title: Ca799-fat body-24h_3

status: Public on Oct 12 2025

city: Shang hai

first: li

last: jie

address: No. 320 Yueyang Road

institute: Shanghai lnstitute of lmmunity and Infection

data_processing:
Raw reads were processed with Trim Galore to trim adaptors and remove low-quality reads, then mapped to  the Drosophila melanogaster genome assembly dm6 (Ensembl version 109) using STAR.
Assembly: dm6
Supplementary files format and content: In the processed data file, the first column contains gene IDs, the second column contains gene symbols, the third column contains gene descriptions, and columns four to twenty-seven correspond to individual samples.

organism: Drosophila melanogaster

source_name: fat body

extract_protocol:
RNA was extracted using Trizol. 1 µg of total RNA was used for library construction.
Eukaryotic mRNA was enriched using magnetic beads with Oligo(dT). Subsequently, fragmentation buffer was added to break the mRNA into short fragments. Using the mRNA as a template, first-strand cDNA was synthesized with random hexamer primers. Then, a buffer, dNTPs, DNA polymerase I, and RNase H were added to synthesize the second-strand cDNA, which was purified using AMPure XP beads. The purified double-stranded cDNA underwent end repair, A-tailing, and adapter ligation, followed by size selection using AMPure XP beads. Finally, PCR amplification was performed, and the PCR products were purified with AMPure XP beads to obtain the final library.

value: fat body


title: Ca799-fat body-24h_2

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: treatment

tag: time

tag: tissue


title: pbs-fat body-24h_3

value: PBS


title: Ca799-fat body-24h_1


title: pbs-fat body-24h_2


title: E100parietal

status: Public on Oct 13 2025

city: San Francisco

first: Alex

middle: A

last: Pollen

state: CA

address: 35 Medical Center Way

department: Neurology

country: USA

institute: UCSF

description:
Library name: E100parietal
10X Genomics (V3) 3 capture single cell RNA seq

library_source: transcriptomic single cell

data_processing:
fastq files
Kallisto gene expression quantification
Cellbender ambient RNA removal
Assembly: rheMac10
Supplementary files format and content: H5AD

molecule: polyA RNA

organism: Macaca mulatta

source_name: brain

extract_protocol:
Papain dissociated whole cells
10X Genomics (V3) 3 capture single cell RNA seq

value: brain

tag: developmental stage


title: Ca799-fat body-6h_2


title: Ca799-fat body-6h_3


title: pbs-fat body-6h_2


title: pbs-fat body-6h_1


title: Ca799-whole body-24h_3

source_name: whole body

value: whole body


title: Ca799-fat body-6h_1


title: Ca799-whole body-24h_1


title: pbs-whole body-24h_3


title: pbs-fat body-6h_3


title: E100motor

description:
Library name: E100motor
10X Genomics (V3) 3 capture single cell RNA seq


title: Ca799-whole body-6h_3


title: Ca799-whole body-24h_2


title: Ca799-whole body-6h_1


title: pbs-whole body-6h_3


title: pbs-whole body-24h_1


title: Ca799-whole body-6h_2


title: pbs-whole body-24h_2


title: pbs-whole body-6h_2


title: pbs-whole body-6h_1


title: FACS sorted cells from EB and HB cultures plate008

city: Zürich

first: Nina

last: Schmolka

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description:
Library name: plate008
SORT-seq

data_processing:
During sequencing, read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode, and unique molecular identifier (UMI) [Read 1: 26bp: 12bp 5’ Illumina adaptor -6bp random molecular barcode(UMI)- 8bp cell-specific barcode]. Read 2 was assigned 60 base pairs and used to map to the reference genome Mus musculus (GRCm38) version 99 with STARSolo 2.7.3a4. Briefly, mapping and generation of count tables were automated using the STARSolo 2.7.3a aligner. Unsupervised clustering and differential gene expression analysis was performed with the Seurat5 R toolkit. Count tables were imported into R, where a singleCellExperiment object was constructed and subsequently filtered based on library size, feature count, spike-in count, and mitochondrial count using the isOutlier function from the scater v1.26.1 R package. Following quality control, the dataset was analysed using the Seurat v4.3 R package, using the SCTransform workflow.
Assembly: Mus musculus (GRCm38) version 99
Supplementary files format and content: Tab-separated values files

organism: Mus musculus

source_name: differentiated ESCs

growth_protocol: Murine Embryonic stem cells (ESCs) were differentiated towards mesodermal and endothelial and haematopoietic lineages during embryoid body (EB)  and haemangioblast (HB) cultures. For EB cultures: twenty-four hours prior to the initiation, ESCs were transferred into gelatinized plates containing using Iscove’s Modified Eagle Medium (IMDM) (Gibco). For the generation of embryoid body (EB) cultures, ESCs were trypsinized then plated at 10,000 cells/ml in non-adherent 10 cm2 petri dishes in EB medium (IMDM supplemented with 1% L-glutamine (Gibco), 10% FCS (Gibco), 0.6% transferrin (Roche, 10652), 50 µg/ml ascorbic acid (Sigma, A4544) and 0.03% monothioglycerol (Sigma, M6145). Bmp4 was added from day 0 of EB culture and bFGF, activin A and VEGF from day 2.5 (all Peprotech) all at 5 ng/ml. After five days in culture, EBs were harvested, and TrypLE Express Enzyme (1×) (Gibco, 12605036) was used to generate a single- cell suspension. For HB cultures: Prior to HB cultures, mesodermal populations underwent FACS sorting (for either DP priMes, F_SP HEM or total FLK1+) and 0.5x106 cells were cultured on 0.2%-gelatine-coated plates in IMDM supplemented with 1% penicillin–streptomycin, 1% L-glutamine, 15% FCS (Gibco), transferrin (Roche), 0.03% monothioglycerol (Sigma, M6145), 50 mg/μL of ascorbic acid (Sigma, A4544), 5 ng/ml VEGF (Peprotech) and 10 ng/mL IL6 (Peprotech). After 2.5 days in culture, cells were harvested, and TrypLE Express Enzyme (1×) (Gibco, 12605036) was used to generate a single-cell suspension. The following antibodies were used for FACS sorting: anti-FLK1, anti-Vecad, anti-CD41, anti-cKit.

extract_protocol:
Single-cell RNA sequencing was performed according to an adapted version of the SORT-seq protocol (Muraro et al., 2016) with primers described previously (van den Brink et al., 2017). Cells were heat-lysed at 65° C followed by cDNA synthesis. After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT).
Library preparation was done following the CEL-Seq2 protocol (Hashimshony et al., 2016) to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina).

treatment_protocol: No treatment was applied

tag: cell line

value: differentiated ESCs


title: FACS sorted cells from EB and HB cultures plate007

description:
Library name: plate007
SORT-seq


title: FACS sorted cells from EB and HB cultures plate004

description:
Library name: plate004
SORT-seq


title: FACS sorted cells from EB and HB cultures plate006

description:
Library name: plate006
SORT-seq


title: FACS sorted cells from EB and HB cultures plate003

description:
Library name: plate003
SORT-seq


title: FACS sorted cells from EB and HB cultures plate002

description:
Library name: plate002
SORT-seq


title: C57Bl/6J naked genomic DNA control

city: Boston

first: Jenna

middle: L

last: Galloway

state: MA

address: 185 Cambridge St.

department: Orthopaedics

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
Demultiplexed PE reads were trimmed using NGmerge (Gaspar (2018)) and aligned to the mouse genome using Bowtie2 (Langmead and Salzberg (2012)). Read pairs mapping to the mitochondrial genome were removed using removeChrom (https: //github.com/jsh58/harvard) and PCR duplicates were filtered with the dedup tool in bamUtil (Jun et al. (2015)).
Peaks were called with MACS2 in paired end BAM mode with the options -f BAMPE --nolambda --keep-dup all. Any peaks falling in the ENCODE defined blacklist for mm10 (Davis et al. (2017)) and peaks called from the naked DNA control were deemed spurious and removed using bedtools (Quinlan and Hall (2010)).
Assembly: mm10/GRCm38v91
Supplementary files format and content: quant.sf files (RNAseq): output of Salmon transcript alignment and quantification
Supplementary files format and content: BED files (ATAC-seq): output of MACS2 peak calling significant peaks only, filtered on naked gDNA peaks and ENCODE mm10 blacklist

molecule: genomic DNA

source_name: tail

extract_protocol:
Tendons were digested in 0.2% collagenase II, 0.2% collagenase I, 0.4% dispase in DMEM at 37C. 50,000 FACS sorted ScxCre-tdTomato+ cells per biological replicate were subjected to a modified Fast-ATAC protocol (Corces et al. 2017)
Tn5 transposed DNA was column purified, amplified and barcoded, and bead purified as described in Buenrostro et al. 2015. Library quality was assessed via BioAnalyzer or TapeStation and libraries were quantified using the KAPA qPCR library quantification system. Libraries were multiplexed and paired-end 42 bp reads were sequenced on an Illumina NextSeq 500 using a High-Output 75-cycle kit.

value: tail

tag: time point


title: FACS sorted cells from EB and HB cultures plate001

description:
Library name: plate001
SORT-seq


title: P35 tendon biorep 1, ATACseq

source_name: tendon

value: tendon


title: P35 tendon biorep 2, ATACseq


title: P28 tendon biorep 1, ATACseq


title: P14 tendon biorep 2, ATACseq


title: pbs-fat body-24h_1


title: P28 tendon biorep 2, ATACseq


title: P0 tendon biorep 1, ATACseq


title: P14 tendon biorep 1, ATACseq


title: P0 tendon biorep 2, ATACseq


title: P35 tendon biorep 8, bulk RNAseq

data_processing:
Sequenced RNA-seq reads were demultiplexed, followed by quality filtering and trim- ming using TrimGalore (Andrews et al. (2012)). After quality filtering, the final sample size was between 6 and 9 biological replicates per time point. A Salmon transcript index was built from the Ensembl mouse transcriptome (GRCm38v91) and transcripts were then quantified from quality-trimmed reads using Salmon (Patro et al. (2017)) in mapping-based mode with the --seqBias and --gcBias flags enabled.
Assembly: mm10/GRCm38v91
Supplementary files format and content: quant.sf files (RNAseq): output of Salmon transcript alignment and quantification
Supplementary files format and content: BED files (ATAC-seq): output of MACS2 peak calling significant peaks only, filtered on naked gDNA peaks and ENCODE mm10 blacklist

extract_protocol:
Whole tendons were homogenized in TRIzol using a bead beater and then RNA was extracted using traditional TRIzol-chloroform extraction and cleaned up using the Zymo Direct-Zol RNA kit. RNA quality was determined by Bioanalyzer or TapeStation and quantity was determined using Qubit. Only samples with RIN > 6.7 were processed for sequencing.
Library prep was performed using the Apollo 324 NGS library prep system (IntegenX) and the PrepX mRNA library protocol (Takara Bio) using the polyA selection method. cDNA libraries were barcoded and amplified, then multiplexed into 3 pools. Single end 75 bp reads were sequenced on an Illumina NextSeq 500 using a High-Output 75-cycle kit.


title: P35 tendon biorep 7, bulk RNAseq


title: SBP2(Se), RIP, rep3

city: Shanghai

first: Chenfang

last: Si

address: Haike Road 100

institute: Chinese Academy of Sciences

description:
Library name: SBP2(Se)_RIP_3
Column name in Counts.csv: SBP2(Se)_RIP_3

data_processing:
All sequencing reads were processed using Trim Galore (v0.6.6) with the parameters ‘‘–nextseq 30 –paired’’ to remove adapter sequences, retaining reads longer than 20 bp.
Quality-filtered reads were then mapped to the human genome (GRCh38) using STAR (v2.7.6a) with default settings.
Uniquely mapped read pairs were counted against gene annotations from Homo sapiens (Ensembl: GRCh38.94) using featureCounts (v2.0.1) with the parameters ‘‘-p -B -C’’ to generate gene-level counts.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

organism: Homo sapiens

source_name: HEK 293T cells

growth_protocol: HEK 293 cells were cultured in high-glucose Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (PS) at 37°C under a 5% CO2 atmosphere.

