title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 8

description:
Library name: CSS21_ATAC
BS1314


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 7

status: Public on Jun 05 2026

type: SRA

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description:
Library name: CSS19_GEX
BS1308

library_source: transcriptomic single cell

data_processing:
The fastq files were processed using Cell Ranger ARC 2.0 with default parameters
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: HDF5 10X Genomics file containing features, barcodes and sparse matrix of gene expression counts
Supplementary files format and content: Gzipped BED-like tabular file created by cellranger-atac count, where each line represents a unique ATAC-seq fragment captured by the assay.

molecule: nuclear RNA

organism: Homo sapiens

source_name: lung tumor, NSCLC

extract_protocol:
CD56⁺ NK and T cells were sorted from non-small cell lung cancer (NSCLC) tumor single-cell suspensions. Nuclei were isolated according to protocol and processed using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338, Rev C), following the manufacturer’s instructions.
The libraries were constructed according to 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338, Rev C), following the manufacturer’s instructions.

tag: tissue

value: lung tumor, NSCLC

tag: cell type

value: CD56⁺ NK and T cell


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 8

description:
Library name: CSS21_GEX
BS1314


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 7

description:
Library name: CSS19_ATAC
BS1308

library_source: genomic single cell

molecule: genomic DNA


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 6

description:
Library name: CSS16_ATAC
BS1198


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 6

description:
Library name: CSS16_GEX
BS1198


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 5

description:
Library name: CSS13_ATAC
BS1175


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 5

description:
Library name: CSS13_GEX
BS1175


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 4

description:
Library name: CSS10_ATAC
BS897


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 4

description:
Library name: CSS10_GEX
BS897


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 3

description:
Library name: CSS7_ATAC
BS889


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 3

description:
Library name: CSS7_GEX
BS889


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 2

description:
Library name: CSS4_GEX
BS824


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 2

description:
Library name: CSS4_ATAC
BS824


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 1

description:
Library name: CSS1_ATAC
BS840


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 1

description:
Library name: CSS1_GEX
BS840


title: RA6

city: Suzhou

first: xinyu

last: zhou

address: No. 199 Ren'ai Road, Suzhou Industrial Park

country: China

institute: Soochow University

description: Library name: Sample 18

library_source: transcriptomic

data_processing:
Raw FASTQ files were quality-checked with FastQC (v0.11.9), and adapters/low-quality bases were trimmed using Trimmomatic (v0.39) with parameters:
Clean reads were aligned to the GRCh38 primary assembly (GENCODE v43) using STAR (v2.7.10a) with default parameters.
Gene-level counts were generated with featureCounts (v2.0.3) using paired-end mode and strand-specific counting (-s 2).
Assembly: hg38
Supplementary files format and content: matrix files

molecule: total RNA

source_name: peripheral blood mononuclear cells

extract_protocol:
The supernatant was removed and stored at -80°C in a refrigerator, and RNA was havested using Trizol reagent.
RNA-seq libraries were constructed by Azenta following their standard poly(A)-enriched/ribo-depleted protocol.

value: peripheral blood mononuclear cells

tag: subject status

value: early RA patient


title: RA5

description: Library name: Sample 17


title: RA4

description: Library name: Sample 16


title: RA3

description: Library name: Sample 15


title: RA2

description: Library name: Sample 14


title: RA1

description: Library name: Sample 13


title: OA5

description: Library name: Sample 11

value: osteoarthritis (OA) patient


title: OA6

description: Library name: Sample 12


title: OA4

description: Library name: Sample 10


title: OA3

description: Library name: Sample 9


title: OA2

description: Library name: Sample 8


title: OA1

description: Library name: Sample 7


title: HC8

description: Library name: Sample 6

value: healthy control


title: HC6

description: Library name: Sample 5


title: HC5

description: Library name: Sample 4


title: HC4

description: Library name: Sample 3


title: HC3

description: Library name: Sample 2


title: HC1

description: Library name: Sample 1


title: 336_3xSNCA

city: Esch-Belval

first: Elisa

last: Zuccoli

address: 6, Avenue du Swing

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

description: Library name: S4

data_processing:
Reads were mapped to the human reference genome hg38 using the HISAT2 tool
Assembly: hg38
Supplementary files format and content: count_matrix.csv

source_name: Microglia

growth_protocol: Nickels et al, 2020

extract_protocol:
RNA isolation was done using the RNeasy Mini Kit (Qiagen, cat.no. 74106) following the manufacturer’s protocol.
In-home kit - Novogene NGS  RNA Library Prep Set

value: Microglia

tag: cell line

value: human induced pluripotent stem cells

tag: genotype


title: 277_39

description: Library name: S3

value: wt/wt


title: 232_T12.9

description: Library name: S2


title: 201_Epi

description: Library name: S1


title: MitoRibo_HEK293_mtIF3_KO_1

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

description: Library name: L31

library_source: other

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

molecule: other

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).


title: MitoRibo_HEK293_mtIF3_KO_2

description: Library name: L32


title: p21_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: p21_3wks_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

organism: Mus musculus

source_name: Bone

extract_protocol:
For single-cell RNA sequencing (scRNA-seq) analysis, 3-week-old p21 reporter mice were used. p21 reporter mice received a single intraperitoneal injection of tamoxifen (1 mg/mouse) 48 hours prior to analysis. The diaphysis was trimmed approximately 2 mm distal to the growth plate, and metaphyseal regions of distal femurs and proximal tibias were collected in digestion buffer. Following bone dissociation as described above, FACS was performed using the 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 in 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: MitoRibo_HEK293_2

description: Library name: L30

value: Naive


title: M. wolinskyi QL01-infected WT BMDM, biological replicate 3

city: Jinan

first: Yuxiao

last: Zhao

state: Shandong

address: Qilu Hospital of Shandong University, 107 Wenhua  Xi Road, Jinan, Shandong 250012, China

institute: Qilu Hospital of Shandong University

description:
Library name: Mw_QL01_3
biological replicate 3
B_3

data_processing:
Raw reads were filtered using Cutadapt v1.9 to remove adapters, poly(A)/poly(G), reads with >5% N bases, and low-quality reads in which >20% of bases had Q <= 20. Sequence quality was assessed using FastQC v0.11.9. Clean reads were aligned to the Mus musculus reference genome using HISAT2 v2.2.1 with up to two mismatches allowed. Transcript abundance was quantified using StringTie v2.1.6 and Ballgown as FPKM values. Differential expression analysis between infected and control groups was performed using DESeq2. Genes with FDR < 0.05 and absolute fold change >= 2 (|log2FC| >= 1) were considered differentially expressed genes.
Assembly: mm38
Supplementary files format and content: Tab-delimited text files containing processed RNA-seq results, such as gene-level expression matrices (for example, FPKM) and differential expression analysis results, should be provided.

