title: SMP 23 15022 G14-16

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


title: 6132-EC-S1_ROI_107

status: Public on Feb 04 2026

type: SRA

city: Ann Arbor

first: Eileen

last: Carpenter

state: MI

address: 1137 E Catherine St Med Sci II R 7712

department: Internal Medicine

country: USA

institute: University of Michigan

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

library_source: other

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

molecule: other

organism: Homo sapiens

source_name: Pancreas

growth_protocol: FFPE Blocks

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

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

tag: tissue

value: Pancreas

tag: cell type

value: Stroma

tag: batch


title: 6132-EC-S1_ROI_110

description:
Library name: DSP-1001660011120-D-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: 6132-EC-S1_ROI_106

description:
Library name: DSP-1001660011120-D-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: 207700160098_R08C01

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

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

label: Cy5 and Cy3

molecule: genomic DNA

source_name: human thyroid carcinoma tissue DNA

label_protocol: Standard Illumina Protocol

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

tag: cohort

value: REFERENCE

tag: Stage

value: HI

tag: age

tag: Sex

value: Female

value: Kinase Fusion


title: SMP 23 15022 G14-18

city: HOUSTON

first: HONG

last: ZHAO

state: Texas

address: 6670 Bertner Ave

institute: HOUSTON METHODIST HOSPITAL

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

library_source: transcriptomic

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

molecule: total RNA

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: Rap1_WT_G2_As_Rep2 (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: Rap1_WT_G2_As_Rep2_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: genotype

value: 0.5mM As(III)

tag: chip antibody


title: 6132-EC-S1_ROI_109

description:
Library name: DSP-1001660011120-D-D02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 209269000108_R02C01

description: Thyroid carcinoma tissue DNA

data_processing: SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.

source_name: Human tissue DNA

value: VALIDATION

value: Primary

value: Male


title: 6132-EC-S1_ROI_108

description:
Library name: DSP-1001660011120-D-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: SMP 23 15022 G14-15

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


title: Rap1_WT_G2_As_Rep2 (ChIP)

description: Library name: Rap1_WT_G2_As_Rep2_IP

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


title: 207700160098_R05C01

value: BRAF V600E


title: SMP 23 15022 G14-14

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


title: 207700160098_R01C01


title: SMP 23 15022 G14-13

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


title: 207686140028_R05C01


title: H2A-P_WT_Log_K_Rep1 (Input)

description: Library name: H2A-P_WT_Log_K_Rep1_INP


title: SMP 23 15022 G14-12

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


title: H2A-P_WT_Log_K_Rep1 (ChIP)

description: Library name: H2A-P_WT_Log_K_Rep1_IP

value: Anti-Histone H2A (phospho S129) antibody (Active Motif, 39271)


title: 6132-EC-S1_ROI_103

description:
Library name: DSP-1001660011120-D-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: 6132-EC-S1_ROI_104

description:
Library name: DSP-1001660011120-D-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: 207686140005_R04C01


title: SMP 23 15022 G14-11

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


title: H2A-P_WT_Log_As_Rep1 (Input)

description: Library name: H2A-P_WT_Log_As_Rep1_INP


title: 6132-EC-S1_ROI_105

description:
Library name: DSP-1001660011120-D-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: 207686140005_R01C01


title: 6132-EC-S1_ROI_102

description:
Library name: DSP-1001660011120-D-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: SMP 23 15022 G14-10

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


title: 6132-EC-S1_ROI_101

description:
Library name: DSP-1001660011120-D-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: H2A-P_WT_Log_As_Rep1 (ChIP)

description: Library name: H2A-P_WT_Log_As_Rep1_IP


title: SMP 23 15022 G14-9

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


title: 207700160062_R03C01


title: 6132-EC-S1_ROI_100

description:
Library name: DSP-1001660011120-D-C05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 207700160043_R08C01


title: Pol2_WT_Log_K_Rep2 (Input)

description: Library name: Pol2_WT_Log_K_Rep2_INP


title: 207686140156_R08C01

value: LI

value: Ras-like


title: 6132-EC-S1_ROI_99

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

value: Pancreas

value: IPMN


title: SMP 23 15022 G14-7

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


title: SMP 23 15022 G14-8

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


title: 6132-EC-S1_ROI_98

description:
Library name: DSP-1001660011120-D-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: 207686140043_R02C01

value: REFERENCE

value: LEUKO


title: Pol2_WT_Log_As_Rep2 (Input)

description: Library name: Pol2_WT_Log_As_Rep2_INP


title: Pol2_WT_Log_K_Rep2 (ChIP)

description: Library name: Pol2_WT_Log_K_Rep2_IP

value: Anti-HA  antibody (Roche, 11867423001)


title: 207700160021_R05C01

value: HI

value: Kinase Fusion


title: Pol2_WT_Log_As_Rep2 (ChIP)

description: Library name: Pol2_WT_Log_As_Rep2_IP

value: yeast


title: 6132-EC-S1_ROI_96

description:
Library name: DSP-1001660011120-D-C01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 207686140156_R01C01

value: Female


title: SMP 23 15022 G14-4

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

value: PDAC

value: prehab


title: SMP 23 15022 G14-6

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


title: Pol2_WT_Log_K_Rep1 (Input)

description: Library name: Pol2_WT_Log_K_Rep1_INP


title: SMP 23 15022 G14-5

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


title: 6132-EC-S1_ROI_95

description:
Library name: DSP-1001660011120-D-B12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: SMP 23 15022 G14-3

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


title: Pol2_WT_Log_K_Rep1 (ChIP)

description: Library name: Pol2_WT_Log_K_Rep1_IP


title: 207686140155_R08C01

value: Primary

value: Male


title: 207686140155_R03C01


title: Pol2_WT_Log_As_Rep1 (Input)

description: Library name: Pol2_WT_Log_As_Rep1_INP

value: 0.5mM As(III)


title: 6132-EC-S1_ROI_94

description:
Library name: DSP-1001660011120-D-B11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6132-EC-S1_ROI_97

description:
Library name: DSP-1001660011120-D-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: SMP 23 15022 G14-2

