title: Vegfd-OE, Injured, LST

city: Dallas

first: Sneha

last: Korlakunta

address: 6000 Harry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

description:
Library name: Vegfd-OE LST Injured
10X Genomics

data_processing:
Raw sequence files were analysed by CellRanger software (v5.0.1) with reads mapped to mouse reference mm10-2020-A.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Achilles tendon

extract_protocol:
Cells from the excised tissue were isolated based on previously described methods. Briefly, tissue was digested for 45 min in 0.3% Type 1 Collagenase and 0.4% Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37 °C under constant agitation at 120 rpm. Digestions were quenched with 10% FBS RPMI and filtered through 40μm sterile strainers. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter, and samples with >85% viability were processed for further sequencing. Single-cell 3’ library generation was performed on the 10X Genomics Chromium Controller following the manufacturers’ protocol for the v2 reagent kit (10X Genomics, Pleasanton, CA, USA). Cell suspensions were loaded onto a Chromium Single-Cell A chip along with reverse transcription (RT) master mix and single cell 3’ gel beads, aiming for 2000–6000 cells per channel. Following the generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed, and the resulting Post GEM-RT product was cleaned using DynaBeads MyOne Silane beads (Thermo Fisher Scientific, Waltham, MA, USA). The cDNA was amplified, SPRIselect (Beckman Coulter, Brea, CA, USA) cleaned, quantified, and then enzymatically fragmented and size selected using SPRIselect beads to optimize the cDNA amplicon size prior to library construction. An additional round of double-sided SPRI bead cleanup was performed after end repair and A-tailing. Another single-sided cleanup was done after adapter ligation. Indexes were added during PCR amplification and a final double-sided SPRI cleanup was performed. Libraries were quantified by Kapa qPCR for Illumina Adapters (Roche) and size was determined by Agilent tapestation D1000 tapes. Read 1 primer sequence were added to the molecules during GEM incubation. P5, P7 and sample index and read 2 primer sequence were added during library construction via end repair, A-tailing, adaptor ligation and PCR. Libraries were generated with unique sample indices (SI) for each sample. Libraries were sequenced on a HiSeq 4000, (Illumina, San Diego, CA, USA) using a HiSeq 4000 PE Cluster Kit (PN PE-410-1001) with HiSeq 4000 SBS Kit (100 cycles, PN FC- 410-1002) reagents, loaded at 200 pM following Illumina’s denaturing and dilution recommendations. The run configuration was 26 × 8 × 98 cycles for Read 1, Index and Read 2, respectively.
Library construction was performed according to the manufacturer’s instructions for scRNA (Single Cell 3’ v3 protocol, 10X Genomics).

value: Achilles tendon

value: Burn/tenotomy, injured tendon, post-tenotomy Day 7


title: unstim_2hr_R2

status: Public on Apr 23 2026

type: SRA

city: San Francisco

first: Julie

last: Zikherman

state: CA

address: 513 Parnassus Ave

department: Medicine, Rheumatology

country: USA

institute: University of California, San Francisco

description:
Library name: Unstim2hr2
NovaSeq X Plus Series (PE150)

library_source: transcriptomic

data_processing:
Raw sequencing reads were mapped to GRCm39 with the GENCODE vM36 gene annotation using STAR v2.7.11b.
Differential gene expression analysis was performed using DESeq2 v1.34.0
Assembly: GRCm39
Supplementary files format and content: CSV file of gene-level TPMs and DESeq2 results

molecule: polyA RNA

organism: Mus musculus

source_name: Lymph node

extract_protocol:
TRIzol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.

tag: tissue

value: Lymph node

tag: cell type

value: Naive B cell

tag: genotype

tag: treatment


title: solubleHEL_overnight_R3

description:
Library name: sHELon3
NovaSeq X Plus Series (PE150)


title: unstim_2hr_R1

description:
Library name: Unstim2hr1
NovaSeq X Plus Series (PE150)


title: L. japonicus WT  control conditions, shoots, biological replicate 3

city: Sevilla

first: MARCO

last: BETTI

state: Sevilla

address: C. Prof. García González 1

department: Bioquímica Vegetal y Biología Molecular

country: Spain

institute: Universidad de Sevilla

description:
Library name: WT_0mM3
column name in gene_fpkm.xls: WT_0mM3

data_processing:
Libraries were ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: Lotus japonicus Gifu V 1_3
Supplementary files format and content: excel file contains the FPKM values for all the samples

organism: Lotus japonicus

source_name: shoot

growth_protocol: plants grown in the presence of ‘Hornum’ nutrient solution (control) or ‘Hornum’ nutrient solution + 100mM NaCl (salt stress treatment)

extract_protocol:
Tissue was flash-freezed in liquid N2, ground with mortar and pestle and RNA extracted with a modified CTAB protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP.

value: shoot

value: WT

value: ‘Hornum’ nutrient solution


title: Vegfd-OE, Uninjured, LST

state: TX

description:
Library name: Vegfd-OE LST Uninjured
10X Genomics

library_source: transcriptomic single cell

value: Burn/tenotomy, contralateral uninjured tendon


title: Colonic eosinophils isolated from DSS-treated C57Bl/6 WT mice,1,D6

city: Houston

first: Yang

last: Yang

address: 6432 Fannin St, MSB 6.261

department: Department of Anesthesiology, Critical Care and Pain Medicine

institute: University of Texas Health Science Center at Houston

description: Library name: B1

data_processing:
1.Clean reads were mapped to the reference genome using [STAR / Hisat2] (v2.2.1);2.The number of reads mapped to each gene was counted using [featureCounts / HTSeq-count].3.FPKM/TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.4.Differential expression analysis was performed using the [DESeq2] R package.
Assembly: mm10 (GRCm38)
Supplementary files format and content: The processed data file is a tab-delimited text file containing raw read counts

molecule: total RNA

source_name: Primary colonic eosinophils

extract_protocol:
Total RNA was isolated using the RNA extraction kit (GenDopt) according to the manufacturer’s instructions.
RNA-seq libraries were prepared by Novogene Co., Ltd. (Beijing, China). Briefy, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The final library was obtained after adapter ligation and PCR enrichment, and sequenced on the [Illumina NovaSeq X Plus] platform.

value: Primary colonic eosinophils


title: L. japonicus WT  control conditions, shoots, biological replicate 1

description:
Library name: WT_0mM1
column name in gene_fpkm.xls: WT_0mM1


title: unstim_2hr_R3

description:
Library name: Unstim2hr3
NovaSeq X Plus Series (PE150)


title: Colonic eosinophils isolated from DSS-treated C57Bl/6 WT mice,2,D6

description: Library name: B2


title: solubleHEL_overnight_R2

description:
Library name: sHELon2
NovaSeq X Plus Series (PE150)


title: CO_MECP2-WT,R133C,R168X,R270X_Rep1,2,3_L8

city: Montreal

first: Anthony

last: Flamier

state: QC

address: 3175 chemin de la Côte-Sainte-Catherine

department: Neurosciences

country: Canada

institute: Université de Montreal

description: Library name: Split-seq, snRNAseq, Library 8

data_processing:
Raw paired-end FASTQ files were QC’d (FastQC v0.11.9) and processed with the Parse Biosciences pipeline to generate merged gene–cell count matrices. In R (4.3.2) using Seurat v5.0.1, cells with >15 000 genes, >100 000 UMIs or >15 % mitochondrial reads were removed; counts were log-normalized, 2 000 variable features selected, data scaled, PCA run retaining 30 PCs, graph-based clustering (resolution 0.30) performed, UMAP visualized, and cluster markers identified (min.pct = 0.25, logFC ≥ 0.25).
Assembly: HG38
Supplementary files format and content: snRNAseq has a count matrix file (.mtx), a cell barcode file (.csv) and a features file (.csv)

molecule: nuclear RNA

organism: Homo sapiens

extract_protocol:
Organoids were gently dounced in sucrose-based buffer with detergents and RNase inhibitors, filtered, pelleted, washed, counted, and immediately fixed using the Evercode™ Nuclei Fixation v2 kit.
Eight single-nucleus libraries were prepared with the EVERCODE™ WT v2 kit (Parse Biosciences, #ECW02135) according to the manufacturer’s split-pool protocol.

tag: cell line

value: Cerebral organoid

value: MECP2-WT, MECP2-R133C, MECP2-R168X, MECP2-R270X


title: solubleHELantiCD40_overnight_R2

description:
Library name: sHEL40on2
NovaSeq X Plus Series (PE150)


title: CO_MECP2-WT,R133C,R168X,R270X_Rep1,2,3_L7

description: Library name: Split-seq, snRNAseq, Library 7


title: solubleHELantiCD40_overnight_R3

description:
Library name: sHEL40on3
NovaSeq X Plus Series (PE150)


title: solubleHEL_overnight_R1

description:
Library name: sHELon1
NovaSeq X Plus Series (PE150)


title: solubleHELantiCD40_overnight_R1

description:
Library name: sHEL40on1
NovaSeq X Plus Series (PE150)


title: Colonic eosinophils isolated from water (control)-treated C57Bl/6 WT mice,1,D6

description: Library name: A1


title: CO_MECP2-WT,R133C,R168X,R270X_Rep1,2,3_L6

description: Library name: Split-seq, snRNAseq, Library 6


title: particulateHELT_overnight_R2

description:
Library name: pHELTon2
NovaSeq X Plus Series (PE150)


title: CO_MECP2-WT,R133C,R168X,R270X_Rep1,2,3_L4

description: Library name: Split-seq, snRNAseq, Library 4


title: CO_MECP2-WT,R133C,R168X,R270X_Rep1,2,3_L3

description: Library name: Split-seq, snRNAseq, Library 3


title: CO_MECP2-WT,R133C,R168X,R270X_Rep1,2,3_L1

description: Library name: Split-seq, snRNAseq, Library 1


title: LPS_overnight_R3

description:
Library name: LPSon3
NovaSeq X Plus Series (PE150)


title: particulateHELT_overnight_R3

description:
Library name: pHELTon3
NovaSeq X Plus Series (PE150)


title: LPS_overnight_R1

description:
Library name: LPSon1
NovaSeq X Plus Series (PE150)


title: Neural Stem, d7, MECP2-R270X, rep3

description: Library name: NSC_R270X_Rep3

data_processing:
Raw paired-end reads were QC-checked (FastQC v0.11.9/MultiQC), trimmed (Trimmomatic v0.39), aligned to GRCh38 (STAR v2.7.11a, two-pass), and gene counts generated (featureCounts v2.0.2). After filtering low-abundance genes, DESeq2 v1.40.2 was used (design ~ Genotype + Time) to identify DEGs
Assembly: hg38
Supplementary files format and content: TPM_values.csv contain the TPM value for all detected genes in all RNAseq samples.

extract_protocol:
Total RNA was extracted in biological triplicate (n = 3 per line) with the PureLink™ RNA Mini Kit (Invitrogen, #12183018A)
In total, 48 barcoded libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB, #E7760L) according to the manufacturer’s instructions.

