title: TNBC009|ROI-004|PanCK-

description:
Library name: DSP-1001660016070-F-H08
TNBC009 - 004 - PanCK-
TNBC009-slide.png
TNBC009 - 004.png
TNBC009 - 004 - Segments.png


title: GroupD, mouse 1, antibody H3K4me3, replicate 1

status: Public on Dec 19 2025

type: SRA

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

country: USA

institute: Virginia Tech

description: Library name: D-1-H3K4me3-rep1

library_source: genomic

data_processing:
Read trimming was performed using default settings by Trim Galore!
Trimmed reads were aligned to the mm10 genome with Bowtie2.
Peaks were called using MACS2 (q < 0.05).
Blacklisted regions in the mm10 as defined by ENCODE were removed to improve data quality using SAMtools.
Mapped reads from ChIP and input samples were extended by 100 bp on either side (250 bp total) using BEDtools and a normalized signal was calculated.
For visualization in IGV (Broad Institute), the signal was calculated in 100bp windows over the entire genome and output as a bigWig file.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: Frontal cortex

extract_protocol:
Adult mice were euthanized by cervical dislocation, and bilateral samples of the frontal cortex (spanning bregma 1.90 to 1.40) were rapidly dissected and flash-frozen at –80°C for later processing. For epigenomic analysis via MOWChIP-seq, the frozen frontal cortex tissue was processed to isolate neuronal nuclei. Fluorescence-activated cell sorting (FACS) was used to enrich for NeuN-positive (NeuN⁺) neuronal populations. Each chromatin immunoprecipitation replicate targeting histone marks H3K4me3 and H3K27ac was performed using approximately 10,000 sorted neuronal nuclei.
Chromatin from 10,000 FACS-sorted neuronal nuclei was digested with micrococcal nuclease (MNase) following a published protocol. Chromatin immunoprecipitation was performed using the MOWChIP method (Zhu et al., Nat Protocols, 14, 3366–3394, (2019))with anti-H3K4me3 and anti-H3K27ac antibodies (Active Motif). Libraries were prepared from purified ChIP DNA using the Accel-NGS 2S Plus kit (Swift Biosciences), with experimenters blinded to sample identity and histone mark. Minor protocol modifications were made to optimize PCR amplification and library cleanup. Library were lsequenced on an Illumina HiSeq 4000 (single-end, 50 bp), yielding ~15M reads per ChIP-seq replicate.

treatment_protocol: Pregnant CD1 mice were exposed to maternal immune activation (MIA) via intranasal administration of 5 × 10³ plaque-forming units (pfu) of influenza A/WSN/33 (H1N1) on embryonic day 9.5 (E9.5), or received PBS as a control. At birth, approximately half of the offspring were cross-fostered to surrogate dams—either MIA-exposed or control—to dissociate prenatal from postnatal influences. Offspring were weaned at postnatal day 21 (P21) and housed in same-sex groups of 3–5 per cage. Litters were organized based on their prenatal and postnatal exposure conditions and distributed across multiple cages. Adult mice were sacrificed for tissue collection.

tag: tissue

value: Frontal cortex

tag: cell type

value: Neuron

tag: treatment

value: MIA-MIA

tag: chip antibody


title: scRNA Abd-S79 (VDJ)

city: chongqing

first: Ye

last: qian

address: No. 1 Youyi Road, Yuzhong District, Chongqing

country: China

institute: The First Affiliated Hospital of Chongqing Medical University

description:
Library name: sample38
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

library_source: transcriptomic single cell

data_processing:
The final library pool was sequenced on the Illumina NovaSeq 6000 platform and the sequencing data were processed using the Cell Ranger software (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: The .csv file contains all VDJ data.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Peripheral blood samples were collected and gently rotated to mix thoroughly. Whole blood was first diluted by adding an equal amount of sterile phosphate-buffered saline (PBS), the diluted whole blood was layered onto Ficoll PAQUE, after horizontally centrifuged, the middle mononuclear cell layer was transferred to a new tube, ACK lysis buffer (Miltenyi Biotec) was added to lyse red blood cells. After the last wash, pipet off the supernatant and loosen the pellet by adding PBS with 0.04% BSA.
RNA libraries were generated by 10xGenomics Single Cell 5’ RNA, VDJ Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

value: Peripheral blood

tag: cell line

value: PBMCs

value: Immune cells

tag: gender

value: Male

tag: age

tag: sample collection_site

value: Chongqing Emergency Medical Center, Chongqing, China.

tag: group

value: Adult Sepsis

tag: sepsis infection_source

value: Abdominal

tag: ethnicity

value: East Asian


title: GroupC, mouse 5, antibody H3K4me3, replicate 1

description: Library name: C-5-H3K4me3-rep1

value: Mock-MIA


title: scRNA Abd-S66 (VDJ)

description:
Library name: sample33
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC009|ROI-004|PanCK+

city: Pasadena

first: David

middle: Eugene

last: Frankhouser

state: CA

address: 1500 E Duarte Rd

department: Population Sciences

institute: City of Hope

description:
Library name: DSP-1001660016070-F-H07
TNBC009 - 004 - PanCK+
TNBC009-slide.png
TNBC009 - 004.png
TNBC009 - 004 - Segments.png

library_source: transcriptomic

data_processing:
The "GeomxTools" library in R was used to read in the DCC files using the .pkc file, and the raw counts were output into the "raw_counts.tsv" file
Assembly: Hg38
Supplementary files format and content: "Hs_R_NGS_WTA_v1.0.pkc" is the GeoMx probe code file used to map probes to gene names when producing the "raw_counts.tsv" file
Supplementary files format and content: "raw_counts.tsv" is a gene by sample expression matrix of raw counts where each sample is the "library name" and corresponds to ether a PanCK+/- segmented ROI (AOI); NTC control samples and samples that failed QC are not included

source_name: Breast

extract_protocol:
Tissue sections were prepared following the instruction of GeoMx slide preparation, and the slides were processed using the protocol of RNA slide preparation  for  formalin-fixed paraffin-embedded (FFPE) samples as described in the GeoMx DSP Manual Slide Preparation User Manual (NanoString Technologies, GeoMx-DSP-Manual-Slide-Preparation, MAN-10150). Briefly, deparaffinization and rehydration, antigen retrieval (Invitrogen, IHC Antigen Retrieval Solution, Cat#00-4956-58), and proteinase K digestion (1ug/ml, at 37°C) were performed. Human whole transcriptome atlas (WTA) probes (GeoMx WTA, Mouse RNA Probe for NGS, catalog #121401103) were hybridized in Buffer R (GeoMx RNA Slide Prep Kit PCLN catalog #121300313) and incubated in a hybridization humidity chamber (UVP, HB-1000 Hybridizer) overnight at 37°C. To remove nonspecifically bound probes, slides were washed in 50% Formamide/2x SSC (Thermo Fisher, catalog AM9763, USA) at 37°C (2 washes/25 min each), then slides were blocked and incubated with antibodies diluted with 200 μL Buffer W (GeoMx RNA Slide Prep Kit PCLN catalog 121300313). Then, immunostaining was performed for detection of the region of interest (ROI) . Briefly, Morphology Marker Solution was prepared in the following proportions per slide: 22 μL SYTO (GeoMx Nuclear Stain Morphology Kit, catalog 121300303), 5.5 μL Pan-CK, 5.5 μL CD45 (GeoMx Solid Tumor TME Morphology, Human FFPE RNA Compatible, catalog 121300315), and 181.5 μL Buffer W (GeoMx RNA Slide Prep Kit PCLN catalog 121300313) for a total volume of 220 μL/slide. Slides were incubated in this solution at room temperature for 1 hour followed by 2 consecutive SSC washes, then, slides were loaded into the for ROI selection following GeoMxTM Digital Spatial Profiler Instrument User Manual.
After ROI selection, the WTA probe tags were selectively isolated (UV-cleaved) and collected from each of these ROIs, then transferred to individual wells of a collection plate on the DSP. The collections were processed for library preparation following the manual of MANUAL GeoMx® DSP NGS Readout (MAN-10153-06). The quality of library was assessed by the Bioanalyzer DNA 1000 assay (Agilent, catalog 5067-1504). The library was then sequenced on Illumina NextSeq2000. The fastq files were converted to .DCC files using the software of GeoMx-NGS Pipeline; the DCC files were loaded on GeoMx DSP for QC, normalization.  Q3 data was generated and used for all the analysis.

value: Breast

tag: prognosis

value: GPx


title: TNBC009|ROI-008|PanCK-

description:
Library name: DSP-1001660016071-G-A05
TNBC009 - 008 - PanCK-
TNBC009-slide.png
TNBC009 - 008.png
TNBC009 - 008 - Segments.png


title: TNBC009|ROI-003|PanCK-

description:
Library name: DSP-1001660016070-F-H06
TNBC009 - 003 - PanCK-
TNBC009-slide.png
TNBC009 - 003.png
TNBC009 - 003 - Segments.png


title: Cardiac tissue from AB with LL-VNS 20min starting 4w biological replicate 3

city: Wuhan

first: Zhen

last: Guo

address: Donghu Road 169

institute: 武汉大学

description:
Library name: AB_LLVNS20min_4w_3
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with established heart failure treated with LL-VNS (late intervention: started 4w post-AB 20min daily for 4 weeks). Tissue harvested at 8 weeks post-AB surgery.

data_processing:
1. Quality Control: Raw FASTQ files were assessed using FastQC (v0.11.9). Adapter sequences and low-quality reads (Q<20) were removed using Cutadapt (v1.11).
2. Read Alignment: Clean reads were aligned to the mouse reference genome (GRCm38/mm10) using HISAT2 (v2.1.0). Alignment parameters: up to 2 mismatches allowed per read. Alignment rate: >94% for all samples.
3. Quantification: Gene-level read counts were quantified using featureCounts (v1.6.0) from the Subread package. Reference annotation: Ensembl GRCm38.99. Only uniquely mapped reads were counted.
4. Normalization: FPKM (Fragments Per Kilobase Million) normalization was applied for expression level comparison across samples.
5. Differential Expression Analysis: Performed using edgeR (v3.32.1) in R (v4.0.3). Filtering: genes with CPM >1 in at least 3 samples. Statistical thresholds: FDR < 0.05, |log2FoldChange| > 1.
6. Pathway Analysis: Gene Ontology (GO) enrichment analysis using clusterProfiler (v3.18.1). KEGG pathway enrichment using clusterProfiler. Network analysis using Cytoscape (v3.8.2) and Metascape.
Assembly: GRCm38/mm10
Supplementary files format and content: The processed data file normailzed_counts.txt" is a tab-delimited text file containing FPKM-normalized gene expression values for all 21 samples. The first column contains Ensembl Gene IDs, the second column contains Gene Symbols, and subsequent columns contain FPKM values for each sample. The file includes all genes detected with average FPKM > 0.1 across all samples.

source_name: left ventricle

growth_protocol: Male C57BL/6 mice (8 weeks old, 25-27 g) were obtained from the Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences. Animals were housed under specific pathogen-free conditions at Wuhan University's Experimental Animal Center with controlled temperature (22-24°C), humidity (40-70%), and a 12-hour light-dark cycle. Mice had unrestricted access to food and water and were acclimated for a minimum of 7 days before experimental procedures. All procedures were approved by the Animal Care and Use Committee of Renmin Hospital of Wuhan University (Approval No. WDRM20230901C) and conducted according to NIH guidelines.

extract_protocol:
At 8 weeks post-AB surgery, mice were euthanized by CO2 asphyxiation followed by cervical dislocation. Hearts were rapidly excised, and left ventricular tissue was dissected, snap-frozen in liquid nitrogen, and stored at -80°C until RNA extraction. Total RNA was extracted from left ventricular tissue using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA quality was assessed using Agilent 2100 Bioanalyzer with RNA integrity numbers (RIN) greater than 8.0 required for library construction. RNA concentration was measured using NanoDrop spectrophotometry.
RNA library construction was performed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme Biotech) starting from 1 μg total RNA per sample. The protocol included: (1) PolyA RNA isolation using oligo-dT magnetic beads, (2) RNA fragmentation to approximately 200-300 bp, (3) First-strand cDNA synthesis using random hexamer primers, (4) Second-strand cDNA synthesis, (5) End repair and A-tailing, (6) Adapter ligation, (7) Size selection using AMPure XP beads, (8) PCR amplification (12-15 cycles), (9) Final library quality control using Agilent 2100 Bioanalyzer. Libraries were quantified using Qubit fluorometry and qPCR, pooled at equimolar ratios, and validated for appropriate insert size distribution.Paired-end sequencing (2×150 bp) was performed on the Illumina NovaSeq 6000 platform. Libraries were loaded onto S4 flow cells with target sequencing depth of >40 million read pairs per sample to ensure adequate coverage for differential expression analysis. Sequencing was performed by Wuhan IGENEBOOK Biotechnology Co., Ltd.

