title: 6132-EC-S1_ROI_66

description:
Library name: DSP-1001660005976-G-H06
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_0073_S336 __Day10

status: Public on Feb 04 2026

type: SRA

city: Biberach

first: Siavash

last: Khosravi

address: Birkendorfer Strasse 65

country: Germany

institute: Boehringer Ingelheim

description: Library name: 1080_0073

library_source: transcriptomic

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

molecule: polyA RNA

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.

tag: tissue

value: Retina

tag: genotype

value: wild type

tag: time point


title: 1080_0076_S339 __Day10

description: Library name: 1080_0076


title: 6132-EC-S1_ROI_65

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-1001660005976-G-H05
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.

value: Pancreas

tag: cell type

value: IPMN

tag: batch


title: 1080_0071_S334 __Day10

description: Library name: 1080_0071


title: NM900_008

type: genomic

city: Miaoli County

first: Shih-Sheng

last: Jiang

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

molecule: genomic DNA

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: age

tag: gender

value: Female

tag: smoking status

value: Non-smoking


title: Adipocytes, high-fat diet, large fraction, biological replicate 4 (B4L)

city: Ithaca

first: Claudia

last: Fischbach

state: NY

address: 157 Weill Hall

institute: Cornell University

description: Library name: Sample 25

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

molecule: total RNA

organism: Mus musculus

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: Adipocytes, wild-type, unsorted, biological replicate 3 (C4)

description: Library name: Sample 26


title: Adipocytes, high-fat diet, small fraction, biological replicate 4 (B4S)

description: Library name: Sample 24


title: 1080_0072_S335 __Day10

description: Library name: 1080_0072


title: 6132-EC-S1_ROI_64

description:
Library name: DSP-1001660005976-G-H04
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_0070_S333 __Day10

description: Library name: 1080_0070


title: NM900_002


title: Adipocytes, high-fat diet, unsorted, biological replicate 3 (B4)

description: Library name: Sample 23


title: NM900_003


title: Adipocytes, low-fat diet, unsorted, biological replicate 3 (A4)

description: Library name: Sample 22


title: 6132-EC-S1_ROI_63

description:
Library name: DSP-1001660005976-G-H03
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_61

description:
Library name: DSP-1001660005976-G-H01
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: 209443890176_R08C01

city: Philadelphia

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

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.

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: VALIDATION

tag: Stage

value: Primary

value: HI

tag: Sex

value: Kinase Fusion


title: Adipocytes, lep ob, large fraction, biological replicate 3 (D3L)

description: Library name: Sample 21


title: NM900_004


title: NM900_001


title: 6132-EC-S1_ROI_62

description:
Library name: DSP-1001660005976-G-H02
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_0067_S330 __Day10

description: Library name: 1080_0067


title: NM900_005


title: 209443890176_R07C01

description: Thyroid carcinoma tissue DNA

value: LEUKO


title: 6132-EC-S1_ROI_60

description:
Library name: DSP-1001660005976-G-G12
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, small fraction, biological replicate 3 (D3S)

description: Library name: Sample 20


title: 1080_0069_S332 __Day10

description: Library name: 1080_0069


title: 1080_0068_S331 __Day10

description: Library name: 1080_0068


title: 209443890176_R06C01

description: Thyroid carcinoma tissue DNA

value: LI

value: Ras-like


title: 209443890176_R05C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_58

description:
Library name: DSP-1001660005976-G-G10
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: ChronicPanc


title: Adipocytes, wild-type, unsorted, biological replicate 2 (C3)

description: Library name: Sample 18


title: Adipocytes, lep ob, unsorted, biological replicate 3 (D3)

description: Library name: Sample 19


title: 1080_0065_S328 __Day10

description: Library name: 1080_0065

value: Retina


title: 209443890176_R04C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_59

description:
Library name: DSP-1001660005976-G-G11
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: ADM


title: 1080_0064_S327 __Day7

description: Library name: 1080_0064

value: wild type


title: Adipocytes, high-fat diet, small fraction, biological replicate 3 (B3S)

description: Library name: Sample 16


title: 1080_0066_S329 __Day10

description: Library name: 1080_0066


title: 6132-EC-S1_ROI_57

description:
Library name: DSP-1001660005976-G-G09
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: 1080_0063_S326 __Day7

description: Library name: 1080_0063


title: 6132-EC-S1_ROI_55

description:
Library name: DSP-1001660005976-G-G07
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, high-fat diet, large fraction, biological replicate 3 (B3L)

description: Library name: Sample 17


title: 209443890176_R01C01

description: Thyroid carcinoma tissue DNA

value: BRAF V600E


title: 1080_0062_S325 __Day7

description: Library name: 1080_0062


title: 1080_0061_S324 __Day7

description: Library name: 1080_0061


title: Adipocytes, lep ob, large fraction, biological replicate 2 (D2L)

description: Library name: Sample 15


title: 6132-EC-S1_ROI_56

description:
Library name: DSP-1001660005976-G-G08
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: 209443890032_R07C01

description: Thyroid carcinoma tissue DNA

value: Female


title: 6132-EC-S1_ROI_52

description:
Library name: DSP-1001660005976-G-G04
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_54

description:
Library name: DSP-1001660005976-G-G06
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: PanIN


title: Adipocytes, lep ob, small fraction, biological replicate 2 (D2S)

description: Library name: Sample 14

value: Mammary adipose tissue


title: 6132-EC-S1_ROI_53

description:
Library name: DSP-1001660005976-G-G05
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_0060_S323 __Day7

