title: DRG, N_2 human sample

city: DURHAM

first: Jing

last: Xu

state: NC

address: 816 Louise Circle

institute: Duke university

description:
Library name: N_2
10x 3' gene expression protocol

library_source: transcriptomic single cell

data_processing:
snRNA-seq reads were processed with Cell-Ranger v4.0.0, and aligned to the Human GRCh38 (GENCODE v32/Ensembl98) reference genome performed using default parameters. Downstream analysis was conducted with Seurat v4.3.0 using R v4.3.0. Cells were filtered out if they expressed fewer than 200 genes or had more than 10% mitochondrial reads. Gene expression was then normalized and scaled using the NormalizeData and ScaleData functions from Seurat, respectively, with default settings, as well as the FindVariableFeatures function to identify the highly variable genes. Principal Component Analysis (PCA) was carried out, and downstream analyses were based on the top 20 principal components. To address batch effects, datasets were integrated, re-normalized, scaled, and batch-corrected using Harmony v0.1.1. Unsupervised clustering was done using the FindClusters function from Seurat with a resolution of 0.8. Uniform Manifold Approximation and Projection (UMAP) was applied to reduce the data to two dimensions. FindMarkers with default settings to get gene markers, and cell types within each cluster were annotated based on known marker genes and genes that were differentially expressed within each cluster.
Assembly: Human GRCh38 (GENCODE v32/Ensembl98) reference genome
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Human DRG tissues from were microdissected for nuclei isolation according to the previous report. Microdissected DRG were homogenized in 0.2 ml RNAase-free lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc2, 0.1 mM EDTA, 10 mM Tris-HCl, 1 mM DTT and 0.1% Triton X-100 in diethylpyrocarbonate (DEPC)-treated water) using homogenizer from 10X Genomics nuclei isolation kit (PN-1000493) on ice. The homogenate was loaded into a 3.5-ml polycarbonate ultracentrifuge tube (349622, Beckman-Coulter), and 1.8 ml of sucrose solution (1.8 M sucrose, 3 mM MgAc2, 1 mM DTT, and 10 mM Tris-HCl in DEPC-treated water) was added to the bottom of the tube with the homogenate, and the tube was centrifuged at 24400 RPM for 2.5 h at 4 °C. After removing the supernatants, pellets containing the nuclei were incubated in 100 μl of DEPC-treated water-based PBS for 20 min on ice before resuspending the pellets using the same solution.
Nuclei were counted using a hemocytometer and single-nucleus capture was performed using the 10X Genomics Single-Cell 3′ system (v3.1). Single-nucleus libraries from individual samples were pulled and sequenced on the MGISEQ-2000 machine. RNA integrity analysis was performed using the Agilent 2100 Bioanalyzer.

value: dorsal root ganglion

value: Homo sapiens


title: DDX3i and SMACm combination

status: Public on Feb 01 2026

type: RNA

city: Amsterdam

first: Neeltje

last: Kootstra

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

description: SUPT1 cells treated with DDX3i FH1321 (50uM) and SMACm AZD5582 (1uM) for 6 hours

data_processing: LightCycler 480 1.5.1.62 SP3 software (Roche, Basel, Switzerland) was used for analysis of relative copy numbers and melting curves. TATA-binding protein (TBP), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and hypoxanthine phosphoribosyltransferase 1 (HPRT1) were included as reference genes to correct for cDNA input.

label: SYBR green

molecule: total RNA

organism: Homo sapiens

label_protocol: cDNA was produced using the M-MLV Reverse Transcriptase kit (Promega, Madison, WI) and random hexamers (Promega). PCR arrays were using the 384 well plates Apoptosis and Survival Tier 1-4 from Bio-Rad (Hercules, CA, USA), where 384 primer pairs are lyophilized on the plate. 10 ng cDNA was used for qPCR with GoTaq® qPCR Master Mix (Promega, Madison, WI, USA) on the LightCycler 480 System (Roche, Basel, Switzerland). The following cycling conditions were used: denaturation: 95 °C for 2 min; amplification: 40 cycles of 95°C for 5 sec and 60°C for 30 sec, followed by a melting curve stage.

growth_protocol: SUPT1-CCR5 cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM; Thermo Fisher Scientific, Gibco) supplemented with 10% fetal calf serum (FCS; HyClone, Cytiva, Marlborough, MA, USA) and antibiotics (100U/ml penicillin and 100ug/ml streptomycin) (Invitrogen, Carlsbad, CA, USA) at 37°C in a humidified 10% CO2 incubator.

extract_protocol: RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturers’ instructions.

treatment_protocol: Cells were treated with the different compounds (alone or in combination or solvent (DMSO) control for 6 hours. Coumpounds: DDX3i FH1321 (50uM) and SMACm AZD5582 (1uM)

tag: disease state

value: T-cell non-Hodgkin lymphoma that has been engineered (transfection) to express CCR5


title: AAV-TBG-Vec_2

type: SRA

city: Shanghai

first: Yinkun

last: Fu

address: chongqing Rd

department: school of medicine

country: China

institute: shanghai jiaotong university

description: Library name: GFPHFD-2

library_source: transcriptomic

data_processing:
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
mm10
tab-delimited text file includes raw counts for each sample
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA were extracted from livers using  Trizol method.
1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

tag: tissue

value: Liver


title: SMACm treated

description: SUPT1 cells treated with SMACm AZD5582 (1uM) for 6 hours


title: L1_roots_rep1

city: Kayseri

first: Saffet

last: Teber

address: Erciyes University Faculty of Agriculture, Köşk Mahallesi, Fuat Sezgin Caddesi No:12, Melikgazi/KAYSERİ

country: Turkey

institute: Erciyes University

description: Library name: L1_rep1

data_processing:
ACGT101-miR pipeline (LC Sciences, Houston, TX, USA).
Assembly: CDC Redberry genome v2.0
Supplementary files format and content: xlsx file contains both raw and normalized counts

organism: Lens culinaris

source_name: Roots

extract_protocol:
Total RNA was isolated from pooled samples using TRI Reagent (Sigma Life Science) and the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich), following the manufacturer’s protocols.
Small RNA libraries were prepared using the Illumina TruSeq Small RNA Preparation Kit according to the manufacturer’s protocol.

value: Roots


title: AAV-TBG-Vec_3

description: Library name: GFPHFD-3


title: v4 ko CD8T-1

status: Public on Jan 30 2026

city: Hefei

first: xia

last: zhou

address: huang shan Road 443

institute: university of science and technology of china

description: Library name: Sample-3

data_processing:
MiXCR (v.3.0.13) toolkit.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq

source_name: liver

extract_protocol:
Liver tissues enriched for metastatic MC38 melanomas were harvested from WT or Vsig4-/- mice, cut into small pieces and digested with 0.5 mg/mL collagenase IV (Sigma) and 5 U/mL DNase I (Sigma) for 20 mins at 37℃ under shaking. The cell suspension was filtered through a 70 µm cell strainer and centrifugated at 400g for 5 mins at 4℃, followed by lysis of red blood cell inn ACK buffer (Biolegend).DAPI-CD45+CD3+CD8+ T cells  were sorted by FACS and further processed for bulk TCR-seq.
RNA libraries for TCR-seq were prepared using Evo M-MLV Kit Ver.2 AG11728 kit  following manufacture's protocols.

