description:
Library name: CFZ_uninfected_2
Uninfected BV2 cells treated with 30 nM CFZ, rep2


title: iMGL derived from major allele hiPSC treated with vehicle (replicate1)

status: Public on Apr 21 2026

type: SRA

city: Daegu

first: Jichang

last: Yu

address: 333, Techno jungang-daero

department: Department of Brain Sciences

country: South Korea

institute: DGIST

description: Library name: MajorControl1

library_source: transcriptomic

data_processing:
Raw FASTQ files were quality checked using FastQC. Reads were aligned to the GRCh38.99 human reference genome using HISAT2. Aligned reads were quantified at the gene level using featureCounts. Differential expression analysis was performed using DESeq2 in R. Genes with adjusted p < 0.05 were considered significantly differentially expressed.
Assembly: GRCh38.99 (Ensembl release 99)
Supplementary files format and content: Processed data file is a tab-delimited text file containing FPKM values for each gene across all samples. Rows represent genes and columns represent individual samples.

molecule: polyA RNA

organism: Homo sapiens

source_name: brain

extract_protocol:
Cells were lysed using QIAzol Lysis Reagent (QIAGEN) for the extraction of RNA. The lysates were separated into an aqueous phase containing RNAs using chloroform (Daejung) and centrifuged at 12,000 rpm for 15 mins at 4°C in RNase-free condition. The RNA pellets were washed with RNase-free 75% ethanol, air-dried, and suspended in RNase-free water.
Total RNA concentration was measured using Quant-IT RiboGreen (Invitrogen, #R11490), and RNA integrity was assessed using Agilent TapeStation RNA ScreenTape (#5067-5576). Only samples with RIN > 7.0 were used. Libraries were constructed using 1 µg of total RNA per sample with the Illumina TruSeq Stranded mRNA Library Prep Kit (#20020595). Poly-A containing mRNA was purified using poly-T magnetic beads, fragmented, and reverse-transcribed using SuperScript II reverse transcriptase (Invitrogen, #18064014). Second-strand cDNA synthesis was carried out using DNA Polymerase I, RNase H, and dUTP. The cDNA fragments were end-repaired, A-tailed, adapter-ligated, and PCR-amplified. Libraries were quantified using the KAPA Library Quantification Kit.

tag: tissue

value: brain

tag: cell line

value: hiPSC

tag: cell type

value: Microglia

tag: batch


title: iMGL derived from minor allele hiPSC treated with vehicle (replicate1)

description: Library name: MinorControl1


title: mouse HSPCs with shRen rep3, batch1

city: Chengdu

first: Yiman

last: Peng

state: Sichuan

address: No.1, Keyuan 4th Road, Gaopeng Avenue, Chengdu, Sichuan, China

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University

country: China

institute: Sichuan University

description:
Library name: 1_RNAseq_shRen_rep3
batch1_RNASeq_raw_counts.csv

data_processing:
For RNA-Seq, after removing the adapters, ploy-N, and low-quality reads, clean data were aligned against the reference mouse genome (mm10) using STAR_2.7.10b. Following this, raw counts were normalized and significance scores as well as log2-fold change values were calculated using the DESeq2 (v1.26.0).
Assembly: mm10
Supplementary files format and content: csv files include raw counts and DESeq2 normalized data of RNAseq.

organism: Mus musculus

source_name: HSPC

growth_protocol: For Utx KO/WT samples, WBM cells were freshly isolated from Utxf/f and Utxf/f; Mx1-Cre mice, and then HSPCs were sorted with mouse CD117 magnetic microbeads. Primary mouse cells were cultured in BCM medium (50% IMDM+50% DMEM+10% FBS+5% PS+0.34% BME) with 10% Stem Cell Medium (SCM) including 10% FBS, IL3 (10ng/mL; 1:1000), IL6 (10ng/mL; 1:500), and SCF (50ng/mL; 1:1000). For other RNA-Seq samples, mouse cKit+ HSPCs and AML cells were cultured at 37 °C with 7.5% CO2 in BCM medium [45% IMDM + 45% DMEM + 10% FBS + 50 × 10-6 M β-mercaptoethanol + penicillin (100 U mL-1)/streptomycin (0.1 mg mL-1)] supplemented with 10% stem cell medium (SCM) including mIL-3 (10 ng mL-1, Cat# 403-ML; R&D Systems), mIL-6 (10 ng mL-1, Cat# 406-ML; R&D Systems), and mSCF (50 ng mL-1, Cat# 455-MC; R&D Systems)

extract_protocol:
RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kits (NEB, E7770) according to the manufacturer's protocol.
RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kits (NEB, E7770) according to the manufacturer's protocol.

value: HSPC

tag: genotype

value: shRen


title: iMGL derived from major allele hiPSC treated with argatroban (replicate3)

description: Library name: MajorArg3


city: Guangzhou

first: Shen

last: Weishan

state: Guangdong

address: 58 Zhongshan 2nd Road

department: cirtical care medicine

institute: The First Affiliated Hospital, Sun Yat-sen University (FAH-SYSU)

description:
Library name: CFZ_HSV_3
BV2 cells infected with HSV-1 (MOI=1)  for 24 hours and treated with 30 nM CFZ, rep3

data_processing:
All clean data were mapped to the mouse genome mm10 using HISAT2 v2.1.0 with default parameters and BAM files were sorted by Samtools 1.9. Reads counts were summarized using the feature Counts program as part of the Subread package release 2.0.0 (http://subread.sourceforge.net/) .
Assembly: mm10
Supplementary files format and content: BV2_HSV1_BulkRNAseq.xlsx

extract_protocol:
Total RNA was extracted from BV2 cells using TRIzol reagent
sequencing was conducted by Annoroad Gene Technology Corporation (Beijing). Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed. NA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlus™ Real-Time PCR System (Library valid concentration＞10 nM). The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions.

value: wild-type

tag: treatment


title: mouse HSPCs with shRen rep1, batch1

description:
Library name: 1_RNAseq_shRen_rep1
batch1_RNASeq_raw_counts.csv


title: Human Coronary Smooth Muscle Cells, H3K27ac ChIP-Seq Rep 1

city: Singapore

first: Roger

last: Foo

address: 14 Medical Drive, MD6

country: Singapore

institute: National University of Singapore

description: Library name: HCASMC H3K27ac ChIP-Seq Replicate 1

library_source: genomic

data_processing:
Paired-end sequencing reads were aligned to human genome (hg38) using BWA mem version 0.7.5
Reads were deduplicated using Picard MarkDuplicates function and aligned mapped reads in BAM file were used as input for peak-calling using Dfilter to identify significant H3K27ac peaks using the following setting: -ks=60, -bs=100, -Ipvalue=8.
Bigwig tracks were normalized for sequencing depths and the sum of normalized binned tag-count represents the peak height
Assembly: hg38
Supplementary files format and content: Peak call files for respective samples (Except inputs)
Supplementary files format and content: bigwig tracks for samples (Except inputs)

molecule: genomic DNA

source_name: HCASMC

growth_protocol: human healthy coronary artery smooth muscle cells (HCASMC) (Thermo Scientific, Product code C-017-5C, Lot. 1689414) are cultured in human vascular smooth muscle (VSMC) basal medium (Gibco, M231500), in Smooth Muscle Growth Supplement (SMGS) (Gibco, S00725) and 1% penicillin/streptomycin. human healthy coronary artery endothelial cells (HCAEC) (ATCC, Product code PCS-100-020, Lot 62382179) are cultured in Endothelial Cell Growth medium MV2 (PromoCell, C-22022).

extract_protocol:
Cells were crosslinked with 1% Formaldehyde for 10 min at room temperature and quenched with glycine (125mM) for 5 min. The cells were rinsed twice with cold 1XPBS and sonicated in nuclei lysis buffer.
Library preparation was performed on the eluted ChIP DNA using the NEB Ultra II library preparation kit, according to the manufacturer’s protocol. 10 PCR cycles were performed using indexed primers and the library of DNA fragments with sizes between 300 to 500 bp was selected using the Omega MagBind NGS cleanup Magnetic beads (Omega M1378). The libraries were sent for paired end sequencing with at least 50 million read pairs at 2 x 151 bp read length on the illumina HiSeq 4000 platform.

value: Heart

value: Smooth Muscle Cells

tag: chip antibody

value: anti-H3K27ac (Abcam, ab4729)


title: SFTSV-infected THP-1 cells (48 h post-infection)-2

city: changchun

first: baoyan

last: wang

state: jilin

address: No. 5333, Xi'an Road, Lvyuan District, Changchun City, Jilin Province

department: College of Veterinary Medicine, Jilin University

institute: Jilin University

description: Library name: SF482

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: homo ensemblv112
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

source_name: Peripheral Blood

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Peripheral Blood

value: human monocytic cells

value: WT

value: SFTSV-infected (48 h post-infection)


description:
Library name: CFZ_HSV_2
BV2 cells infected with HSV-1 (MOI=1)  for 24 hours and treated with 30 nM CFZ, rep2


title: SFTSV-infected THP-1 cells (48 h post-infection)-1

description: Library name: SF481


title: Val_5_Pool2

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: VPA

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Assembly: rn6
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 28,307 genes detected.

