title: 11870, Sus scrofa, Cerebellum,Cerebellum

description: Library name: itox011870

source_name: Cerebellum,Cerebellum

value: Cerebellum,Cerebellum


title: 1508, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

status: Public on Mar 25 2026

type: SRA

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

country: USA

institute: Pfizer

description: Library name: itox001508

library_source: transcriptomic

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read count mapped to human

molecule: total RNA

organism: Mus musculus

source_name: Thyroid/parathyroid,Thyroid/parathyroid

extract_protocol:
RNA was isolated from tissues using the RNeasy mini kit (Qiagen #74534) according to manufacturer’s protocol. RNAseq cDNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq stranded mRNA kit (Cat. No. RS-122-2101) according to the manufacturer's instructions.
After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA Assay Kit (ThermoFisher Scientific, #Q32853).

tag: tissue

value: Thyroid/parathyroid,Thyroid/parathyroid

tag: batch


title: 225, Rattus norvegicus, Bone marrow - femoral scoop

description: Library name: itox000225

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read counts mapped to human

organism: Rattus norvegicus

source_name: Bone marrow - femoral scoop

value: Bone marrow - femoral scoop


title: 222, Rattus norvegicus, Muscle - Skeletal (gastrocnemius)

description: Library name: itox000222

source_name: Muscle - Skeletal (gastrocnemius)

value: Muscle - Skeletal (gastrocnemius)


title: 226, Rattus norvegicus, Esophagus (mid)

description: Library name: itox000226

source_name: Esophagus (mid)

value: Esophagus (mid)


title: 1510, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001510


title: TA muscle from control (Cre) female mouse 2

city: Nice

first: Olivier

last: Croce

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

description:
Library name: R247_F_Cre_TA
Column name in gene_counts_matrix.txt: R247_F_Cre_TA

data_processing:
Paired-end sequencing (read length: 2x150 bp) was performed by NovoGene using an Illumina sequencer.
Raw RNA-seq reads were quality filtered and trimmed using Trimmomatic.
Trimmed reads were aligned to the mouse reference genome using STAR.
Gene-level count summaries were generated from STAR output and differential expression analysis was performed using DESeq2.
Submitted FASTQ files correspond to quality-filtered and trimmed reads used for alignment.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing gene-level raw counts for all samples (gene_counts_matrix.txt).
Supplementary files format and content: Tab-delimited text file containing sample-level correlation/QC summary values (sample_correlation_matrix.tsv).

source_name: tibialis anterior muscle

growth_protocol: Specific skeletal muscle TRF2 KO mice (HSA-Cre+/-; Terf2-/-) were generated as previously described (Robin et al., 2020). TRF2 floxed mice from the Jackson Laboratory (strain B6;129P2-Terf2tm1Tdl/J) were backcrossed with C57BL/6 for 6 generations and crossed with the HSA-Cre+/- strain expressing Cre recombinase under the control of the Human Skeletal Actin promoter, specifically expressed in striated muscle fibers. Animal procedures were approved by the appropriate ethics committees and regulatory authorities.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions.
Libraries were prepared by NovoGene from total RNA for paired-end Illumina sequencing.

treatment_protocol: Mice were euthanized by isoflurane-induced loss of consciousness followed by cervical dislocation. Gastrocnemius-plantaris-soleus and tibialis anterior muscles were dissected, snap-frozen in liquid nitrogen, and stored at -80°C.

value: tibialis anterior muscle

tag: genotype

value: HSA-Cre+/-

tag: Sex

value: Female

tag: age

value: 8 months


title: 1511, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001511


title: 11752, Sus scrofa, Kidney,Kidney

description: Library name: itox011752

organism: Sus scrofa

source_name: Kidney,Kidney

value: Kidney,Kidney


title: TA muscle from control (Cre) female mouse 1

description:
Library name: R246_F_Cre_TA
Column name in gene_counts_matrix.txt: R246_F_Cre_TA


title: TA muscle from Terf2 KO male mouse 5

description:
Library name: R569_M_KO_TA
Column name in gene_counts_matrix.txt: R569_M_KO_TA

value: HSA-Cre+/- ; Terf2-/-

value: Male


title: TA muscle from Terf2 KO male mouse 4

description:
Library name: R563_M_KO_TA
Column name in gene_counts_matrix.txt: R563_M_KO_TA


title: 227, Rattus norvegicus, Heart - Atrium

description: Library name: itox000227

source_name: Heart - Atrium

value: Heart - Atrium


title: 11892, Sus scrofa, Kidney,Kidney

description: Library name: itox011892


title: TA muscle from Terf2 KO male mouse 2

description:
Library name: R217_M_KO_TA
Column name in gene_counts_matrix.txt: R217_M_KO_TA


title: TA muscle from Terf2 KO male mouse 1

description:
Library name: R211_M_KO_TA
Column name in gene_counts_matrix.txt: R211_M_KO_TA


title: 1580, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001580

source_name: Brain - Cerebellum,Brain - Cerebellum

value: Brain - Cerebellum,Brain - Cerebellum


title: 11871, Sus scrofa, Corpus Callosum,Corpus Callosum

description: Library name: itox011871

source_name: Corpus Callosum,Corpus Callosum

value: Corpus Callosum,Corpus Callosum


title: 228, Rattus norvegicus, Heart - Ventricle (left)

description: Library name: itox000228

source_name: Heart - Ventricle (left)

value: Heart - Ventricle (left)


title: TA muscle from Terf2 KO male mouse 3

description:
Library name: R562_M_KO_TA
Column name in gene_counts_matrix.txt: R562_M_KO_TA


title: 231, Rattus norvegicus, Thyroid/parathyroid

description: Library name: itox000231

source_name: Thyroid/parathyroid

value: Thyroid/parathyroid


title: 229, Rattus norvegicus, Lung (left lobe)

description: Library name: itox000229

source_name: Lung (left lobe)

value: Lung (left lobe)


title: 1582, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001582


title: TA muscle from Terf2 KO female mouse 3

description:
Library name: R559_F_KO_TA
Column name in gene_counts_matrix.txt: R559_F_KO_TA


title: TA muscle from Terf2 KO female mouse 1

description:
Library name: R208_F_KO_TA
Column name in gene_counts_matrix.txt: R208_F_KO_TA


title: 11876, Sus scrofa, Eye,Eye

description: Library name: itox011876

source_name: Eye,Eye

value: Eye,Eye


title: 11873, Sus scrofa, Esophagus,Esophagus

description: Library name: itox011873

source_name: Esophagus,Esophagus

value: Esophagus,Esophagus


title: 1583, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001583


title: 1579, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001579


title: 1512, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001512

value: Thyroid/parathyroid,Thyroid/parathyroid


title: 11872, Sus scrofa, Dorsal Root Ganglion,Dorsal Root Ganglion

description: Library name: itox011872


title: 1584, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001584


title: 276, Rattus norvegicus, Brown Fat (intrascapular)

description: Library name: itox000276

source_name: Brown Fat (intrascapular)

value: Brown Fat (intrascapular)


title: 11874, Sus scrofa, Eye,Eye

description: Library name: itox011874


title: 11875, Sus scrofa, Eye,Eye

description: Library name: itox011875


title: 1581, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001581


title: 277, Rattus norvegicus, Kidney (left to include cortex and medulla)

description: Library name: itox000277


title: GPS muscle from control (Cre) male mouse 5

description:
Library name: R319_M_Cre_GPS
Column name in gene_counts_matrix.txt: R319_M_Cre_GPS

source_name: gastrocnemius-plantaris-soleus muscle

value: gastrocnemius-plantaris-soleus muscle


title: 230, Rattus norvegicus, Thymus

description: Library name: itox000230

source_name: Thymus

value: Thymus


title: TA muscle from Terf2 KO female mouse 2

description:
Library name: R22_F_KO_TA
Column name in gene_counts_matrix.txt: R22_F_KO_TA

value: tibialis anterior muscle

value: Female


title: 11879, Sus scrofa, Adrenal Gland,Adrenal Gland

description: Library name: itox011879

source_name: Adrenal Gland,Adrenal Gland

value: Adrenal Gland,Adrenal Gland


title: 278, Rattus norvegicus, Mammary Gland/Tissue (female only)

description: Library name: itox000278

source_name: Mammary Gland/Tissue (female only)

value: Mammary Gland/Tissue (female only)


title: GPS muscle from control (Cre) male mouse 4

description:
Library name: R318_M_Cre_GPS
Column name in gene_counts_matrix.txt: R318_M_Cre_GPS

value: HSA-Cre+/-

value: Male

value: 8 months


title: 1585, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001585

value: Brain - Cerebellum,Brain - Cerebellum


title: 279, Rattus norvegicus, Brain - Spinal cord (cervical)

description: Library name: itox000279

source_name: Brain - Spinal cord (cervical)

value: Brain - Spinal cord (cervical)


title: GPS muscle from control (Cre) male mouse 2

description:
Library name: R245_M_Cre_GPS
Column name in gene_counts_matrix.txt: R245_M_Cre_GPS


title: 280, Rattus norvegicus, Skin (inguinal)

description: Library name: itox000280

source_name: Skin (inguinal)

value: Skin (inguinal)


title: 1586, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001586


title: 11994, Sus scrofa, Esophagus,Esophagus

description: Library name: itox011994


title: 11993, Sus scrofa, Epididymis,Epididymis

description: Library name: itox011993

source_name: Epididymis,Epididymis

value: Epididymis,Epididymis


title: 1589, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001589


title: GPS muscle from control (Cre) male mouse 3

description:
Library name: R317_M_Cre_GPS
Column name in gene_counts_matrix.txt: R317_M_Cre_GPS


title: GPS muscle from control (Cre) male mouse 1

description:
Library name: R321_M_Cre_GPS
Column name in gene_counts_matrix.txt: R321_M_Cre_GPS


title: 11996, Sus scrofa, Eye,Eye

description: Library name: itox011996

value: Eye,Eye


title: 281, Rattus norvegicus, Ureter

description: Library name: itox000281

source_name: Ureter

value: Ureter


title: 11995, Sus scrofa, Eye,Eye

description: Library name: itox011995


title: 1588, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001588


title: 1587, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001587


title: 11974, Sus scrofa, Temporal Lobe,Temporal Lobe

description: Library name: itox011974

source_name: Temporal Lobe,Temporal Lobe

value: Temporal Lobe,Temporal Lobe


title: GPS muscle from control (Cre) female mouse 4

description:
Library name: R249_F_Cre_GPS
Column name in gene_counts_matrix.txt: R249_F_Cre_GPS


title: 282, Rattus norvegicus, Urinary Bladder

description: Library name: itox000282

source_name: Urinary Bladder

value: Urinary Bladder


title: 284, Rattus norvegicus, DRG-L4

description: Library name: itox000284


title: 1591, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001591

source_name: Brain - Cerebellum,Brain - Cerebellum


title: GPS muscle from control (Cre) female mouse 5

description:
Library name: R320_F_Cre_GPS
Column name in gene_counts_matrix.txt: R320_F_Cre_GPS

value: gastrocnemius-plantaris-soleus muscle


title: 283, Rattus norvegicus, Adrenal Gland

description: Library name: itox000283

source_name: Adrenal Gland

value: Adrenal Gland


title: 11880, Sus scrofa, Mammary Gland,Mammary Gland

description: Library name: itox011880

source_name: Mammary Gland,Mammary Gland

value: Mammary Gland,Mammary Gland


title: 1590, Mus musculus, Brain-Cerebellum,Brain-Cerebellum

description: Library name: itox001590

source_name: Brain-Cerebellum,Brain-Cerebellum

value: Brain-Cerebellum,Brain-Cerebellum


title: GPS muscle from control (Cre) female mouse 3

description:
Library name: R248_F_Cre_GPS
Column name in gene_counts_matrix.txt: R248_F_Cre_GPS

