title: Slide 5; ROI 022; Segment: SMA

description:
Library name: DSP-1001660008135-B-F01
Sample/column name in raw count matrix = Slide 5 | 022 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_022. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 022; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 022


title: Slide 5; ROI 023; Segment: CK

status: Public on Apr 20 2026

type: SRA

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

country: USA

institute: University of Oklahoma Health Sciences Center

description:
Library name: DSP-1001660008135-B-F02
Sample/column name in raw count matrix = Slide 5 | 023 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_023. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 023; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

library_source: transcriptomic

data_processing:
Raw paired-end reads were processed with Bruker GeoMx NGS Pipeline v3.1.0.194 to assign reads to Human Whole Transcriptome Atlas targets and generate gene-level count outputs. Quality control and downstream normalization were performed in R using standR v1.10.0. ROIs were excluded if they failed preset thresholds for minimum segment reads (1000), percent trimmed (80), percent stitched (80), percent aligned (80), percent sequencing saturation (50), maximum no-template-control count (1000), minimum area (1000), and minimum nuclei (50, when available). For slide 5, nuclei-based filtering was not available. Genes with fewer than 5 counts in more than 60% of regions were removed in the discovery cohort. Normalized expression matrices were generated using trimmed mean of M-values normalization and RUV5 correction for slide-level effects; differential expression testing was performed with limma-voom v3.62.2.
Assembly: hg38
Supplementary files format and content: Raw count matrix of slide 1-4: raw_count14.csv  | Raw count matrix of slide 5: raw_count5.csv | Normalized count matrix of slide 1-4: GeoMx_tmm_ruv_normalized_count_linear_S14.csv | Normalized count matrix of slide 5: GeoMx_tmm_ruv_normalized_count_linear_S5.csv | Metadata of slide 1-4: sampleAnnoFile_S14.csv | Metadata of slide 5: sampleAnnoFile_S5.csv
Supplementary files format and content: In Metadata, "library" column  matches the library name above, "SegmentDisplayName" column matches the columns/samples in the raw count matrix, "sampleID" column matches the columns/samples in the normalized count matrix.
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: breast tissue

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) breast tissues from patients diagnosed with ductal carcinoma in situ (DCIS) or invasive ductal carcinoma (IDC) were obtained from the Department of Pathology at the University of Oklahoma Health Campus (Oklahoma City, OK). A pathologist confirmed the histopathologic diagnosis using routine diagnostic criteria. Patient demographic and clinicopathologic data were abstracted from the medical record, samples were de-identified, and their use was approved under University of Oklahoma IRB 12384. FFPE sections were mounted on Apex BOND Adhesive slides with tissue positioned within the GeoMx imaging area and baked at 60°C for at least 30 minutes. Slides were prepared on the Leica BOND RX using the GeoMx NGS RNA FFPE BOND workflow for breast tissue, including: bake and dewax preparation, ER2 heat-induced epitope retrieval for 10 minutes at 100°C, and Proteinase K digestion at 0.1 μg/mL for 15 minutes. Human Whole Transcriptome Atlas RNA probes containing UV-photocleavable barcoded oligonucleotides were hybridized overnight at 37°C. After stringent washes at 37°C (two 25-minute washes in Stringent Wash solution followed by two 2-minute washes in 2X SSC), slides were blocked in Buffer W for 30 minutes and stained for 1 hour at room temperature with the four-color morphology panel alpha smooth muscle actin (SMA)-647, SYTO 13 nuclear stain, pan-cytokeratin (CK)-532, and leukocyte (CD45)-AF594. Morphology markers guided ROI selection and segmentation of CK+, SMA+, and/or CD45+ compartments. Prepared slides were loaded onto the GeoMx DSP, each ROI was illuminated with UV light, and released oligonucleotides were collected by microcapillary aspiration into separate wells of a 96-well plate.
Region-specific oligonucleotides released on the GeoMx DSP were collected into individual wells of a 96-well plate and converted into sequencing libraries according to the manufacturer’s GeoMx RNA library preparation workflow for the Human Whole Transcriptome Atlas assay. Libraries were indexed according to the GeoMx protocol and sequenced as paired-end 150-bp reads on an Illumina NovaSeq X Plus instrument at the University of Colorado Anschutz Medical Campus shared-resource facility in Aurora, Colorado.

tag: tissue

value: breast tissue

tag: cell type

value: leukocytes

tag: slide

value: Slide 5

tag: roi

value: ROI 023

tag: segment

value: CK

tag: batch


title: Group 3_mIgG-mutmIL15_G3_26_Tumor_14_Run2_1

city: Cambridge

first: Julien

last: Tessier

state: MA

address: 350 Water Street

institute: Sanofi US

description: Library name: Lib-DSP-1001660037469-D-F02

data_processing:
BCL were then converted to FASTQ files which were then processed through the GeoMx NGS Pipeline v1.2 for Digital count conversion (DCC). Finally, counts from the DCC file were mapped back to tissue location on the GeoMx DSP instrument, yielding a spatially resolved digital profile of analyte abundance. In the end, 474 ROIs were successfully sequenced and mapped back to tissue location for this study.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes)
Supplementary files format and content: DCC
Library strategy: Spatial Transcriptomics

organism: Mus musculus

growth_protocol: Female C57BL/6J mice were obtained from the Jackson Laboratory (Bar Harbor, ME). B16-F10-OVA cells were grown in Dulbecco Modified Eagle Medium (DMEM) (Life technologies, Cat No. 11995065) supplemented with 10% heat inactivated Fetal Bovine Serum (HI FBS) (Life technologies, Cat No. 10082-147), Blasticidin at 7.5 µg/ml (Gibco, Cat No. 05756), and incubated at 37°C with 5% CO2. The cells were harvested using 0.25% Trypsin-Ethylenediaminetetraacetic (EDTA) (Life technologies, Cat No. 2520056), and re-suspended in Dulbecco's phosphate-buffered saline (DPBS) (Gibco, Cat No. 14190-144). On day 0, 120 animals were subcutaneously implanted with 0.5 x 106 B16-F10-OVA tumor cells into the right flank.