value: liver

tag: cell type

value: CD8+ T cells

tag: genotype

value: VSIG4 KO

tag: treatment

value: liver bearing metastatic MC38 melanomas


title: AAV-TBG-Vec_1

description: Library name: GFPHFD-1


title: v4 ko CD8T-2

description: Library name: Sample-4


title: WT CD8T-1

description: Library name: Sample-1

value: WT


title: PDE6G

city: 杭州

first: wei

last: zhang

state: 浙江省

address: 浙江省杭州市钱塘区下沙街道东方街150中国科学院杭州医学研究所

institute: 浙江工业大学

description:
Library name: Sample 2
10×Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values (TSV) files for gene expression matrices; matrix files containing unique molecular identifier (UMI) counts per gene per cell

source_name: Tumor tissue

extract_protocol:
Fresh mouse tumor tissues were harvested and immediately placed in ice-cold HBSS supplemented with Mg²⁺ and 0.04% (w/v) BSA. Under sterile conditions, the tissues were minced into 1–2 mm³ pieces, then resuspended in digestion buffer (HBSS with Mg²⁺, containing 2 mg/ml collagenase IV, 0.2 mg/ml hyaluronidase, and 40 U/ml DNase I) and incubated at 37°C for 45–60 minutes with gentle shaking. Digestion was terminated by adding an equal volume of FACS buffer (HBSS + 2% FBS + 5 mM EDTA), and the resulting suspension was filtered through a 70 μm cell strainer to remove undigested tissue debris, followed by centrifugation at 300×g for 5 minutes at 4°C. The collected cell pellet was washed twice with FACS buffer, and cell viability and concentration were assessed via Trypan Blue staining to ensure a viability rate of >80% and a final cell concentration of 700–1,200 cells/μl in HBSS containing 0.04% BSA.
The prepared cell suspension, reaction mixture (Master Mix + Sample), 10X Barcode Gel Beads (VDJ 5’ Gel Beads v1.1), and Partitioning Oil were loaded into separate wells of a Chromium Next GEM Chip G. Through the microfluidic “single cross” system, Gel Beads-in-Emulsions (GEMs) were formed. To achieve single-cell resolution, cells were subjected to limited dilution during GEM generation, resulting in 90–99% of GEMs being cell-free and the remaining GEMs typically containing a single cell. All generated GEMs were pooled together, followed by Gel Bead dissolution and cell lysis within each GEM. The Gel Beads consist of a gel matrix and oligonucleotides conjugated to magnetic beads. Upon dissolution, the Gel Beads release a large quantity of primer sequences, which are composed of: (i) Illumina TruSeq Read 1 sequencing primer, (ii) a 16-nt 10X Barcode (unique to each Gel Bead), (iii) a 10-nt unique molecular identifier (UMI), and (iv) a 13-nt Template Switch Oligo (TSO). The released oligonucleotides were mixed with the lysed cells and Master Mix (containing RT reagents and RT primers) to perform reverse transcription, yielding full-length cDNA sequences tagged with the 10X Barcode. After reverse transcription, the oil-in-water emulsion was disrupted using a Recovery Agent. The cDNA was then recovered, purified, and amplified with DNA polymerase. Following cDNA amplification, an aliquot of the cDNA from a single sample was split into 2–3 portions, which were separately used for TCR/BCR enrichment and library construction, as well as 5’ transcriptome library construction, according to the experimental design. V(D)J Enrichment and Library Construction: The constant (C) regions of TCR and BCR genes are highly conserved. Nested PCR was performed using outer and inner primers designed against these C regions to specifically enrich cDNA fragments containing the V(D)J regions. The enriched cDNA was fragmented by enzymatic digestion, and fragments of appropriate size were selected. After end repair, A-tailing, and ligation of Read 2 sequencing primers, the cDNA library containing P5 and P7 adapters was constructed via PCR.

treatment_protocol: PDE6G-expressing tumor models (experimental group) were immunized with PDE6G mRNA-LNP vaccine

value: Tumor tissue

tag: cell line

value: Tumor cells


title: Luc

address: 浙江省杭州市钱塘区下沙街道东方街150中国科学院杭州医学研究所

description:
Library name: Sample 1
10×Genomics


title: DRG, N_1 human sample

country: USA

description:
Library name: N_1
10x 3' gene expression protocol

molecule: polyA RNA

source_name: dorsal root ganglion


title: (AT)34 chr10

status: Public on Jan 28 2026

city: New York

first: Bertrand

last: Theulot

state: NY

address: 100 WASHINGTON SQ E, Attn: Duncan Smith

institute: NYU

description: Library name: 2258

library_source: genomic

data_processing:
Reads were aligned to the Saccharomyces cerevisiae S288C reference genome (R64-5-1-20240529) using BWA-MEM (v0.7.17). Alignments were converted to BAM, filtered with SAMtools (v1.19) to retain reads with mapping quality ≥30 and to remove secondary and supplementary alignments (-q 30 -F 2304), then sorted and indexed. Strand-specific coverage was computed by extracting reverse-strand reads (flags 0x50 and 0x90) and plus-strand reads (flags 0x40 and 0x80 with 0x10 excluded), and running samtools depth -aa to include all genomic positions, including zero-coverage bases. Plus- and reverse-strand coverage files were merged position-by-position with awk.
Assembly: S288C_reference_sequence_R64-5-1_20240529
Supplementary files format and content: Coverage of okazaki fragments per strand at each position on the genone (chrom,pos,cov_plus _strand, cov_minus_strand)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to mid-log phase in YPD at 30C before treatment

extract_protocol:
Okazaki fragments were enriched and purified as described previously (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).
Libraries were generated as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).

treatment_protocol: Cells carrying a doxycycline-repressible CDC9 gene were grown to mid-log phase before addition of 40 mg/L doxycycline for 2 hrs before harvest. Cells subjected to anchor-away depletion of Cdc9 were grown to mid-log phase and then treated with rapamycin (final, 1 µg/mL) for 1 h. Genomic DNA was extracted from spheroplasts, and Okazaki fragments were isolated, end-labeled, and deep-sequenced as previously described (Smith and Whitehouse, 2012).

value: haploid yeast cells

value: MAT ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+, AT34 2 kb downstream ARS1019 cdc9::tetO7-CDC9 cmv_Laci-NAT

value: 40 mg/L doxycycline for 2 hrs

tag: batch


title: Mouse, Lung,  Saline_1, scRNA

city: Chengdu

first: Bisen

last: Ding

address: Renmin South Road

institute: State Key Laboratory of Biotherapy

description: Library name: Saline_1

data_processing:
The cellranger pipeline (version 3.1.0, 10X Genomics) was used to process raw sequencing output.
Assembly: mm10
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx, or filtered_feature_bc_matrix.h5)

source_name: lung

extract_protocol:
The homogenized lung tissues were suspended in DMEM medium (C11995500BT, GIBCO) containing 1 mg/mL type I collagenase (C8140，Solarbio), 1 mg/mL type IV collagenase (C8160，Solarbio), 1 mg/mL Dispase II (D6430，Solarbio), and 0.2 mg/mL DNAase (D8071, Solarbio) at 37°C for 30 min. The digested lung tissues were filtered through a 70 μm filter membrane (BS-70-XBS, biosharp), and the filtrate was centrifuged and treated with red blood cell lysis buffer (R1010, Solarbio) for 10 min, centrifuged again under the same conditions, the pellet was washed once with sterile PBS (C10010500BT, GIBCO), and centrifuged again under the same conditions. Cell pellet was resuspended again with MACS mixture (2 mM EDTA, 0.1% BSA, 1% penicillin/streptomycin/antimitotic in DPBS) to obtain lung single cell suspension.
Single-cell ATAC sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) were performed using the 10X Chromium 3′ v3 kit (10X Genomics, Pleasanton, CA) according to the manufacturer's instructions.

value: lung

value: saline


title: control

description: SUPT1 cells, with DMSO for 6 hours (control condition only containing the solvent)


title: rad52delta (AT)34 chr10

description: Library name: 2297

value: MAT ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+, AT34 2 kb downstream ARS1019 cdc9::tetO7-CDC9 cmv_Laci-NAT Rad52::KanMX


title: No Repeat control chr10

description: Library name: 2092

value: MAT ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+, Flex1 Control 2 kb downstream ARS1019, cdc9::tetO7-CDC9 cmv_Laci-NAT


title: No Repeat Control chr6

description: Library name: 2442

value: MAT ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3-1, tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1 CDC9-FRB::KanMX, Flex1Control-HPH cassette at Chr6int2 Locus

value: rapamycin (final, 1 µg/mL) for 1 h


title: DDX3i treated

description: SUPT1 cells treated with DDX3i FH1321 (50uM) for 6 hours

value: T-cell non-Hodgkin lymphoma that has been engineered (transfection) to express CCR5


title: rad52delta (AT)34 chr6

description: Library name: 2439

value: MAT ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3-1, tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1 CDC9-FRB::KanMX, rad52::LEU,AT-34-HPH cassette at Chr6int2 Locus


title: WT CD8T-2

description: Library name: Sample-2

value: liver

value: CD8+ T cells


title: Mid DOX-treated in-vitro BMP4 treated sample 1

status: Public on Jan 27 2026

city: Boston

first: April

middle: M

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

description:
Library name: DV48-12wB-midDOX
normalized_counts_BMP.txt

data_processing:
alignment to hg38; Salmon version 1.2.1; default parameters for hg38 alignment
RNA-seq read mapping; Salmon version 1.8.0; salmon -l A --numBootstraps 100 --gcBias –validateMappings
Read abundance normalization; DESeq2 version 1.38.0
Assembly: hg38
Supplementary files format and content: normalized_counts_BMP: Normalized abundance counts across BMP4-treated RNA-seq datasets generated
Supplementary files format and content: CTRL_TvB_Log2FC_normcounts: Normalized abundance counts between CTRL TGF-beta and BMP4 RNA-seq datasets generated

source_name: H9 HESC

growth_protocol: A detailed description of the protocol for generating chondrogenic cells and tissues from human pluripotent stem cells has been published (PMID: 25961409).