description: Library name: 1080_0060


title: 209443890032_R08C01

description: Thyroid carcinoma tissue DNA

value: Male


title: 1080_0059_S322 __Day7

description: Library name: 1080_0059


title: 209443890032_R06C01

description: Thyroid carcinoma tissue DNA

value: VALIDATION


title: Adipocytes, lep ob, unsorted, biological replicate 2 (D2)

description: Library name: Sample 13

value: Adipocyte


title: 209443890032_R05C01

description: Thyroid carcinoma tissue DNA

value: Primary

value: HI


title: 1080_0058_S321 __Day7

description: Library name: 1080_0058


title: Adipocytes, high-fat diet, large fraction, biological replicate 2 (B2L)

description: Library name: Sample 12


title: 6132-EC-S1_ROI_50

description:
Library name: DSP-1001660005976-G-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. \

value: Acinar


title: Adipocytes, high-fat diet, small fraction, biological replicate 2 (B2S)

description: Library name: Sample 11


title: 6132-EC-S1_ROI_51

description:
Library name: DSP-1001660005976-G-G03
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_0057_S320 __Day7

description: Library name: 1080_0057


title: 209443890032_R04C01

description: Thyroid carcinoma tissue DNA

value: Kinase Fusion


title: 6132-EC-S1_ROI_49

description:
Library name: DSP-1001660005976-G-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: 1080_0056_S319 __Day7

description: Library name: 1080_0056


title: 209443890032_R03C01

description: Thyroid carcinoma tissue DNA


title: Adipocytes, high-fat diet, unsorted, biological replicate 2 (B2)

description: Library name: Sample 10


title: Adipocytes, low-fat diet, unsorted, biological replicate 2 (A2)

description: Library name: Sample 9


title: 1080_0055_S318 __Day7

description: Library name: 1080_0055


title: 6132-EC-S1_ROI_48

description:
Library name: DSP-1001660005976-G-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: 209443890032_R02C01

description: Thyroid carcinoma tissue DNA

value: LEUKO


title: 6132-EC-S1_ROI_47

description:
Library name: DSP-1001660005976-G-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. \


title: 209443890032_R01C01

description: Thyroid carcinoma tissue DNA


title: Adipocytes, lep ob, large fraction, biological replicate 1 (D1L)

description: Library name: Sample 8


title: 1080_0054_S317 __Day7

description: Library name: 1080_0054


title: 6132-EC-S1_ROI_46

description:
Library name: DSP-1001660005976-G-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. \

value: IPMN


title: 209434740102_R08C01

description: Thyroid carcinoma tissue DNA


title: 1080_0052_S315 __Day7

description: Library name: 1080_0052

value: Retina


title: Adipocytes, lep ob, unsorted, biological replicate 1 (D1)

description: Library name: Sample 6


title: 6132-EC-S1_ROI_45

description:
Library name: DSP-1001660005976-G-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: 1080_0053_S316 __Day7

description: Library name: 1080_0053


title: Adipocytes, wild-type, unsorted, biological replicate 1 (C1)

description: Library name: Sample 5


title: 209434740102_R07C01

description: Thyroid carcinoma tissue DNA


title: 209434740102_R06C01

description: Thyroid carcinoma tissue DNA

value: LI

value: Indeterminate


title: 6132-EC-S1_ROI_43

description:
Library name: DSP-1001660005976-G-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. \

value: Pancreas


title: 1080_0050_S313 __Day7

description: Library name: 1080_0050

value: wild type


title: Adipocytes, lep ob, small fraction, biological replicate 1 (D1S)

description: Library name: Sample 7


title: 209434740102_R05C01

description: Thyroid carcinoma tissue DNA

value: Female

value: Ras-like


title: Adipocytes, high-fat diet, large fraction, biological replicate 1 (B1L)

description: Library name: Sample 4

value: Mammary adipose tissue


title: 6132-EC-S1_ROI_42

description:
Library name: DSP-1001660005976-G-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: 1080_0049_S312 __Day7

description: Library name: 1080_0049


title: 6132-EC-S1_ROI_44

description:
Library name: DSP-1001660005976-G-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: 209434740102_R04C01

description: Thyroid carcinoma tissue DNA


title: Adipocytes, high-fat diet, unsorted, biological replicate 1 (B1)

description: Library name: Sample 2


title: 209434740102_R03C01

description: Thyroid carcinoma tissue DNA


title: Adipocytes, low-fat diet, unsorted, biological replicate 1 (A1)

description: Library name: Sample 1


title: Adipocytes, high-fat diet, small fraction, biological replicate 1 (B1S)

description: Library name: Sample 3


title: 1080_0051_S314 __Day7

description: Library name: 1080_0051


title: 1080_0047_S310 __Day3

description: Library name: 1080_0047


title: 6132-EC-S1_ROI_39

description:
Library name: DSP-1001660005976-G-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. \

value: Tumor


title: 1080_0046_S309 __Day3

description: Library name: 1080_0046


title: 209434740102_R02C01

description: Thyroid carcinoma tissue DNA

value: VALIDATION

value: BRAF V600E


title: 209434740096_R08C01

description: Thyroid carcinoma tissue DNA

value: Primary


title: 1080_0048_S311 __Day3

description: Library name: 1080_0048


title: S13_XR_183_5 High SiglecF AM. LuAD.