extract_protocol:
Cells were lysed in 0.5 ml of NP40 lysis buffer (50 mM HEPES, pH 7.5, 150 mM KCl, 2 mM EDTA, 1 mM NaF, 0.5% (v/v) NP40, 1 mM DTT, protease inhibitor cocktail, 100 U/ml RNaseOUT recombinant ribonuclease inhibitor) per 10cm dish, and rotated for 30 min at 4°C. After centrifuging at 20,000 g at 4°C for 10 min, the supernatants were collected. Protein concentrations were determined using the BCA method. 4 mg protein with 120 μl anti-flag magnetic beads (Biomake) were used for immunoprecipitation at 4°C for 5h with rotation. Before starting the incubation, 1/5 of the sample was taken as Input. Beads were washed three times with IP wash buffer (50 mM HEPES-KOH, pH 7.5, 300 mM KCl, 0.05% (v/v) NP40, 1 mM DTT, protease inhibitor cocktail), and further washed three times with high-salt wash buffer (50 mM HEPES-KOH, pH 7.5, 500 mM KCl, 0.05% (v/v) NP40, 1 mM DTT, protease inhibitor cocktail). RNA from both Input and IP samples was extracted according to the instructions provided with the TRIzol reagent (Thermo Fisher Scientific), followed by DNA removal with RNase-free DNase (Promega).
RNA-seq libraries were prepared with the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech), following the manufacturer’s instructions using 1 µg of RNA.

treatment_protocol: HEK 293T cells were transiently transfected with Flag or Flag-SBP2 plasmids using PolyJet transfection reagent (SignaGen) following the manufacturer’s protocol. Four hours post-transfection, cells in the Flag-SBP2 group were treated with 100 nM sodium selenite. Cell lysates were harvested 48 hours after transfection.

value: HEK 293T cells

value: Flag-SBP2 overexpression, 100 nM sodium selenite


title: FACS sorted cells from EB and HB cultures plate009

description:
Library name: plate009
SORT-seq


title: P35 tendon biorep 6, bulk RNAseq


title: F_SP_HEM_R3

description:
Library name: F_SP_HEM_003
polyA RNA-seq

data_processing:
Single-end 100bp were sequenced on Novaseq 6000 (Illumina, Inc, California, USA) and an average of ~20 million reads per sample were obtained. Data Analysis: Reads were mapped to the GRCm39.107 genomic reference and count tables generated using STAR-2.7.7 (ref48). Count tables were filtered and only genes with a minimum of 10 reads and occurrences in at least three conditions were retained
Assembly: Mus musculus (GRCm38)
Supplementary files format and content: counttable.tsv

source_name: ESC-derived mesodermal populations

growth_protocol: Murine Embryonic stem cells (ESCs) were differentiated towards mesodermal  during embryoid body (EB). For EB cultures: twenty-four hours prior to the initiation, ESCs were transferred into gelatinized plates containing using Iscove’s Modified Eagle Medium (IMDM) (Gibco). For the generation of embryoid body (EB) cultures, ESCs were trypsinized then plated at 10,000 cells/ml in non-adherent 10 cm2 petri dishes in EB medium (IMDM supplemented with 1% L-glutamine (Gibco), 10% FCS (Gibco), 0.6% transferrin (Roche, 10652), 50 µg/ml ascorbic acid (Sigma, A4544) and 0.03% monothioglycerol (Sigma, M6145). Bmp4 was added from day 0 of EB culture and bFGF, activin A and VEGF from day 2.5 (all Peprotech) all at 5 ng/ml. After five days in culture, EBs were harvested, and TrypLE Express Enzyme (1×) (Gibco, 12605036) was used to generate a single- cell suspension. The following antibodies were used for FACS sorting: anti-FLK1, anti-PDGFRa.

extract_protocol:
0.5x106 cells were collected on day 5 of EB culture and mesodermal populations were FACS sorted using FLK and PDGFRa surface expression. Subsequently RNA was isolated using Qiagen RNAeasy kit (Qiagen cat. 74134). The quality of the isolated RNA was determined with a Fragment Analyzer (Agilent, Santa Clara, California, USA).
The TruSeq Stranded mRNA protocol (Illumina, Inc, California, USA) was used. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using the Fragment Analyzer. The libraries were normalized to 10 nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.

value: ESC-derived mesodermal populations

tag: cell subpopulation

value: FLK1 single- positive haemato-endothelial mesoderm

tag: genotype

value: wild type

value: developmental stage


title: P35 tendon biorep 4, bulk RNAseq


title: P35 tendon biorep 3, bulk RNAseq


title: P35 tendon biorep 2, bulk RNAseq


title: FACS sorted cells from EB and HB cultures plate005

description:
Library name: plate005
SORT-seq


title: P35 tendon biorep 1, bulk RNAseq


title: Control, RIP, rep3

description:
Library name: Control_RIP_3
Column name in Counts.csv: Control_RIP_3

value: Flag overexpression


title: P28 tendon biorep 7, bulk RNAseq


title: F_SP_HEM_R1

description:
Library name: F_SP_HEM_001
polyA RNA-seq


title: SBP2(Se), RIP, rep2

description:
Library name: SBP2(Se)_RIP_2
Column name in Counts.csv: SBP2(Se)_RIP_2


title: P28 tendon biorep 5, bulk RNAseq


title: P28 tendon biorep 6, bulk RNAseq


title: P7 tendon biorep 1, ATACseq


title: DP_priMes_R3

description:
Library name: DP_priMes_003
polyA RNA-seq

value: double-positive primitive mesoderm (FLK1+PDGFRa+)


title: P28 tendon biorep 4, bulk RNAseq


title: P7 tendon biorep 2, ATACseq


title: P28 tendon biorep 2, bulk RNAseq


title: SBP2, RIP, rep2

description:
Library name: SBP2_RIP_2
Column name in Counts.csv: SBP2_RIP_2

value: Flag-SBP2 overexpression


title: P28 tendon biorep 3, bulk RNAseq


title: Control, RIP, rep2

description:
Library name: Control_RIP_2
Column name in Counts.csv: Control_RIP_2


title: DP_priMes_R2

description:
Library name: DP_priMes_002
polyA RNA-seq


title: P35 tendon biorep 5, bulk RNAseq


title: SBP2(Se), RIP, rep1

description:
Library name: SBP2(Se)_RIP_1
Column name in Counts.csv: SBP2(Se)_RIP_1


title: P21 tendon biorep 7, bulk RNAseq


title: PD_SP_R3

description:
Library name: PD_SP_003
polyA RNA-seq

value: PDGFRa- single positive cells


title: P21 tendon biorep 6, bulk RNAseq


title: F_SP_HEM_R2

description:
Library name: F_SP_HEM_002
polyA RNA-seq


title: P21 tendon biorep 5, bulk RNAseq


title: SBP2, RIP, rep1

description:
Library name: SBP2_RIP_1
Column name in Counts.csv: SBP2_RIP_1


title: P21 tendon biorep 4, bulk RNAseq


title: P21 tendon biorep 3, bulk RNAseq


title: Control, RIP, rep1

description:
Library name: Control_RIP_1
Column name in Counts.csv: Control_RIP_1


title: PD_SP_R1

description:
Library name: PD_SP_001
polyA RNA-seq


title: P21 tendon biorep 2, bulk RNAseq


title: P14 tendon biorep 6, bulk RNAseq


title: P21 tendon biorep 1, bulk RNAseq


title: DN_R2

description:
Library name: DN_002
polyA RNA-seq

value: double-negative cells (FLK1-PDGFRa-)


title: P28 tendon biorep 1, bulk RNAseq


title: DP_priMes_R1

description:
Library name: DP_priMes_001
polyA RNA-seq


title: SBP2, Input, rep3

description:
Library name: SBP2_Input_3
Column name in Counts.csv: SBP2_Input_3


title: P14 tendon biorep 5, bulk RNAseq


title: DN_R3

description:
Library name: DN_003
polyA RNA-seq


title: P14 tendon biorep 2, bulk RNAseq


title: P14 tendon biorep 4, bulk RNAseq


title: DN_R1

description:
Library name: DN_001
polyA RNA-seq


title: SBP2, Input, rep2

description:
Library name: SBP2_Input_2
Column name in Counts.csv: SBP2_Input_2


title: P7 tendon biorep7, bulk RNAseq


title: P14 tendon biorep 3, bulk RNAseq


title: P14 tendon biorep 1, bulk RNAseq


title: SBP2(Se), Input, rep2

description:
Library name: SBP2(Se)_Input_2
Column name in Counts.csv: SBP2(Se)_Input_2


title: P7 tendon biorep6, bulk RNAseq


title: Iri_3

city: Nanjing

first: Xinghua

last: Gao

state: Jiangsu

address: #639 Longmian Dadao

institute: China Pharmaceutical University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low-quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads.
Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome.
The gene alignment and FPKM were calculated using featureCounts v1.6.2 / StringTie v1.3.4d.
DESeq2 v1.22.1 / edgeR v3.24.3 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression.
Assembly: GRCm39.104
Supplementary files format and content: tab-delimited text files include FPKM and count for each sample.

extract_protocol:
Total RNA was extracted using Trizol (Takara, Japan) and checked for a RIN number to inspect RNA integrity by an Bioanalyzer 2100 (Agilent technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CT26 tumor cells were treated with Irinotecan (CPT-11) at a concentration of 10 uM for 24 hours.

tag: cell type

value: tumor cell

value: WT

value: CPT-11 treatment


title: PD_SP_R2

description:
Library name: PD_SP_002
polyA RNA-seq


title: Control, Input, rep2

description:
Library name: Control_Input_2
Column name in Counts.csv: Control_Input_2


title: Iri_2


title: SBP2(Se), Input, rep3

description:
Library name: SBP2(Se)_Input_3
Column name in Counts.csv: SBP2(Se)_Input_3


title: P7 tendon biorep3, bulk RNAseq


title: Iri_1


title: P7 tendon biorep4, bulk RNAseq


title: SBP2(Se), Input, rep1

description:
Library name: SBP2(Se)_Input_1
Column name in Counts.csv: SBP2(Se)_Input_1


title: SBP2, RIP, rep3

description:
Library name: SBP2_RIP_3
Column name in Counts.csv: SBP2_RIP_3


title: P7 tendon biorep2, bulk RNAseq


title: Control_DMSO_3

value: DMSO treatment


title: Control_DMSO_2


title: SBP2, Input, rep1

description:
Library name: SBP2_Input_1
Column name in Counts.csv: SBP2_Input_1


title: P0 tendon biorep 8, bulk RNAseq


title: P7 tendon biorep1, bulk RNAseq


title: P0 tendon biorep 7, bulk RNAseq


title: Control, Input, rep3

description:
Library name: Control_Input_3
Column name in Counts.csv: Control_Input_3


title: Control_DMSO_1


title: P0 tendon biorep 4, bulk RNAseq


title: 19145X1 Nevus

city: Salt Lake City

first: Robert

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah

description: BD Rhapsody

data_processing:
Fastq files were processed using the BD WTA Multiplex Rhapsody Analysis Pipeline Version 1.9.1 on SevenBridges (https://igor.sbgenomics.com/public/apps/jiewho/bd-public-project/bd-rhapsody-wta-analysis-pipeline)
Assembly: hg38
Supplementary files format and content: CSV files with molecules per gene per cell based on RSEC error correction and assigned sample tags for each cell

source_name: nevus

growth_protocol: Melanoma cell ilnes were grown in RPMI media supplemented with 10% FBS. NHMs were grown in 254 media supplemented with HGMS.