extract_protocol:
Collagenase digestion
Samples were prepared using HiSeq Illumina RNA library preparation

value: H9 HESC

value: chondrocytes


title: (AT)34 chr6

description: Library name: 2441

value: MAT ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3-1, tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1 CDC9-FRB::KanMX ,AT-34-HPH cassette at Chr6int2 Locus


title: CREB5 Mid DOX-treated in-vitro TGF-beta treated sample 3

description:
Library name: DV59-12wT-midDOX
CREB5_normalized_counts.txt

data_processing:
alignment to hg38
Salmon version 1.2.1; default parameters for hg38 alignment
RNA-seq read mapping
Salmon version 1.8.0; salmon -l A --numBootstraps 100 --gcBias –validateMappings
Read abundance normalization
DESeq2 version 1.38.0
Assembly: hg38
Supplementary files format and content: CREB5_normalized_counts.txt' file contains all normalized counts for each sample

tag: sample group


title: CREB5 Early DOX-treated in-vitro TGF-beta treated sample 3

description:
Library name: DV59-12wT-earDOX
CREB5_normalized_counts.txt


title: Mid DOX-treated in-vitro BMP4 treated sample 2

description:
Library name: DV49-12wB-midDOX
normalized_counts_BMP.txt


title: CREB5 Vehicle treated in-vitro TGF-beta treated sample 3

description:
Library name: DV59-12wT-CTRL
CREB5_normalized_counts.txt


title: CREB5 Mid DOX-treated in-vitro TGF-beta treated sample 1

description:
Library name: DV54-12wT-midDOX
CREB5_normalized_counts.txt


title: Mid DOX-treated in-vitro BMP4 treated sample 3

description:
Library name: DV53-12wB-midDOX
normalized_counts_BMP.txt


title: CREB5 Mid DOX-treated in-vitro TGF-beta treated sample 2

description:
Library name: DV58-12wT-midDOX
CREB5_normalized_counts.txt


title: CREB5 Vehicle treated in-vitro TGF-beta treated sample 2

description:
Library name: DV58-12wT-CTRL
CREB5_normalized_counts.txt


title: ligament, acl, aclfirstfive

city: San Francisco

first: Brian

middle: T

last: Feeley

state: CA

address: 1700 Owens St

department: Orthopedic Surgery

institute: University of California, San Francisco

description:
Library name: aclfirstfive
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: integrated metadata and matrix files

source_name: ligament

extract_protocol:
ACL samples were obtained during ACL reconstruction. All samples were transferred from the operating room on ice and stored in 30% FBS (fetal bovine serum, Gibco, #10437028) in Dulbecco's Modified Eagle Medium (DMEM) (Gibco, #11965084) until processing. Samples were then mechanically and enzymatically digested in 1 mg/ml collagenase III (Worthington Biochemical Corporation, #NC0021929) in DMEM with 10% FBS and 1% Penicillin/Streptomycin (Gibco, #15140122) at 37°C for 70 minutes with intermittent manual needle trituration with an 18-gauge needle. Digests were washed with PBS (Gibco, #10010023) and further digested with 0.25% trypsin-EDTA (Gibco, #25200056) at 37°C for 12–15 min. Suspensions were passed through 40 µm nylon mesh (Corning, #431750), erythrocytes were lysed with ACK lysing buffer (Quality Biological, #188-156-101) for 5–7 minutes on ice and washed in PBS with 2% FBS. Cells were then resuspended in 100 µl flow cytometry buffer (PBS with 2% FBS, 5 mM EDTA (Corning, #MT-46034CI), 2 mM HEPES (Quality Biological, #118-089-721)) per 1 gram of starting tissue weight. Cells were then frozen in 10% Dimethyl sulfoxide (DMSO, Sigma Aldrich, #276855) in FBS (fetal bovine serum, Gibco, #10437028) before flow cytometry and single cell sequencing. Cells were thawed, washed, and resuspended in flow cytometry buffer with 1:1000 SYTOX Blue (ThermoFisher, #S34857). Cells were resuspended in 0.04% BSA in PBS at 1000 cells per μl to prepare for scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: ligament

tag: location

value: anterior cruciate ligament

value: All Live Cells


title: CREB5 Early DOX-treated in-vitro BMP4 treated sample 2

description:
Library name: DV58-12wB-earDOX
CREB5_normalized_counts.txt


title: CREB5 Vehicle treated in-vitro BMP4 treated sample 2

description:
Library name: DV58-12wB-CTRL
CREB5_normalized_counts.txt


title: CREB5 Early DOX-treated in-vitro TGF-beta treated sample 2

description:
Library name: DV58-12wT-earDOX
CREB5_normalized_counts.txt


title: CREB5 Vehicle treated in-vitro BMP4 treated sample 3

description:
Library name: DV59-12wB-CTRL
CREB5_normalized_counts.txt


title: CREB5 Vehicle treated in-vitro TGF-beta treated sample 1

description:
Library name: DV54-12wT-CTRL
CREB5_normalized_counts.txt


title: CREB5 Early DOX-treated in-vitro BMP4 treated sample 3

description:
Library name: DV59-12wB-earDOX
CREB5_normalized_counts.txt


title: CREB5 Mid DOX-treated in-vitro BMP4 treated sample 2

description:
Library name: DV58-12wB-midDOX
CREB5_normalized_counts.txt


title: CREB5 Early DOX-treated in-vitro TGF-beta treated sample 1

description:
Library name: DV54-12wT-earDOX
CREB5_normalized_counts.txt


title: Vehicle treated in-vitro TGF-beta treated sample 3

data_processing:
alignment to hg38: Salmon version 1.2.1 (default parameters for hg38 alignment)
RNA-seq read mapping: Salmon version 1.8.0 (salmon -l A --numBootstraps 100 --gcBias –validateMappings)
Read abundance normalization : DESeq2 version 1.38.0
Assembly: hg38
Supplementary files format and content: Normalized abundance counts across BMP4-treated RNA-seq datasets generated
Supplementary files format and content: Normalized abundance counts between CTRL TGF-beta and BMP4 RNA-seq datasets generated


title: Vehicle treated in-vitro TGF-beta treated sample 2


title: CREB5 Early DOX-treated in-vitro BMP4 treated sample 1

description:
Library name: DV54-12wB-earDOX
CREB5_normalized_counts.txt


title: CREB5 Vehicle treated in-vitro BMP4 treated sample 1

description:
Library name: DV54-12wB-CTRL
CREB5_normalized_counts.txt


title: Vehicle treated in-vitro TGF-beta treated sample 1


title: Vehicle treated in-vitro BMP4 treated sample 1

value: Vehicle treated in-vitro BMP4 treated


title: Vehicle treated in-vitro BMP4 treated sample 2


status: Public on Jan 22 2026

city: Winston-Salem

first: Keith

last: Gagnon

address: 575 Patterson Ave

department: Biochemistry

institute: Wake Forest Baptist Medical Center

description: Library name: IDT synthesized fragment (asp gene, Inosine)