extract_protocol:
On day 21, tumors were harvested. One half was fixed in 10% neutral buffered formalin for 24h, followed by transfer to 70% ethanol before paraffin embedding. Samples were then embedded in paraffin and sectioned for downstream GeoMx DSP spatial transcriptomics analysis. The freshly cut sections were then processed within two weeks of sectioning following the Nanostring GeoMx DSP Automated RNA Slide Preparation user manual (MAN-10151-04, section “Fully Automated RNA Slide Preparation protocol for FFPE”). ISH hybridization was performed using NanoString Mouse Whole Transcriptome Atlas probe mix (>20,000 genes). Acquisition runs of four slides (one slide of each study group) were performed on the Nanostring GeoMx DSP instrument. For each tumor, we defined 3 compartments (“Leading Edge”, “Tumor” and “Necrosis”) based on morphological markers and H&E staining. For each compartment, we then harvested 8 circular (250μm in diameter) ROIs, so a total of 24 per tumor (23 ROIs per tumor for the isotype control group as the first well on each collection plate was dedicated to the no-template control). ROI placement for each compartment was done within the tumor boundaries, including for the “Leading Edge” one.
Libraries were prepared from released tags according to the Nanostring GeoMx DSP NGS readout user manual (MAN-10153-02). Library quality was assessed using Agilent 4200 Tapestation system and the D1000 DNA ScreenTape (Agilent Technologies, catalog# 5067-5582). Library concentration was assessed using Qubit™ Flex Fluorometer and Qubit™ 1X dsDNA BR Assay Kit (ThermoFisher Scientific, catalog# Q33262). Libraries were sequenced on the NovaSeq 6000 platform (Illumina) using Illumina v1.5 reagent kits with a read length of 27 for both reads and i5 reverse sequence orientation.

treatment_protocol: On day 9 post implantation, the mice were pooled and randomly distributed to the control and treatment groups (10 mice per group), with tumor size ranging from 46 to 148 mm3. On day 10, mice started treatment as follow: Isotype Control (intraperitoneal; 10mg/kg; twice weekly), anti-mPD-1 (intraperitoneal; 10mg/kg; twice weekly), mIgG-mutmIL15 (intraveneous; 1 mg/kg; once weekly), anti-mPD-1-mutmIL15 (intraveneous; 1 mg/kg; once weekly).

tag: cell line

tag: treatment

tag: mouse id

tag: region of_interest,_label

value: Tumor

tag: region of_interest,_id


title: Slide 5; ROI 022; Segment: CK

description:
Library name: DSP-1001660008135-B-E12
Sample/column name in raw count matrix = Slide 5 | 022 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_022. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 022; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: fibroblasts/myoepithelial cells


title: Slide 5; ROI 025; Segment: SMA

description:
Library name: DSP-1001660008135-B-F08
Sample/column name in raw count matrix = Slide 5 | 025 | SMA ; in normalized count matrix = DCIS_High_SMA_S5_025. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 025; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: epithelial cells

value: ROI 025

value: SMA


title: Slide 5; ROI 025; Segment: CD45

description:
Library name: DSP-1001660008135-B-F07
Sample/column name in raw count matrix = Slide 5 | 025 | CD45 ; in normalized count matrix = DCIS_High_CD45_S5_025. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 025; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 3_mIgG-mutmIL15_G3_26_Leading Edge_7_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E07

value: Leading Edge


title: Group 3_mIgG-mutmIL15_G3_26_Leading Edge_8_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E08


title: Group 3_mIgG-mutmIL15_G3_26_Leading Edge_6_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E06


title: Slide 5; ROI 021; Segment: CK

description:
Library name: DSP-1001660008135-B-E10
Sample/column name in raw count matrix = Slide 5 | 021 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_021. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 021; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 021


title: Group 3_mIgG-mutmIL15_G3_26_Tumor_11_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E11


title: Group 3_mIgG-mutmIL15_G3_26_Leading Edge_4_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E04


title: Slide 5; ROI 021; Segment: SMA

description:
Library name: DSP-1001660008135-B-E11
Sample/column name in raw count matrix = Slide 5 | 021 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_021. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 021; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 3_mIgG-mutmIL15_G3_26_Leading Edge_3_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E03


title: Group 3_mIgG-mutmIL15_G3_26_Leading Edge_2_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E02


title: Slide 5; ROI 020; Segment: CD45

description:
Library name: DSP-1001660008135-B-E08
Sample/column name in raw count matrix = Slide 5 | 020 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S5_020. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 020; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 020


title: Slide 5; ROI 020; Segment: CK

description:
Library name: DSP-1001660008135-B-E07
Sample/column name in raw count matrix = Slide 5 | 020 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_020. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 020; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 020; Segment: SMA

description:
Library name: DSP-1001660008135-B-E09
Sample/column name in raw count matrix = Slide 5 | 020 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_020. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 020; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 019; Segment: CD45

description:
Library name: DSP-1001660008135-B-E05
Sample/column name in raw count matrix = Slide 5 | 019 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S5_019. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 019; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 019


title: Slide 5; ROI 019; Segment: SMA

description:
Library name: DSP-1001660008135-B-E06
Sample/column name in raw count matrix = Slide 5 | 019 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_019. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 019; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 2_anti-mPD-1_G2_19_Necrosis_23_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D11

value: Necrosis


title: Group 3_mIgG-mutmIL15_G3_26_Leading Edge_5_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E05


title: Group 3_mIgG-mutmIL15_G3_26_Leading Edge_1_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E01


title: Slide 5; ROI 019; Segment: CK

description:
Library name: DSP-1001660008135-B-E04
Sample/column name in raw count matrix = Slide 5 | 019 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_019. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 019; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 2_anti-mPD-1_G2_19_Necrosis_24_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D12


title: Group 2_anti-mPD-1_G2_19_Necrosis_22_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D10


title: Slide 5; ROI 017; Segment: CD45

description:
Library name: DSP-1001660008135-B-D12
Sample/column name in raw count matrix = Slide 5 | 017 | CD45 ; in normalized count matrix = DCIS_High_CD45_S5_017. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 017; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 017


title: Group 2_anti-mPD-1_G2_19_Necrosis_20_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D08


title: Group 2_anti-mPD-1_G2_19_Necrosis_19_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D07


title: Slide 5; ROI 018; Segment: CK

description:
Library name: DSP-1001660008135-B-E02
Sample/column name in raw count matrix = Slide 5 | 018 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_018. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 018; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 018


title: Group 2_anti-mPD-1_G2_19_Necrosis_18_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D06


title: Group 2_anti-mPD-1_G2_19_Necrosis_17_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D05


title: Slide 5; ROI 017; Segment: SMA

description:
Library name: DSP-1001660008135-B-E01
Sample/column name in raw count matrix = Slide 5 | 017 | SMA ; in normalized count matrix = DCIS_High_SMA_S5_017. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 017; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: breast tissue


title: Slide 5; ROI 018; Segment: SMA

description:
Library name: DSP-1001660008135-B-E03
Sample/column name in raw count matrix = Slide 5 | 018 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_018. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 018; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 016; Segment: CD45

description:
Library name: DSP-1001660008135-B-D09
Sample/column name in raw count matrix = Slide 5 | 016 | CD45 ; in normalized count matrix = DCIS_High_CD45_S5_016. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 016; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: leukocytes