city: Glasgow

first: Robin

last: Shaw

address: Switchback Road

country: United Kingdom

institute: CRUK Scotland Institute

description: Library name: S13_XR_183_5

data_processing:
Raw reads underwent QC and trimming with FastQC v0.12.1, fastp v0.23.4 and FastQ Screen v0.15.1. Paired-end reads were aligned with STAR v2.7.11b to the mouse GRCm39.110 genome and annotation; gene-level counts were generated with featureCounts (Subread v2.0.6). Differential expression was performed in R v4.3.2 using Bioconductor packages, with DESeq2 v1.42.0 and adaptive shrinkage via apeglm; significance was defined as fold-change > 1.5 and FDR (adjusted P) ≤ 0.05. MultiQC and notebooks were used to document the workflow.
Assembly: Mouse genome GRCm39.110 (Ensembl) was used for alignment and quantification.
Supplementary files format and content: Tab-separated raw counts tables.

source_name: Lung

extract_protocol:
Cell pellets (150,000–250,000 cells) were resuspended in Buffer RLT (Qiagen) and stored at −70 °C. RNA was extracted with the RNeasy Micro Kit (Qiagen) per manufacturer instructions. RNA quality was assessed on an Agilent TapeStation 4200 (High Sensitivity RNA ScreenTape) with all samples RIN > 8, and concentrations measured on a Qubit Fluorometer (RNA Broad Range assay). 150 ng total RNA was used as input.
Libraries were prepared using the Illumina Stranded mRNA kit and indexed with IDT for Illumina RNA UD Indexes. Post-library QC used Agilent High Sensitivity D1000 ScreenTape for sizing/profiling and Qubit High Sensitivity DNA assay for quantification. Libraries were pooled equimolarly to 4 nM and sequenced on an Illumina NextSeq 500 (High-Output 150-cycle run), paired-end 74 bp.

value: Lung

value: Airway Macrophages


title: 1080_0045_S308 __Day3

description: Library name: 1080_0045


title: 6132-EC-S1_ROI_41

description:
Library name: DSP-1001660005976-G-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: S14_XR_183_6 High SiglecF AM. LuAD.

description: Library name: S14_XR_183_6


title: 6132-EC-S1_ROI_38

description:
Library name: DSP-1001660005976-G-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: 209434740096_R07C01

description: Thyroid carcinoma tissue DNA

value: HI

value: Male


title: 6132-EC-S1_ROI_40

description:
Library name: DSP-1001660005976-G-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: 1080_0044_S307 __Day3

description: Library name: 1080_0044


title: 6132-EC-S1_ROI_37

description:
Library name: DSP-1001660005976-G-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: S12_XR_183_4 High SiglecF AM. LuAD.

description: Library name: S12_XR_183_4


title: 6132-EC-S1_ROI_36

description:
Library name: DSP-1001660005976-G-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: 1080_0043_S306 __Day3

description: Library name: 1080_0043


title: S11_XR_183_3 Low SiglecF AM. LuAD.

description: Library name: S11_XR_183_3


title: 209434740096_R06C01

description: Thyroid carcinoma tissue DNA

value: Kinase Fusion


title: S10_XR_183_2 Low SiglecF AM. LuAD.

description: Library name: S10_XR_183_2


title: 209434740096_R05C01

description: Thyroid carcinoma tissue DNA

value: LEUKO


title: 209434740096_R04C01

description: Thyroid carcinoma tissue DNA


title: 1080_0042_S305 __Day3

description: Library name: 1080_0042

value: Retina


title: 6132-EC-S1_ROI_34

description:
Library name: DSP-1001660005976-G-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: S08_XR_182_6 LuAD Tcrd WT

description: Library name: S08_XR_182_6


title: 209434740096_R03C01

description: Thyroid carcinoma tissue DNA


title: 1080_0041_S304 __Day3

description: Library name: 1080_0041


title: S07_XR_182_5 LuAD Tcrd WT

description: Library name: S07_XR_182_5


title: 6132-EC-S1_ROI_35

description:
Library name: DSP-1001660005976-G-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: 6132-EC-S1_ROI_33

description:
Library name: DSP-1001660005976-G-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: 1080_0040_S303 __Day3

description: Library name: 1080_0040


title: 209434740096_R01C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_32

description:
Library name: DSP-1001660005976-G-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: 209434740094_R08C01

description: Thyroid carcinoma tissue DNA

value: LI


title: 1080_0039_S302 __Day3

description: Library name: 1080_0039


title: 6132-EC-S1_ROI_31

description:
Library name: DSP-1001660005976-G-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. \

value: Pancreas


title: S06_XR_182_4 LuAD Tcrd WT

description: Library name: S06_XR_182_4


title: 1080_0038_S301 __Day3

description: Library name: 1080_0038

value: wild type


title: 6132-EC-S1_ROI_30

description:
Library name: DSP-1001660005976-G-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: S09_XR_183_1 Low SiglecF AM. LuAD.

description: Library name: S09_XR_183_1


title: 1080_0037_S300 __Day3

description: Library name: 1080_0037


title: 209434740094_R07C01

description: Thyroid carcinoma tissue DNA

value: Female


title: S05_XR_182_3 LuAD Tcrd KO

description: Library name: S05_XR_182_3


title: 209434740094_R06C01

description: Thyroid carcinoma tissue DNA


title: S04_XR_182_2 LuAD Tcrd KO

description: Library name: S04_XR_182_2


title: 1080_0036_S299 __Day3

description: Library name: 1080_0036


title: 209434740096_R02C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_29

description:
Library name: DSP-1001660005976-G-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. \

value: NormalDuct


title: 1080_0035_S298 __Day3

description: Library name: 1080_0035


title: 6132-EC-S1_ROI_28

description:
Library name: DSP-1001660005976-G-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: 6132-EC-S1_ROI_27

description:
Library name: DSP-1001660005976-G-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: 1080_0032_S295 __Day1

description: Library name: 1080_0032


title: 1080_0033_S296 __Day3

description: Library name: 1080_0033


title: 6132-EC-S1_ROI_26

description:
Library name: DSP-1001660005976-G-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: S02_XR_174_Low SiglecF AM. LuAD.