molecule: polyA RNA

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages (BMDMs) were generated from mouse bone marrow cells cultured for 5 days in L929 cell-conditioned DMEM/F-12 supplemented with 10% fetal bovine serum, 1% nonessential amino acids, and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol reagent. RNA concentration, purity, and integrity were assessed using NanoDrop ND-1000, Agilent Bioanalyzer 2100, and denaturing agarose gel electrophoresis.
Poly(A) RNA was purified from 5 ug total RNA using Dynabeads Oligo(dT)25 with two rounds of purification. Purified mRNA was fragmented at 94 C for 5-7 min, reverse-transcribed into cDNA, converted to second-strand cDNA, end-repaired/A-tailed, adapter ligated, size selected with AMPure XP beads, treated with heat-labile UDG, PCR amplified, and sequenced as 2 x 150 bp paired-end libraries on an Illumina NovaSeq 6000 platform.

treatment_protocol: BMDMs were infected with Mycobacterium wolinskyi QL01 at a multiplicity of infection (MOI) of 400 for 6 h. Uninfected wild-type BMDMs served as controls. Three biological replicates were included in each group.

value: bone marrow-derived macrophages

value: WT

tag: treatment

value: infected with M. wolinskyi QL01, MOI 400, 6 h


title: AL_168

city: Pittsburgh

first: Neil

last: Carleton

state: PA

address: 5051 Centre Ave

department: Pharmacology & Chemical Biology

country: USA

institute: University of Pittsburgh

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.

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

tag: agerange

value: Elderly

tag: chronologicalage

tag: read length


title: AL_167


title: MitoRibo_HEK293_1

description: Library name: L29


title: p21_3w_1

description:
Library name: p21_3wks_1
10x Genomics


title: M. wolinskyi QL01-infected WT BMDM, biological replicate 2

description:
Library name: Mw_QL01_2
biological replicate 2
B_2


title: M. wolinskyi QL01-infected WT BMDM, biological replicate 1

description:
Library name: Mw_QL01_1
biological replicate 1
B_1


title: AL_166


title: Follow-up sample ADK005-post (week 16-18)

city: Maribor

first: Martina

last: Krušič

address: Taborska ulica 8

country: Slovenia

institute: Faculty of Medicine

description:
Library name: ADK005-post
Column name in RawCounts.txt: ADK005post

data_processing:
A three-stage approach was employed for differential expression analysis, similar to that used in a previously published article by our group. In stage one, differentially expressed genes influenced by dupilumab therapy were identified. These genes were excluded prior to the second stage. Stage two consisted of two substages aimed at identifying differentially expressed genes associated with inflammation. The union of unique differentially expressed genes identified in both substages was considered to represent inflammation-related genes and was subsequently removed from the analysis prior to the third stage. In the final stage, differentially expressed genes that could serve as predictors of response to dupilumab were determined.
Blood transcriptome analysis for each stage was performed using a custom pipeline developed by the Center for Human Molecular Genetics and Pharmacogenomics in the environment R 4.5.2, employing various packages as described in previously published studies. In stage one, genes with an adjusted p-value < 0.05 were considered differentially expressed. In all subsequent stages, a p-value < 0.05 was used as the significance threshold.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file (RawCounts_StageThree.txt) include raw counts for samples included in the stage three analysis.

source_name: Blood

extract_protocol:
RNA samples were extracted from peripheral blood mononuclear cells using the innuPREP Micro RNA Kit (iST Innuscreen GmbH).
RNA samples were sequenced at BGI facilities using BGI Optimal Dual-mode mRNA Library Prep Kit PE150 on the DNBSEQ G400 (China). Raw data containing adapter sequences or low-quality reads were removed using the SOAPnuke tool by BGI.

value: Blood

tag: Sex

value: F

value: Responder to dupilumab


title: Baseline sample ADK005-pre (week 0)

description:
Library name: ADK005-pre
Column name in RawCounts.txt: ADK005pre

value: Naïve to biological treatment


title: Uninfected WT BMDM, biological replicate 3

description:
Library name: Control_3
biological replicate 3
A_3

value: uninfected control


title: AL_164


title: Uninfected WT BMDM, biological replicate 1

description:
Library name: Control_1
biological replicate 1
A_1


title: Uninfected WT BMDM, biological replicate 2

description:
Library name: Control_2
biological replicate 2
A_2


title: AL_162


title: Fibro-adipogenic progenitors, Pge2_3

city: Montreal

first: Nicolas A

last: Dumont

state: Quebec

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

description: Library name: FAPS-PGE2-3

data_processing:
GenPipes an open-source Python-based Workflow Management System (WMS) Sequence reads were trimmed for adaptor sequence/low-quality sequence using GenPipes Trimmed sequence reads were mapped to mm10 Read count extraction and normalization were performed using Genpipes
Assembly: mm10
Supplementary files format and content: a csv file includes raw counts for each samples

source_name: Muscle

growth_protocol: Primary wt FAPs were cultured in DMEM 4,5mg/ml with Glutamax, 10% FBS, 2,5ng/mL hFGF and 2% P/S in humidified atmosphere 5% CO2

extract_protocol:
The RNA samples were obtained from mice and extracted using the RNeasy Mini Kit from QIAGEN, according to the manufacturer’s instructions. 1ug of total RNA was used from construction of libraries
The sequencing libraries and Illumina NovaSeq 6000 for 100-bp PE reads sequencing were performed at the Genome Quebec platform

treatment_protocol: FAPs were treated for 2 consecutive days (once per day) with PGE2 (500nM) or vehicle.

