title: FC00185: Control_52


title: FC00185: Control_51

status: Public on Dec 12 2022

type: SRA

city: Wellington

first: Sotaro

last: Ochiai

address: Gate 7 Victoria University, Keburn Parade

country: New Zealand

institute: Malaghan Institute of Medical Research

description: FC00185: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 2

library_source: transcriptomic single cell

data_processing:
Detected number of molecules for each gene per cell was counted based on molecular barcodes
Number of molecules for each gene per cell was calculated using the detection efficiency of the spike-in RNAs which were measured together with every cell (total input number of spike-in RNA molecules per cell: 39000).
Assembly: mm10 assembly from the UCSC Genome Browser using STAR ver.2.7.3a
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: C1-C8 DRG

extract_protocol:
DRGs collected from Nav1.8-Cre R26CAG-floxStop-tdTomato mice were digested using 0.5 mg/mL liberase TL, 5 mg.mL dispase II, 0.33 mg/mL papain and 0.1mg/mL Dnase I in DMEM (with 2-ME). Samples were incubated for 20 min, mechanically agitated using glass Pasteur pipettes to prepare single cell suspension. tdTomato+ cells were single cell sorted using BD FACS Aria III into tubes containing 0.4uL of 10 x SingleCellProtect and immediiately frozen in LiqN2. Cell collection and sequencing was performed at four separate occasions from 6 naive Nav1.8-Cre R26CAG-floxStop-tdTomato mice . FC00029 contains cells from 2 mice (labelled blue and red), FC00185 contains samples from 1 mouse, FC00355 from 2 mice (Control1 and Control2) and FC00404 from 1 mouse (Control6).
Library was generated as previously described (Tenno et al, 2017,  J Exp Med 214, 2933-2946. 10.1084/jem.20170729.)
scRNA-seq using digital RNA sequencing method (Shiroguchi et al. 2012, Proc Natl Acad Sci U S A 109, 1347-1352. 10.1073/pnas.1118018109.)

tag: cell type

value: Dorsal Root Ganglion

tag: tissue

value: C1-C8 DRG

tag: strain

tag: age

value: 6-12 weeks old


title: FC00185: Control_49


title: Neutrophils from naïve (BALBc/J) mice, gene expression library

city: Bar Harbor

first: Guangwen

last: Ren

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

description: polyA RNA

library_source: transcriptomic

data_processing:
The raw data (FASTQ file) of each library were produced and demultiplexed using Illumina bcl2fastq 2.20.0.422.
For all libraries, R1 contains a 16bp cell barcode + 12bp UMI barcode and R2 contains the biological reads. If present, I1 contains the 8bp i7 index which is needed for 10X CellRanger pipelines.
An unfiltered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mouse reference genome (mm10-2020-A) build using CellRanger v4.0.0
A digital counts matrix was generated for each hashtag library using CITE-Seq-Count v1.4.3. This produces a matrix of counts with hashtag labels for rows and cell barcodes for columns.
Assembly: mm10
Supplementary files format and content: Transcriptomic and HashTag (HTO) counts matrices in Matrix Market sparse CSC matrix format. Rows correspond to genes in the order provided in features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

molecule: polyA RNA

source_name: BM, PB, Lung

extract_protocol:
Neutrophils were sorted from BM, PB and lung, and then labeled with cell hashing antibodies. Around 24,000 cells (8,000 cells from each hashtagged sample) were loaded into one lane of a 10X Chromium microfluidic chip. Cells capture, lysis and RNA extraction were performed using the 10X V3 Chromium technology following the manufacturer’s protocol.
Single cell capture, barcoding and library preparation were performed with the 10x Chromium system using version 3 chemistry, following the manufacturer’s protocol. cDNA was synthesized and amplified as per manufacturer’s protocol and amplified to construct an Illumina sequencing library. cDNA and libraries were checked for quality on an Agilent 4200 TapeStation, quantified by KAPA qPCR.

value: BM, PB, Lung

tag: Sex

value: Female

value: Neutrophils

tag: genotype

value: Wild type

value: BALBc/J


title: FC00185: Control_50


title: epidermis_28h_subject103

type: RNA

city: Berlin

first: Bharath

last: Ananthasubramaniam

address: Philippstr. 13, House 20, R. 209

country: Germany

institute: Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin

description: Gene expression at 4:00h the day after in human epidermis

hyb_protocol: Samples were hybridized to Agilent Whole Genome Oligo Microarrays 4x44k (Agilent Technologies).

scan_protocol: Agilent protocol

data_processing: The RMA algorithm was used to preprocess and extract expression profiles from the raw CEL files. Genes were annotated with ENSEMBL and ENTREZ IDs using Agilent “Human Genome, Whole” annotation data (hgug4112a.db, v3.2). Background correction was performed with the “normexp” function from R package “limma”; normalization between the different arrays was done with the “quantile” function from the same package. Non-annotated probes as well as control probes were filtered out. Genes were considered to be expressed if the signal across the 7 time points was well above the background signal in at least 50% of the samples. Averaged values of probes that mapped to the same gene were used for further analysis.

organism: Homo sapiens

source_name: Skin biopsy from upper back, epidermis, subject P103, taken at 4:00h day after

label_protocol: For each of the samples, RNA was amplified and 1.2–1.65 μg of RNA were labelled with Cyanine 3-CTP according to the manufacturer's instruction (Miltenyi Biotec).

extract_protocol:
3 mm biopsies were obtained from the upper back for seven time points over a period of 24 h (8:00, 12:00, 16:00, 20:00, 00:00, 04:00 and 8:00 the following day).
RNA extraction and quality control was performed with TRIzol following manufacturer's instructions.

treatment_protocol: Skin biopsies were subsequently incubated in PBS at 55oC for 3 min to separate epidermis and dermis. Tissue samples were then frozen in liquid nitrogen and stored at -80oC.

tag: subject

value: Skin – epidermis

tag: time of collection

value: 4:00h day after

value: female


title: epidermis_28h_subject109

source_name: Skin biopsy from upper back, epidermis, subject P109, taken at 4:00h day after

value: male


title: epidermis_28h_subject106

source_name: Skin biopsy from upper back, epidermis, subject P106, taken at 4:00h day after


title: Neutrophils from naïve (BALBc/J) and 4T1 tumor-bearing mice, hashtag library

description: Hashtag-derived oligonucleotide (HTO)


title: FC00185: Control_47


title: FC00185: Control_58


title: epidermis_28h_subject102

source_name: Skin biopsy from upper back, epidermis, subject P102, taken at 4:00h day after


title: Neutrophils from 4T1 tumor-bearing mice, gene expression library

description: polyA RNA


title: epidermis_28h_subject100

source_name: Skin biopsy from upper back, epidermis, subject P100, taken at 4:00h day after


title: FC00185: Control_46


title: Primed Hmg20a DP #26 rep1

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

library_source: genomic

data_processing:
Quality control of FASTQ files was done using FastQC.
trimGalore was used for QC-aware trimming and adapter-removal.
Reads were aligned to a pre-compiled index of the mouse mm9 genome using HISAT2 v2.2.1
Duplicates were removed with Picard tools v2.21.9. Coverage tracks were generated with deepTools.
Peak calling was performed using MACS 2.2.71
Assembly: mm9
Supplementary files format and content: bigwig files (of coverage) at 25 bp resolution

molecule: genomic DNA

source_name: mES V6.5

growth_protocol: mESCs were cultured on 0.1%-gelatin-coated 6-well plates in N2B27 medium supplemented with 50 μM β-mercaptoethanol, 2 mM L-glutamine, 0.1% Sodium bicarbonate, 0.11% bovine serum albumin fraction V, 1000 units/ml recombinant mouse leukemia inhibitory factor (LIF), 1 µM PD0325901 (MEK inhibitor) and 3 µM CHIR99021 (GSK3 inhibitor). Every two days, cells were passaged at a density of 1.4x105 cells/well.

extract_protocol:
ATAC-seq was performed on 1x105 primed mESCs at applying the ATAC-Seq Kit cat. 53150 (Active Motif) according to manufacturer instructions.
ATAC-Seq Kit Cat. 53150 (Active Motif) - transposase based

treatment_protocol: On differentiation day 0, naïve wild type and Hmg20a KO mESCs (2i+LIF) were adapted to primed state in differentiation media (DMEM, Sigma) supplemented with 10% FCS, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1000 U/mL leukemia inhibitory factor (LIF) for 2 days before harvesting.

tag: cell line

value: mES V6.5

value: embryonic stem cell

value: Hmg20A DP

tag: treatment

value: Primed mouse embryonic stem cells


title: epidermis_24h_subject115

description: Gene expression at 00:00h the day after in human epidermis

source_name: Skin biopsy from upper back, epidermis, subject P115, taken at 00:00h day after

value: 00:00h day after


title: mESC Day2_WT RNA_Rep1

description: RNA-seq

data_processing:
Paired end raw FASTQ files were quality and adaptor trimmed using trimGalore v.1.18
Alignment of the trimmed FASTQ files against the  mm9 genome build  was performed using hisat2 v.2.2.1 with “--min-intronlen 30 --max-intronlen 3000” parameters
Based on the BAM files and the mouse mm9 GTF read counts per gene for each sample were calculated using the summarizedOverlaps function of the GenomicAlignments R package
The resulting read counts were normalized using DESeq2 v.1.28.1.
DESeq2 was used for the identification of differentially expressed genes
Assembly: mm9
Supplementary files format and content: CSV of raw sequencing counts per gene

extract_protocol:
At indicated timepoints of differentiation total RNA was harvested using Rneasy mini columns with on-column Dnase digestion (QUIAGEN)
Performed by NOVOGENE using TruSeq® Stranded Total RNA LT-Ribo-Zero Gold kit (Illumina RS-122–2301/2) or others.

treatment_protocol: On differentiation day 0, naïve wild type and Hmg20a KO mESCs (2i+LIF) were adapted to primed state in differentiation media (DMEM, Sigma) supplemented with 10% FCS, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1000 U/mL leukemia inhibitory factor (LIF) for 2 days. Hanging drops containing 1000 cells were prepared in 25 µl of differentiation media (without LIF) supplemented with 50 µg/ml vitamin C. On differentiation day 6 (4 days in suspension), each droplet containing one EB was carefully transferred onto a 0.1%-gelatin-coated 24-well plate.

value: WT

value: Cardiomyocyte differentiation


title: FC00185: Control_44

value: Dorsal Root Ganglion

value: C1-C8 DRG

value: 6-12 weeks old


title: epidermis_24h_subject114

source_name: Skin biopsy from upper back, epidermis, subject P114, taken at 00:00h day after


title: mESC Day0_WT RNA_Rep2

description: RNA-seq


title: FC00185: Control_41


title: FC00185: Control_42


title: FC00185: Control_48


title: FC00185: Control_40


title: mESC Day0_WT RNA_Rep1

description: RNA-seq


title: non-CMs, Sham2

city: Shinjuku

first: Taketaro

last: Sadahiro

state: Tokyo

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

data_processing:
Raw sequence reads were processed from 10X Genomics' Cell Ranger v.5.0.0 pipeline and generated fastq files. In brief, the demultiplexed fastq files were aligned to a custom reference genome with the tdTomato sequence added to the mm10/GRCm38 reference transcriptome, and the gene expression matrix was counted using the Cellranger count program. The processed scRNA-seq data were performed to quality control, dimensionality reduction, cell clustering, and differential expression analysis by Seurat suite versions 3.2.2 used in R version 3.6.3. (Stuart et al., 2019). To exclude low-quality cells from the analysis, cells that met any of the following criteria were excluded: less than 800 or more than 5,000 unique genes expressed, or more than 10% of the reads mapping to mitochondria. After filtering, dimensionality reduction and visualization of the normalized data (NormalizeData function, default scale factor is 10,000) was done using the UMAP (Uniform Manifold Approximation and Projection) algorithm with the RunPCA and RunUMAP functions implemented in the Seurat package. The DoubletFinder package was used to detect doublets (McGinnis et al., 2019).
Assembly: mm10
Supplementary files format and content: Matrix table with raw or filtered gene counts for every gene and each cell

source_name: non-CMs

extract_protocol:
The isolation of non-CMs from the murine heart was performed as previously described with some modifications (Forte et al., 2020a; Skelly et al., 2018). In brief, mice were sacrificed by cervical dislocation, and hearts were immediately cannulated and perfused with cold PBS (50 ml). Remove the heart, separate the atria and valves from the heart, and cut the ventricular myocardium into 1 mm pieces on a bacterial Petri dish on ice. Transfer to a 10 ml tube containing 3 ml of enzyme solution and incubate in a water bath at 37°C for 45 min, trituration every 15 min. Enzyme solution contained 2 mg/ml collagenase type IV (Worthington Biochemical, CLS-4) and 1.2 U/ml Dispase II (Sigma, 255-914-4). After the final trituration, the enzyme/tissue mixture is filtered through a 40 μm cell strainer, FACS buffer and dead cell removal solution (Miltenyi Biotec, 130-109-398) is added, and debris is removed after centrifugation. Further, use RBC lysis buffer (pluriSelect, 60-00050-11) to remove red blood cells, then dye the cell suspension with Live/Dead (Invitrogen, L34975,1:1000), Calcein Violet Working solution (BioLegend, 425203, 0.1μM). Using a BD AriaIIu with a 130 μm nozzle, cells with intact cell membranes and metabolically active cells (Live/Dead-, Calcein+) were sorted (12 psi) while minimizing pressure on the cells.
Libraries from non-CMs suspensions were generated with a Chromium controller from 10X Genomics according to the manufacturer's instructions. Approximately 8,000 whole cells were loaded into each channel and processed using the Chromium Single Cell 3' v3.1 reagent kit (10X Genomics).

