title: HEK293T, Wild type, Arsenite stress, rep1

city: Beijing

first: Yuxin

last: Fang

state: Beijing

address: Yiheyuan Road No.5

institute: Peking University

description: Library name: GLORI2_As_rep1

data_processing:
Sequencing reads were firstly processed with Cutadapt (v.1.18) to remove adaptors (For subcellular transcriptome data, adaptor1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adaptor2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; for cancer cell migration study, adaptor1=CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, adaptor2=CTGTCTCTTATACACATCTGACGCTGCCGACGA; other parameters: -q 20 -O 3 -m 20). For GLORI2 data analysis, raw R2 reads were treated by Trim Galore and Seqkit for adaptor trimming and quality control. The m6A sites were called by GLORI-tools. For each mRNA, an m6A strength score was calculated as the sum of m6A ratios across all identified m6A sites.
Trimmed reads were mapped against the corresponding genome assemblies using hisat2 (v.2.1.0).
Number of reads mapped to each gene was counted with HTSeq (v0.7.2) (-s no)
Differential expression analysis was carried out by DESeq2 (v.1.16.1)
Assembly: GRCh38 (hg38), Rnor_6.0, GRCm39
Supplementary files format and content: Excel tables include raw counts for each sample.
Supplementary files format and content: Python script counts amino acid residues in mutant libraries pre- and post-enrichment.

growth_protocol: HEK293T and MC38 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and maintained at 37°C with 5% CO2. Cortical neurons were dissected from neonatal Sprague Dawley rats (within 24 hours post-birth), plated onto 10-cm dishes, and cultured with GPM for 3-6 h before switching to neural cell culture medium (Neurobasal medium with 2% (v/v) B-27 supplement, 1% (v/v) GlutaMAX supplement, penicillin and streptomycin). Petri dishes were pre-incubated overnight with 50-100 μg/mL PDL at 37°C. The day of rat dissection was designated as DIV 0 (0 days in vitro), and thereafter, half of the spent culture medium was replaced with fresh neural cell culture medium every 3 days.

extract_protocol:
For the profiling of subcellular transcriptomes, cells were lyzed with TRIzol. Total RNAs were extracted, clicked with biotin handles, enriched with streptavidin-coated beads, and purified again with TRIzol. For the study of cancer cell migration, cells with strong biotin signals were sorted by flow cytometry and lyzed with 0.5% (v/v) Triton X-100 and 0.1 U DNase I.
For the profiling of subcellular transcriptomes, 100 ng Input RNA samples or 5 μL Enrich RNA samples were utilized for NGS library construction. For identifying G3BP1-proximal and OMM-proximal RNAs in the HEK293T cells, rRNAs were removed with Ribo-off rRNA Depletion Kit (Vazyme) following the manufacturer’s protocol. The purified RNAs were dissolved in 5 μL nuclease-free water. NEBNext Ultra II RNA Library Prep Kit for Illumina was used for NGS library construction. RNAs were fragmentated to ~300 nt before first strand synthesis. For the study of cancer cell migration, the sorted cells were used for pseudo-bulk RNA-sequencing library construction following the previously published Sherry2 protocol. Libraries constructed from polyA RNAs (OMM-proximal and G3BP1-proximal RNAs of HEK293T cells, and mRNAs of MC38 cells) were sequenced to a depth of 3 G raw base. And libraries constructed from total RNAs (ERM-proximal RNAs of HEK293T cells and G3BP1-proximal RNAs of rat cortical neurons) were sequenced to a depth of 15 G raw base. For GLORI2.0 library construction, mRNA was isolated from total RNA by the Dynabeads® mRNA Purification Kit (Invitrogen) according to the manufacturer’s instructions. These purified mRNA were fragmented in a 20 μL mixture containing 2 μL 10x RNA fragment buffer (NEB, E6150S), incubated for 5 min at 85oC and immediately placed on ice for 2 min. Subsequently, 2 μL 10x stop buffer (NEB, E6150S) was added. The final solution was purified by Zymo RNA Clean & Concentrator column (Zymo, R1016) according to the manufacturer’s instructions. The purified fragment mRNA were added into 50 μL of reaction buffer containing 13 μL glyoxal solution (Sigma, 50649), 10 μL DMSO, 10 μL 5 M NaNO2 (Sigma, S2252), 5 μL saturated H3BO3 solution (Sigma, B0394), 4 μL 500 mM MES (pH 6.0, Sigma, 76039) and nuclease-free water, incubated for 10 min at 50 °C and immediately placed on ice for 2 min for stopping the reaction. The mixture was purified by ethanol precipitation. The pellets were dissolved by 50 μL deprotection buffer containing 0.5 M TEAA (pH 8.6) and 47.5% Formamide. The mixture was incubated at 95°C for 10 min without shaking and immediately placed on ice for 2 min. The mixture was purified by ethanol precipitation. The pellets were dissolved by 8.5 μL nuclease-free water. The RNA library was constructed by SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa, 634413) according to the manufacturer’s instructions, except for replacing the RT primer with a ternary primer.

treatment_protocol: For general CAP-seq labeling experiments, HEK293T cells were cultured until the confluence reached 90%, incubated with 10 mM propargylamine (PA) in HBSS for 5 min, and irradiated with blue light for 1-120 seconds. For the induction of stress granules, HEK293T cells were incubated with 0.5 mM sodium arsenite for 5-60 minutes. Primary cultures of rat cortical neurons were transduced with a lentivirus expressing G3BP1-Lantern or Lantern-NES at 3 days in vitro (DIV3). At DIV8, neurons were stimulated with 0.25 mM sodium arsenite for 3 hours, and conducted with the CAP-seq labeling procedure. For the cancer cell migration assay, MC38 cells were seeded on coverslips with a culture-insert to create a 500-μm cell-free gap. 24 hours after removing the culture-insert, migrating cells near the gap and remaining cells far from the gap were selectively labeled with DMD-controlled 450-nm laser and 2 mM Bio-NH2 probe.

value: embryonic kidney cells

value: WT


title: PHC2 L307R mutant H3K27me3 CUT&RUN (HCT116) rep01

status: Public on Mar 27 2026

type: SRA

city: Boston

first: Philipp

last: Schneider

state: Massachusetts

address: 185 Cambridge Street

country: USA

institute: Massachusetts General Hospital

description:
Library name: CR_L307R_H3K27me3_01
CUT&RUN with H3K27me3 antibody (CST 9733) - used in part 1 of the analysis

library_source: genomic

data_processing:
The raw reads were initially trimmed using Trimmomatic with the empirically determined parameters “HEADCROP:0 ILLUMINACLIP:adapters.fa:2:22:9:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20”. Quality control of the sequencing data was performed with FastQC and MultiQC. Subsequently, the trimmed reads were aligned to the ribosomal DNA references, retrieved from NCBI with bowtie2 using the -N 1 option to allow single mismatches in the alignment. Reads identified as non-ribosomal were subjected to splicing-aware alignment with the STAR aligner using the settings “--bamRemoveDuplicatesType UniqueIdenticalNotMulti --outMultimapperOrder Random”. For this step, we employed the hg38 genome and RefSeq annotations for introns and exons. Unaligned reads were removed for further processing and a subset of the unaligned reads was used with BLAST to confirm the absence of any contamination. Picard's markDuplicate function was used on the aligned read set to identify duplicate reads. Using the Bedtools' genomecov function, we generated bedgraph files from BAM files with single-base-pair resolution. These files were normalized to 1x genome coverage and converted to bigwigs. In parallel to this, BAM files were processed by featureCounts to determine gene-and-exon-wise coverage in all RNA-Seq samples.
Raw CUT&RUN reads were trimmed with Trimmomatic and empirically determined parameters “HEADCROP:5 ILLUMINACLIP:adapters.fa:2:22:9:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20”. Quality control of the CUT&RUN sequencing experiment was performed with FastQC and MultiQC. Mitochondrial reads were removed by alignment to the mitochondrial DNA sequence reference from the hg38 genome using Bowtie2. The remaining non-mitochondrial reads were further aligned to the human genome hg38 using Bowtie 2, allowing for single-base mismatches (parameter -N 1). Poor alignments in the produced BAM alignment file, as determined by score fields AS, YS and MAPQ, multi-aligners, as determined by fields AS and XS, large fragments (TLEN>3500) and flagged singletons were subsequently filtered out with samtools. Replicate marking and removal were accomplished using Picard’s MarkDuplicates. Sample- and antibody-specific CUT&RUN peaks were called with macs3, employing multiple replicates for each experiment and using respective IgG CUT&RUNs as controls with a q-value of 0.01 (-q 0.01). For normalizing CUT&RUN tracks, a "background-interval-set" was generated using the complement of a union peak set derived from all samples and antibodies, extending each peak interval by 10 kbp. Bedgraph files, prepared for each sample with BedTools genomecov, were normalized to a standard 1x coverage on the background intervals.
Assembly: hg38
Supplementary files format and content: raw counts per gene (RNA-Seq) for part 1 and part 2 of the analysis - tab-separated
Supplementary files format and content: raw counts per antibody-wise merged peak set (CUT&RUN) for part 1 and part 2 of the analysis - tab-separated
Supplementary files format and content: bigwigs (merged replicates)

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
We followed the CUT&RUN protocol from Skene et al. with some minor modifications. First, Concanavalin A (Polysciences, 86057-10) beads were prepared by taking 20 µl per sample and washing the beads three times with 1 ml of Bead Activation Buffer (20 mM HEPES with pH 7.9, 10 mM KCl, 1 mM CaCl₂ 1 mM MnCl₂), incubating for ~15 minutes on a rotator each time. After washing, tubes were placed on a magnetic stand, supernatant was removed, and beads were resuspended in 200 µl Bead Activation Buffer. For each CUT&RUN sample, 1×10⁶ cells were harvested by trypsinization, quenched, and counted. Then cells were spun down at 500 RCF for 5 minutes and washed with 10 ml of PBS with pH 7.4. Then, we resuspend cells in 0.5% formaldehyde in PBS with pH 7.4. Cells were fixed for 5 minutes, then quenched with 1:1 volume of 1 M Tris pH 8.0 for 10 minutes at room temperature. Afterwards, we washed cells twice with 5 ml PBS with pH 7.4 in 15 ml Falcon tubes by spinning at 500 ×g for 3 minutes. Then cells were resuspended in 100 µl of PBS per library. Afterwards, we added 100 µl Wash Buffer (20 mM HEPES with pH 7.5, 150 mM NaCl, 2 mM EDTA with pH 8.0, 0.5% BSA, 0.1% Triton, Protease Inhibitor Tablet Roche cOmplete EDTA-free) and 40 µl of washed ConA beads. This mixture was incubated for 10 minutes on a rotator to bind cells to beads. Then, samples were spun at 50  RCF for 1 minute, moved to a magnetic stand, and cleared for 1 minute. Afterwards, the supernatant was removed and beads were resuspended in 100 µl Wash Buffer and transferred to PCR strip tubes. We then prepared the corresponding antibody solutions (all antibodies were used at 1:400) in 150 µl Wash Buffer. PCR tubes with beads were moved to a magnetic stand, incubated for 1 minute, and then the supernatant was removed. We then added the antibody solution and resuspended the beads. Finally, the tubes were placed on a nutator overnight at 4°C. The next day, the samples were washed twice with 100 µl Wash Buffer. After removing the Wash Buffer, we added 50 µl of proteinA MNase at 700 ng/ml final in Wash Buffer and incubated for 1 hour at room temperature. Then, the beads were washed three times with 100 µl Wash Buffer. Afterwards, the samples were chilled on ice. We then added 100 µl of ice cold Wash Buffer with 10 mM CaCl₂ to each sample and digested for 1 hour at 4°C. During the incubation, we prepared RNase-containing 2× STOP buffer by mixing 4 µl of 100 mg/ml RNase A with 3996 µl 2× STOP buffer (340 mM NaCl, 20 mM EDTA with pH 8.0, 4 mM EGTA with pH 8.0). After the 1 hour incubation, we added 100 µl of STOP/RNase buffer per sample and incubated at 37°C for 15 minutes. Then, samples were placed on the magnet, allowed to clear for 1 minute, and then the supernatant was transferred to new tubes. We then added 2 µl of 10% SDS and 2 µl of 19 mg/mL proteinase K to each tube and mixed gently. With this, reverse crosslink was performed at 50°C overnight. The next day, we performed the DNA Clean-Up using Ampure XP beads (Beckman Coulter, A63881) at 0.9x beads to sample ratio (e.g. 180 µl of beads with 200 µl of DNA sample). Beads and samples were mixed and incubated at room temperature for 10 minutes. Afterwards, we moved the tubes to the magnet, discarded the supernatant, and washed with 200 µl of freshly prepared 90% ethanol without resuspending. This wash was repeated and then the beads were allowed to air dry just until no visible liquid remained. We then removed the tubes from the magnet, added 52 µl of 0.1× TE, resuspended beads by pipetting, and incubated for 2 minutes at room temperature. Then, the tubes were returned to the magnet and we transferred 50 µl of supernatant to new PCR tubes.
We grew wild-type and PHC2 L307R HCT116 cells in 6-well plates. The day before harvesting the cells, we plated 2.5×10⁵ cells per well. Cells were harvested by adding 0.5 ml of TRI Reagent (Molecular Research Center, TR118) and transferred to a 1.5 ml tube. Then 0.1 ml of chloroform was added to the tube and vigorously mixed. Afterwards, the sample was incubated at room temperature for 3 minutes and centrifuged at 16,000 RCF for 15 minutes at 4°C. We then carefully transferred the upper aqueous phase to a new tube and added 1 volume of 100% ethanol to 1 volume of sample (1:1 ratio). Then, the RNA was purified using the RNA clean & concentrator kit (Zymo Research, R1016) following the manufacturer’s manual. To remove the DNA we performed the “In-column DNase treatment” and used 5 units of TURBO DNAase (Thermo Fisher Scientific, AM2238) as described in the appendix of the manufacturer manual. The quality and concentration was accessed by nanodrop and Agilent Tapestation. Subsequently, the RNA library was prepared using the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, R3000) following the manufacturer’s manual exactly. We started out with 250 ng of RNA. For the final library amplification we ran 12 PCR cycles. Afterwards library quality was assessed using the Agilent Tapestation. The library concentrations were measured using the NEBNext Library Quant Kit for Illumina (New England Biolabs, E7630L) following the manufacturer’s manual exactly. For PHC2 KO and PHC2 KO with PHC2 overexpression through lentivirus, the NEBnext PolyA mRNA magnetic isolation module (New England Biolabs, E7490L) was used instead of the Zymo-Seq RiboFree Total RNA Library Kit.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®,New England Biolabs, E7645S