value: Muscle

value: Primary cells

value: Fibro-adipogenic progenitors

value: wt, male


title: AL_163

source_name: BreastTumor

value: Tumor


title: mNPC G2_M, MOF-dTAG, dTAG13 (500 nM, 4h), H4K5ac, rep2

status: Public on Jun 06 2026

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Library name: dtag_4h_mNPC_G2_M_H4K5ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz

library_source: genomic

data_processing:
The data were processed using the snakePipes DNA-mapping (v2.1.2) (Bhardwaj et al. 2019). Illumina adaptors were removed using cutadapt (v2.8) (Martin 2011) with default settings. Reads were then mapped to the mm10 genome with Bowtie2 (v2.3.5.1) (Langmead and Salzberg 2012), using the modified options –local –very-sensitive-local –no-mixed –no-discordant –phred33 -I 60 -X 700. Reads mapping to blacklisted regions from the Encode Consortium (Amemiya, Kundaje, and Boyle 2019) were discarded. Finally, only properly paired mapped reads and reads with a mapping quality over 3 were retained for further analysis
Assembly: mm10
Supplementary files format and content: bigwig files from sequencing-depth normalized counts
Library strategy: CUT&Tag

source_name: mNPC

growth_protocol: NPCs were cultured in N2B27 medium supplemented with EGF and FGF on gelatin-coated plates.

extract_protocol:
DNA fragments were isolated using the ChIP DNA Clean & Concentrator kit (Zymo Research) and eluted with 15 l elution buffer (provided by the kit). The library was prepared using 13 l DNA solution, mixed with 1 l of 10 M barcoded i5 and i7 primers separately, and 15 l NEBNext HiFi 2x PCR Master Mix. The PCR program included 72 °C for 5 minutes, 98 °C for 30 seconds, followed by 13 to 16 cycles of 98 °C for 10 seconds and 72 °C for 10 seconds, ending with 72 °C for 1 minute and holding at 8 °C. Ampure beads (39 l) were used for DNA purification.
CUT&Tag

treatment_protocol: MOF-dTAG cells were treated with dTAG13 (5 mg, Tocris) at 500nM, or with TSA at 330nM at different time points before proceeding the downstream experiments.

value: mNPC

value: MOF-dTAG

tag: cut&tag antibody


title: Tumor_treated

city: Singapore

first: Cheng

last: Xu

address: 70 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description: Library name: Sample 1

data_processing:
Fastq files were trimmed and filtered based on quality and then mapped using the Spliced Transcripts.
Assembly: mouse mm10
Supplementary files format and content: xlsx files with counts for each sample

source_name: 4T1 tumor

extract_protocol:
RNA was harvested using PureLink RNA Mini Kit (Invitrogen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNAseq library was constructed via AccuraCode® RNA Library Construction Kit.

value: 4T1 tumor

value: Protein degrader

tag: batch


title: CTCF_CD2_cntrl_rep1

city: Miami

first: Mustafa

last: Tekin

state: Florida

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

description: Library name: CTCF_CD2_cntrl_1

data_processing:
Sequence reads were mapped to hg38 reference genome with Bowtie 2.
Normalized ChIP-seq read densities were visualized using deepTools and/or Integrative Genomics Viewer (IGV).
Assembly: hg38
Supplementary files format and content: bigwig

source_name: CD2 iPSCs

growth_protocol: The generation of inner ear organoids (IEOs) have been described in the Methods of this study (Zafeer et. al. 2026). About 200 organoids were pooled for the downstream ChIP-seq analysis.

extract_protocol:
Cells were lysed as described in Ortabozkoyun et al., 2022 using buffers in the following order: LB1 (50 mM HEPES, pH 7.5 at 4 C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X) for 10 min at 4 C, LB2 (10 mM Tris, pH 8 at 4 C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at RT, and LB3 (10 mM Tris, pH 7.5 at 4 C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sonicated to an average size of ~250 bp using a Covaris sonicator. ChIP was performed by using antibodies listed. Chromatin from Drosophila (1:100 ratio to CD2 cells chromatin), and Drosophila-specific H2Av antibody were used as spike-in control in each sample.
ChIP-seq Libraries were prepared according to manufacturer’s instructions (Illumina) as described in Narendra et al., 2015. Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), ligated to custom adapters, and fragments of 300±100 bp were size-selected. These fragments were amplified through ligation-mediated PCR amplification (LM-PCR) by using Q5 polymerase (NEB M0530).

value: CD2 iPSCs

value: CD2 iPSC-derived inner ear organoids (IEOs)

value: WT

tag: chip antibody

value: CTCF (Abcam, ab128873)


title: AL_161

value: Elderly


title: AL_160


title: Fibro-adipogenic progenitors, Pge2_2

description: Library name: FAPS-PGE2-2


title: catID_35

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

description:
Library name: PAM73681_bc_3.fastq_catID_35
column 4 in Counts File

data_processing:
mapping against felCat9
base-calling using Guppy
pre-processing with fastP
allignment with Minimap2
FeatureCounts
Assembly: felCat9
Supplementary files format and content: tab-delimited file with counts per sample in each collumn

organism: Felis catus

source_name: cardiac biopsy left ventricle

extract_protocol:
RNEasy, Qiagen
SQK-RNA002, Oxford Nanopore

treatment_protocol: cardiac tissue collected post mortem

value: cardiac biopsy left ventricle


title: catID_22

description:
Library name: PAM73696__bc_4.fastq_catID_22
column 8 in Counts File


title: Fibro-adipogenic progenitors, Pge2_1

description: Library name: FAPS-PGE2-1


title: AL_159


title: Fibro-adipogenic progenitors, vehicle3

description: Library name: FAPS-CTRL3

value: vehicle


title: Fibro-adipogenic progenitors, vehicle2

description: Library name: FAPS-CTRL2


title: AL_157


title: AL_158


title: AL_165


title: catID_23

description:
Library name: PAK20671_bc_2.fastq_catID_23
column 12 in Counts File


title: AL_155


title: KO_01

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: Library name: KO_01

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.99 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization, considering only those genes for which expression was at least 1 count per million (CPM) in at least 2 samples.
Assembly: GRCm38.99
Supplementary files format and content: Normalized counts (CPM) for genes with expression level of at least 1 count per million (CPM) in at least 2 samples.