value: Neural Stem Cells


title: Neural Stem, d7, MECP2-WT, rep2

description: Library name: NSC_WT_Rep2


title: Neural Stem, d7, MECP2-WT, rep1

description: Library name: NSC_WT_Rep1


title: GOLPH3 KO, male, liver 1

city: Lausanne

first: Giovanni

last: D'Angelo

address: Station 19

department: SV-IBI

country: Switzerland

institute: EPFL

description: Library name: avid10901

data_processing:
Reads in FASTQ format were aligned to GRCm39 with Ensembl release 115 gene annotations by using STAR v2.7.11b in 2-pass mode.
Gene-level counts were quantified by featureCounts v2.1.1 (Subread) with reverse-strand specificity
DESeq2 on R-Studio for differential gene expression analysis
Assembly: GRCm39
Supplementary files format and content: standard plain-text format file containing FPKM counts for each sample

source_name: Liver

growth_protocol: All cohorts of mice were inbred at the EPFL breeding facility, maintained in the temperature-controlled enviorenment with 12h-light/12h-dark cycle and free access to standard chow diet and water. Animals were sacrificed by cervical dislocation and necropsy was performed and the tissues were snap-frozen.

extract_protocol:
Rneasy Mini Kit (Qiagen, Germany) according to the manufacturer's protocol
A Watchmaker mRNA library prep, starting from 500 ng of RNA was performedaccording to Watchmaker mRNA Library Prep Kit, Version 2.2.1224. Resulting libraries were quantified by qubit DNA HS and profile analysis was done by TapeStation 4200 (Agilent).

treatment_protocol: Dissected liver tissue was powderized with pestle and mortar

value: Liver

tag: batch


title: GOLPH3 KO, male, liver 2

description: Library name: avid10902


title: Neural Stem, d7, MECP2-WT, rep3

description: Library name: NSC_WT_Rep3


title: GOLPH3 KO, female, liver 2

description: Library name: avid10900


title: GOLPH3 KO, female, liver 1

description: Library name: avid10899


title: Neural Stem, d7, MECP2-R270X, rep1

description: Library name: NSC_R270X_Rep1


title: Neural Stem, d7, MECP2-R270X, rep2

description: Library name: NSC_R270X_Rep2


title: Neural Stem, d7, MECP2-R168X, rep2

description: Library name: NSC_R168X_Rep2


title: WT, female, liver 1

description: Library name: avid10895


title: Neural Stem, d7, MECP2-R168X, rep1

description: Library name: NSC_R168X_Rep1


title: LPS_overnight_R2

description:
Library name: LPSon2
NovaSeq X Plus Series (PE150)


title: WT, female, liver 2

description: Library name: avid10896


title: CO_MECP2-WT,R133C,R168X,R270X_Rep1,2,3_L2

description: Library name: Split-seq, snRNAseq, Library 2


title: WT, male, liver 1

description: Library name: avid10897


title: WT, male, liver 2

description: Library name: avid10898


title: Neural Stem, d7, MECP2-R168X, rep3

description: Library name: NSC_R168X_Rep3


title: Muscle, Control, rep8

city: San Diego

first: Pura

last: Muñoz-Cánoves

address: 5510 Morehouse Dr

institute: Altos Labs

description:
Library name: Control_Sample_8
Column name in tmm_all.csv: NT_S8

data_processing:
Sequencing reads were demultiplexed using bcl2fastq (v2.20.0) and preprocessed with fastp (v0.21.0). Gene abundances were quantified using Salmon (v1.5.2). Counts were normalized using the Trimmed Mean of M values (TMM) method implemented in edgeR (v3.34.1) for downstream visualization.
Assembly: GRCh38
Supplementary files format and content: tmm_all.csv: comma separated text file with TMM counts for each sample

source_name: quadriceps

extract_protocol:
Muscle samples were immediately flash-frozen upon biopsy and stored at -80ºC. They were then transported on dry ice to the NIH, where they were uniformly processed. RNA extraction was performed using TRIzol.
Libraries were prepared either using the NeoPrep system with the TruSeq Stranded mRNA Library Prep protocol (Illumina, San Diego, CA) or with the NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs, ref. #E7490 and #E7760).

value: quadriceps

tag: disease state

value: Healthy control


title: Neural Stem, d7, MECP2-R133C, rep1

description: Library name: NSC_R133C_Rep1


title: Neural Stem, d7, MECP2-R133C, rep3

description: Library name: NSC_R133C_Rep3


title: particulateHELT_overnight_R1

description:
Library name: pHELTon1
NovaSeq X Plus Series (PE150)


title: Muscle, Control, rep7

description:
Library name: Control_Sample_7
Column name in tmm_all.csv: NT_S7


title: Muscle, Control, rep6

description:
Library name: Control_Sample_6
Column name in tmm_all.csv: NT_S6


title: Muscle, Control, rep5

description:
Library name: Control_Sample_5
Column name in tmm_all.csv: NT_S5


title: Spatial transcriptomics of Macaca fascicularis pineal gland

city: Shanghai

first: jihong

last: zheng

state: Shanghai

address: XinSongjiang Road, Songjiang District

country: China

institute: Shanghai General Hospital

description:
Library name: Mf_Pineal_Spatial
BMKMANU S3000

data_processing:
For snRNA-seq, the sequencing data were processed using Cell Ranger v7.1.0, where the raw data were aligned to the Macaca fascicularis_6.0 genome to generate a UMI count matrix. Data were quality-controlled by removing cells with UMI counts >25,000, retaining cells with between 200–7,000 detected genes. Doublets were removed using DoubletFinder, and SCTransform normalization was applied. The Seurat package was used for analysis, identifying seven distinct cell populations, which were annotated using marker genes from the NHPCA dataset. The snRNA-seq data were integrated with the NHPCA reference dataset using Canonical Correlation Analysis (CCA), and the harmonized expression matrix was visualized using UMAP.
For snATAC-seq, the data were processed with Cell Ranger ATAC v2.0.0, where the raw data were aligned to the Macaca fascicularis_6.0 reference genome to generate a fragment count matrix. Quality control steps included filtering based on TSS enrichment, fragment counts per cell (1,000–10,000), and fragment lengths (10–2,000 bp). Doublets were removed using the addDoubletScores and filterDoublets functions. Downstream analysis was performed using ArchR, including dimensionality reduction with Iterative LSI and clustering using the Louvain algorithm. The data were integrated with snRNA-seq data, and five major cell types were identified and annotated.
Spatial transcriptomic data were aligned to the Macaca fascicularis_6.0 genome using BSTMatrix (v2.4). Gene expression matrices were generated using aggregation-based superspot strategies, with Level-5 resolution (25 μm diameter) selected for optimal transcript detection sensitivity.
Assembly: Macaca fascicularis_6.0
Supplementary files format and content: Mf_Pineal_snRNA_barcodes.tsv.gz: A tab-delimited file containing the spatial barcodes corresponding to individual cells or nuclei.
Supplementary files format and content: Mf_Pineal_snRNA_features.tsv.gz: A tab-delimited file listing gene IDs (features) that were measured during the experiment.
Supplementary files format and content: Mf_Pineal_snRNA_matrix.mtx.gz: A Matrix Market Exchange Format (MTX) file containing gene expression count data. Rows represent genes, and columns represent cells or nuclei, with values indicating the UMI counts.
Supplementary files format and content: Mf_Pineal_snATAC_rep1_barcodes.tsv: A tab-delimited file containing spatial barcode information for each nucleus or spot.
Supplementary files format and content: Mf_Pineal_snATAC_rep1_peaks.bed: A BED file describing the genomic regions accessible in the sampled nuclei (based on ATAC-seq data).
Supplementary files format and content: Mf_Pineal_snATAC_rep1_matrix.mtx: A Matrix Market file containing gene accessibility data for the peaks identified in the peaks.bed file.
Supplementary files format and content: A CSV file containing metadata for each cell, with columns for various quality control metrics and feature counts. Key columns include barcode (cell identifier), total (total mapped reads), duplicate (duplicate reads), unmapped (unmapped fragments), mitochondrial (mitochondrial fragments), passed_filters (fragments passing quality control), and is__cell_barcode (indicates if the barcode is valid, with 1 = valid and 0 = invalid).
Supplementary files format and content: Mf_Pineal_snATAC_rep1_filtered_peak_bc_matrix.h5: A compressed HDF5 file containing the matrix of peaks versus cell barcodes, with filtered data.
Supplementary files format and content: Mf_Pineal_snATAC_rep1_fragments.tsv.gz: A compressed file containing the transposed fragments from the ATAC-seq data.
Supplementary files format and content: Mf_Pineal_snATAC_rep1_fragments.tsv.gz.tbi: A tabix index file for Mf_Pineal_snATAC_rep1_fragments.tsv.gz, allowing for efficient querying and retrieval of specific fragment data.
Supplementary files format and content: For rep2 (Mf_Pineal_snATAC_rep2), the files follow the same structure as for rep1, with different batch or experimental replicate names:  Mf_Pineal_snATAC_rep2_barcodes.tsv  Mf_Pineal_snATAC_rep2_peaks.bed  Mf_Pineal_snATAC_rep2_matrix.mtx  Mf_Pineal_snATAC_rep2_singlecell.csv  Mf_Pineal_snATAC_rep2_filtered_peak_bc_matrix.h5  Mf_Pineal_snATAC_rep2_fragments.tsv.gz  Mf_Pineal_snATAC_rep2_fragments.tsv.gz.tbi
Supplementary files format and content: Mf_Pineal_Spatial_fluorescence_HE.txt: A text file containing information about fluorescence and H&E stained tissue regions.
Supplementary files format and content: Mf_Pineal_Spatial_fluorescence.tif: A high-resolution TIFF image showing fluorescence of the tissue for spatial analysis.
Supplementary files format and content: Mf_Pineal_Spatial_HE.tif: A high-resolution TIFF image of the H&E stained tissue for anatomical context.
Supplementary files format and content: Mf_Pineal_Spatial_scalefactors_json.json: A JSON file containing scale factors used for aligning spatial coordinates between tissue images and gene expression data.
Supplementary files format and content: Mf_Pineal_Spatial_tissue_lowres_image.png: A low-resolution image of the tissue used for visualization and spatial mapping.
Supplementary files format and content: Mf_Pineal_Spatial_tissue_positions_list.csv: A CSV file mapping the spatial barcode positions to coordinates of tissue spots.
Supplementary files format and content: Mf_Pineal_Spatial_level_5_barcodes_pos.tsv.gz: A compressed tab-delimited file containing spatial barcodes and their corresponding positions on the tissue.
Supplementary files format and content: Mf_Pineal_Spatial_level_5_barcodes.tsv.gz: A compressed tab-delimited file containing a list of spatial barcodes for the dataset.
Supplementary files format and content: Mf_Pineal_Spatial_level_5_features.tsv.gz: A compressed tab-delimited file listing the genes detected in the spatial transcriptomics dataset.
Supplementary files format and content: Mf_Pineal_Spatial_level_5_matrix.mtx.gz: A Matrix Market file containing gene expression count data, formatted as a sparse matrix.
Library strategy: Spatial Transcriptomics