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


title: SMP 23 15022 G14-1

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


title: 6132-EC-S1_ROI_92

description:
Library name: DSP-1001660011120-D-B09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: NormalDuct


title: 207686140005_R03C01


title: 207686140065_R04C01


title: 6132-EC-S1_ROI_93

description:
Library name: DSP-1001660011120-D-B10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: Pol2_WT_Log_As_Rep1 (ChIP)

description: Library name: Pol2_WT_Log_As_Rep1_IP


title: 6132-EC-S1_ROI_91

description:
Library name: DSP-1001660011120-D-B08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: H2A-P_WT_G2_K_Rep2 (Input)

description: Library name: H2A-P_WT_G2_K_Rep2_INP


title: SMP 20 04565 B35-24

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

value: w/o prehab


title: 207222790148_R08C01


title: 6132-EC-S1_ROI_90

description:
Library name: DSP-1001660011120-D-B07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: H2A-P_WT_G2_K_Rep2 (ChIP)

description: Library name: H2A-P_WT_G2_K_Rep2_IP

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


title: H2A-P_WT_G2_As_Rep2 (Input)

description: Library name: H2A-P_WT_G2_As_Rep2_INP


title: SMP 20 04565 B35-23

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


title: 6132-EC-S1_ROI_89

description:
Library name: DSP-1001660011120-D-B06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Pancreas


title: 207222790148_R04C01


title: H2A-P_WT_G2_K_Rep1 (Input)

description: Library name: H2A-P_WT_G2_K_Rep1_INP


title: SMP 20 04565 B35-20

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


title: SMP 20 04565 B35-21

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


title: 6132-EC-S1_ROI_87

description:
Library name: DSP-1001660011120-D-B04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: IPMN


title: 207222790148_R02C01

value: REFERENCE


title: SMP 20 04565 B35-22

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


title: 207222790148_R06C01


title: 6132-EC-S1_ROI_86

description:
Library name: DSP-1001660011120-D-B03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6132-EC-S1_ROI_88

description:
Library name: DSP-1001660011120-D-B05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: H2A-P_WT_G2_K_Rep1 (ChIP)

description: Library name: H2A-P_WT_G2_K_Rep1_IP


title: 6132-EC-S1_ROI_85

description:
Library name: DSP-1001660011120-D-B02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: SMP 20 04565 B35-18

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


title: H2A-P_WT_G2_As_Rep1 (Input)

description: Library name: H2A-P_WT_G2_As_Rep1_INP


title: H2A-P_WT_G2_As_Rep1 (ChIP)

description: Library name: H2A-P_WT_G2_As_Rep1_IP


title: H2A-P_WT_G2_As_Rep2 (ChIP)

description: Library name: H2A-P_WT_G2_As_Rep2_IP


title: 207700160105_R07C01

value: BRAF V600E


title: 207700160105_R06C01

value: LEUKO


title: H2A-P_ku70_G1_K_Rep1 (Input)

description: Library name: H2A-P_ku70_G1_K_Rep1_INP


title: 6132-EC-S1_ROI_84

description:
Library name: DSP-1001660011120-D-B01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 207222790148_R01C01

value: HI


title: 207700160105_R04C01

value: Kinase Fusion


title: SMP 20 04565 B35-15

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


title: H2A-P_ku70_G1_K_Rep1 (ChIP)

description: Library name: H2A-P_ku70_G1_K_Rep1_IP

value: yeast


title: SMP 20 04565 B35-19

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


title: 6132-EC-S1_ROI_83

description:
Library name: DSP-1001660011120-D-A12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 207700160105_R03C01

value: LI

value: Female

value: Ras-like


title: 6132-EC-S1_ROI_82

description:
Library name: DSP-1001660011120-D-A11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: SMP 20 04565 B35-14

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

value: PDAC


title: H2A-P_ku70_G1_As_Rep1 (Input)

description: Library name: H2A-P_ku70_G1_As_Rep1_INP


title: 207700160098_R04C01

value: Primary


title: 207700160098_R03C01

value: Male


title: SMP 20 04565 B35-13

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


title: SMP 20 04565 B35-16

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


title: H2A-P_ku70_G1_As_Rep1 (ChIP)

description: Library name: H2A-P_ku70_G1_As_Rep1_IP

value: 0.5mM As(III)


title: 6132-EC-S1_ROI_81

description:
Library name: DSP-1001660011120-D-A10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: SMP 20 04565 B35-17

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

value: w/o prehab


title: 6132-EC-S1_ROI_80

description:
Library name: DSP-1001660011120-D-A09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 207700160098_R02C01


title: 207700160062_R08C01


title: 207700160062_R06C01


title: NTg, rep 4

city: Atlanta

first: Karen

middle: N

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

description: Library name: 1163

data_processing:
STAR was used to align FASTQ files to genome.
BAM files were used to generate gene counts using Rsamtools and the summarize overlaps function with the Genomic Alignments package.
Differential gene expression analysis was performed with the DESeq2 package.
Assembly: GRCm39/mm39
Supplementary files format and content: csv file with raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: brain

growth_protocol: TgCRND8 mice overexpressing APP were bred in house and housed three to five to a cage and maintained on ad libitum food and water with a 12-h light:dark cycle. Brains were harvested at 18 months. One hemibrane was snap-frozen in isopentane on dry ice and stroed at -80 degrees C until it was pulverized in LN2 for RNA extraction.

extract_protocol:
RNA was extracted from frozen, pulverized forebrains using TRIzol reagent (Invitrogen) followed by an RNeasy mini column (Qiagen) with an on-column DNase treatment.
RNA sequencing libraries were contructed using Illumina's TruSeq RNA Library Prep kit version 2; libraries were sequenced on paired-end, 75-bp runs on a NextSeq 500 using a pooled strategy to minimize batch effects.