source_name: ventricular heart

extract_protocol:
Total RNA from ventricular cardiac tissue of Vhl-KO and WT mice was extracted using the RNeasy Mini Kit (Qiagen) following standard protocols.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The kit for library preparation was the Novogene NGS RNA Library Prep Set (PT042).  The library was checked with Qubit 2.0, real-time PCR for quantification, and a bioanalyzer 2100 for size distribution detection. Sequencing was carried out on the Illumina platform NovaSeq6000 .

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

value: ventricular heart


title: KO_03

description: Library name: KO_03


title: Fibro-adipogenic progenitors, vehicle1

description: Library name: FAPS-CTRL1

value: Muscle


title: AL_154


title: AL_153


title: AL_156


title: DKO_03

description: Library name: DKO_03


title: DKO_01

description: Library name: DKO_01


title: DKO_02

description: Library name: DKO_02


title: AL_152


title: C_03

description: Library name: C_03


title: AL_150


title: C_02

description: Library name: C_02


title: PC3, VprBP sh3

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: sample6
column name in raw_counts_all_samples.txt:S3

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.

value: prostate cancer cells

value: VprBP knockdown


title: AL_148


title: PC3, VprBP sh1

description:
Library name: sample4
column name in raw_counts_all_samples.txt:S1


title: AB1563_B16_rodo-_2

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: AB1563
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

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)

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.

value: rodo-


title: AL_147


title: PC3, Control sh3

description:
Library name: sample3
column name in raw_counts_all_samples.txt:C3


title: AB1562_B16_rodo high_2

description:
Library name: AB1562
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: AB1561_B16_rodo-_3

description:
Library name: AB1561
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: PC3, Control sh1

description:
Library name: sample1
column name in raw_counts_all_samples.txt:C1


title: PC3, Control sh2

description:
Library name: sample2
column name in raw_counts_all_samples.txt:C2


title: MSCs, control, gene expression, biol rep 1

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

description: Library name: control1_MSC

data_processing:
Reads were aligned to the mm10 mouse genome using STAR. Aligned read files were analyzed using HOMER. Differential expression analysis was performed using DESeq2. Gene set enrichment analysis was performed using GSEApy.
Assembly: Mouse mm10
Supplementary files format and content: UCSC bedGraph format files (genome coverage signal tracks, gzip compressed, compatible with UCSC Genome Browser and IGV)

source_name: Mesenchymal stromal cells

extract_protocol:
Tibiae, femurs, and pelvis were harvested from mice (3 sham-operated and 3 TAC mice) and processed separately for isolation of MSCs. Bone marrow was first collected by flushing with cell suspension medium (PBS containing 2% FBS) and digested with collagenase type II (1 mg/mL) and DNase I (25 U/mL) in HBSS for 30 min at 37 °C. Remaining bone fragments were then crushed and further digested with collagenase type I (2.5 mg/mL) and DNase I (25 U/mL) in HBSS for 45 min at 37 °C. Cell suspensions were washed, filtered through a 100 µm strainer, and subjected to red blood cell lysis using PharmLyse solution. Cells were depleted of hematopoietic and endothelial populations using Mouse CD45 MicroBeads, CD31 MicroBeads, and Lineage Cell Depletion Kit (Miltenyi Biotec) via autoMACS separation. The negatively selected cells were washed and maintained in FACS buffer supplemented with actinomycin D (2 µM). Cells were stained with antibodies against lineage markers (Ter119, CD45, CD71, CD144, CD31, CD41, CD61, CD11b, Gr1, CD45R, CD5) and Leptin receptor (Lepr). Lin-Lepr+ cells were sorted as MSCs.
RNA-seq libraries were prepared using a NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocols.

treatment_protocol: Transverse aortic constriction (TAC) surgery was performed to induce cardiac stress. Sham-operated mice underwent identical surgical procedures without aortic constriction.

value: Mesenchymal stromal cells

value: sham


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample11

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

description:
Chem2_B_D3_C03
Chem2_counts_matrix.txt

data_processing:
*library strategy: TempO-Seq (Templated Oligo-Sequencing)
Sample-specific TempO-Seq libraries were pooled together and sequenced on an Illumina sequencer (NextSeq 500), 2 × 50 bp, single-end reads, NovaSeq X 10B reagent kits.
Sequence reads were then demultiplexed based on sample-specific barcodes, and a FASTQ file was generated for each sample using Illumina's bcl2fastq conversion software. Resulting TempO-Seq data were analyzed by Biospyder using TempO-SeqR software implemented in R.
The FASTQ files were aligned to the known transcript composition of the reduced transcriptome, and a count table (columns = samples, genes = rows) was generated.
Assembly: GCA_016745375.1
Supplementary files format and content: count matrices with rows as gene features and columns as samples

organism: Pimephales promelas

source_name: whole body

growth_protocol: not applicable

extract_protocol:
Samples were prepared for transcriptomics analysis by homogenization in a protease lysis buffer as directed by BioSpyder Technologies, Inc. Pimephales promelas were homogenized in 75 µL/well with a 2.3 mm stainless steel bead (BioSpec) at 30 Hz for 2 min using a well plate homogenizer (Bead Ruptor 96, OMNI International). Plates were centrifuged for 3 min at 1000 rpm. Homogenates were pooled (excluding any mortalities) by treatment concentration within each plate, resulting in n=3 replicates per treatment, each containing five pooled organisms (Supplementary Figure 2B). The final plates containing pool homogenates were stored at -80ºC until shipped on dry ice to BioSpyder Technologies, Inc. (Carlsbad, CA) for TempO-seq analysis. Test acceptability criteria were met if control survival was >90 %.
TempO-Seq libraries were prepared by ligating detector oligos to corresponding transcripts present in the whole-body homogenates. Quality control and sample quantification were performed with a DeNovix UV-visible spectrophotometer (DeNovix). Ligated transcripts were subjected to polymerase chain reaction amplification, which also introduces adaptors for sequencing and a sample-specific barcode.

