title: 1B_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_1_B

tag: batch


title: 2A_Donors 289, 292, 310, and 313 with DPI only

status: Public on Mar 18 2026

type: SRA

city: Brest

first: Marie

last: Frutoso

address: 9 rue Félix le Dantec

country: France

institute: LBAI, UMR1227

description: Library name: Cartridge_2_A

library_source: transcriptomic single cell

data_processing:
Fastq files were processed via the standard Rhapsody analysis pipeline (BD Biosciences) on Seven Bridges (www.sevenbridges.com). In brief, after read filtering, reads are aligned to a reference genome and annotated, barcodes and UMIs are counted, followed by determining putative cells. The final output (molecule per cell count matrix) was analysed in R using Seurat.
Assembly: GRCh38
Supplementary files format and content: A Seurat Object in RDS format combining all donors, tissues and cell types (data.integrated)
Supplementary files format and content: A Seurat Object in RDS format containing only NK cells, without chorioamnionitis donors and without cordblood (data.NK.pure)

molecule: total RNA

organism: Homo sapiens

source_name: mfPLAC (renamed DPI in the paper)

extract_protocol:
After thawing, cells from maternal blood, cordblood, DPI and decidua were stained with a cytometry panel and one specific Sample-Tag for multiplexing (BD Biosciences SMK).  Live, CD45+ immune cells were sorted (using the BD Symphony S6 cell sorter equipped with a 70um nozzle for batches 1 and 2 and the FACSAria III equiped with a 100um nozzle). For batches 1 and 2, Live CD45+ cells were enriched for ILC (CD45+CD19-CD14-CD3-CD127+CD34-), NK cells (CD45+CD19-CD14-CD3-CD127-NKp46+) and myeloid cells (CD45+CD3-CD19-NKp46-HLA-DR+). For batch 3 CD45+ were sorted without enrichment of specific cell type. After sorting, cells from all donors and tissues were pooled and stained with 56 oligo-proteins. Stained cells were then loaded on the BD Rhapsody cartridges (between 35 - 45,000 cells were loaded per cartridges).
Libraries were performed according to manufacturer's instructions (BD RhapsodyTM System, mRNA WTA, Abseq and Sample Tag library Preparation protocol). In brief, after sorting, single cells were stained with AbSeq antibodies, washed three times, pooled and counted and subsequently loaded onto a nano-well cartridge (BD Rhapsody), lysed inside the wells followed by mRNA capture on cell capture beads according to manufacturer instructions. Cell Capture Beads were retrieved and washed prior to performing reverse transcription and treatment with Exonuclease I. cDNA underwent random priming extension and amplification using the human primer xtension mix and via PCR (10–11 cycles). PCR products were purified, and mRNA PCR products were separated from Sample-Tag and AbSeq. PCR products with double-sided size selection using SPRIselect magnetic beads (Beckman Coulter). mRNA and Sample Tag products were further amplified using PCR (10 cycles). PCR products were then purified using SPRIselect magnetic beads.Quality of PCR products was determined by using an Agilent 2200TapeStation with High Sensitivity D5000 ScreenTape (Agilent) in the Fred Hutch Genomics Shared Resource laboratory. The quantity of PCR products was determined by Qubit with Qubit dsDNA HS Assay (Q32851). Whole transcriptome mRNA product was diluted at less than 2 nM (8 pcr cycles), and the Sample Tag and AbSeq PCR products were diluted to 0.25 ng μl−1 to prepare final libraries. Final libraries were indexed using PCR (8 cycles for WTA and 7 cycles for SampleTag and AbSeq libraries). Index PCR products were purified using SPRIselect magnetic beads. Quality of all final libraries was assessed by using Agilent 2200 TapeStation with High Sensitivity D5000 ScreenTape and quantified using a Qubit Fluorometer using the Qubit dsDNA HS Kit (ThermoFisher). Final libraries were diluted to 3 nM and multiplexed for paired-end (100 bp) sequencing on a NovaSeq 6000 (Illumina) using S1 and S2 flow cells. For the gene expression library, we targeted 35,000 reads per cell, for the AbSeq library 22,000 reads per cell, and for the Sample-Tag libraries 2,000 reads per cell.

tag: tissue

value: mfPLAC (renamed DPI in the paper)

tag: donor

value: PRI289 PRI313 PRI292 PRI310

tag: group

value: Healthy (PRI289 PRI313) and Chorioamniontis (PRI292 PRI310)

tag: annotation

value: PRI289_mfPLAC; PRI313_mfPLAC; PRI292_mfPLAC; PRI310_mfPLAC

tag: sample tag

value: PRI289_mfPLAC (SMK9); PRI313_mfPLAC (SMK10); PRI292_mfPLAC (SMK11); PRI310_mfPLAC (SMK12)


title: mCherry-6h-rep3

status: Public on Mar 25 2026

city: Guangzhou

first: Shu

last: Meng

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Science Research

country: China

institute: Guangzhou National Laboratory

description: Library name: mChe-6h-rep3

library_source: transcriptomic

data_processing:
Raw sequencing reads were first subjected to basic quality control including removal of potential sequencing adapters, and poor quality bases or reads using TrimGalore (v0.6.10). Then, clean reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.10b) with default arguments, and only uniquely mapped reads were retained. Reads quantification on the gene level was performed using featureCounts (v2.0.6). Genes with a minimal raw count of 10 and detected in at least three samples were retained. Differentially gene expression analysis was conducted using DESeq2 package (v1.40.2, p < 0.05 and fold change > 1.5).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: HUVEC

extract_protocol:
HUVECs were collected at 6h and 24h after IVT mRNA transfection. Then, total RNA was extracted using RNeasy Plus Mini Kit (Cat# 74134, QIAGEN).
RNA-seq libraries were prepared according to the standard protocol of VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Cat# NR603).

treatment_protocol: We co-transfected 6μg mCherry mRNA with 1.2μg Luc, M, and SOCS1 mRNA into HUVECs, respectively.

tag: cell line

value: HUVEC

tag: treatment


title: 3A_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_3_A


title: mCherry-24h-rep1

description: Library name: mChe-24h-rep1


title: 2_Donors 306 and 307 with DPI Decidua mBlood CordBlood

description: Library name: Placenta_1_Cart2

source_name: mfPLAC (renamed DPI in the paper), decidua, maternal blood and cordblood

value: PRI307 and PRI306

value: Healthy (PRI307) and Chorioamniontis (PRI306)

value: PRI307_mfPLAC; PRI307_Decidua; PRI307_mBlood; PRI307_CordBlood; PRI306_mfPLAC; PRI306_Decidua; PRI306_mBlood; PRI306_CordBlood

value: PRI307_mfPLAC (SMK2); PRI307_Decidua (SMK4); PRI307_mBlood (SMK1); PRI307_CordBlood (SMK3); PRI306_mfPLAC (SMK6); PRI306_Decidua (SMK8); PRI306_mBlood (SMK5); PRI306_CordBlood (SMK7)


