title: MDA-MB-231 EA 15 ribo-seq rep2

city: nanjing

first: Zhou

last: Jun

state: jiangsu

address: longmiandadao

department: College of life science and technology

institute: China Pharmaceutical University

description: Library name: 231riboD15R2

data_processing:
For paired-end Ribo-seq sequencing, R1 reads were utilized for all analyses. Raw Ribo-seq reads were initially processed using Cutadapt (v2.8) to remove adapter sequences with the following parameters: --match-read-wildcards -a NNNNNNNNNNAGATCGGAAGAGCACACGTC -m 25 -M 35. Quality-filtered reads were sequentially aligned to human ribosomal RNA (rRNA) and transfer RNA (tRNA) reference sequences using Bowtie2 (v2.3.5.1) to eliminate contaminating reads. The remaining non-rRNA/non-tRNA reads were then aligned to the human reference genome (GRCh38) using HISAT2 (v2.2.1) with default parameters. Resulting alignments were converted to BAM format and sorted using SAMtools (v1.21). Mapped reads were quantified using featureCounts (v2.0.6) with the -t exon parameter. Translational efficiency (TE) was calculated as the ratio of TPM (Transcripts Per Kilobase Million)-normalized Ribo-seq to TPM-normalized RNA-seq data. Differential TE analysis was performed using the riborex package (v2.4.0) with the DESeq2 engine. Genes with p-value < 0.05 and absolute log2 fold change (|log₂FC|) >= 1 were considered significantly differentially translated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with gene counts
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

source_name: cell line

growth_protocol: MDA-MB-231 TNBC cells were cultured in DMEM (BI, Cat#06-1055-57-1ACS) supplemented with 10% FBS (Viva Cell, C04001-500) and 1% Penicillin-Streptomycin (Life,15140122) at 37℃ with 5% CO2.

extract_protocol:
Input RNA was extracted with TRIzol LS followed by chemical fragmentation. Ribo-seq samples were produced by RNase I digestion followed by RNA extraction using TRIzol LS.
40-60nt region for input and 30nt for ribo-seq were selected according to 15% polyacrylamide TBE-urea gel separation. Desired RNA species were excised and soaked overnight followed by ethanol precipitation. The purified RNA was dephosporylated and added with 3’adapter. The 5’ adapter was added after reverse transcription. Eventually, PCR amplification was proceeded using Phusion High-Fidelity DNA Polymerase.

treatment_protocol: MDA-MB-231 cells were treated with DMSO, 15 μM, or 30 μM EA for 24 hours.

value: cell line

value: TNBC

value: Pre-treated with EA for 24h and treated with CHX for 5min,normal culture


title: GCTB

status: Public on Mar 24 2026

type: SRA

city: Chuo-ku

first: Masaki

last: Shimada

state: Kumamoto

address: 1-1-1 Honjo

department: Department of Orthopaedic Surgery

country: Japan

institute: Kumamoto University

description:
Library name: 01450-1
FFPE Spatial transcriptome sequencing

library_source: transcriptomic

data_processing:
The Space Ranger pipeline (version 2.0.0, 10x Genomics) was used to process the Visium spatial gene expression data, including the generation of FASTQ files.
Sequences were aligned to the GRCh38, and barcode and UMI counting were performed.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

organism: Homo sapiens

source_name: Distal femur

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) tumor tissues were sectioned at 5 μm thickness and mounted onto standard glass slides. Sections were deparaffinized, rehydrated, and subjected to hematoxylin and eosin (H&E) staining according to the manufacturer’s instructions for the Visium CytAssist Spatial Gene Expression for FFPE (10x Genomics).
Spatial transcriptome sequencing libraries were prepared with the Visium CytAssist Spatial Gene Expression for FFPE (10x Genomics) following the manufacturer’s instructions.

tag: tissue

value: Distal femur

tag: Sex

value: Male

tag: treatment

value: surgical curettage


title: MDA-MB-231 EA 30 ribo-seq rep2

country: China

description: Library name: 231riboD30R2

tag: cell line

tag: cell type

tag: genotype

value: WT


title: siRbFox2_Rep1

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

country: USA

institute: Medical College of Wisconsin

description: Library name: siRbm9_1

data_processing:
Starting from raw PacBio HiFi reads, lima was used to remove cDNA primers.
Subsequently, the "pbmm2" algorithm in Isoseq 4.3.0 was used to align the resulting BAM file to the Rattus Norvegicus genome (rn7.2).
Isoquant v3.5.0 was used to quantify the aligned BAMs at the gene and transcript level (Rattus_norvegicus.mRatBN7.2.112.chr.gtf)
Assembly: rn7.2
Supplementary files format and content: gene/transcript Ensembl ID with associated counts.

organism: Rattus norvegicus

growth_protocol: A7R5 cells were cultured in Dulbecco’s modified Eagle medium supplemented with 5% fetal bovine serum and 1% penicillin–streptomycin and maintained at 37°C with 5% CO2.

extract_protocol:
Novogene’s RNA detection for RNA samples primarily includes four methods: 1.Agarose gel electrophoresis to analyze the degree of RNA degradation and to check for contamination. 2.Nanodrop to assess the purity of RNA (OD260/280 ratio). 3.Qubit for precise quantification of RNA concentration. 4.Agilent 2100 for accurate assessment of RNA integrity.
The Iso-Seq Express 2.0 kit was used to synthesize cDNA using QC-passed RNA. This was followed by library construction using the Kinnex Full-Length RNA Kit.

treatment_protocol: A7R5 cells were treated with either siRNA targeting RbFox2 and RhoBTB1 mRNA or negative control pool of 4 siRNAs .


title: fetal liver, E14.5, ATAC-seq, RORgt_neg_2

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

institute: Kyushu University

description: Active Motif

library_source: genomic

data_processing:
Raw ATAC-seq reads were trimmed and filtered for quality control using Cutadapt with the adapter sequence "CTGTCTCTTATACACATCT". The trimmed reads were then aligned to the mouse genome (mm10) using Bowtie2 v2.2.5 with the parameter -X 2000. Non-uniquely mapping reads and reads that aligned to the mitochondrial genome were filtered out using Samtools. Only concordantly mapped reads were used for further analysis. Peaks were called using Genrich with the following parameters: -j (ATAC-seq mode), -q 0.01 (FDR threshold), -y (exclude mitochondrial reads), and -e chrM (exclude mitochondrial chromosome).
Assembly: mm10
Supplementary files format and content: Tdf files

molecule: genomic DNA

organism: Mus musculus

source_name: fetal liver

extract_protocol:
The LTi progenitor cells were collected from E14.5 fetal liver, and E17.5 DP thymocytes were collected from E17.5 thymus. Th17 and γΔ17 cells were collected from the small intestine of 8-10 week-old mice. The E14.5 fetal liver and E17.5 thymus were separated under a microscope, and single-cell suspension was generated by pipetting with a 1000-micropipette. The cell suspension  was then filtered through a 100 μm strainer and resuspended in FACS buffer (2% FBS/0.05% NaN3/1% PBS). The collected adult intestines were cut into  1 cm pieces and washed with PBS. After opening the intestines along the longitudinal axis, they were treated with 30mM EDTA-containing PBS at room temperature for 15 minutes to remove the epithelium. The tissues were then digested by incubating at 37°C in DMEM containing 1 mg/mL Collagenase D and 0.33 mg/mL DNase I. Dissociated cells were collected every 30 min and strained with a 100 μm strainer, and then lymphocytes were further enriched on a 40%/80% Percoll gradient.  After staining by antibodies,  cell sorting were performed with  MA900 (Sony Imaging Products & Solutions).
100-200 cells were used for ATAC-seq following the manufacturer's instructions (Active Motif, #53150).

value: fetal liver

tag: strain

value: RORgt-EGFP

tag: age

value: embryonic day 14.5


title: Control_Rep2

description: Library name: Ctrl_2

value: Control


title: Sample 2 - Arc-Liver-D1

city: Houston

first: Narein

last: Rao

state: Texas

address: 6100 Main St

department: Computer Science

institute: RICE University

description:
Library name: Sample 2 - Arc-Liver-D1
Fresh frozen spatial transcriptome sequencing

data_processing:
Pipeline: Space Ranger Count v4.0.1 Parameters (applied to both samples): includeIntrons: false filterProbes: true umiRegistration: true trimTsoMinScore: 20 trimPolyaMinScore: 20 nucleusSegmentation: true skipTissueDetection: false reorientImages: true noBam: true
Assembly: Human (GRCh38) 2024-A
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered gene expression counts
Supplementary files format and content: raw_feature_bc_matrix.h5: unfiltered UMI counts for all detected bins
Supplementary files format and content: raw_probe_bc_matrix.h5: full, unfiltered, probe-level spatial gene expression data at the highest 2 µm resolution
Supplementary files format and content: scalefactors_json.json: scalefactor in json format
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the jpg image
Supplementary files format and content: aligned_tissue_image.jpg: Image capturing the results of the image registration by merging the registered images in a checkerboard pattern with adjacent squares alternating between the two images.
Supplementary files format and content: barcode_mappings.parquet: spatial mapping information that tracks relationships between barcodes (squares), nuclei, cells, and bins within your Visium HD data
Supplementary files format and content: cloupe_008um.cloupe: Symlink to the .cloupe file at 8 µm bin size
Supplementary files format and content: cloupe_cell.cloupe: Symlink to the .cloupe file with cell segmentation
Supplementary files format and content: feature_slice.h5: support efficient fetching of 2 µm resolution image slices for a single gene or multiple genes
Supplementary files format and content: molecule_info.h5:  per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene barcode or bin
Supplementary files format and content: probe_set.csv: input probe set reference CSV file
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Library strategy: Spatial Transcriptomics

molecule: total RNA

source_name: Fetal Liver

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) human liver tissue blocks were sectioned at 5 µm thickness using a microtome. Sections were mounted onto positively charged glass slides according to 10x Genomics Visium HD sample preparation guidelines and stored at 4 °C with desiccant until further processing. Tissue sections were deparaffinized, stained with hematoxylin and eosin (H&E), and subjected to probe hybridization using the Visium Human Transcriptome Probe Set v2.1.0. Following hybridization and templated ligation, probe-derived products were transferred onto 10x Genomics Visium HD Spatial Gene Expression Slides (slide serial: H1-GVJMQ3Q) using the CytAssist instrument according to the manufacturer’s protocol. Subsequent library preparation steps were performed following the Visium HD workflow.
Spatial transcriptomic libraries were generated using the 10x Genomics Visium HD Spatial Gene Expression platform (SPATIAL-HD-v1 chemistry). Formalin-fixed paraffin-embedded (FFPE) human liver tissue sections were placed onto Visium HD capture areas (A1 and D1) of slide H1-GVJMQ3Q. Tissue sections were processed according to the manufacturer’s instructions. Briefly, sections were deparaffinized, stained with hematoxylin and eosin (H&E), and imaged at 20× magnification using a Zeiss Axioscan 7 prior to probe hybridization. Imaging data were used for tissue detection and nucleus segmentation during downstream analysis. Gene expression profiling was performed using the Visium Human Transcriptome Probe Set v2.1.0 (GRCh38-2024-A reference). Probes were hybridized to target transcripts in situ and ligated using a templated ligation approach. Following probe ligation, captured molecules were released and subjected to library construction including amplification and indexing according to the Visium HD workflow. Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 150 bp sequencing. During downstream processing, read 2 was trimmed to 50 bp in Space Ranger Count v4.0.1. Raw sequencing data were processed using Space Ranger Count v4.0.1 with probe filtering enabled, intronic reads excluded, UMI registration applied, and nucleus segmentation performed during image processing.