treatment_protocol: High-throughput in vivo exposures were conducted in 1 mL 96-well deep well plates (NEST, Catalog #502162) for 24 h. Each exposure consisted of two chemicals tested in a 1/2 log dilution series with five replicates per treatment concentration on each of three plates (15 organisms exposed per concentration). Final exposure concentrations ranged from 66.67 – 0.021 µM for all data poor chemicals, except fipronil amide (56.43- 0.018 µM) and fexofenadine hydrochloride (32.2 – 0.011 µM). All chemical stocks were prepared in DMSO and had purities > 95%. For each exposure, a Tecan D300e Bioprinter (Corvallis, OR, USA) was used to prepare an initial chemical dosing plate containing 1800 µL/well of test solution diluted in UV-treated, filtered Lake Superior Water in a 2 mL 96-well deep well plate (NEST, Catalog #503162). The concentration of DMSO was normalized across all wells to match those of the highest % DMSO obtained with the chemical delivery (i.e., the highest exposure concentration; generally 0.34% DMSO). Using the bioprinter, the dosing solutions were arranged to evenly distribute replicate exposure groups along the edges of the plate to avoid confounding any edge effects, if present, with treatment. For each exposure, one organism was loaded with 150 µL of control water (UV-treated, filtered Lake Superior Water) to each well of the three 96-well plates. A multi-channel pipette was used to deliver 550 µL of dosing solution to each well for a final volume of 700 µL per well. Each assay included DMSO controls, with final in-well DMSO concentrations never exceeding 0.34% in the exposure plate wells.

value: whole body

tag: developmental stage

value: larval

value: 3,4-Dichlorophenyl isocyanate


title: MSCs, TAC 4w, gene expression, biol rep 1

description: Library name: TAC1_MSC

value: TAC


title: MitoDiso_HAP1_mtRES1_KO_2

description: Library name: L50

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


title: MitoDiso_HAP1_mtRES1_KO_1

description: Library name: L49


title: AL_145

value: Tumor


title: AB1558_B16_viable only_2

description:
Library name: AB1558
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: viable only


title: AL_144

value: Elderly


title: AB1557_B16_rodo high_2

description:
Library name: AB1557
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: MitoDiso_HeLa_mtRF-R_KO_2

description: Library name: L46

source_name: HeLa

value: HeLa


title: AL_143


title: AB1556_B16_viable only_3

description:
Library name: AB1556
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: MitoDiso_HeLa_6

description: Library name: L44

value: Naive


title: MitoDiso_HeLa_mtRF-R_KO_1

description: Library name: L45


title: AL_142


title: MitoDiso_HeLa_5

description: Library name: L43


title: AB1555_Roi-IN3_PBS-injected myeloid_3

description:
Library name: AB1555
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: Lung

value: Lung

value: PBS-injected myeloid


title: AL_141


title: MitoDiso_HeLa_ICT1_KO_2

description: Library name: L42


title: AB1554_Roi-IN3_PBS-injected myeloid_3

description:
Library name: AB1554
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: MitoDiso_HeLa_mtRF1_KO_2

description: Library name: L40


title: AL_140


title: MitoDiso_HeLa_mtRF1_KO_1

description: Library name: L39


title: AB1553_Roi-IN3_PBS-injected myeloid_3

description:
Library name: AB1553
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_139


title: AB1552_Roi-IN3_non-phago myeloid_3

description:
Library name: AB1552
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: MitoDiso_HeLa_1

description: Library name: L37


title: MitoRibo_mtRES1_KO_2

description: Library name: L24


title: MitoRibo_mtRES1_KO_1

description: Library name: L23


title: AB1551_Roi-IN3_phago myeloid_3

description:
Library name: AB1551
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 myeloid


title: YJ775_Lef1_E10

status: Public on Jun 08 2026

city: Boston

first: Yuemeng

last: Jia

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description: Library name: YJ775_Lef1_E10

data_processing:
The data was process with our customized software (https://gitlab.com/hormozlab/carlin)
Assembly: mm10
Supplementary files format and content: text files

source_name: Liver

extract_protocol:
RNA were extracted with Qiagen RNAeasy
RNA was reverse transcribed using a CARLIN-specific UMI-tagged primer. The DARLIN from Col1a1 was was then PCR amplified by nested PCR

value: Liver


title: whole larval P. promelas, cis-Nonachlordane, sample18

description:
Chem12_C_D2_B11
Chem12_counts_matrix.txt

value: cis-Nonachlordane


title: whole larval P. promelas, cis-Nonachlordane, sample15

description:
Chem12_B_D7_G09
Chem12_counts_matrix.txt


title: AB1550_Roi-IN3_non-phago myeloid_3

description:
Library name: AB1550
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_2

description: Library name: L20

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: MitoRibo_HAP1_2

description: Library name: L22


title: AL_136


title: AB1549_Roi-IN3_PBS-injected myeloid_3

description:
Library name: AB1549
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_2

description: Library name: L18


title: AL_135


title: MitoRibo_HeLa_HEMK1_KO_1

description: Library name: L17


title: AB1548_Roi-IN3_non-phago myeloid_3

description:
Library name: AB1548
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_8

description: Library name: L16


title: AL_134


title: AB1547_Roi-IN3_non-phago myeloid_3

description:
Library name: AB1547
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_mtRF1L_KO_2

