title: 118_Non-Tumor_Normal_Spleen

data_processing:
Genomic DNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA). Enrichment probes were designed against the region of interest and synthesized through Agilent Technologies–SureSelectXT CD Rat All Exon. Library preparation was performed according to the manufacturer’s guidelines. Briefly, the genomic DNA was fragmented by acoustic shearing with a Covaris S220 instrument. Fragmented DNAs were cleaned up and end repaired, as well as adenylated at the 3’ends. Adapters were ligated to the DNA fragments, and adapter-ligated DNA fragments were enriched with limited cycle PCR. Adapter-ligated DNA fragments were validated using Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer. Adapter-ligated DNA fragments were hybridized with biotinylated baits. The hybrid DNAs were captured by streptavidin-coated binding beads. After extensive wash, the captured DNAs were amplified and indexed with Illumina indexing primers. Post-captured DNA libraries were validated using Agilent TapeStation (Agilent, Santa Clara, CA, USA) and quantified using Qubit 2.0 Fluorometer and Real-Time PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and demultiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification
Assembly: Sequencing results were aligned and analyzed using version 3.4.0 of the NF-Core Sarek Pipeline, using Nextflow version 23.10.1, Singularity 3.9.6. Pipeline settings used the Singularity profile, Rnor_6.0 Rat genome, CNVKit and Mutect2 tools, skipped base_recalibrator, WES-only mode with a minimal SLURM config file for the University of Pittsburgh Center for Research Computing High Throughput Computing Cluster.
mutect2.vcf.gz & mutect2.txt
Authors state:     We ran multiple pipelines to analyze WES data with various parameters.     Users can determine their own pipeline and parameters to analyze our WES     data. As the results will be different by a pipeline or parameters, we     determined that we don't upload the processed data files.

organism: Rattus norvegicus

extract_protocol:
Genomic DNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA). Enrichment probes were designed against the region of interest and synthesized through Agilent Technologies–SureSelectXT CD Rat All Exon. Library preparation was performed according to the manufacturer’s guidelines. Briefly, the genomic DNA was fragmented by acoustic shearing with a Covaris S220 instrument.
Fragmented DNAs were cleaned up and end repaired, as well as adenylated at the 3’ends. Adapters were ligated to the DNA fragments, and adapter-ligated DNA fragments were enriched with limited cycle PCR. Adapter-ligated DNA fragments were validated using Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer. Adapter-ligated DNA fragments were hybridized with biotinylated baits. The hybrid DNAs were captured by streptavidin-coated binding beads. After extensive wash, the captured DNAs were amplified and indexed with Illumina indexing primers. Post-captured DNA libraries were validated using Agilent TapeStation (Agilent, Santa Clara, CA, USA) and quantified using Qubit 2.0 Fluorometer and Real-Time PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and demultiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification
The libraries were normalized and pooled, and then sequenced using the NovaSeq 6000 Platform (Illumina) to an average of 25M 101 PE reads. Sequencing data was given as raw data with a Phred Q30 score of 80 or better.

tag: ageclass

value: Older


title: AB1437_B16_viable only_1

status: Public on Jun 05 2026

type: SRA

city: Tel Aviv

first: Merav

last: Cohen

address: Chaim Levanon St 55

department: Clinical microbiology and immunology

country: Israel

institute: Tel Aviv University

description:
Library name: AB1437
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

library_source: transcriptomic single cell

data_processing:
We generated FASTQ files from the raw BCL files using the bcl2fastq software provided by Illumina (v.2.20.0.422) with default parameters.
Sequences were mapped to the mouse genome (GRCm39) using STAR (v.2.7.1a). Reads with multiple mapping positions were excluded. We then assigned gene names for exonic, genomic and mitochondrial regions using featureCounts (v.2.0.0), processed the resulting BAM file using samtools (v.1.10) and finally created gene-cell UMI matrices using the UMI-tools software package (v.1.1.2). Using the Scanpy package (v.1.9.8), we loaded these files to a unified data object.
We performed QC by excluding cells with <500 or >10,000 UMIs, >30% mitochondrial genes or >1 UMIs of hemoglobin genes. We also excluded cells from the in vitro model with any expression of T cell genes (Tcf7, Trbc2, Cd3d, Trbc1, Cd3g, Cd3e, Trac, Cd8b1) and from the in vivo lung model with >1 UMIs of endothelial genes (Pecam1, Cdh5, Col4a1, Plvap).
Assembly: GRCm39
Supplementary files format and content: h5ad files - unified post-QC scRNA-seq data, containing a gene-cell UMI matrix
Supplementary files format and content: csv files - flourescence intensity data where relevant (pHrodo+ cells)

molecule: polyA RNA

organism: Mus musculus

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
in-vitro: For macrophage-thymocyte co-culture, BM-derived macrophages were washed with cold PBS and seeded in 24-well plates at 2.5 x 105 cells per well in culture medium supplemented with 10 ng/ml M-CSF and incubated at 37 °C for 3 hours to settle. pHrodo-labeled apoptotic thymocytes were added to the BM-derived macrophages at 1.25 x 106 cells per well. Cells were co-cultured for 3 or 24 hours before they were collected by gentle scraping. in-vivo lung: To obtain single cell suspensions of lungs from mice inoculated with apoptotic thymocytes or PBS, the mice were perfused with PBS through the right ventricle. Lungs were dissociated using the mouse lung dissociation kit (Miltenyi Biotec) according to the manufacturer’s instructions with the following modifications: After mechanical dissociation using the gentleMACS dissociator program “m_lung_01”, lungs were incubated at 37 °C for 10 minutes with agitation. The sample was subsequently pipetted through 16G, 18G and 19G needles and then incubated again at 37 °C for 10 minutes with agitation and then washed with ice-cold sorting buffer (PBS supplemented with 0.2 mM EDTA, pH 8 and 0.5% BSA), filtered through a 100-µm cell strainer and pelleted. B16: To obtain single cell suspensions of B16 tumors, the tumors were removed and weighed using an analytical scale, and then placed in RPMI-1640 supplemented with DNase (28 μg/ml, Sigma-Aldrich) and collagenase IV (1 mg/ml, Worthington). Tissues were incubated at 37 °C for 10 minutes with agitation and then pipetted through 16G, 18G, 19G and 21G needles before they were incubated again at 37 °C for 10 minutes with agitation. Cell suspensions were then washed with cold sorting buffer and pelleted.
The library preparation was conducted following the previously reported protocol {Jaitin, 2014}. In brief, mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol {Jaitin, 2014}. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.