value: Fetal Liver


title: isolated living cells from young mouse brai after Pacitaxel treatment_2

city: Oklahoma City

first: Roland

last: Patai

state: Oklahoma

address: 975 NE 10th street

department: Department of Neurosurgery

institute: University of Oklahoma Health Campus

description:
Library name: PTX2
10X Genomics Chromium Single Cell 3′ Gene Expression v2

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting were made using the Cell Ranger software count pipeline v.6.0.0.
Assembly: gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Mice were euthanized and transcardially perfused with PBS, after which brains were rapidly harvested, rinsed in ice-cold PBS, and minced into small fragments. Tissue was enzymatically digested using collagenase, hyaluronidase, and elastase at 37 °C, then filtered through a 100 μm cell strainer to obtain a single-cell suspension. Cells were washed, centrifuged, and enriched for cerebrovascular and neurovascular unit cells using an iodixanol (OptiPrep) density gradient. The enriched cell fraction was collected and resuspended in PBS containing 0.4% BSA for downstream processing.
Single-cell suspensions were loaded onto the 10x Genomics Chromium Single Cell 3′ platform for droplet-based capture. Libraries were generated using the Chromium Single Cell 3′ v2 kit following the manufacturer’s protocol, pooled based on molar concentration, and sequenced on an Illumina NovaSeq 6000 system. Raw sequencing data were processed using the Cell Ranger pipeline for read alignment, barcode processing, and gene expression quantification

treatment_protocol: Mice used for single-cell RNA sequencing were transgenic p16-3MR males treated with paclitaxel (PTX; 5 mg/kg/day, intraperitoneally) administered in two cycles of 5 consecutive days with a 7-day interval between cycles. Control animals received vehicle (DMSO + saline). Following treatment and recovery, animals were maintained for up to 6 months post-chemotherapy before brain collection. Whole brains were harvested after perfusion and processed for single-cell dissociation and downstream transcriptomic analysis.

value: brain

value: multiple

value: wild-type  p16- 3MR mouse

value: male

value: 9-10 months

value: Pacitaxel

tag: batch


title: MDA-MB-231 DMSO ribo-seq rep2

description: Library name: 231riboD0R2

value: cell line

value: TNBC

value: Pre-treated with DMSO for 24h and treated with CHX for 5min,normal culture


title: isolated living cells from young mouse brai after Pacitaxel treatment_3

description:
Library name: PTX3
10X Genomics Chromium Single Cell 3′ Gene Expression v2


title: KPCY tumor, PBS1

city: Columbus

first: Mengying

last: Hu

state: Ohio

address: 496 W 12th Ave

department: Pharmaceutics and Pharmacology

institute: The Ohio State University

description: Library name: PBS1

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (version 2.0.11) (http://ccb.jhu.edu/software/tophat/index.shtml), and transcriptome reconstruction was performed by Cufflinks (version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/). The abundance of transcripts was measured with Cufflinks in fragments per kilobase of exon model per million mapped reads (FPKM).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: subcutaneous tumor

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen, 74134) following the manufacturer’s instructions.
TruSeq stranded mRNA library was prepared according to manufacturer's instructions

treatment_protocol: 5 × 10^5 of KPCY (6419c5) cells in 50 µL of Corning Matrigel matrix were subcutaneously injected into the right flank of 8-week-old female C57BL/6 mice. 4 days after tumor inoculation, mice were randomized blindly into different treatment groups, and the investigator was blinded to the group allocation during the animal experiments. Each mice received one intratumoral injection of PBS or 25 µg of ATEVs (containing 10 µg of EVDNA) in the volume of 30 µL every 3 days for in total 6 doses. Mice were euthanized 9 days after the final treatment. Tumors were harvested for flow cytometry analysis and bulk RNAseq.

value: subcutaneous tumor

value: KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre; Rosa26YFP/YFP

value: PBS


title: Control_Rep1

description: Library name: Ctrl_1


title: TSST1_Ad60

city: Aachen

first: Christopher

middle: Thomas

last: Neullens

address: Pauwelsstraße 30, 52074

country: Germany

institute: RWTH Aachen University Medical Faculty

description: Library name: Sample 20

data_processing:
nextflow run nf-core/rnaseq
Assembly: GENCODE_GRCh38_v46
Supplementary files format and content: tsv data, mapped reads

source_name: Adenoid/Tonsillar

growth_protocol: Adenoid/Tonsillar cells were receiving from the surgery department and processed within 4 hours into single cells.

extract_protocol:
Cells were harvested and sorted by CD4, CD45RO and CD69 to collect the Tmem population. RNA of those was harvested using the Rneasy mini Kit (Qiagen).
RNA libraries for RNA Seq were prepared using QuantSeq 3'mRNA-Seq Library Prep Kit FWD for Illumina following manufacturor's protocol

treatment_protocol: 2x10^6 cells were cultured in CMT media for 2 days along with 1 µg/ml PT and 50 ng/ml TSST-1 or CD3/CD28 (5 µg/ml CD3, 2 µg/ml CD28).

value: Adenoid/Tonsillar

value: T cells


title: TSST1_Ad55

description: Library name: Sample 16


title: TSST1_Ad42

description: Library name: Sample 8


title: isolated living cells from young mouse brai after Pacitaxel treatment_4

description:
Library name: PTX4
10X Genomics Chromium Single Cell 3′ Gene Expression v2


title: TSST1_Ad44

description: Library name: Sample 12


title: Sample 1 - Arc-Liver-A1

description:
Library name: Sample 1 - Arc-Liver-A1
Fresh frozen spatial transcriptome sequencing


title: small intestine, 10w, ATAC-seq, RORgt+CD4T

description: Active Motif

source_name: small intestine

value: small intestine

value: RORgt-EGFP


title: isolated living cells from young mouse brain_2

description:
Library name: CTRL2
10X Genomics Chromium Single Cell 3′ Gene Expression v2

value: Vechicle (DMSO+saline)


title: isolated living cells from young mouse brai after Pacitaxel treatment_1

description:
Library name: PTX1
10X Genomics Chromium Single Cell 3′ Gene Expression v2

value: brain


title: Trichoderma atroviride grown on xylan (replicate 2)

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

description: Library name: sample8

data_processing:
Raw sequencing reads were assessed for quality using FastQC. Adapter and low-quality sequences were removed using Trimmomatic with parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:keepBothReads, LEADING:3, TRAILING:3, and MINLEN:36.
Trimmed reads were aligned to the Trichoderma atroviride reference genome using HISAT2 v2.0.4 with default parameters and multithreading (-p 8).
Read counts per gene were generated from aligned reads and organized into a count matrix in R.
Differential gene expression analysis was performed using the edgeR package (v4.6.3) in R.
Assembly: Trichoderma atroviride reference genome v2 available at JGI MycoCosm: https://mycocosm.jgi.doe.gov/Triat2/Triat2.home.html
Supplementary files format and content: Processed data include gene-level read count matrices derived from RNA-seq alignments this in TPMs.
Supplementary files format and content: Files are provided as tab-delimited text files where rows correspond to genes and columns correspond to RNA-seq libraries.

organism: Trichoderma atroviride

source_name: Trichoderma atroviride

growth_protocol: Trichoderma atroviride was grown on solid Vogel’s minimal medium supplemented with glucose for 36 h. A mycelial plug was used to inoculate 50 mL liquid Vogel’s minimal medium containing glucose in 125 mL Erlenmeyer flasks and cultured for 48 h at 28°C in darkness with shaking at 220 rpm.

extract_protocol:
Mycelium was harvested after 12 h, frozen in liquid nitrogen, and ground using a mortar and pestle. Total RNA was extracted using TRIzol (Invitrogen) and purified using the RNeasy Plus kit (Qiagen) following the manufacturer’s instructions.
RNA-seq libraries were prepared from purified total RNA using the TruSeq RNA Sample Preparation Kit v2 (Illumina). Sequencing was performed on an Illumina NovaSeq 6000 platform at the QB3 facility (University of California, Berkeley), generating ~30 million reads per library.

treatment_protocol: After 48 h growth, mycelial pellets were washed three times with Vogel’s minimal medium lacking a carbon source and transferred to fresh Vogel’s minimal medium containing either no carbon source, 1% glucose (10 g/L), or 1% xylan (10 g/L). Cultures were incubated for 12 h at 28°C in darkness with shaking at 220 rpm prior to RNA extraction.

value: Trichoderma atroviride

value: Mycellium

value: WT

value: xylan


title: Trichoderma atroviride grown on xylan (replicate 1)

description: Library name: sample7


title: MDA-MB-231 DMSO input rep2

description: Library name: 231inD0R2

data_processing:
For paired-end Ribo-seq sequencing, R1 reads were utilized for all analyses. Raw Ribo-seq reads were initially processed using Cutadapt (v2.8) to remove adapter sequences with the following parameters: --match-read-wildcards -a NNNNNNNNNNAGATCGGAAGAGCACACGTC -m 25 -M 35. Quality-filtered reads were sequentially aligned to human ribosomal RNA (rRNA) and transfer RNA (tRNA) reference sequences using Bowtie2 (v2.3.5.1) to eliminate contaminating reads. The remaining non-rRNA/non-tRNA reads were then aligned to the human reference genome (GRCh38) using HISAT2 (v2.2.1) with default parameters. Resulting alignments were converted to BAM format and sorted using SAMtools (v1.21). Mapped reads were quantified using featureCounts (v2.0.6) with the -t exon parameter. Translational efficiency (TE) was calculated as the ratio of TPM (Transcripts Per Kilobase Million)-normalized Ribo-seq to TPM-normalized RNA-seq data. Differential TE analysis was performed using the riborex package (v2.4.0) with the DESeq2 engine. Genes with p-value < 0.05 and absolute log2 fold change (|log₂FC|) >= 1 were considered significantly differentially translated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with gene counts


title: TSST1_Ad35

description: Library name: Sample 4


title: isolated living cells from young mouse brain_3

description:
Library name: CTRL3
10X Genomics Chromium Single Cell 3′ Gene Expression v2

value: multiple

value: wild-type  p16- 3MR mouse

value: male

value: 9-10 months


title: isolated living cells from young mouse brain_1

description:
Library name: CTRL1
10X Genomics Chromium Single Cell 3′ Gene Expression v2


title: MDA-MB-231 EA 30 ribo-seq rep1

description: Library name: 231riboD30R1

value: cell line

value: TNBC

value: Pre-treated with EA for 24h and treated with CHX for 5min,normal culture


title: MDA-MB-231 EA 15 input rep2

description: Library name: 231inD15R2


title: Trichoderma atroviride grown without carbon source (replicate 3)

description: Library name: sample6

value: no carbon


title: Trichoderma atroviride grown on xylan (replicate 3)

description: Library name: sample9


title: PT_Ad60

description: Library name: Sample 19

value: Adenoid/Tonsillar

value: T cells

value: Pertussis toxin


title: isolated living cells from  very aged mouse brain after oral RSV treatment_3

description:
Library name: Aged_oral-RSV_3
10X Genomics Next GEM 3' Gene Expression v3