description: Library name: S02_XR_174_L


title: 209434740094_R04C01

description: Thyroid carcinoma tissue DNA

value: Indeterminate


title: S01_XR_174_High SiglecF AM. LuAD.

description: Library name: S01_XR_174_H


title: 209434740091_R06C01

description: Thyroid carcinoma tissue DNA

value: Ras-like


title: 6132-EC-S1_ROI_22

description:
Library name: DSP-1001660005976-G-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. \

value: IPMN


title: 209434740094_R03C01

description: Thyroid carcinoma tissue DNA

value: VALIDATION


title: S03_XR_182_1 LuAD Tcrd KO

description: Library name: S03_XR_182_1


title: 6132-EC-S1_ROI_24

description:
Library name: DSP-1001660005976-G-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: 6132-EC-S1_ROI_20

description:
Library name: DSP-1001660005976-G-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: 209434740091_R08C01

description: Thyroid carcinoma tissue DNA

value: Primary


title: 209434740091_R04C01

description: Thyroid carcinoma tissue DNA

value: BRAF V600E


title: WT2 scATAC-seq

city: College Station

first: Chun Yip

last: Tong

state: Tx

address: 400 Bizzell St

department: Biology

institute: Texas A&M University

description:
Library name: Mouse Liver WT2 scATAC-seq
10X Genomics Multiome RNA + ATAC

data_processing:
For the 10X Genomics Multiome data, we used Cell Ranger ARC (version 2.0.0) to perform sample demultiplexing, barcode processing, peak calling, and counting of RNA and ATAC reads in single cells. Alignment was performed with the cellranger-arc count function. Cells with high percentages of mitochondrial reads, extreme RNA read counts, and/or extreme ATAC fragment counts were removed. Doublet cells, identified by scDblFinder across multiplexed samples corresponding to the treatment groups, were excluded from subsequent analysis. For read count normalization, we used sctransform by Seurat for scRNA-seq and TF-IDF by Signac for scATAC-seq.  This is followed by principal component analysis (PCA) and latent semantic indexing (LSI) for dimension reduction, respectively. We kept the top 50 principal components (PCs) from scRNA-seq and the top 2-50 LSIs from scATAC-seq. Jointly, these are used as input to construct a weighted nearest neighbor (WNN) graph, which is further used for joint UMAP visualization and clustering.  We used the Leiden clustering algorithm for community detection with the resolution parameter visualized and optimized by the clustree algorithm, which builds a tree to visualize and examine how clusters are related to each other at varying resolutions, allowing researchers to assess which clusters are distinct and which are unstable with the use of additional metrics such as the SC3 stability index. For modality-specific processing, we built the unweighted K-nearest neighbor (KNN) and the weighted shared nearest neighbor (SNN) graphs, followed by UMAP visualization and clustering identification. For scATAC-seq data, we also adopted weighted PCA by Destin weighing chromatin accessibilities by existing genomic annotations and publicly available regulomic data. We obtained the position frequency matrices and annotated 633 pairs of TFs and motifs from the JASPAR 2020 database; we further applied chromVAR to derive, for each TF, its motif score, which measures the deviation in chromatin accessibility across the set of peaks containing the corresponding motif, compared to a set of background peaks. We also constructed a pseudo-gene activity matrix, summing ATAC read counts in gene bodies and promoter regions (2Kb upstream of genes' transcription start sites), followed by sctransform normalization.
Assembly: mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix
Library strategy: Genomics Multiome

molecule: nuclear RNA

source_name: Liver

growth_protocol: Adult male wild type (C57BL/6NCrl strain; Charles River laboratories)  was housed under 12 h light:12 h dark, and provided food and water ad libitum.

extract_protocol:
Mice were euthanized by isoflurane anesthesia followed by decapitation, with four biological replicates per group. Livers were dissected quickly after euthanasia, briefly washed in ice-cold 1X PBS, snap-frozen in liquid nitrogen, and stored at -80ºC until nuclei purification.
Flash-frozen mouse liver tissue samples were processed to isolate nuclei using a combination of lysis, purification, and permeabilization steps. Nuclei were prepared by homogenizing the tissue in a lysis buffer, followed by filtration and resuspension in diluted nuclei buffer optimized for subsequent steps. This buffer formulation, containing magnesium and RNase inhibitors, ensured compatibility with downstream transposition and barcoding processes. Purified nuclei were subjected to transposition in a reaction mix containing transposase, which preferentially fragmented open-chromatin regions and appended adapter sequences to the ends of DNA fragments. Polyadenylated RNA molecules within the nuclei were reverse-transcribed into full-length cDNA. These processes occurred within nanoliter-scale Gel Beads-in-emulsion (GEMs), generated using the Chromium Next GEM platform. Each GEM contained the necessary reagents for DNA and RNA barcoding, ensuring unique molecular and nucleus-specific indexing. Following GEM incubation, barcoded DNA and cDNA were recovered, purified, and amplified via PCR to generate sufficient material for library construction. ATAC libraries underwent size selection, while cDNA for gene expression libraries was enzymatically fragmented, end-repaired, and adapter-ligated prior to further amplification. Both libraries were subjected to QC to ensure high fidelity. Sequencing of the final libraries was performed on an Illumina NovaSeq platform using paired-end 150 bp reads (PE150), targeting a depth of ~200 million reads per library.