value: Female


title: 1592, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001592


title: 11975, Sus scrofa, Thalamus,Thalamus

description: Library name: itox011975

source_name: Thalamus,Thalamus

value: Thalamus,Thalamus


title: 286, Rattus norvegicus, Brain- Hippocampus

description: Library name: itox000286

source_name: Brain- Hippocampus

value: Brain- Hippocampus


title: 11997, Sus scrofa, Eye,Eye

description: Library name: itox011997

source_name: Eye,Eye


title: GPS muscle from control (Cre) female mouse 1

description:
Library name: R246_F_Cre_GPS
Column name in gene_counts_matrix.txt: R246_F_Cre_GPS

source_name: gastrocnemius-plantaris-soleus muscle

value: HSA-Cre+/-


title: 285, Rattus norvegicus, Brain-Striatum

description: Library name: itox000285

source_name: Brain-Striatum

value: Brain-Striatum


title: 12001, Sus scrofa, Mammary Gland,Mammary Gland

description: Library name: itox012001


title: 287, Rattus norvegicus, Pituitary

description: Library name: itox000287

source_name: Pituitary

value: Pituitary


title: 1593, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001593

value: Brain - Cerebellum,Brain - Cerebellum


title: 1594, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001594

source_name: Brain - Cortex,Brain - Cortex

value: Brain - Cortex,Brain - Cortex


title: GPS muscle from Terf2 KO male mouse 4

description:
Library name: R569_M_KO_GPS
Column name in gene_counts_matrix.txt: R569_M_KO_GPS

value: HSA-Cre+/- ; Terf2-/-

value: Male

value: 8 months


title: 12000, Sus scrofa, Adrenal Gland,Adrenal Gland

description: Library name: itox012000

source_name: Adrenal Gland,Adrenal Gland

value: Adrenal Gland,Adrenal Gland


title: 12002, Sus scrofa, Parathyroid Gland,Parathyroid Gland

description: Library name: itox012002

source_name: Parathyroid Gland,Parathyroid Gland

value: Parathyroid Gland,Parathyroid Gland


title: 62, Rattus norvegicus, Ileum

description: Library name: itox000062

source_name: Ileum

value: Ileum


title: GPS muscle from Terf2 KO male mouse 3

description:
Library name: R562_M_KO_GPS
Column name in gene_counts_matrix.txt: R562_M_KO_GPS

value: gastrocnemius-plantaris-soleus muscle


title: 1596, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001596


title: 63, Rattus norvegicus, Testis (tubules\, without capsule)

description: Library name: itox000063

source_name: Testis (tubules\, without capsule)

value: Testis (tubules\, without capsule)


title: GPS muscle from control (Cre) female mouse 2

description:
Library name: R247_F_Cre_GPS
Column name in gene_counts_matrix.txt: R247_F_Cre_GPS


title: GPS muscle from Terf2 KO male mouse 2

description:
Library name: R217_M_KO_GPS
Column name in gene_counts_matrix.txt: R217_M_KO_GPS


title: 71, Rattus norvegicus, Muscle - Skeletal (gastrocnemius)

description: Library name: itox000071

source_name: Muscle - Skeletal (gastrocnemius)

value: Muscle - Skeletal (gastrocnemius)


title: 12003, Sus scrofa, Pituitary Gland,Pituitary Gland

description: Library name: itox012003

source_name: Pituitary Gland,Pituitary Gland

value: Pituitary Gland,Pituitary Gland


title: 1598, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001598


title: 72, Rattus norvegicus, Peripheral Nerve (sciatic)

description: Library name: itox000072

source_name: Peripheral Nerve (sciatic)

value: Peripheral Nerve (sciatic)


title: GPS muscle from Terf2 KO male mouse 1

description:
Library name: R211_M_KO_GPS
Column name in gene_counts_matrix.txt: R211_M_KO_GPS


title: 12004, Sus scrofa, Prostate Gland,Prostate Gland

description: Library name: itox012004

source_name: Prostate Gland,Prostate Gland

value: Prostate Gland,Prostate Gland


title: 1599, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001599


title: 168, Rattus norvegicus, Adrenal Gland

description: Library name: itox000168

source_name: Adrenal Gland

value: Adrenal Gland


title: GPS muscle from Terf2 KO female mouse 3

description:
Library name: R559_F_KO_GPS
Column name in gene_counts_matrix.txt: R559_F_KO_GPS

value: Female


title: 12005, Sus scrofa, Salivary Gland,Salivary Gland

description: Library name: itox012005

source_name: Salivary Gland,Salivary Gland

value: Salivary Gland,Salivary Gland


title: GPS muscle from Terf2 KO female mouse 2

description:
Library name: R22_F_KO_GPS
Column name in gene_counts_matrix.txt: R22_F_KO_GPS


title: 169, Rattus norvegicus, DRG-L4

description: Library name: itox000169


title: 12006, Sus scrofa, Thyroid Gland,Thyroid Gland

description: Library name: itox012006

source_name: Thyroid Gland,Thyroid Gland

value: Thyroid Gland,Thyroid Gland


title: 170, Rattus norvegicus, Brain-Striatum

description: Library name: itox000170

value: Brain-Striatum


title: 12031, Sus scrofa, Heart,Heart

description: Library name: itox012031

source_name: Heart,Heart

value: Heart,Heart


title: 1665, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001665


title: GPS muscle from Terf2 KO female mouse 1

description:
Library name: R208_F_KO_GPS
Column name in gene_counts_matrix.txt: R208_F_KO_GPS

value: HSA-Cre+/- ; Terf2-/-


title: PS19 Zbp1-KO (PZKO), hippocampus, pooled

city: Charlottesville

first: Jessica

middle: M.

last: Thanos

state: VA

address: 409 Lane Road

institute: University of Virginia

description:
Library name: PZKO
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw BCL files were converted to FASTQ and processed with Cell Ranger (v7.0.1, 10x Genomics) using the count pipeline and the mm10 mouse reference genome to generate gene-by-cell count matrices for each sample. Cell Ranger outputs were then imported into R and used to construct Seurat objects.
Assembly: mm10
Supplementary files format and content: files ending in "fastq.gz": raw sequencing files
Supplementary files format and content: files ending in "barcodes.tsv.gz": cell identity files
Supplementary files format and content: files ending in "features.tsv.gz": gene annotation files
Supplementary files format and content: files ending in "matrix.tsv.gz": matrix files containing genes, cells, and counts

molecule: nuclear RNA

source_name: Brain, Hippocampus

extract_protocol:
For each genotype, hippocampi from individual animals were processed separately. Nuclei were isolated using a proprietary detergent-based lysis buffer and gentle mechanical disruption, filtered to remove debris, and counted by fluorescent dye exclusion.
Single-nucleus 3′ RNA libraries were generated using the Chromium Single Cell 3′ Reagent Kit (10x Genomics) according to the manufacturer’s protocol and loaded for target capture of ~6,000 nuclei per sample. Libraries were quality-checked by capillary electrophoresis and fluorometric quantification and sequenced on an Illumina NovaSeq platform.

value: Brain, Hippocampus

tag: strain

value: PS19 ZBP1

value: Male

value: PS19 Zbp1-KO (PZKO)

value: 9 months


title: 1666, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001666


title: 1667, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001667


title: 1595, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001595

value: Brain - Cortex,Brain - Cortex


title: 171, Rattus norvegicus, Pituitary

description: Library name: itox000171

value: Pituitary


title: 12033, Sus scrofa, Heart,Heart

description: Library name: itox012033


title: 172, Rattus norvegicus, Small intestine- Jejunum (mid)

description: Library name: itox000172

source_name: Small intestine- Jejunum (mid)

value: Small intestine- Jejunum (mid)


title: PS19 Zbp1-WT (PS19), hippocampus, pooled

description:
Library name: PS19
10x Genomics

value: PS19 Zbp1-WT (PS19)


title: 1668, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001668


title: 12034, Sus scrofa, Heart,Heart

description: Library name: itox012034


title: 173, Rattus norvegicus, Spleen

description: Library name: itox000173

source_name: Spleen

value: Spleen


title: brain section from young mouse brain after Pacitaxel and Ganciclovir treatment_2

city: Oklahoma City

first: Roland

last: Patai

state: Oklahoma

address: 975 NE 10th street

department: Department of Neurosurgery

institute: University of Oklahoma Health Campus

description:
Library name: PTX+GCV2
10X Genomics Visium Spatial Transcriptomics kit

data_processing:
Raw sequencing data were processed using the Space Ranger pipeline (10x Genomics) for read alignment, annotation, and generation of spatially resolved gene expression matrices, including mapping of transcriptomic data to histological images. Downstream analyses were performed in Seurat (v4.0), including SCTransform normalization, dataset integration, dimensionality reduction (PCA), and graph-based clustering. Low-quality spots (low gene counts, low feature counts, or high mitochondrial content) were excluded. Senescent regions were identified based on Cdkn2a expression, and differential gene expression between senescent and non-senescent spots was analyzed using the MAST framework. Functional enrichment analysis was conducted using g:Profiler with false discovery rate correction, and gene set enrichment analysis (AUCell) was applied to assess biological signatures such as microglial activation.
Assembly: gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: fresh frozen brain

extract_protocol:
Mice were euthanized and exsanguinated by transcardial perfusion with PBS, after which brains were rapidly removed and rinsed in ice-cold PBS. Tissues were cryoprotected in 30% sucrose, embedded in OCT, and stored at −80 °C. Coronal brain cryosections (10 μm thickness) were cut and mounted onto Visium Spatial Gene Expression Slides (10x Genomics) containing spatially barcoded capture spots. Sections were subjected to hematoxylin and eosin (H&E) staining and imaging prior to downstream transcriptomic processing.
ollowing imaging, tissue sections were permeabilized to release mRNA, which hybridized to spatially barcoded oligonucleotides on the Visium capture areas. Reverse transcription was performed in situ to generate spatially barcoded cDNA, which was subsequently collected, amplified, and processed into sequencing libraries according to the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform (S4 flow cell, XP chemistry), enabling whole-transcriptome profiling with spatial resolution at ~55 μm spot size.

treatment_protocol: or spatial transcriptomics, p16-3MR mice were assigned to the same in vivo treatment groups used throughout the study: control mice received vehicle, while experimental mice received paclitaxel (PTX; 5 mg/kg/day, i.p.) in two 5-day cycles separated by a 7-day interval. After recovery, PTX-treated mice were further divided into three groups that received either vehicle, ganciclovir (GCV; 25 mg/kg/day, i.p.), or the senolytic drug ABT263/Navitoclax (1.5 mg/kg/day, i.p.), each given for 5 days in two cycles with a 2-week interval between cycles. Brains were collected 6 months after the PTX protocol, and sections from control, PTX, PTX+GCV, and PTX+ABT263 mice were used for spatial transcriptomic analysis of senescence-associated gene expression.