value: ROI 016


title: Group 2_anti-mPD-1_G2_19_Tumor_15_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D03


title: Slide 5; ROI 016; Segment: CK

description:
Library name: DSP-1001660008135-B-D08
Sample/column name in raw count matrix = Slide 5 | 016 | CK ; in normalized count matrix = DCIS_High_CK_S5_016. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 016; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: Slide 5


title: Group 2_anti-mPD-1_G2_19_Necrosis_21_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D09


title: Slide 5; ROI 015; Segment: SMA

description:
Library name: DSP-1001660008135-B-D07
Sample/column name in raw count matrix = Slide 5 | 015 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_015. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 015; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 015


title: Slide 5; ROI 017; Segment: CK

description:
Library name: DSP-1001660008135-B-D11
Sample/column name in raw count matrix = Slide 5 | 017 | CK ; in normalized count matrix = DCIS_High_CK_S5_017. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 017; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: CK


title: Group 2_anti-mPD-1_G2_19_Tumor_16_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D04

value: Tumor


title: Slide 5; ROI 015; Segment: CD45

description:
Library name: DSP-1001660008135-B-D06
Sample/column name in raw count matrix = Slide 5 | 015 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S5_015. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 015; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 016; Segment: SMA

description:
Library name: DSP-1001660008135-B-D10
Sample/column name in raw count matrix = Slide 5 | 016 | SMA ; in normalized count matrix = DCIS_High_SMA_S5_016. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 016; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: fibroblasts/myoepithelial cells


title: Group 2_anti-mPD-1_G2_19_Tumor_11_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C11


title: Group 2_anti-mPD-1_G2_19_Tumor_12_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C12


title: Slide 5; ROI 014; Segment: SMA

description:
Library name: DSP-1001660008135-B-D04
Sample/column name in raw count matrix = Slide 5 | 014 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_014. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 014; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 014


title: Slide 5; ROI 014; Segment: CD45

description:
Library name: DSP-1001660008135-B-D03
Sample/column name in raw count matrix = Slide 5 | 014 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S5_014. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 014; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 2_anti-mPD-1_G2_19_Tumor_14_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D02


title: Slide 5; ROI 015; Segment: CK

description:
Library name: DSP-1001660008135-B-D05
Sample/column name in raw count matrix = Slide 5 | 015 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_015. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 015; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: epithelial cells


title: Group 2_anti-mPD-1_G2_19_Tumor_13_Run2_1

description: Library name: Lib-DSP-1001660037469-D-D01


title: Group 2_anti-mPD-1_G2_19_Tumor_9_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C09


title: Slide 5; ROI 014; Segment: CK

description:
Library name: DSP-1001660008135-B-D02
Sample/column name in raw count matrix = Slide 5 | 014 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_014. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 014; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 2_anti-mPD-1_G2_19_Leading Edge_8_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C08

value: Leading Edge


title: Slide 5; ROI 013; Segment: CK

description:
Library name: DSP-1001660008135-B-C12
Sample/column name in raw count matrix = Slide 5 | 013 | CK ; in normalized count matrix = Mix_Normal_CK_S5_013. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 013; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 013


title: Slide 5; ROI 013; Segment: SMA

description:
Library name: DSP-1001660008135-B-D01
Sample/column name in raw count matrix = Slide 5 | 013 | SMA ; in normalized count matrix = Mix_Normal_SMA_S5_013. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 013; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: SMA


title: Group 2_anti-mPD-1_G2_19_Tumor_10_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C10


title: Group 2_anti-mPD-1_G2_19_Leading Edge_6_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C06


title: Group 2_anti-mPD-1_G2_19_Leading Edge_5_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C05


title: Slide 5; ROI 012; Segment: CK

description:
Library name: DSP-1001660008135-B-C09
Sample/column name in raw count matrix = Slide 5 | 012 | CK ; in normalized count matrix = Mix_Normal_CK_S5_012. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 012; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 012


title: Slide 5; ROI 012; Segment: CD45

description:
Library name: DSP-1001660008135-B-C10
Sample/column name in raw count matrix = Slide 5 | 012 | CD45 ; in normalized count matrix = Mix_Normal_CD45_S5_012. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 012; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 2_anti-mPD-1_G2_19_Leading Edge_3_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C03


title: Group 2_anti-mPD-1_G2_19_Leading Edge_4_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C04


title: Slide 5; ROI 011; Segment: SMA

description:
Library name: DSP-1001660008135-B-C08
Sample/column name in raw count matrix = Slide 5 | 011 | SMA ; in normalized count matrix = Mix_Normal_SMA_S5_011. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 011; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 011


title: Slide 5; ROI 011; Segment: CD45

description:
Library name: DSP-1001660008135-B-C07
Sample/column name in raw count matrix = Slide 5 | 011 | CD45 ; in normalized count matrix = Mix_Normal_CD45_S5_011. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 011; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 2_anti-mPD-1_G2_19_Leading Edge_2_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C02


title: Slide 5; ROI 012; Segment: SMA

description:
Library name: DSP-1001660008135-B-C11
Sample/column name in raw count matrix = Slide 5 | 012 | SMA ; in normalized count matrix = Mix_Normal_SMA_S5_012. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 012; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 011; Segment: CK

description:
Library name: DSP-1001660008135-B-C06
Sample/column name in raw count matrix = Slide 5 | 011 | CK ; in normalized count matrix = Mix_Normal_CK_S5_011. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 011; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 2_anti-mPD-1_G2_19_Leading Edge_1_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C01


title: Group 1_Isotype Control_G1_7_Necrosis_23_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B12

value: Isotype Control

value: Necrosis


title: Group 2_anti-mPD-1_G2_19_Leading Edge_7_Run2_1

description: Library name: Lib-DSP-1001660037469-D-C07


title: Slide 5; ROI 010; Segment: SMA

description:
Library name: DSP-1001660008135-B-C05
Sample/column name in raw count matrix = Slide 5 | 010 | SMA ; in normalized count matrix = Mix_Normal_SMA_S5_010. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 010; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: breast tissue

value: ROI 010


title: Group 1_Isotype Control_G1_7_Necrosis_21_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B10


title: Group 1_Isotype Control_G1_7_Necrosis_22_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B11


title: Slide 5; ROI 009; Segment: SMA

description:
Library name: DSP-1001660008135-B-C03
Sample/column name in raw count matrix = Slide 5 | 009 | SMA ; in normalized count matrix = IDC_Normal_SMA_S5_009. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 009; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 009


title: Group 1_Isotype Control_G1_7_Necrosis_20_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B09


title: Group 1_Isotype Control_G1_7_Necrosis_19_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B08


title: Slide 5; ROI 009; Segment: CD45

description:
Library name: DSP-1001660008135-B-C02
Sample/column name in raw count matrix = Slide 5 | 009 | CD45 ; in normalized count matrix = IDC_Normal_CD45_S5_009. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 009; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: leukocytes

