title: Senescence irradiation + UK5099, Sen(IR+UK5099) 3

status: Public on May 19 2026

city: La Jolla

first: Peter

middle: D.

last: Adams

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: tab-limited text file include raw count for each Sample
Supplementary files format and content: tab-limited text file include TPM value for each Sample

extract_protocol:
RNA was extract with Rneasy mini plus kiy (Qiagen)
Library construction was performed by AZENTA

value: Human Fibroblasts


title: SFFFM_Rox

status: Public on Jun 01 2026

type: SRA

city: Nashville

first: Abraham

middle: Scott

last: McCall

state: TN

department: Medicine

country: USA

institute: Vanderbilt University medical Center

description: Library name: 11001_2

library_source: transcriptomic single cell

data_processing:
Cellranger v9.0.1 with demultiplexing
Doublet calling - scDblFinder
Data integration/annotation -> Seurat, Harmony
Assembly: GRCh38-2020-A
Supplementary files format and content: h5 filtered matrix

molecule: total RNA

organism: Homo sapiens

source_name: lung organoid

growth_protocol: Primary CD326+ enriched human declined donor were cultured under serum-free feeder free conditions in domed matrigel culture the replated in technical triplicate for each condition for sequencing.

extract_protocol:
Cultured alveolar organoid under indicated experimental conditions were liberated from matrigel using Dispase (2mg/ml), rinsed, trypsinized, and quenched with ACF free trypsin inhibitor,  to generate a single cell suspension then fixed per 10X FLEX protocol, counted and pooled for 10X FLEX library preperation.
Chromium Human Transcriptome Probe Set v1.1.0

tag: tissue

value: lung organoid

tag: cell line

value: primary

tag: cell type

value: epithelial

tag: treatment

value: SFFFM//Roxadustat

tag: batch


title: Senescence irradiation + UK5099, Sen(IR+UK5099) 2

state: CA

library_source: transcriptomic


title: Senescence irradiation + CTPI2, Sen(IR+CTPI2) 3


title: Senescence irradiation + UK5099, Sen(IR+UK5099) 1


title: Senescence irradiation + CTPI2, Sen(IR+CTPI2) 2


title: Senescence irradiation + CTPI2, Sen(IR+CTPI2) 1


title: Senescence irradiation Sen(IR) 3


title: Senescence irradiation Sen(IR) 2


title: Proliferative 2


title: Senescence irradiation Sen(IR) 1


title: Proliferative 1


title: H3K27ac MRC5 Sen(IR) CTPI2 3

library_source: genomic

data_processing:
H2K27ac and H3 ChIP-seq samples were processed with nf-core chipseq nextflow pipeline version 2.0.0  using singularity containers and parameters "--aligner bowtie2--read_length 75 --genome GRCh38”. H3K27ac bigwig signal files were normalized by H3 signal using Deeptools bigwigCompare version 3.5.5 with parameters  “—operation subtract --binSize 10”.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: bigWig file average of 3 replicates of H3K27ac normalized by total H3 in proliferatives parkin cells
Supplementary files format and content: bigWig file average of 3 replicates of H3K27ac normalized by total H3 in senescents parkin cells
Supplementary files format and content: bigWig file average of 3 replicates of H3K27ac normalized by total H3 in senescents parkin cells without mitochondria
Supplementary files format and content: bigWig file average of 3 replicates of H3K27ac normalized by total H3 senescent MRC5 treated with DMSO
Supplementary files format and content: bigWig file average of 3 replicates of H3K27ac normalized by total H3 senescent MRC5 treated with CTPI2

molecule: genomic DNA

extract_protocol:
Cells were formalin fixed for 10 minutes in 4%PFA, then lysed and chromatin was sheared to between 250-500bp as confirmed by agarose gel electrophoresis in size using sonication (Biorupter pico, Ref B01060010).
Library preparation of ChIP DNA was performed with the Watchmaker DNA Library Prep Kit (Watchmaker Genomics, Cat: 7K0103) with xGEN Stubby adaptors (IDT, Cat: 10005924) and xGEN 10nt UDI Primers (IDT, Cat: 10008052).


title: H3K27ac MRC5 Sen(IR) CTPI2 2


title: H3K27ac MRC5 Sen(IR) CTPI2 1


title: Proliferative 3


title: H3K27ac MRC5 Sen(IR) DMSO 3


title: H3K27ac MRC5 Sen(IR) DMSO 2


title: H3K27ac MRC5 Sen(IR) DMSO 1


title: H3 MRC5 Sen(IR) CTPI2 2


title: Ries_1_16_600_2

status: Public on Jun 30 2026

city: Brookings

first: Anne

last: Fennell

state: SD

address: Raven Precision Ag Building Box 2100A

department: Agronomy, Horticulture & Plant Science

institute: South Dakota State University

description:
Library name: Ries_1_16_600_2
Total RNA single illumina

data_processing:
1. Quality Control of Raw Reads- Raw RNA-seq reads were assessed for quality using FastQC, and summary reports across all samples were generated using MultiQC.
2. Adapter Trimming and Filtering- Adapter sequences and low-quality bases were removed using Trimmomatic. Since the data consisted of single-end reads, the TruSeq2 single-end adapter file was used during trimming.
3. Reference Genome Preparation- The Vitis vinifera 12Xv2 reference genome assembly and V2.20 GFF3 annotation file were downloaded and prepared for downstream analysis.
4. Genome Index Generation - Genome indices were generated using STAR to facilitate efficient   alignment of RNA-seq reads.
5. Read Alignment - Trimmed reads were aligned to the Vitis vinifera reference genome using STAR, producing BAM alignment files for each sample.
Assembly: 6. Gene Expression Quantification- Gene-level read counts were generated using featureCounts  with the V2.20 GFF3 annotation file, retaining gene IDs for downstream expression analysis.
Supplementary files format and content: geo_processed_read_counts.csv

organism: Vitis vinifera

source_name: Bud

growth_protocol: Standard commercial vineyard management, Ravines Wine Cellar, Geneva, New York

extract_protocol:
RNA was extracted from 3 bud pooled samples. Tissue was homogenized to powder while frozen then promptly extracted using Sigma Plant Total RNA kits with the addition of 3% PVP40 at the lysis buffer stage.
Poly(A)-selected mRNA-seq library, prepared with a TruSeq-compatible kit, random-hexamer primed, sequenced 1×75 SE on Illumina NextSeq 500/550.

treatment_protocol: Field Conditions

value: Bud

tag: genotype

value: total RNA

value: single


title: Ries_1_14_1400_3

description:
Library name: Ries_1_14_1400_3
Total RNA single illumina


title: Ries_1_16_600_3

description:
Library name: Ries_1_16_600_3
Total RNA single illumina


title: H3 MRC5 Sen(IR) CTPI2 3


title: H3 MRC5 Sen(IR) CTPI2 1


title: H3 MRC5 Sen(IR) DMSO 2


title: H3 MRC5 Sen(IR) DMSO 1


title: Ries_1_15_1800_3

description:
Library name: Ries_1_15_1800_3
Total RNA single illumina


title: H3K27ac Parkin Sen(IR) + CCCP 3

value: over expressing Parkin


title: H3 MRC5 Sen(IR) DMSO 3


title: H3K27ac Parkin Sen(IR) + CCCP 1


title: H3K27ac Parkin Sen(IR) + CCCP 2


title: H3K27ac Parkin Sen(IR) 2


title: H3K27ac Parkin Prolif 3


title: H3K27ac Parkin Sen(IR) 3


title: H3K27ac Parkin Sen(IR) 1


title: H3K27ac Parkin Prolif 2


title: H3K27ac Parkin Prolif 1


title: H3 Parkin Sen(IR) + CCCP 3


title: H3 Parkin Sen(IR) + CCCP 1


title: H3 Parkin Sen(IR) + CCCP 2


title: H3 Parkin Sen(IR) 2


title: H3 Parkin Sen(IR) 3


title: H3 Parkin Prolif 3


title: H3 Parkin Sen(IR) 1


title: L, CAR-T-cells, HTO

status: Public on May 18 2026

city: New York

first: Sneha

last: Mitra

state: New York

address: 1265 York Ave

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: L_HTO
CITE-seq feature barcode library containing anitbody-derived tags (ADT); read1 contains cell barcode and UMI; read2 contains transcript sequence

library_source: other

data_processing:
Multiome files we demultiplexed using cellranger-multi mkfastq
Demultiplexed data was processed using the cellranger-arc count pipeline
Assembly: hg38
Supplementary files format and content: Cellranger output files: E_filtered_feature_bc_matrix.h5, F_filtered_feature_bc_matrix.h5, G_filtered_feature_bc_matrix.h5 L_filtered_feature_bc_matrix.h5
Supplementary files format and content: Cellranger output files: E_atac_fragments.tsv.gz, F_atac_fragments.tsv.gz, G_atac_fragments.tsv.gz, L_atac_fragments.tsv.gz

molecule: other

source_name: PBMC

extract_protocol:
Cells were sorted for live, CD3+, and CAR+ cells from 13 patients at early (days 7-14), intermediate (days 25-35), and late (days 60-90 post-infusion) timepoints. Cells were hashed and batched to preserve identity and ensure similar frequencies of cells from both cilta- and ide-cel treated patients.
Libaries construction for both scRNA and CITE followed manufacturer protocols (10X genomics).

value: PBMC

value: T-cell

tag: library type

value: HTO/ADT

value: L


title: H3 Parkin Prolif 2


title: H3 Parkin Prolif 1


title: L, CAR-T-cells, ATAC

description:
Library name: L_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

library_source: genomic single cell

value: ATAC


title: AML116

status: Public on Jun 14 2026

city: Dalian

first: Xuehong

last: Zhang

state: Liaoning

address: No. 9 West Section Lvshun South Road, Dalian 116044, Liaoning, China

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

description: Library name: Sample116

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 27, GRCh38).
The Gene abundances are given as Reads Per Kilobase per Million mapped reads (RPKM) with “cuffnorm” command using the Cufflinks package.
Assembly: human GRCh38
Supplementary files format and content: Excel file includes FPKM values for all Samples

source_name: Bone Marrow

extract_protocol:
Total RNA of mononucleated cells of bone marrow or peripheral blood samples from AML patients and healthy donors were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

value: Bone Marrow

tag: disease stage

value: AML


title: G, CAR-T-cells, ATAC

description:
Library name: G_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

value: G


title: G, CAR-T-cells, HTO

description:
Library name: G_HTO
CITE-seq feature barcode library containing anitbody-derived tags (ADT); read1 contains cell barcode and UMI; read2 contains transcript sequence


title: L, CAR-T-cells, GEX

description:
Library name: L_RNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

molecule: nuclear RNA

value: mRNA


title: F, CAR-T-cells, HTO

description:
Library name: F_HTO
CITE-seq feature barcode library containing anitbody-derived tags (ADT); read1 contains cell barcode and UMI; read2 contains transcript sequence

value: F


title: G, CAR-T-cells, GEX

description:
Library name: G_RNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: F, CAR-T-cells, GEX

description:
Library name: F_RNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: F, CAR-T-cells, ATAC

description:
Library name: F_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: E, CAR-T-cells, ATAC

description:
Library name: E_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

value: E


title: E, CAR-T-cells, HTO

description:
Library name: E_HTO
CITE-seq feature barcode library containing anitbody-derived tags (ADT); read1 contains cell barcode and UMI; read2 contains transcript sequence


