title: K2

city: Taiyuan

first: Yuan

last: Fu

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

institute: Shanxi Medical University

description: Library name: Sample 4

data_processing:
Base Calling and Demultiplexing:Raw sequencing data (BCL files) were converted to FASTQ format using Illumina's bcl2fastq v2.20 (Illumina Inc.).
Raw Data Quality Control:FastQC v0.11.9 was used to assess per-base sequence quality, adapter contamination, GC content, and sequence duplication levels. Summary reports were aggregated with MultiQC v1.11.
Adapter Trimming and Quality Filtering:cutadapt v4.0 was employed to Trim Illumina TruSeq adapters,Remove low-quality bases、Discard reads shorter than 20 bp after trimming and use paired-end mode with default error tolerance.
Alignment to Reference Genome:Filtered reads were aligned to the mm10 (GRCm38) mouse genome using bowtie2 v2.4.5.Post-Alignment Processing:SAM files were converted to sorted BAM files using samtools v1.12.Duplicate reads were marked and removed with Picard MarkDuplicates v2.26.10.BAM files were indexed using samtools v1.12.
Broad histone marks (H3K27me3) were identified using MACS2 v2.2.7.1 with parameters.Normalized genome coverage tracks (bigWig files) were generated with deepTools bamCoverage v3.5.1.Fraction of Reads in Peaks (FRiP) was calculated using MACS2 output.Normalized Strand Cross-Correlation (NSC) and Relative Strand Correlation (RSC) were assessed via phantompeakqualtools v1.2.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

growth_protocol: The cells were maintained in DMEM supplemented with 10% FBS and cultured at 37 °C with 5% CO2. This cell line was validated by short tandem repeat (STR) profiling and was free of mycoplasma contamination.

extract_protocol:
100,000 cells were collected for experiments according to Vazyme #TD903 (Hyperactive Universal CUT&Tag Kit).H3K27me3 (CST #9733) was used for experiments.
Amplified libraries using Vazyme HiFi PCR Master Mix (Catalog #TD903),Index primers (Vazyme kit-provided).PCR program:72°C, 5 min; 98°C, 30 sec;12–15 cycles: 98°C 10 sec, 63°C 30 sec, 72°C 30 sec;72°C, 5 min final extension.Library QC:Quantified with Qubit dsDNA HS Assay.Size distribution verified via Bioanalyzer (peak: 200–700 bp).Pooled equimolar libraries for 150-bp paired-end sequencing on Illumina NovaSeq.


title: HC_16_53, bulk RNA

status: Public on Dec 09 2025

type: SRA

city: Shanghai

first: Tianyi

last: Zhu

address: 639 Zhizaoju Road

department: Ophthalmology

country: China

institute: Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine

description:
Library name: HC_16_53
HC_16_53

library_source: transcriptomic

data_processing:
For PBMCs sequencing, raw fastq data were subjected to quality control using fastp-0.12.4. Alignment was performed using hisat2-2.2.0, referencing the GRCh38 human genome, which included ERCC spike sequences. Sorted SAM files were processed using GATK4-4.2.6.0, and transcript assembly and abundance estimation were carried out using stringtie-2.2.1. Batch effects were corrected using ERCC spike-in as references, employing the R package RUVSeq-1.30.0 for normalization.
Assembly: hg38
Supplementary files format and content: For PBMCs sequencing, tab-delimited text file includes ERCC counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Peripheral blood samples were collected and stored at 4℃ in EDTA anticoagulant tubes and processed promptly. PBMC isolation was performed using a Ficoll density gradient centrifugation with the following steps: whole blood samples were diluted 1:1 with phosphate buffered saline (PBS), and the diluted blood samples were gently layered over Ficoll solution in a centrifuge tube. The mixture was centrifuged at 400g for 30 minutes at room temperature, with the acceleration and brake settings of the centrifuge set to 1. After centrifugation, the intermediate cloudy layer containing the PBMCs was carefully collected. This layer was mixed with three volumes of PBS and centrifuged again at 500g for 10 minutes at room temperature. The resulting PBMC pellet was washed further with PBS and centrifuged to enrich the cells. Samples with significant red blood cell contamination were treated with ACK Lysing Buffer (A10492-01, Gibco) for red blood cell lysis.
For PBMCs sequencing, the total RNA was mixed with ERCC RNA Spike-in Mix (4456740, Invitrogen) in proportion for transcriptome library construction. The sequencing library was prepared using the RNA-seq Library Prep Kit for MGI (NRM605, Vazyme) and sequenced in batches on the DNBSEQ-T7 platform.

tag: cell type

value: PBMC


title: K1

description: Library name: Sample 3

library_source: genomic

molecule: genomic DNA

tag: cell line

tag: genotype


title: HC_16_52, bulk RNA

description:
Library name: HC_16_52
HC_16_52


title: mutant, Pmel treatment, rep2

city: Aurora

first: Sarah

middle: E

last: Clark

state: CO

address: 12700 E 19th Ave, Mail Stop 8333

country: USA

institute: University of Colorado School of Medicine

description: Library name: ZplusM_5_S21

data_processing:
Adapter contamination removal with BBDuk
Tx Quantification with Salmon
Gene-level summaries with Tximport
Assembly: GRCh38 (Gencode H37)
Supplementary files format and content: CSV, rownames are genes, columns are samples, values are Salmon calculated counts

molecule: polyA RNA

extract_protocol:
RNA extraction by Rneasy kit (Qiagen)
Nugen Universal Plus mRNA kit

value: CF

tag: treatment

value: P. melaninogenica strain ATCCÒ 25845, heat-killed


title: C2

description: Library name: Sample 2

value: Control


title: HC_16_50, bulk RNA

description:
Library name: HC_16_50
HC_16_50


title: C1

description: Library name: Sample 1


title: MCF7-ENRICH-2-3, bulkRNAseq

city: Milan

first: Italia

last: Bongarzone

state: Milan

address: Via Amedeo, 42

department: Department of Diagnostic Innovation

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Library name: MCF7-ENRICH-2-3

data_processing:
Raw sequencing data underwent quality assessment using FastQC. High-quality reads were aligned to the human reference genome (hg38) using the STAR aligner (v2.7.10a). Gene-level quantification was performed with featureCounts (v1.6.4) to obtain raw read counts.
Assembly: hg38
Supplementary files format and content: txt file includes raw counts for each Sample

source_name: Breast cancer

extract_protocol:
Total RNA was isolated from MCF-7 cells treated with either vehicle control (0.1% DMSO) or 250 nM doxorubicin for 72 hours using the RNeasy Mini Kit (Qiagen, Santa Clarita, CA) on an automated QIAcube extractor (Qiagen, Santa Clarita, CA), following the manufacturer's instructions.
RNA-seq libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero™ Plus kit (Illumina, San Diego, CA, USA, Cat# 20040525), following the manufacturer's protocol. Libraries were generated from 100 ng of total RNA, which was initially depleted of abundant ribosomal RNA (rRNA). The remaining RNA was then reverse transcribed into cDNA, followed by ligation and amplification steps to add adapters for clustering and sequencing. The final library concentrations were measured using Qubit 4, and quality control was performed with the TapeStation 4200. All libraries were purified and diluted to a starting concentration of 0.5 nM. The pooled libraries were sequenced at 2×75 base pairs on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) using a NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles).

tag: tissue

value: Breast cancer

value: ENRICH


title: HC_17_58, bulk RNA

description:
Library name: HC_17_58
HC_17_58


title: HC_17_57, bulk RNA

description:
Library name: HC_17_57
HC_17_57


title: HC_16_49, bulk RNA

description:
Library name: HC_16_49
HC_16_49


title: MCF7-ENRICH-2-2, bulkRNAseq

description: Library name: MCF7-ENRICH-2-2


title: HC_16_48, bulk RNA

description:
Library name: HC_16_48
HC_16_48


title: HC_14_47, bulk RNA

description:
Library name: HC_14_47
HC_14_47


title: HC_14_46, bulk RNA

description:
Library name: HC_14_46
HC_14_46


title: MCF7-ENRICH-2-1, bulkRNAseq

description: Library name: MCF7-ENRICH-2-1


title: MCF7-ENRICH-1-3, bulkRNAseq

description: Library name: MCF7-ENRICH-1-3


title: HC_14_44, bulk RNA

description:
Library name: HC_14_44
HC_14_44


title: MCF7-ENRICH-1-1, bulkRNAseq

description: Library name: MCF7-ENRICH-1-1


title: MCF7-ENRICH-1-2, bulkRNAseq

description: Library name: MCF7-ENRICH-1-2


title: A549 cells, Control, Experiment 2

city: Kalyani

first: Kaushik

last: Das

state: West Bengal

address: N.S.S. Kalyani Nadia

country: India

institute: National Institute of Biomedical Genomics

description: Library name: Sample 2

data_processing:
Raw sequencing reads were subjected to quality control using FastQC
Adapter trimming and quality filtering were performed using Trim Galore! (v0.6.6)
High-quality reads were aligned to the human reference genome (Ensembl release 112) and miRBase miRBase (release 22.1) and  using STAR aligner (v2.7.9a)
read counts were quantified using HTSeq (v0.13.5)
Assembly: hg38
Supplementary files format and content: excel, gene count

source_name: Lung cancer

growth_protocol: The human lung epithelial adenocarcinoma cell line, A549 was maintained in F-12K, supplemented with 10% fetal bovine serum and 1X penicillin-streptomycin solution. The cells were grown at 37°C with 5% CO2 in a humidified atmosphere.

extract_protocol:
MicroRNA was isolated from equal number of control- or aPC-treated EVs by using mirPremier microRNA Isolation Kit (Sigma) and subjected to miR expression analysis by deep-sequencing.
Illumina NovaSeq 6000 platform, generating 50 bp single-end reads

treatment_protocol: A549 cells were serum starved for 1 h followed by the treatment with a control vehicle or aPC (Sigma). After 16 h, the supernatant was subjected to EV isolation by differential centrifugation. After counting the EVs by NTA Nano-Sight, the EVs were subjected to miR isolation.

value: Lung cancer

value: A549 cells

value: Non-small cell lung cancer cells

value: control


title: HC_14_45, bulk RNA

description:
Library name: HC_14_45
HC_14_45


title: MCF7-DOXO-2-3, bulkRNAseq

description: Library name: MCF7-DOXO-2-3

value: DOXO


title: HC_17_59, bulk RNA

description:
Library name: HC_17_59
HC_17_59


title: HC_14_43, bulk RNA

description:
Library name: HC_14_43
HC_14_43


title: MCF7-DOXO-2-2, bulkRNAseq

description: Library name: MCF7-DOXO-2-2


title: HC_14_42, bulk RNA

description:
Library name: HC_14_42
HC_14_42


title: HC_14_41, bulk RNA

description:
Library name: HC_14_41
HC_14_41


title: HC_16_51, bulk RNA

description:
Library name: HC_16_51
HC_16_51


title: MCF7-DOXO-2-1, bulkRNAseq

description: Library name: MCF7-DOXO-2-1


title: MCF7-DOXO-1-2, bulkRNAseq

description: Library name: MCF7-DOXO-1-2


title: HC_14_40, bulk RNA

description:
Library name: HC_14_40
HC_14_40


title: MCF7-DOXO-1-1, bulkRNAseq

description: Library name: MCF7-DOXO-1-1


title: HC_14_38, bulk RNA

description:
Library name: HC_14_38
HC_14_38


title: MCF7-CONTROL-2-3, bulkRNAseq

description: Library name: MCF7-CONTROL-2-3

value: CONTROL


title: HC_16_36, bulk RNA

description:
Library name: HC_16_36
HC_16_36


title: HC_16_37, bulk RNA

description:
Library name: HC_16_37
HC_16_37


title: MCF7-CONTROL-2-1, bulkRNAseq

description: Library name: MCF7-CONTROL-2-1


title: MCF7-CONTROL-1-3, bulkRNAseq

description: Library name: MCF7-CONTROL-1-3


title: MCF7-CONTROL-2-2, bulkRNAseq

description: Library name: MCF7-CONTROL-2-2


title: HC_14_34, bulk RNA

description:
Library name: HC_14_34
HC_14_34


title: MCF7-CONTROL-1-2, bulkRNAseq

description: Library name: MCF7-CONTROL-1-2


title: HC_16_35, bulk RNA

description:
Library name: HC_16_35
HC_16_35


title: HC_14_33, bulk RNA

description:
Library name: HC_14_33
HC_14_33


title: HC_14_31, bulk RNA

description:
Library name: HC_14_31
HC_14_31


title: HC_14_30, bulk RNA

description:
Library name: HC_14_30
HC_14_30


title: HDFs irradiated with 4Gy gamma irradiation sample 3

city: Minneapolis

first: Louise

middle: Eileen

last: Pitcher

state: MN

address: 312 Church Street SE RM 4-210 NILS HASSELMO HALL

department: Biochemistry, Molecular Biology and Biophysics

institute: Masonic Institute on the Biology of Aging and Metabolism

description:
Library name: 4Gy-gamma-3
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed

data_processing:
Fastqc files were processed using Trimmomatic for the removal of adapter sequences and bases having a Q-score < 30.
Paired-end reads were aligned to the GRCh38 reference genome using Hisat2 v2.0.5 and feature Counts v1.5.0 was used to count and map each gene.
Assembly: The human reference genome build 38 (GRCh38)
Supplementary files format and content: a tab-deliminated text file that include raw counts per sample

source_name: dermal skin tissue

growth_protocol: Primary Human dermal cells (HDFs) were cultured in alpha-MEM with nucleosides and glutamine (Gibco), supplemented with 10% FBS, 1% penicillin/streptomycin (Gibco), and non-essential amino acids. The cells were maintained at 37°C, 5% CO2 and 20% O2.  All cells were seeded at 50% confluence and replicate cultures were shipped overnight to the National Aeronautics and Space Administration (NASA) Laboratory at Brookhaven National Laboratory. Upon arrival cells were allowed to recover from shipment overnight prior to radiation exposure and irradiation occurred as described previously. Briefly, irradiations occurred using particle beams for Hydrogen (H), Silicon (Si), Iron (Fe) using particle energies of 150, 238 and 600 MeV/n with LET values of 0.5, 79 and 174 ke V/µm respectively. For γ-irradiation, a 137Cs source (JL Shepard and Associates, CA) was used, all cells regardless of types of radiation exposure received final doses of 4.0Gy. Following exposure to space radiation, a media change was preformed, and cells were allowed to rest overnight prior to overnight shipment back to the University of Minnesota where they were allowed to rest another 13 days to allow senescence induction. During senescence induction medium was replaced and collected every 2-3 days and routine passaging was conducted.

extract_protocol:
RNA extraction was done using 1mL TRIZOL as described above, with the addition of an on-column DNase digestion as described by the from Invitrogen PureLink RNA Mini Kit’s instructions and was eluted in ultra-pure sterile water (Invitrogen).
Library preparation and sequencing was performed at the University of Minnesota Genomics Center. Unique dual indexed paired-end TruSeq stranded libraries were created and pooled following rRNA depletion using the Ribo-Zero Plus rRNA Depletion kit. All libraries were gel size selected (≈ 200bp) and sequenced using an Illumina NovaSeq X Lane with a 2 x 150bp flow cell. Libraries were sequenced to a mean depth of ≥20M reads.

treatment_protocol: Irradiation treatments occurred using particle beams for Hydrogen (H), Silicon (Si), Iron (Fe) using particle energies of 150, 238 and 600 MeV/n with LET values of 0.5, 79 and 174 ke V/µm respectively. For γ-irradiation, a 137Cs source (JL Shepard and Associates, CA) was used, all cells regardless of types of radiation exposure received final doses of 4.0Gy. Following exposure to space radiation, a media change was preformed, and cells were allowed to rest overnight prior to overnight shipment back to the University of Minnesota where they were allowed to rest another 13 days to allow senescence induction. During senescence induction medium was replaced and collected every 2-3 days and routine passaging was conducted.

value: dermal skin tissue

value: primary

value: dermal fibroblast

value: WT

value: 4Gy Gamma irradiation

tag: batch

value: all on one


title: HC_14_29, bulk RNA

description:
Library name: HC_14_29
HC_14_29

value: PBMC


title: HDFs irradiated with 4Gy gamma irradiation sample 2

description:
Library name: 4Gy-gamma-2
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HC_14_32, bulk RNA

description:
Library name: HC_14_32
HC_14_32


title: MCF7-DOXO-1-3, bulkRNAseq

description: Library name: MCF7-DOXO-1-3


title: HDFs irradiated with 4Gy Hydrogen irradiation sample 3

description:
Library name: 4Gy-Hydrogen-3
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed

value: 4Gy Hydrogen irradiation


title: HDFs irradiated with 4Gy gamma irradiation sample 1

description:
Library name: 4Gy-gamma-1
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HC_16_27, bulk RNA

description:
Library name: HC_16_27
HC_16_27


title: HC_16_28, bulk RNA

description:
Library name: HC_16_28
HC_16_28


title: HDFs irradiated with 4Gy Hydrogen irradiation sample 2

description:
Library name: 4Gy-Hydrogen-2
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HC_14_39, bulk RNA

description:
Library name: HC_14_39
HC_14_39


title: HC_16_26, bulk RNA

description:
Library name: HC_16_26
HC_16_26


title: HDFs irradiated with 4Gy Hydrogen irradiation sample 1

description:
Library name: 4Gy-Hydrogen-1
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HDFs irradiated with 4Gy Iron irradiation sample 3

description:
Library name: 4Gy-Iron-3
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed

value: 4Gy Iron irradiation


title: HC_13_24, bulk RNA

description:
Library name: HC_13_24
HC_13_24


title: HC_15_25, bulk RNA

description:
Library name: HC_15_25
HC_15_25


title: HDFs irradiated with 4Gy Silicon irradiation sample 3

description:
Library name: 4Gy-Silicon-3
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed

value: 4Gy Silicon irradiation


title: MCF7-CONTROL-1-1, bulkRNAseq

description: Library name: MCF7-CONTROL-1-1

value: Breast cancer


title: HC_13_23, bulk RNA

description:
Library name: HC_13_23
HC_13_23


title: HDFs irradiated with 4Gy Silicon irradiation sample 2

description:
Library name: 4Gy-Silicon-2
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HC_13_21, bulk RNA

description:
Library name: HC_13_21
HC_13_21


title: HDFs irradiated with 4Gy Iron irradiation sample 1

description:
Library name: 4Gy-Iron-1
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HC_13_22, bulk RNA

description:
Library name: HC_13_22
HC_13_22


title: Non-irradiated HDF control for gamma irradiation sample 3

description:
Library name: Mock_gamma-3
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed

value: Gamma irradiation control shipped not irradiated


title: HC_15_18, bulk RNA

description:
Library name: HC_15_18
HC_15_18


title: HDFs irradiated with 4Gy Silicon irradiation sample 1

description:
Library name: 4Gy-Silicon-1
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HC_13_19, bulk RNA

description:
Library name: HC_13_19
HC_13_19


title: HC_13_20, bulk RNA

description:
Library name: HC_13_20
HC_13_20


title: Non-irradiated HDF control for gamma irradiation sample 2

description:
Library name: Mock_gamma-2
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: Non-irradiated HDF control for gamma irradiation sample 1

description:
Library name: Mock_gamma-1
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HC_16_16, bulk RNA

description:
Library name: HC_16_16
HC_16_16


title: HC_15_17, bulk RNA

description:
Library name: HC_15_17
HC_15_17


title: Low passage, non-shipped, not irradiated HDF sample 3

description:
Library name: Healthy_CTRL-3
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed

value: Low passage, unshipped


title: Low passage, non-shipped, not irradiated HDF sample 2

description:
Library name: Healthy_CTRL-2
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HC_15_15, bulk RNA

description:
Library name: HC_15_15
HC_15_15


title: HC_15_14, bulk RNA

description:
Library name: HC_15_14
HC_15_14


title: HC_15_13, bulk RNA

description:
Library name: HC_15_13
HC_15_13


title: Non-irradiated HDF control for charged particle irradiation sample 1

description:
Library name: mock-1
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed

value: Irradiation control shipped not irradiated


title: Non-irradiated HDF control for charged particle irradiation sample 3

description:
Library name: mock-3
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: Low passage, non-shipped, not irradiated HDF sample 1

description:
Library name: Healthy_CTRL-1
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HDFs irradiated with 4Gy Iron irradiation sample 2

description:
Library name: 4Gy-Iron-2
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed


title: HC_13_12, bulk RNA

description:
Library name: HC_13_12
HC_13_12


title: HC_13_11, bulk RNA

description:
Library name: HC_13_11
HC_13_11


title: HC_13_8, bulk RNA

description:
Library name: HC_13_8
HC_13_8


title: Iron

description:
Library name: Fe_GEX_FL
10X genomics

library_source: transcriptomic single cell

data_processing:
Subsequent analysis of obtained read count matrices was carried out using the R package Seurat, version 5.0. Using Seurat, we filtered out cells with low feature count (<200 genes), high mitochondrial RNA content (>10%) with more stringent cutoffs being determined through examination of the coefficient of determination value (R2 = 0.95) for the line describing the relationship for nCount_RNA vs nFeature_RNA leading to an nCount < 20000 threshold. Each sample was normalized using the ‘LogNormalize’ method using the ‘NormalizeData’ function, and the top 3000 highly variable genes were selected from individual samples with the function ‘FindVariableFeatures’. The top 50 principal components, determined by the ‘ElbowPlot’ method, were applied for two-dimensional data visualization with the uniform manifold approximation and projection (UMAP) via ‘RunUMAP’ function. Clusters were identified using the Louvain algorithm with a resolution of 0.8. All functions utilized default parameters.
Using the machine learning program SenCID we identified senescent IMR-90 fibroblasts using the SenCID5 gene signature as using the standard described workflow and parameters
Assembly: The human reference genome build 38 (GRCh38)
Supplementary files format and content: The process data file "mytree_rep2.rds" is and rds file of the whole Seurat object with samples Mock, Silicon, Hydrogen and Iron irradiated IMR-90cells. Origin of samples is included in the metadata under origin identitiy. Also in the metadata you will find clusting info for resolutions 0 to 1.5 and SenCID scores.

source_name: normal lung

growth_protocol: IMR-90 human fibroblasts were obtained from ATCC and cultures in MEM (Gibco), supplemented with 10% FBS, 1% penicillin/streptomycin (Gibco), and non-essential amino acids (Gibco) and sodium pyruvate (Gibco). The cells were maintained at 37C, 5% CO2 and 20% O2.  All cells were seeded at 50% confluence and replicate cultures were shipped overnight to the National Aeronautics and Space Administration (NASA) Laboratory at Brookhaven National Laboratory. Upon arrival cells were allowed to recover from shipment overnight prior to radiation exposure and irradiation occurred as described previously. Briefly, irradiations occurred using particle beams for Hydrogen (H), Silicon (Si), Iron (Fe) using particle energies of 150, 238 and 600 MeV/n with LET values of 0.5, 79 and 174 ke V/m respectively. For -irradiation, a 137Cs source (JL Shepard and Associates, CA) was used, all cells regardless of types of radiation exposure received final doses of 4.0Gy. Following exposure to space radiation, a media change was preformed, and cells were allowed to rest overnight prior to overnight shipment back to the University of Minnesota where they were allowed to rest another 13 days to allow senescence induction. During senescence induction medium was replaced and collected every 2-3 days and routine passaging was conducted.