value: Liver

value: Wildtype


title: WT4 scATAC-seq

description:
Library name: Mouse Liver WT4 scATAC-seq
10X Genomics Multiome RNA + ATAC


title: WT5 scATAC-seq

description:
Library name: Mouse Liver WT5 scATAC-seq
10X Genomics Multiome RNA + ATAC


title: 1080_0034_S297 __Day3

description: Library name: 1080_0034


title: 6132-EC-S1_ROI_21

description:
Library name: DSP-1001660005976-G-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: 1080_0029_S292 __Day1

description: Library name: 1080_0029


title: 1080_0031_S294 __Day1

description: Library name: 1080_0031


title: 209434740091_R07C01

description: Thyroid carcinoma tissue DNA

value: HI


title: 6132-EC-S1_ROI_25

description:
Library name: DSP-1001660005976-G-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: 209434740091_R03C01

description: Thyroid carcinoma tissue DNA

value: Kinase Fusion


title: 1080_0028_S291 __Day1

description: Library name: 1080_0028


title: WT6 scATAC-seq

description:
Library name: Mouse Liver WT6 scATAC-seq
10X Genomics Multiome RNA + ATAC


title: 209434740091_R01C01

description: Thyroid carcinoma tissue DNA

value: LEUKO

value: Male


title: 1080_0030_S293 __Day1

description: Library name: 1080_0030

value: Retina


title: WT3 scATAC-seq

description:
Library name: Mouse Liver WT3 scATAC-seq
10X Genomics Multiome RNA + ATAC


title: WT1 scATAC-seq

description:
Library name: Mouse Liver WT1 scATAC-seq
10X Genomics Multiome RNA + ATAC


title: 209434740091_R02C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_19

description:
Library name: DSP-1001660005976-G-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. \

value: Pancreas


title: 209411850003_R08C01

description: Thyroid carcinoma tissue DNA


title: WT5 scRNA-seq

description:
Library name: Mouse Liver WT5 scRNA-seq
10X Genomics Multiome RNA + ATAC


title: 1080_0027_S290 __Day1

description: Library name: 1080_0027

value: wild type


title: WT6 scRNA-seq

description:
Library name: Mouse Liver WT6 scRNA-seq
10X Genomics Multiome RNA + ATAC


title: 6132-EC-S1_ROI_17

description:
Library name: DSP-1001660005976-G-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. \


title: 6132-EC-S1_ROI_18

description:
Library name: DSP-1001660005976-G-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: 1080_0025_S288 __Day1

description: Library name: 1080_0025


title: 1080_0026_S289 __Day1

description: Library name: 1080_0026


title: 6132-EC-S1_ROI_16

description:
Library name: DSP-1001660005976-G-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: 1080_0024_S287 __Day1

description: Library name: 1080_0024


title: 209411850003_R05C01

description: Thyroid carcinoma tissue DNA

value: Female


title: 209411850003_R06C01

description: Thyroid carcinoma tissue DNA


title: WT4 scRNA-seq

description:
Library name: Mouse Liver WT4 scRNA-seq
10X Genomics Multiome RNA + ATAC


title: 209411850003_R07C01

description: Thyroid carcinoma tissue DNA


title: 209411850003_R04C01

description: Thyroid carcinoma tissue DNA

value: LI


title: 6132-EC-S1_ROI_15

description:
Library name: DSP-1001660005976-G-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: WT2 scRNA-seq

description:
Library name: Mouse Liver WT2 scRNA-seq
10X Genomics Multiome RNA + ATAC


title: 6132-EC-S1_ROI_14

description:
Library name: DSP-1001660005976-G-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: WT1 scRNA-seq

description:
Library name: Mouse Liver WT1 scRNA-seq
10X Genomics Multiome RNA + ATAC


title: 1080_0022_S285 __Day1

description: Library name: 1080_0022


title: WT3 scRNA-seq

description:
Library name: Mouse Liver WT3 scRNA-seq
10X Genomics Multiome RNA + ATAC


title: 1080_0023_S286 __Day1

description: Library name: 1080_0023


title: 1080_0021_S284 __Day1

description: Library name: 1080_0021


title: 209411850003_R03C01

description: Thyroid carcinoma tissue DNA

value: Indeterminate


title: 6132-EC-S1_ROI_12

description:
Library name: DSP-1001660005976-G-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: 209411850003_R02C01

description: Thyroid carcinoma tissue DNA


title: NR3C2-OE-RNA-3

city: WUHAN

first: heng

middle: zhi

last: du

address: 1095 Jiefang Dadao, Wuhan City, Hubei Province, China

country: China

institute: Wuhan Tongji Hospital

description: Library name: Sample6

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (Version 1.2.1) (Martin M, 2011) was used to remove 3' end joints, at least 10 bp Overlap (AGATCGGAAG), and 20% base error rate was allowed.
Reads per kilobase of exon per megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Ensembl 38.85
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: HK2 cells

growth_protocol: The human renal proximal tubular epithelial cell line (HK2) (Boster Biological Technology, Cat# CX0044) was cultured in DMEM/F12 medium (KeyGEN Bio TECH, Cat# KGL1202-500) supplemented with 10% fetal bovine serum (FBS, HyClone, Cat# SH30084-03) and 1% penicillin/streptomycin (Thermo Fisher Scientific, Cat# 10378016) at 37°C in a 5% CO₂ humidified atmosphere.