title: E, CAR-T-cells, GEX

description:
Library name: E_RNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: MND, HTO, ADT

description:
Library name: MND_HTO_ADT
CITE-seq feature barcode library containing both anitbody-derived tags (ADT) and hashtag-oligonucleotides; read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
CITE-seq files were demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: hg38
Supplementary files format and content: Cellranger output files: E_C_M1_filtered_feature_bc_matrix.h5, E_C_M2_filtered_feature_bc_matrix.h5, E_C_M3_filtered_feature_bc_matrix.h5, E_C_M4_filtered_feature_bc_matrix.h5, E_C_M5_filtered_feature_bc_matrix.h5
Supplementary files format and content: Cellranger output files: E_C_M1_airr_rearrangement.tsv, E_C_M2_airr_rearrangement.tsv, E_C_M3_airr_rearrangement.tsv, E_C_M4_airr_rearrangement.tsv, E_C_M5_airr_rearrangement.tsv

extract_protocol:
At indicated timepoints, T cells were obtained by either bone marrow aspiration under sedation as per institutional protocols (MSKCC Antitumor Assessment Core), or animals were euthanized with C02 asphyxiation for femur harvest. Femurs were dissected, cleaned of muscle tissue, and both ends were snipped to expose the marrow cavity. Bone marrow was was flushed using a 25G needle and cold PBS into a 50 mL conical tube. The cell suspension was filtered through a 70 μm cell strainer, and cells were pelleted by centrifugation at 400 × g for 5 minutes at 4°C. Bone marrow was obtained from femurs of euthanized mice. Cells were washed and labeled with anti-human CD45 BV650 (Biolegend #304044), Sytox Blue Dead Cell Stain (Thermo Scientific, Cat# S34857, 1:1000), and recombinant human BCMA Fc chimera protein (A647, R&D Systems, Cat# AFR193, 1:100). Live hCD45+ CAR+ were isolated using Fluorescence-Activated Cell Sorting on a BD FACSymphony S6 cell sorter (MSK Flow Cytometry Core facility).
Libaries construction for both scRNA, CITE, scTCR followed manufacturer protocols (10X genomics).

treatment_protocol: 8–12-week-old NOD.Cg-Prkdc scid Il2rg tm1Wjl /SzJ (NSG) male or female mice (Jackson Laboratory) were inoculated with 4 × 106 mCherry-MM1.s cells by tail vein injection. Seven days later, CAR T cells at the indicated dose were administered by tail vein injection. Bioluminescence imaging used the IVIS Spectrum in vivo imaging system (PerkinElmer) with Living Image software (Xenogen) for acquisition of imaging datasets. Mice were euthanized if showing signs of distress due to excessive tumour burden or xeno-GVHD by unblinded investigators per institutional procedures.

value: MND

tag: hto/adt

value: TotalSeq


title: EF1a, HTO, ADT

description:
Library name: EF1a_HTO_ADT
CITE-seq feature barcode library containing both anitbody-derived tags (ADT) and hashtag-oligonucleotides; read1 contains cell barcode and UMI; read2 contains transcript sequence


title: MND, TCR

description:
Library name: MND_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
CITE-seq files were demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: hg38
Supplementary files format and content: Cellranger output files: E_C_M1_filtered_feature_bc_matrix.h5, E_C_M2_filtered_feature_bc_matrix.h5, E_C_M3_filtered_feature_bc_matrix.h5, E_C_M4_filtered_feature_bc_matrix.h5, E_C_M5_filtered_feature_bc_matrix.h5
Supplementary files format and content: Cellranger output files: E_C_M1_airr_rearrangement.tsv, E_C_M2_airr_rearrangement.tsv, E_C_M3_airr_rearrangement.tsv, E_C_M4_airr_rearrangement.tsv, E_C_M5_airr_rearrangement.tsv
Library strategy: TCR-seq

value: VDJ


title: MND, CAR-T-cells, GEX

description:
Library name: MND_RNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

molecule: polyA RNA


title: EF1a, TCR

description:
Library name: EF1a_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: EF1a, CAR-T-cells, GEX

description:
Library name: EF1a_RNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: scRNA-seq of human Coronary artery samples

status: Public on May 09 2026

city: Beijing

first: Fangzhou

last: Li

address: 167 Beilishi Rd, Xicheng District,

department: Fuwai hospital

institute: Peking Union Medical College

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC hg38 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Assembly: hg38
Supplementary files format and content: csv,gene expression matrix for single cell RNASeq
Supplementary files format and content: txt,raw counts of RNA-seq
Supplementary files format and content: xlsx,log fold change of RNA-seq

source_name: Coronary artery

extract_protocol:
Total RNA was extracted from cells using the Quick-RNATM MicroPrep (ZYMO RESEARCH, R1050)
One μg of RNA was used for the generation of sequencing libraries using the TruSeq RNA Library Prep Kit V2 (Illumina, RS-122-2002) according to manufacturer’s instructions.

value: Coronary artery


title: scRNA-seq of human Coronary artery samples 3DE

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC hg38 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
NA
Assembly: hg38
Supplementary files format and content: csv,gene expression matrix for single cell RNASeq
Supplementary files format and content: txt,raw counts of RNA-seq
Supplementary files format and content: xlsx,log fold change of RNA-seq


title: Cab_Franc_1_28_1400_3

description:
Library name: Cab_Franc_1_28_1400_3
Total RNA single illumina

value: Bud

value: total RNA

value: single


title: Tr-NAM-4

status: Public on May 08 2026

first: Bettina

last: Nadorp

state: NY

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The FASTQ files were further processed using the Seq-N-Slide pipeline [ref: https://doi.org/10.5281/zenodo.5550459]. The sequencing reads were adapter and quality trimmed with Trimmomatic (version 0.39) and then aligned to the mouse genome (build mm10/GRCm38) using the Bowtie 2 aligner (version 2.3.4.1), and duplicate reads were removed using Sambamba (version 0.6.8). We used deeptools (version 3.5.1) to generate BigWig files and called peaks with MACS2 (version 2.2.1). Peaks were further filtered for mm10 ENCODE backlist regions (version 2). We established consensus peak sets for each group using bedtools (version 2.30.0), including only peaks present in at least two of the replicates. Peaks were considered overlapping if at least 50% of the peak was overlapping. Differential accessibility analysis was performed using EdgeR, correcting for library size and GC content. Peaks were considered differentially accessible when reaching |logFC|>0.6 and FDR corrected p-value<0.05. Principal component analysis within DESeq2 was used to visualize similarities between samples, and the ChIPseeker (version 1.38) R package was used for peak annotations. Subsequent motif analysis was performed on significantly more or less accessible peaks separately using HOMER (v4.10). All downstream analysis was performed in R (version 4.3.3) and visualizations were generated using ggplot2 (version 2.3.5.1). Tracks of ATAC-seq and RNA-seq data were further visualized using the Integrative Genome Viewer (IGV).
Assembly: mm10
Supplementary files format and content: MAC2 called peaks, bed files

organism: Mus musculus

extract_protocol:
Flow-sorted nerve- and airway-associated macrophages
A total of 50,000 purified macrophage populations per replicate were washed once in cold sterile PBS and resuspended in 20-50 µl of cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Cell lysates were centrifuged at 500g for 30 seconds to 1 min at 4 °C, and nuclei were resuspended in 25 µl of water. The transposition reaction mix consisted of 25 µl of TD buffer, 2.5 µl of Tn5 transposase (Illumina cat. 20034198), and 22.5 µl of nuclease-free water containing the nuclei. The mix was incubated for 30 min at 37 °C. Transposed DNA fragments were purified using a Qiagen Reaction MiniElute kit (Qiagen). Clean DNA was run with PCR amplification to incorporate the indexes, which were a universal index and a unique i7 index per sample. (IDT primers outlined in Buenrostro 2013 paper) and amplified by PCR for 11 cycles using NEBNext high fidelity 2× PCR master mix (New England Biolabs).  PCR products were cleaned with 0.9x volume of Ampure XP beads (Beckman Coulter), and amplified fragment size was verified on an Agilent 2100 Bioanalyzer system (Agilent) with high sensitivity DNA screentape. ATAC-seq libraries were quantified by quantitative PCR with the Roche-kapa Illumina quantification kit. Paired-end sequencing was performed on an Illumina Novaseq6000 system with an SP100 cycle kit sequenced as paired-end 50 bases.

value: Nb-trained


title: Tr-NAM-2

source_name: nerve- and airway-associated macrophages


title: Tr-NAM-1

value: nerve- and airway-associated macrophages


title: SS-NAM-3

value: naïve


title: Tr-NAM-3


title: SS-NAM-2


title: SS-NAM-4


title: SS-NAM-1


title: Nanopore 5mC data from Idh1-R132H expressing 32D cells after 5 days of Aza, rep 1

status: Public on May 07 2026

city: Heidelberg

first: Daniel

middle: B.

last: Lipka

address: INF 581

department: Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology

country: Germany

institute: German Cancer Research Center

description: Library name: 32D_R132H_1_Aza

data_processing:
Basecalling and alignment of ONT data was conducted using dorado (https://github.com/nanoporetech/dorado) with the „dna_r10.4.1_e8.2_400bps_hac@v5.0.0“ basecalling model and modified bases model „dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v3“. Data was thereby aligned against the mm10 reference genome using a dorado “min-qscore” filter of 10. bai files were subsequently sorted using the samtools “sort” function followed by demultiplexing using dorado “demux”. Demultiplexed bai files were indexed using samtools “index” followed by extraction of bedMethyl files using modkit “pileup” with the “--combine-strands” and “—cpg” flags. Output files were processed using the R bedGraph reader methrix (PMID 33346800). Uncovered CpGs were removed from the dataset and global methylation levels determined based on 20,000 randomly selected CpGs.
Assembly: mm10
Supplementary files format and content: bigWig , BAM-fles (basecalls and methylation calls), BAI-files

source_name: 32D cell line

growth_protocol: Empty-vector or Idh1-R132H expressing 32D cells were cultured under steady-state conditions or were treated either with AGI-5198 or 5-acazitidine for 5 days.

extract_protocol:
32D cells expressing either the empty vector (EV) or the Idh1-R132 mutant were treated with AGI or AZA for 5 days. At the end of treatment period, 106 cells were harvested for DNA isolation. For each genotype (EV and Idh1-R132) and treatment condition (AGI and AZA), two biological replicates were collected. DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s protocol for cultured cells. DNA was eluted in 50 µL pre-warmed Buffer EB twice. DNA concentrationswas quantified using the Qubit High Sensitivity (HS) dsDNA Assay kit according to the manufacturer’s instructions.
A total of 1000 ng of genomic DNA per sample was sheared with Covaris g-TUBE by centrifuging at 4200 rpm for 1 min, followed by an additional 1 min at 4200 rpm after inverting the tube. Fragment size distribution was assessed using 1 µl of sheared DNA with Agilent Genomic DNA ScreenTape Assay following manufacturer’s instructions. Libraries were prepared using the ONT Ligation sequencing gDNA protocol with the Multiplex Sequencing Kit V14 (Cat # SQK-MLK114.96-XL, ONT, Oxford, UK) by incorporating native barcoding and long fragment buffer. For sequencing, libraries were multiplexed equimolarly and sequenced together. Sequencing was performed on a PromethION P24 ONT device (ONT, Oxford, UK) using R10.4.1 flow cells (Cat# FLO-PRO114M, ONT, Oxford, UK), with basecalling configured to detect 5mC and 5hmC in the CpG context.