extract_protocol:
Single-cell libraries were prepared by trypsinizing and pooling replicate cultures of IMR-90 fibroblasts (n =3) exposed to 4Gy radiation and mock control. Cells were trypsinized using TrpLE (Gibco) and examined for viability (>80%) through trypan blue staining. Cells were resuspended in MEM (Gibco) supplemented with 10% FBS in 100uL at 1500 cells/uL for subsequent library preparation and sequencing provided by the University of Minnesota’s Genomics Center.
Library construction was done using Chromium Next GEM Single Cell 3ʹ dual index Kits v3.1 with Chip G (10x Genomics). Live suspensions of ~10,000 single cells were loaded for generation of gel bead-in-emulsions (GEMs), the captured cells were lysed, and the RNA was barcoded while reverse-transcribed in each GEM. GEMs were then broken, and the synthesized cDNA was used for library preparation following the manufacturer’s protocol. cDNA quality was assessed on the Agilent Bioanalyzer with Pico-green (Agilent). The libraries underwent additional QC by shallow-sequencing using an Illumina NextSeq instrument. Final library sequencing was done using an Illumina Nova Seq S4 lane capturing ~ 20,000 paired-end reads per cell.  10x sequencing libraries were converted into feature-barcode matrices following the Cell Ranger (10x Genomics, version 5.0.0) pipeline. After demultiplexing, the function ‘cellranger count’ was used with default parameters, reads were mapped using the Cell Ranger prebuilt annotation platform GRCh38.

treatment_protocol: Irradiation treatments occurred using particle beams for Hydrogen (H), Silicon (Si), Iron (Fe) using particle energies of 150, 238 and 600 MeV/n with LET values of 0.5, 79 and 174 ke V/m respectively. For -irradiation, a 137Cs source (JL Shepard and Associates, CA) was used, all cells regardless of types of radiation exposure received final doses of 4.0Gy. Following exposure to space radiation, a media change was preformed, and cells were allowed to rest overnight prior to overnight shipment back to the University of Minnesota where they were allowed to rest another 13 days to allow senescence induction. During senescence induction medium was replaced and collected every 2-3 days and routine passaging was conducted.

value: normal lung

value: fibroblasts isolated from normal lung tissue derived from a 16-week-old female


title: HC_13_7, bulk RNA

description:
Library name: HC_13_7
HC_13_7


title: Hydrogen

description:
Library name: H_GEX_FL
10X genomics


title: Silicon

description:
Library name: Si_GEX_FL
10X genomics


title: Gamma

description:
Library name: Gamma_GEX_FL
10X genomics


title: HC_13_9, bulk RNA

description:
Library name: HC_13_9
HC_13_9


title: HC_13_6, bulk RNA

description:
Library name: HC_13_6
HC_13_6


title: HC_13_10, bulk RNA

description:
Library name: HC_13_10
HC_13_10


title: HC_13_4, bulk RNA

description:
Library name: HC_13_4
HC_13_4


title: SB17, induced Skeletal Muscles, 24 hrs ARD-1676, rep 2

city: Ann Arbor

first: Andrew

last: Lieberman

state: Michigan

address: 1150 W Medical Center Drive

institute: University of Michigan

description: Library name: 13214.AS.22

data_processing:
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000, Control Software Version: 1.8.1, RTA Version: v3.4.4).BCL Convert Conversion Software v4.3.13 (Illumina) was used to generate de-multiplexed fastq files.
Assembly: Reads were mapped to the reference genome GRCh38 (ENSEMBL),  using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Cells were lysed in TRIzol (Invitrogen 15596018) for RNA extraction according to manufacturer’s instructions
A TruSeq-based kit was used during library preparation. The adapter sequences for this kit are R1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA R2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT The product name of the library preparation kit is NEB.

value: induced skeletal muscle


title: SB17, iInduced Skeletal Muscles, 24 hrs ARD-1676, rep 3

description: Library name: 13214.AS.24


title: SB17, induced Skeletal Muscles, 24 hrs vehicle, rep 3

description: Library name: 13214.AS.23

value: 24 hrs vehicle


title: Mock

description:
Library name: mock_GEX_FL
10X genomics

value: Irradiation Control


title: HC_13_2, bulk RNA

description:
Library name: HC_13_2
HC_13_2


title: HC_13_5, bulk RNA

description:
Library name: HC_13_5
HC_13_5


title: SB17, induced Skeletal Muscles, 24 hrs vehicle, rep 2

description: Library name: 13214.AS.21


title: HC_13_3, bulk RNA

description:
Library name: HC_13_3
HC_13_3


title: SB17, induced Skeletal Muscles, 24 hrs vehicle, rep 1

description: Library name: 13214.AS.19


title: Non-irradiated HDF control for charged particle irradiation sample 2

description:
Library name: mock-2
column in HDF_ALL_compiles_counts.txt: "libraryname"_HISAT2.trimmed

value: dermal skin tissue

value: primary

value: dermal fibroblast


title: HC_13_1, bulk RNA

description:
Library name: HC_13_1
HC_13_1


title: SB3, iInduced Skeletal Muscles, 24 hrs ARD-1676, rep 3

description: Library name: 13214.AS.18


title: SB17, induced Skeletal Muscles, 24 hrs ARD-1676, rep 1

description: Library name: 13214.AS.20


title: GH_1_18, bulk RNA

description:
Library name: GH_1_18
GH_1_18


title: Healthy

description:
Library name: Healthy_GEX_FL
10X genomics

value: WT

value: Healthy low passage

value: all on one


title: SB3, induced Skeletal Muscles, 24 hrs vehicle, rep 3

description: Library name: 13214.AS.17


title: GH_1_20, bulk RNA

description:
Library name: GH_1_20
GH_1_20

value: PBMC


title: GH_1_19, bulk RNA

description:
Library name: GH_1_19
GH_1_19


title: SB3, induced Skeletal Muscles, 24 hrs ARD-1676, rep 1

description: Library name: 13214.AS.14


title: GH_1_17, bulk RNA

description:
Library name: GH_1_17
GH_1_17


title: SB3, induced Skeletal Muscles, 24 hrs vehicle, rep 2

description: Library name: 13214.AS.15


title: GH_1_15, bulk RNA

description:
Library name: GH_1_15
GH_1_15


title: GH_1_16, bulk RNA

description:
Library name: GH_1_16
GH_1_16


title: SB3, induced Skeletal Muscles, 24 hrs vehicle, rep 1

description: Library name: 13214.AS.13


title: GH_1_13, bulk RNA

description:
Library name: GH_1_13
GH_1_13


title: H180, iInduced Skeletal Muscles, 24 hrs ARD-1676, rep 3

description: Library name: 13214.AS.12


title: GH_1_12, bulk RNA

description:
Library name: GH_1_12
GH_1_12


title: SB3, induced Skeletal Muscles, 24 hrs ARD-1676, rep 2

description: Library name: 13214.AS.16


title: GH_1_14, bulk RNA

description:
Library name: GH_1_14
GH_1_14


title: H180, induced Skeletal Muscles, 24 hrs vehicle, rep 3

description: Library name: 13214.AS.11


title: H180, induced Skeletal Muscles, 24 hrs ARD-1676, rep 2

description: Library name: 13214.AS.10


title: GH_1_9, bulk RNA

description:
Library name: GH_1_9
GH_1_9


title: Patient 1_ROI 003_ PanCK+

status: Public on Dec 10 2025

city: Hospitalet de Llobregat

first: Barbara

last: Rivera

address: Granvia de l'Hospitalet de Llobregat, 199

country: Spain

institute: IDIBELL

description:
Library name: Sample_DSP-1001660005657-A-A05
FFPE spatial transcriptomics (NanoString DSP WTA)

data_processing:
Fastq files containing sequencing of UV-cleaved probes were processed into Digital count conversion (DCC) files using the Nanostring GeoMx NGS Pipeline v2.3.3.10. The DCC files were imported into R v4.3.0 for further analysis. Using GeomxTools v3.3.0, areas of Illumination (AOI) were assessed for sequencing quality. AOIs retained for analysis if they met the following criteria: Minimum reads per AOI greater than 1000, the percentage of trimmed reads, stitched reads and aligned reads all greater than 80%, the sequencing saturation greater than 50%, the minimum count of negative control probes greater 0.5, No Template Control (NTC) counts greater than 1300, number of nuclei per AOI is greater than 100, the area per AOI is greater than 1000 µm, and greater than 5% of genes detected above limit of quantification (LOQ, mean of negative control counts + 2 standard deviation). 6 AOIs were discarded for not meeting the criteria, for a total of 78 AOIs. Genes were retained in the analysis if detected above LOQ in at least 5% of AOIs for a total of 12236 genes. Counts were normalized using the quartile 3 (Q3) method.
Assembly: GRCh38
Supplementary files format and content: Matrix of Q3-normalized counts for the 78 AOIs
Library strategy: Spatial Transcriptomics

source_name: Normal thyroid 3, non-DICER1-mutated, PanCK+

extract_protocol:
GeoMx™ digital spatial profiling was performed as per the supplier’s protocol using the human Whole Transcriptome Atlas probe set with read-out by next-generation sequencing (Nanostring Technologies). Briefly, 5 µm FFPE sections of a sporadic DICER1-thyroid case and a germline DGCR8- thyroid case, were processed through deparaffinization, antigen retrieval (Tris-EDTA ph9 for 20 min at 98°C), and Proteinase K digestion (1 ug/mL Proteinase K for 15 min at 37°C) prior to overnight incubation at 37°C with the human Whole Transcriptome Atlas diluted in hybridization Buffer R. The next day, slides were washed twice in 2XSSC/formamide (25 min at 37°C), blocked with Buffer W (30 min at RT) and incubated with an antibody cocktail consisting of PanCK-AF532, CD45-AF594, VIM-AF647, and SYTO13 for 1 hr in a humidity chamber. Slides were washed 3 times in 2XSSC and then scanned on the GeoMx™ DSP instrument (at 20X), after which regions-of-interest (ROIs) in each case were laid down to capture different histological components in triplicates at least. For the DICER1-case, this included a tumour core from a DICER1-mutated PDTC, the tumor’s capsule, a non-neoplastic nodular area (DICER1-wildtype benign thyroid lesion) and normal area (DICER1-wildtype). For the DGCR8-case, this included a tumour core from a DGCR8-mutated microPTC, a normal adjacent area, non-neoplastic nodular areas (DGCR8-mutated benign thyroid lesions) and normal area (DGCR8-mutated). A total of 51 ROIs were selected and were segmented further into PanCK+ and/or VIM+ areas, and Whole Transcriptome barcodes were released from these distinct populations by UV light illumination and microfluidic collection.
The UV-released barcodes from each of the 84 area-of-illuminations (AOIs) were PCR-amplified to add unique dual-index Illumina i5 and i7 indices and bead-purified twice using AMPure XP beads (Beckman Coutler, A63881). Pooled libraries were sequenced on two 75-cycle High Output flowcells on an Illumina NextSeq sequencer, generating 916M unique raw reads. FASTQ files were converted to DCC files and uploaded onto the GeoMx™ DSP for trimming, stitching, aligning, and deduplication.