value: brain

value: NTg

value: 18 mon

value: F


title: 6132-EC-S1_ROI_79

description:
Library name: DSP-1001660011120-D-A08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Pancreas

value: IPMN


title: NTg, rep 3

description: Library name: 1154


title: SMP 20 04565 B35-11

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


title: SMP 20 04565 B35-12

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


title: SMP 20 04565 B35-10

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


title: 6132-EC-S1_ROI_78

description:
Library name: DSP-1001660011120-D-A07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 207700160062_R02C01

value: REFERENCE

value: HI

value: BRAF V600E


title: Tg, rep 3

description: Library name: 1152

value: Tg


title: 207700160062_R05C01

value: Female


title: Tg, rep 4

description: Library name: 1160


title: SMP 20 04565 B35-8

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


title: Tg, rep 2

description: Library name: 1151


title: 6132-EC-S1_ROI_77

description:
Library name: DSP-1001660011120-D-A06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 207700160043_R07C01

value: Kinase Fusion


title: 6132-EC-S1_ROI_74

description:
Library name: DSP-1001660011120-D-A03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 207700160043_R06C01

value: LI


title: SMP 20 04565 B35-9

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

value: PDAC


title: SMP 20 04565 B35-6

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


title: 6132-EC-S1_ROI_73

description:
Library name: DSP-1001660011120-D-A02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6132-EC-S1_ROI_76

description:
Library name: DSP-1001660011120-D-A05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: NTg, rep 1

description: Library name: 1143


title: Tg, rep 1

description: Library name: 1142


title: NTg, rep 2

description: Library name: 1144


title: Rap1_WT_G2_K_Rep1 (Input)

description: Library name: Rap1_WT_G2_K_Rep1_INP

value: yeast


title: SMP 20 04565 B35-7

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


title: 207700160043_R04C01

value: Primary


title: 207700160043_R05C01


title: SMP 20 04565 B35-5

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

value: w/o prehab


title: 6132-EC-S1_ROI_75

description:
Library name: DSP-1001660011120-D-A04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: NES061

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

description: Library name: NES061

data_processing:
RNA-seq FASTQ reads were aligned to the GRCh37 human genome using HISAT2 v2.2.1 with GENCODE v19 annotation. Gene-level counts were obtained using featureCounts (Subread v2.0.3) and normalized to counts per million (CPM) using the trimmed mean of M-values (TMM) method. Genes with CPM >0.5 in at least 10% of samples were retained (18,390 genes). CPM values were inverse-rank transformed to a standard normal distribution and used for principal component analysis (PCA). Sex, age, RIN, the top 3 genotype PCs, and the top 5 expression PCs were regressed out. The residuals were inverse-rank transformed again to generate the final processed RNA-seq expression data.
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text file containing the final processed expression values for each sample.

source_name: lung

extract_protocol:
Freshly frozen tissue specimens were homogenized in RLT buffer, and total RNA was extracted using the Qiagen RNeasy Mini Kit following the manufacturer’s protocol. RNA was eluted in RNase-free water. RNA quantity and purity were assessed using NanoDrop spectrophotometry, and RNA integrity was evaluated with Agilent Bioanalyzer.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Exome (RNA Access) Library Preparation Kit according to the manufacturer’s instructions. Briefly, 50–100 ng of total RNA was subjected to rRNA depletion, followed by first- and second-strand cDNA synthesis. The resulting cDNA fragments were end-repaired, A-tailed, and ligated to Illumina indexed adapters. Libraries were amplified by PCR and subjected to exome capture using the TruSeq RNA Exome probe set. Captured libraries were enriched, purified, quantified, and assessed for library size distribution prior to sequencing on an Illumina NovaSeq 6000.

value: lung

tag: sample source

value: Normal lung tissue adjacent to lung adenocarcinoma

tag: smoking status

value: Non-smoking

tag: rin

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: expression pc1

tag: expression pc2

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: NES060

description: Library name: NES060

tag: tissue


title: NES059

description: Library name: NES059

tag: age


title: 207700160043_R03C01

tag: cohort

tag: Stage

tag: Sex

value: Indeterminate


title: SMP 20 04565 B35-4

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

tag: treatment


title: Rap1_WT_G2_As_Rep1 (Input)

description: Library name: Rap1_WT_G2_As_Rep1_INP

tag: cell type

tag: genotype

value: 0.5mM As(III)

tag: chip antibody


title: SMP 20 04565 B35-3

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


title: 207700160024_R06C01


title: 207700160043_R02C01


title: NES058

description: Library name: NES058

tag: sample source

tag: smoking status

tag: rin

tag: genotype pc1


title: Rap1_WT_G2_K_Rep1 (ChIP)

description: Library name: Rap1_WT_G2_K_Rep1_IP

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


title: SMP 20 04565 B35-2

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


title: SMP 23 15779 C38-24

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


title: NES057

description: Library name: NES057

tag: genotype pc2

tag: genotype pc3

tag: expression pc1

tag: expression pc2


title: Rap1_WT_G2_As_Rep1 (ChIP)

description: Library name: Rap1_WT_G2_As_Rep1_IP


title: Cdc13_WT_G2_K_Rep2 (Input)

description: Library name: Cdc13_WT_G2_K_Rep2_INP


title: 207700160024_R02C01

value: REFERENCE


title: SMP 23 15779 C38-23

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

tag: tissue


title: Cdc13_WT_G2_K_Rep2 (ChIP)

description: Library name: Cdc13_WT_G2_K_Rep2_IP


title: NES056

description: Library name: NES056

tag: age

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: SMP 20 04565 B35-1

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

tag: treatment


title: NES055

description: Library name: NES055

tag: Sex


title: 207700160024_R01C01

tag: cohort

tag: Stage

value: HI


title: Cdc13_WT_G2_As_Rep2 (Input)

description: Library name: Cdc13_WT_G2_As_Rep2_INP

tag: cell type

tag: genotype

tag: chip antibody


title: 207700160021_R08C01

value: Male

value: Ras-like


title: SMP 23 15779 C38-22

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


title: NES053

description: Library name: NES053

tag: sample source

value: Female

tag: smoking status

tag: rin

tag: genotype pc1


title: NES054

description: Library name: NES054

tag: genotype pc2

tag: genotype pc3

tag: expression pc1

tag: expression pc2


title: SMP 23 15779 C38-21

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

tag: tissue


title: Cdc13_WT_G2_K_Rep1 (Input)

description: Library name: Cdc13_WT_G2_K_Rep1_INP


title: 207700160021_R06C01

tag: age


title: 207700160021_R07C01


title: Cdc13_WT_G2_As_Rep2 (ChIP)

description: Library name: Cdc13_WT_G2_As_Rep2_IP

tag: treatment


title: SMP 23 15779 C38-20

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


title: NES052

description: Library name: NES052

tag: Sex

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: NES051

description: Library name: NES051


title: 207700160021_R04C01

tag: cohort

tag: Stage

value: Kinase Fusion


title: Cdc13_WT_G2_K_Rep1 (ChIP)

