title: HSV-201_Day180

description: RNAseq data from PBMC extracted from individual HSV-201


title: Subject SU146

status: Public on Jan 12 2023

type: protein

city: Stanford

first: Allan

last: Feng

state: CA

address: 269 Campus Dr

department: Imm/Rheum

country: USA

institute: Stanford School of Medicine

description: Antibodies in samples bind to conjugated beads in array. The fluorescence measured as MFI from the secondary antibody was used to determine antibody reactivity.

hyb_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

scan_protocol: A Luminex FlexMAP 3D instrument was used to measure fluorescence (in MFI) from each  barcoded bead.

data_processing: Sample replicate MFI values were averaged for each antigen. The average barebead MFI was then subtracted from the average MFI of each sample and antigen.

label: R-PE conjugated goat anti-human IgG secondary antibody

molecule: protein

organism: Homo sapiens

source_name: Serum/Plasma

extract_protocol: Blood was collected from patients and healthy controls. The blood was then processed into serum or plasma which was then run on our arrays.

tag: disease

value: ICU Patient from Stanford


title: Subject SU149

label_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.


title: Subject SU142


title: Subject SU143


title: HSV-206_Day1

type: SRA

city: Bethesda

first: Foo

last: Cheung

address: Bethesda

institute: NIH

description: RNAseq data from PBMC extracted from individual HSV-206

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
The Spliced Transcripts Alignment to a Reference (STAR) software was used for RNA-seq alignment
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for genes and every sample

molecule: total RNA

source_name: PBMC

extract_protocol:
PBMCs were isolated with Ficoll-Hypaque reagent and lysed in QIAzol (Qiagen, Hilden, Germany) and stored at -80°C until use. Their total RNA was extracted and purified with the miRNeasy kit (Qiagen). RNA quality and quantity were estimated using Nanodrop (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Stranded cDNA sequencing libraries were generated with TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturer’s instructions. Briefly 500 ng of total RNA was used for mRNA selection. After the reverse transcription to 1st strand cDNA, strand info was reserved with dUTPs during 2nd strand synthesis. The dsDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR to create the final cDNA library. The library was qualified with Agilent Bioanalyzer and quantified with Qubit 2.0 fluorometer. The cluster generation and pair-end (2x75 bp) sequencing was run on Illumina HiSeq 3000 at NHLBI Sequencing Core. Up to 96 barcoded samples were pooled for one single run, which yielded at least 30M passed filter paired reads per sample.

tag: cell type

value: PBMC

tag: age


title: HSV-206_Day0


title: HSV-201_Day187


title: MDM IFNg 8h HC1

city: Paris

first: Jeremie

last: Rosain

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine

data_processing:
The RNA-seq FASTQ files were first inspected with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure that the raw data were of high quality
We retained only genes with at least 1 count-per-million (CPM) in at least two samples
Assembly: For each subject, the two FASTQ files generated were then mapped onto the human reference genome (Ensembl GRCh37 release 75) with STAR v.2.7.3a, in the two-pass mode
Supplementary files format and content: Reads were quantified to generate gene-level feature counts from the read mapping, with HTSeq-count v.0.11.2
Supplementary files format and content: We normalized the datasets with the functions DGEList and calcNormFactors from the edgeR version 3.26.8 package201 implemented in R v.3.6.3

molecule: polyA RNA

source_name: Monocyte-derived macrophages

extract_protocol:
Total RNA was extracted from cells with the Quick-RNA MicroPrep kit (#R1051, Zymo Research), and treated with DNAse (Zymo) to remove residual genomic DNA. Ribosomal RNA (rRNA) and mitochondrial RNA (mRNA) were depleted.
RNA-seq libraries were prepared with the Illumina RiboZero TruSeq Stranded Total RNA Library Prep Kit (Illumina)
Libraries were  sequenced using NovaSeq in the 100 or 150-nt, paired-end configuration

value: Monocyte-derived macrophages

tag: genotype

value: WT/WT

tag: treatment

value: IFN-g 1000 IU/mL 8 hours


title: Subject SU141


title: Subject SU145


title: iPSC non-stimulated STAT1

source_name: iPSC-derived macrophage

value: iPSC-derived macrophage

value: Non-stimulated


title: iPSC IFNg 8h STAT1


title: MDM IFNg 2h HC1

value: IFN-g 1000 IU/mL 2 hours


title: Subject SU140


title: HSV-201_Day37


title: MT.Unique.ID_332

city: Houston

first: David

last: Chen

state: TX

address: One Baylor Plaza Suite 400D

department: Molecular & Human Genetics

institute: BCM

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: total cell-free biofluid RNA

extract_protocol:
RNA Isolation kit was miRNeasy (Qiagen).
Library construction kit was TruSeq Small RNA library prep kit (Illumina). Samples were multiplexed. Type of Starting Material was total RNA.