value: fresh frozen brain

tag: cell type

value: multiple

value: wild-type  p16- 3MR mouse

value: male

value: 9-10 months

tag: treatment

value: Pacitaxel+GCV


title: 1669, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001669


title: brain section from young mouse brain after Pacitaxel and Ganciclovir treatment_1

description:
Library name: PTX+GCV1
10X Genomics Visium Spatial Transcriptomics kit


title: 12032, Sus scrofa, Heart,Heart

description: Library name: itox012032

value: Heart,Heart


title: 175, Rattus norvegicus, Lymph node (mesenteric)

description: Library name: itox000175

source_name: Lymph node (mesenteric)

value: Lymph node (mesenteric)


title: brain section from young mouse brain after Pacitaxel and ABT263 treatment_2

description:
Library name: PTX+ABT2
10X Genomics Visium Spatial Transcriptomics kit


title: 12037, Sus scrofa, Hippocampus,Hippocampus

description: Library name: itox012037

source_name: Hippocampus,Hippocampus

value: Hippocampus,Hippocampus


title: 12036, Sus scrofa, Heart,Heart

description: Library name: itox012036


title: 1671, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001671


title: 1597, Mus musculus, Brain - Cortex,Brain - Cortex

description: Library name: itox001597

source_name: Brain - Cortex,Brain - Cortex


title: 176, Rattus norvegicus, Liver (left lateral lobe)

description: Library name: itox000176

source_name: Liver (left lateral lobe)

value: Liver (left lateral lobe)


title: 12122, Sus scrofa, Corpus Callosum,Corpus Callosum

description: Library name: itox012122

source_name: Corpus Callosum,Corpus Callosum

value: Corpus Callosum,Corpus Callosum


title: brain section from young mouse brain after Pacitaxel and ABT263 treatment_1

description:
Library name: PTX+ABT1
10X Genomics Visium Spatial Transcriptomics kit


title: 12035, Sus scrofa, Heart,Heart

description: Library name: itox012035


title: 174, Rattus norvegicus, Stomach (glandular)

description: Library name: itox000174

source_name: Stomach (glandular)

value: Stomach (glandular)


title: 12146, Sus scrofa, Large Intestine,Large Intestine

description: Library name: itox012146

source_name: Large Intestine,Large Intestine

value: Large Intestine,Large Intestine


title: 12123, Sus scrofa, Dorsal Root Ganglion,Dorsal Root Ganglion

description: Library name: itox012123


title: 1673, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001673


title: 178, Rattus norvegicus, Adipose - Visceral (Omentum)

description: Library name: itox000178

source_name: Adipose - Visceral (Omentum)

value: Adipose - Visceral (Omentum)


title: brain section from young mouse brain after Pacitaxel treatment_1

description:
Library name: PTX1
10X Genomics Visium Spatial Transcriptomics kit

value: Pacitaxel


title: 1674, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001674


title: 179, Rattus norvegicus, Brain - Cerebellum

description: Library name: itox000179

source_name: Brain - Cerebellum

value: Brain - Cerebellum


title: 1670, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001670


title: 180, Rattus norvegicus, Uterus (left horn)

description: Library name: itox000180

source_name: Uterus (left horn)

value: Uterus (left horn)


title: 1675, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001675


title: brain section from young mouse brain_2

description:
Library name: Ctrl2
10X Genomics Visium Spatial Transcriptomics kit

value: fresh frozen brain

value: Vechicle (DMSO+saline)


title: brain section from young mouse brain_1

description:
Library name: Ctrl1
10X Genomics Visium Spatial Transcriptomics kit

value: multiple

value: wild-type  p16- 3MR mouse


title: 1677, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001677


title: 181, Rattus norvegicus, Vagina

description: Library name: itox000181

source_name: Vagina

value: Vagina


title: brain section from young mouse brain after Pacitaxel treatment_2

description:
Library name: PTX2
10X Genomics Visium Spatial Transcriptomics kit

value: male

value: 9-10 months


title: 1676, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001676


title: 177, Rattus norvegicus, Ileum

description: Library name: itox000177

source_name: Ileum

value: Ileum


title: liver, B4-HKO-CDAHFD, rep2

city: Shanghai

first: Youjung

last: Chien

address: 180 Fenglin Road, Shanghai 200032, China.

country: China

institute: Zhongshan Hospital, Fudan University

description: Library name: B4-hep-CDAHFD-76

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Differential expression genes (DEGs) were identified using DESeq2 as those with a cutoff Benjamini-Hochberg adjusted p value of 0.05 and an absolute fold change of greater than 1.5 (|Log2FC| > 0.58).
GO enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0).
Gene Set Enrichment Analysis (GSEA) was conducted utilizing the GSEA software.
Assembly: GRCm39
Supplementary files format and content: Processed data files are tab-delimited text files containing normalized gene expression counts. Columns represent individual samples and rows represent genes. Values are counts or FPKM.

source_name: liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: CDAHFD

value: liver

value: CDAHFD for 15 weeks


title: 12062, Sus scrofa, Thalamus,Thalamus

description: Library name: itox012062

source_name: Thalamus,Thalamus

value: Thalamus,Thalamus


title: 1672, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001672


title: liver, B4-HKO-CDAHFD, rep1

description: Library name: B4-hep-CDAHFD-74


title: liver, B4-HKO-CDAHFD, rep3

description: Library name: B4-hep-CDAHFD-80


title: 12127, Sus scrofa, Eye,Eye

description: Library name: itox012127

source_name: Eye,Eye

value: Eye,Eye


title: 182, Rattus norvegicus, Ovary (left)

description: Library name: itox000182

source_name: Ovary (left)

value: Ovary (left)


title: 1678, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001678


title: 12125, Sus scrofa, Eye,Eye

description: Library name: itox012125


title: 1679, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001679


title: 183, Rattus norvegicus, Brain - Cortex

description: Library name: itox000183

source_name: Brain - Cortex

value: Brain - Cortex


title: 12063, Sus scrofa, Thymus Gland,Thymus Gland

description: Library name: itox012063

source_name: Thymus Gland,Thymus Gland

value: Thymus Gland,Thymus Gland


title: liver, WT-CDAHFD, rep4

description: Library name: B4-f-f-CDAHFD-63

value: WT


title: 185, Rattus norvegicus, Muscle - Skeletal (gastrocnemius)

description: Library name: itox000185

source_name: Muscle - Skeletal (gastrocnemius)

value: Muscle - Skeletal (gastrocnemius)


title: 12064, Sus scrofa, Tongue,Tongue

description: Library name: itox012064

source_name: Tongue,Tongue

value: Tongue,Tongue


title: liver, WT-CDAHFD, rep3

description: Library name: B4-f-f-CDAHFD--67


title: liver, WT-CDAHFD, rep2

description: Library name: B4-f-f-CDAHFD--65


title: 12128, Sus scrofa, Frontal Lobe,Frontal Lobe

description: Library name: itox012128

source_name: Frontal Lobe,Frontal Lobe

value: Frontal Lobe,Frontal Lobe


title: 1681, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001681


title: 1680, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001680


title: 1682, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001682


title: 12124, Sus scrofa, Esophagus,Esophagus

description: Library name: itox012124

source_name: Esophagus,Esophagus

value: Esophagus,Esophagus


title: 12131, Sus scrofa, Mammary Gland,Mammary Gland

description: Library name: itox012131

source_name: Mammary Gland,Mammary Gland

value: Mammary Gland,Mammary Gland


title: Wildtype, male mouse 3

city: Chicago

first: George

last: Chlipala

state: IL

address: 900 S. Ashland Ave

department: Research Informatics Core

institute: University of Illinois Chicago

description: Library name: 3_WTM_SMG_S6

data_processing:
Raw reads were quantiated using Salmon (v1.10.1) with Genocode M35, GRCm39/mm39 as the reference transcriptome
Raw counts per gene were generated using the summarizeToGene() function from the R package tximeta
Assembly: mm39
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: csv file includes median ratio normalized counts for each sample

source_name: mouse submandibular glands

extract_protocol:
Total RNA was extracted directly from the cell pellets using the Qiagen RNAeasy Micor Kit following manufacturer’s protocols. Total RNA was eluted and was quality checked on an Agilent Fragment Analyzer and Qubit (Invitrogen).
Total RNA (100 ng) was used to generate RNA libraries following the Illumina RiboZero Total Stranded RNA library prep kit with ribosomal RNA removal. Following RNA library preparation and quality control, final libraries were pooled to 10 nM and the concentration of the pool was determined using the QuantaBio Universal qPCR reaction kit. After final dilution and denaturing, the pooled library was loaded onto a NovaSeq6000 (PE100) for sequencing at 250 pM as final concentration.

value: mouse submandibular glands


title: 188, Rattus norvegicus, Esophagus (mid)

description: Library name: itox000188

source_name: Esophagus (mid)

value: Esophagus (mid)


title: 186, Rattus norvegicus, Peripheral Nerve (sciatic)

description: Library name: itox000186

source_name: Peripheral Nerve (sciatic)

value: Peripheral Nerve (sciatic)


title: 187, Rattus norvegicus, Peripheral Nerve (tibial)

description: Library name: itox000187

source_name: Peripheral Nerve (tibial)

value: Peripheral Nerve (tibial)


title: liver, WT-CDAHFD, rep1

description: Library name: B4-f-f-CDAHFD--62

value: liver


title: 189, Rattus norvegicus, Heart - Atrium

description: Library name: itox000189

source_name: Heart - Atrium

value: Heart - Atrium


title: 12135, Sus scrofa, Heart,Heart

description: Library name: itox012135

source_name: Heart,Heart

value: Heart,Heart


title: 12134, Sus scrofa, Thyroid Gland,Thyroid Gland

description: Library name: itox012134

source_name: Thyroid Gland,Thyroid Gland

value: Thyroid Gland,Thyroid Gland


title: Wildtype, male mouse 1

description: Library name: 1_WTM_SMG_S4

value: male


title: 1683, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001683


title: 191, Rattus norvegicus, Brain - Hypothalamus

description: Library name: itox000191

source_name: Brain - Hypothalamus

value: Brain - Hypothalamus


title: 12133, Sus scrofa, Salivary Gland,Salivary Gland

description: Library name: itox012133

source_name: Salivary Gland,Salivary Gland

value: Salivary Gland,Salivary Gland


title: 12137, Sus scrofa, Heart,Heart

description: Library name: itox012137


title: Wildtype, male mouse 2

description: Library name: 2_WTM_SMG_S5

value: WT


title: 1346, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001346


title: 1345, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001345


title: 192, Rattus norvegicus, Thyroid/parathyroid

description: Library name: itox000192

source_name: Thyroid/parathyroid

value: Thyroid/parathyroid


title: Wildtype, female mouse 1

description: Library name: 1_WTF_SMG_S1

value: female


title: 1685, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001685


title: Wildtype, female mouse 3

description: Library name: 3_WTF_SMG_S3


title: 12140, Sus scrofa, Heart,Heart

description: Library name: itox012140


title: Wildtype, female mouse 2

description: Library name: 2_WTF_SMG_S2


title: 1686, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001686


title: 184, Rattus norvegicus, Eyes-cornea

description: Library name: itox000184

source_name: Eyes-cornea

value: Eyes-cornea


title: 190, Rattus norvegicus, Heart - Ventricle (left)

description: Library name: itox000190

source_name: Heart - Ventricle (left)

value: Heart - Ventricle (left)


title: 12138, Sus scrofa, Heart,Heart

description: Library name: itox012138


title: 195, Rattus norvegicus, Artery - Aorta (thoracic)

description: Library name: itox000195

source_name: Artery - Aorta (thoracic)

value: Artery - Aorta (thoracic)


title: 1684, Mus musculus, Brain - Spinal cord (cervical),Brain - Spinal cord (cervical)

description: Library name: itox001684


title: 12142, Sus scrofa, Kidney,Kidney

description: Library name: itox012142

source_name: Kidney,Kidney

value: Kidney,Kidney


title: 1347, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001347


title: Knockout, male mouse 3

description: Library name: 3_KOM_SMG_S12

value: mouse submandibular glands

value: C57BL/6J-Pou2f3 knockout


title: 193, Rattus norvegicus, Tongue

description: Library name: itox000193

source_name: Tongue

value: Tongue


title: Knockout, male mouse 1

description: Library name: 1_KOM_SMG_S10


title: 12143, Sus scrofa, Kidney,Kidney

description: Library name: itox012143


title: Knockout, female mouse 3

description: Library name: 3_KOF_SMG_S9


title: 102, Rattus norvegicus, Cervix

description: Library name: itox000102

source_name: Cervix

value: Cervix


title: 1348, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001348


title: 1350, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001350


title: Knockout, male mouse 2

description: Library name: 2_KOM_SMG_S11


title: 12141, Sus scrofa, Hippocampus,Hippocampus

description: Library name: itox012141

source_name: Hippocampus,Hippocampus

value: Hippocampus,Hippocampus


title: 1349, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001349


title: 194, Rattus norvegicus, Trachea

description: Library name: itox000194

source_name: Trachea

value: Trachea


title: 12214, Sus scrofa, Spleen,Spleen

description: Library name: itox012214

source_name: Spleen,Spleen

value: Spleen,Spleen


title: Knockout, female mouse 2

description: Library name: 2_KOF_SMG_S8

source_name: mouse submandibular glands


title: 104, Rattus norvegicus, Eyes-cornea

description: Library name: itox000104


title: 1351, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001351


title: 1352, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001352


title: Knockout, female mouse 1

description: Library name: 1_KOF_SMG_S7


title: 12195, Sus scrofa, Kidney,Kidney

description: Library name: itox012195


title: 106, Rattus norvegicus, Peripheral Nerve (sciatic)

description: Library name: itox000106

source_name: Peripheral Nerve (sciatic)

value: Peripheral Nerve (sciatic)


title: 1353, Mus musculus, Artery- Aorta (abdominal descending),Artery- Aorta (abdominal descending)

description: Library name: itox001353


title: 12196, Sus scrofa, Cecum,Cecum

description: Library name: itox012196

source_name: Cecum,Cecum

value: Cecum,Cecum


title: 12144, Sus scrofa, Large Intestine,Large Intestine

description: Library name: itox012144

source_name: Large Intestine,Large Intestine

value: Large Intestine,Large Intestine


title: DRG RNA-seq WT rep2

city: Suita

first: Akira

last: Nishiura

state: Osaka

country: Japan

institute: The University of Osaka

description: Library name: WT_2

data_processing:
Raw sequencing reads were quality-checked using FastQC.
Adapters and low-quality bases were trimmed using Trimmomatic.
Reads were aligned to the mouse reference genome (GRCm39) using STAR.
Gene-level read counts were generated using featureCounts.
Assembly: GRCm39
Supplementary files format and content: Processed data files include gene-level read count tables generated from aligned RNA-seq reads.

source_name: dorsal root ganglion

growth_protocol: Mice were housed under standard conditions with ad libitum access to food and water.

extract_protocol:
Total RNA was extracted from dorsal root ganglia using a standard phenol-chloroform method or commercial RNA extraction kit according to the manufacturer’s instructions.
Poly(A)+ RNA was enriched and sequencing libraries were prepared using a standard Illumina-compatible RNA-seq library preparation kit.

treatment_protocol: No treatment was applied. Dorsal root ganglia were collected at disease onset.

value: dorsal root ganglion

value: sensory neuron

value: WT


title: 1354, Mus musculus, Artery- Aorta (abdominal descending),Artery- Aorta (abdominal descending)

description: Library name: itox001354


title: 103, Rattus norvegicus, Brain - Cortex

description: Library name: itox000103

source_name: Brain - Cortex

value: Brain - Cortex


title: 107, Rattus norvegicus, Peripheral Nerve (tibial)

description: Library name: itox000107

source_name: Peripheral Nerve (tibial)

value: Peripheral Nerve (tibial)


title: DRG RNA-seq WT rep3

description: Library name: WT_3


title: 105, Rattus norvegicus, Muscle - Skeletal (gastrocnemius)

description: Library name: itox000105

source_name: Muscle - Skeletal (gastrocnemius)

value: Muscle - Skeletal (gastrocnemius)


title: 108, Rattus norvegicus, Bone marrow - femoral scoop

description: Library name: itox000108

source_name: Bone marrow - femoral scoop

value: Bone marrow - femoral scoop


title: 109, Rattus norvegicus, Esophagus (mid)

description: Library name: itox000109

source_name: Esophagus (mid)

value: Esophagus (mid)


title: 1356, Mus musculus, Artery- Aorta (abdominal descending),Artery- Aorta (abdominal descending)

description: Library name: itox001356


title: 12220, Sus scrofa, Tonsil,Tonsil

description: Library name: itox012220

source_name: Tonsil,Tonsil

value: Tonsil,Tonsil


title: 12218, Sus scrofa, Thymus Gland,Thymus Gland

description: Library name: itox012218

source_name: Thymus Gland,Thymus Gland

value: Thymus Gland,Thymus Gland


title: DRG RNA-seq SOD1-G93A rep3

description: Library name: SOD1_G93A_3


title: 1355, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001355


title: 1357, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001357


title: 110, Rattus norvegicus, Heart - Atrium

description: Library name: itox000110

source_name: Heart - Atrium

value: Heart - Atrium


title: DRG RNA-seq SOD1-G93A rep2

description: Library name: SOD1_G93A_2


title: 12239, Sus scrofa, Mammary Gland,Mammary Gland

description: Library name: itox012239

source_name: Mammary Gland,Mammary Gland

value: Mammary Gland,Mammary Gland


title: DRG RNA-seq SOD1-G93A rep1

description: Library name: SOD1_G93A_1


title: 12197, Sus scrofa, Colon,Colon

description: Library name: itox012197

source_name: Colon,Colon

value: Colon,Colon


title: 111, Rattus norvegicus, Heart - Ventricle (left)

description: Library name: itox000111

source_name: Heart - Ventricle (left)

value: Heart - Ventricle (left)


title: 1358, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001358


title: 12221, Sus scrofa, Trachea,Trachea

description: Library name: itox012221

source_name: Trachea,Trachea

value: Trachea,Trachea


title: 112, Rattus norvegicus, Lung (left lobe)

description: Library name: itox000112

source_name: Lung (left lobe)

value: Lung (left lobe)


title: DRG RNA-seq WT rep1

description: Library name: WT_1


title: 1360, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001360


title: DKO1

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

description: Library name: DKO1

data_processing:
Base call files from the Illumina sequencer were demultiplexed using the 10X Genomics Cell Ranger (v8.0.1) ‘mkfastq’ pipeline and reads from each library were assembled and aligned to the mouse reference genome assembly ‘mm10-2020-A’ using the Cell Ranger ‘count’ pipeline.
Assembly: mm10-2020-A
Supplementary files format and content: The filtered_feature_bc_matrix.h5 files contain the filtered gene-by-cell expression count matrix generated by Cell Ranger, including only high-quality cells and detected features after quality control.

source_name: skin

growth_protocol: The DKO*K15 mice and their respective Cre-negative controls were generated by genetic crosses of the junBf/f and c-junf/f  alleles with the K15-CrePR1 in mixed C57BL/6.

extract_protocol:
Tissue samples were collected 48 hrs post last TPA application. Skin samples were harvested in PBS, cut in small pieces using a scalpel and digested with 100 μg/ml LiberaseTM (Roche) and 100 μg/ml of DNase I (Sigma-Aldrich) for 1 hr at 37 °C.
30,000 cells per sample were processed for single-cell RNA sequencing on a Chromium X Instrument using the GEM-X Single Cell 5’ Reagent Kit (10X Genomics, Pleasanton, CA) and a single-cell gel bead emulsion was generated. cDNA amplification and library preparation were performed according to the manufacturer’s instructions.

treatment_protocol: Psoriasis-like disease was induced in 8-week-old mice by intraperitoneal injections of 2 mg Mifepristone (RU486) (Merck) for 5 consecutive days. Mice were treated with DMBA and TPA to induce skin tumorigenesis. Briefly, the back skin of 6-week-old mice was shaved 24 hrs before treated once with 50 μg of DMBA (Sigma-Aldrich) and then 3 times per week with 4 μg of TPA (Sigma-Aldrich) for the duration of 15 weeks.

value: skin

value: whole skin


title: DKO2

description: Library name: DKO2


title: 12222, Sus scrofa, Bladder,Bladder

description: Library name: itox012222

source_name: Bladder,Bladder

value: Bladder,Bladder


title: 113, Rattus norvegicus, Brain - Hypothalamus

description: Library name: itox000113

source_name: Brain - Hypothalamus

value: Brain - Hypothalamus


title: 1359, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001359


title: 12223, Sus scrofa, Adipose,Adipose

description: Library name: itox012223

source_name: Adipose,Adipose

value: Adipose,Adipose


title: 1383, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001383

source_name: Heart - Atrium,Heart - Atrium

value: Heart - Atrium,Heart - Atrium


title: Ctrl2

description: Library name: Ctrl2

value: Cre negative control


title: 12224, Sus scrofa, Adipose,Adipose

description: Library name: itox012224


title: 114, Rattus norvegicus, Thymus

description: Library name: itox000114

source_name: Thymus

value: Thymus


title: 1384, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001384


title: Ctrl1

description: Library name: Ctrl1


title: 12225, Sus scrofa, Aorta,Aorta

description: Library name: itox012225

source_name: Aorta,Aorta

value: Aorta,Aorta


title: 115, Rattus norvegicus, Thyroid/parathyroid

description: Library name: itox000115

source_name: Thyroid/parathyroid

value: Thyroid/parathyroid


title: 1386, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001386


title: 116, Rattus norvegicus, Tongue

description: Library name: itox000116

source_name: Tongue

value: Tongue


title: HF2

first: Yufei

last: Wu

address: Siping Campus,1239 Siping Road, Yangpu District, Shangha.

institute: School of Medicine, Tongji University

description:
Library name: Sample 4
10X Genomics

data_processing:
The data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform (www.novelbrain.com). We applied fastp with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve clean data. Then the feature-barcode matrices were obtained by aligning reads to the mouse genome (mm10, Ensembl 100) using CellRanger v5.0.1. We applied the down sample analysis among samples sequenced according to the mapped barcoded reads per cell of each sample and finally achieved the aggregated matrix. Cells contained over 200 expressed genes and mitochondria UMI rate below 20% passed the cell quality filtering and mitochondria genes were removed in the expression table.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: heart

extract_protocol:
RFP-positive cells from isolated cardiac left ventricle were obtained from FACS, then subjected to single-cell RNA sequencing and analyses by NovelBio Bio-pharm Techonology Co., Ltd.
The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA). Briefly, cells were concentrated to approximately 1000 cells/μL and loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by Illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: heart

value: endothelial cell

value: HFD plus L-NAME


title: 1385, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001385


title: HF1

description:
Library name: Sample 3
10X Genomics


title: 12227, Sus scrofa, Bone Marrow,Bone Marrow

description: Library name: itox012227

source_name: Bone Marrow,Bone Marrow

value: Bone Marrow,Bone Marrow


title: 117, Rattus norvegicus, Trachea

description: Library name: itox000117

source_name: Trachea

value: Trachea


title: 1387, Mus musculus, Heart - Ventricle (left),Heart - Ventricle (left)

description: Library name: itox001387


title: NC2

description:
Library name: Sample 2
10X Genomics

value: Chow diet


title: NC1

description:
Library name: Sample 1
10X Genomics


title: 1389, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001389


title: 119, Rattus norvegicus, Artery- Aorta (abdominal descending)

description: Library name: itox000119

source_name: Artery- Aorta (abdominal descending)

value: Artery- Aorta (abdominal descending)


title: 1390, Mus musculus, Heart - Ventricle (left),Heart - Ventricle (left)

description: Library name: itox001390


title: 12228, Sus scrofa, Brainstem,Brainstem

description: Library name: itox012228

source_name: Brainstem,Brainstem

value: Brainstem,Brainstem


title: 118, Rattus norvegicus, Artery - Aorta (thoracic)

description: Library name: itox000118

source_name: Artery - Aorta (thoracic)

value: Artery - Aorta (thoracic)


title: 1391, Mus musculus, Heart - Ventricle (left),Heart - Ventricle (left)

description: Library name: itox001391


title: 12232, Sus scrofa, Esophagus,Esophagus

description: Library name: itox012232

source_name: Esophagus,Esophagus

value: Esophagus,Esophagus


title: 12226, Sus scrofa, Coronary Artery,Coronary Artery

description: Library name: itox012226

source_name: Coronary Artery,Coronary Artery

value: Coronary Artery,Coronary Artery


title: Mouse IUE YAP1-Fus(Y38),10xMultiome, snATAC

city: Memphis

first: Stephen

middle: C.

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

description:
Library name: EPN-Y38 ATAC
10xGenomics

library_source: other

data_processing:
The CellRanger-arc count pipelines (v2.0.2, 10X Genomics) were used to process sequenced 10xMultiome data. The CellRanger-arc pipeline performs filtering and alignment of  snATAC-seq/snRNA reads and identifies the transposase cut sites for snATAC.
Assembly: mm10 (10x Genomics, refdata-cellranger-arc-mm10-2020-A-2.0.0)
Supplementary files format and content: filtered_feature_bc_matrix.h5: the file includes barcodes,  gene IDs, peak regions, gene expression, and atac count data
Supplementary files format and content: atac_fragments.tsv.gz: snATAC fragment data
Supplementary files format and content: atac_fragments.tsv.gz.tbi: snATAC fragment index data

molecule: other

source_name: Supratentorial ependymomas (with YAP1-MAMLD1 fusion)

extract_protocol:
10-30mg of tissue was cut from tumors and was input into the 10x Nuclei Isolation Kit (PN-1000494). Kit instructions were followed but lysis buffer incubation time was increased to 15 minutes to isolate quality nuclei. Mouse embryonic forebrain was isolated with the 10x Demonstrated Protocol CG000366 RevD, but lysis buffer incubation was decreased to 2 minutes. Nuclei were resuspended in nuclei buffer, counted via hemocytometer, and 10,000 were loaded onto the 10x Chromium Chip.
Libraries were assessed via Agilent TapeStation and sent for sequencing at St. Jude’s Hartwell Center on a NovaSeq 6000. Gene Expression libraries had 400 million reads with a 28-10-10-90 cycle configuration and ATAC libraries had 500 million reads with a 50-8-24-49 cycle configuration.


title: 1392, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001392

value: Heart - Atrium,Heart - Atrium


title: 120, Rattus norvegicus, Brown Fat (intrascapular)

description: Library name: itox000120

source_name: Brown Fat (intrascapular)

value: Brown Fat (intrascapular)


title: 122, Rattus norvegicus, Mammary Gland/Tissue (female only)

description: Library name: itox000122

source_name: Mammary Gland/Tissue (female only)

value: Mammary Gland/Tissue (female only)


title: 12233, Sus scrofa, Eye,Eye

description: Library name: itox012233

source_name: Eye,Eye

value: Eye,Eye


title: 121, Rattus norvegicus, Kidney (left to include cortex and medulla)

description: Library name: itox000121


title: 12231, Sus scrofa, Dorsal Root Ganglion,Dorsal Root Ganglion

description: Library name: itox012231


title: 12229, Sus scrofa, Cerebellum,Cerebellum

description: Library name: itox012229

source_name: Cerebellum,Cerebellum

value: Cerebellum,Cerebellum


title: 12230, Sus scrofa, Corpus Callosum,Corpus Callosum

description: Library name: itox012230

source_name: Corpus Callosum,Corpus Callosum

value: Corpus Callosum,Corpus Callosum


title: P6 healthy forebrain,10xMultiome, snATAC

description:
Library name: P6 ATAC
10xGenomics

source_name: Healthy forebrain (postnatal day 6)

value: Healthy forebrain (postnatal day 6)


title: 1388, Mus musculus, Heart - Ventricle (left),Heart - Ventricle (left)

description: Library name: itox001388


title: 123, Rattus norvegicus, Brain - Spinal cord (cervical)

description: Library name: itox000123

source_name: Brain - Spinal cord (cervical)

value: Brain - Spinal cord (cervical)


title: 1393, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001393

source_name: Heart - Atrium,Heart - Atrium


title: P1 healthy forebrain,10xMultiome, snATAC

description:
Library name: P1 ATAC
10xGenomics

source_name: Healthy forebrain (postnatal day 1)

value: Healthy forebrain (postnatal day 1)


title: 12234, Sus scrofa, Cornea,Cornea

description: Library name: itox012234

source_name: Cornea,Cornea

value: Cornea,Cornea


title: P0 healthy forebrain,10xMultiome, snATAC

description:
Library name: P0 ATAC
10xGenomics

source_name: Healthy forebrain (postnatal day 0)

value: Healthy forebrain (postnatal day 0)


title: Mouse IUE YAP1-Fus(Y56),10xMultiome, snATAC

description:
Library name: EPN-Y56 ATAC
10xGenomics

value: Supratentorial ependymomas (with YAP1-MAMLD1 fusion)


title: 1394, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001394


title: Mouse IUE YAP1-Fus(Y55),10xMultiome, snATAC

description:
Library name: EPN-Y55 ATAC
10xGenomics


title: 1395, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001395


title: 232, Rattus norvegicus, Tongue

description: Library name: itox000232

source_name: Tongue

value: Tongue


title: 233, Rattus norvegicus, Trachea

description: Library name: itox000233

source_name: Trachea

value: Trachea


title: 12299, Sus scrofa, Blood,Blood

description: Library name: itox012299

source_name: Blood,Blood

value: Blood,Blood


title: 12301, Sus scrofa, Blood,Blood

description: Library name: itox012301


title: 234, Rattus norvegicus, Salivary Gland (mandibular)

description: Library name: itox000234

source_name: Salivary Gland (mandibular)

value: Salivary Gland (mandibular)


title: 235, Rattus norvegicus, Artery - Aorta (thoracic)

description: Library name: itox000235

source_name: Artery - Aorta (thoracic)

value: Artery - Aorta (thoracic)


title: 12300, Sus scrofa, Blood,Blood

description: Library name: itox012300


title: 236, Rattus norvegicus, Artery- Aorta (abdominal descending)

description: Library name: itox000236

source_name: Artery- Aorta (abdominal descending)

value: Artery- Aorta (abdominal descending)


title: Mouse IUE YAP1-Fus(Y56),10xMultiome, snRNA

description:
Library name: EPN-Y56 RNA
10xGenomics

source_name: Supratentorial ependymomas (with YAP1-MAMLD1 fusion)


title: 12303, Sus scrofa, Parathyroid Gland,Parathyroid Gland

description: Library name: itox012303

source_name: Parathyroid Gland,Parathyroid Gland

value: Parathyroid Gland,Parathyroid Gland


title: 12302, Sus scrofa, Corpus Callosum,Corpus Callosum

description: Library name: itox012302


title: E16.5 healthy forebrain,10xMultiome, snATAC

description:
Library name: E16 ATAC
10xGenomics

source_name: Healthy forebrain (E16.5)

value: Healthy forebrain (E16.5)


title: E18.5 healthy forebrain,10xMultiome, snATAC

description:
Library name: E18 ATAC
10xGenomics

source_name: Healthy forebrain (E18.5)

value: Healthy forebrain (E18.5)


title: E12.5 healthy forebrain,10xMultiome, snATAC

description:
Library name: E12 ATAC
10xGenomics

source_name: Healthy forebrain (E12.5)

value: Healthy forebrain (E12.5)


title: 1398, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001398

value: Heart - Atrium,Heart - Atrium


title: 1396, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001396


title: 238, Rattus norvegicus, Kidney (left to include cortex and medulla)

description: Library name: itox000238


title: 12297, Sus scrofa, Vagina,Vagina

description: Library name: itox012297

source_name: Vagina,Vagina

value: Vagina,Vagina


title: 1397, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001397


title: 237, Rattus norvegicus, Brown Fat (intrascapular)

description: Library name: itox000237

source_name: Brown Fat (intrascapular)

value: Brown Fat (intrascapular)


title: 1399, Mus musculus, Heart - Ventricle (left),Heart - Ventricle (left)

description: Library name: itox001399


title: Mouse IUE YAP1-Fus(Y55),10xMultiome, snRNA

description:
Library name: EPN-Y55 RNA
10xGenomics


title: 239, Rattus norvegicus, Mammary Gland/Tissue (female only)

description: Library name: itox000239

source_name: Mammary Gland/Tissue (female only)

value: Mammary Gland/Tissue (female only)


title: Mouse IUE YAP1-Fus(Y38),10xMultiome, snRNA

description:
Library name: EPN-Y38 RNA
10xGenomics


title: 12298, Sus scrofa, Blood,Blood

description: Library name: itox012298


title: P6 healthy forebrain,10xMultiome, snRNA

description:
Library name: P6 RNA
10xGenomics

source_name: Healthy forebrain (postnatal day 6)

value: Healthy forebrain (postnatal day 6)


title: 1403, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001403

source_name: Heart - Atrium,Heart - Atrium


title: P1 healthy forebrain,10xMultiome, snRNA

description:
Library name: P1 RNA
10xGenomics

source_name: Healthy forebrain (postnatal day 1)

value: Healthy forebrain (postnatal day 1)


title: 241, Rattus norvegicus, Skin (inguinal)

description: Library name: itox000241

source_name: Skin (inguinal)

value: Skin (inguinal)


title: 11735, Sus scrofa, Eye,Eye

description: Library name: itox011735

source_name: Eye,Eye

value: Eye,Eye


title: 240, Rattus norvegicus, Brain - Spinal cord (cervical)

description: Library name: itox000240

source_name: Brain - Spinal cord (cervical)

value: Brain - Spinal cord (cervical)


title: 11736, Sus scrofa, Cerebral Cortex,Cerebral Cortex

description: Library name: itox011736

source_name: Cerebral Cortex,Cerebral Cortex

value: Cerebral Cortex,Cerebral Cortex


title: 1404, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001404


title: 242, Rattus norvegicus, Ureter

description: Library name: itox000242

source_name: Ureter

value: Ureter


title: E18.5 healthy forebrain,10xMultiome, snRNA

description:
Library name: E18 RNA
10xGenomics


title: 1400, Mus musculus, Heart - Ventricle (left),Heart - Ventricle (left)

description: Library name: itox001400


title: 1449, Mus musculus, Stomach (glandular),Stomach (glandular)

description: Library name: itox001449

source_name: Stomach (glandular),Stomach (glandular)

value: Stomach (glandular),Stomach (glandular)


title: 11739, Sus scrofa, Mammary Gland,Mammary Gland

description: Library name: itox011739

source_name: Mammary Gland,Mammary Gland

value: Mammary Gland,Mammary Gland


title: 1402, Mus musculus, Heart - Ventricle (left),Heart - Ventricle (left)

description: Library name: itox001402


title: 11904, Sus scrofa, Occipital Lobe,Occipital Lobe

description: Library name: itox011904

source_name: Occipital Lobe,Occipital Lobe

value: Occipital Lobe,Occipital Lobe


title: P0 healthy forebrain,10xMultiome, snRNA

description:
Library name: P0 RNA
10xGenomics

source_name: Healthy forebrain (postnatal day 0)

value: Healthy forebrain (postnatal day 0)


title: 1450, Mus musculus, Stomach (glandular),Stomach (glandular)

description: Library name: itox001450


title: 1448, Mus musculus, Stomach (glandular),Stomach (glandular)

description: Library name: itox001448


title: 11738, Sus scrofa, Adrenal Gland,Adrenal Gland

description: Library name: itox011738

source_name: Adrenal Gland,Adrenal Gland

value: Adrenal Gland,Adrenal Gland


title: E16.5 healthy forebrain,10xMultiome, snRNA

description:
Library name: E16 RNA
10xGenomics

source_name: Healthy forebrain (E16.5)

value: Healthy forebrain (E16.5)


title: 11740, Sus scrofa, Parathyroid Gland,Parathyroid Gland

description: Library name: itox011740

source_name: Parathyroid Gland,Parathyroid Gland

value: Parathyroid Gland,Parathyroid Gland


title: 1452, Mus musculus, Stomach (glandular),Stomach (glandular)

description: Library name: itox001452


title: 244, Rattus norvegicus, Adrenal Gland

description: Library name: itox000244

source_name: Adrenal Gland

value: Adrenal Gland


title: 245, Rattus norvegicus, DRG-L4

description: Library name: itox000245


title: IUE-ZR-6 (K10), Tracker-seq

description:
Library name: IUE-ZR-6 (K10)
10xGenomics

data_processing:
Process cellranger (v9.0.0) counts to generate filtered_feature_bc_matrix.h5
Assembly: mm10 (10x Genomics, refdata-gex-mm10-2020-A)
Supplementary files format and content: filtered_feature_bc_matrix.h5: the file includes barcodes,  gene IDs, and gene expression

source_name: ST-EPN tumor

extract_protocol:
Tumors were dissociated using the Miltenyi Brain Tumor dissociation kit. Live GFP+ cells were sorted and loaded on a 10x Chromium Chip.
Libraries were constructed using the 10x Chromium Next GEM Gene Expression Kit and assessed via Agilent High Sensitivity D5000 TapeStation. They were then sent for sequencing at St. Jude’s Hartwell Center on a NovaSeq 6000. Libraries had 400 million reads with a 28-10-10-90 cycle configuration.

