title: 2DR6F501LU_S113

description: Library name: 2DR6F501LU_S113_R1_001

value: Lung


title: protein75

status: Public on Jun 01 2026

type: SRA

city: Houston

first: Stephen

last: Wong

address: 6565 Fannin St

country: USA

institute: Houston Methodist

description:
Library name: DSP-1001660022162-A-B10-Y
DSP-1001660022162-A-B10.stats.txt
DSP-1001660022162-A-B10.dcc

library_source: other

data_processing:
Spatial proteogenomic and transcriptomic data were generated on the GeoMx DSP platform and processed with the GeoMxWorkflows R package (v1.0+) following the standard NanoString pipeline. Raw DCC files were imported with corresponding PKC files and sample annotations using readNanoStringGeoMxSet. Segment-level QC required: minimum total reads ≥1,000, trimmed reads ≥80%, stitched reads ≥80%, aligned reads ≥75%, sequencing saturation ≥50%, negative control counts ≥1, NTC counts ≤9,000, nuclei count ≥20, and segment area ≥1,000 μm². Probe-level QC was performed with setBioProbeQCFlags (minimum probe ratio 0.1; maximum percentage failing Grubbs test 20%; local outlier removal enabled), and probes failing these metrics or flagged as global Grubbs outliers were excluded. Probe counts were aggregated to genes with aggregateCounts. For each segment, the limit of quantification (LOQ) was defined as the geometric mean of negative controls plus 2 SD, with a minimum LOQ of 2 counts. Segments with <5% gene detection were removed, and genes detected above LOQ in <10% of segments were excluded (negative control probes retained for normalization). The final dataset comprised 7,709 genes across 65 high-quality segments. Spatial multi-omics data from all metastases samples were obtained from both PanCK+ tumor cell regions and CD45+ immune cell regions. Sample identifiers were standardized by combining scan names with ROI identifiers to ensure proper matching between expression data and metadata across both data modalities. Low-expression gene filtering was applied independently to brain and bone datasets using stringent criteria: genes were retained only if they showed ≥1 count in ≥3 samples per tissue type to ensure adequate gene coverage.
The PKC are
(v1.0) Human Procode NGS Core Protein (Lot Number: 519184)
(v1.1) Human Procode NGS IPA Protein (Lot Number: 512044)
(v1.0) Human NGS Whole Transcriptome Atlas RNA (Lot Number: HW0050423)
In the following link
https://brukerspatialbiology.com/products/geomx-digital-spatial-profiler/geomx-dsp-configuration-files/
Assembly: GRCh38
Supplementary files format and content: .csv, dcc
Supplementary files format and content: The RNA_Pro__Exp.csv, WTAONLY_Exp_NEW.csv files were generated from the .dcc file, the readout of gene expression and the protein (the first row =  the sample id,  and the first column = RNA/protein name).
Supplementary files format and content: When dcc was generated from merged/multiple samples, the file is linked to the first sample records and listed in the corresponding sample description field
Library strategy: Spatial Transcriptomics

molecule: protein

organism: Homo sapiens

source_name: Brain

extract_protocol:
We retrospectively collected metastatic tissue samples from six breast cancer patients with one or more metastatic lesions. The samples included two bone metastases, two brain metastases, one pericardial metastasis, and one chest wall metastasis. Formalin-fixed, paraffin-embedded (FFPE) tissue sections (5 μm) were mounted on standard microscope slides and processed for spatial proteogenomics analysis using the NanoString GeoMx Digital Spatial Profiler (DSP). To enable tissue compartmentalization and spatial segmentation, sections were stained with a panel of three fluorescently labeled morphological markers: anti-pancytokeratin (PanCK-AF532) to identify epithelial tumor cells, anti-CD45 (CD45-AF594) to delineate immune cell populations, and Syto13 nucleic acid stain to visualize nuclei and define cellular boundaries. Staining was performed according to standard immunofluorescence protocols with overnight incubation at 4°C.
DNA barcodes corresponding to RNA and protein targets were photocleaved and collected from each segmented AOI using sequential UV light exposure. Collected barcodes were processed using the GeoMx library preparation protocol with unique dual indexing (i7/i5) for each AOI to enable multiplexed analysis.

tag: tissue

value: Brain


title: 2DR4F301LI_S103

city: Durham

first: Scott

last: Auerbach

state: NC

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description: Library name: 2DR4F301LI_S103_R1_001

library_source: transcriptomic

data_processing:
TempO-Seq sequences were aligned to the rat S1500+ probe sequences using Bowtie version 1.3.1. The Bowtie configuration allowed up to three mismatches and selected the single best alignment for reporting.
The aligned read counts for attenuated probes were properly readjusted to calculate unattenuated equivalent counts using the attenuation factors provided in the platform manifest.
Assembly: BioSpyder TempO-seq rat S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver Left Lobe

extract_protocol:
The majority of all tissues from all animals were collected within approximately 10 minutes of euthanasia. Tissue samples were collected following organ weight measurements in the following order: lung, heart, liver (left lobe), kidney, and ovary (no ovary weights were taken) from all remaining animals on study day 5 for transcriptomic analysis. Two samples of lung, heart, liver, and kidney tissue (approximately 5 mm3) were collected and placed into cryotubes containing RNAlater. The ovaries were collected whole bilaterally (one sample) and placed into cryotubes containing RNAlater. The tissue samples were stored at 2°C to 8°C for approximately 55 hours for rats or up to 48 hours for mice. The RNAlater was then removed and the samples were stored in a −85°C to −60°C freezer until processed for RNA isolation. Tissues were homogenized in QIAzol lysis buffer (Qiagen Inc., Valencia, CA) using the TissueLyser II bead-beating system followed by RNA extraction using the RNeasy 96 QIAcube HT kits (Qiagen Inc., Valencia, CA) with a DNA digestion step.
Isolated RNA was utilized for analysis using either the Rat S1500+ v1.2 TempO-Seq (BioSpyder, Carlsbad, CA) platform with a minimum of 500 mapped read counts/transcript and approximately 1.5 million counts/sample. Work instructions developed by Battelle using the BioSpyder User Guide (https://www.biospyder.com/s/100802-TempO-Seq-User-Guide-rev-C-r8r7.pdf) were followed.

value: Liver Left Lobe

tag: strain

value: Sprague-Dawley

tag: Sex

value: female

tag: age

value: 9 weeks

tag: treatment

tag: concentration (ppm)

tag: sample status

value: Used in Analysis

tag: qc issue


title: 2DR4F301LU_S103

description: Library name: 2DR4F301LU_S103_R1_001

source_name: Lung


title: protein49

description:
Library name: DSP-1001660022162-A-D12-Y
DSP-1001660022162-A-D12.stats.txt
DSP-1001660022162-A-D12.dcc

source_name: Bone

value: Bone


title: 2DR4F301KI_S95

description: Library name: 2DR4F301KI_S95_R1_001

source_name: Kidney

value: Kidney


title: Homozygous LAKI treated with CHBA biological replicate 3

city: Buffalo

first: Stelios

middle: T.

last: Andreadis

state: NY

address: 908 Furnas Hall

department: Chemical and Biological Engineering

institute: University at Buffalo

description: Library name: LAKI-CHBA_3

data_processing:
Sequenced reads were processed using nf-core/rnaseq (v3.14.0) pipeline.
Quality of the reads was assessed using FastQC (v0.12.1). Sequencing reads were trimmed using Trim Galore (v0.6.7) to filter reads that were shorter than 20 bp.
The filtered reads were then mapped to the mouse genome (GRCm39, Ensembl) using STAR (v2.7.9a) and quantified using Salmon (v1.10.1).
The abundance estimates were imported into R using tximport (v1.26.1) package. The resulting gene-level counts were used for differential gene expression and PCA analysis using the DESeq2 (v1.38.3) package.
Assembly: GRCm39
Supplementary files format and content: csv file of raw counts suitable for differential expression analysis with DESeq2.

organism: Mus musculus

source_name: Gastrocnemius

extract_protocol:
RNA was extracted from 10 mg of GA muscle tissue using the RNeasy Fibrous Tissue Mini Kit (Qiagen)
Sequencing libraries were prepared as per standard Illumina protocols (Illumina Stranded Total RNA Prep with Ribo-Zero Plus), quality checked and quantified by Kapa Biosystems qPCR.

treatment_protocol: Mixed sex homozygous LAKI mice were used in the study. Young wildtype (WT) mice of similar age were used as controls.  LAKI mice were intraperitoneally injected with CHBA (10 mg/kg dissolved in 5% (v/v) DMSO in corn oil; abbreviated as LAKI-CHBA: 7 males and 6 females) or vehicle control (5% (v/v) DMSO in corn oil; LAKI: 7 females and 6 males), three times a week for 4 weeks. Young WT mice (WT: 2 females, 3 males) were also administered vehicle (5% (v/v) DMSO in corn oil). Injections were started when the mice were 2.5 months or 10 weeks old.

value: Gastrocnemius

tag: genotype

value: 3-chloro-5-hydroxy BA (CHBA)


title: 2DR4F301HE_S95

description: Library name: 2DR4F301HE_S95_R1_001

source_name: Heart

value: Heart


title: 2DR6F501KI_S105

description: Library name: 2DR6F501KI_S105_R1_001


title: 2DR4F303OV_S37

description: Library name: 2DR4F303OV_S37_R1_001

source_name: Ovary

value: Ovary


title: S3-LCM65

city: San Diego

first: Young Chul

last: Kim

address: 3350 La Jolla Village Dr

institute: University of California-San Diego

description: Library name: S3-LCM65

data_processing:
nf-core/rnaseq analysis pipeline (v3.16.0) with the Nextflow workflow manager (v23.10.0)
Assembly: GRCm38, Ensembl release 101
Supplementary files format and content: txt file with log10 (TPM) of genes for each sample

extract_protocol:
Total RNA was isolated from 70-80 microdissected SGLT2-negative LTL-positive tubules per sample using Arcturus PicoPure frozen RNA isolation kit and additional gDNA digestion was performed via Arcticzymes Heat & Run gDNA removal kit.
Quality and quantity of total RNA were determined by High Sensitive Tape Analysis, and cDNA library was prepared using SMARTer Stranded Total RNA-seq Kit v3-Pico Input Mammalian with 0.5 ng total RNA (DV200>30%).

treatment_protocol: Experimental mice were treated with vehicle, dapagliflozin (10mg/kg diet) or semaglutide (3nmol/kg body weight per day) for 2 weeks.

value: Sglt1 KO

value: Dapagliflozin


title: 2DR3F205OV_S24

description: Library name: 2DR3F205OV_S24_R1_001


title: protein48

description:
Library name: DSP-1001660022162-A-E01-Y
DSP-1001660022162-A-E01.stats.txt
DSP-1001660022162-A-E01.dcc


title: Homozygous LAKI treated with CHBA biological replicate 2

description: Library name: LAKI-CHBA_2


title: 2DR3F205LU_S98

description: Library name: 2DR3F205LU_S98_R1_001


title: protein47

description:
Library name: DSP-1001660022162-A-E02-Y
DSP-1001660022162-A-E02.stats.txt
DSP-1001660022162-A-E02.dcc


title: 2DR3F205LI_S98

description: Library name: 2DR3F205LI_S98_R1_001


title: 2DR3F205KI_S90

description: Library name: 2DR3F205KI_S90_R1_001


title: Homozygous LAKI treated with CHBA biological replicate 1

description: Library name: LAKI-CHBA_1


title: protein46

description:
Library name: DSP-1001660022162-A-E03-Y
DSP-1001660022162-A-E03.stats.txt
DSP-1001660022162-A-E03.dcc


title: Homozygous LAKI biological replicate 7

description: Library name: LAKI_7

value: Vehicle (corn oil)


title: 2DR3F205HE_S90

description: Library name: 2DR3F205HE_S90_R1_001


title: 2DR3F204OV_S5

description: Library name: 2DR3F204OV_S5_R1_001


title: protein45

description:
Library name: DSP-1001660022162-A-E04-Y
DSP-1001660022162-A-E04.stats.txt
DSP-1001660022162-A-E04.dcc


title: 2DR3F204LU_S79

description: Library name: 2DR3F204LU_S79_R1_001


title: Homozygous LAKI biological replicate 6

description: Library name: LAKI_6


title: 2DR3F204LI_S79

description: Library name: 2DR3F204LI_S79_R1_001


title: protein44

description:
Library name: DSP-1001660022162-A-E05-Y
DSP-1001660022162-A-E05.stats.txt
DSP-1001660022162-A-E05.dcc