tag: cell line

tag: genotype

value: PHC2 L307R mutant

tag: batch


title: LLC-Thy1.1 P2 tumour-bearing lung 2

type: other

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

data_processing: Raw data were processed using MERSCOPE Vizualizer software v2.3 (Vizgen Technologies). The processed data files include detected.transcripts.csv file with the spatial coordinates of the detected transcripts, cell_by_gene.csv file, containing the gene expression matrix, and cell_metadata.csv, containing the field of view index and the spatial coordinates of the centroids and cell segmentation boundaries.

molecule: other

organism: Mus musculus

source_name: LLC-Thy1.1 P2 tumour-bearing lung

extract_protocol: All methods listed in Bardet et al. Multiomics immune profiling of a patient-relevant orthotopic lung cancer model using SEPARATE-Seq.

tag: tissue

value: tumour-bearing lung


title: CD34, empty vector, HA, merged

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

description: Library name: CUTRUN_CD34_Empty_HA_merge

data_processing:
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1) and converted to paired-end fragment intervals (BEDPE). For coverage calculation, fragments with inferred insert size < 2000 bp were counted and used to compute a library-size scaling factor to normalize signal to a fixed library size. The center 80 bp of these fragments were used to generate genome-wide coverage tracks using bedtools genomecov in bedGraph format (-bg), applying the scaling factor for depth normalization (-scale). BedGraph files were converted to BigWig format using UCSC tools (bedGraphToBigWig) for visualization in IGV and for creating heatmaps. To increase detection of BCL11BdTAG and RUNX1 binding events in CD34+ HSPCs without DMSO or dTAGV-1 treatment, the mapped bam files from both replicates were merged prior to downstream processing.
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. The first 15 bp of each read were clipped to reduce the GC bias introduced by the Tn5 enzyme. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1). The center 80 bp of nucleosome-free fragments (fragment size < 109 bp) were extracted using bedtools and converted to scaled genome coverage tracks for visualization on IGV and in heatmaps. The scaling factor was computed from the total number of nucleosome-free fragments to normalize signal to a fixed library size. Peaks were called with MACS2 (v2.1.1.20160309) using nucleosome-free fragments with parameters -f BEDPE --keep-dup all -q 0.01
For CD34+ HSPCs: Paired-end RNA-seq reads were adapter and quality trimmed using Trim Galore (v0.4.4), and read quality was assessed with FastQC. Reads were aligned to the GRCh38 reference genome with STAR (v2.7) in two-pass mode. Coordinate-sorted BAM files, transcriptome alignments, gene counts, and strand-specific RPM-normalized coverage tracks were generated during alignment, and wiggle files were converted to BigWig format using wigToBigWig. Duplicate reads were marked with GATK MarkDuplicates, alignments were indexed with SAMtools, and RNA-seq quality metrics were collected using Picard CollectRnaSeqMetrics. Gene- and isoform-level expression was quantified with RSEM. Differential expression analysis was performed using the edgeR/limma-voom workflow. Genes with counts per million (CPM) ≥ 1 in at least 3 samples were retained using edgeR, and normalized expression values were generated by voom as log2-counts per million. Differentially expressed genes between treatment groups and transduction conditions were identified using linear models with empirical Bayes moderation implemented in limma.
For Jurkat BRU-seq: Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2. Unaligned reads were subsequently mapped strand-specifically to human genome build hg38/GRCh38 using STAR and GENCODE annotation version 27. Gene expression was quantified as previously described (Magnuson et al., 2022) and differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: .bw files contain coverage files in bigwig format
Supplementary files format and content: .narrowPeak files contain MACS2 called peaks
Supplementary files format and content: .txt file contains transcripts per million (TPM) values
Library strategy: CUT&Run

source_name: Cord Blood

growth_protocol: CD34+ HSPCs were expanded in Stemspan media supplemented with 1X penicillin-streptomycin-glutamine, 100ng/mL SCF, TPO, IL-6 and FLT3-L, and 1 µM stemregenin-1. Jurkat cells were cultured in RPMI-1640 supplemented with 1X penicillin-streptomycin-glutamine and 10% FBS.

extract_protocol:
CUT&RUN was performed on 0.1 – 0.5 million CD34+ HSPCs using the CUTANA ChIC/CUT&RUN kit from EpiCypher (#14-1048-24) following manufacturer’s instructions.
ATAC-seq was performed with 50,000 cells using the Omni-ATAC protocol as described (Corces et al., 2017). Cells were washed once with 1X PBS and then lysed in 50µl cold Cell Lysis Buffer containing 0.01% digitonin for 3 minutes on ice. After cell lysis, 1mL cold Resuspension Buffer was added and cells were immediately spun at 600xg for 10 minutes at 4°C. After removing the supernatant, the nuclei were transposed in 50µl Transposition reaction using the Tn5 enzyme from Illumina for 30 minutes at 37°C. Transposed DNA was purified using a Qiagen MinElute PCR clean-up kit and DNA was eluted in 10µl Elution Buffer.
CD34+ HSPCs were harvested following DMSO or dTAGV-1 treatment and resuspended in TRI Reagent (Sigma). RNA was isolated using the Direct-zol RNA miniprep kit (Zymo Research #R2050). For BRU-seq, cells were lysed directly in Trizol followed by isolation of total RNA and treatment with DNAse (TURBO DNA-free Kit; Invitrogen). The Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
Libraries were constructed using library prep kits from EpiCypher (#14-1001) following manufacturer’s instructions.
Libraries were constructed by amplifying eluted DNA with barcoded primers described in Corces et al., 2017 for 10-12 cycles. The optimal number of cycles was determined by performing a quantitative PCR analysis after the initial 5 PCR cycles. Amplified libraries were purified using AMPure beads to remove fragments less than 200bp and larger than 700 bp. Final barcoded libraries were pooled and sequenced in paired-end mode.
CD34+ HSPCs: RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation. Libraries were prepared from total RNA with the Illumina Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20040529). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).
Jurkat (BRU-seq): Strand-specific libraries were prepared from a modified protocol using the TruSeq Kit (Illumina) as previously described (Paulsen et al., 2013)

treatment_protocol: Cells were treated with 500nM dTAGV-1 or an equivalent volume of DMSO(1ul/mL media) for 6 hours and then immediately harvested for downstream processing.

value: Cord Blood

tag: cell type

value: CD34+ HSPC

tag: genetic modifiction

value: Empty vector

tag: treatment

tag: antibody

value: HA (CST3724S)


title: HEK293T, Wild type, unstressed, rep2

country: China

description: Library name: GLORI2_basal_rep2

library_source: transcriptomic

molecule: polyA RNA


title: CD34, BCL11B-dTAG, HA, merged

description: Library name: CUTRUN_CD34_BCL11BdTAG_HA_merge


title: PHC2 L307R mutant H3K27me3 CUT&RUN (HCT116) rep03

description:
Library name: CR_L307R_H3K27me3_03
CUT&RUN with H3K27me3 antibody (CST 9733) - not used in the analysis


title: FFPE NSCLC patient (L6) sample profiled with the Xenium human lung gene panel

type: RNA

city: Lausanne

first: Raphael

last: Gottardo

state: Vaud

address: Rue du Bugnon 21

department: Biomedical Data Science Center

country: Switzerland

institute: Lausanne University Hospital

description: Lung cancer tissues analyzed with Xenium human lung gene panel

label: Xenium probe set

molecule: total RNA

source_name: primary NSCLC

label_protocol: Xenium probe set

growth_protocol: Not applicable

treatment_protocol: Not applicable

value: primary NSCLC

tag: tissue preservation method

value: FFPE


title: PHC2 L307R mutant H3K27ac CUT&RUN (HCT116) rep03

description:
Library name: CR_L307R_H3K27ac_03
CUT&RUN with H3K27ac antibody (CST 8173) - not used in the analysis


title: FFPE NSCLC patient (L7) sample profiled with the Xenium human lung gene panel


title: FFPE NSCLC patient (L4) sample profiled with the Xenium human lung gene panel


title: HaCaT cells, MoCe_TNF_2

city: Shanghai

first: Lian

last: Cui

state: China

address: 1278 Baode Road

institute: Shanghai Skin Disease Hospital

data_processing:
The libraries were sequenced on an llumina Hiseq platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
Assembly: hg38
Supplementary files format and content: txt file includes raw counts and FPKM values for each sample

source_name: HaCaT cell

extract_protocol:
RNA from the HaCaT cell was extracted using TRIzol.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit following manufacturer’s protocols.

value: HaCaT cell

value: Mo90Ce10+TNF-α treatment


title: 0223

city: Singapore

first: Solomonraj

last: Wilson

address: 8A Biomedical Grove

country: Singapore

institute: SIgN

description: Library name: Sample 6

data_processing:
Analyses were conducted in R (version 4.3.2). Fiducial detection and tissue alignment were performed on H&E images using Loupe Browser (10x Genomics), followed by alignment of reads and UMI counting against the GRCh38 human reference genome using Space Ranger (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: 10x Genomics Visium binary HDF5 file storing sparse gene-expression data for spatial spots.
Supplementary files format and content: Tissue Image
Library strategy: Spatial Transcriptomics

source_name: Colorectal cancer tissue

extract_protocol:
Using the Visium FFPE Reagents Kit and Visium Human Transcriptome Probe Kit (10x Genomics, Pleasanton, CA, USA), gene panel probe hybridization was performed overnight at 50 C for 18-24 hours. The slides were then washed with post-hybridization buffer and 2 x SSC buffer the next day to remove the unbound probes. Ligation was then performed at 37 C for 1 hour and the slides were then washed in 2 x SSC buffer. The slides then underwent RNA digestion (37 C for 30 mins) followed immediately by permeabilization (37 C for 40 mins) and washed in 2 x SSC buffer. Probe extension (45 C for 15 mins) and elution (Room temperature for 10 mins) were then performed to obtain the released mRNA molcules (10x Genomics, Pleasanton, CA, USA).
The tissue sections were then permeabilized, and mRNA molecules captured by the poly(dT) sequence on the slide surface were reverse transcribed, leaving cDNA molecules complementary to the spatial barcode and UMI covalently attached to the slide. The spatially barcoded molecules were released from the slide, PCR-amplified, and sequenced at the recommended depth of 50 K raw reads per capture spot covered by the tissue.

