title: Matched adjacent non-tumor lung tissue sample N51

description:
Library name: N51
Local paired bulk RNA-seq library; pair_id=51; tissue_status=adjacent non-tumor; sample_id=N51.


title: Matched adjacent non-tumor lung tissue sample N75

status: Public on Jun 03 2026

type: SRA

city: Suzhou

first: Jiaqian

last: Qi

state: Jiangsu

address: No.188 Shizi Road

country: China

institute: The First Affiliated Hospital of Soochow University

description:
Library name: N75
Local paired bulk RNA-seq library; pair_id=75; tissue_status=adjacent non-tumor; sample_id=N75.

library_source: transcriptomic

data_processing:
Raw sequencing reads were processed by the sequencing provider to generate a gene-level raw-count matrix.
Assembly: GRCh38
Supplementary files format and content: CSV file containing gene-level raw counts. Rows correspond to Ensembl gene identifiers and columns correspond to sample IDs.

molecule: total RNA

organism: Homo sapiens

source_name: matched adjacent non-tumor lung tissue

extract_protocol:
Total RNA was extracted from each surgically resected tissue specimen using a standard total-RNA extraction workflow according to the sequencing provider's protocol. RNA quantity and quality were assessed before library construction, and samples passing RNA quality-control criteria were used for bulk RNA-seq.
Bulk RNA-seq libraries were prepared from total RNA using an Illumina-compatible RNA-seq library preparation workflow according to the sequencing provider's protocol. Libraries were generated for paired-end sequencing.

tag: tissue

value: matched adjacent non-tumor lung tissue

tag: cell type

value: bulk tissue


title: 2S04_D7

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

description: Library name: 2S04_D7

data_processing:
Nextpresso pipeline was used for analysis. Brieffly, reads were aligned to hg19 genome using bowtie and TopHat aligners. Feature counting was performed by htseq count command. Read count normalization and diffrential expression analysis was performed using DEseq2 package.
Assembly: hg19
Supplementary files format and content: raw counts as plain text file

molecule: polyA RNA

source_name: H&N squamous cel carcinoma

extract_protocol:
Tumor biopies were obtained prior to treatment, on day 8, and day 28 after treatment and and placed in RNAlater® (Invitrogen). RNA wasextracted using the guanidine isothiocyanate (GTC) method.
Total RNA samples [1µg, but 70-100ng from samples 1S24RNAD-7 and 1S25RNASCR; RQS/RIN= 7.3, range 5.3-9.3 (samples 1S24RNAD-7 and 1S25RNASCR RQS under 6)] were converted into sequencing libraries with the "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760), as recommended by the manufacturer. Briefly, polyA+ fraction is purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters. Adapter-ligated library is completed by PCR with Illumina PE primers. {This kit generates directional libraries stranded in the antisense orientation [the read1 (the only read in single read format) has the antisense orientation (--library-type fr-firststrand in TopHat, --stranded=reverse in HTSeq]} The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's protocols.

value: H&N squamous cel carcinoma

tag: treatment

value: Arm II LD D8


title: N035_Day_0

city: Durham

first: Andrew

last: Hudson

state: NC

address: 1328 Campus Drive

department: Surgery

country: USA

institute: Duke University

description: Library name: N035_Day_0

data_processing:
Raw sequence reads were trimmed using Trimmomatic1
Raw sequence reads were trimmed using Trimmomatic1
Sequenced reads were aligned to the reference genome (MMul_10, GCA_003339765.3) using the STAR aligner2.
Transcripts were annotated using Ensembl build Mmul_10.109.
Assembly: MMul_10 (Available at https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_003339765.1/)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Macaca mulatta

source_name: Peripheral NK

extract_protocol:
Peripheral NK cells were isolated from PBMC by fluorescence-activated cell sorting. RNA extraction was performed from frozen cell pellets using the QIAGEN AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, Maryland), following the manufacturer’s instructions.
Library prep was conducted using the Takara v4 ultra-low input kit (Takara Bio, Otsu, Shiga, Japan), and indexed sequence libraries were sequenced using Illumina NovaSeq X Plus instrument.

treatment_protocol: Macaques were infected intrarectally with SIVmac251 as described [Hudson et al. J Virol 2025]

value: Peripheral NK

tag: time


title: 1S01_D7

description: Library name: 1S01_D7


title: Sextuple-AA rep3

city: Kaifeng

first: Xiaohong

last: Zhu

address: Jinming Street

institute: Henan University

data_processing:
HiSeq2500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seedlings were grown vertically on 1/2 MS medium with 1% sucrose and 1.2% agar.

extract_protocol:
Total RNA was isolated usingTRIzol for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ten day old seedlings were transferred from MS plates to 9-well plate containing 1mL 1/2 liquid MS medium per well and treated with 50uM antimycin for 5 hours (sample named as Col_AA), or treated with DMSO (sample named as Col_CK).

value: whole seedling

tag: age

value: ten day old

tag: genotype

value: sextuple mutant line

value: AA


title: NSCLC tumor tissue sample C51

description:
Library name: C51
Local paired bulk RNA-seq library; pair_id=51; tissue_status=tumor; sample_id=C51.

source_name: non-small cell lung cancer tumor tissue

value: non-small cell lung cancer tumor tissue


title: 1S25_D15

description: Library name: 1S25_D15

value: Arm II HD D28


title: Sextuple1-CK rep3

value: CK


title: M491_Day_70

description: Library name: M491_Day_70


title: 1S22_D15

description: Library name: 1S22_D15


title: 2S13_D15

description: Library name: 2S13_D15


title: 1S21_D15

description: Library name: 1S21_D15


title: NSCLC tumor tissue sample C71

description:
Library name: C71
Local paired bulk RNA-seq library; pair_id=71; tissue_status=tumor; sample_id=C71.


title: M488_Day_70

description: Library name: M488_Day_70


title: 2S09_D15

description: Library name: 2S09_D15

value: Arm II LD D28


title: M488_Day_7

description: Library name: M488_Day_7


title: Matched adjacent non-tumor lung tissue sample N50

description:
Library name: N50
Local paired bulk RNA-seq library; pair_id=50; tissue_status=adjacent non-tumor; sample_id=N50.


title: fctx_HET2 snATAC-seq

city: Toronto

first: Paul

middle: M

last: McKeever

state: ON

address: 60 Leonard Ave., 4th floor - 4KD481

department: Tanz CRND

country: Canada

institute: University of Toronto

description:
Library name: ATAC_fctx_HET2
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_HET2_fragments.tsv.gz
fctx_HET2_fragments.tsv.gz.tbi

library_source: genomic single cell

data_processing:
Raw base call files were demultiplexed using Illumina software to generate FASTQ files.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
FASTQ files were processed using Cell Ranger ARC (10x Genomics) to perform alignment, barcode assignment, and generation of paired gene expression and chromatin accessibility count matrices.
Gene expression reads were aligned to the mouse reference genome mm10 using STAR within the Cell Ranger ARC pipeline.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
Assembly: mm10
Supplementary files format and content: Processed data files include filtered gene expression count matrices, chromatin accessibility peak count matrices, fragment files, and associated cell metadata generated from Cell Ranger ARC and downstream Seurat/Signac analyses.
Supplementary files format and content: Processed files are provided in standard formats including HDF5 (.h5), Matrix Market (.mtx), tab-delimited text (.tsv), and compressed fragment files (.tsv.gz) containing single-nucleus transcriptomic and chromatin accessibility measurements.

molecule: genomic DNA

organism: Mus musculus

source_name: frontal cortex

growth_protocol: C9orf72 wild-type, heterozygous knockout, and homozygous knockout mice were maintained under standard laboratory housing conditions with ad libitum access to food and water on a 12 h light/dark cycle. Brain tissue was collected from approximately 3-month-old animals.

extract_protocol:
Nuclei were isolated from frozen hippocampus and frontal cortex tissue using region-specific nuclei isolation workflows optimized for each brain region. Hippocampal nuclei were isolated using an iodixanol density gradient purification protocol following mechanical homogenization and filtration to enrich for intact nuclei and reduce debris contamination. Frontal cortex nuclei were isolated using the 10x Genomics Nuclei Isolation Kit according to the manufacturer’s protocol. Purified nuclei were counted and assessed prior to loading onto the 10x Genomics Chromium platform. RNA and chromatin accessibility information were simultaneously captured from individual nuclei using the Chromium Single Cell Multiome ATAC + Gene Expression workflow.
Single-nucleus multiomic libraries were generated using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression platform according to the manufacturer’s instructions. Briefly, isolated nuclei were subjected to transposition using Tn5 transposase to generate ATAC fragments, followed by GEM generation for simultaneous barcoding of gene expression and chromatin accessibility molecules from individual nuclei. Gene expression and ATAC libraries were amplified separately and sequenced on Illumina NovaSeq 6000 and NovaSeq X Plus instruments.

treatment_protocol: No experimental treatments were applied prior to tissue collection. Hippocampus and frontal cortex tissues were rapidly dissected from frozen brain samples for downstream single-nucleus isolation.

value: frontal cortex

value: C9orf72 heterozygous knockout


title: 2S04_D15

description: Library name: 2S04_D15


title: 1S01_D15

description: Library name: 1S01_D15


title: M488_Day_74

description: Library name: M488_Day_74


title: 1S25_SCR

description: Library name: 1S25_SCR

value: Arm II HD D0


title: fctx_KO1 snATAC-seq

description:
Library name: ATAC_fctx_KO1
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_KO1_fragments.tsv.gz
fctx_KO1_fragments.tsv.gz.tbi

value: C9orf72 homozygous knockout


title: 1S22_SCR

description: Library name: 1S22_SCR


title: M491_Day_74

description: Library name: M491_Day_74


title: fctx_KO2 snATAC-seq

description:
Library name: ATAC_fctx_KO2
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_KO2_fragments.tsv.gz
fctx_KO2_fragments.tsv.gz.tbi


title: 1S21_SCR

description: Library name: 1S21_SCR


title: M636_Day_74

description: Library name: M636_Day_74


title: 2S13_SCR

description: Library name: 2S13_SCR


title: 2S11_SCR

description: Library name: 2S11_SCR


title: fctx_KO3 snATAC-seq

description:
Library name: ATAC_fctx_KO3
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_KO3_fragments.tsv.gz
fctx_KO3_fragments.tsv.gz.tbi