extract_protocol:
Nevus cells were obtained by excising nevi and sorting for KIT positive cells
BD Rhapsody library prep

value: Primary human nevus cells

value: nevus


title: P0 tendon biorep 6, bulk RNAseq

value: tendon


title: 19145X2 Cultured melanomas and melanocytes

description: BD Rhapsody

source_name: melanoma

value: Human melanoma and melanocyte cell lines

value: melanoma

tag: strain


title: P7 tendon biorep5, bulk RNAseq


title: P0 tendon biorep 5, bulk RNAseq


title: Pool2_Ldb1KO_Six4KO_Zbtb7b_KO

description:
Library name: Pool2
scRNA-seq

data_processing:
For sequencing, the resulting libraries were processed on two lanes of an Illumina NovaSeq X Plus 10 billion flow cell with a 150 bp paired-end read configuration. An average sequencing depth of around 25,000 reads per cell was achieved. Data Analysis: Single-cell RNA-seq reads were processed with the 10x software CellRanger Multi version 7.2.062 with the Mus Musculus GENCODE GRCm39 annotation (Release M31-2023-01-30) to generate the single-cell gene expression matrix. Count tables were imported into R using the Read10X function of Seurat v4. A Seurat object was created and filtered based on library size, feature count and mitochondrial count, using the isOutlier function of the scater v1.26.1 R package. Normalisation, scaling and variable feature detection were performed using the SCTransform workflow in Seurat. Subsequently, linear dimensionality scaling, unsupervised clustering and differential gene expression analysis/positive marker finding discovery were performed in Seurat. Integration with other scRNA-seq datasets was performed using Seurat functions SelectIntegrationFeatures, PrepSCTIntegration, FindIntegrationAnchors and IntegrateData with SCT as normalisation method. For the MouseGastrulationAtlas in vivo dataset, condition-wise integration was conducted on (per-condition) down- sampled subsets. Within the mixed dataset, labels have been propagated to the k=3 nearest neighbours. During integration with our previous in vitro EB dataset (sort-seq) a single per-cluster down-sampled dataset was used. For pseudo-time analysis, the Seurat object was exported to a cds object using the SeuratWrap- pers package. A trajectory graph was predicted using Monocle3 and the cells were ordered in pseudo-time. Individual cluster markers were found using the Seurat Find- Markers function, with parameters min.pct=0.05 and logfc.threshold=0.05.
Assembly: Mus musculus (GRCm38)
Supplementary files format and content: Tab-separated values files

source_name: ESC-derived FLK1+ mesodermal populations

growth_protocol: Murine Embryonic stem cells (ESCs) were differentiated towards mesodermal  during embryoid body (EB). For EB cultures: twenty-four hours prior to the initiation, ESCs were transferred into gelatinized plates containing using Iscove’s Modified Eagle Medium (IMDM) (Gibco). For the generation of embryoid body (EB) cultures, ESCs were trypsinized then plated at 10,000 cells/ml in non-adherent 10 cm2 petri dishes in EB medium (IMDM supplemented with 1% L-glutamine (Gibco), 10% FCS (Gibco), 0.6% transferrin (Roche, 10652), 50 µg/ml ascorbic acid (Sigma, A4544) and 0.03% monothioglycerol (Sigma, M6145). Bmp4 was added from day 0 of EB culture and bFGF, activin A and VEGF from day 2.5 (all Peprotech) all at 5 ng/ml. After five days in culture, EBs were harvested, and TrypLE Express Enzyme (1×) (Gibco, 12605036) was used to generate a single- cell suspension. The following antibodies were used for FACS sorting: anti-FLK1.

extract_protocol:
Cells were collected on day 5 of EB culture and 1x106 mesodermal cells were FACS sorted using FLK surface expression. Isolated cells were fixed using the 10x Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (PN-1000414) and stored at -80°C. The quantity of fixed cell suspension was assessed using an automated cell counter (LUNA-FX7, Logos).
Library preparation was conducted using the 10x Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples. Briefly, four fixed samples underwent probe hybridization, pooling, and loading onto the chip. Approximately 66,000 cells from the sample pools were loaded into the 10x Chromium X. Library preparation followed the manufacturer's guidelines (Guide CG000527, Rev E).


title: KO3

status: Public on Oct 11 2025

first: Li

middle: jing

last: yu

address: south Chongqing road 280

institute: Shanghai Jiaotong university school of medcine

data_processing:
Differential expression analysis was performed by Bioconductor package edgeR v3.18.1. Significantly changed genes were chosen according to two criteria: (1) significance level p < 0.05; (2) fold change >2, and were used for gene ontology enrichment analysis using the website of Gene Ontology Consortium (http://www.geneontology.org). Gene set enrichment analysis was performed using GSEA software (Broad Institute). Normalized heatmap was based on the standard score (Z score) and generated with oebiotech cloud platform (https://cloud.oebiotech.com/task/). The standard score of a raw score x is Z=x−μσ, where μ is the mean of the FPKM value of each sample and σ is the standard deviation of the FPKM value of each sample.
Assembly: GRCm39/mm39
Supplementary files format and content: Comma-Separated Values, RPKM for each sample

source_name: Colon

extract_protocol:
About 1× 104 ILC3s (Lin−CD45.2intThy1.2hi) were sorted from the large intestine of Trmt61a△Rorc and Trmt61afl/fl mice separately and were lysed in Trizol (Invitrogen). The total RNA was extracted. Biological duplicates were generated for each group.
The total RNA sample was digested by DNaseІ (NEB), and purified by oligo-dT beads (Dynabeads mRNA purification kit, Invitrogen), then poly(A) containing mRNA were fragmented into 130 bp with First-strand buffer. First-strand cDNA was generated by N6 primer, First Strand Master Mix and Super Script II reverse transcription (Invitrogen) (reaction condition: 25 °C for 10 min; 42 °C for 40 min; 70 °C for 15 min). Then add Second Strand Master Mix to synthesize the second-strand cDNA (16 °C for 1 h). Purified the cDNA with Ampure XP Beads (AGENCOURT), then combine with End Repair Mix, incubate at 20 °C for 30 min. Purified and add A-Tailing Mix, incubate at 37 °C for 30 min. Then combine the Adenylate 3′ ends DNA, Adapter and Ligation Mix, incubate the ligate reaction at 20 °C for 20 min. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix were performed to enrich the cDNA fragments. Then the PCR products were purified with Ampure XP Beads (AGENCOURT). The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3–cBot–HS, Illumina). The amplified flowcell will be sequenced pair end on the HiSeq 2000 System (TruSeq SBS KIT-HS V3, Illumina), read length 50.

value: Colon

value: Primary cell

value: KO


title: KO2


title: KO1


title: P0 tendon biorep 1, bulk RNAseq


title: Pool1_Ctrl_Smad1KO_Etv2_KO

description:
Library name: Pool1
scRNA-seq

value: ESC-derived FLK1+ mesodermal populations

value: wild type, Smad1KO, Etv2KO


title: WT3


title: WT1


title: Lung tissue with AAH of patient 25 [snRNA-seq]

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Library name: P25_AAH

data_processing:
snRNA-seq experiment: Raw data were pre-processed (demultiplex cellular barcodes, read alignment and generation of gene count matrix) using Cell Ranger Single Cell Software Suite provided by 10x Genomics. For read alignment of human data, human reference GRCh38 (hg38) was used. Detailed QC metrics were generated and evaluated, and cells were carefully and rigorously filtered to obtain high-quality data for downstream analyses. In brief, for basic quality filtering, cells with low-complexity libraries (in which detected transcripts were aligned to <200 genes such as cell debris, empty drops and low-quality cells) were filtered out and excluded from subsequent analyses, and genes detected in less than 3 cells were also excluded. In addition, like with scRNA-seq analysis, nuclei with less than 500 detected genes or with less than 1000 reads count or with a mitochondrial gene fraction that is ≥20% were filtered out using Seurat (v5.1.0). Doublets were identified based on library complexity. First, a python-based software Scrublet was applied to identify the doublets by each sample. Second, based on cluster distribution and marker gene expression, doublets forming distinct clusters with hybrid expression features were also removed. Expression levels and proportions of canonical lineage-related marker genes in each identified cluster were carefully reviewed. Clusters co-expressing discrepant lineage markers were identified and removed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include barcodes, features/genes, and raw counts for each sample

source_name: Lung

extract_protocol:
snRNA experiment: snRNA-seq was done on the same samples analyzed by ST, using FFPE scrolls consecutive to ST-analyzed sections. Scrolls were processed for single nucleus extraction following instructions demonstrated in 10x Genomics’ protocol for sample preparation from FFPE tissue sections and for Chromium Fixed RNA profiling (CG000632). Specifically, scroll digestion was achieved using gentleMACS Octo Dissociator with heaters (Miltenyi Biotec, 130-096-427), operating under the program settings recommended by the manufacturer for optimal tissue dissociation. Throughout the process of digestion and washing of nuclei, efficiency of digestion and enumeration of nuclei was evaluated by staining with ViaStain PI Staining Solution (Revvity Health Sciences Inc, CS101095ML) and assessing nuclei samples on a Countess II FL Automated Cell Counter (Thermofisher Scientific, AMAQAF1000). Cell counts following each of the tissue homogenization, probe hybridization, and pooling steps were an average of 3 per sample. For sample multiplexing, sample barcoding (BC) and pooling was done using Chromium Fixed RNA Human transcriptome kits (10x Genomics, 4 rxns × 4 BC 1000475, or 4 rxns × 16 BC 100476). To capture more cells from precursor and invasive samples with a lower undetected multiplet rate, cells from each of AAH, AIS, MIA and LUAD samples were sub-pooled over two probe barcodes each, to target up to 20,000 cells per sample. Cells from normal lung tissue samples were assigned one barcode, to target up to 10,000 cells. Pooled samples were processed Chromium X instrument (10x Genomics, 1000331) and libraries were generated following manufacturer’s recommendations outlined in Chromium Fixed RNA Profiling Reagent kits (10x Genomics, CG000527). Libraries were sequenced on NovaSeq 6000 or NovaSeq X platforms (Illumina) to achieve a depth of at least 50,000 mean read pairs per cell.
cDNA

value: Lung

value: Formalin-fixed paraffin embedded human lung tissue

tag: age

tag: Sex

value: Male

tag: ethnicity

value: White/Caucasian

tag: smoking

value: Yes


title: Lung tissue with LUAD of patient 25 [snRNA-seq]

description: Library name: P25_LUAD


title: WT2

value: WT


title: Lung tissue with LUAD of patient 24 [snRNA-seq]

description: Library name: P24_LUAD


title: Normal lung tissue of patient 25 [snRNA-seq]

description: Library name: P25_Normal


title: Lung tissue with AIS of patient 23 [snRNA-seq]

description: Library name: P23_AIS

value: East Asian

value: No


title: Lung tissue with second AIS of patient 23 [snRNA-seq]

description: Library name: P23_AIS-1


title: Lung tissue with LUAD of patient 23 [snRNA-seq]

description: Library name: P23_LUAD


title: Control, Input, rep1

description:
Library name: Control_Input_1
Column name in Counts.csv: Control_Input_1

value: HEK 293T cells

value: Flag overexpression


title: Normal lung tissue of patient 24 [snRNA-seq]

description: Library name: P24_Normal


title: Lung tissue with AAH of patient 24 [snRNA-seq]

description: Library name: P24_AAH


title: Lung tissue with AAH of patient 22 [snRNA-seq]

description: Library name: P22_AAH

value: Female


title: Normal lung tissue of patient 23 [snRNA-seq]

description: Library name: P23_Normal


title: P0 tendon biorep 3, bulk RNAseq

value: tendon


title: Lung tissue with LUAD of patient 22 [snRNA-seq]

description: Library name: P22_LUAD


title: Lung tissue with AIS of patient 21 [snRNA-seq]

description: Library name: P21_AIS


title: Normal lung tissue of patient 21 [snRNA-seq]

description: Library name: P21_Normal


title: Normal lung tissue of patient 22 [snRNA-seq]

description: Library name: P22_Normal


title: Lung tissue with AAH of patient 20 [snRNA-seq]

description: Library name: P20_AAH


title: Lung tissue with LUAD of patient 20 [snRNA-seq]

description: Library name: P20_LUAD


title: Lung tissue with AIS of patient 22 [snRNA-seq]

description: Library name: P22_AIS


title: Lung tissue with AIS of patient 19 [snRNA-seq]

description: Library name: P19_AIS


title: Normal lung tissue of patient 20 [snRNA-seq]

description: Library name: P20_Normal


title: Normal lung tissue of patient 19 [snRNA-seq]

description: Library name: P19_Normal


title: Lung tissue with LUAD of patient 18 [snRNA-seq]

