title: TNBC012|ROI-027|PanCK+

description:
Library name: DSP-1001660016269-H-E06
TNBC012 - 027 - PanCK+
TNBC012-slide.png
TNBC012 - 027.png
TNBC012 - 027 - Segments.png


title: TNBC012|ROI-025|PanCK-

status: Public on Dec 19 2025

type: SRA

city: Pasadena

first: David

middle: Eugene

last: Frankhouser

state: CA

address: 1500 E Duarte Rd

department: Population Sciences

country: USA

institute: City of Hope

description:
Library name: DSP-1001660016269-H-E03
TNBC012 - 025 - PanCK-
TNBC012-slide.png
TNBC012 - 025.png
TNBC012 - 025 - 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

molecule: total RNA

organism: Homo sapiens

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.

tag: tissue

value: Breast

tag: prognosis

value: PPx


title: TNBC012|ROI-025|PanCK+

description:
Library name: DSP-1001660016269-H-E02
TNBC012 - 025 - PanCK+
TNBC012-slide.png
TNBC012 - 025.png
TNBC012 - 025 - Segments.png


title: C26_female_20day3

city: Fayetteville

first: Nicholas

middle: P

last: Greene

state: Arkansas

address: 155 Stadium Dr. HPER Building 321

institute: University of Arkansas

description: Library name: zr5492_39_S41

library_source: genomic

data_processing:
Base calling with Illumina Software
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore
The effect of trimming and overall quality distribution was determined using FastQC
Alignment was performed using Bismark
Read totals were called using Bismark Methylation Extractor
Assembly: mm39
Supplementary files format and content: Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome

molecule: genomic DNA

organism: Mus musculus

source_name: Tibialis anterior

extract_protocol:
DNA was isolated from the TA tissue using the Quick-DNA™ Miniprep Plus kit (Zymo Research, D4068) as specified in the protocol.
The DNA RRBS was rered to Zymo Research Corporation (RRBS Basic Srvise Package, 15-20 million read pairs per sample)

value: Tibialis anterior

tag: timepoint

tag: Sex

value: female

tag: treatment

tag: batch


title: TNBC012|ROI-024|PanCK-

description:
Library name: DSP-1001660016269-H-E01
TNBC012 - 024 - PanCK-
TNBC012-slide.png
TNBC012 - 024.png
TNBC012 - 024 - Segments.png


title: TNBC012|ROI-024|PanCK+

description:
Library name: DSP-1001660016269-H-D12
TNBC012 - 024 - PanCK+
TNBC012-slide.png
TNBC012 - 024.png
TNBC012 - 024 - Segments.png


title: CD69+DP-Satb1KO-Smart-Rep3

city: Guangzhou

first: Hao

last: bingtao

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

country: China

institute: Southern Medical University

description: Library name: Sample 123

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.

molecule: polyA RNA

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

tag: cell type

tag: genotype


title: C26_female_20day1

description: Library name: zr5492_37_S39


title: C26_female_20day2

description: Library name: zr5492_38_S40


title: C26_female_pbs3

description: Library name: zr5492_49_S51

value: control

value: pbs


title: CD69+DP-Satb1KO-Smart-Rep4

description: Library name: Sample 124


title: TNBC013|ROI-002|PanCK+

description:
Library name: DSP-1001660016269-H-F04
TNBC013 - 002 - PanCK+
TNBC013-slide.png
TNBC013 - 002.png
TNBC013 - 002 - Segments.png


title: CD69+DP-Satb1KO-Smart-Rep2

description: Library name: Sample 122


title: TNBC012|ROI-023|PanCK+

description:
Library name: DSP-1001660016269-H-D10
TNBC012 - 023 - PanCK+
TNBC012-slide.png
TNBC012 - 023.png
TNBC012 - 023 - Segments.png


title: TNBC012|ROI-022|PanCK-

description:
Library name: DSP-1001660016269-H-D09
TNBC012 - 022 - PanCK-
TNBC012-slide.png
TNBC012 - 022.png
TNBC012 - 022 - Segments.png


title: TNBC012|ROI-026|PanCK-

description:
Library name: DSP-1001660016269-H-E05
TNBC012 - 026 - PanCK-
TNBC012-slide.png
TNBC012 - 026.png
TNBC012 - 026 - Segments.png


title: TNBC012|ROI-022|PanCK+

description:
Library name: DSP-1001660016269-H-D08
TNBC012 - 022 - PanCK+
TNBC012-slide.png
TNBC012 - 022.png
TNBC012 - 022 - Segments.png


title: C26_female_10day4

description: Library name: zr5492_36_S38


title: CD69+DP-Satb1KO-Smart-Rep1

description: Library name: Sample 121


title: C26_female_10day3

description: Library name: zr5492_35_S37


title: TNBC012|ROI-021|PanCK-

description:
Library name: DSP-1001660016269-H-D07
TNBC012 - 021 - PanCK-
TNBC012-slide.png
TNBC012 - 021.png
TNBC012 - 021 - Segments.png


title: C26_female_10day2

description: Library name: zr5492_34_S36


title: TNBC012|ROI-020|PanCK+

description:
Library name: DSP-1001660016269-H-D04
TNBC012 - 020 - PanCK+
TNBC012-slide.png
TNBC012 - 020.png
TNBC012 - 020 - Segments.png


title: TNBC012|ROI-021|PanCK+

description:
Library name: DSP-1001660016269-H-D06
TNBC012 - 021 - PanCK+
TNBC012-slide.png
TNBC012 - 021.png
TNBC012 - 021 - Segments.png


title: CD69+DP-Satb1WT-Smart-Rep3

description: Library name: Sample 119


title: CD69+DP-Satb1WT-Smart-Rep2

description: Library name: Sample 118


title: CD69+DP-Satb1WT-Smart-Rep4

description: Library name: Sample 120


title: C26_male_pbs8

description: Library name: zr5492_32_S34

value: male


title: TNBC012|ROI-023|PanCK-

description:
Library name: DSP-1001660016269-H-D11
TNBC012 - 023 - PanCK-
TNBC012-slide.png
TNBC012 - 023.png
TNBC012 - 023 - Segments.png


title: TNBC012|ROI-018|PanCK-

description:
Library name: DSP-1001660016269-H-D01
TNBC012 - 018 - PanCK-
TNBC012-slide.png
TNBC012 - 018.png
TNBC012 - 018 - Segments.png


title: TNBC012|ROI-019|PanCK+

description:
Library name: DSP-1001660016269-H-D02
TNBC012 - 019 - PanCK+
TNBC012-slide.png
TNBC012 - 019.png
TNBC012 - 019 - Segments.png


title: CD69+DP-Satb1WT-Smart-Rep1

description: Library name: Sample 117


title: TNBC012|ROI-018|PanCK+

description:
Library name: DSP-1001660016269-H-C12
TNBC012 - 018 - PanCK+
TNBC012-slide.png
TNBC012 - 018.png
TNBC012 - 018 - Segments.png


title: TNBC012|ROI-020|PanCK-

description:
Library name: DSP-1001660016269-H-D05
TNBC012 - 020 - PanCK-
TNBC012-slide.png
TNBC012 - 020.png
TNBC012 - 020 - Segments.png


title: C26_female_10day1

description: Library name: zr5492_33_S35


title: C26_male_pbs7

description: Library name: zr5492_31_S33


title: TNBC012|ROI-019|PanCK-

description:
Library name: DSP-1001660016269-H-D03
TNBC012 - 019 - PanCK-
TNBC012-slide.png
TNBC012 - 019.png
TNBC012 - 019 - Segments.png


title: TNBC012|ROI-017|PanCK-

description:
Library name: DSP-1001660016269-H-C11
TNBC012 - 017 - PanCK-
TNBC012-slide.png
TNBC012 - 017.png
TNBC012 - 017 - Segments.png


