title: 6971-EC-S1_ROI_13

description:
Library name: DSP-1001660013356-E-B02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_24

status: Public on Feb 04 2026

type: SRA

city: Ann Arbor

first: Eileen

last: Carpenter

state: MI

address: 1137 E Catherine St Med Sci II R 7712

department: Internal Medicine

country: USA

institute: University of Michigan

description:
Library name: DSP-1001660013356-E-C01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

library_source: other

data_processing:
We used the GeoMxWorkflows package [https://bioconductor.org/packages/release/workflows/html/GeoMxWorkflows.html] for quality control and processing of Nanostring GeoMx data. Briefly, Quality control was performed to exclude the ROIs with less than 10% genes detection rate (less than 10% of the original WTA panel genes were detected) and exclude genes detected in less than 10% of the ROIs. Q3-normalization was performed for each ROI in the gene expression matrix followed by log normalization. For visualization purposes, we performed PCA analysis which clearly showed a batch effect. We used limma package batch correction function to regress out the batch effect which showed clustering of ROIs from the same cell type together. To define cell-type-specific markers, we used a linear mixed model to perform DGE between each cell type and the rest of the ROIs, similar to how we define markers in single cells data.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts of genes for each ROI
Library strategy: Spatial Transcriptomics

molecule: other

organism: Homo sapiens

source_name: Pancreas

growth_protocol: FFPE Blocks

extract_protocol:
Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 310 regions of interest (ROIs), segmented into panCK positive areas of interest (AOIs) for spatial transcriptomics. During collection, each capture area was exposed to UV light that cleaved the linker and released the barcoded oligos for capture by microfluidics. The released barcodes were collected in 96-well plates and were used in the NGS readout library preparation procedure protocol.
The resulted libraries were sequenced by the Illumina NextSeq 6000 platform using reversed, 2 x 27 base paired reads. The resulting GeoMx DSP data was then coupled to next generation sequencing (NGS) readout. This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). BCL Convert Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

treatment_protocol: Slides were deparaffinized and subjected to antigen retrieval (Tris-EDTA, pH 9.0; 15 minutes; >99°C), and enzymatic exposure of RNA targets (1.0µg/ml Proteinase K; 15 minutes; 37°C). Slides were then hybridized with human whole transcriptome overnight (nanoString) at 37°C.  The next morning slides underwent stringent washes and were prepared for morphology marker staining. Slides were co-incubated with fluorescently labeled visualization antibodies to detect tumor cells (pan-cytokeratin [CK]), all immune cells (CD45), and with SYTO 13 for nuclei detection. The samples were imaged, and regions of interest (ROIs) were selected.

tag: tissue

value: Pancreas

tag: cell type

value: IPMN

tag: batch


title: ce_sperm2

city: Philadelphia

first: Colin

last: Conine

state: Pennsylvania

address: 421 Curie Blvd BRB 1213

department: Genetics and Neonatology

institute: UPenn Perelman SOM and CHOP

description:
Library name: ce_sperm2
small RNA-seq on sperm

data_processing:
Bioinformatic pipelines were assembled using Via Foundry, formerly DolphinNext, pipeline generator for all RNA-sequencing data analyzed in this study.
mRNA libraries were first aligned to the C. elegans genome (WS245) using STAR and quantified and normalized to transcripts per million (TPM) using the RSEM package. Significance calls were made based on t-tests (unpaired, two-tailed), where we identified up- and down-regulated genes using the following cutoff:  log2(fold change) >1 or less than –1 and an adjusted P-value ≤0.01. For differentially expressed genes WormBase enrichment analysis was used to determine tissue, pathway, and gene ontology enrichment.
Small RNA libraries were trimmed of adapter sequences using trimmomatic and aligned (in order) sequentially to C. elegans rRNAs, miRNAs, tRNAs, and piRNAs using Bowtie 2. STAR was used to align small RNAs to the C. elegans genome (WS245), featureCounts was then used to quantify reads mapping to genomic features (mRNA fragments, and endo siRNA). Mapped reads were normalized to reads per million using custom python scripts, to total genome mapping reads or to a specific RNA class, for subsequent analysis.
Assembly: WS245
Supplementary files format and content: csv files for small RNA data include raw count values for each Sample
Supplementary files format and content: csv files for mRNA data include TPM values for each Sample