source_name: Testis

extract_protocol:
RNA was extracted using kit (Qiagen) according to manufacturer’s instructions
The initial reverse transcription and template switching were done using 4 µL total RNA with 2.5 ng/µL. 50 ng of ds cDNA was used to build the sequencing libraries by tagmentation with the Illumina Nextera XT Kit. Library was sequenced using an Illumina NovaSeq 6000 sequencing system.
3'Bulk RNA Barcoding sequencing

value: Testis

value: 10-5M valproic acid


title: skeletal muscle cells from PBS liposome-treated mice, biological replicate 3

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

country: Italy

institute: IRCCS, Ospedale San Raffaele

description:
Library name: SHAM_9
10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files with the 'mkfastq' command in Cell Ranger (v6.1.2) with default setting.
The counts were generated using 10X Genomic Cellranger analysis pipelines (CellRanger v6.1.2), with the 'count' command, using the parameter --expect-cells 10000.
Assembly: mm10 (refdata-cellranger-mm10-2020-A) with addition of transgenic gene tdTOMATO (https://www.addgene.org/22799/)
Supplementary files format and content: barcode.tsv.gz: Barcode sequences correspond to column indices, single column with barcode Ids. Content of the Cellranger output folder "filtered_feature_bc_matrix".
Supplementary files format and content: features.tsv.gz: features correspond to row indices. Tab separeted file: first column is feature ID, second clumn feature name, third column feature type. Content of the Cellranger output folder "filtered_feature_bc_matrix".
Supplementary files format and content: matrix.mtx.gz: counts matrix. Content of the Cellranger output folder "filtered_feature_bc_matrix".

source_name: skeletal muscle

extract_protocol:
Freshly isolated quadriceps were minced into small pieces and enzymatically dissociated with 1.5mg/mL Dispase (Gibco, 17105-041) and 0.12% (w/v) Collagenase type I (Sigma-Aldrich, C0130) in two cycles of 30min at 37°C under constant 240 rpm agitation. The suspension was then passed through a 16G needle, followed by a 26G needle and filtered through a 40μm sterile strainer. Then cold CMF was added to inactivate enzymes and red blood cells lysed. To remove cell debris from the suspensions, Ficoll separation was performed. Cells were resuspended in 7 mL of pre-warmed DMEM High Glucose (Gibco, 41965-039) supplemented with 10% FBS (Gibco, 10270-106), in a 15 mL falcon, and 3.5 mL of Ficoll slowly layered on top. Samples were spined at 300g for 30min with no brake nor acceleration and the cell layer formed aspirated to another falcon and washed with cell medium.
Chromium Single Cell 3′ Reagent Kit v3.1 (10xGenomics)

value: skeletal muscle

value: Cdh5-CreERT2:R26R-tdTomato mice

value: SHAM


title: iBEC-RA,Control,Rep3

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

description: Library name: EMFBS-RA1491

data_processing:
Raw sequence data were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software.
Assembly: GRCH38.p14
Supplementary files format and content: Raw count data in excel file format

source_name: iBEC

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep Kit (Zymo Research, Cat. No. R2050) according to the manufacturer's protocol
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (Cat. No. E7760) following manufacturer’s instructions for sequencing on the Illumina NextSeq 500/550 Mid Output Kit v2.5 (150 cycles; Cat. No. 20024904)

value: iBEC

value: Control with Retinoic Acid

value: Control


title: SFTSV-infected THP-1 cells (24 h post-infection)-2

description: Library name: SF242

value: SFTSV-infected (24 h post-infection)


title: mouse HSPCs with shRen rep2, batch1

description:
Library name: 1_RNAseq_shRen_rep2
batch1_RNASeq_raw_counts.csv

value: HSPC

value: shRen


title: iMGL derived from major allele hiPSC treated with argatroban (replicate2)

description: Library name: MajorArg2

value: brain

value: hiPSC

value: Microglia


description:
Library name: CFZ_uninfected_1
Uninfected BV2 cells treated with 30 nM CFZ, rep1

value: wild-type

value: Uninfected treated with 30 nM CFZ


title: SFTSV-infected THP-1 cells (24 h post-infection)-3

description: Library name: SF243

value: Peripheral Blood

value: human monocytic cells

value: WT


title: SFTSV-infected THP-1 cells (48 h post-infection)-3

description: Library name: SF483

value: SFTSV-infected (48 h post-infection)


title: iMGL derived from major allele hiPSC treated with argatroban (replicate1)

description: Library name: MajorArg1


title: skeletal muscle cells from PBS liposome-treated mice, biological replicate 2

description:
Library name: SHAM_8
10x Genomics

value: skeletal muscle

value: Cdh5-CreERT2:R26R-tdTomato mice


title: SFTSV-infected THP-1 cells (24 h post-infection)-1

description: Library name: SF241


title: skeletal muscle cells from PBS liposome-treated mice, biological replicate 1

description:
Library name: SHAM_3
10x Genomics

value: SHAM


title: skeletal muscle cells from Clodronate liposome (CLL)-treated mice, biological replicate 3

description:
Library name: CLL_5
10x Genomics

value: CLL


title: Val_5_EH2710

description: VPA

value: Testis

value: 10-5M valproic acid


title: iBEC-RA,Control,Rep2

description: Library name: EMFBS-RA1324

value: iBEC

value: Control with Retinoic Acid

value: Control


title: iBEC-RA,Control,Rep1

description: Library name: EMFBS-RA1155


description:
Library name: CFZ_HSV_1
BV2 cells infected with HSV-1 (MOI=1)  for 24 hours and treated with 30 nM CFZ, rep1


title: Val_5_EH2384

description: VPA


title: Val_5_Pool1

description: VPA


title: DMSO_Pool2

description: Ctrl

value: Ctrl (DMSO)


title: iBEC,Control,Rep2

description: Library name: EMFBS551


title: DMSO_Pool1

description: Ctrl


title: Val_5_EH2817

description: VPA


title: Val_5_EH3657

description: VPA


title: DMSO_EH2710

description: Ctrl


title: Control THP-1 cells (without SFTSV infection)-1

description: Library name: Control1

value: Control (without SFTSV infection)


title: iBEC,Control,Rep1

description: Library name: EMFBS343


title: iBEC,EndothelialGenes,Rep2

description: Library name: 4EGiBECR2

data_processing:
Raw sequence data were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software.
Assembly: GRCH38.p14
Supplementary files format and content: Raw count and normalized data in excel file format

value: CRISPRa:CLDN5, PECAM1, CDH5, KDR

value: CRISPRa Reprogramming


title: Control THP-1 cells (without SFTSV infection)-3

description: Library name: Control3

value: Peripheral Blood


title: iBEC,EndothelialGenes,Rep1

description: Library name: 4EGiBECR1


title: Control + HFD

city: Houston

first: Yi

last: Zhao

state: Texas

address: 6770 Bertner Avenue

country: USA

institute: The Texas Heart Institute at Baylor College of Medicine

description: Control postnatal day 12 whole heart given maternal high-fat diet

data_processing:
Raw sequencing reads were aligned to the genome (build mm10) using the 10X Genomics toolkit CellRanger version 7.1.0 (cellranger count) with default parameters.
Assembly: mm10
Supplementary files format and content: TSV files: Tab-separated tables. MTX files: long-format matrix files

molecule: nuclear RNA

source_name: Whole heart

extract_protocol:
Single-nuclei were extracted following 10X nucleus extraction kits following manufacturer's protocols
SnRNA-seq was performed by using the 10X Genomics platform. Isolated nuclei were loaded into the 10X Genomics Chromium Controller to obtain the gel beads in emulsion. The sequencing libraries were then prepared according to the manufacturer’s protocols for the Single-cell 3’ Reagents Kits v3. Sequencing was performed by using the NovaSeq 6000 system.

treatment_protocol: Neonate P7 mice were injected with/without AAV-cTNT-YAP5SA, treated with maternal chow/HFD for 5 days.

value: Whole heart

value: Saline injection, maternal chow diet


title: CFBE410_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Genome_build: hg19
Supplementary_files_format_and_content: text files containing counts

growth_protocol: 2.5 × 105 cells were plated in a 6-well plate.