title: 2S09_SCR

description: Library name: 2S09_SCR

value: Arm II LD D0


title: N035_Day_7

description: Library name: N035_Day_7


title: 2S08_SCR

description: Library name: 2S08_SCR


title: 2S04_SCR

description: Library name: 2S04_SCR


title: M636_Day_7

description: Library name: M636_Day_7


title: 1S01_SCR

description: Library name: 1S01_SCR


title: sputum_control_608

city: Frankfurt am Main

first: Ralf

last: Schubert

address: Theodor-Stern-Kai 7

country: Germany

institute: Goethe University Frankfurt

description: Library name: DE_X_608

data_processing:
Unprocessed sequencing reads were adapter-trimmed and quality-trimmed using Cutadapt (version 3.4)
Deduplication based on UMIs (Unique Molecular Identifier) was performed using in-house tools. FastQC (0.11.9) was used to assess the quality of sequencing reads.
Processed sequencing reads were mapped with a reference genome using Bowtie2 (2.4.4)
Quantification of mapped reads to each gene was performed using HTSeq (version 2.0.2). Raw counts were TPM-normalized by dividing each count with the sum of all counts for each sample multiplied by one million.
Differential gene expression analysis was performed using DESeq2 (version 1.38)
Assembly: GRCh38
Supplementary files format and content: Excel file including all raw counts for each sample
Supplementary files format and content: Excel file including all normalized counts and statistical results

source_name: sputum cells

extract_protocol:
RNA was isolated from samples using the miRNeasy mini kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany). Cells were lyzed in QIAzol lysis reagent and chloroform was added to perform a two-phase extraction. After centrifugation, the RNA in the aqueous phase was precipitated by ethanol and washed with the provided buffers from the kit using spin columns. Finally, it was eluted in 30 μL RNase-free water and the concentration was determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Dreieich, Germany) and RNA integrity (RIN) was assessed using the Agilent RNA 6000 Nano Kit and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Carla, CA, USA).
Rapid MACE-seq was used to prepare 3’ RNA sequencing libraries. Samples of 100 ng of DNA-depleted RNA were used for library preparation, using the Rapid MACE-Seq kit (GenXPro GmbH, Germany). Fragmented RNA underwent reverse transcription using barcoded oligo(dT) primers containing TrueQuant unique molecular identifiers, followed by template switching. PCR amplified libraries were purified by solid phase reversible immobilization beads and subsequent sequencing was performed using the Illumina platform NextSeq 500

value: sputum cells

tag: group

value: control


title: sputum_control_607

description: Library name: DE_X_607


title: fctx_WT3 snATAC-seq

description:
Library name: ATAC_fctx_WT3
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_WT3_fragments.tsv.gz
fctx_WT3_fragments.tsv.gz.tbi

value: wild-type


title: DHGZ_Day_74

description: Library name: DHGZ_Day_74

value: Peripheral NK


title: sputum_control_603

description: Library name: DE_X_603


title: sputum_control_602

description: Library name: DE_X_602


title: 9-VP-020-01-X, healthy skin biopsy

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

description: Library name: 9_VP_020_01_X_gezond_A2

data_processing:
Raw read QC was done using FastQC (v0.12.1)
Adapter and quality trimming was done using cutadapt (v5.0)
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.11b)
UMI-based removal of mapped PCR duplicates was done using umi_tools (v1.1.6)
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.1)
Assembly: Homo sapiens  GRCh38 (Ensembl release 112)
Supplementary files format and content: all_samples_rsem_gene_counts.tsv: raw expression count table in tab separated format, with genes as rows and samples as columns

source_name: skin

extract_protocol:
The sampled tissue was lysed mechanically using a 1000 µL pipette tip, followed by shearing through a syringe (Terumo Corporation, Tokyo, Japan) fitted with a 20Gx1½ needle (Terumo Corporation). Total RNA was extracted using the conventional TriReagent/chloroform method and subsequently purified with the Direct-zol Microprep RNA Kit (Zymo Research), including on-column DNase I treatment, according to the manufacturer’s instructions. As residual genomic DNA was detected in some samples, an additional DNase treatment was performed using the TURBO DNA-free™ Kit (Invitrogen, Thermo Fisher Scientific) on all RNA extracts.
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen)

value: skin


title: sputum_patient_F043

description: Library name: DE_F_043

value: patient


title: sputum_patient_F034

description: Library name: DE_F_034


title: 8-VP-020-01-X, perilesional skin biopsy

description: Library name: 8_VP_020_01_X_perilesioneel_H1


title: hippo_HET1 snATAC-seq

description:
Library name: ATAC_hippo_HET1
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_HET1_fragments.tsv.gz
hippo_HET1_fragments.tsv.gz.tbi

source_name: hippocampus

value: hippocampus


title: sputum_patient_F025

description: Library name: DE_F_025


title: fctx_WT6 snATAC-seq

description:
Library name: ATAC_fctx_WT6
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_WT6_fragments.tsv.gz
fctx_WT6_fragments.tsv.gz.tbi


title: sputum_patient_F030

description: Library name: DE_F_030


title: sputum_patient_F017

description: Library name: DE_F_017


title: hippo_HET2 snATAC-seq

description:
Library name: ATAC_hippo_HET2
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_HET2_fragments.tsv.gz
hippo_HET2_fragments.tsv.gz.tbi


title: sputum_patient_F009

description: Library name: DE_F_009


title: 6-VP-017-01, healthy skin biopsy

description: Library name: 6_VP_017_01_gezond_F1


title: sputum_patient_F006

description: Library name: DE_F_006


title: Sham12  mouse muscle, after transplantation

status: Public on Jun 04 2026

city: Beijing

first: xupeng

last: liu

state: Beijing

address: No.3 Datun Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

data_processing:
CLC Genomics Workbench v11.0.1
Seguence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were maped to GrcM38/mm0 using CLc genomic benchwoank (parameters-mismath cost. 2 insertion cost: 3 deletion cost:3 engthfaction. .8 similanity faction. 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: quadriceps femoris muscle

growth_protocol: 10-week-old male 129 mice (n=10) were used and had free access to water and food. The lights were on from 08.00 to 20.00, the temperature was maintained at 21 to 24°C, and the humidity was maintained at 40–70%.

extract_protocol:
RNA is extracted from tissues or cells using standard extraction methods (Trizol), followed by rigorous quality control of RNA samples through Agilent 2100 bioanalyzer.
RNA libraryis for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to the manufacturer's instructions.

treatment_protocol: The muscle stem cells were obtained from the mice by biopsy, and after autologous muscle stem cell transplantation or sham surgery, the muscle stem cells or tissues of the mice were obtained for analysis.

value: quadriceps femoris muscle

value: WT

value: after transplantation


title: 7-VP-020-01-X, lesional skin biopsy

description: Library name: 7_VP_020_01_X_lesioneel_G1


title: hippo_HET3 snATAC-seq

description:
Library name: ATAC_hippo_HET3
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_HET3_fragments.tsv.gz
hippo_HET3_fragments.tsv.gz.tbi


title: sputum_patient_F002

description: Library name: DE_F_002


title: NSCLC tumor tissue sample C50

description:
Library name: C50
Local paired bulk RNA-seq library; pair_id=50; tissue_status=tumor; sample_id=C50.

value: non-small cell lung cancer tumor tissue

value: bulk tissue


title: N035_Day_74

description: Library name: N035_Day_74


title: 5-VP-017-01, perilesional skin biopsy

description: Library name: 5_VP_017_01_perilesioneel_E1


title: 2S08_D15

description: Library name: 2S08_D15

value: H&N squamous cel carcinoma

value: Arm II LD D28


title: fctx_HET3 snATAC-seq

description:
Library name: ATAC_fctx_HET3
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_HET3_fragments.tsv.gz
fctx_HET3_fragments.tsv.gz.tbi

value: frontal cortex

value: C9orf72 heterozygous knockout


title: hippo_HET4 snATAC-seq

description:
Library name: ATAC_hippo_HET4
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_HET4_fragments.tsv.gz
hippo_HET4_fragments.tsv.gz.tbi


title: sputum_control_F509

description: Library name: DE_F_509


title: sputum_control_F507

description: Library name: DE_F_507


title: Control 27, skin biopsy

description: Library name: 53_Control_27_E7


title: sputum_control_F500

description: Library name: DE_F_500


title: 2S11_D15

description: Library name: 2S11_D15

value: Arm II HD D28


title: hippo_KO1 snATAC-seq

description:
Library name: ATAC_hippo_KO1
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_KO1_fragments.tsv.gz
hippo_KO1_fragments.tsv.gz.tbi

value: C9orf72 homozygous knockout


title: sputum_patient_F054

description: Library name: DE_F_054

value: sputum cells


title: Control 26, skin biopsy

description: Library name: 52_Control_26_D7


title: hippo_KO2 snATAC-seq

description:
Library name: ATAC_hippo_KO2
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_KO2_fragments.tsv.gz
hippo_KO2_fragments.tsv.gz.tbi


title: Control 25, skin biopsy

description: Library name: 51_Control_25_C7


title: hippo_KO3 snATAC-seq

description:
Library name: ATAC_hippo_KO3
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_KO3_fragments.tsv.gz
hippo_KO3_fragments.tsv.gz.tbi


title: Control 24, skin biopsy

description: Library name: 50_Control_24_B7


title: fctx_KO4 snATAC-seq

description:
Library name: ATAC_fctx_KO4
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_KO4_fragments.tsv.gz
fctx_KO4_fragments.tsv.gz.tbi


title: hippo_KO4 snATAC-seq

description:
Library name: ATAC_hippo_KO4
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_KO4_fragments.tsv.gz
hippo_KO4_fragments.tsv.gz.tbi


title: YL28

type: RNA

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Affymetrix  430A2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were normalized by RMA by Parteck Genomic Suite 6.6 and analyzed with ANOVA.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse cell line culture

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: in vitro treated

tag: set number

tag: exp number

tag: cell line

value: rhabdomyosarcoma

value: PD48:treated with PD, 20µM MAPK inhibitor PD98059 for 48 hours


title: YL30


title: YL27

value: PD24:treated with PD, 20µM MAPK inhibitor PD98059 for 24 hours


title: YL29


title: YL26


title: YL25


title: 4-VP-017-01, lesional skin biopsy

description: Library name: 4_VP_017_01_lesioneel_D1

value: skin


title: YL24

source_name: Rap

value: Rap:treated with 10nM Rapamycin for 48 hours


title: fctx_WT2 snATAC-seq

description:
Library name: ATAC_fctx_WT2
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_WT2_fragments.tsv.gz
fctx_WT2_fragments.tsv.gz.tbi

value: wild-type


title: M491_Day_0

description: Library name: M491_Day_0

value: Peripheral NK


title: hippo_WT1 snATAC-seq

description:
Library name: ATAC_hippo_WT1
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_WT1_fragments.tsv.gz
hippo_WT1_fragments.tsv.gz.tbi

value: hippocampus


title: YL23


title: sputum_control_606

description: Library name: DE_X_606

value: control


title: Control 23, skin biopsy

description: Library name: 49_Control_23_A7


title: YL20

source_name: CalC

value: CalC:treated with 100 nM calphostin C for 48 hours


title: YL21


title: hippo_WT2 snATAC-seq

description:
Library name: ATAC_hippo_WT2
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_WT2_fragments.tsv.gz
hippo_WT2_fragments.tsv.gz.tbi


title: Control 22, skin biopsy

description: Library name: 48_Control_22_H6


title: YL22


title: hippo_WT3 snATAC-seq

description:
Library name: ATAC_hippo_WT3
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_WT3_fragments.tsv.gz
hippo_WT3_fragments.tsv.gz.tbi


title: YL19


title: mPFC, Ketamine-2, Day15

city: Yokohama City

first: Waki

last: Nakajima

state: Kanazawa-Ku

address: 3-9, Fukuura

department: Physiology

country: Japan

institute: Yokohama City University

description: Library name: Sample 8

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to rn6 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Brain (mPFC)

extract_protocol:
Total RNA was harvested using the RNeasy plus universal kits (Qiagen). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacture's protocols.