title: 2DR5F404KI_S77

description: Library name: 2DR5F404KI_S77_R1_001


title: 2DR5F403OV_S31

description: Library name: 2DR5F403OV_S31_R1_001


title: 2DR3F204KI_S111

description: Library name: 2DR3F204KI_S111_R1_001


title: protein43

description:
Library name: DSP-1001660022162-A-E06-Y
DSP-1001660022162-A-E06.stats.txt
DSP-1001660022162-A-E06.dcc


title: Homozygous LAKI biological replicate 4

description: Library name: LAKI_4


title: 2DR3F203OV_S28

description: Library name: 2DR3F203OV_S28_R1_001


title: 2DR3F203LU_S102

description: Library name: 2DR3F203LU_S102_R1_001


title: Homozygous LAKI biological replicate 5

description: Library name: LAKI_5


title: protein42

description:
Library name: DSP-1001660022162-A-E07-Y
DSP-1001660022162-A-E07.stats.txt
DSP-1001660022162-A-E07.dcc


title: 2DR3F204HE_S111

description: Library name: 2DR3F204HE_S111_R1_001


title: 2DR3F203LI_S102

description: Library name: 2DR3F203LI_S102_R1_001


title: Homozygous LAKI biological replicate 3

description: Library name: LAKI_3


title: 2DR3F203KI_S94

description: Library name: 2DR3F203KI_S94_R1_001


title: 2DR3F203HE_S94

description: Library name: 2DR3F203HE_S94_R1_001


title: protein41

description:
Library name: DSP-1001660022162-A-E08-Y
DSP-1001660022162-A-E08.stats.txt
DSP-1001660022162-A-E08.dcc


title: S3-LCM11

description: Library name: S3-LCM11

value: Sglt1 WT


title: Homozygous LAKI biological replicate 2

description: Library name: LAKI_2


title: 2DR3F202OV_S17

description: Library name: 2DR3F202OV_S17_R1_001


title: 2DR3F202LU_S91

description: Library name: 2DR3F202LU_S91_R1_001

value: Lung


title: 2DR3F202LI_S91

description: Library name: 2DR3F202LI_S91_R1_001


title: 2DR3F202KI_S83

description: Library name: 2DR3F202KI_S83_R1_001


title: Young WT biological replicate 7

description: Library name: WT_7


title: Homozygous LAKI biological replicate 1

description: Library name: LAKI_1


title: protein38

description:
Library name: DSP-1001660022162-A-E11-Y
DSP-1001660022162-A-E11.stats.txt
DSP-1001660022162-A-E11.dcc


title: 2DR3F201OV_S23

description: Library name: 2DR3F201OV_S23_R1_001


title: protein39

description:
Library name: DSP-1001660022162-A-E10-Y
DSP-1001660022162-A-E10.stats.txt
DSP-1001660022162-A-E10.dcc


title: Young WT biological replicate 6

description: Library name: WT_6


title: 2DR3F201LU_S97

description: Library name: 2DR3F201LU_S97_R1_001


title: 2DR3F201LI_S97

description: Library name: 2DR3F201LI_S97_R1_001


title: Young WT biological replicate 5

description: Library name: WT_5


title: 2DR3F201KI_S89

description: Library name: 2DR3F201KI_S89_R1_001


title: protein36

description:
Library name: DSP-1001660022162-A-F01-Y
DSP-1001660022162-A-F01.stats.txt
DSP-1001660022162-A-F01.dcc


title: 2DR3F201HE_S89

description: Library name: 2DR3F201HE_S89_R1_001


title: Young WT biological replicate 4

description: Library name: WT_4


title: 2DR2F105OV_S7

description: Library name: 2DR2F105OV_S7_R1_001


title: 2DR2F105LU_S81

description: Library name: 2DR2F105LU_S81_R1_001


title: Young WT biological replicate 3

description: Library name: WT_3


title: protein35

description:
Library name: DSP-1001660022162-A-F02-Y
DSP-1001660022162-A-F02.stats.txt
DSP-1001660022162-A-F02.dcc


title: protein34

description:
Library name: DSP-1001660022162-A-F03-Y
DSP-1001660022162-A-F03.stats.txt
DSP-1001660022162-A-F03.dcc


title: 2DR2F105KI_S73

description: Library name: 2DR2F105KI_S73_R1_001


title: 2DR2F105LI_S81

description: Library name: 2DR2F105LI_S81_R1_001


title: Young WT biological replicate 2

description: Library name: WT_2


title: 2DR2F105HE_S73

description: Library name: 2DR2F105HE_S73_R1_001


title: 2DR2F104OV_S13

description: Library name: 2DR2F104OV_S13_R1_001


title: protein33

description:
Library name: DSP-1001660022162-A-F04-Y
DSP-1001660022162-A-F04.stats.txt
DSP-1001660022162-A-F04.dcc


title: 2DR2F104LU_S87

description: Library name: 2DR2F104LU_S87_R1_001


title: protein32

description:
Library name: DSP-1001660022162-A-F05-Y
DSP-1001660022162-A-F05.stats.txt
DSP-1001660022162-A-F05.dcc


title: old_bleo_5

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: Library name: S5

library_source: genomic

data_processing:
We use FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample.
We use TrimGalore (Trim Galore) (v0.4.5) with the following parameters: –adapter AGATCGGAAGAGC -e 0.1 –stringency 6 –length 20 –nextseq 20 –rrbs.
Reads are aligned to mm10 with Bismark (Krueger and Andrews, 2011) (v0.22.1) using Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4) with default settings (multi-seed length of 20bp with 0 mismatches).
Alignments below a MAPQ threshold are removed with samtools (Li et al., 2009) (v1.2) and the parameters: -q 10.
MethylDackel (MethylDackel) (v0.4.0) then calls methylation rates with parameters -d 5 -D 2000 –mergeContext.
Assembly: mm10
Supplementary files format and content: bedGraph of methylation calls from MethylDackel

molecule: genomic DNA

source_name: Lung fibroblasts

extract_protocol:
Lungs were minced with a razor blade and tissue was digested with 0.2 mg/mL of Liberase DL and 100 U/mL DNase I (Roche, Indianapolis, IN, USA) for 40 min at 37 °C. Digestion was stopped with medium containing 10% FBS and cells were passed through a 40 µm cell strainer (ThermoFisherScientific, Waltham, MA). Cells were incubated with 2 mL with red cell lysis buffer for 90 seconds. Cells were centrifuged before undergoing FACS sorting using antibodies against CD45:PerCpCy5.5 (1:200, Biolegend, San Diego, CA, USA, Cat# 103132), CD31:PE (1:200, Biolegend, San Diego, CA, USA, Cat#102408), EpCAM:APC (1:200,Biolegend, San Diego, CA, USA, Cat#118214). They were also stained with DAPI (1:1000, Biolegend, San Diego, CA, USA, Cat#422801). DAPI-positive, GFP-positive cells were sorted by FACS using the BD FACS Aria II (BD Biosciences, San Jose, CA, USA).
25-75 ng of genomic DNA was digested for 16-18 hours with the MspI restriction enzyme. The digested DNA was purified by phenol-chloroform extraction, then ethanol precipitated in the presence of glycogen and sodium acetate. The precipitated DNA was resuspended in 10mM Tris-Cl pH8.5 (Buffer EB) and processed for end-repair, A-tailing, and ligation of hairpin adapters with methylated cytosines. The ligated DNA was next ran on a 1.8% Low-Range Ultra Agarose Gel in TBE buffer, and fragments of 100-200bp and 200-300bp were excised and separately purified using Qiagen Gel Extraction kit. A 2ul aliquot of each fragment was used to verify proper adapter ligation and size selection by PCR. Samples passing this QC were then subjected to bisulfite conversion with the EZ DNA Methylation Kit, but with the following changes: the samples were incubated in a thermal cycler using the following conditions: 55 cycles: 95C for 30 sec, 50C for 15 min. Hold at 4C. The bisulfite converted samples were cleaned up according to the manufacturer’s protocol and eluted in 40ul of nuclease free water. The samples were next amplified using Roche High Fidelity FastStart system with the following protocol: 94C for 5 minutes; 18 cycles of: denaturing at 94C for 20 seconds, annealing at 60C for 30 seconds, extension at 72C for 1 min. A final extension was done at 72C for 3 minutes and the reactions were kept at 4C until they were cleaned. This final library cleanup was done with Agencourt’s AMPure XP SPRI beads according to the following protocol: The beads were brought to room temperature with gentle agitation for a minimum of 30 minutes. A 1.2X volume (for short fragments) and 1.1X volume (for long fragments) of SPRI beads was added to each sample fragment, and the PCR products were purified per manufacturer’s recommendation using 500ul of 80% ethanol for washes. Each library was eluted into 33ul of elution buffer (10mM Tris-Cl pH 8.5). The libraries were quantified using Qubit’s High Sensitivity ds DNA kit, and the quality was assessed with Agilent’s High Sensitivity D1000 ScreenTape assay.

treatment_protocol: Col1a1-GFP mice on a FVB background  were obtained from Derek Radisky (Mayo Clinic, Jacksonville, Florida, USA) and were maintained in breeding colonies. Mice were allowed to mature to either 6-8 weeks (young) or > 18 months (aged) of age. Nine mice in each group (aged and young) were treated with 50 µl of either intratracheal bleomycin (1.2 U/kg, APP Pharmaceutical, Schaumburg, IL) (five mice per group) or saline (four mice per group), delivered using a MicroSprayer (Penn-Century). Mice were euthanized at day 30 post-intratracheal treatment. Fibroblasts were isolated by FACS sorting for GFP.

tag: cell type

value: Lung fibroblasts

value: old

value: bleo


title: protein31

description:
Library name: DSP-1001660022162-A-F06-Y
DSP-1001660022162-A-F06.stats.txt
DSP-1001660022162-A-F06.dcc


title: 2DR2F104KI_S79

description: Library name: 2DR2F104KI_S79_R1_001

value: Sprague-Dawley

value: female


title: old_bleo_4

description: Library name: S4


title: 2DR2F103OV_S38

description: Library name: 2DR2F103OV_S38_R1_001

value: 9 weeks

value: Used in Analysis


title: 2DR2F104HE_S79

description: Library name: 2DR2F104HE_S79_R1_001


title: protein30

description:
Library name: DSP-1001660022162-A-F07-Y
DSP-1001660022162-A-F07.stats.txt
DSP-1001660022162-A-F07.dcc

value: Bone


title: 2DR2F103LU_S112

description: Library name: 2DR2F103LU_S112_R1_001


title: old_bleo_3

description: Library name: S3


title: protein29

description:
Library name: DSP-1001660022162-A-F08-Y
DSP-1001660022162-A-F08.stats.txt
DSP-1001660022162-A-F08.dcc


title: 2DR2F103LI_S112

description: Library name: 2DR2F103LI_S112_R1_001

value: Liver Left Lobe


title: 2DR2F103KI_S104

description: Library name: 2DR2F103KI_S104_R1_001

value: Kidney


title: 2DR2F102OV_S6

description: Library name: 2DR2F102OV_S6_R1_001


title: 2DR2F103HE_S104

description: Library name: 2DR2F103HE_S104_R1_001

value: Heart


title: protein27

description:
Library name: DSP-1001660022162-A-F10-Y
DSP-1001660022162-A-F10.stats.txt
DSP-1001660022162-A-F10.dcc


title: 2DR2F102LU_S80

description: Library name: 2DR2F102LU_S80_R1_001


title: 2DR2F102KI_S112

description: Library name: 2DR2F102KI_S112_R1_001


title: young_saline_3

description: Library name: S28

value: young

value: saline


title: protein26

description:
Library name: DSP-1001660022162-A-F11-Y
DSP-1001660022162-A-F11.stats.txt
DSP-1001660022162-A-F11.dcc


title: young_saline_2

description: Library name: S27


title: 2DR2F101OV_S34

description: Library name: 2DR2F101OV_S34_R1_001

value: Ovary


title: protein25

description:
Library name: DSP-1001660022162-A-F12-Y
DSP-1001660022162-A-F12.stats.txt
DSP-1001660022162-A-F12.dcc