extract_protocol:
Total RNA was isolated using miRVana RNA isolation kit using 1.25 volumes of ethanol
Sequencing library was constructed using Illumina TruSeq Stranded mRNA Library prep kit according to manufacturer’s protocol (Illumina, San Diego, CA)

treatment_protocol: Cells were transfected with a vector encoding SFPQ (500 ng) using lipofectamine 2000

value: Bronchial epithelial cell

tag: disease state

value: Cystic Fibrosis

value: Untreated


title: SFPQ_2

source_name: CFBE41o- + SFPQ

value: SFPQ cDNA


title: Control THP-1 cells (without SFTSV infection)-2

description: Library name: Control2

value: human monocytic cells

value: WT


title: SFPQ_1


title: DMSO_EH2384

description: Ctrl

value: Testis


title: iBEC,Control,Rep3

description: Library name: EMFBS687

value: iBEC


title: skeletal muscle cells from Clodronate liposome (CLL)-treated mice, biological replicate 1

description:
Library name: CLL_12
10x Genomics

value: skeletal muscle

value: Cdh5-CreERT2:R26R-tdTomato mice

value: CLL


title: E12.5 Mouse Embryo, D1

city: Ann Arbor

first: Joshua

last: Welch

state: MI

address: Palmer Commons, 100 Washtenaw Ave

department: Department of Computational Medicine & Bioinformatics

institute: University of Michigan

description:
Library name: D1
Fresh frozen Spatial transciprome sequencing

data_processing:
Raw sequencing data were processed using the 10X sGenomics Space Ranger pipeline (v3.1.1) to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings  (v3.1.1)
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings (v3.1.1)
Assembly: mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: clusters_graphclust.csv.gz: graph-based cluster assignments
Supplementary files format and content: tissue_fullres_image.jpg.gz: full-res imgae of tissue
Supplementary files format and content: tissue_positions.parquet.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Whole embryo

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10 µm frozen sections were cut with cryostat. Hematoxylin and eosin (H&E) staining was performed using a kit (ab245880/Abcam, Cambridge, UK) according to the manufacturer’s instructions. H&E stained slides were cover slipped using glycerol, scanned using a Hamamatsu NanoZoomer S20 slide scanner system (C16300-01/Hamamatsu, Shizuoka, Japan) at 400x resolution. H&E scanned slides were de-cover slipped after a brief incubation in room temperature nuclease-free water, then given for Visium HD.
Spatial transcriptome seqeuncing libraries were prepared with 10X Genomics Visium HD spatial Gene Expression Slides & Reagent kit according to manufacture's construction.

value: Whole embryo


title: iPSC,EndothelialGenes,Rep1

description: Library name: 4EGhiPSCs

source_name: iPSC

value: iPSC

value: CRISPRa:CLDN5, PECAM1, CDH5, KDR


title: skeletal muscle cells from Clodronate liposome (CLL)-treated mice, biological replicate 2

description:
Library name: CLL_2
10x Genomics


title: E12.5 Mouse Embryo, A1

description:
Library name: A1
Fresh frozen Spatial transciprome sequencing


title: iBEC,TranscriptionFactor,Rep2

description: Library name: 3TFiBECR2

value: CRISPRa:ETV2,FLI1, ERG

value: CRISPRa Reprogramming


title: SFPQ_3


title: YAP5SA + Chow

description: YAP5SA postnatal day 12 whole heart

value: Whole heart

value: AAV9-YAP5SA injection, maternal high-fat diet


title: DMSO_EH3657

description: Ctrl

value: Ctrl (DMSO)


title: YAP5SA + HFD

description: YAP5SA postnatal day 12 whole heart given maternal high-fat diet


title: CFBE410_2

value: Bronchial epithelial cell

value: Cystic Fibrosis

value: Untreated


title: Control + Chow

description: Control postnatal day 12 whole heart

value: WT

value: Saline injection, maternal chow diet


title: DMSO_EH2817

description: Ctrl

value: Testis


title: HepG2.2.15 cells, Input

status: Public on Apr 20 2026

city: 武汉市

first: jiangpeng

last: FENG

state: 湖北省

address: 武昌区小洪山中区

institute: Wuhan institute of virus

description: Library name: HepG2.2.15, Input

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.The clean reads were used for protein binding site analysis. They were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters. The RSeQC（version 2.6）was used for reads distribution analysis.The MACS2 software（Version 2.1.7.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis. The differentially binding peaks were identified by csaw(version 1.30.1). The Homer（version 4.10）was used for motifs analysis.
Assembly: hg38
Supplementary files format and content: bigwig, narrow peak
Library strategy: iCLIP

extract_protocol:
The samples were irradiated twice with 254 nm UV-C light on ice at 400mJ, and lysed on ice for 15 min with lysis buffer (20 mM Tris, pH 8.0, 1 mM EDTA, 400 mM NaCl, 0.1% SDS, 0.5% Triton X-100 (Merck, cat. no. X100), 1×Protease Inhibitor (Thermo Fisher, cat. no. 87785), 200 U/mL RNasin Plus (Promega, cat. no. N2611) and 20 U/mL DNase I (NEB, cat. no. M0303S)). The lysate was further treated with 40 U RNase I (Thermo Fisher, cat. no. EN0601) and rotary incubated at 37°C for 5 min. The reaction was quenched by adding RNasin® Plus. The mixture was centrifuged at 4°C for 15 minutes at 15,000 g, and 2% of the supernatant was was taken for Input sample. The remain of supernatant was incubated with XRCC5,XRCC6 and PUS1 antibody for immunoprecipitation, rotating slowly at 4°C for 4 h. 10 μL protein A/G magnetic beads (Thermo Fisher, cat. no. 88802) was added and incubated with immune complexes for 2 h followed by successive washes. The 3' phosphate groups on the RNA were removed using FastAP enzyme (Thermo Fisher, cat. no. EF0654) to facilitate subsequent ligation steps. A 3' App-DNA linker is ligated to the RNA molecules using T4 RNA ligase (NEB, cat. no. M0204). The RNA-protein complexes were then separated by Nupage 4-12% Bis-Tris protein gels (Thermo Fisher, cat. no. WG1401BX10) electrophoresis and transferred to a nitrocellulose (NC) membrane. The NC membrane was cut to extract the RNA bound to the protein of interest. The protein-bound RNA was extracted from the NC membrane by incubation with proteinase K (NEB, cat. no. P8107) at 37°C for 20 min and subsequent TRIzol (Thermo Fisher, cat. no. 15596018CN) treatment. The purified RNA was subsequently concentrated, desalted, reverse transcribed. The resulted cDNA was recovered, ligated with a 3' UMI (Unique Molecular Identity) adapter, and amplified by PCR to generate sequencing libraries, which was sequenced on a DNBSEQ-T7 sequencer (MGI) using PE150 mode.eCLIP-seq experiment and high through-put sequencing and data analysis were conducted by Seqhealth Technology Co., LTD., Wuhan, China.
The purified RNA was subsequently concentrated, desalted, reverse transcribed. The resulted cDNA was recovered, ligated with a 3' UMI (Unique Molecular Identity) adapter, and amplified by PCR to generate sequencing libraries, which was sequenced on a DNBSEQ-T7 sequencer (MGI) using PE150 mode.eCLIP-seq experiment and high through-put sequencing and data analysis were conducted by Seqhealth Technology Co., LTD., Wuhan, China.

value: human hepatocellular carcinoma cell line

tag: antibody


title: HepG2.2.15 cells, XRCC6(iCLIP)

description: Library name: HepG2.2.15, iCLIP_XRCC6

value: XRCC6(Proteintech, 10723-1-AP)


title: HepG2.2.15 cells, PUS1(iCLIP)

description: Library name: HepG2.2.15, iCLIP_PUS1


title: iBEC,TranscriptionFactor,Rep1

description: Library name: 3TFiBECR1

value: iBEC


title: HepG2.2.15 cells, XRCC5(Chip)

description: Library name: HepG2.2.15, Chip_XRCC5

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.The clean reads were used for protein binding site analysis. They were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters. The RSeQC（version 2.6）was used for reads distribution analysis.The MACS2 software（Version 2.1.7.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis. The differentially binding peaks were identified by csaw(version 1.30.1). The Homer（version 4.10）was used for motifs analysis.
Assembly: hg38
Supplementary files format and content: bigwig, narrow peak