treatment_protocol: Experiments were performed in 8-week-old randomly allocated male mice. To generate the mouse MI model, mice were intubated and anesthetized with isoflurane gas. The chest cavity was exposed by cutting the intercostal muscle and then the left coronary artery was ligated with a 7-0 silk suture. The mouse surgeon was blinded to the study. Transthoracic echocardiography was performed after 2 days of MI, and mice with an ejection fraction (EF) > 45% were removed from the study.

value: Sham

value: non-CMs

value: Hearts were harvested 3 months after Sham operation


title: epidermis_24h_subject113

source_name: Skin biopsy from upper back, epidermis, subject P113, taken at 00:00h day after

value: Skin – epidermis


title: FC00185: Control_39


title: mESC Day2_WT RNA_Rep2

description: RNA-seq


title: FC00185: Control_45


title: mESC Day6_WT RNA_Rep1

description: RNA-seq


title: epidermis_24h_subject111

source_name: Skin biopsy from upper back, epidermis, subject P111, taken at 00:00h day after


title: FC00185: Control_37


title: mESC Day4_WT RNA_Rep2

description: RNA-seq


title: FC00185: Control_33


title: mESC Day4_WT RNA_Rep1

description: RNA-seq


title: FC00185: Control_34


title: FC00185: Control_35


title: FC00185: Control_43


title: epidermis_24h_subject109

source_name: Skin biopsy from upper back, epidermis, subject P109, taken at 00:00h day after


title: FC00185: Control_32


title: epidermis_24h_subject108

source_name: Skin biopsy from upper back, epidermis, subject P108, taken at 00:00h day after


title: epidermis_24h_subject107

source_name: Skin biopsy from upper back, epidermis, subject P107, taken at 00:00h day after


title: epidermis_24h_subject106

source_name: Skin biopsy from upper back, epidermis, subject P106, taken at 00:00h day after


title: mESC Day7.5_WT RNA_Rep2

description: RNA-seq


title: FC00185: Control_31

source_name: C1-C8 DRG


title: mESC Day6_WT RNA_Rep2

description: RNA-seq


title: epidermis_24h_subject103

source_name: Skin biopsy from upper back, epidermis, subject P103, taken at 00:00h day after


title: mESC Day2_HMG20A KO RNA_Rep2

description: RNA-seq

value: Hmg20A knock out


title: FC00185: Control_27


title: FC00185: Control_28


title: FC00185: Control_29


title: FC00185: Control_36


title: mESC Day2_HMG20A KO RNA_Rep1

description: RNA-seq


title: FC00185: Control_26


title: FC00185: Control_25


title: mESC Day7.5_WT RNA_Rep1

description: RNA-seq


title: FC00185: Control_38


title: FC00185: Control_24


title: epidermis_24h_subject102

source_name: Skin biopsy from upper back, epidermis, subject P102, taken at 00:00h day after


title: FC00185: Control_23


title: FC00185: Control_22


title: epidermis_24h_subject100

source_name: Skin biopsy from upper back, epidermis, subject P100, taken at 00:00h day after


title: mESC Day0_HMG20A KO RNA_Rep2

description: RNA-seq


title: epidermis_28h_subject108

source_name: Skin biopsy from upper back, epidermis, subject P108, taken at 4:00h day after

value: 4:00h day after


title: FC00185: Control_21


title: FC00185: Control_30


title: mESC Day0_HMG20A KO RNA_Rep1

description: RNA-seq


title: FC00185: Control_20


title: FC00185: Control_18


title: epidermis_20h_subject115

description: Gene expression at 20:00h in human epidermis

source_name: Skin biopsy from upper back, epidermis, subject P115, taken at 20:00h

value: female


title: mESC Day6_HMG20A KO RNA_Rep2

description: RNA-seq

value: mES V6.5


title: FC00185: Control_19


title: FC00185: Control_17


title: epidermis_20h_subject113

source_name: Skin biopsy from upper back, epidermis, subject P113, taken at 20:00h

value: male


title: mESC Day6_HMG20A KO RNA_Rep1

description: RNA-seq

source_name: mES V6.5

value: embryonic stem cell


title: FC00185: Control_15


title: FC00185: Control_13


title: FC00185: Control_14


title: epidermis_20h_subject114

source_name: Skin biopsy from upper back, epidermis, subject P114, taken at 20:00h


title: epidermis_20h_subject111

source_name: Skin biopsy from upper back, epidermis, subject P111, taken at 20:00h


title: epidermis_20h_subject108

source_name: Skin biopsy from upper back, epidermis, subject P108, taken at 20:00h


title: epidermis_20h_subject109

source_name: Skin biopsy from upper back, epidermis, subject P109, taken at 20:00h


title: mESC Day4_HMG20A KO RNA_Rep1

description: RNA-seq


title: mESC Day4_HMG20A KO RNA_Rep2

description: RNA-seq


title: FC00185: Control_11


title: FC00185: Control_10


title: mESC Day7.5_HMG20A KO RNA_Rep2

description: RNA-seq


title: FC00185: Control_9


title: FC00185: Control_8


title: epidermis_20h_subject107

source_name: Skin biopsy from upper back, epidermis, subject P107, taken at 20:00h


title: FC00185: Control_7


title: mESC Day7.5_HMG20A KO RNA_Rep1

description: RNA-seq


title: WT Day2_IgG CNR_Rep2

description: Cut and Run-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
trimGalore was used for QC-aware trimming and adapter-removal.
Reads were aligned to a pre-compiled index of the mouse mm9 genome using HISAT2 v2.2.1
Duplicates were removed with Picard tools v2.21.9
Coverage tracks were generated with deepTools.
Peak calling was performed using MACS 2.2.71
Assembly: mm9
Supplementary files format and content: bigwig files (of coverage) at 25 bp resolution
Library strategy: Cut & Run-Seq

extract_protocol:
CUT&RUN was performed on 5x105 mESCs at Day 2 of cardiomyocyte differentiation protocol. Applying the CUTANA® CUT&RUN Kit (version 2) according to manufacturer instructions.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs)

value: Primed mouse embryonic stem cells


title: FC00185: Control_16


title: FC00185: Control_6


title: epidermis_20h_subject106

source_name: Skin biopsy from upper back, epidermis, subject P106, taken at 20:00h


title: epidermis_20h_subject103

source_name: Skin biopsy from upper back, epidermis, subject P103, taken at 20:00h


title: FC00185: Control_4


title: WT Day2_HMG20A CNR_Rep2

description: Cut and Run-seq


title: WT Day2_IgG CNR_Rep1

description: Cut and Run-seq


title: FC00185: Control_3


title: FC00185: Control_2


title: FC00185: Control_1


title: epidermis_20h_subject102

source_name: Skin biopsy from upper back, epidermis, subject P102, taken at 20:00h


title: WT Day2_HMG20A CNR_Rep1

description: Cut and Run-seq


title: FC00185: Control_12


title: FC00029: Red_128

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1


title: HMG20AKO Day2_IgG CNR_Rep2

description: Cut and Run-seq


title: FC00029: Red_127


title: epidermis_20h_subject100

source_name: Skin biopsy from upper back, epidermis, subject P100, taken at 20:00h


title: FC00029: Red_125

source_name: C1-C8 DRG


title: epidermis_16h_subject115

description: Gene expression at 16:00h in human epidermis

source_name: Skin biopsy from upper back, epidermis, subject P115, taken at 16:00h


title: HMG20AKO Day2_HMG20A CNR_Rep2

description: Cut and Run-seq


title: FC00029: Red_126


title: FC00029: Red_123


title: FC00029: Red_124


title: HMG20AKO Day2_IgG CNR_Rep1

description: Cut and Run-seq


title: epidermis_16h_subject113

source_name: Skin biopsy from upper back, epidermis, subject P113, taken at 16:00h


title: FC00185: Control_5


title: epidermis_16h_subject114

source_name: Skin biopsy from upper back, epidermis, subject P114, taken at 16:00h


title: FC00029: Red_121


title: HMG20AKO Day2_HMG20A CNR_Rep1

description: Cut and Run-seq


title: FC00029: Red_122


title: epidermis_16h_subject111

source_name: Skin biopsy from upper back, epidermis, subject P111, taken at 16:00h


title: FC00029: Red_120


title: FC00029: Red_119


title: epidermis_16h_subject109

source_name: Skin biopsy from upper back, epidermis, subject P109, taken at 16:00h


title: FC00029: Red_118


title: eWAT_KO4

city: Columbus

first: Wa

last: Du

state: OH

address: 460 West 12th Avenue, Biomedical Research Tower, Rm 360A

department: Department of Surgery, Division of Vascular Diseases and Surgery

institute: The Ohio State University

data_processing:
The reads were aligned to mouse reference genome version GRCm38.p6
Reads per gene was quantified by STAR 2.7.7 using Ensembl GRCm38.p6 GTF file
After obtaining gene counts, the counts were internally normalized by DESeq2.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample

source_name: epididymal white adipose tissue

extract_protocol:
eWAT and liver RNA was extracted using Qiagen RNeasy Lipid Tissue Mini Kit and RNeasy mini kit, respectively. Illumina TruSeq RNA Sample Prep Kit and 1 ug of total RNA were used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male Ccdc92 KO mice and age-matched littermate WT mice (C57BL/6 background) were fed a high-fat diet (HFD, 20% protein, 60% fat, 20% carbohydrate by calories) for 14 weeks.

value: adipose tissue

value: High fat diet

value: Ccdc92 KO


title: eWAT_KO3


title: FC00029: Red_116

value: Dorsal Root Ganglion


title: epidermis_16h_subject108

source_name: Skin biopsy from upper back, epidermis, subject P108, taken at 16:00h


title: FC00029: Red_117

value: C1-C8 DRG


title: eWAT_KO2


title: FC00029: Red_115

value: 6-12 weeks old


title: FC00029: Red_114


title: FC00029: Red_111


title: eWAT_WT4

value: wild type


title: eWAT_KO1


title: FC00029: Red_113


title: epidermis_16h_subject103

source_name: Skin biopsy from upper back, epidermis, subject P103, taken at 16:00h


title: FC00029: Red_112


title: epidermis_16h_subject102

source_name: Skin biopsy from upper back, epidermis, subject P102, taken at 16:00h


title: FC00029: Red_110


title: eWAT_WT3


title: FC00029: Red_109


title: epidermis_16h_subject100

source_name: Skin biopsy from upper back, epidermis, subject P100, taken at 16:00h


title: eWAT_WT2


title: FC00029: Red_108


title: FC00029: Red_104


title: FC00029: Red_107


title: epidermis_16h_subject107

source_name: Skin biopsy from upper back, epidermis, subject P107, taken at 16:00h


title: FC00029: Red_105


title: FC00029: Red_106


title: FC00029: Red_103


title: eWAT_WT1


title: epidermis_12h_subject115

description: Gene expression at 12:00h in human epidermis

source_name: Skin biopsy from upper back, epidermis, subject P115, taken at 12:00h


title: epidermis_16h_subject106

source_name: Skin biopsy from upper back, epidermis, subject P106, taken at 16:00h


title: Ab7

city: Guangzhou

first: sujun

last: xiao

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

country: China

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters.
Reads Per Kilobase of exon per Megabase of labray size (RPKM) were calculated using a protocol from Chepelev et al, Nucleic Acids Research, 2009. In short, exons from all isoforms.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each Sample.