title: 2DR2F101LI_S108

description: Library name: 2DR2F101LI_S108_R1_001


title: protein24

description:
Library name: DSP-1001660022162-A-G01-Y
DSP-1001660022162-A-G01.stats.txt
DSP-1001660022162-A-G01.dcc


title: 2DR2F101KI_S100

description: Library name: 2DR2F101KI_S100_R1_001


title: 2DR2F101HE_S100

description: Library name: 2DR2F101HE_S100_R1_001


title: protein23

description:
Library name: DSP-1001660022162-A-G02-Y
DSP-1001660022162-A-G02.stats.txt
DSP-1001660022162-A-G02.dcc


title: old_bleo_1

description: Library name: S1


title: 2DR1F9OV_S27

description: Library name: 2DR1F9OV_S27_R1_001


title: 2DR1F9LU_S101

description: Library name: 2DR1F9LU_S101_R1_001


title: young_bleo_3

description: Library name: S19


title: 2DR1F9KI_S93

description: Library name: 2DR1F9KI_S93_R1_001


title: protein22

description:
Library name: DSP-1001660022162-A-G03-Y
DSP-1001660022162-A-G03.stats.txt
DSP-1001660022162-A-G03.dcc


title: protein21

description:
Library name: DSP-1001660022162-A-G04-Y
DSP-1001660022162-A-G04.stats.txt
DSP-1001660022162-A-G04.dcc


title: protein20

description:
Library name: DSP-1001660022162-A-G05-Y
DSP-1001660022162-A-G05.stats.txt
DSP-1001660022162-A-G05.dcc


title: 2DR1F8OV_S4

description: Library name: 2DR1F8OV_S4_R1_001


title: 2DR1F8LU_S78

description: Library name: 2DR1F8LU_S78_R1_001


title: young_bleo_1

description: Library name: S17


title: 2DR1F8LI_S78

description: Library name: 2DR1F8LI_S78_R1_001


title: protein19

description:
Library name: DSP-1001660022162-A-G06-Y
DSP-1001660022162-A-G06.stats.txt
DSP-1001660022162-A-G06.dcc


title: protein40

description:
Library name: DSP-1001660022162-A-E09-Y
DSP-1001660022162-A-E09.stats.txt
DSP-1001660022162-A-E09.dcc


title: 2DR3F202HE_S83

description: Library name: 2DR3F202HE_S83_R1_001


title: protein37

description:
Library name: DSP-1001660022162-A-E12-Y
DSP-1001660022162-A-E12.stats.txt
DSP-1001660022162-A-E12.dcc


title: 2DR1F8KI_S110

description: Library name: 2DR1F8KI_S110_R1_001


title: old_saline_4

description: Library name: S15


title: 2DR1F8HE_S110

description: Library name: 2DR1F8HE_S110_R1_001


title: protein18

description:
Library name: DSP-1001660022162-A-G07-Y
DSP-1001660022162-A-G07.stats.txt
DSP-1001660022162-A-G07.dcc


title: 2DR1F7OV_S20

description: Library name: 2DR1F7OV_S20_R1_001


title: old_saline_3

description: Library name: S14


title: 2DR1F7LU_S94

description: Library name: 2DR1F7LU_S94_R1_001


title: Young WT biological replicate 1

description: Library name: WT_1

value: Gastrocnemius

value: Vehicle (corn oil)


title: protein17

description:
Library name: DSP-1001660022162-A-G08-Y
DSP-1001660022162-A-G08.stats.txt
DSP-1001660022162-A-G08.dcc


title: 2DR2F104LI_S87

description: Library name: 2DR2F104LI_S87_R1_001


title: 2DR1F7LI_S94

description: Library name: 2DR1F7LI_S94_R1_001


title: old_saline_2

description: Library name: S13


title: 2DR1F7KI_S86

description: Library name: 2DR1F7KI_S86_R1_001


title: 2DR1F7HE_S86

description: Library name: 2DR1F7HE_S86_R1_001


title: protein16

description:
Library name: DSP-1001660022162-A-G09-Y
DSP-1001660022162-A-G09.stats.txt
DSP-1001660022162-A-G09.dcc


title: old_saline_1

description: Library name: S12


title: old_bleo_2

description: Library name: S2


title: 2DR1F6OV_S33

description: Library name: 2DR1F6OV_S33_R1_001


title: protein15

description:
Library name: DSP-1001660022162-A-G10-Y
DSP-1001660022162-A-G10.stats.txt
DSP-1001660022162-A-G10.dcc


title: protein28

description:
Library name: DSP-1001660022162-A-F09-Y
DSP-1001660022162-A-F09.stats.txt
DSP-1001660022162-A-F09.dcc


title: young_saline_4

description: Library name: S29


title: 2DR2F102LI_S80

description: Library name: 2DR2F102LI_S80_R1_001


title: 2DR1F6LU_S107

description: Library name: 2DR1F6LU_S107_R1_001

value: Lung


title: 2DR1F6LI_S107

description: Library name: 2DR1F6LI_S107_R1_001


title: Experiment two, Eomes KO, a41BB treatment, VDJ

city: Toulouse

first: Anne

middle: S

last: Dejean

state: Midi-Pyrenees

address: CHU Purpan – BP 3028

country: France

institute: Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)

description: Library name: ASD2_Eomes_KO_41BB_VDJ

data_processing:
fastq files were generated from Illumina BCL files with the 'mkfastq' pipeline of cellranger v7.1.0, which employs bcl2fastq v2.20.0
Assembly: Mouse GRCm38
Supplementary files format and content: rds files : Seurat objects containing normalized counts, UMAP coordinates and clusters. Can be opened with LoadSeuartRds() function.
Library strategy: TCR-Seq

source_name: spleen

extract_protocol:
At day 18, CD44high CD4+ T cells were isolated from spleen using CD4+ T Cells isolation Kit (Invitrogen) then FACS Aria Fusion (BD Biosciences).
Single-cell libraries (5′ gene expression) were generated using the Chromium Controller Instrument and Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit vXXX according to the manufacturer’s protocol (10× Genomics)

treatment_protocol: Mice were injected i.v. with NK1.1-depleting mAbs (50μg/mice, days -2 and 5), engrafted with Vk12653 MM cells (2.106, day 0), subsequently treated with 4-1BBa or control IgG mAbs (20μg/mice, days 10, 13, 16) and mice were euthanized at day 18.

value: spleen

value: CD4 T lymphocyte

value: Vk*Myc tumor injection, aNK1.1 depeleting antibody injection, agonistic a41BB (also called aCD137) antibody injection, tamoxifen injection

tag: batch


title: 2DR1F6KI_S99

description: Library name: 2DR1F6KI_S99_R1_001

value: Sprague-Dawley


title: 2DR2F102HE_S112

description: Library name: 2DR2F102HE_S112_R1_001

value: female


title: Experiment one, Eomes KO, a41BB treatment, VDJ

description: Library name: ASD1_Eomes_KO_41BB_VDJ

value: Vk*Myc tumor injection, aNK1.1 depeleting antibody injection, agonistic a41BB (also called aCD137) antibody injection


title: 2DR1F6HE_S99

description: Library name: 2DR1F6HE_S99_R1_001

value: 9 weeks

value: Used in Analysis


title: young_saline_1

description: Library name: S26

value: Lung fibroblasts


title: 2DR1F5OV_S32

description: Library name: 2DR1F5OV_S32_R1_001


title: protein12

description:
Library name: DSP-1001660022162-A-H01-Y
DSP-1001660022162-A-H01.stats.txt
DSP-1001660022162-A-H01.dcc

value: Bone


title: 2DR1F5LI_S106

description: Library name: 2DR1F5LI_S106_R1_001

value: Liver Left Lobe


title: Experiment one, Eomes WT, a41BB treatment, VDJ

description: Library name: ASD1_Eomes_WT_41BB_VDJ

value: Eomes-IRES-GFP


title: 2DR1F5HE_S98

description: Library name: 2DR1F5HE_S98_R1_001

value: Heart


title: Experiment two, Eomes KO, Ig ctrl treatment, VDJ

description: Library name: ASD2_Eomes_KO_Ig_VDJ

value: Vk*Myc tumor injection, aNK1.1 depeleting antibody injection, Ig control antibody injection, tamoxifen injection


title: 2DR1F4OV_S22

description: Library name: 2DR1F4OV_S22_R1_001

value: Ovary


title: protein10

description:
Library name: DSP-1001660022162-A-H03-Y
DSP-1001660022162-A-H03.stats.txt
DSP-1001660022162-A-H03.dcc


title: 2DR1F5LU_S106

description: Library name: 2DR1F5LU_S106_R1_001


title: protein14

description:
Library name: DSP-1001660022162-A-G11-Y
DSP-1001660022162-A-G11.stats.txt
DSP-1001660022162-A-G11.dcc


title: 2DR1F4LI_S96

description: Library name: 2DR1F4LI_S96_R1_001


title: Experiment one, Eomes KO, Ig ctrl treatment, VDJ

description: Library name: ASD1_Eomes_KO_Ig_VDJ

value: Vk*Myc tumor injection, aNK1.1 depeleting antibody injection, Ig control antibody injection


title: protein9

description:
Library name: DSP-1001660022162-A-H04-Y
DSP-1001660022162-A-H04.stats.txt
DSP-1001660022162-A-H04.dcc


title: 2DR1F4KI_S88

description: Library name: 2DR1F4KI_S88_R1_001

value: Kidney


title: Experiment two, Eomes WT, Ig ctrl treatment, VDJ

description: Library name: ASD2_Eomes_WT_Ig_VDJ

value: spleen


title: 2DR1F4HE_S88

description: Library name: 2DR1F4HE_S88_R1_001


title: protein8

description:
Library name: DSP-1001660022162-A-H05-Y
DSP-1001660022162-A-H05.stats.txt
DSP-1001660022162-A-H05.dcc


title: 2DR1F3OV_S25

description: Library name: 2DR1F3OV_S25_R1_001


title: Experiment one, Eomes WT, Ig ctrl treatment, VDJ

description: Library name: ASD1_Eomes_WT_Ig_VDJ

value: CD4 T lymphocyte


title: 2DR1F3LU_S99

description: Library name: 2DR1F3LU_S99_R1_001

value: Lung


title: protein7

description:
Library name: DSP-1001660022162-A-H06-Y
DSP-1001660022162-A-H06.stats.txt
DSP-1001660022162-A-H06.dcc


title: 2DR1F3LI_S99

description: Library name: 2DR1F3LI_S99_R1_001

value: Sprague-Dawley


title: Experiment two, Eomes KO, a41BB treatment, GEX

description: Library name: ASD2_Eomes_KO_41BB_GEX

library_source: transcriptomic single cell

data_processing:
fastq files were generated from Illumina BCL files with the 'mkfastq' pipeline of cellranger v7.1.0, which employs bcl2fastq v2.20.0
Assembly: Mouse GRCm38
Supplementary files format and content: rds files : Seurat objects containing normalized counts, UMAP coordinates and clusters. Can be opened with LoadSeuartRds() function.