organism: Macaca fascicularis

source_name: Pineal gland

extract_protocol:
In this experiment, pineal gland tissue from the Crab Monkey (Macaca fascicularis) was used to construct the single-nucleus RNA-seq library. The tissue was processed to extract single nuclei, ensuring that the nuclei quality met the standards for downstream snRNA-seq analysis. The extracted nuclei were encapsulated with barcoded gel beads (GEMs) using the 10X Genomics Chromium Single Cell 3' Reagent Kit v3.1, enabling the capture and labeling of poly(A)+ RNA for downstream sequencing.
For snATAC-seq, pineal gland tissue from the Crab Monkey (Macaca fascicularis) was used as the source material. The tissue was processed to extract high-quality nuclei. Tn5 transposase was used to cleave the DNA in open chromatin regions within the nuclei, inserting sequencing adapters. The transposition products were encapsulated with ATAC reagents in GEMs on a microfluidic chip, allowing for the capture of chromatin accessibility information for subsequent analysis.
For spatial transcriptomics, pineal gland tissue from the Crab Monkey (Macaca fascicularis) was prepared using the BMKMANU Spatial Transcriptomics Gene Expression Kit. The tissue was sectioned into 10 μm slices, which were then transferred to a BMKMANU S3000 Gene Expression Slide for further processing. After fixation and H&E staining, permeabilization was performed, followed by imaging to determine the optimal conditions for library construction.
For snRNA-seq, Illumina adapters (P7 and Index sequences) were added to the transposed DNA, followed by PCR amplification to construct the library. The libraries were quantified using Qubit 4.0 to ensure that the concentration met the necessary specifications. The libraries were then sequenced on the Illumina NovaSeq 6000 platform using a PE150 sequencing strategy to ensure sufficient read depth for each nucleus.
For snATAC-seq, Illumina adapters (P7 and Index sequences) were added to the transposed DNA, followed by PCR amplification to construct the library. The libraries were quantified using Qubit 4.0 to ensure that the concentration met the necessary specifications. The libraries were then sequenced on the Illumina NovaSeq 6000 platform using a PE150 sequencing strategy to ensure sufficient read depth for each nucleus.
For spatial transcriptomics, libraries were constructed following the TruSeq Illumina library preparation method. Illumina adapters were added to the library, followed by PCR amplification. The libraries were quantified using Qubit 4.0. After ensuring the library quality, sequencing was conducted on the Illumina NovaSeq X Plus platform using the PE150 strategy, targeting at least 150,000 read pairs per spatial point.

value: Pineal gland

value: Mixed:Pinealocytes, Astrocytes, Microglia, Oligodendrocytes, Oligodendrocyte Precursor Cells (OPCs), Neurons, Endothelial cells, and Vascular Leptomeningeal Cells (VLMCs).

value: wild type

tag: age

value: 4 to 5 years

tag: Sex

value: female


title: Neural Progenitor, d21, MECP2-WT, rep2

description: Library name: NPC_WT_Rep2

value: Neural Progenitor Cells


title: Neural Stem, d7, MECP2-R133C, rep2

description: Library name: NSC_R133C_Rep2


title: Neural Progenitor, d21, MECP2-R168X, rep2

description: Library name: NPC_R168X_Rep2


title: Neural Progenitor, d21, MECP2-WT, rep1

description: Library name: NPC_WT_Rep1


title: Muscle, Control, rep2

description:
Library name: Control_Sample_2
Column name in tmm_all.csv: NT_S2


title: Neural Progenitor, d21, MECP2-R270X, rep3

description: Library name: NPC_R270X_Rep3


title: Muscle, Control, rep1

description:
Library name: Control_Sample_1
Column name in tmm_all.csv: NT_S1


title: Neural Progenitor, d21, MECP2-R133C, rep3

description: Library name: NPC_R133C_Rep3


title: Muscle, Control, rep3

description:
Library name: Control_Sample_3
Column name in tmm_all.csv: NT_S3


title: Muscle, Control, rep4

description:
Library name: Control_Sample_4
Column name in tmm_all.csv: NT_S4


title: Neural Progenitor, d21, MECP2-R270X, rep1

description: Library name: NPC_R270X_Rep1


title: CO_MECP2-WT,R133C,R168X,R270X_Rep1,2,3_L5

description: Library name: Split-seq, snRNAseq, Library 5


title: Neural Progenitor, d21, MECP2-R168X, rep3

description: Library name: NPC_R168X_Rep3


title: Neuroectoderm, d3, MECP2-WT, rep3

description: Library name: NE_WT_Rep3

value: Neuroectodermal


title: Neural Progenitor, d21, MECP2-WT, rep3

description: Library name: NPC_WT_Rep3


title: 1686, microglia, MG IFNAR KO control

city: Iowa City

first: Michael

last: Chimenti

state: Iowa

address: 431 Newton Road

institute: University of Iowa

description: Library name: 1686

data_processing:
Raw sequencing reads were processed using the 10x Genomics Cell Ranger pipeline (version 7.1.0). Reads were aligned to the mouse reference genome mm10-2020-A (GENCODE vM23/Ensembl 98) with default parameters to perform barcode processing, unique molecular identifier (UMI) counting, and generation of filtered gene-barcode expression matrices. Downstream analysis, including quality control, normalization, clustering, and visualization, was performed in R using the Seurat package
Assembly: mm10
Supplementary files format and content: filtered feature barcode matrix (cellranger output)

source_name: ipsilesional forebrain

extract_protocol:
Single-cell suspensions were prepared as described previously. Viable cells were counted and loaded at the recommended concentration into the 10x Genomics Chromium Controller using Chromium Single Cell 5′ chemistry reagents. Cells were partitioned into nanoliter-scale Gel Bead-in-Emulsions (GEMs) together with barcoded gel beads, reverse-transcription reagents, and partitioning oil. Within each GEM, cells were lysed and polyadenylated mRNA was captured by oligo(dT)-primed reverse transcription, generating barcoded full-length cDNA that incorporates a 10x cell barcode and Unique Molecular Identifier (UMI). GEMs were then broken, and the barcoded cDNA was purified and amplified by PCR (following the 10x Genomics Chromium Single Cell 5′ Reagent Kit user guide).
Amplified full-length cDNA derived from polyadenylated transcripts was used for 5′ gene expression library construction with the Chromium Single Cell 5′ Library Construction Kit (10x Genomics). The cDNA was enzymatically fragmented and size-selected, followed by end-repair, A-tailing, adaptor ligation, and sample-index PCR to add P5/P7 Illumina sequences and dual indexes. Final libraries were quantified (e.g., by qPCR or fluorometry) and size-selected prior to sequencing. All steps were performed according to the manufacturer’s protocol for Chromium Single Cell 5′ chemistry (v2, GEM-X, or the specific reagent kit version used in your experiment).

value: ipsilesional forebrain

value: microglia

value: MG IFNAR KO

value: control

tag: time

value: 7 days


title: Neural Progenitor, d21, MECP2-R168X, rep1

description: Library name: NPC_R168X_Rep1


title: Neural Progenitor, d21, MECP2-R270X, rep2

description: Library name: NPC_R270X_Rep2


title: Neural Progenitor, d21, MECP2-R133C, rep2

description: Library name: NPC_R133C_Rep2


title: 1684, microglia, WT control

description: Library name: 1684

value: WT


title: 1685, microglia, WT TBI, 7 days post injury

description: Library name: 1685

value: TBI

value: 7 days post-injury


title: Neuroectoderm, d3, MECP2-WT, rep2

description: Library name: NE_WT_Rep2


title: Neural Progenitor, d21, MECP2-R133C, rep1

description: Library name: NPC_R133C_Rep1


title: 1681, microglia, MG IFNAR KO TBI, 7 days post injury

description: Library name: 1681


title: 1690, microglia, WT control

description: Library name: 1690


title: 1689, microglia, MG IFNAR KO TBI, 7 days post injury

description: Library name: 1689


title: 1673, microglia, WT control

description: Library name: 1673


title: Neuroectoderm, d3, MECP2-R270X, rep3

description: Library name: NE_R270X_Rep3


title: 1683, microglia, MG IFNAR KO control

description: Library name: 1683


title: Neuroectoderm, d3, MECP2-R270X, rep2

description: Library name: NE_R270X_Rep2


title: 1679, microglia, WT TBI, 7 days post injury

description: Library name: 1679


title: Neuroectoderm, d3, MECP2-R168X, rep2

description: Library name: NE_R168X_Rep2


title: 1675, microglia, MG IFNAR KO control

description: Library name: 1675


title: Neuroectoderm, d3, MECP2-R168X, rep3

description: Library name: NE_R168X_Rep3


title: Neuroectoderm, d3, MECP2-WT, rep1

description: Library name: NE_WT_Rep1


title: 1664, microglia, WT TBI, 7 days post injury

description: Library name: 1664


title: H22-LR2

first: Yunkai

last: Lin

address: Qianju Road 366

department: National Center for Liver Cancer

institute: Second Military Medical University

description: Library name: Sample 5

data_processing:
Fastp software was used to remove reads that contained adapter contamination and low-quality bases with default parameters and to verify sequence quality.
HISAT2 was used to map the reads to the reference genome of Homo sapiens GRCh381. The mapped reads of each sample were assembled using StringTie.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare.
StringTie was used to determine the expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs were selected with fold change >2 or fold change <0.5 and with the parametric F test comparing nested linear models (p value <0.05) by the R package edgeR.
Assembly: gffcompare.
Supplementary files format and content: excel includes raw counts for each Sample
Supplementary files format and content: excel file includes FPKM values for each Sample

source_name: HCC tumor

growth_protocol: H22 murine hepatocellular carcinoma cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin at 37°C in a 5% CO₂ humidified incubator. For subcutaneous tumor implantation, 1×10⁶ H22 cells suspended in 100 μl PBS were injected into the right flank of 6-week-old male C57BL/6 mice. Tumor volumes were monitored using a caliper and calculated as (length × width²)/2.

extract_protocol:
Total RNA of tumor tissue was isolated after the intervention using TRIzol reagent (Invitrogen).
RNA libraries for RNA-seq were prepared using VAHTS Universal V6RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer's protocols.

treatment_protocol: For establishment of the lenvatinib-resistant model, mice bearing H22 tumors were treated with lenvatinib (100 mg/kg/day, i.p.) twice a week. This cycle was repeated twice to induce acquired resistance. Lenvatinib-sensitive tumors (H22-NR) were collected from control mice receiving lenvatinib only (PBS with 0.1% DMSO). Lenvatinib-resistant tumors (H22-LR) were harvested from mice that completed two cycles of lenvatinib treatment and exhibited stable resistance. Tumor tissues were immediately snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.buffer (Qiagen) for RNA extraction and further analysis.