value: Slide 5


title: Group 1_Isotype Control_G1_7_Necrosis_18_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B07


title: Slide 5; ROI 009; Segment: CK

description:
Library name: DSP-1001660008135-B-C01
Sample/column name in raw count matrix = Slide 5 | 009 | CK ; in normalized count matrix = IDC_Normal_CK_S5_009. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 009; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: CK


title: Slide 5; ROI 008; Segment: SMA

description:
Library name: DSP-1001660008135-B-B12
Sample/column name in raw count matrix = Slide 5 | 008 | SMA ; in normalized count matrix = IDC_High_SMA_S5_008. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 008; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 008


title: Slide 5; ROI 008; Segment: CD45

description:
Library name: DSP-1001660008135-B-B11
Sample/column name in raw count matrix = Slide 5 | 008 | CD45 ; in normalized count matrix = IDC_High_CD45_S5_008. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 008; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 010; Segment: CK

description:
Library name: DSP-1001660008135-B-C04
Sample/column name in raw count matrix = Slide 5 | 010 | CK ; in normalized count matrix = Mix_Normal_CK_S5_010. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 010; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 1_Isotype Control_G1_7_Necrosis_17_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B06


title: Group 1_Isotype Control_G1_7_Tumor_16_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B05

value: Tumor


title: Slide 5; ROI 007; Segment: SMA

description:
Library name: DSP-1001660008135-B-B09
Sample/column name in raw count matrix = Slide 5 | 007 | SMA ; in normalized count matrix = DCIS_High_SMA_S5_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 007; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: fibroblasts/myoepithelial cells

value: ROI 007


title: Group 1_Isotype Control_G1_7_Tumor_15_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B04


title: Group 1_Isotype Control_G1_7_Tumor_13_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B02


title: Slide 5; ROI 008; Segment: CK

description:
Library name: DSP-1001660008135-B-B10
Sample/column name in raw count matrix = Slide 5 | 008 | CK ; in normalized count matrix = IDC_High_CK_S5_008. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 008; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: epithelial cells


title: Slide 5; ROI 007; Segment: CK

description:
Library name: DSP-1001660008135-B-B07
Sample/column name in raw count matrix = Slide 5 | 007 | CK ; in normalized count matrix = DCIS_High_CK_S5_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 007; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 007; Segment: CD45

description:
Library name: DSP-1001660008135-B-B08
Sample/column name in raw count matrix = Slide 5 | 007 | CD45 ; in normalized count matrix = DCIS_High_CD45_S5_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 007; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 1_Isotype Control_G1_7_Tumor_12_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B01


title: Slide 5; ROI 006; Segment: SMA

description:
Library name: DSP-1001660008135-B-B06
Sample/column name in raw count matrix = Slide 5 | 006 | SMA ; in normalized count matrix = IDC_High_SMA_S5_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 006; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 006


title: Group 1_Isotype Control_G1_7_Tumor_11_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A12


title: Group 1_Isotype Control_G1_7_Tumor_14_Run2_1

description: Library name: Lib-DSP-1001660037469-D-B03


title: Group 1_Isotype Control_G1_7_Tumor_10_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A11


title: Slide 5; ROI 006; Segment: CK

description:
Library name: DSP-1001660008135-B-B04
Sample/column name in raw count matrix = Slide 5 | 006 | CK ; in normalized count matrix = IDC_High_CK_S5_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 006; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 1_Isotype Control_G1_7_Tumor_9_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A10


title: Group 1_Isotype Control_G1_7_Leading Edge_8_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A09

value: Leading Edge


title: Slide 5; ROI 005; Segment: SMA

description:
Library name: DSP-1001660008135-B-B03
Sample/column name in raw count matrix = Slide 5 | 005 | SMA ; in normalized count matrix = DCIS_High_SMA_S5_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 005; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 005

value: SMA


title: Slide 5; ROI 005; Segment: CD45

description:
Library name: DSP-1001660008135-B-B02
Sample/column name in raw count matrix = Slide 5 | 005 | CD45 ; in normalized count matrix = DCIS_High_CD45_S5_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 005; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 005; Segment: CK

description:
Library name: DSP-1001660008135-B-B01
Sample/column name in raw count matrix = Slide 5 | 005 | CK ; in normalized count matrix = DCIS_High_CK_S5_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 005; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 004; Segment: CD45

description:
Library name: DSP-1001660008135-B-A12
Sample/column name in raw count matrix = Slide 5 | 004 | CD45 ; in normalized count matrix = IDC_High_CD45_S5_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 004; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 004


title: Group 1_Isotype Control_G1_7_Leading Edge_6_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A07

value: Isotype Control


title: Slide 5; ROI 006; Segment: CD45

description:
Library name: DSP-1001660008135-B-B05
Sample/column name in raw count matrix = Slide 5 | 006 | CD45 ; in normalized count matrix = IDC_High_CD45_S5_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 006; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: breast tissue


title: Group 1_Isotype Control_G1_7_Leading Edge_5_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A06


title: Slide 5; ROI 003; Segment: SMA

description:
Library name: DSP-1001660008135-B-A10
Sample/column name in raw count matrix = Slide 5 | 003 | SMA ; in normalized count matrix = DCIS_High_SMA_S5_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 003; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 003


title: Group 1_Isotype Control_G1_7_Leading Edge_4_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A05


title: Group 1_Isotype Control_G1_7_Leading Edge_3_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A04


title: Slide 5; ROI 003; Segment: CD45

description:
Library name: DSP-1001660008135-B-A09
Sample/column name in raw count matrix = Slide 5 | 003 | CD45 ; in normalized count matrix = DCIS_High_CD45_S5_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 003; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 1_Isotype Control_G1_7_Leading Edge_7_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A08


title: Slide 5; ROI 003; Segment: CK

description:
Library name: DSP-1001660008135-B-A08
Sample/column name in raw count matrix = Slide 5 | 003 | CK ; in normalized count matrix = DCIS_High_CK_S5_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 003; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 002; Segment: SMA

description:
Library name: DSP-1001660008135-B-A07
Sample/column name in raw count matrix = Slide 5 | 002 | SMA ; in normalized count matrix = IDC_High_SMA_S5_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 002; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 002


title: Group 1_Isotype Control_G1_7_Leading Edge_2_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A03


title: Slide 5; ROI 004; Segment: CK

description:
Library name: DSP-1001660008135-B-A11
Sample/column name in raw count matrix = Slide 5 | 004 | CK ; in normalized count matrix = IDC_High_CK_S5_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 004; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: NTC_NTC_NTC_NTC_NTC_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A01

source_name: NTC

value: NTC


title: Group 1_Isotype Control_G1_7_Leading Edge_1_Run2_1

description: Library name: Lib-DSP-1001660037469-D-A02


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Necrosis_24_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H12

value: Necrosis


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Necrosis_23_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H11


title: Slide 5; ROI 002; Segment: CK

description:
Library name: DSP-1001660008135-B-A05
Sample/column name in raw count matrix = Slide 5 | 002 | CK ; in normalized count matrix = IDC_High_CK_S5_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 002; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: Slide 5

value: CK


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Necrosis_22_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H10


title: Slide 5; ROI 001; Segment: SMA

description:
Library name: DSP-1001660008135-B-A04
Sample/column name in raw count matrix = Slide 5 | 001 | SMA ; in normalized count matrix = IDC_High_SMA_S5_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 001; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 001