treatment_protocol: In control group, rats were recieved no treatment. In K4 group, rats were administered K4 intravenously through a cannula for 7 days. In ketamine group, rats were administered ketamine subcutaneously for 7days. After continuous treatment, withdrawal was done for 7 days.

value: Brain (mPFC)

value: Wistar Kyoto rats

value: Ketamine


title: Control 21, skin biopsy

description: Library name: 47_Control_21_G6


title: fctx_WT4 snATAC-seq

description:
Library name: ATAC_fctx_WT4
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_WT4_fragments.tsv.gz
fctx_WT4_fragments.tsv.gz.tbi

value: frontal cortex


title: YL18

source_name: DMSO

value: DMSO


title: hippo_WT4 snATAC-seq

description:
Library name: ATAC_hippo_WT4
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds
hippo_WT4_fragments.tsv.gz
hippo_WT4_fragments.tsv.gz.tbi


title: YL17


title: NSCLC tumor tissue sample C70

description:
Library name: C70
Local paired bulk RNA-seq library; pair_id=70; tissue_status=tumor; sample_id=C70.

value: non-small cell lung cancer tumor tissue

value: bulk tissue


title: Control 20, skin biopsy

description: Library name: 46_Control_20_F6


title: YL16

value: rhabdomyosarcoma


title: Control 19, skin biopsy

description: Library name: 45_Control_19_E6


title: fctx_HET2 snRNA-seq

description:
Library name: GEX_fctx_HET2
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds

library_source: transcriptomic single cell

molecule: nuclear RNA

value: C9orf72 heterozygous knockout


title: YL14

value: melanoma

value: LY48:treated with 10µM PI3K/AKT inhibitor LY294002 for 48 hours


title: YL15


title: 44-VP-027-01, healthy skin biopsy

description: Library name: 44_VP_027_01_gezond_D6

value: skin


title: fctx_HET3 snRNA-seq

description:
Library name: GEX_fctx_HET3
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds


title: NSCLC tumor tissue sample C68

description:
Library name: C68
Local paired bulk RNA-seq library; pair_id=68; tissue_status=tumor; sample_id=C68.


title: YL13


title: YL12

value: LY24:treated with 10µM PI3K/AKT inhibitor LY294002 for 24 hours


title: fctx_KO1 snRNA-seq

description:
Library name: GEX_fctx_KO1
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds

value: C9orf72 homozygous knockout


title: YL11


title: 43-VP-027-01, perilesional skin biopsy

description: Library name: 43_VP_027_01_perilesioneel_C6


title: fctx_KO2 snRNA-seq

description:
Library name: GEX_fctx_KO2
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds


title: YL10


title: 42-VP-027-01, lesional skin biopsy

description: Library name: 42_VP_027_01_lesioneel_B6


title: YL08

value: Rap:treated with 10nM Rapamycin for 48 hours


title: YL07


title: fctx_KO3 snRNA-seq

description:
Library name: GEX_fctx_KO3
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds


title: 41-VP-025-01, healthy skin biopsy

description: Library name: 41_VP_025_01_gezond_A6


title: YL05


title: fctx_KO4 snRNA-seq

description:
Library name: GEX_fctx_KO4
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds


title: YL06


title: 40-VP-025-01, perilesional skin biopsy

description: Library name: 40_VP_025_01_perilesioneel_H5


title: YL04


title: fctx_WT2 snRNA-seq

description:
Library name: GEX_fctx_WT2
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds

value: wild-type


title: YL09


title: YL03

value: control


title: YL02


title: male, intestinal epithelium, Tacr2null, low fat diet, biological replicate 2

city: La Jolla

first: Supriya

last: Srinivasan

state: CA

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

description: Library name: Sample 38

data_processing:
Raw sequencing reads were quality-assessed using FastQC, and adapters were removed using Cutadapt.
Trimmed reads were aligned to the mouse reference genome (ENSEMBL GRCm38) using STAR aligner version 2.6.1d.
The distribution of mapped reads across genomic features was analyzed with RSeQC v3.0.1.
Differential gene expression analysis was performed using DESeq2 (v2.11.40.8) implemented in R (v4.2.2) via the Galaxy platform.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: intestinal epithelium

extract_protocol:
NOTE for intestinal intestinal epithelium: the small intestine was cut longitudanally, and the intestinal epithelium was scraped using microscope slides from the middle of the length of the entire intestine (roughly 16-20 cm in a typical 34 cm small intestine). The tissues (isolated intestinal epithelium or perigonadal white adipose tissues) were processed via commercial RNeasy RNA purification kits using manufacturers protocols.
Total RNA samples were prepared into RNA-Seq libraries using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommended protocol. Briefly, for each sample, 200 ng total RNA was polyA selected, and converted to double-stranded cDNA followed by fragmentation and ligation of sequencing adapters. The libraries were then PCR amplified 12 cycles using barcoded PCR primers, purified, and size selected using AMPure XP Beads before loading onto an Illumina NextSeq 2000 for 100 base single-read sequencing.

treatment_protocol: Mice (8-12 weeks) were maintained on a low fat diet. Test mice were then given an high fat diet for 1 or 12 weeks. The intestines and perigonadal tissues were collected and flash frozen.

value: intestinal epithelium

tag: Sex

value: male

value: low fat diet


title: male, intestinal epithelium, Tacr2null, low fat diet, biological replicate 3

description: Library name: Sample 39


title: male, intestinal epithelium, Tacr2null, low fat diet, biological replicate 4

description: Library name: Sample 40


title: 39-VP-025-01, lesional skin biopsy

description: Library name: 39_VP_025_01_lesioneel_G5


title: fctx_WT3 snRNA-seq

description:
Library name: GEX_fctx_WT3
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds

value: frontal cortex


title: YL01

value: DMSO


title: Plasma EV RNA-Seq, B18 (PLWoH)

city: Atlanta

first: Erica

middle: L

last: Johnson

state: GA

address: 720 Westview Dr SW

department: Department of Microbiology, Biochemistry, and Immunology

institute: Morehouse School of Medicine

description:
Library name: B18
Maternal plasma-derived EV RNA; sex: F; RIN: 1.0; strand-specific; 2×150 bp; ~20M reads/sample

data_processing:
Quality control / trimming with COMPSRA Quality Control module: adapter removal and filtering of low-quality bases using Phred≥20 thresholds (COMPSRA defaults; e.g., -rh 20 -rt 20 -rr 20). Reads with kit-specific randomized bases at ligation junctions were trimmed; qualified small-RNA read lengths retained.
Alignment with COMPSRA Alignment module using STAR against the human reference GRCh38/hg38 (update here to hg19 if that is what you used). Unmapped reads were retained by COMPSRA but only human-mapped reads were taken forward for annotation/quantification.
Annotation with COMPSRA Annotation module against pre-built small-RNA databases: miRNA (miRBase), piRNA (piRNABank, piRBase, piRNAcluster), tRNA (gtRNAdb), snRNA/snoRNA (GENCODE r27), and circRNA (circBase). Where needed, coordinates were harmonized to the selected human assembly using UCSC LiftOver (built into COMPSRA).
Quantification: feature-level raw read counts were produced per sample and aggregated into a sample × feature matrix. The submitted processed file contains untransformed integer counts (no DE-based filtering). Downstream DE analyses for the manuscript were performed in R/DESeq2 and are supplied only as supplementary analysis files if included.
Assembly: Homo sapiens GRCh38 (hg38)
Supplementary files format and content: smRNA_expression_count.csv — comma-separated matrix of raw integer counts.

source_name: Plasma

extract_protocol:
Plasma was separated by centrifugation. Extracellular vesicles (EVs) were isolated per manufacturer’s instructions, and EV RNA was extracted using the Qiagen exoRNeasy midi kit. RNA quantity/quality were assessed; RIN values are reported but are not a reliable quality metric for EV RNA.
Plasma was separated by centrifugation. Extracellular vesicles (EVs) were isolated per manufacturer’s instructions, and EV RNA was extracted using the Qiagen exoRNeasy midi kit. RNA quantity/quality were assessed; RIN values are reported but are not a reliable quality metric for EV RNA.

treatment_protocol: No experimental treatment was administered. Maternal peripheral blood was collected during pregnancy from two groups: cART-suppressed people living with HIV (PLWH) and HIV-negative controls (PLWoH). Group (PLWH vs PLWoH) is recorded in sample attributes.

value: Plasma

value: HIV negative


title: Plasma EV RNA-Seq, B17 (PLWoH)

description:
Library name: B17
Maternal plasma-derived EV RNA; sex: F; RIN: 1.0; strand-specific; 2×150 bp; ~20M reads/sample


title: 38-VP-023-01, healthy skin biopsy

description: Library name: 38_VP_023_01_gezond_F5


title: fctx_WT4 snRNA-seq

description:
Library name: GEX_fctx_WT4
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds


title: fctx_WT6 snRNA-seq

description:
Library name: GEX_fctx_WT6
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds


title: Plasma EV RNA-Seq, B15 (PLWoH)

description:
Library name: B15
Maternal plasma-derived EV RNA; sex: F; RIN: 1.0; strand-specific; 2×150 bp; ~20M reads/sample


title: 37-VP-023-01, perilesional skin biopsy

description: Library name: 37_VP_023_01_perilesioneel_E5


title: Plasma EV RNA-Seq, B16 (PLWoH)

description:
Library name: B16
Maternal plasma-derived EV RNA; sex: F; RIN: 1.3; strand-specific; 2×150 bp; ~20M reads/sample


title: hippo_HET1 snRNA-seq

description:
Library name: GEX_hippo_HET1
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds

value: hippocampus


title: 36-VP-023-01, lesional skin biopsy

description: Library name: 36_VP_023_01_lesioneel_D5


title: Plasma EV RNA-Seq, B13 (PLWoH)

description:
Library name: B13
Maternal plasma-derived EV RNA; sex: F; RIN: 1.0; strand-specific; 2×150 bp; ~20M reads/sample


title: Control 18, skin biopsy

description: Library name: 35_Control_18_C5


title: Plasma EV RNA-Seq, B10 (PLWoH)