tag: tissue

value: Plasma

tag: subject id

tag: time point

tag: frequency

value: 1 hr

tag: condition

value: Healthy Subject

tag: anatomical location

value: Plasma cell


title: HSV-201_Day7


title: Subject SU144


title: Subject SU138


title: MT.Unique.ID_331


title: HSV-201_Day30


title: MT.Unique.ID_330


title: MT.Unique.ID_328


title: HSV-118_Day187

description: RNAseq data from PBMC extracted from individual HSV-118


title: Subject SU136


title: MT.Unique.ID_329


title: Subject SU139


title: iPSC IFNg 2h STAT1


title: iPSC IFNg 8h P1


title: iPSC IFNg 2h P1


title: HSV-118_Day180


title: HSV-201_Day1


title: iPSC non-stimulated P1


title: Subject SU137


title: MT.Unique.ID_327


title: HSV-118_Day30


title: MT.Unique.ID_323


title: MT.Unique.ID_324


title: HSV-201_Day0


title: Subject SU135


title: MT.Unique.ID_326


title: Subject SU134


title: HSV-118_Day37


title: iPSC IFNg 8h HC16


title: HSV-118_Day1


title: HSV-118_Day0


title: MT.Unique.ID_240

value: 30 min


title: MT.Unique.ID_325


title: MT.Unique.ID_322


title: HSV-118_Day7


title: Subject SU132


title: Subject SU131


title: iPSC non-stimulated HC11


title: HSV-113_Day187

description: RNAseq data from PBMC extracted from individual HSV-113


title: iPSC non-stimulated HC16


title: MT.Unique.ID_238


title: Subject SU133


title: Subject SU129


title: MT.Unique.ID_239


title: Subject SU130


title: Fibroblast non-stimulated 9844

source_name: primary fibroblast

value: primary fibroblast


title: iPSC IFNg 2h HC16


title: Subject SU127


title: Subject SU128


title: HSV-113_Day180


title: donor 1, RPE, macula, atac

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

description:
donor_1_mac_atac
ATAC portion of a 10X Multiome sample

library_source: genomic single cell

data_processing:
FASTQ files were generated from base calls with the bcl2fastq software (Illumina). Sequencing reads were mapped to the GRCh38 reference genome (GRCh38 Reference - 2020-A-2.0.0 prepared by 10X Genomics). Mapping and quantification were carried out by Cell Ranger ARC (v2.0.0, 10X Genomics) using the ‘count’ function with all parameters at default values. Nuclei passing default Cell Ranger quality control cutoffs were used for subsequent filtering and analysis.
For gene expression libraries, nuclei were first filtered with the Seurat (v3.1) subset() function prior to integration (5). Nuclei with nUMI less than 100 (to remove nuclei with poor read quality) or greater than 4000 (to remove nuclei likely to be doublets) were removed. Nuclei with greater than 10% of reads originating from mitochondrial genes or greater than 2.5% of reads originating from ribosomal RNA genes were also removed, as these metrics indicate incomplete lysis. A “neural_retina_genes” score was then assigned to each nucleus in order to identify and remove contamination of the desired RPE sample. Nuclei with greater than 50% of their counts originating from known neural retina cell-specific genes (i.e. CNGB1, PDE6A, CA10, CADPS, and NRXN3) were removed.
For each of the gene expression libraries, reads were normalized with the Seurat (v3.1) NormalizeData() function, and variable features were identified with the FindVariableFeatures() function. Integration anchors between datasets were identified using the FindIntegrationAnchors() function with the following parameters: dims=1:25, k.filter=100, k.score=20. Nuclei were integrated using the IntegrateData() function with the following parameters: dims=1:25, k.weight=30. Uniform manifold approximation and projection (UMAP) was performed using the first 15 principal components. Seurat clusters were identified using the FindClusters() function with the following parameters: resolution=0.5, algorithm=3 (indicating use of the smart local moving (SLM) algorithm. Data scaling, principal component analysis, and clustering of the gene expression data were all performed using Seurat (v3.1).
For ATAC libraries, nuclei were filtered with the Signac (v1.4.0) subset function. Nuclei with fewer than 1000 or greater than 30000 peak region fragments were removed. Term frequency inverse document frequency (TF-IDF) normalization and partial singular value decomposition were performed on each ATAC library using RunTFIDF() and RunSVD() (Signac) with default settings. Gene activities were computed using GeneActivity().
Integration anchors between ATAC datasets were identified using reciprocal LSI projection using FindIntegrationAnchors() in Signac. Dimensions 2-30 were used. LSI embeddings were integrated using IntegrateEmbeddings based on these anchors and using dimensions 1-30.
Gene expression and ATAC portions of the experiment were combined using Weighted Nearest Neighbor (WNN) analysis (Seurat). Integrated ATAC and gene expression objects were subset to include only common cells (i.e., cells that passed both ATAC and gene expression quality control thresholds). UMAP and cluster identification were performed on the resulting object. Cluster identification used the SLM algorithm with a resolution of 0.5 (5).
Assembly: GRCh38
Supplementary files format and content: Processed gene expression data matrix files are provided in comma-delimited format for count(*_count.csv) and processed/normalized (*_normalized.csv) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).
Supplementary files format and content: Processed gene activity data matrix files are provided in comma-delimited format for count (*_count.csv) and processed/normalized (*_normalized.csv) activity values. For processed/normalized files, log-normalized activity values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene activity values. For count files, raw gene activity level were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

molecule: genomic DNA

source_name: retinal pigment epithelium

extract_protocol:
Donor eyes were obtained from the Iowa Lions Eye Bank following full consent of the next of kin and in full compliance with the Declaration of Helsinki. Anterior segments were removed at the limbus and posterior poles were dissected with 4 cuts at 90 degree intervals. Following removal of the vitreous and neural retina, the RPE was gently scraped away from the underlying Bruch’s membrane and choroid using a Beaver-Visitec #6900 surgical blade (TestEquity). RPE cells were collected from either the submacular region (corresponding to the central ~8mm) or from the temporal quadrant. Cryopreserved RPE samples were thawed rapidly at 37˚C and washed once in PBS-/-. Cells were then pelleted and nuclei were isolated using the Chromium Nuclei Isolation Kit (10X Genomics) following manufacturer’s suggested protocol for Single Cell Multiome ATAC and Gene Expression libraries. Briefly, cells were resuspended in Lysis Buffer on ice and dissociated with a pestle. Dissociated material was filtered with the supplied column and nuclei were subsequently washed once with Wash Buffer. Nuclei were resuspended in diluted Nuclei Buffer supplemented with RNase Inhibitor (10X Genomics).
Nuclei were counted using trypan blue exclusion on a Luna automated counter. Nuclei were then processed following the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (Rev. E). For each sample, 6,000 nuclei were targeted. Eight cycles were used for ATAC library index PCR. Nine cycles were used for cDNA amplification. Sixteen cycles were used for Gene Expression Library sample index PCR. Library quality was checked using the Bioanalyzer system prior to sequencing. Gene expression and ATAC libraries were sequenced separately on the Novaseq 6000 platform (Illumina). Sequencing was carried out by the Genomics Division of the Iowa Institute of Human Genetics.