treatment_protocol: Aortic banding (AB) was performed under isoflurane anesthesia (2-3% in oxygen). Following thoracotomy, the ascending aorta was ligated with 7-0 silk suture using a 27-gauge needle as a spacer, which was subsequently removed to create standardized constriction. Doppler echocardiography verified complete aortic constriction immediately post-surgery. Sham-operated controls underwent identical surgical procedures without aortic ligation. Post-operative analgesia was provided using buprenorphine (0.05 mg/kg subcutaneously) every 12 hours for 48 hours. Low-level vagus nerve stimulation (LL-VNS) was delivered using a biodegradable triboelectric nanogenerator (BTENG) implanted subcutaneously with electrode cuffs positioned on the left cervical vagus nerve. Stimulation parameters: 4 μA peak-to-peak current at 2 Hz frequency. Three intervention timepoints were evaluated: (1) Preventive intervention: LL-VNS initiated 1 week post-AB, administered daily for 7 weeks (either 10 or 20 minutes per session); (2) Early intervention: LL-VNS initiated 2 weeks post-AB, administered 20 minutes daily for 6 weeks; (3) Late intervention: LL-VNS initiated 4 weeks post-AB, administered 20 minutes daily for 4 weeks. All interventions were performed at consistent morning hours to minimize circadian variation. All groups reached the same endpoint at 8 weeks post-AB surgery for tissue collection.

value: left ventricle

tag: genotype

value: wild type

value: aortic banding with LL-VNS (20 min daily 4 uA 2 Hz started 4 weeks post-AB 4 weeks duration)


title: scRNA Abd-S59 (VDJ)

description:
Library name: sample32
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: GroupC, mouse 5, antibody H3K4me3, replicate 2

description: Library name: C-5-H3K4me3-rep2

value: Frontal cortex


title: Cardiac tissue from AB with LL-VNS 10min starting 1w biological replicate 1

description:
Library name: AB_LLVNS10min_1w_1
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload treated with LL-VNS (preventive intervention: started 1w post-AB 10min daily for 7 weeks). Tissue harvested at 8 weeks post-AB surgery.

value: aortic banding with LL-VNS (10 min daily 4 uA 2 Hz started 1 week post-AB 7 weeks duration)


title: TNBC009|ROI-003|PanCK+

description:
Library name: DSP-1001660016070-F-H05
TNBC009 - 003 - PanCK+
TNBC009-slide.png
TNBC009 - 003.png
TNBC009 - 003 - Segments.png


title: scRNA Abd-S58 (VDJ)

description:
Library name: sample31
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China


title: GroupC, mouse 5, antibody H3K27ac, replicate 2

description: Library name: C-5-H3K27ac-rep2

value: Neuron


title: GroupC, mouse 5, antibody H3K27ac, replicate 1

description: Library name: C-5-H3K27ac-rep1


title: Cardiac tissue from AB with LL-VNS 20min starting 4w biological replicate 2

description:
Library name: AB_LLVNS20min_4w_2
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with established heart failure treated with LL-VNS (late intervention: started 4w post-AB 20min daily for 4 weeks). Tissue harvested at 8 weeks post-AB surgery.


title: TNBC009|ROI-002|PanCK-

description:
Library name: DSP-1001660016070-F-H04
TNBC009 - 002 - PanCK-
TNBC009-slide.png
TNBC009 - 002.png
TNBC009 - 002 - Segments.png


title: Cardiac tissue from AB with LL-VNS 20min starting 2w biological replicate 3

description:
Library name: AB_LLVNS20min_2w_3
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload treated with LL-VNS (early intervention: started 2w post-AB 20min daily for 6 weeks). Tissue harvested at 8 weeks post-AB surgery.

value: aortic banding with LL-VNS (20 min daily 4 uA 2 Hz started 2 weeks post-AB 6 weeks duration)


title: TNBC009|ROI-002|PanCK+

description:
Library name: DSP-1001660016070-F-H03
TNBC009 - 002 - PanCK+
TNBC009-slide.png
TNBC009 - 002.png
TNBC009 - 002 - Segments.png


title: Cardiac tissue from AB with LL-VNS 20min starting 2w biological replicate 2

description:
Library name: AB_LLVNS20min_2w_2
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload treated with LL-VNS (early intervention: started 2w post-AB 20min daily for 6 weeks). Tissue harvested at 8 weeks post-AB surgery.


title: GroupC, mouse 4, antibody H3K27ac, replicate 2

description: Library name: C-4-H3K27ac-rep2


title: scRNA Abd-S55 (VDJ)

description:
Library name: sample29
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood

value: PBMCs

value: Immune cells


title: GroupC, mouse 4, antibody H3K4me3, replicate 1

description: Library name: C-4-H3K4me3-rep1


title: GroupC, mouse 4, antibody H3K27ac, replicate 1

description: Library name: C-4-H3K27ac-rep1


title: scRNA Abd-S67 (VDJ)

description:
Library name: sample34
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Male

value: Adult Sepsis


title: scRNA Abd-S53 (VDJ)

description:
Library name: sample27
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Abdominal

value: East Asian


title: TNBC008|ROI-025|PanCK-

description:
Library name: DSP-1001660016070-F-G12
TNBC008 - 025 - PanCK-
TNBC008-slide.png
TNBC008 - 025.png
TNBC008 - 025 - Segments.png

value: Breast


title: scRNA Abd-S51 (VDJ)

description:
Library name: sample26
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Chongqing Emergency Medical Center, Chongqing, China.


title: GroupC, mouse 3, antibody H3K4me3, replicate 2

description: Library name: C-3-H3K4me3-rep2

value: Mock-MIA


title: Cardiac tissue from AB with LL-VNS 20min starting 1w biological replicate 2

description:
Library name: AB_LLVNS20min_1w_2
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload treated with LL-VNS (preventive intervention: started 1w post-AB 20min daily for 7 weeks). Tissue harvested at 8 weeks post-AB surgery.

value: left ventricle

value: wild type

value: aortic banding with LL-VNS (20 min daily 4 uA 2 Hz started 1 week post-AB 7 weeks duration)


title: scRNA Abd-S54 (VDJ)

description:
Library name: sample28
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Abd-S47 (VDJ)

description:
Library name: sample24
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Female


title: scRNA CNS-S189 (VDJ)

description:
Library name: sample47
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

value: Central Nervous System


title: Cardiac tissue from AB with LL-VNS 20min starting 1w biological replicate 1

description:
Library name: AB_LLVNS20min_1w_1
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload treated with LL-VNS (preventive intervention: started 1w post-AB 20min daily for 7 weeks). Tissue harvested at 8 weeks post-AB surgery.


title: TNBC008|ROI-025|PanCK+

description:
Library name: DSP-1001660016070-F-G11
TNBC008 - 025 - PanCK+
TNBC008-slide.png
TNBC008 - 025.png
TNBC008 - 025 - Segments.png

value: GPx


title: Cardiac tissue from AB with device implant biological replicate 3

description:
Library name: AB_Implant_3
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload and BTENG device implanted at 1 week post-AB but not activated. Tissue harvested at 8 weeks post-AB surgery.

value: aortic banding with device implant without electrical stimulation


title: TNBC009|ROI-001|PanCK-

description:
Library name: DSP-1001660016070-F-H02
TNBC009 - 001 - PanCK-
TNBC009-slide.png
TNBC009 - 001.png
TNBC009 - 001 - Segments.png


title: GroupC, mouse 3, antibody H3K27ac, replicate 2

description: Library name: C-3-H3K27ac-rep2

value: Frontal cortex

value: Neuron


title: Cardiac tissue from AB with LL-VNS 20min starting 2w biological replicate 1

description:
Library name: AB_LLVNS20min_2w_1
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload treated with LL-VNS (early intervention: started 2w post-AB 20min daily for 6 weeks). Tissue harvested at 8 weeks post-AB surgery.

value: aortic banding with LL-VNS (20 min daily 4 uA 2 Hz started 2 weeks post-AB 6 weeks duration)


title: Reaction2_HT

city: Gosselies

first: Meggy

last: Suarez-Carmona

address: Rue des Professeurs Jeener et Brachet, 12

country: Belgium

institute: ULB

description: Library name: Sample2_HT

library_source: other

data_processing:
Cell Ranger 9.0.1 (10x Genomics) function count were used to demultiplex the sequencing data, generate gene-barcode matrices, and align the sequences to the GRCh38 genome. Resulted matrices were used to generate a single cell seurat object using Seurat 5.1.0 R package.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz
Supplementary files format and content: Meggy_Reaction1_HT.csv, Meggy_Reaction2_HT.csv
Library strategy: CITE-seq

molecule: protein

source_name: CD45 pos

extract_protocol:
FACS-sorted, life human CD45+ cells isolated from MDA-MB-231 tumor cell suspensions were filtered through a 40 μm cell strainer and the concentration adjusted to 1000 cells/μL before single cell capture using the Chromium controller (10x Genomics).
Cells were loaded on the Chromium Controller (10x Genomics) and Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ v3.1 Reagent Kit (10x Genomics) according to manufacturer’s protocol.

value: CD45 pos


title: TNBC008|ROI-024|PanCK+

description:
Library name: DSP-1001660016070-F-G09
TNBC008 - 024 - PanCK+
TNBC008-slide.png
TNBC008 - 024.png
TNBC008 - 024 - Segments.png


title: Cardiac tissue from AB with device implant biological replicate 2

description:
Library name: AB_Implant_2
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload and BTENG device implanted at 1 week post-AB but not activated. Tissue harvested at 8 weeks post-AB surgery.


title: scRNA Abd-S42 (VDJ)

description:
Library name: sample22
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood

value: PBMCs

value: Immune cells

value: Male

value: Adult Sepsis

value: Abdominal


title: GroupC, mouse 6, antibody H3K27ac, replicate 2

description: Library name: C-6-H3K27ac-rep2

value: Mock-MIA


title: TNBC008|ROI-023|PanCK-

description:
Library name: DSP-1001660016070-F-G08
TNBC008 - 023 - PanCK-
TNBC008-slide.png
TNBC008 - 023.png
TNBC008 - 023 - Segments.png

value: Breast


title: GroupC, mouse 6, antibody H3K27ac, replicate 1

description: Library name: C-6-H3K27ac-rep1


title: GroupC, mouse 3, antibody H3K27ac, replicate 1

description: Library name: C-3-H3K27ac-rep1


title: Cardiac tissue from AB with LL-VNS 20min starting 1w biological replicate 3

description:
Library name: AB_LLVNS20min_1w_3
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload treated with LL-VNS (preventive intervention: started 1w post-AB 20min daily for 7 weeks). Tissue harvested at 8 weeks post-AB surgery.

value: left ventricle

value: wild type

value: aortic banding with LL-VNS (20 min daily 4 uA 2 Hz started 1 week post-AB 7 weeks duration)


title: scRNA Abd-S45 (VDJ)

description:
Library name: sample23
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

value: East Asian


title: GroupC, mouse 2, antibody H3K4me3, replicate 1

description: Library name: C-2-H3K4me3-rep1

value: Frontal cortex


title: GroupC, mouse 4, antibody H3K4me3, replicate 2

description: Library name: C-4-H3K4me3-rep2

value: Neuron


title: TNBC008|ROI-024|PanCK-

description:
Library name: DSP-1001660016070-F-G10
TNBC008 - 024 - PanCK-
TNBC008-slide.png
TNBC008 - 024.png
TNBC008 - 024 - Segments.png

value: GPx


title: TNBC008|ROI-022|PanCK-

description:
Library name: DSP-1001660016070-F-G06
TNBC008 - 022 - PanCK-
TNBC008-slide.png
TNBC008 - 022.png
TNBC008 - 022 - Segments.png


title: Cardiac tissue from AB with device implant biological replicate 1

description:
Library name: AB_Implant_1
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload and BTENG device implanted at 1 week post-AB but not activated. Tissue harvested at 8 weeks post-AB surgery.

value: aortic banding with device implant without electrical stimulation


title: GroupC, mouse 3, antibody H3K4me3, replicate 1

description: Library name: C-3-H3K4me3-rep1


title: Cardiac tissue from aortic banding without therapy biological replicate 2

description:
Library name: AB_2
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload-induced heart failure. Tissue harvested at 8 weeks post-AB surgery.