value: HCC tumor

value: No treatment


title: Neuroectoderm, d3, MECP2-R133C, rep2

description: Library name: NE_R133C_Rep2


title: Neuroectoderm, d3, MECP2-R133C, rep3

description: Library name: NE_R133C_Rep3


title: 1667, microglia, WT TBI, 7 days post injury

description: Library name: 1667


title: H22-LR3

description: Library name: Sample 6


title: Neuroectoderm, d3, MECP2-R168X, rep1

description: Library name: NE_R168X_Rep1


title: Neuroectoderm, d3, MECP2-R133C, rep1

description: Library name: NE_R133C_Rep1


title: H22-LR1

description: Library name: Sample 4


title: H22-NR2

description: Library name: Sample 2


title: H22-NR1

description: Library name: Sample 1


title: Neuroectoderm, d3, MECP2-R270X, rep1

description: Library name: NE_R270X_Rep1


title: 1669, microglia, MG IFNAR KO TBI, 7 days post injury

description: Library name: 1669


title: hESC, d0, MECP2-WT, rep2

description: Library name: ESC_WT_Rep2

value: hESC


title: H22-NR3

description: Library name: Sample 3


title: hESC, d0, MECP2-R270X, rep3

description: Library name: ESC_R270X_Rep3


title: hESC, d0, MECP2-WT, rep3

description: Library name: ESC_WT_Rep3


title: Knockout_2

city: Guangzhou

first: Tao

last: Gui

address: Huangpu Ave

institute: Jinan University

description:
Library name: Sample 5
Bulk RNA sequencing
KO-2

data_processing:
DEGs between experimental groups were identified using the DESeq2 R package. Genes meeting the criteria of a false discovery rate (FDR) < 0.05 and an absolute |log2 fold change| ≥ 1 were deemed statistically significant. Heatmaps displaying hierarchical clustering of DEGs were generated using the Pheatmap package, while ggplot2 was employed to construct both volcano plots and KEGG pathway enrichment diagrams, offering insights into the biological processes and pathways influenced by experimental treatments.
Assembly: GRCm39
Supplementary files format and content: csv file

source_name: Bone marrow

extract_protocol:
For the isolation of mBMDMs, bone marrow cells were harvested from the femurs of 8-week-old WT mice. Red blood cells were lysed using ACK lysis buffer (Beyotime, C3702, China), and the remaining cells were centrifuged at 300 × g for 5 min. The cell pellet was resuspended in α-Minimum Essential Medium (α-MEM, Gibco, C12571500BT, USA) containing 10% heat-inactivated FBS, 1% PS, and 30 ng/mL mouse macrophage colony-stimulating factor (M-CSF, MCE, HYP70553, USA). To induce macrophage polarization, cells were treated with 100 ng/mL lipopolysaccharide (LPS, Beyotime, S1732, China) for 24 h to induce inflammatory polarization.Total RNA was isolated from CD74+/+ and CD74-/- mBMDMs pre-stimulated with LPS. RNA quality and integrity were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
High-throughput RNA sequencing libraries were prepared and sequenced on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA), enabling the acquisition of high-resolution transcriptomic datasets.

value: Bone marrow

value: BMDMs

value: KO

value: LPS


title: hESC, d0, MECP2-WT, rep1

description: Library name: ESC_WT_Rep1


title: Knockout_3

description:
Library name: Sample 6
Bulk RNA sequencing
KO-3


title: hESC, d0, MECP2-R270X, rep1

description: Library name: ESC_R270X_Rep1


title: Control_3

description:
Library name: Sample 3
Bulk RNA sequencing
NC-3

value: Con


title: hESC, d0, MECP2-R168X, rep3

description: Library name: ESC_R168X_Rep3


title: hESC, d0, MECP2-R168X, rep1

description: Library name: ESC_R168X_Rep1


title: hESC, d0, MECP2-R270X, rep2

description: Library name: ESC_R270X_Rep2


title: Input for K27me3, K4me3

city: Hong Kong

last: Fu

address: Prince of Wales Hospital, N.T, H.K, 32 Ngan Shing St, Sha Tin

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
Library name: Input for K27me3, K4me3
Input for K27me3, K4me3

library_source: genomic

data_processing:
ATAC-Seq and ChIP-Seq reads were trimmed using Trim Galore (v0.6.10) (https://github.com/FelixKrueger/TrimGalore) and aligned to the mm10 genome using BWA (v0.7.17-r1188).56 Reads with a mapping quality <30 and duplicate reads were removed using SAMtools (v1.5)57 and Sambamba (v1.0.0).58 To improve peak-calling accuracy, blacklisted regions (ENCODE mm10 v2)59 were removed using BEDTools.60 Tn5 offsets were corrected for ATAC-Seq data using alignmentSieve (deepTools v3.5.5).61 Peaks calling was performed using MACS2 (v2.2.6).62 To calculate the average signal intensity over target regions, only replicate 1 of epigenomic data was used. The BAM files were converted to BigWig format using BamCoverage (v3.5.5)61 with RPGC normalization. Subsequently, input-subtracted BigWig files were generated using bigwigCompare (v3.5.5)63 to account for background signal. Next, bigWigAverageOverBed (v2)64 was employed to calculate the average intensity over bases, treating non-covered bases as zeroes in each target. Spearman’s correlation was calculated between the average intensity of each target and its corresponding average TIF across replicates for all targets. Correlations of average intensity with other variables were performed similarly.
Assembly: Not applicable.
Supplementary files format and content: Excel files showing bw and peaks.
Supplementary files format and content: Table S3. SIQ outcomes for single-sgRNA sites.xlsx is the indel profiles for GSM9129596 to GSM9129681.
Supplementary files format and content: Table S5. SIQ outcomes for dual-sgRNA sites is the indel profiles for GSM9129682 to GSM9129779.
Supplementary files format and content: Table S8. SIQ outcomes for AAV dose groups is the indel profiles for GSM9129780 to GSM9129797.
Supplementary files format and content: Table S9. SIQ outcomes for in vivo perturbation is the indel profiles for GSM9129798 to GSM9129853.

molecule: genomic DNA

source_name: skeletal muscle

extract_protocol:
MuSCs were isolated by fluorescence-activated cell sorting (FACS) based on established protocols.49 Briefly, hindlimb muscles from Pax7Cas9 mice were collected and digested with collagenase II (1000 U/ml; Worthington) for 90 minutes at 37°C. The tissue suspension was then washed in washing medium [Ham’s F-10 medium (Sigma-Aldrich), 10% heat-inactivated horse serum (HIHS) (Gibco), penicillin/streptomycin (1×, Gibco)]. MuSCs were further liberated by collagenase II (1000 U/ml) and dispase (11 U/ml) treatment for 40 minutes at 37°C. Mononuclear cells were filtered through a 40 μm cell strainer, and GFP+ MuSCs were sorted using a BD FACSAria Fusion cell sorter (BD Biosciences).
ATAC-seq was performed using the Hyperactive ATAC-Seq Library Prep Kit (Vazyme, TD711-01) according to the manufacturer's standard protocol and sequenced on an Illumina NovaSeq X platform (150 bp paired-end reads). ChIP-seq was performed as previously described.33,34 Briefly, about 5× 105 cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature and quenched with 125 mM glycine. Cells were washed, pelleted by centrifugation (700 g, 5 minutes, 4°C), flash-frozen in liquid nitrogen, and stored at −80°C. The cell pellet was resuspended in 130 μL of shearing buffer [10 mM Tris-HCl (pH 8.0), 0.1% SDS, 1 mM EDTA, and 1× protease inhibitor cocktail (PIC)] and sonicated using a Covaris S220 (140 W intensity, 5% duty cycle, 200 cycles per burst, 7 minutes). The lysate was adjusted to a final concentration of 150 mM NaCl and 1% Triton X-100, then clarified by centrifugation (20,000 g, 20 minutes, 4°C). To reduce non-specific binding, the supernatant was pre-cleared by incubation with pre-washed Dynabeads Protein G (Invitrogen, 10004D) for 2 hours at 4°C. A 1/50 volume of the cleared lysate was reserved as Input control. The remaining lysate was incubated overnight at 4°C with 0.75 μg of the appropriate antibody. The following day, 10 μL of pre-washed Dynabeads Protein G was added to each reaction in IP buffer [10 mM Tris-HCl (pH 8.0), 150 mM NaCl, 0.1% SDS, 1 mM EDTA, 1% Triton X-100, and 1× PIC] and incubated for an additional 2 hours at 4°C. Beads were washed sequentially: twice with IP buffer, twice with high-salt wash buffer [10 mM Tris-HCl (pH 8.0), 500 mM NaCl, 0.1% SDS, 1 mM EDTA, 1% Triton X-100], twice with LiCl wash buffer [10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate], and once with cold TE buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 50 mM NaCl]. Immunocomplexes were eluted in ChIP elution buffer [50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS] at 65°C for 30 minutes, and cross-links were reversed by incubation at 65°C for 16 hours. For the Input sample, three volumes of ChIP elution buffer were added, and samples were processed in parallel with the IP samples. DNA was purified following treatment with RNase A (0.2 mg/mL, 37°C, 2 hours) and Proteinase K (0.2 mg/mL, 55°C, 3 hours) via phenol:chloroform extraction and ethanol precipitation, then resuspended in 1× TE buffer. ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit (NEB, E7645S) and sequenced on an Illumina NovaSeq X platform (150 bp paired-end reads). The following antibodies were used: H3K4me3 (Cell Signaling Technology, #9751), H3K27ac (Cell Signaling Technology, #8173), and H3K27me3 (Cell Signaling Technology, #9733).

value: skeletal muscle


title: Control_2

description:
Library name: Sample 2
Bulk RNA sequencing
NC-2


title: hESC, d0, MECP2-R133C, rep2

description: Library name: ESC_R133C_Rep2


title: Control_1

description:
Library name: Sample 1
Bulk RNA sequencing
NC-1


title: H3K27ac rep2

description:
Library name: H3K27ac rep2
H3K27ac rep2


title: Knockout_1

description:
Library name: Sample 4
Bulk RNA sequencing
KO-1


title: Input for K27ac

description:
Library name: Input for K27ac
Input for K27ac


title: H3K27ac rep1

description:
Library name: H3K27ac rep1
H3K27ac rep1


title: hESC, d0, MECP2-R133C, rep1

description: Library name: ESC_R133C_Rep1


title: H3K27me3 rep1

description:
Library name: H3K27me3 rep1
H3K27me3 rep1


title: hESC, d0, MECP2-R168X, rep2

description: Library name: ESC_R168X_Rep2


title: H3K4me3 rep2

description:
Library name: H3K4me3 rep2
H3K4me3 rep2


title: H3K4me3 rep1

description:
Library name: H3K4me3 rep1
H3K4me3 rep1


title: hESC, d0, MECP2-R133C, rep3

description: Library name: ESC_R133C_Rep3


title: hESC, d0, MECP2-WT, MECP2-R133C, MECP2-R168X, MECP2-R270X, L1

description: Library name: Library 1

data_processing:
Raw paired-end FASTQ files were QC’d (FastQC v0.11.9) and processed with the Parse Biosciences pipeline to generate merged gene–cell count matrices. In R (4.3.2) using Seurat v5.0.1, cells with >15 000 genes, >100 000 UMIs or >15 % mitochondrial reads were removed; counts were log-normalized, 2 000 variable features selected, data scaled, PCA run retaining 30 PCs, graph-based clustering (resolution 0.30) performed, UMAP visualized, and cluster markers identified (min.pct = 0.25, logFC ≥ 0.25).
Assembly: HG38
Supplementary files format and content: scRNAseq has a count matrix file (.mtx), a cell barcode file (.csv) and a features file (.csv)

extract_protocol:
Human ESCs (WT, R133C, R168X and R270X) were harvested at the pluripotent stage, dissociated with Gentle Cell Dissociation (Stem Cell Technologies) and resuspended in ice-cold PBS + 0.04 % BSA.
Two single-cell libraries were constructed from the four fixed samples using the EVERCODE™ WT Mini v2 Kit (Parse Biosciences, #ECW02115).


title: hESC, d0, MECP2-WT, MECP2-R133C, MECP2-R168X, MECP2-R270X, L2

description: Library name: Library 2


title: ATAC-Seq rep2

description:
Library name: ATAC-Seq rep2
ATAC-Seq rep2


title: H3K27me3 rep2

description:
Library name: H3K27me3 rep2
H3K27me3 rep2


title: Patient n.36 whole blood DNA after exercise

type: genomic

city: Divinopolis

first: Camila

middle: Fernanda Cunha

last: Brandao

state: Minas Gerais

address: Av. Paraná, 3001 - Jardim Belvedere I

department: Center for Chronic Non-Communicable Diseases of the Central-West Region of Minas Gerais

country: Brazil

institute: State University of Minas Gerais, Divinópolis, Brazil

description: whole peripheral blood DNA from women with obesity

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to the human Infinium MethylationEPIC BeadChip (Illumina)

scan_protocol: Arrays were imaged using the BeadArray Reader (iScan) according to the standard recommended Illumina scanner settings.