value: Colorectal cancer tissue

value: pre-and-post-treatment


title: PHC2 L307R mutant H3K27ac CUT&RUN (HCT116) rep01

description:
Library name: CR_L307R_H3K27ac_01
CUT&RUN with H3K27ac antibody (CST 8173) - used in part 1 of the analysis


title: HEK293T, Wild type, Arsenite stress, rep2

description: Library name: GLORI2_As_rep2


title: HaCaT cells, MoCe_TNF_1


title: PHC2 L307R mutant H3K27me3 CUT&RUN (HCT116) rep02

description:
Library name: CR_L307R_H3K27me3_02
CUT&RUN with H3K27me3 antibody (CST 9733) - used in part 1 of the analysis


title: 0674_pre

description: Library name: Sample 8

value: pre-treatment


title: FFPE NSCLC patient (L2) sample (2) profiled with the Xenium human lung gene panel


title: PHC2 L307R mutant BAF155 CUT&RUN (HCT116) rep04

description:
Library name: CR_L307R_BAF155_04
CUT&RUN with BAF155 antibody (CST 11956) - not used in the analysis


title: FFPE NSCLC patient (L5) sample profiled with the Xenium human lung gene panel


title: HEK293T, Wild type, unstressed, rep1

description: Library name: GLORI2_basal_rep1


title: 0326

description: Library name: Sample 7


title: HaCaT cells, MoCe_3

value: Mo90Ce10 treatment


title: PHC2 L307R mutant H3K27ac CUT&RUN (HCT116) rep04

description:
Library name: CR_L307R_H3K27ac_04
CUT&RUN with H3K27ac antibody (CST 8173) - not used in the analysis


title: PHC2 L307R mutant BAF155 CUT&RUN (HCT116) rep02

description:
Library name: CR_L307R_BAF155_02
CUT&RUN with BAF155 antibody (CST 11956) - used in part 1 of the analysis


title: 0022_pre

description: Library name: Sample 3


title: PHC2 L307R mutant H3K27ac CUT&RUN (HCT116) rep02

description:
Library name: CR_L307R_H3K27ac_02
CUT&RUN with H3K27ac antibody (CST 8173) - used in part 1 of the analysis


title: HaCaT cells, MoCe_1


title: FFPE NSCLC patient (L1) sample profiled with the Xenium human lung gene panel


title: PHC2 L307R mutant BAF155 CUT&RUN (HCT116) rep01

description:
Library name: CR_L307R_BAF155_01
CUT&RUN with BAF155 antibody (CST 11956) - used in part 1 of the analysis


title: FFPE NSCLC patient (L3) sample profiled with the Xenium human lung gene panel


title: FFPE NSCLC patient (L4) sample profiled with the custom immunooncology gene panel

description: Lung cancer tissues analyzed with a custom Xenium immunooncology 340 gene panel


title: HaCaT cells, Ctrl_TNF_3

value: TNF-α treatment


title: HaCaT cells, Ctrl_TNF_2


title: PHC2 L307R mutant RNA-Seq (HCT116) rep05

description:
Library name: RNA_L307R_05
RNA-Seq - used in part 1 of the analysis


title: iPSC-induced neuron, ABE-corrected, Day28, rep5

city: Shatin

first: Yao

last: Zhu

address: CUHK

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
Library name: Sample 17
Column name in raw_counts_All_Samples.txt: T2_2

data_processing:
FastQC was used to estimate the quality of the files. Read mapping, counting, and differential gene expression analysis of these neurons were performed using HISAT2, FeatureCounts and DESeq2 respectively.
Assembly: hg19
Supplementary files format and content: cvs files include raw counts for each sample

source_name: ns

extract_protocol:
And total RNA from iN cells were extracted using TRIzol (Thermo Fisher Scientific, 15596026CN) according to the manufacturer’s protocols. RNA concentration and quality were assessed using a NanoDrop 2000.
Library construction was generated by Novogene (Beijing).

value: ns

value: iPSC

value: iPSC-induced neuron

value: CDKL5 Mut-corrected

value: Ngn2-induced differentiation

value: Batch 2


title: PHC2 L307R mutant RNA-Seq (HCT116) rep06

description:
Library name: RNA_L307R_06
RNA-Seq - used in part 1 of the analysis

value: PHC2 L307R mutant


title: PHC2 L307R mutant RNA-Seq (HCT116) rep03

description:
Library name: RNA_L307R_03
RNA-Seq - used in part 1 of the analysis


title: HaCaT cells, Ctrl_2

value: PBS treatment


title: iPSC-induced neuron, ABE-corrected, Day28, rep2

description:
Library name: Sample 14
Column name in raw_counts_All_Samples.txt: T1_2

value: Batch 1


title: HaCaT cells, Ctrl_1


title: FFPE NSCLC patient (L8) sample profiled with the Xenium Prime 5K gene panel

description: Lung cancer tissues analyzed with Xenium human Prime 5k gene panel

value: primary NSCLC

value: FFPE


title: PHC2 L307R mutant RNA-Seq (HCT116) rep01

description:
Library name: RNA_L307R_01
RNA-Seq - used in part 1 of the analysis


title: 0119_pre

description: Library name: Sample 5


title: PDX3SiPDLIM4_3

city: Shenyang

first: Sun

middle: Xiang

last: Hao

state: Liaoning

address: puhe road 77th

institute: CMU

description: Library name: PDX3_6

data_processing:
CLC Genomics Workbench y 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKl values for each Sample

source_name: brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug oftotal RNA was used for the construction ofsequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

value: brain


title: 0086_pre

description: Library name: Sample 4

value: Colorectal cancer tissue


title: FFPE NSCLC patient (L7) sample profiled with the Xenium Prime 5K gene panel


title: HaCaT cells, MoCe_TNF_3

value: HaCaT cell

value: Mo90Ce10+TNF-α treatment


title: FFPE NSCLC patient (L2) sample (1) profiled with the Xenium human lung gene panel

description: Lung cancer tissues analyzed with Xenium human lung gene panel


title: HS980_notrans_MUX

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

description: Cell Multiplexing: processed files are linked to the matching GEX sample

library_source: transcriptomic single cell

data_processing:
For non-multiplexed samples, barcoded processing, gene counting were made using “cellranger count” pipeline (v.6.1.1)  with default parameters
For multiplexed sample, demultiplexing, barcoded processing, gene counting were made using “cellranger multi” pipeline (v.6.1.1)  with default parameters for m
To filter out the mouse cells in Grafted, reads were also mapped to the mouse mm10 reference genome, By using pre-transplantation samples as the negative control, cells with 2.25-fold higher number of expressed human genes compared to number of expressed mouse genes were retained as human cells
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: S6 SC-islets generated from H1 and HS980 cells were collected for single-cell RNA sequencing (scRNA-seq) on day 43 of differentiation.

extract_protocol:
The SC-islets were rinsed twice in D-PBS without Ca2+ and Mg2+ and then incubated with TrypLE for 15-20 minutes on an orbit shaker at 37°C. The SC-islets were dissociated into single cells by pipetting 15 times using a P1000 pipette, centrifuged at 300 g for 5 minutes, resuspended into D-PBS without Ca2+ and Mg2+ containing 0.04% BSA (Sigma; A7284), and then filtered using a 40 μm cell strainer (VWR; 732-2760).  Mouse iris transplanted with 300 SC-islets was excised at 20 weeks post-transplantation. Excess iris tissue surrounding SC-islet grafts was removed with a scalpel under a stereomicroscope. The remaining iris tissue with SC-islet grafts was washed twice with 2.5 ml D-PBS without Ca2+ and Mg2+ and then incubated in 2.5 ml dissociation buffer (D-PBS without Ca2+ and Mg2+) containing 2 mg/ml Collagenase IV (ThermoFisher; 17104019), 10 U/ml DNase I (Merck; 04716728001), and 1 mg/ml Papain (Sigma; 76216) for 50 minutes in ULA 6-well plate on an orbit shaker at 37°C. The iris tissue was dissociated into single cells by pipetting 15 times using P1000 pipette every 10 minutes. At the end of dissociation, 2.5 ml D-PBS without Ca2+ and Mg2+ containing 10% FBS were added to block the enzymes. Cells were filtered through 40 μm cell strainer, pelleted at 300g for 5 minutes, and resuspended into 0.8 x 106 cells/ml in D-PBS without Ca2+ and Mg2+ containing 1% BSA.
The 10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x genomics, CG000315 or CG000388) was used for construction of scRNA-seq libraries, sometimes together with Cell Multiplexing Oligo Labeling protocol (10x Genomics, CG000391), followed by RNA sequencing on Illumina Nextseq 2000 machine.

treatment_protocol: Single cell dissociation of stem cell derived islets

value: hESC

value: pancreatic islet differentiation


title: PDX3SiPDLIM4_2

description: Library name: PDX3_5


title: PHC2 L307R mutant BAF155 CUT&RUN (HCT116) rep03

description:
Library name: CR_L307R_BAF155_03
CUT&RUN with BAF155 antibody (CST 11956) - not used in the analysis


title: HaCaT cells, MoCe_2

value: Mo90Ce10 treatment


title: FFPE NSCLC patient (L6) sample profiled with the Xenium Prime 5K gene panel


title: 0022_post

description: Library name: Sample 2

value: post-treatment


title: PDX3SiPDLIM4_1

description: Library name: PDX3_4


title: FFPE NSCLC patient (L9) sample profiled with the Xenium human lung gene panel


title: HS980_notrans_GEX

description: Cell Multiplexing


title: iPSC-induced neuron, CDKL5-R550*, Day28, rep4

description:
Library name: Sample 10
Column name in raw_counts_All_Samples.txt: R2_1

value: ns

value: iPSC

value: iPSC-induced neuron

value: CDKL5 Mut


title: FFPE NSCLC patient (L5) sample profiled with the Xenium Prime 5K gene panel


title: PDX3SiNC3

description: Library name: PDX3_3


title: 0010_pre

description: Library name: Sample 1

value: pre-treatment


title: iPSC-induced neuron, ABE-corrected, Day28, rep6

description:
Library name: Sample 18
Column name in raw_counts_All_Samples.txt: T2_3

value: CDKL5 Mut-corrected

value: Ngn2-induced differentiation

value: Batch 2


title: FFPE NSCLC patient (L3) sample profiled with the custom immunooncology gene panel

value: primary NSCLC

value: FFPE


title: HaCaT cells, Ctrl_TNF_1

value: TNF-α treatment


title: iPSC-induced neuron, ABE-corrected, Day28, rep4

description:
Library name: Sample 16
Column name in raw_counts_All_Samples.txt: T2_1


title: HaCaT cells, Ctrl_3

value: HaCaT cell

value: PBS treatment


title: Wild type isolated mitochondria untreated rep3

city: Göttingen

first: Peter

last: Rehling

address: Humboldtallee

department: Cellular Biochmeistry

country: Germany

institute: University medical center Göttingen

description: Library name: WT_C

data_processing: Samples were demultiplexed and resulting FASTQ-files adapter sequences were removed using cutadapt v3.2 and the command: cutadapt --cores=11 -m15 --discard-untrimmed -O6 -a ATCG-TAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o ‘<output_path>/‘outfile.fastq.gz’ ‘<input_path>/infile.fastq.gz’ 1> ‘<output_path>/‘Cutadapt_report.txt.. Unique molecular identifiers are handled as described in Bertolini et al.,20 using the published scripts and commands. Noncoding RNAs are removed using bowtie2 and reference fasta files containing sequences of non-coding RNAs: bowtie2 -p16 -t -x ‘<ref_file_path>‘ -q infile.fastq.gz’ --un ‘<outfile_path>/outfile.fastq’ -S /dev/null 2> ‘<outfile_path>/Bowtie2_report.txt’. Sequences not matching noncoding RNAs are further aligned to a modified genome of the human chromosome M (GRCh38.p14 Primary Assemblyusing) STAR v2.7.1: STAR --runThreadN 7 --genomeDir ‘<ref_file_path>‘ --readFilesIn ‘<infile_path>/infile.fastq’ --outSAMmultNmax 3 --outFilterType BySJout --outFilterMismatchNmax 2 --alignIntronMin 5 --outFileNamePrefix ‘<outfile_path>‘ --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic --limitBAMsortRAM 1185598524. The modified chromosome M includes open reading frames for noncoding regions of genes and additional short polyA tails at the end of each mRNA to mimic post transcriptional mRNA maturation. Assignment of ribosomal A-, P- and E- site was performed using the Julia scripts described in Bertolini et al., 2021 as well as the removal of PCR duplicates based on UMIs: julia -p 8 <script_path>script.jl -g <annotation_file_path > /annotation_file.gff3 -o <out-put_path>/<input_path>/infile.bam” -u -c 1. Further analysis was performed as described in Günningmann et al., 2023 using the RiboSeqTools package https://github.com/ilia-kats/RiboSeqTools.