value: Patient 1_Normal thyroid 3_ PanCK+

tag: patient

value: Patient 1

tag: histological type

value: Normal thyroid

tag: Sex

value: Female

tag: label (panck/vim)

value: PanCK+ (Cy3)


title: GH_1_8, bulk RNA

description:
Library name: GH_1_8
GH_1_8


title: GH_1_7, bulk RNA

description:
Library name: GH_1_7
GH_1_7


title: GH_10_10, bulk RNA

description:
Library name: GH_10_10
GH_10_10


title: H179, iInduced Skeletal Muscles, 24 hrs ARD-1676, rep 3

description: Library name: 13214.AS.6


title: H180, induced Skeletal Muscles, 24 hrs vehicle, rep 1

description: Library name: 13214.AS.7


title: H179, induced Skeletal Muscles, 24 hrs ARD-1676, rep 2

description: Library name: 13214.AS.4


title: GH_1_4, bulk RNA

description:
Library name: GH_1_4
GH_1_4


title: H180, induced Skeletal Muscles, 24 hrs vehicle, rep 2

description: Library name: 13214.AS.9


title: GH_1_6, bulk RNA

description:
Library name: GH_1_6
GH_1_6


title: H179, induced Skeletal Muscles, 24 hrs vehicle, rep 3

description: Library name: 13214.AS.5


title: GH_1_5, bulk RNA

description:
Library name: GH_1_5
GH_1_5


title: H180, induced Skeletal Muscles, 24 hrs ARD-1676, rep 1

description: Library name: 13214.AS.8


title: H179, induced Skeletal Muscles, 24 hrs vehicle, rep 2

description: Library name: 13214.AS.3


title: GH_1_3, bulk RNA

description:
Library name: GH_1_3
GH_1_3


title: GH_1_2, bulk RNA

description:
Library name: GH_1_2
GH_1_2


title: H179, induced Skeletal Muscles, 24 hrs ARD-1676, rep 1

description: Library name: 13214.AS.2


title: TED_18_155, bulk RNA

description:
Library name: TED_18_155
TED_18_155


title: GH_1_1, bulk RNA

description:
Library name: GH_1_1
GH_1_1


title: SW620 3D cells cultivated in 3D

city: Belgrade

first: Dunja

last: Pavlovic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetics and Genetic Engineering

description: Library name: SW620

data_processing:
The quality of reads was evaluated using FASTQC.
The cleaned reads were aligned to the human genome (hg38) using HISAT2.
Reads were assembled into transcripts and quantified using StrigTie.
Assembly: hg38
Supplementary files format and content: txt file includes FPKM values for each sample

source_name: colon cancer

growth_protocol: HCEC-1CT, HCT116, DLD-1 and SW620 cell lines  were cultivated in 3D as spheroids. Approximately 2x105 cells/well were seeded in 24-well plate Nunclon™ Sphera™ Dish (Thermo Fisher Scientific, USA), specified as the low cell attachment surface, containing 1mL of Dulbecco's Modified Eagle's Medium supplemented with 10% fetal bovine serum and 1% antibiotic/antimycotic solution. Spheroids were cultured for 7 days in humidified incubator at 37°C with 5% CO2. Collection of compact spheroids, without cell debris, was performed under the microscope to enable picking up only live cells for further extraction of total RNA.

extract_protocol:
Total RNA was isolated from spheroids from two 24-well plates using PureLink™ RNA Mini Kit (Thermo Fisher Scientific, USA) according to the manufacturer’s protocol.
RNA-seq libraries were constructed according to standard Illumina protocols.

value: colon cancer

value: epithelial cell


title: GH_1_11, bulk RNA

description:
Library name: GH_1_11
GH_1_11


title: TED_18_154, bulk RNA

description:
Library name: TED_18_154
TED_18_154


title: TED_18_150, bulk RNA

description:
Library name: TED_18_150
TED_18_150


title: HCT116 3D cells cultivated in 3D

description: Library name: HCT116


title: DLD-1 3D cells cultivated in 3D

description: Library name: DLD-1


title: TED_18_151, bulk RNA

description:
Library name: TED_18_151
TED_18_151


title: DE_IPRiboSeq_Rep2

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

description: Library name: NM2022_0008

data_processing:
RNA-seq data analysis - Salmon (Patro et al. 2017) was used for quantifying transcript levels from all libraries using Gencode v26 transcriptome assembly (parameters -l A ‐‐allowDovetail ‐‐validateMappings). All downstream analysis was performed in R. Briefly, Salmon data were imported using the tximport library (Soneson et al. 2015). Differential gene expression was performed using the DESeq2 library (Love et al. 2014).
Riboseq Data analysis - Read 2, the reverse complement read, was used to analyze the RPF data. First, the 12-nt UMI was extracted from the 3' end using umi_tools (Smith et al. 2017). 3’ and 5’ reverse complement adapters (ATTGATGGTGCCTACAGTT and GATCGTCGGACTGTAGAACTCTGAAC) were trimmed using cutadapt (Martin 2011). Reads shorter than 18 nt were removed. The reverse complement of each read was obtained using fastx-toolkit (FASTX-Toolkit) and rRNA reads were removed using bowtie (Langmead and Salzberg 2012). The bam file was deduplicated using umi-tools and transcript expression was quantified using Salmon (Smith et al. 2017; Patro et al. 2017) as described above. All further analysis was performed in R. Salmon files were imported using the tximport library (Soneson et al. 2015). Quality control metrics such as periodicity and read size were analyzed using the ribosomeProfilingQC package (Ou and Hoye 2023).
Assembly: GRCh38
Supplementary files format and content: comma separated file containing Salmon counts for all samples
Library strategy: IPRibo-Seq

source_name: undifferentiated hES

growth_protocol: Undifferentiated human embryonic stem (hES) MEL1 INSGFP/W reporter cells (Micallef et al , 2012) were maintained on hES qualified Matrigel in mTeSR+ media. Differentiation to stem cell derived beta like cells (sBCs) was carried out in suspension‐based, bioreactor magnetic stirring system as done previously.

extract_protocol:
RNA-seq: Total RNA was extracted from GFP+ and GFP- sorted samples in trizol using the DirectZol RNA Microprep kit (Zymo Research) following the manufacturer’s instructions with on-column DNaseI treatment.    Ribo-seq: Ribosome footprinting was performed as described previously (Ingolia et al. 2012) with a few modifications. The GFP+ sorted cell pellets were lysed in buffer without cycloheximide. Following lysis and clarification by centrifugation, total RNA was quantified using the Qubit RNA BR assay kit. The remaining lysate was used as input into the footprinting reaction with 750 U RNase I (Invitrogen Ambion). The digestion was stopped with SUPERaseIN then flash frozen in liquid nitrogen. The lysate was then used as input into immunoprecipitation with RNA immunoprecipitation protocol adapted from (Wessels et al. 2016) using prepared Anti-FLAG M2 Magnetic beads (Sigma). The IP was incubated for two hours at room temperature tumbling end-over-end, followed by post-IP washes with NT2 buffer. The immunoprecipitated RNA was released from the bead complex using TRIzol LS reagent (Invitrogen) and further isolated using chloroform and isopropanol precipitation.
RNA-seq: rRNA was depleted from each total RNA sample following our previously published RNaseH-based method (Baldwin et al. 2021), then input into the KAPA RNA Hyper prep RNAseq library prep kit (Roche). Libraries were prepared according to the manufacturer’s instructions with dual-index adapters, followed by quality check of the final libraries by Qubit dsDNA HS assay and Tapestation High Sensitivity D1000 screentape. Libraries were pooled and submitted for 2x 150bp paired end sequencing on the Illumina NovaSeq6000 platform to a depth of 40 million paired end reads per library (University of Colorado Anschutz Genomics and Microarray Core Facility).        Ribo-seq: The isolated RNA was depleted of rRNA using the siTOOLs riboPOOLs kit for ribosome profiling following the kit instructions. The samples were resolved on a 15% TBE-Urea PAGE gel and ribosome protected fragments 28-29nt in size were extracted and recovered. RPFs were treated with T4-PNK then used as input into the Qiagen QIAseq miRNA library prep kit following the manufacturer’s instructions with provided single index adapters. The resulting libraries were pooled and submitted for 2x 150bp paired end sequencing on the Illumina NovaSeq6000 platform to a depth of 60 million paired end reads (Supplemental Table 6) per library (University of Colorado Anschutz Genomics and Microarray Core Facility).

value: undifferentiated hES

value: DefinitiveEndoderm

tag: library type

value: IP-RiboSeq

tag: antibody used

value: FLAG


title: HCEC-1CT cells cultivated in 3D

description: Library name: HCEC-1CT

source_name: colon

value: colon


title: TED_17_148, bulk RNA

description:
Library name: TED_17_148
TED_17_148


title: DE_IPRiboSeq_Rep1

description: Library name: NM2022_0007


title: TED_17_147, bulk RNA

description:
Library name: TED_17_147
TED_17_147


title: hPSC_IPRiboSeq_Rep2

description: Library name: NM2022_0006

value: hPSC


title: TED_17_145, bulk RNA

description:
Library name: TED_17_145
TED_17_145


title: hPSC_IPRiboSeq_Rep1

description: Library name: NM2022_0005


title: DE_RiboSeq_Rep2

description: Library name: NM2022_0004

data_processing:
RNA-seq data analysis - Salmon (Patro et al. 2017) was used for quantifying transcript levels from all libraries using Gencode v26 transcriptome assembly (parameters -l A ‐‐allowDovetail ‐‐validateMappings). All downstream analysis was performed in R. Briefly, Salmon data were imported using the tximport library (Soneson et al. 2015). Differential gene expression was performed using the DESeq2 library (Love et al. 2014).
Riboseq Data analysis - Read 2, the reverse complement read, was used to analyze the RPF data. First, the 12-nt UMI was extracted from the 3' end using umi_tools (Smith et al. 2017). 3’ and 5’ reverse complement adapters (ATTGATGGTGCCTACAGTT and GATCGTCGGACTGTAGAACTCTGAAC) were trimmed using cutadapt (Martin 2011). Reads shorter than 18 nt were removed. The reverse complement of each read was obtained using fastx-toolkit (FASTX-Toolkit) and rRNA reads were removed using bowtie (Langmead and Salzberg 2012). The bam file was deduplicated using umi-tools and transcript expression was quantified using Salmon (Smith et al. 2017; Patro et al. 2017) as described above. All further analysis was performed in R. Salmon files were imported using the tximport library (Soneson et al. 2015). Quality control metrics such as periodicity and read size were analyzed using the ribosomeProfilingQC package (Ou and Hoye 2023).
Assembly: GRCh38
Supplementary files format and content: comma separated file containing Salmon counts for all samples
Library strategy: Ribo-Seq

value: Riboseq


title: TED_17_142, bulk RNA

description:
Library name: TED_17_142
TED_17_142


title: TED_17_139, bulk RNA

description:
Library name: TED_17_139
TED_17_139


title: hPSC_RiboSeq_Rep1

description: Library name: NM2022_0001


title: TED_17_137, bulk RNA

description:
Library name: TED_17_137
TED_17_137


title: DE_RiboSeq_Rep1

description: Library name: NM2022_0003


title: TED_17_141, bulk RNA

description:
Library name: TED_17_141
TED_17_141


title: TED_16_136, bulk RNA

description:
Library name: TED_16_136
TED_16_136


title: DE_RNAseq_Rep1

description: Library name: NM2022_0043

data_processing:
RNA-seq data analysis - Salmon (Patro et al. 2017) was used for quantifying transcript levels from all libraries using Gencode v26 transcriptome assembly (parameters -l A ‐‐allowDovetail ‐‐validateMappings). All downstream analysis was performed in R. Briefly, Salmon data were imported using the tximport library (Soneson et al. 2015). Differential gene expression was performed using the DESeq2 library (Love et al. 2014).
Riboseq Data analysis - Read 2, the reverse complement read, was used to analyze the RPF data. First, the 12-nt UMI was extracted from the 3' end using umi_tools (Smith et al. 2017). 3’ and 5’ reverse complement adapters (ATTGATGGTGCCTACAGTT and GATCGTCGGACTGTAGAACTCTGAAC) were trimmed using cutadapt (Martin 2011). Reads shorter than 18 nt were removed. The reverse complement of each read was obtained using fastx-toolkit (FASTX-Toolkit) and rRNA reads were removed using bowtie (Langmead and Salzberg 2012). The bam file was deduplicated using umi-tools and transcript expression was quantified using Salmon (Smith et al. 2017; Patro et al. 2017) as described above. All further analysis was performed in R. Salmon files were imported using the tximport library (Soneson et al. 2015). Quality control metrics such as periodicity and read size were analyzed using the ribosomeProfilingQC package (Ou and Hoye 2023).
Assembly: GRCh38
Supplementary files format and content: comma separated file containing Salmon counts for all samples

value: RNAseq


title: TED_14_132, bulk RNA

description:
Library name: TED_14_132
TED_14_132


title: TED_16_133, bulk RNA

description:
Library name: TED_16_133
TED_16_133


title: H179, induced Skeletal Muscles, 24 hrs vehicle, rep 1

description: Library name: 13214.AS.1

value: induced skeletal muscle

value: 24 hrs vehicle


title: hPSC_RNAseq_Rep2

description: Library name: NM2022_0042


title: hPSC_RNAseq_Rep1

description: Library name: NM2022_0041


title: TED_14_131, bulk RNA

description:
Library name: TED_14_131
TED_14_131

value: PBMC


title: HepG2 cells, m6A, Rep1

city: Nanjing

first: Facai

last: Yang

state: jiangsu

address: No. 87 Dingjiaqiao, Gulou District, Nanjing

institute: Southeast University

description:
Library name: SAMPLES12
MeRIP-Seq of human liver cell line
HepG2_peaks_anno.xlsx
HepG2_1_anno.xlsx

data_processing:
*library strategy: meRIP-seq
Raw data was trimmed using Trim Galore to remove adapters and low-quality bases.
Assembly: Sequencing data were aligned to the human reference genome (hg38) using HISAT2, and transcript quantification was performed using featureCounts.
Supplementary files format and content: Processed data files are in BAM format, containing mapped read sequences with quality scores.