description: Library name: L14


title: AL_133


title: MitoRibo_HeLa_mtRF-R_KO_2

description: Library name: L12


title: AL_132


title: MitoRibo_HeLa_mtRF-R_KO_1

description: Library name: L11


title: MitoRibo_HeLa_6

description: Library name: L10


title: AL_131


title: AB1545_Roi-IN3_phago myeloid_3

description:
Library name: AB1545
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_5

description: Library name: L9


title: whole larval P. promelas, cis-Nonachlordane, sample9

description:
Chem12_B_D1_A09
Chem12_counts_matrix.txt


title: MitoRibo_HeLa_ICT1_KO_2

description: Library name: L8


title: AL_130


status: Public on Jun 07 2026

city: La Jolla

first: Pandurangan

last: Vijayanand

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description:
Library name: HIPC-1_09_Hu_TL19_4D
10x single-cell library of lung sample from donor L019

data_processing:
Processing of scRNA-seq libraries: Sequencing reads from single-cell (sc)RNA-seq data were demultiplexed using Cell Ranger (v7.1.0, 10x Genomics) with the mkfastq module and aligned to the GRCh38 reference genome (pre-built reference “2020-A”) with the count module. This generated UMI-collapsed gene expression matrices for 46 single-cell libraries. Independent gene expression libraries were aggregated into combined datasets using the aggr module, yielding a dataset of lung CD3⁺ T cells from 40 donors and a dataset of lung-draining LN CD3⁺ T cells from 8 donors. Aggregated datasets were processed in R (v3.6.1) using Seurat (v3.2.3; Stuart et al., Cell, 2019). Genes expressed in fewer than 0.1% of cells were excluded. To minimize doublets and eliminate low-quality transcriptomes while still allowing for variability in the distribution of UMI and gene counts, we excluded cells that did not meet the following lenient criteria: 500≤ UMI count ≤10,000; 400≤ gene count ≤3,000; and mitochondrial UMI percentage ≤15%. Data normalization was performed using NormalizeData with default parameters. Highly variable genes (HVGs) were identified with the FindVariableFeatures function using the vst method and default settings; selection was restricted to genes with a mean expression >0.01 and contributing 30% of the standardized variance. Gene-wise scaling was performed using ScaleData, with regression of total UMI counts and mitochondrial UMI percentages (vars.to.regress argument), while retaining default settings for other arguments. Dimensionality reduction was performed via principal component analysis (PCA), followed by UMAP embedding using RunUMAP with the top 40 PCs, 15 neighbors (n.neighbors = 15), and a minimum distance of 0.1 (min.dist = 0.1). Unsupervised clustering was conducted with FindNeighbors and FindClusters, with a defined resolution and 30 PCs specified per iteration and all other parameters left unchanged. For the last iteration, 0.2 and 0.3 were chosen as the resolution values for lung and LN T cells, respectively, and irrespective of lineage. Lineage-specific subsets of CD4⁺ and CD8⁺ T cells were defined through iterative rounds of clustering and phenotype-guided filtering. In each round, contaminant clusters were reassigned to the appropriate lineage-specific dataset for further refinement. A total of 16 and 10 rounds of deconvolution were performed for lung and LN T cells, respectively, at which point no lineage contaminating clusters could be discerned.
Processing of hashtag oligonucleotide (HTO)-seq libraries: In the study cohort, hashtag barcoding was used in a subset of libraries to pool cells from multiple donors prior to sequencing. Specifically, 5 coupled scRNA-seq and scTCR-seq libraries included pooled samples and required demultiplexing during analysis. In the resource cohort, all scTCR-seq libraries consisted of pooled, hashtag-barcoded samples that were also demultiplexed during analysis. Reads from hashtag oligonucleotide (HTO) feature barcoding were demultiplexed using Cell Ranger mkfastq (v7.1.0, 10x Genomics) and processed with the count module adapted for feature barcoding (v7.1.0). For each library, cell calling was performed, and barcodes were demultiplexed into separate samples and donor identities with Seurat’s MULTIseqDemux function (v3.2.3; McGinnis et al., Nat. Methods, 2019), as detailed previously (Meckiff et al., Cell, 2020; Kusnadi et al., Science Immunol., 2021). Barcodes classified as doublets were removed from downstream analyses at the initial round of clustering.
Processing of single-cell T-cell receptor (TCR)-seq libraries: Reads from single-cell TCR sequencing (scTCR-seq) data were processed using cellranger vdj (v7.1.0) with the pre-built GCRh38 reference (“vdj-GRCh38-alts-ensembl-7.1.0”) and aggregated following previously described workflows (Meckiff et al., Cell, 2020; Kusnadi et al., Science Immunol., 2021). For the study cohort, one aggregated dataset was generated for lung CD3+ T cells (n=40 libraries, one per donor) and another for lung-draining LN CD3+ T cells (n=6 libraries spanning 8 donors). For the resource cohort, 45 libraries derived from putative pathogen-specific CD4+ T cells were aggregated into a single TCR dataset. For this type of data (single-cell resolution), a clonotype was defined as a unique set of CDR3 α and β sequences and the V and J gene segments encompassing each of them.
Clonotype group-bias assignment problem: Given a clonotype observed across n groups (n>1), let f_g denote its absolute frequency in group g, and let r_g denote its relative frequency in that group, computed as f_g normalized by the total clonotype counts within group g. The task is to classify each clonotype as either biased toward a particular group or unbiased across groups. Proposed solution: First, sort all groups by the clonotype’s relative frequency r_g, identifying the top-ranked group (g_1) and the second-ranked group (g_2). Compute the bias ratio as: bias_ratio=r_(g_1 )/r_(g_2 ) . A clonotype is then assigned as biased to group g_1 if and only if: (i) f_(g_1 )>2 and (ii) bias_ratio>2.
Assignment of uniquely defined antigen specificities to TCR clonotypes: In this study, the ARTE assay was employed to capture antigen-specific T cells, with concomitant TCR repertoires profiled at single-cell resolution. These data have : (i) a readout consisting of CDR3 sequences and the V and J gene segments that encompass them; (ii) clonotypes with an absolute frequency of 1 unit—with cell barcodes as units, referred to as singletons—represented a substantial proportion across the board; (iii) a division of expanded (non-singleton) clonotypes into two classes with regard to antigen specificity—those that were detected with a single peptide MP (unambiguous) and those that were detected with multiple peptide MPs (ambiguous); and (iv) for ambiguous clonotypes, when their associated peptide MPs were ranked by relative frequency and the ratio of the top-to-the-second-highest ranked MP was calculated (reminiscent of the bias_ratio), the resulting distributions were highly similar between assays and data types. Unambiguous clonotypes were directly deemed specific to the antigen corresponding to the peptide MP with which they were detected. In contrast, the assignment of unique specificities to ambiguous clonotypes can be framed as an instance of the clonotype group-bias assignment problem described above. The proposed solution was implemented as a common framework, such that an ambiguous clonotype was defined as specific to antigen g_1 when (i) f_(g_1 )>2, where f_(g_1 ) denotes its absolute frequency for that antigen and (ii) bias_ratio>2.
Assembly: GRCh38 (2020-A reference prebuilt and provided by 10x cellranger).
Supplementary files format and content: This submission includes seurat objects (v3.2.3; Stuart et al., Cell, 2019) created as described above for the sets of CD4+ (HIPC-1_LG-CD4-ALL_SeuratObject.RDS) and CD8+ (HIPC-1_LG-CD8-ALL_SeuratObject.RDS) lung T cells and the sets of CD4+ (HIPC-1_LN-CD4-ALL_SeuratObject.RDS) and CD8+ (HIPC-1_LN-CD8-ALL_SeuratObject.RDS) lung-draining LN T cells.
Supplementary files format and content: TCR clonotype metadata including CDR3 sequences and V and J gene usage, as well as antigen specificity-associated metrics, are provided in file: DICE-TCR_BL-CD4-ALL_ProcessedObject.csv