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Necrosis_21_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H09


title: Slide 5; ROI 001; Segment: CD45

description:
Library name: DSP-1001660008135-B-A03
Sample/column name in raw count matrix = Slide 5 | 001 | CD45 ; in normalized count matrix = IDC_High_CD45_S5_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 001; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: leukocytes


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Necrosis_20_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H08


title: Slide 5; ROI 002; Segment: CD45

description:
Library name: DSP-1001660008135-B-A06
Sample/column name in raw count matrix = Slide 5 | 002 | CD45 ; in normalized count matrix = IDC_High_CD45_S5_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 002; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 001; Segment: CK

description:
Library name: DSP-1001660008135-B-A02
Sample/column name in raw count matrix = Slide 5 | 001 | CK ; in normalized count matrix = IDC_High_CK_S5_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 001; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 4; ROI 013; Segment: CK

description:
Library name: DSP-1001660008101-A-H11
Sample/column name in raw count matrix = Slide 4 | 013 | CK ; in normalized count matrix = IDC_High_CK_S4_013. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 013; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: Slide 4

value: ROI 013


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Necrosis_19_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H07


title: Slide 4; ROI 013; Segment: SMA

description:
Library name: DSP-1001660008101-A-H12
Sample/column name in raw count matrix = Slide 4 | 013 | SMA ; in normalized count matrix = IDC_High_SMA_S4_013. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 013; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: fibroblasts/myoepithelial cells


title: Slide 4; ROI 013; Segment: CD45

description:
Library name: DSP-1001660008101-A-H10
Sample/column name in raw count matrix = Slide 4 | 013 | CD45 ; in normalized count matrix = IDC_High_CD45_S4_013. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 013; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Necrosis_18_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H06


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Tumor_16_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H04

value: Tumor


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Necrosis_17_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H05


title: Slide 4; ROI 012; Segment: CK

description:
Library name: DSP-1001660008101-A-H08
Sample/column name in raw count matrix = Slide 4 | 012 | CK ; in normalized count matrix = IDC_High_CK_S4_012. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 012; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: epithelial cells

value: ROI 012


title: Slide 4; ROI 012; Segment: SMA

description:
Library name: DSP-1001660008101-A-H09
Sample/column name in raw count matrix = Slide 4 | 012 | SMA ; in normalized count matrix = IDC_High_SMA_S4_012. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 012; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: SMA


title: Slide 4; ROI 011; Segment: SMA

description:
Library name: DSP-1001660008101-A-H07
Sample/column name in raw count matrix = Slide 4 | 011 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S4_011. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 011; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 011


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Tumor_15_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H03


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Tumor_14_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H02


title: Slide 4; ROI 011; Segment: CK

description:
Library name: DSP-1001660008101-A-H06
Sample/column name in raw count matrix = Slide 4 | 011 | CK ; in normalized count matrix = DCIS_Normal_CK_S4_011. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 011; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: breast tissue


title: Slide 4; ROI 011; Segment: CD45

description:
Library name: DSP-1001660008101-A-H05
Sample/column name in raw count matrix = Slide 4 | 011 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S4_011. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 011; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Tumor_11_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G11


title: Slide 4; ROI 010; Segment: CD45

description:
Library name: DSP-1001660008101-A-H02
Sample/column name in raw count matrix = Slide 4 | 010 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S4_010. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 010; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 010


title: Slide 4; ROI 010; Segment: CK

description:
Library name: DSP-1001660008101-A-H03
Sample/column name in raw count matrix = Slide 4 | 010 | CK ; in normalized count matrix = DCIS_Normal_CK_S4_010. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 010; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Tumor_12_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G12


title: Slide 4; ROI 009; Segment: SMA

description:
Library name: DSP-1001660008101-A-H01
Sample/column name in raw count matrix = Slide 4 | 009 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S4_009. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 009; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 009


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Tumor_9_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G09


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Leading Edge_7_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G07

value: Leading Edge


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Leading Edge_8_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G08


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Leading Edge_6_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G06


title: Slide 4; ROI 010; Segment: SMA

description:
Library name: DSP-1001660008101-A-H04
Sample/column name in raw count matrix = Slide 4 | 010 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S4_010. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 010; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Tumor_13_Run1_3

description: Library name: Lib-DSP-1001660037468-C-H01


title: Slide 4; ROI 009; Segment: CK

description:
Library name: DSP-1001660008101-A-G12
Sample/column name in raw count matrix = Slide 4 | 009 | CK ; in normalized count matrix = DCIS_Normal_CK_S4_009. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 009; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Tumor_10_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G10


title: Slide 4; ROI 007; Segment: SMA

description:
Library name: DSP-1001660008101-A-G07
Sample/column name in raw count matrix = Slide 4 | 007 | SMA ; in normalized count matrix = DCIS_High_SMA_S4_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 007; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 007


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Leading Edge_3_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G03


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Leading Edge_5_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G05


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Leading Edge_2_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G02


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Leading Edge_4_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G04


title: Slide 4; ROI 008; Segment: SMA

description:
Library name: DSP-1001660008101-A-G10
Sample/column name in raw count matrix = Slide 4 | 008 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S4_008. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 008; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 008


title: Slide 4; ROI 008; Segment: CD45

description:
Library name: DSP-1001660008101-A-G08
Sample/column name in raw count matrix = Slide 4 | 008 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S4_008. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 008; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_36_Leading Edge_1_Run1_3

description: Library name: Lib-DSP-1001660037468-C-G01


title: Slide 4; ROI 006; Segment: SMA

description:
Library name: DSP-1001660008101-A-G04
Sample/column name in raw count matrix = Slide 4 | 006 | SMA ; in normalized count matrix = DCIS_High_SMA_S4_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 006; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 006


title: Group 3_mIgG-mutmIL15_G3_25_Necrosis_24_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F12