extract_protocol:
ChIP-seq was performed using the BeyoChIP Enzymatic ChIP Kit (Beyotime, P2083S) with minor modifications. Briefly, cells were cross-linked with 1% formaldehyde for 10 min at 37°C and quenched with 0.125M of glycine. Nuclei were isolated using Buffer A and Buffer B, followed by Micrococcal Nuclease (MNase) digestion. After adding ChIP Buffer, soluble chromatin was collected by centrifugation. An aliquot (2%) was saved as input, and the remainder was pre-cleared with Protein A/G magnetic beads, then incubated overnight at 4°C with XRCC5/6 antibodies. The next day, fresh beads were added for 2 h at 4°C, washed sequentially with low salt, high salt, LiCl, and TE buffers. Immune complexes were eluted and reverse-crosslinked overnight at 65°C, followed by phenol-chloroform extraction and ethanol precipitation. Purified DNA was used for library preparation and sequenced by Seqhealth (Wuhan).
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: XRCC5(Proteintech, 16389-1-AP)


title: HepG2.2.15 cells, IgG(iCLIP)

description: Library name: HepG2.2.15, iCLIP_IgG

value: IgG(Abclonal, AC005)


title: HepG2.2.15 cells, IgG(Chip)

description: Library name: HepG2.2.15, Chip_IgG


title: MGG152_coculture_rep1

city: New Haven

first: Kevin

middle: C

last: Johnson

state: CT

address: 333 Cedar Street

department: Neurosurgery

institute: Yale University

description: Library name: RV11_m152-1

data_processing:
cellranger-9.0.1 using include-introns parameter set to `True`.
Assembly: GRCh38_and_mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: Brain

growth_protocol: Macrophages were isolated from the peritoneal cavity of stimulated mice (C57BL/6 - wild type). The macrophages were collected from 3 male and 3 female mice aged 10 weeks, pooled together, divided into aliquots, and frozen for downstream experiments. Frozen murine primary macrophages were later thawed quickly on Day 1 of the co-culture experiment and 250,000 cells were seeded in 6-well plates in DMEM medium (ThermoFisher, Gibco 11965092) with 10% FBS (ThermoFisher, Gibco A5670701) supplemented and 10 ng/ml of recombinant M-CSF (BioLegend 576406). After 12 hours, macrophage cells were washed with MGG152 complete medium --- Neurobasal (ThermoFisher, Gibco 21103049) with 0.5% N-2 supplement (100x) (ThermoFisher, Gibco 17502048), 2% B-27 Supplement (50X) (ThermoFisher, Gibco 17504044), 1.5% L-Glutamine (Corning 25-005-CI), 0.5% Antibiotic-antimycotic (Corning 30-004-CI), 20 ng/ml human FGF (PeproTech AF-100-26), 40 ng/ml human EGF (PeproTech AF-100-15), and 10 ng/ml recombinant M-CSF --- for 4 times to remove FBS. 450,000 dissociated MGG152 cells were seeded into the wells with macrophage cells for co-culture.

extract_protocol:
Cells were dissociated into single cells and submitted for 10x single cell RNA-sequencing.
The four different experimental conditions were performed with the same parental MGG152 line per batch. The four different experimental conditions were submitted as a single batch to 10x single-cell RNA sequencing  3' v4 (polyA) OCM.

treatment_protocol: Monoculture and co-culture cells were irradiated using Irradiator X-RAD 320 (Precision X-ray) with 2 Gy dose on each of the following 3 days. After 72-hour recovery period, the cells were harvested.

value: Brain

value: Glioma

value: IDH1 R132H

value: coculture

value: Replicate 1


title: HepG2.2.15 cells, XRCC5(iCLIP)

description: Library name: HepG2.2.15, iCLIP_XRCC5


title: HepG2.2.15 cells, XRCC6(Chip)

description: Library name: HepG2.2.15, Chip_XRCC6


title: MGG152_coculture_irradiation_rep1

description: Library name: RV11_m152-r-1

value: coculture plus irradiation


title: CD11b-positive brain cells (cerebellum removed) RNA-seq of 5xFAD/Cd5l tg/wt mouse 3

city: Shinjuku

first: Natsumi

last: Maehara

state: Tokyo

address: 8-1, Kawata-cho

department: Department of Molecular Biomedicine for Pathogenesis

country: Japan

institute: The Institute for AIM Medicine

description:
Library name: ABAD3
RNA extracted from brain tissue (cerebellum removed) of a 5xFAD/Cd5l tg/wt mouse.

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor sequences and low-quality reads.
Clean reads were aligned to the mouse reference genome.
Aligned reads were summarized at the gene level to obtain read counts.
Gene expression levels were normalized and calculated as FPKM values.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Processed data files contain gene-level expression matrices for each sample, including raw read counts.

source_name: Brain (cerebellum removed)

growth_protocol: Mice were maintained under standard laboratory conditions with free access to food and water. Seven-month-old mice were used for RNA extraction.

extract_protocol:
Total RNA was extracted from CD11b-positive brain cells with the cerebellum removed using a standard RNA extraction protocol according to the manufacturer’s instructions (Promega, Z6011).
RNA-seq libraries were prepared from total RNA following standard library preparation protocols and sequenced on an Illumina platform.

treatment_protocol: Mice of three genotypes (5xFAD,  5xFAD/Cd5l tg/wt) were analyzed.

value: Brain (cerebellum removed)

value: 5xFAD/Cd5l tg/wt


title: CFBE410_1

value: Bronchial epithelial cell

value: Cystic Fibrosis

value: Untreated


title: MGG152_coculture_irradiation_rep3

description: Library name: LZ1_m152-r-3

value: Replicate 3


title: MGG152_coculture_rep2

description: Library name: RV12_m152-2

value: Replicate 2


title: HepG2.2.15 cells(Input)

description: Library name: HepG2.2.15, Input

value: human hepatocellular carcinoma cell line


title: MGG152_coculture_rep3

description: Library name: LZ1_m152-3


title: MGG152_coculture_irradiation_rep2

description: Library name: RV12_m152-r-2


title: MGG152_coculture_rep4

description: Library name: LZ2_m152-4

value: Replicate 4


title: MGG152_coculture_irradiation_rep4

description: Library name: LZ2_m152-r-4


title: CD11b-positive brain cells (cerebellum removed) RNA-seq of 5xFAD mouse 3

description:
Library name: AD3
RNA extracted from brain tissue (cerebellum removed) of a 5xFAD mouse.


title: CD11b-positive brain cells (cerebellum removed) RNA-seq of 5xFAD/Cd5l tg/wt mouse 2

description:
Library name: ABAD2
RNA extracted from brain tissue (cerebellum removed) of a 5xFAD/Cd5l tg/wt mouse.


title: CD11b-positive brain cells (cerebellum removed) RNA-seq of 5xFAD mouse 1

description:
Library name: AD1
RNA extracted from brain tissue (cerebellum removed) of a 5xFAD mouse.


title: Brain tissue (cerebellum removed) RNA-seq of 5xFAD/Cd5l tg/wt mouse 3

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor sequences and low-quality reads.
Clean reads were aligned to the mouse reference genome.
Aligned reads were summarized at the gene level to obtain read counts.
Gene expression levels were normalized and calculated as FPKM values.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Processed data files contain gene-level expression matrices for each sample, including raw read counts and normalized expression values (FPKM).

extract_protocol:
Total RNA was extracted from whole brain tissue with the cerebellum removed using a standard RNA extraction protocol according to the manufacturer’s instructions (Takara, U0955C).
RNA-seq libraries were prepared from total RNA following standard library preparation protocols and sequenced on an Illumina platform.

treatment_protocol: Mice of three genotypes (5xFAD,  5xFAD/Cd5l tg/wt and wild-type) were analyzed.


title: CD11b-positive brain cells (cerebellum removed) RNA-seq of 5xFAD/Cd5l tg/wt mouse 1

description:
Library name: ABAD1
RNA extracted from brain tissue (cerebellum removed) of a 5xFAD/Cd5l tg/wt mouse.


title: Brain tissue (cerebellum removed) RNA-seq of 5xFAD mouse 1


title: Brain tissue (cerebellum removed) RNA-seq of 5xFAD/Cd5l tg/wt mouse 2


title: Brain tissue (cerebellum removed) RNA-seq of 5xFAD mouse 3


title: Brain tissue (cerebellum removed) RNA-seq of 5xFAD/Cd5l tg/wt mouse 1


title: Brain tissue (cerebellum removed) RNA-seq of 5xFAD mouse 2

description:
Library name: AD2
RNA extracted from brain tissue (cerebellum removed) of a 5xFAD mouse.


title: Brain tissue (cerebellum removed) RNA-seq of wild-type mouse 3

description:
Library name: HC3
RNA extracted from brain tissue (cerebellum removed) of a healthy wild-type mouse.

value: wild-type


title: Brain tissue (cerebellum removed) RNA-seq of wild-type mouse 1

description:
Library name: HC1
RNA extracted from brain tissue (cerebellum removed) of a healthy wild-type mouse.


title: Brain tissue (cerebellum removed) RNA-seq of wild-type mouse 2

description:
Library name: HC2
RNA extracted from brain tissue (cerebellum removed) of a healthy wild-type mouse.