source_name: liver

extract_protocol:
Mice livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 1 µg RNA of per mice liver was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

tag: strain background

tag: diet and treatment

value: high fat diet and recomninant human IgG3

value: ApoE-/-

value: liver


title: epidermis_12h_subject114

source_name: Skin biopsy from upper back, epidermis, subject P114, taken at 12:00h

value: Skin – epidermis


title: epidermis_12h_subject113

source_name: Skin biopsy from upper back, epidermis, subject P113, taken at 12:00h


title: Ab6

value: high fat diet and recomninant human IgG2


title: FC00029: Red_101

source_name: C1-C8 DRG


title: epidermis_12h_subject111

source_name: Skin biopsy from upper back, epidermis, subject P111, taken at 12:00h

value: female


title: FC00029: Red_100


title: FC00029: Red_98


title: FC00029: Red_99


title: FC00029: Red_97


title: FC00029: Red_96


title: PBS6

value: high fat diet


title: FC00029: Red_102


title: epidermis_12h_subject109

source_name: Skin biopsy from upper back, epidermis, subject P109, taken at 12:00h

value: male


title: FC00029: Red_95


title: PBS4


title: PBS3


title: FC00029: Red_92


title: N6

value: normal diet


title: epidermis_12h_subject107

source_name: Skin biopsy from upper back, epidermis, subject P107, taken at 12:00h


title: FC00029: Red_93


title: FC00029: Red_94


title: FC00029: Red_90


title: FC00029: Red_89


title: FC00029: Red_91


title: N5


title: epidermis_12h_subject106

source_name: Skin biopsy from upper back, epidermis, subject P106, taken at 12:00h


title: epidermis_12h_subject102

source_name: Skin biopsy from upper back, epidermis, subject P102, taken at 12:00h


title: N4


title: epidermis_12h_subject103

source_name: Skin biopsy from upper back, epidermis, subject P103, taken at 12:00h


title: epidermis_12h_subject108

source_name: Skin biopsy from upper back, epidermis, subject P108, taken at 12:00h


title: FC00029: Red_85


title: non-CMs, TTg-MI

data_processing:
Raw sequence reads were processed from 10X Genomics' Cell Ranger v.5.0.0 pipeline and generated fastq files. In brief, the demultiplexed fastq files were aligned to a custom reference genome with the tdTomato sequence added to the mm10/GRCm38 reference transcriptome, and the gene expression matrix was counted using the Cellranger count program. The processed scRNA-seq data were performed to quality control, dimensionality reduction, cell clustering, and differential expression analysis by Seurat suite versions 3.2.2 used in R version 3.6.3. (Stuart et al., 2019). To exclude low-quality cells from the analysis, cells that met any of the following criteria were excluded: less than 800 or more than 5,000 unique genes expressed, or more than 10% of the reads mapping to mitochondria. After filtering, dimensionality reduction and visualization of the normalized data (NormalizeData function, default scale factor is 10,000) was done using the UMAP (Uniform Manifold Approximation and Projection) algorithm with the RunPCA and RunUMAP functions implemented in the Seurat package. The DoubletFinder package was used to detect doublets (McGinnis et al., 2019).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw or filtered gene counts for every gene and each cell

source_name: non-CMs

extract_protocol:
The isolation of non-CMs from the murine heart was performed as previously described with some modifications (Forte et al., 2020a; Skelly et al., 2018). In brief, mice were sacrificed by cervical dislocation, and hearts were immediately cannulated and perfused with cold PBS (50 ml). Remove the heart, separate the atria and valves from the heart, and cut the ventricular myocardium into 1 mm pieces on a bacterial Petri dish on ice. Transfer to a 10 ml tube containing 3 ml of enzyme solution and incubate in a water bath at 37°C for 45 min, trituration every 15 min. Enzyme solution contained 2 mg/ml collagenase type IV (Worthington Biochemical, CLS-4) and 1.2 U/ml Dispase II (Sigma, 255-914-4). After the final trituration, the enzyme/tissue mixture is filtered through a 40 μm cell strainer, FACS buffer and dead cell removal solution (Miltenyi Biotec, 130-109-398) is added, and debris is removed after centrifugation. Further, use RBC lysis buffer (pluriSelect, 60-00050-11) to remove red blood cells, then dye the cell suspension with Live/Dead (Invitrogen, L34975,1:1000), Calcein Violet Working solution (BioLegend, 425203, 0.1μM). Using a BD AriaIIu with a 130 μm nozzle, cells with intact cell membranes and metabolically active cells (Live/Dead-, Calcein+) were sorted (12 psi) while minimizing pressure on the cells.
Libraries from non-CMs suspensions were generated with a Chromium controller from 10X Genomics according to the manufacturer's instructions. Approximately 8,000 whole cells were loaded into each channel and processed using the Chromium Single Cell 3' v3.1 reagent kit (10X Genomics).
single cell RNA-seq

value: TTg-MI

value: non-CMs

value: Hearts were harvested 3 months after MI


title: epidermis_12h_subject100

source_name: Skin biopsy from upper back, epidermis, subject P100, taken at 12:00h


title: FC00029: Red_83


title: FC00029: Red_88


title: FC00029: Red_87


title: Ab5

value: high fat diet and recomninant human IgG1


title: epidermis_8h_subject115

description: Gene expression at 8:00h in human epidermis

source_name: Skin biopsy from upper back, epidermis, subject P115, taken at 8:00h


title: non-CMs, Ctrl-MI

value: Ctrl-MI


title: FC00029: Red_82

value: Dorsal Root Ganglion

value: C1-C8 DRG


title: epidermis_8h_subject114

source_name: Skin biopsy from upper back, epidermis, subject P114, taken at 8:00h


title: non-CMs, Sham

value: Sham


title: FC00029: Red_79

value: 6-12 weeks old


title: FC00029: Red_78


title: FC00029: Red_76


title: FC00029: Red_80


title: epidermis_8h_subject111

source_name: Skin biopsy from upper back, epidermis, subject P111, taken at 8:00h


title: FC00029: Red_81


title: Unc-1; nhr-1 double mutant, biological rep 6

city: Valencia

first: Carlos

last: Mora-Martínez

state: Comunidad Valenciana

address: Emilio Lluch 4Dup 16

country: Spain

institute: Universidad Internacional de Valencia

description:
R6_U_N
genes.readcount.annot.xls
genes.FPKM.annot.xls
U_N_vs_WT.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls

data_processing:
Data filtering: Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses. The filtering process is as follows: (1) Discard reads with adaptor contamination. (2) Discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%). (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50% of the read. RNA-seq Adapter sequences (Oligonucleotide sequences of adapters from TruSeqTM RNA and DNA Sample Prep Kits): RNA 5' Adapter (RA5): 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' RNA 3' Adapter (RA3): 5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC(6-nucleotide index)ATCTCGTATGCCGTCTTCTGCTTG-3'
Mapping: HISAT2 v2.0.5 with default parameters
Quantification: HTSeq v0.6.1 with -m union option.
Differential expression analysis: DESeq2 v1.24.0
Assembly: WBCel235
Supplementary files format and content: .bam file for each sample (24 total)
Supplementary files format and content: .xls file with raw counts for each sample (1 column per sample)
Supplementary files format and content: .xls file with FPKM counts for each sample (1 column per sample)
Supplementary files format and content: .xls file from differential expression analysis for each pair of experimental groups (10 files total)

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Synchronized L1 animals were cultured in NGM plates at 20 °C until they reached the young adult stage.

extract_protocol:
Yound adults were collected in M9 buffer, frozen, thawed and mechanically lysed with 200 mg of glass beads (Sigma-Aldrich-Merck) for 30 sec using a Fastprep shaker apparatus (Thermofisher Scientific, FP120 model) . tRNA was extracted using NZY total RNA isolation kit, Nzytech. Supernatant was recovered from lysate samples by centrifuging extracts at maximum speed for 1 min. The purified RNA was treated with DNAse, quantified and sent for sequencing by Novogene (Cambridge, UK).
Library preparation was performed at Novogene facilities (Cambridge, UK). mRNA was enriched using oligo(dT) beads and then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick- translation. To build the final cDNA library, a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment were performed. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies). Insert size was checked on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).

treatment_protocol: We sequenced 4 different genotypes, with 6 biological replicates per genotype.

value: whole organism

value: 20 ºC, young adult


title: FC00029: Red_84


title: FC00029: Red_75


title: Unc-1 mutant, biological rep 6

description:
R6_unc_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
unc_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls


title: FC00029: Red_74


title: Nhr-1 mutant, biological rep 6

description:
R6_nhr_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: FC00029: Red_86


title: FC00029: Red_77


title: FC00029: Red_73


title: FC00029: Red_72


title: FC00029: Red_71


title: Unc-1; nhr-1 double mutant, biological rep 5

description:
R5_U_N
genes.readcount.annot.xls
genes.FPKM.annot.xls
U_N_vs_WT.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: FC00029: Red_70


title: epidermis_8h_subject109

source_name: Skin biopsy from upper back, epidermis, subject P109, taken at 8:00h

value: Skin – epidermis


title: epidermis_8h_subject107

source_name: Skin biopsy from upper back, epidermis, subject P107, taken at 8:00h


title: FC00029: Red_69


title: Unc-1 mutant, biological rep 5

description:
R5_unc_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
unc_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls


title: epidermis_8h_subject108

source_name: Skin biopsy from upper back, epidermis, subject P108, taken at 8:00h


title: epidermis_8h_subject113

source_name: Skin biopsy from upper back, epidermis, subject P113, taken at 8:00h


title: Nhr-1 mutant, biological rep 5

description:
R5_nhr_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: epidermis_8h_subject106

source_name: Skin biopsy from upper back, epidermis, subject P106, taken at 8:00h


title: FC00029: Red_68

source_name: C1-C8 DRG


title: epidermis_8h_subject103

source_name: Skin biopsy from upper back, epidermis, subject P103, taken at 8:00h


title: epidermis_8h_subject102

source_name: Skin biopsy from upper back, epidermis, subject P102, taken at 8:00h


title: FC00029: Red_67


title: Unc-1; nhr-1 double mutant, biological rep 4

description:
R4_U_N
genes.readcount.annot.xls
genes.FPKM.annot.xls
U_N_vs_WT.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: FC00029: Red_66


title: FC00029: Red_64


title: FC00029: Red_65


title: Nhr-1 mutant, biological rep 4

description:
R4_nhr_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: FC00029: Red_61


title: FC00029: Red_60


title: dermis_32h_subject114

description: Gene expression at 8:00h the day after in human dermis

source_name: Skin biopsy from upper back, dermis, subject P114, taken at 8:00h day after

value: Skin – dermis

value: 8:00h day after


title: dermis_32h_subject115

source_name: Skin biopsy from upper back, dermis, subject P115, taken at 8:00h day after

value: female


title: dermis_32h_subject113

source_name: Skin biopsy from upper back, dermis, subject P113, taken at 8:00h day after

value: male


title: FC00029: Red_59


title: FC00029: Red_57


title: FC00029: Red_56


title: FC00029: Red_55


title: Nhr-1 mutant, biological rep 3

description:
R3_nhr_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: dermis_32h_subject111

source_name: Skin biopsy from upper back, dermis, subject P111, taken at 8:00h day after


title: Unc-1; nhr-1 double mutant, biological rep 2

description:
R2_U_N
genes.readcount.annot.xls
genes.FPKM.annot.xls
U_N_vs_WT.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: FC00029: Red_54


title: FC00029: Red_53


title: dermis_32h_subject109

source_name: Skin biopsy from upper back, dermis, subject P109, taken at 8:00h day after


title: FC00029: Red_62


title: Unc-1 mutant, biological rep 2

description:
R2_unc_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
unc_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls


title: Unc-1 mutant, biological rep 4

description:
R4_unc_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
unc_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls


title: FC00029: Red_63

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1


title: epidermis_8h_subject100

source_name: Skin biopsy from upper back, epidermis, subject P100, taken at 8:00h


title: FC00029: Red_52


title: Unc-1; nhr-1 double mutant, biological rep 3

description:
R3_U_N
genes.readcount.annot.xls
genes.FPKM.annot.xls
U_N_vs_WT.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: FC00029: Red_51