value: Vk*Myc tumor injection, aNK1.1 depeleting antibody injection, agonistic a41BB (also called aCD137) antibody injection, tamoxifen injection


title: 2DR1F3KI_S91

description: Library name: 2DR1F3KI_S91_R1_001

value: female


title: protein6

description:
Library name: DSP-1001660022162-A-H07-Y
DSP-1001660022162-A-H07.stats.txt
DSP-1001660022162-A-H07.dcc


title: Experiment one, Eomes KO, a41BB treatment, GEX

description: Library name: ASD1_Eomes_KO_41BB_GEX

value: Vk*Myc tumor injection, aNK1.1 depeleting antibody injection, agonistic a41BB (also called aCD137) antibody injection


title: 2DR1F3HE_S91

description: Library name: 2DR1F3HE_S91_R1_001

value: 9 weeks

value: Used in Analysis


title: 2DR1F2OV_S3

description: Library name: 2DR1F2OV_S3_R1_001


title: protein5

description:
Library name: DSP-1001660022162-A-H08-Y
DSP-1001660022162-A-H08.stats.txt
DSP-1001660022162-A-H08.dcc

value: Bone


title: 2DR1F2LU_S77

description: Library name: 2DR1F2LU_S77_R1_001


title: 2DR1F2LI_S77

description: Library name: 2DR1F2LI_S77_R1_001

value: Liver Left Lobe


title: protein4

description:
Library name: DSP-1001660022162-A-H09-Y
DSP-1001660022162-A-H09.stats.txt
DSP-1001660022162-A-H09.dcc


title: 2DR1F2KI_S109

description: Library name: 2DR1F2KI_S109_R1_001


title: protein3

description:
Library name: DSP-1001660022162-A-H10-Y
DSP-1001660022162-A-H10.stats.txt
DSP-1001660022162-A-H10.dcc


title: 2DR1F1OV_S12

description: Library name: 2DR1F1OV_S12_R1_001


title: Experiment two, Eomes KO, Ig ctrl treatment, GEX

description: Library name: ASD2_Eomes_KO_Ig_GEX


title: 2DR1F1LU_S86

description: Library name: 2DR1F1LU_S86_R1_001


title: protein2

description:
Library name: DSP-1001660022162-A-H11-Y
DSP-1001660022162-A-H11.stats.txt
DSP-1001660022162-A-H11.dcc


title: protein11

description:
Library name: DSP-1001660022162-A-H02-Y
DSP-1001660022162-A-H02.stats.txt
DSP-1001660022162-A-H02.dcc


title: 2DR1F1LI_S86

description: Library name: 2DR1F1LI_S86_R1_001


title: Experiment one, Eomes KO, Ig ctrl treatment, GEX

description: Library name: ASD1_Eomes_KO_Ig_GEX


title: protein1

description:
Library name: DSP-1001660022162-A-H12-Y
DSP-1001660022162-A-H12.stats.txt
DSP-1001660022162-A-H12.dcc


title: 2DR1F1HE_S78

description: Library name: 2DR1F1HE_S78_R1_001


title: Experiment two, Eomes WT, Ig ctrl treatment, GEX

description: Library name: ASD2_Eomes_WT_Ig_GEX

value: Eomes-IRES-GFP


title: 2DR1F10OV_S26

description: Library name: 2DR1F10OV_S26_R1_001


title: hipsc_young_control_4

first: Zhen

last: Yan

address: 955 Main St

department: Physiology and Biophysics

description: Library name: YC4

data_processing:
deseq2
Assembly: mm39, hg38
Supplementary files format and content: count matrix

source_name: hi-psc-N

extract_protocol:
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature.
The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

value: hi-psc-N

tag: disease

value: Young control

value: human stem cell derived neuron


title: Experiment one, Eomes WT, Ig ctrl treatment, GEX

description: Library name: ASD1_Eomes_WT_Ig_GEX

value: Vk*Myc tumor injection, aNK1.1 depeleting antibody injection, Ig control antibody injection


title: 2DR1F10LI_S100

description: Library name: 2DR1F10LI_S100_R1_001


title: hipsc_young_control_3

description: Library name: YC3


title: 2DR1F10LU_S100

description: Library name: 2DR1F10LU_S100_R1_001


title: 2DR1F10KI_S92

description: Library name: 2DR1F10KI_S92_R1_001

value: Kidney


title: primary chondrocyte, control 3

city: Hangzhou

first: Liao

last: junguang

state: Zhejiang

address: 928 2nd Street

country: China

institute: Zhejiang Sci-Tech University

description: Library name: Nf2_D7_CTL3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the mus_musculus reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: ensembl.v101
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

molecule: polyA RNA

source_name: Cartilage tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Cartilage tissue

value: primary chondrocyte

value: control


title: hipsc_young_control_2

description: Library name: YC2


title: 2DR1F10HE_S92

description: Library name: 2DR1F10HE_S92_R1_001

value: Heart

value: Sprague-Dawley


title: AO168O_10000_rep3

city: Shanghai

first: Yanbin

last: Zhao

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong university

description: Library name: c10000_3

data_processing:
Raw image data were converted to sequence reads in FASTQ format by CASAVA.
Raw reads were filtered to remove adaptor-containing reads, reads containing ambiguous bases (N), and low-quality reads.
Clean reads were aligned to the Caenorhabditis elegans reference genome ensembl_114_caenorhabditis_elegans_wbcel235_toplevel using HISAT2 v2.2.1.
Gene-level read counts were generated using featureCounts v2.0.6. Differential expression analysis was performed using DESeq2 v1.42.0.
Assembly: ensembl_114_caenorhabditis_elegans_wbcel235_toplevel
Supplementary files format and content: Processed data files are tab-delimited text files containing gene-level raw read counts for all samples and normalized gene expression values (FPKM) for all samples.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Caenorhabditis elegans strains were maintained under standard laboratory conditions on nematode growth medium (NGM) agar plates seeded with Escherichia coli OP50 and incubated at 25 °C.

extract_protocol:
Approximately 1,000 worms per sample were washed thoroughly with M9 buffer, snap-frozen in liquid nitrogen, and stored at -80 °C until processing. Total RNA was extracted using TRIzol reagent (Invitrogen), and RNA integrity was assessed using an Agilent Bioanalyzer 2100 system.
mRNA was enriched from total RNA using an Oligo(dT)-based workflow, followed by fragmentation, first-strand cDNA synthesis using random hexamer primers, second-strand cDNA synthesis, end repair, A-tailing, adaptor ligation, size selection, PCR enrichment, and purification. Libraries were initially quantified using Qubit 2.0, assessed for insert size using an Agilent 2100 Bioanalyzer, and further quantified by qRT-PCR before pooling and sequencing on an Illumina platform in paired-end 150-bp mode.

treatment_protocol: Synchronized eggs were obtained by alkaline bleaching and exposed from the embryonic stage on NGM agar containing AO168=O at 0, 400, 2000, or 10000 ng/g. AO168=O was dissolved in ethanol and added to molten NGM before plate pouring. The final ethanol concentration was 0.01% (v/v) in both control and treatment groups. Worms were collected at the L4 stage after approximately 46 h exposure.

value: whole organism

value: Bristol N2

value: batch 1


title: primary chondrocyte, control 2

description: Library name: Nf2_D7_CTL2


title: Experiment two, Eomes WT, a41BB treatment, GEX

description: Library name: ASD2_Eomes_WT_41BB_GEX

value: spleen

value: CD4 T lymphocyte

value: Vk*Myc tumor injection, aNK1.1 depeleting antibody injection, agonistic a41BB (also called aCD137) antibody injection, tamoxifen injection


title: AO168O_10000_rep2

description: Library name: c10000_2


title: 2DR1F2HE_S109

description: Library name: 2DR1F2HE_S109_R1_001

value: female

value: 9 weeks

value: Used in Analysis


title: hipsc_young_control_1

description: Library name: YC1

value: hi-psc-N

value: Young control

value: human stem cell derived neuron


title: Experiment one, Eomes WT, a41BB treatment, GEX

description: Library name: ASD1_Eomes_WT_41BB_GEX

value: Eomes-IRES-GFP

value: Vk*Myc tumor injection, aNK1.1 depeleting antibody injection, agonistic a41BB (also called aCD137) antibody injection


title: AO168O_10000_rep1

description: Library name: c10000_1


title: primary chondrocyte, control 1

description: Library name: Nf2_D7_CTL1

value: Cartilage tissue

value: primary chondrocyte

value: control


title: AO168O_2000_rep3

description: Library name: c2000_3

value: whole organism


title: hipsc_ASD_4

description: Library name: AU4

value: Autism Spectrum Disorder


title: AO168O_2000_rep2

description: Library name: c2000_2

value: Bristol N2

value: batch 1


title: AO168O_2000_rep1

description: Library name: c2000_1


title: hipsc_ASD_3

description: Library name: AU3


title: AO168O_400_rep2

description: Library name: c400_2


title: AO168O_400_rep3

description: Library name: c400_3


title: primary chondrocyte, Nf2-knockout 2

description: Library name: Nf2_D7_cKO2

value: TCF21 overexpressing


title: priamry chondrocyte, Nf2-knockout 3

description: Library name: Nf2_D7_cKO3


title: hipsc_ASD_2

description: Library name: AU2


title: 2DR1F1KI_S78

description: Library name: 2DR1F1KI_S78_R1_001

value: Kidney

value: Sprague-Dawley

value: Not Used in Analysis

value: TOTAL ALIGNMENT RATE < 40%


title: AO168O_400_rep1

description: Library name: c400_1


title: AO168O_Ctrl_rep3

description: Library name: control_3

value: no treatment


title: hipsc_ASD_1

description: Library name: AU1

value: hi-psc-N


title: AO168O_Ctrl_rep2

description: Library name: control_2


title: primary chondrocyte, Nf2-knockout 1

description: Library name: Nf2_D7_cKO1


title: Lung cells, N protein + GRP75 shRNA

city: hangzhou

first: REN

last: YICHAO

state: zhejiang

address: zhejianghangzhou

institute: zhejiang university

description:
Library name: Sample_3
10x Genomics scRNA-seq; FACS-sorted macrophages (DAPI- Ly6G- F4/80+ CD11b/c+) mixed with unfractionated lung cells at 4:1 ratio

data_processing:
Demultiplexing and barcode processing were performed using Cell Ranger v9.0 with default settings.
Reads were aligned to mouse reference genome mm10 using Cell Ranger count pipeline.
Gene expression matrices were generated using Cell Ranger with default parameters.
Downstream analysis was performed using Seurat v4.0.0. Cells with <200 or >6000 detected genes, >10% mitochondrial reads, or <500 UMI counts were excluded.
Clustering was performed at resolution 0.8. Cell types were annotated using canonical marker genes.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs (Ensembl)
Supplementary files format and content: matrix.mtx.gz: gene expression count matrix in Matrix Market format

extract_protocol:
Lung tissues were digested in HBSS with collagenase I (2 mg/mL) and DNase I (40 U/mL) at 37°C for 30 min. Single-cell suspensions were prepared and stained with DAPI, anti-Ly6G, anti-F4/80, and anti-CD11b/c antibodies. Macrophages (DAPI- Ly6G- F4/80+ CD11b/c+) were sorted by FACS and mixed with unfractionated lung cells at 4:1 ratio.
Libraries were prepared using 10× Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (PN-1000268) according to manufacturer's protocol. Briefly, cells were loaded onto Chromium Controller to generate gel bead-in-emulsion (GEM). Reverse transcription, cDNA amplification, and library construction were performed following standard 10x Genomics workflow.

value: Lung

tag: cell line

value: mixed (macrophage-enriched)

value: wild type

value: N protein + GRP75 shRNA


title: AO168O_Ctrl_rep1

description: Library name: control_1


title: CUT-Tag of HepG2 :sh-TRIM68-2

city: hefei

first: Yousong

last: Xu

address: huaihe road

department: Department of Critical Care Medicine

institute: The First Affiliated Hospital of Anhui Medical University

description: Library name: SH_H4_2

data_processing:
Raw data were processed with fastp v0.44, including adapter trimming, sliding window quality filtering (Q15), and a minimum read length of 30 bp. Clean reads were aligned to the mouse genome (mm10) with Bowtie2 v2.5 (--very-sensitive preset). SAMtools (v1.19) was used to filter and sort the BAM files, and duplicates were removed with sambamba v0.8. Mitochondrial reads were excluded. CPM-normalized bigWig files were generated using deepTools v3.5 and visualized in IGV v2.16.
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag assays were performed in accordance with the manufacturer's instructions (Novoprotein, N259-YH01).
In brief, 1 × 10⁵ cells were immobilized on Concanavalin A-coated magnetic beads for 15 minutes and permeabilized with 0.05% digitonin. After overnight incubation with primary antibody (Anti-acetyl-Histone H4 Antibody, Merck, 06866) at 4 °C, the cells were incubated with a secondary antibody conjugated to protein A/G. Tagmentation was performed using pA–Tn5 transposase at 37 °C for 1 hour and then terminated with 10% SDS and proteinase K at 55 °C for 10 minutes. Libraries were amplified by PCR (12–18 cycles), purified, and size-selected.


title: Lung cells, N protein + Control shRNA

description:
Library name: Sample_2
10x Genomics scRNA-seq; FACS-sorted macrophages (DAPI- Ly6G- F4/80+ CD11b/c+) mixed with unfractionated lung cells at 4:1 ratio

value: N protein + Control shRNA


title: cldc1 ko larvae BG-input

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

description: Library name: Sample 6

data_processing:
Adaptor sequences were trimmed from raw reads with Trimmomatic to generate clean reads, which were then aligned to the GRCZ11/danRer11 reference genome using BWA.
Peak calling was carried out with MACS2, and read distribution analyses were performed with deepTools toolset.
Assembly: GRCZ11
Supplementary files format and content: BigWig

organism: Danio rerio

source_name: whole body

growth_protocol: The larval fish were maintained in E3 medium and cultured in an incubator at 28°C.