data_processing:
Reads were called from the POD5 files with Dorado software (v1.0.0) with settings for RNA modifications (RNA basecalling model rna004_130bps_sup@v5.2.0), and aligned to a HIV-1 genome (AF324493.2, included as NL43_AF324493.2_R2R.fasta), producing a BAM file.
modkit was used to generate a bedgraph of each modification, using a command such as: modkit pileup [location_of_BAM] --ref [loc_of_reference] -t 18 --region NL43_AF324493.2_R2R --max-depth 10000000 --bedgraph ./ --filter-threshold .7 --motif DRACH 2 --prefix m6A
Bedgraph files were filtered to remove modification calls at positions with fewer than 10 reads to reduce noise from low-call areas.
Reads unaligned to HIV-1 reference genome were removed from BAM file to reduce file size and protect PLWH data.
Assembly: NL43_AF324493.2_R2R.fasta
Supplementary files format and content: bedgraph files. Tab-seperated text files, one per modification. Columns in file are: column | name | description ------------------------------------ 1 | chrom | name of reference sequence from BAM header 2 | start position | 0-based start position 3 | end position | 0-based exclusive end position 4 | fraction modified | Number of calls passing filters that were classified as a residue with a specified base modification divided by total number of calls passing filters 5 | total calls | Number of calls passing filters, both modified and unmodified column | name | description ------------------------------------ 1 | chrom | name of reference sequence from BAM header 2 | start position | 0-based start position 3 | end position | 0-based exclusive end position  int 4 | fraction modified | Number of calls passing filters that were classified as a residue with a specified base modification divided by total number of calls passing filters float 5 | total calls | Number of calls passing filters, both modified and unmodified column  name  description  type ------------------------------------ 1  chrom  name of reference sequence from BAM header  str 2  start position  0-based start position  int 3  end position  0-based exclusive end position  int 4 fraction modified Number of calls passing filters that were classified as a residue with a specified base modification divided by total number of calls passing filters float 5 total calls Number of calls passing filters, both modified and unmodified int

organism: Human immunodeficiency virus 1

source_name: Synthesized

growth_protocol: Jurkat cells (HIV repository) were cultured in RPMI-1640 medium supplemented with 10% FBS, 1x P/S, and non-essential amino acids (NEAA).  CD4+ T cells were harvested from whole blood tubes from unidentified healthy donors or leukopaks (Red Cross Blood). Negative cell separation was conducted following the vendors protocol with EasySep Direct Human CD4+ T cell Isolation Kits or RosetteSep Human CD4+ T cell Enrichment Cocktail (Stem Cell Technologies) with Lymphoprep (Stem Cell Technologies) as density medium, respectively. Before infection, we activated T cells by adding anti-CD3 and anti-CD28 antibodies along with IL-2.

extract_protocol:
Total RNA was harvested via TRIZol (Invitrogen), using the manufacturer's protocol.
After extraction, total RNA was divided, and approximately 15-20 μg was used for poly-A selection and RNaseH ribosomal RNA depletion. For poly-A selection, the NEBNext High Input Poly(A) mRNA Isolation Module (E3370S) was used according to the manufacturer's protocol. For the RNaseH treatment, total RNA was hybridized with DNA oligonucleotides complementary to rRNA. The solution was heated to 95°C and slow cooled to 65°C to enable oligonucleotide hybridization. RNase H (McLabs, HTRH-200) was added (200 U) and the solution incubated at 65°C for 5 min to degrade rRNA. DNA was then degraded using 150 U of Turbo DNase (Invitrogen, AM2239) at 37°C for 20 min. RNA was then purified using AMPure XP beads. A polyadenylation reactions was performed using E. coli Poly(A) Polymerase (New England Biolabs, M0276L).  The final library was loaded on a PromethION RNA flow cell (FLO-PRO004RA) and sequenced on a PromethION P2 solo using MinKNOW (v. 24.06.10) with POD5 and live base-calling on.

treatment_protocol: Jurkat cells: When infecting with replicative NL4-3 and pHIVdEnv-GFP, we used a high cell density of ~2.5 x 106 cells/mL with a working concentration of HIV p24 (determined by ELISA) of 500-600 ng/mL. Cells were harvested at 45-48 h post-infection.  CD4+ T cells: Activation was confirmed 3 days post-treatment by measuring CD4+/CD69+ double-positive cell percentage by flow cytometry.  Day 0, isolate CD4+ T cells from blood and activate T cells  Day 3: test activation % and infect CD4+ T cells with WT-HIV.  Day 4: TRIUMEQ cART treatment when applicable  Day 6: harvest CD4+ T cells for TRIzol lysis as well as quantify infection rate by flow cytometry with KC57 antibody  cART treatment: To model current cART therapy, we added TRIUMEQ with the respective concentrations for each of the antiretrovirals based on reported plasma levels: ABC 140 ng/mL, 3TC 670 ng/mL, DTG 3.9 ug/mL.

value: Synthesized


title: CREB5 Mid DOX-treated in-vitro BMP4 treated sample 3

description:
Library name: DV59-12wB-midDOX
CREB5_normalized_counts.txt


title: snATAC-seq of nuclei isolated from cropreserved endosteal cells

status: Public on Jan 26 2026

city: SYDNEY

first: Peter

last: Croucher

state: NSW

address: 384 VICTORIA ST, DARLINGHURST NSW 2010

country: Australia

institute: Garvan Institute of Medical Research

description: Library name: 9w_endosteal_cryo

library_source: genomic single cell

data_processing:
Raw data were processed with Cell Ranger ATAC (v2.1.0) and analysed using Signac (v1.15.0) and Seurat. Low-quality nuclei were filtered. Data was normalised (TF-IDF), reduced (SVD), and clustered (SNN/UMAP). Gene activity scores were computed and integrated with scRNA-seq via CCA. Differential accessibility was assessed using logistic regression and enriched transcription factor binding motifs identified using FindMotifs.
Assembly: Mouse GRCm39
Supplementary files format and content: Filtered peak matrix file, Per-barcode fragment metrics file and Barcoded alignment fragment file generated from Cell Ranger ATAC
Supplementary files format and content: Seurat object saved as Rds format

source_name: Femora and tibiae

extract_protocol:
Endosteal cells were isolated from femora and tibiae of 9-week-old male C57BL/6J mice as described above. Single-cell suspensions were washed with PBS containing 1% BSA and pelleted (500 × g, 5 min, 4 °C). Cells were lysed in 100 µL custom lysis buffer (0.0075% digitonin, 0.05 mg/mL protease inhibitor [Millipore Sigma, 114298668001], 20 mM Tris-HCl [pH 7.4], 150 mM NaCl, 3 mM MgCl₂, 2% BSA) on ice for 1–2 min with gentle pipetting to facilitate lysis. Nuclei were washed with washing buffer (0.025 mg/mL protease inhibitor, 20 mM Tris-HCl [pH 7.4], 150 mM NaCl, 3 mM MgCl₂, 1% BSA) and pelleted (300 × g, 8 min, 4°C).
Single-nucleus ATAC-seq (snATAC-seq) was performed using the 10x Genomics Chromium Single Cell ATAC v2 platform, following the manufacturer’s protocol. Briefly, nuclei were counted using a LUNA counter and haemocytometer to assess concentration and nuclear integrity. Nuclei were diluted to the recommended loading concentration and transposed using the Tn5 transposase in the ATAC transposition mix. Following transposition, gel bead-in-emulsions (GEMs) were generated using the Chromium Controller, enabling barcoding of accessible chromatin fragments in individual nuclei. Post-GEM amplification and library construction were carried out according to the 10x Genomics protocol. Final libraries were quantified using Qubit and assessed for fragment distribution using the Agilent Bioanalyzer or Tapestation.

value: Femora and tibiae

tag: sample preparation

value: Tissue digested with collagenase A and dispase

tag: age

tag: Sex

value: male

tag: strain


title: Vehicle treated in-vitro BMP4 treated sample 3


description: Library name: IDT synthesized fragment (asp gene, no Mods)


title: CREB5 Mid DOX-treated in-vitro BMP4 treated sample 1

description:
Library name: DV54-12wB-midDOX
CREB5_normalized_counts.txt


title: Damha synthesized fragment (m6A)

description:
Library name: damha synthesized fragment (m6A)
Aligned against damha_reference.fasta, rather than full HIV-1 reference.


title: IDT synthesized fragments (2OMe)

description: Library name: IDT synthesized fragments (2OMe)


title: t7inVitro HIV full Psi

description: Library name: t7inVitro HIV full Psi

source_name: IVT

value: IVT


title: Damha synthesized fragment (unmodified)

description:
Library name: damha synthesized fragment (unmodified)
Aligned against damha_reference.fasta, rather than full HIV-1 reference.


title: t7inVitro HIV full m5C

description: Library name: t7inVitro HIV full m5C


title: t7inVitro HIV unmodified

description: Library name: t7inVitro HIV unmodified


title: P6S PLWH

description:
Library name: P6S PLWH
Reads bioinformatically filtered for only those aligning to HIV-1 genome. Contains no homo sapien RNA.