title: CT-6h-rep3

description: Library name: CT-6h-rep3


title: 3B_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_3_B


title: 3_Donors 306 and 307 with DPI Decidua mBlood CordBlood

description: Library name: Placenta_1_Cart3

value: mfPLAC (renamed DPI in the paper), decidua, maternal blood and cordblood


title: 4A_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_4_A


title: mCherry-6h-rep1

description: Library name: mChe-6h-rep1


title: articular chondrocytes, Control4

city: maastricht

first: Marjolein

last: Caron

department: Orthopedic Surgery

country: Netherlands

institute: Maastricht University

description:
Library name: Sample4
contrl.contrl8-24h

data_processing:
Pooled libraries consisting of equal molar samples were sequenced on a high-output 75-bp single read on the NextSeq500 (Illumina). For each sample, the number of reads covering one or more exons of a given transcript was extracted. Triplicates of samples that were treated with either p[62-83] peptide or nothing (control) were grouped separately and compared to one another. The fold-change difference and the p-value were calculated using the R package edgeR15, 16, after which the p-value was corrected for multiple testing [false discovery rate (FDR)-corrected].
For each sample, the number of reads covering one or more exons of a given transcript was extracted. Triplicates of samples that were treated with either p[62-83] peptide or nothing (control) were grouped separately and compared to one another. The fold-change difference and the p-value were calculated using the R package edgeR15, 16, after which the p-value was corrected for multiple testing [false discovery rate (FDR)-corrected].
Assembly: Hg19
Supplementary files format and content: tab-delimited txt file representing counts per gene

source_name: Cartilage

growth_protocol: Human articular chondrocytes (HACs) were isolated from the articular cartilage of patients with late-stage OA who underwent total knee arthroplasty. Ethical permission was received from the Local Ethical Committee (METC approval ID: 2017-0183). Cartilage was removed from the femoral bone, cut into small pieces, and digested in Collagenase II (300 units/ml in HEPES-buffered Dulbecco's Modified Eagle's Medium (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffered DMEM)/F-12 with 1% antibiotics). HACs were cultured until passage two in DMEM/F12 (Gibco Life Technologies), supplemented with 10% fetal calf serum (FCS; Sigma-Aldrich), 1% antibiotic/antimitotic (Gibco Life Technologies), and 1% non-essential amino acids (Gibco Life Technologies) in a humidified atmosphere at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated with the RNeasy kit with gDNA eliminator (Qiagen) according to the manufacturer's protocol and subjected to rRNA depletion. Was checked for quality and integrity on the Agilent 2100 Bioanalyzer (Santa Clara, CA, United States) via 2100.
An Expert Eukaryotic Total RNA Nano chip was used according to the manufacturer’s protocol. The mRNA sequencing library was generated using the TruSeq mRNA Sample Preparation Kit (Illumina, Eindhoven, Netherlands). In short, mRNA was enriched using magnetic beads coated with poly(dT), then fragmented. The fragmented mRNA-enriched samples were subjected to cDNA synthesis by reverse transcriptase, followed by dA-tailing and ligation of specific double-stranded bar-coded adapters. Next, the library was amplified, followed by a cleanup. The library sizes were determined using an Agilent 2100 Bioanalyzer with a DNA 1000 chip, according to the manufacturer’s protocol. Pooled libraries consisting of equal molar samples were sequenced on a high-output 75-bp single read on the NextSeq500 (Illumina).

treatment_protocol: For the experiments, a pool of HACs from six donors was used; cells were plated in replicates at a seeding density of 30.000 cells/cm2 and stimulated for 24 hours with or without 100 nM p[63-82] peptide (H-AAYYSEGESAFPLNSYMNAT-OH; Biosynth)

value: Cartilage

tag: cell type

value: Chondrocytes

value: Vehicle


title: 4B_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_4_B


title: 2_Donors 302 and 316 with DPI Decidua mBlood CordBlood

description: Library name: Cart_2

value: PRI316 and PRI302

value: Healthy (PRI316) and Chorioamniontis (PRI302)

value: PRI316_mfPLAC; PRI316_Decidua; PRI316_mBlood; PRI316_CordBlood; PRI302_mfPLAC; PRI302_Decidua; PRI302_mBlood; PRI302_CordBlood

value: PRI316_mfPLAC (SMK6); PRI316_Decidua (SMK8); PRI316_mBlood (SMK5); PRI316_CordBlood (SMK7); PRI302_mfPLAC (SMK10); PRI302_Decidua (SMK12); PRI302_mBlood (SMK9); PRI302_CordBlood (SMK11)


title: 1A_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_1_A

value: mfPLAC (renamed DPI in the paper)

value: PRI289 PRI313 PRI292 PRI310


title: articular chondrocytes, Peptide p[63-82] treatment3

description:
Library name: Sample7
peptl.L1-peptl4-24h

value: Peptide p[63-82]


title: 3_Donors 302 and 316 with DPI Decidua mBlood CordBlood

description: Library name: Cart_3


title: 4_Donors 306 and 307 with DPI Decidua mBlood CordBlood

description: Library name: Placenta_1_Cart4


title: 1_Donors 306 and 307 with DPI Decidua mBlood CordBlood

description: Library name: Placenta_1_Cart1


title: articular chondrocytes, Peptide p[63-82] treatment4

description:
Library name: Sample8
peptl.L1-peptl5-24h


title: articular chondrocytes, Peptide p[63-82] treatment2

description:
Library name: Sample6
peptl.L1-peptl3-24h


title: articular chondrocytes, Peptide p[63-82] treatment1

description:
Library name: Sample5
peptl.L1-peptl2-24h


title: 1_Donors 302 and 316 with DPI Decidua mBlood CordBlood

description: Library name: Cart_1


title: articular chondrocytes, Control2

description:
Library name: Sample2
contrl.contrl2-24h


title: DSS_cellulose_MC_3

status: Public on Mar 12 2026

city: Champaign

first: Wenyan

last: Mei

state: IL

address: 2001 S Lincoln Ave, VMBSB3411

country: USA

institute: University of Illinois at Urbana-Champaign

description: Library name: DSS_Blank_MC_3

data_processing:
Adaptor sequences and low-quality bases were removed from the raw sequencing data using Trimmomatic v0.39(PMID: 24695404). Transcript abundance was quantified using Kallisto v0.44.0(PMID: 27043002), aligning reads to the mouse transcriptome (GRCm39).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts and tpm for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: middle colon

extract_protocol:
RNAs were extracted from the colons and spleens using PureLink RNA Mini Kit (Ambion, Cat. 12183025).
RNA-seq libraries were constructed and sequenced at the UIUC Biotechnology Center High-Throughput Sequencing Core.

value: middle colon


title: DSS_Inwax_MC_3

description: Library name: DSS_Inwax_MC_3


title: articular chondrocytes, Control3

description:
Library name: Sample3
contrl.contrl4-24h


title: DSS_cellulose_MC_1

description: Library name: DSS_Blank_MC_1


title: DSS_Inwax_MC_1

description: Library name: DSS_Inwax_MC_1


title: DSS_Inwax_MC_2

description: Library name: DSS_Inwax_MC_2


title: Water_Inwax_DC_1

description: Library name: Water_Inwax_DC_1

source_name: distal colon

value: distal colon


title: Water_Inwax_DC_2

description: Library name: Water_Inwax_DC_2


title: DSS_cellulose_MC_2

description: Library name: DSS_Blank_MC_2


title: DSS_Inwax_Spleen_3

description: Library name: DSS_Inwax_Spleen_3

source_name: spleen

value: spleen


title: DSS_cellulose_Spleen_2

description: Library name: DSS_Blank_Spleen_2


title: Water_Inwax_DC_4

description: Library name: Water_Inwax_DC_4


title: articular chondrocytes, Control1

description:
Library name: Sample1
contrl.contrl1-24h


title: DSS_Inwax_Spleen_2

description: Library name: DSS_Inwax_Spleen_2


title: Water_cellulose_DC_4

description: Library name: Water_Blank_DC_4


title: Water_cellulose_DC_3

description: Library name: Water_Blank_DC_3


title: DSS_Inwax_Spleen_1

description: Library name: DSS_Inwax_Spleen_1


title: Water_cellulose_DC_1

description: Library name: Water_Blank_DC_1


title: DSS_cellulose_Spleen_3

description: Library name: DSS_Blank_Spleen_3


title: DSS_cellulose_Spleen_1

description: Library name: DSS_Blank_Spleen_1


title: M5_OZ5001C

status: Public on Mar 11 2026

city: Louisville

first: Jan

last: Potempa

state: Kentucky

address: ULSD, 501 S. Preston St.

institute: University of Louisville

description: Library name: M5_OZ5001C

data_processing:
Single-end reads were aligned with STAR v2.7.0f. Gene counts were quantified using featureCounts v2.0.0 with no strand specificity parameter.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from human blood using density gradient centrifugation. Monocytes were isolated from the PBMC fraction using magnetic sorting beads (Miltenyi Biotec). Monocytes were differentiated to monocyte-derived macrophages (MDMs) by culturing for 1 week in RPMI 1640 10% FBS with 50 ng/ml human recombinant GM-CSF (Biolegend).