data_processing: Champ package

label: Cy3 and Cy5

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA from whole blood extraction was performed using an automated extractor with the Maxwell kit (Promega, WI, EUA)

treatment_protocol: Combined Physical Exercise

value: female

value: obesity

value: Blood

value: combined exercise

value: After

tag: bmi

tag: weight

tag: wc

tag: fm

tag: ffm

tag: rfm

tag: rmr

tag: qr

tag: cho

tag: lip

tag: tmao

tag: tel


title: Patient n.37 whole blood DNA before exercise

tag: tissue

tag: treatment

value: Before


title: Patient n.30 whole blood DNA after exercise

tag: disease state

tag: age


title: Patient n.34  whole blood DNA after exercise

tag: Sex


title: Patient n.37 whole blood DNA after exercise

tag: bmi


title: Patient n.36 whole blood DNA before exercise

tag: weight


title: Patient n.30 whole blood DNA before exercise

tag: wc


title: B6 HP tumor organoid cells

city: Durham

first: Wei

state: NC

address: 303 Research Drive

department: Anesthesiology

institute: Duke University Medical Center

description:
Library name: B6-HP_Tumor_Organoid
cultured organoid cells

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using Cell Rnager v10.0.0
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab seperated values files and matrix files

source_name: breast tumor-derived organoid

growth_protocol: B6-HP tumor organoids were seeded the day prior to processing and dissociated with TrypLE the following day. Live and dead cells were assessed using Trypan blue staining. Cells were resuspended in PBS containing 0.04% BSA, with a viability of 82%. The sample was centrifuged pg. 18 at 400 × g for 5 minutes at 4 °C and resuspended to a final concentration of 4,900 cells/µL in a total volume of approximately 90 µL.

extract_protocol:
B6-HP tumor organoids were s dissociated using TrypLE. Cell viability was assessed using Trypan blue staining. Cells were then resuspended in PBS containing 0.04% BSA, with a viability of 82%. The cell suspension was centrifuged at 400 × g for 5 minutes at 4 °C and resuspended to a final concentration of 4,900 cells/µL in a total volume of approximately 90 µL.
Utilizing the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead kit v.3.3 and Chromium instrument, cells were partitioned into nanoliter droplets to achieve single-cell resolution for a maximum of 10,000–15,000 individual cells per sample (10x Genomics). The resulting cDNA was tagged with a common 16-nt cell barcode and 10-nt unique molecular identifier (UMI) during the reverse transcriptase (RT) reaction. Full-length cDNA from poly-A mRNA transcripts was enzymatically fragmented and size selected to optimize the cDNA amplicon size for library construction (10x Genomics). The concentration of the 10x single-cell library was accurately determined through qPCR to produce cluster counts appropriate for the NovaSeq-6000 platform (Illumina). The sequence data were generated targeting 50,000 read pairs per cell, which provided digital gene expression profiles for each individual cell.

value: breast tumor-derived organoid

tag: cell line

value: B6-HP Tumor Organoid

tag: cell type

value: mouse tumor organoid cell

tag: genotype

value: HP

value: NO treatment


title: ATAC-Seq rep1

description:
Library name: ATAC-Seq rep1
ATAC-Seq rep1


title: ccRCC tumor, Lenvatinib/Pembrolizumab treated, sc58

city: New York

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: sc58T
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger software
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: single cell barcodes
Supplementary files format and content: features.tsv.gz: gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format

source_name: Primary Tumor

extract_protocol:
Tumors were coarsely minced using a scalpel and enzymatically dissociated using the human tumor dissociation kit (Miltenyi) for 25mins at 37c using the Octo-dissociator (Miltenyi). Digested cells were neutralized in DMEM + 10% FBS and successively washed in PBS and strained through 100um, 70μm and 45μm cell strainers with an RBC lysis step in between (Ack lysis buffer; Gibco). Single cell suspensions were stained with DAPI (BD Pharmingen) and calcein AM (Invitrogen) and FACS sorted for live single cells. Cells were counted using a hemocytometer and up to 10,000 cells were loaded into the Chromium Controller (10x genomics).
Cells were processed using the Next GEM 5’ mRNA V2 kit (10x genomics) with strict adherence to manufacturer’s protocols. Gene expression libraries were sequenced at a target depth of 200 million reads per sample.

treatment_protocol: Advanced ccRCC tumors surgically resected following various tyrosine kinase inhibitor (TKI) or immune checkpoint blockade (ICB) therapy combinations.

value: Primary Tumor

tag: histopathology

value: rhabdoid (+focal sarcomatoid) ccRCC

tag: pre-surgery treatment

value: Lenvatinib/Pembrolizumab

tag: pathological response

value: PR

tag: age at_time_of_surgery

value: F


title: Patient n.28 whole blood DNA after exercise

tag: fm

tag: ffm

tag: rfm

tag: rmr

tag: qr

tag: cho

tag: lip

tag: tmao


title: Patient n.28 whole blood DNA before exercise

tag: Sex

tag: disease state

tag: tissue

tag: treatment

tag: age

tag: bmi

tag: weight

tag: tel


title: Patient n.29 whole blood DNA after exercise

tag: wc


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc60

description:
Library name: sc60T
10x Genomics

tag: histopathology

tag: pre-surgery treatment

value: Ipilimumab/Nivolumab

tag: pathological response

value: CR

tag: age at_time_of_surgery

value: M


title: E0771 tumor uPAR KO host replicate 4

first: Shafaat

last: Ahmed Rabbani

state: Quebec

address: 1001 Decarie Blvd

department: Department of Medicine

institute: McGill University Health Center - Glen Site

description: Library name: KO_4

data_processing:
Reads were processed and analyzed using DESeq2 (v1.30.1) in R (v4.0.4).
Quality control included PCA, sample-to-sample distance heatmaps, MA plots, and p-value distribution analysis.
Assembly: GRCm39
Supplementary files format and content: Processed RNA-seq data include a gene-level raw count matrix and differential expression results generated using DESeq2. Raw sequencing files (FASTQ) are unavailable due to third-party analysis and data retention limits at the sequencing facility. Processed RNA-seq data include a raw count matrix (Raw_counts.numbers) and differential expression results (cases_vs_controls_results.csv) and also normalized counts file (Normalized counts.numbers.

source_name: breast tumor

growth_protocol: Orthotopic mammary fat pad implantation of E0771 cells in wild-type or uPAR knockout mice.

extract_protocol:
Total RNA was extracted from tumor tissue using column-based kit following manufacturer instructions.
RNA-seq libraries were prepared using poly(A) selection and sequenced on an Illumina platform.

value: breast tumor

tag: cell line

tag: host

value: mouse

tag: host genotype

value: uPAR knockout


title: Patient n.29 whole blood DNA before exercise

value: female

value: obesity

value: Blood

value: combined exercise

value: Before

tag: fm

tag: ffm

tag: rfm

tag: rmr

tag: qr

tag: cho

tag: lip

tag: tmao


title: Patient n.25 whole blood DNA after exercise

tag: Sex

tag: disease state

tag: tissue

tag: treatment

value: After

tag: age

tag: bmi

tag: weight

tag: tel


title: Patient n.34  whole blood DNA before exercise

tag: wc


title: dorsal PFC nuclei, DMS-projecting, male

city: Iowa

first: Nandakumar

last: Narayanan

state: IA

address: 169 Newton Road

department: Neurology

description:
Library name: dDMS_M
10x Chromium universal 3’ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (90nt) contains transcript

data_processing:
Raw sequencing reads were processed into count matrices using Cell Ranger (10x Genomics; version 7.2.0) and using the mm10-2020-A mouse assembly.
Ambient RNA was removed from the Cell Ranger counts matrices using CellBender (version 0.2.0)
Assembly: 10X genomics mm10-2020-A mouse assembly
Supplementary files format and content: Cell Ranger output files: *filtered_feature_bc_matrix.h5
Supplementary files format and content: CellBender output files *Bent.h5

source_name: prefrontal cortex

extract_protocol:
H2B-TRAP mice aged 3-4 months received bilateral stereotaxic injections of AAVrg-hSyn-Cre into either the DMS or MD. After 2 weeks of recovery, mice were sacrificed between 9:00 am – 12:00 pm by rapid decapitation immediately after removal from the home cage. Brains were extracted and chilled in DMEM/F12 media slush (Thermo Fisher Scientific). Brains were then placed ventral side up in a chilled stainless steel brain matrix (Stoelting, Wood Dale, IL) and 1 mm coronal sections of the PFC were collected. Tissue from the PFC was placed in chilled RNAprotect solution (QIAGEN, Aarhus, Denmark) and then microdissected under a fluorescent stereoscope. During dissections tissue was pooled according to projection target (DMS or MD) and PFC subregion (dorsal or ventral), with male and female samples pooled separately. All pooled samples were incubated overnight at 4°C in RNAprotect® before being removed and stored dry at -80°C.
Each sample underwent nuclear dissociation and purification procedures before being incubated with NucBlue (Thermo fisher scientific). After incubation, nuclei were flow sorted together into RT Reagent B (10x Genomics) using a  Cytek Aurora CS cell sorter with a 70 μm nozzle to remove poor quality nuclei and count the number of nuclei per sample. Sorted nuclei were immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol. Single Cell 3’ v3.1 chemistry was used to process all samples. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). Gene expression libraries were multiplexed and sequenced on a NovaSeq 6000 (Illumina) sequencer using a 100-cycle kit with  the following read structure: Read 1 = 28 cycles followed by Read 2 = 90 cycles.

treatment_protocol: No Treatment

value: prefrontal cortex

tag: genotype

value: AAVrg-Cre, DMS

value: male


title: dorsal MD nuclei, MD-projecting, female

description:
Library name: dMD_F
10x Chromium universal 3’ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (90nt) contains transcript

value: AAVrg-Cre, MD


title: dorsal MD nuclei, MD-projecting, male

description:
Library name: dMD_M
10x Chromium universal 3’ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (90nt) contains transcript


title: ventral MD nuclei, MD-projecting, female

description:
Library name: vMD_F
10x Chromium universal 3’ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (90nt) contains transcript


title: ventral PFC nuclei, DMS-projecting, male

description:
Library name: vDMS_M
10x Chromium universal 3’ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (90nt) contains transcript


title: ventral MD nuclei, MD-projecting, male

description:
Library name: vMD_M
10x Chromium universal 3’ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (90nt) contains transcript


title: HP-F1 +cre breast tumor organoid transplanted cerebellum tumor slide

description:
Library name: Replicate1
FFPE slide

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline version 2.1.1 to generate FASTQ files
Sequences were aligned to mm10 genome to generate gene expression count using Space Ranger's default setting
Assembly: mm10-2020-A
Supplementary files format and content: tab seperated files and matrix files
Supplementary files format and content: aligned fudicials of the tissue image
Supplementary files format and content: image of tissue and spots
Supplementary files format and content: scalefactors in json format
Supplementary files format and content: hi-res image of tissue
Supplementary files format and content: low-res image of tissue
Supplementary files format and content: list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: mouse cerebellum tissue

extract_protocol:
Tumor tissues were fixed with 10% formalin, embedded in paraffin, and cut into 5-µm  sections. For H&E, slides were stained with hematoxylin, rinsed, and then counterstained with eosin, before being mounted and imaged. Tissue prepared for sectioning and staining starts with RNA quality assessment. RNA quality assessment of FFPE tissue blocks (RNA extraction and QC) need meets the DV200 Quality Score = >30% to proceed with assay using Agilent BioAnalyzer or TapeStation Instruments.
Approved slides thickness at 5 μm sections compatible with the Visium CytAssist. 20x resolution imaging on Zeiss Axio Scan 7 Brightfield / Fluorescence Slide Scanner was used for downstream Space Ranger Analysis. Sample/Slide was prepared with decrosslinking and library Construction on 6.5mmx 6.5mm capture area. Visium CytAssist Spatial Gene Expression kit was used for FFPE (Mouse Transcriptome, 6.5 mm, 4 rxns, PN-1000521,10x Genomics). The probe processes include probe hybridization/Wash, probe ligation/Wash, RNA digestion and tissue removal, probe extension and elution, preamplification and cleanup and Index PCR. CytAssist Brightfield images generated for downstream Space Ranger Analysis. For sequencing information, 100M total read pairs was targeted for each sample on the Illumina NovaSeqX Plus instrument (NovaSeq X Plus 10B at 300 cycle, 10M targeted 2x150 Clusters).