tag: tissue

tag: cell type

value: viable only


title: AL_112

city: Pittsburgh

first: Neil

last: Carleton

state: PA

address: 5051 Centre Ave

department: Pharmacology & Chemical Biology

country: USA

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
For processing, we used Rsubread (Bioconductor release 2.16) to align sequence reads to reference genome and used edgeR and limma R packages (Bioconductor release 4.0 and 3.58 respectively) to normalize gene expression level to log2 transcripts per million (TPM)
Assembly: We aligned sequence reads to GRCh38 release 14 human genome reference sequence and mapped the aligned sequences to Entrez Genes
Supplementary files format and content: After normalization, we removed genes of which expression level is zero across all samples to get 39,404 genes for further pathway analysis.

organism: Homo sapiens

source_name: BreastTumor

extract_protocol:
We used the standard procedure of RNeasy kit to extract total RNA from ER+ breast cancer samples of 83 tumor or 85 tumor-adjacent normal tissue obtained from Pitt Biospecimen Core (PBC) and grouped them by chronological age.
The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer.
Library size and quality were checked using Fragment Analyzer (Agilent) and fluorescent quantification on the Infinite F Nano + (Tecan). The libraries were normalized and pooled, and then sequenced using the NovaSeq 6000 Platform (Illumina) to an average of 25M 101 PE reads. Sequencing data was given as raw data with a Phred Q30 score of 80 or better.

tag: tumor or adjacent

value: Tumor

tag: agerange

value: Middle

tag: chronologicalage

tag: read length


title: AB1841_Roi E. Coli rep 2_rodo+_2

description:
Library name: AB1841
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.

source_name: Lung

value: Lung

value: rodo+


title: AB1436_B16_rodo high_1

description:
Library name: AB1436
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: rodo high


title: 167_Tumor_Younger

value: Younger


title: AL_111


title: AB1840_Roi E. Coli rep 1_rodo+_1

description:
Library name: AB1840
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.


title: AB1435_B16_rodo high_1

description:
Library name: AB1435
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB1439_B16_viable only_1

description:
Library name: AB1439
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 158_Tumor_Younger


title: AL_110


title: AB1839_Roi E. Coli rep 1_rodo-_1

description:
Library name: AB1839
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.

value: rodo-


title: AB1876_Roi Zymo rep 2_rodo+_2

description:
Library name: AB1876
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.


title: AL_123


title: AB1438_B16_viable only_1

description:
Library name: AB1438
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB1434_B16_rodo-_1

description:
Library name: AB1434
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AL_109


title: 157_Tumor_Younger


title: AB1838_Roi E. Coli rep 1_rodo-_1

description:
Library name: AB1838
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.


title: AB1433_B16_rodo-_1

description:
Library name: AB1433
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 107_Tumor_Older


title: AL_108


title: AB1837_Roi E. Coli rep 1_rodo+_1

description:
Library name: AB1837
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.


title: AB1432_B16_rodo-_1

description:
Library name: AB1432
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 116_Tumor_Older


title: AL_107


title: AB1836_Roi E. Coli rep 1_rodo-_1

description:
Library name: AB1836
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.


title: AB1431_B16_rodo-_1

description:
Library name: AB1431
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 102_Tumor_Older


title: AL_106


title: AB1835_Roi E. Coli rep 1_rodo-_1

description:
Library name: AB1835
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.


title: AB1430_B16_rodo+_1

description:
Library name: AB1430
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: Lee_021924_Nuclei_6

data_processing:
We used CellRanger (v.8) to process the raw fastq.gz files and used Seurat R package (v.5.1.0) to analyze the snRNA-seq data.
Assembly: We aligned sequence reads to GCA_000002265.1_Rn_Celera_genomic.fna Rattus norvegicus genome reference sequence obtained from NCBI FTP and mapped the aligned sequences to Entrez Genes
Supplementary files format and content: barcode.tsv, features.tsv, and matrix.mtx

extract_protocol:
We performed 3’v3.1 Nuclei Isolation and GEX library preparation with the 10X Genomics Platform. Snap frozen tissues are dissociated with the 10X Genomics Nuclei Isolation Kit. After dissociation, nuclei suspension concentration and nuclei integrity are assessed using AOPI on the Nexcelom Cellometer Auto 2000. Libraries are then prepared according to the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) protocol using the 10X Genomics Chromium iX Instrument.
The resulting full-length cDNA is checked for size and concentration on the Agilent Tapestation 4150 before proceeding with gene expression library preparation and sample indexing. Final libraries are checked for size on the Agilent Tapestation and concentration using the Invitrogen Qubit 2.0. Libraries are pooled and sequenced on the Illumina NovaSeq 6000 Instrument.
The libraries were normalized and pooled, and then sequenced using the NovaSeq 6000 Platform (Illumina) to an average of 25M 101 PE reads. Sequencing data was given as raw data with a Phred Q30 score of 80 or better.


title: AL_105


title: AB1834_Roi E. Coli rep 1_rodo+_1

description:
Library name: AB1834
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.


title: AB1429_B16_rodo+_1

description:
Library name: AB1429
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: Lee_021924_Nuclei_5


title: AL_104


title: AB1833_Roi E. Coli rep 1_rodo+_1

description:
Library name: AB1833
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.