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen)
Total RNA was used as input material for the RNA sample preparations. 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 First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Prior to infection, the culture medium was replaced with RPMI 1640 2% FBS. MDMs were infected for 24 h at 20 MOI with the P. gingivalis  ATCC 33277 WT strain (ATCC WT) and its isogenic PPAD (delPPAD) and fimbriae: main FimA subunit (delFimA) and accessory subunits - FimE (K04) and FimC (OZ5001C) – mutants or W83 WT (W83) strain. Cells obtained from 5 different donors were used for this analysis.

value: Monocyte-derived macrophages

value: Pg ATCC 33277-derived FimC mutant infection


title: M5_K04

description: Library name: M5_K04

value: Pg ATCC 33277-derived FimE mutant infection


title: M5_W83

description: Library name: M5_W83

value: Pg W83 WT infection


title: M5_delPPAD

description: Library name: M5_delPPAD

value: Pg ATCC 33277-derived PPAD mutant infection


title: M5_delFimA

description: Library name: M5_delFimA

value: Pg ATCC 33277-derived FimA mutant infection


title: M4_delFimA

description: Library name: M4_delFimA


title: M3_delPPAD

description: Library name: M3_delPPAD


title: M3_control

description: Library name: M3_control

value: non infected control cells


title: M5_control

description: Library name: M5_control


title: M2_W83

description: Library name: M2_W83


title: M3_W83

description: Library name: M3_W83


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_Dox_7d_Rep2

status: Public on Apr 01 2026

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

description: Library name: Sample 100

data_processing:
Raw sequencing reads (FASTQ files) were processed using the nf-core/slamseq pipeline (v1.0.0). Initial read quality was assessed with FastQC (v0.11.9). Adapters and low-quality sequences were trimmed using TrimGalore! (v0.6.4_dev). The core processing, including conversion-aware alignment, filtering, SNP masking, and quantification, was performed using Slamdunk (v0.4.3) with default parameters. Reads were aligned to the human genome reference (GRCh38), using gene and 3' UTR annotations derived from the UCSC Table Browser for GRCh38. Slamdunk was used to quantify reads at the gene level, specifically generating counts for total reads and counts for reads containing T>C conversions (indicative of newly synthesized RNA, defined in the analysis as reads with >2 T>C conversions). The submitted processed data files consist of these gene-level count matrices generated by Slamdunk.
Assembly: hg38
Supplementary files format and content: Each processed data file corresponds to a single experimental sample and is provided in comma-separated value (.csv) format. Within each file, rows represent individual transcripts identified by their RefSeq transcript ID. The columns contain transcript-level quantification and metric data generated by Slamdunk, including:
* readCount: Raw count of total reads mapping to the transcript.
* tcReadCount: Raw count of reads identified as containing T>C conversions (representing newly synthesized RNA, based on the pipeline's criteria, e.g., >2 T>C conversions per read).
* length: The length of the transcript.
* readsCPM: Reads Per Million mapped reads (calculated for total reads).
* conversionRate: The calculated T>C conversion rate for reads mapping to this transcript.
* Tcontent: The proportion of thymine bases within the transcript sequence.
* coverageOnTs: Coverage depth specifically over thymine bases.
* conversionsOnTs: Number of T>C conversions observed at thymine positions.
* multimapCount: Count related to multi-mapping reads assigned to the transcript.

growth_protocol: KMS-11 cells are cultured in RPMI-1640 supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
Cells were metabolically labeled with 100 µM 4-thiouridine (4sU) for 1 hour. Total RNA was extracted using TRIzol reagent followed by purification with the RNA Clean & Concentrator-5 kit (Zymo Research). 10 µg of RNA was then alkylated with iodoacetamide, followed by another cleanup using the RNA Clean & Concentrator-5 kit. 1 µg of the resulting RNA was used as input for library construction.
Sequencing libraries were prepared from 1 µg of alkylated total RNA using the QuantSeq 3’mRNA-Seq Library Prep FWD Kit for Illumina (Lexogen #015), following the manufacturer's protocol.

treatment_protocol: NSD2dTAG KMS-11 cells were treated with dTAGV-1 (100 nM) to induce NSD2 degradation. For specific experiments, NSD2-depleted cells were subsequently treated either with doxycycline (100 ng/ml) for reconstitution studies, or with the PRC2 inhibitors EPZ-6438 (200 nM) or MAK-658 (50 nM), or a DMSO vehicle control. The specific duration of each treatment varied according to the experimental condition and is indicated in the metadata associated with each sample.

tag: genotype

value: NSD2_dTAG knockin and NSD2WT reconstitution

value: Doxycycline for 7d


title: M4_OZ5001C

description: Library name: M4_OZ5001C


title: M4_K04

description: Library name: M4_K04


title: M2_OZ5001C

description: Library name: M2_OZ5001C


title: M3_ATCC_WT

description: Library name: M3_ATCC_WT

value: Pg ATCC 33277 WT infection


title: M4_control

description: Library name: M4_control


title: M3_delFimA

description: Library name: M3_delFimA


title: M3_OZ5001C

description: Library name: M3_OZ5001C


title: M4_delPPAD

description: Library name: M4_delPPAD


title: M5_ATCC_WT

description: Library name: M5_ATCC_WT


title: M4_W83

description: Library name: M4_W83


title: M3_K04

description: Library name: M3_K04


title: M4_ATCC_WT

description: Library name: M4_ATCC_WT


title: M2_delFimA

description: Library name: M2_delFimA


title: M2_ATCC_WT

description: Library name: M2_ATCC_WT


title: M2_control

description: Library name: M2_control


title: M2_K04

description: Library name: M2_K04


title: M1_W83

description: Library name: M1_W83


title: M1_OZ5001C

description: Library name: M1_OZ5001C


title: M1_delFimA

description: Library name: M1_delFimA


title: P. maniculatus bairdii replicate 3

status: Public on Mar 07 2026

city: Cambridge, MA

first: KT

last: Tyssowski

state: Massachusetts

address: 16 Divinity Ave

institute: Harvard University

description:
Library name: BW4
Parse Evercode WT Mega kit

data_processing:
Data were demultiplexed using python-based pipelines from Parse and aligned to the P. maniculatus bairdii genome. To avoid confounds from mapping to the genome of one of the subspecies, before alignment, genomes were “personalized” to each subspecies, using a method similar to the generation of the P. polionotus genome (see Bendesky et al., PMID 28424518). Briefly, we aligned our data to the P. maniculatus bairdii genome using STAR aligner. Then we performed variant calling for the individuals we sequenced for each subspecies using GATK. We then incorporated variants back into the final genomes to which we mapped reads. We did the final alignment using STAR aligner as a part of the Parse pipeline. Cells that passed a UMI threshold determined automatically by the Parse preprocessing script were carried on to the next steps.
Data were analyzed as a cell x gene count matrix in Seurat version 4.3.0 Data were normalized with the SCTransform method and integrated across samples and subspecies using harmony. Data were then clustered using the default Seurat settings with the FindClusters and FindNeighbors functions. Data were then mapped to the BICNN mouse motor cortex dataset using Azimuth to identify cell types. Clusters with low prediction scores for the mapping (median prediction score < 0.75 out of 1.0) were further assessed by finding marker genes. If clusters showed markers of multiple larger cell types (e.g., neurons and oligodendrocytes) or if they appeared to be non-cortical cell types (e.g., from dissection error), they were removed from the dataset. After removing this contaminating signal, this alignment resulted in 96% of cells with a prediction score greater than 0.75 when mapping to gene classes. The remaining clusters were then re-normalized, re-integrated, and re-clustered.
Assembly: HU_Pman_2.1.3 (Peromyscus maniculatus bairdii)
Supplementary files format and content: RDS file with Seurat object. Genes x cells matrix with metadata labeling sample and cell type information