organism: Caenorhabditis elegans

source_name: sperm

extract_protocol:
Unless otherwise stated all RNA-seq experiments, beyond single embryo experiments (below) were conducted on adult animals. To generate rnst-2 mutant males, heterozygous rnst-2/tmc16 males and females were mated to generate progeny that’s parents had equivalent genotypes. Individual ~50 F1 L4 from these crosses, propagated at 20°C, were then picked as males and females separately to NGM OP50 plates.  These animals were then developed at 20°C for 24 hours to generate adult animals. These animals were then picked into 1X M9 media with 0.5% polyethylene glycol (mPEG) in a 1.5 mL low adhesion microcentrifuge tube. Worms were washed three times with M9/mPEG and once with cold nuclease free water before resuspending in 1 volume 2X worm lysis buffer (1% SDS, 80mM Tris HCl, 400 mM NaCl, 20 mM EDTA, 0.8 mg/mL Proteinase K). The samples were then incubated at 55°C for 15 minutes while shaking and visually inspected to ensure complete lysis. Following worm lysis, 2X volume of TRI reagent (Invitrogen, AM9738) was added followed by 1/5th volume of BCP (catalog #). This solution was mixed thoroughly and transferred a Phase Lock Gel Heavy tube (QuantaBio, 2302830; pre-spun at 14,000 RPM for 1 minute) and spun at 14,000 RPM for 4 minutes at 4°C. The aqueous layer was then transferred to a new low-adhesion microcentrifuge tube, and 15 μg of GlycoBlue coprecipitant (Invitrogen AM9515) was added prior to the addition of 1.1 volume isopropanol. Samples were then precipitated at -20°C for at least 1 hours, and up to a month in isopropanol (longer storage times at -80°C) to purify total RNA. To generate small RNA and mRNA-seq libraries RNA samples in isopropanol were centrifuged at 14,000 RPM for 15 minutes at 4°C, then washed with cold 70% ethanol, spun again at 14,000 RPM for 5 minutes at 4°C, and finally reconstituted in nuclease-free water. RNA isolation from 50 adult male and females, yields ~500ng and ~1µg, respectively.
For small RNA 200 ng of total RNA was used as input for all small RNA sequencing experiments with library construction carried out using a modified Illumina Tru-Seq small RNA library prep protocol (Illumina RS-200). Small RNAs (18 – 40 nt) were first purified by was size selection from denaturing 15% polyacrylamide 7M urea TBE gel electrophoresis. Small RNAs from eluted in 10mM Tris-HCl pH 7.5, 300mM NaCl, and 1mM EDTA shaking overnight at room temperature. Small RNAs were then precipitated by separating the gel debris using 0.45µM cellulose-acetate filters, adding 1ul GlycoBlue and 1.1 volume of isopropanol, mixing well, and placing the samples at -20°C for at least 1 hour. The samples then were centrifuged at 14,000 RPM for 15 minutes at 4°C and the supernatant was discarded before washing with 1X volume of cold 70% ethanol. Following a 14,000 RPM spin at 4°C for five minutes and after complete ethanol removal, the pellet was reconstituted in RNA 5´ Pyrophosphohydrolase (RppH - NEB M0356S) per manufacturers guidelines and incubated at 37°C for one hour. Following RppH treatment, small RNAs were precipitated and ligated to the 3´ adapter using Truncated T4 RNA ligase (Lucigen LR2D11310K). Small RNAs were then ligated to the 5´ adapter using T4 ligase, and subsequently reverse transcribed using Superscript II (Invitrogen 18064014) following the Tru-Seq small RNA protocol. Following PCR optimization, to determine the proper number of cycles for amplification, the libraries were amplified, gel purified on a 8% TBE polyacrylamide gel (to remove cloned products with no insert) and combined at equimolar concentration. Libraries were then sequenced using an Illumina NextSeq1000 (75-bp single read).
For standard  mRNA-seq library construction was carried out using the Illumina stranded mRNA kit as per manufacturer’s instructions (Illumina 20040534). In brief, poly-adenylated RNAs were captured using oligo(dT) magnetic beads from 200-800ng total RNA. The RNA was then fragmented, primed for cDNA synthesis and subsequently cleaned up using AMPure XP beads (Beckman Coulter, Cat# A63881). Following PCR optimization, to determine the proper number of cycles from amplification, the libraries were amplified and combined at equimolar concentrations before being purified using non-denaturing PAGE. Paired-end sequencing (50 bp per read) was performed using an Illumina NextSeq1000.
For single embryo RNA-seq cross plates were prepared by placing 50 WT (fog-2(q71) L4-stage females and 50 rnst-2 Δ/Δ (pen1); fog-2(q71) L4-stage males on 60 mM NGM plates seeded with OP50. The next day mated females full of eggs were picked and washed several times with M9 mPEG and then subjected to a 5-minute hypochlorite treatment. Early-stage embryos, identified under the microscope, were then transferred to 10ug/ul chitanase in M9 mPEG treatment and incubated at room temperature for 8-10 minutes. Following chitinase treatment 2-cell and 8-cell embryos, identified visually under a dissecting microscope were placed in RNA worm lysis buffer in PCR tubes and incubated at 55°C for 10 minutes. Embryo lysates were then stored at -80°C before proceeding to library preparation. Single-embryo mRNA-seq libraries were constructed using the SMART-Seq protocol, used previously for single mouse preimplantation embryos. RNA was isolated with RNAClean-XP beads (Beckman Coulter, Cat# A63987) and full-length polyadenylated RNA was reverse transcribed using Superscript II (Invitrogen, Cat# 18064014). The cDNA was then amplified using 10 cycles and subsequently 0.33 ng of cDNA was used to construct a pool of uniquely indexed samples using the Nextera XT kit (Illumina, Cat# FC-131-1096). Finally, pooled libraries were sequenced on a NextSeq1000 with paired-end sequencing (50 bp per read).

value: sperm

tag: genotype


title: F2FM_41

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

description: Library name: F2FM_41

library_source: transcriptomic

data_processing:
Data cleaning involved the removal of adapters and reads with a Phred-Score < 30. Quality control (QC) and read statistics were assessed using FastQC v0.11.8 and MultiQC v1.9. The reads were mapped to the Bos taurus reference genome (ARS-UCD 1.2) available at http://www.ensembl.org/Bos_taurus/Info/Index/, using the STAR aligner v. 2.7.3a. Raw counts per gene were obtained using the –quantMode GeneCounts parameter from STAR and the gene annotation file from Ensembl (release 100). Post-mapping quality control was conducted using the tools MultiQC, NOISeq v.2.26.0, and edgeR v.3.24.3.
Assembly: Bos taurus reference genome (ARS-UCD 1.2, releas 100)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample. (BM - Samples at birth - F1, SM; Samples at slaugther - F1; FM, fetal samples day84 generation 2) TXT file

molecule: polyA RNA

organism: Bos taurus

source_name: Longissimus dorsi (muscle)

extract_protocol:
Samples were first disrupted and homogenized in TRIzol Reagent (Invitrogen™, Thermo Fisher Scientific, Waltham, MA, USA), and the aqueous phase was then processed using the RNeasy Plus Universal Mini Kit (Qiagen®, Germantown, MD, USA) according to the manufacturer’s instructions. Sample integrity and purity were assessed using the Agilent 2100 Bioanalyzer and agarose gel electrophoresis.
Sixteen samples (8 per treatment) at birth, 15 at the harvest of F1 heifers (LG n = 7; MG n = 8), and 16 samples (8 per treatment) from F2 fetuses met the quantity and quality parameters for library preparation. This process was carried out using the NEBNext® Ultra™ II non-directional RNA Library Prep Kit for Illumina (New England BioLabs®, Ipswich, MA, USA). The libraries were sequenced on the Illumina® NovaSeq 6000 platform, generating 150 bp reads at 20 million per sample depth. Both library preparation and paired-end sequencing were conducted by Novogene Co. (Nanjing, China).

value: Longissimus dorsi (muscle)

tag: generation

tag: treatment

value: LG

tag: timepoint

value: fetal(day 84)


title: 6971-EC-S1_ROI_14

description:
Library name: DSP-1001660013356-E-B03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Acinar


title: 6971-EC-S1_ROI_23

description:
Library name: DSP-1001660013356-E-B12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_16

description:
Library name: DSP-1001660013356-E-B05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F2FM_31

description: Library name: F2FM_31

value: MG


title: F2FM_39

description: Library name: F2FM_39


title: 6971-EC-S1_ROI_15

description:
Library name: DSP-1001660013356-E-B04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F2FM_29

description: Library name: F2FM_29


title: 6971-EC-S1_ROI_12

description:
Library name: DSP-1001660013356-E-B01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_11

description:
Library name: DSP-1001660013356-E-A12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_10

description:
Library name: DSP-1001660013356-E-A11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F2FM_22

description: Library name: F2FM_22


title: F2FM_32

description: Library name: F2FM_32


title: F2FM_20

description: Library name: F2FM_20


title: F2FM_15

description: Library name: F2FM_15


title: F2FM_23

description: Library name: F2FM_23


title: 6971-EC-S1_ROI_7

description:
Library name: DSP-1001660013356-E-A08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_8