source_name: lung

growth_protocol: Study cohort samples: A total of 40 individuals undergoing standard-of-care surgical resection for primary lung non-small cell lung cancer (NSCLC) at Liverpool Heart and Chest NHS Foundation Trust Hospital were enrolled. The cohort included 16 men and 24 women, all of White British ethnicity, with a median age of 70 years (range: 61–83). Background lung tissue, along with matched peripheral blood and LLNs, was collected intraoperatively. Background lung samples were obtained from macroscopically uninvolved, non-tumor-bearing regions of the parenchyma, typically distant from the primary tumor. All samples were de-identified and cryopreserved in freezing medium (90% fetal bovine serum (FBS) and 10% DMSO) prior to downstream processing. Reference cohort samples: Peripheral blood mononuclear cells (PBMCs) were obtained from a total of 61 healthy donors through the San Diego Blood Bank (SDBB) between December 2021 and February 2022. Each donor provided approximately 8 mL of LRS-WBC (Leukoreduction System - Whole Blood Collection) material. Donor ages ranged from 27 to 79 years (median of 65). Of the 61 donors, 47 were male, 12 were female, and 2 had unspecified sex information. No clinical or immunological abnormalities were reported for these donors at the time of collection. PBMCs were isolated and cryopreserved according to standard protocols for downstream immunological assays.

extract_protocol:
Single-cell (sc)RNA-seq library preparation was performed alongside TCR repertoire immune profiling (scTCR-seq) and cell surface protein technology to enable hashtag oligonucleotide (HTO) -based sample demultiplexing. Up to 100,000 CD3⁺ T cells from each of 40 lung samples, up to 100,000 CD3+ T cells of 8 LLN samples—from a single- or 2-donor pools—, and up to 120,000 circulating,  pathogen-specific CD4+ T cells—from up to 16 pooled donors—were processed using the 10x Genomics Chromium Next GEM Single Cell 5′ HT Reagent Kit v2 (Dual Index), following the manufacturer’s instructions.
Initial amplification of cDNA (concomitantly, for gene expression library preparation) was carried out with 13 cycles of amplification; scTCR and HTO libraries were both generated with 8 cycles of amplification. All libraries were quantified and pooled according to equivalent molar concentrations. Libraries from lung CD3+ T cells and circulating, pathogen-specific CD4+ T cells were sequenced on an Illumina NovaSeq6000 sequencing instrument (read 1 and read 2 – 100 cycles; i5 and i7 index - 10 cycles). Libraries from LLN CD3+ T cells were sequenced on an Illumina NovaSeq X instrument (150 x 150 cycle paired-end configuration with index reads ).

treatment_protocol: Study cohort samples: Human lung tissue and LLN samples were thawed in a 37°C water bath for ~5 minutes until only a small ice fragment remained, followed by washing with FBS and dilution in MACS buffer to reduce DMSO concentration. The thawed tissue suspension was filtered through a 70 µm strainer, with retained tissue pieces collected and finely diced using a scalpel (this step only in case of lung tissue). The minced tissue was transferred to a gentleMACS C tube (Miltenyi Biotec,130-096-334) and supplemented with RPMI, after which enzymatic digestion was initiated by adding DNase I (Sigma, D4527-200K) and Liberase (Sigma, 5401127001). The sample underwent mechanical and enzymatic dissociation using an OctoDissociator (Miltenyi Biotec) set at 37°C for 15 minutes. Following dissociation, the cell suspension was filtered through a MACS SmartStrainer, gently pressing residual tissue to maximize cell yield. The resulting cell suspension was centrifuged, and the pellet resuspended in MACS buffer containing FcR Blocking Reagent, followed by the addition of Cell-hashtag TotalSeq-C antibody (1 μg/condition) to enable hashtag oligonucleotide (HTO)-based sample deconvolution at the analysis stage. Cells were then stained with a panel of antibodies optimized to sort for CD3+ T cells while incubating at 4°C. After washing, the cells were underlaid with FBS and centrifuged again. The final cell pellet was resuspended in cold MACS buffer supplemented with DAPI for viability staining and sorted for CD3+ T cells on a FACSAria Fusion Cell Sorter (Becton Dickinson). Resource cohort samples: The enrichment and FACS sort of pathogen-specific CD4+ memory T cells from the PBMC samples of the resource cohort (n=61 donors) was performed using a modified protocol based on Bacher et al., J Immunol., 2016. PBMCs from donors were thawed, washed, and cultured overnight (5% CO2, 37 °C) in serum-free TexMACS medium at a concentration of 10 × 10^6 cells/mL. The cells were then stimulated with pathogen peptide MPs (1ug/ml) for 6 hours, with a CD40 blocking antibody (1 μg/mL; Miltenyi Biotec) present. To enrich CD154+ cells, a series of staining steps were carried out, including surface antibodies, Cell-hashtag TotalSeq-C antibody (1ug/condition), and a biotin-conjugated CD154 antibody, followed by anti-biotin microbeads. The labeled cells underwent positive selection using MS columns, with the CD154+ cells being eluted for subsequent FACS sorting. The enriched populations were immediately sorted using a FACSAria Fusion Cell Sorter (Becton Dickinson) based on dual expression of CD154 and CD69.