organism: Peromyscus maniculatus bairdii

source_name: frontal cortex

extract_protocol:
The anterior half of the cortex was extracted from both hemispheres for each animal (this includes all of sensorimotor cortex, as well as other areas) and flash-frozen in liquid nitrogen. Samples were stored at -70°C until further processing. Nuclei were extracted as described in Matson et al. (PMID 30371670) except that the high sucrose buffer had 1.2M sucrose. Nuclei were fixed using the Parse Evercode Fixation kit, according to the instructions of the manufacturer. Fixed nuclei were stored at -80C for up to 3 months.
Library construction was performed using the Parse Evercode WT Mega kit according to the instructions of the manufacturer. Samples from other projects were included in the run. The data here is de-multiplexed by sample, so as to include only the data for this project.

value: frontal cortex

tag: age

value: 3-6 months

tag: Sex

value: female


title: P. maniculatus nubiterrae replicate 4

description:
Library name: NB5
Parse Evercode WT Mega kit

organism: Peromyscus maniculatus nubiterrae

value: male


title: BT245 FID treatment day 7, biol rep 5

status: Public on Mar 05 2026

city: Montréal

first: Jacek

last: Majewski

state: QC

address: 740 Av. du Docteur-Penfield

country: Canada

institute: McGill University

description: Library name: FID_2

data_processing:
Raw reads trimmed with Atropos
Trimmed reads mapped with STAR aligner
Feature counts extracted with featureCounts
TPM quantification with salmon
Assembly: hg38
Supplementary files format and content: raw counts (CSV)

source_name: Brain

growth_protocol: BT245 pediatric glioma cells were cultured in NeuroCult NS-A media (StemCell Technologies) supplemented with bFGF (10 ng/mL), rhEGF (20 ng/mL), and heparin (0.0002%). Plates were pre-coated with poly-L-ornithine (0.01%) and laminin (0.01 mg/mL) to support adhesion. Cells were maintained in a humidified incubator at 37°C with 5% CO₂.

extract_protocol:
miRNeasy Mini Kit (QIAGEN) with DNase digest using RNase-free DNase Set (QIAGEN)
Library preparation was performed with ribosomal RNA (rRNA) depletion (done at the McGill Genome Center using NEBNextUltra II Directional RNA)

treatment_protocol: Cells were treated with either FID (Forskolin 10 µM, ISX9 10 µM, DAPT 5 µM, Laduviglusib 3 µM, IBET151 2 µM) or FTT (Fasudil 50 µM, Tranilast 100 µM, Temozolomide 50 µM) drug combinations. Stock solutions were prepared in DMSO and diluted into media to final concentrations, with the same DMSO volume administered in control conditions. Treatments were applied for 5–10 days depending on the group, in either standard NeuroCult or BrainPhys media.

value: Brain

value: Glioblastoma

value: FID


title: M1_control

description: Library name: M1_control

value: Monocyte-derived macrophages


title: BT245 FID treatment day 7, biol rep 4

description: Library name: FID_1


title: P. maniculatus nubiterrae replicate 5

description:
Library name: NB6
Parse Evercode WT Mega kit


title: P. maniculatus bairdii replicate 1

description:
Library name: BW1
Parse Evercode WT Mega kit


title: P. maniculatus bairdii replicate 4

description:
Library name: BW5
Parse Evercode WT Mega kit


title: P. maniculatus bairdii replicate 5

description:
Library name: BW6
Parse Evercode WT Mega kit


title: M1_delPPAD

description: Library name: M1_delPPAD


title: male C57BL/6NJ mice 1, rectal tissue, control, Day7

city: Akabanedai

first: Takumi

last: Iwasawa

state: KIta

department: Institute of Life Innovation Studies

country: Japan

institute: Toyo University

description:
Library name: Control sample 1
Column name in raw_counts_All_Samples.csv: 501RC

data_processing:
Adapter trimming, quality trimming, and downsampling were conducted using FASTQ Toolkit (v2.2.6). For downsampling, 20 million reads per sample were randomly selected. Secondary transcriptome analysis was performed using DRAGEN Differential Expression (v4.3.7) (Illumina) with mm10 as the reference genome. Differential expres-sion was assessed within the DESeq2 framework (DESeq2 v1.38.3); for each gene, p-values were calculated using the Wald test based on raw counts.
Assembly: mm10
Supplementary files format and content: Processed data are provided as text-based tables in TSV/CSV format and include:  1. Gene-level raw count matrix (rows: genes; columns: samples; values: integer counts).  2. Normalized expression matrix (e.g., DESeq2-normalized counts and/or variance-stabilized/rlog values; rows: genes; columns: samples).  3. Differential expression results table(s) comparing IBM vs vehicle (gene ID/symbol, log2 fold change, standard error, Wald statistic, p-value, FDR-adjusted p-value).  4. Sample metadata table describing group assignment, dose, and collection time point.

source_name: rectal

growth_protocol: Male C57BL/6NJ mice (8 weeks old) were maintained under specific pathogen-free conditions with ad libitum access to standard chow and water. Mice were acclimated for at least 7 days prior to treatment and housed under a 12 h light/12 h dark cycle at controlled temperature and humidity.

extract_protocol:
At day 7, mice were euthanized and rectal tissue was collected, rinsed briefly in cold PBS to remove luminal contents, and immediately preserved by snap-freezing in liquid nitrogen (or immersion in RNAlater) and stored at −80°C until processing. Total RNA was extracted from rectal tissue using FastGene RNA Premium Kit (FastGene, FG-81050) according to the manufacturer’s instructions, including on-column (or in-solution) DNase treatment. RNA quantity was measured by Qubit and RNA integrity was assessed using Bioanalyzer; samples with RIN ≥ 9.0 were used for library preparation.
NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA)

treatment_protocol: Mice were randomly assigned to receive intestinal bacterial metabolites (IBM) or vehicle once daily by oral gavage for 7 consecutive days. IBM is a cell-free fermented soybean extract generated by co-culturing 31 Lactobacillus/Bifidobacterium-related strains (strain list provided in Supplementary Table S1 of the associated manuscript). The administered dose was 2 mL/kg/day. Control mice received an equivalent volume of vehicle.