value: aortic banding without therapy


title: TNBC009|ROI-001|PanCK+

description:
Library name: DSP-1001660016070-F-H01
TNBC009 - 001 - PanCK+
TNBC009-slide.png
TNBC009 - 001.png
TNBC009 - 001 - Segments.png


title: TNBC008|ROI-022|PanCK+

description:
Library name: DSP-1001660016070-F-G05
TNBC008 - 022 - PanCK+
TNBC008-slide.png
TNBC008 - 022.png
TNBC008 - 022 - Segments.png


title: scRNA Abd-S57 (VDJ)

description:
Library name: sample30
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood

value: PBMCs


title: scRNA Abd-S23 (VDJ)

description:
Library name: sample20
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Immune cells

value: Male


title: TNBC008|ROI-023|PanCK+

description:
Library name: DSP-1001660016070-F-G07
TNBC008 - 023 - PanCK+
TNBC008-slide.png
TNBC008 - 023.png
TNBC008 - 023 - Segments.png


title: scRNA Abd-S39 (VDJ)

description:
Library name: sample21
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Adult Sepsis

value: Abdominal


title: Cardiac tissue from aortic banding without therapy biological replicate 1

description:
Library name: AB_1
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload-induced heart failure. Tissue harvested at 8 weeks post-AB surgery.


title: TNBC008|ROI-021|PanCK-

description:
Library name: DSP-1001660016070-F-G04
TNBC008 - 021 - PanCK-
TNBC008-slide.png
TNBC008 - 021.png
TNBC008 - 021 - Segments.png

value: Breast


title: Cardiac tissue from aortic banding without therapy biological replicate 3

description:
Library name: AB_3
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with pressure overload-induced heart failure. Tissue harvested at 8 weeks post-AB surgery.

value: left ventricle


title: Cardiac tissue from AB with LL-VNS 20min starting 4w biological replicate 1

description:
Library name: AB_LLVNS20min_4w_1
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) with established heart failure treated with LL-VNS (late intervention: started 4w post-AB 20min daily for 4 weeks). Tissue harvested at 8 weeks post-AB surgery.

value: wild type

value: aortic banding with LL-VNS (20 min daily 4 uA 2 Hz started 4 weeks post-AB 4 weeks duration)


title: GroupC, mouse 2, antibody H3K4me3, replicate 2

description: Library name: C-2-H3K4me3-rep2

value: Mock-MIA


title: Cardiac tissue from sham-operated mouse biological replicate 3

description:
Library name: Sham_3
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) that underwent sham operation. Tissue harvested at 8 weeks post-surgery.

value: sham operation (thoracotomy without aortic ligation)


title: scRNA Abd-S123 (VDJ)

description:
Library name: sample17
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Female

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

value: East Asian


title: scRNA Abd-S156 (VDJ)

description:
Library name: sample19
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Abd-S120 (VDJ)

description:
Library name: sample16
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC008|ROI-020|PanCK-

description:
Library name: DSP-1001660016070-F-G02
TNBC008 - 020 - PanCK-
TNBC008-slide.png
TNBC008 - 020.png
TNBC008 - 020 - Segments.png

value: GPx


title: GroupC, mouse 1, antibody H3K4me3, replicate 2

description: Library name: C-1-H3K4me3-rep2

value: Frontal cortex

value: Neuron


title: GroupC, mouse 1, antibody H3K27ac, replicate 1

description: Library name: C-1-H3K27ac-rep1


title: GroupC, mouse 1, antibody H3K4me3, replicate 1

description: Library name: C-1-H3K4me3-rep1


title: GroupC, mouse 2, antibody H3K27ac, replicate 2

description: Library name: C-2-H3K27ac-rep2


title: scRNA Abd-S13 (VDJ)

description:
Library name: sample18
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood

value: PBMCs


title: TNBC008|ROI-021|PanCK+

description:
Library name: DSP-1001660016070-F-G03
TNBC008 - 021 - PanCK+
TNBC008-slide.png
TNBC008 - 021.png
TNBC008 - 021 - Segments.png


title: scRNA Abd-S49 (VDJ)

description:
Library name: sample25
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Immune cells


title: TNBC008|ROI-020|PanCK+

description:
Library name: DSP-1001660016070-F-G01
TNBC008 - 020 - PanCK+
TNBC008-slide.png
TNBC008 - 020.png
TNBC008 - 020 - Segments.png


title: scRNA Abd-S12 (VDJ)

description:
Library name: sample15
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Adult Sepsis


title: scRNA Abd-S111 (VDJ)

description:
Library name: sample14
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Male

value: Abdominal


title: WGS: JM1558 Duct M

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

description:
Library name: MCmg70_JM1558_Duct_M
Mammary Gland

data_processing:
Basecalls performed using CASAVA version 1.7
low-passw WGS reads were aligned to the GRCm38 genome assembly using BWA with the default configurations
Control-FREEC was used to generate segment data and to detect copy number alterations
Assembly: GRCm38
Supplementary files format and content: tab-delimited text (tsv) file includes copy number segment data for each tumor sample

source_name: Mammary Gland

growth_protocol: MaPR245W/+ mice were intraductally injected with adenovirus packaged Cre recombinase to induce expression of p53R245W in the mammary ductal epithelium; mammary tumors and DCIS were collected at endpoint for genomic profiling.

extract_protocol:
Laser-capture microdissected DCIS duct DNA was isolated using the Qiagen QiaAmp DNA Micro Kit using carrier RNA according to manufacturer's instructions, with the exception of digesting samples overnight instead of for one hour. Tumor DNA was isolated using the Qiagen DNeasy Blood & Tissue kit according to  manufacturer’s instructions.
Illumina compatible, dual indexed libraries were created from samples prepared using the KAPA Hyper Prep Kit and SureSelectXT Exon. Sample shearing was done using the Whole genome seq 350bp Biorupter. All libraries were constructed in the  University of Texas MD Anderson Cancer Center Advanced Technology Genomics Core (ATGC).

value: Mammary Gland


title: GroupC, mouse 1, antibody H3K27ac, replicate 2

description: Library name: C-1-H3K27ac-rep2


title: scRNA Abd-S11 (VDJ)

description:
Library name: sample13
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC008|ROI-019|PanCK+

description:
Library name: DSP-1001660016070-F-F11
TNBC008 - 019 - PanCK+
TNBC008-slide.png
TNBC008 - 019.png
TNBC008 - 019 - Segments.png

value: Breast


title: Cardiac tissue from sham-operated mouse biological replicate 2

description:
Library name: Sham_2
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) that underwent sham operation. Tissue harvested at 8 weeks post-surgery.

value: left ventricle

value: wild type


title: GroupB, mouse 6, antibody H3K4me3, replicate 1

description: Library name: B-6-H3K4me3-rep1

value: MIA-Mock


title: GroupB, input

description: Library name: B-input


title: GroupC, mouse 2, antibody H3K27ac, replicate 1

description: Library name: C-2-H3K27ac-rep1

value: Mock-MIA


title: WGS: JM1558 Duct J

description:
Library name: MCmg70_JM1558_Duct_J
Mammary Gland


title: scRNA Abd-S103 (VDJ)

description:
Library name: sample12
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Chongqing Emergency Medical Center, Chongqing, China.


title: TNBC008|ROI-019|PanCK-

description:
Library name: DSP-1001660016070-F-F12
TNBC008 - 019 - PanCK-
TNBC008-slide.png
TNBC008 - 019.png
TNBC008 - 019 - Segments.png


title: WGS: JM1558 Duct L

description:
Library name: MCmg70_JM1558_Duct_L
Mammary Gland


title: GroupB, mouse 6, antibody H3K4me3, replicate 2

description: Library name: B-6-H3K4me3-rep2


title: Cardiac tissue from sham-operated mouse biological replicate 1

description:
Library name: Sham_1
Left ventricular tissue from male C57BL/6 mouse (8 weeks at surgery) that underwent sham operation. Tissue harvested at 8 weeks post-surgery.

value: sham operation (thoracotomy without aortic ligation)


title: TNBC008|ROI-018|PanCK-

description:
Library name: DSP-1001660016070-F-F10
TNBC008 - 018 - PanCK-
TNBC008-slide.png
TNBC008 - 018.png
TNBC008 - 018 - Segments.png

value: GPx


title: GroupB, mouse 6, antibody H3K27ac, replicate 1

description: Library name: B-6-H3K27ac-rep1

value: Frontal cortex


title: GroupB, mouse 6, antibody H3K27ac, replicate 2

description: Library name: B-6-H3K27ac-rep2

value: Neuron


title: WGS: JM1582 Duct I

description:
Library name: MCmg70_JM1582_Duct_I
Mammary Gland


title: scRNA Abd-PS27 (VDJ)

description:
Library name: sample9
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood

value: Children's Hospital of Chongqing Medical University, Chongqing, China

value: Pediatric Sepsis

value: East Asian


title: TNBC008|ROI-017|PanCK+

description:
Library name: DSP-1001660016070-F-F07
TNBC008 - 017 - PanCK+
TNBC008-slide.png
TNBC008 - 017.png
TNBC008 - 017 - Segments.png


title: TNBC008|ROI-018|PanCK+

description:
Library name: DSP-1001660016070-F-F09
TNBC008 - 018 - PanCK+
TNBC008-slide.png
TNBC008 - 018.png
TNBC008 - 018 - Segments.png


title: WGS: JM1582 Duct H

description:
Library name: MCmg70_JM1582_Duct_H
Mammary Gland


title: scRNA Abd-S101 (VDJ)

description:
Library name: sample10
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: PBMCs

value: Immune cells

value: Male

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

value: Adult Sepsis


title: TNBC008|ROI-017|PanCK-

description:
Library name: DSP-1001660016070-F-F08
TNBC008 - 017 - PanCK-
TNBC008-slide.png
TNBC008 - 017.png
TNBC008 - 017 - Segments.png

value: Breast


title: TNBC008|ROI-016|PanCK-

description:
Library name: DSP-1001660016070-F-F06
TNBC008 - 016 - PanCK-
TNBC008-slide.png
TNBC008 - 016.png
TNBC008 - 016 - Segments.png


title: WGS: JM1582 Duct G

description:
Library name: MCmg70_JM1582_Duct_G
Mammary Gland

value: Mammary Gland


title: GroupB, mouse 5, antibody H3K4me3, replicate 2

description: Library name: B-5-H3K4me3-rep2

value: MIA-Mock


title: scRNA Abd-PS23 (VDJ)

description:
Library name: sample8
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Abdominal


title: WGS: YZ-21

description:
Library name: MCmg69_Yun21_BT
Mammary Tumor

source_name: Mammary Tumor

value: Mammary Tumor


title: GroupB, mouse 5, antibody H3K27ac, replicate 2

description: Library name: B-5-H3K27ac-rep2


title: TNBC008|ROI-016|PanCK+

description:
Library name: DSP-1001660016070-F-F05
TNBC008 - 016 - PanCK+
TNBC008-slide.png
TNBC008 - 016.png
TNBC008 - 016 - Segments.png

value: GPx


title: GroupB, mouse 5, antibody H3K4me3, replicate 1

description: Library name: B-5-H3K4me3-rep1

value: Frontal cortex


title: scRNA Abd-S102 (VDJ)

description:
Library name: sample11
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Abd-PS20 (VDJ)

description:
Library name: sample7
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: GroupB, mouse 5, antibody H3K27ac, replicate 1

description: Library name: B-5-H3K27ac-rep1

value: Neuron


title: GroupB, mouse 4, antibody H3K4me3, replicate 2

description: Library name: B-4-H3K4me3-rep2


title: TNBC008|ROI-015|PanCK-

description:
Library name: DSP-1001660016070-F-F04
TNBC008 - 015 - PanCK-
TNBC008-slide.png
TNBC008 - 015.png
TNBC008 - 015 - Segments.png


title: scRNA Abd-PS18 (VDJ)

description:
Library name: sample5
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood

value: Female


title: TNBC008|ROI-015|PanCK+

description:
Library name: DSP-1001660016070-F-F03
TNBC008 - 015 - PanCK+
TNBC008-slide.png
TNBC008 - 015.png
TNBC008 - 015 - Segments.png


title: WGS: JM1262

description:
Library name: MCmg69_JM1262_BT
Mammary Tumor

value: MaPR245W/+; Rosa26LSL-TdTomato/+


title: scRNA Abd-PS19 (VDJ)

description:
Library name: sample6
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Children's Hospital of Chongqing Medical University, Chongqing, China

value: Pediatric Sepsis

value: East Asian


title: WGS: YZ-14

description:
Library name: MCmg69_Yun14_BT
Mammary Tumor


title: TNBC008|ROI-014|PanCK-

description:
Library name: DSP-1001660016070-F-F02
TNBC008 - 014 - PanCK-
TNBC008-slide.png
TNBC008 - 014.png
TNBC008 - 014 - Segments.png


title: scRNA Abd-PS13 (VDJ)

description:
Library name: sample4
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: PBMCs

value: Immune cells


title: WGS: YZ-20

description:
Library name: MCmg69_Yun20_BT
Mammary Tumor


title: GroupB, mouse 4, antibody H3K4me3, replicate 1

description: Library name: B-4-H3K4me3-rep1


title: TNBC008|ROI-014|PanCK+

description:
Library name: DSP-1001660016070-F-F01
TNBC008 - 014 - PanCK+
TNBC008-slide.png
TNBC008 - 014.png
TNBC008 - 014 - Segments.png


title: WGS: YZ-5

description:
Library name: MCmg69_Yun_5_BT
Mammary Tumor


title: GroupB, mouse 4, antibody H3K27ac, replicate 1

description: Library name: B-4-H3K27ac-rep1


title: GroupB, mouse 4, antibody H3K27ac, replicate 2

description: Library name: B-4-H3K27ac-rep2


title: WGS: YZ-24

description:
Library name: MCmg69_Yun24_BT
Mammary Tumor


title: GroupB, mouse 3, antibody H3K4me3, replicate 2

description: Library name: B-3-H3K4me3-rep2


title: scRNA Abd-PS05 (VDJ)

description:
Library name: sample2
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Male


title: WGS: JM885

description:
Library name: MCmg69_JM885_BT
Mammary Tumor


title: GroupB, mouse 3, antibody H3K4me3, replicate 1

description: Library name: B-3-H3K4me3-rep1


title: TNBC008|ROI-013|PanCK-

description:
Library name: DSP-1001660016070-F-E12
TNBC008 - 013 - PanCK-
TNBC008-slide.png
TNBC008 - 013.png
TNBC008 - 013 - Segments.png

value: Breast


title: scRNA Abd-PS07 (VDJ)

description:
Library name: sample3
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC008|ROI-013|PanCK+

description:
Library name: DSP-1001660016070-F-E11
TNBC008 - 013 - PanCK+
TNBC008-slide.png
TNBC008 - 013.png
TNBC008 - 013 - Segments.png


title: scRNA Abd-PS04 (VDJ)

description:
Library name: sample1
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: WGS: JM1173 T2

description:
Library name: MCmg69_JM1173_R45_BT
Mammary Tumor


title: WGS: JM1558

description:
Library name: MCmg69_JM1558_BT
Mammary Tumor


title: MOLM13, Combo, 24h, rep3

city: Mainz

first: Daniel

last: Sasca

address: Langenbeckstr 1

department: Department of Hematology and Oncology

country: Germany

institute: University Medical Center Mainz

description: Library name: Sample 15

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000 technology.
Adapters sequences were trimmed from raw reads using Trim Galore v0.6.5.
Trimmed reads were aligned to the human reference genome (GRCh37/hg19) and both total and nascent mRNA were deconvoluted using the tools software SLAM-DUNK v0.6.5.
Assembly: hg19
Supplementary files format and content: Tab-delimited txt file with raw counts for total RNA from all samples
Supplementary files format and content: Tab-delimited txt file with raw counts for nascent RNA from all samples

extract_protocol:
Cells were snap-frozen usingliquid nitrogen, and RNA was isolated using the RNeasy miniprep kit (Qiagen), with minimalexposure to light. RNA was purified using ethanol precipitation, and RNA concentration and quality were assessed using Nanodrop.
Libraries were constructed using the QuantSeq 3' mRNA-Seq V2 Prep Library Kit with UDI from Lexogen

treatment_protocol: Briefly, 5x10^6 cells were treated with the specified dose scheme or DMSO. One hour prior to RNA isolation, 100μM 4-Thiouridine (S4U) was added to label newly transcribed RNA.

value: Acute Myeloid Leukemia

value: Combo

tag: time


title: GroupB, mouse 3, antibody H3K27ac, replicate 2

description: Library name: B-3-H3K27ac-rep2

value: MIA-Mock


title: TNBC008|ROI-012|PanCK-

description:
Library name: DSP-1001660016070-F-E10
TNBC008 - 012 - PanCK-
TNBC008-slide.png
TNBC008 - 012.png
TNBC008 - 012 - Segments.png


title: MOLM13, Combo, 24h, rep2

description: Library name: Sample 14


title: WGS: YZ-4 T1

description:
Library name: MCmg69_Yun4_BT
Mammary Tumor

value: Mammary Tumor


title: GroupB, mouse 3, antibody H3K27ac, replicate 1

description: Library name: B-3-H3K27ac-rep1


title: TNBC008|ROI-012|PanCK+

description:
Library name: DSP-1001660016070-F-E09
TNBC008 - 012 - PanCK+
TNBC008-slide.png
TNBC008 - 012.png
TNBC008 - 012 - Segments.png

value: GPx


title: WGS: RM0058

description:
Library name: MCmg69_RM0058_Breast
Mammary Tumor


title: MOLM13, Combo, 24h, rep1

description: Library name: Sample 13


title: GroupB, mouse 2, antibody H3K4me3, replicate 2

description: Library name: B-2-H3K4me3-rep2

value: Frontal cortex


title: WGS: JM1566 T2

description:
Library name: MCmg69_JM1566_BT_2
Mammary Tumor


title: WGS: JM1566 T1

description:
Library name: MCmg69_JM1566_BT_1
Mammary Tumor


title: MOLM13, BETi, 24h, rep2

description: Library name: Sample 11

value: BETi


title: TNBC008|ROI-010|PanCK-

description:
Library name: DSP-1001660016070-F-E06
TNBC008 - 010 - PanCK-
TNBC008-slide.png
TNBC008 - 010.png
TNBC008 - 010 - Segments.png


title: TNBC008|ROI-011|PanCK+

description:
Library name: DSP-1001660016070-F-E07
TNBC008 - 011 - PanCK+
TNBC008-slide.png
TNBC008 - 011.png
TNBC008 - 011 - Segments.png


title: MOLM13, BETi, 24h, rep3

description: Library name: Sample 12


title: GroupB, mouse 2, antibody H3K4me3, replicate 1

description: Library name: B-2-H3K4me3-rep1

value: Neuron


title: GroupB, mouse 2, antibody H3K27ac, replicate 2

description: Library name: B-2-H3K27ac-rep2


title: MOLM13, BETi, 24h, rep1

description: Library name: Sample 10


title: TNBC008|ROI-010|PanCK+

description:
Library name: DSP-1001660016070-F-E05
TNBC008 - 010 - PanCK+
TNBC008-slide.png
TNBC008 - 010.png
TNBC008 - 010 - Segments.png


title: WGS: RM0087

description:
Library name: MCmg69_RM0087_BT
Mammary Tumor


title: GroupB, mouse 2, antibody H3K27ac, replicate 1

description: Library name: B-2-H3K27ac-rep1


title: TNBC008|ROI-009|PanCK-

description:
Library name: DSP-1001660016070-F-E04
TNBC008 - 009 - PanCK-
TNBC008-slide.png
TNBC008 - 009.png
TNBC008 - 009 - Segments.png


title: WGS: JM1384

description:
Library name: MCmg69_JM1384_BT
Mammary Tumor


title: TNBC008|ROI-009|PanCK+

description:
Library name: DSP-1001660016070-F-E03
TNBC008 - 009 - PanCK+
TNBC008-slide.png
TNBC008 - 009.png
TNBC008 - 009 - Segments.png


title: TNBC008|ROI-011|PanCK-

description:
Library name: DSP-1001660016070-F-E08
TNBC008 - 011 - PanCK-
TNBC008-slide.png
TNBC008 - 011.png
TNBC008 - 011 - Segments.png


title: WGS: RM249

description:
Library name: MCmg69_RM249_BT
Mammary Tumor


title: GroupB, mouse 1, antibody H3K4me3, replicate 1

description: Library name: B-1-H3K4me3-rep1


title: MOLM13, dCBP, 4h, rep1

description: Library name: Sample 7

value: dCBP


title: GroupB, mouse 1, antibody H3K27ac, replicate 2

description: Library name: B-1-H3K27ac-rep2


title: MOLM13, BETi, 4h, rep3

description: Library name: Sample 6


title: CD69-DP-Satb1KO-HIC-Rep2

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

description: Library name: Sample 14

data_processing:
For ScRNA-seq, FASTQ files from 4 samples were processed using the Cell Ranger count pipeline (https://github.com/10XGenomics/cellranger), with the mouse mm10 reference genome, to generate feature-barcode matrices for each sample.
For HiC-seq,  FASTQ files were obtained following quality filtering and adaptor trimming using fastp (v0.20.0). Using HiC-Pro (v2.11.1) aligned the filtered paired-end by minSzie >=50, and reads to the mouse mm10 genome then filtering self-circle ligation, dangling ends, re-ligation, and the other dumped types. We merged the allValidPairs files generated by HiC-Pro based on experimental grouping. On this basis, the hicpro2juicebox.sh script will convert the merged allValidPairs into Juicebox hic format at fragment resolution. Visualization of Hi-C contact matrices was done with Juicerbox(v1.5.1) .
For CUT&Tag, raw reads were first processed using fastp (v0.20.0) to remove adapter sequences and low-quality reads. Subsequently, the filtered reads were aligned to the mouse reference genome (mm10) by Bowtie2 (v2.4.5) with parameters configured as -p 8 –sensitive. PCR duplicate fragments were then eliminated using Picard (v2.22.8), followed by further filtering to exclude three types of reads: unmapped reads, multi-mapped reads, and those aligning to the mitochondrial chromosome (chrM). The Fragments Ratio in Peaks (FRiP) value— a core metric for assessing CUT&Tag data quality— was calculated through a combined workflow of Bedtools (v2.29.2) and awk (version 4.0.2). To enable visualization in the Integrative Genomics Viewer (IGV), deepTools (version 3.5.0) was used to generate bigWig file.
For ATAC-seq, The rawdata reads were first processed using fastp (version 0.20.0) to remove adapter sequences and low-quality reads. Following this quality control step, the filtered reads were aligned to the mouse reference genome (mm10) via Bowtie2 (version 2.4.5) with the parameters set as -p 8 –sensitive. PCR duplicate fragments were then eliminated using Picard (version 2.22.8). Further filtering was applied to exclude unmapped reads, multi-mapped reads, and those aligning to the mitochondrial chromosome (chrM). The Fragments Ratio in Peaks (FRiP) value— a key metric for assessing ChIP-seq data quality— was calculated through a combination of Bedtools (version 2.29.2) and awk (version 4.0.2). To facilitate visualization in the Integrative Genomics Viewer (IGV), deepTools (version 3.5.0) was employed to generate bigWig files normalized by Counts Per Million (CPM). For subsequent peak calling analyses, SAM files were converted to the binary BAM format using SAMtools (version 1.9). Peaks were identified using MACS2 (version 2.2.4) with the specified parameters: –nomodel –shift -100 –extsize 200 -B –keep-dup all –broad –broad-cutoff 0.1.
For ACC-seq, The rawdata reads were first processed using fastp (version 0.20.0) to remove adapter sequences and low-quality reads. Following this quality control step, the filtered reads were aligned to the mouse reference genome (mm10) via Bowtie2 (version 2.4.5) with the parameters set as -p 8 –sensitive. PCR duplicate fragments were then eliminated using Picard (version 2.22.8). Further filtering was applied to exclude unmapped reads, multi-mapped reads, and those aligning to the mitochondrial chromosome (chrM). The Fragments Ratio in Peaks (FRiP) value— a key metric for assessing ChIP-seq data quality— was calculated through a combination of Bedtools (version 2.29.2) and awk (version 4.0.2). To facilitate visualization in the Integrative Genomics Viewer (IGV), deepTools (version 3.5.0) was employed to generate bigWig files normalized by Counts Per Million (CPM). For subsequent peak calling analyses, SAM files were converted to the binary BAM format using SAMtools (version 1.9). Peaks were identified using MACS2 (version 2.2.4) with the specified parameters: –nomodel –shift -100 –extsize 200 -B –keep-dup all –broad –broad-cutoff 0.1.
For SMART-seq2, raw sequencing data were trimmed using TrimGalore (version 0.6.6) with the following parameters. Subsequently, the processed sequencing data were aligned to the mouse reference genome (mm10) using Hisat2 (v2.2.1). The abundance and coverage of each transcript were quantified by read counting, and normalized using the reads per kilobase of exon per million mapped reads (RPKM) method. Genome browser tracks in bigWig format were generated using the bamCoverage function of deepTools (v3.5.0).
Assembly: mm10
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.
Supplementary files format and content: The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format.