title: TNBC012|ROI-016|PanCK+

description:
Library name: DSP-1001660016269-H-C08
TNBC012 - 016 - PanCK+
TNBC012-slide.png
TNBC012 - 016.png
TNBC012 - 016 - Segments.png


title: TNBC012|ROI-016|PanCK-

description:
Library name: DSP-1001660016269-H-C09
TNBC012 - 016 - PanCK-
TNBC012-slide.png
TNBC012 - 016.png
TNBC012 - 016 - Segments.png


title: C26_male_pbs6

description: Library name: zr5492_30


title: CD69-DP-Satb1KO-Smart-Rep4

description: Library name: Sample 116


title: TNBC012|ROI-017|PanCK+

description:
Library name: DSP-1001660016269-H-C10
TNBC012 - 017 - PanCK+
TNBC012-slide.png
TNBC012 - 017.png
TNBC012 - 017 - Segments.png


title: CD69-DP-Satb1KO-Smart-Rep3

description: Library name: Sample 115


title: TNBC012|ROI-015|PanCK+

description:
Library name: DSP-1001660016269-H-C06
TNBC012 - 015 - PanCK+
TNBC012-slide.png
TNBC012 - 015.png
TNBC012 - 015 - Segments.png


title: TNBC012|ROI-015|PanCK-

description:
Library name: DSP-1001660016269-H-C07
TNBC012 - 015 - PanCK-
TNBC012-slide.png
TNBC012 - 015.png
TNBC012 - 015 - Segments.png


title: TNBC012|ROI-014|PanCK-

description:
Library name: DSP-1001660016269-H-C05
TNBC012 - 014 - PanCK-
TNBC012-slide.png
TNBC012 - 014.png
TNBC012 - 014 - Segments.png


title: C26_male_pbs5

description: Library name: zr5492_29


title: C26_male_pbs4

description: Library name: zr5492_28


title: CD69-DP-Satb1KO-Smart-Rep2

description: Library name: Sample 114


title: C26_male_25day8

description: Library name: zr5492_27_S29


title: TNBC012|ROI-014|PanCK+

description:
Library name: DSP-1001660016269-H-C04
TNBC012 - 014 - PanCK+
TNBC012-slide.png
TNBC012 - 014.png
TNBC012 - 014 - Segments.png


title: TNBC012|ROI-013|PanCK-

description:
Library name: DSP-1001660016269-H-C03
TNBC012 - 013 - PanCK-
TNBC012-slide.png
TNBC012 - 013.png
TNBC012 - 013 - Segments.png


title: CD69-DP-Satb1WT-Smart-Rep4

description: Library name: Sample 112


title: TNBC012|ROI-013|PanCK+

description:
Library name: DSP-1001660016269-H-C02
TNBC012 - 013 - PanCK+
TNBC012-slide.png
TNBC012 - 013.png
TNBC012 - 013 - Segments.png


title: C26_male_25day7

description: Library name: zr5492_26_S28


title: CD69-DP-Satb1WT-Smart-Rep3

description: Library name: Sample 111


title: TNBC012|ROI-012|PanCK-

description:
Library name: DSP-1001660016269-H-C01
TNBC012 - 012 - PanCK-
TNBC012-slide.png
TNBC012 - 012.png
TNBC012 - 012 - Segments.png


title: TNBC012|ROI-012|PanCK+

description:
Library name: DSP-1001660016269-H-B12
TNBC012 - 012 - PanCK+
TNBC012-slide.png
TNBC012 - 012.png
TNBC012 - 012 - Segments.png


title: C26_male_25day6

description: Library name: zr5492_25_S27


title: CD69-DP-Satb1WT-Smart-Rep2

description: Library name: Sample 110


title: TNBC012|ROI-011|PanCK-

description:
Library name: DSP-1001660016269-H-B11
TNBC012 - 011 - PanCK-
TNBC012-slide.png
TNBC012 - 011.png
TNBC012 - 011 - Segments.png


title: TNBC012|ROI-011|PanCK+

description:
Library name: DSP-1001660016269-H-B10
TNBC012 - 011 - PanCK+
TNBC012-slide.png
TNBC012 - 011.png
TNBC012 - 011 - Segments.png


title: C26_male_25day5

description: Library name: zr5492_24_S26


title: CD69-DP-Satb1WT-Smart-Rep1

description: Library name: Sample 109


title: TNBC012|ROI-010|PanCK+

description:
Library name: DSP-1001660016269-H-B08
TNBC012 - 010 - PanCK+
TNBC012-slide.png
TNBC012 - 010.png
TNBC012 - 010 - Segments.png


title: TNBC012|ROI-010|PanCK-

description:
Library name: DSP-1001660016269-H-B09
TNBC012 - 010 - PanCK-
TNBC012-slide.png
TNBC012 - 010.png
TNBC012 - 010 - Segments.png


title: TNBC012|ROI-009|PanCK-

description:
Library name: DSP-1001660016269-H-B07
TNBC012 - 009 - PanCK-
TNBC012-slide.png
TNBC012 - 009.png
TNBC012 - 009 - Segments.png


title: Thymus-Satb1KO-HexFix-ACC-Rep2

description: Library name: Sample 108

value: Thymocyte


title: C26_male_20day8

description: Library name: zr5492_23


title: CD69-DP-Satb1KO-Smart-Rep1

description: Library name: Sample 113


title: TNBC012|ROI-009|PanCK+

description:
Library name: DSP-1001660016269-H-B06
TNBC012 - 009 - PanCK+
TNBC012-slide.png
TNBC012 - 009.png
TNBC012 - 009 - Segments.png


title: C26_male_20day7

description: Library name: zr5492_22


title: TNBC012|ROI-008|PanCK-

description:
Library name: DSP-1001660016269-H-B05
TNBC012 - 008 - PanCK-
TNBC012-slide.png
TNBC012 - 008.png
TNBC012 - 008 - Segments.png


title: Thymus-Satb1KO-HexFix-ACC-Rep1

description: Library name: Sample 107


title: TNBC012|ROI-008|PanCK+

description:
Library name: DSP-1001660016269-H-B04
TNBC012 - 008 - PanCK+
TNBC012-slide.png
TNBC012 - 008.png
TNBC012 - 008 - Segments.png


title: C26_male_20day6

description: Library name: zr5492_21_S23


title: C26_male_25day4

description: Library name: zr5492_20_S22


title: Thymus-Satb1KO-Fix-ACC-Rep2

description: Library name: Sample 106


title: TNBC012|ROI-007|PanCK+

description:
Library name: DSP-1001660016269-H-B02
TNBC012 - 007 - PanCK+
TNBC012-slide.png
TNBC012 - 007.png
TNBC012 - 007 - Segments.png


title: Thymus-Satb1KO-Fix-ACC-Rep1

description: Library name: Sample 105


title: TNBC012|ROI-006|PanCK+

description:
Library name: DSP-1001660016269-H-A12
TNBC012 - 006 - PanCK+
TNBC012-slide.png
TNBC012 - 006.png
TNBC012 - 006 - Segments.png


title: TNBC012|ROI-005|PanCK-

description:
Library name: DSP-1001660016269-H-A11
TNBC012 - 005 - PanCK-
TNBC012-slide.png
TNBC012 - 005.png
TNBC012 - 005 - Segments.png


title: C26_male_25day3

description: Library name: zr5492_18


title: TNBC012|ROI-005|PanCK+

description:
Library name: DSP-1001660016269-H-A10
TNBC012 - 005 - PanCK+
TNBC012-slide.png
TNBC012 - 005.png
TNBC012 - 005 - Segments.png


title: Thymus-Satb1KO-native-ACC-Rep2

description: Library name: Sample 104


title: TNBC012|ROI-004|PanCK-

description:
Library name: DSP-1001660016269-H-A09
TNBC012 - 004 - PanCK-
TNBC012-slide.png
TNBC012 - 004.png
TNBC012 - 004 - Segments.png


title: Thymus-Satb1WT-HexFix-ACC-Rep2

description: Library name: Sample 102


title: TNBC012|ROI-004|PanCK+

description:
Library name: DSP-1001660016269-H-A08
TNBC012 - 004 - PanCK+
TNBC012-slide.png
TNBC012 - 004.png
TNBC012 - 004 - Segments.png


title: C26_male_25day2

description: Library name: zr5492_17_S19


title: GroupG, input

city: Blacksburg

first: Chang

last: Lu

state: VA

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

department: Chemical Engineering

institute: Virginia Tech

description: Library name: G-input

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

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.