source_name: Embryonic Kidney

extract_protocol:
RNA from frozen ribosome fractions was extracted using the hot acid phenol method as described in Galmozzi and Merker et al. 2019
Libraries from isolated ribosome footprints were prepared following the previously published protocol (Galmozzi and Merker et al. 2019)

value: Embryonic Kidney

value: Wild-type


title: PHC2 L307R mutant RNA-Seq (HCT116) rep04

description:
Library name: RNA_L307R_04
RNA-Seq - used in part 1 of the analysis

value: PHC2 L307R mutant


title: iPSC-induced neuron, CDKL5-R550*, Day28, rep2

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.txt: R1_2

value: Batch 1


title: iPSC-induced neuron, CDKL5-R550*, Day28, rep1

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.txt: R1_1

value: ns


title: Hepg2, TNF-a, 6h, mRNA-seq, rep2

city: weifang

first: yongqi

last: liu

state: shandong

address: 699 Binhu Road, Xiashan District

institute: Peking University Institute of Advanced Agricultural Sciences

description: Library name: Hepg2-TNF-a-6-2

data_processing:
Raw sequencing data quality was assessed using FastQC to evaluate read quality.
Cleaned reads were aligned to the human reference genome (GRCh38) using HISAT2 with default parameters.
Aligned reads were processed with StringTie for quantification. Expression levels were estimated as transcripts per million (FPKM) for downstream analysis.
Count matrices generated by StringTie were imported into DESeq2 in R to identify differentially expressed genes.
Assembly: GRCh38 (human reference genome)
Supplementary files format and content: Submitted files include raw expression matrix (FPKM) and differential gene analysis (DESeq2 output) for all samples.
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: HepG2 and HCT116 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C with 5% CO₂. Cells were seeded at a density of 2 × 10⁵ cells per well in 6-well plates and allowed to adhere overnight.

extract_protocol:
Total RNA extracted using Trizol reagent (Invitrogen). RNA purity verified by Nanodrop (A260/A280 >1.8), integrity by Agilent 2100 Bioanalyzer (RIN >8.0).
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V8 RNA - seq Library Prep Kit for MGI.
Bulk RNA-seq libraries prepared with VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (Vazyme): 2 μg RNA underwent polyA selection, fragmentation, cDNA synthesis, end repair, adapter ligation, and PCR amplification. Libraries sequenced on MGISEQ-2000RS (paired-end).

treatment_protocol: Treatments included IL-6 (50 ng/mL, MedChemExpress, HY-P7044, China), TNF-α (100 ng/mL, MedChemExpress, HY-P7058, China), and Torin1 (1 μM, MedChemExpress, HY-13003, China), with incubation times of 3 and 6 hours. Control groups (MOCK) were treated with an equal volume of complete medium. Followed by one PBS rinse prior to sample collection. Each condition was performed in triplicate.

value: liver cancer stem cell


title: FFPE NSCLC patient (L1) sample (1) profiled with the custom immunooncology gene panel

description: Lung cancer tissues analyzed with a custom Xenium immunooncology 340 gene panel


title: iPSC-induced neuron, ABE-corrected, Day28, rep1

description:
Library name: Sample 13
Column name in raw_counts_All_Samples.txt: T1_1

value: iPSC

value: iPSC-induced neuron


title: FFPE NSCLC patient (L1) sample (2) profiled with the custom immunooncology gene panel


title: PHC2 L307R mutant RNA-Seq (HCT116) rep02

description:
Library name: RNA_L307R_02
RNA-Seq - used in part 1 of the analysis


title: iPSC-induced neuron, CDKL5-R550*, Day28, rep6

description:
Library name: Sample 12
Column name in raw_counts_All_Samples.txt: R2_3

value: CDKL5 Mut


title: FFPE NSCLC patient (L2) sample profiled with the custom immunooncology gene panel


title: iPSC-induced neuron, CDKL5-R550*, Day28, rep5

description:
Library name: Sample 11
Column name in raw_counts_All_Samples.txt: R2_2


title: Hepg2, TNF-a, 3h, mRNA-seq, rep3

description: Library name: Hepg2-TNF-a-3-3


title: iPSC-induced neuron, isogenic Control, Day28, rep5

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt: W2_2

value: WT


title: PDX2SiPDLIM4_1

description: Library name: PDX2_4

value: brain


title: iPSC-induced neuron, isogenic Control, Day28, rep4

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt: W2_1

value: Ngn2-induced differentiation

value: Batch 2


title: Hepg2, TNF-a, 3h, mRNA-seq, rep2

description: Library name: Hepg2-TNF-a-3-2


title: FFPE NSCLC patient (L3) sample profiled with the Xenium Prime 5K gene panel

description: Lung cancer tissues analyzed with Xenium human Prime 5k gene panel

value: primary NSCLC

value: FFPE


title: HEK293 translation stalled with CAP rep3

description: Library name: WT_8_CAP


title: HS980_trans

value: hESC

value: Transplantation of HS980 islets


title: iPSC-induced neuron, CDKL5-R550*, Day28, rep3

description:
Library name: Sample 9
Column name in raw_counts_All_Samples.txt: R1_3


title: iPSC-induced neuron, ABE-corrected, Day28, rep3

description:
Library name: Sample 15
Column name in raw_counts_All_Samples.txt: T1_3

value: CDKL5 Mut-corrected


title: PDX3SiNC2

description: Library name: PDX3_2


title: H1

value: pancreatic islet differentiation


title: FFPE NSCLC patient (L1) sample profiled with the Xenium Prime 5K gene panel


title: PDX2SiNC2

description: Library name: PDX2_2


title: PDX2SiPDLIM4_3

description: Library name: PDX2_6


title: PDX3SiNC1

description: Library name: PDX3_1


title: PDX2SiNC1

description: Library name: PDX2_1


title: iPSC-induced neuron, isogenic Control, Day28, rep2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt: W1_2


title: Hepg2, TNF-a, 6h, mRNA-seq, rep1

description: Library name: Hepg2-TNF-a-6-1


title: Wild type isolated mitochondria untreated rep2

description: Library name: WT_B

value: Embryonic Kidney

value: Wild-type


title: Wild type isolated mitochondria untreated rep1

description: Library name: WT_A


title: iPSC-induced neuron, isogenic Control, Day28, rep6

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt: W2_3

value: ns


title: PDX2SiPDLIM4_2

description: Library name: PDX2_5


title: Hepg2, NC, mRNA-seq, rep1

description: Library name: Hepg2-NC-1

value: liver cancer stem cell


title: Hepg2, NC, mRNA-seq, rep2

description: Library name: Hepg2-NC-2


title: HEK293 translation stalled by SNAP freezing rep1

description: Library name: WT_9_SF


title: HEK293 translation stalled by SNAP freezing rep2

description: Library name: WT_7_SF


title: PDX2SiNC3

description: Library name: PDX2_3


title: iPSC-induced neuron, isogenic Control, Day28, rep3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt: W1_3

value: iPSC

value: Batch 1


title: HEK293 translation stalled by SNAP freezing rep3

description: Library name: WT_8_SF


title: Hepg2, NC, mRNA-seq, rep3

description: Library name: Hepg2-NC-3


title: Hepg2, TNF-a, 3h, mRNA-seq, rep1

description: Library name: Hepg2-TNF-a-3-1


title: HEK293 translation stalled with CAP rep2

description: Library name: WT_7_CAP


title: iPSC-induced neuron, isogenic Control, Day28, rep1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt: W1_1

value: iPSC-induced neuron


title: PDX1SiPDLIM4_3

description: Library name: PDX1_6


title: MCF7 cells, -E2, 13 month plus 666-15 24 hours.

city: Chicago

first: Lei

last: Duan

state: IL

address: 1653 W Congress Pkwy

department: Anatomy and Cell Biology

institute: Rush University Medical Center

description: Library name: Sample 5

data_processing:
RNA-seq libraries were sequenced on Illumina NovaSeq 6000 and NovaSeq X Plus platforms to generate paired-end reads.
Raw sequencing reads were subjected to quality control using FastQC to assess read quality, GC content, and adapter contamination.
Adapter sequences and low-quality bases were trimmed using Trimmomatic.
Cleaned reads were aligned to the human reference genome using STAR aligner.
Gene-level read counts were quantified using featureCounts, and normalized expression values were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: Human reference genome GRCh38 (hg38).
Supplementary files format and content: Processed data files are provided as tab-delimited text files containing gene-level expression values.
Supplementary files format and content: Files include raw read counts and FPKM-normalized expression values for each gene, with rows corresponding to genes and columns corresponding to individual samples and experimental conditions.

growth_protocol: MCF7 cells were grown in DMEM medium, with 10% fetal bovine serum (FBS), penicillin (100 U/mL) and streptomycin (100 µg/mL). For estrogen deprivation, cells were grown in phenol-red free DMED supplemented with Charcoal-striped FBS. Long term estrogen deprived (LTED) cells were obtained by continuously growing MCF7 cells in phenol-red free DMEM supplemented with Charcoal-striped FBS for more than 13 months.

extract_protocol:
Total RNA was prepared using Total RNA Mini Kit (IBI Scientific, IA). 1 µg of total RNA was used for the construction of the sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis using either dTTP for non–strand-specific libraries or dUTP for strand-specific libraries. Libraries were end-repaired, A-tailed, adaptor-ligated, and PCR-amplified according to the manufacturer’s protocol prior to sequencing.

treatment_protocol: To develop abemaciclib resistant cells, LTED cells were grown in phenol-red free DMEM supplemented with Charcoal-striped FBS and 0.5 µM  abemaciclib for 8 months.  To test the effect of Creb inhibition, LTED cells were treated with 1 µM 666-15 for 24 hours.