extract_protocol:
WT and cldc1-/- Zebrafish larvae at 2 dpf received β-glucan training through yolk sac microinjection. Four days post-training, larval cells were collected and cross-linked with formaldehyde (37%, Sigma) at 37 °C for 10 min. After fixation, cells were resuspended in SDS buffer and sonicated. Chromatin immunoprecipitation (ChIP) was conducted using a commercial ChIP Assay Kit (Beyotime) with an H3K4me3-specific antibody (GeneTex), following the manufacturer's protocols.
DNA was recovered by phenol/chloroform precipitation and library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit prior to Illumina sequencing (Novaseq PE150).

value: whole body

value: cldc2 KO

value: BG


title: cldc1 ko larvae BG-H3K4me3 ChIP

description: Library name: Sample 5

value: cldc1 KO


title: CUT-Tag of HepG2 :sh-TRIM68-1

description: Library name: SH_H4_1


title: Lung cells, Control shRNA

description:
Library name: Sample_1
10x Genomics scRNA-seq; FACS-sorted macrophages (DAPI- Ly6G- F4/80+ CD11b/c+) mixed with unfractionated lung cells at 4:1 ratio

value: Control shRNA


title: WT larvae BG-input

description: Library name: Sample 4

value: WT


title: CUT-Tag of HepG2 :WT-2

description: Library name: CTRL_H4_2


title: WT larvae BG-H3K4me3 ChIP

description: Library name: Sample 3


title: scSeq night

city: Tel Aviv

first: Yoav

last: Gothilf

address: Sherman Building, room 405

department: Neurobiology

country: Israel

institute: Tel Aviv University

description: Library name: zebrafish_pineal_night

data_processing:
Raw sequencing reads were processed using the 10x Genomics Cell Ranger pipeline (cellranger count). Read 1 (R1) contained cell barcode and UMI sequences (~28 bp). Read 2 (R2) contained cDNA/transcript sequences (~150 bp) and was split into three FASTQ files (001, 002, 003). Reads were aligned to the Danio rerio reference genome GRCz11. Cell Ranger was used for barcode processing, UMI counting, transcript quantification, and generation of filtered gene-barcode count matrices.
Assembly: GRCz11
Supplementary files format and content: Processed data files include filtered sparse gene-barcode count matrices in Matrix Market format (matrix.mtx.gz), barcode tables (barcodes.tsv), and gene feature annotations (features.tsv.gz) generated using 10x Genomics Cell Ranger.

source_name: Pineal gland

growth_protocol: 14h-10h light/dark cycles, at 28°C

extract_protocol:
Pineal glands were dissected and enzymatically dissociated in papain to produce isolated cells. This single-cell suspension was then loaded onto a commercially available droplet-based 10x Chromium system (v3 platform, 10x genomics).
Libraries were constructed using 10x Genomics' Single Cell 3’ Reagent Kit v3 according to the manufacturer's instructions

value: Pineal gland


title: Cerebral Cortex, E14.5, KO

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Library name: Sample 4

data_processing:
Raw sequencing reads were processed through a standard UMI based preprocessing pipeline. FASTQ files were assessed with FastQC v0.12.1 to evaluate per base sequence quality and potential adapter contamination. Gene quantification was performed by collapsing UMIs per gene per cell to remove PCR duplicates, yielding a digital gene expression matrix. Droplet filtering was based on total UMI content to distinguish high complexity cell-containing droplets from background. All droplets were retained regardless of gene count, transcript count, or mitochondrial transcript percentage thresholds, and no upper limits were applied to these metrics. Genes were included in the dataset if expressed in at least three cells. The resulting matrix was filtered only for genes with zero detection across all cells.
Data preprocessing was performed using Cytonaut cloud service by Scipio Bioscience. Raw count matrices for WT and TSK-KO E14.5 and P0 samples were imported using the ReadMtx function in Seurat v5 (Hao et al., 2024) using R v4.3.2. Each dataset consisted of a sparse matrix file together with the associated barcode and feature annotation tables. Separate Seurat objects were generated for each sample with a minimum cell filter of 10 detected cells.  Quality control metrics were computed by quantifying the proportion of mitochondrial transcripts using PercentageFeatureSet. Normalization and variance stabilization were performed with SCTransform (Stuart et al., 2019) while regressing out mitochondrial content and highly variable genes (HVG, n=3000) were identified. Principal component analysis was applied to the transformed expression matrix.
Assembly: GRCm39
Supplementary files format and content: barcodes, features in tab delimited files and matrix files (mtx)

source_name: cerebral cortex

extract_protocol:
Cerebral cortex tissues were dissected from one WT and one TSK-KO mouse at E14.5 and P0, cut into small pieces, and dissociated by trypsin treatment for 8 minutes at 37 oC and gentle pipetting in the presence of trypsin inhibitors. Each sample was then diluted with DMEM/F12 + 10% FCS medium, passed through a 70 μm siever and centrifuged at 1200 rpm for 3 minutes. The resulting cell pellets were resuspended with 1 ml DMEM/F12 + 10% FCS medium, followed by cell counting.
50000 cells of each sample were processed with the Asteria(TM) single-cell RNA-seq benchtop kit (Scipio Bioscence) according to manufacturer instructions, using 15000 cells per sample as input for cell coupling to capture beads, cell lysis, reverse transcription and amplification steps. Amplified DNAs were quantified using Qubit (Invitrogen) and run on TapeStation (Agilent). 3 ng of each DNA were used for library preparation using NEBNext Ultra II FS DNA Library Prep kit for Illumina and NEBNext Multiplex Oligos for Illumina (New England Biolabs) along with the Library Prep Primer included in the Asteria kit. The librariers were quantified using Qubit, run on TapeStation and sequenced with Illumina NovaSeq 6000 SP Reagent Kit (100 cycles; read 1: 25 cycles; index: 6 cycles; read 2: 75 cycles) using the Read1 Custom Primer included in the Asteria kit.

value: cerebral cortex

value: KO


title: WT larvae PBS-input

description: Library name: Sample 2

value: PBS


title: WT larvae PBS-H3K4me3 ChIP

description: Library name: Sample 1


title: PC-3 cells, untreated, replicate 3

city: Nanjing

first: Congjie

last: He

state: Jiangsu

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine

description:
Library name: PC-3_Control_3
PC-3 cells cultured in standard conditions.

data_processing:
Raw data (raw reads) of fastq format were first processed using fastp. 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.
Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome (GRCh38) using STAR (v2.7.6a).
Gene expression levels were quantified using featureCounts (v1.6.4) by counting the number of reads mapped to each gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing gene identifiers (Gene Symbol or Ensembl ID) and normalized expression values (FPKM or TPM) as well as raw counts for each sample.Each column corresponds to a sample listed in the SAMPLES section.

source_name: Prostate

growth_protocol: LNCaP and PC-3 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer's protocol. RNA integrity was assessed using the Agilent 2100 Bioanalyzer, and only high-quality RNA (RIN ≥ 7.0) was used for library construction.
Sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer's recommendations. Poly(A) mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in the NEBNext First Strand Synthesis Reaction Buffer (5X).

treatment_protocol: Cells were treated with Genistein or Baicalein at concentrations of 10 µM or 20 µM for 24 hours. The control group was treated with the vehicle (DMSO) only.

value: Prostate

value: prostate cancer cell

value: untreated


title: Cerebral Cortex, E14.5, WT

description: Library name: Sample 3


title: CUT-Tag of HepG2 :WT-1

description: Library name: CTRL_H4_1


title: WT rep 2, 2 wpi

city: Singapore

first: Chao

last: Gao

address: 14 Science Drive 4

country: Singapore

institute: National University of Singapore

data_processing:
Quality check was using FastQC v0.11.5
Genome mapping was using Kallisto 0.45.0
Read counting was using sleuth 0.30.0
Assembly: GRCz11
Supplementary files format and content: Raw counts for each sample

source_name: Liver

extract_protocol:
RNA was extracted using TRIzol reagent following manufacturer's protocol
RNA libraries for RNA-seq were prepared using the TruSeq Stranded Total RNA sample preparation kit

value: Liver

value: Mifepristone


title: WT rep 3, 2 wpi


title: Cerebral Cortex, P0, KO

description: Library name: Sample 2


title: WT rep 1, 2 wpi


title: ATG5 rep 3, 2 wpi

value: ATG5 overexpression


title: PC-3 cells, untreated, replicate 2

description:
Library name: PC-3_Control_2
PC-3 cells cultured in standard conditions.

value: wild type


title: Cerebral Cortex, P0, WT

description: Library name: Sample 1


title: ATG5 rep 2, 2 wpi


title: PC-3 cells, untreated, replicate 1

description:
Library name: PC-3_Control_1
PC-3 cells cultured in standard conditions.


title: protein13

description:
Library name: DSP-1001660022162-A-G12-Y
DSP-1001660022162-A-G12.stats.txt
DSP-1001660022162-A-G12.dcc

data_processing:
Spatial proteogenomic and transcriptomic data were generated on the GeoMx DSP platform and processed with the GeoMxWorkflows R package (v1.0+) following the standard NanoString pipeline. Raw DCC files were imported with corresponding PKC files and sample annotations using readNanoStringGeoMxSet. Segment-level QC required: minimum total reads ≥1,000, trimmed reads ≥80%, stitched reads ≥80%, aligned reads ≥75%, sequencing saturation ≥50%, negative control counts ≥1, NTC counts ≤9,000, nuclei count ≥20, and segment area ≥1,000 μm². Probe-level QC was performed with setBioProbeQCFlags (minimum probe ratio 0.1; maximum percentage failing Grubbs test 20%; local outlier removal enabled), and probes failing these metrics or flagged as global Grubbs outliers were excluded. Probe counts were aggregated to genes with aggregateCounts. For each segment, the limit of quantification (LOQ) was defined as the geometric mean of negative controls plus 2 SD, with a minimum LOQ of 2 counts. Segments with <5% gene detection were removed, and genes detected above LOQ in <10% of segments were excluded (negative control probes retained for normalization). The final dataset comprised 7,709 genes across 65 high-quality segments. Spatial multi-omics data from all metastases samples were obtained from both PanCK+ tumor cell regions and CD45+ immune cell regions. Sample identifiers were standardized by combining scan names with ROI identifiers to ensure proper matching between expression data and metadata across both data modalities. Low-expression gene filtering was applied independently to brain and bone datasets using stringent criteria: genes were retained only if they showed ≥1 count in ≥3 samples per tissue type to ensure adequate gene coverage.
The PKC are
(v1.0) Human Procode NGS Core Protein (Lot Number: 519184)
(v1.1) Human Procode NGS IPA Protein (Lot Number: 512044)
(v1.0) Human NGS Whole Transcriptome Atlas RNA (Lot Number: HW0050423)
In the following link
https://brukerspatialbiology.com/products/geomx-digital-spatial-profiler/geomx-dsp-configuration-files/
Assembly: GRCh38
Supplementary files format and content: .csv, dcc
Supplementary files format and content: The RNA_Pro__Exp.csv, WTAONLY_Exp_NEW.csv files were generated from the .dcc file, the readout of gene expression and the protein (the first row =  the sample id,  and the first column = RNA/protein name).
Supplementary files format and content: When dcc was generated from merged/multiple samples, the file is linked to the first sample records and listed in the corresponding sample description field
Library strategy: Spatial Transcriptomics

value: Bone


title: ATG5 rep 1, 2 wpi


title: Experiment two, Eomes WT, a41BB treatment, VDJ

description: Library name: ASD2_Eomes_WT_41BB_VDJ

value: spleen

value: CD4 T lymphocyte

value: Eomes-IRES-GFP

value: Vk*Myc tumor injection, aNK1.1 depeleting antibody injection, agonistic a41BB (also called aCD137) antibody injection, tamoxifen injection


title: not5 S288C, AZC 45min, biol rep 4, flowcell 2

city: Baltimore

first: Jeff

last: Coller

state: MD

address: 725 N Wolfe St

institute: Johns Hopkins University

description:
Library name: not5_AZC_4_f2
flowcell 2

data_processing:
All FASTQ files were passed through FASTQC (v0.12.1) to identify possible adapter contamination or sequencing biases prior to mapping. Untrimmed FASTQs were ultimately piped directly to Salmon v1.10.2 for quasi-mapping and transcript abundance estimation using the following parameters: -l  A --validateMappings, using a decoy-aware index generated from the NCBI RefSeq S288C genome assembly R64 GCF_000146045.2.
Assembly: NCBI Saccharomyces cerevisiae S288C Genome Assembly R64 (GCF_000146045.2)
Supplementary files format and content: The processed data is a data frame in tab-delimited format with samples as columns and genes as rows (using RefSeq accessions). Cells contain estimated counts output directly from Salmon quasi-mapping. Samples from the two flowcells used in this study are joined into one data frame, and annotated accordingly (flowcell 1 = f1, flowcell 2 = f2). The gene accessions are under row 'geneID'.