value: Necrosis


title: Slide 4; ROI 006; Segment: CK

description:
Library name: DSP-1001660008101-A-G03
Sample/column name in raw count matrix = Slide 4 | 006 | CK ; in normalized count matrix = DCIS_High_CK_S4_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 006; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: CK


title: Slide 4; ROI 009; Segment: CD45

description:
Library name: DSP-1001660008101-A-G11
Sample/column name in raw count matrix = Slide 4 | 009 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S4_009. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 009; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: leukocytes

value: Slide 4


title: Group 3_mIgG-mutmIL15_G3_25_Necrosis_23_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F11


title: Slide 4; ROI 007; Segment: CK

description:
Library name: DSP-1001660008101-A-G06
Sample/column name in raw count matrix = Slide 4 | 007 | CK ; in normalized count matrix = DCIS_High_CK_S4_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 007; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 4; ROI 006; Segment: CD45

description:
Library name: DSP-1001660008101-A-G02
Sample/column name in raw count matrix = Slide 4 | 006 | CD45 ; in normalized count matrix = DCIS_High_CD45_S4_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 006; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 3_mIgG-mutmIL15_G3_25_Necrosis_22_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F10


title: Slide 4; ROI 007; Segment: CD45

description:
Library name: DSP-1001660008101-A-G05
Sample/column name in raw count matrix = Slide 4 | 007 | CD45 ; in normalized count matrix = DCIS_High_CD45_S4_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 007; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 3_mIgG-mutmIL15_G3_25_Necrosis_20_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F08


title: Slide 4; ROI 005; Segment: CD45

description:
Library name: DSP-1001660008101-A-F12
Sample/column name in raw count matrix = Slide 4 | 005 | CD45 ; in normalized count matrix = IDC_Normal_CD45_S4_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 005; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 005


title: Group 3_mIgG-mutmIL15_G3_25_Necrosis_18_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F06


title: Group 3_mIgG-mutmIL15_G3_25_Necrosis_21_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F09


title: Slide 4; ROI 004; Segment: SMA

description:
Library name: DSP-1001660008101-A-F11
Sample/column name in raw count matrix = Slide 4 | 004 | SMA ; in normalized count matrix = IDC_Normal_SMA_S4_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 004; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: fibroblasts/myoepithelial cells

value: ROI 004


title: Group 3_mIgG-mutmIL15_G3_25_Necrosis_19_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F07


title: Slide 4; ROI 004; Segment: CK

description:
Library name: DSP-1001660008101-A-F10
Sample/column name in raw count matrix = Slide 4 | 004 | CK ; in normalized count matrix = IDC_Normal_CK_S4_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 004; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: epithelial cells


title: Group 3_mIgG-mutmIL15_G3_25_Necrosis_17_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F05


title: Slide 4; ROI 003; Segment: CK

description:
Library name: DSP-1001660008101-A-F09
Sample/column name in raw count matrix = Slide 4 | 003 | CK ; in normalized count matrix = IDC_Normal_CK_S4_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 003; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 003


title: Slide 4; ROI 005; Segment: CK

description:
Library name: DSP-1001660008101-A-G01
Sample/column name in raw count matrix = Slide 4 | 005 | CK ; in normalized count matrix = IDC_Normal_CK_S4_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 005; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 4; ROI 002; Segment: SMA

description:
Library name: DSP-1001660008101-A-F07
Sample/column name in raw count matrix = Slide 4 | 002 | SMA ; in normalized count matrix = IDC_High_SMA_S4_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 002; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 002

value: SMA


title: Group 3_mIgG-mutmIL15_G3_25_Tumor_15_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F03

value: Tumor


title: Group 3_mIgG-mutmIL15_G3_25_Tumor_16_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F04


title: Slide 4; ROI 002; Segment: CK

description:
Library name: DSP-1001660008101-A-F06
Sample/column name in raw count matrix = Slide 4 | 002 | CK ; in normalized count matrix = IDC_High_CK_S4_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 002; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: breast tissue


title: Group 3_mIgG-mutmIL15_G3_25_Tumor_13_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F01


title: Slide 4; ROI 003; Segment: CD45

description:
Library name: DSP-1001660008101-A-F08
Sample/column name in raw count matrix = Slide 4 | 003 | CD45 ; in normalized count matrix = IDC_Normal_CD45_S4_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 003; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 4; ROI 002; Segment: CD45

description:
Library name: DSP-1001660008101-A-F05
Sample/column name in raw count matrix = Slide 4 | 002 | CD45 ; in normalized count matrix = IDC_High_CD45_S4_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 002; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 4; ROI 001; Segment: CD45

description:
Library name: DSP-1001660008101-A-F03
Sample/column name in raw count matrix = Slide 4 | 001 | CD45 ; in normalized count matrix = IDC_High_CD45_S4_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 001; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 001


title: Group 3_mIgG-mutmIL15_G3_25_Tumor_11_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E11


title: Group 3_mIgG-mutmIL15_G3_25_Tumor_12_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E12


title: Slide 3; ROI 013; Segment: SMA

description:
Library name: DSP-1001660008101-A-F02
Sample/column name in raw count matrix = Slide 3 | 013 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S3_013. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 013; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: Slide 3

value: ROI 013


title: Slide 3; ROI 013; Segment: CK

description:
Library name: DSP-1001660008101-A-F01
Sample/column name in raw count matrix = Slide 3 | 013 | CK ; in normalized count matrix = DCIS_Normal_CK_S3_013. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 013; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 4; ROI 001; Segment: CK

description:
Library name: DSP-1001660008101-A-F04
Sample/column name in raw count matrix = Slide 4 | 001 | CK ; in normalized count matrix = IDC_High_CK_S4_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 001; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 3_mIgG-mutmIL15_G3_25_Tumor_10_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E10


title: Group 3_mIgG-mutmIL15_G3_25_Tumor_14_Run1_3

description: Library name: Lib-DSP-1001660037468-C-F02


title: Group 3_mIgG-mutmIL15_G3_25_Leading Edge_8_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E08

value: Leading Edge


title: Slide 3; ROI 013; Segment: CD45

description:
Library name: DSP-1001660008101-A-E12
Sample/column name in raw count matrix = Slide 3 | 013 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S3_013. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 013; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 3; ROI 012; Segment: SMA

description:
Library name: DSP-1001660008101-A-E11
Sample/column name in raw count matrix = Slide 3 | 012 | SMA ; in normalized count matrix = DCIS_High_SMA_S3_012. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 012; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 012


title: Slide 3; ROI 012; Segment: CD45

description:
Library name: DSP-1001660008101-A-E09
Sample/column name in raw count matrix = Slide 3 | 012 | CD45 ; in normalized count matrix = DCIS_High_CD45_S3_012. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 012; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 3_mIgG-mutmIL15_G3_25_Leading Edge_5_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E05