description:
Library name: DSP-1001660013356-E-A09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_5

description:
Library name: DSP-1001660013356-E-A06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F2FM_07

description: Library name: F2FM_07


title: F2FM_11

description: Library name: F2FM_11


title: F1SM_47

description: Library name: F1SM_47

source_name: Longissimus thoracis (muscle)

value: Longissimus thoracis (muscle)

value: slaugther


title: 6971-EC-S1_ROI_6

description:
Library name: DSP-1001660013356-E-A07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F2FM_02

description: Library name: F2FM_02


title: 6971-EC-S1_ROI_9

description:
Library name: DSP-1001660013356-E-A10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F2FM_14

description: Library name: F2FM_14


title: F1SM_41

description: Library name: F1SM_41


title: 6971-EC-S1_ROI_4

description:
Library name: DSP-1001660013356-E-A05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1SM_39

description: Library name: F1SM_39


title: 6971-EC-S1_ROI_1

description:
Library name: DSP-1001660013356-E-A02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: NormalDuct


title: F1SM_45

description: Library name: F1SM_45


title: 6276-EC-S1_ROI_165

description:
Library name: DSP-1001660012908-H-G02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_164

description:
Library name: DSP-1001660012908-H-G01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_3

description:
Library name: DSP-1001660013356-E-A04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_2

description:
Library name: DSP-1001660013356-E-A03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1SM_36

description: Library name: F1SM_36


title: 6276-EC-S1_ROI_162

description:
Library name: DSP-1001660012908-H-F11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Stroma


title: F1SM_31

description: Library name: F1SM_31


title: 6276-EC-S1_ROI_163

description:
Library name: DSP-1001660012908-H-F12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1SM_32

description: Library name: F1SM_32


title: 6276-EC-S1_ROI_161

description:
Library name: DSP-1001660012908-H-F10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1SM_29

description: Library name: F1SM_29


title: F1SM_23

description: Library name: F1SM_23


title: 6276-EC-S1_ROI_158

description:
Library name: DSP-1001660012908-H-F07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1SM_20

description: Library name: F1SM_20


title: 6276-EC-S1_ROI_157

description:
Library name: DSP-1001660012908-H-F06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_160

description:
Library name: DSP-1001660012908-H-F09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_159

description:
Library name: DSP-1001660012908-H-F08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_153

description:
Library name: DSP-1001660012908-H-F02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_156

description:
Library name: DSP-1001660012908-H-F05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1SM_22

description: Library name: F1SM_22


title: F1BM_31

description: Library name: F1BM_31

value: birth


title: 6276-EC-S1_ROI_151

description:
Library name: DSP-1001660012908-H-E12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_155

description:
Library name: DSP-1001660012908-H-F04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1SM_07

description: Library name: F1SM_07


title: F1SM_02

description: Library name: F1SM_02


title: 6276-EC-S1_ROI_150

description:
Library name: DSP-1001660012908-H-E11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1BM_37

description: Library name: F1BM_37


title: F1BM_22

description: Library name: F1BM_22


title: F1SM_11

description: Library name: F1SM_11


title: 6276-EC-S1_ROI_148

description:
Library name: DSP-1001660012908-H-E09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1BM_28

description: Library name: F1BM_28


title: 6276-EC-S1_ROI_149

description:
Library name: DSP-1001660012908-H-E10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_152

description:
Library name: DSP-1001660012908-H-F01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1SM_14

description: Library name: F1SM_14


title: 6276-EC-S1_ROI_147

description:
Library name: DSP-1001660012908-H-E08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_154

description:
Library name: DSP-1001660012908-H-F03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1BM_17

description: Library name: F1BM_17


title: F1BM_15

description: Library name: F1BM_15


title: F1BM_14

description: Library name: F1BM_14


title: F1BM_25

description: Library name: F1BM_25


title: 6276-EC-S1_ROI_145

description:
Library name: DSP-1001660012908-H-E06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_144

description:
Library name: DSP-1001660012908-H-E05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_143

description:
Library name: DSP-1001660012908-H-E04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: daf-16(lf), all cells, rep 2

city: Toronto

first: Shifei

last: Wu

state: Ontario

address: 1 King's College Cir

country: Canada

institute: University of Toronto

description: Library name: Sample18

data_processing:
Salmon 1.4.0 was used to quantify transcript abundance
Assembly: WBcel235
Supplementary files format and content: csv file includes TPM values for all samples

source_name: all

extract_protocol:
RNA was extracted from sorted cells using TRIzol LS followed by chloroform and cleaned up using Zymo RNA Clean & Concentrator-5.
For single-end samples, RNA was assessed by Fragment Analyzer, and high quality total RNA was subjected to library preparation using the Illumina TruSeq Stranded mRNA Library Preparation Kit (Cat# 20020594) according to the manufacturer’s instructions. For paired-end samples, RNA quality was assessed by Agilent Bioanalyzer 2100. The full length cDNA library was first generated from high quality total RNA using TaKaRa SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Cat# 634890) according to manufacturer protocol. The final barcoded sequencing libraries were prepared from the full length cDNA using Illumina Nextera Flex according to manufacturer protocol.

value: all


title: F1BM_13

description: Library name: F1BM_13


title: F1BM_20

description: Library name: F1BM_20


title: F1BM_21

description: Library name: F1BM_21


title: 6276-EC-S1_ROI_146

description:
Library name: DSP-1001660012908-H-E07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: daf-16(lf), muscle cells, rep 4

description: Library name: Sample8

source_name: muscle

value: muscle


title: F1BM_11

description: Library name: F1BM_11


title: 6276-EC-S1_ROI_140

description:
Library name: DSP-1001660012908-H-E01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: wild-type, all cells, rep 1

description: Library name: Sample15

value: wild-type


title: daf-16(lf), all cells, rep 1

description: Library name: Sample17


title: 6276-EC-S1_ROI_142

description:
Library name: DSP-1001660012908-H-E03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: daf-16(lf), muscle cells, rep 1

description: Library name: Sample5


title: daf-16(lf), muscle cells, rep 3

description: Library name: Sample7


title: 6276-EC-S1_ROI_139

description:
Library name: DSP-1001660012908-H-D12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1BM_07

description: Library name: F1BM_07


title: F1BM_12

description: Library name: F1BM_12


title: 6276-EC-S1_ROI_141

description:
Library name: DSP-1001660012908-H-E02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F1BM_10

description: Library name: F1BM_10


title: 6276-EC-S1_ROI_138

description:
Library name: DSP-1001660012908-H-D11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: wild-type, muscle cells, rep 2

description: Library name: Sample2


title: daf-16(lf), muscle cells, rep 2

description: Library name: Sample6


title: F1BM_05

description: Library name: F1BM_05


title: wild-type, muscle cells, rep 4

description: Library name: Sample4


title: wild-type, muscle cells, rep 3

description: Library name: Sample3


title: wild-type, all cells, rep 2

description: Library name: Sample16


title: 6276-EC-S1_ROI_137

description:
Library name: DSP-1001660012908-H-D10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_136

description:
Library name: DSP-1001660012908-H-D09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: wild-type, muscle cells, rep 1

description: Library name: Sample1


title: RV23-6

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Library name: Sample 36

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases and to crop the 150bp PE reads to 50bp PE. This cropping was done to match previously collected sequencing data.
The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options.
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR p-value was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR p-value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Assembly: Rnor_6.0
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.
Supplementary files format and content: Some samples don't have processed data. The sequencing quality was too low for these samples to be included in the differential analysis.