title: cardiac cells, Left Atrial Ligated, collected at day4

city: La Jolla

first: Stephanie

middle: E

last: Lindsey

state: CA

address: 9500 Gilman Dr.

institute: UC San Diego

description:
Library name: Day4_LAL
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v5.0.1, 10x Genomics) with default parameters
Assembly: Gallus gallus
Supplementary files format and content: Matrix Market format files (mtx) and tab-separated files (barcodes and features)

organism: Gallus gallus

source_name: Heart

extract_protocol:
Cardiac neural crest cell (CNCC)-derived cells were isolated from chick embryos collected at days 4 to 7 from normal control and left atrial ligation (LAL) conditions. Embryonic cardiac tissues containing CNCC derivatives were dissected and dissociated into single-cell suspensions using enzymatic digestion and gentle mechanical trituration. Cell suspensions were filtered to remove clumps and debris, and viable fluorescently labeled cells were enriched by fluorescence-activated cell sorting based on H2B-RFP signal. Sorted cells were collected in buffer compatible with single-cell capture and immediately processed for 10x Genomics library preparation.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Gene Expression workflow following the manufacturer’s protocol. Briefly, sorted single cells were partitioned into nanoliter-scale gel bead-in-emulsions (GEMs), where cell lysis and reverse transcription were performed. cDNA molecules were labeled with cell barcodes and unique molecular identifiers (UMIs), followed by cDNA amplification, purification, and construction of sequencing-ready libraries. Libraries were sequenced and the resulting reads were processed using Cell Ranger to generate raw and filtered feature-barcode matrices. Downstream analysis was performed in R using Seurat.

value: cardiac cells

value: Heart

tag: age


title: cardiac cells, Left Atrial Ligated, collected at day5

description:
Library name: Day5_LAL
10x Genomics


title: cardiac cells, Left Atrial Ligated, collected at day6

description:
Library name: Day6_LAL
10x Genomics


title: cardiac cells, sham control, collected at day7

description:
Library name: Day7_control
10x Genomics


title: cardiac cells, sham control, collected at day6

description:
Library name: Day6_control
10x Genomics


title: cardiac cells, sham control, collected at day5

description:
Library name: Day5_control
10x Genomics


title: Day 6 wound, C57BL/6 mouse, 24 months old

city: Boston

first: Danny

last: Roh

state: MA

address: 609 Albany Street

institute: Boston University School of Medicine

description:
Library name: RD_SM_24month
10x Genomics Chromium 3' v3; cells isolated from day 6 full-thickness dorsal skin wounds; 24-month-old C57BL/6 male mice; multiple mice pooled per sample; sequenced across 2 lanes (L001, L002); processed files also include RD_SM_24month_matrix.mtx

data_processing:
Raw FASTQ files were processed using Cell Ranger v9.0 (10x Genomics) with default parameters.
Reads were aligned to the mouse reference genome GRCm38/mm10 (Ensembl 98 annotation) using STAR aligner as implemented in Cell Ranger.
Per-cell gene expression matrices (barcodes, features, matrix) were output by Cell Ranger count pipeline.
Downstream analysis was performed in R using Seurat v4. Doublets were removed using DoubletFinder. Low-quality cells were filtered (nFeature_RNA < 200 or > 6000, percent.mt > 20%). Data were normalized using SCTransform. Batch correction across samples was performed using Harmony. Cell clusters were annotated using canonical marker genes.
Differential expression and gene set enrichment analysis (GSEA) were performed using Seurat/presto and clusterProfiler with Hallmark and curated senescence/SASP gene sets.
Assembly: GRCm38/mm10
Supplementary files format and content: barcodes.tsv.gz: cell barcodes output from Cell Ranger count
Supplementary files format and content: features.tsv.gz: gene IDs and names; matrix.mtx.gz: UMI count matrix in Matrix Market Exchange Format; combined_seu_postHarmony.rds: Seurat object with Harmony-integrated, annotated clusters

source_name: dorsal skin wound

growth_protocol: C57BL/6 male mice (2-month and 24-month) were maintained under standard specific pathogen-free conditions with ad libitum access to food and water. All animal experiments were approved by the Boston University Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Total RNA was extracted from single-cell suspensions prepared from day 6 dorsal wound tissue. Single cells were encapsulated using the 10x Genomics Chromium Controller. Reverse transcription and cDNA amplification were performed per manufacturer instructions (10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1).
Gene expression libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1 following manufacturer's protocol. Library quality was assessed using an Agilent Bioanalyzer High Sensitivity DNA chip and quantified by qPCR prior to sequencing on an Illumina NovaSeq 6000 (paired-end, 28x91 bp).

treatment_protocol: Full-thickness 10mm dorsal skin wounds were created on the dorsum of anesthetized mice. Wound tissue was harvested at day 6 post-wounding. For single-cell isolation, wound tissue was minced and enzymatically dissociated in collagenase/dispase solution at 37°C, followed by red blood cell lysis and filtration through a 40-micron strainer. Cell viability was confirmed by trypan blue exclusion prior to loading.

value: dorsal skin wound

value: 24 months old

value: total wound cells (pooled)

value: wild type

value: full-thickness dorsal excisional wound, day 6


title: Mouse Arid1aWt Bcl2 Mutant rep 3

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

description: Library name: CB_Arid1aWt_Bcl2Mut_3

data_processing:
Trimming by TrimGalore
Alignment by BWA
Filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Assembly: hg38 / mm10
Supplementary files format and content: bed files of MACS2 narrowPeaks

source_name: Spleen

extract_protocol:
Omni ATAC-Seq protocol (Corces et al., 2017; Nature Methods)
Amplification with Q5® High-Fidelity 2X Master Mix and Illumina dual indexes.

treatment_protocol: Inhibitor or DMSO treatment for 24h.

value: Spleen

value: B Cells

value: Arid1a WT Bcl2 Mutant


title: Mouse Arid1aWt Bcl2 Mutant rep 5

description: Library name: CB_Arid1aWt_Bcl2Mut_5


title: Mouse Arid1aWt Bcl2 Mutant rep 4

description: Library name: CB_Arid1aWt_Bcl2Mut_4


title: Day 6 wound, C57BL/6 mouse, 2 months old

description:
Library name: RD_SM_2month
10x Genomics Chromium 3' v3; cells isolated from day 6 full-thickness dorsal skin wounds; 2-month-old C57BL/6 male mice; multiple mice pooled per sample; sequenced across 2 lanes (L001, L002); processed files also include RD_SM_2month_matrix.mtx

value: 2 months old


title: Mouse Arid1aWt Bcl2 Mutant rep 6

description: Library name: CB_Arid1aWt_Bcl2Mut_6


title: Mouse Arid1aWt Bcl2 Mutant rep 1

description: Library name: CB_Arid1aWt_Bcl2Mut_1


title: Mouse Arid1aHet Bcl2 Mutant rep 10

description: Library name: CB_Arid1aHet_Bcl2Mut_10

value: Arid1a Het Bcl2 Mutant


title: Mouse Arid1aHet Bcl2 Mutant rep 11

description: Library name: CB_Arid1aHet_Bcl2Mut_11


title: Mouse Arid1aWt Bcl2 Mutant rep 2

description: Library name: CB_Arid1aWt_Bcl2Mut_2


title: Mouse Arid1aHet Bcl2 Mutant rep 12

description: Library name: CB_Arid1aHet_Bcl2Mut_12


title: Mouse Arid1aHet Bcl2 Mutant rep 9

description: Library name: CB_Arid1aHet_Bcl2Mut_9


title: Mouse Arid1aHet Bcl2 Mutant rep 8

description: Library name: CB_Arid1aHet_Bcl2Mut_8


title: Mouse Arid1aHet Bcl2 Mutant rep 4

description: Library name: CB_Arid1aHet_Bcl2Mut_4


title: Mouse Arid1aHet Bcl2 Mutant rep 3

description: Library name: CB_Arid1aHet_Bcl2Mut_3


title: Mouse Arid1aHet Bcl2 Mutant rep 7

description: Library name: CB_Arid1aHet_Bcl2Mut_7


title: Mouse Arid1aHet Bcl2 Mutant rep 1

description: Library name: CB_Arid1aHet_Bcl2Mut_1


title: Mouse Arid1aHet Bcl2 Mutant rep 5

description: Library name: CB_Arid1aHet_Bcl2Mut_5


title: Ang II+Tec heart 3

city: Chongqing

first: Yanghao

last: Chen

address: No. 288, Tianwen Avenue, Nan'an District, Chongqing

institute: Chongqing Medical University

description:
Library name: S3
S3

data_processing:
Illumina novaseq 6000 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted from samples using the RNAiso Plus reagent (Cat# 9108; Takara, Japan) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 8-week-old male C57BL/6J mice were housed under specific pathogen-free conditions with controlled environmental parameters (temperature: 20–25℃; humidity: 50 ± 5%; standard 12/12-hour light/dark cycle). Mice had free access to sterile water and chow. Pathological cardiac hypertrophy was induced by continuous four-week infusion of angiotensin II (1 μg/kg/min) via osmotic pumps.In the Tec efficacy assessment experiment, mice were infused with Ang II for 4 weeks and treated with Tec 5 mg/kg for the last 2 weeks of the infusion period.