growth_protocol: HepG2 cells were cultured in RPMI-1640 medium, whereas Huh7 cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM), both supplemented with 10% fetal bovine serum (FBS). Cells were incubated at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol.
Library was prepared using the NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: Huh7 cells were infected with lentivirus to knock down FKBP9, and wild-type HepG2 cells were used.

value: mesenchymal HCC cells

value: wild-type

value: Pull down

value: Batch 2


title: HepG2 cells, m6A, Rep2

description:
Library name: SAMPLES13
MeRIP-Seq of human liver cell line
HepG2_peaks_anno.xlsx
HepG2_2_anno.xlsx


title: HepG2 cells, Input, Rep2

description:
Library name: SAMPLES11
MeRIP-Seq of human liver cell line
HepG2_peaks_anno.xlsx
HepG2_2_anno.xlsx

value: Input


title: TED_14_128, bulk RNA

description:
Library name: TED_14_128
TED_14_128


title: TED_14_130, bulk RNA

description:
Library name: TED_14_130
TED_14_130


title: TED_17_144, bulk RNA

description:
Library name: TED_17_144
TED_17_144


title: TED_14_127, bulk RNA

description:
Library name: TED_14_127
TED_14_127


title: TED_14_126, bulk RNA

description:
Library name: TED_14_126
TED_14_126


title: hPSC_RiboSeq_Rep2

description: Library name: NM2022_0002


title: Huh7 cells, shIGF2BP1, Rep3

description:
Library name: SAMPLES9
RNA-Seq of human liver cell line
RNA-Seq_Cont and FPKM.xlsx
RNA-Seq_DE_results.xlsx

data_processing:
Raw data was trimmed using Trim Galore to remove adapters and low-quality bases.
Assembly: Sequencing data were aligned to the human reference genome (hg38) using HISAT2, and transcript quantification was performed using featureCounts.
Supplementary files format and content: Processed data files are in BAM format, containing mapped read sequences with quality scores.

value: knockdown

value: Knockdown

value: Batch 1


title: TED_14_125, bulk RNA

description:
Library name: TED_14_125
TED_14_125


title: Huh7 cells, shIGF2BP1, Rep1

description:
Library name: SAMPLES7
RNA-Seq of human liver cell line
RNA-Seq_Cont and FPKM.xlsx
RNA-Seq_DE_results.xlsx


title: HepG2 cells, Input, Rep1

description:
Library name: SAMPLES10
MeRIP-Seq of human liver cell line
HepG2_peaks_anno.xlsx
HepG2_1_anno.xlsx


title: TED_16_123, bulk RNA

description:
Library name: TED_16_123
TED_16_123


title: Huh7 cells, shFKBP9, Rep3

description:
Library name: SAMPLES6
RNA-Seq of human liver cell line
RNA-Seq_Cont and FPKM.xlsx
RNA-Seq_DE_results.xlsx


title: DE_RNAseq_Rep2

description: Library name: NM2022_0044

value: undifferentiated hES

value: DefinitiveEndoderm


title: TED_16_121, bulk RNA

description:
Library name: TED_16_121
TED_16_121


title: Huh7 cells, shFKBP9, Rep1

description:
Library name: SAMPLES4
RNA-Seq of human liver cell line
RNA-Seq_Cont and FPKM.xlsx
RNA-Seq_DE_results.xlsx


title: Huh7 cells, shFKBP9, Rep2

description:
Library name: SAMPLES5
RNA-Seq of human liver cell line
RNA-Seq_Cont and FPKM.xlsx
RNA-Seq_DE_results.xlsx


title: TED_16_120, bulk RNA

description:
Library name: TED_16_120
TED_16_120


title: Huh7 cells, shControl, Rep3

description:
Library name: SAMPLES3
RNA-Seq of human liver cell line
RNA-Seq_Cont and FPKM.xlsx
RNA-Seq_DE_results.xlsx

value: Control


title: TED_13_118, bulk RNA

description:
Library name: TED_13_118
TED_13_118


title: Huh7 cells, shControl, Rep1

description:
Library name: SAMPLES1
RNA-Seq of human liver cell line
RNA-Seq_Cont and FPKM.xlsx
RNA-Seq_DE_results.xlsx


title: Huh7 cells, shControl, Rep2

description:
Library name: SAMPLES2
RNA-Seq of human liver cell line
RNA-Seq_Cont and FPKM.xlsx
RNA-Seq_DE_results.xlsx


title: TED_16_119, bulk RNA

description:
Library name: TED_16_119
TED_16_119


title: TED_14_129, bulk RNA

description:
Library name: TED_14_129
TED_14_129


title: TED_13_116, bulk RNA

description:
Library name: TED_13_116
TED_13_116


title: TED_13_115, bulk RNA

description:
Library name: TED_13_115
TED_13_115


title: HDLEC_IFNG replicate 3

city: New York

first: Amanda

last: Lund

state: New York

address: 522 First Ave

institute: NYU Langone Health

description: Library name: y_c

data_processing:
RNA was harvested using the Rneasy mini kit (Qiagen, 74104)
Assembly: hg19
Supplementary files format and content: counts.raw.csv

source_name: Juvenile foreskin

extract_protocol:
RNA was harvested using the Rneasy mini kit (Qiagen, 74104)
bulk RNA-seq

treatment_protocol: HDLECs were seeded in 6-well plates at 60K per well. The following day they were treated with PBS control or IFNγ (0.5ug/ml) in fresh media. Treatment was replenished every day.

value: Juvenile foreskin

value: HDLEC

value: Endothelial cells

value: IFNG


title: Huh7 cells, shIGF2BP1, Rep2

description:
Library name: SAMPLES8
RNA-Seq of human liver cell line
RNA-Seq_Cont and FPKM.xlsx
RNA-Seq_DE_results.xlsx


title: TED_13_113, bulk RNA

description:
Library name: TED_13_113
TED_13_113


title: HDLEC_PBS replicate 3

description: Library name: NC_C

value: PBS


title: TED_16_124, bulk RNA

description:
Library name: TED_16_124
TED_16_124

value: PBMC


title: TED_12_112, bulk RNA

description:
Library name: TED_12_112
TED_12_112


title: TED_12_108, bulk RNA

description:
Library name: TED_12_108
TED_12_108


title: TED_12_111, bulk RNA

description:
Library name: TED_12_111
TED_12_111


title: HDLEC_IFNG replicate 2

description: Library name: y_b


title: TED_12_106, bulk RNA

description:
Library name: TED_12_106
TED_12_106


title: HDLEC_IFNG replicate 1

description: Library name: y_a


title: HDLEC_PBS replicate 2

description: Library name: NC_B


title: 3D - Day7 replicate 2

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

institute: SR-TIGET

data_processing:
Raw FASTQ data underwent quality assessment using FastQC. Subsequently, reads were trimmed for adapter sequences and low-quality bases at the 3' end with TrimGalore (v0.5.0) and aligned to the GRCh38 reference genome using STAR (v2.7.0d). The Gencode primary assembly gene transfer file (GTF) v35 served as the reference gene annotation. Post-alignment metrics, such as coverage distribution across gene lengths and the percentage of reads mapping to exons, were gathered using Qorts (v1.3.5). Reads were assigned to genes with featureCounts (v1.6.3), considering reads that overlapped exons by at least 10 nucleotides (--minOverlap 10) and excluding chimeric reads. Data preprocessing, exploratory analyses, and differential gene expression assessments were conducted using built-in functions from the DESeq2 (v1.30.0) R package
Assembly: GRCh38
Supplementary files format and content: tabular text file with raw gene counts matrix

source_name: Cord Blood

growth_protocol: After thawing, HSPCs were seeded at the concentration of 5x105 cells/ml in serum-free StemSpan SFEM medium (StemCell Technologies) supplemented with 2mM L-glutamine and Penicillin-Streptomycin (100IU/ml penicillin, 100mg/ml streptomycin), 1μM SR-1 (Biovision), 50nM UM171 (STEMCell Technologies), and recombinant human cytokines (100ng/ml SCF, 100ng/ml FLT3-L, 20ng/ml TPO, and 20ng/ml IL-6; Peprotech). 10μM 16,16-Dimethyl Prostaglandin E2 (Cayman) was added only at thawing.

extract_protocol:
RNA extraction was performed with RNeasy Plus Micro Kit (QIAGEN) following the manufacturer’s instructions.
Library preparation was performed by Genewiz/AZENTA life sciences using illumina-compatible adapters; samples were sequenced with NovaSeq 2x150 configuration

treatment_protocol: Cells from the two experimental groups were cultured ex vivo either on traditional 2D culture (plastic wells) or on an innovative 3D culture substrate (nichoid).

value: Cord Blood

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

tag: time

value: 3D culture


title: TED_12_109, bulk RNA

description:
Library name: TED_12_109
TED_12_109


title: HDLEC_PBS replicate 1

description: Library name: NC_a


title: TED_12_110, bulk RNA

description:
Library name: TED_12_110
TED_12_110


title: TED_12_100, bulk RNA

description:
Library name: TED_12_100
TED_12_100


title: 3D - Day7 replicate 1


title: TED_12_102, bulk RNA

description:
Library name: TED_12_102
TED_12_102


title: 3D - Day4 replicate 3


title: TED_12_98, bulk RNA

description:
Library name: TED_12_98
TED_12_98


title: TED_12_97, bulk RNA

description:
Library name: TED_12_97
TED_12_97


title: 3D - Day4 replicate 2


title: 3D - Day4 replicate 1


title: 2D - Day7 replicate 3

value: 2D culture


title: TED_12_96, bulk RNA

description:
Library name: TED_12_96
TED_12_96


title: 2D - Day7 replicate 2


title: 2D - Day7 replicate 1


title: 3D - Day7 replicate 3


title: TED_12_93, bulk RNA

description:
Library name: TED_12_93
TED_12_93


title: TED_12_92, bulk RNA

description:
Library name: TED_12_92
TED_12_92


title: 2D - Day4 replicate 1


title: TED_12_95, bulk RNA

description:
Library name: TED_12_95
TED_12_95


title: PY20 for PANDORA-seq

city: Guangzhou

first: Yi

last: Li

state: Guangdong

address: 107 Yanjiang Xi  Ave.