value: mouse cerebellum tissue

tag: cell line

value: B6-HP Tumor Organoid injected cerebellum

tag: cell type

value: mouse brain

value: HP

value: NO treatment


title: ventral PFC nuclei, DMS-projecting, female

description:
Library name: vDMS_F
10x Chromium universal 3’ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (90nt) contains transcript


title: dorsal PFC nuclei, DMS-projecting, female

description:
Library name: dDMS_F
10x Chromium universal 3’ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (90nt) contains transcript


title: Patient n.25 whole blood DNA before exercise

tag: fm

tag: ffm

tag: rfm

tag: rmr


title: HP-B6 +cre breast tumor organoid transplanted cerebellum tumor slide

description:
Library name: Replicate2
FFPE slide


title: E0771 tumor uPAR KO host replicate 3

description: Library name: KO_3

value: breast tumor

tag: host

value: mouse

tag: host genotype


title: Patient n.20 whole blood DNA after exercise

tag: Sex

value: female

tag: disease state

tag: qr

tag: cho

tag: lip

tag: tmao


title: Patient n.20 whole blood DNA before exercise

value: obesity

tag: tissue

tag: treatment

tag: age

tag: bmi

tag: weight

tag: tel


title: E0771 tumor WT host replicate 3

description: Library name: WT_3

tag: cell line

value: wild-type


title: Patient n.16 whole blood DNA after exercise

value: Blood

value: combined exercise

tag: wc

tag: fm

tag: ffm

tag: rfm


title: E0771 tumor uPAR KO host replicate 2

description: Library name: KO_2

tag: host

tag: host genotype

value: uPAR knockout


title: Patient n.16 whole blood DNA before exercise

tag: Sex

tag: disease state

value: Before

tag: rmr

tag: qr


title: E0771 tumor WT host replicate 2

description: Library name: WT_2

tag: tissue


title: Patient n.15 whole blood DNA after exercise

tag: treatment

value: After

tag: cho

tag: lip

tag: tmao


title: Patient n.15 whole blood DNA before exercise

tag: age

tag: bmi

tag: weight

tag: tel


title: E0771 tumor WT host replicate 1

description: Library name: WT_1

tag: cell line


title: Patient n.13 whole blood DNA after exercise

tag: wc

tag: fm

tag: ffm

tag: rfm


title: m7314

city: Indianapolis

first: Afrin

last: Chowdhury

address: Walter hall

institute: Indiana University School of Medicine

description:
Library name: Sample 11
Bex_3

data_processing:
FeatureCounts software v1.5.0-p3 was used for quantification
Read counts are filtered from raw data: (1)Remove reads with adaptor contamination. (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
STAR software v2.6.1d was used to map reads to the reference genome
read counts are normalized to fpkm
PCA analysis was used for analysis of outliers
Assembly: limma and IPA were used for differential expression analysis between treatment groups
Supplementary files format and content: counts and fpkm

source_name: Mammary tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the polyA enrichment procedure.

value: Mammary tumor

tag: genotype

value: MMTV-neu

value: Bexarotene


title: m7285

description:
Library name: Sample 10
Bex_2


title: Patient n.13 whole blood DNA before exercise

tag: Sex

tag: disease state

tag: rmr


title: m7339

description:
Library name: Sample 12
Bex_4

tag: tissue

tag: treatment


title: m7278

description:
Library name: Sample 9
Bex_1


title: Patient n.1 whole blood DNA before exercise

tag: qr

tag: cho

tag: lip


title: Patient n.11 whole blood DNA after exercise

tag: age

tag: bmi

tag: tmao


title: 20-1922 non-granuloma

city: Sendai

first: Koji

last: Murakami

address: 1-1, Seiryo-machi. Aoba-ku

department: Respiratory Medicine

country: Japan

institute: Tohoku University Graduate School of Medicine

description:
Library name: 20-1922-N
Laser-microdissected adjacent non-granuloma region from FFPE lung tissue of pulmonary sarcoidosis

data_processing:
Raw sequencing reads were quality-checked and preprocessed prior to downstream analysis. Adapter sequences and low-quality bases were removed using Trimmomatic; bases with quality scores lower than 3 at read ends were trimmed, sliding-window trimming was performed with a window size of 4 and a required mean quality of 15, and reads shorter than 36 bp were discarded. Trimmed reads were aligned to the human reference genome (GRCh38) using HISAT2. Transcript assembly and expression quantification were performed using StringTie, and gene/transcript abundance was calculated as read counts, FPKM, and TPM. Differential expression analysis comparing granuloma and adjacent non-granuloma regions was performed using DESeq after Relative Log Expression (RLE) normalization.
Assembly: GRCh38
Supplementary files format and content: Processed data files include gene-level expression tables containing read counts, FPKM values, TPM values, and differential expression statistics for granuloma and adjacent non-granuloma regions.

source_name: lung

extract_protocol:
FFPE lung tissue sections were prepared from pulmonary sarcoidosis specimens and mounted on membrane slides. For histologic identification of target regions, the sections were stained using RNase-free H&E staining. Granuloma and adjacent non-granuloma regions were then isolated by PALM laser microdissection and collected into 1.5-mL tubes. Total RNA was extracted from the microdissected FFPE tissue using the RNeasy FFPE Kit (Qiagen). RNA was eluted in 20 μL of RNase-free water.
RNA-seq libraries were prepared from RNA extracted from laser-microdissected FFPE lung tissue using the TruSeq RNA Access Library Prep Kit (Illumina) according to the manufacturer’s instructions. Libraries were sequenced as 101-bp paired-end reads on an Illumina platform.

value: lung

tag: cell type

value: laser-microdissected adjacent non-granuloma tissue

tag: batch


title: 20-1922 granuloma

description:
Library name: 20-1922-G
Laser-microdissected granuloma region from FFPE lung tissue of pulmonary sarcoidosis

value: laser-microdissected granuloma tissue


title: E0771 tumor uPAR KO host replicate 1

description: Library name: KO_1

tag: cell line

tag: host

tag: host genotype


title: 14-3010 non-granuloma

description:
Library name: 14-3010-N
Laser-microdissected adjacent non-granuloma region from FFPE lung tissue of pulmonary sarcoidosis


title: m7296

description:
Library name: Sample 8
v125_4

tag: genotype


title: m7323

description:
Library name: Sample 4
Ctrl_4

value: Control


title: E0771 tumor WT host replicate 4

description: Library name: WT_4

value: breast tumor


title: m7280

description:
Library name: Sample 6
V125_2


title: m7295

description:
Library name: Sample 7
V125_3


title: Patient n.11 whole blood DNA before exercise

tag: Sex

tag: weight

tag: wc

tag: fm

tag: ffm

tag: rfm

tag: tel


title: 14-3010 granuloma

description:
Library name: 14-3010-G
Laser-microdissected granuloma region from FFPE lung tissue of pulmonary sarcoidosis

tag: tissue

tag: treatment


title: m7277

description:
Library name: Sample 5
V125_1


title: Patient n.1 whole blood DNA after exercise

tag: disease state

tag: age

tag: bmi

tag: rmr

tag: qr

tag: cho

tag: lip


title: 14-1549 non-granuloma

description:
Library name: 14-1549-N
Laser-microdissected adjacent non-granuloma region from FFPE lung tissue of pulmonary sarcoidosis

tag: cell type

tag: batch


title: m7288

description:
Library name: Sample 3
Ctrl_3

tag: genotype


title: 14-1549 granuloma

description:
Library name: 14-1549-G
Laser-microdissected granuloma region from FFPE lung tissue of pulmonary sarcoidosis


title: m7284

description:
Library name: Sample 2
Ctrl_2


title: 12-1780 non-granuloma

description:
Library name: 12-1780-N
Laser-microdissected adjacent non-granuloma region from FFPE lung tissue of pulmonary sarcoidosis


title: m7283

description:
Library name: Sample 1
Ctrl_1


title: 12-1780 granuloma

description:
Library name: 12-1780-G
Laser-microdissected granuloma region from FFPE lung tissue of pulmonary sarcoidosis


title: 11-881 non-granuloma

description:
Library name: 11-881-N
Laser-microdissected adjacent non-granuloma region from FFPE lung tissue of pulmonary sarcoidosis obtained during corticosteroid treatment

value: Corticosteroid


title: Aged normal 4

city: Obu

first: Naoki

last: Ito

state: Aichi

address: 7-430, Morioka-cho

department: Geroscience Research Center

institute: National Center for Geriatrics and Gerontology

description: Library name: Sample 11

data_processing:
The transcriptome sequencing was performed on an llumina Novaseq 6000 and 150 bp paired-end reads were generated.
The sequenced reads were aligned to the mouse reference genome (GRCm39 / mm39) using DRAGEN.
TPM normalized gene expression were calculated using DRAGEN.
Assembly: GRCm39
Supplementary files format and content: csv files include TPM values for each Sample

source_name: Skeletal muscle

extract_protocol:
RNA from isolated myofibers was purified by TRIzol. After DNase digestion, RNA was purified by NucleoSpin® RNA Clean-up XS (TAKARA). Ten ng of total RNA was used for the construction of sequencing.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input NRA kit following manufacturer's protocols

value: Skeletal muscle

value: myofibers

value: Aged

tag: tissue type

value: normal


title: Aged abnormal 3

description: Library name: Sample 10

value: abnormal


title: Aged abnormal 4

description: Library name: Sample 12


title: 11-7090 granuloma

description:
Library name: 11-7090-G
Laser-microdissected granuloma region from FFPE lung tissue of pulmonary sarcoidosis obtained during corticosteroid treatment


title: 10-1078 non-granuloma

description:
Library name: 10-1078-N
Laser-microdissected adjacent non-granuloma region from FFPE lung tissue of pulmonary sarcoidosis obtained during corticosteroid treatment


title: 11-881 granuloma

description:
Library name: 11-881-G
Laser-microdissected granuloma region from FFPE lung tissue of pulmonary sarcoidosis obtained during corticosteroid treatment