value: rectal

value: Control

tag: time

value: Day 7


title: P. maniculatus nubiterrae replicate 3

description:
Library name: NB4
Parse Evercode WT Mega kit


title: SampleA, HTO, ADT

status: Public on Feb 19 2026

city: New York

first: Sneha

last: Mitra

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: SampleA_HTO_ADT
CITE-seq feature barcode library containing both anitbody-derived tags (ADT) and hashtag-oligonucleotides; read1 contains cell barcode and UMI; read2 contains transcript sequence

library_source: other

data_processing:
CITE-seq files were demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: hg38
Supplementary files format and content: Cellranger output files: NFIL3KO-D0-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D0-B_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D14-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D14-B_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D7-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D7-B_sample_filtered_feature_bc_matrix.h5, WT-D0-A_sample_filtered_feature_bc_matrix.h5, WT-D0-B_sample_filtered_feature_bc_matrix.h5, WT-D14-A_sample_filtered_feature_bc_matrix.h5, WT-D14-B_sample_filtered_feature_bc_matrix.h5, WT-D7-A_sample_filtered_feature_bc_matrix.h5, WT-D7-B_sample_filtered_feature_bc_matrix.h5,
Supplementary files format and content: Cellranger output files: NFIL3KO-D0-A_airr_rearrangement.tsv,   WT-D0-A_airr_rearrangement.tsv, NFIL3KO-D0-B_airr_rearrangement.tsv,   WT-D0-B_airr_rearrangement.tsv, NFIL3KO-D14-A_airr_rearrangement.tsv,  WT-D14-A_airr_rearrangement.tsv, NFIL3KO-D14-B_airr_rearrangement.tsv,  WT-D14-B_airr_rearrangement.tsv, NFIL3KO-D7-A_airr_rearrangement.tsv,   WT-D7-A_airr_rearrangement.tsv, NFIL3KO-D7-B_airr_rearrangement.tsv,   WT-D7-B_airr_rearrangement.tsv

molecule: protein

extract_protocol:
1 million cells per condition were stained in cell staining buffer containing cell hashing antibodies for 30 minutes at 4°C. 3ml cell staining buffer was added and centrifuged at 400g for 5 mins. Repeated wash two more times for a total of three washes. Cells were resuspended in 500 μl of cell staining buffer and slowly filtered through a 40 μM cell strainer. Cell concentration and viability were verified and loaded on the 10X Chromium Next GEM Chip K Kit. Libraries were prepared according to manufacturer’s protocol (5’V2 kit, 10x Genomics) and sequenced on a NovaSeq X System using the 10B 100C kit (Illumina).
Libaries construction for both scRNA, CITE, scTCR followed manufacturer protocols (10X genomics).

value: spleen

value: T-cell

tag: library type

value: HTO/ADT

value: A

tag: hto/adt

value: TotalSeq C


title: M1_K04

description: Library name: M1_K04

value: Pg ATCC 33277-derived FimE mutant infection


title: M1_ATCC_WT

description: Library name: M1_ATCC_WT

value: Pg ATCC 33277 WT infection


title: SampleB, TCR

description:
Library name: SampleB_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
CITE-seq files were demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: hg38
Supplementary files format and content: Cellranger output files: NFIL3KO-D0-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D0-B_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D14-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D14-B_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D7-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D7-B_sample_filtered_feature_bc_matrix.h5, WT-D0-A_sample_filtered_feature_bc_matrix.h5, WT-D0-B_sample_filtered_feature_bc_matrix.h5, WT-D14-A_sample_filtered_feature_bc_matrix.h5, WT-D14-B_sample_filtered_feature_bc_matrix.h5, WT-D7-A_sample_filtered_feature_bc_matrix.h5, WT-D7-B_sample_filtered_feature_bc_matrix.h5,
Supplementary files format and content: Cellranger output files: NFIL3KO-D0-A_airr_rearrangement.tsv,   WT-D0-A_airr_rearrangement.tsv, NFIL3KO-D0-B_airr_rearrangement.tsv,   WT-D0-B_airr_rearrangement.tsv, NFIL3KO-D14-A_airr_rearrangement.tsv,  WT-D14-A_airr_rearrangement.tsv, NFIL3KO-D14-B_airr_rearrangement.tsv,  WT-D14-B_airr_rearrangement.tsv, NFIL3KO-D7-A_airr_rearrangement.tsv,   WT-D7-A_airr_rearrangement.tsv, NFIL3KO-D7-B_airr_rearrangement.tsv,   WT-D7-B_airr_rearrangement.tsv
Library strategy: TCR-seq

value: VDJ

value: B


title: SampleB, CAR-T-cells, GEX

description:
Library name: SampleB_RNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

value: mRNA


title: SampleB, HTO, ADT

description:
Library name: SampleB_HTO_ADT
CITE-seq feature barcode library containing both anitbody-derived tags (ADT) and hashtag-oligonucleotides; read1 contains cell barcode and UMI; read2 contains transcript sequence


title: P. maniculatus bairdii replicate 2

description:
Library name: BW3
Parse Evercode WT Mega kit

value: frontal cortex

value: 3-6 months

value: female


title: P. maniculatus nubiterrae replicate 1

description:
Library name: NB2
Parse Evercode WT Mega kit

value: male


title: P. maniculatus nubiterrae replicate 2

description:
Library name: NB3
Parse Evercode WT Mega kit


title: SAP_3

status: Public on Feb 18 2026

city: Jinan

first: Shulei

last: Zhao

state: China

address: Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwu Weiqi Rd, Jinan 250021, China.

department: Gastroenterology

description:
Library name: Sample6
snRNA-seq library, ileum tissue.

data_processing:
snRNA-seq: Raw sequencing data were processed using dnbc4tools (v2.1.3) to generate the gene expression (UMI count) matrix. Quality control and downstream analyses were performed in Seurat (v4.3.0). Low-quality nuclei (UMI <1200, genes <500, or percent.mt >5%) and genes detected in fewer than 10 nuclei were excluded. Samples were merged and integrated using Harmony; clustering was performed using the top 30 PCs and resolution 0.8, and cell types were annotated using marker genes and ScType.
Assembly: Rattus norvegicus reference genome mRatBN7.2 (GCF_015227675.2).
Supplementary files format and content: Processed data include (1) snRNA-seq gene-by-nucleus UMI count matrices, cell metadata tables (cell type/cluster/group annotations), and marker gene lists;

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: ileum

growth_protocol: Male Sprague–Dawley rats (6 weeks old, SPF grade) were housed under SPF conditions (22–26°C, 50–60% humidity, 12 h light/dark cycle) with free access to water and acclimatized for 7 days before experimentation.

extract_protocol:
For snRNA-seq, ileal tissue (~100 mg) was processed for nuclei isolation using the Boyou® Cell Nucleus Isolation Kit (SHBIO, 52009-10, China) according to the manufacturer’s protocol. Nuclei were counted and quality assessed using a fluorescence cell analyzer (Countstar® Rigel S2/Mira FL) and microscopy. For spatial transcriptomics, ileal tissues were embedded in OCT within 30 min after resection, snap-frozen on dry ice, stored at −80°C, sectioned at 10 μm on a cryostat, and mounted onto Stereo-seq chips for downstream permeabilization and reverse transcription.
snRNA-seq libraries were prepared using the DNBelab C High-throughput Single-cell RNA Library Preparation Kit V3.0 (MGI Tech). Single nuclei were co-encapsulated with barcoded gel beads and reverse transcriptase mix into droplets using the DNBelab C-TaiM 4 system, followed by cDNA synthesis, emulsion breakage, cDNA purification and amplification, fragmentation, end repair/A-tailing, adaptor ligation, size selection (300–600 bp), PCR amplification, and library purification.