data_processing:
The demultiplexing, barcode processing, gene counting were made using the Cell Ranger software count pipeline v.8.0.1.
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
After euthanasia, mice were transcardially perfused with ice-cold PBS, and brains were immediately collected into ice-cold PBS. For the scRNA-seq experiment, brains were obtained from young and aged mice, with n = 3-4 per group. The brains were then washed in ice-cold PBS and cut into ~1 mm pieces. Single-cell suspensions for scRNA-seq were generated by adapting the authors’ brain flow-cytometry dissociation protocol. In the base protocol, the olfactory bulb, cerebellum, and brainstem were removed, and meningeal vessels were stripped by rolling the brain on Whatman paper. The tissue was finely chopped, and enzymatic digestion was performed using 50 μL collagenase, 2 μL elastase, 2 μL dispase I, and 3 μL hyaluronidase for 45 min at 37°C in a rotating incubator. Following digestion, the tissue was mechanically dissociated by pipetting with 10 mL and 5 mL pipettes, filtered through 100 μm and subsequently 30 μm nylon mesh, and centrifuged. For cleanup, Debris Removal Solution (Miltenyi Biotec) was used. In the flow-cytometry protocol, cells were resuspended in 3.1 mL PBS, 0.9 mL Debris Removal Solution was added, and the mixture was inverted five times to mix. The suspension was then slowly overlaid with 4 mL PBS and centrifuged at 3000 × g for 10 min. After centrifugation, the top buffer layer and the white myelin–debris interphase were removed, and the pelleted cells were washed in PBS and centrifuged again at 1000 × g for 10 min at 4°C. The scRNA-seq section confirms that digestion and purification using Debris Removal Solution were performed, although every enzyme quantity and centrifugation parameter was not explicitly restated; therefore, these values were inferred from the referenced flow-cytometry protocol that was adapted. After cleanup for scRNA-seq, the cell pellet was resuspended in PBS + 0.1% BSA and stained with SYTOX Green to identify live cells. The suspension was then subjected to low-pressure FACS using the WOLF Cell Sorter (NanoCellect) to remove debris and dead cells and to enrich for viable cells. Cells were maintained on ice pending sequencing. After sorting, cells were centrifuged at 2200 rpm for 10 min at 4°C and finally resuspended in 30–50 μL of 0.04% BSA, with the volume adjusted according to the number of recovered cells.
Following cell sorting, the recovered viable cells were processed using a droplet-based single-cell RNA sequencing workflow on the Chromium platform (10x Genomics). In this system, individual cells were partitioned into nanoliter-scale droplets together with barcoded gel beads to generate gel bead-in-emulsion (GEM) partitions. Within each GEM, cell lysis occurred and reverse transcription was carried out, allowing newly synthesized cDNA molecules to be labeled with both a unique molecular identifier (UMI) and a cell-specific barcode. This barcoding strategy enabled transcripts originating from individual cells to be distinguished during downstream analysis. After reverse transcription, the GEMs were broken and the pooled barcoded cDNA was recovered and purified. The resulting cDNA was then amplified through PCR to generate sufficient material for library preparation. Amplified cDNA products were subsequently processed through a series of enzymatic steps to generate sequencing-compatible fragments. During this stage, cDNA molecules were fragmented and end-repaired to produce fragments of an appropriate size distribution for sequencing. Fragmented DNA was then subjected to adaptor ligation so that sequencing adaptors required for Illumina sequencing platforms were incorporated. Following adaptor ligation, additional purification and size-selection steps were performed to remove small fragments, adaptor dimers, and other reaction by-products. The adaptor-ligated DNA fragments were then amplified through sample index PCR to introduce sample-specific index sequences and to produce the final sequencing-ready library. These index sequences enabled multiplexing of multiple samples within the same sequencing run while maintaining the ability to demultiplex reads during data processing. After library amplification, final cleanup and size-selection steps were performed to ensure a consistent fragment size distribution and to remove residual primers or adaptor fragments. Library quality and fragment size distribution were then assessed using capillary electrophoresis-based quality control. Libraries were quantified, pooled according to molar concentration, and prepared for sequencing.

treatment_protocol: For the scRNA-seq study, C57BL/6 mice were assigned to young, aged, and aged treatment groups receiving oral RSV, FL/RSV, or ApoE-FL/RSV. Liposomal formulations were administered by retro-orbital injection under isoflurane anesthesia (3% for induction, 2% during the procedure), using the lower-concentration formulation applied for biological-effect studies (2 mg/mL). Oral RSV was given as a chronic control treatment in a strawberry-flavored, sugar-free gelatin vehicle, corresponding to approximately 6 mg RSV per mouse per day on weekdays. For the long-term molecular analyses associated with BBB and vascular outcomes, animals were treated for one month before brain collection. The manuscript further notes that this liposomal dose delivered approximately 0.117 mg/kg/day RSV, which is about 2000-fold lower than the oral dose of 200 mg/kg/day, enabling comparison of targeted low-dose liposomal delivery with conventional high-dose oral administration.

value: wild-type  C57/BL6

value: 18-20 months

value: resveratrol administered orally (in Jell-O)


title: MDA-MB-231 EA 15 ribo-seq rep1

description: Library name: 231riboD15R1


title: MDA-MB-231 EA 30 input rep2

description: Library name: 231inD30R2


title: PT_Ad55

description: Library name: Sample 15


title: Trichoderma atroviride grown without carbon source (replicate 1)

description: Library name: sample4

value: Trichoderma atroviride

value: Mycellium


title: Trichoderma atroviride grown without carbon source (replicate 2)

description: Library name: sample5

value: WT


title: MDA-MB-231 EA 30 input rep1

description: Library name: 231inD30R1


title: isolated living cells from  very aged mouse brain after oral RSV treatment_1

description:
Library name: Aged_oral-RSV_1
10X Genomics Next GEM 3' Gene Expression v3

value: brain

value: multiple


title: MDA-MB-231 DMSO ribo-seq rep1

description: Library name: 231riboD0R1

value: Pre-treated with DMSO for 24h and treated with CHX for 5min,normal culture


title: isolated living cells from  very aged mouse brain after oral RSV treatment_2

description:
Library name: Aged_oral-RSV_2
10X Genomics Next GEM 3' Gene Expression v3

value: male


title: VB124_2

type: RNA

city: Providence

first: William

last: Oldham

state: RI

address: 55 Claverick Street

department: Medicine

institute: Brown University

hyb_protocol: Slides were processed according to the Xenium Prime In Situ Gene Expression workflow. Tissue sections were hybridized with probes from the Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10x Genomics, PN-1000672) at 50 °C for 18 h. Following hybridization, slides were washed and incubated with ligation reaction mix and subjected to rolling-circle amplification according to the Xenium Prime In Situ Gene Expression User Guide (10x Genomics, CG000760 Rev A). Cell segmentation staining was then performed and slides were treated with an autofluorescence quencher and DAPI prior to loading onto the 10x Genomics Xenium Analyzer.

scan_protocol: Prepared Xenium slides were loaded into the 10x Genomics Xenium Analyzer and imaged according to the Xenium Analyzer User Guide (10x Genomics, CG000584 Rev F). The Xenium instrument performed iterative cycles of probe detection and fluorescence imaging to identify individual RNA molecules within the tissue sections. Following completion of imaging, slides were removed from the instrument and subjected to post-run hematoxylin and eosin staining according to the Xenium In Situ Gene Expression Post-Xenium Analyzer H&E Staining protocol (10x Genomics, CG000613 Rev A).

data_processing: Raw imaging data were processed using the Xenium onboard analysis pipeline to identify transcripts, assign spatial coordinates, and perform cell segmentation. Transcript counts were aggregated to generate cell-level gene expression matrices.

label: Xenium probe set

source_name: lung

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Formalin-fixed paraffin-embedded (FFPE) lung tissue blocks were sectioned onto Xenium slides according to the Xenium In Situ for FFPE Tissue Preparation Guide (10x Genomics, CG000578 Rev C). Slides were baked at 60 °C for 30 min and sequentially immersed in xylene, ethanol, and nuclease-free water to deparaffinize and rehydrate the tissue. Tissue sections were then incubated in decrosslinking and permeabilization solution at 80 °C for 30 min followed by washing with PBS-T according to the Xenium In Situ for FFPE Deparaffinization and Decrosslinking protocol (10x Genomics, CG000580 Rev D). Tissue sections from eight samples were distributed across two slides to balance treatment groups and minimize batch effects.

value: lung

tag: tissue preservation method

value: FFPE

tag: disease

value: bleomycin

value: Male


title: Trichoderma atroviride grown on glucose (replicate 2)

description: Library name: sample2

value: glucose


title: PT_Ad42

description: Library name: Sample 7

value: Adenoid/Tonsillar

value: T cells


title: MDA-MB-231 EA 15 input rep1

description: Library name: 231inD15R1

value: cell line

value: TNBC

value: Pre-treated with EA for 24h and treated with CHX for 5min,normal culture


title: MDA-MB-231 EA 15 rep2 6h

description: Library name: 23196R2

data_processing:
Raw RNA-seq reads were quality-controlled using FastQC (v0.11.8) and processed with TrimGalore (v0.6.10) to remove adapter sequences and low-quality bases. Clean reads were aligned to the mouse reference genome (GRCm38) and Saccharomyces cerevisiae genome (R64) using HISAT2 (v2.2.1) with default parameters, and the resulting alignments were converted to BAM format using SAMtools (v1.9). Gene expression was quantified using featureCounts (v2.0.1) with the -t exon parameter against Ensembl mouse gene annotation (Mus_musculus.GRCm38.108.gtf) and S. cerevisiae gene annotation (Saccharomyces_cerevisiae.R64-1-1.108.gtf), with gene count values normalized to S. cerevisiae spike-in controls to account for global RNA content changes. mRNA half-life was calculated based on first-order kinetics exponential decay model Y(t) = C × e^(-kt), where Y(t) represents normalized mRNA expression at time t, C is the initial concentration, and k is the decay constant. For each gene, expression levels at time points (0, 3, and 6 hours) were fitted to this model using non-linear least squares regression (nls function in R v4.3.0), and half-life was calculated as t₁/₂ = -ln(2)/k.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with gene half-life
Supplementary files format and content: tab-delimited text file with gene counts

extract_protocol:
Equal amounts of cells were then harvested using Trizol containing S. cerevisiae RNA as a spike-in control.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer protocols

treatment_protocol: MDA-MB-231 cells were treated with DMSO, or 15 μM EA for 24 hours, followed by treatment with 500 ng/mL actinomycin D (ActD) for 0, 3, or 6 hours.

value: Pre-treated with EA for 24h and treated with ActD for 6h, normal culture


title: isolated living cells from  very aged mouse brain after ApoE-FL-RSV treatment_2

description:
Library name: Aged_ApoEFL-RSV_2
10X Genomics Next GEM 3' Gene Expression v3

value: wild-type  C57/BL6

value: 18-20 months

value: resveratrol in ApoE fusogenic liposomes


title: Ctrl_Ad55

description: Library name: Sample 13

value: Control


title: isolated living cells from  very aged mouse brain after ApoE-FL-RSV treatment_1

description:
Library name: Aged_ApoEFL-RSV_1
10X Genomics Next GEM 3' Gene Expression v3

value: brain

value: multiple


title: PT_Ad44

description: Library name: Sample 11

value: Pertussis toxin


title: MDA-MB-231 EA 15 rep1 6h

description: Library name: 23196R1

value: WT


title: PT_Ad35

description: Library name: Sample 3


title: Ctrl_Ad60

description: Library name: Sample 17


title: VB124_1

value: lung

value: FFPE

value: bleomycin


title: MDA-MB-231 EA 15 rep2 3h

description: Library name: 23193R2

value: Pre-treated with EA for 24h and treated with  ActD for 3h, normal culture


title: isolated living cells from aged mouse brain after FL-RSV treatment_2

description:
Library name: Aged_FL-RSV_2
10X Genomics Next GEM 3' Gene Expression v3

value: male

value: resveratrol in fusogenic liposomes


title: Ctrl_Ad44

description: Library name: Sample 9

value: Adenoid/Tonsillar

value: T cells


title: Ctrl_Ad35

description: Library name: Sample 1


title: MDA-MB-231 DMSO input rep1

description: Library name: 231inD0R1

value: cell line

value: TNBC

value: Pre-treated with DMSO for 24h and treated with CHX for 5min,normal culture


title: MDA-MB-231 DMSO 6h

description: Library name: 231D6R1

value: Pre-treated with DMSO for 24h and treated with ActD for 6h, normal culture


title: isolated living cells from aged mouse brain after FL-RSV treatment_3

description:
Library name: Aged_FL-RSV_3
10X Genomics Next GEM 3' Gene Expression v3