title: FC00029: Red_50


title: Nhr-1 mutant, biological rep 2

description:
R2_nhr_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: dermis_32h_subject107

source_name: Skin biopsy from upper back, dermis, subject P107, taken at 8:00h day after


title: dermis_32h_subject108

source_name: Skin biopsy from upper back, dermis, subject P108, taken at 8:00h day after


title: Unc-1 mutant, biological rep 3

description:
R3_unc_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
unc_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls

source_name: whole organism


title: FC00029: Red_58


title: FC00029: Red_49


title: FC00029: Red_48


title: FC00029: Red_47


title: Unc-1 mutant, biological rep 1

description:
R1_unc_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
unc_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls


title: Unc-1; nhr-1 double mutant, biological rep 1

description:
R1_U_N
genes.readcount.annot.xls
genes.FPKM.annot.xls
U_N_vs_WT.genes.DEA.xls
U_N_vs_unc_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: FC00029: Red_46


title: Nhr-1 mutant, biological rep 1

description:
R1_nhr_1
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_nhr_1.genes.DEA.xls
U_N_vs_nhr_1.genes.DEA.xls


title: dermis_32h_subject106

source_name: Skin biopsy from upper back, dermis, subject P106, taken at 8:00h day after


title: FC00029: Red_43


title: FC00029: Red_45


title: FC00029: Red_44


title: dermis_32h_subject102

source_name: Skin biopsy from upper back, dermis, subject P102, taken at 8:00h day after


title: FC00029: Red_41


title: FC00029: Red_42


title: dermis_28h_subject115

description: Gene expression at 4:00h the day after in human dermis

source_name: Skin biopsy from upper back, dermis, subject P115, taken at 4:00h day after

value: 4:00h day after


title: FC00029: Red_40


title: dermis_32h_subject100

source_name: Skin biopsy from upper back, dermis, subject P100, taken at 8:00h day after


title: wildtype, biological rep 4

description:
A4_WT
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_WT.genes.DEA.xls
U_N_vs_WT.genes.DEA.xls


title: wildtype, biological rep 5

description:
A5_WT
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_WT.genes.DEA.xls
U_N_vs_WT.genes.DEA.xls


title: FC00029: Red_39


title: FC00029: Red_37


title: dermis_28h_subject114

source_name: Skin biopsy from upper back, dermis, subject P114, taken at 4:00h day after


title: dermis_32h_subject103

source_name: Skin biopsy from upper back, dermis, subject P103, taken at 8:00h day after


title: wildtype, biological rep 3

description:
A3_WT
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_WT.genes.DEA.xls
U_N_vs_WT.genes.DEA.xls


title: wildtype, biological rep 2

description:
A2_WT
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_WT.genes.DEA.xls
U_N_vs_WT.genes.DEA.xls


title: FC00029: Red_36

source_name: C1-C8 DRG


title: FC00029: Red_33


title: FC00029: Red_34


title: dermis_28h_subject109

source_name: Skin biopsy from upper back, dermis, subject P109, taken at 4:00h day after


title: wildtype, biological rep 1

description:
A1_WT
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_WT.genes.DEA.xls
U_N_vs_WT.genes.DEA.xls


title: dermis_28h_subject111

source_name: Skin biopsy from upper back, dermis, subject P111, taken at 4:00h day after


title: dermis_28h_subject113

source_name: Skin biopsy from upper back, dermis, subject P113, taken at 4:00h day after


title: FC00029: Red_32


title: FC00029: Red_31


title: wildtype, biological rep 6

description:
A6_WT
genes.readcount.annot.xls
genes.FPKM.annot.xls
nhr_1_vs_WT.genes.DEA.xls
unc_1_vs_WT.genes.DEA.xls
U_N_vs_WT.genes.DEA.xls


title: FC00029: Red_30


title: FC00029: Red_29


title: FC00029: Red_28


title: FC00029: Red_38


title: mESC CLAM-Cap-seq 1

city: New York

first: Vladimir

last: Despic

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

description: mESC-TSN-list.xlsx

data_processing:
Removal of low quality reads and 3'-end adapter trimming was performed with flexbar v2.5.
Removal of duplicated reads was accomplished with pyFastqDuplicateRemover.py within the pyCRAC package v1.3.2.
Read trimming was performed using seqtk package v1.3.
Read alignement to fly, mouse or human genome was conducted using Bowtie v1.2.3.
5'-end read coverage was calculated per each genomic position using BEDTools v2.28.0.
Genome_build: Drosohila melanogaster; dm6, Mus musculus; mm10, Homo sapiens; hg38.

source_name: cell culture

growth_protocol: mES cells were maintained in Knockout DMEM supplemented with 15% heat-inactivated FBS, 100 U Penicillin-Streptomycin, 55 µM beta-mercaptoethanol, 1x MEM non-essential amino acid solution, 1,000 U ml-1LIF, 3 µM CHIR99021, and 1 µM PD0325901 at 37°C and 5% CO2.

extract_protocol:
CLAM-Cap-seq
Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  Poly(A)+ RNA was isolated from total RNA using magnetic oligo(dT)25 beads (NEB).

tag: cell line/tissue

value: mESC

value: wild type

tag: purification

value: oligo(dT)25 beads


title: dermis_28h_subject108

source_name: Skin biopsy from upper back, dermis, subject P108, taken at 4:00h day after


title: mESC CLAM-Cap-seq 2

description: mESC-TSN-list.xlsx


title: dermis_28h_subject107

source_name: Skin biopsy from upper back, dermis, subject P107, taken at 4:00h day after


title: FC00029: Red_26


title: FC00029: Red_27


title: FC00029: Red_35


title: Spleen CapQuant-seq 2

source_name: mouse organ

growth_protocol: CL57B/L wild type female mice were purchased from Charles River Laboratory, housed and maintained in standard cages with unrestricted supplies of water and food.

extract_protocol:
CapTag-seq
Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  Poly(A)+ RNA was isolated from total RNA using magnetic oligo(dT)25 beads (NEB).

value: spleen

value: C57BL/6 wild type


title: dermis_28h_subject106

source_name: Skin biopsy from upper back, dermis, subject P106, taken at 4:00h day after


title: dermis_28h_subject103

source_name: Skin biopsy from upper back, dermis, subject P103, taken at 4:00h day after


title: FC00029: Red_24

value: Dorsal Root Ganglion


title: FC00029: Red_22

value: C1-C8 DRG


title: FC00029: Red_25


title: dermis_28h_subject102

source_name: Skin biopsy from upper back, dermis, subject P102, taken at 4:00h day after


title: FC00029: Red_21


title: FC00029: Red_20


title: dermis_28h_subject100

source_name: Skin biopsy from upper back, dermis, subject P100, taken at 4:00h day after


title: FC00029: Red_18


title: FC00029: Red_17


title: FC00029: Red_16


title: dermis_24h_subject115

description: Gene expression at 00:00h the day after in human dermis

source_name: Skin biopsy from upper back, dermis, subject P115, taken at 00:00h day after

value: 00:00h day after


title: FC00029: Red_13

value: 6-12 weeks old


title: FC00029: Red_12


title: FC00029: Red_23


title: FC00029: Red_11


title: dermis_24h_subject114

source_name: Skin biopsy from upper back, dermis, subject P114, taken at 00:00h day after


title: FC00029: Red_10


title: FC00029: Red_19


title: dermis_24h_subject111

source_name: Skin biopsy from upper back, dermis, subject P111, taken at 00:00h day after


title: FC00029: Red_9


title: dermis_24h_subject113

source_name: Skin biopsy from upper back, dermis, subject P113, taken at 00:00h day after


title: dermis_24h_subject109

source_name: Skin biopsy from upper back, dermis, subject P109, taken at 00:00h day after


title: FC00029: Red_8

source_name: C1-C8 DRG


title: Early-onset B-cell lymphoma case X3

type: genomic

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 24 hours at 67°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 in an ozone-depleted hood.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

source_name: Early-onset precursor B-cell lymphoma by the irradiation of X-rays at 1 week of age

label_protocol: Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Mice were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 3°C) and humidity (50 ± 10%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet and sterilized water ad libitum.

extract_protocol: Genomic DNA of B-cell lymphomas and normal normal ears were extarcted by AllPrep DNA/RNA/Protein Mini Kit and DNeasy Blood & Tissue Kit (Qiagen), respectively.

treatment_protocol: Mice were left untreated or were subjected to whole-body irradiated with gamma-rays (4 Gy) or X-rays (3.8 Gy) at 1 or 7 weeks of age.

tag: gender

value: Male

value: irradiation of X-rays at 1 week of age

tag: disease state

value: Early-onset precursor B-cell lymphoma

value: B-cell lymphoma

source_name: Normal ear

value: Ear skin


title: Early-onset B-cell lymphoma case X4


title: Early-onset B-cell lymphoma case 19

source_name: Early-onset precursor B-cell lymphoma by the irradiation of gamma-rays at 1 week of age

value: Female


title: Early-onset B-cell lymphoma case X1


title: dermis_24h_subject108

source_name: Skin biopsy from upper back, dermis, subject P108, taken at 00:00h day after

value: Skin – dermis

value: male


title: FC00029: Red_15


title: FC00029: Red_7


title: Early-onset B-cell lymphoma case 12

value: irradiation of gamma-rays at 1 week of age


title: Monkey_Uvea_Male_1003

city: North Chicago

first: Terry

last: Van Vleet

state: IL

address: 1 N Waukegan Rd

institute: AbbVie

description:
Monkey_Uvea_Male_1003
Cyno_FPKM_table_Mar22.xlsx

data_processing:
ArrayStudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using ArrayStudio
Trimmed sequence reads were mapped to Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Read count extraction and normalization were performed using ArrayStudio
Assembly: Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Macaca fascicularis

source_name: Uvea

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 200-300ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit Gold following manufacturer's protocols.

treatment_protocol:
NA
NA

value: Uvea

value: untreated


title: FC00029: Red_6


title: FC00029: Red_14


title: FC00029: Red_5


title: Monkey_Uvea_Male_1002

description:
Monkey_Uvea_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: dermis_24h_subject106

source_name: Skin biopsy from upper back, dermis, subject P106, taken at 00:00h day after


title: Early-onset B-cell lymphoma case 7

source_name: Early-onset precursor B-cell lymphoma by the irradiation of gamma-rays at 7 weeks of age


title: FC00029: Red_4

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1


title: Early-onset B-cell lymphoma case 11


title: dermis_24h_subject103

source_name: Skin biopsy from upper back, dermis, subject P103, taken at 00:00h day after

value: female


title: Early-onset B-cell lymphoma case 5


title: Early-onset B-cell lymphoma case 14

value: irradiation of gamma-rays at 7 weeks of age


title: dermis_24h_subject107

source_name: Skin biopsy from upper back, dermis, subject P107, taken at 00:00h day after


title: FC00029: Red_2

value: Dorsal Root Ganglion


title: FC00029: Red_1

value: C1-C8 DRG


title: FC00029: Red_3


title: FC00029: Blue_128


title: FC00029: Blue_127


title: Monkey_UrinaryBladder_Male_1002

description:
Monkey_UrinaryBladder_Male_1002
Cyno_FPKM_table_Mar22.xlsx

source_name: Urinary Bladder

value: Urinary Bladder


title: dermis_24h_subject102

source_name: Skin biopsy from upper back, dermis, subject P102, taken at 00:00h day after

value: 00:00h day after


title: FC00029: Blue_125

value: 6-12 weeks old


title: Monkey_UrinaryBladder_Male_1001

description:
Monkey_UrinaryBladder_Male_1001
Cyno_FPKM_table_Mar22.xlsx

value: Male


title: Monkey_Trachea_Male_1003

description:
Monkey_Trachea_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Trachea

value: Trachea


title: FC00029: Blue_122


title: FC00029: Blue_124


title: Monkey_Trachea_Male_1002

description:
Monkey_Trachea_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_123


title: FC00029: Blue_121


title: dermis_20h_subject114

description: Gene expression at 20:00h in human dermis

source_name: Skin biopsy from upper back, dermis, subject P114, taken at 20:00h


title: Monkey_Uvea_Male_1001

description:
Monkey_Uvea_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_120


title: dermis_20h_subject115

source_name: Skin biopsy from upper back, dermis, subject P115, taken at 20:00h


title: FC00029: Blue_119


title: dermis_24h_subject100

source_name: Skin biopsy from upper back, dermis, subject P100, taken at 00:00h day after