value: ER+ breast cancer

value: WT

value: E2 deprivation plus 666-15

tag: time

value: Month 13 plus day 1


title: HEK293 translation stalled with CAP rep1

description: Library name: WT_9_CAP


title: Hepg2, IL6, 6h, mRNA-seq, rep3

description: Library name: Hepg2-IL6-6-3


title: PDX1SiPDLIM4_2

description: Library name: PDX1_5

value: brain


title: PDX1SiNC3

description: Library name: PDX1_3


title: PDX1SiNC2

description: Library name: PDX1_2


title: MCF7 cells, -E2, 13 months plus Abemaciclib 8 months

description: Library name: Sample 4

value: E2 deprivation plus abemaciclib

value: Month 13 plus month 8


title: Wild type isolated mitochondria COX1.1-19 morpholino treated rep3

description: Library name: COX1_C


title: MCF7 cells, -E2, 13 months (LTED)

description: Library name: Sample 3

value: E2 deprivation

value: Month 13


title: Wild type isolated mitochondria COX2.1-23 morpholino treated rep1

description: Library name: COX2_A


title: Wild type isolated mitochondria COX2.1-23 morpholino treated rep3

description: Library name: COX2_C


title: Hepg2, IL6, 3h, mRNA-seq, rep2

description: Library name: Hepg2-IL6-3-2


title: Hepg2, IL6, 3h, mRNA-seq, rep1

description: Library name: Hepg2-IL6-3-1


title: Wild type isolated mitochondria COX1.1-19 morpholino treated rep1

description: Library name: COX1_A


title: Hepg2, IL6, 6h, mRNA-seq, rep2

description: Library name: Hepg2-IL6-6-2


title: MCF7 cells, -E2, 1 month (ED)

description: Library name: Sample 2

value: Day 30


title: PDX1SiPDLIM4_1

description: Library name: PDX1_4


title: Hepg2, IL6, 6h, mRNA-seq, rep1

description: Library name: Hepg2-IL6-6-1


title: Cells, OE_PDK4, R1

city: Suzhou

first: You

last: Yu

state: Jiangsu province

address: No.178 Ganjiang Rd

department: Institute for Cardiovascular Science

institute: Soochow University

description:
Library name: Cells_OE_PDK4_R1
OE_PDK4

data_processing:
High quality clean reads, reads were further filtered by fastp and aliged with the reference genome followed by standard pepline. Read count extraction and normalization were performed using default benchwork.
Assembly: GRCm39 (Genome Reference Consortium Mouse Reference 39), INSDC Assembly GCA_000001635.9, Jun 2020
Supplementary files format and content: Table.xlsx files include raw FPKM and Count values for each sample

source_name: Cell line

extract_protocol:
Total RNA was isolated from aorta tissues, and HAECs using RNA isolation reagent (Takara, 9108) according to the manufacturer’s protocol as described. 1 μg total RNA from every sample was subjected to library preparation.
The library was constructed by PolyA method according to the manufacturor's ptotocols.

value: Cell line


title: Hepg2, IL6, 3h, mRNA-seq, rep3

description: Library name: Hepg2-IL6-3-3


title: MCF7 cells, +E2, 1 month (MCF7)

description: Library name: Sample 1


title: Wild type isolated mitochondria COX2.1-23 morpholino treated rep2

description: Library name: COX2_B

value: Embryonic Kidney

value: Wild-type


title: SB_Sh1

description: Library name: SB4


title: Hepg2, IL10, 6h, mRNA-seq, rep2

description: Library name: Hepg2-IL10-6-2

value: liver cancer stem cell


title: Cells, OE_PDK4, R3

description:
Library name: Cells_OE_PDK4_R3
OE_PDK4


title: SB_NC3

description: Library name: SB3


title: PDX1SiNC1

description: Library name: PDX1_1


title: Wild type isolated mitochondria COX1.1-19 morpholino treated rep2

description: Library name: COX1_B


title: Cells, OE_PDK4, R2

description:
Library name: Cells_OE_PDK4_R2
OE_PDK4


title: SB_Sh3

description: Library name: SB6


title: patient 521, non-severe, COVID-19, TA

city: San Francisco

first: Lucile

middle: P A

last: Neyton

state: CA

address: 505 Parnassus Ave

institute: UCSF

description:
Library name: MVIR1-HS521
H5 count matrix

data_processing:
The BCL files from sequencer were demultiplexed into individual libraries using mkfastqs command in Cellranger 3.0.1 suite of tools (https://support.10xgenomics.com).
The feature-barcode matrices were obtained for each library by aligning the TA raw fastq files to GRCh38 (annotated with Ensembl v85) + SARS-CoV-2 reference genome using default parameters in Cellranger count (v3.0.1).
Assembly: GRCh38
Supplementary files format and content: raw count matrices (H5)

source_name: tracheal aspirate

extract_protocol:
The tracheal aspirate (TA) samples were transported to a BSL-3 laboratory, 3 mL of TA was dissociated using 50 µg/mL collagenase type 4 (Worthington), and 0.56 ku/mL of Dnase I (Worthington). The cells were collected by centrifugation and counted, and the CD45-positive cells were enriched using MojoSort Human CD45 beads (Biolgenend) and counted again before library preparation.
The Chromium Controller was loaded with 15,000 cells per sample following the manufacturer’s instructions (10X Genomics). A Chromium Single Cell 5′ Reagent Kit v2 (10X Genomics) was used for reverse transcription, cDNA amplification and library construction of the gene expression libraries (following the detailed protocol provided by 10X Genomics). Libraries were sequenced on an Illumina NovaSeq 6000.

value: tracheal aspirate

tag: severity

value: non-severe


title: [CUT&Run] Human ESC_CTCF-FKBP Clone 1, untreated

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: Library name: Sample 3

data_processing:
Data were processed using a modified version of Cut&RunTools (Zhu et al., 2019).  Reads were adapter trimmed using fastp v.0.20.0 (Chen et al., 2018).  An additional trimming step was performed to remove up to 6bp adapter from each read.
Trimmed reads were aligned the hg38 genome using bowtie2 (Langmead et al., 2012) with the ‘dovetail’ and ‘sensitive’ settings enabled.
Normalized reads per genomic signal (RPGC) signal tracks were generated from the alignments using the ‘bamCoverage’ utility from deepTools (Ramirez et al., 2016) with parameters  bin-size=25, smooth length=75, and with ‘center_reads’ and ‘extend_reads’ options enabled.
Assembly: hg38
Supplementary files format and content: bigwig files containing reads per genomic content (RGPC) normalized read density.
Library strategy: CUT&Run

growth_protocol: Human ESC were cultured in wells coated with growth factor reduced Matrigel (354230, Corning) in mTeSR plus medium (Stemcell, #100-0276) with daily changes of media. Cells were passaged at 80% confluency using 1mg/mL Dispase (Stemcell, #07923) and manual scrapping and cultured at 37°C and 5% CO2. Mouse ESC were grown on 0.1% gelatin-coated plates in high-glucose DMEM (Gibco) supplemented with 15% FBS, 1:500 LIF (made in house), 0.1 mM non-essential amino acids, 1% glutamax, 1mM Sodium Pyruvate, 55 mM β-mercaptoethanol, and 1% penicillin/streptomycin (all from ThermoFisher Scientific) at 37°C and 5% CO2. Cells were routinely passaged with Trypsin 0.05% (Gibco). Media was changed every other day and passaged every 2-3 days.

extract_protocol:
In brief, 450,000 hESC were individualized with Accutase, washed a total of three times with Wash Buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, Roche complete Protease Inhibitor tablet EDTA free) and bound to activated Concanavalin A beads (Polysciences) for 10 minutes at room temperature. Cell permeabilization was performed in 200ml of Digitonin Buffer (0.05 % Digitonin and 0.1% BSA in Wash Buffer) followed by incubation with 4ml of the antibody against CTCF (07-729, Millipore) at 4°C for 2 hours. For negative controls, we used a Guinea Pig anti-Rabbit IgG (ABIN101961, Antibodies-online). After antibody incubation, cells were washed with Digitonin Buffer, followed by incubation with purified hybrid protein A-protein G-Micrococcal nuclease (pAG-MNase) at 4°C for 1 hour. Samples were washed again in Digitonin Buffer, resuspended in 150 μl Digitonin Buffer and equilibrated to 0°C on ice water for 5 minutes. 3 μl of 100 mM CaCl2 was added to cells to start with MNase cleavage, and after 1 hour of digestion, reactions were stopped with the addition of 150 μl 2x Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02 % Digitonin, 50 μg/ml RNase A, 50 μg/ml Glycogen). Samples were incubated at 37°C for 10 minutes to release DNA fragments and centrifuged at 16,000 g for 5 minutes. Supernatants were collected and a mix of 1.5 μl 20% SDS / 2.25 μl 20 mg/ml Proteinase K was added to each sample followed by incubation at 65°C for 35 minutes. DNA was precipitated with ethanol and sodium acetate and pelleted by centrifugation at 4°C, washed, air-dried and resuspended in 10 μl 0.1x TE.
In brief, end-repair was performed in 50 μl of T4 ligase reaction buffer, 0.4 mM dNTPs, 3 U of T4 DNA polymerase (NEB), 9 U of T4 Polynucleotide Kinase (NEB) and 1 U of Klenow fragment (NEB) at 20°C for 30 minutes. Following this step, end-repair reaction was cleaned using AMPure XP beads (Beckman Coulter) and eluted in 16.5 μl of Elution Buffer (10 mM Tris-HCl pH 8.5) followed by A-tailing reaction in 20 μl of dA-Tailing reaction buffer (NEB) with 2.5 U of Klenow fragment exo- (NEB) at 37°C for 30 minutes. The total volume of the A-tailing reaction was mixed with Quick Ligase buffer 2X (NEB), 3000 U of Quick Ligase (NEB) and 10 nM of annealed adaptor (Illumina truncated adaptor) in a final volume of 50 μl and incubated for 20 min at room temperature. The adaptor was prepared by annealing the following HPLC-purified oligos: 5′-Phos/GATCGGAAGAGCACACGTCT-3′ and 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATC∗T-3′ (∗phosphorothioate bond). Ligation was stopped by adding 50 mM of EDTA, cleaned with AMPure XP beads and eluted in 14 μl of Elution Buffer. All volume was used for PCR amplification in a 50 μl reaction with 1 μM primers TruSeq barcoded primer p7, 5′-CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC∗T-3′ and TruSeq barcoded primer p5 5′-AATGATACGGCGACCACCGAGATCTACACXXXXXXXXACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ (∗ represents a phosphothiorate bond and XXXXXXXX a barcode index sequence), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). PCR amplification was performed with the following program: 45 s at 98°C followed by 15 cycles of 15 s at 98°C, 30 s at 63°C, 30 s at 72°C and a final 5 min extension at 72°C. PCR reactions were cleaned with AMPure XP beads (Beckman Coulter), run on a 2% agarose gel and a band of 300bp approximately was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina NextSeq2000 (50bp pair-end reads).

treatment_protocol: ESC were untreated or treated for the indicated times with dTAG at a final concentration of 500nM.

value: Human embryonic stem cell

value: Untreated

value: CTCF


title: Hepg2, IL10, 3h, mRNA-seq, rep3

description: Library name: Hepg2-IL10-3-3


title: Hepg2, IL10, 6h, mRNA-seq, rep3

description: Library name: Hepg2-IL10-6-3


title: [CUT&Run] Human ESC untreated, IgG

description: Library name: Sample 7

value: WT

value: IgG


title: Frontal cortex, CORT+DFP+LPS, 24 h, A278

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

description: Library name: CTX_A278

data_processing:
Raw FASTQ files were processed to remove adaptor sequences and low-quality bases (q < 30) using TrimGalore (v0.4.1), and read quality was assessed with FastQC.
Trimmed reads were aligned using STAR (v2.6.0a) in two-pass mode to the mouse reference genome GRCm38 (mm10) with GENCODE annotations.
Resulting BAM files were processed with GenomicAlignments and DESeq2 following the standard DESeq2 workflow to generate gene-level count data and differential expression statistics.
One control hippocampus sample was excluded from analysis because of poor sample quality; the deposited processed count matrix reflects the analysed 30-sample dataset used in the manuscript.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data file is a gzip-compressed CSV matrix with Ensembl gene IDs in the first column and raw gene-level counts for 30 analysed samples in the remaining columns.

source_name: Frontal cortex

growth_protocol: Adult male C57BL/6J mice (8-12 weeks old, approximately 30 g) were obtained from Jackson Laboratory and housed individually under controlled temperature and humidity on a 12 h light/12 h dark cycle with ad libitum access to food and water.

extract_protocol:
Total RNA was extracted from hippocampus and frontal cortex tissue using the E.Z.N.A. RNA/DNA Isolation Kit (Omega Bio-tek).
For RNA-seq, poly(A)-selected, stranded mRNA libraries were prepared with the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer's protocol. Whole-genome mRNA sequencing was performed on an Illumina NovaSeq 6000 using paired-end 150 bp reads.

treatment_protocol: To model Gulf War Illness-related stress and toxicant exposure, mice received corticosterone (CORT; 200 mg/L in 0.6% ethanol) in the drinking water for 7 days, followed on day 8 by a single intraperitoneal injection of diisopropyl fluorophosphate (DFP; 4 mg/kg). Mice then received periodic CORT administration for 7 days every other week to a total of 5 weeks. On the final day, mice received either saline or lipopolysaccharide (LPS; 0.5 mg/kg, subcutaneous). Hippocampus and frontal cortex were collected 6 h, 12 h, or 24 h after challenge, depending on group.