source_name: Thymus

growth_protocol: All experiments involving mice were performed using protocols approved by  Southern Medical University Animal Studies Committee. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol:
For ScRNA-seq, the  single-cell suspension was loaded onto a Chromium Single Cell Chip (Chromium Single Cell G Chip Kit, 10x Genomics, PN-1000120) according to the manufacturer’s instructions by Guangzhou Yiyue Biotechnology Co., Ltd with the use of a Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, for co-encapsulation with barcoded Gel Beads at a target capture rate of about 10000 individual cells per sample. We lysed captured cells and released RNA was barcoded through reverse-transcription in individual single-cell gel beads in the emulsion (GEMS). In each droplet, complementary DNA (cDNA) was generated and amplified through reverse-transcription on a T100 PCR Thermal Cycler (Bio Rad) at 53 ℃ for 45 min, followed by 85 ℃ for 5 min and a hold at 4 ℃. Then, cDNA concentration and quality were assessed using Qubit Fluorometer (Thermo Scientific) and bioanalyzer2100 (Agilent), respectively. According to the manufacturer’s introduction, scRNA-seq libraries were constructed and sequenced to a depth of 40000 reads per cell on illumina platform.
For HiC-seq, one million cells were cross-linked at a final concentration of 1% formaldehyde and in room temperature for 10 min and quenched by 200 mM glycine for 5 min at room temperature. After washing with cold 1×PBS, cells were pelleted and kept at −80 ℃ until use. Subsequently, cross-linked cells were lysed to obtain nucleus, and chromatin was digested with DpnII and DdeI overnight at 37 ℃. DpnII and DdeI was inactivated at 65 ℃for 15 min, DNA fragment ends were biotinylated with biotin-dATP using Klenow large fragment (NEB, M0210V) for 90 min at 37 ℃, and the sample was diluted, and proximity ligated for 4 h at room temperature. DNA was treated with Lambda Exonuclease and Exonuclease I to remove unligated biotinylated ends. Cross-linked DNA was reversed by the addition of SDS, proteinase K, and allowed to incubate 4h at 55 ℃. DNA was purified by phenol-chloroform, followed by ethanol precipitation, and resuspended in 50 μl 1X TE. DNA was sheared to 300–500 bp by sonication subsequently, the ligated junctions were pulled down with Dynabeads MyOne Streptavidin C1 magnetic beads (Thermo Fisher Scientific, 65001). End repair, dA tailing, adapter ligation, and PCR amplification were performed on biotinylated DNA fragments bound to beads. After purification, libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads. The recommended sequencing volume gene is 100G every sample.
For CUT&Tag, cells were ﬁxed by 0.5% v/v formalin in PBS for 10 min and quenched using 2.5 M glycine. The ﬁxed cells were permeabilized with TritonX-100 ; Then, cells were immobilized on a polylysine-coated coverslip instead of ConA beads and treated with different primary antibodies(anti-SATB1, Abcam 109122; anti-H3K4me3, Merck millipore 04-745; anti-H3K27ac, Abcam 4729; anti-CTCF, Merck millipore 07-729; anti-RAD21, Abcam 217678) and secondary antibodies (Goat anti-Rabbit IgG). Afterward, cells were incubated with pG-Tn5 transposase(Vazyme, S614-02) for 1 h at 37℃. Sample DNA was extracted using phenol-chloroform-isoamyl alcohol and ampliﬁed by PCR. All CUT&Tag libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode.
For ATAC-seq,  approximately 5 × 10⁴ cell pellets were washed once with cold phosphate-buffered saline (PBS). Cells were then lysed on ice for 3 minutes in 50 μL of ice-cold Lysis Buffer, which contained the following components: 10 mM Tris (pH 7.4), 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1% TWEEN 20, and 0.01% Digitonin. Following lysis, the cell lysate was resuspended in 1 mL of ice-cold RBS-Wash Buffer (10 mM Tris [pH 7.4], 10 mM NaCl, 3 mM MgCl₂, and 0.1% TWEEN 20) and centrifuged at 4°C and 500 ×g for 5 minutes to pellet the cellular material. The tagmentation process was performed in 1× Tagmentation Buffer (comprising 10 mM Tris [pH 7.4], 5 mM MgCl₂, 10% dimethylformamide [DMF], 33% PBS, 0.1% TWEEN 20, and 0.01% Digitonin) with the addition of 100 nM Tn5 Transposase, and the reaction was incubated at 37°C for 30 minutes. Immediately after tagmentation, free DNA fragments were purified according to the standard protocol provided with the QIAquick PCR Purification Kit (QIAGEN, Cat. No. 28106, Germany). This purification step was followed by a final PCR amplification, which included 10–15 cycles using P5 and P7 primers. After post-amplification purification, the prepared libraries were subjected to sequencing on the Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads (PE150).
For ACC-seq,  thymocytes were dissociated into single cells. The cell suspension was then plated onto 0.3% gelatin-coated plates and incubated for 30 minutes at 37 ℃ in RPMI-1640 medium to remove adherent cells. A total of 3×10⁵ cells were divided into three aliquots and centrifuged at 500 rcf. For the native condition, cells were resuspended, washed with ice-cold PBS, permeabilized, and tagmented using Tn5 as in the standard ATAC-seq protocol. For the 1,6-Hex+Fix and Fix-only conditions, cells were centrifuged at 500 rcf for 5 minutes and washed once with PBS. In the 1,6-Hex+Fix group, cells were resuspended in PBS containing 10% (w/v) 1,6-hexanediol (Sigma-Aldrich, 240117) for 60 seconds at room temperature. Then, 16% formaldehyde (Invitrogen, 28906) was quickly added to the PBS to a final concentration of 1%, followed by fixation at room temperature for 10 minutes. The reaction was quenched with 0.6 M glycine (final concentration) for 5 minutes at room temperature. Cells were then washed once with ice-cold PBS and centrifuged at 500 rcf for 5 minutes. Subsequent steps were performed as in the ATAC-seq protocol.
For SMART-seq2, 2000 cells sorted in 2x lysis buffer(0.4% triton x-100, 4U/ul RNase inhibitor) through BD FACS.The lysate samples were vortexed and centrifuged, and placed on a preheated PCR machine for heat-treatment. Then, Smart RT buffer and RT enzyme(SuperScript II reverse transcriptase) were added, and the reverse transcription reaction was carried out according to the program. Add 2x phanta enzyme and IS PCR primers to the cDNA product obtained in the previous step and carry out the amplification reaction according to the procedure. And take out a small amount of product and run electrophoresis gel for quality control. Quantitative purification of cDNA was performed using a DNA purification kit. The purified cDNA samples were added to Tn5 buffer and Tn5 enzyme, and the reaction was interrupted according to the program. After the reaction, mix Smart Amp buffer-2, Smart Amp enzyme-2, S5XX, N7XX for library construction, purify and send for testing. Illumina NovaSeq 6000 sequencing platform was usually used, and PE150 sequencing mode was adopted.
Construction of libraries were described as the above extract protocol

value: Thymus


title: GroupB, mouse 1, antibody H3K27ac, replicate 1

description: Library name: B-1-H3K27ac-rep1


title: MOLM13, BETi, 4h, rep2

description: Library name: Sample 5


title: GroupA, input

description: Library name: A-input

value: Mock-Mock


title: TNBC008|ROI-007|PanCK-

description:
Library name: DSP-1001660016070-F-D12
TNBC008 - 007 - PanCK-
TNBC008-slide.png
TNBC008 - 007.png
TNBC008 - 007 - Segments.png


title: WGS: RM247

description:
Library name: MCmg69_RM247_BT
Mammary Tumor

value: MaPR245W/+; Rosa26LSL-TdTomato/+


title: WGS: JM967

description:
Library name: MCmg69_JM967_BT
Mammary Tumor


title: TNBC008|ROI-007|PanCK+

description:
Library name: DSP-1001660016070-F-D11
TNBC008 - 007 - PanCK+
TNBC008-slide.png
TNBC008 - 007.png
TNBC008 - 007 - Segments.png


title: MOLM13, dCBP, 4h, rep3

description: Library name: Sample 9


title: GroupA, mouse 6, antibody H3K4me3, replicate 2

description: Library name: A-6-H3K4me3-rep2


title: MOLM13, DMSO control, rep3

description: Library name: Sample 3

value: DMSO


title: GroupB, mouse 1, antibody H3K4me3, replicate 2

description: Library name: B-1-H3K4me3-rep2


title: TNBC008|ROI-006|PanCK-

description:
Library name: DSP-1001660016070-F-D10
TNBC008 - 006 - PanCK-
TNBC008-slide.png
TNBC008 - 006.png
TNBC008 - 006 - Segments.png


title: WGS: Pooled Ear-JM1262, JM583, JM1581

description:
Library name: POOLmg_JM583_JM1262_JM1581_Ear
Ear Control

source_name: Ear Control

value: Ear Control


title: GroupA, mouse 6, antibody H3K4me3, replicate 1

description: Library name: A-6-H3K4me3-rep1


title: WGS: JM583

description:
Library name: MCmg69_JM583_BT
Mammary Tumor


title: TNBC008|ROI-006|PanCK+

description:
Library name: DSP-1001660016070-F-D09
TNBC008 - 006 - PanCK+
TNBC008-slide.png
TNBC008 - 006.png
TNBC008 - 006 - Segments.png


title: MOLM13, DMSO control, rep2

description: Library name: Sample 2


title: MOLM13, dCBP, 4h, rep2

description: Library name: Sample 8


title: RMme_Ear

description:
Library name: RMme_Ear
Ear Control

data_processing:
Basecalls performed using CASAVA version 1.7
WES reads were aligned to the GRCm38 genome assembly using BWA with the default configurations
GATK pipeline was used to detect the somatic mutations
Control-FREEC was used to generate segment data and to detect copy number alterations
Assembly: GRCm38
Supplementary files format and content: tab-delimited text (tsv) file includes copy number segment data for each tumor sample

extract_protocol:
Laser-capture microdissected DCIS duct DNA was isolated using the Qiagen QiaAmp DNA Micro Kit using carrier RNA according to manufacturer's instructions, with the exception of digesting samples overnight instead of for one hour. Tumor DNA was isolated using the Qiagen DNeasy Blood & Tissue kit according to  manufacturer’s instructions.
Illumina compatible, dual indexed libraries were created from enzymatically fragmented, RNase treated genomic DNA using the Twist Library Preparation Kit and the Twist Universal Adapter System, according to the manufacturer’s protocol. All libraries were constructed in the University of Texas MD Anderson Cancer Center Advanced Technology Genomics Core (ATGC).


title: TNBC008|ROI-008|PanCK+

description:
Library name: DSP-1001660016070-F-E01
TNBC008 - 008 - PanCK+
TNBC008-slide.png
TNBC008 - 008.png
TNBC008 - 008 - Segments.png


title: WGS: JM1561

description:
Library name: MCmg69_JM1561_BT
Mammary Tumor


title: TNBC009|ROI-010|PanCK+

description:
Library name: DSP-1001660016071-G-A08
TNBC009 - 010 - PanCK+
TNBC009-slide.png
TNBC009 - 010.png
TNBC009 - 010 - Segments.png


title: MOLM13, DMSO control, rep1

description: Library name: Sample 1


title: GroupA, mouse 6, antibody H3K27ac, replicate 2

description: Library name: A-6-H3K27ac-rep2


title: GroupA, mouse 6, antibody H3K27ac, replicate 1

description: Library name: A-6-H3K27ac-rep1


title: JMme1582_Ear_E1

description:
Library name: JMme1582_Ear_E1
Ear Control


title: JMme1558_Ear_E1

description:
Library name: JMme1558_Ear_E1
Ear Control


title: TNBC008|ROI-005|PanCK-

description:
Library name: DSP-1001660016070-F-D08
TNBC008 - 005 - PanCK-
TNBC008-slide.png
TNBC008 - 005.png
TNBC008 - 005 - Segments.png


title: TNBC008|ROI-005|PanCK+

description:
Library name: DSP-1001660016070-F-D07
TNBC008 - 005 - PanCK+
TNBC008-slide.png
TNBC008 - 005.png
TNBC008 - 005 - Segments.png


title: GroupA, mouse 5, antibody H3K4me3, replicate 1

description: Library name: A-5-H3K4me3-rep1


title: GroupA, mouse 5, antibody H3K4me3, replicate 2

description: Library name: A-5-H3K4me3-rep2


title: TNBC008|ROI-004|PanCK-

description:
Library name: DSP-1001660016070-F-D06
TNBC008 - 004 - PanCK-
TNBC008-slide.png
TNBC008 - 004.png
TNBC008 - 004 - Segments.png


title: TNBC008|ROI-004|PanCK+

description:
Library name: DSP-1001660016070-F-D05
TNBC008 - 004 - PanCK+
TNBC008-slide.png
TNBC008 - 004.png
TNBC008 - 004 - Segments.png


title: MOLM13, BETi, 4h, rep1

description: Library name: Sample 4


title: Participant 09, untreated, scRNAseq

city: Cleveland

first: Konstantin

last: Leskov

state: OHIO

address: 2109 Adelbert Rd, Wood W200

department: Molecular Biology and Microbiology

institute: Case Western Reserve University School of Medicine

description:
Library name: RD09Un
BD Rhapsody WTA

data_processing:
Count tables were analyzed using Seurat package for R. Single-cell profiles with a minimum of 500 genes per cell, containing less than 25% mitochondrial mRNA and predicted doublets removed (DoubletFinder package for R) resulting in a total of ~275,000 scRNA-Seq/ABseq profiles for the 8 samples (4 participants, 2 samples per participant). Denoising of RNA and protein counts were performed using DecontX package for R.
Assembly: Fastq files were mapped against the GRCh38 human genome reference and ABseq barcodes.
Supplementary files format and content: We used Seurat for gene count normalization, scaling, identifying variable genes, principal component and cluster analysis and UMAP dimensionality reduction. Cell types were predicted by computational mapping to a reference PBMC dataset. Unfiltered count tables are in csv.gz format. Integrated Seurat objects with all participant and treatment conditions are in .rds format and split my cell type: CD4, CD8, Monocytes and NK cells. Participant codes in count tables and Seurat objects correspond to the codes in publication as follows: Donor 1855 = participant 01; Donor 2881 = participant 03; Donor 5353 = participant 08 and Donor 6088 = participant 09. Count tables and Seurat objects contain combined scRNA-seq and CITE-seq (AB-seq, ADT) data. R code for data processing and analysis is in .R format.