value: wild-type  C57/BL6

value: 18-20 months


title: Trichoderma atroviride grown on glucose (replicate 3)

description: Library name: sample3

value: Trichoderma atroviride

value: Mycellium

value: glucose


title: Bleomycin_2

value: lung

value: vehicle

value: Male


title: isolated living cells from aged untreated mouse brain_4

description:
Library name: Aged_nontreated_4
10X Genomics Next GEM 3' Gene Expression v3

value: brain

value: multiple


title: isolated living cells from aged mouse brain after FL-RSV treatment_1

description:
Library name: Aged_FL-RSV_1
10X Genomics Next GEM 3' Gene Expression v3

value: male

value: resveratrol in fusogenic liposomes


title: Ctrl_Ad42

description: Library name: Sample 5

value: Adenoid/Tonsillar

value: T cells

value: Control


title: Bleomycin_1

value: FFPE

value: bleomycin


title: Trichoderma atroviride grown on glucose (replicate 1)

description: Library name: sample1

value: WT


title: isolated living cells from  very aged mouse brain after ApoE-FL-RSV treatment_3

description:
Library name: Aged_ApoEFL-RSV_3
10X Genomics Next GEM 3' Gene Expression v3

value: wild-type  C57/BL6

value: 18-20 months

value: resveratrol in ApoE fusogenic liposomes


title: AZD3965_1


title: AZD3965_2


title: MDA-MB-231 EA 15 rep1 3h

description: Library name: 23193R1

value: cell line

value: TNBC

value: Pre-treated with EA for 24h and treated with ActD for 3h, normal culture


title: isolated living cells from aged untreated mouse brain_3

description:
Library name: Aged_nontreated_3
10X Genomics Next GEM 3' Gene Expression v3


title: CD328_Ad55

description: Library name: Sample 14


title: MDA-MB-231 DMSO 3h

description: Library name: 231D3R1

value: Pre-treated with DMSO for 24h and treated with ActD for 3h, normal culture


title: MDA-MB-231 EA 15 rep2 0h

description: Library name: 23190R2

value: Pre-treated with EA for 24h and treated with ActD for 0h, normal culture


title: Control_2

value: lung

value: vehicle

value: control

value: Male


title: isolated living cells from aged untreated mouse brain_2

description:
Library name: Aged_nontreated_2
10X Genomics Next GEM 3' Gene Expression v3

value: brain

value: multiple

value: male


title: CD328_Ad60

description: Library name: Sample 18

value: Adenoid/Tonsillar

value: T cells


title: CD328_Ad44

description: Library name: Sample 10


title: MDA-MB-231 EA 15 rep1 0h

description: Library name: 23190R1

value: WT


title: isolated living cells from aged untreated mouse brain_1

description:
Library name: Aged_nontreated_1
10X Genomics Next GEM 3' Gene Expression v3

value: wild-type  C57/BL6

value: 18-20 months


title: Control_1

value: FFPE


title: CD328_Ad42

description: Library name: Sample 6


title: C256_CD4Pos

first: Jin Seon

last: Im

address: 7455 Fannin St

department: HBM

institute: MD Anderson Cancer Center

description: Library name: sample 18

data_processing:
Raw FASTQ sequences were assessed or quality control using FastQC (version 0.11.5), followed by adapter removal. The trimmed reads were mapped to the CRCh38/hg38 reference genome using TopHat2 (version 2.0.14). Samtools (version 1.2) was used to sort, convert between formats, and calculate mapping statistics. Gene annotation was carried out using the GENCODE annotation (version 25)[31], and aligned reads were summarized at the gene level using HTseq-count. R (3.5.1) and Bioconductor package DESeq2 was used to identify differentially expressed genes as follow: the read count was first pre-filtered to remove extremely low expressed genes. Then, DESeq2 was carried out for read count filtering, normalization, dispersion estimation, identification of differential expression. DESeq2 modeled the counts using a negative binomial distribution, followed by the Wald test. The final p-value was adjusted using the Benjamini & Hochberg method. Principal component analysis (PCA) was conducted using DESeq2 on variance-stabilizing transformed data from differentially expressed genes across the three pairwise comparisons (cord iNKT cells, adult CD4+ iNKT cells, adult CD4- iNKT cells).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: cord blood

extract_protocol: Total RNA was extracted from adult (CD4+ and CD4-) and cord iNKT cells using the RNeasy Plus Micro Kit, following the manufacturer’s protocol. Subsequent assessment of total RNAs for both quantity and integrity were conducted using an RNA 6000 Nano chip on a 2100 BioAnalyzer (Agilent; Santa Clara, CA).

value: cord blood

value: cord iNKT cell

tag: cell subset

value: CD4 Pos


title: isolated living cells from young untreated mouse brain_4

description:
Library name: Young_nontreated_4
10X Genomics Next GEM 3' Gene Expression v3

value: 4-6 months


title: CD328_Ad35

description: Library name: Sample 2


title: PC9 sheIF4E2-1 Input

description: Library name: PC9-4E2-1Input

data_processing:
For paired-end Ribo-seq libraries, R1 reads were retained for downstream analyses. Raw reads from the PC9/DDPr and PC9_shEIF4E2 libraries were first trimmed with Cutadapt (v2.8) to remove the adapter NNNNNNNNNNAGATCGGAAGAGCACACGTC. After quality filtering, reads were sequentially aligned to ribosomal RNA (rRNA) and transfer RNA (tRNA) reference sequences with Bowtie2 (v2.3.5.1) to eliminate contaminating reads. The remaining on-rRNA/non-tRNA reads were aligned to the human reference genome (GRCh38) with HISAT2 (v2.2.1) using the -k 1 parameter. The resulting alignments were converted to BAM format and sorted using SAMtools (v1.21). The mapped reads were quantified with featureCounts (v2.0.6) using the -t exon parameter. Translational efficiency (TE) was calculated as the ratio of TPM (Transcripts Per Kilobase Million)-normalized Ribo-seq to TPM-normalized RNA-seq data. Differential TE analysis was performed with the “riborex” package (v2.4.0) employing DESeq2 as the statistical engine. Genes with a p-value < 0.05 and an absolute log2 fold change (|log2FC|) > 1 were deemed significantly differentially translated in PC9/DDPr Ribo-seq data. In the PC9_shEIF4E2 Ribo-seq, genes with |log₂FC| > 1 were classified as translationally down- or up-regulated.
Assembly: GRCh38
Supplementary files format and content: Excel (.xlsx) files containing processed gene expression count matrices. Each file includes genes in rows and samples in columns. Values represent raw counts per gene.

growth_protocol: The cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. The PC9 cisplatin-resistant (PC9/DDPr) cells were maintained in cisplatin at concentrations of 6.6 μM to preserve their cisplatin-resistant phenotypes, then cultured in drug-free medium for one week prior to experimental use. All cells were cultured in a 5% CO2 incubator at 37 °C.

treatment_protocol: Cells were incubated with fresh medium for 2 h and 100ug/mL Cycloheximide treatment for 5 min before harvesting.

value: lung

value: Non-Small Cell Lung Cancer


title: PC3_Hx_rep4_S8

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: PC3_Hx_rep4_S8

data_processing:
RNA-seq reads were sequentially aligned to the ERCC sequence library (ERCC92.fa - https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip) and to the Human GRCh37 genome using HISAT2 (2.05). The output SAM files were converted to BAM using SAMtools view (0.1.19) and the number of ERCC mapped reads were counted with SAMtools flagstat for later normalisation.
The final normalised read counts for each RNA-seq sample were calculated by dividing the total number of Human mapped reads by the total number of ERCC mapped reads to provide a scaling factor for normalisation of each sample.
HTSeq (0.5.4p3) set to “intersection-strict” mode was utilised to count the total number of reads mapping within each Refseq-defined gene. Finally, differential expression between normoxia and hypoxia conditions was quantified using DESeq2.
Assembly: Human GRCh37 genome
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: prostate cancer

growth_protocol: PC3 cells were grown in DMEM/Hams F12 medium and HCT116 cells were grown in McCoy's 5a medium. Cells were grown at 37oC in a humidified incubator with 5% CO2 with 100 U/mL penicillin, 100 mg/mL streptomycin, 2mM L-glutamine and 10% fetal bovine serum (Sigma-Aldrich) and regularly tested for mycoplasma infection.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with an on-column Dnase-treatment (Qiagen). Poly-A mRNA was purified using NEBNext Poly-A mRNA Magnetic Isolation Module. 1-4 µl of 1:10 diluted ERCC RNA Spike-in Mix 1 (Ambion, 4456740) was added to each sample.
Messenger RNA (mRNA) isolation and library preparation was performed by the US NCI CCR Genomics Core using the NEB Ultra II RNA-seq kit and PolyA (mRNA) selection.

treatment_protocol: Hypoxia incubations were performed at 0.5% O2 for 16 hours in a hypoxia chamber (In Vivo2 400 Hypoxia Work Station, Ruskinn Technology)

value: prostate cancer

value: prostate cancer cell line

value: hypoxia


title: C246_CD4Pos

description: Library name: sample 17


title: isolated living cells from young untreated mouse brain_3

description:
Library name: Young_nontreated_3
10X Genomics Next GEM 3' Gene Expression v3

value: brain

value: multiple


title: C252_CD4pos

description: Library name: sample 15


title: PC3_Nx_rep4_S7

description: Library name: PC3_Nx_rep4_S7

value: normoxia


title: PC9 sheIF4E2-2 Input

description: Library name: PC9-4E2-2Input


title: C240_CD4Pos

description: Library name: sample 16


title: isolated living cells from young untreated mouse brain_2

description:
Library name: Young_nontreated_2
10X Genomics Next GEM 3' Gene Expression v3

value: male


title: PC9 shScramble rep1 Input

description: Library name: PC9-scr-1Input

value: shScramble


title: PC9 shScramble rep2 Input

description: Library name: PC9-scr-2Input


title: LZ27-RM

city: Singapore

first: Damien

last: Chua

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University, Singapore

description:
Library name: LZ27-RM
LZ27-RM

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 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 . FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: lungs