description:
Library name: B10
Maternal plasma-derived EV RNA; sex: F; RIN: 1.9; strand-specific; 2×150 bp; ~20M reads/sample


title: hippo_HET3 snRNA-seq

description:
Library name: GEX_hippo_HET3
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds

value: C9orf72 heterozygous knockout


title: Plasma EV RNA-Seq, B9 (PLWoH)

description:
Library name: B9
Maternal plasma-derived EV RNA; sex: F; RIN: 3.9; strand-specific; 2×150 bp; ~20M reads/sample


title: Plasma EV RNA-Seq, B8 (PLWH)

description:
Library name: B8
Maternal plasma-derived EV RNA; sex: F; RIN: 1.6; strand-specific; 2×150 bp; ~20M reads/sample

value: cART-suppressed PLWH


title: Plasma EV RNA-Seq, B7 (PLWH)

description:
Library name: B7
Maternal plasma-derived EV RNA; sex: F; RIN: 1.3; strand-specific; 2×150 bp; ~20M reads/sample


title: Control 17, skin biopsy

description: Library name: 34_Control_17_B5


title: hippo_KO1 snRNA-seq

description:
Library name: GEX_hippo_KO1
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds


title: Control 16, skin biopsy

description: Library name: 33_Control_16_A5


title: hippo_HET4 snRNA-seq

description:
Library name: GEX_hippo_HET4
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds


title: Plasma EV RNA-Seq, B5 (PLWH)

description:
Library name: B5
Maternal plasma-derived EV RNA; sex: F; RIN: 1.3; strand-specific; 2×150 bp; ~20M reads/sample


title: Plasma EV RNA-Seq, B6 (PLWH)

description:
Library name: B6
Maternal plasma-derived EV RNA; sex: F; RIN: 2.1; strand-specific; 2×150 bp; ~20M reads/sample


title: Plasma EV RNA-Seq, B4 (PLWH)

description:
Library name: B4
Maternal plasma-derived EV RNA; sex: F; RIN: 1.2; strand-specific; 2×150 bp; ~20M reads/sample


title: hippo_KO2 snRNA-seq

description:
Library name: GEX_hippo_KO2
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds


title: Plasma EV RNA-Seq, B3 (PLWH)

description:
Library name: B3
Maternal plasma-derived EV RNA; sex: F; RIN: 1.1; strand-specific; 2×150 bp; ~20M reads/sample


title: 31-VP-026-01, perilesional skin biopsy

description: Library name: 31_VP_026_01_perilesioneel_G4


title: Plasma EV RNA-Seq, B2 (PLWH)

description:
Library name: B2
Maternal plasma-derived EV RNA; sex: F; RIN: 2.7; strand-specific; 2×150 bp; ~20M reads/sample


title: hippo_KO3 snRNA-seq

description:
Library name: GEX_hippo_KO3
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds


title: 30-VP-026-01, lesional skin biopsy

description: Library name: 30_VP_026_01_lesioneel_F4


title: mouse-muscle-cell-differentiating-8A-H3K27ac-ChIP

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

library_source: genomic

data_processing:
Sequencing reads were aligned to mm9 using BWA (Li and Durbin, 2009). Mapped reads were filtered for quality, and duplicates were removed for further analysis.
The bamCoverage script was used to generate and normalize bigwig files with the RPKM formula.
The peak calling was performed with the MACS2 (Zhang et al., 2008) against a reference input sample from the same cell line with standard settings and a q value of 0.05.
Assembly: mm9
Supplementary files format and content: bigwig file
Supplementary files format and content: peak file with H3K27ac peaks

source_name: C2C12 myoblasts

extract_protocol:
Chromatin for ChIP was prepared as previously described(Kouwenhoven et al., 2010). ChIP assays were performed following a standard protocol (Novakovic et al., 2016) with minor modifications. Antibodies against H3K27ac (1.2 μg) was used in each ChIP assay.
Resulted DNA fragments from four independent ChIP assays were purified and subjected to a ChIP-qPCR quality check. Afterward 5ng DNA fragments were pooled and proceeded on with library construction using KAPA Hyper Prep Kit according to the standard protocol. The prepared libraries were then sequenced using the NextSeq 500 (Illumina) according to standard Illumina protocols.

value: C2C12 myoblasts

value: muscle cells

value: 72h differentiation

tag: antibody

value: Anti-H3K27ac, Diagenode, Cat#C15410174


title: 2-VP-008-01-X, perilesional skin biopsy

description: Library name: 2_VP_008_01_X_perilesioneel_huid_B1

value: skin


title: hippo_KO4 snRNA-seq

description:
Library name: GEX_hippo_KO4
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds

value: C9orf72 homozygous knockout


title: mouse-muscle-cell-differentiating-5A-H3K27ac-ChIP

value: 36h differentiation


title: WT1

first: Manuel

middle: J

last: Gomez

institute: CNIC

description: Library name: WT1

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.99 mouse transcriptome, with RSEM, to obtain expression estimates at gene level.
Assembly: GRCm38.99
Supplementary files format and content: Estimated raw counts for each gene in each sample, as calculated by RSEM

growth_protocol: !0T1/2 cells were maintained in DMEM supplemented with 10% FBS and 1% Pen/Strep, and growth in humidified atmosphere at 5% CO2 and 37C.

extract_protocol:
RNA was extracted using Qiagen miniRNeasy kit (74004, Qiagen, Germany) following manufacturer’s instructions.
mRNA was captured and libraries were prepared using the KAPA mRNA HyperPrep kit (08098115702, Roche, Switzerland) following manufacturer’s instructions. Pooled libraries were sequenced using illumina NextSeq500 at Children’s Research Institute Sequencing Facility.

treatment_protocol: No treatments were applied to the biological material prior to extraction.

value: Embryonic fibroblast

value: WT


title: female, intestinal epithelium, Tacr2null, high fat diet, acute, biological replicate 4

description: Library name: Sample 32

value: intestinal epithelium

value: female

value: high fat diet one week


title: 29-VP-022-01, healthy skin biopsy

description: Library name: 29_VP_022_01_gezond_E4


title: mouse-muscle-cell-differentiating-5A-ChIP-input

value: input


title: Wild Type 48hpf CNCCs

city: Aurora

first: James

middle: T

last: Nichols

state: CO

department: Craniofacial Biology

institute: University of Colorado Anschutz Medical Campus

description:
Library name: Wild_Type
10x genomics

data_processing:
Recovered sequencing reads were mapped to a custom Cell Ranger reference based on the GRCz11/danRer11 genome assembly using the Cell Ranger pipeline (10X Genomics). This Cell Ranger reference contained the alx3 transcript from Ensembl release 91 (GRCz10) mapped to the GCRz11 genome in place of the release 101 (GRCZ11) version due to inaccurate truncation of the 3’ UTR in the most recent version7. The 10X Genomics Cell Ranger pipeline was used to identify cell-associate barcodes.
Assembly: GRCz11/danRer11 genome assembly with the alx3 transcript from Ensembl release 91 (GRCz10) mapped to the GCRz11 genome in place of the release 101 (GRCZ11) version due to inaccurate truncation of the 3’ UTR in the most recent version7.
Supplementary files format and content: wt.barcodes.tsv.gz : barcodes for WT dataset in tsv file
Supplementary files format and content: alx3M.barcodes.tsv.gz : barcodes for alx3M dataset in tsv file
Supplementary files format and content: alx3Malx4aM.barcodes.tsv.gz : barcodes for alx3Malx4aM dataset in tsv file
Supplementary files format and content: wt.features.tsv.gz : features for WT dataset in tsv file
Supplementary files format and content: alx3M.features.tsv.gz : features for alx3M dataset in tsv file
Supplementary files format and content: alx3Malx4aM.features.tsv.gz : features for alx3Malx4aM dataset in tsv file
Supplementary files format and content: wt.matrix.mtx.gz : matrix for WT dataset in mtx file
Supplementary files format and content: alx3M.matrix.mtx.gz : matrix for alx3M dataset in mtx file
Supplementary files format and content: alx3Malx4aM.matrix.mtx.gz : matrix for alx3Malc4aM dataset in mtx file
Supplementary files format and content: 230724_A00405_0714_BH55GNDSX7_L3_Nichols_demux.csv : csv of all data files

organism: Danio rerio

source_name: 48hpf zebrafish embryo

growth_protocol: Zebrafish were grown to 48hpf in E2 embryo media

extract_protocol:
33 double transgenic fli1:EGFP;sox10:mRFP embryos per genotype were dissociated into single-cell suspension using cold-active protease from Bacillus licheniformis, DNase, EDTA, and trituration.
Sorted cells (at 3.27 x 105 cells/ml in wild type, at 2.72 x 105 cells/ml in alx3-/-, and at 2.86 x 105 cells/ml in alx3-/-;alx4a-/- with ~85% viability) were loaded into the 10X Chromium Controller aiming to capture > 10,000 cells per sample. 2x150 paired-end sequencing Chromium 10X Genomics libraries were sequenced using the NovaSEQ6000.

value: 48hpf zebrafish embryo

value: Cranial neural crest

value: wild type


title: hippo_WT1 snRNA-seq

description:
Library name: GEX_hippo_WT1
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds

value: hippocampus

value: wild-type


title: hippo_WT2 snRNA-seq

description:
Library name: GEX_hippo_WT2
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds


title: mouse-muscle-cell-proliferating-3A-ChIP-input

value: C2C12 myoblasts

value: muscle cells

value: proliferation


title: mouse-muscle-cell-differentiating-6B-RNASeq

data_processing:
Sequencing reads were aligned to mm9 using STAR 2.5.0 (Dobin et al., 2013) with default options.
For data visualization, wigToBigWig from the UCSC genome browser tools was used to generate bigwig files and uploaded to UCSC genome browser.
Assembly: mm9
Supplementary files format and content: bigwig file

growth_protocol: C2C12 myoblasts (Yaffe and saxel, 1977) were grown in D-MEM supplemented with 20% fetal bovine serum (FBS) or 10% FBS respectively and penicillin-streptomycin (100 U/ml).

extract_protocol: After purification with the MinElute Reaction Cleanup Kit, 3 ng ds-cDNA was processed for library construction using KAPA Hyper Prep Kit according to the standard protocol except that a 15-minute USER enzyme incubation step was added before library amplification. The prepared libraries were quantified with the KAPA Library Quantification Kit, and then sequenced in a paired-ended manner using the NextSeq 500 (Illumina) according to standard Illumina protocols.

treatment_protocol: Myoblasts were differentiated switching them in differentiation medium D-MEM supplemented with 2% horse serum and penicillin-streptomycin (100 U/ml).