title: Aged normal 3

description: Library name: Sample 9


title: 10-1078 granuloma

description:
Library name: 10-1078-G
Laser-microdissected granuloma region from FFPE lung tissue of pulmonary sarcoidosis obtained during corticosteroid treatment


title: Aged abnormal 1

description: Library name: Sample 6


title: 11-7090 non-granuloma

description:
Library name: 11-7090-N
Laser-microdissected adjacent non-granuloma region from FFPE lung tissue of pulmonary sarcoidosis obtained during corticosteroid treatment


title: Aged normal 2

description: Library name: Sample 7


title: Aged abnormal 2

description: Library name: Sample 8


title: H1299_ribo_sgM5_R2

city: nanjing

first: Zhou

last: Jun

state: jiangsu

address: longmiandadao

department: College of life science and technology

institute: China Pharmaceutical University

description: Library name: Sample 16

library_source: other

data_processing:
For paired-end sequencing data, only read 2 from the raw FASTQ files was used for subsequent analyses. Adapter sequences and low-quality bases were trimmed from ribosome-protected fragment (RPF) samples using Cutadapt (v2.8) with the following parameters: -a AGATCGGAAGAGCGT -u 10 -q 20 -e 0.1 -O 6 -m 25 -M 35 --discard-untrimmed. For the corresponding input samples, the minimum fragment length parameter was set to -m 20, without applying an upper fragment length limit (-M). To remove rRNA and tRNA contamination, reads were aligned to human rRNA and tRNA reference sequences using Bowtie2 (v2.2.5), and unmapped reads were retained as clean reads. These clean reads were then aligned to the human reference genome (GRCh38) using HISAT2 (v2.2.1) with the -k 1 parameter. Gene-level read counts were quantified using featureCounts (v2.0.1) with the -t exon parameter, based on the GRCh38.106 GTF annotation file from the Ensembl database. The protein-coding genes were retained for downstream analysis. To correct for batch effects across different datasets, the ComBat_seq function from the R package sva (v3.58.0) was applied to the count matrix. The batch-corrected count data were then used for differential translation efficiency (TE) analysis. TE differences were calculated using Riborex (v2.4.0) with the edgeR (v4.8.0) engine. Genes with an absolute fold change ≥ 1.5 and a p-value < 0.05 were considered significantly regulated at the translational level. Downstream quality control of Ribo-seq data was performed using the riboTransVis (v0.99.0) R package, focusing on the 5’end of reads.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values (CSV) file with gene counts
Library strategy: Ribo-Seq

molecule: other

growth_protocol: A549 and H1299 lung cancer cells were cultured in DMEM (BI, Cat#06-1055-57-1ACS) and RPMI 1640(BI, Cat#01-100-1ACS) 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: A549 with H1299 lung cancer cells are treated with fresh complete medium for 2 h

tag: cell line

value: Non-Small Cell Lung Cancer

value: METTL5 knockout

value: treated with CHX for 5min,normal culture


title: H1299_rna_sgCtrl_R1

description: Library name: Sample 19

value: WT


title: Young 2

description: Library name: Sample 2

value: Young


title: Young 4

description: Library name: Sample 4


title: Aged normal 1

description: Library name: Sample 5


title: Young 1

description: Library name: Sample 1


title: A549_rna_sgCtrl_R1

description: Library name: Sample 7


title: Young 3

description: Library name: Sample 3


title: A549_rna_sgM5_R2

description: Library name: Sample 10


title: UEIS KI

city: Harbin

first: Xingwen

last: Wang

state: Heilongjiang

address: Xidazhi

institute: HIT

description: Library name: LC_3_CD45

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: Mouse mm10
Supplementary files format and content: Each sample includes three processed files generated by 10x Genomics Cell Ranger: a count matrix (matrix.mtx.gz), feature information (features.tsv.gz), and cell barcodes (barcodes.tsv.gz).
Supplementary files format and content: matrix.mtx.gz: Gene-cell count matrix in Matrix Market Exchange format (sparse format), generated by Cell Ranger v2.1.1.
Supplementary files format and content: features.tsv.gz: Tab-separated file containing gene or feature identifiers and annotations.
Supplementary files format and content: barcodes.tsv.gz: Tab-separated file listing cell barcodes corresponding to each column in the matrix.

source_name: Subcutaneous tumour tissue

growth_protocol: MC38 cells were implanted into C57BL/6 mice to form tumors.

extract_protocol:
The MC38 tumour tissue grown in UEISLSL and UEISKI mice were dissected and digested into single-cell suspension with 0.1 mg/ml DNAase I, and 0.6 mg/ml Collagenase II at 37 °C for 30 min. The cells were filtered through a sterile 70 µm cell strainer to remove red blood cells.
Library preparation was performed following the manufacturer's instructions (Single Cell 3' v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded with partitioning oil and gel beads into the microfluidic chip to generate gel bead-in-emulsions (GEMs). Within each GEM, poly-A RNA from lysed cells was reverse-transcribed into cDNA containing an Illumina R1 primer, a Unique Molecular Identifier (UMI), and a 10x barcode. The barcoded cDNA was then purified using Silane DynaBeads, amplified by PCR, and size-selected with SPRIselect reagent. During library construction, Illumina R2 primer sequences, paired-end adapters (P5 and P7), and sample indices were added.

value: Subcutaneous tumour tissue

value: Tumour-infiltrating immune cells


title: UEIS LSL

description: Library name: LC_2_CD45


title: A549_ribo_sgM5_R2

description: Library name: Sample 4

value: lung


title: Muscle, visium, 7d post-overloading, D1

description:
Library name: STExp2_D1_7dOVL_Plant_Young
10X Genomics

data_processing:
scRNA-seq and snRNA-seq data were processed using cellranger (v7.1.0) mapped to GRCm39 genome.
Visium spatial data were processed using 10X Genomics Space Ranger (v.2.0.0) mapped to Mm10-2020-A genome.
Human bulk RNA-seq data was processed using the nfcore pipeline: reads were trimmed using Trimgalore (v.0.6.10), and quantified using Salmon (v.1.10.3) with GRCh38 genome.
Assembly: GRCm39 for single-cell and single-nuclei. Mm10-2020-A for spatial transcriptomics. GRCh38 for human bulk RNA-seq.
Supplementary files format and content: CellRanger output files
Supplementary files format and content: tab-delimited text files with raw counts and TPM for each sample: human_gene_raw_counts.tsv, human_gene_tpm.tsv
Supplementary files format and content: Space Ranger output files
Library strategy: Spatial Transcriptomics

source_name: plantaris muscle

extract_protocol:
scRNA-seq: Plantaris muscles were manually minced and dissociated in digestion media containing Dulbecco's Modified Eagle's medium (DMEM), liberase (0.1 mg/g muscle weight) (Roche, #5401020001; 5 mg/ml), and dispase 0.3% (Sigma-Aldrich, #D4693-1G) at 37°C for 1.5 h in a shaker incubator. The muscle homogenate was filtered, pelleted, and frozen in freezing media containing FBS (Gibco, # 26-170-043) with 10% DMSO (Sigma, C6164-50ML) for storage at -80 °C. For FACS-sorting, cells were thawed in a water bath and resuspended in PBS with 1% goat serum (FACS buffer). PE-Cy7-conjugated anti-CD45 (1/200, Biolegend, 103114) and anti-Sca-1 (1/200, Biolegend, 108114) were used for lineage-negative selection, and BV605-conjugated anti-CD31 (1/200, Biolegend, 102418) was used for positive staining of ECs. Cells were pelleted and then incubated with the corresponding Cell Multiplexing Oligos (CMOs)(10x Genomics) for 5 min at RT. Cells were then washed, pelleted, and resuspended in 0.05% UltraPure BSA (ThermoFisher, #AM2616) diluted in calcium- and magnesium-free PBS. Cells from all conditions were pooled together, sorted using a FACS Aria II (BD) sorte,r and collected in 0.05 % UltraPure BSA. ECs were selected based on CD31+ staining, while from the CD31- fraction, Sca1-/ CD45- cells were selected (Lin-) to enrich for MuSCs and SCs. Cell concentration was determined using an automatic cell counter (BioRad T20 Cell Counter) and the concentration was adjusted if needed to meet the optimal range for loading on the 10X Chromium chip. The nuclei were loaded into the 10X Chromium system using the Single Cell 3’ Reagent Kit v3.1 (dual index) following the manufacturer’s protocol. Following library construction, libraries were sequenced on the Illumina NextSeq system.
snRNA-seq: Plantaris muscles were isolated from mice immediately following euthanasia and snap-frozen in liquid nitrogen for storage at -80 °C. The Chromium Nuclei Isolation Kit was used following the manufacturer’s protocol with slight optimizations that were found to be most effective for skeletal muscle tissue. In brief, two plantaris muscles were mechanically disrupted with a pestle in Lysis Buffer. Tissue homogenate was then transferred to a Nuclei Isolation Column and centrifuged (16,000 g for 20 seconds at 4°C). The column was then discarded, and flowthrough transferred to a 1.5 ml LoBind Eppendorf. Nuclei suspension was centrifuged at 700 g for 5 minutes at 4°C before adding Debris Removal Buffer and 700 g for 10 minutes at 4 ºC after incubation. Nuclei were then resuspended in Wash Buffer followed by a final centrifugation step (700 g for 5 minutes at 4°C). Then, nuclei were resuspended in 70 μl when using two plantaris muscles as starting material. Nuclei concentration was determined using an automatic cell counter (BioRad T20 Cell Counter) and the concentration was adjusted if needed to meet the optimal range for loading on the 10X Chromium chip. DAPI was added to a small aliquot of the nuclei that were quality-controlled with a fluorescent microscope to ensure that they were intact, had rounded borders, the majority occurring as singlets, and that there was no residual debris. The nuclei were loaded into the 10X Chromium system using the Single Cell 3’ Reagent Kit v3 following the manufacturer’s protocol. We aimed to load ~15,000 nuclei for each run.
Spatial transcriptomics: sagittal cryo-sections of the plantaris muscle were directly collected onto a Visium slide (10x Genomics PN-1000193), ensuring each section was within the 8x8 µm fiducial frame. The Visium slide was fixed in 100% methanol at -20°C for 30 minutes, followed by Hematoxylin staining for 6 minutes (Sigma-Aldrich MH16-500ML) and Eosin staining for 1 minute (Sigma-Aldrich HT110216-500ML). The slide was then mounted with 30% glycerol and a cover slip. For each section, a white-field H&E image with a fiducial frame was captured using a Leica SP8 system.
human bulk RNA-seq: Human muscle biopsies from 3 patients with disrupted innervation and 3 patients subjected to pre- and post-exercise training were analyzed by bulk RNA-seq
scRNA-seq: Library was performed according to the manufacturer's instructions (Single Cell 3’ Reagent Kit v3.1 (dual index), 10X Genomics).
snRNA-seq: Library was performed according to the manufacturer's instructions (Single Cell 3’ Reagent Kit v3, 10X Genomics).
Spatial transcriptomics: Library was performed accordiing to the manufacturer's instructions (Visium Spatial Gene Expression Slides and Reagent kit, PN-1000193, 10X Genomics).
human bulk RNA-seq: Library was performed according to the manufacturer's instructions (SMART-Seq® mRNA LP)

value: plantaris muscle

value: 7d post-overloading


title: hADSC CCN treatment - 3

city: Suwon

first: Hyun Su

last: Park

address: 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do

country: South Korea

institute: Sungkyunkwan University

description: Library name: C3

data_processing:
Raw sequencing data were quality-checked using FastQC and processed with Fastp for adapter trimming and removal of low-quality reads. Trimmed reads were aligned to the reference genome using STAR, and transcript quantification was performed using Salmon. Data proceesed with ExDEGA v5.1.1
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing gene-level expression values for all samples. Rows represent genes and columns represent individual samples (N1–N4, S1–S4, C1–C4).