value: retinal pigment epithelium

tag: region

value: macula

tag: donor

tag: disease status

value: healthy


title: iPSC IFNg 8h HC11


title: Fibroblast IFNg 8h 9844


title: MT.Unique.ID_237


title: MT.Unique.ID_235


title: HSV-113_Day30


title: MT.Unique.ID_234


title: HSV-113_Day7


title: Fibroblast IFNa 8h 9844

value: IFN-a2b 1000 IU/mL 8 hours


title: HSV-113_Day1

value: PBMC


title: MT.Unique.ID_233


title: HSV-113_Day0


title: Subject SU123

value: ICU Patient from Stanford


title: HSV-113_Day37


title: Subject SU126


title: MT.Unique.ID_231


title: MT.Unique.ID_232


title: MT.Unique.ID_236


title: Fibroblast IFNg 30min 9844

value: WT/WT

value: IFN-g 1000 IU/mL 30 min


title: Subject SU121


title: HSV-110_Day180

description: RNAseq data from PBMC extracted from individual HSV-110


title: MT.Unique.ID_230


title: Subject SU125


title: MT.Unique.ID_227


title: Fibroblast IFNg 30min 9843


title: Subject SU124


title: Fibroblast IFNg 2h 9844


title: iPSC IFNg 2h HC11

value: iPSC-derived macrophage


title: Fibroblast IFNa 30min 9844

value: IFN-a2b 1000 IU/mL 30 min


title: HSV-110_Day30


title: Fibroblast IFNa 2h 9844

value: IFN-a2b 1000 IU/mL 2 hours


title: Subject SU118


title: Subject SU122


title: Subject SU117


title: HSV-110_Day187


title: Fibroblast IFNa 8h 9843


title: MT.Unique.ID_224

value: Plasma


title: HSV-110_Day1


title: Fibroblast non-stimulated 9843

value: Non-stimulated


title: HSV-110_Day0


title: MT.Unique.ID_223

value: Healthy Subject


title: Subject SU120


title: MT.Unique.ID_222

value: Plasma cell


title: HSV-106_Day187

description: RNAseq data from PBMC extracted from individual HSV-106


title: Fibroblast IFNg 8h 9843

value: IFN-g 1000 IU/mL 8 hours


title: Fibroblast non-stimulated 4279

value: primary fibroblast


title: HSV-110_Day37


title: HSV-106_Day180


title: Fibroblast IFNg 2h 9843

value: IFN-g 1000 IU/mL 2 hours


title: MT.Unique.ID_225

value: 30 min


title: HSV-110_Day7


title: Subject SU119


title: HSV-106_Day37


title: Subject SU116


title: Fibroblast IFNa 30min 9843


title: Fibroblast IFNg 30min 4279


title: MT.Unique.ID_220


title: Subject SU111


title: Subject SU115


title: Fibroblast IFNa 2h 9843


title: MT.Unique.ID_226


title: HSV-106_Day7


title: MT.Unique.ID_221


title: Subject SU113


title: Fibroblast IFNa 8h 4279


title: Subject SU112


title: MT.Unique.ID_318

value: 1 hr


title: Fibroblast IFNa 30min 4279


title: HSV-106_Day30


title: MT.Unique.ID_219


title: MT.Unique.ID_317


title: Subject SU108


title: Fibroblast IFNa 2h 4279


title: Fibroblast IFNg 2h 4279


title: MT.Unique.ID_218


title: Subject SU110


title: Subject SU109


title: Fibroblast IFNg 8h 4279


title: HSV-104_Day180

description: RNAseq data from PBMC extracted from individual HSV-104


title: Subject SU114


title: HSV-106_Day1


title: MT.Unique.ID_315


title: HSV-106_Day0


title: HSV-104_Day187


title: Fibroblast non-stimulated 4277


title: Subject SU107


title: HSV-104_Day37


title: Fibroblast IFNg 30min 4277


title: HSV-104_Day30


title: Fibroblast IFNg 2h 4277


title: Fibroblast IFNg 8h 4277


title: MT.Unique.ID_312


title: MT.Unique.ID_316


title: Subject SU106


title: Subject SU105


title: Fibroblast IFNa 8h 4277

value: IFN-a2b 1000 IU/mL 8 hours


title: MT.Unique.ID_314


title: MT.Unique.ID_313


title: MT.Unique.ID_311


title: Fibroblast IFNa 2h 4277


title: MT.Unique.ID_309


title: Subject SU104


title: Fibroblast non-stimulated 24564


title: Subject SU100


title: Subject SU102


title: HSV-104_Day0

value: PBMC


title: Subject SU101

value: ICU Patient from Stanford


title: Sample15NSD

first: Yann

last: Vanrobaeys

address: 169 Newton Road

department: Neuroscience and Pharmacology

data_processing:
Raw files were processed with spaceranger-1.3.1.
Outputs for each samples are provided in tar.gz files.
Assembly: mm10
Supplementary files format and content: Compressed directory containing spaceranger output. filtered_feature_bc.matrix.h5 contains expression data. Images are provided as low and high resolution PNG, and scaling information is provided in scalefactors_json.json. Mapping between image coordinates and spot identifiers are provided in tissue_positions_list.csv.

organism: Mus musculus

source_name: brain

extract_protocol:
Mouse brain section per mouse was cut at 10 µm thickness and mounted onto each Visium slide capture area. After H&E staining, each bright-field image was taken as described in the Spatial Transcriptomics procedure. Tissue permeabilization was performed for 18 minutes, as established in the tissue optimization assay. The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to generate sequencing libraries for Visium samples.
Libraries were constructed according to the 10x Visium library construction protocol and sequenced by Illumina NovaSeq6000.

value: brain

tag: Sex

value: male

tag: strain

value: C57BL/6J (Jackson Laboratory #000664)

value: non sleep deprived


title: Sample14SD

value: sleep deprived


title: Fibroblast IFNg 30min 24564

value: IFN-g 1000 IU/mL 30 min


title: HSV-104_Day1


title: MT.Unique.ID_305

value: Plasma


title: MT.Unique.ID_310

value: Healthy Subject


title: Fibroblast IFNa 30min 4277

value: IFN-a2b 1000 IU/mL 30 min


title: Sample16SD


title: Subject SU099


title: Subject SU098


title: MT.Unique.ID_304

value: Plasma cell


title: Subject SU096


title: MT.Unique.ID_308


title: Subject SU095


title: Fibroblast IFNg 8h 24564

value: primary fibroblast

value: IFN-g 1000 IU/mL 8 hours


title: MT.Unique.ID_306


title: Sample13NSD


title: Subject SU103


title: Subject SU097


title: Fibroblast IFNg 2h 24564

value: IFN-g 1000 IU/mL 2 hours


title: Sample10SD


title: MT.Unique.ID_302

value: 1 hr


title: Sample12SD


title: Fibroblast IFNa 8h 24564

value: IFN-a2b 1000 IU/mL 8 hours


title: Sample11NSD


title: MT.Unique.ID_303


title: Subject SU093


title: Fibroblast IFNa 2h 24564

value: IFN-a2b 1000 IU/mL 2 hours


title: Fibroblast IFNa 30min 24564


title: Subject SU092

value: ICU Patient from Stanford


title: Sample6NSD

value: brain


title: Fibroblast IFNg 2h 15474

value: WT/WT


title: MT.Unique.ID_301


title: Sample9NSD

value: male

value: C57BL/6J (Jackson Laboratory #000664)


title: Fibroblast non-stimulated 15474

value: Non-stimulated


title: HSV-104_Day7

value: PBMC


title: Subject SU094


title: MT.Unique.ID_298

value: Plasma


title: MT.Unique.ID_297

value: Healthy Subject


title: MT.Unique.ID_296


title: Sample3SD

value: sleep deprived


title: Subject SU087


title: MT.Unique.ID_292

value: Plasma cell


title: Subject SU088


title: Subject SU089


title: MT.Unique.ID_300


title: Sample8NSD

value: non sleep deprived


title: Fibroblast IFNg 8h 15474

value: primary fibroblast

value: IFN-g 1000 IU/mL 8 hours


title: Subject SU086


title: Fibroblast IFNg 30min 15474

value: IFN-g 1000 IU/mL 30 min


title: MT.Unique.ID_299

value: 1 hr


title: Sample7SD


title: Sample5SD


title: Subject SU090


title: Fibroblast IFNa 30min 15474

value: IFN-a2b 1000 IU/mL 30 min


title: Fibroblast IFNa 8h 15474

value: IFN-a2b 1000 IU/mL 8 hours


title: Sample4NSD

value: brain


title: Sample1SD


title: MT.Unique.ID_290


title: MT.Unique.ID_289


title: Subject SU083

value: ICU Patient from Stanford


title: Subject SU084


title: Subject SU082


title: Subject SU085


title: Fibroblast non-stimulated 15405


title: Fibroblast IFNg 30min 15405


title: Sample2NSD

value: male


title: MT.Unique.ID_288


title: Periost - host, steady state, sample 4

city: Bronx

first: Kira

last: Gritsman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description:
P4
re-analysis of GSM6696280

data_processing:
Raw sequencing data was checked and controlled for quality using FastQC (v0.11.5).
Adapters of RNAseq reads were trimmed out using cutadapt (v1.15)
The RNAseq reads were aligned to the reference genome GRCm39 Release 104 using STAR (v2.5).
Read summarization and gene counts were performed using the featureCounts function from the Subread package (v1.4.6).
Data normalization and differential gene expression were performed with the DESeq2 R package (v1.26.0). Data were filtered using HTSFilter R package (v1.26.0).
Significant genes were defined as p < 0.05 after adjustment for False Discovery Rate (FDR) correction and used for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample reported after HTS Filtering

source_name: periosteum

extract_protocol:
RNA was harvested using Rneasy plus micro kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library

treatment_protocol: Cells were isolated fresh from mice and then digested, stained and sorted using MoFlo Astrios

value: periosteum

value: skeletal stem cells

value: Wild-type

tag: time

value: host, steady state


title: Subject SU091

tag: disease


title: Fibroblast IFNg 2h 15405

tag: cell type

value: IFN-g 1000 IU/mL 2 hours


title: Periost - host, steady state, sample 2+5

description:
P2P5
re-analysis of GSM6696279


title: Subject SU080


title: Subject SU081


title: Fibroblast IFNa 2h 15474

value: WT/WT

value: IFN-a2b 1000 IU/mL 2 hours


title: MT.Unique.ID_287

value: Plasma

value: Healthy Subject

value: Plasma cell


title: Fibroblast IFNa 8h 15405

value: primary fibroblast


title: Periost - host, steady state, sample 1

description:
P1
re-analysis of GSM6696278


title: MT.Unique.ID_291

value: 1 hr


title: Fibroblast non-stimulated 12783

value: Non-stimulated


title: MT.Unique.ID_284


title: Bone marrow - host, steady state, sample 1

description:
BM1
re-analysis of GSM6696275

source_name: Bone marrow

value: Bone marrow

value: mesenchymal stem cells


title: MT.Unique.ID_286


title: Bone marrow - host, steady state, sample 2+4

description:
BM2BM4
re-analysis of GSM6696276


title: Fibroblast IFNg 8h 15405

value: IFN-g 1000 IU/mL 8 hours


title: MT.Unique.ID_283


title: Subject SU078

value: ICU Patient from Stanford


title: Fibroblast IFNg 8h 12783


title: Bone marrow - host, steady state, sample 3

description:
BM3
re-analysis of GSM6696277


title: Fibroblast IFNa 2h 15405


title: Bone marrow - graft at 5 months, sample 4

value: transgenic (POSTN-CRE)

value: Tamoxifen induction

value: graft at 5 months


title: Bone marrow - graft at 5 months, sample 3


title: MT.Unique.ID_285


title: Subject SU076


title: Subject SU077


title: MT.Unique.ID_212

value: 30 min


title: MT.Unique.ID_282


title: Subject SU079


title: Fibroblast IFNa 30min 15405

value: IFN-a2b 1000 IU/mL 30 min


title: CD45-, sorted from tumor, Control DAY7, Rep11

city: Ann Arbor

first: Clifford

last: Cho

address: 2215 Fuller Road

institute: University of Michigan Ann Arbor

description:
Total RNA SEQ
RNASeq CD45- D7.csv

data_processing:
Bcl2fastq2 Controlversion Software (Illumina) was used to generate de-multiplexed Fastq files.  Reads were trimmed using Trim Galore (v0.5.0) using default settings.  Reads were aligned using STAR (v 2.6.0) using default settings .  Unique molecular identifiers were collapsed using Lexogen Quantseq (v2.3.6). Reads were mapped to the mouse genome GRCm38 from the Ensembl genome database.  Reads were counted using BioControlductor R package Rsubread and featureCounts function .  RNASeq data analysis and visualizations were performed using BioJupies.
Assembly: GRCm38

source_name: TUM

extract_protocol: RNA was  submitted to the University of Michigan Advanced Genomics Core for library preparation and QuantSeq analysis.  Pooled libraries were subjected to 101 bp single-end sequencing with Illumina NovaSeq following manufacturer protocols .

treatment_protocol: Flow-sorted CD45+ and CD45- cells were lysed and RNA was extracted per manufacturer instructions using the Qiagen RNeasy Mini Kit.

value: TUM

value: Sorted Tumor and tumor supporting CD45- cells from tumor

value: Control


title: Fibroblast IFNg 30min 12783

value: IFN-g 1000 IU/mL 30 min


title: Subject SU074


title: MT.Unique.ID_213

value: Plasma

value: Healthy Subject

value: Plasma cell


title: MT.Unique.ID_210


title: Fibroblast IFNa 2h 12783

value: primary fibroblast

value: IFN-a2b 1000 IU/mL 2 hours


title: Subject SU072


title: CD45-, sorted from tumor, Control DAY7, Rep10

description:
Total RNA SEQ
RNASeq CD45- D7.csv


title: Bone marrow - graft at 5 months, sample 2

value: Bone marrow

value: mesenchymal stem cells


title: MT.Unique.ID_209


title: Fibroblast IFNg 2h 12783

value: IFN-g 1000 IU/mL 2 hours


title: Bone marrow - graft at 5 months, sample 1

value: transgenic (POSTN-CRE)


