title: Patient 003,PostNeo, PBMC, RNAseq

description:
Library name: P003-PostNeo
RNA-seq of patients' PBMCs


title: Patient 002,Baseline, PBMC, RNAseq

status: Public on Jul 21 2026

type: SRA

city: Los Angeles

first: Lu

last: Sun

state: California

address: 10833 Le Conte Avenue

country: USA

institute: University of California, LA

description:
Library name: P002-Baseline
RNA-seq of patients' PBMCs

library_source: transcriptomic

data_processing:
Paired-end, 2 × 100 base pair (bp) transcriptome reads were mapped to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome using HISAT2 (version 2.0.6)
The gene level counts were generated by the HTSeq-count program (version 0.5.4p5)
We utilized the edgeR (version 3.40.2) R package's cpm() function to compute the normalized gene expression values from the raw gene expression counts. These normalized expression values were log2 transformed after adding a pseudo count of 1.
Assembly: GRCh38
Supplementary files format and content: Gene level raw counts of each sample as computed by htseq-count (tab delimited)

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
RNA and genomic DNA were extracted from resected tumor specimens preserved in AllProtect tissue reagent (Qiagen) at the time of surgery. We divided the tumor tissue in half and employed the Qiagen RNeasy Mini Kit (#74104) for RNA isolation and the Qiagen DNeasy Blood and Tissue Kit (#69504) for DNA isolation. Total RNA from PBMCs was extracted using the Qiagen RNeasy Mini Kit.
TruSeq RNA exome kit is used to construct the RNA sequencing libraries

tag: tissue

value: PBMC

tag: treatment

value: nivolumab+ipilimumab trial

tag: arm

tag: Sex

value: Male

tag: ethnicity

value: Non-Hispanic

tag: age

tag: os


title: AB13078

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Sample 125

library_source: transcriptomic single cell

data_processing:
RNA sequencing data were processed starting with the Cell Ranger software (10x Genomics) to perform quality control, read alignment to the mouse reference genome (GRCm38), and quantification of gene expression levels. Unique Molecular Identifiers (UMIs) were used to count individual mRNA molecules, ensuring accurate expression levels.
The resultant data were then normalized to account for variations in sequencing depth and cell count discrepancies.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: tab delimited cell metadata

molecule: polyA RNA

organism: Mus musculus

source_name: spinal cord

extract_protocol:
Mice were transcardially perfused with sterile PBS, and brain, spinal cord, spleen, lung and CSF were extracted 10 days post CAR T administration.
Next Gem single-cell 3′ with Feature Barcode technology for Cell Surface Protein v3.1.

treatment_protocol: For each mouse, 4 days after EAE induction, 3x10^⁶ cells in 100ul were injected retro-orbitally under isoflurane anesthesia, or 100ul of PBS for the control EAE untreated group. Tissues were harvested for scRNA-seq on day 14.

value: spinal cord

tag: gate

tag: mouse

tag: score

value: Untreated (PBS)

tag: eae model

value: peptide MOG

tag: batch


title: DRG culture, Atf4 mRNA+Cebpg mRNA, t=42h, rep2

city: San Francisco

first: Trent

middle: A.

last: Watkins

state: CA

address: 675 Nelson Rising Lane, Rm 214A

institute: University of California at San Francisco

description: Library name: ATF4_CEBPG_2

data_processing:
Kallisto paired-end quantification
Assembly: Mus_musculus.GRCm39.108
Supplementary files format and content: A comma-separated values (.csv) file contains kallisto estimated counts for siRNA samples.
Supplementary files format and content: A comma-separated values (.csv) file contains kallisto estimated counts for mRNA samples.

source_name: primary adult dorsal root ganglia cell culture

growth_protocol: Dissociated cells cultured in Neurobasal-A medium with B27 supplement.

extract_protocol:
RNA was extracted using the Qiagen RNeasy micro kit (#74004).
Illumina Stranded mRNA Prep

treatment_protocol: Dharnafect 2-mediated transfection of Dharnacon ON-TARGETplus siRNA pools or custom mRNA generated by GenScript.

tag: cell type

tag: genotype

value: wildtype


title: AB17776

description:
Library name: Sample1851
MARS_v2

data_processing:
bcl2fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used (most samples) i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Samples467 up to Samples733 Pool-barcode used is 5N (random) + 4N (Pool barcode) On R1 1 humming error was allowed. Well-barcode N7 folowed by UMI N8 in read 2.
Samples 259, 295, 297, 299, 232 and 234 Utilized a 9 Nucleotide cell barcode and compose of 768 cells per sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cells_annotation_for_geo_ver_20250306.xlsx

source_name: BM

extract_protocol:
BM aspirates were collected from the posterior iliac crest into EDTA-coated tubes (BD Biosciences), diluted 1:1 with ice-cold FACS buffer (PBS supplemented with 2 mM EDTA, pH 8.0, and 0.5% bovine serum albumin), and maintained on ice. Samples were immediately transported to the laboratory for downstream processing and single-cell analysis.
mRNA from cells sorted into barcoded cell capture plates and converted into cDNA, later pooled by using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina adapters during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration was assessed as described earlier. Overall, barcoding was done in three levels: Cell barcodes allow attribution of each sequence read to its cell of origin, thus enabling pooling; Unique Molecular Identifiers (UMIs) allow tagging each original molecule to avoid amplification bias; and plate barcodes allow elimination of the batch effect.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

value: BM

value: PC


title: AB17777

description:
Library name: Sample1852
MARS_v2


title: AB13077

description: Library name: Sample 124


title: Patient 001,C2D1, PBMC, RNAseq

description:
Library name: P001-C2D1
RNA-seq of patients' PBMCs


title: DRG culture, Atf4 mRNA+Cebpg mRNA, t=42h, rep1

description: Library name: ATF4_CEBPG_1

value: primary adult dorsal root ganglia cell culture


title: Patient 001,Baseline, PBMC, RNAseq

description:
Library name: P001-Baseline
RNA-seq of patients' PBMCs


title: AB17775

description:
Library name: Sample1850
MARS_v2


title: AB13076

description: Library name: Sample 123


title: AB17774

description:
Library name: Sample1849
MARS_v2


title: DRG culture, Atf4 mRNA, t=42h, rep4

description: Library name: ATF4_4


title: Patient 062, Tumor, RNAseq

description:
Library name: P062_Tumor
RNA-seq of resected patient tumor specimens

source_name: Tumor

value: Tumor


title: AB12199

description: Library name: Sample 122


title: DRG culture, Atf4 mRNA, t=42h, rep3

description: Library name: ATF4_3


title: AB17773

description:
Library name: Sample1848
MARS_v2


title: AB12198

description: Library name: Sample 121


title: Patient 058, Tumor, RNAseq

description:
Library name: P058_Tumor
RNA-seq of resected patient tumor specimens


title: DRG culture, Atf4 mRNA, t=42h, rep2

description: Library name: ATF4_2


title: AB17772

description:
Library name: Sample1847
MARS_v2


title: Patient 057, Tumor, RNAseq

description:
Library name: P057_Tumor
RNA-seq of resected patient tumor specimens


title: AB12197

description: Library name: Sample 120


title: DRG culture, Atf4 mRNA, t=42h, rep1

description: Library name: ATF4_1


title: AB17771

description:
Library name: Sample1846
MARS_v2


title: AB12196

description: Library name: Sample 119


title: Patient 056, Tumor, RNAseq

description:
Library name: P056_Tumor
RNA-seq of resected patient tumor specimens


title: DRG culture, GFP mRNA, t=42h, rep4

description: Library name: GFP_4


title: Patient 054, Tumor, RNAseq

description:
Library name: P054_Tumor
RNA-seq of resected patient tumor specimens

value: Female


title: AB12195

description: Library name: Sample 118


title: DRG culture, GFP mRNA, t=42h, rep3

description: Library name: GFP_3


title: AB17770

description:
Library name: Sample1845
MARS_v2


title: AB17769

description:
Library name: Sample1844
MARS_v2


title: Patient 053, Tumor, RNAseq

description:
Library name: P053_Tumor
RNA-seq of resected patient tumor specimens


title: DRG culture, GFP mRNA, t=42h, rep2

description: Library name: GFP_2


title: AB17768

description:
Library name: Sample1843
MARS_v2


title: Patient 052, Tumor, RNAseq

description:
Library name: P052_Tumor
RNA-seq of resected patient tumor specimens


title: AB12194

description: Library name: Sample 117


title: DRG culture, GFP mRNA, t=42h, rep1

description: Library name: GFP_1


title: Patient 051, Tumor, RNAseq

description:
Library name: P051_Tumor
RNA-seq of resected patient tumor specimens


title: AB17767

description:
Library name: Sample1842
MARS_v2


title: AB12192

description: Library name: Sample 115


title: DRG culture, siAlyref, t=42h, rep4

description: Library name: siAlyref_4

value: siAlyref


title: AB12193

description: Library name: Sample 116


title: AB17766

description:
Library name: Sample1841
MARS_v2


title: Patient 050, Tumor, RNAseq

description:
Library name: P050_Tumor
RNA-seq of resected patient tumor specimens


title: AB12191

description: Library name: Sample 114


title: DRG culture, siAlyref, t=42h, rep3

description: Library name: siAlyref_3


title: AB17765

description:
Library name: Sample1840
MARS_v2


title: Patient 049, Tumor, RNAseq

description:
Library name: P049_Tumor
RNA-seq of resected patient tumor specimens


title: AB12190

description: Library name: Sample 113


title: DRG culture, siAlyref, t=42h, rep2

description: Library name: siAlyref_2


title: AB17764

description:
Library name: Sample1839
MARS_v2


title: Patient 047, Tumor, RNAseq

description:
Library name: P047_Tumor
RNA-seq of resected patient tumor specimens


title: AB12189

description: Library name: Sample 112


title: DRG culture, siAlyref, t=42h, rep1

description: Library name: siAlyref_1


title: AB17763

description:
Library name: Sample1838
MARS_v2


title: Patient 045, Tumor, RNAseq

description:
Library name: P045_Tumor
RNA-seq of resected patient tumor specimens

value: Hispanic or Latino


title: AB12188

description: Library name: Sample 111


title: DRG culture, siRest, t=42h, rep4

description: Library name: siRest_4

value: siRest


title: AB17762

description:
Library name: Sample1837
MARS_v2


title: Patient 043, Tumor, RNAseq

description:
Library name: P043_Tumor
RNA-seq of resected patient tumor specimens


title: AB12187

description: Library name: Sample 110


title: DRG culture, siRest, t=42h, rep3

description: Library name: siRest_3


title: AB17761

description:
Library name: Sample1836
MARS_v2


title: Patient 042, Tumor, RNAseq

description:
Library name: P042_Tumor
RNA-seq of resected patient tumor specimens


title: AB12186

description: Library name: Sample 109


title: DRG culture, siRest, t=42h, rep2

description: Library name: siRest_2


title: AB17760

description:
Library name: Sample1835
MARS_v2


title: Patient 041, Tumor, RNAseq

description:
Library name: P041_Tumor
RNA-seq of resected patient tumor specimens


title: AB12114

description: Library name: Sample 108


title: DRG culture, siRest, t=42h, rep1

description: Library name: siRest_1


title: AB13004

description:
Library name: Sample1323
MARS_v2


title: Patient 040, Tumor, RNAseq

description:
Library name: P040_Tumor
RNA-seq of resected patient tumor specimens


title: AB17759

description:
Library name: Sample1834
MARS_v2


title: AB12113

description: Library name: Sample 107


title: DRG culture, siKlf6, t=42h, rep5

description: Library name: siKlf6_5


title: AB17758

description:
Library name: Sample1833
MARS_v2


title: AB12112

description: Library name: Sample 106


title: DRG culture, siKlf6, t=42h, rep2

description: Library name: siKlf6_2


title: AB12111

description: Library name: Sample 105


title: AB17259

description:
Library name: Sample1831
MARS_v2


title: AB17260

description:
Library name: Sample1832
MARS_v2


title: Patient 037, Tumor, RNAseq

description:
Library name: P037_Tumor
RNA-seq of resected patient tumor specimens