description: Library name: Cdc13_WT_G2_K_Rep1_IP

tag: cell type

tag: genotype

tag: chip antibody


title: SMP 23 15779 C38-19

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


title: Cdc13_WT_G2_As_Rep1 (Input)

description: Library name: Cdc13_WT_G2_As_Rep1_INP


title: 207700160021_R03C01

value: BRAF V600E


title: NES050

description: Library name: NES050

tag: sample source

tag: smoking status

tag: rin

tag: genotype pc1


title: SMP 23 15779 C38-18

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

value: PDAC


title: Cdc13_WT_G2_As_Rep1 (ChIP)

description: Library name: Cdc13_WT_G2_As_Rep1_IP

value: yeast


title: NES049

description: Library name: NES049

tag: genotype pc2

tag: genotype pc3

tag: expression pc1

tag: expression pc2


title: H2A-P_rpb1-1_Log_37C_Rep2 (Input)

description: Library name: H2A-P_rpb1-1_Log_37C_Rep2_INP

tag: treatment


title: SMP 23 15779 C38-17

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

tag: tissue


title: 207700160021_R02C01

value: Primary

tag: age

tag: Sex


title: 207700160021_R01C01

tag: cohort

value: LI


title: SMP 23 15779 C38-16

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

value: w/o prehab


title: NES048

description: Library name: NES048

value: lung

value: Normal lung tissue adjacent to lung adenocarcinoma

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: H2A-P_rpb1-1_Log_37C_Rep2 (ChIP)

description: Library name: H2A-P_rpb1-1_Log_37C_Rep2_IP

tag: cell type

tag: genotype

tag: chip antibody

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


title: NES047

description: Library name: NES047

tag: sample source

tag: smoking status

value: Non-smoking

tag: rin


title: 207686140156_R07C01

tag: Stage


title: SMP 23 15779 C38-15

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


title: NES046

description: Library name: NES046

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: expression pc1


title: SMP 23 15779 C38-14

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

tag: tissue

tag: treatment


title: H2A-P_rpb1-1_Log_37C_Rep1 (Input)

description: Library name: H2A-P_rpb1-1_Log_37C_Rep1_INP


title: H2A-P_rpb1-1_Log_37C_Rep1 (ChIP)

description: Library name: H2A-P_rpb1-1_Log_37C_Rep1_IP


title: 207686140156_R05C01

tag: cohort

value: LEUKO

tag: age

tag: Sex


title: 207686140156_R06C01

value: REFERENCE


title: 207686140156_R03C01

value: HI


title: SMP 23 15779 C38-13

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


title: SMP 23 15779 C38-11

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


title: NES045

description: Library name: NES045

tag: expression pc2

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: SMP 23 15779 C38-12

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


title: SMP 23 15779 C38-10

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


title: NES044

description: Library name: NES044

tag: sample source


title: H2A-P_rpb1-1_Log_25C_Rep2 (Input)

description: Library name: H2A-P_rpb1-1_Log_25C_Rep2_INP

tag: cell type

tag: genotype

tag: chip antibody


title: 207686140156_R04C01

tag: Stage


title: NES043

description: Library name: NES043

value: Male

tag: smoking status

tag: rin

tag: genotype pc1

tag: genotype pc2


title: H2A-P_rpb1-1_Log_25C_Rep1 (Input)

description: Library name: H2A-P_rpb1-1_Log_25C_Rep1_INP

tag: treatment


title: NES042

description: Library name: NES042

tag: tissue

tag: genotype pc3

tag: expression pc1


title: H2A-P_rpb1-1_Log_25C_Rep2 (ChIP)

description: Library name: H2A-P_rpb1-1_Log_25C_Rep2_IP


title: 207686140156_R02C01

tag: cohort

tag: age

tag: Sex

value: Ras-like


title: 207686140155_R05C01

value: Female


title: SMP 23 15779 C38-9

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


title: Rad52_WT_Log_K_Rep2 (Input)

description: Library name: Rad52_WT_Log_K_Rep2_INP


title: SMP 23 15779 C38-8

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


title: 207686140155_R07C01


title: NES040

description: Library name: NES040

tag: expression pc2

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: Rad52_WT_Log_K_Rep2 (ChIP)

description: Library name: Rad52_WT_Log_K_Rep2_IP

tag: cell type

tag: genotype

tag: chip antibody

value: Anty-GFP antibody (Invitrogen, A-11122)


title: 207686140144_R08C01

tag: Stage


title: 207686140155_R04C01


title: SMP 23 15779 C38-7

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


title: NES038

description: Library name: NES038

tag: sample source

tag: smoking status

tag: rin

tag: genotype pc1


title: SMP 23 15779 C38-6

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

tag: tissue

tag: treatment


title: 207686140144_R07C01

tag: cohort


title: Rad52_WT_Log_As_Rep2 (ChIP)

description: Library name: Rad52_WT_Log_As_Rep2_IP

value: 0.5mM As(III)


title: SMP 23 15779 C38-5

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

value: PDAC


title: Rad52_WT_Log_As_Rep2 (Input)

description: Library name: Rad52_WT_Log_As_Rep2_INP

value: yeast


title: RPA_WT_Log_K_Rep2 (Input)

description: Library name: RPA_WT_Log_K_Rep2_INP


title: SMP 23 15779 C38-4

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


title: 207686140144_R05C01

value: Primary

tag: age


title: NES036

description: Library name: NES036

tag: Sex

tag: genotype pc2

tag: genotype pc3

tag: expression pc1


title: 207686140144_R04C01

value: LI


title: H2A-P_rpb1-1_Log_25C_Rep1 (ChIP)

description: Library name: H2A-P_rpb1-1_Log_25C_Rep1_IP


title: NES039

description: Library name: NES039

tag: expression pc2

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: RPA_WT_Log_K_Rep2 (ChIP)

description: Library name: RPA_WT_Log_K_Rep2_IP

tag: cell type

tag: genotype

tag: chip antibody

value: Any-RFA (Agrisera, AS07 214)


title: RPA_WT_Log_As_Rep2 (Input)

description: Library name: RPA_WT_Log_As_Rep2_INP


title: NES035

description: Library name: NES035

value: lung

tag: sample source

tag: smoking status

tag: rin


title: SMP 23 15779 C38-3

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

tag: tissue

tag: treatment

value: w/o prehab


title: NES041

description: Library name: NES041

value: Normal lung tissue adjacent to lung adenocarcinoma

tag: age

tag: genotype pc1


title: SMP 23 15779 C38-2

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


title: SMP 23 15779 C38-1

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


title: 207686140144_R03C01

tag: cohort

tag: Stage

tag: Sex

value: BRAF V600E


title: RPA_WT_Log_As_Rep2 (ChIP)