title: Fibroblast non-stimulated 11980

value: Non-stimulated


title: Fibroblast IFNa 8h 12783

value: IFN-a2b 1000 IU/mL 8 hours


title: Fibroblast IFNg 8h 11980

value: IFN-g 1000 IU/mL 8 hours


title: Subject SU075

value: ICU Patient from Stanford


title: Subject SU071


title: Fibroblast IFNa 30min 12783

value: IFN-a2b 1000 IU/mL 30 min


title: Fibroblast IFNg 2h 11980


title: MT.Unique.ID_211

value: 30 min


title: CD45-, sorted from tumor, Control DAY7, Rep8

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: TUM

value: Sorted Tumor and tumor supporting CD45- cells from tumor

value: Control


title: CD45+, sorted from tumor, Control DAY7, Rep10

description:
Total RNA SEQ
RNASeq CD45+ D7.csv

source_name: IMM

value: IMM

value: Sorted Immune CD45+ cells from tumor


title: MT.Unique.ID_205

value: Plasma

value: Healthy Subject

value: Plasma cell


title: Subject SU073


title: Subject SU068


title: CD45+, sorted from tumor, Control DAY7, Rep9

description:
Total RNA SEQ
RNASeq CD45+ D7.csv


title: MT.Unique.ID_204


title: Subject SU067


title: MT.Unique.ID_208


title: CD45-, sorted from tumor, Control DAY3, Rep4

description:
Total RNA SEQ
RNASeq CD45- D3.csv


title: Fibroblast IFNa 30min 11980

value: primary fibroblast


title: CD45-, sorted from tumor, Control DAY7, Rep9

description:
Total RNA SEQ
RNASeq CD45- D7.csv


title: MT.Unique.ID_207


title: CD45+, sorted from tumor, Control DAY7, Rep8

description:
Total RNA SEQ
RNASeq CD45+ D7.csv


title: MT.Unique.ID_206


title: Fibroblast IFNg 8h 10547


title: Subject SU069


title: CD45-, sorted from tumor, Abscopal DAY7, Rep4

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: Abscopal


title: MT.Unique.ID_198


title: MT.Unique.ID_202


title: CD45+, sorted from tumor, Control DAY7, Rep7

description:
Total RNA SEQ
RNASeq CD45+ D7.csv


title: Subject SU063


title: Fibroblast IFNg 2h 10547

value: IFN-g 1000 IU/mL 2 hours


title: CD45+, sorted from tumor, Control DAY3, Rep4

description:
Total RNA SEQ
RNASeq CD45+ D3.csv


title: Subject SU066


title: CD45+, sorted from tumor, Abscopal DAY7, Rep4

description:
Total RNA SEQ
RNASeq CD45+ D7.csv


title: Subject SU061


title: MT.Unique.ID_201


title: Subject SU070


title: Subject SU065


title: Fibroblast non-stimulated 10547

value: Non-stimulated


title: Subject SU064


title: Fibroblast IFNa 2h 11980

value: IFN-a2b 1000 IU/mL 2 hours


title: CD45-, sorted from tumor, Control DAY7, Rep7

description:
Total RNA SEQ
RNASeq CD45- D7.csv


title: Subject SU060


title: CD45-, sorted from tumor, Control DAY3, Rep3

description:
Total RNA SEQ
RNASeq CD45- D3.csv


title: Subject SU062


title: Fibroblast IFNa 8h 11980

value: IFN-a2b 1000 IU/mL 8 hours


title: CD45+, sorted from tumor, Control DAY7, Rep6

description:
Total RNA SEQ
RNASeq CD45+ D7.csv


title: CD45+, sorted from tumor, Control DAY3, Rep3

description:
Total RNA SEQ
RNASeq CD45+ D3.csv


title: MT.Unique.ID_195


title: Fibroblast IFNg 30min 10547

value: IFN-g 1000 IU/mL 30 min


title: MT.Unique.ID_199


title: Subject SU059

value: ICU Patient from Stanford


title: Fibroblast IFNa 2h 10547


title: MT.Unique.ID_197

value: 30 min


title: Fibroblast IFNa 8h 10547


title: Patient P2, mRNA-derived cDNA

city: MONTREAL

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
IRF1-02-MM-GEX_LAN1403A4-1_IRF1-02-MM-CSP_LAN1403A6-1_filtered_barcodes.tsv.gz
IRF1-02-MM-GEX_LAN1403A4-1_IRF1-02-MM-CSP_LAN1403A6-1_filtered_features.tsv.gz
IRF1-02-MM-GEX_LAN1403A4-1_IRF1-02-MM-CSP_LAN1403A6-1_filtered_matrix.mtx.gz

data_processing:
QC: Sequence reads quality was assessed using BVAtools (https://bitbucket.org/mugqic/bvatools)
Pre-processing: Cell Ranger v6.0.1 for CITE-seq was used to map reads to the hg38 human reference genome assembly, perform filtering, and count barcodes and unique molecular indexes (UMIs).
Filtering: Genes that were not expressed in any of the datasets were discarded. Cells with >20% of mitochondrial genes were excluded. To filter out low quality cells and doublets, cells falling outside the [-1SD;+2.5SD] interval for the UMI and gene count distribution were excluded. To further identify and remove doublets, we first manually remove cells which co-express cell-specific markers (CD14, CD79A, TRBC1, HBA2 and LILRA4) then the DoubletFinder package v2.0.3 was used to identify and filter out remaining cell doublets (McGinnis et al., 2019).
Joint sample analysis: After dead cells and doublet removal, the patient and control samples were jointly analyzed using the Seurat v4.0.2 R package (Stuart et al., 2019) and cell clustering was performed using the Uniform Manifold Approximation and Projection dimension reduction method (Becht et al., 2019) using the most variable genes, but excluding mitochondrial and ribosomal protein genes, as well as sex-related genes since the two patients are females. Based on the clustering, we performed subclustering for the large immune cell lineages separately (myeloid/pDC, T/NK lymphocytes, and B cells) to identify residual remaining doublets, hence small residual cell clusters expressing multiple cell-specific markers were excluded. A final UMAP clustering identified fourteen distinct 11 T cell and 2 B cells; myeloid cells were excluded from further analyses because of the low number of cells found in patient samples, which is likely due to poor survival of these cells during sample freezing and shipping. The protein markers identified using CITE-seq were used to ascertain the cell identity to each cluster, in conjunction with the MAST approach (Finak et al., 2015) to identify the marker genes for each cluster, in conjunction with the MAST approach (Finak et al., 2015) to identify the marker genes for each cluster.
Differential gene expression analysis:  was performed using MAST for each lymphoid cell cluster by comparing the RNA expression from P1.2 and P2 vs the 5 healthy controls. Adjusted p-values were estimated using the Benjamini-Hochberg (BH) procedure. Every significant differentially expressed gene (absolute FC >=1.5 and adj-p-value ≤0.001) was extracted as down- or up-regulated and used for downstream analysis.
Assembly: hg38
Supplementary files format and content: Filtered Cell Ranger output files: barcodes, features, matrix
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Whole blood