value: Frontal cortex

value: Neuron

tag: chip antibody


title: Thymus-Satb1WT-HexFix-ACC-Rep1

description: Library name: Sample 101


title: TNBC012|ROI-003|PanCK-

description:
Library name: DSP-1001660016269-H-A07
TNBC012 - 003 - PanCK-
TNBC012-slide.png
TNBC012 - 003.png
TNBC012 - 003 - Segments.png


title: TNBC012|ROI-007|PanCK-

description:
Library name: DSP-1001660016269-H-B03
TNBC012 - 007 - PanCK-
TNBC012-slide.png
TNBC012 - 007.png
TNBC012 - 007 - Segments.png


title: TNBC012|ROI-003|PanCK+

description:
Library name: DSP-1001660016269-H-A06
TNBC012 - 003 - PanCK+
TNBC012-slide.png
TNBC012 - 003.png
TNBC012 - 003 - Segments.png


title: Thymus-Satb1WT-Fix-ACC-Rep2

description: Library name: Sample 100


title: C26_male_20day4

description: Library name: zr5492_16_S18


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

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


title: C26_male_10day7

description: Library name: zr5492_14_S16


title: C26_male_10day8

description: Library name: zr5492_15_S17


title: TNBC012|ROI-002|PanCK-

description:
Library name: DSP-1001660016269-H-A05
TNBC012 - 002 - PanCK-
TNBC012-slide.png
TNBC012 - 002.png
TNBC012 - 002 - Segments.png


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

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


title: TNBC012|ROI-006|PanCK-

description:
Library name: DSP-1001660016269-H-B01
TNBC012 - 006 - PanCK-
TNBC012-slide.png
TNBC012 - 006.png
TNBC012 - 006 - Segments.png


title: Thymus-Satb1WT-Fix-ACC-Rep1

description: Library name: Sample 99


title: Thymus-Satb1WT-native-ACC-Rep2

description: Library name: Sample 98


title: C26_male_10day6

description: Library name: zr5492_13_S15


title: TNBC012|ROI-002|PanCK+

description:
Library name: DSP-1001660016269-H-A04
TNBC012 - 002 - PanCK+
TNBC012-slide.png
TNBC012 - 002.png
TNBC012 - 002 - Segments.png


title: Thymus-Satb1WT-native-ACC-Rep1

description: Library name: Sample 97


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

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


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

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


title: TNBC012|ROI-001|PanCK-

description:
Library name: DSP-1001660016269-H-A03
TNBC012 - 001 - PanCK-
TNBC012-slide.png
TNBC012 - 001.png
TNBC012 - 001 - Segments.png


title: C26_male_20day5

description: Library name: zr5492_19_S21


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

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


title: C26_male_10day4

description: Library name: zr5492_11_S13


title: C26_male_10day5

description: Library name: zr5492_12


title: TNBC012|ROI-001|PanCK+

description:
Library name: DSP-1001660016269-H-A02
TNBC012 - 001 - PanCK+
TNBC012-slide.png
TNBC012 - 001.png
TNBC012 - 001 - Segments.png


title: CD69+DP-Satb1KO-ATAC-Rep4

description: Library name: Sample 96


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

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


title: TNBC011|ROI-013|PanCK+

description:
Library name: DSP-1001660016071-G-H12
TNBC011 - 013 - PanCK+
TNBC011-slide.png
TNBC011 - 013.png
TNBC011 - 013 - Segments.png

value: GPx


title: CD69+DP-Satb1KO-ATAC-Rep3

description: Library name: Sample 95


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

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


title: CD69+DP-Satb1KO-ATAC-Rep2

description: Library name: Sample 94


title: TNBC011|ROI-012|PanCK-

description:
Library name: DSP-1001660016071-G-H11
TNBC011 - 012 - PanCK-
TNBC011-slide.png
TNBC011 - 012.png
TNBC011 - 012 - Segments.png


title: scRNA Uri-S93 (VDJ)

city: chongqing

first: Ye

last: qian

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

institute: The First Affiliated Hospital of Chongqing Medical University

description:
Library name: sample133
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.

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: Female

tag: age

tag: sample collection_site

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

tag: group

value: Adult Sepsis

tag: sepsis infection_source

value: Urinary

tag: ethnicity

value: East Asian


title: scRNA Uri-S85 (VDJ)

description:
Library name: sample131
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: TNBC011|ROI-012|PanCK+

description:
Library name: DSP-1001660016071-G-H10
TNBC011 - 012 - PanCK+
TNBC011-slide.png
TNBC011 - 012.png
TNBC011 - 012 - Segments.png

value: Breast


title: scRNA Uri-S20 (VDJ)

description:
Library name: sample130
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC011|ROI-011|PanCK-

description:
Library name: DSP-1001660016071-G-H09
TNBC011 - 011 - PanCK-
TNBC011-slide.png
TNBC011 - 011.png
TNBC011 - 011 - Segments.png


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

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


title: CD69-DP-Satb1KO-ATAC-Rep4

description: Library name: Sample 92

value: Thymus


title: scRNA Uri-S157 (VDJ)

description:
Library name: sample129
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC011|ROI-010|PanCK-

description:
Library name: DSP-1001660016071-G-H07
TNBC011 - 010 - PanCK-
TNBC011-slide.png
TNBC011 - 010.png
TNBC011 - 010 - Segments.png


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

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


title: scRNA Uri-S147 (VDJ)

description:
Library name: sample128
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: CD69-DP-Satb1KO-ATAC-Rep2

description: Library name: Sample 90


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

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


title: CD69-DP-Satb1KO-ATAC-Rep3

description: Library name: Sample 91


title: CD69+DP-Satb1WT-ATAC-Rep4

description: Library name: Sample 88


title: scRNA Uri-S116 (VDJ)

description:
Library name: sample126
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69-DP-Satb1KO-ATAC-Rep1

description: Library name: Sample 89


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

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


title: scRNA Uri-S88 (VDJ)

description:
Library name: sample132
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC011|ROI-010|PanCK+

description:
Library name: DSP-1001660016071-G-H06
TNBC011 - 010 - PanCK+
TNBC011-slide.png
TNBC011 - 010.png
TNBC011 - 010 - Segments.png


title: CD69+DP-Satb1KO-ATAC-Rep1

description: Library name: Sample 93


title: CD69+DP-Satb1WT-ATAC-Rep3

description: Library name: Sample 87


title: TNBC011|ROI-009|PanCK+

description:
Library name: DSP-1001660016071-G-H04
TNBC011 - 009 - PanCK+
TNBC011-slide.png
TNBC011 - 009.png
TNBC011 - 009 - Segments.png


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

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


title: TNBC011|ROI-011|PanCK+

description:
Library name: DSP-1001660016071-G-H08
TNBC011 - 011 - PanCK+
TNBC011-slide.png
TNBC011 - 011.png
TNBC011 - 011 - Segments.png


title: CD69+DP-Satb1WT-ATAC-Rep2

description: Library name: Sample 86


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

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


title: TNBC011|ROI-008|PanCK-

description:
Library name: DSP-1001660016071-G-H03
TNBC011 - 008 - PanCK-
TNBC011-slide.png
TNBC011 - 008.png
TNBC011 - 008 - Segments.png


title: scRNA Uri-S112 (VDJ)

description:
Library name: sample125
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Male


title: scRNA Uri-S134 (VDJ)

description:
Library name: sample127
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Chongqing Emergency Medical Center, Chongqing, China.