organism: Saccharomyces cerevisiae S288C

growth_protocol: Cells were seeded at an OD600 of 0.1 in YPD media and grown at room temperature to an OD600 of 0.4, at which time treatment was performed.

extract_protocol:
Cell pellets were resuspended in 200 µL Phenol/LET (100 mM LiCl, 20 mM EDTA, 25 mM Tris-HCl pH 8) and approximately 200 µL of glass microbeads were added to lyse the cells. After vortexing for 5 minutes at room temperature, 300 µL of Phenol/Chloroform/LET and 300 µL DEPC-treated water was added. After 5 minutes of additional vortexing, and spinning down for 5 minutes at 16,000 x g at room temperature, aqueous phase was collected and added to 500 µL Phenol/Chloroform/LET, vortexed for 5 minutes and spun down. Aqueous phase was collected and added to 500 µL Chloroform, vortexed for 5 minutes, and spun down. Aqueous phase was collected, 40 µL of 3 M Sodium Acetate (final concentration 0.3 M), 1 mL 100% ethanol was added to precipitate RNA at -20°C for approximately 1 hour. RNA was pelleted by spinning at 16,000 x g for 20 minutes at room temperature, washed with 75% ethanol, air dried, and resuspended in DEPC-treated water.
RNA was isolated by Phenol-Chloroform extraction and ethanol precipitation. After confirming the quality of RNA via ScreenTape Analysis (Agilent 5067-5576, 5577, 5578), 1 µg total RNA was poly(A)-selected using oligo-dT beads (NEB E7490S) and mRNA libraries were prepared using Ultra II RNA library prep kit (NEB E7770L) and Unique Dual Index (NEB E6440S, E6442S). Libraries were quantified with DNA High Sensitivity ScreenTape Analysis (Agilent 5067-5584, 5585) and the pooled library was sequenced on a NovaSeq X Plus in Johns Hopkins Genetic Resources Core Facility.

treatment_protocol: Once samples reached an OD600 of 0.4, AZC (final 2mg/mL) or an equal volume of sterile water vehicle was added, and cells were grown at room temperature for 45 minutes before pelleting via centrifugation, freezing, and RNA extraction.

value: AZC


title: FOLFOX+PROBIOTICS38

city: lanzhou

first: Hu

last: Chen

state: Gansu

address: Lanzhou University, Lanzhou City, Gansu Province, China, lanzhou, Gansu, 730000, China

institute: Lanzhou University

description: Library name: Sample 9

data_processing:
Raw sequencing data in BCL format were converted to FASTQ files using bcl2fastq (Illumina). Subsequent data processing involved alignment to the reference genome, barcode processing, and unique molecular identifier (UMI) counting for each cell using the CellRanger pipeline (10X Genomics). Downstream analysis was performed with Seurat (version 4.1.0) in R. Low-quality cells were filtered out based on user-defined thresholds for metrics such as the number of detected genes and mitochondrial gene content. The filtered gene-cell matrix was then normalized, scaled, and subjected to dimensionality reduction.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: subcutaneous tumor

extract_protocol:
Subcutaneous tumors were harvested from tumor-bearing mice and processed into single-cell suspensions. Approximately 12,000 cells per sample were targeted for capture using the 10X Genomics Chromium Single Cell 3' Kit (v3) on a 10X Chromium chip.
Library preparation and sequencing were conducted by LC-Bio Technology Co., Ltd. (Hangzhou, China) on an Illumina NovaSeq 6000 platform, employing a paired-end 150 bp sequencing strategy to achieve a minimum sequencing depth of 20,000 reads per cell.

value: subcutaneous tumor

value: combined probiotic consortium plus FOLFOX intervention


title: LNCaP cells, baicalein20μM, replicate 3

description:
Library name: LNCaP--baicalein20μM_3
LNCaP cells cultured in standard conditions.

value: LNCaP

value: baicalein 20 µM


title: 2DR1F5KI_S98

first: Scott

last: Auerbach

address: 111 TW Alexander Drive

description: Library name: 2DR1F5KI_S98_R1_001

data_processing:
TempO-Seq sequences were aligned to the rat S1500+ probe sequences using Bowtie version 1.3.1. The Bowtie configuration allowed up to three mismatches and selected the single best alignment for reporting.
The aligned read counts for attenuated probes were properly readjusted to calculate unattenuated equivalent counts using the attenuation factors provided in the platform manifest.
Assembly: BioSpyder TempO-seq rat S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

extract_protocol:
The majority of all tissues from all animals were collected within approximately 10 minutes of euthanasia. Tissue samples were collected following organ weight measurements in the following order: lung, heart, liver (left lobe), kidney, and ovary (no ovary weights were taken) from all remaining animals on study day 5 for transcriptomic analysis. Two samples of lung, heart, liver, and kidney tissue (approximately 5 mm3) were collected and placed into cryotubes containing RNAlater. The ovaries were collected whole bilaterally (one sample) and placed into cryotubes containing RNAlater. The tissue samples were stored at 2°C to 8°C for approximately 55 hours for rats or up to 48 hours for mice. The RNAlater was then removed and the samples were stored in a −85°C to −60°C freezer until processed for RNA isolation. Tissues were homogenized in QIAzol lysis buffer (Qiagen Inc., Valencia, CA) using the TissueLyser II bead-beating system followed by RNA extraction using the RNeasy 96 QIAcube HT kits (Qiagen Inc., Valencia, CA) with a DNA digestion step.
Isolated RNA was utilized for analysis using either the Rat S1500+ v1.2 TempO-Seq (BioSpyder, Carlsbad, CA) platform with a minimum of 500 mapped read counts/transcript and approximately 1.5 million counts/sample. Work instructions developed by Battelle using the BioSpyder User Guide (https://www.biospyder.com/s/100802-TempO-Seq-User-Guide-rev-C-r8r7.pdf) were followed.

value: Kidney

value: Sprague-Dawley

value: female

value: 9 weeks

value: Used in Analysis


title: FOLFOX+PROBIOTICS33

description: Library name: Sample 8


title: not5 S288C, AZC 45min, biol rep 3, flowcell 2

description:
Library name: not5_AZC_3_f2
flowcell 2


title: not5 S288C, AZC 45min, biol rep 2, flowcell 2

description:
Library name: not5_AZC_2_f2
flowcell 2


title: not5 S288C, AZC 45min, biol rep 1, flowcell 2

description:
Library name: not5_AZC_1_f2
flowcell 2


title: LNCaP cells, baicalein20μM, replicate 1

description:
Library name: LNCaP--baicalein20μM_1
LNCaP cells cultured in standard conditions.

value: Prostate

value: prostate cancer cell


title: not5 S288C, veh 45min, biol rep 4, flowcell 2

description:
Library name: not5_veh_4_f2
flowcell 2

value: Vehicle


title: FOLFOX+PROBIOTICS32

description: Library name: Sample 7


title: not5 S288C, veh 45min, biol rep 3, flowcell 2

description:
Library name: not5_veh_3_f2
flowcell 2


title: FOLFOX25

description: Library name: Sample 6

value: FOLFOX chemotherapy‑only


title: 2DR1F4LU_S96

description: Library name: 2DR1F4LU_S96_R1_001

source_name: Lung

value: Lung


title: LNCaP cells, baicalein20μM, replicate 2

description:
Library name: LNCaP--baicalein20μM_2
LNCaP cells cultured in standard conditions.

value: wild type


title: not5 S288C, veh 45min, biol rep 2, flowcell 2

description:
Library name: not5_veh_2_f2
flowcell 2


title: not5 S288C, veh 45min, biol rep 1, flowcell 2

description:
Library name: not5_veh_1_f2
flowcell 2


title: WT S288C, AZC 45min, biol rep 4, flowcell 2

description:
Library name: WT_AZC_4_f2
flowcell 2

value: WT


title: LNCaP cells, genistein20μM, replicate 3

description:
Library name: LNCaP--genistein20μM_3
LNCaP cells cultured in standard conditions.

value: genistein 20 µM


title: FOLFOX18

description: Library name: Sample 5

value: subcutaneous tumor


title: LNCaP cells, genistein20μM, replicate 2

description:
Library name: LNCaP--genistein20μM_2
LNCaP cells cultured in standard conditions.


title: WT S288C, AZC 45min, biol rep 3, flowcell 2

description:
Library name: WT_AZC_3_f2
flowcell 2

value: AZC


title: FOLFOX17

description: Library name: Sample 4


title: WT S288C, AZC 45min, biol rep 1, flowcell 2

description:
Library name: WT_AZC_1_f2
flowcell 2


title: LNCaP cells, genistein20μM, replicate 1

description:
Library name: LNCaP--genistein20μM_1
LNCaP cells cultured in standard conditions.

value: LNCaP


title: WT S288C, AZC 45min, biol rep 2, flowcell 2

description:
Library name: WT_AZC_2_f2
flowcell 2


title: WT S288C, veh 45min, biol rep 4, flowcell 2

description:
Library name: WT_veh_4_f2
flowcell 2


title: NC12

description: Library name: Sample 3

value: untreated


title: LNCaP cells, baicalein10μM, replicate 3

description:
Library name: LNCaP--baicalein10μM_3
LNCaP cells cultured in standard conditions.

value: baicalein 10 µM


title: WT S288C, veh 45min, biol rep 3, flowcell 2

description:
Library name: WT_veh_3_f2
flowcell 2


title: WT S288C, veh 45min, biol rep 2, flowcell 2

description:
Library name: WT_veh_2_f2
flowcell 2


title: LNCaP cells, baicalein10μM, replicate 2

description:
Library name: LNCaP--baicalein10μM_2
LNCaP cells cultured in standard conditions.


title: NC6

description: Library name: Sample 2


title: WT S288C, veh 45min, biol rep 1, flowcell 2

description:
Library name: WT_veh_1_f2
flowcell 2


title: NC2

description: Library name: Sample 1


title: zuo1 S288C, AZC 45min, biol rep 3, flowcell 1

description:
Library name: zuo1_AZC_3_f1
flowcell 1


title: zuo1 S288C, AZC 45min, biol rep 4, flowcell 1

description:
Library name: zuo1_AZC_4_f1
flowcell 1


title: Retroperitoneal leiomyosarcoma,Adjacent non-tumor tissue3

city: guangzhou

first: mengye

last: he

state: guangdong

address: guangzhou

institute: guangzhoucunzhongkeji

description: Library name: FMC3

data_processing:
Raw sequencing reads in FASTQ format were first assessed for quality using FastQC (v0.11.9). Adapter sequences and low-quality bases (Q < 20) were trimmed with Trimmomatic (v0.39) or fastp (v0.23.2) with the following parameters: leading:3, trailing:3, sliding_window:4:20, minlen:50. Cleaned reads were then aligned to the reference genome (Homo sapiens GRCh38.p13 or Mus musculus GRCm39) using STAR (Spliced Transcripts Alignment to a Reference, v2.7.10b) with two-pass alignment for improved splice junction detection.  Gene-level read counts were quantified from aligned BAM files using featureCounts (part of Subread package, v2.0.3), based on annotations from Ensembl Release 104 (or GENCODE v44). Only primary alignments were included, and reads overlapping exons of protein-coding genes were counted under a union model.  To enable cross-sample comparison, raw read counts were normalized into Transcripts Per Million (TPM) values as follows:  For each gene, fragments per kilobase (FPK) was calculated by dividing the number of mapped fragments by the gene length in kilobases. The sum of FPK values across all genes in each sample was computed and divided by 1,000,000 to obtain a scaling factor. TPM for each gene = FPK / scaling factor. TPM values were used for downstream analyses including gene expression profiling, clustering (hierarchical clustering and PCA), differential expression analysis (using edgeR or DESeq2), and pathway enrichment (e.g., GO, KEGG via clusterProfiler)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: control 3

extract_protocol:
RNA was harvested using  Trizol Kit (BeyoPure). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was extracted from [tissue/cell line] samples using the BeyoPure™ Total RNA Extraction and Purification Kit (Beyotime Biotechnology, China, Cat# RN0516) according to the manufacturer’s instructions. RNA quality was assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies), with all samples exhibiting RNA Integrity Number (RIN) > 8.0. Poly(A)+ mRNA was enriched from total RNA using oligo(dT) magnetic beads. The RNA was then fragmented into short fragments (approximately 200–300 bp) under elevated temperature in fragmentation buffer. First-strand cDNA was synthesized using reverse transcriptase and random hexamer primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The double-stranded cDNA libraries were constructed by end repair, 3'-end adenylation, adapter ligation, and size selection using AMPure XP beads (Beckman Coulter). Libraries were amplified by PCR and purified again. Finally, library quality was validated on the Bioanalyzer, and quantification was performed using qPCR. Libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp (PE150) reads

value: control 3


title: zuo1 S288C, AZC 45min, biol rep 2, flowcell 1

description:
Library name: zuo1_AZC_2_f1
flowcell 1


title: LNCaP cells, genistein10μM, replicate 3

description:
Library name: LNCaP--genistein10μM_3
LNCaP cells cultured in standard conditions.