extract_protocol:
The frozen PBMCs were quickly thawed at 37°C and gently resuspended by serial additions of DMEM + 10% heat-inactivated FBS, for a final volume of 14ml. Following centrifugation at 300g for 5 min, cells were washed twice with 5ml DMEM + 10% HI-FBS to remove cell debris. Cell counting and viability assessment was done using the LIVE/DEAD™ Viability kit (ThermoFisher Scientific), according to manufacturer’s guidelines. Residual red blood cells were removed using 25ul of the antibody cocktail and beads from the StemCell EasySep PBMC isolation kit.
CITE-seq antibody labeling: One million cells were resuspended in 1ml Biolegend Cell Staining Buffer and passed through a 40μm Flowmi cell strainer (Sigma) to remove aggregates. Cells were then spun at 400g for 5 min and resuspended in 45ul of Biolegend Cell Staining Buffer complemented with 5ul of Human TruStain FcX Fc block (Biolegend). Cells were then incubated for 30 min at 4°C with a cocktail of TotalSeq-B antibodies (Biolegend) that are DNA-barcoded: CD11c (S-HCL-3), CD141 (M80), CD161 (HP-3G10), CD14 (Me5E2), CD16 (3G8), CD19 (HIB19), CD1c (L161), CD28 (CD28.2), CD370 (CLEC9A) (8F9), CD38 (HB-7), CD3e (UCHT1), CD4 (RPA-T4), CD45RA (HI100), CD45RO (UCHL1), CD56 (NCAM) (5.1H11), CD66b (6/40c), CD69 (FN50), CD8a (RPA-T8), TCR gd (B1), TCR Va7.2 (3C10), IgG1 k Isotype Ctl (MOPC-21). Cells were washes twice in Cell Staining Buffer, once in PBS + 0.04% BSA, and resuspended at a concentration of 1000 cells/μl in PBS + 0.04% BSA.
Single-cell library: The samples were loaded onto a 10X Genomics Chromium G chip aiming to capture 10,000 cells per samples. The reverse transcription and library preparation was performed using the Chromium Single Cell 3′ v3.1 Reagent Kits following manufacturers guidelines. The cDNA and feature barcode library quality was assessed using a TapeStation (Agilent).
Sequencing: The cDNA and feature barcode libraries were sequenced on S4 flowcells of an Illumina NovaSeq 6000 sequencer.

tag: individual

value: Patient P2

value: Whole blood

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: library type

value: mRNA

tag: antibodies/tags


title: Subject SU057


title: CD45-, sorted from tumor, Abscopal DAY7, Rep3

description:
Total RNA SEQ
RNASeq CD45- D7.csv

tag: tissue

value: TUM

value: Sorted Tumor and tumor supporting CD45- cells from tumor

tag: treatment


title: MT.Unique.ID_196

value: Plasma

tag: subject id

tag: time point

value: Healthy Subject


title: Pediatric Healthy Control 1, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
PED-CONT-MM-GEX_LAN1403A3-1_PED-CONT-MM-CSP_LAN1403A5-1_filtered_barcodes.tsv.gz
PED-CONT-MM-GEX_LAN1403A3-1_PED-CONT-MM-CSP_LAN1403A5-1_filtered_features.tsv.gz
PED-CONT-MM-GEX_LAN1403A3-1_PED-CONT-MM-CSP_LAN1403A5-1_filtered_matrix.mtx.gz

library_source: other

value: Pediatric Healthy Control 1

value: ADT

value: Anti-CD11c/TotalSeq-B0053; Anti-CD14/TotalSeq-B0081; Anti-CD141/TotalSeq-B0163; Anti-CD16/TotalSeq-B0083; Anti-CD161/TotalSeq-B0149; Anti-CD19/TotalSeq-B0050; Anti-CD1c/TotalSeq-B0160; Anti-CD28/TotalSeq-B0386; Anti-CD370/TotalSeq-B0207; Anti-CD38/TotalSeq-B0410; Anti-CD3e/TotalSeq-B0034; Anti-CD4/TotalSeq-B0072; Anti-CD45RA/TotalSeq-B0063;Anti-CD45RO/TotalSeq-B0087; Anti-CD56/TotalSeq-B0047; Anti-CD66b/TotalSeq-B0166; Anti-CD69/TotalSeq-B0146; Anti-CD8a/TotalSeq-B0080; Anti-TCRgd/TotalSeq-B0139; Anti-TCR Va7.2/TotalSeq-B0581; IgG1 k Isotype Control/TotalSeq-B0090


title: MT.Unique.ID_192

tag: frequency

tag: condition

value: Plasma cell


title: CD45-, sorted from tumor, Histotripsy DAY7, Rep3

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: Histotripsy


title: Fibroblast IFNa 30min 10547

value: primary fibroblast

tag: genotype

value: IFN-a2b 1000 IU/mL 30 min


title: Subject SU058

value: ICU Patient from Stanford


title: CD45+, sorted from tumor, Histotripsy DAY7, Rep3

description:
Total RNA SEQ
RNASeq CD45+ D7.csv

value: IMM

value: Sorted Immune CD45+ cells from tumor


title: Subject SU056


title: Patient P2, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
IRF1-02-MM-GEX_LAN1403A4-1_IRF1-02-MM-CSP_LAN1403A6-1_filtered_barcodes.tsv.gz
IRF1-02-MM-GEX_LAN1403A4-1_IRF1-02-MM-CSP_LAN1403A6-1_filtered_features.tsv.gz
IRF1-02-MM-GEX_LAN1403A4-1_IRF1-02-MM-CSP_LAN1403A6-1_filtered_matrix.mtx.gz

value: Patient P2

value: Whole blood


title: MT.Unique.ID_193

value: 30 min

tag: anatomical location


title: MT.Unique.ID_280

value: 1 hr


title: MT.Unique.ID_194


title: Subject SU055


title: Adult Healthy Control 2, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: Adult Healthy Control 2

value: Peripheral Blood Mononuclear Cells (PBMC)

value: mRNA


title: Subject SU053


title: CD45-, sorted from tumor, Control DAY7, Rep5

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: TUM

value: Sorted Tumor and tumor supporting CD45- cells from tumor

value: Control


title: CD45+, sorted from tumor, Abscopal DAY7, Rep3

description:
Total RNA SEQ
RNASeq CD45+ D7.csv

value: Abscopal


title: Pediatric Healthy Control 1, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
PED-CONT-MM-GEX_LAN1403A3-1_PED-CONT-MM-CSP_LAN1403A5-1_filtered_barcodes.tsv.gz
PED-CONT-MM-GEX_LAN1403A3-1_PED-CONT-MM-CSP_LAN1403A5-1_filtered_features.tsv.gz
PED-CONT-MM-GEX_LAN1403A3-1_PED-CONT-MM-CSP_LAN1403A5-1_filtered_matrix.mtx.gz

value: Pediatric Healthy Control 1


title: Adult Healthy Control 1, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

value: Adult Healthy Control 1

value: ADT

value: Anti-CD11c/TotalSeq-B0053; Anti-CD14/TotalSeq-B0081; Anti-CD141/TotalSeq-B0163; Anti-CD16/TotalSeq-B0083; Anti-CD161/TotalSeq-B0149; Anti-CD19/TotalSeq-B0050; Anti-CD1c/TotalSeq-B0160; Anti-CD28/TotalSeq-B0386; Anti-CD370/TotalSeq-B0207; Anti-CD38/TotalSeq-B0410; Anti-CD3e/TotalSeq-B0034; Anti-CD4/TotalSeq-B0072; Anti-CD45RA/TotalSeq-B0063;Anti-CD45RO/TotalSeq-B0087; Anti-CD56/TotalSeq-B0047; Anti-CD66b/TotalSeq-B0166; Anti-CD69/TotalSeq-B0146; Anti-CD8a/TotalSeq-B0080; Anti-TCRgd/TotalSeq-B0139; Anti-TCR Va7.2/TotalSeq-B0581; IgG1 k Isotype Control/TotalSeq-B0090