value: ST-EPN tumor

tag: cell line

value: IUE

value: ZFTA-RELA fusion positive


title: 243, Rattus norvegicus, Urinary Bladder

description: Library name: itox000243

source_name: Urinary Bladder

value: Urinary Bladder


title: 246, Rattus norvegicus, Brain-Striatum

description: Library name: itox000246

source_name: Brain-Striatum

value: Brain-Striatum


title: IUE-ZR-5, replicate 2 (K96b), Tracker-seq

description:
Library name: IUE-ZR-5-rep2 (K96b)
10xGenomics


title: 11906, Sus scrofa, Fallopian tube,Fallopian tube

description: Library name: itox011906

source_name: Fallopian tube,Fallopian tube

value: Fallopian tube,Fallopian tube


title: IUE-ZR-5, replicate 1 (K96a), Tracker-seq

description:
Library name: IUE-ZR-5-rep1 (K96a)
10xGenomics


title: 247, Rattus norvegicus, Brain- Hippocampus

description: Library name: itox000247

source_name: Brain- Hippocampus

value: Brain- Hippocampus


title: 1454, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001454


title: 11907, Sus scrofa, Pancreas,Pancreas

description: Library name: itox011907

source_name: Pancreas,Pancreas

value: Pancreas,Pancreas


title: IUE-ZR-4, replicate 3 (C08c), Tracker-seq

description:
Library name: IUE-ZR-4-rep3 (C08c)
10xGenomics


title: 248, Rattus norvegicus, Pituitary

description: Library name: itox000248

source_name: Pituitary

value: Pituitary


title: 11908, Sus scrofa, Cerebral Cortex,Cerebral Cortex

description: Library name: itox011908

source_name: Cerebral Cortex,Cerebral Cortex

value: Cerebral Cortex,Cerebral Cortex


title: 1456, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001456


title: 11905, Sus scrofa, Ovary,Ovary

description: Library name: itox011905

source_name: Ovary,Ovary

value: Ovary,Ovary


title: 1455, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001455


title: 1453, Mus musculus, Stomach (glandular),Stomach (glandular)

description: Library name: itox001453

source_name: Stomach (glandular),Stomach (glandular)

value: Stomach (glandular),Stomach (glandular)


title: IUE-ZR-4, replicate 2 (C08b), Tracker-seq

description:
Library name: IUE-ZR-4-rep2 (C08b)
10xGenomics


title: E12.5 healthy forebrain,10xMultiome, snRNA

description:
Library name: E12 RNA
10xGenomics

source_name: Healthy forebrain (E12.5)

value: Healthy forebrain (E12.5)


title: 249, Rattus norvegicus, Spleen

description: Library name: itox000249

source_name: Spleen

value: Spleen


title: 1457, Mus musculus, Salivary Gland (mandibular),Salivary Gland (mandibular)

description: Library name: itox001457


title: 250, Rattus norvegicus, Stomach (glandular)

description: Library name: itox000250

source_name: Stomach (glandular)

value: Stomach (glandular)


title: 11889, Sus scrofa, Heart,Heart

description: Library name: itox011889

source_name: Heart,Heart

value: Heart,Heart


title: 11890, Sus scrofa, Heart,Heart

description: Library name: itox011890


title: 1777, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001777

source_name: Ovary (left),Ovary (left)

value: Ovary (left),Ovary (left)


title: 252, Rattus norvegicus, Lymph node (mesenteric)

description: Library name: itox000252

source_name: Lymph node (mesenteric)

value: Lymph node (mesenteric)


title: 11911, Sus scrofa, Ileum,Ileum

description: Library name: itox011911

source_name: Ileum,Ileum

value: Ileum,Ileum


title: 251, Rattus norvegicus, Colon (mid)

description: Library name: itox000251

source_name: Colon (mid)

value: Colon (mid)


title: IUE-ZR-3, replicate 3 (Z12c), Tracker-seq

description:
Library name: IUE-ZR-3-rep3 (Z12c)
10xGenomics

source_name: ST-EPN tumor

value: ST-EPN tumor

value: IUE

value: ZFTA-RELA fusion positive


title: IUE-ZR-3, replicate 2 (Z12b), Tracker-seq

description:
Library name: IUE-ZR-3-rep2 (Z12b)
10xGenomics


title: 11976, Sus scrofa, Thymus Gland,Thymus Gland

description: Library name: itox011976

source_name: Thymus Gland,Thymus Gland

value: Thymus Gland,Thymus Gland


title: IUE-ZR-3, replicate 1 (Z12a), Tracker-seq

description:
Library name: IUE-ZR-3-rep1 (Z12a)
10xGenomics


title: IUE-ZR-4, replicate 1 (C08a), Tracker-seq

description:
Library name: IUE-ZR-4-rep1 (C08a)
10xGenomics


title: 2475, Mus musculus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002475


title: 1776, Mus musculus, Ovary (left),Ovary (left)

description: Library name: itox001776


title: 59, Rattus norvegicus, Spleen

description: Library name: itox000059


title: 11977, Sus scrofa, Tongue,Tongue

description: Library name: itox011977

source_name: Tongue,Tongue

value: Tongue,Tongue


title: 64, Rattus norvegicus, Brain - Cerebellum

description: Library name: itox000064

source_name: Brain - Cerebellum

value: Brain - Cerebellum


title: IUE-ZR-1 (P4), Tracker-seq

description:
Library name: IUE-ZR-1 (P4)
10xGenomics

source_name: P4 brain

value: P4 brain


title: 11913, Sus scrofa, Spinal Cord,Spinal Cord

description: Library name: itox011913

source_name: Spinal Cord,Spinal Cord

value: Spinal Cord,Spinal Cord


title: IUE-ZR-2 (T1), Tracker-seq

description:
Library name: IUE-ZR-2 (T1)
10xGenomics


title: 11912, Sus scrofa, Jejunum,Jejunum

description: Library name: itox011912

source_name: Jejunum,Jejunum

value: Jejunum,Jejunum


title: 65, Rattus norvegicus, Epididymus (head)

description: Library name: itox000065

source_name: Epididymus (head)

value: Epididymus (head)


title: CD4 T cells, DKO 2 Treg

city: Cologne

first: Mauro

last: Corrado

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: University of Cologne

description: Library name: Sample 10

data_processing:
RNA‐seq data were analyzed using the Cologne Center for Genomics’ in‐house pipeline for RNA‐Seq analysis based on the nextflow DSL (version 20.01.0 build 5264)
Assembly: GRCm38
Supplementary files format and content: countTables_All.xlsx  (including raw counts, FPKM, DeSEQ2 normalized counts)

source_name: CD4 T cells

growth_protocol: CD4+ T cell were cultured in RPMI medium + 10%FCS supplemented with 100 U/mL human recombinant IL-2 (10ngr/mL) (PeproTech, Cat# 200-02), TGF-β (10ngr/mL) (Thermo Fisher Scientific,  Cat#100-21-100UG), anti-IFNγ (4mg/mL) (Bio X Cell, Cat#BP0055), anti-IL4 (mg/mL) (Bio X Cell, Cat# BP0045)

extract_protocol:
RNA was extracted using Rneasy mini kit (qiagen)
Libraries were prepared using the Illumina® Stranded TruSeq® RNA sample preparation Kit. Library preparation started with 500ng total RNA. After poly-A selection (poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This was followed by second-strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (15 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent Tape Station), equimolar amounts of the library were pooled. The pools were quantified using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The pool was sequenced on an Illumina NovaSeq6000 sequencing instrument with a PE100 protocol.

treatment_protocol: no treatment

value: CD4 T cells

value: DKO

value: no treatment


title: 253, Rattus norvegicus, Liver (left lateral lobe)

description: Library name: itox000253

source_name: Liver (left lateral lobe)

value: Liver (left lateral lobe)


title: 2495, Mus musculus, Vagina,Vagina

description: Library name: itox002495

source_name: Vagina,Vagina

value: Vagina,Vagina


title: 66, Rattus norvegicus, Seminal Vesicles

description: Library name: itox000066

source_name: Seminal Vesicles

value: Seminal Vesicles


title: CD4 T cells, DKO 1 Treg

description: Library name: Sample 9


title: 2477, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002477


title: 1778, Mus musculus, Testis (tubules\, without capsule),Testis (tubules\, without capsule)

description: Library name: itox001778


title: 2476, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002476


title: 11915, Sus scrofa, Stomach,Stomach

description: Library name: itox011915

source_name: Stomach,Stomach

value: Stomach,Stomach


title: 11916, Sus scrofa, Temporal Lobe,Temporal Lobe

description: Library name: itox011916

source_name: Temporal Lobe,Temporal Lobe

value: Temporal Lobe,Temporal Lobe


title: CD4 T cells, CHOP KO 3 Treg

description: Library name: Sample 8

value: CHOP KO


title: 11914, Sus scrofa, Spleen,Spleen

description: Library name: itox011914

source_name: Spleen,Spleen

value: Spleen,Spleen


title: CD4 T cells, CHOP KO 2 Treg

description: Library name: Sample 7


title: 125, Rattus norvegicus, Ureter

description: Library name: itox000125

source_name: Ureter

value: Ureter


title: 2478, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002478


title: 2499, Mus musculus, Cervix -Pooled,Cervix -Pooled

description: Library name: itox002499

source_name: Cervix -Pooled,Cervix -Pooled

value: Cervix -Pooled,Cervix -Pooled


title: 11962, Sus scrofa, Testis,Testis

description: Library name: itox011962

source_name: Testis,Testis

value: Testis,Testis


title: 11963, Sus scrofa, Thalamus,Thalamus

description: Library name: itox011963

source_name: Thalamus,Thalamus

value: Thalamus,Thalamus


title: 11964, Sus scrofa, Thymus Gland,Thymus Gland

description: Library name: itox011964

source_name: Thymus Gland,Thymus Gland

value: Thymus Gland,Thymus Gland


title: 126, Rattus norvegicus, Urinary Bladder

description: Library name: itox000126

source_name: Urinary Bladder

value: Urinary Bladder


title: 2479, Mus musculus, Spleen,Spleen

description: Library name: itox002479


title: 124, Rattus norvegicus, Skin (inguinal)