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: lungs

value: WT


title: isolated living cells from young untreated mouse brain_1

description:
Library name: Young_nontreated_1
10X Genomics Next GEM 3' Gene Expression v3

value: wild-type  C57/BL6


title: PC3_Hx_rep3_S6

description: Library name: PC3_Hx_rep3_S6


title: PC3_Nx_rep3_S5

description: Library name: PC3_Nx_rep3_S5


title: MDA-MB-231 DMSO 0h

description: Library name: 231D0R1

value: cell line

value: TNBC

value: Pre-treated with DMSO for 24h and treated with ActD for 0h, normal culture


title: PC9 sheIF4E2-2 Ribo-seq

description: Library name: PC9-4E2-2Ribo

data_processing:
For paired-end Ribo-seq libraries, R1 reads were retained for downstream analyses. Raw reads from the PC9/DDPr and PC9_shEIF4E2 libraries were first trimmed with Cutadapt (v2.8) to remove the adapter NNNNNNNNNNAGATCGGAAGAGCACACGTC. After quality filtering, reads were sequentially aligned to ribosomal RNA (rRNA) and transfer RNA (tRNA) reference sequences with Bowtie2 (v2.3.5.1) to eliminate contaminating reads. The remaining on-rRNA/non-tRNA reads were aligned to the human reference genome (GRCh38) with HISAT2 (v2.2.1) using the -k 1 parameter. The resulting alignments were converted to BAM format and sorted using SAMtools (v1.21). The mapped reads were quantified with featureCounts (v2.0.6) using the -t exon parameter. Translational efficiency (TE) was calculated as the ratio of TPM (Transcripts Per Kilobase Million)-normalized Ribo-seq to TPM-normalized RNA-seq data. Differential TE analysis was performed with the “riborex” package (v2.4.0) employing DESeq2 as the statistical engine. Genes with a p-value < 0.05 and an absolute log2 fold change (|log2FC|) > 1 were deemed significantly differentially translated in PC9/DDPr Ribo-seq data. In the PC9_shEIF4E2 Ribo-seq, genes with |log₂FC| > 1 were classified as translationally down- or up-regulated.
Assembly: GRCh38
Supplementary files format and content: Excel (.xlsx) files containing processed gene expression count matrices. Each file includes genes in rows and samples in columns. Values represent raw counts per gene.
Library strategy: Ribo-Seq


title: C250_CD4pos

description: Library name: sample 13

value: cord blood

value: cord iNKT cell

value: CD4 Pos


title: LZ25-RM

description:
Library name: LZ25-RM
LZ25-RM


title: B343_CD4Neg

description: Library name: sample 12

source_name: peripheral blood

value: peripheral blood

value: adult iNKT cell

value: CD4 Neg


title: PC9 shScramble rep2 Ribo-seq

description: Library name: PC9-scr-2Ribo

value: lung

value: Non-Small Cell Lung Cancer


title: C251_CD4pos

description: Library name: sample 14


title: B342_CD4Neg

description: Library name: sample 11


title: PC3_Hx_rep2_S4

description: Library name: PC3_Hx_rep2_S4

value: prostate cancer

value: prostate cancer cell line

value: hypoxia


title: PC9 shScramble rep1 Ribo-seq

description: Library name: PC9-scr-1Ribo

value: shScramble


title: PC3_Nx_rep1_S1

description: Library name: PC3_Nx_rep1_S1

value: normoxia


title: LZ22-RM

description:
Library name: LZ22-RM
LZ22-RM

value: lungs

value: WT


title: PC9 sheIF4E2-1 Ribo-seq

description: Library name: PC9-4E2-1Ribo


title: PC3_Hx_rep1_S2

description: Library name: PC3_Hx_rep1_S2


title: LZ20-RM

description:
Library name: LZ20-RM
LZ20-RM


title: PC9/DDPr rep2 Input

description: Library name: PC9-DInputR2

value: cisplatin-resistant


title: LZ19-RM

description:
Library name: LZ19-RM
LZ19-RM


title: B340_CD4Neg

description: Library name: sample 10


title: B338_CD4neg

description: Library name: sample 9


title: LZ24-RM

description:
Library name: LZ24-RM
LZ24-RM


title: PC3_Nx_rep2_S3

description: Library name: PC3_Nx_rep2_S3


title: B337_CD4neg

description: Library name: sample 8


title: B336_CD4neg

description: Library name: sample 7


title: LZ17-RM

description:
Library name: LZ17-RM
LZ17-RM


title: PC9/DDPr rep1 Input

description: Library name: PC9-DInputR1


title: PC3_33_HIF1bKOclone13_Nx_input

description: Library name: PC3_33_HIF1bKOclone13_Nx_input

data_processing:
ChIP-seq reads were sequentially aligned to the Drosophila melanogaster BDGP6 genome and to the Human GRCh37 genome using BWA (0.7.5a-r405). The output SAM files were converted to BAM using SAMtools view (0.1.19) and the number of mapped reads were counted with SAMtools flagstat for later normalisation.
Reads mapping to both genomes and human reads mapping to the Duke Encode blacklist regions were excluded using Bedtools (2.17.0)34. Less than 0.001% of all reads mapped to both species.
The final normalised read counts for each ChIP-seq sample were calculated by dividing the total number of Human mapped reads by the total number of Drosophila mapped reads to provide a scaling factor for normalisation of each sample.
Assembly: Human GRCh37 and Drosophila melanogaster BDGP6 genomes.
Supplementary files format and content: BAM files were firstly indexed with SAMtools (0.1.19). Next, Bedtools genomecov (2.17.0) was used to assess genome-wide sequencing coverage. The bedGraph output files were then normalised using the scaling factors above and converted to BigWig using the bedGraphtoBigWig tool.

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed using anti-H3K4me3 (Cell Signaling, 9751S), anti-H3K9me3 (Cell Signaling, 13969S), anti-H3K27me3 (Cell Signaling, 9733S), anti-H3K36me3 (Cell Signaling, 4909S), anti-H3 (Abcam, ab1791) antibodies. In addition, 10ng of Drosophila melanogaster chromatin (Active Motif, 53083) and 1µg of Drosophila-specific histone variant H2Av antibody (Active Motif, 61686) were added to each reaction as a spike-in control for downstream normalisation.
All libraries were prepared and sequenced by the US NCI CCR Genomics Core.

value: HIF1b KO


title: PC3_36_HIF1bKOclone19_Hx_input

description: Library name: PC3_36_HIF1bKOclone19_Hx_input


title: PC9/DDPr rep2 Ribo-seq

description: Library name: PC9-DRiboR2


title: PC9/Nor rep1 Input

description: Library name: PC9-NInputR1

value: non


title: PC3_35_HIF1bKOclone19_Nx_input

description: Library name: PC3_35_HIF1bKOclone19_Nx_input


title: PC9/Nor rep2 Input

description: Library name: PC9-NInputR2


title: PC3_34_HIF1bKOclone13_Hx_input

description: Library name: PC3_34_HIF1bKOclone13_Hx_input


title: LZ21-RM

description:
Library name: LZ21-RM
LZ21-RM


title: B342_CD4Pos

description: Library name: sample 5


title: B343_CD4Pos

description: Library name: sample 6


title: LZ16-RM

description:
Library name: LZ16-RM
LZ16-RM


title: LZ14-RM

description:
Library name: LZ14-RM
LZ14-RM


title: PC3_32_Parental_Hx_input

description: Library name: PC3_32_Parental_Hx_input

value: parental


title: PC3_31_Parental_Nx_input

description: Library name: PC3_31_Parental_Nx_input


title: B340_CD4Pos

description: Library name: sample 4

value: CD4 Pos


title: LZ11-RM

description:
Library name: LZ11-RM
LZ11-RM


title: PC9/Nor rep2 Ribo-seq

description: Library name: PC9-NRiboR2


title: B337_CD4pos

description: Library name: sample 2

value: peripheral blood


title: LZ9-RM

description:
Library name: LZ9-RM
LZ9-RM

value: ASO


title: B338_CD4pos

description: Library name: sample 3

value: adult iNKT cell


title: Library4: Lung, PPFE, control, other

city: Hannover

first: Jonas

last: Schupp

address: Carl-Neuberg-Str. 1

department: Respiratory Medicine

institute: Hannover Medical School

description:
Library name: FLEX9_D5
10x Genomics

data_processing:
Basecalls were converted to reads using the software Cell Ranger (v7.1.0) and its bcl2fastq implementation “mkfastq”.
Subsequent read processing was conducted using the the software Cell Ranger (v7.1.0).
Reads of probes were aligned to the human reference genome GRCh38  (GENCODE v32/Ensembl 98, “GRCh38-2020-A”) using the Chromium Human Transcriptome Probe Set _v1.0.1 for GRCh38-2020-A
Nuclei-UMI count matrices were analyzed using the R package Seurat. UMI counts were normalized with a scale factor of 10,000 UMIs per nuclei and then natural log transformed using a pseudocount of 1. To filter structural lung cells from immune cells, a recursive process of integration, graph embedding, and cluster analysis was employed
Assembly: GRCh38-2020
Supplementary files format and content: PPFE.raw.counts.mtx: sparce matrix of UMI counts in MatrixMarket format; PPFE.genes.tsv: tab-separated text file of gene names; PPFE.barcodes.tsv: tab-separated text file of cell identifiers; PPFE.Seurat.obj.final.rds: final Seurat object

source_name: lung tissue

extract_protocol:
Nuclei isolation from formalin fixed lung tissue, Fluorescence Activated Nuclei Sorting of DAPI+ single nuclei
Library construction according to the 10x Genomivs Chromium Fixed RNA Profiling  for Multiplexed Samples protocol (CG000527, Rev B)

value: lung tissue


title: PC3_29_HIF1bKOclone19_Nx_H3

description: Library name: PC3_29_HIF1bKOclone19_Nx_H3


title: F9-RM

description:
Library name: F9-RM
F9-RM


title: PC9/Nor rep1 Ribo-seq

description: Library name: PC9-NRiboR1

extract_protocol:
Input RNA was extracted with TRIzol LS followed by chemical fragmentation. Ribo-seq samples were produced by RNase I digestion followed by RNA extraction using TRIzol LS.
40-60nt region for input and 30nt for ribo-seq were selected according to 15% polyacrylamide TBE-urea gel separation. Desired RNA species were excised and soaked overnight followed by ethanol precipitation. The purified RNA was dephosporylated and added with 3’adapter. The 5’ adapter was added after reverse transcription. Eventually, PCR amplification was proceeded using Phusion High-Fidelity DNA Polymerase.

value: lung

value: Non-Small Cell Lung Cancer


title: PC3_28_HIF1bKOclone13_Hx_H3

description: Library name: PC3_28_HIF1bKOclone13_Hx_H3

value: prostate cancer

value: prostate cancer cell line


title: F6-RM

description:
Library name: F6-RM
F6-RM


title: DARNA plasmid, gp2.5 induced

city: Missoula

middle: Nicholas

last: Vassallo

state: MT

address: 32 Campus Dr.

department: Biological Sciences

institute: University of Montana

description:
Library name: Sample 4
3202
readends_SSB_induced.csv

data_processing:
Sequencing and demultiplexing were done by the MIT BioMicro Center
Adaptor sequences were trimmed from reads using BBduk (ktrim = r k = 20 mink = 10 hdist = 1 tpe tbo, minlen=17)
Aligned using bowtie2 with default parameters
Read ends and coverage depth were determined using samtools
Assembly: Reads were aligned to NC_000913 (MG1655) or NC_001604 (Enterobacteria phage T7)
Supplementary files format and content: readends, normalized counts of read ends per genome position; depth, coverage depth per genome position

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacterial cell

growth_protocol: Growth at 37 degrees celsius in LB broth

extract_protocol:
Trizol
Lexogen Small RNA-seq Library Prep Kit

treatment_protocol: Infection with bacteriophage T7 or induced expression of T7gp2.5

value: Bacterial cell

value: pCV1-DARNA, pBAD-T7gp2.5

value: Arabinose-induced


title: F7-RM

description:
Library name: F7-RM
F7-RM

value: lungs

value: WT


title: Library3: Lung, PPFE, control, other

description:
Library name: FLEX8_C5
10x Genomics


title: Library2: Lung, PPFE, control, other

description:
Library name: PPFE_Pool2
10x Genomics


title: Empty plasmid control, T7 gp2.5 induced

description:
Library name: Sample 3
3201
readends_SSB_induced.csv

value: pCV1-Empty, pBAD-T7gp2.5


title: DARNA plasmid, T7 infected

description:
Library name: Sample 2
3204
readends_T7_12minPI_mapToMG.csv
readends_T7_12minPI_mapToT7.csv


title: PC3_26_Parental_Hx_H3

description: Library name: PC3_26_Parental_Hx_H3

value: hypoxia


title: PC3_30_HIF1bKOclone19_Hx_H3

description: Library name: PC3_30_HIF1bKOclone19_Hx_H3

value: HIF1b KO


title: PC3_27_HIF1bKOclone13_Nx_H3

description: Library name: PC3_27_HIF1bKOclone13_Nx_H3

value: normoxia


title: Library1: Lung, PPFE, control, other

description:
Library name: PPFE_Pool1
10x Genomics


title: F5-RM

description:
Library name: F5-RM
F5-RM

value: Ctrl


title: PC9/DDPr rep1 Ribo-seq

description: Library name: PC9-DRiboR1

value: cisplatin-resistant


title: F8-RM

description:
Library name: F8-RM
F8-RM

value: ASO


title: B336_CD4pos

description: Library name: sample 1

value: peripheral blood

value: adult iNKT cell

value: CD4 Pos


title: Empty plasmid control, T7-infected

description:
Library name: Sample 1
3203
readends_T7_12minPI_mapToMG.csv
readends_T7_12minPI_mapToT7.csv