source_name: blood

value: blood

value: T cells


title: Jurkat HIV-GFP + 0uM STM2457

description: Library name: Jurkat HIV-GFP + 0uM STM2457

source_name: Jurkat

value: Jurkat

value: HIV-1 infection, STM2457 treatment


title: 13B P8C PLWH

description:
Library name: 13B P8C PLWH
Reads bioinformatically filtered for only those aligning to HIV-1 genome. Contains no homo sapien RNA.


title: 10D CD4+ HIV

description: Library name: 10D CD4+ HIV

value: HIV-1 infection


title: Jurkat HIV-GFP + 30uM STM2457

description: Library name: Jurkat HIV-GFP + 30uM STM2457


title: 11CI Jurkat HIV-GFP + cART

description: Library name: 11CI Jurkat HIV-GFP + cART

value: HIV-1 infection, cART treatment


title: Jurkat Combined Antisense

description: Library name: Jurkat Combined Antisense


title: 11BH Jurkat HIV-GFP (PAS Only)

description: Library name: 11BH Jurkat HIV-GFP (PAS Only)


title: t7inVitro HIV full m6A

description: Library name: t7inVitro HIV full m6A


title: 14H CD4+ HIV Virion

description: Library name: 14H CD4+ HIV Virion


title: P5S2 PLWH

description:
Library name: P5S2 PLWH
Reads bioinformatically filtered for only those aligning to HIV-1 genome. Contains no homo sapien RNA.


title: 11BH Jurkat HIV-GFP (RNaseH Only)

description: Library name: 11BH Jurkat HIV-GFP (RNaseH Only)


title: 11F Jurkat HIV-GFP + cART

description: Library name: 11F Jurkat HIV-GFP + cART


title: 11BH Jurkat HIV-GFP

description: Library name: 11BH Jurkat HIV-GFP


title: ovary, recurrent, patient23

status: Public on Jan 15 2026

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

country: South Korea

institute: Incheon National University

description: Library name: RNA_R_23

data_processing:
Low-quality adapter sequences were trimmed using TrimGalore.
The STAR 2-pass method was used to align the raw sequencing data to the human reference genome (GRCh38.p14) using the STAR aligner.
Read count was extracted using featureCounts.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-deliminated text file includes normalized counts for each sample.

source_name: Ovary

extract_protocol:
A total of 100 ng of total RNA was subjected to a sequencing library construction using the Agilent SureSelect RNA Direct kit as per the manufacturer's protocol.
The final purified product was quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854).

value: Ovary

tag: tissue type

value: recurrent ovarian cancer tissues

tag: subject id


title: ovary, recurrent, patient20

description: Library name: RNA_R_20


title: ovary, recurrent, patient21

description: Library name: RNA_R_21


title: 7E Jurkat HIV-GFP + cART

description: Library name: 7E Jurkat HIV-GFP + cART


title: ovary, recurrent, patient19

description: Library name: RNA_R_19


title: 11E Jurkat HIV-GFP

description: Library name: 11E Jurkat HIV-GFP


title: ovary, recurrent, patient22

description: Library name: RNA_R_22


title: ovary, recurrent, patient16

description: Library name: RNA_R_16


title: ovary, recurrent, patient13

description: Library name: RNA_R_13


title: ovary, recurrent, patient18

description: Library name: RNA_R_18


title: ovary, recurrent, patient15

description: Library name: RNA_R_15


title: 7C Jurkat HIV-GFP

description: Library name: 7C Jurkat HIV-GFP


title: ovary, recurrent, patient24

description: Library name: RNA_R_24


title: ovary, recurrent, patient14

description: Library name: RNA_R_14


title: ovary, recurrent, patient7

description: Library name: RNA_R_07


title: ovary, recurrent, patient17

description: Library name: RNA_R_17


title: ovary, recurrent, patient8

description: Library name: RNA_R_08


title: ovary, recurrent, patient9

description: Library name: RNA_R_09


title: ovary, recurrent, patient11

description: Library name: RNA_R_11


title: ovary, recurrent, patient6

description: Library name: RNA_R_06


title: ovary, recurrent, patient10

description: Library name: RNA_R_10


title: ovary, recurrent, patient4

description: Library name: RNA_R_04


title: ovary, recurrent, patient12

description: Library name: RNA_R_12


title: ovary, recurrent, patient2

description: Library name: RNA_R_02


title: ovary, recurrent, patient5

description: Library name: RNA_R_05


title: ovary, primary, patient22

description: Library name: RNA_P_22

value: primary ovarian cancer tissues


title: ovary, primary, patient18

description: Library name: RNA_P_18


title: ovary, primary, patient24

description: Library name: RNA_P_24


title: ovary, recurrent, patient3

description: Library name: RNA_R_03


title: ovary, primary, patient19

description: Library name: RNA_P_19


title: ovary, primary, patient17

description: Library name: RNA_P_17


title: ovary, primary, patient23

description: Library name: RNA_P_23


title: ovary, primary, patient20

description: Library name: RNA_P_20


title: ovary, primary, patient16

description: Library name: RNA_P_16


title: ovary, primary, patient11

description: Library name: RNA_P_11


title: ovary, recurrent, patient1

description: Library name: RNA_R_01


title: ovary, primary, patient15

description: Library name: RNA_P_15


title: ovary, primary, patient14

description: Library name: RNA_P_14


title: ovary, primary, patient21

description: Library name: RNA_P_21


title: ovary, primary, patient8

description: Library name: RNA_P_08


title: ovary, primary, patient10

description: Library name: RNA_P_10


title: ovary, primary, patient13

description: Library name: RNA_P_13


title: ovary, primary, patient4

description: Library name: RNA_P_04


title: ovary, primary, patient2

description: Library name: RNA_P_02


title: ovary, primary, patient12

description: Library name: RNA_P_12


title: ovary, primary, patient3

description: Library name: RNA_P_03


title: ME_CnT_H3K27ac_replicate2

city: Cambridge

first: Somdutta

last: Dhir

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

description: Library name: Sample22

data_processing:
Fastq files from tagmentation-based duet evoC were processed through a modified version of biomodal’s duet analysis pipeline. 9nt scar sequences, AAGAGATAG and AAAAAACAA were trimmed from the 5`-ends of Reads 1 and 2. Read pairs that lacked either scar sequence were discarded. Adapters containing the full 19nt Tn5 ME sequence and 2 Uracils (ME2U) hairpin were trimmed from the 3`-ends of Reads 1 and 2. A further 9nt were trimmed from the 3`-ends of Read 1 and 2.The trimmed read pairs were then resolved using the bespoke resolution algorithm described in Füllgrabe et al. (2023). The resolved, single-end reads were aligned against a GRCm38 reference (gencode vM25) that contained additional sequences for pUC19, bacteriophage lambda and short spike-in oligonucleotides using bwa-mem2 (v2.2.1).
For Mosaic end CUT&Tag, raw fastq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to mm10 genome, and only the reads within the whitelist have been retained.
Bigwig files were created using bamCoverage with counts per milion normalisation (CPM) after extending the paired-end reads.
Assembly: mm10 and GRCm38(gencode vM25)
Supplementary files format and content: CG_quant reports , BigWigs
Library strategy: CUT&Tag

source_name: Embryonic stem cells

growth_protocol: E14TG2A mouse embryonic stem cells were cultured in serum/LIF conditions on gelatin-coated plates. Serum/LIF medium was prepared with high-glucose DMEM (Sigma, D6546-500mL) supplemented with 10% FBS (Gibco, 16141079), 1X GlutaMax-I (Gibco, 35050-038), 1X NEAA (Gibco, 11140-035), 0.1 mM β-mercaptoethanol (Sigma, M3148) and 1,000 U/mL LIF (PeproTech, murine LIF, 250-02-25UG).

extract_protocol:
Cells were harvested by Accutase dissociation and used in CUT&Tag (Kaya-Okur et al. 2020, PMID: 32913232) assays for different histone mark antibodies (H3K27ac, H3K4me1, H3K4me3, H3K27me3). Genomic DNA was extracted from cells after CUT&Tag using proteinase K digestion and Zymo DNA clean and concentrator clean-up.
Genomic DNA isolated from each CUT&Tag cell sample replicate was subjected to end repair and 6-letter-seq library construction (Fullgrabe and Gosal et al. 2023, PMIID: 36747096).