value: heart

value: WT

value: Ang II + Tec treatment


title: Ang II heart 3

description:
Library name: A3
A3

value: Ang II


title: Ang II heart 2

description:
Library name: A2
A2


title: Ang II+Tec heart 1

description:
Library name: S1
S1


title: Mouse Arid1aHet Bcl2 Mutant rep 2

description: Library name: CB_Arid1aHet_Bcl2Mut_2


title: Ang II heart 1

description:
Library name: A1
A1


title: Id3 oe rep2, Stem, Cut&Run

city: washington dc

first: Shaoqi

last: Zhu

state: WASHINGTON

address: 725 21st st nw

institute: the george washington university

description:
Library name: Id3_oe_rep2_Stem
Day-6-3xT7-ID3-OE-1-Fix-Stem_peaks.narrowPeak
Day-6-3xT7-ID3-OE-1-Fix-Stem_scaled.bw

data_processing:
Cut&Run reads were trimmed remaining 100 bp from 5'end using trim_galore (v3.5).
Cut&Run reads were aligned to the mm10 genome using Bowtie2 version 2.3.4.1.
Sam files were then processed to bam files using samtools (v1.7) and duplication reads were removed using picard MarkDuplicates (v2.21.6).
Bam files were then processed by macs2 (v2.1.1) with qval<0.05, fold enrichment>3 to call narrowPeak.
BigWig files were transfered from macs2 output bdg files normalized by reads on peaks.
Assembly: mm10
Supplementary files format and content: narrowPeak
Supplementary files format and content: bw
Library strategy: CUT&Run

source_name: spleen

growth_protocol: Naive P14 TCR transgenic CD8+ T cells were primed in vitro with plate-bound anti-CD3/CD28 for 24 hours and then spin-infected with retroviral constructs encoding 3×T7-tagged Id2, 3×T7-tagged Id3, or empty vector control. After overnight culture, transduced cells were adoptively transferred into CD45.1 recipient mice, which were subsequently infected with LCMV Clone 13. On day 6 post-infection, Tim3+Slamf6− 3×T7-Id2 P14 cells were sorted as Tex-eff cells, and Tim3−Slamf6+ 3×T7-Id3 P14 cells were sorted as Tpex cells for downstream analyses.

extract_protocol:
CD8+ T cell subsets were crossed-linked with formaldehyde, and then incubated with T7 antibody overnight, followed by incubation with Protein A/G-MNase, calcium-mediated MNase activation. The reaction was stopped and then genomic DNA fragments were extracted.
The DNA segments from T7 Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Nova-seq platform.

treatment_protocol: Sorted cells were used directly for downstream analyses without further treatment.

value: spleen

value: CD45.2+ CD8+ T cells

value: 3xT7 Id3 overexpression

value: day 6 post-infection with LCMV Cl13


title: Mouse Arid1aHet Bcl2 Mutant rep 6

description: Library name: CB_Arid1aHet_Bcl2Mut_6


title: Id2 oe rep1, Term, Cut&Run

description:
Library name: Id2_oe_rep1_Term
Day-6-3xT7-ID2-OE-1-Fix-Term_peaks.narrowPeak
Day-6-3xT7-ID2-OE-1-Fix-Term_scaled.bw

value: 3xT7 Id2 overexpression


title: Id2 oe rep2, Term, Cut&Run

description:
Library name: Id2_oe_rep2_Term
Day-6-3xT7-ID2-OE-1-Fix-Term_peaks.narrowPeak
Day-6-3xT7-ID2-OE-1-Fix-Term_scaled.bw


title: Runx3 rep1, Id2KO Term, Cut&Run

description:
Library name: Day-6-SgID2-Term-Runx3_rep1
Day-6-SgID2-Term-Runx3-CR_peaks.narrowPeak
Day-6-SgID2-Term-Runx3-CR_scaled.bw

growth_protocol: Naive P14 TCR transgenic CD8+ T cells were nucleofected with sgRNAs targeting Thy1 (as a negative control) and those targeting Id2. The nucleofected P14 cells were adoptively transferred into CD45-disparate recipients and subsequently infected with LCMV-Clone 13 to induce chronic viral infection. On day 8 post-infection,  Tim3+Slamf6- P14 cells were sorted and purified as effector exhausted CD8+ T (Tex-eff) cells were sorted forfor downstream analysis.

extract_protocol:
CD8+ T cell subsets incubated with Runx3 antibody overnight, followed by incubation with Protein A/G-MNase, calcium-mediated MNase activation. The reaction was stopped and then genomic DNA fragments were extracted
The DNA segments from Runx3 Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Nova-seq platform.

value: Id2 KO with sgRNA


title: Id3 oe rep1, Stem, Cut&Run

description:
Library name: Id3_oe_rep1_Stem
Day-6-3xT7-ID3-OE-1-Fix-Stem_peaks.narrowPeak
Day-6-3xT7-ID3-OE-1-Fix-Stem_scaled.bw


title: Runx3 rep2, WT Term, Cut&Run

description:
Library name: Day-6-SgTHy1.2-Term-Runx3_rep2
Day-6-SgTHy1.2-Term-Runx3-CR_peaks.narrowPeak
Day-6-SgTHy1.2-Term-Runx3-CR_scaled.bw


title: Runx3 rep2, Id2KO Term, Cut&Run

description:
Library name: Day-6-SgID2-Term-Runx3_rep2
Day-6-SgID2-Term-Runx3-CR_peaks.narrowPeak
Day-6-SgID2-Term-Runx3-CR_scaled.bw


title: IgG, Cut&Run

description: Library name: IgG

value: 3xT7 backbone overexpression


title: E2A rep1, Id2KO Term, Cut&Run

description:
Library name: Day-6-SgID2-Term-E2A_rep1
Day-6-SgID2-Term-E2A-CR_peaks.narrowPeak
Day-6-SgID2-Term-E2A-CR_scaled.bw

extract_protocol:
CD8+ T cell subsets incubated with E2A antibody overnight, followed by incubation with Protein A/G-MNase, calcium-mediated MNase activation. The reaction was stopped and then genomic DNA fragments were extracted
The DNA segments from E2A Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Nova-seq platform.


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Necrosis_24_Run2_2

city: Cambridge

first: Julien

last: Tessier

address: 350 Water Street

institute: Sanofi US

description: Library name: Lib-DSP-1001660035636-E-H12

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

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

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

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

tag: mouse id

tag: region of_interest,_label

value: Necrosis

tag: region of_interest,_id


title: E2A rep1, WT Term, Cut&Run

description:
Library name: Day-6-SgTHy1.2-Term-E2A_rep1
Day-6-SgTHy1.2-Term-E2A-CR_peaks.narrowPeak
Day-6-SgTHy1.2-Term-E2A-CR_scaled.bw


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Necrosis_22_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H10


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Necrosis_20_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H08


title: Runx3 rep1, WT Term, Cut&Run

description:
Library name: Day-6-SgTHy1.2-Term-Runx3_rep1
Day-6-SgTHy1.2-Term-Runx3-CR_peaks.narrowPeak
Day-6-SgTHy1.2-Term-Runx3-CR_scaled.bw


title: E2A rep2, Id2KO Term, Cut&Run

description:
Library name: Day-6-SgID2-Term-E2A_rep2
Day-6-SgID2-Term-E2A-CR_peaks.narrowPeak
Day-6-SgID2-Term-E2A-CR_scaled.bw


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Necrosis_23_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H11


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Tumor_15_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H03

value: Tumor


title: E2A rep2, WT Term, Cut&Run

description:
Library name: Day-6-SgTHy1.2-Term-E2A_rep2
Day-6-SgTHy1.2-Term-E2A-CR_peaks.narrowPeak
Day-6-SgTHy1.2-Term-E2A-CR_scaled.bw


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Necrosis_21_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H09


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Necrosis_19_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H07


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Tumor_14_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H02


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Necrosis_17_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H05


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Necrosis_18_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H06


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Tumor_16_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H04


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Tumor_11_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G11


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Leading Edge_5_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G05

value: Leading Edge


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Leading Edge_4_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G04


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Leading Edge_2_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G02


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Leading Edge_1_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G01


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Tumor_12_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G12


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Leading Edge_6_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G06