molecule: polyA RNA

source_name: Blood

growth_protocol: Primary PBMC were used

extract_protocol:
PBMCs (~500,000 cells/sample) were stained with the BD Immune Discovery Panel (IDP) of 30 oligonucleotide-conjugated antibodies supplemented with an additional pool of 52 antibodies including the functional markers for T-cell subsets (Supplemental Table, fasta file of ABseq barcodes). ScRNA-Seq/ABseq was performed using the BD Rhapsody Express platform.
Whole transcriptome and ABseq libraries were sequenced at Medgenome Inc., using Illumina NovaSeq 6000, PE150

treatment_protocol: Recombinant IL-2 administration (aldesleukin; subcutaneous injections of 5 million international units, twice daily, for four consecutive days) (Clinical Trials[dot]gov #NCT03308786).

value: Blood

value: PBMC

value: Wild type

value: Untreated

tag: infection

value: HIV


title: Participant 08, IL2-treated, scRNAseq

description:
Library name: RD08IL2
BD Rhapsody WTA


title: TNBC008|ROI-003|PanCK-

description:
Library name: DSP-1001660016070-F-D04
TNBC008 - 003 - PanCK-
TNBC008-slide.png
TNBC008 - 003.png
TNBC008 - 003 - Segments.png

value: Breast


title: GroupA, mouse 5, antibody H3K27ac, replicate 1

description: Library name: A-5-H3K27ac-rep1


title: TNBC008|ROI-003|PanCK+

description:
Library name: DSP-1001660016070-F-D03
TNBC008 - 003 - PanCK+
TNBC008-slide.png
TNBC008 - 003.png
TNBC008 - 003 - Segments.png


title: Participant 03, untreated, scRNAseq

description:
Library name: RD03Un
BD Rhapsody WTA


title: JMme1558_Duct_E1_M

description:
Library name: JMme1558_Duct_E1_M
Mammary Gland

value: Mammary Gland


title: GroupA, mouse 4, antibody H3K4me3, replicate 1

description: Library name: A-4-H3K4me3-rep1


title: Participant 01, untreated, scRNAseq

description:
Library name: RD01Un
BD Rhapsody WTA


title: TNBC008|ROI-008|PanCK-

description:
Library name: DSP-1001660016070-F-E02
TNBC008 - 008 - PanCK-
TNBC008-slide.png
TNBC008 - 008.png
TNBC008 - 008 - Segments.png

value: GPx


title: GroupA, mouse 5, antibody H3K27ac, replicate 2

description: Library name: A-5-H3K27ac-rep2

value: Frontal cortex


title: JMme1558_Duct_E1_J

description:
Library name: JMme1558_Duct_E1_J
Mammary Gland


title: JMme1558_Duct_E1_L

description:
Library name: JMme1558_Duct_E1_L
Mammary Gland


title: JMme1582_Duct_E1_G

description:
Library name: JMme1582_Duct_E1_G
Mammary Gland


title: Participant 01, IL2-treated, scRNAseq

description:
Library name: RD01IL2
BD Rhapsody WTA


title: TNBC008|ROI-001|PanCK-

description:
Library name: DSP-1001660016070-F-C12
TNBC008 - 001 - PanCK-
TNBC008-slide.png
TNBC008 - 001.png
TNBC008 - 001 - Segments.png


title: Participant 08, untreated, scRNAseq

description:
Library name: RD08Un
BD Rhapsody WTA


title: GroupA, mouse 4, antibody H3K27ac, replicate 1

description: Library name: A-4-H3K27ac-rep1


title: GroupA, mouse 4, antibody H3K4me3, replicate 2

description: Library name: A-4-H3K4me3-rep2


title: RMme_Duct8

description:
Library name: RMme_Duct8
Mammary Gland


title: JMme1582_Duct_E1_I

description:
Library name: JMme1582_Duct_E1_I
Mammary Gland


title: Participant 09, IL2-treated, ADT

description:
Library name: AD09IL2
BD Rhapsody ABseq

data_processing:
Count tables were analyzed using Seurat package for R. Single-cell profiles with a minimum of 500 genes per cell, containing less than 25% mitochondrial mRNA and predicted doublets removed (DoubletFinder package for R) resulting in a total of ~275,000 scRNA-Seq/ABseq profiles for the 8 samples (4 participants, 2 samples per participant). Denoising of RNA and protein counts were performed using DecontX package for R.
Assembly: Fastq files were mapped against the GRCh38 human genome reference and ABseq barcodes.
Supplementary files format and content: We used Seurat for gene count normalization, scaling, identifying variable genes, principal component and cluster analysis and UMAP dimensionality reduction. Cell types were predicted by computational mapping to a reference PBMC dataset. Unfiltered count tables are in csv.gz format. Integrated Seurat objects with all participant and treatment conditions are in .rds format and split my cell type: CD4, CD8, Monocytes and NK cells. Participant codes in count tables and Seurat objects correspond to the codes in publication as follows: Donor 1855 = participant 01; Donor 2881 = participant 03; Donor 5353 = participant 08 and Donor 6088 = participant 09. Count tables and Seurat objects contain combined scRNA-seq and CITE-seq (AB-seq, ADT) data. R code for data processing and analysis is in .R format.
Library strategy: CITE-seq


title: WGS: RM0008-T1-Cut1

description:
Library name: MCmg69_RM0008_BT
Mammary Tumor

value: Mammary Tumor


title: TNBC008|ROI-002|PanCK-

description:
Library name: DSP-1001660016070-F-D02
TNBC008 - 002 - PanCK-
TNBC008-slide.png
TNBC008 - 002.png
TNBC008 - 002 - Segments.png


title: Participant 03, IL2-treated, scRNAseq

description:
Library name: RD03IL2
BD Rhapsody WTA


title: JMme1582_Duct_E1_H

description:
Library name: JMme1582_Duct_E1_H
Mammary Gland


title: TNBC007|ROI-013|PanCK+

description:
Library name: DSP-1001660016070-F-C09
TNBC007 - 013 - PanCK+
TNBC007-slide.png
TNBC007 - 013.png
TNBC007 - 013 - Segments.png


title: TNBC008|ROI-002|PanCK+

description:
Library name: DSP-1001660016070-F-D01
TNBC008 - 002 - PanCK+
TNBC008-slide.png
TNBC008 - 002.png
TNBC008 - 002 - Segments.png


title: Participant 08, untreated, ADT

description:
Library name: AD08Un
BD Rhapsody ABseq


title: TNBC008|ROI-001|PanCK+

description:
Library name: DSP-1001660016070-F-C11
TNBC008 - 001 - PanCK+
TNBC008-slide.png
TNBC008 - 001.png
TNBC008 - 001 - Segments.png


title: Participant 08, IL2-treated, ADT

description:
Library name: AD08IL2
BD Rhapsody ABseq


title: GroupA, mouse 3, antibody H3K27ac, replicate 1

description: Library name: A-3-H3K27ac-rep1

value: Neuron


title: RMme_Duct4

description:
Library name: RMme_Duct4
Mammary Gland


title: Participant 09, untreated, ADT

description:
Library name: AD09Un
BD Rhapsody ABseq


title: GroupA, mouse 2, antibody H3K4me3, replicate 2

description: Library name: A-2-H3K4me3-rep2


title: TNBC007|ROI-012|PanCK+

description:
Library name: DSP-1001660016070-F-C07
TNBC007 - 012 - PanCK+
TNBC007-slide.png
TNBC007 - 012.png
TNBC007 - 012 - Segments.png


title: Participant 03, untreated, ADT

description:
Library name: AD03Un
BD Rhapsody ABseq


title: GroupA, mouse 3, antibody H3K27ac, replicate 2

description: Library name: A-3-H3K27ac-rep2


title: GroupA, mouse 3, antibody H3K4me3, replicate 2

description: Library name: A-3-H3K4me3-rep2


title: RMme_Duct6

description:
Library name: RMme_Duct6
Mammary Gland


title: GroupA, mouse 3, antibody H3K4me3, replicate 1

description: Library name: A-3-H3K4me3-rep1


title: TNBC007|ROI-013|PanCK-

description:
Library name: DSP-1001660016070-F-C10
TNBC007 - 013 - PanCK-
TNBC007-slide.png
TNBC007 - 013.png
TNBC007 - 013 - Segments.png


title: Participant 03, IL2-treated, ADT

description:
Library name: AD03IL2
BD Rhapsody ABseq


title: TNBC007|ROI-012|PanCK-

description:
Library name: DSP-1001660016070-F-C08
TNBC007 - 012 - PanCK-
TNBC007-slide.png
TNBC007 - 012.png
TNBC007 - 012 - Segments.png


title: RM0053 Ear

description: Library name: RMme0053_Ear

extract_protocol:
mice with germline p53 alterations were sacrificed and tumors collected at end point
Genomic DNA libraries were constructed following standard Illumina protocols for DNA sequencing in a sequencing and microarray core facility. Indexed DNA libraries were minimally PCR amplified, pooled and sequenced.


title: TNBC007|ROI-011|PanCK-

description:
Library name: DSP-1001660016070-F-C06
TNBC007 - 011 - PanCK-
TNBC007-slide.png
TNBC007 - 011.png
TNBC007 - 011 - Segments.png


title: RMme_Duct5

description:
Library name: RMme_Duct5
Mammary Gland


title: RMme_Duct2

description:
Library name: RMme_Duct2
Mammary Gland


title: TNBC007|ROI-011|PanCK+

description:
Library name: DSP-1001660016070-F-C05
TNBC007 - 011 - PanCK+
TNBC007-slide.png
TNBC007 - 011.png
TNBC007 - 011 - Segments.png


title: GroupA, mouse 2, antibody H3K4me3, replicate 1

description: Library name: A-2-H3K4me3-rep1


title: Participant 01, IL2-treated, ADT

description:
Library name: AD01IL2
BD Rhapsody ABseq


title: Participant 01, untreated, ADT

description:
Library name: AD01Un
BD Rhapsody ABseq


title: GroupA, mouse 2, antibody H3K27ac, replicate 2

description: Library name: A-2-H3K27ac-rep2


title: GroupA, mouse 2, antibody H3K27ac, replicate 1

description: Library name: A-2-H3K27ac-rep1


title: TNBC007|ROI-010|PanCK-

description:
Library name: DSP-1001660016070-F-C04
TNBC007 - 010 - PanCK-
TNBC007-slide.png
TNBC007 - 010.png
TNBC007 - 010 - Segments.png


title: MDA-MB-231 cells, c-di-GMP 5uM_4

city: New Orleans

first: HUA

last: LU

state: LA

address: 1430 Tulane Ave

department: Biochemistry and Molecular Biology

institute: TULANE UNIVERSITY

description:
Library name: Sample 8
G4

data_processing:
RNA-seq
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

growth_protocol: MDA-MB-231 breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: MDA-MB-231 breast cancer cells were treated with 5uM c-di-GMP or Vehicle (1*PBS) for 24 hours

value: Breast cancer cells

value: c-di-GMP, 5uM, 24h


title: JM1581 Ear

description: Library name: JMme1581_Ear


title: TNBC007|ROI-010|PanCK+

description:
Library name: DSP-1001660016070-F-C03
TNBC007 - 010 - PanCK+
TNBC007-slide.png
TNBC007 - 010.png
TNBC007 - 010 - Segments.png