treatment_protocol: Cells were treated either with 1 µM AGI-5198 or 500 nM 5-acazitidine for 5 days.

value: 32D cell line


title: Nanopore 5mC data from empty-vector expressing 32D cells after 5 days of Aza, rep 2

description: Library name: 32D_EV_2_Aza

value: Control


title: Nanopore 5mC data from empty-vector expressing 32D cells after 5 days of Aza, rep 1

description: Library name: 32D_EV_1_Aza


title: Nanopore 5mC data from empty-vector expressing 32D cells after 5 days of AGI-5198, rep 2

description: Library name: 32D_EV_2_AGI-5198


title: Nanopore 5mC data from Idh1-R132H expressing untreated 32D cells, rep 2

description: Library name: 32D_R132H_2_untreated


title: Nanopore 5mC data from Idh1-R132H expressing untreated 32D cells, rep 1

description: Library name: 32D_R132H_1_untreated


title: Nanopore 5mC data from empty-vector expressing untreated 32D cells, rep 2

description: Library name: 32D_EV_2_untreated


title: Nanopore 5mC data from empty-vector expressing 32D cells after 5 days of AGI-5198, rep 1

description: Library name: 32D_EV_1_AGI-5198


title: Nanopore 5mC data from Idh1-R132H expressing 32D cells after 5 days of AGI-5198, rep 1

description: Library name: 32D_R132H_1_AGI-5198


title: Nanopore 5mC data from empty-vector expressing untreated 32D cells, rep 1

description: Library name: 32D_EV_1_untreated


title: SK-N-BE(2), c-IDR, rep2

status: Public on May 05 2026

city: Lund

first: Stina

last: Östenberg

address: Sölvegatan 19

country: Sweden

institute: Lund University

description: Library name: BE2c_CIDR_rep2_S7

data_processing:
Raw sequencing reads were quality trimmed using fastp, and ribosomal RNA reads were removed.
Reads were aligned to the human reference genome (GRCh38) using STAR, and transcript quantification was performed with Salmon.
Gene-level counts were generated using featureCounts based on GENCODE v45 annotation.
Data processing was performed using the nf-core/rnaseq pipeline.
Assembly: GRCh38 (Homo sapiens)
Supplementary files format and content: salmon.merged.gene_counts.tsv contains raw read count of all genes.
Supplementary files format and content: salmon.merged.gene_tpm.tsv contains TPM normalized values of all genes.

growth_protocol: Cells were cultured at 37°C, 21% O2, and 5% CO2 in DMEM suplemented with 10% FBS.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit according to manufacturer’s instructions.
Total RNA (~250 ng input) was used for library preparation with the Illumina Stranded mRNA Prep kit (poly(A) selection and fragmentation), followed by first- and second-strand cDNA synthesis, end repair, A-tailing, and adapter ligation. Libraries were amplified using 13 PCR cycles and indexed with unique dual indexes. Library quality and concentration were assessed using TapeStation (Agilent) and Qubit fluorometry (Thermo Fisher Scientific).

value: Neuroblastoma

value: cIDR


title: SK-N-BE(2), c-IDR, rep3

description: Library name: BE2c_CIDR_rep3_S11


title: SK-N-BE(2), N‑CTAD, rep3

description: Library name: BE2c_NTAD_rep3_S10

value: NCTAD


title: SK-N-BE(2), N‑CTAD, rep1

description: Library name: BE2c_NTAD_rep1_S2


title: SK-N-BE(2), N‑CTAD, rep2

description: Library name: BE2c_NTAD_rep2_S6


title: SK-N-BE(2), c-IDR, rep1

description: Library name: BE2c_CIDR_rep1_S3


title: SK-N-BE(2), FL, rep4

description: Library name: BE2c_WT_rep4_S13

value: FL


title: SK-N-BE(2), FL, rep2

description: Library name: BE2c_WT_rep2_S5


title: SK-N-BE(2), WT, rep4

description: Library name: BE2c_CTRL_rep4_S16

value: WT


title: control_11_2

status: Public on Apr 27 2026

type: genomic

city: Edinburgh

first: Dan

last: Sarni

address: Crewe Road

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Infinium® MethylationEPIC BeadChip performed according to manufacturer instructions by Edinburgh ECRF

data_processing:
Raw idat files were processed to beta and detection p-values using the Bioconducter package minfi (v1.50.0) using single-sample normal exponential out of band (ss noob) background correction and dye bias normalization together with Bioconductor EPIC array annotations (IlluminaHumanMethylationEPICmanifest and IlluminaHumanMethylationEPICanno.ilm10b4.hg19). Probes overlapping known SNPs (MAF>1% and within 5 bp of the probe’s CpG target, based on Zhou et al PMID: 27924034), located on sex chromosomes, or with detection p-value > 0.01 were excluded.
Normalized mean Beta and detection p-value.

label: Cy3 and Cy5

source_name: blood

extract_protocol: Genomic DNA was extracted using Dneasy Blood and Tissue Kit (QIAGEN).

value: blood

value: peripheral blood leukocytes

tag: age


title: patient_10

scan_protocol: Infinium® MethylationEPIC BeadChip performed according to manufacturer instructions by Edinburgh ECRF

value: DNMT3A p.S304del heterozygous


title: patient_7

label_protocol: Infinium® MethylationEPIC BeadChip performed according to manufacturer instructions by Edinburgh ECRF

value: DNMT3A p.W330S heterozygous


title: control_9_1

value: unknown


title: control_9_2


title: patient_8

value: DNMT3A p.W306R heterozygous


title: control_7_2


title: control_7_1


title: patient_11

value: DNMT3A p.L300R heterozygous


title: patient_4


title: patient_2

value: DNMT3A p.W330R heterozygous


title: control_4


title: control_3


title: UNCseq1757 ROI2 ARID1A Negitive_Mutated

status: Public on Apr 22 2026

city: Chapel Hill

first: Andrew

middle: B

last: Gladden

state: NC

address: 160 N. Medical Drive

department: Department of Pathology & Laboratory Medicine

institute: The University of North Carolina at Chapel Hill

description: Library name: UNCseq1757 ROI2 ARID1A Neg

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

source_name: Endometrium

growth_protocol: No growth protocol

extract_protocol:
Nanostring antigen retrieval protocol
Nanostring library construction protocol

treatment_protocol: No treatment protocol

value: Endometrium

value: ARID1A Mutated

value: total RNA


title: UNCseq1758 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq1757 ROI3 ARID1A Neg


title: UNCseq1757 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq1757 ROI1 ARID1A Neg


title: UNCseq1084 ROI5 ARID1A Negitive_Mutated

description: Library name: UNCseq1084 ROI5 ARID1A Neg


title: UNCseq1804 ROI4 ARID1A Negitive_Mutated

description: Library name: UNCseq1804 ROI4 ARID1A Neg


title: UNCseq1804 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq1804 ROI1 ARID1A Neg


title: UNCseq0585 ROI6 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI6 ARID1A Neg


title: UNCseq0585 ROI5 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI5 ARID1A Neg


title: UNCseq0585 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI2 ARID1A Neg


title: UNCseq0585 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI1 ARID1A Neg


title: SK-N-BE(2), FL, rep3

description: Library name: BE2c_WT_rep3_S9


title: control_11_1

value: Control


title: UNCseq0886 ROI6 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI6 ARID1A Pos


title: SK-N-BE(2), WT, rep2

description: Library name: BE2c_CTRL_rep2_S8

value: Neuroblastoma


title: UNCseq0886 ROI5 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI5 ARID1A Pos


title: UNCseq0886 ROI4 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI4 ARID1A Pos


title: UNCseq0886 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI3 ARID1A Pos


title: UNCseq0886 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI2 ARID1A Pos


title: UNCseq0886 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI1 ARID1A Pos


title: UNCseq2451 ROI6 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI6 ARID1A Neg

value: ARID1A Wild-Type


title: UNCseq2451 ROI5 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI5 ARID1A Neg


title: UNCseq2451 ROI3 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI3 ARID1A Neg


title: UNCseq2451 ROI4 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI4 ARID1A Neg


title: UNCseq2451 ROI2 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI2 ARID1A Neg


title: UNCseq2451 ROI1 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI1 ARID1A Neg


title: UNCseq1480 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq1480 ROI3 ARID1A Neg


title: UNCseq1480 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq1480 ROI2 ARID1A Neg


title: UNCseq1480 ROI1  ARID1A Negitive_Mutated

description: Library name: UNCseq1480 ROI1  ARID1A Neg


title: UNCseq1480 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq1480 ROI3 ARID1A Pos


title: UNCseq1480 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq1480 ROI2 ARID1A Pos


title: UNCseq1480 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq1480 ROI1 ARID1A Pos


title: UNCseq1357 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq1357 ROI1 ARID1A Neg


title: UNCseq1357 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq1357 ROI3 ARID1A Neg


title: UNCseq1357 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq1357 ROI2 ARID1A Neg


title: UNCseq1357 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq1357 ROI3 ARID1A Pos


title: UNCseq1357 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq1357 ROI1 ARID1A Pos


title: UNCseq0451 ROI6 ARID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI6 ARID1A Neg


title: UNCseq0451 ROI5 RID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI5 RID1A Neg


title: UNCseq0451 ROI4 ARID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI4 ARID1A Neg


title: UNCseq0451 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI3 ARID1A Neg


title: UNCseq0451 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI2 ARID1A Neg


title: UNCseq1531 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq1531 ROI3 ARID1A Neg


title: UNCseq0451 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI1 ARID1A Neg


title: UNCseq1531 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq1531 ROI2 ARID1A Neg


title: UNCseq1531 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq1531 ROI1 ARID1A Neg


title: UNCseq1531 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq1531 ROI3 ARID1A Pos


title: UNCseq1531 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq1531 ROI2 ARID1A Pos


title: UNCseq1531 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq1531 ROI1 ARID1A Pos


title: UNCseq2155 ROI3 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2155 ROI3 ARID1A Neg


title: Nanopore 5mC data from Idh1-R132H expressing 32D cells after 5 days of Aza, rep 2

description: Library name: 32D_R132H_2_Aza

value: 32D cell line


title: UNCseq2155 ROI2 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2155 ROI2 ARID1A Neg


title: Nanopore 5mC data from Idh1-R132H expressing 32D cells after 5 days of AGI-5198, rep 2

description: Library name: 32D_R132H_2_AGI-5198


title: UNCseq2155 ROI1 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2155 ROI1 ARID1A Neg


title: SK-N-BE(2), c-IDR, rep4

description: Library name: BE2c_CIDR_rep4_S15

value: cIDR


title: UNCseq2155 ROI3 ARID1A Positive_Wild-Type

description: Library name: UNCseq2155 ROI3 ARID1A Pos


title: UNCseq2155 ROI2 ARID1A Positive_Wild-Type

description: Library name: UNCseq2155 ROI2 ARID1A Pos


title: SK-N-BE(2), N‑CTAD, rep4

description: Library name: BE2c_NTAD_rep4_S14

value: NCTAD


title: UNCseq2171 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq2171 ROI3 ARID1A Neg


title: SK-N-BE(2), WT, rep3

description: Library name: BE2c_CTRL_rep3_S12

value: WT


title: SK-N-BE(2), FL, rep1

description: Library name: BE2c_WT_rep1_S1

value: FL


title: UNCseq1357 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq1357 ROI2 ARID1A Pos


title: UNCseq2171 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq2171 ROI2 ARID1A Neg


title: UNCseq2155 ROI1 ARID1A Positive_Wild-Type

description: Library name: UNCseq2155 ROI1 ARID1A Pos


title: SK-N-BE(2), WT, rep1

description: Library name: BE2c_CTRL_rep1_S4


title: control_10

value: blood

value: peripheral blood leukocytes


title: A549 Cells, U2AF1 S34S, sample 4

status: Public on Apr 29 2026

city: Boston

first: David

middle: M

last: Walter

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description:
Library name: A549 S34S 3.6
A549_S3_6
This Sample contains 2 separate sequencing runs in SRA: SRR38227765 and SRR38227766. SRR38227766 is a repeated sequencing of the sample.