description: Library name: RPA_WT_Log_As_Rep2_IP


title: NES037

description: Library name: NES037

value: Non-smoking

tag: genotype pc2

tag: genotype pc3

tag: expression pc1

tag: expression pc2


title: NES033

description: Library name: NES033

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: NES034

description: Library name: NES034

tag: sample source


title: KD-21-5_Control

city: Dallas

first: Maria

middle: H

last: Chahrour

address: 6000 Harry Hines Boulevard, NB10.104

institute: UT Southwestern Medical Center

description: Library name: KD-21-5

data_processing:
Raw sequencing data were de-multiplexed and converted to FASTQ files using bcl2fastq (v2.17, Illumina). FASTQ files were quality-checked using FastQC (v0.11.2). Reads were aligned to the human reference genome (hg19) using STAR (v2.5.3a). Read counts were then generated using featureCounts (Subread v1.4.6). Differential expression analysis was performed using DESeq2. Differentially expressed genes (DEGs) were identified in individuals with ASD compared to those without ASD using two approaches: (1) by comparing all individuals with ASD across families, and (2) by analyzing differences within each family.
Assembly: hg19
Supplementary files format and content: Tab delimited text file containing raw counts, CPM, and TPM values per sample

source_name: Blood

extract_protocol:
RNA was extracted from LCL pellets derived from patients, parents, and siblings, when available, using TRIzol reagent (Invitrogen), and purified with the RNeasy Mini Kit (Qiagen). Genomic DNA was removed using the RNase-free DNase kit (Qiagen). RNA quality was assessed using the Agilent TapeStation 4200, and all samples had a RIN score of ≥ 8.
RNA concentrations were measured using a Qubit fluorometer, and 1 μg of DNase-treated total RNA was used for library preparation with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Poly-A RNA was purified and fragmented, and strand-specific libraries were amplified and purified using AmpureXP beads. Samples were sequenced on the Illumina NextSeq 500 using V2.5 reagents.

value: Blood

tag: cell line

value: lymphoblastoid cell lines


title: 207686140144_R02C01

value: REFERENCE


title: NES032

description: Library name: NES032

value: Male

tag: smoking status

tag: rin


title: 207686140144_R01C01

value: HI

value: Female

value: Kinase Fusion


title: RPA_WT_Log_K_Rep1 (Input)

description: Library name: RPA_WT_Log_K_Rep1_INP

tag: cell type

tag: genotype

tag: treatment

tag: chip antibody


title: RPA_WT_Log_K_Rep1 (ChIP)

description: Library name: RPA_WT_Log_K_Rep1_IP


title: 207686140131_R07C01

tag: cohort

tag: Stage

tag: age


title: KD-21-4_Control

description: Library name: KD-21-4

tag: tissue


title: KD-21-3_Affected

description: Library name: KD-21-3


title: NES031

description: Library name: NES031

tag: Sex

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: expression pc1


title: RPA_WT_Log_As_Rep1 (Input)

description: Library name: RPA_WT_Log_As_Rep1_INP

value: 0.5mM As(III)


title: NES030

description: Library name: NES030

tag: sample source

tag: expression pc2

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: 207686140131_R05C01


title: 207686140131_R06C01


title: NES029

description: Library name: NES029

tag: smoking status

tag: rin


title: Tel1_WT_Log_K_Rep1 (Input)

description: Library name: Tel1_WT_Log_K_Rep1_INP

tag: cell type

value: yeast

tag: genotype

tag: treatment

tag: chip antibody


title: RPA_WT_Log_As_Rep1 (ChIP)

description: Library name: RPA_WT_Log_As_Rep1_IP


title: 207686140131_R03C01

tag: cohort

tag: Stage

value: Primary

tag: age


title: 207686140131_R04C01

value: LI

tag: Sex

value: Ras-like


title: Tel1_WT_Log_K_Rep1 (ChIP)

description: Library name: Tel1_WT_Log_K_Rep1_IP

value: V5-Tag antibody (BioRad, MCA1360)


title: KD-21-2_Control

description: Library name: KD-21-2

tag: tissue

tag: cell line


title: KD-21-1_Control

description: Library name: KD-21-1


title: NES028

description: Library name: NES028

value: lung

tag: sample source

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: expression pc1


title: NES027

description: Library name: NES027

value: Normal lung tissue adjacent to lung adenocarcinoma

tag: smoking status

tag: expression pc2

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: KD-20-3_Affected

description: Library name: KD-20-3


title: Tel1_WT_Log_As_Rep1 (Input)

description: Library name: Tel1_WT_Log_As_Rep1_INP

tag: cell type

tag: genotype

tag: treatment

tag: chip antibody


title: KD-20-2_Control

description: Library name: KD-20-2


title: 207686140131_R01C01

tag: cohort

tag: Stage

tag: age

tag: Sex


title: NES026

description: Library name: NES026

tag: tissue

tag: sample source

tag: rin

tag: genotype pc1


title: 207686140131_R02C01

value: BRAF V600E


title: KD-19-3_Affected

description: Library name: KD-19-3

tag: cell line


title: Tel1_WT_Log_As_Rep1 (ChIP)

description: Library name: Tel1_WT_Log_As_Rep1_IP


title: 207686140065_R06C01


title: Rpb1_WT_Log_K_Rep2 (Input)

description: Library name: Rpb1_WT_Log_K_Rep2_INP


title: NES025

description: Library name: NES025

tag: smoking status

value: Non-smoking

tag: genotype pc2

tag: genotype pc3

tag: expression pc1

tag: expression pc2


title: Rpb1_WT_Log_K_Rep2 (ChIP)

description: Library name: Rpb1_WT_Log_K_Rep2_IP

tag: cell type

tag: genotype

value: anti-RNA Polymerase II Antibody, clone 8WG16 (Sigma-Aldrich, 05-952-I)


title: 207686140065_R03C01

value: LEUKO


title: NES024

description: Library name: NES024

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: KD-8-3_Affected

description: Library name: KD-8-3

value: Blood

value: lymphoblastoid cell lines


title: Rpb1_WT_Log_As_Rep2 (Input)