value: lung

value: CD3+ T cells

value: Ex-vivo


title: AB1543_Roi-IN3_phago myeloid_3

description:
Library name: AB1543
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_129


title: MitoRibo_HeLa_3

city: Wako city

first: Taisei

last: Wakigawa

address: 2-1, Hirosawa

institute: RIKEN

description: Library name: L5

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).


title: AB1536_B16_viable only_3

description:
Library name: AB1536
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: AB1544_Roi-IN3_phago myeloid_3

description:
Library name: AB1544
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_128


title: AB1535_B16_rodo+_2

description:
Library name: AB1535
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+


title: MitoRibo_HeLa_2

description: Library name: L2


title: AL_127


title: AB1534_B16_rodo+_3

description:
Library name: AB1534
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: AB1886_Roi Zymo rep 1_rodo-_1

description:
Library name: AB1886
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: AL_126


title: AB1885_Roi Zymo rep 1_rodo+_1

description:
Library name: AB1885
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: AB1533_B16_rodo+_3

description:
Library name: AB1533
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: AB1884_Roi Zymo rep 1_rodo-_1

description:
Library name: AB1884
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_125

value: Middle


title: AB1883_Roi Zymo rep 1_rodo+_1

description:
Library name: AB1883
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: AB1532_B16_rodo-_3

description:
Library name: AB1532
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: AB1878_Roi Zymo rep 3_rodo-_3

description:
Library name: AB1878
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: AB1877_Roi Zymo rep 2_rodo-_2

description:
Library name: AB1877
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: AB1531_B16_rodo high_3

description:
Library name: AB1531
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: AB1873_Roi Zymo rep 3_rodo-_3

description:
Library name: AB1873
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: AB1530_B16_viable only_2

description:
Library name: AB1530
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: viable only


title: AB1872_Roi Zymo rep 3_rodo+_3

description:
Library name: AB1872
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_122

value: Tumor


title: AB1871_Roi Zymo rep 3_rodo+_3

description:
Library name: AB1871
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: AB1529_B16_rodo+_2

description:
Library name: AB1529
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_3_batch3

city: Freiburg im Breisgau

first: Linus

middle: Rudolf

last: Schoemig

state: Baden-Wuerttemberg

address: Breisacherstr. 66

department: Department of Medicine II, Faculty of Medicine

institute: University of Freiburg - Medical Centre

description:
Library name: Sample_20
Column name in "Raw_Counts_Matrix.tsv": L2-LKP_3_batch3

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


title: AL_121

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.


title: AL_151

value: Elderly


title: C_01

description: Library name: C_01

value: ventricular heart


title: AL_124


title: AL_149


title: AL_146


title: AB1870_Roi E. Coli rep 3_rodo-_3

description:
Library name: AB1870
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: Lung


title: L2-LKP_2_batch3

description:
Library name: Sample_19
Column name in "Raw_Counts_Matrix.tsv": L2-LKP_2_batch3


title: AB1869_Roi E. Coli rep 3_rodo-_3

description:
Library name: AB1869
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_120


title: AB1527_B16_rodo-_3

description:
Library name: AB1527
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_119


title: L2-LKP_1_batch3

description:
Library name: Sample_18
Column name in "Raw_Counts_Matrix.tsv": L2-LKP_1_batch3


title: AB1868_Roi E. Coli rep 3_rodo+_3

description:
Library name: AB1868
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: AB1526_B16_rodo high_3

description:
Library name: AB1526
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_118


title: L2-LK_1_batch3

description:
Library name: Sample_13
Column name in "Raw_Counts_Matrix.tsv": L2-LK_1_batch3


title: AB1525_B16_rodo-_2

description:
Library name: AB1525
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_3_batch3

description:
Library name: Sample_12
Column name in "Raw_Counts_Matrix.tsv": L2-LP_3_batch3


title: AL_117


title: AB1866_Roi Zymo rep 2_rodo-_2

description:
Library name: AB1866
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: AB1524_B16_rodo-_2

description:
Library name: AB1524
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_2_batch3

description:
Library name: Sample_11
Column name in "Raw_Counts_Matrix.tsv": L2-LP_2_batch3


title: AL_116


title: AB1865_Roi Zymo rep 2_rodo+_2

description:
Library name: AB1865
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: AB1440_B16_viable only_1

description:
Library name: AB1440
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_batch3

description:
Library name: Sample_10
Column name in "Raw_Counts_Matrix.tsv": L2-LP_1_batch3


title: AL_115


title: AB1844_Roi E. Coli rep 2_rodo+_2

description:
Library name: AB1844
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: L2-L_2_batch3

description:
Library name: Sample_7
Column name in "Raw_Counts_Matrix.tsv": L2-L_2_batch3


title: AL_114


title: AB1843_Roi E. Coli rep 2_rodo-_2

description:
Library name: AB1843
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: L2-L_1_batch3

description:
Library name: Sample_6
Column name in "Raw_Counts_Matrix.tsv": L2-L_1_batch3


title: AL_113


title: AB1842_Roi E. Coli rep 2_rodo+_2

description:
Library name: AB1842
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.