value: 72h differentiation


title: hippo_WT3 snRNA-seq

description:
Library name: GEX_hippo_WT3
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds


title: mouse-muscle-cell-differentiating-5B-RNASeq


title: 27-VP-022-01, lesional skin biopsy

description: Library name: 27_VP_022_01_lesioneel_C4

value: skin


title: mouse-muscle-cell-differentiating-3B-RNASeq

value: 36h differentiation


title: hippo_WT4 snRNA-seq

description:
Library name: GEX_hippo_WT4
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds


title: mouse-muscle-cell-proliferating-2B-RNASeq


title: 26-VP-015-01, healthy skin biopsy

description: Library name: 26_VP_015_01_gezond_B4


title: mouse-muscle-cell-differentiating-4B-RNASeq


title: mouse-muscle-cell-proliferating-1B-RNASeq


title: BoMac475,H3K27ac, ChIP

city: Yinchuan

first: Gang

last: Zhao

address: 489 Helan West Road, Xixia District

institute: ningxia university

data_processing:
The reads were trimmed from 3' end until the final base had a quality score>30, using Trim-glore, discarding reads left with <20bp.
The reads were aligned to ARS-UCD1.2 genome using bwa-mem version 0.7.17 with default settings (BWA-MEM).
Peaks were called using MACS2 v2.2.6 with f = BAMPE; nomodel; shift = 0; extsize = 200; q = 0.05; keep-dup all
Assembly: ARS-UCD1.2
Supplementary files format and content: bigWig, Peak (except for Input sample)

organism: Bos taurus

source_name: BoMac

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator.
ChIP-Seq libraries were prepared by ChIP-IT ChIP-Seq Kit (Active Motif).

value: BoMac


title: BoMacWT,H3K27ac, ChIP

value: BoMacWT


title: 24-VP-013-01, perilesional skin biopsy

description: Library name: 24_VP_013_01_perilesioneel_huid_H3


title: HYP.IP.3

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Library name: Pool2_36

data_processing:
The reads were trimmed for adapter "AGATCGGAAGAGCACACGTCT" and polyX tails by using fastp.
Adapter-trimmed reads were aligned to mouse genome (mm10) by using STAR.
featureCounts was used to assign mapped sequencing reads to genomic features. For reads mapped to multiple features, it assigns fractions (1/number of features).
Assembly: mm10
Supplementary files format and content: miRNA_count_table.csv, CSV file

source_name: Hypothalamus

growth_protocol: Male mice (8-12 weeks old, fed standard chow) were used.

extract_protocol:
RNA was extracted by Trizol-chloroform.
Libraries were prepared using the NEBNext® Multiplex Small RNA Library Prep Kit for Illumina® (Index Primers 1-48) Cat#E7560S, per manufacturer's instructions.

treatment_protocol: 4-thiouracil was injected intraperitoneally (50mg/kg) 4 times every 48hrs to label BAT-miRNAs.

value: Hypothalamus

tag: type

value: IP

tag: mouse id


title: BoMacWT,H3K4me3, ChIP


title: HYP.IP.2

description: Library name: Pool2_34


title: BoMac475,H3K4me3, ChIP


title: Control 14, skin biopsy

description: Library name: 22_Controle_14_F3


title: AngII+MOTS-c3

city: Shanghai

first: Ying

middle: ying

last: Liao

address: 150 Jimo Road，Pudongxin,Shanghai

institute: Shanghai East Hospital

description: Library name: NGS20250703-021-00006_M3-2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. 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, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Alignment files were sorted and duplicates removed using Picard tools (v1.41) and SAMtools (v0.1.18).
Supplementary files format and content: csv files include Reads count for each Sample

source_name: atrial

extract_protocol:
After 48 h of treatment, total RNA was extracted using Trizol and subjected to RNA sequencing.
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

value: atrial

value: Primary atrial  fibroblasts


title: HYP.IP.1

description: Library name: Pool2_32


title: AngII+MOTS-c2

description: Library name: NGS20250703-021-00006_M3-1


title: Control 13, skin biopsy

description: Library name: 21_Controle_13_E3


title: MUS.IP.5

description: Library name: Pool2_29

source_name: Muscle (gastrocnemius)

value: Muscle (gastrocnemius)


title: AngII+MOTS-c1

description: Library name: NGS20250703-021-00006_M2


title: AngII+HNG4

description: Library name: NGS20250703-021-00006_H4


title: 20-VP-024-01, healthy skin biopsy

description: Library name: 20_VP_024_01_gezond_huid_D3


title: AngII+HNG3

description: Library name: NGS20250703-021-00006_H3-2


title: AngII+HNG2

description: Library name: NGS20250703-021-00006_H3-1


title: 1-VP-008-01-X, lesional skin biopsy

description: Library name: 1_VP_008_01_X_lesioneel_huid_A1


title: MUS.IP.3

description: Library name: Pool2_23


title: 19-VP-024-01, perilesional skin biopsy

description: Library name: 19_VP_024_01_perilesioneel_huid_C3


title: AngII4

description: Library name: NGS20250703-021-00006_A4


title: RNA-seq in Donor 30 macrophages, untreated

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

data_processing:
RNA-seq data was aligned to the hg38 assembly of the human genome using STAR v2.7.10b (parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000). Gene counts were computed using featureCounts v2.0.0 and the latest refFlat annotation from UCSC (parameters: -M -p). Differential expression analysis was performed using DESeq2 v1.40.1. Pathway enrichment analysis was performed using the package pathfindR v2.2.0.
Assembly: hg38
Supplementary files format and content: BigWig files of RNA-seq coverage

source_name: macrophage

growth_protocol: CD14+ peripheral blood mononuclear cells (PBMC) were obtained from buffy coats of human blood donors from the Dutch blood bank. All blood donors were informed about the research and granted their consent to the blood bank. The research is exempt from ethical approval by the Dutch Medical Research with Human Subjects Law, because samples were provided fully anonymized to the researchers and the blood donors did not have to undergo extra procedures. Gradient centrifugation was performed at 1250 ×g for 22 minutes at room temperature in SepMate-50 tubes (STEMCELL, 85450) containing ficoll (STEMCELL, 07851). CD14+ monocytes were isolated from PBMC using CD14 MicroBeads (Miltenyi Biotech, 130-050-201) for LS column (Miltenyi Biotech, 130-042-401) magnetic antibody cell sorting (MACS) according to the manufacturer’s supplied protocol. Human peripheral blood monocyte-derived macrophages were generated in ultra-low adherent 6-well plates (Corning, 3471) in 2 mL complete RPMI 1640 Medium (Gibco, 11875093) including 10% Fetal Bovine Serum (FBS) (Hyclone, 10309433), 1% antibiotic-antimitotic (Gibco, 15240062), 1% L-glutamine (Gibco, 15430614), and 100 ng/mL M-CSF (RnD, 216-MC) in 5% CO2 at 37 °C and for 7 days. On day 4, macrophages were supplemented with 1 mL complete RPMI 1640 Medium containing 50 ng/mL M-CSF.

extract_protocol:
Samples were washed twice in PBS and lysed by direct addition of 1 mL TRIzol reagent (ThermoFisher Scientific, 15596026). RNA extraction was performed as per manufacturer instructions, and RNA integrity was assessed by electrophoresis.
Library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, E7770L), as per manufacturer instructions.

treatment_protocol: PBMC-differentiated macrophages were seeded in 6-well plate at 1,000,000 cells/well, cells were treated with 1 μg/mL LPS, 20 ng/mL IFN-γ and 0.1 mM, 1 mM or 10 mM sodium butyrate for 24 hours.