title: DRG culture, siKlf6, t=42h, rep1

description: Library name: siKlf6_1


title: AB17258

description:
Library name: Sample1830
MARS_v2


title: AB12109

description: Library name: Sample 103


title: AB17257

description:
Library name: Sample1829
MARS_v2


title: Patient 035, Tumor, RNAseq

description:
Library name: P035_Tumor
RNA-seq of resected patient tumor specimens


title: AB12108

description: Library name: Sample 102


title: DRG culture, siStat3, t=42h, rep3

description: Library name: siStat3_3


title: AB12107

description: Library name: Sample 101


title: AB17256

description:
Library name: Sample1828
MARS_v2


title: DRG culture, siStat3, t=42h, rep2

description: Library name: siStat3_2


title: Patient 032, Tumor, RNAseq

description:
Library name: P032_Tumor
RNA-seq of resected patient tumor specimens


title: DRG culture, siStat3, t=42h, rep1

description: Library name: siStat3_1


title: AB17254

description:
Library name: Sample1826
MARS_v2


title: Patient 031, Tumor, RNAseq

description:
Library name: P031_Tumor
RNA-seq of resected patient tumor specimens


title: AB12105

description: Library name: Sample 99


title: V(D)J library of CD34 positive rxn 4 replicate 1

city: La Jolla

first: Bryan

last: Briney

address: 10550 N Torrey Pines Rd

department: Immunology and Microbiology

institute: Scripps Research

description:
Library name: CD34_1_220524_BCR
10x Genomic HT, V(D)J

data_processing:
FASTQ files were generated from raw base call files using CellRanger, and downstream analyses were performed with scab (Hurtado et al. 2022). Matrices of VDJ contigs and counts were assembled by alignment to VDJ and transcriptome reference genomes, outputting full-length per cell VDJ sequences as FASTA files and expression profiles (cells x genes) as an .h5 file, differentiating individual cells by barcode. Antibody sequences were annotated using abstar (Briney and Burton 2018) and integrated with gene expression and cellhash data using scab. Donors were demultiplexed by cellhash using scab. Because samples had different read depths, cell hash thresholds were incorrectly high for some of the samples with fewer reads per cell. Reads were thus normalized to ensure equal representation from each donor. To further refine the expression matrix, cells with fewer than 200 and greater than 6000 genes were removed. Genes which appeared in fewer than 50 cells were also removed. Normalization, log plus one transformation, and scaling were performed using scab and scanpy. Scab’s dimensionality reduction tool performed principle component analysis, neighborhood graphing, and cell clustering according to the Leiden algorithm and utilized UMAP for embedding (Traag, Waltman, and van Eck 2019; Becht et al. 2018; McInnes, Healy, and Melville 2018). Doublets were identified using Scrublet (Wolock, Lopez, and Klein 2019) and all doublets, including entire clusters containing primarily doublets, were removed. Cells were then re-clustered without doublets and identified as lymphoid, myeloid, erythroid, plasma cells, T cells, or B cells according to gene expression profiles. B cells were then separated out, clustered again for granularity, and subset into developmental phases also according to gene expression profiles.
Assembly: gene expression assembly - refdata-gex-GRCh38-2020-A, for V(D)J assembly - refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, all_contig.fasta, all_contig_annotations.csv
Library strategy: CITE-seq

source_name: Bone marrow

extract_protocol:
Bone marrow samples from four healthy adult donors were obtained through our commercial clinical partner (ALLCELLS). Lymphocytes were isolated by density gradient centrifugation using Lymphoprep (StemCell Technologies). To ensure representation of early progenitors and developing B cell populations, donor samples were individually enriched for B cells and hematopoietic stem cells by EasySep Human B Cell Enrichment and Human CD34+ Selection Kits (StemCell Technologies).
Single-cell RNA sequencing (scRNAseq) was performed on over 3.8x105 cells from bone marrow and enriched samples with the 10x Genomics 5’ Single Cell Immune Profiling Kit (v2). Briefly, donor samples were individually labelled with Totalseq Anti-Human Hashtags (Biolegend) and pooled prior to overloading the 10x Genomic reaction, targeting 4-6x104 cells per run (Stoeckius et al. 2018). Single-cell emulsion generation, barcoding, V(D)J enrichment, and sequencing library construction were carried out according to theChromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) protocol (CG000330 Rev A). Final libraries were sequenced on a NovaSeq 6000 using a 26-10-10-90 read configuration, with minimum target sequencing depths of 5,000 reads per cell for Cell Surface Protein libraries, 10,000 reads per cell for V(D)J libraries, and 30,000 reads per cell for Gene expression libraries.

value: Bone marrow

value: Lymphocyte

tag: library type

value: mRNA


title: AB17253

description:
Library name: Sample1825
MARS_v2


title: Patient 030, Tumor, RNAseq

description:
Library name: P030_Tumor
RNA-seq of resected patient tumor specimens

value: nivolumab+ipilimumab trial

value: Male


title: AB12104

description: Library name: Sample 98

value: spinal cord


title: AB17252

description:
Library name: Sample1824
MARS_v2


title: DRG culture, siJun, t=42h, rep3

description: Library name: siJun_3

value: siJun


title: Patient 027, Tumor, RNAseq

description:
Library name: P027_Tumor
RNA-seq of resected patient tumor specimens

value: Non-Hispanic


title: AB12103

description: Library name: Sample 97

value: Untreated (PBS)

value: peptide MOG


title: DRG culture, siJun, t=42h, rep2

description: Library name: siJun_2

value: wildtype


title: AB17251

description:
Library name: Sample1823
MARS_v2

value: BM

value: PC


title: Patient 026, Tumor, RNAseq

description:
Library name: P026_Tumor
RNA-seq of resected patient tumor specimens

value: Tumor


title: AB12102

description: Library name: Sample 96


title: DRG culture, siJun, t=42h, rep1

description: Library name: siJun_1

value: primary adult dorsal root ganglia cell culture


title: Patient 024, Tumor, RNAseq

description:
Library name: P024_Tumor
RNA-seq of resected patient tumor specimens


title: AB17250

description:
Library name: Sample1822
MARS_v2


title: AB12101

description: Library name: Sample 95


title: AB17249

description:
Library name: Sample1821
MARS_v2


title: Patient 022, Tumor, RNAseq

description:
Library name: P022_Tumor
RNA-seq of resected patient tumor specimens


title: AB11921

description: Library name: Sample 94


title: DRG culture, siAtf3, t=42h, rep3

description: Library name: siAtf3_3


title: AB17248

description:
Library name: Sample1820
MARS_v2


title: Patient 021, Tumor, RNAseq

description:
Library name: P021_Tumor
RNA-seq of resected patient tumor specimens

value: Hispanic or Latino


title: AB11920

description: Library name: Sample 93


title: DRG culture, siAtf3, t=42h, rep2

description: Library name: siAtf3_2


title: AB17247

description:
Library name: Sample1819
MARS_v2


title: Patient 018, Tumor, RNAseq

description:
Library name: P018_Tumor
RNA-seq of resected patient tumor specimens


title: DRG culture, siAtf3, t=42h, rep1

description: Library name: siAtf3_1


title: AB11919

description: Library name: Sample 92


title: AB17246

description:
Library name: Sample1818
MARS_v2


title: Patient 017, Tumor, RNAseq

description:
Library name: P017_Tumor
RNA-seq of resected patient tumor specimens

value: Female


title: AB17245

description:
Library name: Sample1817
MARS_v2


title: Patient 016, Tumor, RNAseq

description:
Library name: P016_Tumor
RNA-seq of resected patient tumor specimens


title: DRG culture, siAtf4, t=42h, rep3

description: Library name: siAtf4_3


title: AB17244

description:
Library name: Sample1816
MARS_v2


title: DRG culture, siAtf3, t=42h, rep4

description: Library name: siAtf3_4


title: Patient 014, Tumor, RNAseq

description:
Library name: P014_Tumor
RNA-seq of resected patient tumor specimens


title: AB11916

description: Library name: Sample 89


title: DRG culture, siAtf4, t=42h, rep2

description: Library name: siAtf4_2


title: AB17243

description:
Library name: Sample1815
MARS_v2


title: Patient 013, Tumor, RNAseq

description:
Library name: P013_Tumor
RNA-seq of resected patient tumor specimens


title: AB11915

description: Library name: Sample 88


title: DRG culture, siAtf4, t=42h, rep1

description: Library name: siAtf4_1


title: AB17242

description:
Library name: Sample1814
MARS_v2


title: Patient 012, Tumor, RNAseq

description:
Library name: P012_Tumor
RNA-seq of resected patient tumor specimens


title: AB11918

description: Library name: Sample 91


title: AB11914

description: Library name: Sample 87


title: DRG culture, siCONTROL, t=42h, rep4

description: Library name: siCTL_4

value: siCONTROL


title: AB11917

description: Library name: Sample 90


title: AB17241

description:
Library name: Sample1813
MARS_v2


title: Patient 039, Tumor, RNAseq

description:
Library name: P039_Tumor
RNA-seq of resected patient tumor specimens


title: Patient 011, Tumor, RNAseq

description:
Library name: P011_Tumor
RNA-seq of resected patient tumor specimens


title: AB11090

description: Library name: Sample 86


title: DRG culture, siKlf6, t=42h, rep4

description: Library name: siKlf6_4


title: DRG culture, siCONTROL, t=42h, rep3

description: Library name: siCTL_3


title: AB12110

description: Library name: Sample 104


title: Patient 038, Tumor, RNAseq

description:
Library name: P038_Tumor
RNA-seq of resected patient tumor specimens


title: AB17240

description:
Library name: Sample1812
MARS_v2


title: Patient 036, Tumor, RNAseq

description:
Library name: P036_Tumor
RNA-seq of resected patient tumor specimens


title: AB11089

description: Library name: Sample 85


title: Patient 010, Tumor, RNAseq

description:
Library name: P010_Tumor
RNA-seq of resected patient tumor specimens


title: DRG culture, siCONTROL, t=42h, rep2

description: Library name: siCTL_2


title: AB17239

description:
Library name: Sample1811
MARS_v2


title: DRG culture, siStat3, t=42h, rep4

description: Library name: siStat3_4


title: Patient 009, Tumor, RNAseq

description:
Library name: P009_Tumor
RNA-seq of resected patient tumor specimens


title: AB11088

description: Library name: Sample 84


title: Patient 033, Tumor, RNAseq

description:
Library name: P033_Tumor
RNA-seq of resected patient tumor specimens


title: DRG culture, siCONTROL, t=42h, rep1

description: Library name: siCTL_1


title: AB17238

description:
Library name: Sample1810
MARS_v2


title: Patient 008, Tumor, RNAseq

description:
Library name: P008_Tumor
RNA-seq of resected patient tumor specimens


title: AB17255

description:
Library name: Sample1827
MARS_v2


title: Pool2B, CMO, with cells from samples ZW28, ZW29, ZW30, ZW31, ZW32, ZW33, ZW34, ZW35, ZW36

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description: Library name: Pool2B, CMO

data_processing:
Raw sequencing reads were aligned to a STAR index of mouse reference genome provided by 10X Genomics (mm10-2020-A) using Cell Ranger multi (10x Genomics, v7.0.1). Downstream analyses were performed in R (v4.4.1) using Seurat (v5.3.0).
Assembly: mm10
Supplementary files format and content: The filtered_feature_bc_matrix.h5 file is an HDF5 file generated with the following command: cellranger aggr --normalize="none" --csv=aggregation.csv. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). The aggregation.csv file used by the cellranger aggr command specifies the mapping between sample (animal) and the cell barcode suffix, e.g. cells with the _1 suffix are from the sample listed in the first row of the aggregation.csv file, those with suffix _2 are from the sample in the second row, etc.
Supplementary files format and content: The aggregation.csv file is a comma-separated text file with two columns: sample_id,molecule_h5 that was used to run the cellranger aggr command (see above)
Supplementary files format and content: The sample_metadata.csv file is a comma-separated text file with experimental metadata for each animal in this study.
Supplementary files format and content: The cell_metadata.csv file is a comma-separated text file with one row for each cell, mapping the experimental metadata to the cell barcodes.
Supplementary files format and content: The feature_reference.csv file is a comma-separated text file with the gene identifiers, gene symbols and feature_type for each quantified gene feature.
Supplementary files format and content: The cmo_sequences.csv file is a comma-separated text file mapping the sample- and pool-identifiers to the CMO tags and to the CMO sequences.