title: MT.Unique.ID_279

value: Plasma

value: Healthy Subject

value: Plasma cell


title: Subject SU054

value: ICU Patient from Stanford


title: MT.Unique.ID_278


title: Subject SU051


title: CD45-, sorted from tumor, Histotripsy DAY3, Rep7

description:
Total RNA SEQ
RNASeq CD45- D3.csv

value: Histotripsy


title: Adult Healthy Control 1, mRNA-derived cDNA

value: Whole blood


title: MT.Unique.ID_277

value: 1 hr


title: CD45+, sorted from tumor, Histotripsy DAY3, Rep6

description:
Total RNA SEQ
RNASeq CD45+ D3.csv

value: IMM

value: Sorted Immune CD45+ cells from tumor


title: MT.Unique.ID_276


title: Subject SU052


title: Subject SU050


title: Adult Healthy Control 2, ADT-derived cDNA

value: Adult Healthy Control 2

value: Peripheral Blood Mononuclear Cells (PBMC)


title: CD45-, sorted from tumor, Abscopal DAY3, Rep7

description:
Total RNA SEQ
RNASeq CD45- D3.csv

value: TUM

value: Sorted Tumor and tumor supporting CD45- cells from tumor


title: Patient P1, mRNA-derived cDNA

value: Patient P1

value: mRNA


title: CD45+, sorted from tumor, Abscopal DAY3, Rep7

description:
Total RNA SEQ
RNASeq CD45+ D3.csv

value: Abscopal


title: CD45-, sorted from tumor, Control DAY7, Rep6

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: Control


title: Patient P1, ADT-derived cDNA

value: ADT

value: Anti-CD11c/TotalSeq-B0053; Anti-CD14/TotalSeq-B0081; Anti-CD141/TotalSeq-B0163; Anti-CD16/TotalSeq-B0083; Anti-CD161/TotalSeq-B0149; Anti-CD19/TotalSeq-B0050; Anti-CD1c/TotalSeq-B0160; Anti-CD28/TotalSeq-B0386; Anti-CD370/TotalSeq-B0207; Anti-CD38/TotalSeq-B0410; Anti-CD3e/TotalSeq-B0034; Anti-CD4/TotalSeq-B0072; Anti-CD45RA/TotalSeq-B0063;Anti-CD45RO/TotalSeq-B0087; Anti-CD56/TotalSeq-B0047; Anti-CD66b/TotalSeq-B0166; Anti-CD69/TotalSeq-B0146; Anti-CD8a/TotalSeq-B0080; Anti-TCRgd/TotalSeq-B0139; Anti-TCR Va7.2/TotalSeq-B0581; IgG1 k Isotype Control/TotalSeq-B0090


title: Subject SU048


title: MT.Unique.ID_273

value: Plasma

value: Healthy Subject

value: Plasma cell


title: MT.Unique.ID_274


title: Subject SU047

value: ICU Patient from Stanford


title: Subject SU049


title: CD45+, sorted from tumor, Control DAY7, Rep5

description:
Total RNA SEQ
RNASeq CD45+ D7.csv


title: MT.Unique.ID_272

value: 1 hr


title: RV1-SMAD4KD-rep3 [RNA-seq]

city: Baltimore

first: Jianfei

last: Qi

state: MD

address: 655W baltimore street

department: Biochemistry and Molecular Biology

institute: University of Maryland

data_processing:
the sequenced reads with low quality or adaptor contamination were removed
Clear reads were mapped to the human reference genome (hg19) using Hisat2 v2.0.5 software
To count the reads numbers mapped to each gene, featureCounts v1.5.0-p3 was used.
The fragments per kilobase of transcript per million mapped reads (FPKM) method was used to estimate expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Cells were maintained in RPMI 1640 media supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were incubated at 37C and 5% CO2.

extract_protocol:
Rv1 cells were transduced with sh-Control, sh-SMAD2, sh-SMAD3, or sh-SMAD4 lentivirus for 48 hours. Total RNAs were extracted using a total RNA miniprep kit (Sigma-Aldrich, St. Louis, MO).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina

tag: cell line

value: Human prostate cancer cell line

value: SMAD4 knock down


title: CD45-, sorted from tumor, Histotripsy DAY3, Rep6

description:
Total RNA SEQ
RNASeq CD45- D3.csv

value: Histotripsy


title: CD45+, sorted from tumor, Histotripsy DAY3, Rep5

description:
Total RNA SEQ
RNASeq CD45+ D3.csv

value: IMM

value: Sorted Immune CD45+ cells from tumor


title: MT.Unique.ID_275


title: MT.Unique.ID_271


title: RV1-SMAD4KD-rep1 [RNA-seq]


title: MT.Unique.ID_270


title: Subject SU046


title: CD45+, sorted from tumor, Abscopal DAY3, Rep6

description:
Total RNA SEQ
RNASeq CD45+ D3.csv


title: CD45-, sorted from tumor, Abscopal DAY3, Rep6

description:
Total RNA SEQ
RNASeq CD45- D3.csv

value: TUM

value: Sorted Tumor and tumor supporting CD45- cells from tumor


title: RV1-SMAD2KD-rep2 [RNA-seq]

value: SMAD2 knock down


title: Subject SU045


title: MT.Unique.ID_188

value: 30 min


title: Subject SU044


title: RV1-SMAD2KD-rep1 [RNA-seq]


title: MT.Unique.ID_187


title: Subject SU042


title: RV1-SMAD3KD-rep3 [RNA-seq]

value: SMAD3 knock down


title: CD45-, sorted from tumor, Histotripsy DAY3, Rep5

description:
Total RNA SEQ
RNASeq CD45- D3.csv


title: MT.Unique.ID_185


title: RV1-SMAD3KD-rep2 [RNA-seq]


title: MT.Unique.ID_186


title: CD45+, sorted from tumor, Abscopal DAY3, Rep5

description:
Total RNA SEQ
RNASeq CD45+ D3.csv

value: Abscopal


title: Fibroblast IFNg 30min 11980

value: primary fibroblast

value: IFN-g 1000 IU/mL 30 min


title: CD45+, sorted from tumor, Histotripsy DAY3, Rep4

description:
Total RNA SEQ
RNASeq CD45+ D3.csv


title: MT.Unique.ID_184

value: Plasma

value: Healthy Subject


title: Subject SU040

value: ICU Patient from Stanford


title: CD45-, sorted from tumor, Abscopal DAY3, Rep5

description:
Total RNA SEQ
RNASeq CD45- D3.csv


title: RV1-SMAD2KD-rep3 [RNA-seq]