value: Frontal cortex

value: wild type

value: CORT+DFP+LPS, 24 h


title: Cells, OE_Scramble, R3

description:
Library name: Cells_OE_Scramble_R3
OE_Scramble control

value: Scramble


title: Hippocampus, CORT+DFP+LPS, 24 h, A278

description: Library name: HPC_A278

source_name: Hippocampus

value: Hippocampus


title: Hepg2, IL10, 6h, mRNA-seq, rep1

description: Library name: Hepg2-IL10-6-1


title: [CUT&Run] Human ESC dTAG, 72h

description: Library name: Sample 2

value: dTAG

value: 24 hours


title: patient 510, non-severe, COVID-19, TA

description:
Library name: MVIR1-HS510
H5 count matrix


title: Cells, OE_Scramble, R2

description:
Library name: Cells_OE_Scramble_R2
OE_Scramble control

value: Cell line


title: [CUT&Run] Human ESC_CTCF-FKBP Clone 2, untreated

description: Library name: Sample 5


title: Human ESC dTAG, 72h, rep2

description: Library name: Sample 19

data_processing:
Briefly, RNAseq reads were adapter trimmed using cutadapt v4.4. Trimmed reads were aligned to either the hg38 genome with the GENCODE transcriptome annotation release 35  orthe mm10 genome with the GENCODE transcriptome annotation release 25 using STAR v2.7.6a. Transcript and transposable element expression was quantified using TEcount from tetoolkit v2.1.4. Differential expression analysis was performed using the DESeq2 package.
Assembly: hg38, mm10
Supplementary files format and content: Processed data files represent count files obtained from TEcount. This file is a plain-text, tab-separated file with with the following information: Gene or TE, and raw counts.

growth_protocol: Human ESC were cultured in wells coated with growth factor reduced Matrigel (354230, Corning) in mTeSR plus medium (Stemcell, #100-0276) with daily changes of media. Cells were passaged at 80% confluency using 1mg/mL Dispase (Stemcell, #07923) and manual scrapping and cultured at 37°C and 5% CO2. Mouse ESC were grown on 0.1% gelatin-coated plates in high-glucose DMEM (Gibco) supplemented with 15% FBS, 1:500 LIF (made in house), 0.1 mM non-essential amino acids, 1% glutamax, 55 mM β-mercaptoethanol, and 1% penicillin/streptomycin (all from ThermoFisher Scientific) at 37°C and 5% CO2.

extract_protocol:
Cells were collected and isolation of total RNA was performed by using the Isolate II RNA Mini Kit (Bioline).
RNAseq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, NEB) and NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB) according to the manufacturer’s protocol. RNA quality and yield were measured using RNA integrity number (RIN) algorithm, using the Fragment Analyzer (Agilent) or LabChip Gx Touch 24 (Perkin Elmer). Samples with 7.0-10.0 RIN value were used for library preparation. 2 μg of total RNA was used as input for VAHTS Stranded mRNAseq Library preparation. Sequencing was performed on an Illumina NextSeq550 (75bp pair-end reads) or or an Illumina NextSeq2000 (60bp pair-end reads).

treatment_protocol: Human ESC were untreated or treated for the indicated times with dTAG at a final concentration of 500nM. Mouse ESC were untreated or treated for the indicated times with IAA at a final concentration of 500nM and DOX for 1mg/ml


title: patient 508, non-severe, COVID-19, TA

description:
Library name: MVIR1-HS508
H5 count matrix


title: SB_NC1

description: Library name: SB1

value: brain


title: SB_NC2

description: Library name: SB2


title: Frontal cortex, CORT+DFP+LPS, 24 h, A276

description: Library name: CTX_A276


title: Hepg2, IL10, 3h, mRNA-seq, rep2

description: Library name: Hepg2-IL10-3-2

value: liver cancer stem cell


title: SB_Sh2

description: Library name: SB5


title: [CUT&Run] Human ESC_CTCF-FKBP Clone 1, dTAG 24h

description: Library name: Sample 4


title: Human ESC untreated, rep2

description: Library name: Sample 18


title: HCT116, Torin1, 3h, mRNA-seq, rep2

description: Library name: HCT116-Torin1-3-2

value: colonic cancer cell line


title: HCT116, Torin1, 3h, mRNA-seq, rep3

description: Library name: HCT116-Torin1-3-3


title: [CUT&Run] Human ESC_CTCF-FKBP Clone 2, dTAG 24h

description: Library name: Sample 6


title: Hippocampus, CORT+DFP+LPS, 24 h, A276

description: Library name: HPC_A276


title: Human ESC_WAPL-FKBP Clone 2, dTAG 24h

description: Library name: Sample 16


title: Hepg2, IL10, 3h, mRNA-seq, rep1

description: Library name: Hepg2-IL10-3-1


title: patient 51, non-severe, COVID-19, TA

description:
Library name: MVIR1-HS51
H5 count matrix

value: tracheal aspirate

value: non-severe


title: Hippocampus, CORT+DFP+LPS, 24 h, A274

description: Library name: HPC_A274


title: HCT116, Torin1, 6h, mRNA-seq, rep3

description: Library name: HCT116-Torin1-6-3


title: Cells, OE_Scramble, R1

description:
Library name: Cells_OE_Scramble_R1
OE_Scramble control


title: [CUT&Run] Human ESC untreated

description: Library name: Sample 1

value: Human embryonic stem cell

value: Untreated


title: HCT116, Torin1, 6h, mRNA-seq, rep2

description: Library name: HCT116-Torin1-6-2


title: patient 145, severe, COVID-19, TA

description:
Library name: MVIR1-HS145
H5 count matrix

value: severe


title: HCT116, Torin1, 6h, mRNA-seq, rep1

description: Library name: HCT116-Torin1-6-1


title: patient 494, non-severe, COVID-19, TA

description:
Library name: MVIR1-HS494
H5 count matrix


title: patient 489, severe, COVID-19, TA

description:
Library name: MVIR1-HS489
H5 count matrix


title: Human ESC_WAPL-FKBP Clone 1, dTAG 24h

description: Library name: Sample 13


title: patient 31, non-severe, COVID-19, TA

description:
Library name: MVIR1-HS31
H5 count matrix


title: HCT116, TNF-a, 6h, mRNA-seq, rep2

description: Library name: HCT116-TNF-a-6-2


title: Human ESC_WAPL-FKBP Clone 1, untreated

description: Library name: Sample 12


title: patient 38, severe, COVID-19, TA

description:
Library name: MVIR1-HS38
H5 count matrix


title: Human ESC_WAPL-FKBP Clone 2, dTAG 48h

description: Library name: Sample 17


title: Frontal cortex, CORT+DFP+LPS, 24 h, A275

description: Library name: CTX_A275


title: Control EVT_1

city: Madrid

first: Vicente

middle: Pérez

last: García

state: Madrid

address: C/ Nicolás Cabrera 1

department: Tissue and organ homeostasis

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

description: Library name: EVT_1

data_processing:
Reads were mapped to Homo sapiens GRCh38 genome  assembly using HISAT2 v2.1.0.
Read counts and normalization were performed with SeqMonk software.
Assembly: GRCh38
Supplementary files format and content: Matrix with raw counts for each sample per column

extract_protocol:
Total RNA was extracted using RNeasy mini-Kit and RNase-free DNase (QIAGEN 74106)
RNA-seq libraries were generated from 500ng using TruSeq Stranded mRNA library prop (Illumina, 20020594).

value: Trophoblast stem cells

tag: sample group

value: Control EVT


title: Frontal cortex, CORT+DFP+LPS, 24 h, A274

description: Library name: CTX_A274

value: Frontal cortex

value: wild type


title: HCT116, Torin1, 3h, mRNA-seq, rep1

description: Library name: HCT116-Torin1-3-1


title: Frontal cortex, CORT+DFP+LPS, 12 h, A261

description: Library name: CTX_A261

value: CORT+DFP+LPS, 12 h


title: Human ESC_WAPL-FKBP Clone 2, untreated

description: Library name: Sample 15


title: Hippocampus, CORT+DFP+LPS, 24 h, A275

description: Library name: HPC_A275

value: Hippocampus

value: CORT+DFP+LPS, 24 h


title: HCT116, TNF-a, 3h, mRNA-seq, rep2

description: Library name: HCT116-TNF-a-3-2


title: Frontal cortex, CORT+DFP+LPS, 12 h, A259

description: Library name: CTX_A259


title: Hippocampus, CORT+DFP+LPS, 12 h, A260

description: Library name: HPC_A260


title: Human ESC_CTCF-FKBP Clone 3, dTAG 24h

description: Library name: Sample 10

value: dTAG


title: HCT116, NC, mRNA-seq, rep3

description: Library name: HCT116-NC-3


title: Human ESC_WAPL-FKBP Clone 1, dTAG 48h

description: Library name: Sample14


title: Hippocampus, CORT+DFP+LPS, 12 h, A259

description: Library name: HPC_A259


title: HCT116, TNF-a, 6h, mRNA-seq, rep3

description: Library name: HCT116-TNF-a-6-3


title: Hippocampus, CORT+DFP+LPS, 12 h, A261

description: Library name: HPC_A261


title: Control EVT_2

description: Library name: EVT_2


title: Frontal cortex, CORT+DFP+LPS, 12 h, A260

description: Library name: CTX_A260


title: HCT116, TNF-a, 3h, mRNA-seq, rep3

description: Library name: HCT116-TNF-a-3-3


title: HCT116, TNF-a, 6h, mRNA-seq, rep1

description: Library name: HCT116-TNF-a-6-1


title: BAP1-OE EVT_4

description: Library name: EVTh_4

value: BAP1-OE EVT


title: BAP1-OE EVT_3

description: Library name: EVTh_3


title: Control Organoid_4

description: Library name: ORG_C_4

value: Control Organoid


title: HCT116, TNF-a, 3h, mRNA-seq, rep1

description: Library name: HCT116-TNF-a-3-1


title: Control Organoid_1

description: Library name: ORG_C_1


title: Human ESC_CTCF-FKBP Clone 3, untreated

description: Library name: Sample 9


title: Control Organoid_3

description: Library name: ORG_C_3


title: BAP1-OE Organoid_4

description: Library name: ORG_B_4

value: BAP1-OE Organoid


title: Control Organoid_2

description: Library name: ORG_C_2


title: Human ESC_CTCF-FKBP Clone 2, dTAG 48h

description: Library name: Sample 8


title: Human ESC_CTCF-FKBP Clone 3, dTAG 48h

description: Library name: Sample 11


title: Frontal cortex, CORT+DFP+LPS, 12 h, A258

description: Library name: CTX_A258


title: HCT116, NC, mRNA-seq, rep1

description: Library name: HCT116-NC-1

value: colonic cancer cell line


title: Hippocampus, CORT+DFP+LPS, 12 h, A258

description: Library name: HPC_A258


title: HCT116, NC, mRNA-seq, rep2

description: Library name: HCT116-NC-2


title: HCT116, IL6, 6h, mRNA-seq, rep3

description: Library name: HCT116-IL6-6-3


title: BAP1-OE Organoid_3

description: Library name: ORG_B_3


title: Human ESC_CTCF-FKBP Clone 1, dTAG 24h

description: Library name: Sample 4


title: Human ESC_CTCF-FKBP Clone 2, untreated

description: Library name: Sample 6


title: HCT116, IL6, 6h, mRNA-seq, rep2

description: Library name: HCT116-IL6-6-2


title: HCT116, IL6, 6h, mRNA-seq, rep1

description: Library name: HCT116-IL6-6-1


title: Frontal cortex, CORT+DFP+LPS, 6 h, A243

description: Library name: CTX_A243

value: CORT+DFP+LPS, 6 h


title: Human ESC_CTCF-FKBP Clone 1, untreated

description: Library name: Sample 3


title: BAP1-OE Organoid_1

description: Library name: ORG_B_1


title: Human ESC_CTCF-FKBP Clone 2, dTAG 24h

description: Library name: Sample 7


title: BAP1-OE Organoid_2

description: Library name: ORG_B_2


title: Human ESC_CTCF-FKBP Clone 1, dTAG 48h

description: Library name: Sample 5


title: Hippocampus, CORT+DFP+LPS, 6 h, A243

description: Library name: HPC_A243


title: HCT116, IL6, 3h, mRNA-seq, rep3

description: Library name: HCT116-IL6-3-3


title: Hippocampus, CORT+DFP+LPS, 6 h, A242

description: Library name: HPC_A242


title: Human ESC untreated, rep1

description: Library name: Sample 1

value: WT


title: Frontal cortex, CORT+DFP+LPS, 6 h, A242

description: Library name: CTX_A242


title: Control STB_5

description: Library name: SYN_5

value: Control STB


title: ESC-CTCF/WAPL-AID, IAA-treated, 48h, REPLICATE 2

description: Library name: Sample 5

data_processing:
ChIP-seq data were processed using nf-core/chipseq (v2.1.0; DOI: 10.5281/zenodo.3240506). Reads were aligned using BWA (as implemented in the pipeline) to a custom mouse genome (mm10_intDUX) derived from mm10, in which the genomic region chr10:56,747,354–62,384,650 was replaced with the Dux contig (RefSeq accession: MW810794; Grow et al., 2021).  The --keep_multi_map parameter was enabled to retain reads mapping to repetitive elements.
Assembly: A custom genome was generated based on mm10 (GRCm38) by replacing the region chr10:56,747,354–62,384,650 with the Dux contig (RefSeq accession: MW810794).
Supplementary files format and content: bigwig files