source_name: brain

growth_protocol: Generation of hNLRP3 WT and hNLRP3 D305N mice was described by Snouwaert, J. N. et al, Cell reports, 2016. mNlrp3 WT mice were littermates of hNLRP3 D305N mice, bred using hNLRP3 D305N heterozygotes. Mice were bred and maintained by The Jackson Laboratory and shipped to Denali Therapeutics no less than one week before initiating any experimental procedures. All mouse procedures adhered to regulations and protocols approved by Denali Therapeutics Institutional Animal Care and Use Committee (IACUC)

extract_protocol:
Single-cell suspensions were co-labeled with SyTox and CD45 for 30 min on ice. After washing, 0.5–1 × 10⁶ cells per sample were labeled with unique 10x Genomics Cell Multiplexing Oligos (CMO) per the manufacturer’s protocol, substituting PBS with NbActiv-1 + 1% BSA.
CMO-labeled cells from each sample were counted by hemocytometer. ~ 3,000 cells from each of nine animals were pooled at equal cell numbers, FACS-sorted for CD45⁺ immune cells, and loaded onto a Chromium Chip G following the Chromium NextGEMS Single Cell 3′ v3.1 Cell Multiplexing Rev B protocol (CG000388). Following reverse transcription, GEM cleanup, and cDNA amplification, products were separated into 3′ gene expression (GEX) and CMO fractions via dual-sided size selection. Five microliters of CMO cDNA were PCR-amplified to add Illumina indices, and one-quarter of the GEX cDNA was used for library preparation. GEX libraries were pooled equimolarly and quality-checked on an Illumina MiSeq to estimate cell recovery. Based on these results, GEX and CMO libraries were re-pooled and sequenced on an Illumina NovaSeq S2 (28 × 10 × 10 × 90 cycles) at SeqMatic (Fremont, CA), targeting 50,000 reads per cell for mRNA and 5,000 reads per cell for CMO demultiplexing.

treatment_protocol: For all tissue collection, animals are anesthetized via intraperitoneal injection of 2.5% avertin. Whole brains (excluding olfactory bulb and cerebellum) were dissociated using the Miltenyi Adult Mouse Brain Dissociation Kit with modifications. Enzyme Mix 1 was supplemented with anisomycin (2 μM), actinomycin D (5 μM), and hyaluronidase Type I-S (5,600 U/mL) to enhance extracellular matrix digestion and inhibit transcription and translation.

value: CMO

value: brain

tag: strain

value: primary microglia

value: Human NLRP3 WT

tag: sample id

tag: animal id

value: 12.43 weeks

tag: pool

tag: cmo

tag: cmo sequence

value: AACGTTAATCACTCA


title: Patient 007, Tumor, RNAseq

description:
Library name: P007_Tumor
RNA-seq of resected patient tumor specimens

tag: tissue

tag: treatment

value: nivolumab+ipilimumab trial

tag: arm

tag: Sex

value: Male

tag: ethnicity

value: Non-Hispanic


title: AB17237

description:
Library name: Sample1809
MARS_v2

tag: gate


title: AB11087

description: Library name: Sample 83

value: spinal cord

tag: mouse

tag: score

value: Untreated (PBS)

tag: eae model

value: peptide MOG


title: AB11086

description: Library name: Sample 82

tag: batch


title: Hydra vulgaris (AEP), siLb1, rep3

city: Innsbruck

first: Birgit

last: Lengerer

address: Technikerstr. 25

country: Austria

institute: University of Innsbruck

description: Library name: siLb1_rep3

data_processing:
Sequencing reads were aligned to the Hydra vulgaris AEP (PMID: 36639202) reference genome using the Minimap2 aligner (version 2.28).
The BAM files were aligned using the Hydra AEP Genome Project Portal assembly provided by the NHGRI Hydra portal (https://research.nhgri.nih.gov/HydraAEP/). This corresponds directly to the NCBI assembly accession GCA_024232925.2.
Read counting and differential gene expression analysis was performed with the Rsubread (version 2.22.1) and edgeR (version 4.6.3) packages in R (version 4.5.0).
Assembly: Hydra vulgaris AEP (PMID: 36639202); GCA_024232925.2
Supplementary files format and content: counts.txt: tab delimited count matrix file with gene identifier in first column.
Supplementary files format and content: The sequence identifiers present in our processed data (e.g., HVAEP1.G000001) are the official gene model identifiers derived from the GFF3 annotation provided by the NHGRI group for the Hydra AEP Genome Project. These identifiers are fully traceable and searchable in a public database. They can be queried directly via the official NHGRI Hydra AEP Gene Wiki search engine at:
Supplementary files format and content: https://research.nhgri.nih.gov/HydraAEP/genewiki/

organism: Hydra vulgaris

source_name: Whole animal

growth_protocol: Hydra vulgaris (AEP) grown asexually at 18°C in Hydra medium and fed with Artemia nauplii.

extract_protocol:
RNA was isolated with Monarch® Total Miniprep Kit (New England BioLabs) according to manufacturers protocoll
Library preparation, sequencing and gene expression analysis were performed at the company XPseq Analytics GmbH (Austria) using their ExpressoSeq rapid 3' RNA-Seq service

treatment_protocol: Budless Hydra vulgaris (AEP) were electroporated with a square pulse of 250 V and 25 ms in a Gene Pulser X cellTM (Biorad). Immediately after electroporation precooled recovery medium was added and the polyps were gently transferred to a Petri dish prefilled with cooled recovery medium. After 24 hours the polyps were transferred from recovery medium to Hydra medium. Electroporation was performed on 0, 2, and 4 days past electroporation (dpe).  Animals were fed four times (7, 8, 9 and 14 dpe). Basal discs were amputated at 10dpe and animals allowed to regenerate. RNA was isolated at 15dpe.

value: Whole animal

tag: genotype

value: AEP

value: siRNA against Lb1


title: liver, normoxia, 4 h, rep1

city: heze

first: guosong

last: zhang

state: shandong

address: No. 1, University Road, Heze City

country: China

institute: Heze University

description: Library name: B1

library_source: other

data_processing:
Raw miRNA sequencing reads were processed by the in-house program ACGT101-miR (v4.2) to remove adapter dimers, junk sequences, low-complexity sequences, and common non-coding RNA sequences (rRNA, tRNA, snRNA, snoRNA) and repeat sequences.
Unique sequences with a length of 18~26 nucleotides were screened, and BLAST search was performed against miRBase 22.1 species precursor database to identify known miRNAs and novel 3p/5p-derived miRNAs, allowing 3’/5’ end length variation and one internal sequence mismatch.
Unmapped unique sequences were aligned with Pelteobagrus vachellii reference genome, and RNAfold software was used to predict hairpin secondary structures of flank 80nt sequences to screen novel miRNA candidates based on standardized secondary structure prediction criteria.
miRNA expression levels were normalized based on deep-sequencing counts, and Student’s t-test was used to screen differentially expressed miRNAs (DEMIs) with the significance threshold set as P < 0.05.
Integrated analysis of differentially expressed miRNAs and liver tissue differentially expressed mRNAs was performed, miRNA target genes were predicted, and miRNA-mRNA negative regulatory network with opposite expression patterns was constructed, followed by KEGG pathway enrichment analysis (P < 0.05).
Assembly: Pelteobagrus vachellii reference genome (GCF_030014155.1) from NCBI datasets
Supplementary files format and content: Processed data (liver miRNA).xlsx: Normalized expression counts of known and novel miRNAs in Norm-EVs and Hypo-EVs samples

molecule: other

organism: Tachysurus vachellii

source_name: liver

growth_protocol: Healthy Pelteobagrus vachellii with uniform specifications (body length 11.5 ± 1.5 cm, body weight 15 ± 0.94 g) were purchased from Sichuan Rongsen Fishery Co., Ltd. All experimental fish were acclimated for two weeks under conventional breeding conditions and fasted for 48 h before hypoxic stress treatment to eliminate the influence of food metabolism on experimental results.

extract_protocol:
Total small RNA was extracted and purified from 6 groups of Norm-EVs and Hypo-EVs samples using the Norgen 58000 kit (Norgen biotech, CA). The RNA concentration was quantified by Qubit (Invitrogen, USA), and RNA integrity was assessed via Agilent 5400 (Agilent, USA) to ensure qualified RNA samples for library construction and sequencing.
1. RNA and 3’ adapter were denatured at 70°C for 2 min, then ligated overnight at 16°C using T4 RNA Ligase 2 (NEB, M0351L, USA), followed by purification. 2. Single-stranded DNA 3’ adapters were neutralized and removed by RTP reagent incubation at 37°C for 30 min. 3. RNA 5’ adapter was ligated with the product using T4 RNA Ligase 1 (NEB, M0204L, USA) at 37°C for 1 h, then purified. 4. Reverse transcription was performed with SuperScript™ II Reverse Transcriptase (Thermo, 18064014, USA) at 50°C for 1 h, followed by 80°C for 10 min termination. 5. Second-strand synthesis and PCR amplification were carried out using Phusion® High-Fidelity DNA Polymerase (NEB, M0530L, USA) with specific indexes. 6. The miRNA library was purified and enriched via PAGE electrophoresis, and finally sequenced on NovaSeq X Plus platform with PE150 strategy, and reads were truncated to single-end 50 bp for subsequent analysis.

treatment_protocol: The dissolved oxygen (DO) of aquaculture water was reduced from 6.8 mg/L to 1.0±0.1 mg/L by sealing the water body and bubbling pure nitrogen to establish a stable hypoxic stress environment. Experimental fish were subjected to continuous hypoxic treatment, and hepatic tissues were collected at different hypoxia and reoxygenation time points. Hepatic tissue-derived extracellular vesicles (EVs) were isolated from normoxic (Norm-EVs) and hypoxic-treated (Hypo-EVs) fish liver tissues for subsequent small RNA sequencing.

value: liver

value: normoxia, 4 h


title: Pool1B, CMO, with cells from samples ZW19, ZW20, ZW21, ZW22, ZW23, ZW24, ZW25, ZW26, ZW27

description: Library name: Pool1B, CMO

tag: library type

value: CMO

tag: strain

tag: cell type

value: Mouse Nlrp3 WT

value: Female

tag: age

value: 15.29 weeks

value: ATGAGGAATTCCTGC


title: AB17236

description:
Library name: Sample1808
MARS_v2

value: BM

value: PC


title: AB11085

description: Library name: Sample 81


title: Patient 005, Tumor, RNAseq

description:
Library name: P005_Tumor
RNA-seq of resected patient tumor specimens

value: Tumor

value: nivolumab+ipilimumab trial

value: Male

tag: os


title: Pool2B, GEX, with cells from samples ZW28, ZW29, ZW30, ZW31, ZW32, ZW33, ZW34, ZW35, ZW36

description: Library name: Pool2B, GEX

value: mRNA

value: brain

value: primary microglia

value: Human NLRP3 WT

tag: sample id

tag: animal id

value: 12.43 weeks

tag: pool

tag: cmo

tag: cmo sequence

value: AACGTTAATCACTCA


title: Patient 006, Tumor, RNAseq

description:
Library name: P006_Tumor
RNA-seq of resected patient tumor specimens

tag: tissue

tag: treatment

tag: arm

tag: Sex

tag: ethnicity

value: Non-Hispanic


title: AB11084

description: Library name: Sample 80

value: spinal cord

tag: gate

tag: mouse

tag: score

value: Untreated (PBS)

tag: eae model

value: peptide MOG

tag: batch


title: Patient 004, Tumor, RNAseq

description:
Library name: P004_Tumor
RNA-seq of resected patient tumor specimens

value: Female

tag: age


title: AB17234

description:
Library name: Sample1806
MARS_v2


title: AB11083

description: Library name: Sample 79


title: Pool2A, CMO, with cells from samples ZW28, ZW29, ZW30, ZW31, ZW32, ZW33, ZW34, ZW35, ZW36

description: Library name: Pool2A, CMO

tag: library type

value: CMO

tag: strain

tag: cell type

tag: genotype


title: AB11082

description: Library name: Sample 78


title: AB17232

description:
Library name: Sample1804
MARS_v2

value: BM


title: Patient 002, Tumor, RNAseq

description:
Library name: P002_Tumor
RNA-seq of resected patient tumor specimens

tag: os


title: AB11081

description: Library name: Sample 77


title: Pool2A, GEX, with cells from samples ZW28, ZW29, ZW30, ZW31, ZW32, ZW33, ZW34, ZW35, ZW36

description: Library name: Pool2A, GEX

tag: sample id

tag: animal id

tag: pool

tag: cmo

tag: cmo sequence


title: AB17231

description:
Library name: Sample1803
MARS_v2

tag: tissue

value: PC


title: Patient 001, Tumor, RNAseq

description:
Library name: P001_Tumor
RNA-seq of resected patient tumor specimens

value: Tumor

tag: treatment

tag: arm

tag: Sex

tag: ethnicity


title: AB11080

description: Library name: Sample 76

tag: gate

tag: mouse

tag: score

tag: eae model

tag: batch


title: Pool1A, GEX, with cells from samples ZW19, ZW20, ZW21, ZW22, ZW23, ZW24, ZW25, ZW26, ZW27

description: Library name: Pool1A, GEX

tag: library type

tag: strain

tag: cell type

tag: genotype

value: Mouse Nlrp3 WT

tag: age

value: 15.29 weeks

value: ATGAGGAATTCCTGC


title: AB17230

description:
Library name: Sample1802
MARS_v2


title: ob/ob mice treated with 100 mg/kg VE_WAT_rep3

type: RNA

city: TSUKUBA

first: ELDA NURAFNIE

last: IBNU RASID

state: IBARAKI

address: 1-1-1 TENNODAI

country: Japan

institute: UNIVERSITY OF TSUKUBA

description:
100 mg/kg 3
1003 Avg (log2)