description: Library name: itox000124

source_name: Skin (inguinal)

value: Skin (inguinal)


title: CD4 T cells, KO 2 Treg

description: Library name: Sample 5

value: CD4 T cells

value: PTPMT1 KO


title: 128, Rattus norvegicus, DRG-L4

description: Library name: itox000128


title: 2480, Mus musculus, Spleen,Spleen

description: Library name: itox002480


title: CD4 T cells, KO 1 Treg

description: Library name: Sample 4

value: no treatment


title: 11965, Sus scrofa, Tongue,Tongue

description: Library name: itox011965

source_name: Tongue,Tongue

value: Tongue,Tongue


title: 2502, Mus musculus, Eye-lens -Pooled,Eye-lens -Pooled

description: Library name: itox002502

source_name: Eye-lens -Pooled,Eye-lens -Pooled

value: Eye-lens -Pooled,Eye-lens -Pooled


title: 11966, Sus scrofa, Tonsil,Tonsil

description: Library name: itox011966

source_name: Tonsil,Tonsil

value: Tonsil,Tonsil


title: 129, Rattus norvegicus, Brain-Striatum

description: Library name: itox000129

source_name: Brain-Striatum

value: Brain-Striatum


title: 2481, Mus musculus, Spleen,Spleen

description: Library name: itox002481


title: 127, Rattus norvegicus, Adrenal Gland

description: Library name: itox000127

source_name: Adrenal Gland

value: Adrenal Gland


title: 130, Rattus norvegicus, Brain- Hippocampus

description: Library name: itox000130

source_name: Brain- Hippocampus

value: Brain- Hippocampus


title: 11967, Sus scrofa, Trachea,Trachea

description: Library name: itox011967

source_name: Trachea,Trachea

value: Trachea,Trachea


title: 132, Rattus norvegicus, Spleen

description: Library name: itox000132

source_name: Spleen

value: Spleen


title: 2482, Mus musculus, Stomach (glandular),Stomach (glandular)

description: Library name: itox002482

source_name: Stomach (glandular),Stomach (glandular)

value: Stomach (glandular),Stomach (glandular)


title: CD4 T cells, Wt 1 Treg

description: Library name: Sample 1

source_name: CD4 T cells

value: Wt


title: CD4 T cells, Wt 3 Treg

description: Library name: Sample 3


title: CD4 T cells, CHOP KO 1 Treg

description: Library name: Sample 6

value: CHOP KO


title: 2483, Mus musculus, Stomach (glandular),Stomach (glandular)

description: Library name: itox002483


title: 11989, Sus scrofa, Brainstem,Brainstem

description: Library name: itox011989

source_name: Brainstem,Brainstem

value: Brainstem,Brainstem


title: 12038, Sus scrofa, Kidney,Kidney

description: Library name: itox012038

source_name: Kidney,Kidney

value: Kidney,Kidney


title: 2J NSG-CSF1 With iMGL engrafted

city: Braine L'Alleud

first: Jan

middle: R

last: Detrez

address: Chemin du Foriest 1

country: Belgium

institute: UCB

description: Library name: 2J

data_processing:
Raw bcl files were converted to FASTQ by 10X’s tool cellranger mkfastq v.7.1, Followed by creation of gene expression matrices by cellranger count v.7.1 using the provided merged GRCh38 and mm10 genome. Samples were pre-filtered during import in R with Seurat::CreateSeuratObject  set to filter keeping a minimum of 10 cells per gene and 200 genes per cell. Following visualisation of the distribution of features, samples were additionally filtered, keeping cells with more than 2000 genes per cell and less than 10% mitochondrial genes. Normalisation was done using Seurat::SCTransform using glmGamPoi, regressing out the cell cycle gene score, the percentage of mitochondrial genes, the processing batch, number of features, and the original identity. Multi-resolution clustering was performed initially, and an appropriate resolution was chosen based on its alignment with the biology. A processing batch effect was observed between subsequent 10X chip runs, and harmony:: RunHarmony was performed, effectively mering separated clusters. Automated cluster annotation was performed by ScType 39, followed by manual curation of the clusters based on canonical marker expression. Cluster pseudo-bulk differential gene expression (DEG) analysis was done by aggregating the count matrix to sample levels, followed by re-clustering of the raw count matrix per cluster and DESeq2::DESeq analysis and visualisation in volcano plots with cut-offs for false discovery rate (FDR) corrected p-values at 0.05 and an absolute log10 fold change (FC) at 1. All figures were generated by pseudo-bulk clustering, unless indicated otherwise. Gene enrichment was done through fgsea::fgsea, using GO database m5.all.v2022.1.Mm.
Assembly: refdata-gex-GRCh38-and-mm10-2020
Supplementary files format and content: delimited file containing aligned cellular barcodes

source_name: Brain

extract_protocol:
Mice were perfused with ice-cold 1X HBSS with 10 U/ml heparin, together with transcriptional inhibitors were added actinomycin D (5 µg/ml), triptolide (10 µM) as was done in other studies 12. Samples were collected on ice in 1X HBSS that contained anisomycin (27.1 µg/ml) as a third transcription inhibitor, as well as RNase Inhibitor (0.2 U/μl) and DTT (1 mM). All compounds were used in all subsequent solutions at the same concentrations, together with and sample were kept at 4°C throughout the process. Brain dissociations were performed based on an adapted protocol previously described for CyTOF tissue processing. Brains were dissociated using a papain-based dissociation kit at 37 C and 5% CO2 for 30 min (according to the manufacturer’s instructions) with gentle titurations using 10 and 5 ml serological pipettes in 10 min intervals. Papain was inhibited by albumin-ovomucoid solution mixed with DNAse. Single cell suspensions were filtered through a 40 µm cell strainer and resuspended in Myelin Removal Beads II solution according to manufacturer’s instructions. Dynamag magnets were used to remove myelin from the solution. For cell culture cells, cells were detached using 37°C PBS and a cell scraper. After passing through a 40 µm cell strainer, cell suspensions were spun at 300 g for 5 min and resuspended in 1X PBS with 0.1% before loading on the Chromium device.
10X single-cell libraries were prepared following the manufacturer’s guidelines per mouse, without pooling. As 10X chips are limited to 8 samples per run, some experiments were run in multiple processing batches.

value: Brain

value: Engrafted iPSC-derived Microglia

value: HO


title: 2484, Mus musculus, Stomach (glandular),Stomach (glandular)

description: Library name: itox002484


title: 133, Rattus norvegicus, Stomach (glandular)

description: Library name: itox000133

source_name: Stomach (glandular)

value: Stomach (glandular)


title: CD4 T cells, Wt 2 Treg

description: Library name: Sample 2

value: CD4 T cells

value: no treatment


title: 2K NSG-CSF1 With iMGL engrafted

description: Library name: 2K

value: HE


title: 134, Rattus norvegicus, Colon (mid)

description: Library name: itox000134

source_name: Colon (mid)

value: Colon (mid)


title: 2I NSG-CSF1 Without iMGL engrafted

description: Library name: 2I


title: 2H NSG-CSF1 Without iMGL engrafted

description: Library name: 2H


title: 1728, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001728

source_name: Eye (minus lens),Eye (minus lens)

value: Eye (minus lens),Eye (minus lens)


title: 131, Rattus norvegicus, Pituitary

description: Library name: itox000131

source_name: Pituitary

value: Pituitary


title: 12041, Sus scrofa, Colon,Colon

description: Library name: itox012041

source_name: Colon,Colon

value: Colon,Colon


title: 12040, Sus scrofa, Cecum,Cecum

description: Library name: itox012040

source_name: Cecum,Cecum

value: Cecum,Cecum


title: 2488, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002488


title: 1729, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001729


title: 136, Rattus norvegicus, Liver (left lateral lobe)

description: Library name: itox000136

source_name: Liver (left lateral lobe)

value: Liver (left lateral lobe)


title: 137, Rattus norvegicus, Ileum

description: Library name: itox000137

source_name: Ileum

value: Ileum


title: 2489, Mus musculus, Lymph node (mesenteric),Lymph node (mesenteric)

description: Library name: itox002489


title: 12039, Sus scrofa, Kidney,Kidney

description: Library name: itox012039


title: 11998, Sus scrofa, Frontal Lobe,Frontal Lobe

description: Library name: itox011998

source_name: Frontal Lobe,Frontal Lobe

value: Frontal Lobe,Frontal Lobe


title: 2485, Mus musculus, Cecum,Cecum

description: Library name: itox002485


title: 2G NSG-CSF1 Without iMGL engrafted

description: Library name: 2G


title: 2490, Mus musculus, Adipose - Visceral (Omentum),Adipose - Visceral (Omentum)

description: Library name: itox002490


title: 1F NSG-CSF1 Without iMGL engrafted

description: Library name: 1F


title: 1E NSG-CSF1 Without iMGL engrafted

description: Library name: 1E


title: 12045, Sus scrofa, Lymph Node,Lymph Node

description: Library name: itox012045

source_name: Lymph Node,Lymph Node

value: Lymph Node,Lymph Node


title: 139, Rattus norvegicus, Brain - Cerebellum

description: Library name: itox000139

source_name: Brain - Cerebellum

value: Brain - Cerebellum


title: 2491, Mus musculus, Adipose - Visceral (Omentum),Adipose - Visceral (Omentum)

description: Library name: itox002491


title: 138, Rattus norvegicus, Adipose - Visceral (Omentum)

description: Library name: itox000138

source_name: Adipose - Visceral (Omentum)

value: Adipose - Visceral (Omentum)


title: 11999, Sus scrofa, Gallbladder,Gallbladder

description: Library name: itox011999

source_name: Gallbladder,Gallbladder

value: Gallbladder,Gallbladder


title: 12046, Sus scrofa, Skeletal Muscle,Skeletal Muscle

description: Library name: itox012046

source_name: Skeletal Muscle,Skeletal Muscle

value: Skeletal Muscle,Skeletal Muscle


title: 2492, Mus musculus, Uterus (left horn),Uterus (left horn)

description: Library name: itox002492

source_name: Uterus (left horn),Uterus (left horn)

value: Uterus (left horn),Uterus (left horn)


title: 135, Rattus norvegicus, Lymph node (mesenteric)

description: Library name: itox000135

source_name: Lymph node (mesenteric)

value: Lymph node (mesenteric)


title: 140, Rattus norvegicus, Uterus (left horn)

description: Library name: itox000140

source_name: Uterus (left horn)

value: Uterus (left horn)


title: 1C NSG-CSF1 With iMGL engrafted

description: Library name: 1C

source_name: Brain

value: Brain

value: Engrafted iPSC-derived Microglia

value: HO


title: 1D NSG-CSF1 With iMGL engrafted

description: Library name: 1D

value: HE


title: 2493, Mus musculus, Uterus (left horn),Uterus (left horn)

description: Library name: itox002493


title: 1B NSG-CSF1 Without iMGL engrafted

description: Library name: 1B


title: 2561, Mus musculus, Peripheral Nerve (sciatic)-Pooled,Peripheral Nerve (sciatic)-Pooled

description: Library name: itox002561


title: 141, Rattus norvegicus, Ovary (left)

description: Library name: itox000141

source_name: Ovary (left)

value: Ovary (left)


title: 12047, Sus scrofa, Optic Nerve,Optic Nerve

description: Library name: itox012047

source_name: Optic Nerve,Optic Nerve

value: Optic Nerve,Optic Nerve


title: 1A NSG-CSF1 With iMGL engrafted

description: Library name: 1A


title: 12048, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox012048

source_name: Peripheral nerve,Peripheral nerve

value: Peripheral nerve,Peripheral nerve


title: 142, Rattus norvegicus, Oviduct (Fallopian tube)