molecule: genomic DNA

organism: Rattus norvegicus

growth_protocol: Male and female rats were obtained from an outbred strain Hsd: Sprague Dawley®™SD®™ from Envigo (Indianapolis, IN) at about the age of 70-100 days and were then held in ventilated isolator cages. While in these cages, the rats were in cages with dimensions of 10 “W x 191/4” Dx 10” H, 143 square inch floor space where there would be up to 50 air exchanges per hour. The cages used the bedding of Aspen Sani chips and had 14 hours of light and then 10 hours of dark. The room had a temperature of 70 F and humidity of 25% to 35% daily. The rats were fed a steady diet of ad lib with food pellets (8640 Teklad 22/5 Rodent Diest; Harlan) and an ad lib drinking water from the tap. The rats were checked daily for behavioral records and as well as overall wellness. All protocols used for this experiment and procedures with the rats were approved by the Washington State University Animal Care and Use Committee (IACUC approval #6252).

extract_protocol:
The epididymis cauda had a small slit made and then placed in 6 mL of phosphate-buffered saline (PBS) for 15 minutes and then kept at 4 degrees Celsius until the processing begins. The epididymal tissue was minced, releasing the rest of the sperm, and promptly collected. The sperm was centrifuged at 3,000 g for 10 minutes, and the supernatant was discarded. The pellet found at the bottom of the tube was resuspended in NIM buffer. Once the sperm was resuspended in NIM buffer, the sperm was held in a negative 80-degree Celsius freezer until the DNA isolation protocol began. For molecular analysis 100 µl of rat sperm suspension was used. The rat sperm was sonicated for five seconds at 25% (Fisher sonic dismembrator model 300) to remove the tails. Once sample was resuspended and glycoblue was added, the blue pellet was washed with 70% cold ethanol 2-3 times, and then added 500 µl of 70% ethanol and returned to the freezer for 20 minutes. The samples were then centrifuged for ten minutes at 4 degrees Celsius at maximum speed, 18,200 g. The supernatant was discarded and the blue pellet dried entirely before adding 100 µl of nuclease-free water. Sperm DNA from individual animals were obtained and pooled with 4-6 different animals DNA samples, with equal amounts of DNA from each animal present in each pool. 2 µg of DNA was taken from each sperm DNA sample and pooled to be diluted with 130 µl TE buffer (10mM Tris-HCl, pH7.5; 1mM EDTA) and micro pipetted into covaries tubes (M220) and sonicated to 300 bp. Add 100 µl cold 5X IP buffer and add 5 µg of antibody (monoclonal mouse anti-5-methyl cytidine; Diagenode #C15200006). Once incubation is complete, prewash the magnetic bead (Dynabeads M-280 Sheep anti-Mouse IgG; Life Technologies 11201D) by transferring 50 µl of beads per sample into a tube and at least 1 mL of washing buffer. Allow samples to incubate for 2 hours on a rotating platform at 4 degrees Celsius. After complete incubation, wash the beads three times with 1x IP buffer. Place the tubes on a magnetic rack and discard supernatant.   Add 1 mL of cold 1 x IP buffer and mix by inverting tubes several times. Resuspend the beads in 250 µl digestion buffer and add 3.5 µl proteinase K mix (20mg/ml). After incubation, add 250 µl of phenol-chloroform-isoamyl alcohol to each sample. After adding 250 µl of chloroform, vortex for 30 seconds and centrifuge for 5 minutes at 14,000 g at room temperature. Add 500 µl ethanol and then add 20 µl of 5 M NaCl as well as adding 2 µl of glycoblue. Vortex samples well and place in a negative 20-degree Celsius freezer overnight. After incubation, centrifuge samples at 14,000 g for 20 minutes at 4 degrees Celsius and remove the supernatant leaving the blue pellet behind. Wash the pellet with 500 µl 75% ethanol and leave it in the freezer at negative 20 degrees Celsius for 15 minutes. Remove from freezer, centrifuge at 14,000 g at 4 degrees Celsius for five minutes, and remove supernatant. Completely dry the samples and add 25 µl of nuclease-free water. The concentration of the DNA was then measured using the Qubit ssDNA kit (Life Technologies Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed.

treatment_protocol: The treatment involved an intraperitoneal injection of vinclozolin to an F0 generation gestating female during the time of embryonic development of day E8-E15. The gestating females of the control lineage were exposed to a DMSO solvent through intraperitoneal injection during the time of embryonic development of day E8-E15. To avoid any inbreeding within the controls or the vinclozolin lineages each generation and breeding was bred with a wild-type rat. In this study, each generation included two breeding types which were a reverse outcross for the maternal lineage (MOC) and an outcross for the paternal lineage (POC). The same breeding protocol was applied to the control lineage where the outcross represented the maternal lineage (CMOCF4 and the outcross represented the paternal lineage (CPOCF4). This breeding protocol was followed through the F23 generation for the exposure lineages and F4 for control lineage. Once the pups of each generation were born, weaning of pups occurred at 25 days of age where weaning weight (g) was taken. All rats were maintained and then euthanized and dissected at one year of age where tissues and epididymal sperm were collected. In addition to the collection of tissue and sperm, the body weight (g) and length (cm) of the rat were taken for further use in body mass index BMI. Further analysis was done on the collected tissue and sperm for analysis of the generational stability of transgenerational effects on the F13 and F23 generations.