title: PC3_25_Parental_Nx_H3

description: Library name: PC3_25_Parental_Nx_H3

value: prostate cancer

value: parental


title: adult iNKT cells, scTCR

description:
Library name: Sample 2_scTCR
primary cell
10x Genomics

data_processing:
The raw scRNA-seq data were demultiplexed, pre-processed, and aligned to the human genome (hg38) using CellRanger 3.1 (10X Genomics). The resulting expression matrices were imported into R and Seurat version 5.0.3. was used for subsequent downstream analysis. The quality controls included excluding doublets and cells with fewer than 250 genes or 500 features or high mitochondrial content (>10%) or low ribosomal content (<10%). After the filtered read matrix was log-normalized, samples were combined, and potential batch effects were corrected using the Harmony R package. For TCR-seq analysis, the raw TCR reads were processed using CellRanger VDJ (10X Genomics) to assemble T-cell receptor (TCR) sequences and annotate clonotypes. The output containing clonotype information, including CDR3 sequences, V(D)J gene usage, and clonotype frequencies, was imported into R using the Seurat and scRepertoire package.
Assembly: GRCh38/hg38
Supplementary files format and content: CellRanger output files: SC319_1_barcodes.tsv.gz, SC319_1_features.tsv.gz, SC319_1_matrix.mtx.gz
Supplementary files format and content: SC319_1_barcodes.tsv.gz: Contains a list of cell barcodes representing individual cells identified during sequencing.
Supplementary files format and content: SC319_1_features.tsv.gz: Contains the list of genes or features detected in the sample.
Supplementary files format and content: SC319_1_matrix.mtx.gz: A sparse matrix representing the gene expression levels for each cell, with gene counts per barcode.
Supplementary files format and content: SC319_1_filtered_contig_annotations.csv: Contains information on the assembled TCR contigs, including CDR3 sequences, V(D)J gene assignments, contig quality, and clonotype assignments.
Supplementary files format and content: CellRanger output files: SC319_2_barcodes.tsv.gz, SC319_2_features.tsv.gz, SC319_2_matrix.mtx.gz
Supplementary files format and content: SC319_2_barcodes.tsv.gz: Contains a list of cell barcodes representing individual cells identified during sequencing.
Supplementary files format and content: SC319_2_features.tsv.gz: Contains the list of genes or features detected in the sample.
Supplementary files format and content: SC319_2_matrix.mtx.gz: A sparse matrix representing the gene expression levels for each cell, with gene counts per barcode.
Supplementary files format and content: SC319_2_filtered_contig_annotations.csv: Contains information on the assembled TCR contigs, including CDR3 sequences, V(D)J gene assignments, contig quality, and clonotype assignments.
Library strategy: TCR-Seq

extract_protocol:
First, iNKT cells were enriched from PBMCs and CBMCs using MACS with anti-iNKT-Microbeads according to the manufacturer’s guidelines, then stimulated with 2x10e5 allo-DCs in one well of a 24-well tissue culture plate in TCM containing αGalCer (100 nM) and IL-2 (200 IU/mL) for a 14-days. Growth factors and TCM were replenished every 2-3 days and iNKT cells were expanded into multiple wells if needed. Then, the freshly-expanded adult and cord-derived iNKT cells were stimulated by αGalCer-pulsed allogeneic dendritic cells for 24 hours and stained for CD3 and iNKTCR. Live iNKT cells were then sorted using BD FACSAria II Cell Sorter and submitted for single cells RNAseq analysis.
The cells were processed through the 10X Genomics Chromium Next GEM Single Cell 5' V2 chemistry with TCR enrichment amplification following the manufacturer's protocol (CG000331). Briefly, cells were loaded onto a Chromium Next GEM Chip K (10X Genomics PN#1000286) at the recommended concentration to capture between 7,000 and 10,000 cells along with Single Cell 5' Gel Beads containing barcoded oligos. Using the Chromium Controller thousands of cells were partitioned into nanoliter-scale Gel Bead-in-Emulsion (GEM) droplets for single cell reactions. Within the droplets cells were lysed and the cellular RNA was barcoded using reverse transcriptase from the poly(dT) RT primers resulting in full-length cDNA from polyadenylated mRNA. The barcoded RNA is released, and pool of single cell libraries are amplified and cleaned up and then split. One portion is used for the full-length TCR are captured using TCR enrichment, and the second portion for the RNA library construction. The TCR region is selected using TCR primers using Chromium Single Cell Human TCR Amplification Kit (10X Genomics PN#1000252) and NGS libraries are constructed. The other portion of the amplified full length mRNA library is used to construct 5’ RNA libraries using Chromium Next GEM Single Cell 5' Reagent Kit v2 (10X Genomics PN#1000263).

value: aGC stimulation

tag: library type

value: TCR


title: F4-RM

description:
Library name: F4-RM
F4-RM


title: cord iNKT cells, scTCR

description:
Library name: Sample 1_scTCR
primary cell
10x Genomics

value: cord blood

value: iNKT cell


title: PC3_24_HIF1bKOclone19_Hx_K36me3

description: Library name: PC3_24_HIF1bKOclone19_Hx_K36me3

value: prostate cancer cell line


title: SU-DIPGXIII_K27KO_RNA002_rep2

city: Sydney

first: Samuel

middle: Ernest

last: Ross

state: NSW

address: The University of Sydney

country: Australia

institute: The University of Sydney

description:
Library name: Sample 30
RNA002

data_processing:
RNA-seq reads were trimmed using Trimmomatic  and aligned to the GRCh38 genome using STAR. Quantification of transcript and gene abundance was then performed using RSEM.
RNA002 Direct RNA-seq libraries were mapped to the GRCh38 Ensembl annotations release version 91 using minimap2 (minimap2 -ax map-ont -uf --secondary=no -k 14 -w 10 ) and m6A modifications called using singleMod-V1
RNA004 libraries were mapped and called using dorado and rna004_130bps_hac@v5.1.0_inosine_m6A@v1 model (--min-qscore 10 --mm2-opts "-k 14 -w 10 --secondary=no") and modkit PILEUP and modkit DMR PAIR
Assembly: hg38
Supplementary files format and content: tab-delimited text files provide TPM counts for RNAseq experiments
Supplementary files format and content: RNA002_m6A.txt files provide m6A stochiometry calls from singeMod. RNA004_DMR.txt files provide output from modkit DMR PAIR

source_name: SU-DIPGXIII (K27KO)

extract_protocol:
total RNA was extracted using the ISOLATE II RNA Mini Kit from Bioline
cDNA libraries were prepared at the Ramaciotti Centre for Genomics using the Illumina Stranded mRNA prep kit. Direct RNA-seq libraries were prepared by the Garvan Sequencing Platform using the SQK-RNA002 kit or SQK-RNA004 kits sequences on PromethION  flow cells

value: SU-DIPGXIII (K27KO)

value: H3K27 altered DMG

value: untreated


title: PC3_23_HIF1bKOclone19_Nx_K36me3

description: Library name: PC3_23_HIF1bKOclone19_Nx_K36me3

value: HIF1b KO

value: normoxia


title: F3-RM

description:
Library name: F3-RM
F3-RM

value: lungs

value: WT

value: Ctrl


title: F2-RM

description:
Library name: F2-RM
F2-RM


title: SU-DIPGXIII_K27KO_RNA002_rep1

description:
Library name: Sample 29
RNA002


title: P000302_RNA004_rep2

description:
Library name: Sample 28
RNA004

value: Patient-derived, non-neoplastic, brain cells


title: adult iNKT cells, scRNA

description:
Library name: Sample 2_scRNA
primary cell
10x Genomics

data_processing:
The raw scRNA-seq data were demultiplexed, pre-processed, and aligned to the human genome (hg38) using CellRanger 3.1 (10X Genomics). The resulting expression matrices were imported into R and Seurat version 5.0.3. was used for subsequent downstream analysis. The quality controls included excluding doublets and cells with fewer than 250 genes or 500 features or high mitochondrial content (>10%) or low ribosomal content (<10%). After the filtered read matrix was log-normalized, samples were combined, and potential batch effects were corrected using the Harmony R package. For TCR-seq analysis, the raw TCR reads were processed using CellRanger VDJ (10X Genomics) to assemble T-cell receptor (TCR) sequences and annotate clonotypes. The output containing clonotype information, including CDR3 sequences, V(D)J gene usage, and clonotype frequencies, was imported into R using the Seurat and scRepertoire package.
Assembly: GRCh38/hg38
Supplementary files format and content: CellRanger output files: SC319_1_barcodes.tsv.gz, SC319_1_features.tsv.gz, SC319_1_matrix.mtx.gz
Supplementary files format and content: SC319_1_barcodes.tsv.gz: Contains a list of cell barcodes representing individual cells identified during sequencing.
Supplementary files format and content: SC319_1_features.tsv.gz: Contains the list of genes or features detected in the sample.
Supplementary files format and content: SC319_1_matrix.mtx.gz: A sparse matrix representing the gene expression levels for each cell, with gene counts per barcode.
Supplementary files format and content: SC319_1_filtered_contig_annotations.csv: Contains information on the assembled TCR contigs, including CDR3 sequences, V(D)J gene assignments, contig quality, and clonotype assignments.
Supplementary files format and content: CellRanger output files: SC319_2_barcodes.tsv.gz, SC319_2_features.tsv.gz, SC319_2_matrix.mtx.gz
Supplementary files format and content: SC319_2_barcodes.tsv.gz: Contains a list of cell barcodes representing individual cells identified during sequencing.
Supplementary files format and content: SC319_2_features.tsv.gz: Contains the list of genes or features detected in the sample.
Supplementary files format and content: SC319_2_matrix.mtx.gz: A sparse matrix representing the gene expression levels for each cell, with gene counts per barcode.
Supplementary files format and content: SC319_2_filtered_contig_annotations.csv: Contains information on the assembled TCR contigs, including CDR3 sequences, V(D)J gene assignments, contig quality, and clonotype assignments.

value: peripheral blood

value: adult iNKT cell

value: mRNA


title: PC3_22_HIF1bKOclone13_Hx_K36me3

description: Library name: PC3_22_HIF1bKOclone13_Hx_K36me3

value: prostate cancer

value: hypoxia


title: PC3_21_HIF1bKOclone13_Nx_K36me3

description: Library name: PC3_21_HIF1bKOclone13_Nx_K36me3


title: cord iNKT cells, scRNA

description:
Library name: Sample 1_scRNA
primary cell
10x Genomics

value: cord blood

value: aGC stimulation


title: P000302_RNA004_rep1

description:
Library name: Sample 27
RNA004


title: Whole Exome Sequencing (WES)-p53null STIFF mammary tumors Sample A9

city: San Francisco

first: Hugo

middle: A

last: Gonzalez

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California San Francisco

description:
Library name: Sample_A9
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene

data_processing:
Paired-end sequencing reads (FASTQ format) were aligned to the Mus musculus reference genome (GRCm39, Ensembl release) using bwa-mem2 (version 2.2.1). The resulting SAM files were converted to BAM format, sorted, and indexed using SAMtools (version 1.19.2). Duplicate reads were identified and marked using the MarkDuplicates tool from the Genome Analysis Toolkit (GATK; version 4.4.0.0). Base quality score recalibration (BQSR) was performed with GATK, with recalibration tables generated using BaseRecalibrator and known variant sites from the Mouse Genomes Project (mgp_REL2021), followed by application of the recalibration using ApplyBQSR with default parameters. A Panel of Normals (PoN) was constructed from two normal samples (wild-type Balb/c tail tissue) processed with GATK Mutect2 in tumor-only mode. Variant calls from the normal samples were jointly processed using GenomicsDBImport and combined with CreateSomaticPanelOfNormals to generate the final PoN. Somatic variant calling was then performed using Mutect2, incorporating the PoN to filter recurrent technical artifacts and germline variants. Variant calls were further refined using GATK FilterMutectCalls to retain high-confidence somatic variants. Functional annotation of variants was carried out using SnpEff (version 5.3a).
Assembly: Mus musculus reference genome (GRCm39) Ensembl release
Supplementary files format and content: VCF including the variants from GATK annotated using snpEff and ,txt file with variant per gene exported from snpEff.