title: Participant 09, IL2-treated, scRNAseq

description:
Library name: RD09IL2
BD Rhapsody WTA


title: GroupA, mouse 1, antibody H3K4me3, replicate 2

description: Library name: A-1-H3K4me3-rep2

value: Mock-Mock


title: MDA-MB-231 cells, c-di-GMP 5uM_3

description:
Library name: Sample 7
G3


title: GroupA, mouse 4, antibody H3K27ac, replicate 2

description: Library name: A-4-H3K27ac-rep2


title: GroupA, mouse 1, antibody H3K4me3, replicate 1

description: Library name: A-1-H3K4me3-rep1


title: JM1419 Ear

description: Library name: JMme1419_Ear

value: MaPR245W/+; Rosa26LSL-TdTomato/+


title: TNBC007|ROI-009|PanCK-

description:
Library name: DSP-1001660016070-F-C02
TNBC007 - 009 - PanCK-
TNBC007-slide.png
TNBC007 - 009.png
TNBC007 - 009 - Segments.png


title: RMme_Duct7

description:
Library name: RMme_Duct7
Mammary Gland


title: GroupA, mouse 1, antibody H3K27ac, replicate 2

description: Library name: A-1-H3K27ac-rep2


title: TNBC007|ROI-008|PanCK-

description:
Library name: DSP-1001660016070-F-B12
TNBC007 - 008 - PanCK-
TNBC007-slide.png
TNBC007 - 008.png
TNBC007 - 008 - Segments.png


title: TNBC007|ROI-009|PanCK+

description:
Library name: DSP-1001660016070-F-C01
TNBC007 - 009 - PanCK+
TNBC007-slide.png
TNBC007 - 009.png
TNBC007 - 009 - Segments.png


title: MDA-MB-231 cells, c-di-GMP 5uM_2

description:
Library name: Sample 6
G2


title: MDA-MB-231 cells, c-di-GMP 5uM_1

description:
Library name: Sample 5
G1


title: RM221 Ear

description: Library name: RMme221_Ear


title: JM825 Ear

description: Library name: JMme825_Ear


title: GroupA, mouse 1, antibody H3K27ac, replicate 1

description: Library name: A-1-H3K27ac-rep1


title: TNBC007|ROI-008|PanCK+

description:
Library name: DSP-1001660016070-F-B11
TNBC007 - 008 - PanCK+
TNBC007-slide.png
TNBC007 - 008.png
TNBC007 - 008 - Segments.png


title: JM731 Ear

description: Library name: JMme731_Ear


title: GroupG, mouse 6, RNA, replicate 2

description: Library name: G-6-RNA-rep2

data_processing:
Read trimming was performed using default settings by Trim Galore!
The trimmed reads were mapped to GRCm38 genome by hisat2.
Mapped bam files were imported into SeqMonk v1.47.1 (Babraham Institute).
Datasets with poor quality (percentage of reads aligned to exons < 40%) were discarded.
FeatureCounts was used to count reads and DEGs were determined by pairwise comparison using DESeq2 (FDR < 0.05).
Assembly: mm10
Supplementary files format and content: featureCounts txt file

extract_protocol:
Adult mice were euthanized by cervical dislocation, and bilateral samples of the frontal cortex (spanning bregma 1.90 to 1.40) were rapidly dissected and flash-frozen at –80°C for later processing. For transcriptomic analysis via RNA-seq, frozen frontal cortex tissue was processed to isolate neuronal nuclei. Fluorescence-activated cell sorting (FACS) was used to enrich for NeuN-positive (NeuN⁺) neuronal populations. Each RNA-seq replicate was prepared from approximately 6,000 sorted neuronal nuclei.
For transcriptomic analysis via RNA-seq, frozen frontal cortex tissue (bregma 1.90–1.40) was processed to isolate neuronal nuclei. Fluorescence-activated cell sorting (FACS) was used to enrich for NeuN-positive (NeuN⁺) populations. A total of 100 μL of sorted neuronal nuclei suspension (~12,000 nuclei) was used for RNA extraction using the RNeasy Mini Kit (Qiagen) and RNase-Free DNase Set, following the manufacturer’s instructions. RNA from ~6,000 nuclei (in 30 μL) was concentrated by ethanol precipitation and resuspended in 4.6 μL of RNase-free water. Libraries were prepared using the SMART-seq v4 Ultra Low Input RNA kit (Clontech) and the Nextera XT DNA Library Preparation kit (Illumina), with ~600 pg of purified cDNA used per replicate. Library quality was assessed using the Agilent High Sensitivity DNA kit on a TapeStation system. Libraries were pooled with ChIP-seq samples (18–22 total per run), quantified with a KAPA Library Quantification Kit, and sequenced on an Illumina HiSeq 4000 (single-end, 50 bp), yielding ~11 million reads per RNA-seq sample.


title: MDA-MB-231 cells, Vehicle Control_4

description:
Library name: Sample 4
C4

value: control


title: MDA-MB-231 cells, Vehicle Control_3

description:
Library name: Sample 3
C3


title: JM1582 Ear

description: Library name: JMme1582_Ear

value: Ear Control


title: TNBC007|ROI-007|PanCK-

description:
Library name: DSP-1001660016070-F-B10
TNBC007 - 007 - PanCK-
TNBC007-slide.png
TNBC007 - 007.png
TNBC007 - 007 - Segments.png


title: TNBC007|ROI-007|PanCK+

description:
Library name: DSP-1001660016070-F-B09
TNBC007 - 007 - PanCK+
TNBC007-slide.png
TNBC007 - 007.png
TNBC007 - 007 - Segments.png


title: GroupG, mouse 6, RNA, replicate 1

description: Library name: G-6-RNA-rep1


title: MDA-MB-231 cells, Vehicle Control_2

description:
Library name: Sample 2
C2


title: GroupG, mouse 5, RNA, replicate 2

description: Library name: G-5-RNA-rep2


title: JM1491 Ear

description: Library name: JMme1491_Ear


title: JM1561 Ear

description: Library name: JMme1561_Ear


title: JM1261 Ear

description: Library name: JMme1261_Ear


title: JM1384 Ear

description: Library name: JMme1384_Ear


title: GroupG, mouse 5, RNA, replicate 1

description: Library name: G-5-RNA-rep1


title: MDA-MB-231 cells, Vehicle Control_1

description:
Library name: Sample 1
C1


title: TNBC007|ROI-006|PanCK+

description:
Library name: DSP-1001660016070-F-B07
TNBC007 - 006 - PanCK+
TNBC007-slide.png
TNBC007 - 006.png
TNBC007 - 006 - Segments.png


title: GroupG, mouse 4, RNA, replicate 2

description: Library name: G-4-RNA-rep2


title: SMG33_T

city: Beijing

first: XINYUAN

last: ZHANG

address: No.22 ,Zhongguancun South  Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

description:
Library name: Sanple4
10x Genomics

data_processing:
Raw reads were filtered using fastp (v0.21.0) to remove adaptors and low-quality sequences. Clean reads were aligned to the human genome (GRCh38, Ensembl v104) using Cell Ranger v7.1.0 to generate feature-barcode matrices. Cells with >200 genes and mitochondrial UMI rates <20% (organoid samples) or <50% (tissue samples) were retained. Mitochondrial genes were removed from the expression matrix. Aggregated matrices were generated by downsampling based on barcoded reads per cell.
Assembly: RCh38 (Ensembl release 104)
Supplementary files format and content: Tab-separated values files (.tsv) and sparse matrix files (.mtx.gz) representing filtered gene-barcode matrices and annotations.

source_name: Salivary gland

extract_protocol:
Organoids were enzymatically dissociated into single-cell suspensions using TrypLE (Thermo Fisher Scientific) at 37°C for 15 minutes. Cell viability was assessed using acridine orange/propidium iodide (AO/PI) staining and analyzed with a Countstar Fluorescence Cell Analyzer. Cells were then resuspended in PBS or loading buffer and prepared for scRNA-seq library construction.
Single-cell RNA-seq libraries were constructed using the Chromium Single Cell 3’ v3 Reagent Kits on the 10X Genomics Chromium Controller (10X Genomics, Pleasanton, CA). Approximately 1000 cells/μL were loaded to generate single-cell Gel Bead-In-Emulsions (GEMs). Reverse transcription was performed in each GEM, and barcoded cDNA was purified and amplified. The resulting cDNA was fragmented, end-repaired, A-tailed, and ligated with sequencing adapters, followed by indexed PCR amplification. Final libraries were quantified using the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific) and sized using the High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). Libraries were sequenced on an Illumina platform with 150 bp paired-end reads.

value: Salivary gland

value: Epithelial cells


title: TNBC007|ROI-006|PanCK-

description:
Library name: DSP-1001660016070-F-B08
TNBC007 - 006 - PanCK-
TNBC007-slide.png
TNBC007 - 006.png
TNBC007 - 006 - Segments.png


title: TNBC007|ROI-005|PanCK-

description:
Library name: DSP-1001660016070-F-B06
TNBC007 - 005 - PanCK-
TNBC007-slide.png
TNBC007 - 005.png
TNBC007 - 005 - Segments.png


title: JM967 Ear

description: Library name: JMme967_Ear


title: TNBC007|ROI-005|PanCK+

description:
Library name: DSP-1001660016070-F-B05
TNBC007 - 005 - PanCK+
TNBC007-slide.png
TNBC007 - 005.png
TNBC007 - 005 - Segments.png


title: GroupG, mouse 4, RNA, replicate 1

description: Library name: G-4-RNA-rep1


title: SMG32_T

description:
Library name: Sanple2
10x Genomics


title: JM1262 Ear

description: Library name: JMme1262_Ear


title: JM964 Ear

description: Library name: JMme964_Ear


title: TNBC007|ROI-004|PanCK-

description:
Library name: DSP-1001660016070-F-B04
TNBC007 - 004 - PanCK-
TNBC007-slide.png
TNBC007 - 004.png
TNBC007 - 004 - Segments.png


title: GroupG, mouse 3, RNA, replicate 1

description: Library name: G-3-RNA-rep1


title: SMG32_O

description:
Library name: Sanple1
10x Genomics

source_name: Salivary gland organoid

value: Salivary gland organoid

value: Organoid-derived epithelial cells


title: TNBC007|ROI-004|PanCK+

description:
Library name: DSP-1001660016070-F-B03
TNBC007 - 004 - PanCK+
TNBC007-slide.png
TNBC007 - 004.png
TNBC007 - 004 - Segments.png


title: LH914982

first: Dingding

last: Wang

state: None Selected

address: 56 Nanlishi Road

institute: Beijing Children Hospital, Capital Medical University

description: Library name: sample45

data_processing:
The paired-end reads were gene-annotated by STAR[2] 2.7.9a and quantified gene expression using Stringtie[3] v2.1.4 with Ensembl gene annotation (GRCh38/hg38 assembly).
Assembly: GRCh38/hg38 assembly
Supplementary files format and content: A combined file include FPKM value for each sample

source_name: liver

extract_protocol:
Total RNA was extracted from liver tissues. RNA libraries were constructed using a poly(A) protocol. cDNA libraries were constructed using a random hexamer primer, M-MuLV Reverse Transcriptase (RNase H Minus), DNA polymerase I, and RNase H.
The Illumina NovaSeq 6000 system was used to sequence the cDNA libraries with paired-end 150 bp reads.

value: liver

value: Ctrl


title: GroupG, mouse 2, RNA, replicate 2

description: Library name: G-2-RNA-rep2


title: JM747 Ear

description: Library name: JMme747_Ear


title: TNBC007|ROI-003|PanCK-

description:
Library name: DSP-1001660016070-F-B02
TNBC007 - 003 - PanCK-
TNBC007-slide.png
TNBC007 - 003.png
TNBC007 - 003 - Segments.png

value: Breast


title: LH910594

description: Library name: sample44


title: GroupG, mouse 2, RNA, replicate 1

description: Library name: G-2-RNA-rep1


title: JM596 Ear

description: Library name: JMme596_Ear


title: GroupG, mouse 1, RNA, replicate 2

description: Library name: G-1-RNA-rep2


title: SMG33_O

description:
Library name: Sanple3
10x Genomics


title: GroupG, mouse 1, RNA, replicate 1

description: Library name: G-1-RNA-rep1


title: LH907175

description: Library name: sample43


title: Yun Ear

description: Library name: JMme_Yun_Ear


title: GroupF, mouse 6, RNA, replicate 2

description: Library name: F-6-RNA-rep2


title: GroupG, mouse 3, RNA, replicate 2

description: Library name: G-3-RNA-rep2


title: LH899917

description: Library name: sample40


title: RM249 Ear

description: Library name: RMme249_Ear


title: JM756 Ear

description: Library name: JMme756_Ear


title: RM247 Ear

description: Library name: RMme247_Ear


title: TNBC007|ROI-002|PanCK-

description:
Library name: DSP-1001660016070-F-A12
TNBC007 - 002 - PanCK-
TNBC007-slide.png
TNBC007 - 002.png
TNBC007 - 002 - Segments.png

value: GPx


title: LH904185

description: Library name: sample41


title: TNBC007|ROI-002|PanCK+

description:
Library name: DSP-1001660016070-F-A11
TNBC007 - 002 - PanCK+
TNBC007-slide.png
TNBC007 - 002.png
TNBC007 - 002 - Segments.png