treatment_protocol: Severe acute pancreatitis (SAP) was induced by retrograde infusion of 3% sodium taurocholate (0.1 mL/100 g, 0.1 mL/min) into the pancreatic duct under anesthesia (3% pentobarbital sodium, 40 mg/kg, i.p.), followed by clamping for 5 min. Control animals underwent sham laparotomy without infusion. Animals were sacrificed 24 h after induction, and ileal tissues were harvested and processed for downstream assays.

value: ileum

value: wild type

value: SAP


title: SampleA, CAR-T-cells, GEX

description:
Library name: SampleA_RNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

value: spleen


title: SampleA, TCR

description:
Library name: SampleA_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains transcript sequence

value: T-cell


title: SAP_2

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

description:
Library name: Sample5
snRNA-seq library, ileum tissue.


title: SAP_1

description:
Library name: Sample4
snRNA-seq library, ileum tissue.


title: M2_delPPAD

description: Library name: M2_delPPAD

value: Monocyte-derived macrophages

value: Pg ATCC 33277-derived PPAD mutant infection


title: CON_2

description:
Library name: Sample2
snRNA-seq library, ileum tissue.

value: Control


title: CON_1

description:
Library name: Sample1
snRNA-seq library, ileum tissue.


title: S54_AS_9_Lung

status: Public on Feb 13 2026

city: Canyon

first: Matthew

last: Scott

state: TX

address: 3201 Russell Long Blvd

institute: Texas A&M University

description: Library name: S54_AS.9.Lung

data_processing:
Following sample demultiplexing via bcl2fastq2 v2.20, raw sequenced reads were quality assessed with FastQC v0.11.9. Reads were subsequently trimmed for ambiguous base calling, retained Illumina adaptors, and minimum read lengths with Trimmomatic v0.39 using the following parameters: “ILLUMINACLIP:TruSeq3.fa:2:30:10:2:TRUE”, “SLIDINGWINDOW:4:20”, “MINLEN:28”, “LEADING:3”, and “TRAILING:3”.
Retained trimmed reads were mapped and indexed to the sheep reference genome assembly ARS-UI_Ramb_v3.0 (Ovis aries) with HISAT2 v2.2.1 utilizing default parameters.
Prior to transcript assembly, Sequence Alignment Map (.sam) files generated from HISAT2 were converted to Binary Alignment Map (.bam) files via Samtools v1.14, utilizing default parameters. Transcript assembly and relative gene-level expression estimation was performed via StringTie2 v2.2.0, with default parameters. Following merged Gene Transfer Format (.gtf) file generation of expression estimates for each sample, post-processing for the appending of ambiguous gene-level identifications (“MSTRG” tags) was performed with a custom Perl script.
Assembly: GCF_016772045.2
Supplementary files format and content: Tab-delimited file of raw gene count data for each sample.

organism: Ammotragus lervia

source_name: Lung

extract_protocol:
Total RNA was collected from approximately 20mg of sterilely dissected frozen tissue via Rneasy Plus Mini Kits (Qiagen) using manufactorer's instruction.
mRNA library preparation was performed with the Stranded mRNA Library Kit (Illumina) using manufactorer's instruction.

value: Lung

tag: animal id

tag: mycoplasma ovipneumoniae_presence

value: Yes

tag: pasteruella multocida_presence

value: No

tag: bibersteinia trehalosi_presence

tag: mannheimia haemolytica_presence

tag: trueperella pyogenes_presence


title: S49_AS_4_Lung

description: Library name: S49_AS.4.Lung

tag: tissue


title: S42_DBS_11_LN

description: Library name: S42_DBS.11.LN

organism: Ovis canadensis

source_name: Lymph node

value: Lymph node


title: S39_DBS_8_Lung

description: Library name: S39_DBS.8.Lung


title: S53_AS_8_Lung

description: Library name: S53_AS.8.Lung


title: CON_3

description:
Library name: Sample3
snRNA-seq library, ileum tissue.

tag: batch


title: S57_AS_11_LN

description: Library name: S57_AS.11.LN


title: S51_AS_6_Lung

description: Library name: S51_AS.6.Lung


title: S52_AS_7_Lung

description: Library name: S52_AS.7.Lung


title: S45_DBS_13_LN

description: Library name: S45_DBS.13.LN


title: S48_AS_3_Lung

description: Library name: S48_AS.3.Lung


title: DAP_1

status: Public on Feb 15 2026

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

description:
Library name: Sample 1
4T1 cells were collected from DAP-treated group for 24 h

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 Hiseq 6000 platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Assembly: reference sequence used for mice
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: breast

growth_protocol: 4T1 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. 4T1 cells transcriptomics were analyzed by Illumina NovaSeq 6000 for high-throughput deep sequencing. The mRNA libraries were constructed and sequenced. In brief, mRNA was purified with poly-T oligo beads and fragmented. First-strand cDNA was synthesized by random hexamer primers, and followed by second-strand synthesis. cDNA products were end-repaired and A-tailed before size selection and adapter ligation. The AMPure XP system was preferentially selected cDNA fragments between 150 and 200 bp in length. Individual sequence libraries were amplified by PCR. Libraries were pooled, and 150 basepair paired-end reads were sequenced.
the mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4T1 cells (5 × 10^5) were seeded in six-well plates and incubated for 24 h, and then DAP (1.62 mg·mL1) was added to the wells and incubated overnight.

value: breast

tag: cell line

value: cancer cell

value: WT


title: S40_DBS_9_LN

description: Library name: S40_DBS.9.LN


title: S58_AS_12_Lung

description: Library name: S58_AS.12.Lung


title: Control_1

description:
Library name: Sample 4
4T1 cells were collected from control group for 24 h

treatment_protocol: 4T1 cells (5 × 10^5) were seeded in six-well plates and incubated for 24 h, and then cultured in fresh medium overnight without DAP treatment.

tag: treatment


title: DAP_2

description:
Library name: Sample 2
4T1 cells were collected from DAP-treated group for 24 h

tag: cell type


title: S50_AS_5_Lung

description: Library name: S50_AS.5.Lung


title: DAP_3

description:
Library name: Sample 3
4T1 cells were collected from DAP-treated group for 24 h

tag: genotype


title: S56_AS_11_Lung

description: Library name: S56_AS.11.Lung


title: S46_DBS_14_Lung

description: Library name: S46_DBS.14.Lung


title: Control_2

description:
Library name: Sample 5
4T1 cells were collected from control group for 24 h


title: Control_3

description:
Library name: Sample 6
4T1 cells were collected from control group for 24 h


title: S41_DBS_11_Lung

description: Library name: S41_DBS.11.Lung


title: S43_DBS_12_Lung

description: Library name: S43_DBS.12.Lung


title: 15_WT_fin_amputation_plane_21_dpa

status: Public on Feb 11 2026

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

institute: Morgridge Institute For Research

description: Library name: dpa21_REP3

data_processing:
RNA-seq reads were trimmed by Trim Galore (v 0.6.7, with cutadapt v 3.5) and counted by salmon (v 1.4.0) by supplying the UCSC danRer11 annotation
The counts were normalized to transcripts per million (TPM)
Assembly: danRer11
Supplementary files format and content: csv file with TPM counts

organism: Danio rerio

source_name: Fin

extract_protocol:
Tissue was homogenized with a stainless-steel bead (5mm, Cat. No. 69989) in Tri-Reagent. RNA was extracted by cholorform followed by an isopropanol precipitation. Remaining DNA was digested by DNase. RNA was purified with a Zymo RNA Clean & Concentrator Kit.
For amputation plane tissue samples, cDNA was prepared by Maxima H-minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adapter primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel-cutting and extraction, and 300 - 800 bp DNA fragments were collected for sequencing.