value: macrophage


title: AngII3

description: Library name: NGS20250703-021-00006_A3-2


title: MUS.IP.2

description: Library name: Pool2_22


title: AngII2

description: Library name: NGS20250703-021-00006_A3-1


title: 18-VP-024-01, lesional skin biopsy

description: Library name: 18_VP_024_01_lesioneel_huid_B3


title: MUS.IP.1

description: Library name: Pool2_21


title: AngII1

description: Library name: NGS20250703-021-00006_A1


title: CUMS3

first: mao yang

address: No. 27 Courtyard, Taiping Road, Haidian District, Beijing

institute: Academy of Military Medical Sciences

description: Library name: sample6

data_processing:
Quality Control Quality statistics of the raw reads was evaluated using FastQC (fastqc_v0.11.3). Raw reads in FASTQ format were pre-processed through fastp (fastp 0.20.0). The remaining reads after filtering were proceeded to subsequent analyses. The quality statistics of clean reads was also performed using FastQC. Reference Data Preparation before Analysis.Prior to conducting the analysis, we obtained or prepared the necessary reference datasets for the studied species. This included the reference genome sequence in FASTA format, gene annotation in GTF format, Gene Ontology (GO) annotation files, functional description files, and a BEDfile specifying gene regions. Repetitive elements in the genome were identified and masked using RepeatMasker, which screens for interspersed repeats and low-complexity DNA sequences by referencing curated repeat libraries such as Dfam or RepBase. Additionally, CpG islands (CGIs) were predicted from the genome sequence using the cpgIslandExt tool, generating a track of these genomic features for downstream analysis. Reads Mapping to the Reference Genome The alignment of bisulfite-treated reads to the reference genome was performed using Bismark software (version 0.16.3) with the parameter-X 700 to set the maximum fragment length for valid paired-end alignments and--dovetail to allow dovetailed pairs. Prior to alignment, the reference genome was  in silico converted into bisulfite-converted versions: one with all cytosines (C) transformed to thymines (T) and another with all guanines (G) transformed to adenines (A). These converted genomes were indexed using  Bowtie2 to facilitate efficient alignment. Clean sequencing reads were similarly converted into fully bisulfite-transformed versions (C-to-T and G-to-A) and aligned  directionallyto theconverted reference genomes. For each read, alignments to both the original top strand andthe complementary bottom strand were evaluated. Reads producing a  unique bestalignment across these processes were retained. The methylation state of each cytosineposition was inferred by comparing these alignments to the unconverted genomic sequence. PCR duplicates were identified as reads aligning to identical genomic regions and removed using Bismark's deduplication function to ensure accurate methylation calling. Sequencing depth and coverage statistics were calculated based on deduplicated reads. Methylation calls were extracted using  “bismark_methylation_extractor with the--no_overlap” option to avoid double-counting overlapping read pairs in paired-end data. The results were converted into  bigWig format for visualization in the  IGV browser . To assess bisulfite conversion efficiency, the  non-conversion rate was calculated as the percentage of cytosines remaining unconverted (i.e., still sequenced as cytosine) at reference cytosine positions in the lambda phage genome (spike-in control), providing a quality control metric for the bisulfite treatment step.
Estimating Methylation Level Methylated sites were identified using a binomial test based on methylated read counts (mC), total read counts (mC + umC), and the non-conversion rate (r). Sites with a methylation level (ML) ≥ 0.05 and an FDR-adjusted p-value < 0.01 were considered significantly methylated. To analyze methylation across the sequence, the genome was divided into 10 kb bins. For each window, the total methylated and unmethylated counts were summed. The methylation level for each window or cytosine site was calculated as the proportion of methylated cytosines, defined as ML = mC / (mC + umC).
Differentially Methylated Analysis Differentially methylated regions (DMRs) were identified using the DSS software, The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions. According to the distribution of DMRs through the genome, we defined the genes related to DMRs as genes whose gene body region (from TSS to TES) or promoter region (2 kb upstream from the TSS) have an overlap with the DMRs
Assembly: mRatBN7.2 (rn7)
Supplementary files format and content: All processed data files are provided for the 5mC methylation profiling (e.g., whole-genome bisulfite sequencing or reduced representation bisulfite sequencing) from hippocampal endothelial cells of control (Ctrl) and CUMS rats (n=3 per group). The files include summary plots, tables of differentially methylated regions (DMRs), and gene-body methylation data.  1. Individual sample methylation level plots  Files: Ctrl1.mC_genomic_feature_level.png, Ctrl2.mC_genomic_feature_level.png, Ctrl3.mC_genomic_feature_level.png, CUMS1.mC_genomic_feature_level.png, CUMS2.mC_genomic_feature_level.png, CUMS3.mC_genomic_feature_level.png  Format: PNG image (bitmap).  Content: For each sample, the plot shows the distribution of 5mC methylation levels (e.g., proportion of methylated cytosines) across different genomic features (e.g., promoter, exon, intron, intergenic, and CpG islands). The y-axis typically represents methylation percentage (0–100%) and the x-axis indicates feature categories or methylation contexts (CG, CHG, CHH).  2. All DMR results (Excel)  File: CUMS_vs_Ctrl.DMR.all.result.xls  Format: Microsoft Excel (XLS) file; can be opened as a spreadsheet.  Content: Contains all differentially methylated regions (DMRs) identified between CUMS and Ctrl groups. Column headers likely include: chromosome, start position, end position, DMR length, number of CpG sites, mean methylation difference (CUMS – Ctrl), statistical significance (p-value, q-value or adjusted p-value), and DMR direction (hyper/hypo-methylation).  3. Heatmap of all DMRs  File: CUMS_vs_Ctrl.DMR.heatmap.all.png  Format: PNG image.  Content: A heatmap visualizing the methylation levels (e.g., beta values) of all DMRs across the six individual samples (Ctrl1-3, CUMS1-3). Rows represent DMRs, columns represent samples. Color scale indicates low (e.g., blue) to high (e.g., red) methylation. Hierarchical clustering of rows and columns is often applied.  4. Annotated DMR results  File: CUMS_vs_Ctrl.DMR.result.annotation.xls  Format: XLS spreadsheet.  Content: Annotation of each DMR with respect to nearby genes and genomic elements. Columns typically include DMR coordinates (chr, start, end), associated gene symbol, gene ID, distance to TSS, genomic region type (e.g., promoter, exon, intron, intergenic), and possibly functional consequences.  5. Gene up/down summary plot  File: CUMS_vs_Ctrl.gene_updown.png  Format: PNG image.  Content: A bar chart or dot plot summarizing the number of genes with hyper-methylated DMRs (up) versus hypo-methylated DMRs (down) in the CUMS group compared to controls. Alternatively, it may show the distribution of methylation changes in gene bodies or promoter regions.  6. Gene-body methylation data  File: CUMS_vs_Ctrl.genebody_methlyation.txt  Format: Plain text, tab-delimited.  Content: Methylation levels across gene bodies for each gene. Columns likely include: gene identifier (e.g., gene symbol or Ensembl ID), mean methylation in Ctrl group, mean methylation in CUMS group, difference (CUMS – Ctrl), and p-value. This file allows gene-level analysis of methylation changes.  7. All DMR results (text version)  File: DMR.ALL.result.txt  Format: Plain text, tab-delimited.  Content: Similar to CUMS_vs_Ctrl.DMR.all.result.xls but in text format. Contains the complete list of DMRs with coordinates, statistics, and methylation differences. This file is machine-readable and can be easily parsed for downstream analyses.  Note: DMR.ALL.result.txt and CUMS_vs_Ctrl.DMR.all.result.xls contain essentially the same DMR data but in different file formats (plain text vs. Excel). Users may choose either format for convenience.
Library strategy: EM-seq

source_name: Hippocampus

extract_protocol:
Hippocampal tissues were dissected from control and CUMS rats after modeling and immediately placed in ice-cold PBS. Tissues were minced into small pieces (approximately 1 mm³) using sterile scissors, then digested with a mixture of collagenase type Ⅱ(1 mg/mL) and DNase I (0.1 mg/mL) in Hank’s balanced salt solution at 37 ℃ for 30 min with gentle agitation. The digestion reaction was terminated by adding an equal volume of ice-cold PBS containing 10% FBS. The resulting cell suspension was filtered through a 70 μm cell strainer to remove undigested tissue fragments and cell aggregates, then centrifuged at 300 × g for 5 min at 4 °C. The cell pellet was washed twice with cold PBS containing 1% FBS to remove residual enzymes. For immunostaining, the single-cell suspension was adjusted to a concentration of 1 × 10⁶ cells per 100 μL in staining buffer (PBS with 2% FBS). Cells were then stained with FITC-conjugated anti-rat CD45 antibody (BD Biosciences, 554877) and PE-conjugated anti-rat CD31 antibody (BD Biosciences, 555027) at optimized dilutions (1:100) for 30 min at 4 °C in the dark. Following antibody incubation, cells were washed twice with staining buffer and centrifuged at 300 × g for 5 min. After the final wash, cells were resuspended in staining buffer for immediate flow cytometric sorting. Endothelial cells were identified as CD45⁻/CD31⁺ population and sorted using a flow cytometer (BD FACSAria™ III) equipped with appropriate lasers and filters. Sorted cells were collected into sterile tubes containing RNase inhibitor or lysis buffer for downstream analyses as required. Sorted endothelial cells were collected into sterile 1.5 mL microcentrifuge tubes containing 500 μL of ice-cold PBS and centrifuged at 300 × g for 5 min at 4 °C. The supernatant was carefully aspirated, and the cell pellet was washed once with 500 μL of ice-cold PBS to remove residual staining buffer and antibodies. After centrifugation under the same conditions, the supernatant was discarded, and the cell pellet was snap-frozen in liquid nitrogen and stored at -80 °C until DNA extraction. After DNA were extracted from the samples (Animals: TIANGEN DP705; Plants: TIANGEN DP342; cfDNA: QIAamp MinElute cfDNA Midi Kit (Qiagen 55284)), Genomic DNA degradation and contamination was checked using agarose gels. DNA purity was evaluated by NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). Fragment distribution of cfDNA or Genomic DNA waschecked using Agilent 2100. DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA)
Unmethylated Lambda DNA was spiked into each sample (10–100 ng total DNA input) as a negative control for methylation analysis. The DNA was then sheared to 200–350 bp fragments using the Bioruptor Pico ultrasonicator. Library preparation was performed using the Enzymatic Methylation sequencing Kit. Final library quality and fragment size distribution were assessed using the Agilent Bioanalyzer 2100 system.

value: Hippocampus

value: chronic unpredictable mild stress (CUMS) for 8 weeks


title: 17-VP-021-01, healthy skin biopsy

description: Library name: 17_VP_021_01_gezond_A3

source_name: skin


title: CUMS2

description: Library name: sample5


title: LIV.IP.5

description: Library name: Pool2_20

source_name: Liver

value: Liver


title: CUMS1

description: Library name: sample4


title: 16-VP-021-01, perilesional skin biopsy

description: Library name: 16_VP_021_01_perilesioneel_H2


title: LIV.IP.4

description: Library name: Pool2_19


title: male, intestinal epithelium, wildtype, high fat diet, acute, biological replicate 3

description: Library name: Sample 19

value: intestinal epithelium

value: male

value: wildtype

value: high fat diet one week


title: MitoRibo_HeLa_mtRF1L_KO_1

status: Public on Jun 05 2026

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

institute: RIKEN

description: Library name: L13

library_source: other

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Assembly: Read quantitation using custom scripts
Supplementary files format and content: The human or mouse nuclear genomes (human, hg38; mouse, mm10) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpframing text files contain nine columns:  1. the length of ribosome footprint; 2. the fraction of ribosome footprint; 3~5. the number of ribosome footprint at each frames;  6~8,the fraction of ribosome footprint at each frames; 9. the relative entropy of ribosome footprint.
Library strategy: MitoIP-Thor-Ribo-Seq

molecule: other

source_name: HeLa

extract_protocol:
MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq: Cells were cultured in 15-cm dishes, washed with ice-cold PBS, and lysed with 1200 µl of hypotonic buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol). The lysate was incubated with anti-TOM22 antibody-conjugated beads from Mitochondria Isolation Kit, Human (Miltenyi Biotec) for 60 min at 4°C. The subsequent wash and elution steps were performed with wash buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 15 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol), according to the manufacturer’s instructions. The eluted mitochondrial fraction was pelleted by centrifugation at 7,000 × g for 10 min at 4°C and resuspended in modified lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide, 100 µg/ml chloramphenicol, and 2.5 U/ml TURBO DNase). After clarification by centrifugation at 20,000 × g for 10 min at 4°C, the supernatant was used for library preparation. Ribo-Seq and RNA-Seq: Cells in a 10-cm dish were lysed with 600 µl of lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol) and treated with 25 U/ml TURBO DNase (Thermo Fisher Scientific). Then, the lysate was clarified by centrifugation at 20,000 × g for 10 min at 4°C.
MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. RNA-seq: the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).

value: HeLa


title: Ctrl2

description: Library name: sample2

value: Control


title: Ctrl1

description: Library name: sample1


title: VP-008_01, healthy skin biopsy

description: Library name: 14_VP_008_01_gezond_F2

value: skin


title: Male_PAE_VEH_Adolescent N180

city: Binghamton

first: Anny

last: Gano

state: NY

address: 4400 Vestal Parkway East

institute: SUNY Binghamton

description:
Library name: N180
column names are library name - c#, etc

data_processing:
Raw fastq files processed with fastp to remove adapter and low-quality reads, index built using Hisat2 v2.0.5, paired-end clean reads aligned to the genome.
Assembly: Rattus norvegicus, PPI Taxid: 10116, KEGG rno, ncbi_rattus_norvegicus_gcf_036323735_1_grc8
Supplementary files format and content: text file includes gene counts per sample
Supplementary files format and content: text file includes FPKM per sample as well

source_name: brain (nucleus accumbens)

extract_protocol:
RNA was extracted using high-lipid extraction and RNA integrity was assessed using Bioanalyzer 2100 (Agilent Technologies, CA, USA) and purity via the Nanodrop, with all RIN values > 6.3 (except one 5.8), average = 7.2.
cDNA was synthesized using random hexamer primers, second strand synthesis using dTTP for non-strand-specific library construction.