department: Department of Obstetrics and Gynecology

institute: Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University

data_processing:
Bowtie v1.2.3
Sequence data was trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence was mapped to hg38 using CLC genomic benchwork
Read count extraction and normalization was performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each unique sequence

source_name: culture media

extract_protocol:
The RNA was extracted using Trizol
The RNA library was contructed using QIAseq® miRNA Library Kit

value: culture media

tag: sample group

value: second batch :control group of culture media


title: PY19 for PANDORA-seq


title: 2D - Day4 replicate 3


title: PY15 for PANDORA-seq


title: PY18 for PANDORA-seq


title: PY16 for PANDORA-seq


title: TED_12_91, bulk RNA

description:
Library name: TED_12_91
TED_12_91

data_processing:
For PBMCs sequencing, raw fastq data were subjected to quality control using fastp-0.12.4. Alignment was performed using hisat2-2.2.0, referencing the GRCh38 human genome, which included ERCC spike sequences. Sorted SAM files were processed using GATK4-4.2.6.0, and transcript assembly and abundance estimation were carried out using stringtie-2.2.1. Batch effects were corrected using ERCC spike-in as references, employing the R package RUVSeq-1.30.0 for normalization.
Assembly: hg38
Supplementary files format and content: For PBMCs sequencing, tab-delimited text file includes ERCC counts for each Sample


title: TED_11_86, bulk RNA

description:
Library name: TED_11_86
TED_11_86


title: TED_11_87, bulk RNA

description:
Library name: TED_11_87
TED_11_87


title: TED_11_85, bulk RNA

description:
Library name: TED_11_85
TED_11_85


title: TED_12_90, bulk RNA

description:
Library name: TED_12_90
TED_12_90


title: TED_11_83, bulk RNA

description:
Library name: TED_11_83
TED_11_83


title: TED_11_82, bulk RNA

description:
Library name: TED_11_82
TED_11_82


title: PY13 for PANDORA-seq


title: PY11 for PANDORA-seq


title: PY12 for PANDORA-seq


title: TED_12_94, bulk RNA

description:
Library name: TED_12_94
TED_12_94


title: PY10 for PANDORA-seq


title: 2D - Day4 replicate 2


title: TED_11_76, bulk RNA

description:
Library name: TED_11_76
TED_11_76


title: TED_11_75, bulk RNA

description:
Library name: TED_11_75
TED_11_75


title: PY9 for PANDORA-seq


title: PY8 for PANDORA-seq


title: TED_12_99, bulk RNA

description:
Library name: TED_12_99
TED_12_99


title: PY7 for PANDORA-seq


title: TED_11_89, bulk RNA

description:
Library name: TED_11_89
TED_11_89


title: TED_11_70, bulk RNA

description:
Library name: TED_11_70
TED_11_70


title: TED_10_67, bulk RNA

description:
Library name: TED_10_67
TED_10_67


title: TED_10_69, bulk RNA

description:
Library name: TED_10_69
TED_10_69


title: PY14 for PANDORA-seq


title: TED_11_71, bulk RNA

description:
Library name: TED_11_71
TED_11_71


title: TED_10_66, bulk RNA

description:
Library name: TED_10_66
TED_10_66


title: PY2 for PANDORA-seq


title: PY5 for PANDORA-seq


title: TED_10_64, bulk RNA

description:
Library name: TED_10_64
TED_10_64


title: TED_10_65, bulk RNA

description:
Library name: TED_10_65
TED_10_65


title: P20 for PANDORA-seq

source_name: embryo

value: embryo

value: second batch :control group of embryo


title: PY6 for PANDORA-seq


title: PY1 for PANDORA-seq


title: TED_10_63, bulk RNA

description:
Library name: TED_10_63
TED_10_63


title: P19 for PANDORA-seq


title: TED_11_77, bulk RNA

description:
Library name: TED_11_77
TED_11_77


title: PY3 for PANDORA-seq


title: sorted CD3- CD56+ cells from tonsillar explant, uninfected

city: Barcelona

first: María José

last: Buzón Gómez

state: Barcelona

address: Passeig Vall d'Hebron, 119-129

department: Infectious Diseases

institute: Vall d'Hebron Research Institute

description:
Library name: L759
10x Genomics

data_processing:
CellRanger software v8.0.1 was used to perform the alignment, filtering, barcode counting, and UMI counting for each library. Available online at: https://support.10xgenomics.com/single-cell-gene-expression/software/
Seurat v4.3 ecosystem was used for single cell count data quality control, analysis and exploration. Available online at: https://satijalab.org/seurat/
SingleR v1.10 was used for reference-based single-cell RNA-seq annotation. Available online at: https://github.com/SingleR-inc/SingleR
slingshot v2.4 was used for trajectory analysis. Available online at: https://github.com/kstreet13/slingshot
During the initial clustering steps, we identified a small cluster (55 cells in L759 and 62 cells in L760) that was automatically annotated as B cells by the SingleR method using the Monaco Immune Data Set as a reference. We excluded these potentially contaminating B cells from subsequent analyses
Assembly: Human reference GRCh38 - 2024-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tonsils

extract_protocol:
To prepare tonsillar cell suspensions, 12 tissue blocks were placed into 1.5 mL Eppendorf tubes containing 400 µL of RPMI-1640 medium supplemented with 5% FBS (R5 medium). The tissues were mechanically digested using pestles (Labolan) attached to a handheld homogenizer (Labolan). The resulting cell suspensions were filtered sequentially through 70 µm cell strainers (LabClinics) and 30 µm CellTrics® filters (Sysmex) to remove debris. Filtered cells were washed twice with 1X PBS, and residual red blood cells were lysed using ACK Lysis Buffer (Fisher Scientific). Cell count and viability were evaluated with the LUNA Automated Cell Counter (Logos Biosystems). CD56+ cells were enriched from both HIV-infected and uninfected tissue suspensions using the MagniSort™ Human CD56 Positive Selection Kit. After enrichment, the cells were washed and resuspended in 1X PBS for viability assessment with LIVE/DEAD Viability dye, incubated for 20 minutes. Subsequently, the cells were washed, resuspended in a staining buffer (1X PBS with 3% FBS), and labeled with surface antibodies targeting lineage markers. Finally, the stained cells were washed again in staining buffer and resuspended in PBS containing 0.04% BSA. The CD3-CD56+ cell population was sorted from the tonsillar CD56+ cell suspensions of HIV-infected and uninfected tissue blocks using a FACS instrument (Cytek Aurora CS), achieving a final purity of >95%
The cellular concentration and viability were verified staining the sample with Trypan Blue (Fisher SC) and evaluated by microscopy. Individual cells were partitioned into Gel Bead‑In‑Emulsions with a Target Cell Recovery of 3478 and 5594 total cells, by using the Chromium X System (10X Genomics). Single cell suspensions were converted to barcoded scRNA-seq libraries using the Chromium GEM-X Single Cell 3' Reagent Kits v4 (10X Genomics) following manufacturer's instructions. After cell lysis and barcoded reverse transcription of RNA, cDNA was amplified during 12 cycles and cDNA QC and quantification were performed on an Agilent TapeStation D5000 DNA ScreenTape (Agilent Technologies). cDNA libraries were indexed by PCR during 15 cycles using PN- 3000431 Chromium Dual Index Kit TT Set A. Size distribution and concentration of 3' cDNA libraries were verified on an Agilent TapeStation D5000 DNA ScreenTape (Agilent Technologies). Finally, sequencing cDNA libraries was carried out on a Nova Seq 6000 sequencer (Illumina) to obtain approximately 40,000 paired-end 150 bp reads per cell.