title: TNBC011|ROI-008|PanCK+

description:
Library name: DSP-1001660016071-G-H02
TNBC011 - 008 - PanCK+
TNBC011-slide.png
TNBC011 - 008.png
TNBC011 - 008 - Segments.png


title: CD69+DP-Satb1WT-ATAC-Rep1

description: Library name: Sample 85


title: scRNA Skin-S52 (VDJ)

description:
Library name: sample123
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Skin


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

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


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

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


title: scRNA Skin-S46 (VDJ)

description:
Library name: sample122
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69-DP-Satb1WT-ATAC-Rep4

description: Library name: Sample 84


title: TNBC011|ROI-007|PanCK-

description:
Library name: DSP-1001660016071-G-H01
TNBC011 - 007 - PanCK-
TNBC011-slide.png
TNBC011 - 007.png
TNBC011 - 007 - Segments.png


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

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


title: TNBC011|ROI-009|PanCK-

description:
Library name: DSP-1001660016071-G-H05
TNBC011 - 009 - PanCK-
TNBC011-slide.png
TNBC011 - 009.png
TNBC011 - 009 - Segments.png


title: CD69-DP-Satb1WT-ATAC-Rep3

description: Library name: Sample 83


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

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


title: TNBC011|ROI-007|PanCK+

description:
Library name: DSP-1001660016071-G-G12
TNBC011 - 007 - PanCK+
TNBC011-slide.png
TNBC011 - 007.png
TNBC011 - 007 - Segments.png


title: TNBC011|ROI-006|PanCK-

description:
Library name: DSP-1001660016071-G-G11
TNBC011 - 006 - PanCK-
TNBC011-slide.png
TNBC011 - 006.png
TNBC011 - 006 - Segments.png


title: scRNA Skin-S38 (VDJ)

description:
Library name: sample120
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: TNBC011|ROI-006|PanCK+

description:
Library name: DSP-1001660016071-G-G10
TNBC011 - 006 - PanCK+
TNBC011-slide.png
TNBC011 - 006.png
TNBC011 - 006 - Segments.png


title: scRNA Skin-S142 (VDJ)

description:
Library name: sample119
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: CD69+DP-Satb1KO-H3K27AC-Rep3

description: Library name: Sample 80

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.
Library strategy: CUT&Tag


title: scRNA Skin-S74 (VDJ)

description:
Library name: sample124
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC011|ROI-005|PanCK-

description:
Library name: DSP-1001660016071-G-G09
TNBC011 - 005 - PanCK-
TNBC011-slide.png
TNBC011 - 005.png
TNBC011 - 005 - Segments.png


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

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


title: CD69+DP-Satb1KO-H3K27AC-Rep2

description: Library name: Sample 79


title: scRNA Skin-152 (VDJ)

description:
Library name: sample117
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Res-S77 (VDJ)

description:
Library name: sample116
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Respiratory


title: TNBC011|ROI-005|PanCK+

description:
Library name: DSP-1001660016071-G-G08
TNBC011 - 005 - PanCK+
TNBC011-slide.png
TNBC011 - 005.png
TNBC011 - 005 - Segments.png


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

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

value: Frontal cortex


title: CD69+DP-Satb1KO-H3K27AC-Rep1

description: Library name: Sample 78


title: scRNA Res-S56 (VDJ)

description:
Library name: sample115
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: GroupF, input

description: Library name: F-input

value: Neuron


title: CD69-DP-Satb1WT-ATAC-Rep2

description: Library name: Sample 82


title: CD69+DP-Satb1WT-H3K27AC-Rep3

description: Library name: Sample 77


title: CD69+DP-Satb1WT-H3K27AC-Rep2

description: Library name: Sample 76


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

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


title: scRNA Res-S41 (VDJ)

description:
Library name: sample114
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC011|ROI-003|PanCK-

description:
Library name: DSP-1001660016071-G-G05
TNBC011 - 003 - PanCK-
TNBC011-slide.png
TNBC011 - 003.png
TNBC011 - 003 - Segments.png

value: GPx


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

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


title: CD69+DP-Satb1WT-H3K27AC-Rep1

description: Library name: Sample 75


title: TNBC011|ROI-003|PanCK+

description:
Library name: DSP-1001660016071-G-G04
TNBC011 - 003 - PanCK+
TNBC011-slide.png
TNBC011 - 003.png
TNBC011 - 003 - Segments.png


title: scRNA Res-S40 (VDJ)

description:
Library name: sample113
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood


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

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


title: CD69-DP-Satb1WT-ATAC-Rep1

description: Library name: Sample 81


title: scRNA Skin-S140 (VDJ)

description:
Library name: sample118
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: PBMCs


title: CD69-DP-Satb1KO-H3K27AC-Rep3

description: Library name: Sample 74


title: TNBC011|ROI-002|PanCK-

description:
Library name: DSP-1001660016071-G-G03
TNBC011 - 002 - PanCK-
TNBC011-slide.png
TNBC011 - 002.png
TNBC011 - 002 - Segments.png


title: scRNA Res-S32 (VDJ)

description:
Library name: sample112
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Immune cells


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

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


title: TNBC011|ROI-004|PanCK-

description:
Library name: DSP-1001660016071-G-G07
TNBC011 - 004 - PanCK-
TNBC011-slide.png
TNBC011 - 004.png
TNBC011 - 004 - Segments.png


title: CD69-DP-Satb1KO-H3K27AC-Rep2

description: Library name: Sample 73


title: TNBC011|ROI-004|PanCK+

description:
Library name: DSP-1001660016071-G-G06
TNBC011 - 004 - PanCK+
TNBC011-slide.png
TNBC011 - 004.png
TNBC011 - 004 - Segments.png


title: TNBC011|ROI-002|PanCK+

description:
Library name: DSP-1001660016071-G-G02
TNBC011 - 002 - PanCK+
TNBC011-slide.png
TNBC011 - 002.png
TNBC011 - 002 - Segments.png


title: scRNA Res-S3 (VDJ)

description:
Library name: sample111
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Res-S22 (VDJ)

description:
Library name: sample110
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: CD69-DP-Satb1KO-H3K27AC-Rep1

description: Library name: Sample 72


title: CD69-DP-Satb1WT-H3K27AC-Rep3

description: Library name: Sample 71


title: TNBC011|ROI-001|PanCK+

description:
Library name: DSP-1001660016071-G-F12
TNBC011 - 001 - PanCK+
TNBC011-slide.png
TNBC011 - 001.png
TNBC011 - 001 - Segments.png


title: TNBC011|ROI-001|PanCK-

description:
Library name: DSP-1001660016071-G-G01
TNBC011 - 001 - PanCK-
TNBC011-slide.png
TNBC011 - 001.png
TNBC011 - 001 - Segments.png


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

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


title: TNBC010|ROI-020|PanCK-

description:
Library name: DSP-1001660016071-G-F11
TNBC010 - 020 - PanCK-
TNBC010-slide.png
TNBC010 - 020.png
TNBC010 - 020 - Segments.png


title: CD69-DP-Satb1WT-H3K27AC-Rep2

description: Library name: Sample 70


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

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


title: scRNA Res-S184 (VDJ)

description:
Library name: sample108
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Female


title: scRNA Res-S183 (VDJ)

description:
Library name: sample107
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: scRNA Res-S18 (VDJ)

description:
Library name: sample106
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Adult Sepsis


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

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


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

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


title: CD69+DP-Satb1KO-H3K4ME3-Rep2

description: Library name: Sample 67


title: scRNA Res-S21 (VDJ)

description:
Library name: sample109
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69+DP-Satb1KO-H3K4ME3-Rep3

description: Library name: Sample 68


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

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


title: TNBC010|ROI-020|PanCK+

description:
Library name: DSP-1001660016071-G-F10
TNBC010 - 020 - PanCK+
TNBC010-slide.png
TNBC010 - 020.png
TNBC010 - 020 - Segments.png


title: scRNA RES-S177 (VDJ)

description:
Library name: sample105
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69+DP-Satb1KO-H3K4ME3-Rep1

description: Library name: Sample 66


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

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


title: TNBC010|ROI-019|PanCK+

description:
Library name: DSP-1001660016071-G-F08
TNBC010 - 019 - PanCK+
TNBC010-slide.png
TNBC010 - 019.png
TNBC010 - 019 - Segments.png


title: CD69+DP-Satb1WT-H3K4ME3-Rep3

description: Library name: Sample 65


title: TNBC010|ROI-018|PanCK-

description:
Library name: DSP-1001660016071-G-F07
TNBC010 - 018 - PanCK-
TNBC010-slide.png
TNBC010 - 018.png
TNBC010 - 018 - Segments.png


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

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


title: CD69-DP-Satb1KO-H3K4ME3-Rep3

description: Library name: Sample 62


title: TNBC010|ROI-017|PanCK+

description:
Library name: DSP-1001660016071-G-F04
TNBC010 - 017 - PanCK+
TNBC010-slide.png
TNBC010 - 017.png
TNBC010 - 017 - Segments.png


title: scRNA Res-S167 (VDJ)

description:
Library name: sample100
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69-DP-Satb1KO-H3K4ME3-Rep1

description: Library name: Sample 60


title: TNBC010|ROI-018|PanCK+

description:
Library name: DSP-1001660016071-G-F06
TNBC010 - 018 - PanCK+
TNBC010-slide.png
TNBC010 - 018.png
TNBC010 - 018 - Segments.png


title: CD69+DP-Satb1WT-H3K4ME3-Rep1

description: Library name: Sample 63


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

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


title: CD69+DP-Satb1WT-H3K4ME3-Rep2

description: Library name: Sample 64


title: TNBC010|ROI-017|PanCK-

description:
Library name: DSP-1001660016071-G-F05
TNBC010 - 017 - PanCK-
TNBC010-slide.png
TNBC010 - 017.png
TNBC010 - 017 - Segments.png


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

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


title: scRNA Res-S170 (VDJ)

description:
Library name: sample102
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69-DP-Satb1WT-H3K4ME3-Rep3

description: Library name: Sample 59


title: scRNA RES-S174 (VDJ)

description:
Library name: sample103
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA RES-S164 (VDJ)

description:
Library name: sample98
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69-DP-Satb1KO-H3K4ME3-Rep2

description: Library name: Sample 61


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

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


title: TNBC010|ROI-016|PanCK-

description:
Library name: DSP-1001660016071-G-F03
TNBC010 - 016 - PanCK-
TNBC010-slide.png
TNBC010 - 016.png
TNBC010 - 016 - Segments.png


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

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


title: TNBC010|ROI-015|PanCK+

description:
Library name: DSP-1001660016071-G-E12
TNBC010 - 015 - PanCK+
TNBC010-slide.png
TNBC010 - 015.png
TNBC010 - 015 - Segments.png


title: scRNA RES-S176 (VDJ)

description:
Library name: sample104
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69-DP-Satb1WT-H3K4ME3-Rep2

description: Library name: Sample 58


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

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


title: scRNA Res-S166 (VDJ)

description:
Library name: sample99
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Res-S168 (VDJ)

description:
Library name: sample101
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: TNBC010|ROI-016|PanCK+

description:
Library name: DSP-1001660016071-G-F02
TNBC010 - 016 - PanCK+
TNBC010-slide.png
TNBC010 - 016.png
TNBC010 - 016 - Segments.png


title: TNBC010|ROI-015|PanCK-

description:
Library name: DSP-1001660016071-G-F01
TNBC010 - 015 - PanCK-
TNBC010-slide.png
TNBC010 - 015.png
TNBC010 - 015 - Segments.png


title: TNBC010|ROI-019|PanCK-

description:
Library name: DSP-1001660016071-G-F09
TNBC010 - 019 - PanCK-
TNBC010-slide.png
TNBC010 - 019.png
TNBC010 - 019 - Segments.png


title: scRNA Res-S15 (VDJ)

description:
Library name: sample96
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: CD69-DP-Satb1WT-H3K4ME3-Rep1

description: Library name: Sample 57


title: scRNA Res-S150 (VDJ)

description:
Library name: sample97
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69+DP-Satb1KO-RAD21-Rep3

description: Library name: Sample 56


title: TNBC010|ROI-014|PanCK+

description:
Library name: DSP-1001660016071-G-E10
TNBC010 - 014 - PanCK+
TNBC010-slide.png
TNBC010 - 014.png
TNBC010 - 014 - Segments.png


title: CD69+DP-Satb1KO-RAD21-Rep1

description: Library name: Sample 54


title: scRNA Res-S145 (VDJ)

description:
Library name: sample93
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: scRNA Res-S149 (VDJ)

description:
Library name: sample95
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


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

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


title: scRNA Res-S146 (VDJ)

description:
Library name: sample94
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Res-S144 (VDJ)

description:
Library name: sample92
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69+DP-Satb1WT-RAD21-Rep3

description: Library name: Sample 53


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

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


title: TNBC010|ROI-013|PanCK+

description:
Library name: DSP-1001660016071-G-E08
TNBC010 - 013 - PanCK+
TNBC010-slide.png
TNBC010 - 013.png
TNBC010 - 013 - Segments.png


title: TNBC010|ROI-012|PanCK-

description:
Library name: DSP-1001660016071-G-E07
TNBC010 - 012 - PanCK-
TNBC010-slide.png
TNBC010 - 012.png
TNBC010 - 012 - Segments.png


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

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


title: scRNA Res-S139 (VDJ)

description:
Library name: sample91
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC010|ROI-012|PanCK+

description:
Library name: DSP-1001660016071-G-E06
TNBC010 - 012 - PanCK+
TNBC010-slide.png
TNBC010 - 012.png
TNBC010 - 012 - Segments.png


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

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


title: CD69+DP-Satb1WT-RAD21-Rep2

description: Library name: Sample 52


title: CD69+DP-Satb1WT-RAD21-Rep1

description: Library name: Sample 51


title: TNBC010|ROI-011|PanCK-

description:
Library name: DSP-1001660016071-G-E05
TNBC010 - 011 - PanCK-
TNBC010-slide.png
TNBC010 - 011.png
TNBC010 - 011 - Segments.png


title: TNBC010|ROI-014|PanCK-

description:
Library name: DSP-1001660016071-G-E11
TNBC010 - 014 - PanCK-
TNBC010-slide.png
TNBC010 - 014.png
TNBC010 - 014 - Segments.png


title: scRNA Res-S136 (VDJ)

description:
Library name: sample90
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69+DP-Satb1KO-RAD21-Rep2

description: Library name: Sample 55


title: GroupE, input

description: Library name: E-input


title: TNBC010|ROI-011|PanCK+

description:
Library name: DSP-1001660016071-G-E04
TNBC010 - 011 - PanCK+
TNBC010-slide.png
TNBC010 - 011.png
TNBC010 - 011 - Segments.png


title: TNBC010|ROI-013|PanCK-

description:
Library name: DSP-1001660016071-G-E09
TNBC010 - 013 - PanCK-
TNBC010-slide.png
TNBC010 - 013.png
TNBC010 - 013 - Segments.png


title: CD69-DP-Satb1KO-RAD21-Rep3

description: Library name: Sample 50


title: CD69-DP-Satb1KO-RAD21-Rep2

description: Library name: Sample 49


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

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


title: CD69-DP-Satb1KO-RAD21-Rep1

description: Library name: Sample 48


title: scRNA RES-S118 (VDJ)

description:
Library name: sample87
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Res-S110 (VDJ)

description:
Library name: sample86
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC010|ROI-009|PanCK-

description:
Library name: DSP-1001660016071-G-E01
TNBC010 - 009 - PanCK-
TNBC010-slide.png
TNBC010 - 009.png
TNBC010 - 009 - Segments.png