description: Library name: P18_LUAD


title: Lung tissue with MIA of patient 18 [snRNA-seq]

description: Library name: P18_MIA


title: Normal lung tissue of patient 18 [snRNA-seq]

description: Library name: P18_Normal


title: Lung tissue with LUAD of patient 17 [snRNA-seq]

description: Library name: P17_LUAD


title: Lung tissue with AIS of patient 17 [snRNA-seq]

description: Library name: P17_AIS


title: Lung tissue with LUAD lesion of patient 16 [snRNA-seq]

description: Library name: P16_LUAD


title: Normal lung tissue of patient 17 [snRNA-seq]

description: Library name: P17_Normal


title: Lung tissue with AIS lesion of patient 16 [snRNA-seq]

description: Library name: P16_AIS


title: Lung tissue with LUAD of patient 15 [snRNA-seq]

description: Library name: P15_LUAD


title: Normal lung tissue of patient 16 [snRNA-seq]

description: Library name: P16_Normal


title: Lung tissue with MIA of patient 15 [snRNA-seq]

description: Library name: P15_MIA


title: Lung tissue with LUAD of patient 14 [snRNA-seq]

description: Library name: P14_LUAD


title: Lung tissue with LUAD of patient 12 [snRNA-seq]

description: Library name: P12_LUAD


title: Lung tissue with LUAD of patient 21 [snRNA-seq]

description: Library name: P21_LUAD


title: Normal lung tissue of patient 14 [snRNA-seq]

description: Library name: P14_Normal


title: Lung tissue with LUAD of patient 13 [snRNA-seq]

description: Library name: P13_LUAD


title: Normal lung tissue of patient 15 [snRNA-seq]

description: Library name: P15_Normal


title: Lung tissue with MIA of patient 13 [snRNA-seq]

description: Library name: P13_MIA


title: Lung tissue with second AIS of patient 21 [snRNA-seq]

description: Library name: P21_AIS-1


title: Lung tissue with AIS of patient 14 [snRNA-seq]

description: Library name: P14_AIS


title: Lung tissue with AIS of patient 12 [snRNA-seq]

description: Library name: P12_AIS


title: Normal lung tissue of patient 12 [snRNA-seq]

description: Library name: P12_Normal


title: P0 tendon biorep 2, bulk RNAseq


title: Lung tissue with AAH of patient 11 [snRNA-seq]

description: Library name: P11_AAH


title: Lung tissue with LUAD of patient 10 [snRNA-seq]

description: Library name: P10_LUAD


title: Normal lung tissue of patient 13 [snRNA-seq]

description: Library name: P13_Normal


title: Lung tissue with LUAD of patient 11 [snRNA-seq]

description: Library name: P11_LUAD


title: Lung tissue with LUAD of patient 19 [snRNA-seq]

description: Library name: P19_LUAD


title: Normal lung tissue of patient 10 [snRNA-seq]

description: Library name: P10_Normal


title: Lung tissue with LUAD of patient 9 [snRNA-seq]

description: Library name: P9_LUAD


title: Lung tissue with AIS of patient 9 [snRNA-seq]

description: Library name: P9_AIS


title: Normal lung tissue of patient 9 [snRNA-seq]

description: Library name: P9_Normal


title: Lung tissue with LUAD of patient 8 [snRNA-seq]

description: Library name: P8_LUAD


title: Lung tissue with AIS of patient 8 [snRNA-seq]

description: Library name: P8_AIS


title: Normal lung tissue of patient 8 [snRNA-seq]

description: Library name: P8_Normal


title: Lung tissue with LUAD of patient 7 [snRNA-seq]

description: Library name: P7_LUAD


title: Normal lung tissue of patient 7 [snRNA-seq]

description: Library name: P7_Normal


title: Normal lung tissue of patient 6 [snRNA-seq]

description: Library name: P6_Normal


title: Lung tissue with LUAD of patient 4 [snRNA-seq]

description: Library name: P4_LUAD


title: Lung tissue with AIS of patient 5 [snRNA-seq]

description: Library name: P5_AIS


title: Lung tissue with LUAD of patient 5 [snRNA-seq]

description: Library name: P5_LUAD


title: Lung tissue with AAH of patient 4 [snRNA-seq]

description: Library name: P4_AAH


title: Lung tissue with second AAH of patient 4 [snRNA-seq]

description: Library name: P4_AAH-1


title: Lung tissue with AAH of patient 6 [snRNA-seq]

description: Library name: P6_AAH


title: Second normal lung tissue of patient 4 [snRNA-seq]

description: Library name: P4_Normal-1


title: Lung tissue with MIA of patient 10 [snRNA-seq]

description: Library name: P10_MIA


title: Normal lung tissue of patient 4 [snRNA-seq]

description: Library name: P4_Normal


title: Lung tissue with AIS of patient 3 [snRNA-seq]

description: Library name: P3_AIS


title: Lung tissue with LUAD of patient 3 [snRNA-seq]

description: Library name: P3_LUAD


title: Normal lung tissue of patient 5 [snRNA-seq]

description: Library name: P5_Normal


title: Normal lung tissue of patient 11 [snRNA-seq]

description: Library name: P11_Normal


title: Lung tissue with LUAD of patient 25 [ST]

description: Library name: P25_LUAD

data_processing:
Visium ST experiment: Demultiplexed reads were pre-processed using Space Ranger (v2.0.0, 10x Genomics) and aligned to the GRCh38 reference genome. ST profiling of human FFPE tissues from P1-P25 was performed using the CytAssist-enabled Visium platform with 11 x 11 mm fiducial frames (each frame comprises roughly 14,000 spots) from 10x Genomics according to the manufacturer’s recommendations. ST RNA-seq libraries were generated according to the manufacturer’s instructions with an average of ~11,000 uniquely barcoded spots/tissue. Libraries were sequenced on NovaSeq 6000 or NovaSeq X platforms (Illumina) to achieve an average depth of ~65,000 mean reads per spot and ~3,400 median genes per spot. The resulting unique molecular identifier (UMI) count matrices were analyzed using Seurat (v5.1.0) in the R platform. Spot-level histopathological annotation and visualization were generated using loupe browser (v.7.1). An experienced pathologist then checked and annotated each spot by using the Loupe Browser with the corresponding high-resolution images. Spots annotated as “Space”, "Foreign body", "Tissue artifacts" were filtered out during QC processing. 18Detailed QC metrics were generated and evaluated, and spots were carefully filtered to obtain high-quality data for downstream analyses. Briefly, for basic quality filtering, spots with nUMI < 500 and nFeature < 200 and relative high percentage of mitochondrial genes >15% were filtered out.
Assembly: GRCh38
Supplementary files format and content: images, tab-delimited text files include barcodes, features/genes, coordinates, and raw counts for each sample
Library strategy: Spatial transcriptomics

extract_protocol:
Visium ST experiment: 5 µm FFPE tissue sections were placed on regular plus stained slides and were stained with H&E using Leica ST5010 Autostainer XL using manufacturer-recommended protocols. H&E-stained slides were then cover-slipped and scanned at 40× magnification with previously standardized high-resolution settings on an Aperio ScanScope Turbo slide scanner (Leica Microsystems). Before proceeding with CytAssist assay, each high-resolution image was carefully evaluated by a pathologist to determine the presence of previously selected regions, including precursor and invasive lesions, as well as the quality of the tissue: sectioning (e.g., correct tissue area placement, absence of tissue folds or contamination), staining (intensity and balance), and scanning (resolution and sharpness).
cDNA


title: Lung tissue with AAH of patient 25 [ST]

description: Library name: P25_AAH


title: Lung tissue with LUAD of patient 24 [ST]

description: Library name: P24_LUAD


title: Lung tissue with AAH of patient 24 [ST]

description: Library name: P24_AAH


title: Lung tissue with AAH of patient 9 [snRNA-seq]

description: Library name: P9_AAH


title: Lung tissue with LUAD of patient 23 [ST]

description: Library name: P23_LUAD


title: Lung tissue with second AIS of patient 23 [ST]

description: Library name: P23_AIS-1


title: Lung tissue with AIS of patient 23 [ST]

description: Library name: P23_AIS


title: Lung tissue with AIS of patient 22 [ST]

description: Library name: P22_AIS


title: Lung tissue with LUAD of patient 22 [ST]

description: Library name: P22_LUAD


title: Lung tissue with AAH of patient 22 [ST]

description: Library name: P22_AAH


title: Lung tissue with second LUAD of patient 7 [snRNA-seq]

description: Library name: P7_LUAD-1


title: Lung tissue with LUAD of patient 6 [snRNA-seq]

description: Library name: P6_LUAD


title: Lung tissue with LUAD of patient 21 [ST]

description: Library name: P21_LUAD


title: Lung tissue with second AIS of patient 21 [ST]

description: Library name: P21_AIS-1


title: Lung tissue with LUAD of patient 20 [ST]

description: Library name: P20_LUAD


title: Lung tissue with LUAD of patient 19 [ST]

description: Library name: P19_LUAD


title: Lung tissue with AIS of patient 21 [ST]

description: Library name: P21_AIS


title: Lung tissue with LUAD of patient 17 [ST]

description: Library name: P17_LUAD


title: Lung tissue with AAH of patient 20 [ST]

description: Library name: P20_AAH


title: Lung tissue with AIS of patient 17 [ST]

description: Library name: P17_AIS


title: Lung tissue with AIS of patient 16 [ST]

description: Library name: P16_AIS


title: Lung tissue with LUAD of patient 16 [ST]

description: Library name: P16_LUAD


title: Normal lung tissue of patient 3 [snRNA-seq]

description: Library name: P3_Normal


title: Lung tissue with AIS of patient 19 [ST]

description: Library name: P19_AIS


title: Lung tissue with LUAD of patient 18 [ST]

description: Library name: P18_LUAD


title: Lung tissue with MIA of patient 18 [ST]

description: Library name: P18_MIA


title: Lung tissue with LUAD of patient 15 [ST]

description: Library name: P15_LUAD


title: Lung tissue with LUAD of patient 13 [ST]

description: Library name: P13_LUAD


title: Lung tissue with MIA of patient 13 [ST]

description: Library name: P13_MIA


title: Lung tissue with MIA of patient 15 [ST]

description: Library name: P15_MIA


title: Lung tissue with LUAD of patient 14 [ST]

description: Library name: P14_LUAD


title: Lung tissue with LUAD of patient 12 [ST]

description: Library name: P12_LUAD


title: Lung tissue with AIS of patient 14 [ST]

description: Library name: P14_AIS


title: Lung tissue with AIS of patient 12 [ST]

description: Library name: P12_AIS


title: Arabidopsis Col-0 leaf, CMV-2

city: Shenzhen

first: yujing

last: lin

address: No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen City, Guangdong Province

institute: Southern University of Science and Technology

description:
Library name: CMV-2
Nanopore PromitION 24

data_processing:
The raw sequencing data were aligned to the reference transcriptome using Minimap2. Subsequently, N6-methyladenosine (m6A) modifications were identified at specific sites through the pileup mode of the Modkit software.
Assembly: virus_rna.fa
Supplementary files format and content: txt files that represent significant m6A modification

organism: Cucumber mosaic virus

source_name: Leaf

growth_protocol: Wild type Arabidopsis Col-0 plants were grown in a condition-controlled greenhouse (8 h:16 h, 22 ℃:22 ℃, light:dark cycle).