treatment_protocol: No treatment

value: Embryonic stem cells


title: ovary, primary, patient9

description: Library name: RNA_P_09


title: ovary, primary, patient5

description: Library name: RNA_P_05


title: ME_CnT_H3K27ac_replicate1

description: Library name: Sample21


title: ME_CnT_H3K27ac_replicate3

description: Library name: Sample23


title: ovary, primary, patient6

description: Library name: RNA_P_06


title: ovary, primary, patient1

description: Library name: RNA_P_01


title: ME_CnT_H3K4Me3_replicate2

description: Library name: Sample19


title: ovary, primary, patient7

description: Library name: RNA_P_07


title: ME_CnT_H3K4Me1_replicate2

description: Library name: Sample16


title: ME_CnT_H3K4Me3_replicate1

description: Library name: Sample18


title: ME_CnT_H3K4Me1_replicate1

description: Library name: Sample15


title: ME_CnT_H3K4Me1_replicate3

description: Library name: Sample17


title: ME_CnT_H3K27Me3_replicate3

description: Library name: Sample14


title: ME_CnT_H3K27Me3_replicate1

description: Library name: Sample12


title: ME_CnT_H3K4Me3_replicate3

description: Library name: Sample20


title: IP-CTL, puromycin, replicate A

status: Public on Jan 13 2026

city: Montpellier cedex 05

first: Séverine

last: Boulon

address: 141 rue de la Cardonille

country: France

institute: CNRS

description:
Library name: Sample 23
Column name in Raw_Counts_All.txt: vide_puro_A4

data_processing:
Image analysis and base calling were realized in real-time using the NovaSeq Control Software and the Real-Time Analysis 3 software respectively (Illumina, San Diego, CA, USA). Demultiplexing and FASTQ files generation were carried out using Illumina’s bcl2fastq software (v2.20.0.422). Adapter sequences were trimmed during this step.
The quality control of raw data and demultiplexed reads was assessed using respectively Illumina’s Sequencing Analysis Viewer (SAV) software and the FastQC (v0.11.9) software from the Babraham Institute.Contaminant screening was performed using FastQ Screen (v0.14.0, Babraham Institute). Quality checks for each samples was summarised using MultiQC software (v1.12).
TopHat2 software (v2.1.1) was used to align the obtained reads on the human genome (hg38 version) and to annotate them according to NBCI database. FeatureCounts (v2.0.3) software was then used to obtain read counts per gene.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

growth_protocol: HCT116 cells were maintained in McCoy media supplemented with 10% fetal bovine serum (FBS) and antibiotics in humified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA extraction was performed using Qiagen Rneasy kit after immunoprecipitation of RUVBL1/RPAP3 using GFP-Trap or agarose control beads by Chromotek.
RNA libraries were prepared with SMART-seq Stranded kit from Takara Bio according to manufacturer's protocols.

treatment_protocol: Inhibition of translation was induced by 30 minutes of puromycin at 100µg/mL. Inhibition of RUVBL1/2 ATPase activity was induced by 16 hours of CB-6644 at 0,5µM.

value: RPAP3 GFP-knock-in

tag: rna selection

value: immmunoprecipitated mRNA using uncoupled beads

value: puromycin


title: IP-CTL, puromycin, replicate B

description:
Library name: Sample 24
Column name in Raw_Counts_All.txt: vide_puro_B4


title: IP-CTL, untreated, replicate A

description:
Library name: Sample 21
Column name in Raw_Counts_All.txt: vide_un_A3

value: untreated


title: IP-GFP, puromycin, replicate A

description:
Library name: Sample 19
Column name in Raw_Counts_All.txt: gfp_puro_A2

value: immmunoprecipitated mRNA using beads coupled to anti-GFP


title: IP-CTL, untreated, replicate B

description:
Library name: Sample 22
Column name in Raw_Counts_All.txt: vide_un_B3


title: IP-GFP, puromycin, replicate B

description:
Library name: Sample 20
Column name in Raw_Counts_All.txt: gfp_puro_B2


title: IP-GFP, untreated, replicate B

description:
Library name: Sample 18
Column name in Raw_Counts_All.txt: gfp_un_B1


title: IP-CTL, puromycin+CB-6644, replicate 1

description:
Library name: Sample 15
Column name in Raw_Counts_All.txt: vide_CB-6644_puro_1

value: RUVBL1 GFP-knock-in


title: IP-CTL, puromycin+CB-6644, replicate 2

description:
Library name: Sample 16
Column name in Raw_Counts_All.txt: vide_CB-6644_puro_2


title: ME_CnT_H3K27Me3_replicate2

description: Library name: Sample13


title: IP-CTL, CB-6644, replicate 2

description:
Library name: Sample 12
Column name in Raw_Counts_All.txt: vide_CB-6644_2


title: IP-GFP, CB-6644, replicate 2

description:
Library name: Sample 10
Column name in Raw_Counts_All.txt: GFP_CB-6644_2


title: IP-CTL, puromycin, replicate 1

description:
Library name: Sample 7
Column name in Raw_Counts_All.txt: vide_Puro_1


title: IP-CTL, untreated, replicate 1

description:
Library name: Sample 5
Column name in Raw_Counts_All.txt: vide_untreated_1


title: IP-GFP, puromycin, replicate 1

description:
Library name: Sample 3
Column name in Raw_Counts_All.txt: GFP_Puro_1


title: IP-GFP, untreated, replicate 2

description:
Library name: Sample 2
Column name in Raw_Counts_All.txt: GFP_untreated_2


title: IP-GFP, CB-6644, replicate 1

description:
Library name: Sample 9
Column name in Raw_Counts_All.txt: GFP_CB-6644_1


title: IP-CTL, CB-6644, replicate 1

description:
Library name: Sample 11
Column name in Raw_Counts_All.txt: vide_CB-6644_1


title: IP-CTL, puromycin, replicate 2

description:
Library name: Sample 8
Column name in Raw_Counts_All.txt: vide_Puro_2


title: IP-GFP, puromycin, replicate 2

description:
Library name: Sample 4
Column name in Raw_Counts_All.txt: GFP_Puro_2


title: IP-GFP, puromycin+CB-6644, replicate 1

description:
Library name: Sample 13
Column name in Raw_Counts_All.txt: GFP_CB-6644_puro_1


title: LHS019354678_2

type: genomic

city: Memphis

first: Zhaoming

last: Wang

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description:
207558990021_R07C01
blood from survivor of childhood cancer and control

hyb_protocol: Bisulfite-converted DNA was processed by following the Illumina Infinium Methylation Assay protocol for hybridization to MethylationEPIC BeadChips.

scan_protocol: Scanning used the Illumina HiScan system followed the Illumina Infinium Methylation Assay protocol.

data_processing: Genome-wide DNAm data were generated using Illumina Infinium MethylationEPIC BeadChip v1 (Illumina, San Diego, CA, USA), with DNA extracted from peripheral blood mononuclear cells (PBMCs) or saliva. Preprocessing was conducted using the minfi package in R, following established quality control procedures including a detection p-value ≤ 0.01. CpGs were excluded if they were located on sex chromosomes, contained single nucleotide polymorphisms (SNPs), or were previously identified as cross-reactive or non-specific. Quantile normalization was applied at the probe level to ensure comparability across samples.

label: Cy5 and Cy3

source_name: genomic DNA derived from blood samples from survivor of childhood cancer and community control

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA (250 ng per sample) were treated with bisulfite using the Zymo EZ DNA Methylation Kit under the following thermos-cycling conditions: 16 cycles: 95 degrees Celsius for 30 sec, 50 degrees Celsius for 1 hour. Following bisulfite treatment, DNA samples were desulphonated, column purified, then eluted using 12 µl of elution buffer (Zymo Research Corp.). Treating DNA with sodium bisulfite selectively converts cytosine to uracil but preserves 5-methylcytosine, which is immune from deamination.