title: Lee_021924_Nuclei_4


title: AL_103


title: AB1428_B16_rodo+_1

description:
Library name: AB1428
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB650_Roi-thymo-24h-2_non-phago-macs_2

description:
Library name: AB650
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

source_name: in-vitro

value: in-vitro

value: non-phago-macs


title: AB1427_B16_rodo+_1

description:
Library name: AB1427
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: Lee_021924_Nuclei_3


title: AB1528_B16_rodo-_3

description:
Library name: AB1528
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AL_102


title: AB649_Roi-thymo-24h-2_non-phago-macs_2

description:
Library name: AB649
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB1373_Roi-thymo-24h-4_non-phago-macs_4

description:
Library name: AB1373
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AL_101


title: Lee_021924_Nuclei_2


title: AB646_Roi-thymo-24h-2_phago_2

description:
Library name: AB646
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: phago


title: AB1372_Roi-thymo-24h-4_non-phago-macs_4

description:
Library name: AB1372
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: Lee_021924_Nuclei_1


title: AL_100


title: AB645_Roi-thymo-24h-2_non-phago-macs_2

description:
Library name: AB645
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB1371_Roi-thymo-24h-4_phago_4

description:
Library name: AB1371
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 167_Tumor_Younger

data_processing:
For processing, we ran HTSeq/0.13.5 to count the reads and then DESeq2 to identify differentially expressed genes.
Assembly: We aligned sequence reads to the mRatBN7.2 genome.
Supplementary files format and content: Reads count

extract_protocol:
Total RNA was extracted from fresh frozen tissue samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). ERCC Ex-fold RNA reagent (Cat: 4456739) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The next steps included performing rRNA depletion using QIAseq® FastSelect™−rRNA HMR kit (Qiagen, Germantown, MD, USA), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.
The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer.
Library size and quality were checked using Fragment Analyzer (Agilent) and fluorescent quantification on the Infinite F Nano + (Tecan). The libraries were normalized and pooled, and then sequenced using the NovaSeq 6000 Platform (Illumina) to an average of 25M 101 PE reads. Sequencing data was given as raw data with a Phred Q30 score of 80 or better.


title: AL_099


title: AB644_Roi-thymo-3h-2_phago_2

description:
Library name: AB644
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB1370_Roi-thymo-3h-4_non-phago-macs_4

description:
Library name: AB1370
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 158_Tumor_Younger


title: AL_098


title: AB1867_Roi E. Coli rep 3_rodo+_3

description:
Library name: AB1867
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.


title: AB643_Roi-thymo-3h-2_non-phago-macs_2

description:
Library name: AB643
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB1369_Roi-thymo-24h-4_non-phago-macs_4

description:
Library name: AB1369
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 157_Tumor_Younger


title: AL_097


title: AB641_Roi-thymo-24h-2_phago_2

description:
Library name: AB641
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 107_Tumor_Older


title: AB1368_Roi-thymo-24h-4_phago_4

description:
Library name: AB1368
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AL_096


title: AB1367_Roi-thymo-3h-4_non-phago-macs_4

description:
Library name: AB1367
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB640_Roi-thymo-3h-2_non-phago-macs_2

description:
Library name: AB640
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 116_Tumor_Older


title: AL_095


title: AB637_Roi-thymo-3h-2_phago_2

description:
Library name: AB637
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB1366_Roi-thymo-3h-4_phago_4

description:
Library name: AB1366
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 102_Tumor_Older


title: AL_094


title: AB594_Roi-IN1_non-phago myeloid_1

description:
Library name: AB594
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: non-phago myeloid


title: LuT722_Lung_Adenocarcinoma_invasive_front

type: RNA

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: 10x Genomics; CG000749, Rev. B

scan_protocol: 10x Genomics; CG000584, Rev. K

data_processing: Xenium Onboard Analysis (v.4.0.1.0), R (v.4.5.0), Seurat (v.5.2.1)

label: Xenium probe set

molecule: total RNA

source_name: margin at lung adenocacinoma

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: 10x Genomics; CG000578, Rev. A

value: margin at lung adenocacinoma

tag: tissue type

value: Tumor invasive front region, 4x4 mm tissue

tag: tissue preservation method

value: FFPE

tag: treatment

tag: Sex

value: male

tag: age

tag: disease

value: NSCLC


title: AB1365_Roi-thymo-24h-4_non-phago-macs_4

description:
Library name: AB1365
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AL_093


title: PC3, VprBP sh2

city: Los Angeles

first: Sungmin

last: Kim

state: CA

address: 1450 Biggy St, NRT 6517

department: Department of Cancer Biology

institute: University of Southern California

description:
Library name: sample5
column name in raw_counts_all_samples.txt:S2

data_processing:
Partek Flow Server (ver.12.7.0)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow (End min quality level (Phred=35))
Trimmed sequence reads were mapped to Homo sapience (human) - hg38 using Partek Flow (parameters: generate unaligned read: false; quality encoding: auto-detect; ambiguous charaters function: L,0.0, 0.15; Ignore mismatch qualities: false; align to strand: both; mismatch penalty range: max 6 and min: 2 mismatch penalties; mismatch penalty range for soft-clipping: 2 mismatch penalties)
Read count extraction and normalization were performed using Partek Flow
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: PC3 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
RNA was harvested using RNAqueous-4PCR kit (ThermoFisher Scientific). 1.0 ug of total RNA was used for the construction of sequencing libraries.