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent, and Poly (A) RNA is purified from 50 μg total RNA using Dynabeads Oligo (dT) using two rounds of purification.
The poly(A) RNA was reverse transcribed with adaptors. The reverse transcription product was purified by magnetic beads and connected to the purified product using the sequencing adapter in the SQK-RNA002 kit. The constructed cDNA library was accurately quantified using Qubit. After the library was constructed, a certain amount of cDNA library was added to the Flow Cell and transferred to the Oxford Nanopore PromethION sequencer for real-time single-molecule sequencing.

treatment_protocol: Arabidopsis plants at 3-week-old were inoculated by wild-type cucumber mosaic virus (CMV) and the mutated virus deficient in 2b protein (CMVΔ2b) for 14 days.

tag: host

value: Arabidopsis thaliana

value: Leaf

value: Arabidopsis Col-0 plants were inoculated by wild-type cucumber mosaic virus (CMV)


title: Lung tissue with LUAD of patient 11 [ST]

description: Library name: P11_LUAD


title: Arabidopsis Col-0 leaf, CMV-1

description:
Library name: CMV-1
Nanopore PromitION 24


title: Lung tissue with MIA of patient 10 [ST]

description: Library name: P10_MIA


title: Lung tissue with LUAD of patient 9 [ST]

description: Library name: P9_LUAD


title: Lung tissue with AIS of patient 9 [ST]

description: Library name: P9_AIS


title: shNr4a3 replicate 2, P3-CFs

city: wuhan

first: yu

middle: zhang

last: yi

state: hubei

address: donghu street

department: wuhan

institute: wuhan university

description: Library name: shNr4a3_2

data_processing:
Raw sequencing data was initially filtered by Trimmomatic (version 0.36), with the discarding of low-quality reads and the trimming of reads contaminated with adaptor sequences.
Clean reads were mapped to the reference genome of mouse (mm10) using STRA software (version 2.5.3a) with default parameters.
The counting of reads mapped to the exon regions of each gene was carried out by featureCounts (Subread-1.5.1; Bioconductor).
Resulting BAM files were sorted and indexed using SAMtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: heart

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, cat. NO15596026). 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina) with PE150 model.

value: heart

value: Primary cell

value: cardiac fibroblast

tag: batch

value: neonatal


title: Lung tissue with LUAD of patient 8 [ST]

description: Library name: P8_LUAD

value: Lung

value: Formalin-fixed paraffin embedded human lung tissue


title: Lung tissue with AIS of patient 8 [ST]

description: Library name: P8_AIS


title: Lung tissue with AAH of patient 9 [ST]

description: Library name: P9_AAH


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 3 months post-NNK, ST, replicate 2

description: Library name: B_Il1b_3m_5252

data_processing:
Raw FASTQ data (demultiplexed clean reads) were aligned against the GRCm38 (mm10) mouse reference genomes by Spaceranger (version 2.0.0 for mouse ST data) with the Visium transcriptome probe set (mouse data probeset v1.0) and default parameter settings. The resulting unique molecular identifier (UMI) count matrices were analyzed using Seurat (v5.1.0) in the R platform. An experienced pathologist (A.G.S.) then checked and annotated each spot by using the Loupe Browser with the corresponding high-resolution images. A spot’s annotation was based on the cell type or structure that covered at least 50% of the spot. Spots annotated as “Space”, "Foreign body", "Tissue artifacts" were filtered out during QC processing. Detailed QC metrics were generated and evaluated, and spots were carefully filtered to obtain high-quality data for downstream analyses. Briefly, for basic quality filtering, spots with nUMI < 500 and nFeature < 200 and relative high percentage of mitochondrial genes >15% were filtered out. Data normalization was then performed using Seurat on the filtered gene-cell matrix.
Assembly: GRCm38 (mm10)
Supplementary files format and content: images, tab-delimited text files include barcodes, features/genes, coordinates, and raw counts for each sample
Library strategy: Spatial transcriptomics

extract_protocol:
Visium ST experiment n = 13 samples: For Gprc5a−/− mouse lung tissues analyzed by ST, we studied mice at EOE and at 7 months post exposure to either saline or NNK (2 mice per treatment and timepoint with each mouse lung split across two 6.5 x 6.5 mm regions of interest/capture areas; n = 8 mice; n = 16 libraries total). ST data was generated from 2 regions per mouse (i.e. 4 regions per treatment and timepoint) using 10x Genomics’ Visium platform (6.5 × 6.5 mm ROI and capture areas) and following manufacturer’s recommendations outlined in Visium Spatial Gene Expression Reagent Kits for FFPE User Guide (10x Genomics, CF000407). Visium ST experiment n = 6 samples: For ST profiling of lungs of NNK-exposed Gprc5a−/− mice which received anti- IL-1𝛽 or control IgG and analyzed at 3 and at 7 months post end of NNK, we employed the Visium CytAssist platform from 10x Genomics. One 11 × 11 mm region of interest was selected for each mouse lung and ST was performed on the selected archived and de-cover-slipped H&E slides by carefully positioning the 10x Genomics CytAssist gaskets to select and process these regions of interest. ST profiling was done following manufacturer recommendations outlined in Visium CytAssist Spatial Gene Expression Reagent Kits User Guide (10x Genomics, CG000495).
cDNA

value: Formalin-fixed paraffin embedded mouse lung tissue

tag: exposure

value: NNK

tag: treatment starting_point

value: End of NNK exposure

tag: treatment endpoint

value: 3 months post-NNK

value: 7 months


title: shNT replicate 1,P3-CFs

description: Library name: shNT_1

tag: tissue

value: WT

tag: treatment

value: shNT


title: shNT replicate 2,P3-CFs

description: Library name: shNT_2

tag: cell line


title: Lung tissue with second LUAD of patient 7 [ST]

description: Library name: P7_LUAD-1

value: Female

value: East Asian

value: No


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 7 months post-NNK, ST, replicate 2

description: Library name: B_Il1b_7mo_4963

value: 3 months post end of NNK exposure

value: 7 months post-NNK

value: 11 months


title: Lung tissue with LUAD of patient 6 [ST]

description: Library name: P6_LUAD

value: Male

value: Yes


title: Lung tissue with LUAD of patient 5 [ST]

description: Library name: P5_LUAD

value: Lung


title: Lung tissue with LUAD of patient 7 [ST]

description: Library name: P7_LUAD

value: Formalin-fixed paraffin embedded human lung tissue


title: Lungs of Gprc5a-/- mice exposed to Control IgG and analyzed at 7 months post-NNK, ST

description: Library name: B_IgG_7m_4955

value: Formalin-fixed paraffin embedded mouse lung tissue

value: Control IgG


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 7 months post-NNK, ST, replicate 1

description: Library name: A_Il1b_7mo_4912

value: NNK


title: Lung tissue with AAH of patient 11 [ST]

description: Library name: P11_AAH


title: shNr4a3 replicate 1,P3-CFs

description: Library name: shNr4a3_1

value: heart

value: Primary cell

value: cardiac fibroblast

value: neonatal


title: Lung tissue with LUAD of patient 10 [ST]

description: Library name: P10_LUAD

value: Female


title: Lungs of Gprc5a-/- mice exposed to Control IgG and analyzed at 3 months post-NNK, ST

description: Library name: A_IgG_3m_5241

value: End of NNK exposure

value: 3 months post-NNK

value: 7 months


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 3 months post-NNK, ST, replicate 1

description: Library name: A_Il1b_3m_5318


title: Tumor-bearing Gprc5a-/- lung tissue 16 [ST-D3]

description: Library name: D3

value: Saline


title: Lung tissue with LUAD of patient 4 [ST]

description: Library name: P4_LUAD

value: East Asian

value: No


title: Lung tissue with AIS of patient 5 [ST]

description: Library name: P5_AIS

value: Male

value: Yes


title: Lung tissue with AAH of patient 4 [ST]

description: Library name: P4_AAH

value: Lung

value: Formalin-fixed paraffin embedded human lung tissue


title: Tumor-bearing Gprc5a-/- lung tissue 14 [ST-B3]

description: Library name: B3

value: Formalin-fixed paraffin embedded mouse lung tissue

value: 11 months


title: Tumor-bearing Gprc5a-/- lung tissue 13 [ST-A3]

description: Library name: A3


title: Tumor-bearing Gprc5a-/- lung tissue 15 [ST-C3]

description: Library name: C3


title: Lung tissue with second AAH of patient 4 [ST]

description: Library name: P4_AAH-1


title: Normal lung tissue of patient 4 [ST]

description: Library name: P4_Normal


title: Tumor-bearing Gprc5a-/- lung tissue 12 [ST-D2]

description: Library name: D2

value: NNK

value: 4 months


title: Tumor-bearing Gprc5a-/- lung tissue 11 [ST-C2]

description: Library name: C2


title: Lung tissue with LUAD of patient 3 [ST]

description: Library name: P3_LUAD


title: Lung tissue with AAH of patient 6 [ST]

description: Library name: P6_AAH


title: Lung tissue with AIS of patient 3 [ST]

description: Library name: P3_AIS


title: Tumor-bearing Gprc5a-/- lung tissue 10 [ST-B2]

description: Library name: B2


title: Lung tissue with AAH of patient 2 [ST]

description: Library name: P2_AAH


title: Tumor-bearing Gprc5a-/- lung tissue 8 [ST-D1]

description: Library name: D1


title: Tumor-bearing Gprc5a-/- lung tissue 9 [ST-A2]

description: Library name: A2


title: Lung tissue with LUAD of patient 2 [ST]

description: Library name: P2_LUAD


title: Tumor-bearing Gprc5a-/- lung tissue 7 [ST-C1]

description: Library name: C1


title: Lung tissue with LUAD of patient 1 [ST]

description: Library name: P1_LUAD


title: Lung tissue with AAH of patient 25 [WES]

description: Library name: P25_AAH

data_processing:
WES experiment: Reads were mapped to the human reference genome GRCh38 (hg38) using BWA-mem. Duplicates were marked for filtering and base quality scores were recalibrated using GATK61. Somatic single nucleotide variants and indels were called using MuTect2 with default settings followed by post-calling filtering, and they were subsequently annotated using GATK Funcotator and ANNOVAR. The following criteria were applied to filter variants: (i) only variants marked as "PASS" by MuTect2 were considered; (ii) a minimum coverage of 10× for normal samples and 20× for non-normal samples (AAH, AIS, MIA and LUAD) was required; (iii) variants were required to have at least 4 alternate reads or a variant allele frequency (VAF) of ≥5% in the non-normal regions, while having fewer than 3 alternate reads and a VAF of <5% in the corresponding normal regions, and a VAF ratio (normal/non-normal) of <0.2; (iv) only variants with a median distance of at least 5 bases from the read ends were considered; (v) common variants reported by gnomAD (the Genome Aggregation Database, https://gnomad.broadinstitute.org/), Phase-3 1000 Genome Project (http://phase3browser.1000genomes.org/Homo_sapiens/Info/Index) or the NHLBI GO Exome Sequencing Project (ESP6500) (http://evs.gs.washington.edu/EVS/) with minor allele frequencies greater than 0.5% were removed. Somatic mutations located within introns, untranslated regions (UTRs), UTR-flanking regions, or those classified as silent mutations were also excluded from subsequent analyses. The somatic mutation burden for each sample was calculated based on 3 major mutation types (missense, truncating, and in-frame indels), as previously described.
Assembly: GRCh38
Supplementary files format and content: text files of mutation calling reults

extract_protocol:
WES experiment: Total DNA was isolated from 25 µm FFPE scrolls of the same human lung tissues used for multimodal analysis. Deparaffinization was done using Deparaffinization Solution (Qiagen, 939018) followed by DNA isolation using Qiagen AllPrep mini kit (Qiagen, 80204) and according to the manufacturer’s recommendations. DNA yield was assessed using Qubit™ 1X dsDNA HS Assay Kit (Thermo Fisher Scientific, Q33231) on a Qubit 4 Fluorometer (Thermo Fisher Scientific). DNA quality was assessed using Agilent High Sensitivity DNA Kit (Agilent, 5067-4626) on an Agilent 2100 Bioanalyzer System. TWIST-WES was performed on a NovaSeq 6000 platform (Illumina) at a depth of 100× for tumor samples and 300× for normal, pre-invasive, or mildly invasive samples and using matched normal lung tissues as germline control.
PCR

value: White/Caucasian


title: Tumor-bearing Gprc5a-/- lung tissue 5 [ST-A1]

description: Library name: A1


title: Lung tissue with AAH of patient 1 [ST]

description: Library name: P1_AAH


title: Lung tissue with AAH of patient 24 [WES]

description: Library name: P24_AAH


title: Tumor-bearing Gprc5a-/- lung tissue 6 [ST-B1]

description: Library name: B1


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 7 months post-NNK, replicate 4