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

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


title: scRNA Res-S127 (VDJ)

description:
Library name: sample89
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: CD69-DP-Satb1WT-RAD21-Rep2

description: Library name: Sample 46


title: TNBC010|ROI-010|PanCK+

description:
Library name: DSP-1001660016071-G-E02
TNBC010 - 010 - PanCK+
TNBC010-slide.png
TNBC010 - 010.png
TNBC010 - 010 - Segments.png


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

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


title: scRNA Res-S125 (VDJ)

description:
Library name: sample88
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC010|ROI-010|PanCK-

description:
Library name: DSP-1001660016071-G-E03
TNBC010 - 010 - PanCK-
TNBC010-slide.png
TNBC010 - 010.png
TNBC010 - 010 - Segments.png


title: scRNA Res-S100 (VDJ)

description:
Library name: sample85
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69-DP-Satb1WT-RAD21-Rep3

description: Library name: Sample 47


title: CD69-DP-Satb1WT-RAD21-Rep1

description: Library name: Sample 45


title: scRNA Res-S10 (VDJ)

description:
Library name: sample84
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC010|ROI-008|PanCK-

description:
Library name: DSP-1001660016071-G-D11
TNBC010 - 008 - PanCK-
TNBC010-slide.png
TNBC010 - 008.png
TNBC010 - 008 - Segments.png


title: TNBC010|ROI-009|PanCK+

description:
Library name: DSP-1001660016071-G-D12
TNBC010 - 009 - PanCK+
TNBC010-slide.png
TNBC010 - 009.png
TNBC010 - 009 - Segments.png


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

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


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

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


title: CD69+DP-Satb1KO-CTCF-Rep3

description: Library name: Sample 44


title: TNBC010|ROI-008|PanCK+

description:
Library name: DSP-1001660016071-G-D10
TNBC010 - 008 - PanCK+
TNBC010-slide.png
TNBC010 - 008.png
TNBC010 - 008 - Segments.png


title: scRNA RES-PS26 (VDJ)

description:
Library name: sample83
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


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

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


title: CD69+DP-Satb1KO-CTCF-Rep2

description: Library name: Sample 43


title: scRNA Res-PS25 (VDJ)

description:
Library name: sample82
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: East Asian


title: TNBC010|ROI-007|PanCK-

description:
Library name: DSP-1001660016071-G-D09
TNBC010 - 007 - PanCK-
TNBC010-slide.png
TNBC010 - 007.png
TNBC010 - 007 - Segments.png

value: Breast


title: CD69+DP-Satb1KO-CTCF-Rep1

description: Library name: Sample 42

value: Thymus


title: TNBC010|ROI-007|PanCK+

description:
Library name: DSP-1001660016071-G-D08
TNBC010 - 007 - PanCK+
TNBC010-slide.png
TNBC010 - 007.png
TNBC010 - 007 - Segments.png


title: scRNA Res-PS21 (VDJ)

description:
Library name: sample80
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Male


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

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


title: TNBC010|ROI-006|PanCK-

description:
Library name: DSP-1001660016071-G-D07
TNBC010 - 006 - PanCK-
TNBC010-slide.png
TNBC010 - 006.png
TNBC010 - 006 - Segments.png


title: TNBC010|ROI-006|PanCK+

description:
Library name: DSP-1001660016071-G-D06
TNBC010 - 006 - PanCK+
TNBC010-slide.png
TNBC010 - 006.png
TNBC010 - 006 - Segments.png


title: CD69+DP-Satb1WT-CTCF-Rep2

description: Library name: Sample 40


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

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


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

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


title: scRNA Res-PS16 (VDJ)

description:
Library name: sample79
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Res-PS12 (VDJ)

description:
Library name: sample78
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69+DP-Satb1WT-CTCF-Rep1

description: Library name: Sample 39


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

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


title: TNBC010|ROI-005|PanCK-

description:
Library name: DSP-1001660016071-G-D05
TNBC010 - 005 - PanCK-
TNBC010-slide.png
TNBC010 - 005.png
TNBC010 - 005 - Segments.png


title: scRNA Res-PS03 (VDJ)

description:
Library name: sample77
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69-DP-Satb1KO-CTCF-Rep3

description: Library name: Sample 38


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

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


title: TNBC010|ROI-005|PanCK+

description:
Library name: DSP-1001660016071-G-D04
TNBC010 - 005 - PanCK+
TNBC010-slide.png
TNBC010 - 005.png
TNBC010 - 005 - Segments.png


title: CD69-DP-Satb1KO-CTCF-Rep2

description: Library name: Sample 37


title: TNBC010|ROI-004|PanCK-

description:
Library name: DSP-1001660016071-G-D03
TNBC010 - 004 - PanCK-
TNBC010-slide.png
TNBC010 - 004.png
TNBC010 - 004 - Segments.png


title: scRNA Res-PS02 (VDJ)

description:
Library name: sample76
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: CD69-DP-Satb1KO-CTCF-Rep1

description: Library name: Sample 36


title: scRNA Res-PS22 (VDJ)

description:
Library name: sample81
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Res-S70 (VDJ)

description:
Library name: sample75
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: CD69+DP-Satb1WT-CTCF-Rep3

description: Library name: Sample 41


title: TNBC010|ROI-004|PanCK+

description:
Library name: DSP-1001660016071-G-D02
TNBC010 - 004 - PanCK+
TNBC010-slide.png
TNBC010 - 004.png
TNBC010 - 004 - Segments.png


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

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


title: CD69-DP-Satb1WT-CTCF-Rep3

description: Library name: Sample 35


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

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


title: CD69-DP-Satb1WT-CTCF-Rep2

description: Library name: Sample 34


title: scRNA Res-S26 (VDJ)

description:
Library name: sample74
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Res-S19 (VDJ)

description:
Library name: sample73
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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


title: TNBC010|ROI-003|PanCK+

description:
Library name: DSP-1001660016071-G-C12
TNBC010 - 003 - PanCK+
TNBC010-slide.png
TNBC010 - 003.png
TNBC010 - 003 - Segments.png


title: TNBC010|ROI-003|PanCK-

description:
Library name: DSP-1001660016071-G-D01
TNBC010 - 003 - PanCK-
TNBC010-slide.png
TNBC010 - 003.png
TNBC010 - 003 - Segments.png


title: TNBC010|ROI-002|PanCK-

description:
Library name: DSP-1001660016071-G-C11
TNBC010 - 002 - PanCK-
TNBC010-slide.png
TNBC010 - 002.png
TNBC010 - 002 - Segments.png


title: CD69-DP-Satb1WT-CTCF-Rep1

description: Library name: Sample 33


title: scRNA PIC05 (VDJ)

description:
Library name: sample72
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Pediatric ICU Control


title: CD69+DP-Satb1KO-SATB1-Rep3

description: Library name: Sample 32


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

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


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

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


title: scRNA PIC04 (VDJ)

description:
Library name: sample71
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC010|ROI-001|PanCK-

description:
Library name: DSP-1001660016071-G-C09
TNBC010 - 001 - PanCK-
TNBC010-slide.png
TNBC010 - 001.png
TNBC010 - 001 - Segments.png


title: scRNA PIC02 (VDJ)

description:
Library name: sample70
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC010|ROI-002|PanCK+

description:
Library name: DSP-1001660016071-G-C10
TNBC010 - 002 - PanCK+
TNBC010-slide.png
TNBC010 - 002.png
TNBC010 - 002 - Segments.png