growth_protocol: ESC were grown on 0.1% gelatin-coated plates in high-glucose DMEM (Gibco) supplemented with 15% FBS, 1:500 LIF (made in house), 0.1 mM non-essential amino acids, 1% glutamax, 1mM Sodium Pyruvate, 55 mM β-mercaptoethanol, and 1% penicillin/streptomycin (all from ThermoFisher Scientific) at 37°C and 5% CO2. Cells were routinely passaged with Trypsin 0.05% (Gibco). Media was changed every other day and passaged every 2-3 days.

extract_protocol:
Twenty million of untreated or IAA-treated mESCWAPL/CTCF-AID cells were fixed using 1% Formaldehyde (Sigma, F1635) at room temperature for 10 min. Fixation was then quenched with 125 mM glycine (Sigma). Cell pellets were washed twice with cold PBS and samples were snap-frozen and stored in −80 °C. Frozen pellets were resuspended in 1 mL RIPA buffer (10 mM Tris-HCl pH 7.5, 1 mM ethylenediaminetetraacetic acid (EDTA), 0.1% sodium dodecyl sulfate, 0.1% sodium deoxycholate, 1% Triton X-100, and 1 Complete Mini EDTA-free proteinase inhibitor tablet (Roche)). Sonication was performed using Covaris S220 (duty cycle 20%, peak incident power 175, and cycle/burst 200 for 30 min at 4 °C). Chromatin was pre-clarified with 40 μL prewashed Dynabeads Protein G (ThermoFisher) for 30 min at 4 °C and then incubated with 40 μL Dynabeads Protein G bound to 5 μg of anti-DPPA2 antibody (Millipore Sigma MAB4356) in 900 μL of RIPA buffer overnight at 4 °C. Beads were then collected in a magnetic separator (DynaMag-2 Invitrogen), washed twice with cold RIPA buffer, twice with RIPA buffer containing 0.3 M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (10 mM Tris pH 8.0, 1 mM EDTA) + 0.2% Triton X-100, and once with TE. Crosslinking was reversed by incubating the chromatin bound beads at 65 °C for 4 h in the presence of 0.3% SDS and 1 mg/mL of Proteinase K (Qiagen). Chromatin DNA extraction from beads and library preparation were performed as described (Canela et al, 2019).
In brief, end-repair was performed in 50 μl of T4 ligase reaction buffer, 0.4 mM dNTPs, 3 U of T4 DNA polymerase (NEB), 9 U of T4 Polynucleotide Kinase (NEB) and 1 U of Klenow fragment (NEB) at 20°C for 30 minutes. Following this step, end-repair reaction was cleaned using AMPure XP beads (Beckman Coulter) and eluted in 16.5 μl of Elution Buffer (10 mM Tris-HCl pH 8.5) followed by A-tailing reaction in 20 μl of dA-Tailing reaction buffer (NEB) with 2.5 U of Klenow fragment exo- (NEB) at 37°C for 30 minutes. The total volume of the A-tailing reaction was mixed with Quick Ligase buffer 2X (NEB), 3000 U of Quick Ligase (NEB) and 10 nM of annealed adaptor (Illumina truncated adaptor) in a final volume of 50 μl and incubated for 20 min at room temperature. The adaptor was prepared by annealing the following HPLC-purified oligos: 5′-Phos/GATCGGAAGAGCACACGTCT-3′ and 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATC∗T-3′ (∗phosphorothioate bond). Ligation was stopped by adding 50 mM of EDTA, cleaned with AMPure XP beads and eluted in 14 μl of Elution Buffer. All volume was used for PCR amplification in a 50 μl reaction with 1 μM primers TruSeq barcoded primer p7, 5′-CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC∗T-3′ and TruSeq barcoded primer p5 5′-AATGATACGGCGACCACCGAGATCTACACXXXXXXXXACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ (∗ represents a phosphothiorate bond and XXXXXXXX a barcode index sequence), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). PCR amplification was performed with the following program: 45 s at 98°C followed by 17 cycles of 15 s at 98°C, 30 s at 63°C, 30 s at 72°C and a final 5 min extension at 72°C. PCR reactions were cleaned with AMPure XP beads (Beckman Coulter), run on a 2% agarose gel and a band of 300bp approximately was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina NextSeq2000 (50bp pair-end reads).

treatment_protocol: ESC were untreated or treated for the indicated times with indole-3-acetic acid (IAA) at a final concentration of 500nM.

value: Mouse embryonic stem cell

value: ESC-CTCF/WAPL-AID

value: IAA

value: 48 hours


title: Control STB_4

description: Library name: SYN_4

value: Trophoblast stem cells


title: HCT116, IL6, 3h, mRNA-seq, rep1

description: Library name: HCT116-IL6-3-1


title: Hippocampus, CORT+DFP+LPS, 6 h, A241

description: Library name: HPC_A241

value: wild type


title: Frontal cortex, CORT+DFP+LPS, 6 h, A241

description: Library name: CTX_A241

value: Frontal cortex


title: Control STB_2

description: Library name: SYN_2


title: HCT116, IL6, 3h, mRNA-seq, rep2

description: Library name: HCT116-IL6-3-2


title: ESC-CTCF/WAPL-AID, untreated, REPLICATE 2

description: Library name: Sample 3

value: Untreated


title: Frontal cortex, CORT+DFP+Saline, 6 h, A226

description: Library name: CTX_A226

value: CORT+DFP+Saline, 6 h


title: HCT116, IL10, 6h, mRNA-seq, rep3

description: Library name: HCT116-IL10-6-3


title: ESC-CTCF/WAPL-AID, IAA-treated, 48h, REPLICATE 1

description: Library name: Sample 4


title: Human ESC dTAG, 72h, rep1

description: Library name: Sample 2

value: Human embryonic stem cell

value: dTAG


title: Frontal cortex, CORT+DFP+LPS, 6 h, A240

description: Library name: CTX_A240


title: HCT116, IL10, 6h, mRNA-seq, rep2

description: Library name: HCT116-IL10-6-2


title: Control STB_3

description: Library name: SYN_3


title: HCT116, IL10, 3h, mRNA-seq, rep3

description: Library name: HCT116-IL10-3-3


title: BAP1-OE STB_9

description: Library name: SYNh_9

value: BAP1-OE STB


title: ESC-CTCF/WAPL-AID, untreated, REPLICATE 1

description: Library name: Sample 2


title: Control STB_1

description: Library name: SYN_1


title: HCT116, IL10, 6h, mRNA-seq, rep1

description: Library name: HCT116-IL10-6-1


title: BAP1-OE STB_8

description: Library name: SYNh_8


title: HCT116, IL10, 3h, mRNA-seq, rep2

description: Library name: HCT116-IL10-3-2


title: Hippocampus, CORT+DFP+Saline, 6 h, A224

description: Library name: HPC_A224

value: Hippocampus


title: Frontal cortex, CORT+DFP+Saline, 6 h, A224

description: Library name: CTX_A224


title: HCT116, IL10, 3h, mRNA-seq, rep1

description:
Library name: HCT116-IL10-3-1
mRNA purified from 2 microgram total RNA fragments were used to generate the cDNA libraries, respectively, according to VAHTS Universal V8 RNA - seq Library Prep Kit for MGI.

value: colonic cancer cell line


title: Mouse ESC_WAPL/CTCF-AID indARID3A Clone 2, IAA/DOX 48h

description: Library name: Sample 27

value: ESC_WAPL/CTCF-AID indARID3A

value: DOX/IAA


title: BAP1-OE STB_7

description: Library name: SYNh_7


title: Hippocampus, CORT+DFP+Saline, 6 h, A226

description: Library name: HPC_A226


title: Mouse ESC_WAPL/CTCF-AID indARID3A Clone 2, IAA 48h

description: Library name: Sample 26


title: RS-04372481_7-36-2

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description: Library name: RS-04372481_7-36-2

data_processing:
CDR3 clonotypes were assembled using MiXCR preset workflows for mouse Takara Smart-Seq.
Assembly: mm10
Supplementary files format and content: csv file countaining TCRB-CDR3 clonotype calls for each sample
Library strategy: TCR-Seq

source_name: T cells

growth_protocol: The syngeneic metastatic SCLC model was induced by intravenous tail vein injection of 1×10⁶ N2N1G-GFP/Luc cells into C57BL/6J mice

extract_protocol:
500ng of total RNA was used as input for cDNA synthesis.
T-cell receptor (TCR) repertoire profiling was performed using the SMART-Seq Mouse TCR (with UMIs) kit (Takara Bio, USA) according to the manufacturer’s protocol. First-strand cDNA was generated using SMART (Switching Mechanism at the 5′ end of RNA template) technology, which incorporates unique molecular identifiers (UMIs) during reverse transcription. A 5′-RACE strategy was applied to capture the full-length variable regions of the TRA and TRB chains. Amplified cDNA underwent two rounds of PCR: the first to enrich TCR α/β libraries, and the second to incorporate unique dual indexes (UDIs) for sample multiplexing on patterned flow cells. Libraries were purified using AMPure XP beads (Beckman Coulter) and quantified with Qubit fluorometry (Thermo Fisher Scientific). Library size distribution and quality were assessed on an Agilent 4200 TapeStation using High Sensitivity D1000 ScreenTape. Indexed libraries were pooled equimolarly and sequenced on an Illumina NextSeq platform with 150-bp paired-end read length optimized for CDR3 assembly using a MiXCR preset workflow.

treatment_protocol: 24 days after tumor inoculation, 3×10⁶ untransduced T cells or CAR T cells were administered via tail vein injection.