title: LH891697

description: Library name: sample39


title: GroupF, mouse 5, RNA, replicate 2

description: Library name: F-5-RNA-rep2

value: Frontal cortex


title: TNBC006|ROI-025|PanCK-

description:
Library name: DSP-1001660016070-F-A08
TNBC006 - 025 - PanCK-
TNBC006-slide.png
TNBC006 - 025.png
TNBC006 - 025 - Segments.png

value: PPx


title: JM0087 Ear

description: Library name: RMme0087_Ear


title: JM594 Ear

description: Library name: JMme594_Ear


title: LH906482

description: Library name: sample42


title: JM0058 Ear

description: Library name: RMme0058_Ear


title: LH888022

description: Library name: sample37


title: TNBC007|ROI-003|PanCK+

description:
Library name: DSP-1001660016070-F-B01
TNBC007 - 003 - PanCK+
TNBC007-slide.png
TNBC007 - 003.png
TNBC007 - 003 - Segments.png


title: GroupF, mouse 4, RNA, replicate 2

description: Library name: F-4-RNA-rep2

value: Neuron


title: TNBC006|ROI-024|PanCK-

description:
Library name: DSP-1001660016070-F-A06
TNBC006 - 024 - PanCK-
TNBC006-slide.png
TNBC006 - 024.png
TNBC006 - 024 - Segments.png


title: GroupF, mouse 4, RNA, replicate 1

description: Library name: F-4-RNA-rep1


title: RM0008 Ear

description: Library name: RMme0008_Ear


title: JM1566 Ear

description: Library name: JMme1566_Ear


title: GroupF, mouse 6, RNA, replicate 1

description: Library name: F-6-RNA-rep1


title: LH879491

description: Library name: sample36


title: TNBC007|ROI-001|PanCK-

description:
Library name: DSP-1001660016070-F-A10
TNBC007 - 001 - PanCK-
TNBC007-slide.png
TNBC007 - 001.png
TNBC007 - 001 - Segments.png


title: TNBC006|ROI-024|PanCK+

description:
Library name: DSP-1001660016070-F-A05
TNBC006 - 024 - PanCK+
TNBC006-slide.png
TNBC006 - 024.png
TNBC006 - 024 - Segments.png


title: TNBC006|ROI-023|PanCK-

description:
Library name: DSP-1001660016070-F-A04
TNBC006 - 023 - PanCK-
TNBC006-slide.png
TNBC006 - 023.png
TNBC006 - 023 - Segments.png


title: TNBC007|ROI-001|PanCK+

description:
Library name: DSP-1001660016070-F-A09
TNBC007 - 001 - PanCK+
TNBC007-slide.png
TNBC007 - 001.png
TNBC007 - 001 - Segments.png


title: LH871657

description: Library name: sample35


title: GroupF, mouse 3, RNA, replicate 2

description: Library name: F-3-RNA-rep2


title: LH852362

description: Library name: sample34


title: JM1558 Ear

description: Library name: JMme1558_Ear


title: TNBC006|ROI-023|PanCK+

description:
Library name: DSP-1001660016070-F-A03
TNBC006 - 023 - PanCK+
TNBC006-slide.png
TNBC006 - 023.png
TNBC006 - 023 - Segments.png


title: JM1039 Ear

description: Library name: JMme1039_Ear


title: GroupF, mouse 5, RNA, replicate 1

description: Library name: F-5-RNA-rep1


title: LH840056

description: Library name: sample33


title: LH891344

description: Library name: sample38


title: GroupF, mouse 2, RNA, replicate 2

description: Library name: F-2-RNA-rep2


title: JM1173 Ear

description: Library name: JMme1173_Ear


title: TNBC006|ROI-025|PanCK+

description:
Library name: DSP-1001660016070-F-A07
TNBC006 - 025 - PanCK+
TNBC006-slide.png
TNBC006 - 025.png
TNBC006 - 025 - Segments.png


title: LH839945

description: Library name: sample32


title: TNBC006|ROI-022|PanCK+

description:
Library name: DSP-1001660016069-E-H12
TNBC006 - 022 - PanCK+
TNBC006-slide.png
TNBC006 - 022.png
TNBC006 - 022 - Segments.png


title: GroupF, mouse 2, RNA, replicate 1

description: Library name: F-2-RNA-rep1


title: LH812313

description: Library name: sample31


title: GroupF, mouse 1, RNA, replicate 1

description: Library name: F-1-RNA-rep1


title: LH796000

description: Library name: sample30


title: JM590 Ear

description: Library name: JMme590_Ear


title: JM733 Ear

description: Library name: JMme733_Ear


title: JM583 Ear

description: Library name: JMme583_Ear


title: TNBC006|ROI-021|PanCK+

description:
Library name: DSP-1001660016069-E-H10
TNBC006 - 021 - PanCK+
TNBC006-slide.png
TNBC006 - 021.png
TNBC006 - 021 - Segments.png


title: LH783521

description: Library name: sample29


title: GroupE, mouse 6, RNA, replicate 2

description: Library name: E-6-RNA-rep2


title: TNBC006|ROI-021|PanCK-

description:
Library name: DSP-1001660016069-E-H11
TNBC006 - 021 - PanCK-
TNBC006-slide.png
TNBC006 - 021.png
TNBC006 - 021 - Segments.png


title: JM714 Ear

description: Library name: JMme714_Ear


title: GroupF, mouse 3, RNA, replicate 1

description: Library name: F-3-RNA-rep1


title: TNBC006|ROI-020|PanCK-

description:
Library name: DSP-1001660016069-E-H09
TNBC006 - 020 - PanCK-
TNBC006-slide.png
TNBC006 - 020.png
TNBC006 - 020 - Segments.png


title: GroupE, mouse 6, RNA, replicate 1

description: Library name: E-6-RNA-rep1


title: LH768186

description: Library name: sample28


title: YZ-2 Ear

description: Library name: JMme_Yun2_Ear


title: LH760308

description: Library name: sample27


title: TNBC006|ROI-022|PanCK-

description:
Library name: DSP-1001660016070-F-A02
TNBC006 - 022 - PanCK-
TNBC006-slide.png
TNBC006 - 022.png
TNBC006 - 022 - Segments.png


title: TNBC006|ROI-020|PanCK+

description:
Library name: DSP-1001660016069-E-H08
TNBC006 - 020 - PanCK+
TNBC006-slide.png
TNBC006 - 020.png
TNBC006 - 020 - Segments.png


title: GroupE, mouse 5, RNA, replicate 2

description: Library name: E-5-RNA-rep2


title: TNBC006|ROI-019|PanCK-

description:
Library name: DSP-1001660016069-E-H07
TNBC006 - 019 - PanCK-
TNBC006-slide.png
TNBC006 - 019.png
TNBC006 - 019 - Segments.png


title: JM1275 Ear

description: Library name: JMme1275_Ear


title: GroupE, mouse 5, RNA, replicate 1

description: Library name: E-5-RNA-rep1


title: YZ-1 Ear

description: Library name: JMme_Yun1_Ear


title: TNBC006|ROI-019|PanCK+

description:
Library name: DSP-1001660016069-E-H06
TNBC006 - 019 - PanCK+
TNBC006-slide.png
TNBC006 - 019.png
TNBC006 - 019 - Segments.png


title: LB938991

description: Library name: sample25

value: BA


title: LH751350

description: Library name: sample26


title: GroupE, mouse 4, RNA, replicate 2

description: Library name: E-4-RNA-rep2


title: JM884 Ear

description: Library name: JMme884_Ear


title: GroupF, mouse 1, RNA, replicate 2

description: Library name: F-1-RNA-rep2


title: TNBC006|ROI-018|PanCK-

description:
Library name: DSP-1001660016069-E-H05
TNBC006 - 018 - PanCK-
TNBC006-slide.png
TNBC006 - 018.png
TNBC006 - 018 - Segments.png


title: JM731

description: Library name: JMme731_Breast_Tumor

value: Mammary Tumor


title: GroupE, mouse 4, RNA, replicate 1

description: Library name: E-4-RNA-rep1


title: LB937117

description: Library name: sample24


title: LB935905

description: Library name: sample23


title: TNBC006|ROI-018|PanCK+

description:
Library name: DSP-1001660016069-E-H04
TNBC006 - 018 - PanCK+
TNBC006-slide.png
TNBC006 - 018.png
TNBC006 - 018 - Segments.png


title: RM221

description: Library name: RMme221_BT


title: GroupE, mouse 3, RNA, replicate 2

description: Library name: E-3-RNA-rep2


title: TNBC006|ROI-017|PanCK-

description:
Library name: DSP-1001660016069-E-H03
TNBC006 - 017 - PanCK-
TNBC006-slide.png
TNBC006 - 017.png
TNBC006 - 017 - Segments.png


title: GroupE, mouse 3, RNA, replicate 1

description: Library name: E-3-RNA-rep1


title: LB935827

description: Library name: sample22


title: RM0053

description: Library name: RMme0053_Breast_Tumor


title: TNBC006|ROI-017|PanCK+

description:
Library name: DSP-1001660016069-E-H02
TNBC006 - 017 - PanCK+
TNBC006-slide.png
TNBC006 - 017.png
TNBC006 - 017 - Segments.png


title: LB934150

description: Library name: sample21


title: LB933758

description: Library name: sample20


title: GroupE, mouse 2, RNA, replicate 2

description: Library name: E-2-RNA-rep2


title: TNBC006|ROI-016|PanCK-

description:
Library name: DSP-1001660016069-E-H01
TNBC006 - 016 - PanCK-
TNBC006-slide.png
TNBC006 - 016.png
TNBC006 - 016 - Segments.png


title: GroupE, mouse 2, RNA, replicate 1

description: Library name: E-2-RNA-rep1


title: LB931342

description: Library name: sample19


title: JM1582-T2

description: Library name: JMme1582_Breast_Tumor_2


title: GroupE, mouse 1, RNA, replicate 2

description: Library name: E-1-RNA-rep2


title: TNBC006|ROI-015|PanCK-

description:
Library name: DSP-1001660016069-E-G11
TNBC006 - 015 - PanCK-
TNBC006-slide.png
TNBC006 - 015.png
TNBC006 - 015 - Segments.png


title: JM1582-T1

description: Library name: JMme1582_Breast_Tumor_1


title: LB927089

description: Library name: sample18


title: GroupE, mouse 1, RNA, replicate 1

description: Library name: E-1-RNA-rep1


title: JM1581

description: Library name: JMme1581_BT


title: TNBC006|ROI-015|PanCK+

description:
Library name: DSP-1001660016069-E-G10
TNBC006 - 015 - PanCK+
TNBC006-slide.png
TNBC006 - 015.png
TNBC006 - 015 - Segments.png


title: LB926266

description: Library name: sample17


title: GroupD, mouse 6, RNA, replicate 2

description: Library name: D-6-RNA-rep2

value: MIA-MIA


title: LB924547

description: Library name: sample16


title: JM1261

description: Library name: JMme1261_BT


title: TNBC006|ROI-014|PanCK-

description:
Library name: DSP-1001660016069-E-G09
TNBC006 - 014 - PanCK-
TNBC006-slide.png
TNBC006 - 014.png
TNBC006 - 014 - Segments.png


title: JM590 -T2

description: Library name: JMme590_R45_BT

value: MaPR245W/+; Rosa26LSL-TdTomato/+


title: GroupD, mouse 6, RNA, replicate 1

description: Library name: D-6-RNA-rep1


title: LB924057

description: Library name: sample15


title: TNBC006|ROI-014|PanCK+

description:
Library name: DSP-1001660016069-E-G08
TNBC006 - 014 - PanCK+
TNBC006-slide.png
TNBC006 - 014.png
TNBC006 - 014 - Segments.png


title: GroupD, mouse 5, RNA, replicate 2

description: Library name: D-5-RNA-rep2


title: JM825

description: Library name: JMme825_Breast_Tumor


title: LB923613

description: Library name: sample14


title: RM0057

description: Library name: RMme0057_BT


title: JM1419

description: Library name: JMme1419_BT


title: GroupD, mouse 5, RNA, replicate 1

description: Library name: D-5-RNA-rep1


title: TNBC006|ROI-013|PanCK-

description:
Library name: DSP-1001660016069-E-G07
TNBC006 - 013 - PanCK-
TNBC006-slide.png
TNBC006 - 013.png
TNBC006 - 013 - Segments.png


title: TNBC006|ROI-016|PanCK+

description:
Library name: DSP-1001660016069-E-G12
TNBC006 - 016 - PanCK+
TNBC006-slide.png
TNBC006 - 016.png
TNBC006 - 016 - Segments.png


title: GroupD, mouse 4, RNA, replicate 2

description: Library name: D-4-RNA-rep2


title: JM967

description: Library name: JMme967_BT