tag: treatment lineage

value: vinclozolin

tag: outcross

value: maternal


title: PBMCs,HealthyControl,HC18,T0

city: Pavia

first: Francesca

last: Dragoni

state: Italy

address: Via Mondino, 2

country: Italy

institute: IRCCS Mondino Foundation

description: Library name: HC18

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differental expression analysis for mRNA and lncRNA was performed using R package DESeq2
Assembly: HG19
Supplementary files format and content: fastq.gz

molecule: total RNA

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were prepared by centrifugation. Peripheral blood was layered (density=1.077) and centrifuged at 950g for 30 min. After isolation on a Ficoll-Histopaque layer (Sigma, Italy), cell viability was assayed by a trypan blue

extract_protocol:
Total RNA was isolated from PBMCs using Trizol® reagent. The specifications from the manufacturer were followed.
Illumina TruSeqStranded RNA Library Prep, version 2, Protocol D,  using 500-ng total RNA. Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagnt kit. RNA processing has been carried out using Illumina NextSeq 550 Sequencing.

value: Blood

tag: cell line

value: Peripheral Blood Mononuclear Cells

value: Healthy control


title: RV23-5

description: Library name: Sample 35

value: sperm


title: RV23-4

description: Library name: Sample 34


title: PBMCs,HealthyControl,HC19,T0

description: Library name: HC19


title: PBMCs,HealthyControl,HC14,T0

description: Library name: HC14


title: PBMCs,HealthyControl,HC16,T0

description: Library name: HC16


title: PBMCs,HealthyControl,HC13,T0

description: Library name: HC13


title: PBMCs,HealthyControl,HC11,T0

description: Library name: HC11


title: 6276-EC-S1_ROI_133

description:
Library name: DSP-1001660012908-H-D06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Pancreas

value: IPMN


title: PBMCs,HealthyControl,HC15,T0

description: Library name: HC15


title: RV23-3

description: Library name: Sample 33


title: 6276-EC-S1_ROI_134

description:
Library name: DSP-1001660012908-H-D07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,HealthyControl,HC12,T0

description: Library name: HC12


title: 6276-EC-S1_ROI_132

description:
Library name: DSP-1001660012908-H-D05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,HealthyControl,HC17,T0

description: Library name: HC17


title: RV23-1

description: Library name: Sample 31


title: PBMCs,HealthyControl,HC10,T0

description: Library name: HC10


title: 6276-EC-S1_ROI_135

description:
Library name: DSP-1001660012908-H-D08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,HealthyControl,HC7,T0

description: Library name: HC7


title: RV23-2

description: Library name: Sample 32


title: 6276-EC-S1_ROI_131

description:
Library name: DSP-1001660012908-H-D04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: RV13-6

description: Library name: Sample 30


title: PBMCs,HealthyControl,HC6,T0

description: Library name: HC6


title: PBMCs,HealthyControl,HC4,T0

description: Library name: HC4


title: PBMCs,HealthyControl,HC5,T0

description: Library name: HC5


title: PBMCs,HealthyControl,HC3,T0

description: Library name: HC3


title: PBMCs,HealthyControl,HC8,T0

description: Library name: HC8


title: PBMCs,ALS,P8,T0

description: Library name: P8

value: Pyramidal phenotype


title: 6276-EC-S1_ROI_128

description:
Library name: DSP-1001660012908-H-D01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,HealthyControl,HC9,T0

description: Library name: HC9


title: 6276-EC-S1_ROI_130

description:
Library name: DSP-1001660012908-H-D03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,HealthyControl,HC2,T0

description: Library name: HC2


title: 6276-EC-S1_ROI_129

description:
Library name: DSP-1001660012908-H-D02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_127

description:
Library name: DSP-1001660012908-H-C12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,P7,T0

description: Library name: P7


title: RC4-6

description: Library name: Sample 24

value: control


title: 6276-EC-S1_ROI_125

description:
Library name: DSP-1001660012908-H-C10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,P6,T0

description: Library name: P6


title: PBMCs,ALS,P5,T0

description: Library name: P5


title: PBMCs,ALS,P4,T0

description: Library name: P4


title: RV13-3

description: Library name: Sample 27


title: PBMCs,ALS,P2,T0

description: Library name: P2


title: RC4-5

description: Library name: Sample 23


title: 6276-EC-S1_ROI_124

description:
Library name: DSP-1001660012908-H-C09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,FL10,T0

description: Library name: FL10

value: Flail leg phenotype


title: RV13-1

description: Library name: Sample 25


title: RV13-2

description: Library name: Sample 26


title: 6276-EC-S1_ROI_123

description:
Library name: DSP-1001660012908-H-C08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: RC4-4

description: Library name: Sample 22


title: PBMCs,ALS,P9,T0

description: Library name: P9


title: PBMCs,HealthyControl,HC1,T0

description: Library name: HC1


title: PBMCs,ALS,P3,T0

description: Library name: P3


title: 6276-EC-S1_ROI_126

description:
Library name: DSP-1001660012908-H-C11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,P1,T0

description: Library name: P1


title: PBMCs,ALS,FL9,T0

description: Library name: FL9


title: 6276-EC-S1_ROI_122

description:
Library name: DSP-1001660012908-H-C07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,FL8,T0

description: Library name: FL8


title: PBMCs,ALS,FL7,T0

description: Library name: FL7


title: RC4-3

description: Library name: Sample 21


title: 6276-EC-S1_ROI_121

description:
Library name: DSP-1001660012908-H-C06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,FL6,T0

description: Library name: FL6


title: PBMCs,ALS,FL5,T0

description: Library name: FL5


title: PBMCs,ALS,FL4,T0

description: Library name: FL4


title: RC4-1

description: Library name: Sample 19


title: RV13-4

description: Library name: Sample 28


title: PBMCs,ALS,FL3,T0

description: Library name: FL3


title: 6276-EC-S1_ROI_119

description:
Library name: DSP-1001660012908-H-C04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: RC4-2

description: Library name: Sample 20


title: 6276-EC-S1_ROI_120

description:
Library name: DSP-1001660012908-H-C05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,FL2,T0

description: Library name: FL2


title: OV23-6

description: Library name: Sample 18

value: paternal


title: 6276-EC-S1_ROI_118

description:
Library name: DSP-1001660012908-H-C03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Stroma


title: OV23-5

description: Library name: Sample 17


title: PBMCs,ALS,FL1,T0

description: Library name: FL1


title: PBMCs,ALS,FA7,T0

description: Library name: FA7

value: Flail Arm phenotype


title: PBMCs,ALS,FA5,T0

description: Library name: FA5


title: 6276-EC-S1_ROI_117

description:
Library name: DSP-1001660012908-H-C02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,FA6,T0

description: Library name: FA6


title: OV23-4

description: Library name: Sample 16


title: 6276-EC-S1_ROI_116

description:
Library name: DSP-1001660012908-H-C01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,FA4,T0