source_name: mammary tumor/end-point

extract_protocol:
Tumor tissues were mechanically digested in DNA lysis buffer (4 M guanidine thiocynate, 100 mM Tris/HCl pH 7.4, 30 mM EDTA pH 8.0, 1% Triton X-100, 100 mM b-mercaptoethanol). Lysates were incubated with acid-washed diatomaceous earth to enhance nucleic acid binding, followed by silica column-based purification (Promega). Column-bound DNA was purified through sequential washes with guanidine- and ethanol-based DNA wash buffers. RNA was isolated from the DNA flowthrough by sodium acetate-phenol:chloroform extraction. The aqueous phase was incubated with acid-washed diatomaceous earth and ethanol to promote RNA binding to the column, followed by purification through guanidine- and ethanol-based RNA wash buffers. DNA was used in WES, and RNA was used in RNA-Seq and RT-qPCR analyses.
WES was performed by Novogene (https://www.novogene.com/us-en/). DNA libraries were prepared using SureSelectXT Mouse Exon Kit (Agilent Technologies) and sequenced on the Illumina NovaSeq 6000 or NovaSeq X Plus platform with paired-end 150 bp reads (PE150), with an effective sequencing depth above 50x (6 Gb / sample).

treatment_protocol: Orthotopic animal models. High concentration rat tail Col1 (Corning, Cat #354249) was incubated with 0.1% acetic acid (non-crosslinked; soft) or 0.1% acetic acid with 500 mM L-ribose (Chem Impex, Cat #28127) (crosslinked; stiff) for 10-14 days. The Col1 mixtures were then combined with BM extract (R&D Systems, Cat #3532-005-02) at a final concentration of 20%. Col1/BM hydrogels were injected into a cleared fourth mammary pat pad of 3- to 4-week-old mice prior to implantation of a mammary fragment isolated from an 8- to 10-week-old syngeneic p53null mouse. For LysM-Cre GPX4 mice, a p53null mammary fragment was implanted into the mammary fat pad as described. Mice were euthanized at a tumor end-point of a maximum tumor diameter of 2 cm for tissue analysis.

value: mammary tumor/end-point

value: Mammary Breast Tumor

value: Balb/c mammary p53null

value: non-metabolizable L-ribose crosslinked) collagen 1/ basement membrane (Col1/BM) hydrogels (STIFF Group)


title: BEAS2B, week 34, PTP treated with CSC+PET, replicate 4

city: Bellaterra

first: Alba

last: Hernández

state: Barcelona

address: Campus UAB, s/n

department: Genetics and Microbiology

country: Spain

institute: Universitat Autònoma de Barcelona

description: Library name: PTP_CTP_4

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

source_name: Lung

growth_protocol: BEAS-2B PTP cells were mantained in DMEM +10%FBS medium with 2.5ug/mL plasmocin. Cells were incubated at 37°C, 5% CO2 atmosphere.

extract_protocol:
Cells were extracted on 70-80% confluence with TRI® Reagent according to the manufacturer’s instructions. DNA contamination was removed using RNase-free DNase I.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold kit following manufacter's protocol.

treatment_protocol: Cells were treated with 100ug/mL PET, 25 ug/mL CSC or both during 4 weeks, changing medium twice a week and doing a cell passage once a week.

value: Lung

value: Bronchial epithelial

value: CSC+PET

tag: time

value: 4 weeks


title: PC3_20_Parental_Hx_K36me3

description: Library name: PC3_20_Parental_Hx_K36me3

value: prostate cancer cell line

value: parental


title: PC3_18_HIF1bKOclone19_Hx_K27me3

description: Library name: PC3_18_HIF1bKOclone19_Hx_K27me3

value: HIF1b KO


title: BEAS2B, week 34, PTP treated with CSC+PET, replicate 3

description: Library name: PTP_CTP_3


title: PC3_19_Parental_Nx_K36me3

description: Library name: PC3_19_Parental_Nx_K36me3

value: normoxia


title: SU-DIPGXVII_DMSO_RNA004_rep2

source_name: SU-DIPGXVII

extract_protocol:
total RNA was extracted using the ISOLATE II RNA Mini Kit from Bioline
cDNA libraries were prepared at the Ramaciotti Centre for Genomics using the Illumina Stranded mRNA prep kit. Direct RNA-seq libraries were prepared by the Garvan Sequencing Platform using the SQK-RNA002 kit or SQK-RNA004 kits sequences on PromethION  flow cells
RNA-seq and directRNA-seq

value: SU-DIPGXVII

value: H3K27 altered DMG

value: DMSO


title: SU-DIPGXVII_FB232_RNA004_rep2


title: BEAS2B, week 34, PTP treated with CSC+PET, replicate 1

description: Library name: PTP_CTP_1


title: Whole Exome Sequencing (WES)-p53null SOFT mammary tumors Sample A3

description:
Library name: Sample_A3
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene

value: collagen 1/ basement membrane (Col1/BM) hydrogels (SOFT group)


title: SU-DIPGXVII_FB232_RNA004_rep1


title: Whole Exome Sequencing (WES)-p53null STIFF mammary tumors Sample A8

description:
Library name: Sample_A8
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene


title: F1-RM

description:
Library name: F1-RM
F1-RM

value: lungs

value: WT

value: Ctrl


title: BEAS2B, week 34, PTP treated with CSC+PET, replicate 2

description: Library name: PTP_CTP_2


title: Whole Exome Sequencing (WES)-p53null STIFF mammary tumors Sample A7

description:
Library name: Sample_A7
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene

value: mammary tumor/end-point

value: Mammary Breast Tumor

value: Balb/c mammary p53null


title: PC3_17_HIF1bKOclone19_Nx_K27me3

description: Library name: PC3_17_HIF1bKOclone19_Nx_K27me3

value: prostate cancer


title: BEAS2B, week 34, PTP treated with PET, replicate 4

description: Library name: PTP_PET_4

value: Lung

value: Bronchial epithelial

value: PET


title: SU-DIPGXVII_DMSO_RNA004_rep1


title: SU-DIPGXIII_RNA002_rep2

source_name: SU-DIPGXIII

value: SU-DIPGXIII

value: untreated


title: BEAS2B, week 34, PTP treated with PET, replicate 3

description: Library name: PTP_PET_3

value: 4 weeks


title: Whole Exome Sequencing (WES)-p53null SOFT mammary tumors Sample A1

description:
Library name: Sample_A1
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene


title: BEAS2B, week 34, PTP treated with PET, replicate 2

description: Library name: PTP_PET_2


title: DTR (bio rep 4)

city: Bergen

first: Salwa

last: Suliman

address: Årstadveien 19

department: Department of Clinical Dentistry

country: Norway

institute: Faculty of Medicine, University of Bergen

description: Library name: Sample 24

data_processing:
Broad picard pipeline
HiSat2 version 2.0.5
Quantification FeatureCounts (v 1.5.2) (Counts_genocode_vM13_UiB-S10-2022.txt)
Normalization and Differential Expression : DESeq2 version 1.42.0
Assembly: Reference gencode M13 Mus musculus
Fastq files (FASTQ files were extracted from BAMs aligned using STAR and deduplicated using Picard MarkDuplicates)
Bam files(STAR aligned, Picard deduplicated with mm13 reference)
Supplementary files format and content: Counts_genocode_vM13_UiB-S10-2022.txt

source_name: subcutaneous implant

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen) following manufacturer's protocol
Illumina TruSeq Stranded mRNA sample preparation

value: subcutaneous implant


title: PC3_15_HIF1bKOclone13_Nx_K27me3

description: Library name: PC3_15_HIF1bKOclone13_Nx_K27me3

value: prostate cancer cell line

value: HIF1b KO

value: normoxia


title: PC3_16_HIF1bKOclone13_Hx_K27me3

description: Library name: PC3_16_HIF1bKOclone13_Hx_K27me3

value: hypoxia


title: SU-DIPGXVII_FB232_directRNAseq

data_processing:
RNA-seq reads were trimmed using Trimmomatic  and aligned to the GRCh38 genome using STAR. Quantification of transcript and gene abundance was then performed using RSEM.
Direct RNA-seq libraries were mapped to the GRCh38 Ensembl annotations release version 91  using minimap2 (-ax map-ont -uf  --secondary=no). m6A site probabilities were calculated using nanopolish and m6anet (--num_iterations 1000)
Assembly: hg38
Supplementary files format and content: tab-delimited text files provide TPM counts for RNAseq experiments
Supplementary files format and content: csv files provide m6A site scores from m6Anet for direct-RNAseq experiments

extract_protocol:
total RNA was extracted using the ISOLATE II RNA Mini Kit from Bioline
cDNA libraries were prepared at the Ramaciotti Centre for Genomics using the Illumina Stranded mRNA prep kit. Direct RNA-seq libraries were prepared by the Garvan Sequencing Platform using the SQK-RNA002 kit and sequences on PromethION using FLO-PRO002 flow cells
RNA-seq and directRNA-seq

value: SU-DIPGXVII

value: H3K27 altered DMG


title: BEAS2B, week 34, PTP treated with PET, replicate 1

description: Library name: PTP_PET_1


title: DTR (bio rep 3)

description: Library name: Sample 23


title: SU-DIPGXVII_DMSO_directRNAseq

value: DMSO


title: PC3_14_Parental_Hx_K27me3

description: Library name: PC3_14_Parental_Hx_K27me3

value: parental


title: BEAS2B, week 34, PTP treated with CSC, replicate 4

description: Library name: PTP_CSC_4

value: CSC


title: SU-DIPGXIII_RNA002_rep1


title: BEAS2B, week 34, PTP treated with CSC, replicate 3

description: Library name: PTP_CSC_3


title: DTR (bio rep 2)

description: Library name: Sample 22


title: Whole Exome Sequencing (WES)-p53null SOFT mammary tumors Sample A2

description:
Library name: Sample_A2
Fastq.gz files of WES, annotated variants in .vcf files, and a .txt file of variants per gene

value: mammary tumor/end-point

value: Mammary Breast Tumor

value: Balb/c mammary p53null

value: collagen 1/ basement membrane (Col1/BM) hydrogels (SOFT group)


title: BEAS2B, week 34, PTP treated with CSC, replicate 2

description: Library name: PTP_CSC_2

value: Lung

value: Bronchial epithelial


title: CONVD_PBS, 5 dpf_3

city: LEIDEN

first: Li

last: Liu

address: Verbeekstraat 29D

country: Netherlands

institute: Leiden University

description:
Library name: Sample 12
150 nucleotides

data_processing:
RNAseq reads were aligned and mapped to the zebrafish genome GRCz11 using Salmon v1.2.1
Differential gene expression was analyzed by using DESeq2 v1.24.0. Statistical significance was determined by a padj value of ≤ 0.05 by utilizing apeglm.
Assembly: the zebrafish genome GRCz11
Supplementary files format and content: excel files include RPKM values for each sample
Supplementary files format and content: excel files include fold change values and FDR p value

organism: Danio rerio

source_name: whole embryos

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://zfin.org).