description: Library name: aIL1B_38

data_processing:
Raw scRNA-seq data were pre-processed (demultiplex cellular barcodes, read alignment, and generation of gene count matrix) using Cell Ranger Single Cell Software Suite (version 3.0.1) provided by 10X Genomics. For read alignment of mouse scRNA-seq data, the mouse reference GRCm38 (mm10) genomes were used, respectively. Detailed quality control (QC) metrics were generated and evaluated, and cells were carefully and rigorously filtered to obtain high-quality data for downstream analyses. Briefly, for basic quality filtering, cells with low complexity libraries (in which detected transcripts are aligned to < 200 genes such as cell debris, empty drops, and low-quality cells) were filtered out and excluded from subsequent analyses. Likely dying or apoptotic cells where > 15% of transcripts derived from the mitochondrial genome were also excluded. Doublets or multiplets were identified and carefully removed through a multi-step approach. Briefly, doublets or multiplets were identified based on library complexity, whereby cells with high-complexity libraries in which detected transcripts are aligned to > 6,500 genes were removed, and also, based on cluster distribution and marker gene expression, whereby doublets or multiplets forming distinct clusters with hybrid expression features and/or exhibiting an aberrantly high gene count were also removed. Expression levels and proportions of canonical lineage-related marker genes in each identified cluster were carefully reviewed. Clusters co-expressing discrepant lineage markers were identified and removed. Doublets or multiplets were also identified using the doublet detection algorithm Scrublet. Data normalization was then performed using Seurat on the filtered gene-cell matrix.
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files include barcodes, features/genes, and raw counts for each sample

extract_protocol:
scRNA-seq experiment n = 31 mice: Lungs were obtained from Gprc5a−/− exposed to NNK and one of four antibody treatments. At each defined end point, lungs were processed into single cells by enzymatic digestion in a solution composed of collagenase type I (CLS-1 LS004197, Worthington), elastase (ESL LS002294, Worthington) and DNase I (D LS002007, Worthington). Samples were transferred to 5 ml LoBind Eppendorf tubes and incubated in a 37 °C oven for 20 min with gentle rotation. Samples were then filtered through 70 μm strainers (Miltenyi Biotech, 130-098-462) and washed with ice-cold HBSS. Filtrates were then centrifuged and resuspended in ice-cold ACK lysis buffer (A1049201, Thermo Fisher Scientific) for red blood cell lysis. Following red blood cell lysis, samples were centrifuged and resuspended in ice-cold FBS, filtered (using 40 μm FlowMi tip filters; H13680-0040, Millipore) and an aliquot was taken to count cells and check for viability by Trypan blue (T8154, Sigma Aldrich) exclusion analysis. Cell suspensions were then sorted to enrich for epithelial cells. Namely, mouse lung single cells were stained with Sytox Green and the following cocktail of antibodies: CD45-PE/Cy7 (BioLegend, 103114), ICAM2-A647 (Life Technologies, A15452), EPCAM-BV421 (BioLegend, 118225) and ECAD-A488 (eBioscience, 53-3249-80). To enrich epithelial cells, live (Sytox-) epithelial singlets (CD45-; ICAM2; EpCAM+ &/or ECAD+) were sorted and mixed at a 1:1 ratio with live cells from each sample. Mixtures were then loaded on a Chromium Controller (10x Genomics, 110211) and 5′ single-cell gene expression libraries were prepared using the Chromium Next GEM Single Cell 5′ Gel Bead kit v.1.1 (10x Genomics, 1000169).
cDNA

value: 3 months post end of NNK exposure

value: 7 months post-NNK


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and anti-PD-1 and analyzed at 7 months post-NNK, replicate 4

description: Library name: aIL1B_40

value: anti-IL-1𝛽 and anti-PD-1


title: Lung tissue with LUAD of patient 25 [WES]

description: Library name: P25_LUAD


title: Lung tissue with LUAD of patient 24 [WES]

description: Library name: P24_LUAD


title: Lung tissue with AIS of patient 23 [WES]

description: Library name: P23_AIS


title: Tumor-bearing Gprc5a-/- lung tissue 4 [ST-D4]

description: Library name: D4


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and anti-PD-1 and analyzed at 7 months post-NNK, replicate 3

description: Library name: aIL1B_36


title: Lung tissue with second AIS of patient 23 [WES]

description: Library name: P23_AIS-1


title: Lungs of Gprc5a-/- mice exposed to anti-PD-1 and analyzed at 7 months post-NNK, replicate 4

description: Library name: aIL1B_39


title: Lung tissue with LUAD of patient 23 [WES]

description: Library name: P23_LUAD


title: Lung tissue with LUAD of patient 22 [WES]

description: Library name: P22_LUAD

value: Female


title: Lung tissue with AIS of patient 22 [WES]

description: Library name: P22_AIS


title: Lung tissue with AAH of patient 22 [WES]

description: Library name: P22_AAH


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 7 months post-NNK, replicate 3

description: Library name: aIL1B_34


title: Lungs of Gprc5a-/- mice exposed to Control IgG and analyzed at 7 months post-NNK, replicate 3

description: Library name: aIL1B_33

value: Control IgG


title: Lung tissue with second AIS of patient 21 [WES]

description: Library name: P21_AIS-1


title: Lungs of Gprc5a-/- mice exposed to anti-PD-1 and analyzed at 7 months post-NNK, replicate 2

description: Library name: aIL1B_31


title: Lungs of Gprc5a-/- mice exposed to Control IgG and analyzed at 7 months post-NNK, replicate 2

description: Library name: aIL1B_29


title: Lung tissue with LUAD of patient 21 [WES]

description: Library name: P21_LUAD


title: Lung tissue with LUAD of patient 20 [WES]

description: Library name: P20_LUAD


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and anti-PD-1 and analyzed at 7 months post-NNK, replicate 2

description: Library name: aIL1B_32


title: Lung tissue with LUAD of patient 19 [WES]

description: Library name: P19_LUAD


title: Lungs of Gprc5a-/- mice exposed to anti-PD-1 and analyzed at 7 months post-NNK, replicate 1

description: Library name: aIL1B_27


title: Lung tissue with AAH of patient 20 [WES]

description: Library name: P20_AAH


title: Lung tissue with AIS of patient 21 [WES]

description: Library name: P21_AIS


title: Lung tissue with MIA of patient 18 [WES]

description: Library name: P18_MIA


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and anti-PD-1 and analyzed at 7 months post-NNK, replicate 1

description: Library name: aIL1B_28


title: Lungs of Gprc5a-/- mice exposed to Control IgG and analyzed at 7 months post-NNK, replicate 1

description: Library name: aIL1B_25


title: Lungs of Gprc5a-/- mice exposed to Control IgG and analyzed at 7 months post-NNK, replicate 4

description: Library name: aIL1B_37


title: Lung tissue with AIS of patient 19 [WES]

description: Library name: P19_AIS


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 7 months post-NNK, replicate 1

description: Library name: aIL1B_26


title: Lungs of Gprc5a-/- mice exposed to anti-PD-1 and analyzed at 3 months post-NNK, replicate 4

description: Library name: aIL1B_19

value: End of NNK exposure

value: 3 months post-NNK

value: 7 months


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and anti-PD-1 and analyzed at 3 months post-NNK, replicate 4

description: Library name: aIL1B_20


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 3 months post-NNK, replicate 4

description: Library name: aIL1B_18


title: Lung tissue with LUAD of patient 17 [WES]

description: Library name: P17_LUAD

value: Male

value: East Asian


title: Lungs of Gprc5a-/- mice exposed to anti-PD-1 and analyzed at 7 months post-NNK, replicate 3

description: Library name: aIL1B_35

value: Lung


title: Lung tissue with LUAD of patient 18 [WES]

description: Library name: P18_LUAD

value: Formalin-fixed paraffin embedded human lung tissue

value: No


title: Lungs of Gprc5a-/- mice exposed to Control IgG and analyzed at 3 months post-NNK, replicate 4

description: Library name: aIL1B_17

value: Formalin-fixed paraffin embedded mouse lung tissue


title: at the onset of AE [AE_73]

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

country: Japan

institute: Tsukuba university

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 20.0.0; Qiagen, Redwood City, CA).
Assembly: hg19

source_name: Whole blood cells

extract_protocol:
Silica-membrane-based RNA isolation and purification in a spin-column format were performed using the PAXgene Blood RNA kit (Qiagen). Extracted RNA was globin-cleared using the Ambion GLOBINclear kit (Thermo Fisher, Waltham, MA). Then, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) and converted to an Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole blood cells

tag: group

value: at the onset of AE


title: Lung tissue with LUAD of patient 16 [WES]

description: Library name: P16_LUAD

value: Yes


title: at the onset of AE [AE_69]


title: at the onset of AE [AE_51]


title: Lung tissue with AIS of patient 17 [WES]

description: Library name: P17_AIS


title: at the onset of AE [AE_48]


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 7 months post-NNK, replicate 2

description: Library name: aIL1B_30

value: NNK

value: 3 months post end of NNK exposure

value: 11 months


title: at the onset of AE [AE_34]


title: Lung tissue with AIS of patient 16 [WES]

description: Library name: P16_AIS

value: Female


title: Lungs of Gprc5a-/- mice exposed to anti-PD-1 and analyzed at 3 months post-NNK, replicate 3

description: Library name: aIL1B_15


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and anti-PD-1 and analyzed at 3 months post-NNK, replicate 3

description: Library name: aIL1B_16

value: anti-IL-1𝛽 and anti-PD-1


title: at the onset of AE [AE_45]


title: Lung tissue with MIA of patient 15 [WES]

description: Library name: P15_MIA


title: at the onset of AE [AE_14]


title: at the onset of AE [AE_26]


title: Lung tissue with LUAD of patient 15 [WES]

description: Library name: P15_LUAD


title: at the onset of AE [AE_7]


title: Lung tissue with LUAD of patient 14 [WES]

description: Library name: P14_LUAD


title: Nonresponder 3M [3M_87]

value: Nonresponder 3M


title: Nonresponder 3M [3M_85]


title: Responder 3M [3M_86]

value: Responder 3M


title: Lungs of Gprc5a-/- mice exposed to Control IgG and analyzed at 3 months post-NNK, replicate 3

description: Library name: aIL1B_13

value: Control IgG

value: End of NNK exposure

value: 3 months post-NNK

value: 7 months


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and anti-PD-1 and analyzed at 3 months post-NNK, replicate 2

description: Library name: aIL1B_12

value: Lung


title: Lung tissue with MIA of patient 13 [WES]

description: Library name: P13_MIA

value: Formalin-fixed paraffin embedded human lung tissue

value: Male

value: East Asian


title: Lung tissue with AIS of patient 14 [WES]

description: Library name: P14_AIS


title: Responder 3M [3M_83]

value: Whole blood cells


title: Lungs of Gprc5a-/- mice exposed to anti-PD-1 and analyzed at 3 months post-NNK, replicate 2

description: Library name: aIL1B_11

value: Formalin-fixed paraffin embedded mouse lung tissue


title: Nonresponder 3M [3M_82]


title: Lung tissue with LUAD of patient 13 [WES]

description: Library name: P13_LUAD

value: Yes


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 3 months post-NNK, replicate 2

description: Library name: aIL1B_10

value: NNK


title: Lungs of Gprc5a-/- mice exposed to Control IgG and analyzed at 3 months post-NNK, replicate 2

description: Library name: aIL1B_9


title: Nonresponder 3M [3M_81]


title: Nonresponder 3M [3M_80]


title: Responder 3M [3M_79]


title: Lung tissue with LUAD of patient 12 [WES]

description: Library name: P12_LUAD

value: No


title: Nonresponder 3M [3M_77]