description: Library name: FA4


title: PBMCs,ALS,FA2,T0

description: Library name: FA2


title: PBMCs,ALS,FA3,T0

description: Library name: FA3


title: OV23-3

description: Library name: Sample 15


title: PBMCs,ALS,FA1,T0

description: Library name: FA1


title: OV23-2

description: Library name: Sample 14


title: PBMCs,ALS,C12,T0

description: Library name: C12

value: Classic phenotype


title: 6276-EC-S1_ROI_114

description:
Library name: DSP-1001660012908-H-B11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Nerve


title: PBMCs,ALS,C10,T0

description: Library name: C10


title: OV23-1

description: Library name: Sample 13


title: PBMCs,ALS,C9,T0

description: Library name: C9


title: 6276-EC-S1_ROI_113

description:
Library name: DSP-1001660012908-H-B10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,C8,T0

description: Library name: C8


title: PBMCs,ALS,C7,T0

description: Library name: C7


title: 6276-EC-S1_ROI_112

description:
Library name: DSP-1001660012908-H-B09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: OV13-5

description: Library name: Sample 11


title: OV13-6

description: Library name: Sample 12


title: 6276-EC-S1_ROI_115

description:
Library name: DSP-1001660012908-H-B12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,C6,T0

description: Library name: C6


title: PBMCs,ALS,C2,T0

description: Library name: C2


title: OV13-2

description: Library name: Sample 8


title: PBMCs,ALS,C5,T0

description: Library name: C5


title: PBMCs,ALS,C4,T0

description: Library name: C4


title: OV13-3

description: Library name: Sample 9


title: 6276-EC-S1_ROI_110

description:
Library name: DSP-1001660012908-H-B07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: RV13-5

description: Library name: Sample 29


title: 6276-EC-S1_ROI_109

description:
Library name: DSP-1001660012908-H-B06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_111

description:
Library name: DSP-1001660012908-H-B08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,C1,T0

description: Library name: C1


title: PBMCs,ALS,C3,T0

description: Library name: C3


title: OV13-4

description: Library name: Sample 10


title: No Template Control

city: HOUSTON

first: HONG

last: ZHAO

state: Texas

address: 6670 Bertner Ave

institute: HOUSTON METHODIST HOSPITAL

description:
Library name: DSP-1001660038458-A-A01
Spatial transcriptomic profiling was performed using the NanoString GeoMx Digital Spatial Profiling (DSP) platform with the Cancer Transcriptome Atlas panel (8,600 probes). For each tissue section, eight circular regions of interest (ROIs; 300 μm diameter) were selected. Within each ROI, three biological segments—immune, tumor, and stromal—were independently profiled

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

organism: synthetic construct

source_name: PDAC

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

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

value: PDAC

value: w/o prehab


title: OV13-1

description: Library name: Sample 7

value: vinclozolin


title: Induced neurons, untreated library 2, 10 cell lines pooled

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description:
Library name: C2
10X Multiome Kit

library_source: transcriptomic single cell

data_processing:
Base-calling was performed by the sequencing service (Novogene)
Fastq files were processed using 10X Genomics cellranger-arc software
Counts matrices were loaded into Seurat for sample merging, filtering, clustering and analysis of gene expression
Individual cells were matched with known SNPs using demuxlet software.
Following clustering, a neuron cluster was extracted and the barcodes x genes counts table was exported
Pseudobulk analysis of cells from each cell line was completed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: The matrix of barcodes x genes counts were exported prior to aggregation for pseudobulk analysis
Supplementary files format and content: Pseudobulk normalized counts were extracted from the DESeq2 object with counts(normalized=T).
Supplementary files format and content: Data from selected neurons matching only three cell lines were included here in the aggregated pseudobulk table, matching those shown in our manuscript.

molecule: nuclear RNA

organism:
Homo sapiens
Mus musculus

source_name: Mixture of 10 cell lines

growth_protocol: Excitatory (Ngn2) neurons were prepared by lentiviral induction of pluripotent stem cells and grown on mouse primary glia in Neurobasal medium. Cultures were harvested 4 weeks after induction.

extract_protocol:
Cells were dissociated using Accutase and Papain
Nuclei were prepared and run through 10X Chromium device following manufacturer's recommendation.  Libraries were prepared using the 10X Multiome kit.

value: Mixture of 10 cell lines

value: Induced glutamatergic neuron

value: Mixed


title: PBMCs,ALS,B10,T0

description: Library name: B10

value: Blood

value: Peripheral Blood Mononuclear Cells

value: Bulbar phenotype


title: Induced neurons, untreated library 1, 10 cell lines pooled

description:
Library name: C1
10X Multiome Kit


title: 6276-EC-S1_ROI_108

description:
Library name: DSP-1001660012908-H-B05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Pancreas

value: IPMN


title: 6276-EC-S1_ROI_107

description:
Library name: DSP-1001660012908-H-B04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: OC4-6

description: Library name: Sample 6

value: sperm

value: control


title: OC4-5

description: Library name: Sample 5

value: paternal


title: PBMCs,ALS,B9,T0

description: Library name: B9


title: 6276-EC-S1_ROI_106

description:
Library name: DSP-1001660012908-H-B03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: PBMCs,ALS,B8,T0

description: Library name: B8


title: 6276-EC-S1_ROI_105

description:
Library name: DSP-1001660012908-H-B02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: HepG2.D11 si-Nontarget

type: RNA

city: Yoshida-gun

first: Shouichi

last: Namikawa

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: The Department of Gastroenterology

country: Japan

institute: University of Fukui

hyb_protocol: Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in fragmentation buffer with blocking agent, and then mixed with hybridization buffer. The samples were hybridized to SurePrint G3 Human GE 8×60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, arrays were washed with GE Wash Buffer 1 for 1 minute at room temperature and with GE Wash Buffer 2 for 1 minute at 37°C.

scan_protocol: Slides were scanned immediately after washing using the Agilent SureScan Microarray Scanner (G2600D) with one-color settings (Green channel; scan area 61 × 21.6 mm; 3 μm resolution; PMT 100%).

data_processing: Scanned images were analyzed using Feature Extraction Software 12.0.3.1 (Agilent Technologies) with default parameters to obtain background-subtracted and spatially detrended processed signal intensities. Processed signals were normalized by the global scaling method using a trimmed mean (excluding the lowest and highest 2% of probe intensities), and the trimmed mean target intensity of each array was set to 2500.

source_name: HepG2.D11 cell

label_protocol: Cy3-labeled cRNA was synthesized from total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions, followed by purification with an RNeasy column (QIAGEN). Dye incorporation and cRNA yield were evaluated using a NanoDrop ND-2000 spectrophotometer.