data_processing:
Paired-end clean reads were aligned to the reference genome GRCh3870 using Hisat2 (v2.0.5). FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. rMATS (4.1.0) was used for alternative splicing analysis.
Assembly: GRCh38
Supplementary files format and content: Gene counts for short-read RNA-sequencing data

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 50 ug/ml gentamicin

extract_protocol:
RNA for each cell clone was extracted using the RNeasy Plus Mini Kit (QIAGEN, 74134) and quantified using the Qubit RNA Broad Range Quantification Assay Kit (Invitrogen, Q10210)
Short-read RNA-sequencing was performed with Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. The samples were then processed by end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library quality was checked with Qubit and real-time PCR for quantification and BioAnalyzer for size distribution detection.

treatment_protocol: A subset of cells underwent genome engineering by prime editing

value: lung adenocarcinoma


title: UNCseq2171 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq2171 ROI1 ARID1A Neg


title: patient_9

value: DNMT3A p.K335E heterozygous


title: UNCseq2171 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq2171 ROI2 ARID1A Pos


title: UNCseq2171 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq2171 ROI3 ARID1A Pos


title: UNCseq1550 ROI6 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI6 ARID1A Pos


title: UNCseq2171 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq2171 ROI1 ARID1A Pos


title: UNCseq1550 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI3 ARID1A Pos


title: UNCseq1550 ROI4 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI4 ARID1A Pos


title: UNCseq1550 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI2 ARID1A Pos


title: UNCseq1550 ROI5 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI5 ARID1A Pos


title: UNCseq2101 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq2101 ROI3 ARID1A Pos


title: UNCseq2101  ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq2101  ROI2 ARID1A Pos


title: UNCseq2101 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq2101 ROI3 ARID1A Neg


title: UNCseq2101 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq2101 ROI1 ARID1A Pos


title: UNCseq2101 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq2101 ROI2 ARID1A Neg


title: UNCseq2101 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq2101 ROI1 ARID1A Neg


title: UNCseq1945 ROI6  ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI6  ARID1A Pos


title: UNCseq1945 ROI5 ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI5 ARID1A Pos


title: UNCseq1757 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq1757 ROI3 ARID1A Pos


title: UNCseq1945 ROI4  ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI4  ARID1A Pos


title: UNCseq1945 ROI3  ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI3  ARID1A Pos


title: UNCseq1757 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq1757 ROI2 ARID1A Pos


title: UNCseq1945 ROI1  ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI1  ARID1A Pos


title: UNCseq0468 ROI5 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI5 ARID1A Pos


title: UNCseq1945 ROI2  ARID1A Positive_Wild-Type

description: Library name: UNCseq1945 ROI2  ARID1A Pos


title: UNCseq0468 ROI2 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI2 ARID1A Pos


title: UNCseq0468 ROI4 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI4 ARID1A Pos


title: UNCseq0468 ROI3 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI3 ARID1A Pos


title: UNCseq1550 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI1 ARID1A Pos


title: UNCseq0468 ROI1 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI1 ARID1A Pos


title: UNCseq0591 ROI3 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI3 ARID1A Pos


title: UNCseq0591 ROI6 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI6 ARID1A Pos


title: UNCseq0591 ROI2 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI2 ARID1A Pos


title: No Template Control

description: Library name: No Template Control

value: No Template Control


title: UNCseq0590 ROI1 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI1 ARID1A Pos


title: LN229,CRISPRa,RM6RSL3,rep3

status: Public on Apr 16 2026

first: Thomas

last: O'Loughlin

address: 1470 Madison Avenue

institute: Icahn School of Medicine

description:
Library name: Sample_31
CRISPRa_counts_raw.txt
i24a

data_processing:
ScreenPro2 package (v0.2.10) used for processing dual-guide (V3) CRISPRa/i screens – https://github.com/ArcInstitute/ScreenPro2. Paired-end deep sequencing FASTQ files are first processed using the `GuideCounter` module to capture guide pairs counts mapped to the reference guide sequences provided in a library table. Then, the output count matrix per sample is then used to calculate drug screen phenotypes using the `PhenoScore` module.
Supplementary files format and content: .txt file of raw counts
Library strategy: CRISPR Screen

source_name: LN229 dCas9-Suntag

growth_protocol: LN229 cells were cultured in DMEM (Gibco # 11965-084) supplemented with 10% FBS (VWR Seradigm # 97068-085), 1 mM sodium pyruvate (Gibco # 11360-070), and 100 U/mL penicillin plus 100 µg/mL streptomycin (Gibco # 15140-122). Cells were cultured at 37°C and 5% CO2 in a humidified atmosphere.

extract_protocol:
Genomic DNA was purified from cell pellets using NucleoSpin Blood L gDNA extraction kits (Nacherey-Nagel # 740954) in accordance with the manufacturer’s instructions and yields and purity were confirmed by nanodrop.
Amplicons were generated by PCR to introduce sequencing adaptors and sample-specific indexes using a common forward primer within the U6 promoter and reverse primers which bind the sgRNA constant region downstream of the second sgRNA and contain the sample-specific indexes. PCR reactions comprised 2x NEB Next Ultra II Q5 polymerase (NEB # M0544), 10 µg of purified gDNA and 1 µl of each 100 µM primer per 100 μl reaction. PCR amplification was performed with the following cycling conditions: denaturation at 98ºC for 30 secs, 22 cycles of denaturation at 98ºC for 10 secs then annealing and extension at 67ºC for 75 secs, and a final extension at 72ºC for 5 mins. All gDNA was PCR amplified and all reactions for each sample were mixed post-amplification. 300 µl of amplified PCR was subject to a 0.5-0.65X double-sided SPRI selection to enrich for the amplicon and remove excess primer. Sample purity and concentration were determined using an Agilent Tapestation and used to calculate equimolar sample pooling. Pooled libraries were sequenced on a NextSeq550 or NovaSeq 6000 platform with paired end reads using custom read 1, read 2 and index read 1 primers and 10% PhiX achieving a minimum of 6 million reads per sample (i.e. ≥300 reads/library element).

treatment_protocol: LN229 CRISPRi or CRISPRa cells were transduced with compact genome-scale dual-sgRNA libraries generously donated by Jonathan Weissman. Cells were transduced at an MOI of ~0.3 to achieve representation of each sgRNA in an average of >500 cells (500x coverage). At 48 and 72 hrs post-transduction cells were dosed with 3 µg/ml puromycin to select for sgRNA-positive cells. Following selection, sgRNA-positive cells were subsequently recovered in fresh medium for an additional 3 days. 6 days post-transduction cells pellets of 25 million cells were frozen to determine sgRNA composition at selection initiation (T0). Remaining cells were split into treatment conditions in triplicate. For CRISPRi screens conditions were: DMSO, RM-006 1.56 nM, and RM-006 0.098 nM. For CRISPRa screens conditions were: DMSO, RM-006 1.56 nM, RSL3 46.875 nM, and RM-006 1.56 nM+RSL3 46.875 nM. Cells were maintained under selection pressure at 1000x library coverage with passaging every 1 to 4 days as necessary for a total of 14-15 days for the CRISPRi and 12 days for the CRISPRa screens. At the screen endpoint cells were harvested and frozen in 25 million cell pellets prior to library preparation for sequencing.

value: LN229 dCas9-Suntag

value: glioblastoma


title: LN229,CRISPRa,RM6RSL3,rep2

description:
Library name: Sample_30
CRISPRa_counts_raw.txt
i23a


title: UNCseq0591 ROI5 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI5 ARID1A Pos

value: Endometrium


title: LN229,CRISPRa,RM6RSL3,rep1

description:
Library name: Sample_29
CRISPRa_counts_raw.txt
i22a


title: LN229,CRISPRa,RSL3,rep3

description:
Library name: Sample_28
CRISPRa_counts_raw.txt
i21a


title: LN229,CRISPRa,RSL3,rep2

description:
Library name: Sample_27
CRISPRa_counts_raw.txt
i20a


title: LN229,CRISPRa,RM6,rep3

description:
Library name: Sample_25
CRISPRa_counts_raw.txt
i18a


title: LN229,CRISPRa,RSL3,rep1

description:
Library name: Sample_26
CRISPRa_counts_raw.txt
i19a


title: LN229,CRISPRa,RM6,rep2

description:
Library name: Sample_24
CRISPRa_counts_raw.txt
i17a


title: LN229,CRISPRa,veh,rep2

description:
Library name: Sample_21
CRISPRa_counts_raw.txt
i14a

value: DMSO


title: LN229,CRISPRa,T0,rep3

description:
Library name: Sample_19
CRISPRa_counts_raw.txt
i12a


title: LN229,CRISPRa,veh,rep1

description:
Library name: Sample_20
CRISPRa_counts_raw.txt
i13a


title: LN229,CRISPRi,RM6lo,rep3,exp2

description:
Library name: Sample_16
CRISPRi_counts_raw.txt
i18i

source_name: LN229 dCas9-KRAB

value: LN229 dCas9-KRAB


title: LN229,CRISPRa,T0,rep1

description:
Library name: Sample_17
CRISPRa_counts_raw.txt
i10a


title: LN229,CRISPRi,veh,rep3,exp2

description:
Library name: Sample_13
CRISPRi_counts_raw.txt
i15i


title: LN229,CRISPRi,RM6lo,rep1,exp2

description:
Library name: Sample_14
CRISPRi_counts_raw.txt
i16i


title: LN229,CRISPRi,veh,rep1,exp2

description:
Library name: Sample_11
CRISPRi_counts_raw.txt
i13i


title: LN229,CRISPRi,veh,rep2,exp2

description:
Library name: Sample_12
CRISPRi_counts_raw.txt
i14i


title: LN229,CRISPRi,RM6hi,rep3,exp1

description:
Library name: Sample_10
CRISPRi_counts_raw.txt
i12i


title: LN229,CRISPRi,veh,rep3,exp1

description:
Library name: Sample_7
CRISPRi_counts_raw.txt
i09i


title: LN229,CRISPRi,RM6hi,rep1,exp1

description:
Library name: Sample_8
CRISPRi_counts_raw.txt
i10i


title: LN229,CRISPRi,veh,rep2,exp1

description:
Library name: Sample_6
CRISPRi_counts_raw.txt
i08i


title: LN229,CRISPRi,T0,rep2,exp2

description:
Library name: Sample_4
CRISPRi_counts_raw.txt
i06i


title: LN229,CRISPRi,veh,rep1,exp1

description:
Library name: Sample_5
CRISPRi_counts_raw.txt
i07i


title: LN229,CRISPRi,T0,rep1,exp2

description:
Library name: Sample_3
CRISPRi_counts_raw.txt
i05i


title: LN229,CRISPRi,T0,rep2,exp1

description:
Library name: Sample_2
CRISPRi_counts_raw.txt
i04i


title: LN229,RM6,0.39nM,rep2

description:
Library name: Sample_8
R6-M2

data_processing:
UMIs were extracted from the fastq files with umi_tools and cutadapt was used to remove short and low-quality reads. The reads were aligned to the human GENCODE v.34 reference genome using STAR aligner and the duplicate reads were collapsed using umi_tools. Gene level counts were measured using HTSeq.
Assembly: GRCh38.p13
Supplementary files format and content: .txt file of raw counts