title: dermis_20h_subject113

source_name: Skin biopsy from upper back, dermis, subject P113, taken at 20:00h


title: FC00029: Blue_126

source_name: C1-C8 DRG


title: Monkey_Trachea_Male_1001

description:
Monkey_Trachea_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_118


title: Monkey_UrinaryBladder_Male_1003

description:
Monkey_UrinaryBladder_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_116


title: dermis_20h_subject108

source_name: Skin biopsy from upper back, dermis, subject P108, taken at 20:00h


title: Monkey_Tongue_Male_1003

description:
Monkey_Tongue_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Tongue

value: Tongue


title: FC00029: Blue_117


title: dermis_20h_subject109

source_name: Skin biopsy from upper back, dermis, subject P109, taken at 20:00h


title: Monkey_Tongue_Male_1002

description:
Monkey_Tongue_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_115


title: FC00029: Blue_113


title: dermis_20h_subject111

source_name: Skin biopsy from upper back, dermis, subject P111, taken at 20:00h


title: FC00029: Blue_110


title: FC00029: Blue_112


title: dermis_20h_subject107

source_name: Skin biopsy from upper back, dermis, subject P107, taken at 20:00h


title: FC00029: Blue_108


title: dermis_20h_subject106

source_name: Skin biopsy from upper back, dermis, subject P106, taken at 20:00h


title: FC00029: Blue_111


title: FC00029: Blue_109


title: Monkey_Tongue_Male_1001

description:
Monkey_Tongue_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_107


title: FC00029: Blue_106


title: Monkey_ThyroidParathyroid_Male_1002

description:
Monkey_ThyroidParathyroid_Male_1002
Cyno_FPKM_table_Mar22.xlsx

source_name: Thyroid Gland

value: Thyroid Gland


title: Monkey_ThyroidParathyroid_Male_1001

description:
Monkey_ThyroidParathyroid_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_ThyroidParathyroid_Male_1003

description:
Monkey_ThyroidParathyroid_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: dermis_20h_subject103

source_name: Skin biopsy from upper back, dermis, subject P103, taken at 20:00h


title: FC00029: Blue_114


title: FC00029: Blue_105


title: Monkey_Thalamus_Male_1003

description:
Monkey_Thalamus_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Thalamus

value: Thalamus


title: FC00029: Blue_104


title: FC00029: Blue_103


title: dermis_20h_subject102

source_name: Skin biopsy from upper back, dermis, subject P102, taken at 20:00h

value: Skin – dermis


title: FC00029: Blue_102


title: Monkey_Thalamus_Male_1002

description:
Monkey_Thalamus_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_Thalamus_Male_1001

description:
Monkey_Thalamus_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_101

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1


title: dermis_20h_subject100

source_name: Skin biopsy from upper back, dermis, subject P100, taken at 20:00h

value: male


title: FC00029: Blue_100


title: dermis_16h_subject115

description: Gene expression at 16:00h in human dermis

source_name: Skin biopsy from upper back, dermis, subject P115, taken at 16:00h


title: dermis_16h_subject114

source_name: Skin biopsy from upper back, dermis, subject P114, taken at 16:00h


title: FC00029: Blue_99


title: Monkey_Testes_Male_1003

description:
Monkey_Testes_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Testis

value: Testis


title: Monkey_Testes_Male_1002

description:
Monkey_Testes_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_98


title: dermis_16h_subject113

source_name: Skin biopsy from upper back, dermis, subject P113, taken at 16:00h


title: FC00029: Blue_97


title: FC00029: Blue_95


title: Monkey_Testes_Male_1001

description:
Monkey_Testes_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Rat_Pancreas_Male

description:
Rat_Pancreas_Male
Rat_FPKM_table_Mar22.xlsx

organism: Rattus norvegicus

source_name: Pancreas

value: Sprague Dawley

value: Pancreas


title: Rat_Pancreas_Female

description:
Rat_Pancreas_Female
Rat_FPKM_table_Mar22.xlsx

value: Female

value: untreated


title: dermis_16h_subject111

source_name: Skin biopsy from upper back, dermis, subject P111, taken at 16:00h

value: female


title: dermis_16h_subject109

source_name: Skin biopsy from upper back, dermis, subject P109, taken at 16:00h


title: dermis_16h_subject108

source_name: Skin biopsy from upper back, dermis, subject P108, taken at 16:00h


title: Rat_Cartilage_Female

description:
Rat_Cartilage_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Ear Cartilage

value: Ear Cartilage


title: FC00029: Blue_94

source_name: C1-C8 DRG

value: Dorsal Root Ganglion

value: C1-C8 DRG


description:
Monkey_SubmandibularSalivaryGland_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Submandibular Gland

value: Submandibular Gland


description:
Monkey_SubmandibularSalivaryGland_Male_1002
Cyno_FPKM_table_Mar22.xlsx

value: Male


title: dermis_16h_subject107

source_name: Skin biopsy from upper back, dermis, subject P107, taken at 16:00h


title: FC00029: Blue_93

value: 6-12 weeks old


title: FC00029: Blue_92


description:
Monkey_SubmandibularSalivaryGland_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Rat_Cartilage_Male

description:
Rat_Cartilage_Male
Rat_FPKM_table_Mar22.xlsx


title: Rat_Skin_Female

description:
Rat_Skin_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Skin

value: Skin


title: dermis_16h_subject106

source_name: Skin biopsy from upper back, dermis, subject P106, taken at 16:00h


title: Monkey_SubcorticalWhiteMatter_Male_1003

description:
Monkey_SubcorticalWhiteMatter_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: White Matter

value: White Matter


title: FC00029: Blue_96


title: dermis_16h_subject103

source_name: Skin biopsy from upper back, dermis, subject P103, taken at 16:00h


title: FC00029: Blue_90


title: dermis_16h_subject102

source_name: Skin biopsy from upper back, dermis, subject P102, taken at 16:00h


title: Monkey_SubcorticalWhiteMatter_Male_1002

description:
Monkey_SubcorticalWhiteMatter_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Rat_Skin_Male

description:
Rat_Skin_Male
Rat_FPKM_table_Mar22.xlsx


title: Monkey_SubcorticalWhiteMatter_Male_1001

description:
Monkey_SubcorticalWhiteMatter_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_91


title: Rat_Esophagus_Female

description:
Rat_Esophagus_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Esophagus

value: Esophagus


title: Rat_WholeBlood_Female

description:
Rat_WholeBlood_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Blood

value: Blood


title: Monkey_StomachPyloric_Male_1002

description:
Monkey_StomachPyloric_Male_1002
Cyno_FPKM_table_Mar22.xlsx

source_name: Stomach

value: Stomach


title: dermis_16h_subject100

description: Gene expression at 16:00h in human dermis

source_name: Skin biopsy from upper back, dermis, subject P100, taken at 16:00h

value: Skin – dermis

value: male


title: Monkey_StomachPyloric_Male_1003

description:
Monkey_StomachPyloric_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_88

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1


title: FC00029: Blue_89


title: Rat_WholeBlood_Male

description:
Rat_WholeBlood_Male
Rat_FPKM_table_Mar22.xlsx

value: Sprague Dawley


title: Rat_Esophagus_Male

description:
Rat_Esophagus_Male
Rat_FPKM_table_Mar22.xlsx


title: dermis_12h_subject114

description: Gene expression at 12:00h in human dermis

source_name: Skin biopsy from upper back, dermis, subject P114, taken at 12:00h


title: Monkey_StomachPyloric_Male_1001

description:
Monkey_StomachPyloric_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_86


title: Rat_Ovary

description:
Rat_Ovary
Rat_FPKM_table_Mar22.xlsx

source_name: Ovary

value: Ovary

value: Female


title: Monkey_StomachBody_Male_1003

description:
Monkey_StomachBody_Male_1003
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: dermis_12h_subject113

source_name: Skin biopsy from upper back, dermis, subject P113, taken at 12:00h


title: dermis_12h_subject111

source_name: Skin biopsy from upper back, dermis, subject P111, taken at 12:00h

value: female


title: FC00029: Blue_87

value: Dorsal Root Ganglion


title: Rat_Prostate

description:
Rat_Prostate
Rat_FPKM_table_Mar22.xlsx

source_name: Prostate

value: Prostate


title: Monkey_StomachBody_Male_1002

description:
Monkey_StomachBody_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Rat_VenaCava_Female

description:
Rat_VenaCava_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Venae Cavae

value: Venae Cavae


title: FC00029: Blue_83

source_name: C1-C8 DRG

value: C1-C8 DRG


title: Monkey_StomachBody_Male_1001

description:
Monkey_StomachBody_Male_1001
Cyno_FPKM_table_Mar22.xlsx

value: Male


title: Rat_VenaCava_Male

description:
Rat_VenaCava_Male
Rat_FPKM_table_Mar22.xlsx


title: dermis_12h_subject115

source_name: Skin biopsy from upper back, dermis, subject P115, taken at 12:00h


title: dermis_12h_subject109

source_name: Skin biopsy from upper back, dermis, subject P109, taken at 12:00h


title: FC00029: Blue_84

value: 6-12 weeks old


title: Monkey_Spleen_Male_1003

description:
Monkey_Spleen_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Spleen

value: Spleen


title: Rat_SubcutaneousAdipose_Female

description:
Rat_SubcutaneousAdipose_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: FC00029: Blue_82


title: Monkey_Spleen_Male_1002

description:
Monkey_Spleen_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: dermis_12h_subject107

source_name: Skin biopsy from upper back, dermis, subject P107, taken at 12:00h


title: Rat_SubcutaneousAdipose_Male

description:
Rat_SubcutaneousAdipose_Male
Rat_FPKM_table_Mar22.xlsx


title: FC00029: Blue_81


title: Monkey_Spleen_Male_1001

description:
Monkey_Spleen_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: dermis_12h_subject106

source_name: Skin biopsy from upper back, dermis, subject P106, taken at 12:00h


title: FC00029: Blue_80


title: FC00029: Blue_85


title: Rat_PituitaryGland_Female

description:
Rat_PituitaryGland_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Pituitary Gland

value: Pituitary Gland


title: Monkey_Soleus_Male_1003

description:
Monkey_Soleus_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Muscle, Skeletal

value: Muscle, Skeletal


title: FC00029: Blue_79

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1


title: Rat_PituitaryGland_Male

description:
Rat_PituitaryGland_Male
Rat_FPKM_table_Mar22.xlsx


title: Monkey_Soleus_Male_1002

description:
Monkey_Soleus_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: dermis_12h_subject103

description: Gene expression at 12:00h in human dermis

source_name: Skin biopsy from upper back, dermis, subject P103, taken at 12:00h

value: Skin – dermis


title: dermis_12h_subject102

source_name: Skin biopsy from upper back, dermis, subject P102, taken at 12:00h

value: male


title: FC00029: Blue_78


title: dermis_12h_subject100

source_name: Skin biopsy from upper back, dermis, subject P100, taken at 12:00h


title: dermis_12h_subject108

source_name: Skin biopsy from upper back, dermis, subject P108, taken at 12:00h


title: dermis_8h_subject115

description: Gene expression at 8:00h in human dermis

source_name: Skin biopsy from upper back, dermis, subject P115, taken at 8:00h


title: Rat_HarderianGland_Female

description:
Rat_HarderianGland_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Harderian Gland

value: Sprague Dawley

value: Harderian Gland


title: Monkey_Soleus_Male_1001

description:
Monkey_Soleus_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_77


title: Rat_HarderianGland_Male

description:
Rat_HarderianGland_Male
Rat_FPKM_table_Mar22.xlsx


title: Monkey_Skin_Male_1003

description:
Monkey_Skin_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Skin

value: Skin


title: dermis_8h_subject113

source_name: Skin biopsy from upper back, dermis, subject P113, taken at 8:00h


title: Rat_Tongue_Female

description:
Rat_Tongue_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Tongue

value: Tongue

value: Female

value: untreated


title: Monkey_Skin_Male_1002

description:
Monkey_Skin_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: dermis_8h_subject114

source_name: Skin biopsy from upper back, dermis, subject P114, taken at 8:00h

value: female


title: Rat_Tongue_Male

description:
Rat_Tongue_Male
Rat_FPKM_table_Mar22.xlsx


title: FC00029: Blue_75

source_name: C1-C8 DRG

value: Dorsal Root Ganglion


title: Monkey_Skin_Male_1001

description:
Monkey_Skin_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_74

value: C1-C8 DRG


title: FC00029: Blue_73


title: dermis_8h_subject109

source_name: Skin biopsy from upper back, dermis, subject P109, taken at 8:00h


title: Monkey_SciaticNerve_Male_1003

description:
Monkey_SciaticNerve_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Sciatic Nerve

value: Sciatic Nerve

value: Male


title: dermis_8h_subject111

source_name: Skin biopsy from upper back, dermis, subject P111, taken at 8:00h


title: Rat_Retina_Male

description:
Rat_Retina_Male
Rat_FPKM_table_Mar22.xlsx

source_name: Retina

value: Retina


title: Monkey_SciaticNerve_Male_1002

description:
Monkey_SciaticNerve_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_72

value: 6-12 weeks old


title: dermis_8h_subject108

source_name: Skin biopsy from upper back, dermis, subject P108, taken at 8:00h


title: Rat_Vagina

description:
Rat_Vagina
Rat_FPKM_table_Mar22.xlsx

source_name: Vagina

value: Vagina


title: FC00029: Blue_76


title: Monkey_Retina_Male_1003

description:
Monkey_Retina_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_71