tag: cell line

value: prostate cancer cells

tag: genotype

value: VprBP knockdown


title: AB593_Roi-IN1_non-phago myeloid_1

description:
Library name: AB593
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB1364_Roi-thymo-3h-4_non-phago-macs_4

description:
Library name: AB1364
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AL_092

value: Tumor

value: Middle


title: AB592_Roi-IN1_phago myeloid_1

description:
Library name: AB592
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: Lung

value: phago myeloid


title: LuT722_Lung_Adenocarcinoma_adjacent_lung

source_name: adjacent lung tissue

value: adjacent lung tissue

value: Adjacent lung tissue region, 4x4 mm tissue


title: AB1363_Roi-thymo-3h-4_phago_4

description:
Library name: AB1363
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: in-vitro


title: AL_091


title: LuT722_Lung_Adenocarcinoma_Tumor_core

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: Tumor core region, 4x4 mm tissue


title: AB591_Roi-IN1_PBS-injected myeloid_1

description:
Library name: AB591
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: PBS-injected myeloid


title: MitoDiso_HeLa_mtRF1L_KO_1

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

description: Library name: L47

library_source: other

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

molecule: other

source_name: HeLa

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

value: HeLa


title: L2-LKP_3_batch2

city: Freiburg im Breisgau

first: Linus

middle: Rudolf

last: Schoemig

state: Baden-Wuerttemberg

address: Breisacherstr. 66

department: Department of Medicine II, Faculty of Medicine

country: Germany

institute: University of Freiburg - Medical Centre

description:
Library name: Sample_17
Column name in "Raw_Counts_Matrix.tsv": L2-LKP_3_batch2

data_processing:
Batch1 and batch 2: Raw data quality control, low-quality sequences and adapter sequences removal was done by using an in-house developed pipeline from BMKGENE (BMKGENE BMKCloud). Mapping was done by BMKGENE using the GRCm38 reference. Batch 3: The exact protocol can be found in "Mueller, S. et al. A disease model resource reveals core principles of tissue-specific cancer evolution. Nature https://doi.org/10.1038/s41586-026-10187-2 (2026) doi:10.1038/s41586-026-10187-2". In brief, raw sequencing data were processed with the Drop-seq pipeline (v1.0) and were aligned to GRCm38.
Raw gene-level count matrices from all three batches were pooled into a unified count matrix and imported into R for downstream analysis (Raw_Counts_Matrix.tsv). Further data processing and normalization was done by using R-software (version 4.5.3) and DeSeq2 package.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values (TSV) file containing a gene expression matrix. Rows represent genes and columns represent samples. Values correspond to raw (unnormalized) read counts obtained after alignment and gene-level quantification.

source_name: Organoids

growth_protocol: Murine organoids were maintained in L-WRN conditioned medium (ATCC, CRL-3276) and L-Wnt3A conditioned medium  (ATCC, CRL-2647) (75/25) supplemented with 1x B27 Supplement, 1x N2 Supplement, 1mM N-acetylcysteine, 10µM ROCK inhibitor, 100µg/mL Primocin and 50ng/mL recombinant murine EGF.

extract_protocol:
RNAfor batch 1 and batch 2 was isolated using the "AllPrep" kit from Qiagen (QIAGEN, 80204). RNA for batch 3 was isolated using the "Rneasy" kit from Qiagen (QIAGEN, 74104).
RNA libraries of batch 1 and batch 2 for sequencing were prepared by "BMKGENE" according to their eukaryotic mRNA sequencing-NGS service. Isolated RNA was sent to BMKGENE and results were obtained 2 months later. RNA library preparation of batch 3 was conducted by our cooperations partners at the Techincal University Munich (Sebastian Mueller and Roland Rad). The exact protocol can be found in "Mueller, S. et al. A disease model resource reveals core principles of tissue-specific cancer evolution. Nature https://doi.org/10.1038/s41586-026-10187-2 (2026) doi:10.1038/s41586-026-10187-2". Batch 3 libraries were sequenced across four independent runs to achieve sufficient read depth per sample, as sequencing was performed as part of a larger multi-sample project. Each sample therefore yielded eight raw FastQ files, corresponding to four sequencing runs with paired-end reads (R1 + R2) each.

treatment_protocol: No treatment

value: Organoids

value: Intestinal metaplasia

value: No

tag: batch


title: AB1362_Roi-thymo-3h-4_phago_4

description:
Library name: AB1362
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: phago


title: AL_090


title: AB590_Roi-IN1_phago myeloid_1

description:
Library name: AB590
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: L2-LKP_2_batch2

description:
Library name: Sample_16
Column name in "Raw_Counts_Matrix.tsv": L2-LKP_2_batch2


title: AB820_Roi-IN2_PBS-injected myeloid_

description:
Library name: AB820
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AL_089


title: AB589_Roi-IN1_non-phago myeloid_1

description:
Library name: AB589
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: non-phago myeloid


title: AB819_Roi-IN2_non-phago myeloid_

description:
Library name: AB819
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: L2-LKP_2_batch1

description:
Library name: Sample_15
Column name in "Raw_Counts_Matrix.tsv": L2-LKP_2_batch1


title: AL_088


title: AB588_Roi-IN1_phago myeloid_1

description:
Library name: AB588
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AB818_Roi-IN2_non-phago myeloid_

description:
Library name: AB818
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: L2-LKP_1_batch1

description:
Library name: Sample_14
Column name in "Raw_Counts_Matrix.tsv": L2-LKP_1_batch1


title: MitoDiso_HeLa_2

description: Library name: L38

value: Naive


title: AL_087

value: Tumor


title: R172HcMyc_3w_2

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

description: Library name: Sp7mTmG_R172HcMyc_3w_2

data_processing:
Illumina RTA version v2.11.3 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Sequenced reads were trimmed to remove low-quality bases and adaptor sequences using cutadapt-4.6. Trimmed reads were mapped to the mouse reference genome (mm10) using STAR v2.7.11a with GENCODE vM23 (mouse). Uniquely mapped reads were summarized at the gene level using HTSeq-count v2.0.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Bone