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and analyzed at 3 months post-NNK, replicate 3

description: Library name: aIL1B_14


title: Lungs of Gprc5a-/- mice exposed to anti-IL-1𝛽 and anti-PD-1 and analyzed at 3 months post-NNK, replicate 1

description: Library name: aIL1B_8


title: Lung tissue with LUAD of patient 11 [WES]

description: Library name: P11_LUAD

value: Female


title: Responder 3M [3M_75]


title: Lung tissue with AAH of patient 11 [WES]

description: Library name: P11_AAH


title: Responder 3M [3M_74]


title: Nonresponder 3M [3M_72]


title: Responder 3M [3M_76]


title: Lungs of Gprc5a-/- mice exposed to Control IgG and analyzed at 3 months post-NNK, replicate 1

description: Library name: aIL1B_5


title: Nonresponder 3M [3M_84]


title: Responder 3M [3M_71]


title: Adult CFs, MGT+shNr4a3 rep 2, Day7

value: heart

value: Primary cell

value: cardiac fibroblast

value: WT

value: 3 months old


title: Nonresponder 3M [3M_70]

value: Nonresponder 3M


title: Lung tissue with MIA of patient 10 [WES]

description: Library name: P10_MIA


title: 3M in AE case [3M_69]

value: 3M in AE case


title: Adult CFs, MGT+shNr4a3 rep 1, Day7


title: Nonresponder 3M [3M_68]


title: Lung tissue with LUAD of patient 10 [WES]

description: Library name: P10_LUAD

value: Lung


title: Lung tissue with LUAD of patient 9 [WES]

description: Library name: P9_LUAD

value: Formalin-fixed paraffin embedded human lung tissue


title: Adult CFs, MGT+shNT rep 2, Day7

value: MGT+shNT


title: Adult CFs, MGT+shNT rep 1, Day7


title: Lung tissue with AIS of patient 12 [WES]

description: Library name: P12_AIS

value: East Asian


title: Responder 3M [3M_66]

value: Whole blood cells

value: Responder 3M


title: Responder 3M [3M_65]


title: Nonresponder 3M [3M_64]


title: Responder 3M [3M_78]


title: Nonresponder 3M [3M_67]


title: Lung tissue with AIS of patient 9 [WES]

description: Library name: P9_AIS


title: Lung tissue with AAH of patient 9 [WES]

description: Library name: P9_AAH


title: MGT Aged 2 replicate 1, MGT, Day3

value: 18 months old

value: MGT


title: Responder 3M [3M_61]


title: Lungs of Gprc5a-/- mice exposed to anti-PD-1 and analyzed at 3 months post-NNK, replicate 1

description: Library name: aIL1B_7

value: Formalin-fixed paraffin embedded mouse lung tissue

value: NNK

value: End of NNK exposure

value: 3 months post-NNK

value: 7 months


title: MGT Aged 1 replicate 1, MGT, Day3

value: heart

value: Primary cell

value: cardiac fibroblast

value: WT


title: Lung tissue with LUAD of patient 8 [WES]

description: Library name: P8_LUAD

value: Lung

value: Female

value: No


title: Nonresponder 3M [3M_60]

value: Nonresponder 3M


title: Responder 3M [3M_59]

value: Whole blood cells


title: Responder 3M [3M_63]

value: Responder 3M


title: Responder 3M [3M_58]


title: MGT Adult 2 replicate 1, MGT, Day3

value: 3 months old


title: Lung tissue with AIS of patient 8 [WES]

description: Library name: P8_AIS

value: Formalin-fixed paraffin embedded human lung tissue

value: East Asian


title: Lung tissue with second LUAD of patient 7 [WES]

description: Library name: P7_LUAD-1


title: Responder 3M [3M_57]


title: MGT Neo 2 replicate 1, MGT, Day3

value: MGT


title: Responder 3M [3M_53]


title: MGT Neo 1 replicate 1, MGT, Day3


title: Responder 3M [3M_52]


title: Responder 3M [3M_62]


title: Responder 3M [3M_50]


title: Responder 3M [3M_49]


title: Nonresponder 3M [3M_47]


title: Lung tissue with AAH of patient 6 [WES]

description: Library name: P6_AAH

value: Male

value: Yes


title: Responder 3M [3M_46]


title: LacZ Aged 1 replicate 1, MGT, Day3

value: 18 months old

value: LacZ


title: Lung tissue with AIS of patient 5 [WES]

description: Library name: P5_AIS


title: LacZ Adult 2 replicate 1, MGT, Day3

value: heart

value: Primary cell


title: Lung tissue with LUAD of patient 5 [WES]

description: Library name: P5_LUAD


title: Responder 3M [3M_42]


title: LacZ Adult 1 replicate 1, MGT, Day3

value: cardiac fibroblast

value: WT


title: MGT Adult 1 replicate 1, MGT, Day3


title: Responder 3M [3M_56]


title: Responder 3M [3M_43]


title: Responder 3M [3M_54]


title: Responder 3M [3M_40]


title: Responder 3M [3M_55]


title: Responder 3M [3M_41]


title: Lung tissue with LUAD of patient 4 [WES]

description: Library name: P4_LUAD

value: Lung

value: Female


title: Responder 3M [3M_39]


title: Lung tissue with LUAD of patient 7 [WES]

description: Library name: P7_LUAD

value: No


title: Lung tissue with AAH of patient 4 [WES]

description: Library name: P4_AAH-1


title: Lung tissue with LUAD of patient 6 [WES]

description: Library name: P6_LUAD


title: LacZ Aged 2 replicate 1, MGT, Day3


title: Responder 3M [3M_38]

value: Whole blood cells


title: Responder 3M [3M_36]

value: Responder 3M


title: Lung tissue with LUAD of patient 3 [WES]

description: Library name: P3_LUAD


title: LacZ Neo 1 replicate 1, MGT, Day3


title: Responder 3M [3M_37]


title: Responder 3M [3M_35]


title: Nonresponder 3M [3M_33]

value: Nonresponder 3M


title: 24m_CFs_replicate 2

value: 24 months old

value: culture 3 days


title: Responder 3M [3M_44]


title: 24m_CFs_replicate 1


title: Responder 3M [3M_32]


title: Lung tissue with AAH of patient 2 [WES]

description: Library name: P2_AAH

value: Formalin-fixed paraffin embedded human lung tissue

value: East Asian


title: Responder 3M [3M_31]


title: Responder 3M [3M_30]


title: LacZ Neo 2 replicate 1, MGT, Day3


title: Lung tissue with LUAD of patient 2 [WES]

description: Library name: P2_LUAD

value: Male

value: Yes


title: 12m_CFs_replicate 1

value: 12 months old


title: Responder 3M [3M_29]


title: Responder 3M [3M_28]


title: 3m_CFs_replicate 2

value: heart

value: 3 months old


title: Lung tissue with LUAD of patient 1 [WES]

description: Library name: P1_LUAD


title: Responder 3M [3M_27]


title: 3m_CFs_replicate 1

value: Primary cell

value: cardiac fibroblast


title: 3M in AE case [3M_26]

value: 3M in AE case


title: Responder 3M [3M_24]


title: Responder 3M [3M_25]


title: 80

city: Chapel Hill

first: Shehzad

middle: Z.

last: Sheikh

address: 111 Mason Farm Road

department: Department of Medicine

institute: University of North Carolina School of Medicine

description: Library name: 80

data_processing:
Salmon was used to quantify transcript expression. Quality control metrics based on distributions of sequencing quality, sequencing error rate, and A/T/G/C base, and RNA integrity number (RIN), were used to exclude low-quality samples
Assembly: hg19
Supplementary files format and content: rownames contain the gene name. colnames conatin the sample names. Matrix values are the rounded transcript expression.

extract_protocol:
Total RNA was isolated from frozen tissue in Trizol and total RNA purification kit (Norgen Biotek).
PolyA enrichment, library preparation, and sequencing (150 bp paired end reads) on the NovaSeq sequencer was performed by Novogene (https://www.novogene.com).

value: Colon

tag: disease

value: UC

tag: sample year

tag: tin scores


title: neo_CFs_replicate 2

tag: cell type

tag: genotype

value: WT


title: Responder 3M [3M_22]

value: Whole blood cells

value: Responder 3M


title: Nonresponder 3M [3M_21]

value: Nonresponder 3M


title: neo_CFs_replicate 1

tag: age

value: culture 3 days


title: 71

description: Library name: 71

tag: Sex

value: Female


title: 626

description: Library name: 626


title: Nonresponder 3M [3M_23]


title: Responder 3M [3M_19]


title: Responder 3M [3M_17]


title: 588

description: Library name: 588

source_name: Sigmoid

value: Sigmoid


title: Lung tissue with AIS of patient 3 [WES]

description: Library name: P3_AIS

value: Lung

value: Formalin-fixed paraffin embedded human lung tissue

value: Male

tag: ethnicity

value: East Asian

tag: smoking


title: Neo CFs, OENr4a3 replicate 2, Day10

city: Wuhan

first: Mengxin

last: Liu

address: 115 Donghu Road

value: heart


title: Responder 3M [3M_16]


title: 583

description: Library name: 583


title: Nonresponder 3M [3M_15]


title: 12m_CFs_replicate 2

value: Primary cell

value: 12 months old


title: Neo CFs, OECtrl replicate 2, Day10

value: cardiac fibroblast

value: OE-Ctrl


title: Responder 3M [3M_13]


title: Lung tissue with AAH of patient 1 [WES]

description: Library name: P1_AAH

value: Yes


title: 564

description: Library name: 564

value: UC


title: Responder 3M [3M_11]

value: Whole blood cells


title: Neo CFs, OECtrl replicate 1, Day10

value: WT


title: Nonresponder 3M [3M_10]

value: Nonresponder 3M


title: Responder 3M [3M_20]

value: Responder 3M


title: aged_icm, scRNAseq

description: 10x genomics

data_processing:
Reads from single-cell RNA-seq were aligned and collapsed into Unique Molecular Identifiers (UMI) counts using 10x Genomics Cell Ranger software (version 7.1.0) and mapped to mm10 reference (version 3.0.0) genome.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Aged reprogramming cells from Day 14 post virus infection were harvested by trypsin and sent to Whan Biobank for library preparation
The libraries were prepared according to the standard outlined in the manual. Briefly, single cells in nanoliter-scale oil droplets by Chromium Controller and to generate Gel Bead-In-EMulsions (GEMs). Full-length cDNA libraries were prepared by incubation of GEMs in a thermocycler machine. GEMs containing cDNAs were crushed and all single-cell cDNA libraries were collected together, and cleaned using DynaBeads MyOne Silane beads (PN 37002D; Fisher). The final constructed single-cell libraries were sequenced by Illumina Novaseq6000 machine (Illumina, San Diego, CA) with total reads per cell targeted, for a minimum of 50,000.

value: primary cell

value: 24 months old

value: MGT


title: Nonresponder 3M [3M_12]


title: 531

description: Library name: 531

value: Sigmoid


title: Responder 3M [3M_18]


title: 3M in AE case [3M_7]

value: 3M in AE case


title: neo_icm, scRNAseq

description: 10x genomics

extract_protocol:
Neonatal reprogramming cells from Day 14 post virus infection were harvested by trypsin and sent to Whan Biobank for library preparation
The libraries were prepared according to the standard outlined in the manual. Briefly, single cells in nanoliter-scale oil droplets by Chromium Controller and to generate Gel Bead-In-EMulsions (GEMs). Full-length cDNA libraries were prepared by incubation of GEMs in a thermocycler machine. GEMs containing cDNAs were crushed and all single-cell cDNA libraries were collected together, and cleaned using DynaBeads MyOne Silane beads (PN 37002D; Fisher). The final constructed single-cell libraries were sequenced by Illumina Novaseq6000 machine (Illumina, San Diego, CA) with total reads per cell targeted, for a minimum of 50,000.


title: Responder 3M [3M_8]


title: 53

description: Library name: 53

value: Colon

value: Male


title: Responder 3M [3M_9]


title: Responder 3M [3M_6]


title: Responder 3M [3M_5]


title: Neo CFs, OENr4a3 replicate 1, Day10

value: heart

value: Primary cell


title: 52

description: Library name: 52


title: Nonresponder 3M [3M_2]


title: 512

description: Library name: 512


title: Responder 3M [3M_4]


title: Responder 3M [3M_1]


title: Adult CFs, MGT+shNr4a3 replicate 1, Day7

data_processing:
The raw reads were subjected to adapter removal (fastp 0.20.1) and mapping genome mm10 (Bowtie version 2.2.5) using –no-unal –no-mixed –no-discordant -X 2000 –local parameters. The null, unmapped and duplicated reads were removed by view and markdup functions in sambamba (version 0.7.1) with default parameter settings and mitochondrial reads were removed by SAMtools (version 1.9).
Bigwig files were generated by bam Coverage function in deepTools (version 3.4.3)
MACS2 (version 2.1.2) were used to call ATAC-seq peaks, using default parameters in -p 1e−5 –nomodel -f BAMPE –keep-dup all -g mm.
Assembly: mm10
Supplementary files format and content: narrowPeak

extract_protocol:
10000-50000 cells were treated with cell lysis buffer and nucleus were collected by centrifuging for 5 min at 2000 g.
Transposition and high-throughput DNA sequencing library were carried out by TruePrep DNA Library Prep Kit V2 for Illumina kit (Catalog No. TD501, Vazyme).