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S Array, Mouse; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome Analysis Console (TAC) software. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, TAC software (CEL files) filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space).
Signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4).

label: biotin

source_name: Gene expression data of ob/ob mice that were treated with 100 mg/kg VE for 42 days

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/uL total RNA.

growth_protocol: C57BL/6JHamSlc-+ /+ (non-obese) and C57BL/6JHamSlc-ob/ob (obese) were used in this study. Six-week-old male C57BL/6JHamSlc-+ /+ and C57BL/6JHamSlc-ob/ob (Japan SLC, Inc., Shizuoka, Japan) were maintained at room temperature in a 12 h light/dark cycle. After one week of acclimatization with standard chow diet and tap water ad libitum, on initiation day of the study (D0), all animals were randomly assigned into respective groups.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: Briefly, ob/ob group mice were given vehicle, and treatment groups were given VE by oral gavage for 6 weeks. Body weight (BW) and food intake were measured on a daily and weekly basis, respectively. From the initiation of the study (D0-D42), all groups were fed with standard chow diet and tap water ad libitum. At the termination of the experiment, blood was collected by cardiac puncture after the mice were anesthetized with isoflurane inhalation.

value: ob/ob mice

value: WAT

value: 100 mg/kg VE for 42 days


title: AB22023

description: Library name: Sample 302

source_name: CSF

value: CSF

value: rhMOG


title: AB17228

description:
Library name: Sample1801
MARS_v2


title: AB11079

description: Library name: Sample 75


title: AB22022

description: Library name: Sample 301


title: ob/ob mice treated with 100 mg/kg VE_WAT_rep2

description:
100 mg/kg 2
1002 Avg (log2)


title: AB11078

description: Library name: Sample 74


title: AB17227

description:
Library name: Sample1800
MARS_v2


title: AB11077

description: Library name: Sample 73


title: ob/ob mice treated with 100 mg/kg VE_WAT_rep1

description:
100 mg/kg 1
1001 Avg (log2)


title: AB17226

description:
Library name: Sample1799
MARS_v2


title: AB17225

description:
Library name: Sample1798
MARS_v2


title: C57BL/6JHamSlc-+/+  mice given vehicle_WAT_rep3

description:
Wild Type 3
WT3 Avg (log2)

source_name: Gene expression data wild-type  mice given vehicle for 42 days

value: wild-type mice

value: vehicle for 42 days


title: AB11075

description: Library name: Sample 71

value: spinal cord

value: Untreated (PBS)


title: AB22018

description: Library name: Sample 298

source_name: spleen

value: spleen


title: AB17224

description:
Library name: Sample1797
MARS_v2


title: AB22017

description: Library name: Sample 297


title: AB11074

description: Library name: Sample 70

value: peptide MOG


title: C57BL/6JHamSlc-+/+  mice given vehicle_WAT_rep1

description:
Wild Type 1
WT1 Avg (log2)


title: AB11073

description: Library name: Sample 69


title: ob/ob mice given vehicle_WAT_rep3

description:
Control 3
OB3 Avg (log2)

source_name: Gene expression data from ob/ob mice that were given vehicle for 42 days


title: AB22016

description: Library name: Sample 296

value: aPD-1 CAR + IL-10


title: AB17221

description:
Library name: Sample1795
MARS_v2

value: BM

value: PC


title: ob/ob mice given vehicle_WAT_rep2

description:
Control 2
OB2 Avg (log2)


title: AB11072

description: Library name: Sample 68


title: AB22015

description: Library name: Sample 295

value: aPD-1 CAR


title: AB17220

description:
Library name: Sample1794
MARS_v2


title: AB11071

description: Library name: Sample 67


title: ob/ob mice given vehicle_WAT_rep1

description:
Control 1
OB1 Avg (log2)


title: AB22014

description: Library name: Sample 294


title: AB17219

description:
Library name: Sample1793
MARS_v2


title: AB11070

description: Library name: Sample 66


title: AB22013

description: Library name: Sample 293


title: AB17218

description:
Library name: Sample1792
MARS_v2


title: ob/ob mice treated with 100 mg/kg VE_liver_rep2

description:
Gene expression data of ob/ob mice that were treated with 100 mg/kg VE for 42 days
100 mg/kg 2
1002(log2)

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome Analysis Console software (sheet 2). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files) filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space).
Signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4).

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/uL total RNA

value: liver


title: AB11076

description: Library name: Sample 72


title: AB22012

description: Library name: Sample 292


title: AB11069

description: Library name: Sample 65


title: AB17217

description:
Library name: Sample1791
MARS_v2


title: AB11068

description: Library name: Sample 64


title: ob/ob mice treated with 100 mg/kg VE_liver_rep1

description:
Gene expression data of ob/ob mice that were treated with 100 mg/kg VE for 42 days
100 mg/kg 1
1001 (log2)


title: AB22011

description: Library name: Sample 291


title: AB17216

description:
Library name: Sample1790
MARS_v2


title: C57BL/6JHamSlc-+/+  mice given vehicle_liver_rep3

description:
Gene expression data wild-type  mice given vehicle for 42 days
Wild Type 3
WT3 Avg (log2)


title: AB11067

description: Library name: Sample 63


title: AB22010

description: Library name: Sample 290


title: AB17215

description:
Library name: Sample1789
MARS_v2


title: C57BL/6JHamSlc-+/+  mice given vehicle_liver_rep2

description:
Gene expression data wild-type  mice given vehicle for 42 days
Wild Type 2
WT2 Avg (log2)


title: AB10568

description: Library name: Sample 62


title: AB22009

description: Library name: Sample 289


title: AB17213

description:
Library name: Sample1788
MARS_v2


title: AB22008

description: Library name: Sample 288


title: AB10567

description: Library name: Sample 61


title: C57BL/6JHamSlc-+/+  mice given vehicle_liver_rep1

description:
Gene expression data wild-type  mice given vehicle for 42 days
Wild Type 1
WT1 Avg (log2)


title: ob/ob mice treated with 100 mg/kg VE_liver_rep3

description:
Gene expression data of ob/ob mice that were treated with 100 mg/kg VE for 42 days
100 mg/kg 3
1003 (log2)


title: AB17212

description:
Library name: Sample1787
MARS_v2


title: AB22007

description: Library name: Sample 287


title: AB10566

description: Library name: Sample 60


title: AB17210

description:
Library name: Sample1786
MARS_v2


title: ob/ob mice given vehicle_liver_rep3

description:
Gene expression data from ob/ob mice that were given vehicle for 42 days
Control 3
OB3 Avg (log2)


title: AB10565

description: Library name: Sample 59


title: ob/ob mice given vehicle_liver_rep2

description:
Gene expression data from ob/ob mice that were given vehicle for 42 days
Control 2
OB2 Avg (log2)


title: AB22006

description: Library name: Sample 286


title: AB17209

description:
Library name: Sample1785
MARS_v2


title: ob/ob mice given vehicle_liver_rep1

description:
Gene expression data from ob/ob mice that were given vehicle for 42 days
Control 1
OB1 Avg (log2)


title: AB22005

description: Library name: Sample 285


title: AB10564

description: Library name: Sample 58


title: AB17207

description:
Library name: Sample1784
MARS_v2


title: AB17235

description:
Library name: Sample1807
MARS_v2


title: AB10560

description: Library name: Sample 57


title: Pool1B, GEX, with cells from samples ZW19, ZW20, ZW21, ZW22, ZW23, ZW24, ZW25, ZW26, ZW27

description: Library name: Pool1B, GEX

value: mRNA

value: brain

value: primary microglia

value: Mouse Nlrp3 WT

tag: sample id

tag: animal id

value: Female

value: 15.29 weeks

tag: pool

tag: cmo

value: ATGAGGAATTCCTGC


title: Patient 003, Tumor, RNAseq

description:
Library name: P003_Tumor
RNA-seq of resected patient tumor specimens

tag: tissue

value: Tumor

tag: treatment

value: nivolumab+ipilimumab trial

tag: arm

value: Male

value: Non-Hispanic

tag: os


title: AB17233

description:
Library name: Sample1805
MARS_v2

tag: gate


title: ob/ob mice treated with 100 mg/kg VE_brain_rep3

description:
100 mg/kg 3
1003 Avg (log2)

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Human; ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4).

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

treatment_protocol: Briefly, wild type and ob/ob group mice were given vehicle, and treatment groups were given VE at 100mg/kg BW by oral gavage for 6 weeks. Body weight (BW) and food intake were measured on a daily and weekly basis, respectively. From the initiation of the study (D0-D42), all groups were fed with standard chow diet and tap water ad libitum. At the termination of the experiment, blood was collected by cardiac puncture after the mice were anesthetized with isoflurane inhalation.

value: ob/ob mice

value: 100 mg/kg VE for 42 days


title: AB17206

description:
Library name: Sample1783
MARS_v2

value: BM


title: AB22004

description: Library name: Sample 284

tag: mouse

tag: score

value: Untreated (PBS)

value: rhMOG


title: Pool1A, CMO, with cells from samples ZW19, ZW20, ZW21, ZW22, ZW23, ZW24, ZW25, ZW26, ZW27

description: Library name: Pool1A, CMO

value: CMO

tag: Sex

tag: cmo sequence


title: AB10559

description: Library name: Sample 56

value: spinal cord

tag: eae model

value: peptide MOG

tag: batch


title: ob/ob mice treated with 100 mg/kg VE_brain_rep2

description:
100 mg/kg 2
1002 (log2)

tag: genotype

value: brain


title: AB17205

description:
Library name: Sample1782
MARS_v2


title: AB22003

description: Library name: Sample 283


title: AB17204

description:
Library name: Sample1781
MARS_v2

value: PC


title: AB22002

description: Library name: Sample 282


title: AB10558

description: Library name: Sample 55


title: AB10557

description: Library name: Sample 54


title: ob/ob mice treated with 100 mg/kg VE_brain_rep1

description:
100 mg/kg 1
1001 Avg (log2)


title: C57BL/6JHamSlc-+/+  mice given vehicle_brain_rep3

description:
Wild Type 3
WT3 Avg (log2)

value: wild-type mice

value: vehicle for 42 days


title: AB22001

description: Library name: Sample 281

value: aPD-1 CAR + IL-10


title: AB17203

description:
Library name: Sample1780
MARS_v2


title: AB10553

description: Library name: Sample 53

value: healthy

value: Untreated naïve control


title: AB22000

description: Library name: Sample 280


title: AB17202

description:
Library name: Sample1779
MARS_v2


title: AB10550

description: Library name: Sample 52


title: C57BL/6JHamSlc-+/+  mice given vehicle_brain_rep2

description:
Wild Type 2
WT2 Avg (log2)