extract_protocol:
To isolate cells specifically from the metaphyseal (MP) region, the epiphysis was carefully removed at the midpoint of the growth plate using forceps. Residual chondrocytes from the growth plate were thoroughly removed under a stereomicroscope. The diaphysis was then trimmed approximately 2 mm (for 3- and 8-week-old Osx-CreERT2; mTmG mice) or 5 mm (for 5-week-old Osx-CreERT2; mTmG; LSL-tTA; Col1a1::TetO–c-Myc and Osx-CreERT2; mTmG; LSL-tTA; Col1a1::TetO–c-Myc; Trp53-LSL-R172H mice) distal to the growth plate. The harvested MP regions from distal femurs and proximal tibias were transferred to digestion buffer containing M199 with Hanks’ salts (Gibco), 250 U/mL type I collagenase (Worthington), 250 U/mL type II collagenase (Worthington), 100 U/mL DNase I (1 mg/mL; Roche), 1 mg/mL poloxamer 188 (Sigma), 1 mg/mL BSA (Fujifilm), and 20 mM HEPES (Nacalai Tesque). The bones were placed in a mortar with 1 mL of digestion buffer and crushed using a pestle for at least 1 minute. The supernatant was collected into a 15 mL conical tube. This process was repeated until the bones appeared completely white (typically ≥3 times). The remaining bone fragments were pooled into the same tube and supplemented with digestion buffer to a final volume of 5 mL per sample. Samples were incubated at 37 °C for 30 minutes at 210 rpm. Following digestion, the supernatant was filtered through a 70 μm cell strainer into a 50 mL tube containing 5–10 mL of ice-cold cell suspension buffer [Ca²⁺/Mg²⁺-free PBS (Nacalai Tesque) with 2% FBS, 1 mg/mL poloxamer 188, and 100 U/mL penicillin/streptomycin (Gibco)]. Bone fragments were further digested with 3–5 mL of prewarmed digestion buffer, and the crushing–filtration process was repeated 4–5 times. Red blood cells were lysed using ACK lysis buffer (Gibco). Bone chips were removed, and single-cell suspensions were obtained by filtering through a 40 μm strainer for subsequent MACS preparation. Magnetic-activated cell sorting (MACS) was performed using LD columns (Miltenyi Biotec, Cat. No. 130-042-901) to deplete hematopoietic and erythroid cells with CD45 microbeads (Cat. No. 130-052-301) and TER119 microbeads (Cat. No. 130-049-901), following the manufacturer’s instructions. Following MACS, single-cell suspensions were incubated on ice and in the dark for 30 minutes with the following fluorophore-conjugated antibodies (1:200 dilution; Invitrogen/eBioscience), prepared in cell suspension buffer: eFluor450-conjugated anti-CD31 (clone 390; Cat. No. 48-0311-82); eFluor450-conjugated anti-CD45 (clone 30F-11; Cat. No. 48-0451-82); eFluor450-conjugated anti-TER119 (clone TER119; Cat. No. 48-5921-82). Fluorescence-activated cell sorting (FACS) was performed using a FACS Melody system (BD Biosciences). mGFP-positive cells were isolated from the CD31⁻CD45⁻TER119⁻ fraction after dead cells were excluded using 7-AAD (1:200; BioLegend, Cat. No. 420403). Sorted cells were immediately collected into Buffer RLT Plus (Qiagen) and stored at −80 °C until RNA extraction.
Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration and purity were assessed using a NanoDrop 2000c spectrophotometer (Thermo Fisher), and RNA quantity was further confirmed using a Qubit fluorometer (Thermo Fisher). amples with an RNAintegrity number (RIN) >= 8, as determined by a Bioanalyzer (Agilent Technologies), were used for library preparation. RNA-seq libraries were generated from 200 ng of high-quality RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). The number of PCR amplification cycles was minimized to prevent amplification bias.

treatment_protocol: mGFP-positive osteoblasts were isolated from 3- and 8-week-old Osx-CreERT2; mTmG mice for RNA sequencing analysis. Two femurs and two tibias were dissected from each mouse, and surrounding soft tissues were carefully removed. For control samples, femurs and tibias from two male mice were pooled per replicate. For c-Myc-induced and c-Myc + Trp53-R172H osteoblasts, mGFP-positive cells were isolated from Osx-CreERT2; mTmG; LSL-tTA; Col1a1::TetO–c-Myc and Osx-CreERT2; mTmG; LSL-tTA; Col1a1::TetO–c-Myc; Trp53-LSL-R172H mice, respectively (both male and female), 7 days after tamoxifen administration.

value: Bone

value: Tamoxifen


title: AB817_Roi-IN2_phago myeloid_

description:
Library name: AB817
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: Lung

value: phago myeloid


title: L2-LP_2_batch2

description:
Library name: Sample_9
Column name in "Raw_Counts_Matrix.tsv": L2-LP_2_batch2


title: AL_086

value: Middle


title: AL_138

value: Elderly


title: R172HcMyc_3w_1

description: Library name: Sp7mTmG_R172HcMyc_3w_1


title: AB816_Roi-IN2_phago myeloid_

description:
Library name: AB816
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: L2-LP_1_batch2

description:
Library name: Sample_8
Column name in "Raw_Counts_Matrix.tsv": L2-LP_1_batch2


title: AL_085


title: cMyc_3w_2

description: Library name: Sp7mTmG_cMyc_3w_2


title: AB810_Roi-IN2_PBS-injected myeloid_

description:
Library name: AB810
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: L2-L_2_batch2

description:
Library name: Sample_5
Column name in "Raw_Counts_Matrix.tsv": L2-L_2_batch2


title: AL_084


title: cMyc_3w_1

description: Library name: Sp7mTmG_cMyc_3w_1


title: AB809_Roi-IN2_phago myeloid_

description:
Library name: AB809
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: MitoRibo_HeLa_HEMK1_KO_HEMK1_resucue_1

description: Library name: L19

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


title: 8w_4

description: Library name: Sp7mTmG_8w_6


title: L2-L_1_batch2

description:
Library name: Sample_4
Column name in "Raw_Counts_Matrix.tsv": L2-L_1_batch2


title: AL_083


title: AB806_Roi-IN2_non-phago myeloid_

description:
Library name: AB806
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: L2-L_3_batch1

description:
Library name: Sample_3
Column name in "Raw_Counts_Matrix.tsv": L2-L_3_batch1


title: AL_082


title: 8w_3

description: Library name: Sp7mTmG_8w_5


title: AB805_Roi-IN2_phago myeloid_

description:
Library name: AB805
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: L2-L_2_batch1