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Tumor_13_Run2_2

description: Library name: Lib-DSP-1001660035636-E-H01


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Leading Edge_8_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G08


title: Group 3_mIgG-mutmIL15_G3_30_Necrosis_23_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F11


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Leading Edge_7_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G07


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Tumor_10_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G10


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Tumor_9_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G09


title: Group 3_mIgG-mutmIL15_G3_30_Necrosis_22_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F10


title: Group 3_mIgG-mutmIL15_G3_30_Necrosis_20_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F08


title: Group 3_mIgG-mutmIL15_G3_30_Necrosis_17_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F05


title: Group 3_mIgG-mutmIL15_G3_30_Necrosis_21_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F09


title: Group 4_anti-mPD-1-mutmIL15_G4_40_Leading Edge_3_Run2_2

description: Library name: Lib-DSP-1001660035636-E-G03


title: Group 3_mIgG-mutmIL15_G3_30_Necrosis_18_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F06


title: Group 3_mIgG-mutmIL15_G3_30_Necrosis_19_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F07


title: Group 3_mIgG-mutmIL15_G3_30_Tumor_15_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F03


title: Group 3_mIgG-mutmIL15_G3_30_Necrosis_24_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F12


title: Group 3_mIgG-mutmIL15_G3_30_Tumor_12_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E12


title: Group 3_mIgG-mutmIL15_G3_30_Tumor_13_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F01


title: Group 3_mIgG-mutmIL15_G3_30_Tumor_14_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F02


title: Ang II+Tec heart 2

description:
Library name: S2
S2


title: Group 3_mIgG-mutmIL15_G3_30_Tumor_9_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E09


title: Group 3_mIgG-mutmIL15_G3_30_Tumor_10_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E10


title: Group 3_mIgG-mutmIL15_G3_30_Leading Edge_8_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E08


title: Group 3_mIgG-mutmIL15_G3_30_Tumor_16_Run2_2

description: Library name: Lib-DSP-1001660035636-E-F04


title: Group 3_mIgG-mutmIL15_G3_30_Leading Edge_7_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E07


title: Group 3_mIgG-mutmIL15_G3_30_Leading Edge_6_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E06


title: Group 3_mIgG-mutmIL15_G3_30_Leading Edge_5_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E05


title: Group 3_mIgG-mutmIL15_G3_30_Tumor_11_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E11


title: Group 2_anti-mPD-1_G2_20_Necrosis_24_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D12


title: Group 3_mIgG-mutmIL15_G3_30_Leading Edge_4_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E04


title: Group 2_anti-mPD-1_G2_20_Necrosis_22_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D10


title: Group 3_mIgG-mutmIL15_G3_30_Leading Edge_3_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E03


title: Group 2_anti-mPD-1_G2_20_Necrosis_21_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D09


title: Group 2_anti-mPD-1_G2_20_Necrosis_23_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D11


title: Group 2_anti-mPD-1_G2_20_Necrosis_19_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D07


title: Group 2_anti-mPD-1_G2_20_Necrosis_20_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D08


title: Group 2_anti-mPD-1_G2_20_Necrosis_18_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D06


title: Group 2_anti-mPD-1_G2_20_Tumor_14_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D02


title: Group 2_anti-mPD-1_G2_20_Tumor_13_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D01


title: Group 2_anti-mPD-1_G2_20_Tumor_16_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D04


title: Group 2_anti-mPD-1_G2_20_Tumor_12_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C12


title: Group 3_mIgG-mutmIL15_G3_30_Leading Edge_1_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E01


title: Group 3_mIgG-mutmIL15_G3_30_Leading Edge_2_Run2_2

description: Library name: Lib-DSP-1001660035636-E-E02


title: Group 2_anti-mPD-1_G2_20_Tumor_11_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C11


title: Group 2_anti-mPD-1_G2_20_Tumor_9_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C09


title: Group 2_anti-mPD-1_G2_20_Tumor_10_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C10


title: Group 2_anti-mPD-1_G2_20_Leading Edge_8_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C08


title: Group 2_anti-mPD-1_G2_20_Leading Edge_7_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C07


title: Group 2_anti-mPD-1_G2_20_Leading Edge_4_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C04


title: Group 2_anti-mPD-1_G2_20_Necrosis_17_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D05


title: Group 2_anti-mPD-1_G2_20_Leading Edge_3_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C03


title: Group 2_anti-mPD-1_G2_20_Leading Edge_5_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C05


title: Group 1_Isotype Control_G1_9_Necrosis_22_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B11

value: Isotype Control


title: Group 2_anti-mPD-1_G2_20_Leading Edge_6_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C06


title: Group 2_anti-mPD-1_G2_20_Leading Edge_1_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C01


title: Group 1_Isotype Control_G1_9_Necrosis_23_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B12


title: Group 2_anti-mPD-1_G2_20_Leading Edge_2_Run2_2

description: Library name: Lib-DSP-1001660035636-E-C02


title: Group 1_Isotype Control_G1_9_Necrosis_20_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B09


title: Group 1_Isotype Control_G1_9_Necrosis_21_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B10


title: Group 1_Isotype Control_G1_9_Necrosis_19_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B08


title: Group 1_Isotype Control_G1_9_Necrosis_17_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B06


title: Group 1_Isotype Control_G1_9_Tumor_16_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B05


title: Group 2_anti-mPD-1_G2_20_Tumor_15_Run2_2

description: Library name: Lib-DSP-1001660035636-E-D03


title: Group 1_Isotype Control_G1_9_Necrosis_18_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B07


title: Group 1_Isotype Control_G1_9_Tumor_14_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B03


title: Group 1_Isotype Control_G1_9_Tumor_13_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B02


title: Group 1_Isotype Control_G1_9_Tumor_12_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B01


title: Group 1_Isotype Control_G1_9_Tumor_11_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A12


title: Group 1_Isotype Control_G1_9_Tumor_9_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A10


title: Group 1_Isotype Control_G1_9_Tumor_10_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A11


title: Group 1_Isotype Control_G1_9_Leading Edge_6_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A07


title: Group 1_Isotype Control_G1_9_Tumor_15_Run2_2

description: Library name: Lib-DSP-1001660035636-E-B04


title: Group 1_Isotype Control_G1_9_Leading Edge_7_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A08


title: Group 1_Isotype Control_G1_9_Leading Edge_4_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A05


title: Group 1_Isotype Control_G1_9_Leading Edge_3_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A04


title: Group 1_Isotype Control_G1_9_Leading Edge_2_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A03


title: Group 1_Isotype Control_G1_9_Leading Edge_1_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A02


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Necrosis_22_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H10


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Necrosis_24_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H12


title: Group 1_Isotype Control_G1_9_Leading Edge_5_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A06


title: NTC_NTC_NTC_NTC_NTC_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A01

source_name: NTC

value: NTC


title: Group 1_Isotype Control_G1_9_Leading Edge_8_Run2_2

description: Library name: Lib-DSP-1001660035636-E-A09


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Necrosis_23_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H11


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Necrosis_21_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H09


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Tumor_16_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H04


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Necrosis_20_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H08


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Necrosis_17_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H05


title: Slide 5; ROI 034; Segment: CD45

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

description:
Library name: DSP-1001660008135-B-H10
Sample/column name in raw count matrix = Slide 5 | 034 | CD45 ; in normalized count matrix = IDC_Normal_CD45_S5_034. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 034; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

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

source_name: breast tissue

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

value: breast tissue

value: leukocytes

tag: slide

value: Slide 5

tag: roi

value: ROI 034

tag: segment


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Necrosis_18_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H06


title: Slide 5; ROI 034; Segment: SMA

description:
Library name: DSP-1001660008135-B-H11
Sample/column name in raw count matrix = Slide 5 | 034 | SMA ; in normalized count matrix = IDC_Normal_SMA_S5_034. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 034; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: fibroblasts/myoepithelial cells

value: SMA


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Tumor_15_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H03


title: Slide 5; ROI 034; Segment: CK

description:
Library name: DSP-1001660008135-B-H09
Sample/column name in raw count matrix = Slide 5 | 034 | CK ; in normalized count matrix = IDC_Normal_CK_S5_034. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 034; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: epithelial cells

value: CK


title: Slide 5; ROI 033; Segment: SMA

description:
Library name: DSP-1001660008135-B-H08
Sample/column name in raw count matrix = Slide 5 | 033 | SMA ; in normalized count matrix = IDC_Normal_SMA_S5_033. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 033; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 033


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Tumor_14_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H02


title: Slide 5; ROI 033; Segment: CD45

description:
Library name: DSP-1001660008135-B-H07
Sample/column name in raw count matrix = Slide 5 | 033 | CD45 ; in normalized count matrix = IDC_Normal_CD45_S5_033. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 033; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Necrosis_19_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H07