title: AB21999

description: Library name: Sample 279


title: C57BL/6JHamSlc-+/+  mice given vehicle_brain_rep1

description:
Wild Type 1
WT1 Avg (log2)


title: AB17201

description:
Library name: Sample1778
MARS_v2


title: AB21998

description: Library name: Sample 278


title: AB22021

description: Library name: Sample 300

value: CSF


title: AB10447

description: Library name: Sample 51


title: ob/ob mice given vehicle_brain_rep3

description:
Control 3
OB3 Avg (log2)


title: AB22020

description: Library name: Sample 299


title: AB17199

description:
Library name: Sample1777
MARS_v2


title: C57BL/6JHamSlc-+/+  mice given vehicle_WAT_rep2

description:
Wild Type 2
WT2 Avg (log2)

value: WAT


title: AB10446

description: Library name: Sample 50


title: AB21997

description: Library name: Sample 277


title: AB17198

description:
Library name: Sample1776
MARS_v2


title: ob/ob mice given vehicle_brain_rep2

description:
Control 2
OB2 Avg (log2)

value: ob/ob mice


title: AB10445

description: Library name: Sample 49


title: AB21996

description: Library name: Sample 276


title: ChIPseq NHEM Promocell_n2 (H3K27ac ChIP)

city: Deggendorf

first: Melanie

last: Kappelmann-Fenzl

address: Dieter-Görlitz Platz 1

department: Applied Computer Science

country: Germany

institute: Deggendorf Institute of Technology

description: Library name: NHEM_Promocell_P3_n2, H3K27ac ChIP

library_source: genomic

data_processing:
Single-end ChIP-seq reads were aligned to the human reference genome (hg38, v44) using bowtie2 (v2.5.1; SCR_016368) and reads with a mapping quality lower than 10 were removed using samtools view.
SAM files were converted into BAM files with samtools and reads aligning to highly repetitive regions according to the ENCODE blacklist (hg38-blacklist.v2) were excluded with bedtools intersect (v2.30.0; SCR_006646).
Replicate correlation between  ChIP-seq samples was analyzed using deepTools functions multiBigwigSummary and plotCorrelation. 1x normalized (RPGC) bigWig tracks were created utilizing deepTools bamCoverage (v3.5.3).
ChIP-seq peaks were called using HOMER’s (v4.10) getDifferentialPeaksReplicates.pl program, including all biological replicates per cell line. Overlapping peaks were identified with HOMER’s mergePeaks program.
Assembly: hg38
Supplementary files format and content: bigwig, per-base numerical data  mapped to genomic coordinates
Supplementary files format and content: bed, called peaks via Homer (v4.10)

molecule: genomic DNA

source_name: juvenil foreskin

growth_protocol: Human melanoma cell lines Sbcl-2 (CVCL_D732), WM3211 (CVCL_6797), WM1366 (CVCL_6789), and WM1158  (CVCL_6785) (a generous gift from Dr. M. Herlyn, Wistar Institute, Philadelphia, USA) were maintained in a culture medium consisting of MCDB153 (Sigma-Aldrich, Steinheim, Germany) with 20% Leibovitz’s L-15 (PAA Laboratories, Coelbe, Germany), 2% FCS, 1.68 mM CaCl2 (Sigma), and 5 µg/ml insulin (Sigma-Aldrich) at 37 °C and 5% CO2. NHEMs were derived from neonatal foreskin (NHEMs, PromoCell, Heidelberg, Germany, or Thermo Fisher Scientific, Waltham, USA) and were cultured in melanocyte growth media as defined by the supplier at 37 °C and 5% CO2.

extract_protocol:
ChIP was performed with the melanoma cell lines and the normal human epidermal melanocytes (NHEM) that had not exceeded six passages. Chromatin  was crosslinked in 1/10th volume of fixation buffer (50 mM HEPES/KOH, pH 7.9, 11% formaldehyde). After quenching with glycine and lysis the chromatin was sheared to an average DNA fragment size of ~400–600 bp using a Covaris ME220.
ChIP-seq libraries were generated using the TruSeq ChIP Library Preparation Kit (IP-202-1012, Illumina Inc., San Diego, CA, USA) following the recommended workflow. Library quality and fragment size distribution were assessed using a 4200 Tape Station (Agilent Technologies), and concentrations were determined by Qubit fluorometric quantification. Prepared libraries were sequenced on an Illumina NextSeq2000 using a P4 Flow-cell with 72 bp single-end reads.

treatment_protocol: no treatment

value: juvenil foreskin

tag: cell line

value: NHEM

tag: cell type

value: normal


title: AB10444

description: Library name: Sample 48

value: Untreated (PBS)


title: AB17197

description:
Library name: Sample1775
MARS_v2

value: BM


title: AB21995

description: Library name: Sample 275

value: rhMOG


title: AB17195

description:
Library name: Sample1774
MARS_v2


title: ob/ob mice given vehicle_brain_rep1

description:
Control 1
OB1 Avg (log2)


title: ChIPseq NHEM Promocell_n2 (PolII ChIP)

description: Library name: NHEM_Promocell_P3_n2_PolII


title: DRG culture, siAtf4, t=42h, rep4

description: Library name: siAtf4_4

value: primary adult dorsal root ganglia cell culture

value: wildtype


title: AB21994

description: Library name: Sample 274

value: brain


title: AB17222

description:
Library name: Sample1796
MARS_v2

value: PC


title: AB10443

description: Library name: Sample 47

value: spinal cord

value: peptide MOG


title: AB17194

description:
Library name: Sample1773
MARS_v2


title: ChIPseq NHEM Promocell_n2 (Input)

description: Library name: NHEM_Promocell_P3_n2, Input


title: AB10439

description: Library name: Sample 46


title: AB21993

description: Library name: Sample 273

value: aPD-1 CAR


title: AB10438

description: Library name: Sample 45


title: ChIPseq NHEM Promocell_n1 (H3K27ac ChIP)

description: Library name: NHEM_Promocell_P3_n1, H3K27ac ChIP


title: AB17193

description:
Library name: Sample1772
MARS_v2


title: AB17190

description:
Library name: Sample1771
MARS_v2


title: AB21992

description: Library name: Sample 272

value: CD45.1+ mCherry+


title: ChIPseq NHEM Promocell_n1 (PolII ChIP)

description: Library name: NHEM_Promocell_P3_n1, PolII ChIP


title: AB10437

description: Library name: Sample 44


title: AB17188

description:
Library name: Sample1770
MARS_v2


title: AB21991

description: Library name: Sample 271


title: ChIPseq NHEM Promocell_n1 (Input)

description: Library name: NHEM_Promocell_P3_n1, Input


title: AB10435

description: Library name: Sample 43


title: AB21990

description: Library name: Sample 270


title: AB17187

description:
Library name: Sample1769
MARS_v2


title: ChIPseq NHEM Thermo_n2 (H3K27ac ChIP)

description: Library name: NHEM_Thermo_P7_n2, H3K27ac ChIP


title: AB21989

description: Library name: Sample 269


title: AB10434

description: Library name: Sample 42


title: ChIPseq NHEM Thermo_n2 (PolII ChIP)

description: Library name: NHEM_Thermo_P7_n2, PolII ChIP


title: AB17186

description:
Library name: Sample1768
MARS_v2


title: AB10428

description: Library name: Sample 41

value: healthy

value: Untreated naïve control


title: AB21988

description: Library name: Sample 268


title: AB17185

description:
Library name: Sample1767
MARS_v2


title: AB10427

description: Library name: Sample 40


title: ChIPseq NHEM Thermo_n2 (Input)

description: Library name: NHEM_Thermo_P7_n2, Input


title: AB17184

description:
Library name: Sample1766
MARS_v2


title: AB21987

description: Library name: Sample 267


title: ChIPseq NHEM Thermo_n1 (H3K27ac ChIP)

description: Library name: NHEM_Thermo_P7_n1, H3K27ac ChIP


title: AB10423

description: Library name: Sample 39


title: AB17183

description:
Library name: Sample1765
MARS_v2


title: AB21986

description: Library name: Sample 266


title: ChIPseq NHEM Thermo_n1 (PolII ChIP)

description: Library name: NHEM_Thermo_P7_n1, PolII ChIP


title: AB10422

description: Library name: Sample 38


title: AB21985

description: Library name: Sample 265


title: ChIPseq NHEM Thermo_n1 (Input)

description: Library name: NHEM_Thermo_P7_n1, Input


title: AB21984

description: Library name: Sample 264


title: AB17182

description:
Library name: Sample1764
MARS_v2


title: AB10421

description: Library name: Sample 37


title: AB17181

description:
Library name: Sample1763
MARS_v2


title: ChIPseq human melanoma WM1158_n2 H3K27ac ChIP)

description: Library name: WM1158_n2, H3K27ac ChIP

source_name: melanoma cell line derived from metastatic site: Lymph node

value: melanoma cell line derived from metastatic site:Lymph node

value: metastasis


title: AB10420

description: Library name: Sample 36


title: AB17180

description:
Library name: Sample1762
MARS_v2


title: AB10418

description: Library name: Sample 35


title: AB21983

description: Library name: Sample 263


title: AB21982

description: Library name: Sample 262


title: ChIPseq human melanoma WM1158_n2 (PolII ChIP)

description: Library name: WM1158_n2, PolII ChIP


title: ChIPseq human melanoma WM1158_n2 (Input)

description: Library name: WM1158_n2, Input


title: AB17179

description:
Library name: Sample1761
MARS_v2


title: AB21981

description: Library name: Sample 261


title: AB10417

description: Library name: Sample 34


title: AB17178

description:
Library name: Sample1760
MARS_v2


title: ChIPseq human melanoma WM1158_n1 H3K27ac ChIP)

description: Library name: WM1158_n1, H3K27ac ChIP


title: AB10416

description: Library name: Sample 33


title: AB17177

description:
Library name: Sample1759
MARS_v2


title: AB21980

description: Library name: Sample 260


title: AB10415

description: Library name: Sample 32


title: ChIPseq human melanoma WM1158_n1 (PolII ChIP)

description: Library name: WM1158_n1, PolII ChIP


title: AB21979

description: Library name: Sample 259


title: AB17176

description:
Library name: Sample1758
MARS_v2


title: ChIPseq human melanoma WM1158_n1 (Input)

description: Library name: WM1158_n1, Input


title: AB10414

description: Library name: Sample 31


title: AB17175

description:
Library name: Sample1757
MARS_v2


title: ChIPseq human melanoma WM1366_n2 H3K27ac ChIP)

description: Library name: WM1366_n2, H3K27ac ChIP

source_name: melanoma cell line derived from primary cunaneous melanoma

value: primary tumor (VGP)


title: AB21978

description: Library name: Sample 258


title: AB10411

description: Library name: Sample 30


title: AB21977

description: Library name: Sample 257


title: ChIPseq human melanoma WM1366_n2 (PolII ChIP)

description: Library name: WM1366_n2, PolII ChIP

value: melanoma cell line derived from primary cunaneous melanoma


title: AB17174

description:
Library name: Sample1756
MARS_v2


title: AB21976

description: Library name: Sample 256

value: Untreated (PBS)


title: AB17173

description:
Library name: Sample1755
MARS_v2

value: BM


title: AB10409

description: Library name: Sample 29


title: ChIPseq human melanoma WM1366_n2 (Input)

description: Library name: WM1366_n2, Input


title: AB9181

description: Library name: Sample 28


title: AB21975

description: Library name: Sample 255

value: rhMOG


title: ChIPseq human melanoma WM1366_n1 H3K27ac ChIP)

description: Library name: WM1366_n1, H3K27ac ChIP


title: AB9180

description: Library name: Sample 27


title: AB21974

description: Library name: Sample 254


title: ChIPseq human melanoma WM1366_n1 (PolII ChIP)

description: Library name: WM1366_n1, PolII ChIP


title: AB17171

description:
Library name: Sample1753
MARS_v2


title: AB17172

description:
Library name: Sample1754
MARS_v2


title: AB9179

description: Library name: Sample 26


title: AB17170

description:
Library name: Sample1752
MARS_v2


title: ChIPseq human melanoma WM1366_n1 (Input)