extract_protocol:
RNA was extracted from cells using Quick-RNA microprep kit (Zymo # R1050) according to the manufacturer's instructions
3’ RNA-seq libraries were generated using a QuantSeq FWD Kit (Lexogen # 015) with UMI add-on module according to the manufacturer’s instructions. Briefly, 350 ng of input RNA was used for first-strand cDNA synthesis with an oligo(dT) primer, RNA was removed, second strand synthesis was performed with random primers containing unique molecular identifiers, and the generated cDNA purified using magnetic beads. Purified cDNA was amplified by 16 cycles of PCR to generate sufficient material for sequencing and to introduce complete sequencing adapters. Amplified libraries were subject to a further purification step and then assessed for yield and composition on an Agilent Bioanalyzer. Samples were pooled equimolarly, and pooled libraries were subsequently sequenced on an Illumina NextSeq550 platform using a High Output Reagent Cartridge v2 (Illumina # 15057934) in single-end 65 bp configuration.

treatment_protocol: Cells were treated with vehicle (DMSO) or 0.098, 0.39, 1.56 nM RM-006 for 72 hours

value: wild-type


title: LN229,RM6,0.39nM,rep1

description:
Library name: Sample_7
R6-M1


title: LN229,RM6,0.098nM,rep1

description:
Library name: Sample_5
R6-L1


title: LN229,RM6,0.098nM,rep2

description:
Library name: Sample_6
R6-L2


title: LN229,RM6,1.56nM,rep1

description:
Library name: Sample_3
R6-H1


title: LN229,veh,rep2

description:
Library name: Sample_2
D-2


title: LN229,veh,rep1

description:
Library name: Sample_1
D-1


title: LN229,RM6,1.56nM,rep2

description:
Library name: Sample_4
R6-H2


title: LN229,GFP,rep2

description: Library name: Sample_2

data_processing:
By Plasmidsaurus: "Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file. Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values. Functional enrichment, when available, is performed using gene set enrichment analysis with gseapy v0.12 using the MSigDB Hallmark gene set."
Assembly: hg38
Supplementary files format and content: .tsv file of raw counts and cpm

extract_protocol:
By Plasmidsaurus: Total RNA extracted using a bead-based extraction approach from cells preserved in Zymo DNA/RNA Shield. Post-extraction RNA concentration assessed using a fluorescence based plate reader assay.
By Plasmidsaurus: mRNA converted into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification. cDNA generated using a poly(dT)VN primer

treatment_protocol: Cells were transduced with GFP or SREBP1 cDNA, puro selected to purity, and then harvested in DNA/RNA shield for RNA extraction

value: GFP


title: LN229,SREBP1,rep2

description: Library name: Sample_4


title: LN229,SREBP1,rep1

description: Library name: Sample_3


title: LN229,GFP,rep1

description: Library name: Sample_1


title: T21, R23877

status: Public on Apr 08 2026

city: New York City

first: Michael

middle: S

last: Breen

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Library name: R23877

data_processing:
Raw sequencing reads were processed using the RAPiD-nf pipeline, with alignment to the GRCh38 reference genome performed using STAR v2.7.3a.
Alignment quality was assessed with RSeQC and Picard. PCR duplicates were marked but not removed prior to quantification.
Gene-level counts were generated using featureCounts (Subread v2.0.1) with GENCODE v32 annotations.
Counts were normalized usingthe VOOM method from the limma package (v3.48.3), and log2-transformed expression matrices were created seperately for DLPFC and hippocampus.
Assembly: GRCh38 (Ensembl release 95)
Supplementary files format and content: tab-delimited text file (T21_raw_counts.txt) includes raw counts for each sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from frozen dorosolateral prefrontal cortex and hippocampal tissues using the AllPrep DNA/RNA Mini Kit, and only samples with RIN ≥ 9.0 were included.
RNA-seq libraries were generatred from 300 ng of high-quality total RNA using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold.

value: Hippocampus

tag: karyotype

tag: rin

tag: gestational age

tag: Sex

value: Male

tag: race

value: Caucasian


title: T21, R23874

description: Library name: R23874


title: T21, R23871

description: Library name: R23871


title: T21, R23872

description: Library name: R23872

value: Female


title: T21, R23870

description: Library name: R23870


title: T21, R23869

description: Library name: R23869


title: T21, R23868

description: Library name: R23868


title: T21, R23852

description: Library name: R23852


title: T21, R23844

description: Library name: R23844


title: T21, R23861

description: Library name: R23861


title: T21, R23843

description: Library name: R23843


title: T21, R23831

description: Library name: R23831


title: T21, R23842

description: Library name: R23842


title: T21, R23835

description: Library name: R23835


title: Control, R23981

description: Library name: R23981

value: Control


title: Control, R23876

description: Library name: R23876


title: Control, R23873

description: Library name: R23873


title: Control, R23863

description: Library name: R23863


title: Control, R23865

description: Library name: R23865


title: Control, R23862

description: Library name: R23862


title: Control, R23858

description: Library name: R23858


title: Control, R23860

description: Library name: R23860


title: Control, R23857

description: Library name: R23857


title: Control, R23856

description: Library name: R23856


title: Control, R23855

description: Library name: R23855


title: T21, R23846

description: Library name: R23846


title: Control, R23853

description: Library name: R23853


title: Control, R23851

description: Library name: R23851


title: Control, R23850

description: Library name: R23850


title: Control, R23849

description: Library name: R23849


title: Control, R23848

description: Library name: R23848


title: Control, R23847

description: Library name: R23847


title: Control, R23845

description: Library name: R23845


title: Control, R23841

description: Library name: R23841


title: AML195

description: Library name: Sample195

value: Bone Marrow

value: AML


title: AML189

description: Library name: Sample189


title: AML176

description: Library name: Sample176


title: Control, R23839

description: Library name: R23839


title: Control, R23838

description: Library name: R23838


title: Control, R23837

description: Library name: R23837


title: Control, R23834

description: Library name: R23834


title: Control, R23836

description: Library name: R23836


title: Control, R23832

description: Library name: R23832


title: T21, R23830

description: Library name: R23830

source_name: DLPFC

value: DLPFC


title: Control, R23833

description: Library name: R23833


title: Control, R23859

description: Library name: R23859


title: UNCseq0468 ROI6 ARID1A Positive_Wild-Type

description: Library name: UNCseq0468 ROI6 ARID1A Pos

value: ARID1A Wild-Type

value: total RNA


title: Control, R23829

description: Library name: R23829


title: T21, R23828

description: Library name: R23828


title: UNCseq0591 ROI4 ARID1A Positive_Wild-Type

description: Library name: UNCseq0590 ROI4 ARID1A Pos


title: T21, R23827

description: Library name: R23827


title: Control, R23826

description: Library name: R23826


title: T21, R23825

description: Library name: R23825


title: T21, R23823

description: Library name: R23823


title: T21, R23824

description: Library name: R23824


title: T21, R23822

description: Library name: R23822


title: T21, R23821

description: Library name: R23821


title: AML155

description: Library name: Sample155


title: AML151

description: Library name: Sample151


title: T21, R23819

description: Library name: R23819


title: LN229,CRISPRa,veh,rep3

description:
Library name: Sample_22
CRISPRa_counts_raw.txt
i15a

value: LN229 dCas9-Suntag


title: LN229,CRISPRa,RM6,rep1

description:
Library name: Sample_23
CRISPRa_counts_raw.txt
i16a

value: glioblastoma


title: T21, R23817

description: Library name: R23817


title: Control, R23818

description: Library name: R23818


title: Control, R18814

description: Library name: R18814


title: Control, R23816

description: Library name: R23816


title: T21, R18809

description: Library name: R18809


title: Control, R23815

description: Library name: R23815


title: LN229,CRISPRa,T0,rep2

description:
Library name: Sample_18
CRISPRa_counts_raw.txt
i11a


title: Control, R23814

description: Library name: R23814


title: Control, R18821

description: Library name: R18821


title: LN229,CRISPRi,RM6lo,rep2,exp2

description:
Library name: Sample_15
CRISPRi_counts_raw.txt
i17i


title: Control, R23813

description: Library name: R23813


title: Control, R23812

description: Library name: R23812


title: Control, R23811

description: Library name: R23811


title: LN229,CRISPRi,RM6hi,rep2,exp1

description:
Library name: Sample_9
CRISPRi_counts_raw.txt
i11i


title: Control, R18820

description: Library name: R18820


title: T21, R23810

description: Library name: R23810


title: T21, R18807

description: Library name: R18807


title: Control, R23809

description: Library name: R23809


title: Control, R23808

description: Library name: R23808


title: Control, R23807

description: Library name: R23807


title: Control, R23805

description: Library name: R23805


title: Control, R23806

description: Library name: R23806


title: T21, R18805

description: Library name: R18805


title: T21, R18806

description: Library name: R18806


title: Control, R23804

description: Library name: R23804


title: T21, R18803

description: Library name: R18803


title: T21, R18804

description: Library name: R18804


title: LN229,CRISPRi,T0,rep1,exp1

description:
Library name: Sample_1
CRISPRi_counts_raw.txt
i03i


title: Control, R18802

description: Library name: R18802


title: Control, R23803

description: Library name: R23803


title: AML124

description: Library name: Sample124


title: Control, R18815

description: Library name: R18815


title: Control, R18818

description: Library name: R18818


title: T21, R18801

description: Library name: R18801


title: Control, R13656

description: Library name: R13656


title: Control, R13654

description: Library name: R13654


title: Control, R18816

description: Library name: R18816


title: T21, R18800

description: Library name: R18800


title: Control, R18811

description: Library name: R18811


title: AP-Seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 3

status: Public on Apr 02 2026

city: Paris

first: Anton

last: Granzhan

address: 45 rue des Saints-Pères

department: UMR8601 LCBPT

country: France

institute: Université Paris Cité

description: Library name: Rep3 XR AP Seq

data_processing:
Data management, quality control, and primary analysis were carried out by the Institut Curie Bioinformatics platform.
Unless stated otherwise, data processing was performed using DeepTools following key tools, including BigwigCompare, multiBigwigSummary, plotCorrelation, computeMatrix, and plotProfile. The BigwigCompare tool was used to calculate the relative enrichment of AP sites by comparing the BigWig file of the enriched sample against the input. This comparison was performed using a log2 transformation across various bin sizes: 100bp, 1kb, 10kb, 100kb, and 1Mb. The resulting relative enrichment files were then processed with multiBigwigSummary to generate a matrix, which was subsequently subjected to statistical correlation analysis using Pearson or Spearman correlation. Data were visualized with the Integrative Genomics Viewer version 2.17.2 (http://software.broadinstitute.org/software/igv/). Genome-wide feature sets were obtained from the UCSC Genome Browser. Chromatin features for HepG2 cells were retrieved from the data repository generated in the context of the ENCODE consortium
BigWig files were generated using the GenomicRanges package in R, where scores correspond to normalized fragment coverage across genomic coordinates. Peaks were identified using MACS2 (v2) with default parameters, and reported in narrowPeak format, representing enriched regions of binding.
AP site enrichment was analyzed with DeepTools using BigwigCompare (log2-transformed, 100 bp–1 Mb bins), multiBigwigSummary for correlation with samples and HepG2 histone marks, and computeMatrix for distribution across genomic features (TSS, TTS, 5′/3′UTRs). Visualization was done with plotCorrelation, plotProfile, and IGV.
Assembly: hg19, T2T-CHM13
Supplementary files format and content: bigWig

growth_protocol: HepG2 were purchased from ATCC and cultivated at 37 °C and 5% CO2 in Dulbecco’s modified Eagle medium (Gibco DMEM+GlutaMax, ThermoFisher, cat. n° 31966021) supplemented with 1% penicillin/ streptomycin, and 10% heat-inactivated fetal bovine serum (FBS) in 75-T flask. Cells were harvested using 1X trypsin (Gibco TrypLE Express, ThermoFisher, cat. n° 12605-010,) and, when needed, cell washing was done using 1X DPBS (Gibco, ThermoFisher, cat. n° 14190-094).