extract_protocol:
RNA was harvested using Trizol reagent following the instructions.
All of our RNA-seq projects used strand specific kits to construct the libraries.By using next-generation sequencing (NGS) technology, paired-end (PE) sequencing of these libraries was performed based on Illumina HiSeq sequencing platform

treatment_protocol: HK2 cells were transfected with an NR3C2-overexpressing (NR3C2-OE) plasmid DNA, both designed and synthesized by Aoke Biotechnology Co., Ltd. Transfection was performed using Lipofectamine 2000 reagent (Invitrogen, Cat# 11668019) according to the manufacturer’s instructions.

tag: cell line

value: HK2 cells

value: Homo sapiens

value: NR3C2 overexpression


title: 6132-EC-S1_ROI_13

description:
Library name: DSP-1001660005976-G-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. \

value: IPMN


title: 1080_0020_S283 __Day1

description: Library name: 1080_0020


title: NR3C2-OE-RNA-2

description: Library name: Sample5


title: 209411850003_R01C01

description: Thyroid carcinoma tissue DNA

value: VALIDATION

value: Primary


title: 1080_0019_S282 __Day1

description: Library name: 1080_0019


title: NR3C2-OE-RNA-1

description: Library name: Sample4


title: 1080_0018_S281 __Day1

description: Library name: 1080_0018


title: 209411840098_R08C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_10

description:
Library name: DSP-1001660005976-G-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: 6132-EC-S1_ROI_11

description:
Library name: DSP-1001660005976-G-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: 209411840098_R07C01

description: Thyroid carcinoma tissue DNA


title: 1080_0017_S280 __Day1

description: Library name: 1080_0017


title: 1080_0016_S279 __Day0

description: Library name: 1080_0016


title: 6132-EC-S1_ROI_8

description:
Library name: DSP-1001660005976-G-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: 209411840098_R06C01

description: Thyroid carcinoma tissue DNA

value: Ras-like


title: 209411840098_R05C01

description: Thyroid carcinoma tissue DNA

value: HI


title: 6132-EC-S1_ROI_9

description:
Library name: DSP-1001660005976-G-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: 6132-EC-S1_ROI_7

description:
Library name: DSP-1001660005976-G-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: Control-RNA-2

description: Library name: Sample2

value: normal


title: 209411840098_R04C01

description: Thyroid carcinoma tissue DNA

value: Kinase Fusion


title: 6132-EC-S1_ROI_6

description:
Library name: DSP-1001660005976-G-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: Control-RNA-1

description: Library name: Sample1


title: SMP 21 18380 A13-22

city: HOUSTON

first: HONG

last: ZHAO

state: Texas

address: 6670 Bertner Ave

institute: HOUSTON METHODIST HOSPITAL

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

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

source_name: PDAC

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

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

value: PDAC

tag: treatment

value: prehab


title: 1080_0014_S277 __Day0

description: Library name: 1080_0014

value: Retina


title: 209411840098_R03C01

description: Thyroid carcinoma tissue DNA

value: LEUKO


title: Control-RNA-3

description: Library name: Sample3


title: 1080_0015_S278 __Day0

description: Library name: 1080_0015

value: wild type


title: 1080_0013_S276 __Day0

description: Library name: 1080_0013


title: 6132-EC-S1_ROI_4

description:
Library name: DSP-1001660005976-G-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. \

value: Pancreas


title: SMP 21 18380 A13-21

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


title: 6132-EC-S1_ROI_5

description:
Library name: DSP-1001660005976-G-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: 1080_0012_S275 __Day0

description: Library name: 1080_0012


title: SMP 21 18380 A13-20

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


title: SMP 21 18380 A13-19

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


title: 209411840098_R02C01

description: Thyroid carcinoma tissue DNA

value: Female

value: BRAF V600E


title: 6132-EC-S1_ROI_2

description:
Library name: DSP-1001660005976-G-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. \


title: 6132-EC-S1_ROI_3

description:
Library name: DSP-1001660005976-G-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: 1080_0011_S274 __Day0

description: Library name: 1080_0011


title: SMP 21 18380 A13-23

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


title: 209392270069_R08C01

description: Thyroid carcinoma tissue DNA


title: 209411840098_R01C01

description: Thyroid carcinoma tissue DNA


title: SMP 21 18380 A13-18

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


title: 1080_0009_S272 __Day0

description: Library name: 1080_0009


title: 6132-EC-S1_ROI_1

description:
Library name: DSP-1001660005976-G-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: 1080_0010_S273 __Day0

description: Library name: 1080_0010


title: 6132-EC-S1_ROI_132

description:
Library name: DSP-1001660011120-D-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. \

value: Stroma


title: 1080_0008_S271 __Day0

description: Library name: 1080_0008


title: 209392270069_R05C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_131

description:
Library name: DSP-1001660011120-D-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: SMP 21 18380 A13-16

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


title: 1080_0007_S270 __Day0

description: Library name: 1080_0007


title: 209392270069_R03C01

description: Thyroid carcinoma tissue DNA


title: 209392270069_R06C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_129

description:
Library name: DSP-1001660011120-D-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: SMP 21 18380 A13-17

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


title: SMP 21 18380 A13-14

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


title: 1080_0006_S269 __Day0

description: Library name: 1080_0006


title: 209392270069_R04C01

description: Thyroid carcinoma tissue DNA

value: LI


title: 6132-EC-S1_ROI_130

description:
Library name: DSP-1001660011120-D-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: 1080_0004_S267 __Day0

description: Library name: 1080_0004


title: SMP 21 18380 A13-12

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


title: SMP 21 18380 A13-13

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


title: 209392270051_R07C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_128

description:
Library name: DSP-1001660011120-D-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. \

value: Lymphoid


title: 209392270051_R08C01

description: Thyroid carcinoma tissue DNA

value: VALIDATION


title: 6132-EC-S1_ROI_127

description:
Library name: DSP-1001660011120-D-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: SMP 21 18380 A13-15