value: genistein 10 µM


title: LNCaP cells, baicalein10μM, replicate 1

description:
Library name: LNCaP--baicalein10μM_1
LNCaP cells cultured in standard conditions.


title: zuo1 S288C, AZC 45min, biol rep 1, flowcell 1

description:
Library name: zuo1_AZC_1_f1
flowcell 1


title: Retroperitoneal leiomyosarcoma,Adjacent non-tumor tissue2

description: Library name: FMC2

source_name: control 2

value: control 2


title: zuo1 S288C, veh 45min, biol rep 4, flowcell 1

description:
Library name: zuo1_veh_4_f1
flowcell 1


title: LNCaP cells, genistein10μM, replicate 2

description:
Library name: LNCaP--genistein10μM_2
LNCaP cells cultured in standard conditions.


title: zuo1 S288C, veh 45min, biol rep 3, flowcell 1

description:
Library name: zuo1_veh_3_f1
flowcell 1


title: Retroperitoneal leiomyosarcoma,Adjacent non-tumor tissue1

description: Library name: FMC1

source_name: control 1

value: control 1


title: zuo1 S288C, veh 45min, biol rep 2, flowcell 1

description:
Library name: zuo1_veh_2_f1
flowcell 1


title: LNCaP cells, genistein10μM, replicate 1

description:
Library name: LNCaP--genistein10μM_1
LNCaP cells cultured in standard conditions.

value: Prostate


title: Retroperitoneal leiomyosarcoma, tumor tissue3

description: Library name: FMT3

source_name: tumor 3

value: tumor 3


title: zuo1 S288C, veh 45min, biol rep 1, flowcell 1

description:
Library name: zuo1_veh_1_f1
flowcell 1

value: Vehicle


title: WT S288C, AZC 45min, biol rep 3, flowcell 1

description:
Library name: WT_AZC_3_f1
flowcell 1


title: WT S288C, AZC 45min, biol rep 4, flowcell 1

description:
Library name: WT_AZC_4_f1
flowcell 1


title: LNCaP cells, untreated, replicate 3

description:
Library name: LNCaP_Control_3
LNCaP cells cultured in standard conditions.

value: prostate cancer cell


title: WT S288C, AZC 45min, biol rep 2, flowcell 1

description:
Library name: WT_AZC_2_f1
flowcell 1


title: 2DR2F101LU_S108

institute: Division of the National Toxicology Program at NIEHS

description: Library name: 2DR2F101LU_S108_R1_001

value: Lung

value: Sprague-Dawley

value: female

value: 9 weeks

value: Used in Analysis


title: Retroperitoneal leiomyosarcoma, tumor tissue2

description: Library name: FMT2

source_name: tumor 2

value: tumor 2


title: LNCaP cells, untreated, replicate 2

description:
Library name: LNCaP_Control_2
LNCaP cells cultured in standard conditions.

value: LNCaP

value: wild type


title: WT S288C, AZC 45min, biol rep 1, flowcell 1

description:
Library name: WT_AZC_1_f1
flowcell 1

value: WT

value: AZC


title: Retroperitoneal leiomyosarcoma, tumor tissue1

description: Library name: FMT1

source_name: tumor 1

value: tumor 1


title: WT S288C, veh 45min, biol rep 4, flowcell 1

description:
Library name: WT_veh_4_f1
flowcell 1


title: LNCaP cells, untreated, replicate 1

description:
Library name: LNCaP_Control_1
LNCaP cells cultured in standard conditions.

value: untreated


title: WT S288C, veh 45min, biol rep 3, flowcell 1

description:
Library name: WT_veh_3_f1
flowcell 1


title: WT S288C, veh 45min, biol rep 2, flowcell 1

description:
Library name: WT_veh_2_f1
flowcell 1


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L single-cell, castrated, Sx682, ICB, replicate 2, hashtag TotalSeq-A0308

city: Notre Dame

first: Ziyu

last: Zeng

state: Indiana

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

description: Library name: TKO_CSI2_HTO

data_processing:
(Bulk RNA-seq) Aligned to GRCm39 with STAR v2.7.11a. Differential expression via DESeq2 v1.48.2, rlog variance stabilization. Pathways analyzed with fgsea v1.34.2 and GSVA v2.2.0.
(scRNA-seq) Cell Ranger Multi v8.0.1 demultiplexing. Seurat v5.3.0: filtered 100-9069 genes/cell, <29430 UMI, <25% mitochondrial, doublets removed (scDblFinder). SCTransform normalization regressing cell cycle and mitochondrial content. Louvain clustering (resolution=1.0), 50 PCs for tSNE. Cell types annotated using SingleR + Azimuth + manual curation.
Assembly: GRCm39 (mm39)
Supplementary files format and content: comma-separated file containing bulk RNA-seq raw read counts for all samples; comma-separated file containing tpm normalized counts
Supplementary files format and content: h5 files for single-cell raw counts each individual sample, demultiplexed from cellranger multi; processed seurat object as R object (rds)

source_name: prostate tumor

growth_protocol: Nkx3.1-CreERT2/+ mice with floxed Pten, Smad4, and Pygo2 alleles received tamoxifen (1 mg IP daily × 5 days) at 1-4 months to induce prostate tumorigenesis. Tumors harvested at 10 weeks (DKO) or 17 weeks (TKO) post-induction for RNA-seq.

extract_protocol:
Total RNA isolated using Direct-zol RNA MiniPrep Kit (Zymo R2050). For scRNA-seq: tumors dissociated with Mouse Tumor Dissociation Kit (Miltenyi 130-096-730), 1-2h 37°C, filtered through 40-μm strainer, dead cell depleted with EasySep Annexin V kit (STEMCELL 17899), TotalSeq-A hashtag A0303-A0308 applied.
Bulk RNA-seq: standard Illumina library prep
scRNA-seq: 10x Chromium Single Cell 3' v3 chemistry. Six tumor samples were individually labeled with TotalSeq-A hashtag oligonucleotides (BioLegend): DKO replicate 1 (A0303), DKO replicate 2 (A0304), TKO replicate 1 (A0305), TKO replicate 2 (A0306), TKO+CSI replicate 1 (A0307), TKO+CSI replicate 2 (A0308). After hashing, samples were pooled in equal proportions and loaded onto 10x Chromium Controller for library preparation with feature barcoding enabled.

treatment_protocol: CSI treatment: surgical castration + SX-682 medicated chow (1428.5 mg/kg, 200 mg/kg/day equivalent) + anti-PD1 (10 mg/kg) + anti-CTLA4 (10 mg/kg) IP twice weekly × 4 doses.

value: prostate tumor


title: WT S288C, veh 45min, biol rep 1, flowcell 1

description:
Library name: WT_veh_1_f1
flowcell 1


title: MM217 H3k27Ac epicypher REP1

first: Giacomo

last: Corleone

address: via chianesi 43

institute: IRCCS Regina Elena National Cancer Institute

description:
Library name: H3k27Ac-REP1-epicypher
BigWig

data_processing:
Peaks built by applying nextflow standard cut&tag pipeline:  NXF_VER=24.10.0 nextflow run nf-core/cutandrun -r 3.2.1 - -profile docker --normalisation_mode CPM --peakcaller macs2
Assembly: HG38
Supplementary files format and content: MACS2 Command line: callpeak --nomodel --shift -75 --extsize 150 --keep-dup all -q 0.01 --gsize 2.7E+9 --format BAMPE
Library strategy: CUT&Tag

source_name: Bone Marrow

growth_protocol: optimem medium supplemented with 15% FBS inactived, 1% L-Glutamine and 0,1% Gentamicin. Cells were cultured at 37°C, in a humidified atmosphere with 5% CO2 and mycoplasma contamination was periodically checked by polymerase chain reaction (PCR) analysis.

extract_protocol:
we followed the experimental procedure of the kits employed.
we followed the experimental procedure of the kits employed.

value: Bone Marrow

value: Plasma Cell CD138+


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L single-cell, castrated, Sx682, ICB, replicate 1, hashtag TotalSeq-A0307

description: Library name: TKO_CSI1_HTO


title: Daily 4PM bat6

city: College Station

first: Michael

last: Smotherman

state: Texas

address: 3258 TAMU

department: Biology

institute: Texas A&M University

description: Library name: 102122121

data_processing:
Quality checking of reads and trimming used TrimGalore 0.6.7
Alignment of trimmed reads to genome used STAR Aligner 2.7.10b
HTSeq-Count 2.0.1 was used to generate counts based on read alignment
Assembly: Tadarida brasiliensis genome, NCBI Accession number: PRJNA972445 under Bat1K BioProject PRJNA489245
Supplementary files format and content: HTSeq-Count output text (.txt) files, counts based on species' genome

organism: Tadarida brasiliensis

source_name: whole eyes

extract_protocol:
Promega Maxwell automated workflow for extraction, conducted at MedGenome Inc
Library prep used Takara SMART-Seq v4 Ultra-low Input RNA kit, conducted at MedGenome Inc

treatment_protocol: Extracted tissue were flash frozen using liquid nitrogen and stored at -80°C before being shipped to sequencing

value: whole eyes

value: male


title: MM217 H3k27Ac epicypher REP2

description:
Library name: H3k27Ac-REP2-epicypher
BigWig


title: Daily 4PM bat4

description: Library name: 102122101


title: MM217 H3k27Ac vazyme REP1

description:
Library name: H3K27Ac-REP1-vazyme
BigWig


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L single-cell, untreated, replicate 2, hashtag TotalSeq-A0306

description: Library name: TKO2_HTO


title: Daily 4PM bat3

description: Library name: 102122091


title: S3-LCM46

first: Young Chul

last: Kim

address: 3350 La Jolla Village Dr

institute: University of California-San Diego

description: Library name: S3-LCM46

data_processing:
nf-core/rnaseq analysis pipeline (v3.16.0) with the Nextflow workflow manager (v23.10.0)
Assembly: GRCm38, Ensembl release 101
Supplementary files format and content: txt file with log10 (TPM) of genes for each sample

source_name: Kidney

extract_protocol:
Total RNA was isolated from 70-80 microdissected SGLT2-negative LTL-positive tubules per sample using Arcturus PicoPure frozen RNA isolation kit and additional gDNA digestion was performed via Arcticzymes Heat & Run gDNA removal kit.
Quality and quantity of total RNA were determined by High Sensitive Tape Analysis, and cDNA library was prepared using SMARTer Stranded Total RNA-seq Kit v3-Pico Input Mammalian with 0.5 ng total RNA (DV200>30%).