value: T cells

value: Wild type


title: BAP1-OE STB_6

description: Library name: SYNh_6


title: Frontal cortex, CORT+DFP+Saline, 6 h, A223

description: Library name: CTX_A223


title: Hippocampus, CORT+DFP+LPS, 6 h, A240

description: Library name: HPC_A240

value: CORT+DFP+LPS, 6 h


title: RS-04372480_6-36-1

description: Library name: RS-04372480_6-36-1


title: Mouse ESC_WAPL/CTCF-AID indARID3A Clone 2, untreated

description: Library name: Sample 24

value: Mouse embryonic stem cell


title: BAP1-OE hTSC_6

description: Library name: SCh_6

value: BAP1-OE hTSC


title: Hippocampus, CORT+DFP+Saline, 6 h, A222

description: Library name: HPC_A222


title: Mouse ESC_WAPL/CTCF-AID indARID3A Clone 2, DOX 48h

description: Library name: Sample 25

value: DOX


title: ESC-CTCF/WAPL-AID, untreated, REPLICATE 1, INPUT

description: Library name: Sample 1

value: ESC-CTCF/WAPL-AID

value: No antibody


title: Mouse ESC_WAPL/CTCF-AID indARID3A Clone 1, IAA/DOX 48h

description: Library name: Sample 23


title: Frontal cortex, CORT+DFP+LPS, 24 h, A511

description:
Library name: CTX_A511
FC-24hr-3
csaw_CTX_24h_vs_CTRL.bed

data_processing:
Raw sequencing reads were processed using Trim Galore (v0.6.7) and FASTQC (v0.11.9) for adapter removal and quality control.
Trimmed reads were aligned to the mouse reference genome GRCm38 (mm10) using Bowtie2 (v2.4.4) with default settings.
ATAC-seq peaks were identified using MACS2 (v2.2.7.1).
Differential accessibility analysis was performed using the Bioconductor package csaw.
Processed BED files correspond to differentially accessible regions in frontal cortex and hippocampus at 6 h, 12 h, and 24 h relative to CORT+DFP+Saline, 6 h baseline controls.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Sample-level MACS2 narrowPeak files containing called accessible chromatin regions for each ATAC-seq library; study-level supplementary BED files contain differentially accessible regions identified by csaw.
Supplementary files format and content: Per-sample processed files are named using sample shorthand (FC or HIP, condition/timepoint, replicate) with the suffix _peaks.narrowPeak. Supplementary csaw BED files are named by tissue (CTX or HPC) and comparison (6 h, 12 h, or 24 h relative to baseline controls).

growth_protocol: Adult male C57BL/6J mice were housed under standard conditions with ad libitum access to food and water.

extract_protocol:
Frozen hippocampus and frontal cortex tissue samples (20–30 mg) were used for ATAC-seq library preparation.
ATAC-seq libraries for hippocampus and frontal cortex were generated from frozen tissue samples (20–30 mg) using the OMNI-ATAC-seq protocol. Sequencing was performed on an Illumina NovaSeq 6000 at the Princess Margaret Genomics Centre (Toronto, ON, Canada) using paired-end 50 bp reads.

treatment_protocol: To model Gulf War Illness-related stress and toxicant exposure, mice received corticosterone (CORT) in the drinking water for 7 days, followed on day 8 by a single intraperitoneal injection of diisopropyl fluorophosphate (DFP), with repeated intermittent CORT administration over 5 weeks. On the final day, mice received either saline or lipopolysaccharide (LPS), and hippocampus and frontal cortex were collected 6 h, 12 h, or 24 h after challenge.

value: Frontal cortex

value: wild type

value: CORT+DFP+LPS, 24 h


title: Hippocampus, CORT+DFP+LPS, 24 h, A513

description:
Library name: HPC_A513
HIP-24hr-4
csaw_HPC_24h_vs_CTRL.bed


title: RS-04372478_4-18-1

description: Library name: RS-04372478_4-18-1


title: Mouse ESC_WAPL/CTCF-AID indARID3A Clone 1, IAA 48h

description: Library name: Sample 22

value: IAA


title: BAP1-OE hTSC_9

description: Library name: SCh_9

value: Trophoblast stem cells


title: BAP1-OE hTSC_8

description: Library name: SCh_8


title: BAP1-OE STB_10

description: Library name: SYNh_10

value: BAP1-OE STB


title: Frontal cortex, CORT+DFP+LPS, 24 h, A513

description:
Library name: CTX_A513
FC-24hr-4
csaw_CTX_24h_vs_CTRL.bed


title: Mouse ESC_WAPL/CTCF-AID indARID3A Clone 1, DOX 48h

description: Library name: Sample 21


title: Hippocampus, CORT+DFP+LPS, 24 h, A511

description:
Library name: HPC_A511
HIP-24hr-3
csaw_HPC_24h_vs_CTRL.bed

value: Hippocampus


title: RS-04372476_2-D-1

description: Library name: RS-04372476_2-D-1


title: Mouse ESC_WAPL/CTCF-AID indARID3A Clone 1, untreated

description: Library name: Sample 20

value: ESC_WAPL/CTCF-AID indARID3A

value: Untreated


title: BAP1-OE hTSC_7

description: Library name: SCh_7


title: RS-04372475_1-UT

description: Library name: RS-04372475_1-UT

value: T cells


title: CD34, BCL11B-dTAG, dTAGV-1, rep3, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_dTAG_0249
TPM_CD34_017.txt

data_processing:
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1) and converted to paired-end fragment intervals (BEDPE). For coverage calculation, fragments with inferred insert size < 2000 bp were counted and used to compute a library-size scaling factor to normalize signal to a fixed library size. The center 80 bp of these fragments were used to generate genome-wide coverage tracks using bedtools genomecov in bedGraph format (-bg), applying the scaling factor for depth normalization (-scale). BedGraph files were converted to BigWig format using UCSC tools (bedGraphToBigWig) for visualization in IGV and for creating heatmaps. To increase detection of BCL11BdTAG and RUNX1 binding events in CD34+ HSPCs without DMSO or dTAGV-1 treatment, the mapped bam files from both replicates were merged prior to downstream processing.
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. The first 15 bp of each read were clipped to reduce the GC bias introduced by the Tn5 enzyme. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1). The center 80 bp of nucleosome-free fragments (fragment size < 109 bp) were extracted using bedtools and converted to scaled genome coverage tracks for visualization on IGV and in heatmaps. The scaling factor was computed from the total number of nucleosome-free fragments to normalize signal to a fixed library size. Peaks were called with MACS2 (v2.1.1.20160309) using nucleosome-free fragments with parameters -f BEDPE --keep-dup all -q 0.01
For CD34+ HSPCs: Paired-end RNA-seq reads were adapter and quality trimmed using Trim Galore (v0.4.4), and read quality was assessed with FastQC. Reads were aligned to the GRCh38 reference genome with STAR (v2.7) in two-pass mode. Coordinate-sorted BAM files, transcriptome alignments, gene counts, and strand-specific RPM-normalized coverage tracks were generated during alignment, and wiggle files were converted to BigWig format using wigToBigWig. Duplicate reads were marked with GATK MarkDuplicates, alignments were indexed with SAMtools, and RNA-seq quality metrics were collected using Picard CollectRnaSeqMetrics. Gene- and isoform-level expression was quantified with RSEM. Differential expression analysis was performed using the edgeR/limma-voom workflow. Genes with counts per million (CPM) ≥ 1 in at least 3 samples were retained using edgeR, and normalized expression values were generated by voom as log2-counts per million. Differentially expressed genes between treatment groups and transduction conditions were identified using linear models with empirical Bayes moderation implemented in limma.
For Jurkat BRU-seq: Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2. Unaligned reads were subsequently mapped strand-specifically to human genome build hg38/GRCh38 using STAR and GENCODE annotation version 27. Gene expression was quantified as previously described (Magnuson et al., 2022) and differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: .bw files contain coverage files in bigwig format
Supplementary files format and content: .narrowPeak files contain MACS2 called peaks
Supplementary files format and content: .txt file contains transcripts per million (TPM) values

extract_protocol:
CUT&RUN was performed on 0.1 – 0.5 million CD34+ HSPCs using the CUTANA ChIC/CUT&RUN kit from EpiCypher (#14-1048-24) following manufacturer’s instructions.
ATAC-seq was performed with 50,000 cells using the Omni-ATAC protocol as described (Corces et al., 2017). Cells were washed once with 1X PBS and then lysed in 50µl cold Cell Lysis Buffer containing 0.01% digitonin for 3 minutes on ice. After cell lysis, 1mL cold Resuspension Buffer was added and cells were immediately spun at 600xg for 10 minutes at 4°C. After removing the supernatant, the nuclei were transposed in 50µl Transposition reaction using the Tn5 enzyme from Illumina for 30 minutes at 37°C. Transposed DNA was purified using a Qiagen MinElute PCR clean-up kit and DNA was eluted in 10µl Elution Buffer.
CD34+ HSPCs were harvested following DMSO or dTAGV-1 treatment and resuspended in TRI Reagent (Sigma). RNA was isolated using the Direct-zol RNA miniprep kit (Zymo Research #R2050). For BRU-seq, cells were lysed directly in Trizol followed by isolation of total RNA and treatment with DNAse (TURBO DNA-free Kit; Invitrogen). The Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
Libraries were constructed using library prep kits from EpiCypher (#14-1001) following manufacturer’s instructions.
Libraries were constructed by amplifying eluted DNA with barcoded primers described in Corces et al., 2017 for 10-12 cycles. The optimal number of cycles was determined by performing a quantitative PCR analysis after the initial 5 PCR cycles. Amplified libraries were purified using AMPure beads to remove fragments less than 200bp and larger than 700 bp. Final barcoded libraries were pooled and sequenced in paired-end mode.
CD34+ HSPCs: RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation. Libraries were prepared from total RNA with the Illumina Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20040529). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).
Jurkat (BRU-seq): Strand-specific libraries were prepared from a modified protocol using the TruSeq Kit (Illumina) as previously described (Paulsen et al., 2013)

value: Cord Blood

value: CD34+ HSPC


title: BAP1-OE hTSC_10

description: Library name: SCh_10


title: RS-04372477_3-D-2

description: Library name: RS-04372477_3-D-2

value: Wild type


title: Hippocampus, CORT+DFP+LPS, 12 h, A503

description:
Library name: HPC_A503
HIP-12hr-4
csaw_HPC_12h_vs_CTRL.bed

value: CORT+DFP+LPS, 12 h


title: Control hTSC_5

description: Library name: SC_5

value: Control hTSC


title: Control hTSC_4

description: Library name: SC_4


title: ESC-DUX, LTR-RFP, DOX treated 16 hours

description: Library name: Sample 8

data_processing:
ATACseq data were processed using the Center for Cancer Research Collaborative Bioinformatics Resource’s ASPEN (ATACseq PipEliNe) version 0.5.2 (https://doi.org /10.5281/zenodo.13755867 and https://github.com/CCBR/ASPEN) to generate signal tracks (bigwigs).
Assembly: mm10
Supplementary files format and content: bigwig files containing reads per genomic content (RGPC) normalized read density.

extract_protocol:
Briefly, 50,000 cells were first washed with 50ul cold 1X PBS and nuclei were isolated by resuspending the cells in 50ul Lysis Buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20, and 0.01% Digitonin) on ice for three minutes. Nuclei were washed once with 1ml Wash Buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20) and further resuspended in 50ul Transposition Reaction Mix (Tn5 Transposase, 1X TD Buffer, 0.1% Tween-20, 0.01% Digitonin) for exactly 30 minutes at 37 °C. Following transposition, DNA was purified using the Zymo DNA Clean and Concentrator kit (Zymo, D4033).
Libraries were prepared using the entire purified DNA, Q5 Polymerase, and unique barcoded primers. An initial PCR amplification was performed at 72 °C for 5 minutes followed by 5 cycles of 98 °C, 10 seconds, 63 °C, 30 seconds, and 72 °C 1 minute. Then, tubes were held on ice while a quantitative PCR was run on 5 ul of the pre-amplified library to determine the additional number of cycles needed. PCR reactions were cleaned up with AMPure XP beads (Beckman Coulter) and concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina NextSeq550 (75 bp pair-end reads).

value: Embryonic stem cell

value: DUX

value: DOX


title: CD34, BCL11B-dTAG, dTAGV-1, rep2, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_dTAG_0205
TPM_CD34_017.txt


title: Frontal cortex, CORT+DFP+LPS, 12 h, A501

description:
Library name: CTX_A501
FC-12hr-3
csaw_CTX_12h_vs_CTRL.bed

value: Frontal cortex

value: wild type


title: Control hTSC_3

description: Library name: SC_3


title: Hippocampus, CORT+DFP+LPS, 12 h, A501

description:
Library name: HPC_A501
HIP-12hr-3
csaw_HPC_12h_vs_CTRL.bed


title: ESC-CTCF/WAPL-AID, E14, IAA treated 48 hours

description: Library name: Sample 7

value: CTCF/WAPL-AID

value: IAA

value: 48 hours


title: CD34, BCL11B-dTAG, dTAGV-1, rep1, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_dTAG_0615
TPM_CD34_017.txt


title: CD34, BCL11B-dTAG, DMSO, rep2, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_DMSO_0205
TPM_CD34_017.txt

value: DMSO