description: Library name: Rpb1_WT_Log_As_Rep2_INP

tag: treatment

tag: chip antibody


title: NES023

description: Library name: NES023

tag: tissue

tag: age

tag: Sex


title: KD-8-2_Control

description: Library name: KD-8-2


title: NES022

description: Library name: NES022

tag: sample source

tag: rin

tag: genotype pc1


title: KD-19-2_Control

description: Library name: KD-19-2

tag: cell line


title: NES021

description: Library name: NES021

tag: smoking status

tag: genotype pc2

tag: genotype pc3


title: Rpb1_WT_Log_As_Rep2 (ChIP)

description: Library name: Rpb1_WT_Log_As_Rep2_IP

tag: cell type


title: 207686140043_R06C01

tag: cohort

value: REFERENCE

tag: Stage


title: KD-8-1_Control

description: Library name: KD-8-1


title: 207686140043_R04C01

value: HI

value: Female


title: Rpb1_WT_Log_K_Rep1 (Input)

description: Library name: Rpb1_WT_Log_K_Rep1_INP

tag: genotype


title: NES020

description: Library name: NES020

value: Male

tag: expression pc1

tag: expression pc2

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: KD-6-3_Affected

description: Library name: KD-6-3

tag: tissue


title: NES019

description: Library name: NES019

tag: sample source

tag: age

tag: Sex


title: KD-6-1_Control

description: Library name: KD-6-1

tag: cell line


title: 207686140043_R08C01


title: 207686140043_R07C01

value: s

value: Kinase Fusion


title: NES018

description: Library name: NES018

tag: smoking status

tag: rin

tag: genotype pc1


title: Rpb1_WT_Log_As_Rep1 (Input)

description: Library name: Rpb1_WT_Log_As_Rep1_INP

tag: cell type

value: yeast

tag: treatment

value: 0.5mM As(III)

tag: chip antibody


title: 207686140043_R01C01

tag: cohort

tag: Stage

value: Primary


title: NES017

description: Library name: NES017

value: lung

tag: genotype pc2

tag: genotype pc3

tag: expression pc1

tag: expression pc2


title: 207686140033_R02C01

value: Indeterminate


title: Rpb1_WT_Log_K_Rep1 (ChIP)

description: Library name: Rpb1_WT_Log_K_Rep1_IP

tag: genotype


title: H2A-P_WT_Log_noPM_Rep1 (Input)

description: Library name: H2A-P_WT_Log_noPM_Rep1_INP


title: KD-5-3_Affected

description: Library name: KD-5-3

tag: tissue


title: 207686140043_R03C01

tag: age


title: KD-6-2_Control

description: Library name: KD-6-2


title: 207686140028_R06C01

value: LI

tag: Sex

value: Ras-like


title: NES016

description: Library name: NES016

tag: sample source

value: Normal lung tissue adjacent to lung adenocarcinoma

value: Non-smoking

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: KD-5-4_Control

description: Library name: KD-5-4

value: Blood

tag: cell line


title: Rpb1_WT_Log_As_Rep1 (ChIP)

description: Library name: Rpb1_WT_Log_As_Rep1_IP

tag: cell type

tag: treatment

value: anti-RNA Polymerase II Antibody, clone 8WG16 (Sigma-Aldrich, 05-952-I)


title: NES015

description: Library name: NES015

tag: smoking status

tag: rin

tag: genotype pc1


title: KD-5-2_Control

description: Library name: KD-5-2

value: lymphoblastoid cell lines


title: NES014

description: Library name: NES014

tag: genotype pc2

tag: genotype pc3


title: H2A-P_WT_Log_50PM_Rep1 (Input)

description: Library name: H2A-P_WT_Log_50PM_Rep1_INP

value: 50 µg/ml phleomycin

tag: chip antibody


title: NES013

description: Library name: NES013

value: Female

tag: expression pc1

tag: expression pc2


title: KD-5-1_Control

description: Library name: KD-5-1

tag: tissue


title: KD-1-4_Control

description: Library name: KD-1-4


title: H2A-P_WT_Log_50PM_Rep1 (ChIP)

description: Library name: H2A-P_WT_Log_50PM_Rep1_IP

tag: genotype

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


title: 207686140028_R03C01

tag: cohort

value: REFERENCE

tag: Stage

value: LEUKO

tag: age

tag: Sex


title: H2A-P_WT_Log_noPM_Rep1 (ChIP)

description: Library name: H2A-P_WT_Log_noPM_Rep1_IP

value: yeast


title: 207686140028_R04C01

value: HI

value: Kinase Fusion


title: 207686140028_R01C01

value: Primary


title: KD-1-2_Control

description: Library name: KD-1-2

tag: cell line


title: 207686140028_R02C01

value: Male


title: H2A-P_WT_Log_2PM_Rep1 (ChIP)

description: Library name: H2A-P_WT_Log_2PM_Rep1_IP

tag: cell type

value: 2 µg/ml phleomycin


title: NES012

description: Library name: NES012

value: lung

tag: sample source

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: NES011

description: Library name: NES011

value: Normal lung tissue adjacent to lung adenocarcinoma

tag: smoking status

tag: rin

tag: genotype pc1

tag: genotype pc2


title: H2A-P_WT_G1_K_Rep1 (Input)

description: Library name: H2A-P_WT_G1_K_Rep1_INP

tag: treatment

tag: chip antibody


title: 207686140005_R08C01

value: LI


title: NES010

description: Library name: NES010

tag: tissue

value: Non-smoking

tag: genotype pc3

tag: expression pc1

tag: expression pc2


title: 207686140005_R07C01

tag: cohort

tag: Stage

tag: age

tag: Sex

value: Ras-like


title: H2A-P_WT_Log_2PM_Rep1 (Input)

description: Library name: H2A-P_WT_Log_2PM_Rep1_INP

tag: cell type

tag: genotype


title: H2A-P_WT_G1_As_Rep1 (Input)

description: Library name: H2A-P_WT_G1_As_Rep1_INP

value: 0.5mM As(III)


title: KD-1-3_Affected

description: Library name: KD-1-3

value: Blood

tag: cell line

value: lymphoblastoid cell lines


title: MCF7 pRb CRISPR cells, T1-44 treated, biological replicate 1

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

data_processing:
RNAseq raw data was processed with fastp software to remove sequencing adaptors and low quality bases.
Processed reads were aligned with human reference genome hg19 using the STAR package (v.020201) with -quatMode Genecounts option
Differential expression analysis was performed with DESeq2 R package.  The aligned data was also used for alternative splicing analysis with rMATS program (v4.0.2).
Alternatively, the cell synchronised RNA-seq data was analysed using the Galaxy web platform at the public server at usegalaxy.org. Raw data was processed with Cutadapt (Galaxy version 4.8) before aligning with human reference genome hg38 using RNA STAR (Galaxy version 2.7.11a) with per gene read counts option selected.
Differential gene expression for cell synchronised experiments was performed with DESeq2 (Galaxy version 2.11.40.8), whilst alternative splicing analysis was performed with rMATS.
Assembly: hg19 or hg38
Supplementary files format and content: tab-delimited files include raw counts for each sample.