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


title: SMP 21 18380 A13-11

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


title: 1080_0005_S268 __Day0

description: Library name: 1080_0005


title: 209392270051_R06C01

description: Thyroid carcinoma tissue DNA

value: Primary


title: 6132-EC-S1_ROI_126

description:
Library name: DSP-1001660011120-D-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: 1080_0002_S265 __Day0

description: Library name: 1080_0002


title: 209392270051_R05C01

description: Thyroid carcinoma tissue DNA


title: 1080_0003_S266 __Day0

description: Library name: 1080_0003


title: 6132-EC-S1_ROI_125

description:
Library name: DSP-1001660011120-D-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: 1080_0001_S264 __Day0

description: Library name: 1080_0001


title: SMP 21 18380 A13-10

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


title: 209392270051_R04C01

description: Thyroid carcinoma tissue DNA


title: SMP 21 18380 A13-9

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


title: 209392270051_R03C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_124

description:
Library name: DSP-1001660011120-D-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: SMP 21 18380 A13-8

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


title: H2A-P_WT_Log_K_Rep3 (Input)

city: Wrocław

first: Ireneusz

middle: Bernard

last: Litwin

address: Kanonia 6/8

department: Department of Genetics and Cell Physiology

country: Poland

institute: University of Wroclaw

description: Library name: H2A-P_WT_Log_K_Rep3_INP

library_source: genomic

data_processing:
Raw sequencing data was quality controlled by Q30.
Low-quality reads and adapter sequences were cut off using Cutadapt.
Filtered reads were then mapped against the target genome (S. cerevisiae S288C assembly SacCer3) and against the spike-in genome (S. pombe assembly ASM294v2) using Bowtie2.
Unmapped reads, mitochondrial DNA and duplicates were filtered out using Samtools.
Samtools was used to count reads uniquely mapped to SacCer3 and ASM294v2 and these values were used to calculate the occupancy ratio value.
Peaks were called using MACS3.
bedGraph files were converted to bigWig format using bedGraphToBigWig utility.
Assembly: Saccharomyces cerevisiae SacCer3
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: All S. cerevisiae strains were cultured in rich YPD medium at 30°C unless indicated otherwise. The S. pombe calibration strain was cultured in YES medium at 30°C

extract_protocol:
4 × 10⁸ S. cerevisiae cells were mixed with ~1 × 10⁸ Schizosaccharomyces pombe cells expressing Rad21–6HA, fixed in 1% formaldehyde for 15 min at room temperature (RT), and quenched with 150 mM glycine for 5 min. Cells were pelleted, washed once with TBS, and resuspended in 600 µl FA lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, protease inhibitor cocktail, 1 mM PMSF). Cells were lysed by four cycles of bead beating (6,500 rpm, 30 s) and lysates were sonicated to an average DNA fragment length of ~600 bp. After centrifugation for 30 min at 15,000 rpm, cleared supernatants were transferred to new tubes and 1% of each was kept as an input sample. For immunoprecipitation, 5 µl of antibody against the S. cerevisiae protein of interest and 2 µl of anti-HA antibody recognizing Rad21–6HA were added to the lysates, and samples were incubated overnight at 4°C with rotation. The next day, DNA-protein complex es were captured with Protein G Dynabeads and sequentially washed with FA-lysis buffer, FA-500 buffer (50 mM HEPES–KOH pH 7.5, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM EDTA), LiCl wash buffer (10 mM Tris–HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA) and TE (10 mM Tris–HCl pH 7.5, 1 mM EDTA) on a rotator for 5 min each time. Beads and input samples were then resuspended in elution buffer (50 mM Tris–HCl pH 7.5, 1% SDS, 10 mM EDTA) and incubated O/N at 65°C on a thermal shaker. The next day, magnetic beads were removed, and all samples were treated with RNase A (100 µg/ml) for 1 h at 37°C, followed by a 1 h incubation at 65°C in the presence of proteinase K (1 mg/ml). DNA from H2A-S129-P, Rap1-13cMyc, Ku70-13cMyc, Tel1-12Pk, Pol2-3HA, and Rpb1 ChIP samples was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). DNA from RPA, Rad52–YFP, Rad51, Rad59–13cMyc, and Cdc13–18cMyc ChIP samples was extracted by phenol–chloroform purification and ethanol precipitation.
Sequencing libraries for H2A-S129-P, Rap1-13cMyc, Ku70-13cMyc, Tel1-12Pk, Pol2-3HA, and Rpb1 ChIP samples were prepared using the Novogene NGS DNA Library Prep Set. Libraries for RPA, Rad52–YFP, Rad51, Rad59–13cMyc, and Cdc13–18cMyc ChIP samples were generated using the xGen™ ssDNA & Low-Input DNA Library Preparation Kit (Integrated DNA Technologies) according to the manufacturer’s instructions.

treatment_protocol: The indicated S. cerevisiae strains were treated with 0.5 mM As(III) for 1 h or 2 h, or left untreated. Wild-type cells were also treated with phleomycin (2 µg/mL or 50 µg/mL). rpb1-1 mutant cells were grown at the permissive temperature (25°C) and shifted to 37°C.