description: Library name: WM1366_n1, Input


title: AB21973

description: Library name: Sample 253


title: AB9178

description: Library name: Sample 25


title: AB21972

description: Library name: Sample 252

value: aPD-1 CAR + IL-10


title: AB17169

description:
Library name: Sample1751
MARS_v2


title: AB9177

description: Library name: Sample 24


title: AB21971

description: Library name: Sample 251


title: ChIPseq human melanoma WM3211_n2 (H3K27ac ChIP)

description: Library name: WM3211_n2, H3K27ac ChIP


title: AB17168

description:
Library name: Sample1750
MARS_v2


title: ChIPseq human melanoma WM3211_n2 (PolII ChIP)

description: Library name: WM3211_n2, PolII ChIP


title: AB9176

description: Library name: Sample 23


title: ChIPseq human melanoma WM3211_n2 (Input)

description: Library name: WM3211_n2, Input


title: AB17167

description:
Library name: Sample1749
MARS_v2


title: AB21970

description: Library name: Sample 250


title: AB21969

description: Library name: Sample 249


title: AB9175

description: Library name: Sample 22


title: AB17166

description:
Library name: Sample1748
MARS_v2


title: ChIPseq human melanoma WM3211_n1 (H3K27ac ChIP)

description: Library name: WM3211_n1, H3K27ac ChIP


title: AB21968

description: Library name: Sample 248


title: AB9171

description: Library name: Sample 21


title: ChIPseq human melanoma WM3211_n1 (PolII ChIP)

description: Library name: WM3211_n1, PolII ChIP


title: AB9170

description: Library name: Sample 20


title: AB21967

description: Library name: Sample 247


title: AB17165

description:
Library name: Sample1747
MARS_v2


title: ChIPseq human melanoma WM3211_n1 (Input)

description: Library name: WM3211_n1, Input


title: AB17164

description:
Library name: Sample1746
MARS_v2


title: AB9168

description: Library name: Sample 19


title: AB21966

description: Library name: Sample 246


title: AB17163

description:
Library name: Sample1745
MARS_v2


title: ChIPseq human melanoma Sbcl2_n2 (H3K27ac ChIP)

description: Library name: Sbcl2_n2, H3K27ac ChIP

value: primary tumor (RGP)


title: AB21965

description: Library name: Sample 245


title: AB9167

description: Library name: Sample 18


title: ChIPseq human melanoma Sbcl2_n2 (PolII ChIP)

description: Library name: Sbcl2_n2, PolII ChIP


title: AB9094

description: Library name: Sample 17


title: AB17162

description:
Library name: Sample1744
MARS_v2


title: AB21964

description: Library name: Sample 244


title: AB17161

description:
Library name: Sample1743
MARS_v2


title: ChIPseq human melanoma Sbcl2_n2 (Input)

description: Library name: Sbcl2_n2, Input


title: AB9093

description: Library name: Sample 16


title: AB21963

description: Library name: Sample 243


title: AB17160

description:
Library name: Sample1742
MARS_v2


title: AB21962

description: Library name: Sample 242


title: AB17159

description:
Library name: Sample1741
MARS_v2


title: ChIPseq human melanoma Sbcl2_n1 (H3K27ac ChIP)

description: Library name: Sbcl2_n1, H3K27ac ChIP


title: AB9092

description: Library name: Sample 15


title: ChIPseq human melanoma Sbcl2_n1 (PolII ChIP)

description: Library name: Sbcl2_n1, PolII ChIP


title: AB9091

description: Library name: Sample 14


title: AB21961

description: Library name: Sample 241


title: AB9087

description: Library name: Sample 13


title: AB21960

description: Library name: Sample 240


title: ChIPseq human melanoma Sbcl2_n1 (Input)

description: Library name: Sbcl2_n1 (Input)


title: AB17157

description:
Library name: Sample1739
MARS_v2


title: Whole Blood, ID18, M5, Booster, 2hour

city: Hamilton

first: Vincent

last: Munster

state: Montana

department: NIAID

institute: NIH

description: Library name: VA0002200016

data_processing:
Bulk RNA-seq FASTQ files were processed using the OpenOmics/RNA-seek (https://doi.org/10.5281/zenodo.13312679) v1.9.5 pipeline to run QC and quantify gene transcript counts.
Assembly: GRCh38
Supplementary files format and content: RSEM counts

source_name: Whole Blood

extract_protocol:
Whole blood RNA was isolated from PAXgene tubes for 221 study samples using the QIAsymphony PAXgene Blood RNA Kit and the QIAsymphony SP instrument (both Qiagen) according to the manufacturer instructions including DNase I digestion and Proteinase K treatment.  RNA concentration was determined by Quant-iT RiboGreen assay (ThermoFisher) using a Biotek Synergy H1 plate reader (Agilent Technologies) and RINs assessed using Agilent 4200 TapeStation (Agilent).
RNA-seq libraries were prepared from 500 ng of total RNA using Universal Plus mRNA-seq Kit with NuQuant Human Globin AnyDeplete kit (Tecan Genomics) on a Biomek Fx robot (Beckman). First, messenger RNA transcripts were captured, fragmented, and converted to complementary DNA. Following second-strand synthesis and end repair, DNA fragments were ligated with dual-indexed adapters compatible with the Illumina platform. Libraries were subjected to strand selection and removal of globin transcripts, followed by 14 cycles of amplification. Purified libraries were analyzed with the Biotek Synergy H1 plate reader and Agilent 4200 TapeStation (Agilent Technologies) to assess concentration and size distribution, respectively, then normalized and pooled for sequencing. Final molarity of the pool was determined by quantitative polymerase chain reaction using the KAPA library quantification kit (Roche). Paired-end sequencing was performed on the NextSeq 2000 (Illumina) using P3 300 cycles kits in 2 × 150-base pair (bp) format.

value: Whole Blood

tag: individual

value: female

tag: age

value: Booster

tag: time

value: Month 5

tag: timepoint

value: 2 hour

tag: reaction type

value: ISRR

tag: reaction type_severity

value: Severe


title: AB9086

description: Library name: Sample 12

source_name: spinal cord

tag: tissue

value: spinal cord

tag: treatment

value: peptide MOG


title: AB21959

description: Library name: Sample 239

tag: gate

tag: mouse


title: AB17156

description:
Library name: Sample1738
MARS_v2


title: Whole Blood, ID18, M5, Booster, 35min

description: Library name: VA0002190017

tag: Sex

value: 35 min


title: AB9085

description: Library name: Sample 11

tag: score


title: AB17155

description:
Library name: Sample1737
MARS_v2

value: PC


title: Whole Blood, ID18, M5, Booster, Baseline

description: Library name: VA0002180010

value: Baseline


title: AB21958

description: Library name: Sample 238

value: Untreated (PBS)

tag: eae model


title: AB9083

description: Library name: Sample 10

value: healthy

value: Untreated naïve control

tag: batch


title: AB21957

description: Library name: Sample 237

value: CD45.1+ mCherry+

value: aPD-1 CAR + IL-10

value: rhMOG


title: Whole Blood, ID18, D2, Vaccine, 24hour

description: Library name: VA0001910005

value: Whole Blood

value: female

value: Vaccine

value: Day 2

value: 24 hour

value: Mild


title: AB17154

description:
Library name: Sample1736
MARS_v2

value: BM


title: AB21956

description: Library name: Sample 236

value: spinal cord


title: AB17153

description:
Library name: Sample1735
MARS_v2


title: AB9082

description: Library name: Sample 9

value: peptide MOG


title: Whole Blood, ID18, D2, Vaccine, 6hour

description: Library name: VA0001900005

value: 6 hour

value: ISRR


title: AB9081

description: Library name: Sample 8

value: Untreated (PBS)


title: AB17151

description:
Library name: Sample1734
MARS_v2


title: AB21954

description: Library name: Sample 234


title: AB17150

description:
Library name: Sample1733
MARS_v2

value: PC


title: Whole Blood, ID18, D2, Vaccine, 35min

description: Library name: VA0001880012

value: 35 min


title: AB9079

description: Library name: Sample 7

value: healthy

value: Untreated naïve control


title: AB9077

description: Library name: Sample 6


title: AB17149

description:
Library name: Sample1732
MARS_v2


title: AB9076

description: Library name: Sample 5


title: Whole Blood, ID18, D1/D2, Placebo/Vaccine, 24hour/Baseline

description: Library name: VA0001870012

value: Placebo/Vaccine

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Severe/Mild


title: AB21952

description: Library name: Sample 232

value: aPD-1 CAR

value: rhMOG


title: AB17148

description:
Library name: Sample1731
MARS_v2

value: BM


title: Whole Blood, ID18, D1, Placebo, 6hour

description: Library name: VA0001860005

value: Whole Blood

value: female

value: Placebo

value: Day 1

value: Severe


title: AB21951

description: Library name: Sample 231

value: spinal cord

value: Untreated (PBS)


title: AB17146

description:
Library name: Sample1730
MARS_v2

value: PC


title: AB9071

description: Library name: Sample 3

value: healthy

value: Untreated naïve control

value: peptide MOG


title: AB21950

description: Library name: Sample 230


title: Whole Blood, ID18, D1, Placebo, 2hour

description: Library name: VA0001850012

value: 2 hour

value: ISRR


title: AB9069

description: Library name: Sample 2


title: Whole Blood, ID18, D1, Placebo, 35min

description: Library name: VA0001840012

value: 35 min


title: AB21949

description: Library name: Sample 229


title: AB17144

description:
Library name: Sample1728
MARS_v2


title: Whole Blood, ID18, D1, Placebo, Baseline

description: Library name: VA0001830016

value: Baseline


title: AB9068

description: Library name: Sample 1


title: AB17143

description:
Library name: Sample1727
MARS_v2


title: AB21948

description: Library name: Sample 228

value: CD45.1+ mCherry+

value: aPD-1 CAR + IL-10

value: rhMOG


title: Whole Blood, ID17, M5, Booster, 2hour

description: Library name: VA0002170012

value: Whole Blood

value: female

value: Booster

value: Month 5

value: Allergic


title: Y3B, scRNA

first: Sheng

last: Li

address: 1450 Biggy St

institute: University of Southern California

description: Library name: Y3B

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger (for scRNA-seq).
Assembly: Mouse mm10
Supplementary files format and content: Tab separated values files and matrix files

extract_protocol:
Freshly collected Wild-type mice were profiled by scRNA-seq of Lineage-c-Kit+ HSPCs for each mouse using Chromium v.3 (10x Genomics).
Library was performed according to the manufacter's instructions.

value: Bone marrow

value: 4.5 months (host age)

tag: gender

value: Female

tag: genotype

value: Wild-type


title: Whole Blood, ID17, M5, Booster, 35min

description: Library name: VA0002160012


title: AB17142

description:
Library name: Sample1726
MARS_v2

value: BM

value: PC


title: Y2B, scRNA

description: Library name: Y2B


title: AB21946

description: Library name: Sample 226

value: spinal cord


title: AB17141

description:
Library name: Sample1725
MARS_v2


title: Y1B, scRNA

description: Library name: Y1B


title: Whole Blood, ID17, M5, Booster, Baseline

description: Library name: VA0002150016


title: AB21945

description: Library name: Sample 225


title: AB17140

description:
Library name: Sample1724
MARS_v2


title: O3B, scRNA

description: Library name: O3B

value: 22.5 months (host age)


title: Whole Blood, ID17, D2, Placebo, 24hour

description: Library name: VA0001760005

value: Placebo

value: Day 2

value: 24 hour

value: ISRR

value: Severe


title: AB21944

description: Library name: Sample 224

value: Untreated (PBS)

value: rhMOG


title: AB17139

description:
Library name: Sample1723
MARS_v2


title: Whole Blood, ID17, D2, Placebo, 6hour

description: Library name: VA0001750005

value: Whole Blood

value: female

value: 6 hour


title: AB21943

description: Library name: Sample 223


title: O2B, scRNA

description: Library name: O2B

value: Bone marrow


title: AB17138

description:
Library name: Sample1722
MARS_v2


title: Whole Blood, ID17, D2, Placebo, 2hour

description: Library name: VA0001740029

value: 2 hour


title: O1B, scRNA

description: Library name: O1B

value: Female

value: Wild-type


title: AB21942

description: Library name: Sample 222


title: AB17137

description:
Library name: Sample1721
MARS_v2

value: BM

value: PC


title: AB21955

description: Library name: Sample 235

value: spinal cord

value: aPD-1 CAR + IL-10


title: Whole Blood, ID17, D2, Placebo, 35min

description: Library name: VA0001730011

value: Placebo

value: Day 2

value: 35 min


title: 6_Oa, scRNAseq

description: Library name: 6_Oa

value: 20 months (donor age)