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Tumor_13_Run2_1

description: Library name: Lib-DSP-1001660037469-D-H01


title: Slide 5; ROI 033; Segment: CK

description:
Library name: DSP-1001660008135-B-H06
Sample/column name in raw count matrix = Slide 5 | 033 | CK ; in normalized count matrix = IDC_Normal_CK_S5_033. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 033; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Tumor_12_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G12


title: Slide 5; ROI 032; Segment: SMA

description:
Library name: DSP-1001660008135-B-H05
Sample/column name in raw count matrix = Slide 5 | 032 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_032. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 032; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 032


title: Slide 5; ROI 032; Segment: CD45

description:
Library name: DSP-1001660008135-B-H04
Sample/column name in raw count matrix = Slide 5 | 032 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S5_032. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 032; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 032; Segment: CK

description:
Library name: DSP-1001660008135-B-H03
Sample/column name in raw count matrix = Slide 5 | 032 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_032. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 032; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Tumor_10_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G10


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Leading Edge_8_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G08


title: Slide 5; ROI 031; Segment: SMA

description:
Library name: DSP-1001660008135-B-H02
Sample/column name in raw count matrix = Slide 5 | 031 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_031. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 031; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 031


title: Slide 5; ROI 031; Segment: CD45

description:
Library name: DSP-1001660008135-B-H01
Sample/column name in raw count matrix = Slide 5 | 031 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S5_031. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 031; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Tumor_11_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G11


title: Slide 5; ROI 031; Segment: CK

description:
Library name: DSP-1001660008135-B-G12
Sample/column name in raw count matrix = Slide 5 | 031 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_031. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 031; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Tumor_9_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G09


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Leading Edge_6_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G06


title: Slide 5; ROI 030; Segment: SMA

description:
Library name: DSP-1001660008135-B-G11
Sample/column name in raw count matrix = Slide 5 | 030 | SMA ; in normalized count matrix = IDC_High_SMA_S5_030. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 030; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 030


title: Slide 5; ROI 030; Segment: CD45

description:
Library name: DSP-1001660008135-B-G10
Sample/column name in raw count matrix = Slide 5 | 030 | CD45 ; in normalized count matrix = IDC_High_CD45_S5_030. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 030; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Leading Edge_5_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G05


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Leading Edge_2_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G02


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Leading Edge_3_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G03


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Leading Edge_4_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G04


title: Slide 5; ROI 029; Segment: SMA

description:
Library name: DSP-1001660008135-B-G08
Sample/column name in raw count matrix = Slide 5 | 029 | SMA ; in normalized count matrix = DCIS_High_SMA_S5_029. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 029; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 029


title: cardiac cells, sham control, collected at day4

description:
Library name: Day4_control
10x Genomics

value: cardiac cells

value: Heart


title: Slide 5; ROI 029; Segment: CD45

description:
Library name: DSP-1001660008135-B-G07
Sample/column name in raw count matrix = Slide 5 | 029 | CD45 ; in normalized count matrix = DCIS_High_CD45_S5_029. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 029; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 3_mIgG-mutmIL15_G3_26_Necrosis_24_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F12

value: Necrosis


title: Slide 5; ROI 028; Segment: SMA

description:
Library name: DSP-1001660008135-B-G05
Sample/column name in raw count matrix = Slide 5 | 028 | SMA ; in normalized count matrix = IDC_High_SMA_S5_028. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 028; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 028


title: Slide 5; ROI 029; Segment: CK

description:
Library name: DSP-1001660008135-B-G06
Sample/column name in raw count matrix = Slide 5 | 029 | CK ; in normalized count matrix = DCIS_High_CK_S5_029. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 029; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: breast tissue


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Leading Edge_1_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G01

value: Leading Edge


title: Group 4_anti-mPD-1-mutmIL15_G4_38_Leading Edge_7_Run2_1

description: Library name: Lib-DSP-1001660037469-D-G07


title: Slide 5; ROI 030; Segment: CK

description:
Library name: DSP-1001660008135-B-G09
Sample/column name in raw count matrix = Slide 5 | 030 | CK ; in normalized count matrix = IDC_High_CK_S5_030. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 030; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: Slide 5


title: Slide 5; ROI 028; Segment: CD45

description:
Library name: DSP-1001660008135-B-G04
Sample/column name in raw count matrix = Slide 5 | 028 | CD45 ; in normalized count matrix = IDC_High_CD45_S5_028. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 028; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: leukocytes


title: Group 3_mIgG-mutmIL15_G3_26_Necrosis_22_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F10


title: Slide 5; ROI 027; Segment: SMA

description:
Library name: DSP-1001660008135-B-G02
Sample/column name in raw count matrix = Slide 5 | 027 | SMA ; in normalized count matrix = DCIS_High_SMA_S5_027. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 027; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: fibroblasts/myoepithelial cells

value: ROI 027


title: Group 3_mIgG-mutmIL15_G3_26_Necrosis_20_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F08


title: Group 3_mIgG-mutmIL15_G3_26_Necrosis_21_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F09


title: Group 3_mIgG-mutmIL15_G3_26_Necrosis_23_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F11


title: Slide 5; ROI 027; Segment: CD45

description:
Library name: DSP-1001660008135-B-G01
Sample/column name in raw count matrix = Slide 5 | 027 | CD45 ; in normalized count matrix = DCIS_High_CD45_S5_027. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 027; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Slide 5; ROI 027; Segment: CK

description:
Library name: DSP-1001660008135-B-F12
Sample/column name in raw count matrix = Slide 5 | 027 | CK ; in normalized count matrix = DCIS_High_CK_S5_027. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 027; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: epithelial cells


title: Group 3_mIgG-mutmIL15_G3_26_Necrosis_19_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F07


title: Slide 5; ROI 026; Segment: SMA

description:
Library name: DSP-1001660008135-B-F11
Sample/column name in raw count matrix = Slide 5 | 026 | SMA ; in normalized count matrix = DCIS_High_SMA_S5_026. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 026; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 026

value: SMA


title: Group 3_mIgG-mutmIL15_G3_26_Necrosis_18_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F06


title: Slide 5; ROI 026; Segment: CD45

description:
Library name: DSP-1001660008135-B-F10
Sample/column name in raw count matrix = Slide 5 | 026 | CD45 ; in normalized count matrix = DCIS_High_CD45_S5_026. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 026; Segment: CD45
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 3_mIgG-mutmIL15_G3_26_Tumor_16_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F04

value: Tumor


title: Slide 5; ROI 026; Segment: CK

description:
Library name: DSP-1001660008135-B-F09
Sample/column name in raw count matrix = Slide 5 | 026 | CK ; in normalized count matrix = DCIS_High_CK_S5_026. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 026; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: CK


title: Slide 5; ROI 028; Segment: CK

description:
Library name: DSP-1001660008135-B-G03
Sample/column name in raw count matrix = Slide 5 | 028 | CK ; in normalized count matrix = IDC_High_CK_S5_028. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 028; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 3_mIgG-mutmIL15_G3_26_Tumor_15_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F03


title: Group 3_mIgG-mutmIL15_G3_26_Tumor_13_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F01


title: Group 3_mIgG-mutmIL15_G3_26_Tumor_12_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E12


title: Slide 5; ROI 024; Segment: SMA

description:
Library name: DSP-1001660008135-B-F05
Sample/column name in raw count matrix = Slide 5 | 024 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_024. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 024; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 024


title: Slide 5; ROI 023; Segment: SMA

description:
Library name: DSP-1001660008135-B-F03
Sample/column name in raw count matrix = Slide 5 | 023 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S5_023. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 023; Segment: SMA
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 023


title: Slide 5; ROI 025; Segment: CK

description:
Library name: DSP-1001660008135-B-F06
Sample/column name in raw count matrix = Slide 5 | 025 | CK ; in normalized count matrix = DCIS_High_CK_S5_025. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 025; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv

value: ROI 025


title: Slide 5; ROI 024; Segment: CK

description:
Library name: DSP-1001660008135-B-F04
Sample/column name in raw count matrix = Slide 5 | 024 | CK ; in normalized count matrix = DCIS_Normal_CK_S5_024. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 5; ROI 024; Segment: CK
raw_count5.csv
GeoMx_tmm_ruv_normalized_count_linear_S5.csv
sampleAnnoFile_S5.csv


title: Group 3_mIgG-mutmIL15_G3_26_Necrosis_17_Run2_1

description: Library name: Lib-DSP-1001660037469-D-F05


title: Group 3_mIgG-mutmIL15_G3_26_Tumor_10_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E10


title: Group 3_mIgG-mutmIL15_G3_26_Tumor_9_Run2_1

description: Library name: Lib-DSP-1001660037469-D-E09