value: peripheral blood mononuclear cells

tag: source

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Hodgkin lymphoma

tag: average dose to whole heart, cgy

tag: anthracyclines_dose_5, mg/m²

tag: race group

value: White


title: IP-GFP, untreated, replicate A

description:
Library name: Sample 17
Column name in Raw_Counts_All.txt: gfp_un_A1

tag: cell line

tag: genotype

tag: treatment


title: IP-GFP, untreated, replicate 1

description:
Library name: Sample 1
Column name in Raw_Counts_All.txt: GFP_untreated_1


title: IP-GFP, puromycin+CB-6644, replicate 2

description:
Library name: Sample 14
Column name in Raw_Counts_All.txt: GFP_CB-6644_puro_2


title: LHS0745563869_2

description:
207558990021_R06C01
blood from survivor of childhood cancer and control

tag: tissue

value: blood

value: Black


title: IP-CTL, untreated, replicate 2

description:
Library name: Sample 6
Column name in Raw_Counts_All.txt: vide_untreated_2


title: LHS019326929_3

description:
207558990011_R08C01
blood from survivor of childhood cancer and control

tag: age

value: male


title: LHS0568443971_3

description:
207558990021_R02C01
blood from survivor of childhood cancer and control

tag: Sex


title: LHS0428892405_3

description:
207558990021_R04C01
blood from survivor of childhood cancer and control


title: LHS0449762497_3

description:
207558990021_R03C01
blood from survivor of childhood cancer and control


title: LHS0420182600_3

description:
207558990011_R07C01
blood from survivor of childhood cancer and control


title: LHS019258698_5

description:
207558990011_R06C01
blood from survivor of childhood cancer and control


title: LHS019359183_5

description:
207558990021_R01C01
blood from survivor of childhood cancer and control


title: LHS0420452089_2

description:
207558990011_R05C01
blood from survivor of childhood cancer and control


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description:
207558990011_R03C01
blood from survivor of childhood cancer and control


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description:
207558990021_R05C01
blood from survivor of childhood cancer and control


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description:
207558990011_R02C01
blood from survivor of childhood cancer and control


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description:
207558990011_R01C01
blood from survivor of childhood cancer and control

value: control


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description:
207534240179_R06C01
blood from survivor of childhood cancer and control


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description:
207534240179_R07C01
blood from survivor of childhood cancer and control


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description:
207534240179_R08C01
blood from survivor of childhood cancer and control


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description:
207558990011_R04C01
blood from survivor of childhood cancer and control


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description:
207534240163_R06C01
blood from survivor of childhood cancer and control


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description:
207534240163_R05C01
blood from survivor of childhood cancer and control


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description:
207534240163_R08C01
blood from survivor of childhood cancer and control


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description:
207534240179_R04C01
blood from survivor of childhood cancer and control


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description:
207534240179_R03C01
blood from survivor of childhood cancer and control


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description:
207534240163_R04C01
blood from survivor of childhood cancer and control


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description:
207534240179_R01C01
blood from survivor of childhood cancer and control


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description:
207534240163_R03C01
blood from survivor of childhood cancer and control


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description:
207534240163_R01C01
blood from survivor of childhood cancer and control


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description:
207534240163_R02C01
blood from survivor of childhood cancer and control


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description:
207534240163_R07C01
blood from survivor of childhood cancer and control


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description:
207534240143_R06C01
blood from survivor of childhood cancer and control


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description:
207534240179_R02C01
blood from survivor of childhood cancer and control


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description:
207534240143_R05C01
blood from survivor of childhood cancer and control


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description:
207534240179_R05C01
blood from survivor of childhood cancer and control


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description:
207534240143_R07C01
blood from survivor of childhood cancer and control


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description:
207534240143_R01C01
blood from survivor of childhood cancer and control


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description:
207534240143_R08C01
blood from survivor of childhood cancer and control


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description:
207534240143_R02C01
blood from survivor of childhood cancer and control


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description:
207534240138_R06C01
blood from survivor of childhood cancer and control

tag: age at death


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description:
207534240143_R03C01
blood from survivor of childhood cancer and control


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description:
207534240138_R07C01
blood from survivor of childhood cancer and control


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description:
207534240138_R04C01
blood from survivor of childhood cancer and control


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description:
207534240138_R03C01
blood from survivor of childhood cancer and control


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description:
207534240138_R01C01
blood from survivor of childhood cancer and control


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description:
207534240129_R08C01
blood from survivor of childhood cancer and control

value: Other


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description:
207534240138_R02C01
blood from survivor of childhood cancer and control


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description:
207534240138_R08C01
blood from survivor of childhood cancer and control


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description:
207534240129_R04C01
blood from survivor of childhood cancer and control


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description:
207534240129_R03C01
blood from survivor of childhood cancer and control


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description:
207534240129_R02C01
blood from survivor of childhood cancer and control


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description:
207534240129_R05C01
blood from survivor of childhood cancer and control


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description:
207534240129_R07C01
blood from survivor of childhood cancer and control


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description:
207534240143_R04C01
blood from survivor of childhood cancer and control


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description:
207534240138_R05C01
blood from survivor of childhood cancer and control


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description:
207534240128_R07C01
blood from survivor of childhood cancer and control


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description:
207534240129_R06C01
blood from survivor of childhood cancer and control


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description:
207534240128_R08C01
blood from survivor of childhood cancer and control


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description:
207534240128_R04C01
blood from survivor of childhood cancer and control


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description:
207534240128_R03C01
blood from survivor of childhood cancer and control


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description:
207534240128_R05C01
blood from survivor of childhood cancer and control


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description:
207534240128_R01C01
blood from survivor of childhood cancer and control


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description:
207534240128_R02C01
blood from survivor of childhood cancer and control


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description:
207534240127_R07C01
blood from survivor of childhood cancer and control


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description:
207534240127_R08C01
blood from survivor of childhood cancer and control


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description:
207534240127_R06C01
blood from survivor of childhood cancer and control


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description:
207534240127_R03C01
blood from survivor of childhood cancer and control


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description:
207534240129_R01C01
blood from survivor of childhood cancer and control


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description:
207534240128_R06C01
blood from survivor of childhood cancer and control


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description:
207534240094_R04C01
blood from survivor of childhood cancer and control


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description:
207534240127_R01C01
blood from survivor of childhood cancer and control


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description:
207534240094_R06C01
blood from survivor of childhood cancer and control


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description:
207534240094_R05C01
blood from survivor of childhood cancer and control


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description:
207261500130_R07C01
blood from survivor of childhood cancer and control


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description:
207534240094_R01C01
blood from survivor of childhood cancer and control


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description:
207261500130_R08C01
blood from survivor of childhood cancer and control


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description:
207534240127_R05C01
blood from survivor of childhood cancer and control


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description:
207261500130_R05C01
blood from survivor of childhood cancer and control


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description:
207534240094_R03C01
blood from survivor of childhood cancer and control


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description:
207534240127_R04C01
blood from survivor of childhood cancer and control


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description:
207534240127_R02C01
blood from survivor of childhood cancer and control


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description:
207534240094_R07C01
blood from survivor of childhood cancer and control


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description:
207261500130_R01C01
blood from survivor of childhood cancer and control

value: Wilms tumor


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description:
207261500130_R04C01
blood from survivor of childhood cancer and control

value: Soft tissue sarcoma


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description:
207261500130_R03C01
blood from survivor of childhood cancer and control

value: Rhabdomyosarcoma


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description:
207179240142_R07C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


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description:
207179240142_R06C01
blood from survivor of childhood cancer and control


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description:
207179240142_R04C01
blood from survivor of childhood cancer and control


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description:
207261500130_R06C01
blood from survivor of childhood cancer and control


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description:
207179240142_R05C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)


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description:
207534240094_R08C01
blood from survivor of childhood cancer and control


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description:
207179240142_R08C01
blood from survivor of childhood cancer and control


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description:
207261500130_R02C01
blood from survivor of childhood cancer and control


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description:
207534240094_R02C01
blood from survivor of childhood cancer and control


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description:
207179240142_R02C01
blood from survivor of childhood cancer and control

value: Osteosarcoma


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description:
207179240142_R03C01
blood from survivor of childhood cancer and control


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description:
207179240142_R01C01
blood from survivor of childhood cancer and control


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description:
207262930139_R06C01
blood from survivor of childhood cancer and control


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description:
207262930139_R07C01
blood from survivor of childhood cancer and control


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description:
207262930139_R04C01
blood from survivor of childhood cancer and control


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description:
207262930139_R03C01
blood from survivor of childhood cancer and control


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description:
207262930139_R01C01
blood from survivor of childhood cancer and control


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description:
207262930139_R05C01
blood from survivor of childhood cancer and control


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description:
207262930139_R02C01
blood from survivor of childhood cancer and control


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description:
207262930137_R08C01
blood from survivor of childhood cancer and control


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description:
207262930137_R06C01
blood from survivor of childhood cancer and control


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description:
207262930137_R07C01
blood from survivor of childhood cancer and control


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description:
207262930137_R02C01
blood from survivor of childhood cancer and control


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description:
207262930137_R05C01
blood from survivor of childhood cancer and control


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description:
207262930137_R01C01
blood from survivor of childhood cancer and control