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

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


title: CD69+DP-Satb1KO-SATB1-Rep2

description: Library name: Sample 31


title: scRNA PIC01 (VDJ)

description:
Library name: sample69
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC010|ROI-001|PanCK+

description:
Library name: DSP-1001660016071-G-C08
TNBC010 - 001 - PanCK+
TNBC010-slide.png
TNBC010 - 001.png
TNBC010 - 001 - Segments.png


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

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


title: CD69+DP-Satb1KO-SATB1-Rep1

description: Library name: Sample 30


title: CD69+DP-Satb1WT-SATB1-Rep3

description: Library name: Sample 29


title: scRNA PHC05 (VDJ)

description:
Library name: sample68
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Pediatric Healthy Control


title: TNBC009|ROI-021|PanCK-

description:
Library name: DSP-1001660016071-G-C07
TNBC009 - 021 - PanCK-
TNBC009-slide.png
TNBC009 - 021.png
TNBC009 - 021 - Segments.png


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

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

value: Frontal cortex


title: CD69+DP-Satb1WT-SATB1-Rep2

description: Library name: Sample 28


title: scRNA PHC03 (VDJ)

description:
Library name: sample67
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA PHC02 (VDJ)

description:
Library name: sample66
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


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

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

value: Neuron


title: TNBC009|ROI-020|PanCK-

description:
Library name: DSP-1001660016071-G-C05
TNBC009 - 020 - PanCK-
TNBC009-slide.png
TNBC009 - 020.png
TNBC009 - 020 - Segments.png

value: GPx


title: CD69+DP-Satb1WT-SATB1-Rep1

description: Library name: Sample 27


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

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


title: TNBC009|ROI-020|PanCK+

description:
Library name: DSP-1001660016071-G-C04
TNBC009 - 020 - PanCK+
TNBC009-slide.png
TNBC009 - 020.png
TNBC009 - 020 - Segments.png


title: TNBC009|ROI-019|PanCK-

description:
Library name: DSP-1001660016071-G-C03
TNBC009 - 019 - PanCK-
TNBC009-slide.png
TNBC009 - 019.png
TNBC009 - 019 - Segments.png


title: scRNA IC22 (VDJ)

description:
Library name: sample63
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood

value: Adult ICU Control


title: GroupD, input

description: Library name: D-input

value: MIA-MIA


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

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


title: CD69-DP-Satb1KO-SATB1-Rep1

description: Library name: Sample 24


title: TNBC009|ROI-019|PanCK+

description:
Library name: DSP-1001660016071-G-C02
TNBC009 - 019 - PanCK+
TNBC009-slide.png
TNBC009 - 019.png
TNBC009 - 019 - Segments.png


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

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


title: CD69-DP-Satb1WT-SATB1-Rep3

description: Library name: Sample 23


title: scRNA IC19 (VDJ)

description:
Library name: sample62
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: PBMCs

value: Immune cells


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

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


title: CD69-DP-Satb1WT-SATB1-Rep2

description: Library name: Sample 22


title: TNBC009|ROI-018|PanCK-

description:
Library name: DSP-1001660016071-G-C01
TNBC009 - 018 - PanCK-
TNBC009-slide.png
TNBC009 - 018.png
TNBC009 - 018 - Segments.png


title: scRNA IC16 (VDJ)

description:
Library name: sample61
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


title: TNBC009|ROI-018|PanCK+

description:
Library name: DSP-1001660016071-G-B12
TNBC009 - 018 - PanCK+
TNBC009-slide.png
TNBC009 - 018.png
TNBC009 - 018 - Segments.png


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

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


title: CD69-DP-Satb1WT-SATB1-Rep1

description: Library name: Sample 21


title: scRNA Skin-S43 (VDJ)

description:
Library name: sample121
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Adult Sepsis

value: Skin


title: TNBC009|ROI-017|PanCK-

description:
Library name: DSP-1001660016071-G-B11
TNBC009 - 017 - PanCK-
TNBC009-slide.png
TNBC009 - 017.png
TNBC009 - 017 - Segments.png

value: Breast


title: CD69-DP-Satb1KO-SATB1-Rep3

description: Library name: Sample 26

value: Thymus


title: TNBC009|ROI-021|PanCK+

description:
Library name: DSP-1001660016071-G-C06
TNBC009 - 021 - PanCK+
TNBC009-slide.png
TNBC009 - 021.png
TNBC009 - 021 - Segments.png


title: scRNA IC10 (VDJ)

description:
Library name: sample59
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Male

value: East Asian


title: CD69-DP-Satb1WT-HIC-Rep4

description: Library name: Sample 20


title: CD69-DP-Satb1WT-HIC-Rep3

description: Library name: Sample 19


title: TNBC009|ROI-017|PanCK+

description:
Library name: DSP-1001660016071-G-B10
TNBC009 - 017 - PanCK+
TNBC009-slide.png
TNBC009 - 017.png
TNBC009 - 017 - Segments.png


title: scRNA IC09 (VDJ)

description:
Library name: sample58
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA PHC01 (VDJ)

description:
Library name: sample65
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 Healthy Control


title: CD69-DP-Satb1WT-HIC-Rep2

description: Library name: Sample 18


title: TNBC009|ROI-016|PanCK-

description:
Library name: DSP-1001660016071-G-B09
TNBC009 - 016 - PanCK-
TNBC009-slide.png
TNBC009 - 016.png
TNBC009 - 016 - Segments.png


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

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

value: Frontal cortex

value: Neuron


title: TNBC009|ROI-016|PanCK+

description:
Library name: DSP-1001660016071-G-B08
TNBC009 - 016 - PanCK+
TNBC009-slide.png
TNBC009 - 016.png
TNBC009 - 016 - Segments.png

value: GPx


title: scRNA IC08 (VDJ)

description:
Library name: sample57
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood

value: Adult ICU Control


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

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

value: MIA-MIA


title: CD69-DP-Satb1WT-HIC-Rep1

description: Library name: Sample 17


title: TNBC009|ROI-015|PanCK-

description:
Library name: DSP-1001660016071-G-B07
TNBC009 - 015 - PanCK-
TNBC009-slide.png
TNBC009 - 015.png
TNBC009 - 015 - Segments.png


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

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


title: scRNA IC15 (VDJ)

description:
Library name: sample60
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: PBMCs

value: Immune cells


title: scRNA HC16 (VDJ)

description:
Library name: sample56
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: Adult Healthy Control


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

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


title: CD69-DP-Satb1KO-HIC-Rep4

description: Library name: Sample 16


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

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


title: TNBC009|ROI-015|PanCK+

description:
Library name: DSP-1001660016071-G-B06
TNBC009 - 015 - PanCK+
TNBC009-slide.png
TNBC009 - 015.png
TNBC009 - 015 - Segments.png

value: Breast


title: scRNA HC13 (VDJ)

description:
Library name: sample55
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA HC12 (VDJ)

description:
Library name: sample54
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC009|ROI-014|PanCK-

description:
Library name: DSP-1001660016071-G-B05
TNBC009 - 014 - PanCK-
TNBC009-slide.png
TNBC009 - 014.png
TNBC009 - 014 - Segments.png


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

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


title: CD69-DP-Satb1KO-HIC-Rep3

description: Library name: Sample 15

value: Thymus


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

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


title: scRNA IC23 (VDJ)

description:
Library name: sample64
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69-DP-Satb1KO-SATB1-Rep2

description: Library name: Sample 25


title: CD69-DP-Satb1KO-HIC-Rep1

description: Library name: Sample 13


title: scRNA HC09 (VDJ)

description:
Library name: sample53
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Male


title: TNBC009|ROI-014|PanCK+

description:
Library name: DSP-1001660016071-G-B04
TNBC009 - 014 - PanCK+
TNBC009-slide.png
TNBC009 - 014.png
TNBC009 - 014 - Segments.png