extract_protocol:
Total genomic DNA was extracted from washed cell pellets using the DNeasy Blood & Tissue Kit (Qiagen, cat. n° 69506), following the manufacturer's instructions with slight modifications. Briefly, each washed cell pellet was resuspended in 200 µL of fresh, cold PBS. To this, 4 µL of RNase A (Qiagen, cat. n° 19101) was added, and the mixture was incubated at room temperature for 2 minutes. Subsequently, 20 µL of Proteinase K (Qiagen, cat. n° 19131) and 200 µL of Buffer AL (without ethanol) were added, and the mixture was thoroughly mixed and incubated at 37 °C for 10 minutes. After incubation, samples were vortexed until homogeneous, and 200 µL of cold absolute ethanol was added to precipitate the DNA. The mixture was transferred to a spin column and centrifuged at 6000 × g for 1 minute at 4 °C. The flow-through was discarded, and the column was washed with 500 µL of Buffer AW1, followed by centrifugation at 6000 × g for 1 min at 4 °C. A second wash was performed using 500 µL of Buffer AW2, followed by centrifugation at 20,000 × g for 3 min at 4 °C to ensure complete drying. Each wash was done in a new Eppendorf tube. Genomic DNA was then eluted by adding 150–200 µL of sterile water to the column, incubating at room temperature for 3 minutes, and centrifuging at 6000 × g for 1 min at 4 °C. DNA concentration and purity (A260 / A280 > 1.8) were assessed using a NanoDrop 2000 spectrophotometer (Thermo Scientific). Throughout the extraction process, samples were kept on ice until processed for DNA-adduct formation analysis.
Library preparation and sequencing were performed by the Institut Curie NGS platform. ChIP-seq libraries were prepared using a 150-bp paired-end (PE150) protocol with the KAPA Biosystems library preparation kit (Ref. No. 07962363001). Sequencing was carried out on the Illumina NextSeq 2000 system in PE150 mode, using P1, P2, or P3 flow cell formats depending on the sequencing run. Data generated from different flow cells were subsequently combined. Briefly, fragmented DNA underwent end-repair and A-tailing in a single enzymatic step by incubation with End Repair & A-Tailing Buffer and Enzyme Mix at 20°C for 30 minutes, followed by 65°C for 30 minutes. Adapter ligation was then performed at 20°C for 15 minutes using KAPA dual-indexed adapters. Post-ligation cleanup was conducted using a 0.8× volume of KAPA HyperPure Beads. Libraries were optionally amplified by PCR using KAPA HiFi HotStart ReadyMix with 14–15 cycles, depending on the input DNA amount. Amplified libraries underwent a second bead-based cleanup, and final elution was performed in H₂O. Library quality and concentration were assessed using Qubit fluorometry and a Bioanalyzer to confirm fragment size distribution and ensure suitability for Illumina sequencing. High-throughput sequencing was performed by the ICGex NGS platform at Institut Curie.

treatment_protocol: To prepare samples for APX-seq and AP-seq, approximately 3–4 × 10⁶ cells were initially seeded in a T-75 flask and cultured for 3–4 days to reach a final count of approximately 9–12 × 10⁶ cells. These were then divided into four groups: untreated, two MMS-treated groups, and X-ray irradiated group. For the MMS-treated groups, cells were incubated for 1 hour in pre-warmed DMEM containing either 5 mM or 10 mM MMS. For the X-ray irradiated group, cells were exposed to 6 Gy of X-ray using an X-RAD 320 Dx irradiator (320 kV), followed by a 30-minute incubation. The untreated control group was maintained in DMEM and processed in parallel, following identical washing and harvesting steps. Following treatment or incubation, the medium was removed and cells were washed with 10 mL of pre-warmed 1X DPBS. Cells were then harvested using 5 mL of 1X trypsin and incubated for 10 minutes at 37°C until fully detached. To neutralize the trypsin, 5 mL of pre-warmed fresh DMEM was added, resulting in a total volume of 10 mL. Cell counts were recorded, and the suspensions were centrifuged at 1200 rpm for 5 minutes. The resulting cell pellets were transferred to 1.5 mL Eppendorf tubes and washed twice with 1 mL of cold 1X PBS, centrifuging at 1200 rpm for 5 minutes at 4 °C each time. The final washed cell pellets were kept on ice and immediately processed for genomic DNA extraction.

value: Human hepatocellular carcinoma

value: 6 Gy X-ray 30min

value: Replicate 3


title: Input DNA control for AP-Seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 3

description: Library name: Rep3 XR AP input


title: AP-Seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M2 AP Seq

value: 10 mM MMS 1h


title: Input DNA control for AP-Seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M2 AP input


title: Input DNA control for AP-Seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M1 AP input

value: 5 mM MMS 1h


title: Input DNA control for AP-Seq in HepG2 cells (untreated control), replicate 3

description: Library name: Rep3 C AP input


title: AP-Seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M1 AP Seq


title: Input DNA control for AP-Seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 2

description: Library name: Rep2 XR AP input

value: Replicate 2


title: AP-Seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M2 AP Seq


title: Input DNA control for AP-Seq in HepG2 cells (untreated control), replicate 2

description: Library name: Rep2 C AP input


title: AP-Seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M1 AP Seq


title: AP-Seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 1

description: Library name: Rep1 XR AP Seq

value: Replicate 1


title: AP-Seq of AP sites in HepG2 cells (untreated control), replicate 2

description: Library name: Rep2 C AP Seq


title: Input DNA control for AP-Seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M2 AP input


title: AP-Seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M1 AP Seq


title: Input DNA control for AP-Seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M1 AP input


title: Input DNA control for AP-Seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 1

description: Library name: Rep1 XR AP input


title: AP-Seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M2 AP Seq


title: Input DNA control for AP-Seq in HepG2 cells (untreated control), replicate 1

description: Library name: Rep1 C AP input


title: AP-Seq of AP sites in HepG2 cells (untreated control), replicate 1

description: Library name: Rep1 C AP Seq


title: Input DNA control for APX-seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 3

description: Library name: Rep3 XR APX input


title: APX-seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 3

description: Library name: Rep3 XR APX Seq


title: Input DNA control for APX-seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M2 APX input


title: Input DNA control for APX-seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M1 APX input


title: APX-seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M1 APX Seq


title: T21, R23820

description: Library name: R23820

value: Male

value: Caucasian


title: APX-seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 3

description: Library name: Rep3 M2 APX Seq


title: Input DNA control for APX-seq in HepG2 cells (untreated control), replicate 3

description: Library name: Rep3 C APX input


title: Input DNA control for APX-seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M2 APX input


title: APX-seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 2

description: Library name: Rep2 XR APX Seq


title: APX-seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M2 APX Seq


title: APX-seq of AP sites in HepG2 cells (untreated control), replicate 3

description: Library name: Rep3 C APX Seq


title: Input DNA control for APX-seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 2

description: Library name: Rep2 XR APX input


title: Input DNA control for APX-seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M1 APX input


title: APX-seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M1 APX Seq


title: Input DNA control for APX-seq in HepG2 cells (untreated control), replicate 2

description: Library name: Rep2 C APX input


title: Input DNA control for APX-seq in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 1

description: Library name: Rep1 XR APX input


title: APX-seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 1

description: Library name: Rep1 XR APX Seq


title: Input DNA control for APX-seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M2 APX input


title: Input DNA control for APX-seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M1 APX input


title: APX-seq of AP sites in HepG2 cells (untreated control), replicate 2

description: Library name: Rep2 C APX Seq


title: APX-seq of AP sites in HepG2 cells (untreated control), replicate 1

description: Library name: Rep1 C APX Seq


title: ATAC HIRAfl/fl_Tbg-Cre_female_rep1

description: Library name: sample 3

data_processing:
Reads were trimmed using Cutadapt v2.3 and then aligned against chrM mm10 using Bowtie2.
Duplicate reads were removed using Picard MarkDuplicates v2.22.0.
MACS2 v2.2.9.1 was used to call peaks.
Reproducible peaks for replicates (n=2) were determined using IDR v2.0.4.2.
Differential accessibility of peaks were tested using edgeR v3.38.4
Assembly: mm10
Supplementary files format and content: genome track files as bigWig

source_name: liver

extract_protocol:
DNA was extracted from cells using the ATAC-seq kit (Active Motif, 53150)
ATAC libraries were prepared using the ATAC-seq kit (Active Motif, 53150) following the manufacturer's protocol.

treatment_protocol: Virus suspension was injected at a dose of 3.33 x 1011 viral genomes per mouse in 100 µl sterile PBS retro-orbitally.

value: liver

value: HIRA fl/fl

value: AAV8 Tbg-Cre


title: Input DNA control for APX-seq in HepG2 cells (untreated control), replicate 1

description: Library name: Rep1 C APX input


title: ATAC WT_Tbg-Cre_female_rep1

description: Library name: sample 1

value: wildtype


title: ATAC WT_Tbg-Cre_female_rep2

description: Library name: sample 2


title: WT_CRISPR_sgHIRA_female_6months_rep4

description: Library name: sample 19

data_processing:
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Assembly: mm10
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene
Supplementary files format and content: FPKM matrix contains FPKM values for each sample and each gene

extract_protocol:
RNA was extracted from tissue using a bead homogenizer with TRIzol and Direct-zol RNA MiniPrep Plus kits (Zymo R2072).
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA).