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description:
207262930137_R03C01
blood from survivor of childhood cancer and control


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description:
207262930136_R08C01
blood from survivor of childhood cancer and control


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description:
207262930137_R04C01
blood from survivor of childhood cancer and control


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207262930136_R04C01
blood from survivor of childhood cancer and control


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description:
207262930136_R02C01
blood from survivor of childhood cancer and control


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description:
207262930136_R05C01
blood from survivor of childhood cancer and control


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description:
207262930136_R06C01
blood from survivor of childhood cancer and control


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207262930125_R07C01
blood from survivor of childhood cancer and control


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description:
207262930136_R01C01
blood from survivor of childhood cancer and control


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description:
207262930125_R05C01
blood from survivor of childhood cancer and control


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description:
207262930125_R08C01
blood from survivor of childhood cancer and control


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description:
207262930136_R03C01
blood from survivor of childhood cancer and control


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description:
207262930125_R04C01
blood from survivor of childhood cancer and control


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description:
207262930125_R06C01
blood from survivor of childhood cancer and control


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description:
207262930125_R03C01
blood from survivor of childhood cancer and control


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description:
207262930125_R02C01
blood from survivor of childhood cancer and control


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description:
207262930136_R07C01
blood from survivor of childhood cancer and control


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description:
207262930043_R04C01
blood from survivor of childhood cancer and control


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description:
207262930043_R06C01
blood from survivor of childhood cancer and control


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description:
207262930125_R01C01
blood from survivor of childhood cancer and control


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description:
207262930043_R07C01
blood from survivor of childhood cancer and control


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description:
207262930043_R05C01
blood from survivor of childhood cancer and control


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description:
207262930043_R08C01
blood from survivor of childhood cancer and control


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description:
207262930043_R03C01
blood from survivor of childhood cancer and control


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description:
207262930043_R02C01
blood from survivor of childhood cancer and control


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207262930016_R04C01
blood from survivor of childhood cancer and control


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207262930016_R06C01
blood from survivor of childhood cancer and control


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207262930016_R07C01
blood from survivor of childhood cancer and control


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207262930016_R08C01
blood from survivor of childhood cancer and control


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207262930043_R01C01
blood from survivor of childhood cancer and control


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207262930016_R02C01
blood from survivor of childhood cancer and control


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description:
207262930016_R05C01
blood from survivor of childhood cancer and control


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207262930009_R08C01
blood from survivor of childhood cancer and control


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description:
207262930016_R01C01
blood from survivor of childhood cancer and control


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description:
207262930016_R03C01
blood from survivor of childhood cancer and control


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description:
207262930009_R05C01
blood from survivor of childhood cancer and control


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description:
207262930007_R08C01
blood from survivor of childhood cancer and control


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description:
207262930009_R03C01
blood from survivor of childhood cancer and control


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description:
207262930009_R04C01
blood from survivor of childhood cancer and control


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description:
207262930009_R01C01
blood from survivor of childhood cancer and control


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description:
207262930007_R07C01
blood from survivor of childhood cancer and control


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207262930009_R02C01
blood from survivor of childhood cancer and control


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207262930009_R07C01
blood from survivor of childhood cancer and control


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description:
207262930007_R02C01
blood from survivor of childhood cancer and control


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description:
207262930007_R01C01
blood from survivor of childhood cancer and control


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description:
207262930007_R03C01
blood from survivor of childhood cancer and control


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description:
207262930009_R06C01
blood from survivor of childhood cancer and control


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207261500057_R08C01
blood from survivor of childhood cancer and control


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description:
207262930007_R04C01
blood from survivor of childhood cancer and control


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description:
207262930007_R06C01
blood from survivor of childhood cancer and control


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description:
207262930007_R05C01
blood from survivor of childhood cancer and control


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description:
207261500057_R02C01
blood from survivor of childhood cancer and control


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description:
207261500057_R07C01
blood from survivor of childhood cancer and control


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description:
207261500057_R01C01
blood from survivor of childhood cancer and control


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description:
207261500057_R04C01
blood from survivor of childhood cancer and control


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description:
207261500057_R03C01
blood from survivor of childhood cancer and control


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description:
207261500057_R05C01
blood from survivor of childhood cancer and control


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description:
207261500050_R08C01
blood from survivor of childhood cancer and control


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description:
207261500050_R06C01
blood from survivor of childhood cancer and control


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description:
207261500050_R04C01
blood from survivor of childhood cancer and control


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description:
207261500050_R02C01
blood from survivor of childhood cancer and control


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description:
207261500050_R03C01
blood from survivor of childhood cancer and control


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description:
207261500050_R01C01
blood from survivor of childhood cancer and control


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description:
207261500049_R07C01
blood from survivor of childhood cancer and control


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description:
207261500049_R05C01
blood from survivor of childhood cancer and control


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description:
207261500049_R02C01
blood from survivor of childhood cancer and control


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description:
207261500049_R08C01
blood from survivor of childhood cancer and control


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description:
207261500050_R07C01
blood from survivor of childhood cancer and control


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description:
207261500042_R06C01
blood from survivor of childhood cancer and control


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description:
207261500049_R03C01
blood from survivor of childhood cancer and control


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description:
207261500042_R08C01
blood from survivor of childhood cancer and control


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description:
207261500042_R04C01
blood from survivor of childhood cancer and control


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description:
207261500042_R05C01
blood from survivor of childhood cancer and control


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description:
207261500049_R01C01
blood from survivor of childhood cancer and control


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description:
207261500050_R05C01
blood from survivor of childhood cancer and control


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description:
207261500057_R06C01
blood from survivor of childhood cancer and control


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description:
207261500042_R03C01
blood from survivor of childhood cancer and control


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description:
207261500042_R07C01
blood from survivor of childhood cancer and control


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description:
207261500021_R06C01
blood from survivor of childhood cancer and control


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description:
207261500049_R06C01
blood from survivor of childhood cancer and control


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description:
207261500042_R02C01
blood from survivor of childhood cancer and control


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description:
207261500021_R04C01
blood from survivor of childhood cancer and control


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description:
207261500042_R01C01
blood from survivor of childhood cancer and control


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description:
207261500021_R07C01
blood from survivor of childhood cancer and control


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description:
207261500020_R08C01
blood from survivor of childhood cancer and control


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description:
207261500021_R03C01
blood from survivor of childhood cancer and control


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description:
207261500021_R05C01
blood from survivor of childhood cancer and control


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description:
207261500049_R04C01
blood from survivor of childhood cancer and control


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description:
207261500020_R07C01
blood from survivor of childhood cancer and control


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description:
207261500020_R06C01
blood from survivor of childhood cancer and control


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description:
207261500021_R02C01
blood from survivor of childhood cancer and control

value: Unknown


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description:
207261500020_R05C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells


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description:
207261500021_R01C01
blood from survivor of childhood cancer and control


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description:
207261500006_R06C01
blood from survivor of childhood cancer and control

value: female


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description:
207261500020_R04C01
blood from survivor of childhood cancer and control

value: cancer survivor


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description:
207261500006_R02C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma


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description:
207261500006_R04C01
blood from survivor of childhood cancer and control

value: White


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description:
207261500020_R01C01
blood from survivor of childhood cancer and control

value: blood


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description:
207261500006_R08C01
blood from survivor of childhood cancer and control


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description:
207261500005_R07C01
blood from survivor of childhood cancer and control


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description:
207261500006_R07C01
blood from survivor of childhood cancer and control


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description:
207261500020_R02C01
blood from survivor of childhood cancer and control


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description:
207261500020_R03C01
blood from survivor of childhood cancer and control


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description:
207261500006_R05C01
blood from survivor of childhood cancer and control


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description:
207261500005_R08C01
blood from survivor of childhood cancer and control


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description:
207261500006_R03C01
blood from survivor of childhood cancer and control


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description:
207261500005_R04C01
blood from survivor of childhood cancer and control


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description:
207261500005_R06C01
blood from survivor of childhood cancer and control


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description:
207255330073_R07C01
blood from survivor of childhood cancer and control


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description:
207261500005_R03C01
blood from survivor of childhood cancer and control


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description:
207261500006_R01C01
blood from survivor of childhood cancer and control


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description:
207261500005_R02C01
blood from survivor of childhood cancer and control


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description:
207255330073_R06C01
blood from survivor of childhood cancer and control


title: LHS0809703965

description:
207261500005_R05C01
blood from survivor of childhood cancer and control


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