description:
Library name: Sample_2
Column name in "Raw_Counts_Matrix.tsv": L2-L_2_batch1


title: AL_081


title: 8w_2

description: Library name: Sp7mTmG_8w_4


title: AL_080


title: AL_079


title: 8w_1

description: Library name: Sp7mTmG_8w_3


title: CdSeNP-3 3mg/L Treatment

city: Chengdu

first: xiumei

last: luo

address: Shuangliu

department: Institute of Urban Agriculture

country: China

institute: Chinese Academy of Agricultural Sciences

description:
Library name: CdSeNP_3
Rice leaves co-treated with Cd and SeNPs

data_processing:
StringTie v2.2.1 was used to assemble transcripts and estimate expression levels in transcripts per million (TPM) for each sample.
Differential gene expression between treatment groups was identified using DESeq2 v1.34.0 with a false discovery rate (FDR) cutoff of 0.05 and fold-change threshold of 2.
Clean reads were mapped to the Oryza sativa reference genome using HISAT2.
Differentially expressed genes were annotated using BLASTP against the NCBI non-redundant protein database and assigned GO terms using InterProScan.
Assembly: Oryza_sativa.IRGSP-1.0
Supplementary files format and content: Processed RNA-seq data are provided as gene-level expression matrices. Raw sequencing reads were quality-filtered, and clean reads were mapped to the Oryza sativa IRGSP-1.0 reference genome. Gene expression levels were quantified as normalized counts and FPKM values. The final processed dataset includes a tab-delimited matrix containing gene IDs, gene expression values across all samples, and corresponding sample annotations for control, Cd, SeNPs, and Cd + SeNP treatments. Differential expression results (log₂ fold change, p-values, and adjusted p-values) are also included for comparative analysis between treatment groups

organism: Oryza sativa

source_name: leaves

growth_protocol: Rice (Oryza sativa L. cv. Quan Youde Zhan) seeds were surface sterilized with 5% H₂O₂ for 10 min and rinsed thoroughly with sterile distilled water. Seeds were germinated in darkness at 25°C and transferred to hydroponic culture in 1/4 Kimura nutrient solution for 7 days, followed by 1/2 strength solution for another 7 days under controlled growth conditions (25°C, 16 h light/8 h dark photoperiod, 400 μmol m⁻² s⁻¹ light intensity, and 75% relative humidity, pH 6.0).

extract_protocol:
Total RNA was extracted from rice leaf tissues using a commercial plant RNA extraction kit following the manufacturer’s instructions. RNA quality and integrity were assessed using agarose gel electrophoresis and a NanoDrop spectrophotometer, and RNA concentration was further verified using a Qubit fluorometer. High-quality RNA samples were used for cDNA library construction and subsequent Illumina sequencing.
High-quality total RNA was used for cDNA library construction following the Illumina TruSeq RNA sample preparation protocol. mRNA was enriched using poly(A) selection and fragmented into short fragments. First-strand and second-strand cDNA were synthesized, followed by end repair, A-tailing, and adapter ligation. The ligated products were purified and amplified by PCR to generate sequencing-ready libraries. Library quality and fragment size distribution were assessed before sequencing on an Illumina platform.

treatment_protocol: Three-week-old rice seedlings were transferred to full-strength Kimura nutrient solution and exposed to cadmium and selenium nanoparticles under hydroponic conditions. Cadmium stress was applied using 10 mg/L CdCl₂·2.5H₂O after preliminary toxicity screening. Selenium nanoparticle (SeNPs) treatments were applied at 1, 3, and 5 mg/L, both alone and in combination with 10 mg/L Cd. Untreated plants served as the control. All treatments were maintained under controlled growth conditions, and leaf samples were collected at the 6-leaf stage (1.5 months) for RNA sequencing analysis.

value: leaves

value: whole leaf

value: Quan Youde Zhan

value: 10+3 mg/L Cd+SeNPs exposure


title: 3w_4

description: Library name: Sp7mTmG_3w_4


title: AB802_Roi-IN2_non-phago myeloid_

description:
Library name: AB802
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AL_078


title: 3w_3

description: Library name: Sp7mTmG_3w_3


title: CdSeNP-1 3mg/L Treatment

description:
Library name: CdSeNP_1
Rice leaves co-treated with Cd and SeNPs


title: AB799_Roi-thymo-3h-3_non-phago-macs_3

description:
Library name: AB799
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: in-vitro

value: non-phago-macs


title: AL_077


title: AB798_Roi-thymo-24h-3_non-phago-macs_3

description:
Library name: AB798
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 3w_2

description: Library name: Sp7mTmG_3w_2


title: AL_076


title: 3w_1

description: Library name: Sp7mTmG_3w_1


title: AB796_Roi-thymo-24h-3_phago_3

description:
Library name: AB796
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: SeNP-2 3mg/L Treatment

description:
Library name: SeNP_2
Rice leaves treated with 3mg/L SeNPs only

value: 3 mg/L SeNPs exposure


title: AL_075


title: 42,Mithra,rep3,Input

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

description: Library name: 42,Mithra,rep3,Input

library_source: genomic

data_processing:
Paired-end FASTQ reads were trimmed with Trim Galore (version 0.6.10) using paired-end mode. Trimmed reads were aligned to the GENCODE human hg38/GRCh38 primary assembly genome using STAR (version 2.7.10b). Reads overlapping ENCODE blacklist regions were removed using bedtools intersect (version 2.31.1) with the hg38 blacklist BED file provided by ENCODE. BAM files were converted, sorted, and indexed with samtools (version 1.6). Read groups were added with Picard AddOrReplaceReadGroups, and duplicate reads were removed with Picard MarkDuplicates (version 3.3.0) using "REMOVE_DUPLICATES=true". Filtered BAM files were used for peak calling with MACS3 (version 3.0.1). Peaks were called as narrow peaks using paired-end BAM mode ("-f BAMPE"). Matched input BAM files were provided as controls for each ChIP sample using the MACS3 "-c" flag. BigWig tracks were generated from filtered BAM files using deepTools bamCoverage (version 3.5.5), with CPM normalization.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: Lf-C2 and Lf-4-2 cells were grown in Fibroblast Basal Medium supplemented with Fibroblast Growth Kit-Low serum and were maintained at 37°C, 100% humidity, and 5% CO2

extract_protocol:
ChIP-seq was performed as per the manufacturer’s protocol (CST, catalog #: 9003) with modifications. Briefly, Lf-C2 and Lf-4-2 cells were treated with either DMSO or 300 nM Mithramycin A for 24 hours. Cells were crosslinked with Cross-link Gold (Diagenode, catalog #: C01019027), followed by 1% formaldehyde for 10 mins at room temperature. Fixed cells were enzymatically digested and sonicated. 750 µg of protein was incubated with anti-EGR1 (Bethyl, catalog #: A303-390A, 45 µg) or control IgG (CST, catalog #: 2729) overnight at 4°C with rotation. The antibody-bound chromatin was immunoprecipitated by protein G magnetic beads and eluted. After reversal of the crosslink, the DNA was purified, and sequencing was performed at the OncoGenomics Shared Resources (OGSR) of the Sylvester Comprehensive Cancer Center.
ChIP-seq libraries were prepared using the KAPA HyperPrep Kit (Roche, Cat # 07962363001). In brief, immunoprecipitated DNA fragments (IP frags) were quantified and qualitatively assessed on the ThermoFisher QuBit Fluorometer’s High Sensitivity DNA (cat. Q32855) and Agilent Femto Pulse Ultra Sensitivity NGS kits (cat. FP-1101-0275), respectively. Input of IP frags. were between 0.17 and 25 ng. HyperPrep kit was used for end repair, A-tailing and adapter ligation followed by PCR amplification. Finished libraries were quantified and qualitatively assessed on the ThermoFisher QuBit using Fluorometer’s High Sensitivity DNA (Cat #Q32855) and Agilent Fragment Analyzer High Sensitivity NGS kits (Cat # DNF-474-0500) prior to normalization and pooling in preparation for sequencing.. Pooled libraries were sequenced using paired-end 150 base pair chemistry on an Illumina NovaSeq X Plus instrument. Targeted average sequencing depth for ChIP-seq broad peak was 30 million clusters per library.

value: human lung fibroblast cell line

value: 300 nM Mithramycin


title: AB794_Roi-thymo-3h-3_phago_3

description:
Library name: AB794
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: phago


title: AL_074

value: Tumor


title: SeNP-1 3mg/L Treatment

description:
Library name: SeNP_1
Rice leaves treated with 3mg/L SeNPs only


title: 42,DMSO,rep3,Input

description: Library name: 42,DMSO,rep3,Input

treatment_protocol: Lf-C2 and Lf-4-2 cells were treated with either DMSO or 300 nM Mithramycin A for 24 hours

value: DMSO


title: AB793_Roi-thymo-24h-3_non-phago-macs_3

description:
Library name: AB793
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: Cd-3 10mg/L Treatment

description:
Library name: Cd_3
Rice leaves exposed to 10 mg/L Cd

value: 10 mg/L CdCl₂ exposure


title: AL_073


title: C2,Mithra,rep3,Input

description: Library name: C2,Mithra,rep3,Input

value: WT


title: AB792_Roi-thymo-24h-3_non-phago-macs_3

description:
Library name: AB792
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: Cd-2 10mg/L Treatment

description:
Library name: Cd_2
Rice leaves exposed to 10 mg/L Cd


title: AL_072


title: C2,DMSO,rep3,Input

description: Library name: C2,DMSO,rep3,Input


title: AB791_Roi-thymo-24h-3_phago_3

description:
Library name: AB791
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: Cd-1 10mg/L Treatment

description:
Library name: Cd_1
Rice leaves exposed to 10 mg/L Cd


title: AL_071


title: 42,Mithra,rep2,Input

description: Library name: 42,Mithra,rep2,Input


title: Control-3 Treatment

description:
Library name: CK_3
Control rice leaves without Cd or SeNP exposure

value: control (0 mg/L CdCl₂)


title: 42,DMSO,rep2,Input

description: Library name: 42,DMSO,rep2,Input


title: AB787_Roi-thymo-24h-3_phago_3

description:
Library name: AB787
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: AL_069

value: Middle


title: C2,Mithra,rep2,Input

description: Library name: C2,Mithra,rep2,Input


title: Control-1 Treatment

description:
Library name: CK_1
Control rice leaves without Cd or SeNP exposure


title: AL_068


title: AB784_Roi-thymo-3h-3_non-phago-macs_3

description:
Library name: AB784
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: dose1_0h_MOD280_muscle

city: Lausanne

first: Gustavo

middle: Agustín

last: Ruiz Buendía

state: Vaud

address: Amphipôle, Quartier UNIL-Sorge

institute: Swiss Institute of Bioinformatics

description: See sample Dose, Time point, and Batch for experimenal condition.

hyb_protocol: Hybridization was performed per the manufacturer’s instructions for Gene Expression Panels with Panel Plus/CodeSet with CodeSet Plus. Briefly, Hybridization was set up with 5 mcL of sample (100 ng of RNA), which was added to 10 mcL of hybridization master mix (5 mcL of hybridization buffer + 3 mcL of Reporter CodeSet + 2 mcL of Reporter Plus) + 3 mcL of Capture Maser Mix. The total hybridization volume was 18uL per sample. Each cartridge was hybridized for 18 hours on a thermal cycler set to 65℃ with a lid heated to 70℃.

scan_protocol: Cartridges were then analyzed on the nCounter Pro Analysis System

data_processing: Nanostring Data was analyzed by ROSALIND (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes, and p-values were calculated using criteria provided by Nanostring.

label: NanoString

source_name: Muscle

label_protocol: standard protocol

growth_protocol: Muscle samples were collected from mice, at multiple time points after 1 dose or 2 doses of a COVID-19 mRNA vaccine. Samples were snap-frozen and stored at -80ºC.

extract_protocol: Tissues were lysed and homogenized in Trizol using Precellys bead mill homogenizer and CK14 tubes (Bertin). RNA extraction was done using the Rneasy midi kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: C57BL/6J mice were vaccinated intramuscularly with 1 dose or 2 doses (21 days apart) of 1 µg of a COVID-19 mRNA vaccine.

value: Muscle

tag: group

tag: dose

tag: time point


title: 42,Mithra,rep1,Input

description: Library name: 42,Mithra,rep1,Input

tag: cell type


title: AB783_Roi-thymo-3h-3_phago_3

description:
Library name: AB783
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

tag: tissue


title: dose1_0h_MOD279_muscle


title: AL_066

tag: tumor or adjacent

tag: agerange


title: AB782_Roi-thymo-3h-3_phago_3

description:
Library name: AB782
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: dose1_0h_MOD278_muscle


title: AL_065

tag: chronologicalage

tag: read length


title: C2,Mithra,rep1,Input

description: Library name: C2,Mithra,rep1,Input


title: AB786_Roi-thymo-24h-3_phago_3

description:
Library name: AB786
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad


title: 8w_2

description:
Library name: B6J_8wks_2
10x Genomics

data_processing:
The 10X Genomics Cell Ranger pipeline (version 7.2.0) was used to perform sample demultiplexing, alignment to the mm10 mouse reference genome, barcode/UMI processing, and gene counting for each cell.
Assembly: mm10
Supplementary files format and content: hdf5 files containing lists of gene names, cell barcodes and UMI counts for each sample

extract_protocol:
For single-cell RNA sequencing (scRNA-seq) analysis, 3- and 8-week-old C57BL/6J wild-type mice were used. The diaphysis was trimmed approximately 2 mm distal to the growth plate, and the metaphyseal (MP) regions of distal femurs and proximal tibias were collected in digestion buffer. Following bone dissociation as described above, FACS was performed using a FACS Melody system (BD Biosciences). CD31/CD45/TER119-negative cells were sorted after dead cells were excluded using 7-AAD (1:200; BioLegend, 420403). Sorted cells were immediately collected into an ice-cold cell suspension buffer and loaded onto a Chromium Controller (10X Genomics).
Single-cell libraries were prepared using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (10X Genomics).

value: Bone


title: C2,DMSO,rep2,Input

description: Library name: C2,DMSO,rep2,Input


title: dose2_0h_MOD277_muscle


title: AL_067


title: AL_064


title: C2,DMSO,rep1,Input

description: Library name: C2,DMSO,rep1,Input


title: 8w_1

description:
Library name: B6J_8wks_1
10x Genomics


title: dose2_0h_MOD276_muscle


title: AL_063


title: 42,Mithra,rep3,IgG

description: Library name: 42,Mithra,rep3,IgG


title: 3w_2

description:
Library name: B6J_3wks_2
10x Genomics


title: 42,DMSO,rep1,Input

description: Library name: 42,DMSO,rep1,Input


title: dose2_0h_MOD275_muscle


title: AL_062


title: 42,DMSO,rep3,IgG

description: Library name: 42,DMSO,rep3,IgG


title: 3w_1

description:
Library name: B6J_3wks_1
10x Genomics


title: dose1_4h30_MOD274_muscle


title: AL_061


title: C2,Mithra,rep3,IgG

description: Library name: C2,Mithra,rep3,IgG


title: MitoDiso_C2C12_mtRF1_KO_2

description: Library name: L54


title: AL_060


title: dose1_4h30_MOD273_muscle


title: C2,DMSO,rep3,IgG

description: Library name: C2,DMSO,rep3,IgG


title: MitoDiso_C2C12_mtRF1_KO_1

description: Library name: L53


title: L2-L_1_batch1

description:
Library name: Sample_1
Column name in "Raw_Counts_Matrix.tsv": L2-L_1_batch1

value: Organoids

value: Intestinal metaplasia

value: No


title: dose1_4h30_MOD272_muscle


title: AB803_Roi-IN2_PBS-injected myeloid_

description:
Library name: AB803
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: Lung

value: PBS-injected myeloid


title: AL_059


title: 42,Mithra,rep2,IgG

description: Library name: 42,Mithra,rep2,IgG


title: MitoDiso_C2C12_2

description: Library name: L52

value: Naive


title: dose2_4h30_MOD271_muscle


title: AL_058


title: CdSeNP-2 3mg/L Treatment

description:
Library name: CdSeNP_2
Rice leaves co-treated with Cd and SeNPs

value: leaves

value: whole leaf

value: Quan Youde Zhan

value: 10+3 mg/L Cd+SeNPs exposure


title: AB800_Roi-thymo-3h-3_non-phago-macs_3

description:
Library name: AB800
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

value: in-vitro

value: non-phago-macs


title: 42,DMSO,rep2,IgG

description: Library name: 42,DMSO,rep2,IgG

value: human lung fibroblast cell line

value: DMSO


title: MitoDiso_C2C12_1

description: Library name: L51


title: dose2_4h30_MOD270_muscle


title: AL_057

value: Tumor

value: Middle


title: C2,Mithra,rep2,IgG

description: Library name: C2,Mithra,rep2,IgG

value: WT

value: 300 nM Mithramycin


title: MitoRibo_C2C12_mtRF1_KO_2

description: Library name: L28


title: AL_056


title: dose2_4h30_MOD269_muscle

value: Muscle


title: SeNP-3 3mg/L Treatment

description:
Library name: SeNP_3
Rice leaves treated with 3mg/L SeNPs only

value: 3 mg/L SeNPs exposure


title: C2,DMSO,rep2,IgG

description: Library name: C2,DMSO,rep2,IgG


title: MitoRibo_C2C12_mtRF1_KO_1

description: Library name: L27


title: AL_055