value: brain (nucleus accumbens)

value: Long Evans rat

value: described in sample name

tag: batch


title: LIV.IP.2

description: Library name: Pool2_14

value: IP


title: VP-008_01, perilesional skin biopsy

description: Library name: 13_VP_008_01_perilesioneel_huid_E2

data_processing:
Raw read QC was done using FastQC (v0.12.1)
Adapter and quality trimming was done using cutadapt (v5.0)
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.11b)
UMI-based removal of mapped PCR duplicates was done using umi_tools (v1.1.6)
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.1)
Assembly: Homo sapiens  GRCh38 (Ensembl release 112)
Supplementary files format and content: all_samples_rsem_gene_counts.tsv: raw expression count table in tab separated format, with genes as rows and samples as columns

extract_protocol:
The sampled tissue was lysed mechanically using a 1000 µL pipette tip, followed by shearing through a syringe (Terumo Corporation, Tokyo, Japan) fitted with a 20Gx1½ needle (Terumo Corporation). Total RNA was extracted using the conventional TriReagent/chloroform method and subsequently purified with the Direct-zol Microprep RNA Kit (Zymo Research), including on-column DNase I treatment, according to the manufacturer’s instructions. As residual genomic DNA was detected in some samples, an additional DNase treatment was performed using the TURBO DNA-free™ Kit (Invitrogen, Thermo Fisher Scientific) on all RNA extracts.
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen)


title: Male_PAE_VEH_Adolescent N175

description:
Library name: N175
column names are library name - c#, etc


title: Control 12, skin biopsy

description: Library name: 12_controle_12_D2


title: Ctrl3

description: Library name: sample3


title: BAT.IP.5

description: Library name: Pool2_10

source_name: Brown fat

value: Brown fat


title: Female_FCL_VEH_Adolescent N152

description:
Library name: N152
column names are library name - c#, etc


title: Control 11, skin biopsy

description: Library name: 11_controle_11_C2


title: Male_PAE_VEH_Adolescent N151

description:
Library name: N151
column names are library name - c#, etc


title: BAT.IP.4

description: Library name: Pool2_7


title: Male_FCL_VEH_Adult N148

description:
Library name: N148
column names are library name - c#, etc


title: Control 10, skin biopsy

description: Library name: 10_controle_10_B2


title: Female_PAE_VEH_Adolescent N144

description:
Library name: N144
column names are library name - c#, etc


title: BAT.IP.3

description: Library name: Pool2_6


title: Female_PAE_VEH_Adolescent N143

description:
Library name: N143
column names are library name - c#, etc


title: VP-021-01, lesional skin biopsy

description: Library name: 15_VP_021_01_lesioneel_G2


title: Female_FCL_VEH_Adolescent N187

description:
Library name: N187
column names are library name - c#, etc


title: LIV.IP.3

description: Library name: Pool2_15


title: Control 9, skin biopsy

description: Library name: 52_Control_9__D6


title: Male_FCL_VEH_Adolescent N140

description:
Library name: N140
column names are library name - c#, etc


title: Male_FCL_VEH_Adult N179

description:
Library name: N179
column names are library name - c#, etc


title: BAT.IP.2

description: Library name: Pool2_4


title: Female_PAE_AAE_Adult N129

description:
Library name: N129
column names are library name - c#, etc


title: Control 8, skin biopsy

description: Library name: 51_Control_8__C6


title: LIV.IP.1

description: Library name: Pool2_13


title: Female_FCL_VEH_Adult N127

description:
Library name: N127
column names are library name - c#, etc


title: BAT.IP.1

description: Library name: Pool2_2


title: Male_FCL_VEH_Adult N126

description:
Library name: N126
column names are library name - c#, etc


title: Control 7, skin biopsy

description: Library name: 50_Control_7__B6


title: Male_FCL_VEH_Adult N172

description:
Library name: N172
column names are library name - c#, etc


title: Male_PAE_VEH_Adolescent N123

description:
Library name: N123
column names are library name - c#, etc


title: HYP5

description: Library name: Pool1_39

value: Hypothalamus

value: Input


title: Female_PAE_AAE_Adult N119

description:
Library name: N119
column names are library name - c#, etc


title: Control 6, skin biopsy

description: Library name: 49_Control_6__A6


title: HYP4

description: Library name: Pool1_38


title: Male_PAE_AAE_Adult N109

description:
Library name: N109
column names are library name - c#, etc


title: Male_PAE_VEH_Adolescent N108

description:
Library name: N108
column names are library name - c#, etc


title: Control 5, skin biopsy

description: Library name: 48_Control_5__H7


title: Female_PAE_AAE_Adult N169

description:
Library name: N169
column names are library name - c#, etc


title: Male_PAE_VEH_Adolescent N107

description:
Library name: N107
column names are library name - c#, etc


title: HYP3

description: Library name: Pool1_36


title: Female_FCL_VEH_Adult N104

description:
Library name: N104
column names are library name - c#, etc


title: Control 4, skin biopsy

description: Library name: 47_Control_4__G7


title: Female_PAE_AAE_Adult N101

description:
Library name: N101
column names are library name - c#, etc


title: Female_PAE_VEH_Adolescent N099

description:
Library name: N099
column names are library name - c#, etc


title: Control 3, skin biopsy

description: Library name: 46_Control_3_F7


title: HYP2

description: Library name: Pool1_34


title: HYP1

description: Library name: Pool1_32


title: Female_FCL_VEH_Adolescent N092

description:
Library name: N092
column names are library name - c#, etc


title: Male_FCL_VEH_Adolescent N091

description:
Library name: N091
column names are library name - c#, etc


title: Female_FCL_VEH_Adult N093

description:
Library name: N093
column names are library name - c#, etc


title: Control 2, skin biopsy

description: Library name: 45_Control_2__E7


title: MUS5

description: Library name: Pool1_29

value: Muscle (gastrocnemius)


title: Female_FCL_VEH_Adolescent N088

description:
Library name: N088
column names are library name - c#, etc


title: Control 1, skin biopsy

description: Library name: 44_Control_1__D7


title: Male_FCL_VEH_Adolescent N087

description:
Library name: N087
column names are library name - c#, etc


title: MUS4

description: Library name: Pool1_28


title: Male_FCL_VEH_Adult N084

description:
Library name: N084
column names are library name - c#, etc


title: VP-019-01, healthy skin biopsy

description: Library name: 43_VP_019_01_gezond_C7


title: Male_PAE_AAE_Adult N081

description:
Library name: N081
column names are library name - c#, etc


title: MUS3

description: Library name: Pool1_23


title: Female_FCL_VEH_Adolescent N080

description:
Library name: N080
column names are library name - c#, etc


title: VP-019-01, perilesional skin biopsy

description: Library name: 42_VP_019_01_perilesioneel_B7


title: Male_FCL_VEH_Adult N076

description:
Library name: N076
column names are library name - c#, etc


title: MUS2

description: Library name: Pool1_22


title: VP-018-01, healthy skin biopsy

description: Library name: 41_VP_018_01_gezond_A7


title: Male_PAE_AAE_Adult N073

description:
Library name: N073
column names are library name - c#, etc


title: Female_FCL_VEH_Adult N072

description:
Library name: N072
column names are library name - c#, etc


title: MUS1

description: Library name: Pool1_21


title: Male_PAE_AAE_Adult N069

description:
Library name: N069
column names are library name - c#, etc


title: VP-018-01, perilesional skin biopsy

description: Library name: 40_VP_018_01_perilesioneel_H8


title: Male_FCL_VEH_Adolescent N068

description:
Library name: N068
column names are library name - c#, etc


title: LIV5

description: Library name: Pool1_20


title: Male_PAE_VEH_Adolescent N067

description:
Library name: N067
column names are library name - c#, etc


title: VP-018-01, lesional skin biopsy

description: Library name: 39_VP_018_01_lesioneel_G8


title: Female_FCL_VEH_Adult N064

description:
Library name: N064
column names are library name - c#, etc


title: LIV4

description: Library name: Pool1_19


title: 3-VP-008-01-X, healthy skin biopsy

description: Library name: 3_VP_008_01_X_gezond_huid_C1


title: VP-016-01, healthy skin biopsy

description: Library name: 38_VP_016_01_gezond_F8


title: Male_PAE_AAE_Adult N061

description:
Library name: N061
column names are library name - c#, etc


title: Female_PAE_VEH_Adolescent N060

description:
Library name: N060
column names are library name - c#, etc


title: LIV3

description: Library name: Pool1_15


title: VP-016-01, perilesional skin biopsy

description: Library name: 37_VP_016_01_perilesioneel_E8


title: Male_PAE_VEH_Adolescent N059

description:
Library name: N059
column names are library name - c#, etc


title: LIV2

description: Library name: Pool1_14


title: Male_FCL_VEH_Adolescent N056

description:
Library name: N056
column names are library name - c#, etc


title: Female_FCL_VEH_Adolescent N048

description:
Library name: N048
column names are library name - c#, etc


title: VP-016-01, lesional skin biopsy

description: Library name: 36_VP_016_01_lesioneel_D8


title: Female_FCL_VEH_Adolescent N038

description:
Library name: N038
column names are library name - c#, etc


title: LIV1

description: Library name: Pool1_13


title: Plasma EV RNA-Seq, B12 (PLWoH)

description:
Library name: B12
Maternal plasma-derived EV RNA; sex: F; RIN: 1.0; strand-specific; 2×150 bp; ~20M reads/sample

value: Plasma

value: HIV negative


title: Male_FCL_VEH_Adolescent N037

description:
Library name: N037
column names are library name - c#, etc


title: VP-014-01, healthy skin biopsy

description: Library name: 35_VP_014_01_gezond_C8


title: Female_FCL_VEH_Adult N036

description:
Library name: N036
column names are library name - c#, etc


title: VP-014-01, perilesional skin biopsy

description: Library name: 34_VP_014_01_perilesioneel_B8


title: Female_FCL_VEH_Adult N029

description:
Library name: N029
column names are library name - c#, etc


title: BAT5

description: Library name: Pool1_8


title: BAT4

description: Library name: Pool1_7


title: Male_FCL_VEH_Adolescent N021

description:
Library name: N021
column names are library name - c#, etc


title: Male_PAE_AAE_Adult N020

description:
Library name: N020
column names are library name - c#, etc


title: VP-014-01, lesional skin biopsy

description: Library name: 33_VP_014_01_lesioneel_A8


title: Male_PAE_VEH_Adolescent N018

description:
Library name: N018
column names are library name - c#, etc


title: Male_FCL_VEH_Adolescent N016

description:
Library name: N016
column names are library name - c#, etc


title: BAT3

description: Library name: Pool1_6


title: VP-012-01, healthy skin biopsy

description: Library name: 32_VP_012_01_gezond_H9


title: Female_FCL_VEH_Adult N015

description:
Library name: N015
column names are library name - c#, etc


title: BAT2

description: Library name: Pool1_4


title: Matched adjacent non-tumor lung tissue sample N68

city: Suzhou

first: Jiaqian

last: Qi

address: No.188 Shizi Road

institute: The First Affiliated Hospital of Soochow University

description:
Library name: N68
Local paired bulk RNA-seq library; pair_id=68; tissue_status=adjacent non-tumor; sample_id=N68.