title: WT_CRISPR_sgHIRA_female_6months_rep3

description: Library name: sample 18


title: WT_CRISPR_sgRosa26_female_6months_rep5

description: Library name: sample 15


title: WT_CRISPR_sgHIRA_female_6months_rep1

description: Library name: sample 16


title: WT_CRISPR_sgRosa26_female_6months_rep4

description: Library name: sample 14


title: WT_CRISPR_sgRosa26_female_6months_rep3

description: Library name: sample 13


title: AML106

description: Library name: Sample106

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 27, GRCh38).
The Gene abundances are given as Reads Per Kilobase per Million mapped reads (RPKM) with “cuffnorm” command using the Cufflinks package.
Assembly: human GRCh38
Supplementary files format and content: Excel file includes FPKM values for all Samples

value: Bone Marrow

value: AML


title: AML104

description: Library name: Sample104


title: WT_CRISPR_sgRosa26_female_6months_rep1

description: Library name: sample 11


title: WT_CRISPR_sgHIRA_female_3weeks_rep5

description: Library name: sample 10


title: WT_CRISPR_sgHIRA_female_6months_rep5

description: Library name: sample 20


title: WT_CRISPR_sgHIRA_female_3weeks_rep4

description: Library name: sample 9


title: WT_CRISPR_sgHIRA_female_3weeks_rep3

description: Library name: sample 8


title: WT_CRISPR_sgHIRA_female_3weeks_rep2

description: Library name: sample 7


title: WT_CRISPR_sgHIRA_female_3weeks_rep1

description: Library name: sample 6


title: WT_CRISPR_sgRosa26_female_3weeks_rep3

description: Library name: sample 3


title: WT_CRISPR_sgRosa26_female_3weeks_rep1

description: Library name: sample 1


title: WT_CRISPR_sgHIRA_male_after_rep2

description: Library name: sample 16


title: WT_CRISPR_sgRosa26_female_3weeks_rep5

description: Library name: sample 5


title: WT_CRISPR_sgRosa26_female_3weeks_rep2

description: Library name: sample 2


title: WT_CRISPR_sgHIRA_male_after_rep1

description: Library name: sample 15


title: HIRAfl/fl_Tbg-Cre_male_after_rep1

description: Library name: sample 13


title: WT_CRISPR_sgRosa26_male_after_rep1

description: Library name: sample 11


title: WT_CRISPR_sgRosa26_male_after_rep2

description: Library name: sample 12


title: WT_Tbg-Cre_male_after_rep2

description: Library name: sample 10


title: WT_Tbg-Cre_male_after_rep1

description: Library name: sample 9


title: WT_CRISPR_sgHIRA_male_before_rep2

description: Library name: sample 8


title: WT_CRISPR_sgHIRA_male_before_rep1

description: Library name: sample 7


title: HIRAfl/fl_Tbg-Cre_male_before_rep2

description: Library name: sample 6


title: HIRAfl/fl_Tbg-Cre_male_before_rep1

description: Library name: sample 5


title: WT_CRISPR_sgRosa26_male_before_rep2

description: Library name: sample 4


title: WT_CRISPR_sgRosa26_male_before_rep1

description: Library name: sample 3


title: WT_Tbg-Cre_male_before_rep2

description: Library name: sample 2


title: WT_Tbg-Cre_male_before_rep1

description: Library name: sample 1


title: WT_Tbg-Cre_female_rep2

description: Library name: sample 17


title: WT_Tbg-Cre_female_rep1

description: Library name: sample 16


title: WT_Tbg-Cre_male rep3

description: Library name: sample 15


title: WT_Tbg-Cre_male rep2

description: Library name: sample 14


title: WT_Tbg-Cre_female_rep3

description: Library name: sample 18


title: APX-seq of AP sites in HepG2 cells treated with 5 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M1 APX Seq


title: APX-seq of AP sites in HepG2 cells treated with 10 mM MMS for 1 h, replicate 1

description: Library name: Rep1 M2 APX Seq


title: WT_Tbg-Cre_male rep1

description: Library name: sample 13


title: ATAC HIRAfl/fl_Tbg-Cre_female_rep2

description: Library name: sample 4


title: HIRAfl/fl_MCS_female_rep3

description: Library name: sample 12

value: AAV8 Tbg-MCS


title: HIRAfl/fl_MCS_female_rep2

description: Library name: sample 11


title: HIRAfl/fl_MCS_female_rep1

description: Library name: sample 10


title: HIRAfl/fl_MCS_male_rep3

description: Library name: sample 9


title: HIRAfl/fl_Tbg-Cre_female_rep3

description: Library name: sample 6


title: HIRAfl/fl_MCS_male_rep2

description: Library name: sample 8


title: WT_CRISPR_sgHIRA_female_6months_rep2

description: Library name: sample 17


title: HIRAfl/fl_Tbg-Cre_female_rep2

description: Library name: sample 5


title: HIRAfl/fl_Tbg-Cre_female_rep1

description: Library name: sample 4


title: HIRAfl/fl_Tbg-Cre_male_rep3

description: Library name: sample 3


title: HIRAfl/fl_Tbg-Cre_male_rep1

description: Library name: sample 1


title: WT_CRISPR_sgRosa26_female_6months_rep2

description: Library name: sample 12


title: HIRAfl/fl_MCS_male_rep1

description: Library name: sample 7


title: HIRAfl/fl_Tbg-Cre_female_H3.3_rep3

description: Library name: sample 18

data_processing:
Raw reads were aligned to mm10 using bowtie2
Duplicates were removed using Picard MarkDuplicates
Signal was normalized by uniquely aligned non-duplicated E.coli spike-in reads
Assembly: mm10
Supplementary files format and content: E.coli spike-in normalized bigWig files
Library strategy: CUT&Tag

extract_protocol:
DNA was extracted from cells using the Cut&Tag-IT kit (Active Motif, 53160, 53165)
Cut&Tag libraries were prepared using the Cut&Tag-IT kit (Active Motif, 53150) following the manufacturer's protocol.


title: HIRAfl/fl_Tbg-Cre_female_H3.3_rep2

description: Library name: sample 17


title: HIRAfl/fl_Tbg-Cre_male_rep2

description: Library name: sample 2


title: Control, R18817

description: Library name: R18817

value: DLPFC

value: Control


title: WT_Tbg-Cre_female_H3.3_rep3

description: Library name: sample 15


title: HIRAfl/fl_Tbg-Cre_female_H3.3_rep1

description: Library name: sample 16


title: WT_Tbg-Cre_female_H3.3_rep1

description: Library name: sample 13


title: WT_Tbg-Cre_female_H3.3_rep2

description: Library name: sample 14


title: HIRAfl/fl_Tbg-Cre_female_H3K36me3_rep3

description: Library name: sample 12


title: HIRAfl/fl_Tbg-Cre_female_H3K36me3_rep2

description: Library name: sample 11


title: HIRAfl/fl_Tbg-Cre_female_H3K36me3_rep1

description: Library name: sample 10


title: WT_Tbg-Cre_female_H3K36me3_rep3

description: Library name: sample 9


title: WT_CRISPR_sgRosa26_female_3weeks_rep4

description: Library name: sample 4


title: WT_Tbg-Cre_female_H3K36me3_rep2

description: Library name: sample 8


title: HIRAfl/fl_Tbg-Cre_female_H3K27ac_rep3

description: Library name: sample 6


title: HIRAfl/fl_Tbg-Cre_female_H3K27ac_rep1

description: Library name: sample 4


title: WT_Tbg-Cre_female_H3K36me3_rep1

description: Library name: sample 7


title: HIRAfl/fl_Tbg-Cre_female_H3K27ac_rep2

description: Library name: sample 5


title: WT_Tbg-Cre_female_H3K27ac_rep3

description: Library name: sample 3


title: WT_Tbg-Cre_female_H3K27ac_rep1

description: Library name: sample 1


title: WT_Tbg-Cre_female_H3K27ac_rep2

description: Library name: sample 2


title: H3f3afl/fl_H3f3bfl/fl_Tbg-Cre_male_rep4

description: Library name: sample 10


title: HIRAfl/fl_Tbg-Cre_male_after_rep2

description: Library name: sample 14


title: H3f3afl/fl_H3f3bfl/fl_Tbg-Cre_male_rep2

description: Library name: sample 8


title: H3f3afl/fl_H3f3bfl/fl_Tbg-Cre_male_rep3

description: Library name: sample 9


title: H3f3afl/fl_H3f3bfl/fl_MCS_male_rep2

description: Library name: sample 5


title: H3f3afl/fl_H3f3bfl/fl_Tbg-Cre_male_rep1

description: Library name: sample 7


title: H3f3afl/fl_H3f3bfl/fl_MCS_male_rep1

description: Library name: sample 4


title: H3f3afl/fl_H3f3bfl/fl_MCS_male_rep3

description: Library name: sample 6


title: WT_Tbg-Cre_male_rep3

description: Library name: sample 3


title: WT_Tbg-Cre_male_rep1

description: Library name: sample 1


title: AP-Seq of AP sites in HepG2 cells (untreated control), replicate 3

description: Library name: Rep3 C AP Seq

value: Human hepatocellular carcinoma


title: WT_Tbg-Cre_male_rep2

description: Library name: sample 2


title: H3f3afl/fl_H3f3bfl/fl_Tbg-Cre_male_H3.3_rep1

description: Library name: sample 2

value: H3f3afl/fl; H3f3bfl/fl


title: WT_Tbg-Cre_male_H3.3_rep1

description: Library name: sample 1


title: HIRAfl/fl_Tbg-Cre_female_rep3

description: mouse DNA methylation array was performed on Illumina iScan System

hyb_protocol: Bisulfite-converted DNA was hybridized to the Infinium Mouse Methylation BeadChip (Illumina) following the manufacturer's standard protocol.

scan_protocol: BeadChips were scanned on an Illumina iScan system at the UCSD Institute for Genomic Medicine (IGM) Genomics Core.

data_processing: SeSAMe package (v1.26.0) in R environment (v4.5.1) with TQCDPB preprocessing

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was isolated from mouse liver tissue using the Monarch Genomic DNA Purification Kit.


title: HIRAfl/fl_Tbg-Cre_female_rep4


title: HIRAfl/fl_Tbg-Cre_female_rep2


title: HIRAfl/fl_Tbg-Cre_female_rep1


title: WT_Tbg-Cre_female_rep3


title: WT_Tbg-Cre_female_rep4


title: WT_Tbg-Cre_female_rep2


title: HIRA_KO_FOV_49

type: RNA

description:
R6289_E3_Liver_exprMat_file.csv
R6289_E3_Liver_metadata_file.csv
R6289_E3_Liver_tx_file.csv
R6289_E3_Liver_fov_positions_file.csv
R6289_E3_Liver-polygons.csv
NanoString CosMx Spatial Molecular Imager

data_processing: AtoMx Spatial Informatics Platform was used to decode transcripts and segment cells from CosMx SMI raw image data.

extract_protocol: Transcript were detected in situ on FFPE tissue sections using the NanoString CosMx Spatial Molecular Imager. FFPE tissue blocks were sectioned at 5 μm thickness and processed according to the manufacturer's CosMx SMI FFPE slide preparation protocol.