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1


title: Rat_Epidydymes

description:
Rat_Epidydymes
Rat_FPKM_table_Mar22.xlsx

source_name: Epididymis

value: Epididymis


title: dermis_8h_subject106

source_name: Skin biopsy from upper back, dermis, subject P106, taken at 8:00h

value: Skin – dermis


title: Rat_Uterus

description:
Rat_Uterus
Rat_FPKM_table_Mar22.xlsx

source_name: Uterus

value: Uterus


title: Monkey_Retina_Male_1002

description:
Monkey_Retina_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_69


title: dermis_8h_subject107

source_name: Skin biopsy from upper back, dermis, subject P107, taken at 8:00h


title: Rat_Testes

description:
Rat_Testes
Rat_FPKM_table_Mar22.xlsx

source_name: Testis

value: Sprague Dawley

value: Testis


title: Rat_Retina_Female

description:
Rat_Retina_Female
Rat_FPKM_table_Mar22.xlsx


title: Monkey_Retina_Male_1001

description:
Monkey_Retina_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Rat_SkeletalMuscle_Female

description:
Rat_SkeletalMuscle_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Muscle, Skeletal

value: Muscle, Skeletal


title: dermis_8h_subject103

description: Gene expression at 8:00h in human dermis

source_name: Skin biopsy from upper back, dermis, subject P103, taken at 8:00h


title: Tcell_d10_post_expansion_GFP-negative_antigen

city: Stanford

first: Howard

middle: Y

last: Chang

state: California

address: 269 Campus Drive, CCSR 2130

department: Center for Personal Dynamic Regulomes

institute: Stanford University

description: pMHC antigen library (10x genomics 5' kit)

data_processing:
The scRNA-seq reads were aligned to GRCh38 genome and quantified using cellranger count (10x genomics). The CITE-seq reads were processed using cellranger count with antibody oligo barcode as feature reference. The TCR-seq reads were mapped to VDJ compatible reference (refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0) using cellranger vdj. pMHC antigen reads were processed either by custom scripts (for cell mixing experiment) or by cellranger count using peptide sequence as feature reference (for primary T cells)
The later analyses for single cell RNA-seq and CITE-seq were performed using SCANPY. TCR relevant analyses were performed using Scirpy
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz. TCR output files: filtered_contig_annotations.csv, clonotypes.csv

source_name: Peripheral blood

extract_protocol:
Primary T cells isolated directly from patient blood samples or peptide stimulated donor PBMC were stained with a mixture of pMHC displayed ENTER viruses. After 2 hr, cells were also stained with barcoded antibodies CD45RA, CD45RO, and IL7R (Biolegend totalseq-C, cat# 304163, cat# 304259, cat# 351356), live dead dye, CD3-APC and CD8-BV711 for 20 min on ice. Sample from each donor is also stained with unique hash-tag barcoded antibody (Biolegend totalseq-C, cat# 394661, cat# 394663). After two washes, CD8+ CD3+ GFP+ cells were sorted to load on two GEM wells of 10x genomics platform and CD8+ CD3+ GFP- cells were loaded on one GEM well, all using 5’ RNA and VDJ kits according to manufacturer’s protocol
Library was prepared using Chromium Single Cell 5ʹ RNA and VDJ kit (10x Genomics).

value: Peripheral blood

value: CD8+ T cells

value: CMV seropositive

value: PBMC ex vivo peptide induced expansion for 10 days, then incubate with pMHC displayed VLP for 2h

tag: library type

value: pMHC antigen

tag: antibodies/tags


title: dermis_8h_subject102

source_name: Skin biopsy from upper back, dermis, subject P102, taken at 8:00h

tag: tissue

value: male


title: FC00029: Blue_68

tag: cell type

value: Dorsal Root Ganglion

value: C1-C8 DRG

tag: strain


title: FC00029: Blue_67

tag: age


title: dermis_8h_subject100

source_name: Skin biopsy from upper back, dermis, subject P100, taken at 8:00h

tag: Sex


title: Monkey_Quadriceps_Male_1002

description:
Monkey_Quadriceps_Male_1002
Cyno_FPKM_table_Mar22.xlsx

source_name: Quadriceps Muscle

value: Quadriceps Muscle

value: Male

value: untreated


title: FC00029: Blue_66

source_name: C1-C8 DRG

value: 6-12 weeks old


title: Rat_SkeletalMuscel_Male

description:
Rat_SkeletalMuscel_Male
Rat_FPKM_table_Mar22.xlsx


title: Monkey_SciaticNerve_Male_1001

description:
Monkey_SciaticNerve_Male_1001
Cyno_FPKM_table_Mar22.xlsx

source_name: Sciatic Nerve

value: Sciatic Nerve


title: Tcell_d10_post_expansion_GFP-positive_GEM-well1_antigen


title: Monkey_Quadriceps_Male_1001

description:
Monkey_Quadriceps_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_65


title: Rat_Lung_Male

description:
Rat_Lung_Male
Rat_FPKM_table_Mar22.xlsx

source_name: Lung

value: Lung


title: Cellmix_antigen

source_name: Jurkat T cell line

value: Jurkat T cell line

value: incubate with pMHC displayed VLP for 2h


title: FC00029: Blue_64


title: Rat_Lung_Female

description:
Rat_Lung_Female
Rat_FPKM_table_Mar22.xlsx

value: Sprague Dawley

value: Female


title: Rat_TransverseColon_Female

description:
Rat_TransverseColon_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Colon, Transverse

value: Colon, Transverse


title: Cellmix_TCR

description: TCR library (10x genomics 5' kit)

value: TCR


title: Tcell_d10_post_expansion_GFP-positive_GEM-well2_antigen

value: Peripheral blood

value: CD8+ T cells

value: CMV seropositive

value: PBMC ex vivo peptide induced expansion for 10 days, then incubate with pMHC displayed VLP for 2h


title: FC00029: Blue_70

value: Dorsal Root Ganglion

value: C1-C8 DRG


title: FC00029: Blue_63


title: Mouse_Male_SciaticNerve

description:
Mouse_Male_SciaticNerve
Mouse_FPKM_table_Mar22.xlsx

value: Male


title: Monkey_Prostate_Male_1003

description:
Monkey_Prostate_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Prostate

value: Prostate

value: untreated


title: Rat_TransverseColon_Male

description:
Rat_TransverseColon_Male
Rat_FPKM_table_Mar22.xlsx


title: FC00029: Blue_62

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

value: 6-12 weeks old


title: Monkey_Prostate_Male_1001

description:
Monkey_Prostate_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_Quadriceps_Male_1003

description:
Monkey_Quadriceps_Male_1003
Cyno_FPKM_table_Mar22.xlsx

value: Quadriceps Muscle


title: Mouse_Male_WholeBlood

description:
Mouse_Male_WholeBlood
Mouse_FPKM_table_Mar22.xlsx

source_name: Serum

value: Serum


title: Monkey_Pituitary_Male_1003

description:
Monkey_Pituitary_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Pituitary Gland

value: Pituitary Gland


title: Mouse_Male_Tongue

description:
Mouse_Male_Tongue
Mouse_FPKM_table_Mar22.xlsx

source_name: Tongue

value: Tongue


title: Rat_WhiteAdipose_Male

description:
Rat_WhiteAdipose_Male
Rat_FPKM_table_Mar22.xlsx

source_name: Adipose Tissue, White

value: Sprague Dawley

value: Adipose Tissue, White


title: Monkey_Pituitary_Male_1001

description:
Monkey_Pituitary_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Rat_BrownAdipose_Female

description:
Rat_BrownAdipose_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Adipose Tissue, Brown

value: Adipose Tissue, Brown

value: Female


title: Rat_WhiteAdipose_Female

description:
Rat_WhiteAdipose_Female
Rat_FPKM_table_Mar22.xlsx


title: Mouse_Male_Thymus

description:
Mouse_Male_Thymus
Mouse_FPKM_table_Mar22.xlsx

source_name: Thymus Gland

value: Thymus Gland


title: FC00029: Blue_61


title: FC00029: Blue_60


title: FC00029: Blue_59


title: Rat_BrownAdipose_Male

description:
Rat_BrownAdipose_Male
Rat_FPKM_table_Mar22.xlsx


title: Mouse_Male_SkeletalMuscle

description:
Mouse_Male_SkeletalMuscle
Mouse_FPKM_table_Mar22.xlsx

source_name: Muscle, Skeletal

value: Muscle, Skeletal


title: FC00029: Blue_58


title: Rat_BoneMarrow_Female

description:
Rat_BoneMarrow_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Bone Marrow

value: Bone Marrow


title: Monkey_Prostate_Male_1002

description:
Monkey_Prostate_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Male_SalivaryGland

description:
Mouse_Male_SalivaryGland
Mouse_FPKM_table_Mar22.xlsx

source_name: Salivary Glands

value: Salivary Glands


title: Monkey_PeyersPatch_Male_1002

description:
Monkey_PeyersPatch_Male_1002
Cyno_FPKM_table_Mar22.xlsx

source_name: Peyer's Patches

value: Peyer's Patches


title: Rat_BoneMarrow_Male

description:
Rat_BoneMarrow_Male
Rat_FPKM_table_Mar22.xlsx

value: Male


title: Monkey_PeyersPatch_Male_1001

description:
Monkey_PeyersPatch_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_55

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

value: Dorsal Root Ganglion

value: C1-C8 DRG


title: Monkey_Pancreas_Male_1003

description:
Monkey_Pancreas_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Pancreas

value: Pancreas

value: untreated


title: Mouse_Male_MesentericLymphNode

description:
Mouse_Male_MesentericLymphNode
Mouse_FPKM_table_Mar22.xlsx

source_name: Lymph Nodes

value: Lymph Nodes


title: Rat_Cecum_Female

description:
Rat_Cecum_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Cecum

value: Cecum


title: FC00029: Blue_56

source_name: C1-C8 DRG

value: 6-12 weeks old


title: Monkey_Pituitary_Male_1002

description:
Monkey_Pituitary_Male_1002
Cyno_FPKM_table_Mar22.xlsx

value: Pituitary Gland


title: Rat_Cecum_Male

description:
Rat_Cecum_Male
Rat_FPKM_table_Mar22.xlsx

value: Sprague Dawley


title: Monkey_Pancreas_Male_1002

description:
Monkey_Pancreas_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Male_Lung

description:
Mouse_Male_Lung
Mouse_FPKM_table_Mar22.xlsx

source_name: Lung

value: Lung


title: Mouse_Male_Spleen

description:
Mouse_Male_Spleen
Mouse_FPKM_table_Mar22.xlsx

source_name: Spleen

value: Spleen


title: Mouse_Male_Esophagus

description:
Mouse_Male_Esophagus
Mouse_FPKM_table_Mar22.xlsx

source_name: Esophagus

value: Esophagus


title: Monkey_Pancreas_Male_1001

description:
Monkey_Pancreas_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Rat_Heart_Female

description:
Rat_Heart_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Heart

value: Heart

value: Female


title: Monkey_MesentericLymphNode_Male_1003

description:
Monkey_MesentericLymphNode_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_53


title: FC00029: Blue_52


title: FC00029: Blue_54


title: FC00029: Blue_57


title: Monkey_PeyersPatch_Male_1003

description:
Monkey_PeyersPatch_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: Rat_Ileum_Female