extract_protocol:
Zebrafish larvae from all groups  groups (n=3) were resuspended and crushed in 0.5 ml of TRIzol Reagent
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) was used to process the samples. Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation of the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

value: wild type

value: whole embryos

value: 5 days post fertilization


title: DTR (bio rep 1)

description: Library name: Sample 21

value: subcutaneous implant


title: PC3_10_HIF1bKOclone13_Hx_K9me3

description: Library name: PC3_10_HIF1bKOclone13_Hx_K9me3

value: prostate cancer

value: prostate cancer cell line

value: HIF1b KO


title: CONVD_PBS, 5 dpf_2

description:
Library name: Sample 11
150 nucleotides


title: CONVD_PBS, 5 dpf_1

description:
Library name: Sample 10
150 nucleotides


title: PC3_12_HIF1bKOclone19_Hx_K9me3

description: Library name: PC3_12_HIF1bKOclone19_Hx_K9me3

value: hypoxia


title: PC3_11_HIF1bKOclone19_Nx_K9me3

description: Library name: PC3_11_HIF1bKOclone19_Nx_K9me3

value: normoxia


title: BEAS2B, week 34, PTP treated with CSC, replicate 1

description: Library name: PTP_CSC_1

value: 4 weeks


title: PC3-sh720-1-3

city: Toon

first: Yuichiro

last: Sawada

address: Shitsukawa

institute: Ehime Univercity

description: Library name: N177-mix-03

data_processing:
Fastq files were trimmed trim galore.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values file includes raw counts for each Sample

extract_protocol:
shControl and CTHRC1 KD cells were pre-cultured in 6-well plates (1 × 105/well) for 24 hours. Total RNA was extracted using RNeasy spin column kits and DNase I (Quiagen, USA).
RNA-seq was performed on the NovaSeq6000, with a read configuration of 75 bp for single reads; 3 million reads were generated per sample.

value: prostatic adenocarcinoma cell line

value: pMSCV-luc transfected cell


title: DT (bio rep 4)

description: Library name: Sample 20


title: DT (bio rep 3)

description: Library name: Sample 19


title: DT (bio rep 2)

description: Library name: Sample 18


title: PC3-sh718-1-3

description: Library name: N177-mix-02


title: PC3_9_HIF1bKOclone13_Nx_K9me3

description: Library name: PC3_9_HIF1bKOclone13_Nx_K9me3


title: PC3_8_Parental_Hx_K9me3

description: Library name: PC3_8_Parental_Hx_K9me3

value: parental


title: DT (bio rep 1)

description: Library name: Sample 17


title: PC3_7_Parental_Nx_K9me3

description: Library name: PC3_7_Parental_Nx_K9me3


title: PC3_13_Parental_Nx_K27me3

description: Library name: PC3_13_Parental_Nx_K27me3


title: CONVD_Ecoli, 5 dpf_1

description:
Library name: Sample 7
150 nucleotides


title: T (biol rep 4)

description: Library name: Sample 16


title: CONVD_Ecoli, 5 dpf_2

description:
Library name: Sample 8
150 nucleotides


title: PC3_6_HIF1bKOclone19_Hx_K4me3

description: Library name: PC3_6_HIF1bKOclone19_Hx_K4me3


title: GF_PBS, 5 dpf_3

description:
Library name: Sample 6
150 nucleotides


title: T (biol rep 3)

description: Library name: Sample 15


title: CONVD_Ecoli, 5 dpf_3

description:
Library name: Sample 9
150 nucleotides


title: GF_PBS, 5 dpf_2

description:
Library name: Sample 5
150 nucleotides


title: T (biol rep 2)

description: Library name: Sample 14


title: Lung, Sarcoidosis, Granuloma, 7

description: Library name: SAR020

data_processing:
Basecalls were converted to reads using the software Cell Ranger and its bcl2fastq implementation “mkfastq”.
Subsequent read processing was conducted using the the software spaceranger
Reads of probes were aligned to the human reference genome GRCh38  (GENCODE v32/Ensembl 98, “GRCh38-2020-A”) using the Chromium Human Transcriptome Probe Set _v1.0.1 for GRCh38-2020-A
Assembly: GRCh38-2020
Supplementary files format and content: matrix.mtx.gz: gene expression count data in MatrixMarket Exchange format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hires image of tissue
Supplementary files format and content: tissue_lowres_image.png: lowres image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
FFPE tissue blocks were cut on a routine microtome into of 5 µm thick sections
Library construction according to the 10x Genomics Visium CytAssist Gene Expression protocol (CG000495 Rev A)

value: lung


title: PC3_5_HIF1bKOclone19_Nx_K4me3

description: Library name: PC3_5_HIF1bKOclone19_Nx_K4me3


title: Lung, Sarcoidosis, Granuloma, 6

description: Library name: SAR019


title: Lung, Sarcoidosis, Granuloma, 5

description: Library name: SAR014


title: PC3_4_HIF1bKOclone13_Hx_K4me3

description: Library name: PC3_4_HIF1bKOclone13_Hx_K4me3


title: PC3-shCtrl-1-3

description: Library name: N177-mix-01


title: PC3_3_HIF1bKOclone13_Nx_K4me3

description: Library name: PC3_3_HIF1bKOclone13_Nx_K4me3


title: T (biol rep 1)

description: Library name: Sample 13


title: GF_PBS, 5 dpf_1

description:
Library name: Sample 4
150 nucleotides


title: Lung, Sarcoidosis, Granuloma, 4

description: Library name: SAR012


title: PC3_1_Parental_Nx_K4me3

description: Library name: PC3_1_Parental_Nx_K4me3


title: R (biol rep 3)

description: Library name: Sample 11


title: PC3_2_Parental_Hx_K4me3

description: Library name: PC3_2_Parental_Hx_K4me3


title: GF_Ecoli, 5 dpf_3

description:
Library name: Sample 3
150 nucleotides


title: R (biol rep 4)

description: Library name: Sample 12


title: GF_Ecoli, 5 dpf_2

description:
Library name: Sample 2
150 nucleotides


title: Lung, Sarcoidosis, Granuloma, 2

description: Library name: SAR006


title: R (biol rep 2)

description: Library name: Sample 10


title: Lung, Sarcoidosis, Granuloma, 3

description: Library name: SAR009


title: GF_Ecoli, 5 dpf_1

description:
Library name: Sample 1
150 nucleotides


title: Lung, Sarcoidosis, Granuloma, 1

description: Library name: SAR001


title: PC3_24_Hx_rep2_input

description: Library name: PC3_24_Hx_rep2_input


title: RD cells, vincristine-resistant, replicate 2

city: Seattle

first: Eleanor

last: Chen

state: WA

address: 1959 NE Pacific St

department: Laboratory Medicine and Pathology

institute: University of Washington

description:
Library name: Sample 4
Column name in Differential_expression_analysis_table.csv: RD-VIN-2

data_processing:
Read were trimmed for adapter sequences and quality using bcl2fastq v2.17 software.
Trimmed reads were aligned to the ENSEMBL reference genome using STAR v2.5.2b software and gene-level counts were obtained with featureCounts (Subread v1.5.2) from uniquely mapped exonic reads.
Differential expression analysis was performed with DESeq2 using the Wald test.
Gene ontology enrichment was assessed with GeneSCF using the MGI GO database.
Principal component analysis (PCA) was performed in DESeq2 (plotPCA) using the 500 most variable genes.
Assembly: GRCh38
Supplementary files format and content: csv file including differential gene analysis for each Sample

source_name: RD

growth_protocol: RD rhabdomyosarcoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit.
mRNA was enriched with oligo(dT) beads, fragmented at 94C for 15 min, converted to double-stranded cDNA, end-repaired, adenylated, ligated to adapters, and PCR-amplified with indexed primers.

treatment_protocol: Vincristine resistance was induced by intially treating with vincristine at a dose of 1-1.5nM which killed approximately 80-90% of the cells. The remaining cells were maintained in culture until they grew to >50% confluency, split to allow regrowth, and then restarted on vincristine at a 10-20% increase in dosage. Incremental increases in drug dosage were continued over the course of 9 months to a year to reach at least a 100-fold increase in the IC50 (half-maximal inhibitory concentration).

value: RD

value: rhabdomyosarcoma fusion negative cells

value: WT

value: Vincristine, IC50 > 100x


title: Line XIII scramble H3K27me3 CutRun rep1

city: Sacramento

first: Paul

last: Knoepfler

state: CA

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

description: Library name: XIII_scramble_H3K27me3_rep1

data_processing:
Reads were trimmed of adapters using bbduk
Reads were aligned to the hg19 genome with bowtie2
Aligned reads were only retained if they aligned to the same chromosome and within 1000bp of eachother.
Bedtools was used to generate bedgraph files of the aligned reads
Peaks were called with SEACR using the stringent setting with a cutoff of the top 1% of peaks.
Assembly: hg19
Supplementary files format and content: bigwig or bed (peak file)
Library strategy: CUT&Run

source_name: DIPG Line XIII

growth_protocol: Cells were grown in Tumor Stem Medium, which contains DMEM/F12 1:1 (Invitrogen), Neurobasal-A (Invitrogen), 10mM HEPES (Invitrogen), 1X MEM sodium pyruvate (Invitrogen), 1X MEM nonessential amino acids (Invitrogen), 1% GlutaMax (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah), human-EGF (20 ng/ml) (Shenandoah), human PDGF-A and PDGF-B (20ng/ml) (Shenandoah), heparin (10 ng/ml) (StemCell Technologies) and B27 without Vitamin A (Invitrogen) (27).

extract_protocol:
Cut&Run was performed for CTCF (rabbit anti-CTCF, Millipore #07-729), H3.3 (Millipore #09-838) and H3K27me3 (Cell Signaling C36B11)  using the ActiveMotif Cut&Run kit (ActiveMotif #53180) according to the protocol. Input was used as the control.
Libaries were prepared using the NEB Next Ultra II DNA Library Prep Kit.

treatment_protocol: For CTCF knockdown and scramble control samples, cells were transfected with 90 nM of either scramble control or CTCF siRNA using the RNAi Max reagent (Invitrogen 13778075) and OptiMEM medium (Gibco 31985070). Samples were collected 72 hours after transfection.

value: DIPG Line XIII

value: pediatric glioma tumor cells


title: Line XIII scramble H3K27me3 CutRun rep2

description: Library name: XIII_scramble_H3K27me3_rep2


title: PC3_22_Hx_rep1_input

description: Library name: PC3_22_Hx_rep1_input


title: RD cells, control, replicate 2

description:
Library name: Sample 2
Column name in Differential_expression_analysis_table.csv: RD-CTRL-2

value: Untreated


title: MSC (biol rep 4)

description: Library name: Sample 8

value: subcutaneous implant


title: RD cells, vincristine-resistant, replicate 1

description:
Library name: Sample 3
Column name in Differential_expression_analysis_table.csv: RD-VIN-1


title: MSC (biol rep 3)

description: Library name: Sample 7


title: PC3_21_Nx_rep1_input

description: Library name: PC3_21_Nx_rep1_input

value: prostate cancer

value: prostate cancer cell line


title: Line XIII siCTCF H3K27me3 CutRun rep2

description: Library name: XIII_siCTCF_H3K27me3_rep2


title: MSC (biol rep 1)

description: Library name: Sample 5


title: PC3_19_Nx_rep2_H3

description: Library name: PC3_19_Nx_rep2_H3


title: RD cells, control, replicate 1

description:
Library name: Sample 1
Column name in Differential_expression_analysis_table.csv: RD-CTRL-1


title: PC3_23_Nx_rep2_input

description: Library name: PC3_23_Nx_rep2_input


title: Line XIII siCTCF H3K27me3 CutRun rep1

description: Library name: XIII_siCTCF_H3K27me3_rep1