value: Fin

tag: time point


title: 11_WT_fin_amputation_plane_14_dpa

description: Library name: dpa14_REP2


title: 9_WT_fin_amputation_plane_7_dpa

description: Library name: dpa7_REP3


title: 3_WT_fin_amputation_plane_0_dpa

description: Library name: dpa0_REP3


title: 4_WT_fin_amputation_plane_4_dpa

description: Library name: dpa4_REP1


title: 5_WT_fin_amputation_plane_4_dpa

description: Library name: dpa4_REP2


title: 14_WT_fin_amputation_plane_21_dpa

description: Library name: dpa21_REP2


title: 10_WT_fin_amputation_plane_14_dpa

description: Library name: dpa14_REP1


title: 6_WT_fin_amputation_plane_4_dpa

description: Library name: dpa4_REP3


title: 1_WT_fin_amputation_plane_0_dpa

description: Library name: dpa0_REP1


title: 13_WT_fin_amputation_plane_21_dpa

description: Library name: dpa21_REP1


title: Pt4-17

status: Public on Feb 04 2026

city: HOUSTON

first: HONG

last: ZHAO

state: Texas

address: 6670 Bertner Ave

institute: HOUSTON METHODIST HOSPITAL

description:
SMP 21 18380 A13-17
Library name: DSP-1001660038458-A-H06
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled

data_processing:
Raw FASTQ files generated from the Illumina sequencer were processed using the NanoString GeoMx NGS Pipeline. Reads were demultiplexed by ROI-specific indices, trimmed, and aligned to the CTA reference oligonucleotide manifest provided by NanoString. Digital count conversion (DCC) files were generated for each ROI. Quality control metrics, including sequencing saturation, percent aligned reads, and probe-level performance, were assessed using the GeoMx DSP Quality Control Dashboard. ROIs failing NanoString-recommended QC thresholds were excluded.  Probe counts were normalized according to NanoString guidelines for CTA data. Background correction was performed using the geometric mean of negative probes. ROI-level signal was normalized using upper quartile or Q3 normalization. Housekeeping gene performance was evaluated for stability, and no additional correction was required unless otherwise noted. Normalized counts were exported in both ROI-by-gene matrices and DCC format for downstream analysis.  Downstream statistical analyses, including differential expression and pathway enrichment, were performed using standard tools in R and Python following normalization.
Assembly: Human genome reference annotations used in the NanoString Cancer Transcriptome Atlas (CTA) probe manifest, based on GRCh38/hg38.
Supplementary files format and content: Processed data files include normalized gene expression matrices generated from NanoString GeoMx DSP CTA profiling. Each file contains ROI-level expression values for all CTA panel genes.
Supplementary files format and content: excel file
Library strategy: Spatial Transcriptomics

source_name: PDAC

growth_protocol: FFPE sections (5μm) were stained with anti-CD45, anti-PanCK, and Syto-13 to enable automated segmentation of immune (CD45⁺), tumor (PanCK⁺), and stromal (CD45⁻/PanCK⁻) compartments.

extract_protocol:
For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled
FFPE tissue sections were processed using the NanoString GeoMx Digital Spatial Profiling (DSP) protocol with the Cancer Transcriptome Atlas (CTA) RNA probe panel. Slides were deparaffinized, subjected to antigen retrieval, and incubated with CTA RNA probe sets together with fluorescent morphology markers to enable ROI selection. After overnight hybridization, regions of interest (ROIs) were selected based on immunofluorescent segmentation markers, and oligonucleotide tags linked to the CTA probes were released by UV photocleavage. Photocleaved indexing oligos from each ROI were collected into separate wells and amplified by PCR using Illumina-compatible adapters and ROI-specific indices. Amplified libraries were purified, quantified, and pooled to create the final sequencing library. Sequencing was performed on an Illumina instrument following NanoString recommendations for CTA panel libraries.

value: PDAC

value: prehab


title: 2_WT_fin_amputation_plane_0_dpa

description: Library name: dpa0_REP2


title: Pt4-13

description:
SMP 21 18380 A13-13
Library name: DSP-1001660038458-A-H02
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-22

description:
SMP 21 18380 A13-22
Library name: DSP-1001660038458-A-H11
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-19

description:
SMP 21 18380 A13-19
Library name: DSP-1001660038458-A-H08
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-15

description:
SMP 21 18380 A13-15
Library name: DSP-1001660038458-A-H04
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: 8_WT_fin_amputation_plane_7_dpa

description: Library name: dpa7_REP2


title: Pt4-16

description:
SMP 21 18380 A13-16
Library name: DSP-1001660038458-A-H05
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-21

description:
SMP 21 18380 A13-21
Library name: DSP-1001660038458-A-H10
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-10

description:
SMP 21 18380 A13-10
Library name: DSP-1001660038458-A-G11
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-18

description:
SMP 21 18380 A13-18
Library name: DSP-1001660038458-A-H07
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-11

description:
SMP 21 18380 A13-11
Library name: DSP-1001660038458-A-G12
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-20

description:
SMP 21 18380 A13-20
Library name: DSP-1001660038458-A-H09
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: 7_WT_fin_amputation_plane_7_dpa

description: Library name: dpa7_REP1


title: Pt4-14

description:
SMP 21 18380 A13-14
Library name: DSP-1001660038458-A-H03
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: 12_WT_fin_amputation_plane_14_dpa

description: Library name: dpa14_REP3


title: Pt4-12

description:
SMP 21 18380 A13-12
Library name: DSP-1001660038458-A-H01
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-23

description:
SMP 21 18380 A13-23
Library name: DSP-1001660038458-A-H12
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-18

description:
SMP 23 15022 G14-18
Library name: DSP-1001660038458-A-F07
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-20

description:
SMP 23 15022 G14-20
Library name: DSP-1001660038458-A-F09
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-21

description:
SMP 23 15022 G14-21
Library name: DSP-1001660038458-A-F10
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-23

description:
SMP 23 15022 G14-23
Library name: DSP-1001660038458-A-F12
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-24

description:
SMP 23 15022 G14-24
Library name: DSP-1001660038458-A-G01
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-10

description:
SMP 23 15022 G14-10
Library name: DSP-1001660038458-A-E11
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-2

description:
SMP 21 18380 A13-2
Library name: DSP-1001660038458-A-G03
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-6

description:
SMP 21 18380 A13-6
Library name: DSP-1001660038458-A-G07
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-9

description:
SMP 21 18380 A13-9
Library name: DSP-1001660038458-A-G10
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-8

description:
SMP 23 15022 G14-8
Library name: DSP-1001660038458-A-E09
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-1

description:
SMP 21 18380 A13-1
Library name: DSP-1001660038458-A-G02
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-22

description:
SMP 23 15022 G14-22
Library name: DSP-1001660038458-A-F11
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-7

description:
SMP 21 18380 A13-7
Library name: DSP-1001660038458-A-G08
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-14

description:
SMP 23 15022 G14-14
Library name: DSP-1001660038458-A-F03
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-11

description:
SMP 23 15022 G14-11
Library name: DSP-1001660038458-A-E12
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-19

description:
SMP 23 15022 G14-19
Library name: DSP-1001660038458-A-F08
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-5

description:
SMP 21 18380 A13-5
Library name: DSP-1001660038458-A-G06
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-3

description:
SMP 21 18380 A13-3
Library name: DSP-1001660038458-A-G04
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-4

description:
SMP 21 18380 A13-4
Library name: DSP-1001660038458-A-G05
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-17

description:
SMP 23 15022 G14-17
Library name: DSP-1001660038458-A-F06
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-12

description:
SMP 23 15022 G14-12
Library name: DSP-1001660038458-A-F01
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt4-8