description:
Rat_Ileum_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Ileum

value: Ileum


title: Mouse_Male_Brain_Cortex

description:
Mouse_Male_Brain_Cortex
Mouse_FPKM_table_Mar22.xlsx

source_name: Cerebral Cortex

value: Cerebral Cortex


title: FC00029: Blue_51


title: Monkey_MesentericLymphNode_Male_1002

description:
Monkey_MesentericLymphNode_Male_1002
Cyno_FPKM_table_Mar22.xlsx

value: Male


title: Mouse_Male_Cerebellum

description:
Mouse_Male_Cerebellum
Mouse_FPKM_table_Mar22.xlsx

source_name: Cerebellum

value: Cerebellum


title: Mouse_Male_Pancreas

description:
Mouse_Male_Pancreas
Mouse_FPKM_table_Mar22.xlsx


title: FC00029: Blue_50

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

value: Dorsal Root Ganglion

value: C1-C8 DRG


title: Mouse_Male_CaudalVenaCava

description:
Mouse_Male_CaudalVenaCava
Mouse_FPKM_table_Mar22.xlsx

source_name: Vena Cava, Inferior

value: Vena Cava, Inferior

value: untreated


title: Monkey_Lung_Male_1003

description:
Monkey_Lung_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: Rat_Jejunum_Female

description:
Rat_Jejunum_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Jejunum

value: Jejunum


title: FC00029: Blue_49

value: 6-12 weeks old


title: Mouse_Male_BoneMarrow

description:
Mouse_Male_BoneMarrow
Mouse_FPKM_table_Mar22.xlsx

value: Bone Marrow


title: FC00029: Blue_48


title: Rat_Jejunum_Male

description:
Rat_Jejunum_Male
Rat_FPKM_table_Mar22.xlsx

value: Sprague Dawley


title: Monkey_Lung_Male_1001

description:
Monkey_Lung_Male_1001
Cyno_FPKM_table_Mar22.xlsx

value: Lung


title: Rat_Duodenum_Female

description:
Rat_Duodenum_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Duodenum

value: Duodenum


title: Rat_Duodenum_Male

description:
Rat_Duodenum_Male
Rat_FPKM_table_Mar22.xlsx


title: Monkey_Lung_Male_1002

description:
Monkey_Lung_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Male_Adipose_Brown

description:
Mouse_Male_Adipose_Brown
Mouse_FPKM_table_Mar22.xlsx

source_name: Adipose Tissue, Brown

value: Adipose Tissue, Brown


title: Monkey_Liver_Male_1002

description:
Monkey_Liver_Male_1002
Cyno_FPKM_table_Mar22.xlsx

source_name: Liver

value: Liver


title: Rat_Spleen_Female

description:
Rat_Spleen_Female
Rat_FPKM_table_Mar22.xlsx

value: Spleen

value: Female


title: Rat_Ileum_Male

description:
Rat_Ileum_Male
Rat_FPKM_table_Mar22.xlsx

value: Ileum


title: Rat_Heart_Male

description:
Rat_Heart_Male
Rat_FPKM_table_Mar22.xlsx

value: Heart

value: Male


title: FC00029: Blue_47

value: Dorsal Root Ganglion


title: Mouse_Male_AdrenalGland

description:
Mouse_Male_AdrenalGland
Mouse_FPKM_table_Mar22.xlsx

source_name: Adrenal Glands

value: Adrenal Glands


title: Monkey_Liver_Male_1003

description:
Monkey_Liver_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_46

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

value: C1-C8 DRG


title: Mouse_Female_WholeBlood

description:
Mouse_Female_WholeBlood
Mouse_FPKM_table_Mar22.xlsx

source_name: Serum

value: Serum

value: untreated


title: Monkey_LacrimalGland_Male_1003

description:
Monkey_LacrimalGland_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Lacrimal Apparatus

value: Lacrimal Apparatus


title: FC00029: Blue_43

value: 6-12 weeks old


title: FC00029: Blue_44


title: Mouse_Male_Bladder

description:
Mouse_Male_Bladder
Mouse_FPKM_table_Mar22.xlsx

source_name: Urinary Bladder

value: Urinary Bladder


title: Monkey_MesentericLymphNode_Male_1001

description:
Monkey_MesentericLymphNode_Male_1001
Cyno_FPKM_table_Mar22.xlsx

source_name: Lymph Nodes

value: Lymph Nodes


title: FC00029: Blue_45

source_name: C1-C8 DRG


title: Rat_Liver_Male

description:
Rat_Liver_Male
Rat_FPKM_table_Mar22.xlsx

value: Sprague Dawley


title: Monkey_LacrimalGland_Male_1002

description:
Monkey_LacrimalGland_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Monkey_Liver_Male_1001

description:
Monkey_Liver_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Female_Tongue

description:
Mouse_Female_Tongue
Mouse_FPKM_table_Mar22.xlsx

source_name: Tongue

value: Tongue


title: Mouse_Female_Thymus

description:
Mouse_Female_Thymus
Mouse_FPKM_table_Mar22.xlsx

source_name: Thymus Gland

value: Thymus Gland


title: Rat_Spleen_Male

description:
Rat_Spleen_Male
Rat_FPKM_table_Mar22.xlsx

source_name: Spleen

value: Spleen


title: Rat_Liver_Female

description:
Rat_Liver_Female
Rat_FPKM_table_Mar22.xlsx

value: Liver

value: Female


title: Mouse_Female_ThyroidGland

description:
Mouse_Female_ThyroidGland
Mouse_FPKM_table_Mar22.xlsx

source_name: Thyroid Gland

value: Thyroid Gland


title: Monkey_LacrimalGland_Male_1001

description:
Monkey_LacrimalGland_Male_1001
Cyno_FPKM_table_Mar22.xlsx

value: Male


title: Rat_Kidney_Male

description:
Rat_Kidney_Male
Rat_FPKM_table_Mar22.xlsx

source_name: Kidney

value: Kidney


title: Monkey_Kidney_Male_1002

description:
Monkey_Kidney_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Female_Stomach

description:
Mouse_Female_Stomach
Mouse_FPKM_table_Mar22.xlsx

source_name: Stomach

value: Stomach


title: Mouse_Female_Spleen

description:
Mouse_Female_Spleen
Mouse_FPKM_table_Mar22.xlsx


title: Mouse_Female_Skin

description:
Mouse_Female_Skin
Mouse_FPKM_table_Mar22.xlsx

source_name: Skin

value: Skin


title: Rat_Thyroid_Female

description:
Rat_Thyroid_Female
Rat_FPKM_table_Mar22.xlsx


title: FC00029: Blue_40

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

value: Dorsal Root Ganglion

value: C1-C8 DRG


title: FC00029: Blue_38


title: Rat_Thymus_Female

description:
Rat_Thymus_Female
Rat_FPKM_table_Mar22.xlsx

value: untreated


title: Monkey_Kidney_Male_1001

description:
Monkey_Kidney_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_42

value: 6-12 weeks old


title: Mouse_Female_SkeletalMuscle

description:
Mouse_Female_SkeletalMuscle
Mouse_FPKM_table_Mar22.xlsx

source_name: Muscle, Skeletal

value: Muscle, Skeletal


title: Monkey_Jejunum_Male_1003

description:
Monkey_Jejunum_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Jejunum

value: Jejunum


title: FC00029: Blue_41


title: FC00029: Blue_37


title: Monkey_Jejunum_Male_1002

description:
Monkey_Jejunum_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Rat_Kidney_Female

description:
Rat_Kidney_Female
Rat_FPKM_table_Mar22.xlsx

value: Sprague Dawley


title: Monkey_Jejunum_Male_1001

description:
Monkey_Jejunum_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Female_Jejunum

description:
Mouse_Female_Jejunum
Mouse_FPKM_table_Mar22.xlsx


title: FC00029: Blue_36


title: Mouse_Female_Lung

description:
Mouse_Female_Lung
Mouse_FPKM_table_Mar22.xlsx

source_name: Lung

value: Lung


title: Mouse_Female_PituitaryGland

description:
Mouse_Female_PituitaryGland
Mouse_FPKM_table_Mar22.xlsx

source_name: Pituitary Gland

value: Pituitary Gland


title: Monkey_Ileum_Male_1003

description:
Monkey_Ileum_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Ileum

value: Ileum


title: FC00029: Blue_39


title: Mouse_Female_Cortex

description:
Mouse_Female_Cortex
Mouse_FPKM_table_Mar22.xlsx

source_name: Cerebral Cortex

value: Cerebral Cortex


title: Rat_Stomach_Female

description:
Rat_Stomach_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Stomach, Ruminant

value: Stomach, Ruminant

value: Female


title: Rat_Stomach_Male

description:
Rat_Stomach_Male
Rat_FPKM_table_Mar22.xlsx

value: Male


title: Rat_Thymus_Male

description:
Rat_Thymus_Male
Rat_FPKM_table_Mar22.xlsx

value: Thymus Gland


title: Monkey_Kidney_Male_1003

description:
Monkey_Kidney_Male_1003
Cyno_FPKM_table_Mar22.xlsx

value: Kidney


title: Rat_Thyroid_Male

description:
Rat_Thyroid_Male
Rat_FPKM_table_Mar22.xlsx

value: Thyroid Gland


title: FC00029: Blue_34

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

value: Dorsal Root Ganglion


title: FC00029: Blue_35

value: C1-C8 DRG


title: Rat_SalivaryGland_Female

description:
Rat_SalivaryGland_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Salivary Glands

value: Salivary Glands

value: untreated


title: FC00029: Blue_33

value: 6-12 weeks old


title: Mouse_Female_Brain_Cerebellum

description:
Mouse_Female_Brain_Cerebellum
Mouse_FPKM_table_Mar22.xlsx

source_name: Cerebellum

value: Cerebellum


title: Rat_SalivaryGland_Male

description:
Rat_SalivaryGland_Male
Rat_FPKM_table_Mar22.xlsx

value: Sprague Dawley


title: Monkey_Ileum_Male_1001

description:
Monkey_Ileum_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Female_CaudalVenaCava

description:
Mouse_Female_CaudalVenaCava
Mouse_FPKM_table_Mar22.xlsx

source_name: Vena Cava, Inferior

value: Vena Cava, Inferior


title: Rat_NerveSciatic_Female

description:
Rat_NerveSciatic_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Sciatic Nerve

value: Sciatic Nerve


title: Monkey_Hippocampus_Male_1003

description:
Monkey_Hippocampus_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Hippocampus

value: Hippocampus


title: FC00029: Blue_31

source_name: C1-C8 DRG


title: Monkey_Hippocampus_Male_1002

description:
Monkey_Hippocampus_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Rat_NerveSciatic_Male

description:
Rat_NerveSciatic_Male
Rat_FPKM_table_Mar22.xlsx


title: FC00029: Blue_30


title: Mouse_Female_Bladder

description:
Mouse_Female_Bladder
Mouse_FPKM_table_Mar22.xlsx

source_name: Urinary Bladder

value: Urinary Bladder


title: Rat_AdrenalGland_Female

description:
Rat_AdrenalGland_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Adrenal Glands

value: Adrenal Glands


title: Monkey_Hippocampus_Male_1001

description:
Monkey_Hippocampus_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_29


title: Monkey_Heart_Male_1003

description:
Monkey_Heart_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Heart

value: Heart


title: Rat_AdreanlGland_Male

description:
Rat_AdreanlGland_Male
Rat_FPKM_table_Mar22.xlsx

value: Male


title: FC00029: Blue_28


title: Mouse_Female_Adipose_Visceral

description:
Mouse_Female_Adipose_Visceral
Mouse_FPKM_table_Mar22.xlsx

source_name: Intra-Abdominal Fat

value: Intra-Abdominal Fat

value: Female


title: Monkey_Heart_Male_1002

description:
Monkey_Heart_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: Rat_BrainSpinalCord_Male

description:
Rat_BrainSpinalCord_Male
Rat_FPKM_table_Mar22.xlsx

source_name: Spinal Cord

value: Spinal Cord


title: FC00029: Blue_27

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

value: Dorsal Root Ganglion


title: Monkey_Ileum_Male_1002

description:
Monkey_Ileum_Male_1002
Cyno_FPKM_table_Mar22.xlsx

value: Ileum


title: Rat_BrainSpinalCord_Female

description:
Rat_BrainSpinalCord_Female
Rat_FPKM_table_Mar22.xlsx


title: Mouse_Female_Adipose_Brown

description:
Mouse_Female_Adipose_Brown
Mouse_FPKM_table_Mar22.xlsx

source_name: Adipose Tissue, Brown

value: Adipose Tissue, Brown


title: FC00029: Blue_32

value: C1-C8 DRG


title: Rat_BarinMedulla_Female

description:
Rat_BarinMedulla_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Medulla Oblongata

value: Medulla Oblongata

value: untreated


title: Monkey_GastrocnemiusTendon_Male_1003

description:
Monkey_GastrocnemiusTendon_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Tendons

value: Tendons


title: FC00029: Blue_25

value: 6-12 weeks old


title: FC00029: Blue_26


title: Mouse_Male_Testis

description:
Mouse_Male_Testis
Mouse_FPKM_table_Mar22.xlsx

source_name: Testis

value: Testis


title: Mouse_Male_ThyroidGland

description:
Mouse_Male_ThyroidGland
Mouse_FPKM_table_Mar22.xlsx

source_name: Thyroid Gland

value: Thyroid Gland


title: Monkey_GastrocnemiusTendon_Male_1002

description:
Monkey_GastrocnemiusTendon_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_24


title: Mouse_Female_Aorta

description:
Mouse_Female_Aorta
Mouse_FPKM_table_Mar22.xlsx

source_name: Aorta

value: Aorta


title: Rat_BrainMedulla_Male

description:
Rat_BrainMedulla_Male
Rat_FPKM_table_Mar22.xlsx

value: Sprague Dawley


title: Rat_BrainFrontalCortex_Female

description:
Rat_BrainFrontalCortex_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Frontal Lobe

value: Frontal Lobe


title: Mouse_Male_Stomach

description:
Mouse_Male_Stomach
Mouse_FPKM_table_Mar22.xlsx

source_name: Stomach

value: Stomach

value: Male


title: Monkey_GastrocnemiusTendon_Male_1001

description:
Monkey_GastrocnemiusTendon_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_23


title: Mouse_Male_Jejunum

description:
Mouse_Male_Jejunum
Mouse_FPKM_table_Mar22.xlsx

source_name: Jejunum

value: Jejunum


title: Rat_BrainFrontalCortex_Male

description:
Rat_BrainFrontalCortex_Male
Rat_FPKM_table_Mar22.xlsx


title: FC00029: Blue_22


title: Mouse_Male_Ileum

description:
Mouse_Male_Ileum
Mouse_FPKM_table_Mar22.xlsx

source_name: Ileum


title: Monkey_Heart_Male_1001

description:
Monkey_Heart_Male_1001
Cyno_FPKM_table_Mar22.xlsx

value: Heart


title: Rat_BrainCortex_Female

description:
Rat_BrainCortex_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Cerebral Cortex

value: Cerebral Cortex

value: Female


title: FC00029: Blue_21

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

source_name: C1-C8 DRG

value: Dorsal Root Ganglion


title: Monkey_Gallbladder_Male_1002

description:
Monkey_Gallbladder_Male_1002
Cyno_FPKM_table_Mar22.xlsx

source_name: Gallbladder

value: Gallbladder


title: Mouse_Male_Duodenum

description:
Mouse_Male_Duodenum
Mouse_FPKM_table_Mar22.xlsx

source_name: Duodenum

value: Duodenum


title: Monkey_Gallbladder_Male_1001

description:
Monkey_Gallbladder_Male_1001
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: Rat_BrainCortex_Male

description:
Rat_BrainCortex_Male
Rat_FPKM_table_Mar22.xlsx


title: Monkey_FrontalLobe_Male_1003

description:
Monkey_FrontalLobe_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: Rat_BrainCerebellum_Female

description:
Rat_BrainCerebellum_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Cerebellum

value: Cerebellum


title: FC00029: Blue_20

value: C1-C8 DRG

value: 6-12 weeks old


title: Rat_BrainCerebellum_Male

description:
Rat_BrainCerebellum_Male
Rat_FPKM_table_Mar22.xlsx


title: Mouse_Female_AdrenalGland

description:
Mouse_Female_AdrenalGland
Mouse_FPKM_table_Mar22.xlsx

source_name: Adrenal Glands

value: Adrenal Glands


title: Mouse_Male_Skin

description:
Mouse_Male_Skin
Mouse_FPKM_table_Mar22.xlsx

source_name: Skin

value: Skin


title: Monkey_FrontalLobe_Male_1002

description:
Monkey_FrontalLobe_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_19


title: FC00029: Blue_17


title: Mouse_Male_PituitaryGland

description:
Mouse_Male_PituitaryGland
Mouse_FPKM_table_Mar22.xlsx

source_name: Pituitary Gland

value: Pituitary Gland


title: Mouse_Male_Prostate

description:
Mouse_Male_Prostate
Mouse_FPKM_table_Mar22.xlsx

source_name: Prostate

value: Prostate


title: FC00029: Blue_18


title: Monkey_FrontalLobe_Male_1001

description:
Monkey_FrontalLobe_Male_1001
Cyno_FPKM_table_Mar22.xlsx

value: Frontal Lobe


title: Rat_Bladder_Male

description:
Rat_Bladder_Male
Rat_FPKM_table_Mar22.xlsx

source_name: Urinary Bladder

value: Sprague Dawley

value: Urinary Bladder

value: Male


title: Rat_Bladder_Female

description:
Rat_Bladder_Female
Rat_FPKM_table_Mar22.xlsx


title: Mouse_Male_Liver

description:
Mouse_Male_Liver
Mouse_FPKM_table_Mar22.xlsx

source_name: Liver

value: Liver


title: Monkey_Gallbladder_Male_1003

description:
Monkey_Gallbladder_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: Rat_ArteryAorta_Female

description:
Rat_ArteryAorta_Female
Rat_FPKM_table_Mar22.xlsx

value: Aorta

value: Female


title: Mouse_Male_Parathyroid

description:
Mouse_Male_Parathyroid
Mouse_FPKM_table_Mar22.xlsx

source_name: Parathyroid Glands

value: Parathyroid Glands


title: Monkey_FemoralVein_Male_1003

description:
Monkey_FemoralVein_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Femoral Vein

value: Femoral Vein


title: FC00029: Blue_16

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

value: Dorsal Root Ganglion


title: Monkey_FemoralVein_Male_1002

description:
Monkey_FemoralVein_Male_1002
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: FC00029: Blue_15

value: C1-C8 DRG


title: Rat_ArteryAorta_Male

description:
Rat_ArteryAorta_Male
Rat_FPKM_table_Mar22.xlsx

source_name: Aorta


title: Mouse_Male_Kidney

description:
Mouse_Male_Kidney
Mouse_FPKM_table_Mar22.xlsx

source_name: Kidney

value: Kidney


title: Monkey_FemoralVein_Male_1001

description:
Monkey_FemoralVein_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Mouse_Male_Heart

description:
Mouse_Male_Heart
Mouse_FPKM_table_Mar22.xlsx

source_name: Heart

value: Heart


title: FC00029: Blue_14

value: 6-12 weeks old


title: Rat_LymphNodeMesenteric_Female

description:
Rat_LymphNodeMesenteric_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Lymph Nodes

value: Lymph Nodes


title: Monkey_Esophagus_Male_1003

description:
Monkey_Esophagus_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Esophagus

value: Esophagus


title: Mouse_Male_Eye

description:
Mouse_Male_Eye
Mouse_FPKM_table_Mar22.xlsx

source_name: Eye

value: Eye


title: FC00029: Blue_13

source_name: C1-C8 DRG


title: Monkey_Esophagus_Male_1002

description:
Monkey_Esophagus_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_12


title: Monkey_Esophagus_Male_1001

description:
Monkey_Esophagus_Male_1001
Cyno_FPKM_table_Mar22.xlsx


title: Rat_MammaryTissue_Female

description:
Rat_MammaryTissue_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Mammary Glands, Animal

value: Sprague Dawley

value: Mammary Glands, Animal


title: FC00029: Blue_11


title: Mouse_Male_Epididymis

description:
Mouse_Male_Epididymis
Mouse_FPKM_table_Mar22.xlsx

source_name: Epididymis

value: Epididymis

value: Male


title: Mouse_Male_Colon

description:
Mouse_Male_Colon
Mouse_FPKM_table_Mar22.xlsx

source_name: Colon

value: Colon


title: FC00029: Blue_10


title: Mouse_Male_Cecum

description:
Mouse_Male_Cecum
Mouse_FPKM_table_Mar22.xlsx

source_name: Cecum

value: Cecum


title: Monkey_Epididymis_Male_1003

description:
Monkey_Epididymis_Male_1003
Cyno_FPKM_table_Mar22.xlsx


title: Rat_Cornea_Female

description:
Rat_Cornea_Female
Rat_FPKM_table_Mar22.xlsx

source_name: Cornea

value: Cornea

value: Female


title: Mouse_Male_Brain_Medulla

description:
Mouse_Male_Brain_Medulla
Mouse_FPKM_table_Mar22.xlsx

source_name: Medulla Oblongata

value: Medulla Oblongata


title: FC00029: Blue_9

description: FC00029: naïve Nav1.8-Cre R26CAG-floxStop-tdTomato, scRNAseq run 1

value: Dorsal Root Ganglion


title: Monkey_Epididymis_Male_1001

description:
Monkey_Epididymis_Male_1001
Cyno_FPKM_table_Mar22.xlsx

value: untreated


title: Mouse_Male_Brain_Spinal_Cord

description:
Mouse_Male_Brain_Spinal_Cord
Mouse_FPKM_table_Mar22.xlsx

source_name: Spinal Cord

value: Spinal Cord


title: Monkey_Epididymis_Male_1002

description:
Monkey_Epididymis_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_8

value: C1-C8 DRG


title: Monkey_Duodenum_Male_1003

description:
Monkey_Duodenum_Male_1003
Cyno_FPKM_table_Mar22.xlsx

source_name: Duodenum

value: Duodenum


title: Rat_Cornea_Male

description:
Rat_Cornea_Male
Rat_FPKM_table_Mar22.xlsx


title: Mouse_Male_Brain_Frontal_Cortex

description:
Mouse_Male_Brain_Frontal_Cortex
Mouse_FPKM_table_Mar22.xlsx

source_name: Frontal Lobe

value: Frontal Lobe


title: FC00029: Blue_7

value: 6-12 weeks old


title: Monkey_Duodenum_Male_1002

description:
Monkey_Duodenum_Male_1002
Cyno_FPKM_table_Mar22.xlsx


title: FC00029: Blue_6


title: Rat_LymphNodeMesenteric_Male

description:
Rat_LymphNodeMesenteric_Male
Rat_FPKM_table_Mar22.xlsx

value: Lymph Nodes


title: Mouse_8_H3K27ac

city: San Francisco

first: Ilia

middle: D.

last: Vainchtein

address: 1550 4th street

department: Psychiatry

institute: UCSF

data_processing:
Reads were mapped using Bowtie2 to mouse genome (mm10).
HOMER was used to create tags and call peaks.
Peak files were merged per group and annotated with HOMER.
ATAC-seq enhancer peaks were anchored onto H3K27ac peaks.
Assembly: GRCm38, mm10
Supplementary files format and content: Excel; H3K27ac_ChIPseq_allNormTags.xlsx (normalized tags for H3K27ac-ChIPseq)
Supplementary files format and content: Excel; H3K27ac_ChIPseq_anchoredATACseq_IL33vsVehicle.xlsx (ATACseq anchored H3K27ac peaks IL33 vs Vehicle)

source_name: Cortex

extract_protocol:
Microglia were isolated using a tissue homogenizer followed by 22% Percoll gradient, all on ice or 4C, and collected with FACS.
H3K27ac ChIP-seq protocol as in Nott et al., 2019.

treatment_protocol: P30 mice were unilaterally i.c.v. injected with IL-33 or vehicle and terminated after 4 hours.

value: Cortex

tag: celltype

value: Microglia

tag: antibody

value: H3K27ac (Active Motif, Cat #39685)


title: Mouse_Male_Aorta

description:
Mouse_Male_Aorta
Mouse_FPKM_table_Mar22.xlsx

source_name: Aorta

value: Aorta

value: Male


title: Mouse_7_H3K27ac


title: Mouse_6_input


title: Monkey_Duodenum_Male_1001

description:
Monkey_Duodenum_Male_1001
Cyno_FPKM_table_Mar22.xlsx