growth_protocol: HCT116 and MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antiniotics in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was extracted using TRIzol, as per the manufacturer's instructions
RNA from MCF7 cells was subsequently enriched using the NEBNext Poly(A) mRNA magnetic isolation module as per the manufacturer's instructions. cDNA libraries were made using the NEBNext ultra directional RNA library prep kit for Illumina, as per the manufacturer's instructions. RNA from HCT116 cells was used to prepare libraries by BGI Genomics.  Briefly, mRNAs were isolated using oligo(dT)-based mRNA enrichment.  mRNA was fragmented and reverse transcribed with random primer, prior to second strand synthesis with dUTP, end repair and 3' A-tailing. This was followed by adaptor ligation and digestion of U-labelled second strand template with UDG, prior to PCR amplification. Library quality control was performed before circularisation and amplification to make DNA nanoballs.

treatment_protocol: HCT116 WT and DP1 Cr cells were grown untreated in culture. MCF7 WT and pRb Cr cells were treated with 5uM PRMT5 inhibitor (T1-44) for 72h, or with DMSO. HCT116 WT and E2F1 Cr cells were synchronised at G1/S by double thymidine block (2mM thymidine for 18h, followed by 10h release, followed by 2mM thymidine for 15h), and then released for either 0 hours (G1/S) or 6h (G2/M).

value: breast adenocarcinoma

value: pRb KO

value: T1-44 treated


title: MCF7 pRb CRISPR cells, T1-44 treated, biological replicate 2


title: H2A-P_WT_G1_K_Rep1 (ChIP)

description: Library name: H2A-P_WT_G1_K_Rep1_IP

value: yeast

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


title: NES009

description: Library name: NES009

tag: sample source

value: Female

tag: smoking status

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: NES008

description: Library name: NES008

tag: rin

tag: genotype pc1

tag: genotype pc2


title: MCF7 pRb CRISPR cells, T1-44 treated, biological replicate 3

tag: treatment


title: 207686140005_R05C01

value: REFERENCE

value: Primary

value: HI

value: Kinase Fusion


title: 207686140005_R06C01


title: Rad59_WT_Log_K_Rep2 (Input)

description: Library name: Rad59_WT_Log_K_Rep2_INP

tag: chip antibody


title: H2A-P_WT_G1_As_Rep1 (ChIP)

description: Library name: H2A-P_WT_G1_As_Rep1_IP


title: 207686140005_R02C01

tag: cohort

value: BRAF V600E


title: MCF7 pRb CRISPR cells, DMSO treated, biological replicate 3

value: DMSO control


title: NES007

description: Library name: NES007

tag: tissue

value: lung

value: Normal lung tissue adjacent to lung adenocarcinoma

value: Non-smoking

tag: genotype pc3

tag: expression pc1

tag: expression pc2


title: MCF7 pRb CRISPR cells, DMSO treated, biological replicate 2

tag: cell type

tag: genotype


title: NES006

description: Library name: NES006

tag: sample source

tag: age

tag: Sex


title: Rad59_WT_Log_K_Rep2 (ChIP)

description: Library name: Rad59_WT_Log_K_Rep2_IP

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


title: MCF7 pRb CRISPR cells, DMSO treated, biological replicate 1

tag: cell line


title: 207222790148_R07C01

tag: Stage


title: NES005

description: Library name: NES005

tag: smoking status

tag: rin

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: Rad59_WT_Log_As_Rep2 (Input)

description: Library name: Rad59_WT_Log_As_Rep2_INP

tag: treatment

value: 0.5mM As(III)

tag: chip antibody


title: 207222790148_R03C01

tag: cohort

value: Male


title: Rad59_WT_Log_As_Rep2 (ChIP)

description: Library name: Rad59_WT_Log_As_Rep2_IP


title: NES004

description: Library name: NES004

tag: tissue

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: expression pc1


title: MCF7 WT cells, T1-44 treated, biological replicate 3

tag: cell type

value: breast adenocarcinoma

tag: genotype

value: WT


title: 207222790148_R05C01

tag: age

tag: Sex


title: MCF7 WT cells, T1-44 treated, biological replicate 2

tag: cell line

value: T1-44 treated


title: NES003

description: Library name: NES003

tag: sample source

tag: smoking status

tag: rin

tag: expression pc2


title: Rad52_WT_Log_K_Rep1 (Input)

description: Library name: Rad52_WT_Log_K_Rep1_INP

value: yeast

tag: treatment


title: MCF7 WT cells, T1-44 treated, biological replicate 1


title: 207219750052_R05C01

tag: Stage

value: LI

value: Ras-like


title: 207219750052_R06C01

tag: cohort

value: REFERENCE

value: Primary

value: Female


title: NES002

description: Library name: NES002

tag: tissue

tag: expression pc3

tag: expression pc4

tag: expression pc5


title: NES001

description: Library name: NES001

tag: genotype pc1

tag: genotype pc2

tag: genotype pc3

tag: expression pc1


title: Rad52_WT_Log_K_Rep1 (ChIP)

description: Library name: Rad52_WT_Log_K_Rep1_IP

tag: cell type

tag: genotype

tag: chip antibody

value: Anty-GFP antibody (Invitrogen, A-11122)


title: Rad52_WT_Log_As_Rep1 (ChIP)

description: Library name: Rad52_WT_Log_As_Rep1_IP


title: 207219750052_R04C01

tag: age

tag: Sex


title: Rad51_WT_Log_K_Rep2 (Input)

