions. RNA concentration and purity were measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with RIN value > 7.0 were used for library construction.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: colon

value: RKO

value: CRC

tag: sample group

value: ENZ


title: Day 17 VNOs-on-chip HF

description: Library name: Sample6

value: Organoids derived from pluripotent stem cells

value: Day 17 VNOs-on-chip HF


title: ENZ-2

description: Library name: ENZ-2


title: MpPIF DAP-seq

description: Library name: MpPIF DAP-seq

value: MpPIF


title: Day 17 VNOs-on-chip LF

description: Library name: Sample5

value: Day 17 VNOs-on-chip LF


title: kd_3

city: Guangzhou，China

first: Jide

last: Wang

state: Guangdong ，China

address: 11838 Guangzhou Avenue North

department: Department of Digestive Medicine

institute: Nanfang Hospital, Southern Medical University

description: Library name: kd_3

data_processing:
Raw data were filtered to remove adapter contamination and low-quality reads.
rRNA contamination was filtered by Bowtie2.
Clean reads were mapped to the genome using TopHat.
The expression levels of mRNA were calculated and normalized as FPKM (Fragments Per Kilobase Per Million reads).
Assembly: hg38
Supplementary files format and content: The .xlsx file includes FPKM values for each Sample

source_name: AGS

growth_protocol: AGS cells were cultured in medium supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was isolated and purified using TRIzol(Life, cat.265709, CA, USA) following the manufacturer's procedure.
VAHTS mRNA Capture Beads with Oligo (dT) (Vazyme, cat.N401-01, Nanjing, China) were used and mRNA was fragmented using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme, cat.NR604, Nanjing, China) under 94°C for 8 min, followed by reverse transcription into cDNA, which was used to synthesize U-labeled second-strand DNA.

treatment_protocol: AGS cells were ttreated with either negative control or ANXA2P1 knockdown, with three biological replicates per group.

value: AGS

value: Human gastric adenocarcinoma cell

value: Treated with ANXA2P1 knockdown


title: Day 17 VNOs in wells

description: Library name: Sample4

value: Day 17 VNOs in wells


title: kd_2

description: Library name: kd_2


title: ENZ-1

description: Library name: ENZ-1


title: Control-3

description: Library name: Control-3

value: Control


title: Day 10 VNOs in wells

description: Library name: Sample2

value: Day 10 VNOs in wells


title: kd_1

description: Library name: kd_1


title: Control-2

description: Library name: Control-2


title: Day 10 VNOs-on-chip

description: Library name: Sample3

value: WTC

value: Day 10 VNOs-on-chip


title: Day 6 VNOs (MVP agg.)

description: Library name: Sample1

value: iPSC

value: Day 6 VNOs (MVP agg.)


title: OCI-Ly7_HDAC3i_AZA_rep3

city: Nice

first: Pilar

middle: M

last: Dominguez

state: Provence-Alpes-Côte d'Azur

address: 151 Route de Saint-Antoine

country: France

institute: Centre Méditerranéen de Médecine Moléculaire: C3M

description: Library name: E49AH_4

data_processing:
Sequencing files were demultiplexed (Bcl2fastq, v2.17.1.14) and QC was performed on FASTQ files using FASTQC (v.12.1).
Sequencing reads were trimmed (cutadapt v5.1) and aligned to the hg38 human reference genome using STAR (v2.7.11b).
Read counting across genomic features was performed using FeatureCounts (Subread, v2.1.2)
Differential gene expression analysis was performed using Voom-Limma in R (v3.64.3)
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: Cells were passaged every 2 days when they were observed to have attained roughly 90% confluency, determined by light microscopy. New frozen vials of cells were thawed every month for use.

extract_protocol:
Lymphoma cells were pelleted, RNA was isolated using Trizol reagent and the Direct-zol RNA MicroPrep kit (Zymo Research) according to the manufacturers instructions
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize DNA double strands. The synthesized doublestranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.

treatment_protocol: Cells were treated daily with 0nM or 100nM 5-AZA from day 0 to day 4; and on day 2 and day 4 they were treated with either 0μM or 15μM HDAC3i

value: Lymphoma cells


title: OCI-Ly7_HDAC3i_AZA_rep2

description: Library name: E49AH_2


title: VNO chip HF 2

description: Library name: Sample 8

data_processing:
Sequencing data was demultiplexed using Illumina’s BCL Convert. De-multiplexed read sequences were then aligned to the Homo sapiens (hg38 no Alts, with decoys) reference sequence using DRAGEN RNA app on Basespace Sequence Hub.
Assembly: hg38 no Alts, with decoys
Supplementary files format and content: count matrices

extract_protocol:
Using a needle, VNOs were meticulously extracted from the chip. For each sample, n = 2 independent microchannels were pooled together, and n = 3 samples were submitted for each condition (static, low flow, and high flow). RNA extraction was done using the Trizol protocol (Invitrogen).
Sample quality control was performed using the Agilent 2100 Bioanalyzer or the Agilent 4200 Tapestation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq2000 with Paired End 59bp x 59bp reads.

tag: condition

value: high flow


title: HUVEC 2

description: Library name: Sample 11

source_name: Pirmary cells

value: Pirmary cells

value: HUVEC-GFP

value: Primary Human Umbilical Vein Endothelial Cells


title: VNO chip HF 3

description: Library name: Sample 9

value: Organoids derived from pluripotent stem cells


title: HUVEC 3

description: Library name: Sample 12


title: VNO chip LF 1

description: Library name: Sample 4

value: low flow


title: VNO chip HF 1

description: Library name: Sample 7


title: VNO chip LF 3

description: Library name: Sample 6


title: OCI-Ly7_HDAC3i_AZA_rep1

description: Library name: E49AH_1


title: ChipSeq of SW620

city: TangShan

first: Wei

last: Fang

state: HeBei

address: 21 Bohai Sea Avenue, Caofeidian New Town

department: College of Life Sciences

institute: North China University of Science and Technology

description: Library name: SW620

data_processing:
Raw reads were trimmed using Trimmomatic v0.39
Clean reads were aligned to reference genome (hg38) using Bowtie2 v2.4.4
Peaks were called using MACS2 v2.2.7.1
Assembly: hg38
Supplementary files format and content: bed

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at RT. Chromatin was sonicated to 200-500 bp. Immunoprecipitation was performed using specific antibody. DNA was reverse cross-linked overnight at 65°C and purified.
Libraries were prepared following standard Illumina DNA library preparation protocol. Size selection was performed. Library quality was assessed.

value: colon


title: VNO chip static 3

description: Library name: Sample 3

value: static


title: Control-1

description: Library name: Control-1

value: RKO

value: CRC


title: OCI-Ly7_AZA_rep2

description: Library name: E49A_2

value: AZA


title: VNO chip LF 2

description: Library name: Sample 5


title: ChipSeq of SW620-IP

description: Library name: SW620-IP


title: HUVEC 1

description: Library name: Sample 10


title: OCI-Ly7_AZA_rep3

description: Library name: E49A_3


title: OCI-Ly7_HDAC3i_rep3

description: Library name: E49H_4


title: St55_PHP37_CMO_library1

city: New York

first: Maria

middle: ANTONIETTA

last: Tosches

address: 1212 Amsterdam Ave

institute: Columbia University

description:
Library name: ST55_PHP37_M1
Deryckere_development_st55.rds

data_processing:
Reads were assigned to the combined Pleurodeles waltl transcriptome using Alevin (Salmon v1.6.0). Library type was set to automatic and keepCBFraction was set to 1. All other parameters were set as default.  Multiplex tag reads were also assigned using Alevin
Assembly: merge_trinity_iso_t2g_GFP_TS.txt, iso_trinity_transcripts_GFP_TS.fasta
Supplementary files format and content: raw count matrix

organism: Pleurodeles waltl

source_name: Forebrain

extract_protocol:
Tissue pieces were dissociated for 30 min at room temperature using the Papain dissociation kit (Worthington) in calcium-free Hibernate A (BrainBits). After processing and concentration, cells were resuspended in calcium and magnesium-free HibernateA (BrainBits) at a concentration of 1000 cells/µl. Cells were counted in a haemocytometerchamber and immediately processed for single-cell GEM formation (10x Genomics, single cellRNA sequencing 3’, Chromium V3.1). Cells  were resuspended at ~1500 cells/µl and multiplexed using 4 distinct Cell Multiplexing Oligos from the 10x Genomics 3’ CellPlex Multiplexing kit prior to GEM formation
The cells were loaded into a 10x Chromium Chip G with a targeted cell recovery of 5000- 8000 cells for GEM Generation and cell barcoding. Single-cell RNA-seq libraries were prepared with 10x Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.0 or v3.1 (Dual Index)

value: Forebrain

tag: library type

value: CMO

value: Injected with PHP-GFP virus at stage 37.


title: VNO chip static 2

description: Library name: Sample 2

value: WTC

value: iPSC


title: St55_PHP37_CMO_library2

description:
Library name: ST55_PHP37_M2
Deryckere_development_st55.rds


title: VNO chip static 1

description: Library name: Sample 1


title: Passage 6 HUVEC Negative control, replicate 3

city: Bellaterra

first: Alba

last: Hernández

state: Barcelona

address: Campus UAB, s/n

department: Genetics and Microbiology

institute: Universitat Autònoma de Barcelona

description: Library name: CTL_3

data_processing:
Illumina packages: RTA (Real Time Analysis) and bcl2fastq
Sequence reads were trimmed for adaptor sequence/low quality sequence using Rfastp 1.12.0 (parameters- cutLowQualFront/cutLowQualTail: TRUE minReadLength: 20)
Trimmed sequences reas were mapped to hg38 using align function from Rsubread 2.16.1 (parameters- type: rna)
Read counts were performed using featureCounts function from Rsubread 2.16.1 (parameters- annot.inbuilt: hg38 isPairedEnd: TRUE maxMOp: 15)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: blood vessel endothelium

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were used as a model to simulate the human endothelial barrier of blood vessels. These cells were obtained commercially from Promocell (Heidelberg, Germany), identified as HUVEC single-donor (C-12200). Derived from the endothelial lining of umbilical cord veins, HUVECs are widely employed in both physiological and pharmacological studies due to their relevance as a primary model for endothelial cells. HUVECs were maintained in Endothelial Cell Growth Medium 2 (EGM-2; C-22011, Promocell, Heidelberg, Germany) and cultured in thin-layer collagen-coated flasks. The collagen coating was prepared by diluting rat tail collagen I (Corning Inc., New York City, NY, USA) in 20 mM acetic acid to achieve a final concentration of 5 μg/cm². This solution was applied to flasks or plates and incubated for one hour. After incubation, excess collagen and acid were removed by washing the surfaces twice with 1X PBS. All experiments were conducted using cells up to passage 6. The cells were incubated at 37°C in a humidified atmosphere containing 5 % CO₂, with media changes every other day.

extract_protocol:
After cells were exposed to 100 μg/mL of PS-C-NPLs (PS-C 30 nm, PS-C 50 nm, and PS-C 100 nm) for 24 hours, RNA isolation and purification were performed using the TRI Reagent® protocol (Merck, Darmstadt, Germany). Briefly, cells were lysed with 1 mL of TRI Reagent, and the homogenized lysates were transferred to Eppendorf tubes (Eppendorf, Hamburg, Germany). Chloroform was added, followed by incubation and centrifugation. The aqueous phase, containing RNA, was transferred to new tubes, and RNA was precipitated with 2-propanol. After centrifugation, RNA pellets were washed with 75 % ethanol and centrifuged again. The pellets were air-dried, resuspended in RNase-free water, and RNA quality and concentration were measured using a NanoDrop® spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). The experiment was conducted with technical quadruplicates for each treatment and triplicates for the negative control.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold kit following manufacter's protocol.

treatment_protocol: To evaluate the toxicological effects of various PS-C-NPLs, cells were exposed to NPLs diluted in EGM-2 medium at a final concentration of 100 μg/mL. The exposure duration varied depending on the specific assay, with standard protocols typically involving 24-hour exposure periods. To ensure consistent cell density across treatments with different exposure times, treatments were applied in a staggered manner and evaluated simultaneously. Typically, cells were plated at a density of 26,300 cells/cm² and cultured for 48 hours in wells pre-coated with a thin layer of collagen. After this incubation period, the culture medium was replaced with the appropriate treatment for the required duration, generally 24 hours. Untreated cells served as the negative control for all experiments.

value: blood vessel endothelium

value: HUVEC

value: Primary

tag: time

value: 24 hours


title: Passage 6 HUVEC Negative control, replicate 2

description: Library name: CTL_2


title: OCI-Ly7_AZA_rep1

description: Library name: E49A_1

value: Lymphoma cells


title: St55_PHP41_transcript_library1

description:
Library name: ST55_PHP41_T1
Deryckere_development_st55.rds

value: GEX

value: Injected with PHP-GFP virus at stage 41.


title: St55_PHP37_transcript_library1

description:
Library name: ST55_PHP37_T1
Deryckere_development_st55.rds


title: St55_PHP37_transcript_library2

description:
Library name: ST55_PHP37_T2
Deryckere_development_st55.rds


title: OCI-Ly7_vehicle_rep3

description: Library name: E49C_4

value: vehicle


title: St55_PHP51_CMO_library2

description:
Library name: ST55_PHP51_M2
Deryckere_development_st55.rds

value: Injected with PHP-GFP virus at stage 51.


title: Passage 6 HUVEC Negative control, replicate 1

description: Library name: CTL_1


title: Passage 6 HUVEC + PS-C 100 nm 24 h treatment, replicate 4

description: Library name: PS_C_100_4

value: PS-C 100nm


title: OCI-Ly7_HDAC3i_rep2

description: Library name: E49H_3


title: St55_PHP51_transcript_library1

description:
Library name: ST55_PHP51_T1
Deryckere_development_st55.rds


title: St55_PHP41_CMO_library1

description:
Library name: ST55_PHP41_M1
Deryckere_development_st55.rds


title: Passage 6 HUVEC + PS-C 100 nm 24 h treatment, replicate 2

description: Library name: PS_C_100_2


title: Passage 6 HUVEC + PS-C 100 nm 24 h treatment, replicate 3

description: Library name: PS_C_100_3


title: Passage 6 HUVEC + PS-C 100 nm 24 h treatment, replicate 1

description: Library name: PS_C_100_1


title: Passage 6 HUVEC + PS-C 50 nm 24 h treatment, replicate 4

description: Library name: PS_C_50_4

value: PS-C 50 nm


title: OCI-Ly7_vehicle_rep2

description: Library name: E49C_3


title: OCI-Ly7_HDAC3i_rep1

description: Library name: E49H_1


title: St55_PHP51_CMO_library1

description:
Library name: ST55_PHP51_M1
Deryckere_development_st55.rds


title: Passage 6 HUVEC + PS-C 50 nm 24 h treatment, replicate 3

description: Library name: PS_C_50_3


title: St53_CMO_library1

description:
Library name: St53_M1
CMO tag sequencing for library 1 |CMO309|CMO310|CMO311|CMO312
Deryckere_development_st53.rds

data_processing:
Reads were assigned to the combined Pleurodeles waltl transcriptome using Alevin (Salmon v1.6.0). Library type was set to automatic and keepCBFraction was set to 1. All other parameters were set as default.  Multiplex tag reads were also assigned using Alevin
The 4 CMO tags: They are only used to identify and exclude doublets. The objects were first demultiplexed independently based on the identity of the Feature Barcode oligonucleotides introduced using the 10x Genomics 3    CellPlex Kit, and only singlets were retained. Singlets were identified using the HTODemux() command within Seurat.
Assembly: GSE198367_iso_trinity_transcripts.fasta.gz, GSE198367_merge_trinity_iso_t2g.txt.gz
Supplementary files format and content: raw count matrix

molecule: other

source_name: Telencephalon

value: Telencephalon

tag: Stage

value: stage 53


title: St53_transcript_library2

description:
Library name: St53_T2
Deryckere_development_st53.rds


title: Passage 6 HUVEC + PS-C 50 nm 24 h treatment, replicate 2

description: Library name: PS_C_50_2


title: St55_PHP51_transcript_library2

description:
Library name: ST55_PHP51_T2
Deryckere_development_st55.rds

value: Forebrain


title: St53_CMO_library2

description:
Library name: St53_M2
CMO tag sequencing for library 2 |CMO309|CMO310|CMO311|CMO312
Deryckere_development_st53.rds

value: CMO


title: Stage_50_transcript_library_2

description: Library name: St_50_T2

value: stage 50


title: St33_CMO_tags_library_2

description: Library name: St33_M2

source_name: Head

value: Head

value: stage 33


title: Stage_50_CMO_library_2

description:
Library name: St_50_M2
CMO tags for library 2. CMO308|CMO309|CMO310|CMO311


title: OCI-Ly7_vehicle_rep1

description: Library name: E49C_1


title: Passage 6 HUVEC + PS-C 30 nm 24 h treatment, replicate 3

description: Library name: PS_C_30_3

value: blood vessel endothelium

value: HUVEC

value: PS-C 30 nm


title: St53_transcript_library1

description:
Library name: St53_T1
Deryckere_development_st53.rds


title: NC_3

description: Library name: NC_3

treatment_protocol: AGS cells were transfected with either scr-shRNA or ANXA2P1-shRNAp.

value: AGS

value: Human gastric adenocarcinoma cell

value: Transfected with scr-shRNA


title: Stage_50_CMO_library_1

description:
Library name: St_50_M1
CMO tags for library 1. CMO308|CMO309|CMO310|CMO311


title: NC_2

description: Library name: NC_2


title: St33_transcript_library_1

description: Library name: St33_T1

value: GEX


title: Stage_50_transcript_library_1

description: Library name: St_50_T1


title: stage_30_mpx_tags_1

description: Library name: ST_30_M1


title: Passage 6 HUVEC + PS-C 50 nm 24 h treatment, replicate 1

description: Library name: PS_C_50_1

value: Primary

value: 24 hours


title: St33_CMO_tags_library_1

description: Library name: St33_M1


title: stage_30_transcripts_1

description: Library name: ST_30_T1


title: NC_1

description: Library name: NC_1


title: strain harbouring mCherry-carrying high copy plasmid, t2, replicate C

type: RNA

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

country: Germany

institute: Saarland University

description: sampling during mid-exponential growth phase

hyb_protocol: Agilent hybridisation kit (600 ng cDNA)

scan_protocol: Agilent SureScan S2600D Microarray Scanner

data_processing: GeneSpring 14.9 GC, Feature extraction,Baseline Transformation: median of all samples Statistical analysis (moderated t-test, Benjamini-Hochberg FDR, p_corr < 0.2, 2fold change), export

organism: Corynebacterium glutamicum

source_name: cell biomass

label_protocol: Agilent labeling kit (one color)

growth_protocol: cultivation in flowerplates in mini-bioreactors (Biolector 1, m2plabs, 1.300 rpm, 30°C, 80% humidity, inoculation OD 0.5)

extract_protocol: mRNA extracted from harvested cell pellets using Qiagen RNeasy kit and Turbo DNAfree kit followed by nano-drop analysis

treatment_protocol: cells (500 µL) were harvested via centrifugation (30 sec, 4°C, 13.000 x g) and snap-frozen in liquid nitrogen

value: BHI medium, mid-exponential growth phase, time point 2


title: Passage 6 HUVEC + PS-C 30 nm 24 h treatment, replicate 2

description: Library name: PS_C_30_2


title: Passage 6 HUVEC + PS-C 30 nm 24 h treatment, replicate 1

description: Library name: PS_C_30_1


title: Passage 6 HUVEC + PS-C 30 nm 24 h treatment, replicate 4

description: Library name: PS_C_30_4


title: strain harbouring mCherry-carrying high copy plasmid, t2, replicate B


title: GBe051s006_WSUAML_sgGLIS2_Rep3

description: Library name: Sample 9

data_processing:
RNA-seq reads were trimmed using TrimGalore v0.6.10 (cutadapt v4.9) and ribosomal RNA reads were removed using SortMeRNA v4.3.7 (nf-core/rnaseq v3.21.0). Reads were aligned to the GRCh38/hg38 reference genome using STAR v2.7.10a and quantified at the gene level using Salmon v1.10.3 (star_salmon workflow). Gene-level counts were imported using tximeta v1.20.1/tximport.
Differential expression analysis was performed using DESeq2 v1.40 with median-of-ratios size-factor normalization. Results for each contrast (sgRNA vs. sgNT non-targeting control) were extracted using Wald statistics with LFC shrinkage via ashr. DEG thresholds: |log2FoldChange| >= 1 and BH-adjusted p-value < 0.05.
Gene Set Enrichment Analysis (GSEA) was performed using clusterProfiler v4.8 with genes ranked by DESeq2 Wald statistic. MSigDB Hallmark (H) and C2 curated (Reactome, KEGG, WikiPathways) gene sets were tested (minGSSize = 5, maxGSSize = 500, eps = 0, seed = 2110; BH FDR < 0.25). Re-analysis of published cord blood RNA-seq data (Le et al. 2022; GEO: GSE181726) comparing CBFA2T3-GLIS2 transduced vs. GFP control cells used the same DESeq2 pipeline.
Assembly: GRCh38
Supplementary files format and content: Gene-level count matrix quantified from STAR alignments using Salmon v1.10.3 (nf-core/rnaseq v3.21.0 star_salmon workflow). The merged count table (salmon.merged.gene_counts.tsv.gz) contains estimated read counts with Ensembl gene IDs (rows) and sample IDs (columns).

growth_protocol: WSU-AML cells stably expressing Cas9 were generated by lentiviral transduction with lentiCas9-Blast (Addgene #52962) modified with a fused mCherry reporter, followed by blasticidin selection. Cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS and 1X GlutaMAX (Gibco) at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted from CRISPR-KO cell lines using the RNeasy Mini Kit (Qiagen, Cat. No. 74104) according to the manufacturer's protocol.
RNA-seq libraries were prepared and sequenced by Novogene. Strand-specific polyA-selected libraries were sequenced paired-end on an Illumina NovaSeq X Plus instrument.

treatment_protocol: WSU-AML Cas9-expressing cells were transduced with single-guide RNA (sgRNA) lentiviral vectors targeting GLIS2 (sgGLIS2: ATCCTTCTCGGGCTTGACA), SMARCA4 (sgSMARCA4: GAGGTACGTGATGAGCGCGA), or a non-targeting control (sgNT: AGAGCCTTGCGCAATTTTG). Cells were selected in puromycin (2.5–5 µg/mL) for at least 1 week. All experiments were performed at least 3 days post-transduction. Knockout efficiency was verified by Western blotting and TIDE analysis.

value: WSU-AML


title: strain harbouring mCherry-carrying high copy plasmid, t2, replicate A


title: St33_transcript_library_2

description: Library name: St33_T2


title: strain harbouring mCherry-carrying high copy plasmid, t1, replicate B

value: BHI medium, mid-exponential growth phase, time point 1


title: GBe051s006_WSUAML_sgGLIS2_Rep2

description: Library name: Sample 8


title: GBe051s005_WSUAML_sgSMARCA4_Rep2

description: Library name: Sample 5


title: MOM_EndoGCD2

city: Taipei

first: Wei-Ting

last: Liao

address: No. 7, Chung-Shan S. Rd., Chung-Cheng District

country: Taiwan

institute: NTU

description:
Library name: Sample5
MOM_EndoGCD2

data_processing:
Trimmomatic was used to filter out low-quality reads, trim adapter sequences, and eliminate poor-quality bases from the raw paired-end reads. Then, the "clean reads" (the resulting high-quality data) was used for downstream analysis. Using HISAT2, the read pairs from each sample were mapped to the corresponding reference genome (H. sapiens, GRCh38). The number of reads mapped to individual genes was counted using featureCounts. To normalized gene expression, we used the "Relative Log Expression" (RLE) normalization using DESeq2. We used DESeq2 to detect differentially expressed genes (DEGs) under two conditions. The p-values obtained from DEG detection were adjusted using Benjamini and Hochberg's approach to control the false discovery rate (FDR).
Assembly: H. sapiens, GRCh38
Supplementary files format and content: DESeq2_normalized_read_counts.txt
Supplementary files format and content: Original_read_count.txt

extract_protocol:
The RNAs from cells were extracted using TRIzol reagent (Invitrogen, #15596018). 1 μg of total RNA of each sample was used to prepared the library.
The RNA sequencing libraries were constructed by KAPA mRNA HyperPrep Kit (KAPA Biosystems) following the manufacturer's protocol.

value: adenocarcinomic alveolar basal epithelial cells

value: MOM-ENDOGH141A overexpression


title: MOM_EndoGCD3

description:
Library name: Sample6
MOM_EndoGCD3


title: GBe051s006_WSUAML_sgGLIS2_Rep1

description: Library name: Sample 7


title: GBe051s005_WSUAML_sgSMARCA4_Rep3

description: Library name: Sample 6


title: GBe051s005_WSUAML_sgSMARCA4_Rep1

description: Library name: Sample 4


title: strain harbouring mCherry-carrying high copy plasmid, t1, replicate C


title: reference strain harbouring mCherry-carrying native pClik 5? plasmid, replicate C

value: BHI medium, mid-exponential growth phase


title: GBe051s004_WSUAML_sgNT_Rep2

description: Library name: Sample 2

value: sgNT


title: strain harbouring mCherry-carrying high copy plasmid, t1, replicate A


title: GBe051s004_WSUAML_sgNT_Rep3

description: Library name: Sample 3


title: reference strain harbouring mCherry-carrying native pClik 5? plasmid, replicate B


title: GBe051s004_WSUAML_sgNT_Rep1

description: Library name: Sample 1


title: MOM_EndoGCD1

description:
Library name: Sample4
MOM_EndoGCD1


title: JFS3041_M07e_FHD286_48hr_GLIS2_rep2

description: Library name: Sample 33

data_processing:
CUT&RUN reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project's unified GRCh38 blacklist  bed file were removed using bedtools v2.30. Technical replicates were then merged using SAMtools merge and peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility and binding was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
Assembly: GRCh38
Supplementary files format and content: CUT&RUN bigWig files give the normalized coverage of protein-DNA interactions across the genome (deepTools bamCoverage --binSize 40 --normalizeUsing CPM --exactScaling).
Library strategy: CUT&RUN

growth_protocol: M-07e cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS, 1X GlutaMAX (Gibco), and 10 ng/mL recombinant human IL-3 (STEMCELL Technologies). WSU-AML cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS and 1X GlutaMAX (Gibco). All cells were maintained at 37°C with 5% CO₂.

extract_protocol:
Cells were harvested, washed in cold PBS, and nuclei were isolated according to the AutoCUT&RUN protocol. Nuclei were incubated overnight at 4°C with antibodies targeting mSWI/SNF subunits (SMARCA4), CBFA2T3::GLIS2 fusion components (CBFA2T3, GLIS2), or histone modifications (H3K27ac, H3K4me3), or IgG isotype control. Following pA-MNase incubation, chromatin cleavage was initiated by CaCl₂ addition at 0°C, and released DNA fragments were purified.
CUT&RUN libraries were prepared at the Fred Hutchinson Cancer Center Genomics Core using the AutoCUT&RUN protocol. Paired-end sequencing was performed on an Illumina instrument.

treatment_protocol: M-07e cells were treated with 100 nM FHD-286 (SMARCA2/4 ATPase inhibitor; provided by Foghorn Therapeutics) for 24 hours. WSU-AML cells were treated with 10 nM FHD-286 for 24 hours. DMSO vehicle controls were treated in parallel for 48 hours.

value: GLIS2 (Invitrogen, PA5-72849)


title: JFS3042_M07e_FHD286_48hr_IgG_rep2

description: Library name: Sample 34

value: IgG (Abcam, AB172730)


title: strain harbouring empty high copy plasmid, replicate C


title: JFS3039_M07e_FHD286_48hr_H3K4me3_rep2

description: Library name: Sample 31

value: H3K4me3 (Active Motif, 39159)


title: MOM_EndoGWT3

description:
Library name: Sample3
MOM_EndoG3

value: MOM-ENDOGWT

value: MOM-ENDOGWT overexpression


title: MOM_EndoGWT2

description:
Library name: Sample2
MOM_EndoG2


title: JFS3038_M07e_FHD286_48hr_H3K27ac_rep2

description: Library name: Sample 30

value: H3K27ac (EMD Millipore, MABE647)


title: strain harbouring empty high copy plasmid, replicate B


title: JFS3035_M07e_FHD286_48hr_SMARCA4_rep2

description: Library name: Sample 29

value: SMARCA4 (Abcam, ab110641)


title: reference strain harbouring mCherry-carrying native pClik 5? plasmid, replicate A


title: MOM_EndoG3

description: Library name: Sample6

data_processing:
Trimmomatic was used to filter out low-quality reads, trim adapter sequences, and eliminate poor-quality bases from the raw paired-end reads. Then, the "clean reads" (the resulting high-quality data) was used for downstream analysis. Using HISAT2, the read pairs from each sample were mapped to the corresponding reference genome (H. sapiens, GRCh38). The number of reads mapped to individual genes was counted using featureCounts. To normalized gene expression, we used the "Relative Log Expression" (RLE) normalization using DESeq2. We used DESeq2 to detect differentially expressed genes (DEGs) under two conditions. The p-values obtained from DEG detection were adjusted using Benjamini and Hochberg's approach to control the false discovery rate (FDR).
Assembly: H. sapiens, GRCh38
Supplementary files format and content: DESeq2_normalized_read_counts.txt


title: MOM_EndoG2

description: Library name: Sample5


title: JFS3032_M07e_FHD286_48hr_CBFA2T3_rep1

description: Library name: Sample 26

value: CBFA2T3 (Sigma-Aldrich, AV33993-100UL)


title: MOM_EndoGWT1

description:
Library name: Sample1
MOM_EndoG1


title: JFS3034_M07e_FHD286_48hr_IgG_rep1

description: Library name: Sample 28


title: JFS3040_M07e_FHD286_48hr_CBFA2T3_rep2

description: Library name: Sample 32


title: JFS3031_M07e_FHD286_48hr_H3K4me3_rep1

description: Library name: Sample 25


title: reference strain harbouring empty native pClik 5? plasmid, replicate C


title: JFS3033_M07e_FHD286_48hr_GLIS2_rep1

description: Library name: Sample 27


title: MOM_EndoG1

description: Library name: Sample4


title: reference strain harbouring empty native pClik 5? plasmid, replicate B


title: JFS3026_M07e_FHD286_24hr_GLIS2_rep2

description: Library name: Sample 22


title: NoTransfect3

description: Library name: Sample3

value: Vehicle control


title: NoTransfect2

description: Library name: Sample2


title: strain harbouring empty high copy plasmid, replicate A


title: reference strain harbouring empty native pClik 5? plasmid, replicate A


title: JFS3024_M07e_FHD286_24hr_H3K4me3_rep2

description: Library name: Sample 20


title: JFS3030_M07e_FHD286_48hr_H3K27ac_rep1

description: Library name: Sample 24


title: NoTransfect1

description: Library name: Sample1


title: JFS3023_M07e_FHD286_24hr_H3K27ac_rep2

description: Library name: Sample 19


title: JFS3019_M07e_FHD286_24hr_IgG_rep1

description: Library name: Sample 17


title: JFS3020_M07e_FHD286_24hr_SMARCA4_rep2

description: Library name: Sample 18


title: JFS3015_M07e_FHD286_24hr_H3K27ac_rep1

description: Library name: Sample 13


title: JFS3016_M07e_FHD286_24hr_H3K4me3_rep1

description: Library name: Sample 14


title: Dynamic_Day5_techRep3_bioRep2

city: Berlin

first: Rainer

last: Glauben

address: Hindenburgdamm 30

department: Klinik für Gastroenterologie, Infektiologie und Rheumatologie

institute: Charite CBF

description: Library name: BD5_3

data_processing:
Paired-end reads were aligned to the human reference genome (GRCh38, GENCODE v33) using HISAT2 v2.0.5 with default parameters. Gene-level counts were obtained using featureCounts v1.5.0-p3.
Assembly: GRCh38
Supplementary files format and content: txt document contains processed data for all samples combined
Supplementary files format and content: Combined raw data folder contains fq.gz files for each paired end sample

source_name: Terminal ileum

growth_protocol: Organoids were cultured in organoid expansion medium consisting of WRN-conditioned medium produced from L-WRN cells (ATCC CRL-3276), supplemented with recombinant human EGF, SB202190, A83-01, Gastrin I, Nicotinamide, and Y-27632 during initial passages. Antibiotics were included during establishment to prevent contamination. Cultures were maintained at 37 °C and 5% CO₂, with medium exchange every other day and passaged weekly. Organoids at passages 5–6 were used for subsequent experiments.

extract_protocol:
Cells were lysed in QIAzol reagent and RNA was extracted using the Direct-zol RNA Microprep kit (Zymo Research). RNA integrity was assessed on an Agilent TapeStation (RNA ScreenTape assay, Software A.02.01 SR1), and samples with RNA integrity number (RIN) ≥ 8 were used for downstream analyses.
Libraries were prepared using the Illumina mRNA library preparation kit with poly-A enrichment from the recommended Novogene RNA input. Sequencing was performed on an Illumina platform using paired-end 150 bp reads, generating approximately 9 Gb of data per sample (~30 million reads per sample).

value: Terminal ileum

value: Primary human intestinal organoids

value: intestinal epithelial cells

value: healthy donor


title: JFS3025_M07e_FHD286_24hr_CBFA2T3_rep2

description: Library name: Sample 21


title: JFS3027_M07e_FHD286_48hr_SMARCA4_rep1

description: Library name: Sample 23


title: Dynamic_Day5_techRep4_bioRep2

description: Library name: BD5_4


title: JFS3012_M07e_FHD286_24hr_SMARCA4_rep1

description: Library name: Sample 12


title: JFS3017_M07e_FHD286_24hr_CBFA2T3_rep1

description: Library name: Sample 15


title: JFS3018_M07e_FHD286_24hr_GLIS2_rep1

description: Library name: Sample 16


title: Dynamic_Day5_techRep2_bioRep2

description: Library name: BD5_2


title: Dynamic_Day5_techRep1_bioRep2

description: Library name: BD5_1


title: JFS3011_M07e_DMSO_48hr_GLIS2_rep2

description: Library name: Sample 11

value: DMSO 48hr


title: JFS3010_M07e_DMSO_48hr_CBFA2T3_rep2

description: Library name: Sample 10


title: Scaffold_Day5_techRep3_bioRep2

description: Library name: BS5_3


title: JFS3009_M07e_DMSO_48hr_H3K4me3_rep2

description: Library name: Sample 9


title: JFS3008_M07e_DMSO_48hr_H3K27ac_rep2

description: Library name: Sample 8


title: JFS3005_M07e_DMSO_48hr_SMARCA4_rep2

description: Library name: Sample 7


title: Scaffold_Day5_techRep2_bioRep2

description: Library name: BS5_2


title: normal-glucose_3

state: Guangdong

address: 1838 Guangzhou Avenue North

description: Gene expression after normal-glucose treatment

hyb_protocol: The Cy3-labeled cRNA samples were purified and hybridized to Agilent Human ceRNA Microarray 2019 (Design ID: 086188) using the manufacturer’s protocol. Hybridization was carried out at 65 °C for 17 hours in an Agilent hybridization oven.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, the raw data were normalized with the quantile algorithm. The probes detected with at least 75.0 percent in any group were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test.

source_name: AGS cells

label_protocol: Cyanine-3-CTP (Cy3-CTP, Agilent Technologies) was incorporated into the cRNA. The labeling procedure was performed according to the manufacturer's standard protocol.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA quantity and purity were assessed by NanoDrop ND-2000 (Thermo Scientific), and integrity was evaluated using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Cells were treated with either low-glucose medium (1.0 mM glucose) or normal-glucose medium (7.0 mM glucose) before RNA extraction.

value: normal-glucose

value: AGS


title: normal-glucose_4


title: Scaffold_Day5_techRep1_bioRep2

description: Library name: BS5_1


title: JFS3002_M07e_DMSO_48hr_CBFA2T3_rep1

description: Library name: Sample 4


title: JFS3000_M07e_DMSO_48hr_H3K27ac_rep1

description: Library name: Sample 2


title: GBe046s006_48

description: Library name: Sample 23

data_processing:
CUT&Tag reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project's unified GRCh38 blacklist  bed file were removed using bedtools v2.30.0. The data was then processed by merging technical replicates using SAMtools merge. Peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility and binding was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
Assembly: GRCh38
Supplementary files format and content: CUT&Tag bigWig files give the normalized coverage of histone modifications and transcription factor binding across the genome (deepTools bamCoverage --binSize 40 --normalizeUsing CPM --exactScaling).
Library strategy: CUT&Tag

extract_protocol:
Cells were harvested, washed in cold PBS, and resuspended in nuclear extraction buffer. Intact nuclei were incubated with primary antibodies targeting mSWI/SNF subunits (SMARCC1, SMARCB1, SMARCA4), CBFA2T3::GLIS2 fusion components (CBFA2T3, GLIS2), histone modifications (H3K4me3), or IgG isotype control, followed by secondary antibody and pA/G-Tn5 incubation. Tagmentation was activated by MgCl₂ at 37°C and resulting DNA fragments were purified.
CUT&Tag libraries were prepared in-house using the CUT&Tag protocol (Kaya-Okur et al., 2019). Libraries were sequenced by Novogene on an Illumina instrument.

treatment_protocol: WSU-AML Cas9-expressing cells were transduced with sgRNA lentiviral vectors targeting CBFA2T3 (sgCBFA2T3: AGTCAACGAGAACGGCAAG), GLIS2 (sgGLIS2: ATCCTTCTCGGGCTTGACA), SMARCA4 (sgSMARCA4: GAGGTACGTGATGAGCGCGA), SMARCA2 (sgSMARCA2: TTGTCATGTATACCATCGA), or a non-targeting control (sgNT: AGAGCCTTGCGCAATTTTG). Experiments were performed 6 days post-transduction. Knockout efficiency was verified by Western blotting and TIDE analysis.

value: WSU-AML

value: SMARCC1 (Cell Signaling Technology, 11956S)


title: Plastic_Day5_techRep3_bioRep2

description: Library name: BP5_3


title: JFS3004_M07e_DMSO_48hr_IgG_rep1

description: Library name: Sample 6

value: IgG (Abcam, AB172730)


title: GBe046s005_46

description: Library name: Sample 21

value: sgCtrl


title: Plastic_Day5_techRep2_bioRep2

description: Library name: BP5_2


title: Plastic_Day5_techRep4_bioRep2

description: Library name: BP5_4


title: GBe046s006_47

description: Library name: Sample 22


title: JFS3001_M07e_DMSO_48hr_H3K4me3_rep1

description: Library name: Sample 3

value: H3K4me3 (Active Motif, 39159)


title: GBe046s008_49

description: Library name: Sample 24


title: hsfa1abd-2, wounded, 24h, r2

city: Yokohama

first: Duncan

middle: Peter

last: Coleman

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

country: Japan

institute: Riken

description: Library name: WabdT24-2

data_processing:
read trimming was carried out using fastp (Chen et al., 2018) with the following settings; -q 15 -l 5 -w 16 -x
Processed reads were mapped to the TAIR10 genome with  STAR (Dobin et al., 2013) with the following settings; --quantMode GeneCounts --outFilterMultimapNmax 1
--alignIntronMax 10000 --alignMatesGapMax 10000
Assembly: TAIR10
Supplementary files format and content: raw read counts for each sample in a tab seperated file (tsv)

organism: Arabidopsis thaliana

source_name: Hypocotyl

growth_protocol: WT and hsfa1abd-2 seedlings were grown in the dark for 7 days on 1x MS

extract_protocol:
RNA was isolated using the RNeasy plant mini kit (Qiagen)
to library preparation with the Kapa stranded mRNA sequencing kit (KK8420, Kapa Biosystems) and Illumina-compatible FastGene adapters (NGSAD24, Nippon Genetics).

treatment_protocol: Hypocotyls were wounded by cutting with a scalple and hypocotyl explants were harvest ), around 50 explants were collected per replicate and three biological replicates were used for each time point

value: Hypocotyl

tag: ecotype

value: whole tissue

value: wounding


title: hsfa1abd-2, wounded, 3h, r3

description: Library name: WabdT3-3


title: hsfa1abd-2, wounded, 24h, r1

description: Library name: WabdT24-1


title: Plastic_Day5_techRep1_bioRep2

description: Library name: BP5_1


title: hsfa1abd-2, wounded, 24h, r3

description: Library name: WabdT24-3


title: normal-glucose_2


title: normal-glucose_1


title: GBe046s008_38

address: 1920 Terry Ave

description: Library name: Sample 19

source_name: WSU-AML

value: SMARCA4 (Abcam, ab110641)


title: GBe046s008_50

description: Library name: Sample 25


title: GBe046s005_45

description: Library name: Sample 20


title: Dynamic_Day1_techRep4_bioRep2

description: Library name: BD1_4


title: low-glucose_4

description: Gene expression after low-glucose treatment

value: low-glucose


title: low-glucose_3


title: hsfa1abd-2, wounded, 3h, r2

description: Library name: WabdT3-2


title: GBe046s006_36

description: Library name: Sample 17


title: hsfa1abd-2, wounded, 3h, r1

description: Library name: WabdT3-1


title: GBe046s008_37

description: Library name: Sample 18


title: Dynamic_Day1_techRep2_bioRep2

description: Library name: BD1_2

value: Terminal ileum


title: GBe046s006_27

description: Library name: Sample 13

value: GLIS2 (Invitrogen, PA5-72849)


title: GBe046s005_34

description: Library name: Sample 15


title: hsfa1abd-2, wounded, 1h, r2

description: Library name: WabdT1-2


title: GBe046s008_28

description: Library name: Sample 14


title: Dynamic_Day1_techRep3_bioRep2

description: Library name: BD1_3

value: Primary human intestinal organoids

value: intestinal epithelial cells


title: GBe046s006_26

description: Library name: Sample 12


title: hsfa1abd-2, wounded, 1h, r3

description: Library name: WabdT1-3


title: low-glucose_1


title: Scaffold_Day1_techRep2_bioRep2

description: Library name: BS1_2

value: healthy donor


title: GBe046s005_25

description: Library name: Sample 11


title: GBe046s008_18

description: Library name: Sample 9


title: GBe046s006_16

description: Library name: Sample 7


title: Dynamic_Day1_techRep1_bioRep2

description: Library name: BD1_1


title: hsfa1abd-2, wounded, 30min, r2

description: Library name: WabdT05-2


title: GBe046s005_14

description: Library name: Sample 5


title: GBe046s005_24

description: Library name: Sample 10


title: hsfa1abd-2, wounded, 30min, r1

description: Library name: WabdT05-1


title: GBe046s005_35

description: Library name: Sample 16


title: Scaffold_Day1_techRep1_bioRep2

description: Library name: BS1_1


title: hsfa1abd-2, wounded, 30min, r3

description: Library name: WabdT05-3


title: GBe046s008_17

description: Library name: Sample 8


title: hsfa1abd-2, wounded, 1h, r1

description: Library name: WabdT1-1


title: Scaffold_Day1_techRep3_bioRep2

description: Library name: BS1_3


title: GBe046s006_15

description: Library name: Sample 6


title: low-glucose_2


title: Plastic_Day1_techRep2_bioRep2

description: Library name: BP1_2


title: Plastic_Day1_techRep4_bioRep2

description: Library name: BP1_4


title: GBe046s005_4

description: Library name: Sample 1


title: GBe046s008_6

description: Library name: Sample 3


title: Plastic_Day1_techRep3_bioRep2

description: Library name: BP1_3


title: hsfa1abd-2, wounded, T0, r2

description: Library name: WabdT0-2


title: Plastic_Day1_techRep1_bioRep2

description: Library name: BP1_1


title: GBe046s005_13

description: Library name: Sample 4


title: GBe046s006_5

description: Library name: Sample 2


title: Scaffold_Day0_techRep3_bioRep2

description: Library name: BS0_3


title: HEK293T cells, KO, rep2, RNA-seq

city: Guangzhou

first: dingdang

last: Yu

address: No. 106, Zhongshan 2nd Road, Yuexiu District

institute: Guangdong Provincial People's Hospital

description: Library name: KO_RNA_rep2

data_processing:
Raw paired-end sequencing reads were subjected to quality control and adapter trimming using Trim Galore (v0.6.6). Processed reads were aligned to the human reference genome (hg38) and spike-in mouse genome (mm39) from GENCODE using Bowtie (v2.3.5.1) with default parameters.Unmapped reads and low-quality alignments were removed using SAMtools (v1.11).To control for technical variation, a spike-in-based normalization strategy was applied. The total number of reads mapped to the mm10 genome (mm10_count) was used to calculate the normalization factor α = 1e5/mm10_count.
Normalized bigWig files were generated using bamCoverage from deepTools (v2.5.7).
Assembly: hg38; mm39
Supplementary files format and content: bigWig; narrowPeak

source_name: Embryonic kidney

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, Chromatin was sheared to an average length of 300-700 bp with a Qsonica sonicator.
ChIP-seq libraries were prepared using VAHTSTM Universal DNA Library Prep Kit for Illumina. After amplification and size selection with DNA clean beads from Vazyme, the size distributions were determined with Agilent 4200 Bioanalyzer.

value: Embryonic kidney

value: Epithelial-like cell

value: KO


title: hsfa1abd-2, wounded, T0, r1

description: Library name: WabdT0-1


title: JFS2997_M07e_DMSO_48hr_SMARCA4_rep1

city: Seattle

first: Jay

last: Sarthy

institute: Seattle Children's Research Institute

description: Library name: Sample 1

value: DMSO 48hr


title: hsfa1abd-2, wounded, T0, r3

description: Library name: WabdT0-3


title: HEK293T cells, KO, rep3, RNA-seq

description: Library name: KO_RNA_rep3


title: HEK293T cells, WT, rep3, RNA-seq

description: Library name: WT_RNA_rep3

value: WT


title: HEK293T cells, KO, rep1, RNA-seq

description: Library name: KO_RNA_rep1


title: Col-0, wounded, 24h, r3

description: Library name: WCol-0T24-3

value: WT Col-0


title: Col-0, wounded, 24h, r2

description: Library name: WCol-0T24-2


title: HEK293T cells, WT, rep1, RNA-seq

description: Library name: WT_RNA_rep1


title: Scaffold_Day0_techRep2_bioRep2

description: Library name: BS0_2


title: Scaffold_Day0_techRep1_bioRep2

description: Library name: BS0_1


title: Plastic_Day0_techRep4_bioRep2

description: Library name: BP0_4


title: Col-0, wounded, 24h, r1

description: Library name: WCol-0T24-1


title: HEK293T cells, KO, rep2, Pro-seq

description: Library name: KO_PRO_rep2

data_processing:
Raw paired-end sequencing reads were subjected to quality control and adapter trimming using Trim Galore (v0.6.6). Processed reads were aligned to the human reference genome (hg38) and spike-in mouse genome (mm39) from GENCODE using Bowtie (v2.3.5.1) with default parameters.Unmapped reads and low-quality alignments were removed using SAMtools (v1.11).To control for technical variation, a spike-in-based normalization strategy was applied. The total number of reads mapped to the mm10 genome (mm10_count) was used to calculate the normalization factor α = 1e5/mm10_count.
Normalized bigWig files were generated using bamCoverage from deepTools (v2.5.7).
Assembly: hg38; mm39
Supplementary files format and content: bigWig; narrowPeak
Library strategy: Pro-seq


title: HEK293T cells, KO, rep1, Pro-seq

description: Library name: KO_PRO_rep1


title: HEK293T cells, WT, rep2, Pro-seq

description: Library name: WT_PRO_rep2


title: HEK293T cells, WT, rep1, Pro-seq

description: Library name: WT_PRO_rep1


title: Col-0, wounded, 3h, r3

description: Library name: WCol-0T3-3


title: Plastic_Day0_techRep3_bioRep2

description: Library name: BP0_3


title: Col-0, wounded, 3h, r2

description: Library name: WCol-0T3-2


title: Plastic_Day0_techRep2_bioRep2

description: Library name: BP0_2


title: HEK293T cells, KO, rep1, TT-seq

description:
Library name: KO_TT_rep1
Transient transcriptome sequencing (TT-seq)


title: HEK293T cells, FH OE, Input

description: Library name: FH_IN

value: FH OE


title: HEK293T cells, FH OE, HA, ChIP

description: Library name: FH_HA

tag: chip-seq antibody

value: HA


title: HEK293T cells, WT, rep2, RNA-seq

description: Library name: WT_RNA_rep2


title: HEK293T cells, KO, rep2, TT-seq

description:
Library name: KO_TT_rep2
Transient transcriptome sequencing (TT-seq)


title: HEK293T cells, KO, Input

description: Library name: KO_IN


title: HEK293T cells, WT, rep1, TT-seq

description:
Library name: WT_TT_rep1
Transient transcriptome sequencing (TT-seq)


title: Col-0, wounded, 3h, r1

description: Library name: WCol-0T3-1

value: Hypocotyl

value: whole tissue


title: Col-0, wounded, 1h, r3

description: Library name: WCol-0T1-3

value: wounding


title: Dynamic_Day5_techRep3_bioRep1

description: Library name: AD5_3


title: HEK293T cells, KO, H3K4me3, ChIP

description: Library name: KO_H3K4me3


title: Plastic_Day0_techRep1_bioRep2

description: Library name: BP0_1


title: Col-0, wounded, 1h, r1

description: Library name: WCol-0T1-1


title: HEK293T cells, WT, Input

description: Library name: WT_IN


title: HEK293T cells, KO, H3K4me1, ChIP

description: Library name: KO_H3K4me1


title: Col-0, wounded, 1h, r2

description: Library name: WCol-0T1-2


title: HEK293T cells, KO, H3K27ac, ChIP

description: Library name: KO_H3K27ac


title: HEK293T cells, FH OE, FLAG, ChIP

description: Library name: FH_FLAG

value: FLAG


title: Dynamic_Day5_techRep2_bioRep1

description: Library name: AD5_2

value: Terminal ileum


title: Col-0, wounded, 30min, r3

description: Library name: WCol-0T05-3


title: HEK293T cells, KO, RPB1, ChIP

description: Library name: KO_RPB1


title: Dynamic_Day5_techRep4_bioRep1

description: Library name: AD5_4


title: HEK293T cells, KO, pSer5, ChIP

description: Library name: KO_pSer5


title: Scaffold_Day5_techRep3_bioRep1

description: Library name: AS5_3


title: HEK293T cells, KO, INTS13, ChIP

description: Library name: KO_INTS13


title: HEK293T cells, KO, pSer2, ChIP

description: Library name: KO_pSer2


title: HEK293T cells, KO, INTS10, ChIP

description: Library name: KO_INTS10


title: Col-0, wounded, 30min, r1

description: Library name: WCol-0T05-1


title: Col-0, wounded, 30min, r2

description: Library name: WCol-0T05-2


title: HEK293T cells, WT, rep2, TT-seq

description:
Library name: WT_TT_rep2
Transient transcriptome sequencing (TT-seq)


title: Col-0, wounded, T0, r3

description: Library name: WCol-0T0-3


title: Dynamic_Day5_techRep1_bioRep1

description: Library name: AD5_1


title: HEK293T cells, WT, H3K4me2, ChIP

description: Library name: WT_H3K4me2


title: HEK293T cells, WT, H3K4me3, ChIP

description: Library name: WT_H3K4me3


title: Scaffold_Day5_techRep1_bioRep1

description: Library name: AS5_1


title: HEK293T cells, WT, H3K4me1, ChIP

description: Library name: WT_H3K4me1


title: Scaffold_Day5_techRep2_bioRep1

description: Library name: AS5_2


title: HEK293T cells, WT, H3K27ac, ChIP

description: Library name: WT_H3K27ac


title: Col-0, wounded, T0, r2

description: Library name: WCol-0T0-2


title: JFS3003_M07e_DMSO_48hr_GLIS2_rep1

description: Library name: Sample 5

value: GLIS2 (Invitrogen, PA5-72849)


title: Plastic_Day5_techRep4_bioRep1

description: Library name: AP5_4

value: Primary human intestinal organoids


title: HEK293T cells, WT, pSer2, ChIP

description: Library name: WT_pSer2


title: Col-0, wounded, T0, r1

description: Library name: WCol-0T0-1


title: HEK293T cells, WT, RPB1, ChIP

description: Library name: WT_RPB1


title: CMT93 spheroids treated with 200 µM palmitate, replicate 3

city: Leuven

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB/KU Leuven

description: Library name: CMT93E.PA.R3

data_processing:
Purified dual-indexed sequence-libraries of each sample were equimolarly pooled and sequenced on an Element Biosciences AVITI (Adept Rapid PCR-Plus conversion, 2 runs, Cloudbreak High Output Sequencing kits, single end, (101-10-10-0)) at the VIB Nucleomics Core (https://nucleomicscore.sites.vib.be/en).
Following demultiplexing, reads from both runs corresponding to each given sample were concatenated, and the resulting merged reads were subject to optical-duplicate removal and adapter trimming using the BBMap suite (v38.98; https://sourceforge.net/projects/bbmap/) clumpify and BBDuk modules, respectively. Trimmed-read quality control was then performed using FastQC (v0.11.8; https://www.bioinformatics.babraham.ac.uk/projects/fastqc). High-quality reads were then mapped to the mm39 reference mouse genome (GRCm39, Gencode build vM30) using STAR (v2.6.1; https://github.com/alexdobin/STAR), and further quantified using HTSeq’s (v0.9.1; https://htseq.readthedocs.io) htseq-count module.
Gene counts for all 6 samples collected under the 2 conditions of interest (palmitate or vehicle treatment) were first filtered to keep only genes expressed in at least 2 out of 3 samples for at least one of the two conditions.
Differential expression analysis was then performed on the remaining 23399 genes within the DESeq2 (v1.34.0; https://bioconductor.org/packages/release/bioc/html/DESeq2.html) framework. DESeq2-derived log fold-changes (log2FC) and their associated p-values for the palmitate vs. vehicle contrast were then combined to derive a ranking metric of the form RM = -log10(p-value) x sign(log2FC).
Pre-ranked gene-set enrichment analysis (GSEA; https://www.gsea-msigdb.org/gsea) was then performed based on this ranking metric RM, using the R package fgsea (v1.20.0; https://github.com/ctlab/fgsea; fgsea-multilevel implementation with 10000 initial permutations and no lower bound for p-value estimation), for a collection of gene sets including all KEGG (https://www.genome.jp/kegg) metabolism gene sets with gene-set sizes in the range 3-1500, obtained by querying KEGG's REST API (https://www.kegg.jp/kegg/rest).
Assembly: mm39 (GRCm39, Gencode build vM30)
Supplementary files format and content: The raw-count matrix for all 6 samples included in the study is provided as a tab-separated text file (rawCounts.txt), after filtering out genes with no expression in at least 2 out of 3 samples for at least one of the two conditions considered in the study. The first two columns of this file contain respectively gene stable IDs and symbols. For genes without defined symbols, stable IDs are used in their place. Genes with different stable IDs but annotated to identical symbols are designated by appending .X to the latter, where X = 2...N, with N being the total number of times the same symbol is annotated to different stable IDs. Text-based tab-separated tables are also provided with the results of DESeq2-based differential expression analysis (DESeq2results.txt) and GSEA (GSEAresults.txt). The latter are accompanied by a text file (DESeq2GSEAColumnDescription.txt) describing the contents of the various columns in each of the two files, and a gmt file with the KEGG metabolism gene-set collection used for GSEA (GeneSets_mmKEGGmet.gmt).

organism: Mus musculus

growth_protocol: CMT93 cells were obtained from ATCC, and were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% penicillin (50 units/mL) and 1% streptomycin (50 µg/mL), in a humidified temperature-controlled incubator at 37°C with 5% CO₂ and 95% relative humidity. For 3D (spheroid) cultures, soft agar-coated plates were prepared by mixing 1% soft agar 1:1 with culture medium, allowing this mixture to solidify at room temperature. Cells were then plated on top of the agar and supplemented with 0.25% Matrigel to enable 3D growth

extract_protocol:
For RNA extraction, spheroids were collected, centrifuged, and washed once with PBS. Cell pellets were then lysed with TRIZOL reagent, and total RNA was isolated according to the manufacturer's instructions. RNA concentration and purity were determined spectrophotometrically using a Nanodrop ND-8000, and RNA integrity and concentration were assessed using an Agilent Bioanalyzer 2100 Eukaryote Total RNA Nano Assay.
1000 ng of total RNA per sample were used as input for library preparation. Using the Illumina Stranded mRNA Sample Prep Kit (protocol version: # 1000000124518 v02 (April 2021)), poly-A containing mRNA molecules were purified from the total RNA input using poly-dT oligo-attached magnetic beads. The purified mRNA was fragmented and in a reverse transcription reaction using random primers and Actinomycin D, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using dUTP to achieve strand specificity. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which pre-index anchors were ligated preparing the fragments for dual indexing. Anchor-ligated fragments were then purified using magnetic beads. Finally, enrichment PCR was carried out to enrich those DNA fragments that have anchor-ligated DNA fragments and to add indexes and primer sequences for cluster generation.

treatment_protocol: For palmitate treatment, sodium palmitate was dissolved in ethanol, conjugated with bovine serum albumin (BSA), and then diluted in culture medium down to a final concentration of 200 µM. The same volume of ethanol was incubated with BSA and then analogously diluted in culture medium to serve as vehicle treatment. CMT93 cells were pre-cultured as a monolayer in medium containing vehicle or 200 µM palmitate for 1 week, before being seeded into 3D (spheroid) culture. Cells were then grown as spheroids in medium containing vehicle or 200 µM palmitate for 5 days, after which total RNA was isolated.

value: Colorectal cancer

value: Wildtype

value: 200 µM palmitate (ethanol + BSA-conjugated sodium palmitate)


title: HEK293T cells, WT, INTS13, ChIP

description: Library name: WT_INTS13

value: Embryonic kidney

value: Epithelial-like cell


title: Plastic_Day5_techRep3_bioRep1

description: Library name: AP5_3

value: intestinal epithelial cells

value: healthy donor


title: Plastic_Day5_techRep2_bioRep1

description: Library name: AP5_2


title: HEK293T cells, FH-ZBTB26 OE, Input

description: Library name: FH-ZBTB26_IN

value: FH-ZBTB26 OE


title: Plastic_Day5_techRep1_bioRep1

description: Library name: AP5_1


title: HEK293T cells, WT, INTS10, ChIP

description: Library name: WT_INTS10

value: WT


title: HEK293T cells, FH-ZBTB26 OE, HA, ChIP

description: Library name: FH-ZBTB26_HA

value: HA


title: CMT93 spheroids treated with vehicle, replicate 3

description: Library name: CMT93E.BSA.R3

value: Vehicle (ethanol + BSA)


title: HEK293T cells, WT, pSer5, ChIP

description: Library name: WT_pSer5


title: CMT93 spheroids treated with 200 µM palmitate, replicate 1

description: Library name: CMT93E.PA.R1


title: Dynamic_Day1_techRep4_bioRep1

description: Library name: AD1_4


title: CUT&RUN_Mitotic_T300_HEK293T_H4K5ac_2

city: Orange

first: Matthew

middle: D

last: Simon

state: CT

address: West Campus, 100 West Campus Drive, Ste MIC312A

department: MBB

institute: Yale University

description: Library name: Sample 95

data_processing:
TimeLapse-seq: Sequencing data was processed using the fastq2EZbakR pipeline (Vock et al., 2025).
TimeLapse-seq: Adapter sequences were trimmed using fastp and reads were aligned to a GRCh38 or combined dm6-GRCh38 genome using STAR. Tracks were normalized using DESeq2 (estimateSizeFactors) or Dm spike-ins with DESeq2 (estimateSizeFactors).
TimeLapse-seq: Final mutation counts and feature assignments were summarized in a cB output file.
ATAC-seq: Sequencing data was processed using the nf-core/atacseq pipeline (version 2.1.2) (Ewels et al., 2020).
ATAC-seq: Adapter sequences were trimmed using Cutadapt.
ATAC-seq: Reads were aligned to the human hg38 genome using the BWA aligner.
ATAC-seq: Duplicate reads and reads mapping to mitochondrial DNA were filtered out.
ATAC-seq: Peaks were called using MACS2 in narrow peak mode, and tracks were normalized using TMM normalization.
CUT&RUN: Reads were trimmed of adaptor sequences using fastp.
CUT&RUN: Reads were aligned to a combined E. coli-GRCh38 genome using bwa-mem2.
CUT&RUN: Aligned reads were processed using SAMtools. Tracks were normalized using TMM normalization or E.coli spike-ins.
CUT&RUN: Peaks were called using MACS2 with default parameters, in broad peak mode for H3K27me3, and in narrow peak mode for all other targets, with IgG samples used as controls.
ChIP-seq: For H3K27ac ChIP-seq samples, reads were trimmed of adaptor sequences using Cutadapt and aligned to the GRCh38 genome using Bowtie2 v2.2.9. Fold enrichment bigwig tracks were created using MACS2 bdgcamp compared to input control.
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, reads were processed using the nf-core/chipseq pipeline (version 2.0.0).
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, adapter sequences were trimmed using Trim Galore and reads were aligned to the GRCh38 genome using the BWA aligner.
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, duplicate reads and reads mapping to blacklisted regions were filtered out. Counts Per Million (CPM) normalization was applied to create scaled bigWig files.
ChIP-seq: For all ChIP-seq samples, peaks were called using MACS2 with default parameters, using inputs as controls.
Assembly: GRCh38 and dm6
Supplementary files format and content: Normalized bigWig, TDF files, and MACS2 called-peak files.
Library strategy: CUT&Run

growth_protocol: HEK-293T cells were cultured at 37°C in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin. S2 cells were cultured at 27°C in Schneider's Drosophila Medium with 10% heat-inactivated FBS and 1% Penicillin/Streptomycin. THP-1 cells were grown at 37°C as single cell suspensions in RPMI-1640 containing 10% FBS, 1% penicillin-streptomycin, and 0.05 mM 2-mercaptoethanol (BME).

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. For TimeLapse-seq, genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for TimeLapse-seq was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018. ATAC-seq was performed in HEK293T cells using the Active Motif ATAC-Seq Kit following the standard protocol. CUT&RUN was performed in HEK293T nuclei using the EpiCypher CUTANA ChIC/CUT&RUN Kit following the standard protocol. For Kacme, H4K5ac, and CTCF CUT&RUN samples, cells were crosslinked (0.1% formaldehyde, 1 min) prior to nuclei isolation. For ChIP-seq, 20-30 million cells per IP were crosslinked with formaldehyde for 10 minutes. Nuclei were sonicated, lysates were clarified, and histone-DNA complexes were isolated with antibody.
TimeLapse-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413). ATAC-seq libraries were generated following the Active Motif ATAC-Seq Kit standard protocol. CUT&RUN library preparation was carried out with the EpiCypher CUTANA CUT&RUN Library Prep Kit. ChIP-seq libraries were prepared using standard Illumina protocols.

treatment_protocol: For transcriptional inhibition datasets, HEK293T cells were treated with 10 uM triptolide (MCE, HY-32735) for 1hr. KDM6A/B inhibition was performed by treating HEK293T cells with 5 uM GSK-J4 (MCE, HY-15648B) for either 6 or 24 hrs. THP-1 differentiation was carried out by treating cells with 40 ng/mL PMA (phorbol 12-myristate 13-acetate, Abcam, ab120297) for 48 hrs, followed by washing away non-adherent cells with PBS and incubating the adherent cells in fresh RPMI medium for an additional 24 hrs. Mitotic arrest and release were performed in HEK293T cells. For each sample, 2 million cells were seeded and allowed to adhere overnight. The following day, nocodazole (Sigma, M1404) was added to the media at a final concentration of 50 ng/mL, and cells were incubated for 16 hrs at 37 °C. Mitotic cells were harvested by manual shake-off.

value: WT HEK293T

value: 300 min post-mitotic release

tag: antibody


title: CUT&RUN_Mitotic_T300_HEK293T_Kacme_2

description: Library name: Sample 94

value: Kacme


title: Dynamic_Day1_techRep3_bioRep1

description: Library name: AD1_3

tag: tissue

value: Terminal ileum


title: CUT&RUN_Mitotic_T300_HEK293T_H4K5ac_1

description: Library name: Sample 93


title: CMT93 spheroids treated with 200 µM palmitate, replicate 2

description: Library name: CMT93E.PA.R2

tag: cell type


title: HEK293T cells, FH-ZBTB26 OE, FLAG, ChIP

description: Library name: FH-ZBTB26_FLAG

value: FLAG


title: Dynamic_Day1_techRep2_bioRep1

description: Library name: AD1_2

value: Primary human intestinal organoids


title: CMT93 spheroids treated with vehicle, replicate 2

description: Library name: CMT93E.BSA.R2

value: Colorectal cancer


title: CUT&RUN_Mitotic_T165_HEK293T_H4K5ac_2

description: Library name: Sample 91

value: 165 min post-mitotic release


title: CMT93 spheroids treated with vehicle, replicate 1

description: Library name: CMT93E.BSA.R1

value: Wildtype


title: CUT&RUN_Mitotic_T105_HEK293T_H4K5ac_2

description: Library name: Sample 87

value: 105 min post-mitotic release


title: Dynamic_Day1_techRep1_bioRep1

description: Library name: AD1_1


title: CUT&RUN_Mitotic_T300_HEK293T_Kacme_1

description: Library name: Sample 92


title: CUT&RUN_Mitotic_T165_HEK293T_Kacme_1

description: Library name: Sample 88


title: Scaffold_Day1_techRep2_bioRep1

description: Library name: AS1_2


title: CUT&RUN_Mitotic_T165_HEK293T_Kacme_2

description: Library name: Sample 90


title: Scaffold_Day1_techRep3_bioRep1

description: Library name: AS1_3


title: CUT&RUN_Mitotic_T165_HEK293T_H4K5ac_1

description: Library name: Sample 89


title: CUT&RUN_Mitotic_T105_HEK293T_Kacme_2

description: Library name: Sample 86


title: CUT&RUN_Mitotic_T105_HEK293T_Kacme_1

description: Library name: Sample 84


title: PPARG KO, 5 months FFD, repeat 3

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

description:
Library name: Sample 12
PPARG KO, 5 months FFD, repeat 3

data_processing:
Perform alignments with HISAT2 to the reference.
Assembly: mm10
Supplementary files format and content: TXT for count expression

source_name: liver

extract_protocol:
Total RNA was extracted using the TRIzol (Sigma) method
Samples were submitted to Novogene for sequencing using Illumina NovaSeq platform.

value: liver

value: FFD

value: PPARG KO

tag: time point

value: 5 months


title: CUT&RUN_Mitotic_T80_HEK293T_H4K5ac_2

description: Library name: Sample 83

tag: treatment

value: 80 min post-mitotic release


title: CUT&RUN_Mitotic_T80_HEK293T_Kacme_2

description: Library name: Sample 82

tag: genotype


title: WT, 5 months FFD, repeat 3

description:
Library name: Sample 9
WT, 5 months FFD, repeat 3

value: WT


title: Plastic_Day1_techRep4_bioRep1

description: Library name: AP1_4

value: intestinal epithelial cells

value: healthy donor