data_processing:
Raw sequencing reads were processed by the sequencing provider to generate a gene-level raw-count matrix.
Assembly: GRCh38
Supplementary files format and content: CSV file containing gene-level raw counts. Rows correspond to Ensembl gene identifiers and columns correspond to sample IDs.

source_name: matched adjacent non-tumor lung tissue

extract_protocol:
Total RNA was extracted from each surgically resected tissue specimen using a standard total-RNA extraction workflow according to the sequencing provider's protocol. RNA quantity and quality were assessed before library construction, and samples passing RNA quality-control criteria were used for bulk RNA-seq.
Bulk RNA-seq libraries were prepared from total RNA using an Illumina-compatible RNA-seq library preparation workflow according to the sequencing provider's protocol. Libraries were generated for paired-end sequencing.

value: matched adjacent non-tumor lung tissue

value: bulk tissue


title: Female_PAE_AAE_Adult N011

description:
Library name: N011
column names are library name - c#, etc


title: VP-012-01, perilesional skin biopsy

first: Yannick

institute: Ghent University

description: Library name: 31_VP_012_01_perilesioneel_G9


title: Male_FCL_VEH_Adolescent N008

description:
Library name: N008
column names are library name - c#, etc


title: BAT1

description: Library name: Pool1_2


title: Female_PF_VEH_Adolescent c194

description:
Library name: c194
column names are library name - c#, etc

source_name: brain (anterior cingulate cortex)

value: brain (anterior cingulate cortex)


title: VP-012-01, lesional skin biopsy

description: Library name: 30_VP_012_01_lesioneel_F9


title: Male_PF_AAE_Adolescent c193

description:
Library name: c193
column names are library name - c#, etc


title: HYP.IP.5

description: Library name: Pool2_39


title: VP-011-01, healthy skin biopsy

description: Library name: 29_VP_011_01_gezond_E9


title: Female_PF_VEH_Adolescent c192

description:
Library name: c192
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 120 h serum starvation, bulk population, dox treatment, RNA-seq biol rep 3

city: Berkeley

first: Oscar

last: Whitney

address: 1951 Oxford St

institute: UC Berkeley

description: Library name: C2C12_iMyoD1_120h_diff_bulk_plusDox_RNAseq_biorep3

data_processing:
core/RNAseq pipeline version 3.14.0
Assembly: mm10
Supplementary files format and content: tab-separated transcript-level estimated count matrices generated from Salmon quantification

source_name: skeletal muscle

growth_protocol: C2C12 skeletal muscle myoblasts were maintained in DMEM supplemented with 20% fetal bovine serum, penicillin streptomycin in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using TriZol following manufacturer protocols
polyA-mRNA enrichment was performed on extracted RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S). Extracted RNA was reverse transcribed following NEBNext Ultra II RNA Library Prep kit, following manufacturer protocol. Libraries were prepared following NEBNext Ultra II RNA Library Prep kit protocol

value: skeletal muscle

value: skeletal muscle cell population

value: endogenous MyoD1 + dox-inducible Halo-MyoD1

value: 120 h dox


title: C2C12 cells, iMyoD1, 120 h serum starvation, bulk population, dox treatment, RNA-seq biol rep 2

description: Library name: C2C12_iMyoD1_120h_diff_bulk_plusDox_RNAseq_biorep2


title: Female_PF_AAE_Adolescent c191

description:
Library name: c191
column names are library name - c#, etc


title: Male_PAE_AAE_Adolescent c189

description:
Library name: c189
column names are library name - c#, etc


title: VP-011-01, perilesional skin biopsy

last: Gansemans

description: Library name: 28_VP_011_01_perilesioneel_D9

value: skin


title: Male_PF_VEH_Adolescent c188

description:
Library name: c188
column names are library name - c#, etc

value: Long Evans rat


title: C2C12 cells, iMyoD1, 120 h serum starvation, bulk population, dox treatment, RNA-seq biol rep 1

description: Library name: C2C12_iMyoD1_120h_diff_bulk_plusDox_RNAseq_biorep1


title: Female_FCL_VEH_Adolescent c187

description:
Library name: c187
column names are library name - c#, etc

value: described in sample name


title: VP-011-01, lesional skin biopsy

description: Library name: 27_VP_011_01_lesioneel_C9


title: Female_FCL_AAE_Adolescent c185

description:
Library name: c185
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 120 h serum starvation, bulk population, untreated, RNA-seq biol rep 3

description: Library name: C2C12_iMyoD1_120h_diff_bulk_noDox_RNAseq_biorep3

value: 120 h vehicle


title: Male_PF_VEH_Adolescent c183

description:
Library name: c183
column names are library name - c#, etc


title: Male_FCL_AAE_Adolescent c181

description:
Library name: c181
column names are library name - c#, etc


title: VP-010-01, healthy skin biopsy

description: Library name: 26_VP_010_01_gezond_B9


title: C2C12 cells, iMyoD1, 120 h serum starvation, bulk population, untreated, RNA-seq biol rep 2

description: Library name: C2C12_iMyoD1_120h_diff_bulk_noDox_RNAseq_biorep2


title: Male_FCL_AAE_Adolescent c182

description:
Library name: c182
column names are library name - c#, etc


title: VP-010-01, perilesional skin biopsy

description: Library name: 25_VP_010_01_perilesioneel_A9


title: Male_PAE_VEH_Adolescent c180

description:
Library name: c180
column names are library name - c#, etc


title: Matched adjacent non-tumor lung tissue sample N66

description:
Library name: N66
Local paired bulk RNA-seq library; pair_id=66; tissue_status=adjacent non-tumor; sample_id=N66.


title: 2OX-AA rep1

city: Kaifeng

first: Xiaohong

last: Zhu

address: Jinming Street

institute: Henan University

data_processing:
HiSeq2500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: seedling

extract_protocol:
Total RNA was isolated usingTRIzol for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole seedling

value: ten day old

value: MCU2 overexpression line

value: AA


title: 4OX-CK rep1

value: MCU4 overexpression line

value: CK


title: C2C12 cells, iMyoD1, 120 h serum starvation, bulk population, untreated, RNA-seq biol rep 1

description: Library name: C2C12_iMyoD1_120h_diff_bulk_noDox_RNAseq_biorep1


title: Male_FCL_VEH_Adult c179

description:
Library name: c179
column names are library name - c#, etc


title: VP-010-01, lesional skin biopsy

city: Ghent

address: Ottergemsesteenweg 460

description: Library name: 24_VP_010_01_lesioneel_H10


title: Female_FCL_AAE_Adult c178

description:
Library name: c178
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 48 h serum starvation, dox treatment, RNA-seq biol rep 3

description: Library name: C2C12_iMyoD1_48h_diff_plusDox_RNAseq_biorep3

value: skeletal muscle myoblast

value: 48 h dox


title: VP-009-01, perilesional skin biopsy

description: Library name: 22_VP_009_01_perilesioneel_F10


title: VP-009-01, healthy skin biopsy

description: Library name: 23_VP_009_01_gezond_G10


title: Male_PAE_VEH_Adolescent c175

description:
Library name: c175
column names are library name - c#, etc

value: brain (anterior cingulate cortex)


title: Male_PF_AAE_Adolescent c174

description:
Library name: c174
column names are library name - c#, etc


title: Female_PF_VEH_Adolescent c176

description:
Library name: c176
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 48 h serum starvation, dox treatment, RNA-seq biol rep 2

description: Library name: C2C12_iMyoD1_48h_diff_plusDox_RNAseq_biorep2

value: skeletal muscle


title: Female_PAE_AAE_Adolescent c173

description:
Library name: c173
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 48 h serum starvation, dox treatment, RNA-seq biol rep 1

description: Library name: C2C12_iMyoD1_48h_diff_plusDox_RNAseq_biorep1


title: Male_FCL_VEH_Adult c172

description:
Library name: c172
column names are library name - c#, etc


title: VP-009-01, lesional skin biopsy

description: Library name: 21_VP_009_01_lesioneel_E10


title: Female_PAE_VEH_Adult c171

description:
Library name: c171
column names are library name - c#, etc


title: Male_FCL_AAE_Adult c170

description:
Library name: c170
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 48 h serum starvation, untreated, RNA-seq biol rep 3

description: Library name: C2C12_iMyoD1_48h_diff_noDox_RNAseq_biorep3

value: 48 h vehicle


title: VP-007-01, healthy skin biopsy

description: Library name: 20_VP_007_01_gezond__D10


title: VP-007-01, perilesional skin biopsy

description: Library name: 19_VP_007_01_perilesioneel__C10


title: C2C12 cells, iMyoD1, 48 h serum starvation, untreated, RNA-seq biol rep 2

description: Library name: C2C12_iMyoD1_48h_diff_noDox_RNAseq_biorep2

value: endogenous MyoD1 + dox-inducible Halo-MyoD1


title: C2C12 cells, iMyoD1, 48 h serum starvation, untreated, RNA-seq biol rep 1

description: Library name: C2C12_iMyoD1_48h_diff_noDox_RNAseq_biorep1


title: Female_FCL_AAE_Adolescent c168

description:
Library name: c168
column names are library name - c#, etc


title: Female_PAE_AAE_Adolescent c166

description:
Library name: c166
column names are library name - c#, etc


title: Female_PAE_AAE_Adult c169

description:
Library name: c169
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 120 h serum starvation, <40 um myoblast-enriched fraction, dox treatment, RNA-seq biol rep 3

description:
Library name: C2C12_iMyoD1_120h_lt40um_plusDox_RNAseq_biorep3
<40 um myoblast-enriched fraction

value: skeletal muscle myoblast-enriched fraction

value: 120 h dox


title: Male_FCL_AAE_Adult c161

description:
Library name: c161
column names are library name - c#, etc

value: Long Evans rat


title: Female_PAE_VEH_Adolescent c159

description:
Library name: c159
column names are library name - c#, etc

value: described in sample name


title: Male_PF_VEH_Adult c154

description:
Library name: c154
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 120 h serum starvation, <40 um myoblast-enriched fraction, dox treatment, RNA-seq biol rep 2

description:
Library name: C2C12_iMyoD1_120h_lt40um_plusDox_RNAseq_biorep2
<40 um myoblast-enriched fraction


title: Female_PAE_AAE_Adolescent c157

description:
Library name: c157
column names are library name - c#, etc


title: VP-006-01, healthy skin biopsy

description: Library name: 17_VP_006_01_gezond_A10

value: skin


title: Female_PF_AAE_Adult c153

description:
Library name: c153
column names are library name - c#, etc


title: VP-006-01, lesional skin biopsy

description: Library name: 15_VP_006_01_lesioneel_G11