value: Kidney

value: Sglt1 KO/Akita

value: Dapagliflozin


title: Daily 4PM bat5

description: Library name: 102122111


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L single-cell, untreated, replicate 1, hashtag TotalSeq-A0305

description: Library name: TKO1_HTO


title: Daily 4PM bat2

description: Library name: 102122081

value: female


title: Daily 4PM bat1

description: Library name: 102122071


title: MM217 H3k27Ac vazyme REP2

description:
Library name: H3K27Ac-REP2-vazyme
BigWig


title: Daily 10AM bat6

description: Library name: 100722061


title: PC_006, Carcinoma, CDC73 mut

city: Seoul

first: Jong-Il

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description: Library name: CHR0387

data_processing:
Base call files were processed with Cell Ranger v8.0.1 (10x Genomics) using the refdata-gex-GRCh38-2024-A reference to generate gene–barcode matrices. To reduce background contamination from ambient RNA, raw feature-barcode matrices were processed using CellBender v0.3.0 remove-background prior to downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file listing cell barcodes.
Supplementary files format and content: Tab-delimited file listing gene symbols.
Supplementary files format and content: Tab-delimited matrix of raw gene expression counts (genes as rows and cells as columns).

source_name: Parathyroid Carcinoma

extract_protocol:
Parathyroid adenoma and carcinoma tissues were dissociated into single-cell suspensions using the Tumor Dissociation Kit, human (Miltenyi Biotec) and the gentleMACS Octo Dissociator with heaters (Miltenyi Biotec) using program 37C_h_TDK_1 for 30–45 min, according to the manufacturer’s protocol.
Cell suspensions were filtered through 100 μm strainers, centrifuged at 400 × g for 5 min at 4 °C, and resuspended in 0.04% bovine serum albumin (BSA) in PBS at an appropriate concentration for 10x Genomics loading. All libraries were sequenced using NovaSeq 6000 system (Illumina) in paired-end mode.

value: Parathyroid Carcinoma

value: CDC73 mutant


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L single-cell, untreated, replicate 2,hashtag TotalSeq-A0304

description: Library name: DKO2_HTO

value: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L


title: Daily 10AM bat5

description: Library name: 100722051


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L single-cell, untreated, replicate 1, hashtag TotalSeq-A0303

description: Library name: DKO1_HTO


title: PA_008, Adenoma, WT

description: Library name: CHR0386

source_name: Parathyroid Adenoma

value: Parathyroid Adenoma

value: CDC73 WT


title: Daily 10AM bat4

description: Library name: 100722041


title: Daily 10AM bat3

description: Library name: 100722031


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L KO single-cell, castrated, Sx682, ICB, replicate 2

description: Library name: TKO_CSI2_cDNA


title: PC_005, Carcinoma, WT

description: Library name: CHR0367


title: Daily 10AM bat2

description: Library name: 100722021


title: Daily 10AM bat1

description: Library name: 100722011


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L single-cell, castrated, Sx682, ICB, replicate 1

description: Library name: TKO_CSI1_cDNA


title: Daily 4AM bat6

description: Library name: 102122061


title: PA_007, Adenoma, WT

description: Library name: CHR0315


title: Daily 4AM bat5

description: Library name: 102122051


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L single-cell, untreated, replicate 2

description: Library name: TKO2_cDNA


title: Daily 4AM bat4

description: Library name: 102122041


title: PC_004, Carcinoma, CDC73 mut

description: Library name: CHR0276


title: Daily 4AM bat3

description: Library name: 102122031


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L single-cell, untreated, replicate 1

description: Library name: TKO1_cDNA


title: Daily 4AM bat2

description: Library name: 102122021


title: PC_002, Carcinoma, WT

description: Library name: CHR0248


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L single-cell, untreated, replicate 2

description: Library name: DKO2_cDNA


title: PA_006, Adenoma, WT

description: Library name: CHR0252


title: O4_Muscle

city: Vienna

first: Peter

last: Pietschmann

state: Vienna

address: Währinger Gürtel 18-20

country: Austria

institute: Institute of Pathophysiology and Allergy Research

description: Library name: O4_Mu_MKRN250005748-1A_22

data_processing:
Base calling used CASAVA, and demultiplexing and FASTQ generation were performed with bcl2fastq (Illumina).
The Nothobranchius furzeri genome (Ensembl Release 113, 2024-08-14) and annotation were downloaded from Ensembl FTP repository (version 2024-08-14) . Read quality was assessed with FastQC v0.12.1 . Available online at:  and summarized using MultiQC v1.28 . Adapter trimming and quality filtering were performed with Trim Galore v0.6.10 . An average of ~40 million reads per sample were aligned to the Nfu genome using STAR v2.7.10b , and BAM files were indexed with samtools v1.13 . Read distribution was evaluated with RSeQC v5.0.2 and gene-level counts were obtained from STAR’s --quantMode GeneCounts output.
Assembly: Nothobranchius furzeri genome (Ensembl Release 113, 2024-08-14) and annotation were downloaded from Ensembl FTP repository (version 2024-08-14)
Supplementary files format and content: all_samples_counts.txt: rows represent Ensembl Gene Identifiers (Ensembl Release 113, 2024-08-14) obtained from STAR’s --quantMode GeneCounts output and columns are each sample analyzed

organism: Nothobranchius furzeri

source_name: Muscle

growth_protocol: Female Nothobranchius furzeri of the GRZ strain were grown in an overflow custom-made system maintained at 28°C on a 12h light/dark cycle.

extract_protocol:
RNA was harvested using ReliaPrep RNA Tissue Miniprep System (Promega GmbH). >10ng/ul of total RNA was used for the construction of sequencing libraries.
RNA sequencing analysis was performed at Novogene GmbH (Munich, Germany). Total RNA quality and integrity were verified using the Agilent 5400 Fragment Analyzer (Agilent Technologies). Libraries were prepared following standard Illumina protocols, quantified with the Qubit™ dsDNA HS Assay Kit (Invitrogen), and validated for fragment size and integrity on the Fragment Analyzer. Final quantification was performed by qPCR. Sequencing was conducted on an Illumina NovaSeq X Plus platform (paired-end 2 × 150 bp).

treatment_protocol: 16 weeks old female Nothobranchius furzeri were treated 3 weeks with 10µM alendronate (PHR1599, Sigma -Aldrich) and the placebo group with the same amount of distilled water added directly to the system water with a daily change of 10%.

value: Muscle

value: Placebo


title: Daily 4AM bat1

description: Library name: 102122011


title: O4_Liver

description: Library name: O4_L_MKRN250005747-1A_22

value: Liver


title: O4_Spleen

description: Library name: O4_M_MKRN250005746-1A_22

source_name: Spleen

value: Spleen


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L single-cell, untreated, replicate 1

description: Library name: DKO1_cDNA

value: prostate tumor

value: untreated


title: PA_005, Adenoma, WT

description: Library name: CHR0211


title: O4_Heart

description: Library name: O4_H_MKRN250005749-1A_22

source_name: Heart

value: Heart


title: protein102

city: Houston

first: Stephen

last: Wong

address: 6565 Fannin St

institute: Houston Methodist

description:
Library name: DSP-1001660022162-A-H07
DSP-1001660022162-A-H07.dcc
DSP-1001660022162-A-H07.stats.txt

source_name: Brain

extract_protocol:
We retrospectively collected metastatic tissue samples from six breast cancer patients with one or more metastatic lesions. The samples included two bone metastases, two brain metastases, one pericardial metastasis, and one chest wall metastasis. Formalin-fixed, paraffin-embedded (FFPE) tissue sections (5 μm) were mounted on standard microscope slides and processed for spatial proteogenomics analysis using the NanoString GeoMx Digital Spatial Profiler (DSP). To enable tissue compartmentalization and spatial segmentation, sections were stained with a panel of three fluorescently labeled morphological markers: anti-pancytokeratin (PanCK-AF532) to identify epithelial tumor cells, anti-CD45 (CD45-AF594) to delineate immune cell populations, and Syto13 nucleic acid stain to visualize nuclei and define cellular boundaries. Staining was performed according to standard immunofluorescence protocols with overnight incubation at 4°C.
DNA barcodes corresponding to RNA and protein targets were photocleaved and collected from each segmented AOI using sequential UV light exposure. Collected barcodes were processed using the GeoMx library preparation protocol with unique dual indexing (i7/i5) for each AOI to enable multiplexed analysis.

value: Brain


title: protein101

description:
Library name: DSP-1001660022162-A-H08
DSP-1001660022162-A-H08.dcc
DSP-1001660022162-A-H08.stats.txt


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L, castrated, Sx682, ICB, replicate 3

description: Library name: TKO_CSI_3


title: HPNE-hTERT cells, FOLFIRINOX, Day 4, N3

city: Montreal

first: Audrey

last: Langlois

state: Qc

address: 900 Saint Denis St

department: Biochemistry

country: Canada

institute: University of Montreal

description: Library name: Sample 6

data_processing:
The quality of the raw reads was assessed with FASTQC v0.12.1. After examining the quality of the raw reads, no trimming was deemed necessary. The reads were aligned to the GRCh38 reference genome with STAR v2.7.11b with mean of 90 % of reads uniquely mapped. The raw counts were calculated with FeatureCounts v2.0.6 based on the GRCh38 reference genome (release 110). Differential expression was performed using DESeq2 R package. DEGs heatmap was drawn based on z-score of normalized count. Functional enrichment analysis of DEGs (gene ontology and pathway enrichment) was performed with the gprofiler2 R package. Bioinformatics analysis were performed at the Bioinformatics core facility from Montreal Clinical Research Institute (IRCM).
Assembly: GRCh38
Supplementary files format and content: TSV files- counts normalized relative to library size
Supplementary files format and content: FOLFI_vs_Veh_counts_normalized_relative_to_library_size.tsv

source_name: pancreas

growth_protocol: HPNE hTERT cells were maintained in 75% DMEM (low glucose), 25% M3 Base medium supplemented with 10% fetal bovin serum (FBS), 200 mM glutamine, 20 ng/ml hEGF and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using the RNA Clean & Concentrator kit (Zymo Research). 1.0 ug of total RNA was used to for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA enrich (NEB) + KAPA RNA hyperprep following manufacturer's protocols.

treatment_protocol: Senescence was induced with the chemotherapy regimen FOLFIRINOX (10 µM 5-Fluorouracil, 25 nM SN-38, 5 µM Oxaliplatin) for 4 days.

value: pancreas

value: HPNE hTERT

value: epithelial ductal cells

value: non-malignant

value: FOLFIRINOX


title: O3_Muscle

description: Library name: O3_Mu_MKRN250005743-1A_22


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L, castrated, Sx682, ICB, replicate 2

description: Library name: TKO_CSI_2


title: O3_Spleen

description: Library name: O3_M_MKRN250005741-1A_22


title: O3_Liver

description: Library name: O3_L_MKRN250005742-1A_22

source_name: Liver


title: HPNE-hTERT cells, Control, Day 4, N3

description: Library name: Sample 5

value: DMSO


title: O3_Kidney

description: Library name: O3_N_MKRN250005740-1A_22

value: Kidney


title: O3_Heart

description: Library name: O3_H_MKRN250005744-1A_22


title: HPNE-hTERT cells, FOLFIRINOX, Day 4, N2

description: Library name: Sample 4


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L, castrated, Sx682, ICB, replicate 1

description: Library name: TKO_CSI_1


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L, tumor, untreated, replicate 2

description: Library name: TKO_2


title: O2_Spleen

description: Library name: O2_M_MKRN250005736-1A_22


title: O2_Muscle

description: Library name: O2_Mu_MKRN250005738-1A_22


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L, tumor, untreated, replicate 1

description: Library name: TKO_1


title: O2_Liver

description: Library name: O2_L_MKRN250005737-1A_22


title: O2_Kidney

description: Library name: O2_N_MKRN250005735-1A_22


title: HPNE-hTERT cells, Control, Day 4, N2

description: Library name: Sample 3


title: HPNE-hTERT cells, FOLFIRINOX, Day 4, N1

description: Library name: Sample 2


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L, tumor, castrated, Sx682, ICB, replicate 3

description: Library name: DKO_CSI_3

value: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L


title: O2_Heart

description: Library name: O2_H_MKRN250005739-1A_22


title: O1_Muscle

description: Library name: O1_Mu_MKRN250005733-1A_22


title: O1_Liver

description: Library name: O1_L_MKRN250005732-1A_22


title: Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L, tumor, castrated, Sx682, ICB, replicate 2

description: Library name: DKO_CSI_2


title: HPNE-hTERT cells, Control, Day 4, N1

description: Library name: Sample 1


title: O1_Heart

description: Library name: O1_H_MKRN250005734-1A_22