growth_protocol: The human liver cancer cell line HepG2 was obtained from the American Type Culture Collection (Manassas, VA, USA) and cultured with RPMI-1640 (Sigma-Aldrich, St. Louis, MO, USA) containing 10% fetal bovine serum (FBS), 2 mmol/L L-glutamine, 1 μmol/L sodium pyruvate, 0.1 mmol/L nonessential amino acids, and 100 U/mL penicillin/50 μg/mL streptomycin (Gibco, Grand Island, NY, USA) at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific). RNA concentration and purity were assessed with a NanoDrop spectrophotometer, and RNA quality was confirmed using a BioAnalyzer.

treatment_protocol: The 1.3-mer HBV genomes [genotype C2, both basal core promoter (BCP) A1762T/G1764A mutation and precore G1896A mutation, accession number AB819615] were inserted into the KpnΙ and NotΙ restriction sites of pBluescript II SK (Agilent Technologies, Santa Clara, USA). Plasmid was transfected into HepG2 cells using LipofectamineTM LTX Reagent (Thermo Fisher Scientific, Waltham, MA, USA). HBV transfected HepG2 cells that were confirmed to stably produce HBsAg in the supernatant were called HepG2.D11 clones. For microarray experiments, HepG2.D11 cells were seeded on day 0, transfected on day 1 with FAH vector or empty vector, or with siFAH or si Nontarget, and collected on day 4.

tag: tag

value: HBV transfected, si-Non target

value: HepG2 cell


title: OC4-3

description: Library name: Sample 3


title: 6276-EC-S1_ROI_104

description:
Library name: DSP-1001660012908-H-B01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: HepG2.D11 si-FAH

value: HBV transfected, si-FAH


title: PBMCs,ALS,B7,T0

description: Library name: B7


title: OC4-4

description: Library name: Sample 4


title: PBMCs,ALS,B5,T0

description: Library name: B5


title: PBMCs,ALS,B6,T0

description: Library name: B6


title: PBMCs,ALS,B4,T0

description: Library name: B4


title: Z3.clean

city: Hangzhou

first: Yuepeng

last: Jiang

address: binwen road

country: China

institute: zhejiang chinese medical university

description: Library name: sample9

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of homo sapiens using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: mm39
Supplementary files format and content: All_reads_counts.xls

organism: Mus musculus

source_name: Z3.clean (Spleen CD4+ T cells from CIA mice treated with luteolin(LUT))

extract_protocol:
Total RNA was extracted from CD4+ T cells by using TRIzol Reagent (Invitrogen, Cat NO. 15596026). The RNA purity, concentration, and integrity were evaluated with an Agilent TapeStation 4200 (Agilent Technologies). RNA sequencing library was prepared by mRNA Library Prep Kit for Illumina®, and the indexed libraries were subjected to sequencing on DNBSEQ-T7 sequencer with PE150 model. Read mapping was performed via STRA software (version 2.5.3a) using CHOK1GS from Ensembl as a reference genome. Afterwards, high-quality reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Differential expression analysis was identified using the edgeR package (version 3.12.1).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: CD4+T cell


title: HepG2.D11 FAH vector

value: HBV transfected, FAH vector


title: OC4-2

description: Library name: Sample 2


title: Z1.clean

description: Library name: sample7

source_name: Z1.clean (Spleen CD4+ T cells from CIA mice treated with luteolin(LUT))


title: 6276-EC-S1_ROI_100

description:
Library name: DSP-1001660012908-H-A09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Stroma


title: 207686140065_R02C01

type: genomic

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

description:
Thyroid carcinoma tissue DNA
additional sample (4of4)
GEO_processed_matrix_GPL33022_additional_samples.csv
signal_intensity_matrix_GPL33022_additional_samples.csv

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.
matrix processed value definition: Normalized average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Human tissue DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol.

tag: cohort

value: REFERENCE

tag: Stage

value: Primary

value: HI

tag: age

tag: Sex

value: Male

value: Kinase Fusion


title: 6276-EC-S1_ROI_103

description:
Library name: DSP-1001660012908-H-A12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6276-EC-S1_ROI_102

description:
Library name: DSP-1001660012908-H-A11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: R3.clean

description: Library name: sample6

source_name: R3.clean (Spleen CD4+ T cells from CIA mice)


title: HepG2.D11 Empty vector

value: HBV transfected, Empty vector


title: PBMCs,ALS,B3,T0

description: Library name: B3

value: Blood

value: Peripheral Blood Mononuclear Cells

value: Bulbar phenotype


title: OC4-1

description: Library name: Sample 1

value: sperm

value: control


title: Z2.clean

description: Library name: sample8

source_name: Z2.clean (Spleen CD4+ T cells from CIA mice treated with luteolin(LUT))


title: 6276-EC-S1_ROI_101

description:
Library name: DSP-1001660012908-H-A10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Pancreas


title: PBMCs,ALS,B2,T0

description: Library name: B2


title: 207686140033_R08C01

description:
Thyroid carcinoma tissue DNA
additional sample (3of4)
GEO_processed_matrix_GPL33022_additional_samples.csv
signal_intensity_matrix_GPL33022_additional_samples.csv

value: Female


title: PBMCs,ALS,B1,T0

description: Library name: B1


title: R2.clean

description: Library name: sample5

source_name: R2.clean (Spleen CD4+ T cells from CIA mice)


title: 6276-EC-S1_ROI_98

description:
Library name: DSP-1001660012908-H-A07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 207686140033_R06C01

description:
Thyroid carcinoma tissue DNA
additional sample (2of4)
GEO_processed_matrix_GPL33022_additional_samples.csv
signal_intensity_matrix_GPL33022_additional_samples.csv


title: R1.clean

description: Library name: sample4

source_name: R1.clean (Spleen CD4+ T cells from CIA mice)


title: 6276-EC-S1_ROI_99

description:
Library name: DSP-1001660012908-H-A08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

source_name: Pancreas


title: 207686140033_R05C01

description:
Thyroid carcinoma tissue DNA
additional sample (1of4)
GEO_processed_matrix_GPL33022_additional_samples.csv
signal_intensity_matrix_GPL33022_additional_samples.csv


title: 6276-EC-S1_ROI_97

description:
Library name: DSP-1001660012908-H-A06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: C3.clean

description: Library name: sample3

source_name: C3.clean (Spleen CD4+ T cells from control mice)


title: Adipocytes, lep ob, large fraction, biological replicate 5 (D5L)

city: Ithaca

first: Claudia

last: Fischbach

state: NY

address: 157 Weill Hall

institute: Cornell University

description: Library name: Sample 37

data_processing:
Libraries were sequenced as 86 bp single-end reads on a NextSeq500 System (Illumina)
Reads were trimmed using fastp (v.0.23.4)
Reads were aligned using STAR (v.2.7.10b)
Reads were counted using the GeneCounts feature of STAR (v.2.7.10b)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Mammary adipose tissue

extract_protocol:
RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen)
Libraries were constructed using the QuantSeq FWD Kit (Lexogen)

value: Mammary adipose tissue

value: Adipocyte


title: NM900_016

city: Miaoli County

first: Shih-Sheng

address: 35, Keyan Road, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: The bisulfite-converted DNA was hybridized to the Illumina HumanMethylation450/EPIC/EPIC v2.0 BeadChips according to the manufacturer’s Infinium HD protocol. Hybridization was performed at 48°C for 16 hours in a humidity-controlled chamber. Following hybridization, chips were washed using Illumina-supplied buffers to remove unbound DNA prior to extension.