description: Library name: itox000142

source_name: Oviduct (Fallopian tube)

value: Oviduct (Fallopian tube)


title: 12049, Sus scrofa, Peripheral nerve,Peripheral nerve

description: Library name: itox012049


title: 144, Rattus norvegicus, Eye-lens

description: Library name: itox000144

source_name: Eye-lens

value: Eye-lens


title: 12050, Sus scrofa, Occipital Lobe,Occipital Lobe

description: Library name: itox012050

source_name: Occipital Lobe,Occipital Lobe

value: Occipital Lobe,Occipital Lobe


title: 2582, Mus musculus, Peripheral Nerve (sciatic)-Pooled,Peripheral Nerve (sciatic)-Pooled

description: Library name: itox002582


title: S3 NSG-CSF1 Without Inhibitors

description: Library name: S3

value: WT


title: S5 NSG-CSF1 Without Inhibitors

description: Library name: S5


title: 143, Rattus norvegicus, Cervix

description: Library name: itox000143

source_name: Cervix

value: Cervix


title: S4 NSG-CSF1 Without Inhibitors

description: Library name: S4


title: S2 NSG-CSF1 With Inhibitors

description: Library name: S2


title: 12051, Sus scrofa, Pancreas,Pancreas

description: Library name: itox012051

source_name: Pancreas,Pancreas

value: Pancreas,Pancreas


title: 145, Rattus norvegicus, Brain - Cortex

description: Library name: itox000145

source_name: Brain - Cortex

value: Brain - Cortex


title: 67, Rattus norvegicus, Epididymus (tail)

description: Library name: itox000067

source_name: Epididymus (tail)

value: Epididymus (tail)


title: 12052, Sus scrofa, Cerebral cortex,Cerebral cortex

description: Library name: itox012052

source_name: Cerebral cortex,Cerebral cortex

value: Cerebral cortex,Cerebral cortex


title: 68, Rattus norvegicus, Prostate

description: Library name: itox000068

source_name: Prostate

value: Prostate


title: 2585, Mus musculus, Lung (left lobe),Lung (left lobe)

description: Library name: itox002585

source_name: Lung (left lobe),Lung (left lobe)

value: Lung (left lobe),Lung (left lobe)


title: 12055, Sus scrofa, Small Intestine,Small Intestine

description: Library name: itox012055

source_name: Small Intestine,Small Intestine

value: Small Intestine,Small Intestine


title: 2563, Mus musculus, Esophagus (mid) -Pooled,Esophagus (mid) -Pooled

description: Library name: itox002563


title: 2565, Mus musculus, Lung (left lobe),Lung (left lobe)

description: Library name: itox002565


title: 2562, Mus musculus, Esophagus (mid) -Pooled,Esophagus (mid) -Pooled

description: Library name: itox002562


title: 12054, Sus scrofa, Small Intestine,Small Intestine

description: Library name: itox012054


title: 12053, Sus scrofa, Skin,Skin

description: Library name: itox012053

source_name: Skin,Skin

value: Skin,Skin


title: DSP-1001660035646-A-H07

city: Boston

first: Sharmila

last: Masli

address: 72 E. Concord St Instructional (L)

institute: Boston University

description: Library name: DSP-1001660035646-A-H07

data_processing:
Raw FASTQ files from the instrument were processed using the GeoMX NGS Pipeline using the instrument provided .ini file generated probe count matrices in dcc format
Images were assessed for presence of each cell type based on established markers (CK, SMA, PTPRC, etc.)
Raw counts were loaded with nanostring packages and then normalized, after which differential expression analysis was conducted by DESeq2, followed by Gene Set Enrichment Analysis through clusterProfiler
Supplementary files format and content: .dcc, count matrix files

source_name: Lacrimal Gland

extract_protocol:
Serial sections of formalin-fixed paraffin-embedded (FFPE) LG tissues harvested from WT (n=3) and TSP-/- (n=4) mice were cut (5 µm thick) and transferred to slides. One set of slides was stained for H&E and another set of slides with consecutive sections were submitted for spatial profiling to the Beth Israel Deaconess Medical Center (BIDMC) Spatial Technologies Unit (STU), MA, USA. The GeoMX Digital Spatial Profiler (DSP) platform was used to generate spatially resolved transcriptomic data, specifically the Whole Transcriptome Atlas (WTA) mouse RNA probe set for Illumina Systems (GMX-RNA-NGS-MsWTA-4) assay. This assay includes RNA probe set for 21,000+ transcripts for mouse protein coding genes plus negative controls designed for Illumina NGS readout with the Seq Code library prep. To visualize tissue structural components and microenvironment, a set of fluorophore-conjugated morphology markers were used. These included Alexa Fluor 532 (green)-conjugated anti-pan-CK (AE1+AE3, Novus, Cat.# NBP2-33200), Alexa Fluor 594 (yellow)-conjugated anti-CD45 (EM-05, Novus, Cat.# NBP1-44763AF594) and Alexa Fluor 647 (red)-conjugated anti-Smooth Muscle Actin (SP171, Abcam, Cat.# ab267537) and nuclear stain SYTO13 (blue). These markers were used to delineate the nuclear, epithelial (acinar and duct), immune and myoepithelial compartments. Immunofluorescence imaging, region of interest (ROI) selection, segmentation into marker-specific areas of interest (AOI) and spatially indexed barcode cleavage and collection were performed on a GeoMx Digital Spatial Profiling instrument (Nanostring). Selected ROIs were exposed to ultraviolet (UV) light to cleave DNA tags in a region-specific manner. The released indexing oligos were then collected using microcapillary aspiration and dispensed into a microplate as per segmentation of each ROI. Four consecutive sections per tissue (total 16 of TSP-1-/- and 12 of WT) were assessed. Approximately, 6-10 ROIs and 11-14 AOIs per tissue sample (total 34 ROIs and 57 AOIs for TSP-1-/- and 21 ROIs and 34 AOIs for WT) were collected.
Library preparation was performed as per manufacturer’s instructions which included PCR amplification to add Illumina adapter sequences and unique dual sample indices. Sequencing was performed to a minimum of 350M PE reads by pooling all 91 uniquely indexed WTA AOIs and sequencing on Illumina NovaSeq 6000 S4 flowcell in a 2x150bp PE, dual index, 8bp i5 and i7 index length configuration.

value: Lacrimal Gland

value: Multiple


title: DSP-1001660035646-A-H06

description: Library name: DSP-1001660035646-A-H06


title: 69, Rattus norvegicus, Brain - Cortex

description: Library name: itox000069


title: 2564, Mus musculus, Esophagus (mid) -Pooled,Esophagus (mid) -Pooled

description: Library name: itox002564


title: 1608, Rattus norvegicus, Brain-Cortex,Brain-Cortex

description: Library name: itox001608

source_name: Brain-Cortex,Brain-Cortex

value: Brain-Cortex,Brain-Cortex


title: 2566, Mus musculus, Lung (left lobe),Lung (left lobe)

description: Library name: itox002566


title: 12057, Sus scrofa, Spinal Cord,Spinal Cord

description: Library name: itox012057

source_name: Spinal Cord,Spinal Cord

value: Spinal Cord,Spinal Cord


title: DSP-1001660035646-A-H04

description: Library name: DSP-1001660035646-A-H04


title: 2567, Mus musculus, Thymus,Thymus

description: Library name: itox002567

source_name: Thymus,Thymus

value: Thymus,Thymus


title: 1462, Rattus norvegicus, Salivary Gland,Salivary Gland

description: Library name: itox001462

source_name: Salivary Gland,Salivary Gland

value: Salivary Gland,Salivary Gland


title: DSP-1001660035646-A-H05

description: Library name: DSP-1001660035646-A-H05


title: 1098, Rattus norvegicus, AoEC,AoEC

description: Library name: itox001098

source_name: AoEC,AoEC

value: AoEC,AoEC


title: DSP-1001660035646-A-H03

description: Library name: DSP-1001660035646-A-H03


title: 12058, Sus scrofa, Spleen,Spleen

description: Library name: itox012058

source_name: Spleen,Spleen

value: Spleen,Spleen


title: 1100, Rattus norvegicus, LSEC,LSEC

description: Library name: itox001100

source_name: LSEC,LSEC

value: LSEC,LSEC


title: 2548, Mus musculus, Ileum,Ileum

description: Library name: itox002548

source_name: Ileum,Ileum

value: Ileum,Ileum


title: 12059, Sus scrofa, Stomach,Stomach

description: Library name: itox012059

source_name: Stomach,Stomach

value: Stomach,Stomach


title: 12168, Sus scrofa, Aorta,Aorta

description: Library name: itox012168

source_name: Aorta,Aorta

value: Aorta,Aorta


title: DSP-1001660035646-A-H02

description: Library name: DSP-1001660035646-A-H02


title: DSP-1001660035646-A-G12

description: Library name: DSP-1001660035646-A-G12


title: DSP-1001660035646-A-H01

description: Library name: DSP-1001660035646-A-H01


title: 2570, Mus musculus, Skin (inguinal),Skin (inguinal)

description: Library name: itox002570

source_name: Skin (inguinal),Skin (inguinal)

value: Skin (inguinal),Skin (inguinal)


title: DSP-1001660035646-A-G11

description: Library name: DSP-1001660035646-A-G11


title: 1735, Mus musculus, Eye (minus lens),Eye (minus lens)

description: Library name: itox001735

source_name: Eye (minus lens),Eye (minus lens)

value: Eye (minus lens),Eye (minus lens)


title: 1549, Rattus norvegicus, Bone marrow - femoral scoop,Bone marrow - femoral scoop

description: Library name: itox001549


title: 12170, Sus scrofa, Bone Marrow,Bone Marrow

description: Library name: itox012170

source_name: Bone Marrow,Bone Marrow

value: Bone Marrow,Bone Marrow


title: 12169, Sus scrofa, Coronary Artery,Coronary Artery

description: Library name: itox012169

source_name: Coronary Artery,Coronary Artery

value: Coronary Artery,Coronary Artery


title: 2572, Mus musculus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002572


title: 12056, Sus scrofa, Small Intestine,Small Intestine

description: Library name: itox012056

source_name: Small Intestine,Small Intestine

value: Small Intestine,Small Intestine


title: 2571, Mus musculus, Small intestine- Jejunum (mid),Small intestine- Jejunum (mid)

description: Library name: itox002571


title: 1538, Rattus norvegicus, Adipose - Visceral (Omentum),Adipose - Visceral (Omentum)

description: Library name: itox001538


title: 2573, Mus musculus, Small intestine-Duodenum,Small intestine-Duodenum

description: Library name: itox002573


title: 1550, Rattus norvegicus, Lymph node (mesentric),Lymph node (mesentric)

description: Library name: itox001550


title: DSP-1001660035646-A-G09

description: Library name: DSP-1001660035646-A-G09

value: Lacrimal Gland


title: 2595, Mus musculus, Whole Blood,Whole Blood

description: Library name: itox002595

source_name: Whole Blood,Whole Blood

value: Whole Blood,Whole Blood


title: 12171, Sus scrofa, Brainstem,Brainstem

description: Library name: itox012171

source_name: Brainstem,Brainstem

value: Brainstem,Brainstem


title: 1553, Rattus norvegicus, Lymph node (mesentric),Lymph node (mesentric)

description: Library name: itox001553


title: 1099, Rattus norvegicus, LMVEC,LMVEC

description: Library name: itox001099

source_name: LMVEC,LMVEC

value: LMVEC,LMVEC


title: 1633, Rattus norvegicus, Brain-Hippocampus,Brain-Hippocampus

description: Library name: itox001633

source_name: Brain-Hippocampus,Brain-Hippocampus

value: Brain-Hippocampus,Brain-Hippocampus