title: Whole Blood, ID18, D2, Vaccine, 2hour

description: Library name: VA0001890012

value: Vaccine

value: ISRR

value: Mild


title: AB17136

description:
Library name: Sample1720
MARS_v2


title: AB21941

description: Library name: Sample 221

value: Untreated (PBS)

value: rhMOG


title: Whole Blood, ID17, D1/D2, Vaccine/Placebo, 24hour/Baseline

description: Library name: VA0001720029

value: Whole Blood

value: female

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: Allergic/ISRR

value: None/Severe


title: AB21953

description: Library name: Sample 233

value: spinal cord

value: aPD-1 CAR


title: 5_Oa, scRNAseq

description: Library name: 5_Oa

value: Bone marrow

value: Female

value: Wild-type


title: AB21940

description: Library name: Sample 220


title: AB17135

description:
Library name: Sample1719
MARS_v2

value: BM


title: 4_Oa, scRNAseq

description: Library name: 4_Oa

value: 20 months (donor age)


title: AB21939

description: Library name: Sample 219


title: Whole Blood, ID17, D1, Vaccine, 6hour

description: Library name: VA0001710005

value: Vaccine

value: Day 1

value: 6 hour

value: Allergic


title: AB17134

description:
Library name: Sample1718
MARS_v2

value: PC


title: AB21938

description: Library name: Sample 218

value: Untreated (PBS)

value: rhMOG


title: Whole Blood, ID17, D1, Vaccine, 2hour

description: Library name: VA0001700029

value: Whole Blood

value: female

value: 2 hour


title: AB9072

description: Library name: Sample 4

value: spinal cord

value: healthy

value: Untreated naïve control

value: peptide MOG


title: Whole Blood, ID17, D1, Vaccine, Baseline

description: Library name: VA0001680034

value: Baseline


title: 3_Ya, scRNAseq

description: Library name: 3_Ya

value: Bone marrow

value: 2 months (donor age)

value: Female

value: Wild-type


title: AB17133

description:
Library name: Sample1717
MARS_v2

value: BM


title: AB17145

description:
Library name: Sample1729
MARS_v2


title: AB21937

description: Library name: Sample 217


title: AB17132

description:
Library name: Sample1716
MARS_v2


title: Whole Blood, ID16, M5, Booster, 2hour

description: Library name: VA0002130034

value: Booster

value: Month 5

value: ISRR

value: Mild


title: 2_Ya, scRNAseq

description: Library name: 2_Ya


title: AB21936

description: Library name: Sample 216

value: CD45.1+ mCherry+

value: aPD-1 CAR

value: rhMOG


title: AB17131

description:
Library name: Sample1715
MARS_v2

value: PC


title: 1_Ya, scRNAseq

description: Library name: 1_Ya


title: Whole Blood, ID16, M5, Booster, 35min

description: Library name: VA0002120016

value: Whole Blood

value: female

value: 35 min


title: AB21935

description: Library name: Sample 215

value: spinal cord


title: YY_CSP, hashtag oligo-based multiplexing(HTO)

description: Library name: YY_CSP

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics). Gene expression reads were aligned to the mouse reference genome (mm10) to generate expression matrices. Feature barcode reads, including CellTag and hashtag oligo (HTO), were processed using Cell Ranger multi for sample demultiplexing and the celltagR pipeline for clonal barcode analysis. Downstream analyses were performed using standard single-cell RNA-seq workflows.
Assembly: Mouse mm10
Supplementary files format and content: Tab or comma separated values files and matrix files

extract_protocol:
Bone marrow cells were isolated from femurs, tibia, iliac crests, and spine of young and old mice. Red blood cells were removed by ACK lysis, and mononuclear cells were enriched by density gradient centrifugation. Hematopoietic stem and progenitor cells (HSPCs) were enriched using CD117 magnetic beads and sorted by flow cytometry as Lineage? Sca1+ c-Kit+ CD48? CD150+ cells.
Single-cell libraries were generated using the 10x Genomics Chromium platform (GEM-X Single Cell 3? v4). Approximately 10,000?20,000 cells were captured per sample. Gene expression libraries were constructed following the manufacturer?s protocol. CellTag and hashtag oligo feature barcode libraries were captured simultaneously. Libraries were sequenced on an Illumina NovaSeq platform. Hashtag oligo-based multiplexing was performed using TotalSeq-B antibodies (BioLegend) following the 10x Genomics Feature Barcode protocol (3? Gene Expression with Antibody Capture). Cells from different biological samples were labeled with unique oligonucleotide-conjugated antibodies prior to pooling. The hashtag oligos (HTOs) enabled sample demultiplexing after sequencing. The following TotalSeq-B hashtag sequences were used: B0301 (ACCCACCAGTAAGAC), B0302 (GGTCGAGAGCATTCA), and B0303 (CTTGCCGCATGTCAT). Feature barcode libraries were generated alongside gene expression libraries and processed to assign cells to their sample of origin.

value: Bone marrow

value: 4.5 months (host age)


title: Whole Blood, ID16, D2, Placebo, 24hour

description: Library name: VA0001530005

value: Placebo

value: Day 2

value: 24 hour

value: Severe


title: YO_CSP, hashtag oligo-based multiplexing(HTO)

description: Library name: YO_CSP

value: 22.5 months (host age)

value: Female

value: Wild-type


title: AB17130

description:
Library name: Sample1714
MARS_v2

value: BM


title: AB17129

description:
Library name: Sample1713
MARS_v2


title: AB21934

description: Library name: Sample 214

value: aPD-1 CAR


title: Whole Blood, ID16, D2, Placebo, 6hour

description: Library name: VA0001520005

value: 6 hour

value: ISRR


title: OY_CSP, hashtag oligo-based multiplexing(HTO)

description: Library name: OY_CSP


title: AB21933

description: Library name: Sample 213

value: rhMOG


title: AB17128

description:
Library name: Sample1712
MARS_v2

value: PC


title: Whole Blood, ID16, D2, Placebo, 2hour

description: Library name: VA0001510030

value: Whole Blood

value: female

value: 2 hour


title: AB21932

description: Library name: Sample 212

value: spleen


title: AB17127

description:
Library name: Sample1711
MARS_v2


title: Whole Blood, ID16, D2, Placebo, 35min

description: Library name: VA0001500012

value: Placebo

value: 35 min


title: OO_CSP, hashtag oligo-based multiplexing(HTO)

description: Library name: OO_CSP

value: Bone marrow


title: Y_vitro_CSP, hashtag oligo-based multiplexing(HTO)

description: Library name: Y_vitro_CSP

value: 2 months (donor age)


title: AB17126

description:
Library name: Sample1710
MARS_v2


title: AB21931

description: Library name: Sample 211

value: spinal cord

value: CD45.1+ mCherry+


title: Whole Blood, ID16, D1/D2, Vaccine/Placebo, 24hour/Baseline

description: Library name: VA0001490030

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Moderate/Severe


title: O_vitro_CSP, hashtag oligo-based multiplexing(HTO)

description: Library name: O_vitro_CSP

value: 20 months (donor age)

value: Female

value: Wild-type


title: AB21930

description: Library name: Sample 210

value: aPD-1 CAR

value: rhMOG


title: AB17125

description:
Library name: Sample1709
MARS_v2

value: BM

value: PC


title: YY_GEX, scRNAseq

description: Library name: YY_GEX

value: 4.5 months (host age)


title: Whole Blood, ID16, D1, Vaccine, 6hour

description: Library name: VA0001480005

value: Whole Blood

value: female

value: Vaccine

value: Day 1

value: 6 hour

value: ISRR

value: Moderate


title: AB21929

description: Library name: Sample 209

value: spinal cord


title: AB17124

description:
Library name: Sample1708
MARS_v2


title: Whole Blood, ID16, D1, Vaccine, 2hour

description: Library name: VA0001470030

value: 2 hour


title: AB21928

description: Library name: Sample 208


title: AB17123

description:
Library name: Sample1707
MARS_v2


title: Whole Blood, ID16, D1, Vaccine, 35min

description: Library name: VA0001460012

value: 35 min


title: OY_GEX, scRNAseq

description: Library name: OY_GEX

value: Bone marrow

value: Female


title: Whole Blood, ID16, D1, Vaccine, Baseline

description: Library name: VA0001450034

value: Baseline


title: AB20938

description: Library name: Sample 207

value: spleen

value: Untreated (PBS)

value: peptide MOG


title: AB17122

description:
Library name: Sample1706
MARS_v2

value: BM

value: PC


title: OO_GEX, scRNAseq

description: Library name: OO_GEX

value: 22.5 months (host age)

value: Wild-type


title: AB20937

description: Library name: Sample 206


title: Whole Blood, ID11, M5, Booster, 2hour

description: Library name: VA0002070012

value: Whole Blood

value: female

value: Booster

value: Month 5

value: Mild


title: AB20936

description: Library name: Sample 205

source_name: lung

value: lung


title: AB17117

description:
Library name: Sample1704
MARS_v2

source_name: BM


title: AB20935

description: Library name: Sample 204


title: O_vitro_GEX, scRNAseq

description: Library name: O_vitro_GEX

value: 20 months (donor age)


title: AB17116

description:
Library name: Sample1703
MARS_v2


title: Whole Blood, ID11, M5, Booster, Baseline

description: Library name: VA0002050016

value: ISRR


title: mHSC_female_vold

description:
Library name: SL20002_Female-22-mo
95-week

value: Bone marrow

value: 95 weeks

value: Female


title: AB20934

description: Library name: Sample 203

value: Untreated (PBS)


title: AB17115

description:
Library name: Sample1702
MARS_v2


title: Whole Blood, ID11, D2, Placebo, 24hour

description: Library name: VA0001340005

value: Placebo

value: Day 2

value: 24 hour


title: mHSC_male_vold

description:
Library name: SL20001_Male-22-mo
95-week

value: Male


title: AB20933

description: Library name: Sample 202

value: spinal cord

value: peptide MOG


title: AB17114

description:
Library name: Sample1701
MARS_v2

value: BM

value: PC


title: AB17158

description:
Library name: Sample1740
MARS_v2


title: Whole Blood, ID11, D2, Placebo, 6hour

description: Library name: VA0001330005

value: Whole Blood

value: female

value: 6 hour


title: mHSC_female_old

description:
Library name: SL19009_Old-Age-Female
79-week

value: 79 weeks

value: Wild-type


title: AB17113

description:
Library name: Sample1700
MARS_v2


title: Whole Blood, ID11, D2, Placebo, 2hour

description: Library name: VA0001320012

value: 2 hour

value: ISRR

value: Mild


title: AB20932

description: Library name: Sample 201

value: Untreated (PBS)


title: AB20931

description: Library name: Sample 200


title: AB17112

description:
Library name: Sample1699
MARS_v2


title: Whole Blood, ID11, D2, Placebo, 35min

description: Library name: VA0001310012

value: Placebo

value: 35 min


title: mHSC_female_mid

description:
Library name: SL19008_Middle-Aged-Female
50-week

value: Bone marrow

value: 50 weeks

value: Female


title: mHSC_female_young

description:
Library name: SL19007_Young-Female
14-week

value: 14 weeks


title: AB20930

description: Library name: Sample 199

value: brain

value: peptide MOG


title: AB17111

description:
Library name: Sample1698
MARS_v2

value: BM


title: Whole Blood, ID11, D1/D2, Vaccine/Baseline, 24hour/Baseline

description: Library name: VA0001300012

value: Whole Blood

value: female

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Moderate/Mild


title: AB20929

description: Library name: Sample 198

value: spinal cord

value: Untreated (PBS)


title: AB17110

description:
Library name: Sample1697
MARS_v2


title: mHSC_male_old

description:
Library name: SL19003_Old-Male
78-week

value: 78 weeks

value: Male

value: Wild-type


title: Whole Blood, ID11, D1, Vaccine, 6hour

description: Library name: VA0001290005

value: Vaccine

value: Day 1

value: 6 hour

value: ISRR

value: Moderate


title: AB20928

description: Library name: Sample 197

value: brain

value: peptide MOG


title: AB17109

description:
Library name: Sample1696
MARS_v2

value: BM

value: PC


title: mHSC_male_mid

description:
Library name: SL19002_Middle-Aged-Male
50-week

value: Bone marrow

value: 50 weeks


title: AB21947

description: Library name: Sample 227

value: aPD-1 CAR + IL-10

value: rhMOG


title: Whole Blood, ID11, D1, Vaccine, 2hour

description: Library name: VA0001280012

value: Whole Blood

value: female

value: 2 hour


title: mHSC_male_young

description:
Library name: SL19001_Young-Male
14-week

value: 14 weeks

value: Male

value: Wild-type


title: AB20927

description: Library name: Sample 196

value: Untreated (PBS)


title: AB17108

description:
Library name: Sample1695
MARS_v2


title: Whole Blood, ID11, D1, Vaccine, 35min

description: Library name: VA0001270014

value: Vaccine

value: Day 1

value: 35 min

value: ISRR


title: FARday90

city: New York

first: Ye

last: Xie

state: New York

address: 1468 Madison Ave

department: Ophthalmology

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 4
3' mRNA (v3.1, 10x Genomics)

data_processing:
Sequencing data was aligned and quantified using the Cell Ranger Software v8.0.1 (10x Genomics) against the mm10 as the reference.
Assembly: mouse mm10
Supplementary files format and content: Cell Ranger outputf files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.mtx.gz

source_name: retina

growth_protocol: All mice were housed under controlled room temperature and a 12-h light/dark cycle with free access to water and food. Mice of either sex at the age of 2-3 months were randomly assigned to different groups for all experiments.