description:
SMP 21 18380 A13-8
Library name: DSP-1001660038458-A-G09
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: No Template Control

description:
No Template Control
Library name: DSP-1001660038458-A-A01
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled

organism: synthetic construct

value: w/o prehab


title: Pt3-15

description:
SMP 23 15022 G14-15
Library name: DSP-1001660038458-A-F04
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-9

description:
SMP 23 15022 G14-9
Library name: DSP-1001660038458-A-E10
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-16

description:
SMP 23 15022 G14-16
Library name: DSP-1001660038458-A-F05
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-13

description:
SMP 23 15022 G14-13
Library name: DSP-1001660038458-A-F02
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-7

description:
SMP 23 15022 G14-7
Library name: DSP-1001660038458-A-E08
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-4

description:
SMP 23 15022 G14-4
Library name: DSP-1001660038458-A-E05
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-22

description:
SMP 20 04565 B35-22
Library name: DSP-1001660038458-A-D11
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-19

description:
SMP 20 04565 B35-19
Library name: DSP-1001660038458-A-D08
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-3

description:
SMP 23 15022 G14-3
Library name: DSP-1001660038458-A-E04
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-23

description:
SMP 20 04565 B35-23
Library name: DSP-1001660038458-A-D12
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-4

description:
SMP 20 04565 B35-4
Library name: DSP-1001660038458-A-C05
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-9

description:
SMP 20 04565 B35-9
Library name: DSP-1001660038458-A-C10
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-2

description:
SMP 23 15022 G14-2
Library name: DSP-1001660038458-A-E03
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-18

description:
SMP 20 04565 B35-18
Library name: DSP-1001660038458-A-D07
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-6

description:
SMP 23 15022 G14-6
Library name: DSP-1001660038458-A-E07
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-11

description:
SMP 20 04565 B35-11
Library name: DSP-1001660038458-A-C12
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-14

description:
SMP 20 04565 B35-14
Library name: DSP-1001660038458-A-D03
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-5

description:
SMP 23 15022 G14-5
Library name: DSP-1001660038458-A-E06
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt3-1

description:
SMP 23 15022 G14-1
Library name: DSP-1001660038458-A-E02
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-10

description:
SMP 20 04565 B35-10
Library name: DSP-1001660038458-A-C11
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-13

description:
SMP 20 04565 B35-13
Library name: DSP-1001660038458-A-D02
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-5

description:
SMP 20 04565 B35-5
Library name: DSP-1001660038458-A-C06
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-21

description:
SMP 20 04565 B35-21
Library name: DSP-1001660038458-A-D10
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-20

description:
SMP 20 04565 B35-20
Library name: DSP-1001660038458-A-D09
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-15

description:
SMP 20 04565 B35-15
Library name: DSP-1001660038458-A-D04
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-24

description:
SMP 20 04565 B35-24
Library name: DSP-1001660038458-A-E01
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-17

description:
SMP 20 04565 B35-17
Library name: DSP-1001660038458-A-D06
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-16

description:
SMP 20 04565 B35-16
Library name: DSP-1001660038458-A-D05
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-12

description:
SMP 20 04565 B35-12
Library name: DSP-1001660038458-A-D01
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-8

description:
SMP 20 04565 B35-8
Library name: DSP-1001660038458-A-C09
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-7

description:
SMP 20 04565 B35-7
Library name: DSP-1001660038458-A-C08
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-6

description:
SMP 20 04565 B35-6
Library name: DSP-1001660038458-A-C07
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-1

description:
SMP 20 04565 B35-1
Library name: DSP-1001660038458-A-C02
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-21

description:
SMP 23 15779 C38-21
Library name: DSP-1001660038458-A-B10
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-8

description:
SMP 23 15779 C38-8
Library name: DSP-1001660038458-A-A09
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-4

description:
SMP 23 15779 C38-4
Library name: DSP-1001660038458-A-A05
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-3

description:
SMP 23 15779 C38-3
Library name: DSP-1001660038458-A-A04
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-1

description:
SMP 23 15779 C38-1
Library name: DSP-1001660038458-A-A02
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-7

description:
SMP 23 15779 C38-7
Library name: DSP-1001660038458-A-A08
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-24

description:
SMP 23 15779 C38-24
Library name: DSP-1001660038458-A-C01
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-15

description:
SMP 23 15779 C38-15
Library name: DSP-1001660038458-A-B04
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-14

description:
SMP 23 15779 C38-14
Library name: DSP-1001660038458-A-B03
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-5

description:
SMP 23 15779 C38-5
Library name: DSP-1001660038458-A-A06
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-19

description:
SMP 23 15779 C38-19
Library name: DSP-1001660038458-A-B08
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-10

description:
SMP 23 15779 C38-10
Library name: DSP-1001660038458-A-A11
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-3

description:
SMP 20 04565 B35-3
Library name: DSP-1001660038458-A-C04
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-12

description:
SMP 23 15779 C38-12
Library name: DSP-1001660038458-A-B01
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt2-2

description:
SMP 20 04565 B35-2
Library name: DSP-1001660038458-A-C03
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-16

description:
SMP 23 15779 C38-16
Library name: DSP-1001660038458-A-B05
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-6

description:
SMP 23 15779 C38-6
Library name: DSP-1001660038458-A-A07
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-13

description:
SMP 23 15779 C38-13
Library name: DSP-1001660038458-A-B02
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-23

description:
SMP 23 15779 C38-23
Library name: DSP-1001660038458-A-B12
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-20

description:
SMP 23 15779 C38-20
Library name: DSP-1001660038458-A-B09
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-22

description:
SMP 23 15779 C38-22
Library name: DSP-1001660038458-A-B11
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-18

description:
SMP 23 15779 C38-18
Library name: DSP-1001660038458-A-B07
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-11

description:
SMP 23 15779 C38-11
Library name: DSP-1001660038458-A-A12
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-17

description:
SMP 23 15779 C38-17
Library name: DSP-1001660038458-A-B06
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-2

description:
SMP 23 15779 C38-2
Library name: DSP-1001660038458-A-A03
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: Pt1-9

description:
SMP 23 15779 C38-9
Library name: DSP-1001660038458-A-A10
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled


title: BMDMs, non-treatment and IL4-treatment, WT or Smyd5 KO

status: Public on Jan 26 2026

city: Xiamen

first: dang

last: buyun

state: Fujian

address: Xiang 'an District Xiang Annan Road

institute: xiamen university

description: Library name: Mix pool library_RNA-seq

data_processing:
We used the iPrimer-seq protocol for sequencing, so there was only one raw data file. In the subsequent analysis process, we divided the raw data files through labels and calculate the counts of each different sample in the file respectively.
The raw data were filtered by bbduk2.sh.
Using the picard merge the forward and reverse sequence
Using the dropseq and STAR to mapping counting the gene count according to different barcode.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: BMDMs

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin, Cells were cultured at 37°C at 5% CO2

extract_protocol:
BMDMs were  lysed for 1 min at 4°C with pre-cold lysis buffer (100 mM Tris-HCl, pH 7.5, 1% SDS, 500mM LiCl, 10mM EDTA, 5mM dithiothreitol). Then, total polyA RNA was extracted by oligodT-beads
Using the primer-seq protocols build the Mix RNA-seq library. Briefly, after marking each sample with a barcode, the samples are mixed to form a mix library and then sequenced simultaneously.

treatment_protocol: Firstly, WT or Smyd5 knockout BMDMs were treated with or without IL-4 for 24 hours, then BMDMs were stimulated with or without LPS for another 4 hours

value: BMDMs

value: Bone marrow-derived macrophages

value: WT and Smyd5 KO

value: non-treatment and IL4-treatment