description: Library name: Rad51_WT_Log_K_Rep2_INP


title: MCF7 WT cells, DMSO treated, biological replicate 1

tag: cell line

value: DMSO control


title: 207219750052_R03C01


title: MCF7 WT cells, DMSO treated, biological replicate 3

tag: treatment


title: 207219750052_R02C01

tag: Stage


title: MCF7 WT cells, DMSO treated, biological replicate 2


title: Rad52_WT_Log_As_Rep1 (Input)

description: Library name: Rad52_WT_Log_As_Rep1_INP


title: Pa03C E96A G8 TMZ 8hr

city: Indianapolis

first: Kelley

last: Mark

state: Indiana

institute: Herman B Wells Center for Pediatric Research

description: Library name: G8-TMZ-8hr_S13

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to human genes using featureCounts (from subread v2.0.1).
Raw count were subject to differential expression analysis using EdgeR
Assembly: hg38
Supplementary files format and content: raw counts file

source_name: pancreas

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM; high glucose) supplemented with 10% fetal bovine serum (FBS) under standard culture conditions (37 °C, 5% CO₂, humidified incubator). Cells were passaged at ~70–80% confluence and seeded for RNA isolation at comparable densities to ensure equivalent growth phase at harvest

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Cat# 74104) according to the manufacturer’s instructions, including on-column DNase treatment (Qiagen RNase-Free DNase Set, Cat# 79254) where applicable. RNA integrity and concentration were assessed prior to library preparation
RNA libraries for RNA-seq were prepared using Qiagen RNeasy Mini Kit (74104) following manufacturers' protocols

value: pancreas

value: pancreatic ductal adenocarcinoma


title: Rad51_WT_Log_K_Rep2 (ChIP)

description: Library name: Rad51_WT_Log_K_Rep2_IP

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


title: Clinical AD Subject 6

city: Durham

first: Bradley

last: Goldstein

state: NC

address: 40 Duke Medicine Cir

institute: Duke University

description: Library name: Subject-21

library_source: transcriptomic single cell

data_processing:
Raw base call files were analyzed using Cell Ranger v.9.0.0 using the Duke Cluster Computing platform. The ‘mkfastq’ command was used to generate FASTQ files from bcl Illumina sequencer output files.
CellRanger v.9.0.0 ‘counts’ command was used to generate raw gene-barcode matrices aligned to the GRCh38-2024-A human genome
Assembly: GRCh38-2024-A
Supplementary files format and content: filtered_feature_bc_matrices.tar.gz contain matrix.mtx, features.tsv, and barcodes.tsv

source_name: Olfactory Epithelium

extract_protocol:
After brush-biopsy specimens were collected in Hibernate-A medium containing 5 µg/mL N-acetylcysteine (NAC), cells were digested for 15 min at 37 °C in a cocktail of papain (4U/mL), DNase I (10 µg/mL), 1mM EDTA, and NAC (0.05 mg/mL), then treated for 1 min with an equal volume of Accutase. The slurry was quenched with FBS, strained through a 70 µm filter, pelleted (400 g, 5 min), washed in PBS with 2% FBS, and resuspended at 1 × 10⁶ cells/mL in Hibernate-A plus 0.2 % BSA, NAC (0.05 mg/mL) 0.05 % anti-clumping reagent for immediate scRNA-seq.
Samples were processed for 3' scRNA-seq using Chromium Single Cell 3' Paired-End, Dual-Index Library & Gel Bead Kit v4 GEMX kit (10X Genomics) targeting 20,000 cells, then sequenced using NovaSeqX (Illumina) flow cells. 5' scRNA-seq was processed identically except the 5' Gel Bead Kit v3 GEMX kit (10X Genomics) was used.

value: Olfactory Epithelium


title: Control Subject 6

description: Library name: Subject-20


title: Clinical AD Subject 7

description: Library name: Subject-22


title: Rad51_WT_Log_As_Rep2 (Input)

description: Library name: Rad51_WT_Log_As_Rep2_INP

value: 0.5mM As(III)


title: TP6

city: Hangzhou

first: Chen

last: Xue

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou

country: China

institute: Zhejiang University

description:
Library name: L01507_TM0012
MobiNova

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the MobiVision software.
Assembly: GRCh38/hg38
Supplementary files format and content: h5ad file

source_name: liver

extract_protocol:
Fresh liver tissue samples were cut into 1 mm3 pieces and digested in HBSS (Gibco, USA) buffer containing 0.05% collagenase IV (Invitrogen, Carlsbad, USA) and 0.002% DNase I (Invitrogen, Carlsbad, USA) at 37°C with gentle agitation for 30 minutes. The dissociated cells were filtered through 70 μm sterile cell strainers. Immune cells were then separated by density gradient centrifugation with 36% Percoll medium (Sigma-Aldrich, St. Louis, USA), and residual erythrocytes were removed using a red blood cell lysate solution (Sigma, USA). The immune cells were subsequently re-suspended in phosphate-buffered saline (PBS) to create a single-cell suspension.
The single-cell suspension was loaded onto the MobiNova®-100 chip with 3' transcriptome microspheres, droplet-generating oil, and reverse transcription reagents. RNA transcripts from individual cells were uniquely barcoded and reverse-transcribed within the droplets formed on the chip. Following this, pooled cDNA was purified and enriched through PCR amplification to construct cDNA libraries.

value: liver

value: immune cells

value: TPPU


title: Pa03C E96A G8 untreated

description: Library name: G8-Untr_S11


title: TP4

description:
Library name: L01507_TM0010
MobiNova

value: WT


title: Pa03C E96A B4 TMZ 8hr

description: Library name: B4-TMZ-8hr_S10


title: 12214-JF

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 12214-JF

data_processing:
CellRanger was used to map the reads (paired end) to the reference genome to generate the bam files.
Assembly: hg19
Supplementary files format and content: cellranger output format

source_name: human skin

extract_protocol:
https://cdn.10xgenomics.com/image/upload/v1721078231/support-documents/CG000632_DemonstratedProtocol_SamplePrep_from__FFPETissueSections_RevD.pdf    Protocol Overview: gentleMACS Octo Dissociator for Isolation of Cells from FFPE Tissue Sections
https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: human skin

value: mixed (single cell)


title: TP5

description:
Library name: L01507_TM0011
MobiNova