extract_protocol:
Retinal dissection was performed in Hank’s balanced salt solution (HBSS). Per dissected retina were incubated at 37ºC for 15 min in the activated Papain mix composed of 40 µL Papain (Worthington, 500 U/mL), 40 µL Cysteine/EDTA mix (25 mM cysteine + 5 mM EDTA [pH 7.0]), and 320 µL HBSS/HEPES (normal HBSS + 10 mM HEPES). Cell pellet was collected after centrifugation for 5 min at 1,000 rpm and treated with 10 µL DNase I (Invitrogen, 2 U/µL) in 400 µL HBSS at room temperature for 3 min with gentle trituration. After incubation of additional 5 min for DNase I digestion, 1 ml HBSS was added, and cell pellet was collected after centrifugation for 5 min at 1,000 rpm. Dissociated cells were resuspended in an appropriate volume of PBS buffer containing 0.5% BSA for future experiments. To purify Sun1-GFP+ MG and their progeny, retinas were isolated from tamoxifen-induced Sun1-GFP MG lineage tracing mice with or without FAR treatment. 4-8 retinas were used for each treatment condition. After retinal dissociation, single-cell resuspension was filtered right before loading on a IMI5L cell sorter (BD Biosciences). DAPI was used as a viability dye to exclude the dead cells.
FACS-purified Sun1-GFP+ cells were processed according to Chromium 3’ Gene Expression V3.1 Kit (10x Genomics, Pleasanton, CA) using manufacturer’s guidelinese. An estaimated 10,000 cells were loaded onto each channel with a targeted cell recovery of 6000 cells per sample. Single-cell libraries were quantified using Tapestation (Agilent) and QuBit (Thermofisher) analysis. Libraries were then sequenced in paired end mode on a NovaSeq 6000 instrument (Illumina, San Diego, CA) targeting a depth of 50,000-100,000 reads per cell.

treatment_protocol: Intravitreal injection of 1.5 μL FGF2 (R&D SYSTEMS, 233-FB, 0.2 μg/μL final concentration in PBS) after 10 and 12 days after intravitreal injection of 1.5 μL AAV-Ascl1 (titer: 1e14 vg/ml) per eye. all-trans-Retinoic acid (RA, Thermo Scientific, 207340010) was dissolved in cottonseed oil at the concentration of 5 mg/mL. RA was administered in mice through intraperitoneal injections at a daily dose of 25 mg/kg body weight for three consecutive days from 10 to 12 days after AAV-Ascl1 injection. Samples were then collected at 13, 20, 90 days after AAV-mediated MG-specific gene transfer of Ascl1.

value: retina

tag: cell type

value: Muller glia

value: Sun1-GFP lineage tracing mice (C57BL/6J background)

value: FAR for 90 days


title: AB20926

description: Library name: Sample 195

value: brain

value: peptide MOG


title: AB17107

description:
Library name: Sample1694
MARS_v2

value: BM

value: PC


title: Whole Blood, ID11, D1, Vaccine, Baseline

description: Library name: VA0001260016

value: Whole Blood

tag: individual

value: female

value: Baseline

value: Moderate


title: FARday20

description:
Library name: Sample 3
3' mRNA (v3.1, 10x Genomics)

value: FAR for 20 days


title: AB20925

description: Library name: Sample 194

value: spleen

value: aPD-1 CAR


title: YO_GEX, scRNAseq

description: Library name: YO_GEX

source_name: Bone marrow

value: Bone marrow

tag: age

value: 22.5 months (host age)

value: Female

value: Wild-type


title: AB17106

description:
Library name: Sample1693
MARS_v2


title: Whole Blood, ID15, M5, Booster, 2hour

description: Library name: VA0002040012

value: Booster

tag: time

value: Month 5

value: 2 hour

value: ISRR

value: VeryMild


title: AB17105

description:
Library name: Sample1692
MARS_v2

value: BM

value: PC


title: FARday13

description:
Library name: Sample 2
3' mRNA (v3.1, 10x Genomics)

value: retina

value: Muller glia

value: Sun1-GFP lineage tracing mice (C57BL/6J background)

value: FAR for 13 days


title: Whole Blood, ID15, M5, Booster, 35min

description: Library name: VA0002030012

value: Whole Blood

value: female

tag: timepoint

value: 35 min


title: AB20924

description: Library name: Sample 193

value: spleen

value: aPD-1 CAR

value: peptide MOG


title: AB17118

description:
Library name: Sample1705
MARS_v2


title: AB20923

description: Library name: Sample 192

value: lung


title: Whole Blood, ID15, M5, Booster, Baseline

description: Library name: VA0002020016

value: Booster

value: Month 5

value: Baseline

tag: reaction type


title: Y_vitro_GEX, scRNAseq

description: Library name: Y_vitro_GEX

value: Bone marrow

value: 2 months (donor age)

value: Female

value: Wild-type


title: Whole Blood, ID11, M5, Booster, 35min

description: Library name: VA0002060012

value: ISRR

tag: reaction type_severity

value: Mild


title: AB20922

description: Library name: Sample 191

tag: tissue


title: Untreated

description:
Library name: Sample 1
3' mRNA (v3.1, 10x Genomics)

value: retina

value: Muller glia

value: Sun1-GFP lineage tracing mice (C57BL/6J background)

tag: treatment

value: Untreated


title: AB17104

description:
Library name: Sample1691
MARS_v2

value: BM

tag: gate

value: PC


title: Foz_WD_12w_3

first: Souradipta

last: Ganguly

address: 9500 Gilman Drive

institute: University of California, San Diego

description:
Library name: FW12w_7114_231010
Column name in All_HTSeq_Counts.txt: FW12w_7114_231010

data_processing:
The paired-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
The reads were then aligned to the GRCm38.p4 reference genome and Gencode M9 annotations using STAR (v 2.6.1).
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
The alignment results were parsed via the SAMtools to generate SAM files.
Read counts to each genomic feature were obtained with featureCounts (v 1.6.5).
Assembly: GRCm38
Supplementary files format and content: Tab seperated values of rxaw counts for each sample

source_name: Heart

extract_protocol:
Total RNA was extracted using RNeasy Mini columns (Qiagen, Valencia, CA). mRNA selection was completed using 500ng of total RNA input using NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were prepped using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: Heart

tag: liver phenotype

tag: heart phenotype

value: Foz


title: AB15667

description:
Library name: Sample1690
MARS_v2


title: Whole Blood, ID15, D2, Vaccine, 24hour

description: Library name: VA0001170005

value: Whole Blood

tag: Sex

value: female

value: Vaccine

value: Day 2

value: 24 hour


title: Foz_WD_12w_2

description:
Library name: FW12w_7117_231010
Column name in All_HTSeq_Counts.txt: FW12w_7117_231010


title: AB20921

description: Library name: Sample 190

value: spinal cord

tag: mouse

tag: score

value: aPD-1 CAR

tag: eae model

value: peptide MOG


title: AB15665

description:
Library name: Sample1689
MARS_v2

tag: batch


title: Whole Blood, ID15, D2, Vaccine, 6hour

description: Library name: VA0001160007

value: 6 hour


title: Foz_WD_12w_1

description:
Library name: FW12w_7151_231010
Column name in All_HTSeq_Counts.txt: FW12w_7151_231010

tag: genotype


title: AB15664

description:
Library name: Sample1688
MARS_v2


title: AB20919

description: Library name: Sample 188


title: WT_Chow_24w_3

description:
Library name: WTChow24w_4_231010
Column name in All_HTSeq_Counts.txt: WTChow24w_4_231010

value: Healthy

value: Normal

value: WT


title: Whole Blood, ID15, D2, Vaccine, 2hour

description: Library name: VA0001150030

tag: individual

value: 2 hour


title: AB20920

description: Library name: Sample 189

value: CD45.1+ mCherry+


title: Whole Blood, ID15, D2, Vaccine, 35min

description: Library name: VA0001140012

tag: age

value: 35 min


title: AB15663

description:
Library name: Sample1687
MARS_v2

value: BM

value: PC


title: AB20918

description: Library name: Sample 187


title: WT_Chow_24w_2

description:
Library name: WTChow24w_2_231010
Column name in All_HTSeq_Counts.txt: WTChow24w_2_231010

value: Heart


title: AB15662

description:
Library name: Sample1686
MARS_v2


title: Whole Blood, ID15, D1/D2, Placebo/Vaccine, 24hour/Baseline

description: Library name: VA0001130030

value: Whole Blood

value: female

value: Placebo/Vaccine

tag: time

value: Day 1/Day 2

value: 24 hour/Baseline

value: None/None


title: WT_Chow_24w_1

description:
Library name: WTChow24w_1_231010
Column name in All_HTSeq_Counts.txt: WTChow24w_1_231010


title: AB20917

description: Library name: Sample 186

value: spinal cord

value: aPD-1 CAR

value: peptide MOG


title: AB15661

description:
Library name: Sample1685
MARS_v2


title: Whole Blood, ID15, D1, Placebo, 6hour

description: Library name: VA0001120005

value: Placebo

value: Day 1

tag: timepoint

value: 6 hour


title: Foz_Chow_24w_3

description:
Library name: FC24w_8143_231010
Column name in All_HTSeq_Counts.txt: FC24w_8143_231010

value: Foz


title: AB20916

description: Library name: Sample 185

value: CD45.1+ mCherry+


title: Foz_Chow_24w_2

description:
Library name: FC24w_8194_231010
Column name in All_HTSeq_Counts.txt: FC24w_8194_231010


title: AB15660

description:
Library name: Sample1684
MARS_v2

value: BM


title: Whole Blood, ID15, D1, Placebo, 2hour

description: Library name: VA0001110030

value: 2 hour

tag: reaction type


title: AB20915

description: Library name: Sample 184

source_name: brain

value: brain


title: Whole Blood, ID15, D1, Placebo, 35min

description: Library name: VA0001100012

value: Whole Blood

value: 35 min

tag: reaction type_severity


title: Foz_Chow_24w_1

description:
Library name: FC24w_8149_231010
Column name in All_HTSeq_Counts.txt: FC24w_8149_231010

tag: tissue

value: Heart


title: AB15657

description:
Library name: Sample1683
MARS_v2

value: PC


title: AB20914

description: Library name: Sample 183

tag: treatment


title: AB15656

description:
Library name: Sample1682
MARS_v2

tag: gate


title: Foz_Regression_3

description:
Library name: R8w_8403_231010
Column name in All_HTSeq_Counts.txt: R8w_8403_231010

tag: liver phenotype

value: Regression


title: Whole Blood, ID15, D1, Placebo, Baseline

description: Library name: VA0001090034

value: female

value: Baseline