title: Group 3_mIgG-mutmIL15_G3_25_Leading Edge_6_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E06


title: Group 3_mIgG-mutmIL15_G3_25_Leading Edge_7_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E07


title: Group 3_mIgG-mutmIL15_G3_25_Tumor_9_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E09


title: Slide 3; ROI 011; Segment: CK

description:
Library name: DSP-1001660008101-A-E08
Sample/column name in raw count matrix = Slide 3 | 011 | CK ; in normalized count matrix = IDC_Normal_CK_S3_011. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 011; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 011

value: CK


title: Slide 3; ROI 012; Segment: CK

description:
Library name: DSP-1001660008101-A-E10
Sample/column name in raw count matrix = Slide 3 | 012 | CK ; in normalized count matrix = DCIS_High_CK_S3_012. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 012; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 3_mIgG-mutmIL15_G3_25_Leading Edge_3_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E03


title: Group 3_mIgG-mutmIL15_G3_25_Leading Edge_2_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E02


title: Group 3_mIgG-mutmIL15_G3_25_Leading Edge_4_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E04


title: Slide 3; ROI 010; Segment: CK

description:
Library name: DSP-1001660008101-A-E05
Sample/column name in raw count matrix = Slide 3 | 010 | CK ; in normalized count matrix = IDC_High_CK_S3_010. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 010; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 010


title: Slide 3; ROI 011; Segment: CD45

description:
Library name: DSP-1001660008101-A-E07
Sample/column name in raw count matrix = Slide 3 | 011 | CD45 ; in normalized count matrix = IDC_Normal_CD45_S3_011. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 011; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: leukocytes


title: Group 2_anti-mPD-1_G2_18_Necrosis_24_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D12

value: Necrosis


title: Group 3_mIgG-mutmIL15_G3_25_Leading Edge_1_Run1_3

description: Library name: Lib-DSP-1001660037468-C-E01


title: Slide 3; ROI 010; Segment: CD45

description:
Library name: DSP-1001660008101-A-E04
Sample/column name in raw count matrix = Slide 3 | 010 | CD45 ; in normalized count matrix = IDC_High_CD45_S3_010. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 010; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 2_anti-mPD-1_G2_18_Necrosis_23_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D11


title: Slide 3; ROI 009; Segment: CK

description:
Library name: DSP-1001660008101-A-E02
Sample/column name in raw count matrix = Slide 3 | 009 | CK ; in normalized count matrix = DCIS_Normal_CK_S3_009. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 009; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 009


title: Group 2_anti-mPD-1_G2_18_Necrosis_21_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D09


title: Group 2_anti-mPD-1_G2_18_Necrosis_22_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D10


title: Group 2_anti-mPD-1_G2_18_Necrosis_20_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D08


title: Slide 3; ROI 010; Segment: SMA

description:
Library name: DSP-1001660008101-A-E06
Sample/column name in raw count matrix = Slide 3 | 010 | SMA ; in normalized count matrix = IDC_High_SMA_S3_010. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 010; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: fibroblasts/myoepithelial cells


title: Group 2_anti-mPD-1_G2_18_Necrosis_19_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D07


title: Slide 3; ROI 008; Segment: SMA

description:
Library name: DSP-1001660008101-A-E01
Sample/column name in raw count matrix = Slide 3 | 008 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S3_008. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 008; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 008


title: Slide 3; ROI 009; Segment: SMA

description:
Library name: DSP-1001660008101-A-E03
Sample/column name in raw count matrix = Slide 3 | 009 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S3_009. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 009; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 2_anti-mPD-1_G2_18_Necrosis_18_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D06


title: Slide 3; ROI 007; Segment: SMA

description:
Library name: DSP-1001660008101-A-D11
Sample/column name in raw count matrix = Slide 3 | 007 | SMA ; in normalized count matrix = DCIS_High_SMA_S3_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 007; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 007


title: Slide 3; ROI 008; Segment: CK

description:
Library name: DSP-1001660008101-A-D12
Sample/column name in raw count matrix = Slide 3 | 008 | CK ; in normalized count matrix = DCIS_Normal_CK_S3_008. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 008; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: epithelial cells


title: Slide 3; ROI 007; Segment: CK

description:
Library name: DSP-1001660008101-A-D10
Sample/column name in raw count matrix = Slide 3 | 007 | CK ; in normalized count matrix = DCIS_High_CK_S3_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 007; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 3; ROI 006; Segment: CK

description:
Library name: DSP-1001660008101-A-D08
Sample/column name in raw count matrix = Slide 3 | 006 | CK ; in normalized count matrix = DCIS_High_CK_S3_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 006; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 006


title: Group 2_anti-mPD-1_G2_18_Necrosis_17_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D05


title: Slide 3; ROI 006; Segment: SMA

description:
Library name: DSP-1001660008101-A-D09
Sample/column name in raw count matrix = Slide 3 | 006 | SMA ; in normalized count matrix = DCIS_High_SMA_S3_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 006; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: breast tissue

value: SMA


title: Slide 3; ROI 005; Segment: CK

description:
Library name: DSP-1001660008101-A-D07
Sample/column name in raw count matrix = Slide 3 | 005 | CK ; in normalized count matrix = IDC_Normal_CK_S3_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 005; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: Slide 3

value: ROI 005


title: Group 2_anti-mPD-1_G2_18_Tumor_16_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D04

value: Tumor


title: Group 2_anti-mPD-1_G2_18_Tumor_15_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D03


title: Slide 3; ROI 005; Segment: CD45

description:
Library name: DSP-1001660008101-A-D06
Sample/column name in raw count matrix = Slide 3 | 005 | CD45 ; in normalized count matrix = IDC_Normal_CD45_S3_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 005; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 3; ROI 004; Segment: CK

description:
Library name: DSP-1001660008101-A-D05
Sample/column name in raw count matrix = Slide 3 | 004 | CK ; in normalized count matrix = IDC_Normal_CK_S3_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 004; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 004


title: Group 2_anti-mPD-1_G2_18_Tumor_12_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C12


title: Group 2_anti-mPD-1_G2_18_Tumor_11_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C11


title: Group 2_anti-mPD-1_G2_18_Tumor_13_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D01


title: Group 2_anti-mPD-1_G2_18_Tumor_14_Run1_3

description: Library name: Lib-DSP-1001660037468-C-D02


title: Slide 3; ROI 003; Segment: CK

description:
Library name: DSP-1001660008101-A-D03
Sample/column name in raw count matrix = Slide 3 | 003 | CK ; in normalized count matrix = IDC_High_CK_S3_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 003; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 003


title: Slide 3; ROI 004; Segment: CD45

description:
Library name: DSP-1001660008101-A-D04
Sample/column name in raw count matrix = Slide 3 | 004 | CD45 ; in normalized count matrix = IDC_Normal_CD45_S3_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 004; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 3; ROI 002; Segment: CK