value: cardiac fibroblast

value: 3 months old


title: Adult CFs, MGT+shNr4a3 replicate 2, Day7


title: 532

description: Library name: 532

value: Female


title: Nonresponder 0M [0M_87]

value: Nonresponder 0M


title: Adult CFs, MGT+shNT replicate 1, Day7

value: MGT+shNT


title: Adult CFs, MGT+shNT replicate 2, Day7

value: WT


title: 511

description: Library name: 511

value: UC


title: 500

description: Library name: 500


title: Nonresponder 0M [0M_85]

value: Whole blood cells


title: MGT_Aged_2_replicate 1, MGT, Day3

value: 18 months old


title: Responder 0M [0M_86]

value: Responder 0M


title: 495

description: Library name: 495


title: Nonresponder 0M [0M_84]


title: Responder 0M [0M_83]


title: MGT_Aged_1_replicate 1, MGT, Day3

value: MGT


title: Nonresponder 0M [0M_82]


title: Nonresponder 0M [0M_81]


title: 46

description: Library name: 46


title: MGT_Adult_2_replicate 1, MGT, Day3


title: 447

description: Library name: 447


title: Responder 0M [0M_79]


title: Nonresponder 3M [3M_3]

value: Nonresponder 3M


title: MGT_Adult_1_replicate 1, MGT, Day3


title: 443

description: Library name: 443


title: Responder 0M [0M_75]


title: MGT_Neo_2_replicate 1, MGT, Day3


title: Responder 0M [0M_74]


title: Nonresponder 0M [0M_77]


title: 43800

description: Library name: 43800


title: Responder 0M [0M_76]


title: Nonresponder 0M [0M_70]


title: Lacz_Aged_1_replicate 1, Lacz, Day3

value: LacZ


title: 43000

description: Library name: 43000

value: Colon


title: Responder 0M [0M_71]


title: Lacz_Aged_2_replicate 1, Lacz, Day3


title: Nonresponder 0M [0M_72]


title: Nonresponder 0M [0M_80]


title: 417

description: Library name: 417

value: Male


title: Nonresponder 0M [0M_68]


title: 43500

description: Library name: 43500


title: Lacz_Adult_2_replicate 1, Lacz, Day3

value: heart


title: 0M in AE case [0M_69]

value: 0M in AE case


title: Nonresponder 0M [0M_67]


title: Lacz_Adult_1_replicate 1, Lacz, Day3

value: Primary cell

value: cardiac fibroblast


title: Responder 0M [0M_66]


title: Responder 0M [0M_65]


title: 41600

description: Library name: 41600


title: Responder 0M [0M_78]


title: Nonresponder 0M [0M_64]


title: Lacz_Neo_2_replicate 1, Lacz, Day3


title: MGT_Neo_1_replicate 1, MGT, Day3


title: 44300

description: Library name: 44300

value: Sigmoid

value: Female


title: 0M in AE case [0M_73]


title: Lacz_Neo_1_replicate 1, Lacz, Day3


title: Responder 0M [0M_61]


title: Responder 0M [0M_63]


title: Adult CF, shNr4a3_2, H3K27me3 CUT&Tag

data_processing:
The raw reads were subjected to adapter removal (Fastp version 0.20.1) and mapping mouse reference genome (mm10) using Bowtie2 (version 2.2.5) using –no-unal –no-mixed –no-discordant –local –very-sensitive-local –phred33 -I 10 -X 700 parameter.
Bigwig files were generated by bam Coverage function in deepTools (version 3.4.3) with default parameter settings.
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol:
50000 cells were harvested, and the CUT&Tag assay was performed by SeqHealth (Wuhan Seqhealth Co., Ltd. China) using a commercial kit (TD903, Vazyme, China) according to the manufacturer’s protocol. The following primary antibodies were used: Rabbit anti-H3K27ac antibody (Abcam; ab4729), anti-H3K27me3 antibody (Active Motif; Catalog No: 39155). Hyperactive pG-Tn5 transposonase was then added to perform tagmentation. The reaction was terminated, and DNA fragments were extracted by PCI, followed by PCR amplification using indexed P5 and P7 primers.
cells were incubated with Rabbit anti-H3K27ac antibody (Abcam; ab4729) and anti-H3K27me3 antibody (Active Motif; Catalog No: 39155) for 2 h, and then 1 h with secondary antibody at room temperature. Hyperactive pG-Tn5 transposonase was then added to perform tagmentation. The reaction was terminated, and DNA fragments were extracted by PCI, followed by PCR amplification using indexed P5 and P7 primers. The library products were enriched, quantified and finally sequenced on a Novaseq 6000 sequencer (Illumina) with PE150 model.

value: primary cell

value: 3 months old

tag: antibody

value: H3K27me3 (Active Motif; Catalog No:39155)


title: Nonresponder 0M [0M_60]

value: Whole blood cells

value: Nonresponder 0M


title: 41200

description: Library name: 41200

value: UC


title: Responder 0M [0M_62]

value: Responder 0M


title: Responder 0M [0M_58]


title: Responder 0M [0M_59]


title: Adult CF, shNr4a3_1, H3K27me3 CUT&Tag

value: WT


title: Adult CF, shNT_2, H3K27me3 CUT&Tag

value: MGT+shNT


title: 412

description: Library name: 412

source_name: Cecum

value: Cecum


title: 41100

description: Library name: 41100

value: Colon


title: 411

description: Library name: 411

value: Male


title: Adult CF, shNT_1, H3K27me3 CUT&Tag

value: heart


title: Responder 0M [0M_57]


title: Responder 0M [0M_52]


title: Responder 0M [0M_53]


title: 0M in AE case [0M_51]

value: 0M in AE case


title: Adult CF, shNr4a3_2, H3K27ac CUT&Tag

value: cardiac fibroblast

value: H3K27ac (Abcam; ab4729)


title: 41000

description: Library name: 41000

value: Female


title: Responder 0M [0M_54]


title: 415

description: Library name: 415


title: Responder 0M [0M_50]


title: Adult CF, shNr4a3_1, H3K27ac CUT&Tag

value: primary cell


title: 410

description: Library name: 410


title: Responder 0M [0M_49]


title: Adult CF, shNT_2, H3K27ac CUT&Tag

value: 3 months old


title: 40

description: Library name: 40


title: 0M in AE case [0M_48]


title: 365

description: Library name: 365


title: Nonresponder 0M [0M_47]


title: Responder 0M [0M_46]


title: Adult CF, shNT_1, H3K27ac CUT&Tag


title: 0M in AE case [0M_45]


title: Responder 0M [0M_55]


title: 191KO AT2 cell

first: Yu

last: Xu

address: 320 Yueyang Road

institute: Shanghai Institue of Biochemistry and Cell Biology

data_processing:
We analysed the quality scores and other metrics using FASTQC.In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data using Trimmomatic (v0.39) . At the same time, Q20, Q30 and GC content of the celan reads were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from HISAT2 website directly.The RNA-seq reads were aligned to the mouse genome (GRCm38/mm10) using HISAT2（v2.0.5）.
Transcript assembly and quantification using StringTie (v1.3.3b) .
The gene annotation files (gtf file) were downloaded from the ENSEMBL database. We analyzed these raw data using DESeq2 (1.28.1) to assess variance and differential expression between sample groups.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw read counts for each RNA-seq sample.

source_name: lung

extract_protocol:
RNA was extracted, purified and checked for integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).
Libraries were generated for sequencing using a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.  After end repair, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification was performed and PCR products were purified (AMPure XP system). The library quality was assessed on the Agilent Bioanalyzer 2100 system and qRT-PCR.

value: lung

value: epithelial cells

value: Med23 knockout in T cells

tag: strain

value: 6 months old


title: Responder 0M [0M_56]

value: Whole blood cells

value: Responder 0M


title: Responder 0M [0M_44]


title: 362

description: Library name: 362

value: UC


title: Responder 0M [0M_42]


title: 179KO AT2 cell


title: Responder 0M [0M_41]


title: Responder 0M [0M_43]


title: 175KO AT2 cell


title: 190WT AT2 cell

value: WT


title: 286

description: Library name: 286

value: Colon


title: 295

description: Library name: 295


title: Responder 0M [0M_38]


title: Responder 0M [0M_39]


title: 277

description: Library name: 277


title: Responder 0M [0M_40]


title: Responder 0M [0M_37]


title: 269

description: Library name: 269

value: Male


title: 177WT AT2 cell


title: Responder 0M [0M_36]


title: Responder 0M [0M_35]


title: 176WT AT2 cell


title: 0M in AE case [0M_34]


title: Nonresponder 0M [0M_33]

value: Nonresponder 0M


title: 260

description: Library name: 260


title: 224KO Adjacent normal tissue

value: mouse lung tissue

value: 18 months old


title: Responder 0M [0M_31]


title: Responder 0M [0M_32]


title: 217KO Adjacent normal tissue


title: Responder 0M [0M_30]


title: 220

description: Library name: 220


title: Responder 0M [0M_29]


title: 188

description: Library name: 188


title: 224KO lung tumor


title: 0M in AE case [0M_26]

value: 0M in AE case


title: 139

description: Library name: 139

value: Female


title: Responder 0M [0M_25]


title: Responder 0M [0M_27]


title: Responder 0M [0M_24]


title: Nonresponder 0M [0M_23]


title: 102KO lung tumor


title: Responder 0M [0M_22]


title: 217KO lung tumor


title: 565

description: Library name: 565

value: NIBD


title: 630

description: Library name: 630


title: Responder 0M [0M_20]


title: 41500

description: Library name: 41500


title: 545

description: Library name: 545


title: Responder 0M [0M_19]


title: Muscle, WT_3, 12 weeks

city: Jining

first: Xiaomei

last: Wang

address: No. 133 Hehua Road，Taibai Lake New District

institute: Jining Medical University

data_processing:
Illumina NovaSeq 6000 software for sequencing.
The image data measured by the high-throughput sequencer of the sequencing fragment is converted into sequence data (reads) through CASAVA base recognition.
The original data filtering mainly includes removing reads with adapters, removing reads containing N (N indicates that the base information cannot be determined), and removing low-quality reads (reads with base numbers of Qphred <=20 accounting for more than 50% of the entire read length).
Index of reference genomes constructed using HISAT2 (v2.0.5)
Compare the paired end clean reads with the reference genome using HISAT2 (v2.0.5).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files includes RPKM values for each Sample

extract_protocol:
Using standard extraction methods to extract RNA from tissues, followed by strict quality control of RNA samples, mainly through Agilent 2100 bioanalyzer
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: heart


title: 230

description: Library name: 230


title: Muscle, WT_2, 12 weeks


title: Nonresponder 0M [0M_21]


title: Responder 0M [0M_18]


title: Responder 0M [0M_17]


title: 102KO Adjacent normal tissue

value: lung


title: Muscle, WT_1, 12 weeks


title: Responder 0M [0M_28]


title: Responder 0M [0M_16]


title: 480

description: Library name: 480


title: 465

description: Library name: 465


title: Muscle, MC4R_KO_3, 12 weeks

value: Mc4r knockout


title: Nonresponder 0M [0M_15]


title: 0M in AE case [0M_14]


title: Muscle, MC4R_KO_2, 12 weeks


title: 397

description: Library name: 397


title: Nonresponder 0M [0M_12]


title: Responder 0M [0M_11]


title: Muscle, MC4R_KO_1, 12 weeks


title: Responder 0M [0M_9]


title: Responder 0M [0M_13]


title: Responder 0M [0M_8]