treatment_protocol: HIV infection

value: Tonsils

tag: age

value: 9 years

value: male

value: CD3- CD56+ lymphocytes

tag: infection

value: uninfected


title: TED_9_62, bulk RNA

description:
Library name: TED_9_62
TED_9_62


title: TED_9_61, bulk RNA

description:
Library name: TED_9_61
TED_9_61


title: P18 for PANDORA-seq


title: TED_11_74, bulk RNA

description:
Library name: TED_11_74
TED_11_74


title: P17 for PANDORA-seq


title: TED_7_53, bulk RNA

description:
Library name: TED_7_53
TED_7_53


title: P16 for PANDORA-seq


title: TED_7_52, bulk RNA

description:
Library name: TED_7_52
TED_7_52


title: PY4 for PANDORA-seq


title: P15 for PANDORA-seq


title: TED_7_51, bulk RNA

description:
Library name: TED_7_51
TED_7_51


title: P14 for PANDORA-seq


title: P12 for PANDORA-seq


title: P13 for PANDORA-seq


title: TED_7_50, bulk RNA

description:
Library name: TED_7_50
TED_7_50


title: P11 for PANDORA-seq


title: TED_6_48, bulk RNA

description:
Library name: TED_6_48
TED_6_48


title: TED_6_46, bulk RNA

description:
Library name: TED_6_46
TED_6_46


title: P9 for PANDORA-seq


title: P8 for PANDORA-seq


title: P7 for PANDORA-seq


title: TED_6_42, bulk RNA

description:
Library name: TED_6_42
TED_6_42


title: TED_6_41, bulk RNA

description:
Library name: TED_6_41
TED_6_41


title: P6 for PANDORA-seq


title: P5 for PANDORA-seq


title: P4 for PANDORA-seq


title: TED_6_40, bulk RNA

description:
Library name: TED_6_40
TED_6_40


title: TED_6_39, bulk RNA

description:
Library name: TED_6_39
TED_6_39


title: TED_7_56, bulk RNA

description:
Library name: TED_7_56
TED_7_56


title: TED_6_37, bulk RNA

description:
Library name: TED_6_37
TED_6_37


title: P2 for PANDORA-seq


title: TED_6_49, bulk RNA

description:
Library name: TED_6_49
TED_6_49


title: P1 for PANDORA-seq


title: GY19 for PANDORA-seq

value: second batch :case group of culture media


title: GY18 for PANDORA-seq


title: TED_6_43, bulk RNA

description:
Library name: TED_6_43
TED_6_43


title: TED_5_34, bulk RNA

description:
Library name: TED_5_34
TED_5_34


title: GY20 for PANDORA-seq


title: TED_11_84, bulk RNA

description:
Library name: TED_11_84
TED_11_84


title: TED_5_33, bulk RNA

description:
Library name: TED_5_33
TED_5_33


title: P10 for PANDORA-seq


title: TED_5_32, bulk RNA

description:
Library name: TED_5_32
TED_5_32


title: GY15 for PANDORA-seq


title: TED_5_29, bulk RNA

description:
Library name: TED_5_29
TED_5_29


title: GY16 for PANDORA-seq


title: TED_4_28, bulk RNA

description:
Library name: TED_4_28
TED_4_28


title: GY14 for PANDORA-seq


title: TED_4_26, bulk RNA

description:
Library name: TED_4_26
TED_4_26


title: P3 for PANDORA-seq


title: GY13 for PANDORA-seq


title: TED_6_38, bulk RNA

description:
Library name: TED_6_38
TED_6_38


title: TED_4_25, bulk RNA

description:
Library name: TED_4_25
TED_4_25


title: GY12 for PANDORA-seq


title: TED_6_45, bulk RNA

description:
Library name: TED_6_45
TED_6_45


title: GY11 for PANDORA-seq


title: TED_4_24, bulk RNA

description:
Library name: TED_4_24
TED_4_24


title: TED_6_35, bulk RNA

description:
Library name: TED_6_35
TED_6_35


title: TED_4_21, bulk RNA

description:
Library name: TED_4_21
TED_4_21


title: GY10 for PANDORA-seq


title: GY9 for PANDORA-seq


title: TED_4_22, bulk RNA

description:
Library name: TED_4_22
TED_4_22


title: TED_6_36, bulk RNA

description:
Library name: TED_6_36
TED_6_36


title: GY17 for PANDORA-seq


title: GY8 for PANDORA-seq


title: TED_3_16, bulk RNA

description:
Library name: TED_3_16
TED_3_16


title: GY5 for PANDORA-seq


title: GY6 for PANDORA-seq


title: GY7 for PANDORA-seq


title: TED_3_18, bulk RNA

description:
Library name: TED_3_18
TED_3_18


title: TED_3_15, bulk RNA

description:
Library name: TED_3_15
TED_3_15


title: GY4 for PANDORA-seq


title: GY3 for PANDORA-seq


title: TED_9_12, bulk RNA

description:
Library name: TED_9_12
TED_9_12


title: TED_9_13, bulk RNA

description:
Library name: TED_9_13
TED_9_13


title: TED_9_11, bulk RNA

description:
Library name: TED_9_11
TED_9_11


title: TED_9_10, bulk RNA

description:
Library name: TED_9_10
TED_9_10


title: TED_9_9, bulk RNA

description:
Library name: TED_9_9
TED_9_9


title: G20 for PANDORA-seq

value: second batch :case group of embryo


title: TED_3_8, bulk RNA

description:
Library name: TED_3_8
TED_3_8


title: G19 for PANDORA-seq


title: TED_2_7, bulk RNA

description:
Library name: TED_2_7
TED_2_7


title: TED_2_6, bulk RNA

description:
Library name: TED_2_6
TED_2_6


title: GY1 for PANDORA-seq


title: G18 for PANDORA-seq


title: G17 for PANDORA-seq


title: G16 for PANDORA-seq


title: G14 for PANDORA-seq


title: TED_3_17, bulk RNA

description:
Library name: TED_3_17
TED_3_17


title: TED_3_20, bulk RNA

description:
Library name: TED_3_20
TED_3_20


title: TED_1_3, bulk RNA

description:
Library name: TED_1_3
TED_1_3


title: G15 for PANDORA-seq


title: TED_2_5, bulk RNA

description:
Library name: TED_2_5
TED_2_5


title: TED_2_4, bulk RNA

description:
Library name: TED_2_4
TED_2_4


title: G12 for PANDORA-seq


title: TED_18_161, smoking patient, bulk RNA

first: Jin

last: Liu

state: Huangpu district

address: 833 Zhizaoju Road

institute: Shanghai Ninth People’s Hospital

data_processing:
For  orbital fibroblasts sequencing, the sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05 (or FDR ≤ 0.001).
For PBMCs sequencing, raw fastq data were subjected to quality control using fastp-0.12.4. Alignment was performed using hisat2-2.2.0, referencing the GRCh38 human genome, which included ERCC spike sequences. Sorted SAM files were processed using GATK4-4.2.6.0, and transcript assembly and abundance estimation were carried out using stringtie-2.2.1. Batch effects were corrected using ERCC spike-in as references, employing the R package RUVSeq-1.30.0 for normalization.
Assembly: hg38
Supplementary files format and content: For orbital fibroblasts sequencing, tab-delimited text file includes raw counts for each cell sample
Supplementary files format and content: For PBMCs sequencing, tab-delimited text file includes ERCC counts for each Sample

extract_protocol:
For cell RNA extraction, Add 600 μL TRIzol to one cell sample. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification.Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
For orbital fibroblast cell bulk RNA-seq, the libraries were sequenced on an MGISEQ-2000RS system. For PBMCs sequencing, the total RNA was mixed with ERCC RNA Spike-in Mix (4456740, Invitrogen) in proportion for transcriptome library construction. The sequencing library was prepared using the RNA-seq Library Prep Kit for MGI (NRM605, Vazyme) and sequenced in batches on the DNBSEQ-T7 platform.

value: thyroid eye disease (TED)


title: TED_18_158, nonsmoking patient, bulk RNA

value: PBMC


title: TED_18_160, nonsmoking patient, bulk RNA


title: G10 for PANDORA-seq


title: G11 for PANDORA-seq


title: TED_18_157, smoking patient, bulk RNA


title: GY2 for PANDORA-seq


title: TED_18_156, smoking patient, bulk RNA


title: G9 for PANDORA-seq


title: G8 for PANDORA-seq


title: TED_17_149, smoking patient, bulk RNA


title: G7 for PANDORA-seq


title: TED_18_153, smoking patient, bulk RNA


title: G6 for PANDORA-seq


title: G5 for PANDORA-seq


title: G4 for PANDORA-seq


title: TED_17_138, smoking patient, bulk RNA


title: TED_17_140, smoking patient, bulk RNA


title: TED_17_143, smoking patient, bulk RNA


title: G3 for PANDORA-seq


title: FY10 for PANDORA-seq


title: TED_16_122, nonsmoking patient, bulk RNA


title: FY9 for PANDORA-seq


title: FY8 for PANDORA-seq


title: TED_16_135, smoking patient, bulk RNA


title: TED_16_134, smoking patient, bulk RNA


title: TED_13_117, nonsmoking patient, bulk RNA


title: FY6 for PANDORA-seq


title: TED_12_107, smoking patient, bulk RNA


title: FY5 for PANDORA-seq


title: FY4 for PANDORA-seq


title: FY2 for PANDORA-seq


title: TED_12_104, smoking patient, bulk RNA


title: TED_13_114, smoking patient, bulk RNA


title: FY3 for PANDORA-seq


title: TED_12_101, nonsmoking patient, bulk RNA


title: G13 for PANDORA-seq


title: TED_11_79, nonsmoking patient, bulk RNA


title: TED_11_72, smoking patient, bulk RNA


title: F10 for PANDORA-seq


title: FY1 for PANDORA-seq


title: TED_10_68, smoking patient, bulk RNA


title: F7 for PANDORA-seq


title: TED_8_59, nonsmoking patient, bulk RNA


title: FY7 for PANDORA-seq


title: TED_17_146, nonsmoking patient, bulk RNA


title: TED_9_60, nonsmoking patient, bulk RNA


title: F9 for PANDORA-seq


title: F6 for PANDORA-seq


title: TED_8_58, nonsmoking patient, bulk RNA


title: TED_7_57, smoking patient, bulk RNA


title: TED_7_55, nonsmoking patient, bulk RNA


title: F4 for PANDORA-seq


title: TED_7_54, nonsmoking patient, bulk RNA


title: F5 for PANDORA-seq


title: F2 for PANDORA-seq


title: TED_6_44, smoking patient, bulk RNA


title: TED_5_30, nonsmoking patient, bulk RNA


title: TED_5_31, nonsmoking patient, bulk RNA


title: TED_6_47, nonsmoking patient, bulk RNA


title: PM4 for PANDORA-seq

value: first batch :control group of culture media


title: F1 for PANDORA-seq


title: TED_4_27, smoking patient, bulk RNA


title: TED_11_88, nonsmoking patient, bulk RNA


title: kdm5a-mo-48hpf

data_processing:
Libraries were constructed with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) per the manufacturer's guidelines, with index codes for sample identification.
Clustering was conducted on a cBot system with HiSeq PE Cluster Kit v4-cBot-HS (Illumina), and 150 bp paired-end reads were generated on an Illumina platform.
Quality control was performed with FastQC (v0.11.5), and low-quality reads were filtered with NGSQC (v2.3.3). Clean reads were aligned to the reference genome (http://asia.ensembl.org/index.html) using HISAT2 (v2.1.0) under default parameters.
Gene expression was quantified with StringTie (v1.3.3b), and differential expression analysis was conducted with DESeq (v1.28.0). DEGs were identified with a fold change of ≥2 (|log2FC| ≥ 1) and significance level of p ≤ 0.05, adjusted by the Benjamini-Hochberg FDR method. DEG annotations were based on ENSEMBL, NCBI, UniProt, GO, and KEGG databases.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

growth_protocol: The zebrafish were kept at 28°C, pH: 7-8, with a photoperiod of 14h light/10h dark. Zebrafish were placed in the same mating tank at about 16:00 on the day before spawning in a ratio of 2:1 males to females, separated by a plastic partition in the middle of the mating tank, which was withdrawn at 9:00 the next morning. Fertilized eggs were collected and recorded as 0hpf.

extract_protocol:
WT zebrafish and KO zebrafish were mated separately and embryos were collected
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Knockout of the Kdm5a gene using crispr/cas9 technology

tag: time point

value: 48h after fertilization.


title: F8 for PANDORA-seq

tag: cell type


title: TED_4_23, nonsmoking patient, bulk RNA


title: kdm5a-mo-24hpf

value: 24h after fertilization.


title: PM2 for PANDORA-seq


title: dmap1_rep2_atri

city: Palo Alto

first: Ben

last: Herken

state: CA

address: 3181 porter dr.

institute: Arc Institute

description: Library name: 98_r2_T_K

data_processing:
Align to library reference file with hamming distance = 1, see github: https://github.com/bherken/herken2024_originalcode & Differential expression analysis from raw counts with DeSeq2, See STAR Methods
Assembly: dualsgrna_alignedlibrary.txt & GRCh38
Supplementary files format and content: .txt,  counts table

extract_protocol:
Genomics DNA using MN Blood XL Kit, see STAR Method & Total RNA from Zymo Direct-Zol kit
PCR from genomic DNA, see STAR Method & Lexogen Quantseq FWD kit with UMI add-on

tag: cell line

value: ATRi


title: TED_1_2, nonsmoking patient, bulk RNA

tag: genotype


title: F3 for PANDORA-seq


title: wt-48hpf

first: Yuan

last: Fu

address: No. 56, Xinjian South Road, Yingze District

value: WT


title: wt-24hpf


title: TED_3_19, smoking patient, bulk RNA


title: PM5 for PANDORA-seq

value: culture media


title: PM1 for PANDORA-seq


title: PE6 for PANDORA-seq

value: embryo

value: first batch :control group of embryo


title: dmap1_rep2_untreated

description: Library name: 98_r2_UT_K

tag: treatment

value: DMSO


title: TED_1_1, nonsmoking patient, bulk RNA


title: PM6 for PANDORA-seq


title: dmap1_rep1_untreated

description: Library name: 98_r1_UT_K


title: dmap1_rep1_atri

description: Library name: 98_r1_T_K


title: PE4 for PANDORA-seq


title: PE5 for PANDORA-seq


title: ChIP_OCR_PU.1_rep2

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description:
Library name: Sample R2
ChIP_Spi1_OCR_rep2

data_processing:
cutadapt
BWA-mem alignment
macs2 peak-calling
Assembly: mm10
Supplementary files format and content: text file and narrow peaks

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
For PU.1 ChIP-seq, 20,000 sorted HSCs were 458 mixed with 50M bacteria, and beads were washed for 1 min instead of 5 min in the sample wash 459 step
Libraries were prepared with TruSeq Nano DNA Low Throughput Library Prep Kit (20015964, 460 Illumina) according to manufacturer's instructions. Sequencing was done with Illumina HiSeq 461 2500 instrument

tag: tissue

value: Bone marrow

value: Hematopoetic stem cells

value: Calorie Restriction


title: PM3 for PANDORA-seq


title: ChIP_OCRRF_PU.1_rep2

description:
Library name: Sample R3
ChIP_Spi1_OCRRF_rep2

value: Calorie Restriction, then refeed

tag: batch


title: brd8_rep2_atri

description: Library name: 96_r2_T_K


title: brd8_rep2_untreated

description: Library name: 96_r2_UT_K


title: brd8_rep1_untreated

description: Library name: 96_r1_UT_K


title: PE3 for PANDORA-seq


title: PE2 for PANDORA-seq


title: ntc_rep2_atri

description: Library name: 100_r2_T_K


title: ntc_rep1_atri

description: Library name: 100_r1_T_K


title: ChIP_OWT_PU.1_rep2

description:
Library name: Sample R1
ChIP_Spi1_OWT_rep2


title: ntc_rep2_untreated

description: Library name: 100_r2_UT_K


title: LG253-NY-200

city: NEW YORK

first: hao

last: chen

state: NY

address: 413 E 69th ST

department: Brain and mind research institute

institute: Weill Cornell Medicine

description:
Library name: Sample15
novogene

data_processing:
reads were aligned to the Mus musculus GRCm38 (mm10) reference genome using STAR v2.7.x
follow novogene standard pipeline
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: frontal cortex

extract_protocol:
RNA was harvested by PureLink RNA Mini Kit (Invitrogen, Cat # 12183025), 500ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocol

value: frontal cortex

value: female


title: PE1 for PANDORA-seq


title: GM16 for PANDORA-seq

value: first batch :case group of culture media


title: LG253-NY-205

description:
Library name: Sample16
novogene


title: GM15 for PANDORA-seq


title: LG253-NY-113

description:
Library name: Sample13
novogene


title: GM14 for PANDORA-seq


title: 02_004_pre

city: Cambridge

first: Roy

last: Zhang

address: Cambridge Biomedical Campus, Francis Crick Ave

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description: Library name: Sample_56

data_processing:
Libraries were sequenced on a NovaSeq sequencer (Ilumina) by Genewiz
Sequencing data was demultiplexed to give individual fastq files using Casava (Illumina)
FASTQC was used for quality control
Fastq files were aligned to the human genome (Hg38) using STAR
A table of gene counts was produced using the featureCounts function within Rsubread
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include unnormalised counts for each sample

source_name: Peripheral blood

extract_protocol:
RNA extracted using a pure-link RNA mini kit (Ambion)
0.3 - 0.75µg of RNA was used to produce sequencing libraries using TruSeq Stranded total RNA library prep kit (Illumina) with 14 PCR amplification cycles

value: Peripheral blood

value: Peripheral blood mononuclear cells

tag: individual

tag: treatment arm

value: Clazakizumab

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

value: Unknown cause

tag: donor type

value: Living

tag: donor age

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

value: CyA, MMF

tag: study centre

value: Berlin

tag: sample timepoint

value: pre

tag: abmr mmdx

tag: abmr banff

tag: egfr

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)

value: male


title: LG253-NY-152

description:
Library name: Sample14
novogene

tag: tissue

tag: genotype

tag: age

tag: Sex


title: 02_003_week12

description: Library name: Sample_54

tag: cell type

tag: individual

tag: treatment arm

value: Placebo

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

value: IgA nephropathy

tag: donor type

tag: donor age

value: Tac, MMF, Methypred

tag: batch


title: 02_004_week52

description: Library name: Sample_58

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

tag: egfr


title: brd8_rep1_atri

description: Library name: 96_r1_T_K

tag: cell line

tag: genotype

tag: treatment

value: ATRi


title: 02_004_week12

description: Library name: Sample_57

tag: tissue

tag: cell type

tag: individual

tag: treatment arm

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)

tag: Sex


title: 02_003_week52

description: Library name: Sample_55

tag: donor type

tag: donor age

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

tag: sample timepoint

tag: abmr mmdx

tag: batch


title: 02_003_pre

description: Library name: Sample_53

tag: tissue

tag: cell type

tag: individual

tag: treatment arm

tag: date of_birth

tag: date of_transplant

tag: abmr banff

tag: egfr


title: 02_002_week12

description: Library name: Sample_51

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

tag: donor age

tag: hla-a mismatch

value: Tac, EC-MPS, Methypred

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)

tag: Sex


title: 02_002_week52

description: Library name: Sample_52

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

tag: sample timepoint

tag: abmr mmdx

tag: batch


title: LG253-NY-72

description:
Library name: Sample11
novogene

tag: tissue

value: frontal cortex

tag: genotype

tag: age


title: GM12 for PANDORA-seq

tag: cell type

value: culture media

tag: sample group


title: 02_001_week52

description: Library name: Sample_49

tag: individual

tag: treatment arm

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

value: RPGN with pANCA

tag: donor type

value: Deceased

tag: donor age

tag: hla-a mismatch

value: CyA, MMF, Methypred

tag: abmr banff

tag: egfr

value: female


title: ntc_rep1_untreated

description: Library name: 100_r1_UT_K

tag: cell line

value: WT

tag: treatment

value: DMSO


title: 02_002_pre

description: Library name: Sample_50

tag: tissue

value: Peripheral blood

value: Peripheral blood mononuclear cells

value: Clazakizumab

value: Living

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

tag: sample timepoint

tag: abmr mmdx

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)

tag: Sex

tag: batch


title: LG253-NY-95

description:
Library name: Sample10
novogene

tag: genotype

tag: age


title: GM11 for PANDORA-seq

tag: cell type

tag: sample group

value: first batch :case group of culture media


title: 02_001_week12

description: Library name: Sample_48

tag: individual

tag: treatment arm

value: Placebo

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

tag: donor age

tag: hla-a mismatch

value: Berlin

tag: abmr banff

tag: egfr


title: LG253-NY-120

description:
Library name: Sample9
novogene

tag: tissue

tag: Sex


title: 01_018_week52

description: Library name: Sample_46

value: IgA nephropathy

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

value: Tac, EC-MPS, Pred

tag: study centre

value: Vienna

tag: sample timepoint

tag: abmr mmdx

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)

value: male

tag: batch


title: GE16 for PANDORA-seq

tag: cell type

value: embryo

tag: sample group

value: first batch :case group of embryo


title: 01_018_week12

description: Library name: Sample_45

tag: individual

tag: treatment arm

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

value: Deceased

tag: donor age

tag: hla-a mismatch


title: 01_018_pre

description: Library name: Sample_44

tag: tissue

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

value: pre

tag: abmr banff

tag: egfr

tag: Sex


title: 01_017_week12

description: Library name: Sample_43

tag: cell type

tag: individual

tag: treatment arm

value: Polycystic kidney disease

value: Tac, MMF, Pred

tag: sample timepoint

tag: abmr mmdx

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)

tag: batch


title: LG253-NY-225

description:
Library name: Sample8
novogene

tag: tissue

value: frontal cortex

tag: genotype

tag: age

value: female


title: GE15 for PANDORA-seq

tag: sample group


title: LG253-NY-134

description:
Library name: Sample12
novogene


title: 01_016_week12

description: Library name: Sample_40

value: Peripheral blood

value: Peripheral blood mononuclear cells

value: Clazakizumab

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

value: RPGN

tag: donor type

tag: donor age

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

value: Tac, EC-MPS,Pred


title: 01_017_pre

description: Library name: Sample_42

tag: cell type

tag: individual

tag: treatment arm

tag: study centre

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

tag: egfr

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)

tag: Sex


title: LG253-NY-218

description:
Library name: Sample7
novogene

tag: tissue

tag: genotype

tag: age


title: 01_016_week52

description: Library name: Sample_41

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

tag: donor age

tag: hla-a mismatch

tag: hla-b mismatch

tag: hla-dr mismatch

tag: batch


title: GM13 for PANDORA-seq

tag: cell type

value: culture media

tag: sample group

value: first batch :case group of culture media


title: GE14 for PANDORA-seq


title: LG253-NY-187

description:
Library name: Sample6
novogene


title: 01_015_week52

description: Library name: Sample_38

tag: individual

tag: treatment arm

value: Placebo

value: Postrenal cause, meningomyelocele

value: Living

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

value: Vienna

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

tag: egfr

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)


title: GE13 for PANDORA-seq

value: embryo

value: first batch :case group of embryo


title: 01_016_pre

description: Library name: Sample_39

tag: tissue

tag: date of_birth

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

value: Deceased

tag: donor age

tag: hla-a mismatch

value: pre

tag: Sex


title: 01_015_week12

description: Library name: Sample_37

tag: cell type

tag: individual

tag: treatment arm

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

value: Tac, MMF, Pred

tag: batch


title: GE12 for PANDORA-seq

tag: sample group


title: 01_015_pre

description: Library name: Sample_36

tag: tissue

tag: date of_birth

tag: study centre

tag: sample timepoint

tag: abmr mmdx

tag: abmr banff

tag: egfr

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)

value: female


title: 02_001_pre

description: Library name: Sample_47

value: Peripheral blood

tag: cell type

tag: individual

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

value: RPGN with pANCA

tag: donor type

tag: donor age

tag: hla-a mismatch

value: CyA, MMF, Methypred

value: Berlin

tag: Sex


title: LG253-NY-196

description:
Library name: Sample3
novogene

tag: tissue

value: frontal cortex

tag: genotype

tag: age


title: 01_014_week52

description: Library name: Sample_35

value: Peripheral blood mononuclear cells

tag: treatment arm

value: Clazakizumab

tag: date of_birth

value: Diabetic nephropathy

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

tag: sample timepoint

tag: abmr mmdx

value: male

tag: batch


title: GE11 for PANDORA-seq

tag: cell type

tag: sample group


title: 01_014_week12

description: Library name: Sample_34

tag: individual

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

tag: donor age

tag: hla-a mismatch

tag: abmr banff

tag: egfr

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)


title: Jurkat cells shBDH1-2

city: Wuhan

last: Xu

address: 115 East Lake Road, Wuhan, Hubei, 430071, P. R. China

institute: Wuhan university

data_processing:
RNA-seq reads were analyzed by FastQC (version 0.11.9) and mapped to the human genome reference assembly (hg38) using Hisat2 software (version 2.2.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text includes  raw counts for each Sample
Supplementary files format and content: tab-delimited text includes  RPKM values for each Sample

source_name: Jurkat cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and subjected to quality control for RNA integrity by Agilent Bioanalyzer 2100 system (Agilent Technologies). Total RNA was further purified by RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN).
mRNA libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme) and sequenced as 150 bp paired-end reads by Illumina NovaSeq 6000 (Annoroad Gene Technology Corporation).

tag: cell line

value: Jurkat cells

value: T-ALL cell lines

tag: genotype

value: WT

tag: treatment


title: 01_014_pre

description: Library name: Sample_33

tag: tissue

tag: treatment arm

tag: date of_birth

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

value: Vienna

tag: sample timepoint

tag: abmr mmdx

tag: Sex

tag: batch


title: LG253-NY-58

description:
Library name: Sample2
novogene

tag: age


title: 01_013_week52

description: Library name: Sample_32

tag: cell type

tag: individual

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

value: Unknown cause

tag: donor type

value: Deceased

tag: donor age

tag: hla-a mismatch

tag: abmr banff

tag: egfr

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)


title: 01_013_week12

description: Library name: Sample_31

tag: tissue

tag: treatment arm

tag: date of_birth

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

value: Tac, MMF, Pred

tag: study centre

tag: sample timepoint


title: Jurkat cells shBDH1-1

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: 01_012_week52

description: Library name: Sample_29

tag: individual

value: Placebo

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

value: Pyelonephritis

tag: donor type

tag: donor age

tag: hla-a mismatch

value: Tac, EC-MPS, Pred

tag: abmr mmdx

tag: abmr banff

tag: Sex

value: female

tag: batch


title: LG253-NY-96

description:
Library name: Sample1
novogene

tag: tissue

tag: age


title: Jurkat cells shcontrol-1

tag: cell line

value: shcontrol


title: Jurkat cells shcontrol-2

tag: cell type


title: LG253-NY-73

description:
Library name: Sample5
novogene

value: frontal cortex

tag: genotype


title: LG253-NY-189

description:
Library name: Sample4
novogene


title: LG253-NY-200

description:
Library name: Sample15
mRNA expression in mouse hippocampus

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.3.1.0) (10× Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than two cells, cells with a unique gene count over 8000 or less than 300, and cells with a high fraction of mitochondrial reads (>5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v3.0.182 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)
RNA-seq

value: hippocampus

value: Female


title: LG253-NY-205

description:
Library name: Sample16
mRNA expression in mouse hippocampus


title: 01_012_pre

description: Library name: Sample_27

value: Peripheral blood

value: Peripheral blood mononuclear cells

tag: treatment arm

tag: date of_birth

tag: hla-b mismatch

tag: hla-dr mismatch

tag: cold ischaemic_time_(hours)

tag: immunosuppression at_screening

tag: study centre

tag: sample timepoint

value: pre

tag: egfr

tag: dsa (%_of_baseline)

tag: igg (%_of_baseline)


title: 01_012_week12

description: Library name: Sample_28

tag: individual

tag: date of_transplant

tag: date of_index_sample

tag: cause of_renal_failure

tag: donor type

tag: donor age

tag: hla-a mismatch

tag: abmr mmdx

tag: abmr banff

tag: Sex

tag: batch