source_name: human adipose derived mesenchymal stem cell

extract_protocol:
RNA was harvested using Trizol reagent (Life Technologies). Harvested total RNA was used for the construction of sequencing libraries.
Library was generated using the CORALL RNA-Seq V2 Library Prep Kit (Lexogen), and high-throughput sequencing was performed as paired-end 100 bp reads on a NovaSeq 6000 platform (Illumina)

value: CCN treatment


title: H1299_rna_sgM5_R2

description: Library name: Sample 22


title: hADSC CCN treatment - 4

description: Library name: C4

value: human adipose derived mesenchymal stem cell


title: H1299_ribo_sgCtrl_R1

description: Library name: Sample 13


title: A549_ribo_sgCtrl_R1

description: Library name: Sample 1


title: Muscle, visium, 7d post-overloading, C1

address: 5510 Morehouse Dr

description:
Library name: STExp2_C1_7dOVL_Plant_Young
10X Genomics


title: Muscle, visium, sham, D1

description:
Library name: STExp1_D1_SHAM_Plant_Young
10X Genomics

value: sham/basal


title: hADSC CN treatment - 3

description: Library name: S3

value: CN treatment


title: hADSC CN treatment - 4

description: Library name: S4


title: Muscle, visium, sham, C1

description:
Library name: STExp1_C1_SHAM_Plant_Young
10X Genomics


title: Muscle, visium, 7d post-denervation, A1

description:
Library name: STExp1_A1_7dDEN_Plant_Young
10X Genomics

value: 7d post-denervation


title: hADSC CCN treatment - 1

description: Library name: C1


title: hADSC no treatment - 4

description: Library name: N4

value: no treatment


title: 24289X4_GEMM_KNH_HED897_input

city: Salt lake City

first: Headtlove

last: Essel Dadzie

state: UT

address: 2000 circle of Hope

department: Oncological Sciences

institute: University of Utah

description: Library name: 24289X4

data_processing:
Fastq alignments were pre-processed with the merge_umi_fastq application from the UMIScripts package (https://github.com/HuntsmanCancerInstitute/UMIScripts) to associate the UMI sequence, provided as a third Fastq file, into the read comment.
Reads were aligned using Bowtie2 v2.2.9 to the standard chromosomes of the mouse genome (version mm10) or the human genome (version hg38).
Duplicate alignments based on the UMI code were removed using the bam_umi_dedup application (UMIScripts) allowing for 1 mismatch.
Peaks were called using MACS2 v2.2.7 with a significance of q-value <1e-8 for exogenous experiments and q-value < 0.01 for endogenous experiments.
Coverage tracks were generated with MACS2 as Reads Per Million.
Assembly: hg38 and mm10
Supplementary files format and content: bigwig, BED files (except for Input samples)

source_name: Lung tissue

growth_protocol: 3D organoid lines were cultured in 50% L-WRN conditioned media.

extract_protocol:
For all organoid ChIP-seq experiments, two 24-well plates (approximately 4 – 8 million cells) were collected in Cell Recovery Solution (500 μl per dome). Organoids were submerged in ice for 30 min before centrifugation at 4°C (300G). Cells were washed three times in cold PBS. On the second wash, PBS was supplemented with DNase solution (containing a final concentration of 200U/ml DNase [Worthington], 2.5 mM MgCl2, 500 mM CaCl2). After the third wash, organoids were resuspended in 5 ml of 2 mM DSG buffer (1X PBS, 1 mM MgCl2) and rotated at room temperature for 35 min. Formaldehyde was then added to a final concentration of 1% and cells were crosslinked for 10 min. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were washed with cold PBS, then frozen at -80. Cell pellets were thawed on ice for 5 min then lysed in 1 ml of Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40) for all TF experiments or 400 ul of Chromatrap Hypotonic buffer (catalog #100007) for all histone experiments. Samples were centrifuged at 4°C (1000G) then resuspended in 1ml of RIPA lysis buffer (1X PBS, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) or 100 μl of Chromatrap Lysis buffer (catalog #100005) for TF and histone ChIPs respectively. All lysis buffers were supplemented with protease inhibitors. Chromatin extract was sonicated with QSonica Q800R (pulse: 30 s on/30 s off; sonication time: 20 min; amplitude: 70%). After sonication, chromatin extract of histone samples was brought up to a volume of 1 ml with RIPA lysis buffer. Chromatin from all samples was immunoprecipitated with antibodies premixed with Protein A/G Dynabeadsper antibody used. For sorted nuclei from GEMMs,  At 14 weeks post-tumor initiation, KN and KNH tumor-bearing mice were euthanized. The rib cage was dissected to expose the trachea and heart, and lungs were perfused with cold PBS, snap-frozen, and minced on ice. Homogenized tissue was centrifuged (300G, 4°C, 5 min) and crosslinked in 2 mM DSG + 1% formaldehyde. After fixation, nuclei were extracted using TST buffer, dounced, and filtered through 70 μm/35 μm strainers. GFP-positive nuclei were sorted using BD FACSAria (85 μm nozzle) into PBS + 1% BSA + protease inhibitors.For ChIP-seq, nuclei (10M for TF ChIP-seq) were pelleted (500G, 4°C, 10 min), lysed, and sonicated (QSonica Q800R, 30s on/off, 20 min, 70%). Chromatin was immunoprecipitated with antibodies premixed with Protein A/G Dynabeads per antibody used.
Library preparation was performed using the ChIP-seq with NEBNext DNA Ultra II library prep kit using Unique Molecular Indexes (UMIs). Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

treatment_protocol: 429A were transiently treated with 2mM 4-OHT (dissolved in 100% Ethanol) or vehicle(100% Ethanol) for 72 (organoid culture) hr to activate CreERT2 nuclear activity and generate isogenic pairs. 1311G#5 were transiently treated with AD5-Cmv-Cre to delete HNF4α in vitro.

value: Lung tissue

value: KNH

value: Tamoxifen IP

tag: chip antibody

value: No Antibody


title: hADSC CN treatment - 1

description: Library name: S1


title: 24289X3_GEMM_KNH_HED931_input

description: Library name: 24289X3


title: hADSC no treatment - 3

description: Library name: N3


title: 24289X6_GEMM_KNH_HED897_FOXA2_rep2

description: Library name: 24289X6

value: FOXA2(CST D56D6)


title: hADSC CN treatment - 2

description: Library name: S2


title: 24289X2_GEMM_KNH_HED931_FOXA2_rep1

description: Library name: 24289X2


title: 24289X1_GEMM_KNH_HED931_FOXA1_rep1

description: Library name: 24289X1

value: FOXA1(Abcam ab170933)


title: Muscle, visium, 7d post-denervation, B1

first: Pura

last: Muñoz-Cánoves

institute: Altos Labs

description:
Library name: STExp1_B1_7dDEN_Plant_Young
10X Genomics


title: hADSC no treatment - 2

description: Library name: N2


title: hADSC CCN treatment - 2

description: Library name: C2


title: 24515X6_GEMM_KNH_HED968_FOXA1_rep2

description: Library name: 24515X6


title: 24515X4_GEMM_KN_HED934_Hnf4a_rep2

description: Library name: 24515X4

value: KN

value: Control

value: HNF4α (Perseus Proteomics PP-H1415)


title: 24515X7_GEMM_KN_HED814_input

description: Library name: 24515X7


title: hADSC no treatment - 1

description: Library name: N1


title: 25798X2_HCI_IMA03_KN_FOXA1_rep1

description:
Library name: 25798X2
ChIP-seq

source_name: Lung

extract_protocol:
For all organoid ChIP-seq experiments, two 24-well plates (approximately 4 – 8 million cells) were collected in Cell Recovery Solution (500 μl per dome). Organoids were submerged in ice for 30 min before centrifugation at 4°C (300G). Cells were washed three times in cold PBS. On the second wash, PBS was supplemented with DNase solution (containing a final concentration of 200U/ml DNase [Worthington], 2.5 mM MgCl2, 500 mM CaCl2). After the third wash, organoids were resuspended in 5 ml of 2 mM DSG buffer (1X PBS, 1 mM MgCl2) and rotated at room temperature for 35 min. Formaldehyde was then added to a final concentration of 1% and cells were crosslinked for 10 min. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were washed with cold PBS, then frozen at -80. Cell pellets were thawed on ice for 5 min then lysed in 1 ml of Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40) for all TF experiments or 400 ul of Chromatrap Hypotonic buffer (catalog #100007) for all histone experiments. Samples were centrifuged at 4°C (1000G) then resuspended in 1ml of RIPA lysis buffer (1X PBS, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) or 100 μl of Chromatrap Lysis buffer (catalog #100005) for TF and histone ChIPs respectively. All lysis buffers were supplemented with protease inhibitors. Chromatin extract was sonicated with QSonica Q800R (pulse: 30 s on/30 s off; sonication time: 20 min; amplitude: 70%). After sonication, chromatin extract of histone samples was brought up to a volume of 1 ml with RIPA lysis buffer. Chromatin from all samples was immunoprecipitated with antibodies premixed with Protein A/G Dynabeadsper antibody used. For sorted nuclei from GEMMs, At 14 weeks post-tumor initiation, KN and KNH tumor-bearing mice were euthanized. The rib cage was dissected to expose the trachea and heart, and lungs were perfused with cold PBS, snap-frozen, and minced on ice. Homogenized tissue was centrifuged (300G, 4°C, 5 min) and crosslinked in 2 mM DSG + 1% formaldehyde. After fixation, nuclei were extracted using TST buffer, dounced, and filtered through 70 μm/35 μm strainers. GFP-positive nuclei were sorted using BD FACSAria (85 μm nozzle) into PBS + 1% BSA + protease inhibitors.For ChIP-seq, nuclei (10M for TF ChIP-seq) were pelleted (500G, 4°C, 10 min), lysed, and sonicated (QSonica Q800R, 30s on/off, 20 min, 70%). Chromatin was immunoprecipitated with antibodies premixed with Protein A/G Dynabeads per antibody used.
Library preparation was performed using the ChIP-seq with NEBNext DNA Ultra II library prep kit using Unique Molecular Indexes (UMIs). Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

value: Lung

value: 3D cell line


title: 25736X4_HCI_IMA03_KN_Hnf4a_rep2

description:
Library name: 25736X4
ChIP-seq


title: 24515X5_GEMM_KNH_HED968_input

description: Library name: 24515X5


title: 24515X8_GEMM_KN_HED814_FOXA2_rep2

description: Library name: 24515X8


title: 24515X3_GEMM_KN_HED934_FOXA2_rep1

description: Library name: 24515X3


title: 25798X1_HCI_IMA03_KN_input_rep2

description:
Library name: 25798X1
ChIP-seq


title: 25736X3_HCI_IMA03_KN_FOXA1_rep2

description:
Library name: 25736X3
ChIP-seq


title: 25736X2_HCI_IMA03_KN_Hnf4a_rep1

description:
Library name: 25736X2
ChIP-seq


title: 24137X3_GEMM_KN_HED798_input_rep1

description: Library name: 24137X3