value: yeast

tag: chip antibody


title: 6132-EC-S1_ROI_123

description:
Library name: DSP-1001660011120-D-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: H2A-P_WT_Log_K_Rep3 (ChIP)

description: Library name: H2A-P_WT_Log_K_Rep3_IP

value: Anti-Histone H2A (phospho S129) antibody (Abcam, ab15083)


title: 209392270039_R08C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_122

description:
Library name: DSP-1001660011120-D-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: SMP 21 18380 A13-7

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


title: 209392270039_R07C01

description: Thyroid carcinoma tissue DNA

value: Indeterminate


title: 6132-EC-S1_ROI_121

description:
Library name: DSP-1001660011120-D-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: SMP 21 18380 A13-5

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


title: H2A-P_WT_Log_As_Rep3 (Input)

description: Library name: H2A-P_WT_Log_As_Rep3_INP

value: 0.5mM As(III)


title: H2A-P_WT_Log_As_Rep3 (ChIP)

description: Library name: H2A-P_WT_Log_As_Rep3_IP


title: SMP 21 18380 A13-6

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

value: PDAC


title: SMP 21 18380 A13-4

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

value: prehab


title: 209367290008_R08C01

description: Thyroid carcinoma tissue DNA

value: HI

value: Kinase Fusion


title: H2A-P_WT_Log_K_Rep2 (Input)

description: Library name: H2A-P_WT_Log_K_Rep2_INP


title: H2A-P_WT_Log_As_Rep2 (Input)

description: Library name: H2A-P_WT_Log_As_Rep2_INP


title: 209392270039_R02C01

description: Thyroid carcinoma tissue DNA

value: Male


title: 209367290008_R07C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_120

description:
Library name: DSP-1001660011120-D-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. \

value: Pancreas


title: 6132-EC-S1_ROI_117

description:
Library name: DSP-1001660011120-D-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: 6132-EC-S1_ROI_118

description:
Library name: DSP-1001660011120-D-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: SMP 21 18380 A13-3

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


title: H2A-P_WT_Log_As_Rep2 (ChIP)

description: Library name: H2A-P_WT_Log_As_Rep2_IP


title: Rad59_WT_Log_K_Rep1 (Input)

description: Library name: Rad59_WT_Log_K_Rep1_INP


title: SMP 21 18380 A13-1

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


title: 6132-EC-S1_ROI_116

description:
Library name: DSP-1001660011120-D-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: SMP 23 15022 G14-24

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


title: 6132-EC-S1_ROI_119

description:
Library name: DSP-1001660011120-D-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: 209367290008_R06C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_115

description:
Library name: DSP-1001660011120-D-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: H2A-P_WT_Log_K_Rep2 (ChIP)

description: Library name: H2A-P_WT_Log_K_Rep2_IP


title: 209367290008_R04C01

description: Thyroid carcinoma tissue DNA

value: LEUKO

value: Female


title: Rad59_WT_Log_K_Rep1 (ChIP)

description: Library name: Rad59_WT_Log_K_Rep1_IP

value: Anti-c-myc antibody (Roche, 11667149001)


title: SMP 23 15022 G14-23

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


title: 209392270039_R04C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_114

description:
Library name: DSP-1001660011120-D-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. \

value: Stroma


title: SMP 21 18380 A13-2

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


title: 209367290008_R02C01

description: Thyroid carcinoma tissue DNA

value: BRAF V600E


title: 209367290008_R05C01

description: Thyroid carcinoma tissue DNA

value: VALIDATION


title: Rad59_WT_Log_As_Rep1 (ChIP)

description: Library name: Rad59_WT_Log_As_Rep1_IP


title: SMP 23 15022 G14-21

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


title: 6132-EC-S1_ROI_113

description:
Library name: DSP-1001660011120-D-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. \


title: 209367290008_R01C01

description: Thyroid carcinoma tissue DNA

value: Primary

value: LI


title: SMP 23 15022 G14-20

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


title: Rad51_WT_Log_K_Rep1 (Input)

description: Library name: Rad51_WT_Log_K_Rep1_INP

value: yeast


title: SMP 23 15022 G14-22

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


title: 209269000108_R05C01

description: Thyroid carcinoma tissue DNA


title: 6132-EC-S1_ROI_111

description:
Library name: DSP-1001660011120-D-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: Rad59_WT_Log_As_Rep1 (Input)

description: Library name: Rad59_WT_Log_As_Rep1_INP


title: 209367290008_R03C01

description: Thyroid carcinoma tissue DNA


title: SMP 23 15022 G14-19

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


title: Rad51_WT_Log_K_Rep1 (ChIP)

description: Library name: Rad51_WT_Log_K_Rep1_IP

value: Anty-Rad51 antibody (Invitrogen, PA5-34905)


title: 209269000108_R03C01

description: Thyroid carcinoma tissue DNA

value: Indeterminate


title: Rad51_WT_Log_As_Rep1 (Input)

description: Library name: Rad51_WT_Log_As_Rep1_INP

value: 0.5mM As(III)


title: Rad51_WT_Log_As_Rep1 (ChIP)

description: Library name: Rad51_WT_Log_As_Rep1_IP


title: SMP 23 15022 G14-17

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

value: PDAC

value: prehab


title: Rap1_WT_G2_K_Rep2 (Input)

description: Library name: Rap1_WT_G2_K_Rep2_INP


title: 6132-EC-S1_ROI_112

description:
Library name: DSP-1001660011120-D-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: 209269000108_R01C01

description: Thyroid carcinoma tissue DNA


title: Rap1_WT_G2_K_Rep2 (ChIP)

description: Library name: Rap1_WT_G2_K_Rep2_IP