description:
Library name: DSP-1001660008101-A-D01
Sample/column name in raw count matrix = Slide 3 | 002 | CK ; in normalized count matrix = IDC_High_CK_S3_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 002; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 002

value: CK


title: Group 2_anti-mPD-1_G2_18_Tumor_9_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C09


title: Slide 3; ROI 003; Segment: CD45

description:
Library name: DSP-1001660008101-A-D02
Sample/column name in raw count matrix = Slide 3 | 003 | CD45 ; in normalized count matrix = IDC_High_CD45_S3_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 003; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: leukocytes


title: Group 2_anti-mPD-1_G2_18_Leading Edge_8_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C08

value: Leading Edge


title: Slide 3; ROI 002; Segment: CD45

description:
Library name: DSP-1001660008101-A-C12
Sample/column name in raw count matrix = Slide 3 | 002 | CD45 ; in normalized count matrix = IDC_High_CD45_S3_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 002; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 2_anti-mPD-1_G2_18_Leading Edge_6_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C06


title: Group 2_anti-mPD-1_G2_18_Leading Edge_5_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C05


title: Slide 3; ROI 001; Segment: CK

description:
Library name: DSP-1001660008101-A-C11
Sample/column name in raw count matrix = Slide 3 | 001 | CK ; in normalized count matrix = IDC_High_CK_S3_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 001; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 001


title: Group 2_anti-mPD-1_G2_18_Tumor_10_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C10


title: Group 2_anti-mPD-1_G2_18_Leading Edge_4_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C04


title: Slide 2; ROI 007; Segment: SMA

description:
Library name: DSP-1001660008101-A-C09
Sample/column name in raw count matrix = Slide 2 | 007 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S2_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 007; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: fibroblasts/myoepithelial cells

value: Slide 2


title: Slide 2; ROI 007; Segment: CK

description:
Library name: DSP-1001660008101-A-C08
Sample/column name in raw count matrix = Slide 2 | 007 | CK ; in normalized count matrix = DCIS_Normal_CK_S2_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 007; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 007


title: Slide 2; ROI 006; Segment: SMA

description:
Library name: DSP-1001660008101-A-C07
Sample/column name in raw count matrix = Slide 2 | 006 | SMA ; in normalized count matrix = DCIS_High_SMA_S2_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 006; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 2_anti-mPD-1_G2_18_Leading Edge_2_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C02


title: Slide 2; ROI 006; Segment: CK

description:
Library name: DSP-1001660008101-A-C06
Sample/column name in raw count matrix = Slide 2 | 006 | CK ; in normalized count matrix = DCIS_High_CK_S2_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 006; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: epithelial cells


title: Group 2_anti-mPD-1_G2_18_Leading Edge_3_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C03


title: Group 1_Isotype Control_G1_6_Necrosis_23_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B12

value: Isotype Control

value: Necrosis


title: Slide 2; ROI 005; Segment: SMA

description:
Library name: DSP-1001660008101-A-C05
Sample/column name in raw count matrix = Slide 2 | 005 | SMA ; in normalized count matrix = DCIS_High_SMA_S2_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 005; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: breast tissue

value: SMA


title: Slide 3; ROI 001; Segment: CD45

description:
Library name: DSP-1001660008101-A-C10
Sample/column name in raw count matrix = Slide 3 | 001 | CD45 ; in normalized count matrix = IDC_High_CD45_S3_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 3; ROI 001; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: Slide 3


title: Group 2_anti-mPD-1_G2_18_Leading Edge_1_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C01


title: Group 2_anti-mPD-1_G2_18_Leading Edge_7_Run1_3

description: Library name: Lib-DSP-1001660037468-C-C07


title: Group 1_Isotype Control_G1_6_Necrosis_22_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B11


title: Slide 2; ROI 003; Segment: CD45

description:
Library name: DSP-1001660008101-A-B12
Sample/column name in raw count matrix = Slide 2 | 003 | CD45 ; in normalized count matrix = IDC_Normal_CD45_S2_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 003; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 1_Isotype Control_G1_6_Necrosis_20_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B09


title: Group 1_Isotype Control_G1_6_Necrosis_19_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B08


title: Slide 2; ROI 005; Segment: CK

description:
Library name: DSP-1001660008101-A-C04
Sample/column name in raw count matrix = Slide 2 | 005 | CK ; in normalized count matrix = DCIS_High_CK_S2_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 005; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 005


title: Slide 2; ROI 002; Segment: CK

description:
Library name: DSP-1001660008101-A-B11
Sample/column name in raw count matrix = Slide 2 | 002 | CK ; in normalized count matrix = IDC_High_CK_S2_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 002; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 1_Isotype Control_G1_6_Necrosis_21_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B10


title: Group 1_Isotype Control_G1_6_Necrosis_18_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B07


title: Slide 2; ROI 002; Segment: CD45

description:
Library name: DSP-1001660008101-A-B10
Sample/column name in raw count matrix = Slide 2 | 002 | CD45 ; in normalized count matrix = IDC_High_CD45_S2_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 002; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 1_Isotype Control_G1_6_Tumor_16_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B05

value: Tumor


title: Slide 2; ROI 004; Segment: CK

description:
Library name: DSP-1001660008101-A-C03
Sample/column name in raw count matrix = Slide 2 | 004 | CK ; in normalized count matrix = IDC_Normal_CK_S2_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 004; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 004


title: Group 1_Isotype Control_G1_6_Necrosis_17_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B06


title: Group 1_Isotype Control_G1_6_Tumor_14_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B03


title: Slide 2; ROI 001; Segment: CK

description:
Library name: DSP-1001660008101-A-B09
Sample/column name in raw count matrix = Slide 2 | 001 | CK ; in normalized count matrix = IDC_High_CK_S2_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 001; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 2; ROI 001; Segment: CD45

description:
Library name: DSP-1001660008101-A-B08
Sample/column name in raw count matrix = Slide 2 | 001 | CD45 ; in normalized count matrix = IDC_High_CD45_S2_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 001; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 2; ROI 004; Segment: CD45

description:
Library name: DSP-1001660008101-A-C02
Sample/column name in raw count matrix = Slide 2 | 004 | CD45 ; in normalized count matrix = IDC_Normal_CD45_S2_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 004; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 1; ROI 007; Segment: SMA

description:
Library name: DSP-1001660008101-A-B07
Sample/column name in raw count matrix = Slide 1 | 007 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S1_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 007; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: Slide 1


title: Slide 1; ROI 007; Segment: CD45

description:
Library name: DSP-1001660008101-A-B05
Sample/column name in raw count matrix = Slide 1 | 007 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S1_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 007; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv