title: Gb21_ET1

description: Library name: Gb21_ET1

data_processing:
BGI took care of the quality control of the samples, the construction of the mRNA library, the sequencing of the mRNAs making at least more than 30 million read lengths with 150 paired-end base pairs facilitating the alignment and therefore the reliability of the analysis as well as the verification and analysis steps of the data generated. Data filtering was done by SOAPnuke (R. Li et al., 2008) to (1) remove the readings from the sequencing adapters used; (2) remove low-quality readings with a baseline ratio ≤ 15 if the reading is greater than 20% of the reading phase; (3) remove reads where the number of unknown databases detected is greater than 5%. Then, the "clean" readings were stored in the standard FASTQ format. These reads were mapped to the reference genome using HISAT (D. Kim et al., 2015). To detect gene fusions and differentially expressed genes, Ericscript (0.5.5-5) (Benelli et al., 2012) and rMATS (v4.1.1) (Shen et al., 2014) were used, respectively. The Bowtie2 software (Langmead & Salzberg, 2012) was used to align the "clean" readings with the gene set. Gene expression levels were calculated by RSEM (v1.2.28) (B. Li & Dewey, 2011) to obtain quantification in read count, fragment per kilobase per million (FPKM) and number of transcripts per kilobase million (TPM). An analysis of differentially expressed genes (DEG) is also possible with DESeq2 (Love et al., 2014) or DEGseg (L. Wang et al., 2010) or PossionDis (Audic & Claverie, 1997) with the Q-value ≤ 0.05. The bioinformatics analyses were performed on the BGI, Dr. Tom software platform to visualize the data and extract gene expression in TPM.
Assembly: Homo Sapiens, NCBI, GCF_000001405.39_GRCh38.p13
Supplementary files format and content: One tab-delimited text file includesFPKM, TPM, Readcount, NormReadcount for all sample

growth_protocol: LGG275, LGG336, BT237, Gb7, Gb21 cells were seeded to 260,000 cells/wells in 3.5 mL of a proliferation medium in 6-well plates (#140685, ThermoFisher Nunclon) and placed in an incubator at 37°C in a humid atmosphere with 5% CO2. Cells were cultured in DMEM/F12 (#21331046, Life Technologies) supplemented with L-glutamine (2mM, #25030024, Thermo Fisher), N-2 supplement (100X) (#17502048, Life Technologies), B-27 without vitamin A (50X) (#12587010, Life Technologies, used at 0,5X), heparin (2μg/mL, H3149-100KU, Sigma), EGF (10ng/mL, #Cat AF-100-15-1MG, Peprotech) and FGF2 (10 ng/mL, Cat#100-18B-500UG, Peprotech). This medium also contained antibiotics with ciprofloxacin (10ug/mL), gentamicin (10ug/ml, #11520506, ThermoFisher) and fungin (10μg/mL, Invivogen) to avoid bacterial and fungal contamination.

extract_protocol:
RNA extraction was performed 8 hours after the last treatment using RNEasy mini kit Qiagen for total RNA and dosage by NanoDrop 2000/2000c spectrophotometer to prepare samples at 20 ng/µl with 200 ng minimum
BGI Genomics-BGISEQ (Poland) to perform sequencing via their DNBSEQTM platform for DNBSEQ stranded mRNA library [DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing]

treatment_protocol: Cells were treated either with endothelin dilution buffer (PBS with BSA 0.1%) for control condition or with ET-1 (25 ng/mL) at 10 nM final right after seeding and once a day for 5 days before proceeding to RNA extraction 8 hours after the last treatment.

value: diffuse IDH-wildtype glioblastoma stem cell line

value: WT

value: 5 days

value: Treated ET1-10nM


title: 336_ET1

status: Public on Sep 05 2025

type: SRA

city: Montpellier

first: Donovan

last: PINEAU

address: 141 Rue de la Cardonille

country: France

institute: IGF

description: Library name: 336_ET1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: diffuse IDH-mutant low-grade astrocytoma cell line

tag: genotype

tag: treatment

tag: batch


title: Gb21_Vhcle

description: Library name: Gb21_Vhcle

value: Vehicle


title: Gb7_Vhcle

description: Library name: Gb7_Vhcle


title: Gb7_ET1

description: Library name: Gb7_ET1


title: 336_Vhcle

description: Library name: 336_Vhcle


title: 275_ET1_3 (Rep3)

description: Library name: 275_ET1_3


title: BT237_Vhcle

description: Library name: BT237_Vhcle

value: diffuse IDH-mutant low-grade oligodendroglioma cell line


title: 275_Vhcle_2 (Rep2)

description: Library name: 275_Vhcle_2


title: 275_ET1_2 (Rep2)

description: Library name: 275_ET1_2


title: 275_Vhcle_3 (Rep3)

description: Library name: 275_Vhcle_3


title: DMSO

description: Library name: DMSO

data_processing:
BGI took care of the quality control of the samples, the construction of the mRNA library, the sequencing of the mRNAs making at least more than 30 million read lengths with 100 paired-end base pairs facilitating the alignment and therefore the reliability of the analysis as well as the verification and analysis steps of the data generated. Data filtering was done by SOAPnuke (R. Li et al., 2008) to (1) remove the readings from the sequencing adapters used; (2) remove low-quality readings with a baseline ratio ≤ 15 if the reading is greater than 20% of the reading phase; (3) remove reads where the number of unknown databases detected is greater than 5%. Then, the "clean" readings were stored in the standard FASTQ format. These reads were mapped to the reference genome using HISAT (D. Kim et al., 2015). To detect gene fusions and differentially expressed genes, Ericscript (0.5.5-5) (Benelli et al., 2012) and rMATS (v4.1.1) (Shen et al., 2014) were used, respectively. The Bowtie2 software (Langmead & Salzberg, 2012) was used to align the "clean" readings with the gene set. Gene expression levels were calculated by RSEM (v1.2.28) (B. Li & Dewey, 2011) to obtain quantification in read count, fragment per kilobase per million (FPKM) and number of transcripts per kilobase million (TPM). An analysis of differentially expressed genes (DEG) is also possible with DESeq2 (Love et al., 2014) or DEGseg (L. Wang et al., 2010) or PossionDis (Audic & Claverie, 1997) with the Q-value ≤ 0.05. The bioinformatics analyses were performed on the BGI, Dr. Tom software platform to visualize the data and extract gene expression in TPM.
Assembly: Homo sapiens, NCBI, GCF_000001405.38_GRCh38.p12
Supplementary files format and content: One tab-delimited text file includes FKPMs-TPMs-Readcounts for All samples

growth_protocol: LGG275 cells were seeded to 260,000 cells/wells in 3.5 mL of a proliferation medium in 6-well plates (#140685, ThermoFisher Nunclon) coated with Poly-D-Lysine (25 mg/mL, P7886, Sigma) and laminin (L2020-1MG, Sigma) and placed in an incubator at 37°C in a humid atmosphere with 5% CO2. Cells were cultured in DMEM/F12 (#21331046, Life Technologies) supplemented with L-glutamine (2mM, #25030024, Thermo Fisher), N-2 supplement (100X) (#17502048, Life Technologies), B-27 without vitamin A (50X) (#12587010, Life Technologies, used at 0,5X), heparin (2μg/mL, H3149-100KU, Sigma), EGF (10ng/mL, #Cat AF-100-15-1MG, Peprotech) and FGF2 (10 ng/mL, Cat#100-18B-500UG, Peprotech). This medium also contained antibiotics with ciprofloxacin (10ug/mL), gentamicin (10ug/ml, #11520506, ThermoFisher) and fungin (10μg/mL, Invivogen) to avoid bacterial and fungal contamination.

extract_protocol:
RNA extraction was performed 8 hours after the last treatment using RNEasy micro kit Qiagen for total RNA and dosage by NanoDrop 2000/2000c spectrophotometer to prepare samples at 20 ng/µl with 200 ng minimum
The 21 samples were sent to BGI Genomics-BGISEQ (Hong Kong) to perform sequencing via their DNBSEQTM platform for DNBSEQ stranded mRNA library

treatment_protocol: Right after seeding, the following compounds were added to the medium at 10ng/mL every day for 5 days (1 well of the 6-well plate = 1 treatment) for LGG275 cells : +PBS/BSA 0,1% for control, hOSM (#300-10, Peprotech); hLIF (#300-05, Peprotech); hBMP2 (#120-02C, Peprotech), hBMP4 (#120-05, Peprotech), hIFNβ (#300-02BC, Peprotech), hIFNγ (#300-02, Peprotech). NaOH (Vehicle control for T3) vs T3 (40ng/mL) and DMSO (Vehicle control for AGI5198) vs AGI5198-540 nM were used. "Diff" condition corresponds to medium without EGF and FGF2. "Diff-FBS" condition is medium without EGF and FGF2 + FBS 5%. On Nunclon plastic plates, BSA coating (control for Dll4) vs Dll4 (10µg/mL) were used. On Nunclon plastic plates, +PBS/BSA 0,1% for control, ET1 (10ng/mL; 4nM), ET3 (10ng/mL; 4nM) were used. Different coatings were tested: Nunclon plastic plate (#140685, ThermoFisher Nunclon), with PolyHEMA (free-floating cultures; 192066-25g, Sigma) or PDL/Laminin noted control with is Poly-D-Lysine (25 mg/mL, P7886, Sigma) and laminin (L2020-1MG, Sigma). For Gb4, Nunclon plastic plate (#140685, ThermoFisher Nunclon) versus ET1 (10ng/mL; 4nM) was carried out.

tag: time

value: Vehicle condition DMSO PDL/Lam


title: ET1

description: Library name: ET1

value: Treated ET1_Nunclon


title: 275_alone1

description: Library name: 275_alone1

data_processing:
BGI took care of the quality control of the samples, the construction of the mRNA library, the sequencing of the mRNAs making at least more than 30 million read lengths with 150 paired-end base pairs facilitating the alignment and therefore the reliability of the analysis as well as the verification and analysis steps of the data generated. Data filtering was done by SOAPnuke (R. Li et al., 2008) to (1) remove the readings from the sequencing adapters used; (2) remove low-quality readings with a baseline ratio ≤ 15 if the reading is greater than 20% of the reading phase; (3) remove reads where the number of unknown databases detected is greater than 5%. Then, the "clean" readings were stored in the standard FASTQ format. These reads were mapped to the reference genome using HISAT (D. Kim et al., 2015). To detect gene fusions and differentially expressed genes, Ericscript (0.5.5-5) (Benelli et al., 2012) and rMATS (v4.1.1) (Shen et al., 2014) were used, respectively. The Bowtie2 software (Langmead & Salzberg, 2012) was used to align the "clean" readings with the gene set. Gene expression levels were calculated by RSEM (v1.2.28) (B. Li & Dewey, 2011) to obtain quantification in read count, fragment per kilobase per million (FPKM) and number of transcripts per kilobase million (TPM). An analysis of differentially expressed genes (DEG) is also possible with DESeq2 (Love et al., 2014) or DEGseg (L. Wang et al., 2010) or PossionDis (Audic & Claverie, 1997) with the Q-value ≤ 0.05. The bioinformatics analyses were performed on the BGI, Dr. Tom software platform to visualize the data and extract gene expression in TPM.
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201
Supplementary files format and content: One tab-delimited text file includes TPM for all samples

growth_protocol: LGG275 were infected with GFP lentivirus (#VB200526-1117awv, Vector Builder) and  hCMEC/D3 cells (Human Umbilical Vein Endothelial Cell, Promocell) were infected with a mCherry lentivirus (#VB010000-9485zvg, Vector Builder) and selected by FACS. 1 day prior to the co-cultures, 3,4.105 HCMEC cells were seeded on 0,2% gelatin coated plates (#G2500, Sigma) in Endothelial Cell Basal Medium (#C-22111, Promocell) supplemented with recombinant human EGF (5 ng/ml), recombinant human basic Fibroblast growth factor (10 ng/ml), recombinant human Insulin-like Growth Factor (Long R3 IGF) (20 ng/ml), recombinant human Vascular Endothelial Growth Factor 165 (0,5 ng/ml), Ascorbic Acid (1 µg/ml), Heparin (22.5 µg/ml) and Hydrocortisone (0.2 µg/ml) and fetal calf serum (0.02 ml/ml). 3,0.105 glioma cells were added on top of HCMEC so that co-cultures experiments were performed at a ratio of 1:1,3 (HCMEC: glioma cells LGG275) for 48 hours before FACS isolation of transduced cells GFP+ and mCherry+ cells and subsequent RNA extractions.

extract_protocol:
RNAs were immediately extracted using the Arcturus Picopure RNA kit (Thermo Fisher) and shipped to BGI platform for RNA sequencing.
BGI Genomics-BGISEQ (Poland) to perform sequencing via their DNBSEQTM platform for DNBSEQ stranded mRNA library [DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing]

value: GFP


title: Diff-FBS

description: Library name: Diff-FBS

value: Treated diff+5%FBS PDL/Lam


title: BT237_ET1

description: Library name: BT237_ET1


title: Gb4-ET1

description: Library name: Gb4-ET1


title: Gb4-Ctrl

description: Library name: Gb4-Ctrl


title: Dll4

description: Library name: Dll4

value: Treated DLL4_Nunclon


title: 275_Vhcle_1 (Rep1)

description: Library name: 275_Vhcle_1


title: ET3

description: Library name: ET3

value: Treated ET3_Nunclon


title: Ctrl-BSA

description: Library name: Ctrl-BSA

value: Vehicle condition BSA_Nunclon


title: IFNg

description: Library name: IFNg

value: Treated, hIFNγ PDL/Lam


title: Ctrl-NaOH

description: Library name: Ctrl-NaOH

value: Vehicle condition NaOH PDL/Lam


title: Diff

description: Library name: Diff

value: Treated diff PDL/Lam


title: T3

description: Library name: T3

value: Treated T3 PDL/Lam


title: BMP4

description: Library name: BMP4

value: WT

value: Treated, hBMP4 PDL/Lam


title: BMP2

description: Library name: BMP2

value: 5 days

value: Treated, hBMP2 PDL/Lam


title: IFNb

description: Library name: IFNb

value: diffuse IDH-mutant low-grade astrocytoma cell line

value: Treated, hIFNβ PDL/Lam


title: PolyHEMA

description: Library name: PolyHEMA

value: PolyHEMA


title: Control-Lam

description: Library name: Control-Lam


title: AGI5198

description: Library name: AGI5198

value: Treated AGI5198 PDL/Lam


title: SENCR-BAC-stomach#1

city: Chongqing

first: Qing

middle: Rex

last: Lyu

state: Chongqing

address: #118 Xingguang Avenue

department: Affiliated Chongqing General Hospital

country: China

institute: Chongqing University

description: Library name: SR-KI-stomach1

data_processing:
Raw reads of fastq format were processed using fastp, and the low quality reads were removed to obtain clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each sample.

organism: Mus musculus

source_name: stomach

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's protocol. RNA quality was evaluated using the NanoDrop 2000 spectrophotometer. RNA integrity was assessed using the Agilent 2100 Bioanalyzer.
RNA libraries for RNA-seq were prepared using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer's instructions.

tag: tissue

value: stomach


title: LIF

description: Library name: LIF

value: Treated, hLIF PDL/Lam


title: SENCR-BAC-stomach#2

description: Library name: SR-KI-stomach2


title: 275_ET1_1 (Rep1)

description: Library name: 275_ET1_1

value: Treated ET1-10nM


title: OSM

description: Library name: OSM

value: Treated, hOSM PDL/Lam


title: SENCR-BAC-lung#2

description: Library name: SR-KI-lung2

source_name: lung

value: lung


title: SENCR-BAC-lung#3

description: Library name: SR-KI-lung3


title: SENCR-BAC-liver#3

description: Library name: SR-KI-liver3

source_name: liver

value: liver


title: SENCR-BAC-spleen#2

description: Library name: SR-KI-spleen2

source_name: spleen

value: spleen


title: SENCR-BAC-liver#1

description: Library name: SR-KI-liver1


title: SENCR-BAC-kidney#3

description: Library name: SR-KI-kidney3

source_name: kidney

value: kidney


title: SENCR-BAC-kidney#1

description: Library name: SR-KI-kidney1


title: SENCR-BAC-kidney#2

description: Library name: SR-KI-kidney2


title: SENCR-BAC-liver#2

description: Library name: SR-KI-liver2


title: SENCR-BAC-heart#3

description: Library name: SR-KI-heart3

source_name: heart

value: heart


title: Ctrl-Nunclon

description: Library name: Ctrl-Nunclon

value: WT


title: SENCR-BAC-heart#1

description: Library name: SR-KI-heart1


title: SENCR-BAC-heart#2

description: Library name: SR-KI-heart2


title: SENCR-BAC-brain#3

description: Library name: SR-KI-brain3

source_name: brain

value: brain


title: SENCR-BAC-aorta#2

description: Library name: SR-KI-aorta2

source_name: aorta

value: aorta


title: SENCR-BAC-stomach#3

description: Library name: SR-KI-stomach3


title: SENCR-BAC-spleen#3

description: Library name: SR-KI-spleen3


title: SENCR-BAC-brain#2

description: Library name: SR-KI-brain2


title: SENCR-BAC-brain#1

description: Library name: SR-KI-brain1


title: SENCR-BAC-aorta#3

description: Library name: SR-KI-aorta3


title: SENCR-BAC-aorta#1

description: Library name: SR-KI-aorta1


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ+S3QEL1.2, rep2

city: New York

first: Adam

middle: L.

last: Orr

state: NY

address: 413 East 69th St

department: Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute

country: USA

institute: Weill Cornell Medicine

description: Library name: Sample 23

data_processing:
The libraries were sequenced with paired-end 50 bps on a NovaSeq6000 sequencer. The raw sequencing reads in BCL format were processed through bcl2fastq (v2.20) (Illumina) for FASTQ conversion and demultiplexing.
The adaptors were trimmed with cutadapt (v1.18) (https://cutadapt.readthedocs.io/en/v1.18/), RNA reads were aligned and mapped to the GRCm39 mouse reference genome by STAR (v2.5.2) (https://github.com/alexdobin/STAR), and transcriptome reconstruction was performed by Cufflinks (v2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/).
The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM). Raw read counts per gene were extracted using HTSeq-count (v0.11.2). Gene expression profiles were constructed for differential expression, cluster, and principle component analyses with the DESeq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
For data analysis in the associated manuscript, conditions that were included in both experiments #1 and #2 were combined to increase power. For example, the IL-1ɑ+S3QEL1.2 vs. IL-1ɑ comparison presented was derived from the combined data from experiments #1 and #2.
Assembly: GRCm39
Supplementary files format and content: FPKM values for all samples are uploaded as XLS and XLSX files.

molecule: polyA RNA

source_name: Cortex/Hippocampus

growth_protocol: All cultures were maintained at 37°C in a humidified 5% CO2-containing atmosphere. Astrocytes were grown, maintained, and treated in high-glucose DMEM without glutamine or pyruvate (Corning) and supplemented with 20% heat-inactivated FBS (VWR), 1X GlutaMAX (ThermoFisher), and 1 mM sodium pyruvate (ThermoFisher).

extract_protocol:
Cultured primary cells were rinsed once with ice-cold PBS and collected in freshly prepared extraction buffer consisting of 1% β-mercaptothanol in RLT (Qiagen). Total RNA was extracted using the RNeasy Mini Kit with on-column DNase treatment (Qiagen).
RNA libraries were prepared using Truseq Standard mRNA Sample Prep (Poly A selection) following manufacturer's instructions (Document #1000000040498v00).

treatment_protocol: Astrocytes were treated for 6 hours during a full media change to include one or more of the following reagents: Vehicle (DMSO), 3 µM S3QEL1.2 (WuXi Apptec), 10 µM S1QEL2.2 (Life Chemicals), or 3 ng/mL IL-1α (Sigma). Stimuli and inhibitors were co-applied for entire treatment durations.

value: Cortex/Hippocampus

value: Primary Cells

value: Astrocyte


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ+S1QEL2.2, rep3

description: Library name: Sample 27


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ+S3QEL1.2, rep3

description: Library name: Sample 24


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ, rep3

description: Library name: Sample 21


title: SENCR-BAC-spleen#1

description: Library name: SR-KI-spleen1


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ, rep1

description: Library name: Sample 19


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ+S1QEL2.2, rep2

description: Library name: Sample 26


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, Vehicle, rep2

description: Library name: Sample 14

value: Vehicle


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ+S3QEL1.2, rep1

description: Library name: Sample 22


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, Vehicle, rep3

description: Library name: Sample 15


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ, rep2

description: Library name: Sample 20


title: SENCR-BAC-lung#1

description: Library name: SR-KI-lung1


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, S1QEL2.2, rep3

description: Library name: Sample 18


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, S1QEL2.2, rep2

description: Library name: Sample 17


title: brain cells, post TBI 3 day, injury site

city: Shanghai

first: Xiaoyu

last: Li

address: Dongan Road

institute: Fudan University

description:
Library name: TBI_d3
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw data of scRNA-seq were processed by using Cell Ranger Single-Cell Software Suite (V5.0.0, 10X Genomics) and aligned to GRCm38 (mm10) mouse reference genome by using STAR V2.5.37. For quality control, multiplets and broken (apoptotic) cells were excluded from analysis. Cells with 200 to 5,500 detected genes per cell and less than 5% mitochondrial genes were included for further analysis. Seurat V3.2.0 was used for downstream analysis, including generating tSNE plots, heatmaps, violin plots and ridge plots. Multiple cell-type-specific or enriched marker genes were used to identify different brain cell types as previously described8. Briefly, these genes included, but were not limited to, Skap1 and Nkg7 for T cells; Kcnj8 and Vtn for Pericyte; Pdgfra for Oligodendrocyte progenitor cell (OPC); Mbp, Plp1 and Mog for Oligodendrocyte (OL); Tubb3 and Dcx for Neuron; S100a8, S100a9 and Il1b for Monocyte; P2ry12 and Tmem119 for Microglia; Mrc1 and Ms4a7 for Macrophage; Ccdc153 for Ependymocyte; Cldn5 for Endothelial cell (EC); Ttr for Choroid plexus cell (CPC); Cd79a for B cell; S100b, Sox9, Aldh1l1 and Gfap for Astrocyte.
Assembly: mm10
Supplementary files format and content: tab-separated text file and matrix file

source_name: brain cells

extract_protocol:
In brief, injured cortical tissues were minced and enzymatically dissociated using 8U/ml papain and 125 U/ml DNase I. Tissues were mechanically dissociated by gentle pipetting until no visible chunks were present and then terminated by adding 10% ovomucoid. Cell clusters were removed by filtering through 70μm strainers and debris were discarded using 30% Percoll density gradient centrifugation in choline chloride solution. Cell viability was measured by Cellometer Auto 2000 Automatic Cell Viability Counter system (Nexcelom, USA) and samples with > 85% viability were proceeded to scRNA-seq library preparation. Approximately 5,188~11,934 cells for each sample were loaded according to the instructions of 10X Chromium single-cell platform (Supplemental Figure S1b). The libraries were then purified, quantified and sequenced on an Illumina HiSeq (Illumina, San Diego, CA, USA).
Single-cell suspensions were processed for library preparation using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v3 according to the manufacturer’s instructions (10x Genomics, Pleasanton, CA, USA). Briefly, viable single cells were encapsulated with barcoded gel beads and reverse transcription reagents in nanoliter-scale Gel Bead-In-Emulsions (GEMs) using the Chromium Controller. Within each GEM, cell lysis and barcoded reverse transcription of RNA occurred to generate uniquely labeled cDNA for each cell. After reverse transcription, GEMs were broken, and cDNA was recovered and amplified by PCR. Amplified cDNA was subjected to enzymatic fragmentation, end repair, A-tailing, and adaptor ligation. Fragmented cDNA was then amplified with sample index primers to generate sequencing-ready libraries.  Library quality and concentration were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Libraries were pooled and sequenced on the Illumina HiSeq platform with a paired-end 150 bp configuration to achieve sufficient depth for transcriptome coverage.

value: brain cells


title: brain cells, post TBI 14 day, injury site

description:
Library name: TBI_d14
10x Genomics


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, S1QEL2.2, rep1

description: Library name: Sample 16


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ+S3QEL1.2, rep3

description: Library name: Sample 12


title: brain cells, post TBI 7 day, injury site

description:
Library name: TBI_d7
10x Genomics


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ+S3QEL1.2, rep2

description: Library name: Sample 11


title: brain cells, post TBI 1 day, injury site

description:
Library name: TBI_d1
10x Genomics


title: brain cells, Sham

description:
Library name: Sham
10x Genomics


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ, rep3

description: Library name: Sample 9


title: KMS11 cells, STK17B overexpression REP1

city: Durham

first: Mikhail

last: Nikiforov

state: NC

address: 210 Research Drive, GSRB II Rm. 4020

institute: Duke University

description: Library name: Sample11

data_processing:
The sequencing data, also known as raw reads or raw data, were subjected to quality control (QC) to determine whether the sequencing data were suitable for subsequent analysis. After QC, the clean reads were aligned to the reference sequences. After alignment, the alignment results were subjected to a second QC to evaluate the alignment quality, including alignment rate and distribution of reads on the reference sequences. After that, gene quantification analysis, various analyses based on gene expression levels (such as principal component analysis, correlation analysis, differential gene screening, etc.) were performed. Differential expressed genes between samples were further analyzed for gene ontology (GO) functional enrichment, pathway enrichment, clustering, protein- protein interaction networks, and transcription factors. The complete analysis pipeline is illustrated below:
The raw data obtained from sequencing were filtered using SOAPnuke.
The filtered data, referred to as clean data, were subsequently analyzed, visualized, and mined using Online Multi-Omics Data Mining System.
HISAT [2] (Hierarchical Indexing for Spliced Alignment of Transcripts) is a software used for aligning RNA-seq reads to a reference genome.
Clean data was aligned to the reference gene set using Bowtie2 (v2.3.4.3) [3]. Gene expression quantification was performed using RSEM (v1.3.1) [4] software, and gene expression clustering heatmaps across different samples were generated using pheatmap (v1.0.8) [5]. DESeq2 (v1.4.5) [6] (or DEGseq [7] or PoissonDis [8]) was employed for differential gene detection, with criteria set as Q value ≤ 0.05 or FDR ≤ 0.001. Gene fusion detection was performed using Ericscript (v0.5.5) [10], and alternative splicing and differential alternative splicing were detected using rMATS (V3.2.5)
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201
Supplementary files format and content: txt file including TPM values

source_name: multiple myeloma

extract_protocol:
RNA was extracted using RNeasy Mini Kit. DNBSEQ-mRNA-Seq-oligo dT(also called polyA selection), stranded.
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 cDNA double strands. The synthesized double- stranded 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.

value: multiple myeloma

value: STK17B overexpression

value: no treatment


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, S3QEL1.2, rep3

description: Library name: Sample 6


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ, rep2

description: Library name: Sample 8


title: KMS11 cells, Vector REP1

description: Library name: Sample9


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ+S1QEL2.2, rep1

description: Library name: Sample 25


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ+S3QEL1.2, rep1

description: Library name: Sample 10


title: Experiment 2, Primary mouse astrocyte, 6 hour treatment, Vehicle, rep1

description: Library name: Sample 13


title: KMS11 cells, Vector REP2

description: Library name: Sample10


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, IL-1ɑ, rep1

description: Library name: Sample 7


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, Vehicle, rep3

description: Library name: Sample 3


title: KMS11 cells, sh2 STK17B REP1

description: Library name: Sample5

value: STK17B shRNA


title: KMS11 cells, STK17B inhibitor REP2

description: Library name: Sample8

value: STK17B inhibitor


title: KMS11 cells, sh1 STK17B REP2

description: Library name: Sample4


title: KMS11 cells, STK17B inhibitor REP1

description: Library name: Sample7


title: LA58_39B_KT

city: Stanford

first: Yuning

last: Tang

state: CA

address: 279 Campus Drive, Beckman Center

institute: Stanford University

description: Library name: LA58_39B

library_source: genomic

data_processing:
Tuba-seq Ultra NGS processing scripts convert read counts for each barcode-sgRNA into absolute cell numbers based on spike-in reads. Tumor metrics for each sgRNA, with clonal resolution, are calculated for log-normal mean, tumor number, and total tumor burden. Confidence intervals and p-values are determined using bootstrap resampling. For detailed information on the analysis, please refer to the "Quantification and Statistical Analysis" section in the Methods of the manuscript titled "Functional Mapping of Epigenomic Regulators Uncovers Coordinated Tumor Suppression by the HBO1 and MLL1 Complexes," available at: https://www.biorxiv.org/content/10.1101/2024.08.19.607671v1.
Assembly: sgRNA library sequences is included in the processed data file
Supplementary files format and content: The processed file is in .csv format. It contains the sequence of each sgRNA and the calculated metrics for tumors initiated with each Lenti-U6-sgRNA-Saturation/Cre vector in KT;H11-LSL-Cas9 mice. 'X_percentile_relative' indicates the size of the tumors at the Xth percentile of the tumor size distribution relative to the tumor size at the same percentile of the sgInert tumor size distribution. 'X_percentile_2.5P' and 'X_percentile_97.5P' represent the 95% confidence intervals for the Xth percentile.

molecule: genomic DNA

source_name: Lung

extract_protocol:
The tissues were homogenized in 20 ml lysis buffer (100mM NaCl, 20mM Tris, 10mM EDTA, 0.5% SDS) with 200 μl of 20 mg/ml Proteinase K (Life Technologies, AM2544). Homogenized tissues were incubated at 55°C overnight.  Genomic DNA was extracted with phenol-chloroform (ThermoFisher Scientific, 15593049) or the Qiagen Puregene Kit (Qiagen, 158063) and precipitated with ethanol. Plasmid DNA extraction was performed following QIAGEN Plasmid Plus Midi Kit instructions
Custom Tuba-seqUltra library construction protocol. For detailed methodology, please refer to the "Tuba-seqUltra library preparation" section in the Methods of the manuscript "Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes," available at: https://www.biorxiv.org/content/10.1101/2024.08.19.607671v1

value: Lung

value: Total lung

value: KT


title: LA58_36_KT

description: Library name: LA58_36


title: LA58_38_KT

description: Library name: LA58_38


title: KMS11 cells, sh2 STK17B REP2

description: Library name: Sample6


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, Vehicle, rep1

description: Library name: Sample 1


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, Vehicle, rep2

description: Library name: Sample 2


title: KMS11 cells, sh1 STK17B REP1

description: Library name: Sample3


title: LA58_34_KT

description: Library name: LA58_34


title: P62_enrichment

city: Shenzhen

first: yuanfang

last: Liu

state: Guangdong

address: Zhenyuan Road

institute: The Seventh Affiliated Hospital of Sun Yat-sen University (Shenzhen)

description: Library name: Sample21

data_processing:
Remove the low-quality sequences and adapters (trim-galore (v.0.6.10))
Align with the reference genome (HISAT2 (v.2.2.1))
File format conversion and sorting after align (samtools (v.1.21))
Remove PCR duplication (picard (v.3.3.0))
peak-calling (Macs2 (v.2.2.9.1))
Assembly: GCA_000001405.28
Supplementary files format and content: The .bw format includes quantified data used to draw conclusions for this study.

source_name: paracancerous

extract_protocol:
30 μg genomic DNA extracted from NCM460 or HCT116 cell lines was fragmented to about 250 bp by sonication, and then mixed with 100 mM of Azide-PEG3-Amino (2 μL) and 25 mM of K2IrBr6 (2 μL) in NaPi buffer (100 mM, pH 8.0) in a 50 μL reaction system for 30 min at 37 °C. The reaction was terminated by adding 300 μL of ice-ethanol, and then purified using MolPure®PCR Purification Kit (Yesean) to obtain the azide-modified cytogenomic DNA. Next, the obtained azide-modified cell genomic DNA was mixed with 0.01 mg of DBCO-IgG in a 100 μL reaction system at 37 ℃ for 2 h. After the reaction was completed, the IgG-coupled DNA product to be enriched was purified by magnetic bead purification and further enriched using protein G magnetic beads (New England Biolabs). In the enrichment process, 10 μL of magnetic beads were washed three times with 500 μL of binding buffer (0.1 M sodium phosphate buffer, pH 8.0). Then 1 μg of fragmented λDNA genome was added and pre-incubated for 1 h. Later, the DNA to be enriched was added to the magnetic beads and incubated at 37 ℃ for 30 min. After that, the beads were washed three times with 500 μL of binding buffer. Next, 50 μL of enzyme-free water was added to the beads for resuspension, and 1 μL of Proteinase K (40 mg/mL) was added and incubated at 55 oC for 1 h. The supernatant was aspirated and purified by the MolPure®PCR Purification Kit.
The enriched nucleic acid product was subjected to end repair, adding A-tails, adapter ligation and PCR library amplification in accordance with conventional methods, and then the prepared cell genome libraries were used for subsequent sequencing analysis.

value: paracancerous

tag: disease state

value: colon cancer


title: KMS11 cells, shControl REP1

description: Library name: Sample1

value: WT


title: KMS11 cells, shControl REP2

description: Library name: Sample2


title: LA58_37_KT

description: Library name: LA58_37


title: T62_unenrichment

description: Library name: Sample24

source_name: cancer tissue from colon cancer

value: cancer tissue from colon cancer


title: LA58_31_KTC

description: Library name: LA58_31

value: KTC


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, S3QEL1.2, rep1

description: Library name: Sample 4

value: Cortex/Hippocampus

value: Primary Cells


title: P62_unenrichment

description: Library name: Sample22


title: Experiment 1, Primary mouse astrocyte, 6 hour treatment, S3QEL1.2, rep2

description: Library name: Sample 5

value: Astrocyte


title: LA58_29_KTC

description: Library name: LA58_29


title: LA58_32_KTC

description: Library name: LA58_32


title: LA58_33_KTC

description: Library name: LA58_33


title: A1849R

city: Ann Arbor

first: Christina

middle: Vadala

last: Angeles

state: MI

address: 1500 E Medical Center Drive

department: Surgery

institute: University of Michigan

description:
Library name: A1849R
1 Patient Tumor Sample

data_processing:
Fastq, raw reads, files were processed through fastp software. Reads were aligned to the reference genome (GRCh38) using Hisat2 v2.05. featureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Assembly: GRCh38
Supplementary files format and content: raw count matrix

source_name: Patient Tumor Sample

extract_protocol:
Patient tumor and normal fat samples were stored in liquid nitrogen or RNAlater stablization solution until extraction. 30 mg of frozen tissue was dissociated using the BeadBug Homogenizer (Southern Labware, D1030). RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen #80204). RNA concentrations were determined using the NanoDrop 2000 (Thermo Fisher Scientific). Messenger RNA was purified from total RNA using poly-T-oligo-attached magnetic beads.
Library construction was performed and completed by Novogene

value: Patient Tumor Sample

tag: condition

value: DDLPS


title: T62_enrichment

description: Library name: Sample23


title: T3_unenrichment

description: Library name: Sample18


title: LA58_28_KTC

description: Library name: LA58_28


title: A1267R

description:
Library name: A1267R
1 Patient Tumor Sample

value: WDLPS


title: P3_enrichment

description: Library name: Sample15


title: A1736R

description:
Library name: A1736R
1 Patient Tumor Sample


title: P3_unenrichment

description: Library name: Sample16


title: A1844R

description:
Library name: A1844R
1 Patient Normal Fat Sample

source_name: Patient Normal Fat Sample

value: Patient Normal Fat Sample

value: Normal Fat


title: LA58_26_KTC

description: Library name: LA58_26


title: LA58_27_KTC

description: Library name: LA58_27


title: LA58_25B_KTC

description: Library name: LA58_25B


title: A1292R

description:
Library name: A1292R
1 Patient Tumor Sample


title: A1675R

description:
Library name: A1675R
1 Patient Normal Fat Sample


title: N3_unenrichment

description: Library name: Sample14

source_name: healthy

value: healthy


title: A1171R

description:
Library name: A1171R
1 Patient Tumor Sample


title: N62_unenrichment

description: Library name: Sample20


title: LA58_24_KTC

description: Library name: LA58_24

value: Lung


title: K7_plib

description: Library name: Kat7_epistasis_plasmids

library_source: other

data_processing:
Custom Tuba-seqUltra library construction protocol. For detailed methodology, please refer to the "Quantification and statistical analysis" section in the Methods of the manuscript "Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes," available at: https://www.biorxiv.org/content/10.1101/2024.08.19.607671v1
Assembly: sgRNA library sequence
Supplementary files format and content: .csv

molecule: other

organism: Escherichia coli


title: A1755R

description:
Library name: A1755R
1 Patient Tumor Sample


title: N62_enrichment

description: Library name: Sample19


title: A1284R

description:
Library name: A1284R
1 Patient Tumor Sample


title: LA58_23B_KTC

description: Library name: LA58_23B

value: Total lung


title: A1330R

description:
Library name: A1330R
1 Patient Tumor Sample


title: A1348R

description:
Library name: A1348R
1 Patient Tumor Sample


title: A1389R

description:
Library name: A1389R
1 Patient Tumor Sample


title: N3_enrichment

description: Library name: Sample13


title: A1694R

description:
Library name: A1694R
1 Patient Tumor Sample


title: NCM460_unenrichment

description: Library name: Sample12


title: NCM460_enrichment

description: Library name: Sample11


title: A1707R

description:
Library name: A1707R
1 Patient Normal Fat Sample


title: T3_enrichment

description: Library name: Sample17


title: A1131R

description:
Library name: A1131R
1 Patient Tumor Sample


title: LA58_21_KTC

description: Library name: LA58_21


title: HCT116_unenrichment

description: Library name: Sample10


title: A1679R

description:
Library name: A1679R
1 Patient Tumor Sample


title: A1576R

description:
Library name: A1576R
1 Patient Normal Fat Sample


title: A1583R

description:
Library name: A1583R
1 Patient Tumor Sample


title: LA58_19_KTC

description: Library name: LA58_19


title: LA58_18_KTC

description: Library name: LA58_18


title: A1168R

description:
Library name: A1168R
1 Patient Normal Fat Sample


title: HEK293T cells, IP M4 3

city: Newark

first: Chun-Chieh (Jack)

last: Hsu

state: New Jersey

address: 205 S. Orange Avenue

department: Department of Medicine

institute: Rutgers University, New Jersey Medical School

description: Library name: Sample 18

data_processing:
FastQC v0.11.9 was used for read-quality control.
Adapters were removed with cutadapt v4.6 (minimum read length: 16 nt).
Alternative splicing was quantified with VAST-TOOLS v2.5.1 against VastDB hg38 (Hs2). For AS events, PSI was computed per replicate. Differential events were called with vast-tools compare using --min_dPSI 15 --min_range 5 (|ΔPSI| ≥ 15 and no-overlap ≥ 5).
For intron retention, PIR was computed per replicate from .IR2 files using a VAST-like coverage rule: (I5 ≥ 10 & I3 ≥ 5) or (I5 ≥ 5 & I3 ≥ 10), and EE ≥ 10; ≥2/3 replicates with coverage were required per condition.
Assembly: hg38
Supplementary files format and content: Tab-delimited TSV tables include per-event PSI/PIR by replicate, condition means, ΔPSI/ΔPIR, GROUP, and annotations. Event IDs follow VastDB naming.

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in Dulbecco’s modified Eagle’s media supplemented with 10% fetal bovine serum and maintained iin humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were harvested and washed with DPBS buffer. Total RNA was extracted using TRIzol reagent (Thermo Scientific) and subsequently purified with Direct-zol RNA MiniPrep (Zymo Research). mRNA was enriched by two rounds of poly(A) purification using oligo(dT)25 magnetic beads (New England Biolabs). RNA concentrations were measured by Nanodrop.
RNA-Seq libraries were prepared using NEBNext Ultra II RNA Library Prep Kit (New England Biolabs).

treatment_protocol:
For DNA plasmid transfection, cells were plated 24 h before transfection and transfected using Lipofectamine 2000 according to the manufacturer’s instructions.
IP RNA samples were immunoprecipitated using m7G antibody overnight

value: HEK293T cells

value: Embrionic kidney cells

value: M4 -protein overexpression

tag: sample processing

value: m7G-immunoprecipitated RNA


title: HCT116_enrichment

description: Library name: Sample9

value: WT


title: A1116R

description:
Library name: A1116R
1 Patient Normal Fat Sample


title: A1165R

description:
Library name: A1165R
1 Patient Tumor Sample


title: HEK293T cells, IP M4 1

description: Library name: Sample 16


title: HEK293T cells, IP M4 2

description: Library name: Sample 17


title: LA58_22B_KTC

description: Library name: LA58_22B

value: KTC


title: A1028R

description:
Library name: A1028R
1 Patient Tumor Sample


title: A1134R

description:
Library name: A1134R
1 Patient Normal Fat Sample


title: HEK293T cells, INPUT M4 3

description: Library name: Sample 15

value: poly (A) -enriched RNA


title: 02_T3BKO2

city: Bethesda

first: Anjali

last: Dhall

state: MD

address: 37 Convent Drive

department: DTB

institute: NCI

description:
Library name: Sample4
dual index (60x8x8x60)

data_processing:
BAM files were generated using BWA aligner and picrad tool used to filter and remove duplicate reads.
MACS2 algorithm was used for peak calling
Assembly: mm39
Supplementary files format and content: BigWig file format of R-loop CUT& Tag seq
Library strategy: CUT&Tag

source_name: Total splenocytes

growth_protocol: Fresh murine primary splenocytes

extract_protocol:
The Cut and Tag protocol was carried out following Zhang et al (80). Briefly, 2 ml 2XCB (0.1 M Tris pH 8.0; 0.3 M NaCl; 0.1% Triton X-100; 25% Glycerol), 2 ml pA-Tn5 tranposome (at 4 mM), and 2 ml S9.6 antibody were mixed in a microcentrifuge tube (mixture A) and kept on ice. One million cells were harvested and transferred to a clean 1.5 mL tube. Cells were washed once with 1 ml of PBS, suspend in 1 mL of 1X CB, and incubated on ice for 10 min. The cells were spun down, suspend in 1 mL of 1X CB. An aliquot of 50 ml was added to mixture A, incubated at room temperature for 60 min with rotation. 500 ml of wash buffer (50 mM Tris pH 8.0; 150 mM NaCl; 0.05% Triton X-100) was added to each tube, centrifuged. The pellets were washed two more time with 500 ml of wash buffer and then suspended in 100 ml of wash buffer. 1 ml of 1 M MgCl2 was added to start the transposome reaction, incubated at 37°C for 60 min. 4 ml of 0.5 M EDTA, 2 ml of 10% SDS and 1 ml of 20 mg/mL Proteinase K were added, and incubated at 55 °C for 60 min. The DNA was purified with ChIP DNA clean & concentrator (Zymo Research). Library was constructed following manufacture’s protocol (Illumina) and sequenced on Next-seq.
The kits used for the library prep were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB, E6440) were used with 13 cycles of PCR amplification. The final 750 pM library was sequenced paired-end with dual index (60x8x8x60) using the Illumina NextSeq2000 P2 Reagents (100cycles) on the Illumina NextSeq2000 instrument.

value: spleen

value: Murine total splenocyes


title: 01_T3BKO1

description:
Library name: Sample3
dual index (60x8x8x60)


title: LA58_16B_KTC

description: Library name: LA58_16B


title: LA58_15B_KTC

description: Library name: LA58_15B


title: LA58_14B_KTC

description: Library name: LA58_14B


title: HEK293T cells, INPUT M4 2

description: Library name: Sample 14


title: A1031R

description:
Library name: A1031R
1 Patient Normal Fat Sample


title: LA58_20_KTC

description: Library name: LA58_20


title: YD14, Day 14 post-resection, Wild Type, young skeletally immature mice, pool of 2 rib calluses, scRNAseq

first: Olivier

last: Duverger

address: 30 Convent Drive - Bldg 30 - Room 202

institute: National Institute of Dental and Craniofacial Research

description: 10x Genomics

data_processing:
Reads were mapped using the 10X Genomics mm10-2020-A reference transcriptome
Libraries were processed using Cell Ranger version 6.0.1
Secondary analysis was performed using Seurat's R package
Assembly: mm10
Supplementary files format and content: Cellranger filtered feature barcode matrix in HDF5 format
Supplementary files format and content: Cellranger raw feature barcode matrix in HDF5 format

source_name: Rib callus at 14 days post-resection

extract_protocol:
Bone repair calluses were dissected from skeletally immature and mature mice at 5 and 14 days post large-scale rib resection, minced into ~1mm sizes, and enzymatically digested at 37 °C using collagenase type XI (0.05%) and dispase (0.06 units/mL) for 60 min and 40 min, respectively, followed by gently pipetting up and down 10 – 15 times. Enzyme was inhibited with 20% FBS, and cells were filtered through 70 µm strainers and re-suspended in PBS supplemented with 0.04% high-quality bovine serum albumin at 1000 cells/µL for single-cell capture. Subsequently, single cell suspensions of each group were pooled (n=2) and loaded onto a chromium chip (10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 3′ kit, 10X Genomics) to generate cDNA and library according to the manufacturer’s protocol.
Single-cell RNA sequencing was performed using 10X Genomics Chromium instruments.

value: Rib callus at 14 days post-resection

tag: age

value: 7 weeks

value: Wild Type


title: HEK293T cells, INPUT M4 1

description: Library name: Sample 13


title: YD5, Day 5 post-resection, Wild Type, young skeletally immature mice, pool of 2 rib calluses, scRNAseq

description: 10x Genomics

source_name: Rib callus at 5 days post-resection

value: Rib callus at 5 days post-resection


title: OD14b, Day 14 post-resection, Wild Type, old skeletally mature mice, pool of 2 rib calluses, scRNAseq

description: 10x Genomics

value: 12 months


title: LA58_13B_KTC

description: Library name: LA58_13B


title: OD5b, Day 5 post-resection, Wild Type, old skeletally mature mice, pool of 2 rib calluses, scRNAseq

description: 10x Genomics


title: HEK293T cells, IP NSP14 3

description:
Library name: Sample 12
AS_events_IP_all_samples.tsv: Nsp14_3

value: NSP14-protein overexpression


title: LA58_12_KTC

description: Library name: LA58_12

value: Lung


title: LA58_17_KTC

description: Library name: LA58_17

value: Total lung


title: mESC_H3K27me3_B2T2S1

city: Copenhagen

first: Mariia

last: Metelova

address: Blegdamsvej 3b

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: Copenhagen University

data_processing:
Micro-C-ChIP paired-end reads were processed with the distiller pipeline (https://github.com/mirnylab/distiller-nf). Briefly, reads were mapped to the reference genome (mm10 and hg38 as mouse and human reference assemblies, respectively) via bwa (v0.7.17) mem with flags –SP.
Alignments were parsed and .pairs files were generated using the pairtools package  (v0.3.0). PCR/optical duplicates were filtered with pairtools dedup function with “-max-mismatch 1”.
Valid pairs with high mapping quality scores on both sides (MAPQ > 30) were aggregated into binned matrices of Micro-C-ChIP interactions using the cooler package (v0.9.2) into multiresolution cooler (mcool) files (100 bp, 200 bp, 500 bp, 1 kb, 2.5 kb, 5 kb, 10 kb, 25 kb, 50 kb, 100 kb, 500 kb, 1 Mb).
Replicates for each condition (histone mark and cell type) were merged after confirming the reproducibility by visual inspection of individual mcool files and calculating reproducibility scores by HiCRep (v0.2.6) for contact maps at 10 kb resolution.
Assembly: mm10, hg38
Supplementary files format and content: mcool
Library strategy: Micro-C-ChIP

growth_protocol: mESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with 15% FBS, home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA. hTERT-RPE1 cells (ATCC, #CRL-4000) were grown in DMEM-GlutaMAX-pyruvate containing 10% FBS and 1× penicillin/streptomycin at 37°C with 5% CO2

extract_protocol:
Nuclei derived from dually crosslinked cells (FA+EGS) were MNase-digested, the DNA ends were biotin-labeled, and proximity ligated. Ligated chromatin was sonicated to solubilize the heavily crosslinked chromatin. Ligated solubilized fragments were immunoprecipitated against H3K4me3 and H3K27me3 histone marks followed by on-bead library preparation and sequencing.
Sequencing libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: Samples were untreated.

value: Embryonic stem cells

value: wildtype

tag: antibody

value: Anti-H3K27me3 (Cell Signaling Technology #9733s)


title: mESC_H3K27me3_B2T1S1


title: LA58_11_KTC

description: Library name: LA58_11


title: mESC_H3K4me3_B2T1S1

value: Anti-H3K4me3 (Cell Signaling Technology #9751S)


title: HEK293T cells, IP NSP14 2

description:
Library name: Sample 11
AS_events_IP_all_samples.tsv: Nsp14_2

value: HEK293T cells

value: Embrionic kidney cells

value: WT

value: m7G-immunoprecipitated RNA


title: mESC_H3K27me3_B1T1S1


title: HEK293T cells, INPUT NSP14 3

description:
Library name: Sample 9
Column name in AS_events_INPUT_all_samples.tsv: Nsp14_3

value: poly (A) -enriched RNA


title: LA58_10_KTC

description: Library name: LA58_10

value: KTC


title: HEK293T cells, INPUT NSP14 2

description:
Library name: Sample 8
Column name in AS_events_INPUT_all_samples.tsv: Nsp14_2


title: LA58_9C_KTC

description: Library name: LA58_9C


title: mESC_H3K4me3_B1T1S1


title: 01_WT1

description:
Library name: Sample1
dual index (60x8x8x60)

value: spleen

value: Murine total splenocyes

value: Wild-type


title: HEK293T cells, IP NSP14 1

description:
Library name: Sample 10
AS_events_IP_all_samples.tsv: Nsp14_1


title: MC-ChIP_HCT116_H3K4me3_UT

description:
Library name: Sample5
merged replicates

data_processing:
Micro-C-ChIP paired-end reads were processed with the distiller pipeline (https://github.com/mirnylab/distiller-nf). Briefly, reads were mapped to the reference genome (mm10 and hg38 as mouse and human reference assemblies, respectively) via bwa (v0.7.17) mem with flags –SP.
Alignments were parsed and .pairs files were generated using the pairtools package  (v0.3.0). PCR/optical duplicates were filtered with pairtools dedup function with “-max-mismatch 1”.
Valid pairs with high mapping quality scores on both sides (MAPQ > 30) were aggregated into binned matrices of Micro-C-ChIP interactions using the cooler package (v0.9.2) into multiresolution cooler (mcool) files (100 bp, 200 bp, 500 bp, 1 kb, 2.5 kb, 5 kb, 10 kb, 25 kb, 50 kb, 100 kb, 500 kb, 1 Mb).
Replicates for each condition (histone mark and cell type) were merged after confirming the reproducibility by visual inspection of individual mcool files and calculating reproducibility scores by HiCRep (v0.2.6) for contact maps at 10 kb resolution.
Assembly: mm10, hg38
Supplementary files format and content: mcool

growth_protocol: mESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with 15% FBS, home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA. hTERT-RPE1 cells (ATCC, #CRL-4000) were grown in DMEM-GlutaMAX-pyruvate containing 10% FBS and 1× penicillin/streptomycin at 37°C with 5% CO2. Human HCT-116-RAD21-mAID-mClover cells were cultured in McCoy’s 5A medium (Gibco #16600082) supplemented with 10% FBS, 100μg/ml Hygromycin (Gibco #10687010) and 100μg/ml Geneticin (Gibco #10131027) at 37 °C with 5% CO2.

treatment_protocol: To induce degradation of the AID-tagged RAD21, cells were treated with 500μM indole-3-acetic acid (IAA) (Sigma Aldrich #I3750-5G-A) for 6 hours.

value: HCT-116 RAD21mAID-mClover

value: untreated

value: Anti-H3K4me3 (Cell Signaling Technology )


title: RPE1_H3K27me3_B2T1S1

value: hTERT-immortalized primary retinal epithelial cells

value: Anti-H3K27me3 (Cell Signaling Technology 9733s)


title: HEK293T cells, INPUT NSP14 1

description:
Library name: Sample 7
Column name in AS_events_INPUT_all_samples.tsv: Nsp14_1

value: NSP14-protein overexpression


title: RPE1_H3K27me3_B1T1S1

value: wildtype


title: RPE1_H3K4me3_B2T1S1

value: Anti-H3K4me3 (Cell Signaling Technology 9751S)


title: LA58_7B_KTC

description: Library name: LA58_7B

value: Lung

value: Total lung


title: LA58_8B_KTC

description: Library name: LA58_8B


title: HEK293T cells, IP Control 3

description:
Library name: Sample 6
AS_events_IP_all_samples.tsv: Ctrl_3

value: HEK293T cells

value: Embrionic kidney cells

value: WT

value: Control


title: LA58_5B_KTC

description: Library name: LA58_5B

value: KTC


title: RPE1_H3K4me3_B1T1S1


title: HEK293T cells, IP Control 1

description:
Library name: Sample 4
AS_events_IP_all_samples.tsv: Ctrl_1

value: m7G-immunoprecipitated RNA


title: T47DS_IgG_R5020_rep1

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

description: Library name: Sample_10

data_processing:
Quality of the reads was assessed using fastqc. Reads were trimmed with bbmap bbdud to remove adapters and poly [AT], [G] and [C] repeat sequences. Reads were aligned to the hg38 genome with bowtie273 with the options –local –very-sensitive-local –no-unal –no-mixed -no-discordant –phred33 –dovetail -I 0 -X 500. Samtools suite was used to remove duplicate and incorrectly paired reads. Bedtools was used to remove reads mapped to the CUT&RUN hg38 suspect list from bam files. Bedgraphs were created using Bedtools genomecov on pair-end mode. Peaks were called on merged replicate files using MACS2 with the options -f BAMPE and -p 1e-3 against the IgG control for narrowPeaks.
Assembly: Hg38
Supplementary files format and content: Bedgraph, Narrowpeak
Library strategy: CUT&Run

growth_protocol: Human T47DS breast cancer cells were routinely cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing GlutaMAX, supplemented with 10% Fetal Bovine Serum (FBS). Cells were split 1:10 every 3-4 days and routinely tested for mycoplasma.

extract_protocol:
CUT&RUN LoV-U was performed as described in Zambanini et al, with the following modifications. Approximately 500,000 T47DS cells per sample were harvested using 0.25% trypsin, and cells were washed three times in nuclear extraction buffer (20 mM HEPES-KOH (pH 8.2), 10 mM KCl, 0.5 mM spermidine, 0.05% IGEPAL, 20% glycerol, and Roche Complete Protease Inhibitor EDTA-Free) to isolate nuclei. Nucleic pellets were flash-frozen in an isopropyl chamber and stored at –80 °C until further processing. Nuclei were thawed, washed once in nuclear extraction buffer and subsequently bound to equilibrated magnetic ConA agarose beads. Following incubation, nuclei-bead complexes were washed for 5 minutes in wash buffer (20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, and Roche Complete Protease Inhibitor EDTA-Free, 0.025% digitonin) supplemented with 2 mM EDTA, and then transferred to PCR tubes. Antibodies were added to the wash buffer and incubated overnight at 4 °C on a rotator. The next day, samples were washed five times with wash buffer, then resuspended in pAG-MN buffer (wash buffer containing 120 ng/sample pAG-MN) and incubated for 30 minutes at 4 °C on a rotator. Following another five washes, digestion was initiated by resuspending the beads in wash buffer supplemented with 2 mM CaCl₂ and incubated at room temperature for 5 minutes, followed by an additional 25 minutes at 4 °C. The reaction was stopped by adding 250 mM EDTA/EGTA mix. Fragment release was initiated by the addition of 5 M NaCl and incubation at 37 °C for 30 minutes. The supernatant was collected, and beads were subsequently resuspended in 1× Urea buffer (100 mM NaCl, 2 mM EDTA, 2 mM EGTA, 0.5% IGEPAL, 8.5 M urea) for a second release step. After 30 minutes at room temperature, the urea release was combined with the initial supernatant. Samples were treated with SDS and proteinase K, followed by phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation.
Library preparation was done using the KAPA Hyper Prep Kit for Illumina sequencing following the manufacturer's guidelines with modifications. 0.4× volume reactions were used for End repair and A-tailing steps, starting with 20 μl CUT&RUN DNA. The thermocycler conditions were 12°C for 15 min, 37°C for 15 min and 58°C for 25 min. Adapter ligation was also performed in 0.4× volume reactions. KAPA Dual Indexed adapters were used at 0.15 μM. A DNA cleanup was performed after ligation with Mag-Bind TotalPure NGS beads at 1.2× the sample volume, and DNA was resuspended in 10 mM Tris–HCl pH 7.5. Library amplification steps were performed in 0.5× volume reactions. The cycling conditions were: 45 sec initial denaturation at 98°C, 15 s denaturation at 98°C, 10 s annealing/elongation at 60°C, 1 min final extension at 72°C, hold at 4°C, for a total of 13 cycles. A post-amplification DNA purification was performed with beads at 1.2× sample volume. Libraries were then size-selected using the E-Gel EX 2% agarose gel and the E-Gel Power Snap Electrophoresis System. Run time was set to 10 min and DNA between 150 and 500 bp was excised from the gel and purified using the QIAquick Gel Extraction Kit according to the manufacturer's instructions. Libraries were quantified using Qubit  and the high sensitivity DNA kit. Libraries were pooled according to nM and sequenced with 36 bp pair-end reads on the NextSeq 550 using the Illumina NextSeq 500/550 High Output Kit v2.5 (75 cycles). Target depth was 5–10 million reads per sample.

treatment_protocol: When treated, T47DS cells were cultured in DMEM containing GlutaMAX, supplemented with 5% Charcoal Stripped Fetal Bovine Serum  for 24 hours, followed by stimulation with 1 nM R5020 for 4 hours, again in stripped-serum conditions.

value: Epithelial breast cancer

value: 1nM R5020 for 4h

tag: cut&run antibody

value: rabbit IgG 1:100, Invitrogen, #100500C)


title: LA58_4B_KTC

description: Library name: LA58_4B


title: HEK293T cells, IP Control 2

description:
Library name: Sample 5
AS_events_IP_all_samples.tsv: Ctrl_2


title: T47DS_GRHL2_R5020_rep1

description:
Library name: Sample_8
GRHL2_R5020_MACS2_p001_peaks.narrowPeak

value: anti-GRHL2 (1:100, Sigma-Aldrich, #HPA004820)


title: T47DS_PR_R5020_rep2

description:
Library name: Sample_7
PR_R5020_MACS2_p001_peaks.narrowPeak

value: anti-PR (1:100, Cell Signaling, #8757S)


title: T47DS_GRHL2_R5020_rep2

description:
Library name: Sample_9
GRHL2_R5020_MACS2_p001_peaks.narrowPeak


title: T47DS_PR_R5020_rep1

description:
Library name: Sample_6
PR_R5020_MACS2_p001_peaks.narrowPeak


title: MC-ChIP_HCT116_H3K4me3_IAA

description:
Library name: Sample6
merged replicates

value: HCT-116 RAD21mAID-mClover

value: IAA-treated


title: T47DS_IgG_non-treated_rep1

description: Library name: Sample_5

value: non-treated


title: LA58_3B_KTC

description: Library name: LA58_3B


title: HEK293T cells, INPUT Control 3

description:
Library name: Sample 3
Column name in AS_events_INPUT_all_samples.tsv: Ctrl_3

value: poly (A) -enriched RNA


title: LA58_2B_KTC

description: Library name: LA58_2B

value: Lung


title: T47DS_PR_non-treated_rep2

description:
Library name: Sample_2
PR_untreated_MACS2_p001_peaks.narrowPeak


title: T47DS_GRHL2_non-treated_rep2

description:
Library name: Sample_4
GRHL2_untreated_MACS2_p001_peaks.narrowPeak


title: T47DS_GRHL2_non-treated_rep1

description:
Library name: Sample_3
GRHL2_untreated_MACS2_p001_peaks.narrowPeak


title: HEK293T cells, INPUT Control 2

description:
Library name: Sample 2
Column name in AS_events_INPUT_all_samples.tsv: Ctrl_2


title: T47DS_PR_non-treated_rep1

description:
Library name: Sample_1
PR_untreated_MACS2_p001_peaks.narrowPeak


title: LA58_1B_KTC

description: Library name: LA58_1B

value: Total lung


title: HEK293T cells, INPUT Control 1

description:
Library name: Sample 1
Column name in AS_events_INPUT_all_samples.tsv: Ctrl_1

value: HEK293T cells


title: 02_WT2

description:
Library name: Sample2
dual index (60x8x8x60)

value: spleen

value: Murine total splenocyes

value: Wild-type


title: FACS sorted eYFP+ EECs from P12 mSI, plate IGB-AA-s025

city: ILLKIRCH

first: Adèle

last: DE ARCANGELIS

address: 1 rue Laurent Fries

department: Development & Stem Cells

institute: IGBMC, CNRS UMR 7104, Inserm U 1258

description:
Library name: mSI_P12_IGB-AA-s025
SORT-seq
adata_P12.h5ad
adata_3stages.h5ad
adata_3stages_pt.h5ad

data_processing:
Demultiplexing, alignment and quantification were performed by Single Cell Discoveries (Utrecht, The Netherlands, https://www.scdiscoveries.com), using scRNAseq analysis  based on Seurat v3.1. For all the additional analyses we carried out, we used the transcript count matrix and the python-based Scanpy API (Wolf et al., 2018).
Assembly: For mouse samples: mm10
Assembly: For HIO and tHIO samples: GRCh38
Supplementary files format and content: Annotated data matrix (adata) objects saved in h5ad-file format are provided. The file contains the preprocessed, normalized and annotated count data of all experiments. Mouse data : adata_e15.h5ad;  adata_e18.h5ad;  adata_P12.h5ad -> adata for each individual stage (E15.5; E18.5; P12 respectively);  adata_3stages.h5ad -> adata including the integration of all 3 stages; adata_3stages_pt.h5ad -> adata including pseudotime analysis of all 3 stages. HIOs data : HIOs.h5ad -> adata for HIOs tHIOs data : tHIOs.h5ad -> adata including all tHIO intestinal epithelial cells (Venus+ EECs and Venus- non EECs) ; tHIOs_ec.h5ad -> adata including only Venus+ EECs ; human_pre-processed.h5ad -> adata including data on human EECs from the study of  Elmentaite et al., 2021; integration_human_thios_scVI.h5ad -> adata integrating the human EECs data from the study of Elmentaite et al, 2021 and the Venus+ EECs data from tHIOs.

source_name: Small Intestine

growth_protocol: Mouse study: Heterozygous Neurog3eYFP/+ mice were collected at embryonic day E15.5 (n=18 embryos from 3 litters) and E18.5 (n=27 embryos from 3 litters), and 12 days after birth (P12) (n=7 pups from 1 litter). Single cells were isolated from the whole small intestine either directly for stages E15.5 and E18.5, or by first separating the epithelial cells  from the rest of the intestine tissue at P12 (Piccand et al., 2019). Human study: HIOs derived from NEUROG3-HA-P2A-Venus hiPSCs were generated using STEMdiff™ Intestinal Organoid Kit (STEMCELL™ Technologies), according to manufacturer’s protocol with some modifications. Spheroids were collected 2-3 days after exposure to MHG (mid-/hindgut) medium, and embedded in Matrigel domes (growth factor reduced-phenol red free Matrigel; Corning) to allow their 3D growth, in presence of STEMdiff™ Intestinal Organoid Growth Medium (OGM). Organoids were split every 10-14 days and embedded in new Matrigel domes. Medium was changed every 3-4 days. HIOs were maintained in 3D culture for 31-42 days. For the HIOs that were subsequently transplanted (tHIOs) into immunocompromised NSG mice, the OGM medium was replaced by a medium containing only EGF (Advanced DMEM/F-12, HEPES 10 mM, GlutaMAX 2 mM, penicillin/streptomycin 100 U/mL, supplement B27 1X, supplement N2 1X (all from Gibco™), human recombinant EGF 50 ng/mL (PeproTech®) in order to promote the development of mesenchyme-rich HIOs, essential to ensure good engraftment and growth of the transplant (Múnera et al., 2017; Watson et al., 2014).

extract_protocol:
Isolation of mouse EECs: Mouse intestinal samples were digested into single cells for 30 to 40 min at 37°C in TrypLETM Express with vigorous up and downs shakings each 5 min. The cells were centrifuged twice at 900rpm, 5min, 4°C in Advanced DMEM, HEPES 10mM, fetal calf serum (FCS) 10%. For the P12 small intestine, an additional filtering step, onto a 70µm cell strainer, was performed before centrifugation. Cells were resuspended in Advanced DMEM F12, HEPES 10mM, FCS 5%, Y-27632 10µM, filtered through a 50µm cell strainer and sorted with a FACS Aria Fusion II (BD) in SORT-seq 384-well cell-capture plates (Single Cell Discoveries). Plates were sealed, centrifuged 2min at 1500g, 4°C, and snap-frozen and stored at -80°C until sequencing. Dissociation of HIOs and tHIOs into single cells and isolation of EECs for single-cell RNA sequencing: Around 40 HIOs (from a single differentiation) were dissociated to single cells as previously described with some modifications (Grün et al., 2015). Briefly, after medium removal, rinsing of each well with PBS1X, and Matrigel disruption, HIOs were dissociated in TrypLE™ Express (1X) (Gibco™) at 37 °C for 20 min, assisted by a mechanical dissociation (up and down with a p1000 pipette). The dissociation was stopped in a basal medium containing Advanced DMEM/F-12, HEPES 10 mM, fetal calf serum 10%, and Y27632 10µM (STEMCELL™ Technologies). After 3 washes, the cells were resuspended in the FACS medium (basal medium containing only 5% of fetal calf serum), strained through a 50 μm cell strainer, and stained with DAPI (to exclude dead cells) before being sorted by flow cytometry (FACSAria Fusion, BD) based on Venus fluorescence levels. Individual cells were sorted directly in pre-filled 384-well cell capture plates (one cell/well) containing the reagents to perform single-cell RNA-sequencing (scRNA-Seq) according to the SORT-Seq technology (Muraro et al. 2016)(Single Cell Discoveries, Utrecht, The Netherlands). tHIOs were dissociated to single cells as described by Yu et al., (2021) with modifications. Briefly, a total of 8 individual tHIOs were harvested 15 weeks post-transplantation. Samples were first minced into small pieces using a scalpel in ice-cold 1X HBSS, then enzymatically digested in the Neural Tissue Dissociation Kit (Miltenyi Biotec, 130-092-628) at 10°C, following the manufacturer’s instructions. After complete dissociation, the cells were filtered through a 70µm cell strainer, centrifuged (500g, 5 min, 10°C) and the pellet was resuspended in the basal medium. The cell suspensions (from 1 to 3 tHIOs, depending on their size) were then labeled using an anti-EpCAM antibody to collect only epithelial cells (APC anti-human CD326 (EpCAM) antibody, BioLegend) and DAPI (to exclude dead cells). Cells were filtered through a 50 μm cell strainer before being sorted by FACS (FACSAria Fusion, BD) directly into the 384-well plates for SORT-Seq analysis (Single Cell Discoveries, Utrecht, The Netherlands), as described above. Both DAPI-; EpCAM+; Venus+ or Venus- cells were harvested. Reads were mapped to the human GRCh38 genome assembly.
Single cells were sequenced with the SORT-seq method (Muraro et al., 2016), a partially robotized version of the CEL-seq2 protocol (Hashimshony et al., 2016). Library preparation and single-cell RNA sequencing were performed by Single Cell Discoveries (Utrecht, The Netherlands, https://www.scdiscoveries.com). Briefly, single cells were sorted by FACS into each well of a cell-capture 384-well plate, containing well-specific barcoded primers. Each primer contains a cell-specific barcode and a unique molecular identifier (UMI). The protocol involves the following steps: 1) lysis of cells by heat (65°C, 5min) and hybridization of primers to the poly-A tail of mRNAs. 2) Reverse transcription & second-strand synthesis (Invitrogen). 3) Pooling of all the wells. 4) In vitro transcription (IVT) (Ambion) to generate many copies of RNA via linear amplification.5) Fragmentation & reverse transcription: the amplified RNA (aRNA) is fragmented into segments of approximately 300-400 base pairs and reverse transcribed. 6) Amplification of the cDNA by PCR and addition of sequencing adapters (10-12 cycles with Illumina TruSeq primers). The resulting cDNA libraries were paired-end sequenced at a depth of 150.000 reads/cell on an Illumina NextSeq 500.

treatment_protocol: In vivo transplantation of HIOs into the renal subcapsular space of NSG immunocompromised mice. Transplantations of HIOs under the kidney capsule were carried out as described by Watson and collaborators (Watson et al. 2014) with some modifications. Prior to transplantation, HIOs were maintained in culture for 40-42 days. Transplants (tHIOs) were harvested 15 weeks post-transplantation and immediately processed to obtain single cells.

value: Small Intestine

value: EECs


title: Cre_8M_TCR

city: Noda

first: Masaki

last: Ohyagi

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

description:
Library name: SAMPLE4
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

source_name: Brain

extract_protocol:
Brains were roughly minced and homogenized with a potter tissue grinder in RPMI-1640. Whole brain homogenates were separated by 37% Percoll gradient centrifugation at 800g for 20 min. The pellets were washed once with RPMI-1640 containing 2% fetal bovine serum. Cells were washed and stained with anti-CD45 antibody and fixable viability dye. Alive CD45-expressing immune cells were sorted using a FACS AriaIII (Becton Dickinson). Brain immune cells were washed and resuspended in PBS supplemented with 0.5% bovine serum albumin. Single-cell suspensions were loaded onto a 10x Genomics Chromium Controller. The Chromium Next GEM Single Cell 5' Kit v2 (dual index) and Chromium Single Cell Mouse TCR Amplification Kit were used separately to generate a cDNA library for transcriptome expression and targeting TCR.
Library was performed according to the manufacter's instructions (Chromium Next GEM Single Cell 5' v2 (dual index) and Chromium Single Cell Mouse TCR Amplification KIt protocol, 10x Genomics). The cDNA content of each sample and libraries were quality-checked sing a high-sensitivity DNA chip with a 2100 Bioanalyzer (Agilent Technologies).

value: Brain

value: 8 months

value: CD45-expressing cells

value: AppNL-G-F; Cd8a-Cre; Nr4a^flox/flox


title: AG-NF2-Men, 1.1 uM brigatinib + 20 nM INK128, biol replicate 3

city: Columbus

first: Long-Sheng

last: Chang

address: 575 Children's Crossroad

institute: Abigail Wexner Institute at Nationwide Children's Hospital

description:
Library name: Sample 12
Differential_Expression_Genes_DMSO-Ctrl_vs_BrigPlusINK.with.shrinkage.xlsx

data_processing:
Non-polyA-tailed RNA species, including mitochondrial transcripts, rRNAs, and tRNAs, were filtered out using Bowtie 2 (v.2.5.1).
STAR v2.7.3a was used to align reads to the GRCh37/hg19 reference human genome (released February 2009).
Raw read counts were estimated via HTSeq v0.11.2 and normalized with the DESeq2 package.
Cufflinks v2.2.1 was used to estimate the gene expression levels, and the values were reported as FPKM (fragments per kilobase per million) units per gene.
DESeq2 was used to estimate the differential expression of gene counts relative to the DMSO-treated controls.
Assembly: GRCh37/hg19 reference human genome (released February 2009)
Supplementary files format and content: Excel (xlsx) file containing the raw and normalized counts (in FPKM) for all replicates
Supplementary files format and content: Excel (xlsx) files containing the log2-fold change (log2FC) of brigatinib, INK128-, and brigatinib+INK128-treated cells compared to DMSO-treated control cells, statistics including P-values and adjusted P-values, and raw and normalized FPKM counts for replicates

growth_protocol: Human telomerase-immortalized meningioma cell lines AG-NF2-Men cells were grown in standard 10-centimeter dishes in high-glucose DMEM with glutamine and 10% heat-inactivated FBS at 37° C in a 5% CO2 humifiied incubator.

extract_protocol:
Maxwell RSC simplyRNA Cells kit (Cat. #AS1390; Promega).
Illumina TruSeq stranded mRNA kit

treatment_protocol: Cells were treated with DMSO as a vehicle control or 1x growth-inhibitory IC50 concentration of brigatinib, INK128, or their combined IC50 doses for 24 hours. Cells were harvested by scraping down on ice, cell pellets rinsed with cold PBS, and snap-frozen on dry ice

value: meningioma

value: 24 hours


title: FACS sorted eYFP+ EECs from P12 mSI, plate IGB-AA-s024

description:
Library name: mSI_P12_IGB-AA-s024
SORT-seq
adata_P12.h5ad
adata_3stages.h5ad
adata_3stages_pt.h5ad


title: WT_8M_TCR

description:
Library name: SAMPLE3
10x Genomics

value: AppNL-G-F; Cd8a-WT; Nr4a^flox/flox


title: FACS sorted eYFP+ EECs from E18.5 mSI, plate IGB-AA-s021

description:
Library name: mSI_E18-5_IGB-AA-s021
SORT-seq
adata_e18.h5ad
adata_3stages.h5ad
adata_3stages_pt.h5ad


title: FACS sorted eYFP+ EECs from E15.5 mSI, plate IGB-AA-003

description:
Library name: mSI_E15-5_IGB-AA-003
SORT-seq
adata_e15.h5ad
adata_3stages.h5ad
adata_3stages_pt.h5ad


title: FACS sorted eYFP+ EECs from E18.5 mSI, plate IGB-AA-s009

description:
Library name: mSI_E18-5_IGB-AA-s009
SORT-seq
adata_e18.h5ad
adata_3stages.h5ad
adata_3stages_pt.h5ad


title: AG-NF2-Men, 1.1 uM brigatinib + 20 nM INK128, biol replicate 2

description:
Library name: Sample 11
Differential_Expression_Genes_DMSO-Ctrl_vs_BrigPlusINK.with.shrinkage.xlsx


title: FACS sorted eYFP+ EECs from E15.5 mouse small intestine (mSI), plate IGB-AA-002

description:
Library name: mSI_E15-5_IGB-AA-002
SORT-seq
adata_e15.h5ad
adata_3stages.h5ad
adata_3stages_pt.h5ad


title: AG-NF2-Men, 20 nM INK128, biol replicate 3

description:
Library name: Sample 9
Differential_Expression_Genes_DMSO-Ctrl_vs_INK128.with.shrinkage.xlsx


title: Cre_8M_GEX

description:
Library name: SAMPLE2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: WT_8M_GEX

description:
Library name: SAMPLE1
10x Genomics


title: LA55_52_KT18049FL-65Q2-02-27

description: Library name: LA55_52

data_processing:
Tuba-seq Ultra NGS processing scripts convert read counts for each barcode-sgRNA into absolute cell numbers based on spike-in reads. Tumor metrics for each sgRNA, with clonal resolution, are calculated for log-normal mean, tumor number, and total tumor burden. Confidence intervals and p-values are determined using bootstrap resampling. For detailed information on the analysis, please refer to the "Quantification and Statistical Analysis" section in the Methods of the manuscript titled "Functional Mapping of Epigenomic Regulators Uncovers Coordinated Tumor Suppression by the HBO1 and MLL1 Complexes," available at: https://www.biorxiv.org/content/10.1101/2024.08.19.607671v1.
Assembly: sgRNA library sequences included in the processed data file
Supplementary files format and content: The processed file is in .csv format. It contains the sequence of each sgRNA and the calculated metrics for tumors initiated with each Lenti-U6-sgRNA-Epigenomics/Cre vector in KT;H11-LSL-Cas9 mice. 'X_percentile_relative' indicates the size of the tumors at the Xth percentile of the tumor size distribution relative to the tumor size at the same percentile of the sgInert tumor size distribution. 'X_percentile_2.5P' and 'X_percentile_97.5P' represent the 95% confidence intervals for the Xth percentile.

value: KT


title: TBI0,INPUT

description: Library name: sample9

data_processing:
Sequencing reads were aligned to GRCm38 (mm10) mouse reference genome using HISAT2. The m6A_enriched peaks were identified with ExomePeak and gene expression levels were quantified as fragments per kilobase of exon per million mapped fragments (FPKM) using StringTie. Motif enrichment within m6A peaks were analyzed using MEME and HOMER. Peak annotation was performed using ChIP_seeker with Ensembl gene annotation information. A four_quadrant plot was generated to illustrate the distribution of transcripts with significant changes in both m6A modification level and expression (│Log2 FC│> 1.0 and p < 0.05).
Assembly: mm10
Supplementary files format and content: xlsx
Library strategy: MeRIP-Seq

source_name: brain cell

extract_protocol:
Total RNAs were extracted from injured cortical tissues using Trizol reagent following the manufacturer's protocol.
Purified RNA was chemically fragmented into ~100nt segments and incubated with beads conjugated to anti_m6A antibodies. Eluted m6A_containing fragments (IP) and untreated input control fragments were converted into the final cDNA library by the dUTP method in accordance with strand_specific library preparation. Sequencing was performed on an Illumina NovaSeq 6000 platform with 100_base paired_end reads at LC_BIO Bio_tech Co., Ltd. (Hangzhou, China) following the vendor's recommended protocol.

value: brain cell

value: Traumatic brain injury

tag: time point

value: sham group


title: FACS sorted eYFP+ EECs from E18.5 mSI, plate IGB-AA-s010

description:
Library name: mSI_E18-5_IGB-AA-s010
SORT-seq
adata_e18.h5ad
adata_3stages.h5ad
adata_3stages_pt.h5ad


title: AG-NF2-Men, 20 nM INK128, biol replicate 1

description:
Library name: Sample 7
Differential_Expression_Genes_DMSO-Ctrl_vs_INK128.with.shrinkage.xlsx


title: LA55_51_KT18049FL-65Q2-02-26

description: Library name: LA55_51

value: Lung

value: Total lung


title: LA55_54_KT18049FL-65Q2-02-29

description: Library name: LA55_54


title: TBI7,IP

description: Library name: sample8

value: 7 days following traumatic brain injury


title: LA55_48_KT18049FL-65Q2-02-23

description: Library name: LA55_48


title: AG-NF2-Men, 20 nM INK128, biol replicate 2

description:
Library name: Sample 8
Differential_Expression_Genes_DMSO-Ctrl_vs_INK128.with.shrinkage.xlsx


title: LA55_50_KT18049FL-65Q2-02-25

description: Library name: LA55_50


title: AG-NF2-Men, 1.1 uM brigatinib + 20 nM INK128, biol replicate 1

description:
Library name: Sample 10
Differential_Expression_Genes_DMSO-Ctrl_vs_BrigPlusINK.with.shrinkage.xlsx


title: LA55_55_KT18049FL-65Q2-02-30

description: Library name: LA55_55


title: LA55_49_KT18049FL-65Q2-02-24

description: Library name: LA55_49


title: AG-NF2-Men, 1.1 uM brigatinib, biol replicate 3

description:
Library name: Sample 6
Differential_Expression_Genes_DMSO-Ctrl_vs_Brigatinib.with.shrinkage.xlsx

value: brigatinib


title: TBI7,INPUT

description: Library name: sample7


title: TBI0,IP

description: Library name: sample10


title: TBI5,IP

description: Library name: sample6

value: 5 days following traumatic brain injury


title: LA55_47_KT18049FL-65Q2-02-22

description: Library name: LA55_47


title: LA55_45_KTC18049FL-65Q2-02-20

description: Library name: LA55_45

value: KTC


title: AG-NF2-Men, 1.1 uM brigatinib, biol replicate 1

description:
Library name: Sample 4
Differential_Expression_Genes_DMSO-Ctrl_vs_Brigatinib.with.shrinkage.xlsx


title: LA55_44_KTC18049FL-65Q2-02-19

description: Library name: LA55_44


title: LA55_43_KTC18049FL-65Q2-02-18

description: Library name: LA55_43


title: AG-NF2-Men, 1.1 uM brigatinib, biol replicate 2

description:
Library name: Sample 5
Differential_Expression_Genes_DMSO-Ctrl_vs_Brigatinib.with.shrinkage.xlsx


title: LA55_46_KT18049FL-65Q2-02-21

description: Library name: LA55_46


title: LA55_42_KTC18049FL-65Q2-02-17

description: Library name: LA55_42


title: AG-NF2-Men, DMSO, biol replicate 3

description: Library name: Sample 3

value: DMSO


title: TBI3,IP

description: Library name: sample4

value: 3 days following traumatic brain injury


title: LA55_41_KTC18049FL-65Q2-02-16

description: Library name: LA55_41


title: AG-NF2-Men, DMSO, biol replicate 2

description: Library name: Sample 2


title: AG-NF2-Men, DMSO, biol replicate 1

description: Library name: Sample 1


title: LA55_38_KTC18049FL-65Q2-02-13

description: Library name: LA55_38


title: TBI1,IP

description: Library name: sample2

value: 1 day following traumatic brain injury


title: TBI1,INPUT

description: Library name: sample1


title: LA55_36_KTC18049FL-65Q2-02-11

description: Library name: LA55_36


title: iPSC Cells

city: Tsukuba

first: Haruki

last: Odaka

state: Ibaraki

address: Tsukuba Central 6, 1-1-1 Higashi

institute: National Institute of Advanced Industrial Science and Technology

description: Library name: iPSC.01

data_processing:
Processing of sc-RNAseq data was performed by Subio Platform (version 1.24.5849, Subio inc.) which uses fastp (version 0.22.0) for quality control of FASTQ and HISAT2 (version 2.2.0) for mapping to the human reference genome (GRCh38), and StringTie (version 2.1.1) for calculation of the raw count data.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: 201B7 hiPSCs were cultured in 2 mL of mTeSR Plus (VERITAS ) on 6 well plate coated with Matrigel (Corning international ).

extract_protocol:
Single-cell cDNA library was prepared using GenNextⓇRamDA-seqTM Single Cell Kit (Toyobo Co., LTD. Tokyo, Japan) followed by manufacturer’s protocol.
cDNA library from each single cell was prepared using GenNextⓇRamDA-seqTM Single Cell Kit (Toyobo Co., LTD. Tokyo, Japan) followed by manufacturer’s protocol.

treatment_protocol: Differentiation into NPCs was performed using STEMdiff SMADi Neural Induction Kit according to the manufacturer’s protocol (VERITAS). NPCs were expanded until P4 in STEMdiff SMADi medium. For differentiation into neurons, the NPCs were detached and dissociated into a single cell with Accutase (Innovative Cell Technologie) and seeded on polyethyleneimine (0.07%, Sigma-Aldrich) and laminin (3.3 μg/ml, FUJIFILM Wako)-coated plates. Cells were cultured with neurobasal medium (Thermo Fisher) supplemented with 2% B27 supplement  (Thermo Fisher), 1% GlutaMax (Thermo Fisher), and 5 μM DAPT (Sigma-Aldrich) for 1 week. At day 7, the medium was changed to neurobasal plus medium (Thermo Fisher) supplemented with 2% B27 plus supplement  (Thermo Fisher) and 1% GlutaMax. Half of the medium was changed twice a week until days 21.

value: iPSC


title: LA55_53_KT18049FL-65Q2-02-28

description: Library name: LA55_53


title: App_TCR

description:
Library name: SAMPLE5
10x Genomics

value: Brain

value: CD45-expressing cells

value: AppNL-G-F


title: LA55_33_KTC18049FL-65Q2-02-08

description: Library name: LA55_33


title: TBI5,INPUT

description: Library name: sample5


title: LA55_40_KTC18049FL-65Q2-02-15

description: Library name: LA55_40


title: TBI3,INPUT

description: Library name: sample3


title: LA55_30_KTC18049FL-65Q2-02-05

description: Library name: LA55_30


title: WT_TCR

description:
Library name: SAMPLE4
10x Genomics

value: wild-type


title: PKP2KO_2, hPSC-EPCs

city: Tucson

first: Jared

last: Churko

state: Arizona

address: 1501 N CAMPBELL AVE LSN 461

department: CMM

institute: University of Arizona

description: Library name: Sample_16

data_processing:
Align raw FASTQ reads to the human GRCh38 reference using STAR.   Generate gene-level count matrix and perform normalization and differential expression analysis in R using DESeq2.
Assembly: GRCh38
Supplementary files format and content: GEO_matrixfile.csv : comma-separated count matrix

growth_protocol: Human iPSCs were maintained on Matrigel-coated plates in E8 medium at 37 °C, 5% CO₂.

extract_protocol:
Total RNA was extracted from epicardial cells using TRIzol reagent and purified with the Direct-zol RNA MiniPrep kit
RNA-seq libraries were prepared from 1 µg total RNA using the Illumina TruSeq Stranded mRNA kit (Novogene), then sequenced on an Illumina NovaSeq (2×150 bp paired-end).

treatment_protocol: Epicardial differentiation was induced by sequential Wnt modulation: Day 0 in DMEM + 128 µg/mL ascorbic acid-2-phosphate + 6 µM CHIR99021; Day 2 fresh DMEM + ascorbic acid; Days 3–5 DMEM + ascorbic acid + 5 µM IWR-1-endo; Day 6 dissociation and reseeding in epicardial maintenance medium (DMEM + 128 µg/mL ascorbic acid + 10 µg/mL insulin + 10 µM Y-27632), then maintained with 3 µM CHIR99021 on days 7–8 and SB431542 from day 12 onward.

value: hPSC-EPCs


title: LA55_39_KTC18049FL-65Q2-02-14

description: Library name: LA55_39


title: App;Cd3e-/-_GEX

description:
Library name: SAMPLE3
10x Genomics

value: AppNL-G-F; Cd3e-/-


title: LA55_27_KTC18049FL-65Q2-02-02

description: Library name: LA55_27


title: LA55_28_KTC18049FL-65Q2-02-03

description: Library name: LA55_28


title: App_GEX

description:
Library name: SAMPLE2
10x Genomics


title: LA55_37_KTC18049FL-65Q2-02-12

description: Library name: LA55_37


title: LA55_35_KTC18049FL-65Q2-02-10

description: Library name: LA55_35


title: Neural Progenitor Cells

description: Library name: NPC.1

value: iPSC-derived NPC


title: PKP2KO_3, hPSC-EPCs

description: Library name: Sample_17


title: LA55_32_KTC18049FL-65Q2-02-07

description: Library name: LA55_32

value: Lung


title: LA55_25_KTC18049FL-65Q2-01-25

description: Library name: LA55_25

value: Total lung


title: WT_GEX

description:
Library name: SAMPLE1
10x Genomics


title: LA55_23_KTC18049FL-65Q2-01-23

description: Library name: LA55_23


title: LA55_31_KTC18049FL-65Q2-02-06

description: Library name: LA55_31


title: LA55_24_KTC18049FL-65Q2-01-24

description: Library name: LA55_24


title: LA55_29_KTC18049FL-65Q2-02-04

description: Library name: LA55_29


title: H7EPC_2, hPSC-EPCs

description: Library name: Sample_13


title: H7EPC_4, hPSC-EPCs

description: Library name: Sample_15


title: LA55_20_KTC18049FL-65Q2-01-20

description: Library name: LA55_20


title: PKP2KO_1, hPSC-EPCs

description: Library name: Sample_12


title: LA55_22_KTC18049FL-65Q2-01-22

description: Library name: LA55_22


title: scr_library3

description:
Library name: scr_lib3
scRNA-seq by split-seq (Parse Biosciences)

data_processing:
The FASTQ files were preprocessed with the data analysis pipeline from Parse Biosciences (split-pipe v1.0.3). Gene expression analysis was performed using Scanpy (v1.9.3)
Assembly: mm10

source_name: Ex vivo primary cells (not cell line)

growth_protocol: All mice were on a C57BL/6 background and kept in standard condition with 12hour light/dark cycle and ad libitum access to food and water.

extract_protocol:
FACS sorted Lin-TdTomato+ neoplastic cells from KT;H11LSL-Cas9 mice transduced with sgRNA. Immediately after FACS, the sorted neoplastic cells were fixed with Evercode Cell Fixation kit (Parse Biosciences, ECF2101). The fixed cells are processed with Parse Biosciences scRNA-seq protocol.
Parse Biosciences scRNA-seq protocol

treatment_protocol: Intratracheal transduction in mouse

value: FACS sorted lung neoplastic cells

value: Kras driven lung neoplastic cells

value: Lenti-sgRNA/Cre


title: H7EPC_3, hPSC-EPCs

description: Library name: Sample_14


title: scr_library4

description:
Library name: scr_lib4
scRNA-seq by split-seq (Parse Biosciences)


title: LA55_21_KTC18049FL-65Q2-01-21

description: Library name: LA55_21

value: KTC


title: H7EPC_1, hPSC-EPCs

description: Library name: Sample_11


title: sub_library8

description:
Library name: sub_lib8
scRNA-seq by split-seq (Parse Biosciences)


title: LA55_19_KTC18049FL-65Q2-01-19

description: Library name: LA55_19


title: LA55_26_KTC18049FL-65Q2-02-01

description: Library name: LA55_26


title: LA55_18_KTC18049FL-65Q2-01-18

description: Library name: LA55_18


title: ACMEPC_5, hPSC-EPCs

description: Library name: Sample_10


title: LA55_17_KTC18049FL-65Q2-01-17

description: Library name: LA55_17


title: LA55_16_KTC18049FL-65Q2-01-16

description: Library name: LA55_16


title: ConEPC_5, hPSC-EPCs

description: Library name: Sample_9


title: LA55_15_KTC18049FL-65Q2-01-15

description: Library name: LA55_15


title: sub_library6

description:
Library name: sub_lib6
scRNA-seq by split-seq (Parse Biosciences)


title: LA55_14_KTC18049FL-65Q2-01-14

description: Library name: LA55_14


title: LA55_13_KTC18049FL-65Q2-01-13

description: Library name: LA55_13


title: ACMEPC_4, hPSC-EPCs

description: Library name: Sample_8


title: LA55_12_KTC18049FL-65Q2-01-12

description: Library name: LA55_12


title: sub_library5

description:
Library name: sub_lib5
scRNA-seq by split-seq (Parse Biosciences)


title: ConEPC_4, hPSC-EPCs

description: Library name: Sample_7


title: LA55_09_KTC18049FL-65Q2-01-09

description: Library name: LA55_09


title: sub_library4

description:
Library name: sub_lib4
scRNA-seq by split-seq (Parse Biosciences)


title: sub_library3

description:
Library name: sub_lib3
scRNA-seq by split-seq (Parse Biosciences)


title: sub_library2

description:
Library name: sub_lib2
scRNA-seq by split-seq (Parse Biosciences)


title: LA55_11_KTC18049FL-65Q2-01-11

description: Library name: LA55_11


title: LA55_08_KTC18049FL-65Q2-01-08

description: Library name: LA55_08


title: ConEPC_3, hPSC-EPCs

description: Library name: Sample_6


title: LA55_04_KTC18049FL-65Q2-01-04

description: Library name: LA55_04


title: ConEPC_1, hPSC-EPCs

description: Library name: Sample_3


title: LA55_06_KTC18049FL-65Q2-01-06

description: Library name: LA55_06


title: LA55_03_KTC18049FL-65Q2-01-03

description: Library name: LA55_03


title: ACMEPC_2, hPSC-EPCs

description: Library name: Sample_2


title: LA55_05_KTC18049FL-65Q2-01-05

description: Library name: LA55_05


title: ConEPC_2, hPSC-EPCs

description: Library name: Sample_4


title: LA52_10B_KTC_18049FL-58Q-31V1

description: Library name: LA52_10B


title: sub_library1

description:
Library name: sub_lib1
scRNA-seq by split-seq (Parse Biosciences)


title: LA55_02_KTC18049FL-65Q2-01-02

description: Library name: LA55_02


title: ACMEPC_3, hPSC-EPCs

description: Library name: Sample_5


title: LA55_07_KTC18049FL-65Q2-01-07

description: Library name: LA55_07


title: sub_library7

description:
Library name: sub_lib7
scRNA-seq by split-seq (Parse Biosciences)


title: LA55_10_KTC18049FL-65Q2-01-10

description: Library name: LA55_10


title: LA52_8B_KTC_18049FL-58Q-28V1

description: Library name: LA52_8B


title: Adductors, Apoa1bp-/-, scRNAseq

city: Changsha

first: Lingping

last: Zhu

address: Xiangya Road

institute: Xiangya hospital

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v2.1.1
Assembly: GRCm39Ensembl_release106
Supplementary files format and content: Tab-separated values files and matrix files

source_name: adductors muscle

extract_protocol:
We performed FAL surgery on four Apoa1bp-/- mice and four control littermates. Ischemic adductor muscles were collected and stored in tissue storage solution. For single-cell suspension preparation, Adductor muscles were collected, minced, and homogenized in 2 mL cold ECM containing 5% FBS. The crude homogenate was digested with Collagenase D (1 mg/mL, Millipore sigma, Cat # 11088866001) for 30 min, passed through a 70-μm cell strainer, and washed three times with DPBS to remove clumps. The homogenate was centrifuged at 500 g for 10 min at 4°C, and the supernatant was discarded. The pellet was resuspended in wash buffer.
The final library was sequenced using Illumina paired-end sequencing, with the 16 bp 10x Barcode and 10 bp UMI encoded in Read 1 and cDNA fragments sequenced in Read 2. Sample index sequences were incorporated into the i7 index read.

value: adductors muscle

value: All cells in adductors

value: AIBP-KO

value: Femoral artery ligation


title: ACMEPC_1, hPSC-EPCs

description: Library name: Sample_1


title: LA52_25_KT_18049FL-58Q-25V1

description: Library name: LA52_25

value: KT


title: Adductors, control, scRNAseq

description: 10X Genomics

value: WT


title: hippocampus, 20CBD, long-term,6

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: GRCm39
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

source_name: hippocampus

extract_protocol:
Tissues were collected and immediately submerged in stayRNA™ (A&A Biotechnology) reagent. After 24 of cooling (4C), tissues were frozen at -80C until the time of RNA isolation. For RNA isolation, tissue scrapes (10-20 mg) were homogenized and used for RNA isolation with AllPrep DNA/RNA (Qiagen) kit. Following isolation, RNA was controlled for quality with the TapeStation4150 system and quantified.
Libraries were prepared using CORALL mRNA-Seq V2 (Lexogen) following standard protocol.
RNA-Seq, stranded

treatment_protocol: The experiment was conducted on C57BL/6J laboratory mice strain (n=48), divided into subgroups receiving CBD at doses of 0.2, 10, or 20 mg/kg of body weight, and a control group receiving placebo, administered for 2 (short-term) or 28 (long-term) days. CBD was administered once a day via intraperitoneal injection. RNA-Seq analysis of the hippocampus was conducted to identify transcriptomic alternations induced by CBD treatment in this brain structure.

value: hippocampus

value: 20CBD, long-term


title: LA52_24_KT_18049FL-58Q-24V1

description: Library name: LA52_24

extract_protocol:
The tissues were homogenized in 20 ml lysis buffer (100mM NaCl, 20mM Tris, 10mM EDTA, 0.5% SDS) with 200 μl of 20 mg/ml Proteinase K (Life Technologies, AM2544). Homogenized tissues were incubated at 55°C overnight.  Genomic DNA was extracted with phenol-chloroform (ThermoFisher Scientific, 15593049) or the Qiagen Puregene Kit (Qiagen, 158063) and precipitated with ethanol. Plasmid DNA extraction was performed following QIAGEN Plasmid Plus Midi Kit instructions
Custom Tuba-seqUltra library construction protocol. For detailed methodology, please refer to the "Tuba-seqUltra library preparation" section in the Methods of the manuscript "Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes," available at: https://www.biorxiv.org/content/10.1101/2024.08.19.607671v1


title: LA52_23_KTC_18049FL-58Q-23V1

description: Library name: LA52_23


title: LA52_22_KTC_18049FL-58Q-22V1

description: Library name: LA52_22


title: PBMC from pediatric SLE donor 8

city: New York

first: Simone

last: Caielli

address: 413 E 69th Street

department: Department of Pediatrics

institute: Weill Cornell Medicine

description:
Library name: SLE_8
10x Genomics

data_processing:
Single cell demultiplxing and gene counting were performed using 10X Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: PBMC

extract_protocol:
Cryopreserved PBMCs were thawed and resuspended in RPMI containing 10% FBS for cell number and viability assessment.
Live PBMCs were enriched using the Dead Cell Removal Kit (Miltenyi) and resuspended in PBS with 1% BSA for scRNAseq processing using Chromium Single Cell 5’ V2 gene expression (10x Genomics). The samples were divided into four batches and loaded into different lanes of a 10x chip, aiming for a cell recovery of 10,000 per sample, following the manufacturer’s instructions. Paired-end sequencing was performed on the Illumina NovaSeq 6000.

value: PBMC

tag: subject status

value: pediatric SLE donor


title: LA55_01_KTC_18049FL-65Q2-01-01

description: Library name: LA55_01

source_name: Lung


title: PBMC from pediatric SLE donor 7

description:
Library name: SLE_7
10x Genomics


title: LA52_21_KTC_18049FL-58Q-21V1

description: Library name: LA52_21


title: LA52_19_KTC_18049FL-58Q-19V1

description: Library name: LA52_19


title: hippocampus, 20CBD, long-term,3


title: LA52_18_KTC_18049FL-58Q-18V1

description: Library name: LA52_18


title: LA52_17_KTC_18049FL-58Q-17V1

description: Library name: LA52_17


title: LA52_16_KTC_18049FL-58Q-16V1

description: Library name: LA52_16


title: hippocampus, 20CBD, long-term,2


title: PBMC from pediatric SLE donor 5

description:
Library name: SLE_5
10x Genomics


title: LA52_15_KTC_18049FL-58Q-15V1

description: Library name: LA52_15


title: hippocampus, 20CBD, long-term,1


title: LA52_12_KTC_18049FL-58Q-12V1

description: Library name: LA52_12


title: PBMC from pediatric SLE donor 9

description:
Library name: SLE_9
10x Genomics