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

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


title: scRNA HC07 (VDJ)

description:
Library name: sample52
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: East Asian


title: TNBC009|ROI-013|PanCK-

description:
Library name: DSP-1001660016071-G-B03
TNBC009 - 013 - PanCK-
TNBC009-slide.png
TNBC009 - 013.png
TNBC009 - 013 - Segments.png


title: CD69+DP-Satb1WT-HIC-Rep4

description: Library name: Sample 12


title: TNBC009|ROI-013|PanCK+

description:
Library name: DSP-1001660016071-G-B02
TNBC009 - 013 - PanCK+
TNBC009-slide.png
TNBC009 - 013.png
TNBC009 - 013 - Segments.png


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

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


title: scRNA HC05 (VDJ)

description:
Library name: sample51
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69+DP-Satb1WT-HIC-Rep3

description: Library name: Sample 11


title: scRNA HC01 (VDJ)

description:
Library name: sample50
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: TNBC009|ROI-012|PanCK-

description:
Library name: DSP-1001660016071-G-B01
TNBC009 - 012 - PanCK-
TNBC009-slide.png
TNBC009 - 012.png
TNBC009 - 012 - Segments.png


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

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


title: CD69+DP-Satb1WT-HIC-Rep2

description: Library name: Sample 10


title: TNBC009|ROI-012|PanCK+

description:
Library name: DSP-1001660016071-G-A12
TNBC009 - 012 - PanCK+
TNBC009-slide.png
TNBC009 - 012.png
TNBC009 - 012 - Segments.png


title: scRNA CNS-S61 (VDJ)

description:
Library name: sample49
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Adult Sepsis

value: Central Nervous System


title: CD69+DP-Satb1WT-HIC-Rep1

description: Library name: Sample 9


title: TNBC009|ROI-011|PanCK-

description:
Library name: DSP-1001660016071-G-A11
TNBC009 - 011 - PanCK-
TNBC009-slide.png
TNBC009 - 011.png
TNBC009 - 011 - Segments.png


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

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

value: Frontal cortex


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

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

value: Neuron


title: CD69+DP-Satb1KO-HIC-Rep4

description: Library name: Sample 8


title: TNBC009|ROI-011|PanCK+

description:
Library name: DSP-1001660016071-G-A10
TNBC009 - 011 - PanCK+
TNBC009-slide.png
TNBC009 - 011.png
TNBC009 - 011 - Segments.png

value: GPx


title: CD69+DP-Satb1KO-HIC-Rep3

description: Library name: Sample 7


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

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


title: TNBC009|ROI-010|PanCK-

description:
Library name: DSP-1001660016071-G-A09
TNBC009 - 010 - PanCK-
TNBC009-slide.png
TNBC009 - 010.png
TNBC009 - 010 - Segments.png


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

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


title: CD69+DP-Satb1KO-HIC-Rep2

description: Library name: Sample 6


title: scRNA Abd-S98 (VDJ)

description:
Library name: sample46
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood

value: Abdominal


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

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

value: MIA-MIA


title: TNBC009|ROI-009|PanCK-

description:
Library name: DSP-1001660016071-G-A07
TNBC009 - 009 - PanCK-
TNBC009-slide.png
TNBC009 - 009.png
TNBC009 - 009 - Segments.png


title: scRNA Abd-S9 (VDJ)

description:
Library name: sample44
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: PBMCs


title: CD69+DP-Satb1KO-HIC-Rep1

description: Library name: Sample 5


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

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


title: CD69+DP-Satb1WT-ScRNASeq-Rep2

description: Library name: Sample 4


title: scRNA Res-S87 (VDJ)

description:
Library name: sample43
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Immune cells

value: Respiratory


title: TNBC009|ROI-009|PanCK+

description:
Library name: DSP-1001660016071-G-A06
TNBC009 - 009 - PanCK+
TNBC009-slide.png
TNBC009 - 009.png
TNBC009 - 009 - Segments.png


title: scRNA CNS-S50 (VDJ)

description:
Library name: sample48
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: CD69+DP-Satb1WT-ScRNASeq-Rep1

description: Library name: Sample 3


title: scRNA Abd-S83 (VDJ)

description:
Library name: sample42
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: CD69+DP-Satb1KO-ScRNASeq-Rep2

description: Library name: Sample 2


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

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


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

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


title: TNBC009|ROI-008|PanCK+

description:
Library name: DSP-1001660016071-G-A04
TNBC009 - 008 - PanCK+
TNBC009-slide.png
TNBC009 - 008.png
TNBC009 - 008 - Segments.png


title: TNBC009|ROI-007|PanCK-

description:
Library name: DSP-1001660016071-G-A03
TNBC009 - 007 - PanCK-
TNBC009-slide.png
TNBC009 - 007.png
TNBC009 - 007 - Segments.png


title: CD69+DP-Satb1KO-ScRNASeq-Rep1

description: Library name: Sample 1


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

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


title: GroupC, input

description: Library name: C-input

value: Mock-MIA


title: scRNA Abd-S91 (VDJ)

description:
Library name: sample45
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Chongqing Emergency Medical Center, Chongqing, China.


title: TNBC009|ROI-007|PanCK+

description:
Library name: DSP-1001660016071-G-A02
TNBC009 - 007 - PanCK+
TNBC009-slide.png
TNBC009 - 007.png
TNBC009 - 007 - Segments.png

value: Breast


title: TNBC009|ROI-006|PanCK-

description:
Library name: DSP-1001660016070-F-H12
TNBC009 - 006 - PanCK-
TNBC009-slide.png
TNBC009 - 006.png
TNBC009 - 006 - Segments.png


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

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


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

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


title: Reaction1_HT

city: Gosselies

first: Meggy

last: Suarez-Carmona

address: Rue des Professeurs Jeener et Brachet, 12

country: Belgium

institute: ULB

description: Library name: Sample1_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: Reaction2_GEX

description: Library name: Sample2_GEX

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


title: TNBC009|ROI-006|PanCK+

description:
Library name: DSP-1001660016070-F-H11
TNBC009 - 006 - PanCK+
TNBC009-slide.png
TNBC009 - 006.png
TNBC009 - 006 - Segments.png


title: scRNA Abd-S75 (VDJ)

description:
Library name: sample37
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Male

value: East Asian


title: scRNA Abd-S81 (VDJ)

description:
Library name: sample41
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Adult Sepsis


title: Reaction1_GEX

description: Library name: Sample1_GEX


title: TNBC009|ROI-005|PanCK-

description:
Library name: DSP-1001660016070-F-H10
TNBC009 - 005 - PanCK-
TNBC009-slide.png
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TNBC009 - 005 - Segments.png


title: scRNA Abd-S80 (VDJ)

description:
Library name: sample40
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Abd-S73 (VDJ)

description:
Library name: sample36
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: scRNA Abd-S8 (VDJ)

description:
Library name: sample39
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452


title: Cardiac tissue from AB with LL-VNS 10min starting 1w biological replicate 3

city: Wuhan

first: Zhen

last: Guo

address: Donghu Road 169

institute: 武汉大学

description:
Library name: AB_LLVNS10min_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 10min daily for 7 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

value: wild type

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


title: scRNA Abd-S72 (VDJ)

description:
Library name: sample35
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452

value: Peripheral blood

value: Female


title: Cardiac tissue from AB with LL-VNS 10min starting 1w biological replicate 2

description:
Library name: AB_LLVNS10min_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 10min daily for 7 weeks). Tissue harvested at 8 weeks post-AB surgery.


title: TNBC009|ROI-005|PanCK+

description:
Library name: DSP-1001660016070-F-H09
TNBC009 - 005 - PanCK+
TNBC009-slide.png
TNBC009 - 005.png
TNBC009 - 005 - Segments.png

value: GPx