title: WT_Tbg-Cre_female_rep1


title: HIRA_KO_FOV_50


title: HIRA_KO_FOV_47


title: HIRA_KO_FOV_48


title: HIRA_KO_FOV_46


title: HIRA_KO_FOV_45


title: HIRA_KO_FOV_44


title: HIRA_KO_FOV_43


title: WT_FOV_42

value: WT


title: WT_FOV_41


title: WT_FOV_40


title: WT_FOV_39


title: WT_FOV_38


title: WT_FOV_37


title: WT_FOV_35


title: WT_FOV_36


title: HIRA_KO_FOV_32


title: HIRA_KO_FOV_31


title: HIRA_KO_FOV_29


title: HIRA_KO_FOV_30


title: HIRA_KO_FOV_28


title: HIRA_KO_FOV_27


title: WT_FOV_25


title: WT_FOV_24


title: HIRA_KO_FOV_26


title: WT_FOV_23


title: WT_FOV_22


title: WT_FOV_20


title: WT_FOV_21


title: WT_FOV_19


title: WT_FOV_18


title: HIRA_KO_FOV_17


title: HIRA_KO_FOV_15


title: HIRA_KO_FOV_16


title: HIRA_KO_FOV_14


title: HIRA_KO_FOV_13


title: HIRA_KO_FOV_11


title: HIRA_KO_FOV_12


title: WT_FOV_9


title: HIRA_KO_FOV_10


title: WT_FOV_8


title: WT_FOV_6


title: WT_FOV_7


title: WT_FOV_5


title: WT_FOV_4


title: WT_FOV_3


title: WT_FOV_2


title: WT_FOV_1


title: mebendazole treated cells

status: Public on Apr 01 2026

city: London

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

institute: UCL GOS ICH

description: Library name: NC6_S6_R1_001.fastq.gz

data_processing:
BCL output from the sequencer were converted to FASTQ, along with index demultiplexing using Illumina's BCL Convert v3.7.5.
All tools in the analysis were invoked through the Galaxy Project for NGS analysis, as follows:
5’ adapters were trimmed from the FASTQ files using the Cutadapt tool
sgRNA read counts were collected using the MAGeCK count tool
MAGeCKs test was used to perform sgRNA and gene ranking
Assembly: hg38
Supplementary files format and content: DMSOvIC90MBZ_Galaxy_MAGeCKs_test_Gene Summary.xlsx
Library strategy: CRISPR Screen

source_name: THP-1 cells, MLL-AF9 positive

growth_protocol: THP-1 cells (Acute Myeloid Leukemia cell line) (ATCC) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 ug/ml streptomycin at 37°C with 5% CO2.

extract_protocol:
genomic DNA isolated using the QIAamp DNA Blood Maxi Kit (Qiagen, Manchester, UK).
The library was produced using forward and reverse barcode primers and the NEBNext High Fidelity PCR Master Mix (New England Biolabs, Hitchin, UK) according to previously published protocols (Joung et al 2017, Nature Protocols, 12(4):828-863. doi: 10.1038/nprot.2017.016) and pooled PCR products purified using the QIAquick PCR Purification Kit (Qiagen).

treatment_protocol: THP-1 cells transduced with the Brunello CRISPR library were exposed to DMSO or 1 micromolar mebendazole for 10 days.

value: THP-1 cells, MLL-AF9 positive

value: Acute Myeloid Leukemia

value: cell line

value: 1uM mebendazole 10 days


title: DMSO treated cells

description: Library name: NC4_S4_R1_001.fastq.gz

value: DMSO 10 days


title: AP-Seq of AP sites in HepG2 cells exposed to 6 Gy X-ray irradiation, replicate 2

description: Library name: Rep2 XR AP Seq

value: 6 Gy X-ray 30min

value: Replicate 2


title: Treatment-6

status: Public on Mar 23 2026

city: Chengdu

first: Bi-Sen

last: Ding

state: Sichuan

address: Wuhou District, Renmin three paragraphs

department: The West China Second UniversityHospital of Sichuan University

institute: Sichuan University

description:
Library name: Treatment-6
Singleron GEXSCOPE®

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the CeleScope software v1.15.0
Assembly: Sscrofa11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: Liver

extract_protocol:
Liver samples were obtained through surgical biopsy, preserved in SCelLiVe® Tissue Storage Solution, and minced into small pieces. The tissue was digested at 37°C for 40 minutes using a digestion solution containing 1 mg/ml Collagenase I, 1 mg/ml Collagenase II, 1 mg/ml Dispase II, and 10 U/ml DNase I. After obtaining the cell suspension, red blood cells were removed, and the sample was centrifuged at 50 g for 2 minutes to isolate non-parenchymal cells (NPCs).
Library was performed according to the manufacter's instruction(GEXSCOPE® Single Cell RNA Library Kit)

treatment_protocol: For the analysis of minipig non-parenchymal cells, a MASH model was successfully established over a 3-month period using a high-fat, high-sugar diet combined with intraperitoneal injection of carbon tetrachloride . Pre-treatment samples were obtained via surgical biopsy. Subsequently, a 9-month treatment regimen with a ROCK2 inhibitor was administered. Post-treatment samples were then collected via surgical biopsy, followed by single-cell library construction and sequencing.

value: Liver

value: NPCs


title: Treatment-5

description:
Library name: Treatment-5
Singleron GEXSCOPE®


title: Treatment-4

description:
Library name: Treatment-4
Singleron GEXSCOPE®


title: Treatment-3

description:
Library name: Treatment-3
Singleron GEXSCOPE®


title: Treatment-1

description:
Library name: Treatment-1
Singleron GEXSCOPE®


title: MASH-6

description:
Library name: MASH-6
Singleron GEXSCOPE®


title: Input DNA control for AP-Seq in HepG2 cells treated with 10 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M2 AP input

value: 10 mM MMS 1h


title: Treatment-2

description:
Library name: Treatment-2
Singleron GEXSCOPE®


title: Input DNA control for AP-Seq in HepG2 cells treated with 5 mM MMS for 1 h, replicate 2

description: Library name: Rep2 M1 AP input

value: 5 mM MMS 1h


title: MASH-4

description:
Library name: MASH-4
Singleron GEXSCOPE®


title: MASH-5

description:
Library name: MASH-5
Singleron GEXSCOPE®


title: MASH-3

description:
Library name: MASH-3
Singleron GEXSCOPE®


title: MASH-2

description:
Library name: MASH-2
Singleron GEXSCOPE®


title: MASH-1

description:
Library name: MASH-1
Singleron GEXSCOPE®


title: Male, Astrocyte, 7 weeks post-Fx, Trap Sample 2

status: Public on Mar 19 2026

city: Palo Alto

first: Vivianne

middle: L.

last: Tawfik

address: 3174 Porter Drive

department: Anesthesiology, Perioperative & Pain Medicine

institute: Stanford University

description:
Library name: Male_7wpFx_Trap_2
Column Y

data_processing:
FASTQ files were passed through the nf-core RNAseq (v3.12.0) pipeline which performed quality control (FastQC), trimming (Trim Galore), alignment to genome reference (STAR; GRCm38), and transcript quantification (RSEM). Genes with ≥ 25 counts in at least 90% of samples were included for analysis.
Assembly: GENCODE GRCm38
Supplementary files format and content: comma-separated values files report raw gene counts for each sample

source_name: Homogenized lumbar spinal cord

extract_protocol:
RNA was isolated by Azenta Life Sciences (formerly GeneWiz) using a routine protocol.
RNA libraries for RNA-seq were prepared by Azenta Life Sciences (formerly GeneWiz) using a standard poly-A selection protocol for mRNA species (eukaryotic).

value: Homogenized lumbar spinal cord

value: Spinal cord astrocytes

value: Fracture


title: Male, Astrocyte, 7 weeks post-Fx, Trap Sample 3

description:
Library name: Male_7wpFx_Trap_3
Column AG


title: Male, Astrocyte, 7 weeks post-Fx, Trap Sample 1

description:
Library name: Male_7wpFx_Trap_1
Column R


title: Male, Astrocyte, 5 weeks post-Fx, Trap Sample 3

description:
Library name: Male_5wpFx_Trap_3
Column AF


title: Male, Astrocyte, 5 weeks post-Fx, Trap Sample 2

description:
Library name: Male_5wpFx_Trap_2
Column X


title: Male, Astrocyte, 3 weeks post-Fx, Trap Sample 3

description:
Library name: Male_3wpFx_Trap_3
Column AE


title: Male, Astrocyte, 3 weeks post-Fx, Trap Sample 2

description:
Library name: Male_3wpFx_Trap_2
Column W


title: Male, Astrocyte, 5 weeks post-Fx, Trap Sample 1

description:
Library name: Male_5wpFx_Trap_1
Column P


title: Male, Astrocyte, 3 weeks post-Fx, Trap Sample 1

description:
Library name: Male_3wpFx_Trap_1
Column N


title: Male, Astrocyte, Uninjured, Trap Sample 2

description:
Library name: Male_Uninjured_ Trap_2
Column Z

value: No fracture


title: Male, Astrocyte, Uninjured, Trap Sample 1

description:
Library name: Male_Uninjured_ Trap_1
Column L


title: Female, Astrocyte, 7 weeks post-Fx, Trap Sample 3

description:
Library name: Female_7wpFx_ Trap_3
Column AC


title: Female, Astrocyte, 7 weeks post-Fx, Trap Sample 2

description:
Library name: Female_7wpFx_ Trap_2
Column U


title: Male, Astrocyte, Uninjured, Trap Sample 3

description:
Library name: Male_Uninjured_ Trap_3
Column AH


title: Female, Astrocyte, 5 weeks post-Fx, Trap Sample 3

description:
Library name: Female_5wpFx_ Trap_3
Column AB


title: Female, Astrocyte, 5 weeks post-Fx, Trap Sample 2

description:
Library name: Female_5wpFx_ Trap_2
Column T


title: Female, Astrocyte, 7 weeks post-Fx, Trap Sample 1

description:
Library name: Female_7wpFx_ Trap_1
Column J


title: Female, Astrocyte, 5 weeks post-Fx, Trap Sample 1

description:
Library name: Female_5wpFx_ Trap_1
Column H


title: Female, Astrocyte, 3 weeks post-Fx, Trap Sample 2

description:
Library name: Female_3wpFx_ Trap_2
Column S


title: Female, Astrocyte, 3 weeks post-Fx, Trap Sample 3

description:
Library name: Female_3wpFx_ Trap_3
Column AA


title: Female, Astrocyte, 3 weeks post-Fx, Trap Sample 1

description:
Library name: Female_3wpFx_ Trap_1
Column F


title: Female, Astrocyte, Uninjured, Trap Sample 1

description:
Library name: Female_Uninjured_ Trap_1
Column D


title: Male, Astrocyte, 7 weeks post-Fx, Input Sample 1

description:
Library name: Male_7wpFx_Input_1
Column Q

value: All spinal cord cell types


title: Female, Astrocyte, Uninjured, Trap Sample 3

description:
Library name: Female_Uninjured_ Trap_3
Column AD


title: Female, Astrocyte, Uninjured, Trap Sample 2

description:
Library name: Female_Uninjured_ Trap_2
Column V


title: Male, Astrocyte, 5 weeks post-Fx, Input Sample 1

description:
Library name: Male_5wpFx_Input_1
Column O


title: Male, Astrocyte, Uninjured, Input Sample 1

description:
Library name: Male_Uninjured_Input_1
Column K


title: Male, Astrocyte, 3 weeks post-Fx, Input Sample 1

description:
Library name: Male_3wpFx_Input_1
Column M


title: Female, Astrocyte, 7 weeks post-Fx, Input Sample 1

description:
Library name: Female_7wpFx_Input_1
Column I


title: Female, Astrocyte, Uninjured, Input Sample 1

description:
Library name: Female_Uninjured_Input_1
Column C


title: Female, Astrocyte, 5 weeks post-Fx, Input Sample 1

description:
Library name: Female_5wpFx_Input_1
Column G