scan_protocol: Arrays were scanned on the Illumina iScan System using default parameters. Images were processed using Illumina GenomeStudio Methylation Module software to extract signal intensities and compute methylation beta values. Quality control was performed using internal control probes.

data_processing: For NM450 (450K), NM850 (EPIC), and NM900 (EPICv2) samples, raw intensities were background-corrected, dye-bias-equalized, and functionally normalized using the ‘preprocessFunnorm’ function in the minfi R package. CpGs on sex chromosomes, containing SNPs (MAF ≥5%), in repetitive regions, or with poor detection p-values were removed. Three processed DNA methylation datasets were generated: NM450-114 (NM450 samples), NMC-47 (combined NM850 and NM900), and NMC-161 (combined NM450, NM850, and NM900), retaining CpGs common to the platforms within each dataset (373,275 CpGs for NM450-114; 558,115 CpGs for NMC-47; 298,801 CpGs for NMC-161). For each dataset, beta values were inverse-rank transformed to a standard normal distribution and regressed on confounders including sex, age, medical operation status, batch, top genotyping PCs, and top methylation PCs. The residuals were inverse-rank transformed again to produce the final processed DNA methylation data.

label: Cy3 and Cy5

source_name: lung

label_protocol: Genomic DNA (500 ng) underwent bisulfite treatment with the EZ DNA Methylation Kit (Zymo Research). Following conversion, samples were processed according to the Illumina Infinium HD Methylation Assay protocol, including amplification, fragmentation, and hybridization steps. Labeling was incorporated during the single-base extension step.

extract_protocol: Tissue DNA was extracted from lung tissues using the QIAamp DNA Mini Kit (Qiagen Inc, USA). Bisulfite conversion of tissue DNA was performed using the EpiTect Fast DNA Bisulfite Kit (Qiagen Inc, USA) according to the manufacturer’s instructions. DNA methylation of bisulfite-converted DNA was measured using the abovementioned platform, according to Illumina’s standard procedure in Genetech Biotech Co., Ltd.

value: lung

tag: gender

tag: smoking status

value: Non-smoking


title: NM900_015

tag: tissue


title: C2.clean

description: Library name: sample2

source_name: C2.clean (Spleen CD4+ T cells from control mice)

tag: cell type

value: CD4+T cell


title: Adipocytes, lep ob, small fraction, biological replicate 5 (D5S)

description: Library name: Sample 36


title: 6276-EC-S1_ROI_96

description:
Library name: DSP-1001660012908-H-A05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Stroma

tag: batch


title: 6276-EC-S1_ROI_95

description:
Library name: DSP-1001660012908-H-A04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: Adipocytes, lep ob, unsorted, biological replicate 5 (D5)

description: Library name: Sample 35

tag: genotype


title: C1.clean

description: Library name: sample1

source_name: C1.clean (Spleen CD4+ T cells from control mice)


title: Adipocytes, wild-type, unsorted, biological replicate 4 (C5)

description: Library name: Sample 34


title: 1080_0080_S343 __Day10

city: Biberach

first: Siavash

last: Khosravi

address: Birkendorfer Strasse 65

country: Germany

institute: Boehringer Ingelheim

description: Library name: 1080_0080

data_processing:
Use paired-end sequencing with a read length of 101 bp. Convert BCL files to FASTQ format using bcl2fastq v2.204
Assembly: FASTQ were aligned files to the Sus scrofa reference genome (assembly 10.2, Ensembl release 86) using STAR aligner v2.5.2b6
Supplementary files format and content: tab deliminited text file includes raw counts for each sample

organism: Sus scrofa

source_name: Retina

extract_protocol:
RNA was extracted using RNeasy 96 Kit (Qiagen) according to the manufacturor protocol
Poly(A) mRNA was seperated with NEBNext Ultra II Directional RNA Library Prep Kit for illumina (NEB). Then NEBNext Multiplex Oligos for Illumina (NEB) was used for adapter ligation according to the manufacturer’s protocol.

value: Retina

value: wild type

tag: time point


title: 6276-EC-S1_ROI_94

description:
Library name: DSP-1001660012908-H-A03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Tumor


title: NM900_014


title: NM900_012


title: 1080_0079_S342 __Day10

description: Library name: 1080_0079


title: Adipocytes, high-fat diet, small fraction, biological replicate 5 (B5S)

description: Library name: Sample 32


title: Adipocytes, high-fat diet, large fraction, biological replicate 5 (B5L)

description: Library name: Sample 33


title: 6132-EC-S1_ROI_71

description:
Library name: DSP-1001660005976-G-H11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: IPMN


title: 6132-EC-S1_ROI_72

description:
Library name: DSP-1001660005976-G-H12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 1080_0078_S341 __Day10

description: Library name: 1080_0078


title: 6132-EC-S1_ROI_70

description:
Library name: DSP-1001660005976-G-H10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: NM900_011


title: Adipocytes, high-fat diet, unsorted, biological replicate 4 (B5)

description: Library name: Sample 31


title: NM900_010


title: NM900_013


title: Adipocytes, low-fat diet, unsorted, biological replicate 4 (A5)

description: Library name: Sample 30


title: 1080_0077_S340 __Day10

description: Library name: 1080_0077


title: 6132-EC-S1_ROI_69

description:
Library name: DSP-1001660005976-G-H09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6132-EC-S1_ROI_68

description:
Library name: DSP-1001660005976-G-H08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: NM900_009


title: 1080_0075_S338 __Day10

description: Library name: 1080_0075


title: Adipocytes, lep ob, small fraction, biological replicate 4 (D4S)

description: Library name: Sample 28


title: Adipocytes, lep ob, large fraction, biological replicate 4 (D4L)

description: Library name: Sample 29


title: NM900_007


title: 1080_0074_S337 __Day10

description: Library name: 1080_0074


title: 6132-EC-S1_ROI_67

description:
Library name: DSP-1001660005976-G-H07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: Adipocytes, lep ob, unsorted, biological replicate 4 (D4)

description: Library name: Sample 27


title: NM900_006