title: RV1-SMAD3KD-rep1 [RNA-seq]


title: Subject SU041


title: RV1-SMAD4KD-rep2 [RNA-seq]


title: CD45-, sorted from tumor, Histotripsy DAY3, Rep4

description:
Total RNA SEQ
RNASeq CD45- D3.csv


title: MT.Unique.ID_183

value: Plasma cell


title: MT.Unique.ID_200


title: RV1-pLKO.1-rep3 [RNA-seq]

value: Human prostate cancer cell line

value: WT


title: RV1-pLKO.1-rep2 [RNA-seq]


title: CD45+, sorted from tumor, Histotripsy DAY3, Rep3

description:
Total RNA SEQ
RNASeq CD45+ D3.csv

value: Histotripsy


title: Subject SU043


title: Subject SU038


title: CD45-, sorted from tumor, Abscopal DAY3, Rep4

description:
Total RNA SEQ
RNASeq CD45- D3.csv


title: Subject SU037


title: MT.Unique.ID_182


title: RV1-pLKO.1-rep1 [RNA-seq]


title: MT.Unique.ID_181


title: CD45+, sorted from tumor, Abscopal DAY3, Rep4

description:
Total RNA SEQ
RNASeq CD45+ D3.csv

value: IMM


title: Subject SU036


title: CD45-, sorted from tumor, Control DAY7, Rep4

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: Control


title: RV1-pLKO.1-IgG

library_source: genomic

data_processing:
library strategy: CUT&RUN
Quality of ChIP-seq read were checked with fastqc
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 28, using trimgalore v0.6.6
ChIP-seq reads were aligned to the UCSC human hg19 reference genome and E. coli K12, MG1655 reference genome using Bowtie2 v2.3.5.1. If one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant (--dovetail)
Samples were normalized compare do total reads counts, and BAM files were processed (remove duplicates, sorting, and indexing) using samtools v1.10 and Picard v2.23.9
Processed Bam files were normalized with spike-in normalization method and formatted in the bigWig and bedgraph file format, using Deeptools v3.5.0
Peaks were called uing MACS2 bdgpeakcall v2.2.6 with the significance cut-off p-value <=0.01 and reproducible peaks were generaged from two replicated peaks using IDR v2.0.4.2
Assembly: hg19, K12 MG1655
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cell nuclei were extracted using nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1 % Triton X-100, 20% glycerol, 1X protease cocktail) and incubated with ConA Beads to absorb nuclei to beads for 10 min at RT. The nuclei-beads were placed in magnet and the supernatant was removed. Antibody buffer and 0.5 μg antibody was added to each sample and incubate overnight at 4°C. After washing the nuclei-beads, 2.5 μl of pAG-NMase was added and incubated for 10 min at RT. After washing, 1 μl of Chromatin Digest additive was added and incubate for 2 hrs at 4°C. Then, stop buffer and 0.5 ng of Spike-in DNA were added and incubate for 10 min at 37 °C. We purified DNA from this using DNA purification kit (EpiCypher).
Using 5 ng of purified CUT&RUN-enriched DNA, we prepared sequencing library using library prep kit for illumine sequencing (E7645, NEB). The library was purified with 1.0 X AMPure beads (Beckman) and library fragment size was checked with Agilent Bioanalyzer.

value: control

tag: antibody

value: IgG


title: RV1-SMAD3KD-AR-rep2

value: AR (millipore, #06-680)


title: MT.Unique.ID_180

value: 30 min


title: Subject SU035


title: Subject SU039


title: CD45+, sorted from tumor, Control DAY7, Rep4

description:
Total RNA SEQ
RNASeq CD45+ D7.csv

value: Sorted Immune CD45+ cells from tumor


title: RV1-SMAD3KD-AR-rep1


title: Subject SU034


title: MT.Unique.ID_179


title: MT.Unique.ID_176


title: MT.Unique.ID_175


title: CD45+, sorted from tumor, Control DAY7, Rep3

description:
Total RNA SEQ
RNASeq CD45+ D7.csv


title: CD45-, sorted from tumor, Control DAY7, Rep3

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: TUM

value: Sorted Tumor and tumor supporting CD45- cells from tumor


title: RV1-pLKO.1-AR-rep2


title: Subject SU033


title: RV1-pLKO.1-AR-rep1


title: MT.Unique.ID_178


title: CD45-, sorted from tumor, Histotripsy DAY7, Rep2

description:
Total RNA SEQ
RNASeq CD45- D7.csv


title: Subject SU031


title: Subject SU032


title: MT.Unique.ID_174


title: MT.Unique.ID_173


title: RV1-pLKO.1-SMAD3-rep1

value: SMAD3 (abcam, #ab28379)


title: Subject SU030


title: MT.Unique.ID_172

value: Plasma


title: CD45-, sorted from tumor, Abscopal DAY7, Rep2

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: Abscopal


title: Subject SU029

value: ICU Patient from Stanford


title: CD45+, sorted from tumor, Abscopal DAY7, Rep2

description:
Total RNA SEQ
RNASeq CD45+ D7.csv


title: MT.Unique.ID_171

value: Healthy Subject

value: Plasma cell


title: RGD_HBL1_CD40L_BiolRep3

city: Ithaca

first: Lauren

middle: D

last: Walter

address: 161 Weill Hall

department: Biomedical Engineering

institute: Cornell University

data_processing:
Reads were trimmed using bcl2fastq. Trimmed sequence reads were mapped to hg38 using TopHat v2.1.1
Reads were counted within features using HTSeq v2.0.1
Assembly: NCBI hg38
Supplementary files format and content: BAM files of aligned reads
Supplementary files format and content: tab-delimited matrix of raw counts

extract_protocol: Sorted lymphoma cells were lysed and collected RNA by TRIzol

value: Human diffuse large B-cell lymphoma

value: RGD; Co-culture with CD40L+ cells

value: 4 days organoid culture


title: MT.Unique.ID_170


title: RGD_HBL1_CD40L_BiolRep1


title: RGD_HBL1_CD40L_BiolRep2


title: CD45-, sorted from tumor, Histotripsy DAY7, Rep1

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: Histotripsy


title: RGD_HBL1_BiolRep3

value: RGD Matrix; No co-culture


title: CD45+, sorted from tumor, Histotripsy DAY7, Rep1

description:
Total RNA SEQ
RNASeq CD45+ D7.csv

value: IMM


title: Subject SU028


title: CD45+, sorted from tumor, Abscopal DAY7, Rep1

description:
Total RNA SEQ
RNASeq CD45+ D7.csv


title: MT.Unique.ID_168


title: Subject SU027


title: Subject SU026


title: RV1-pLKO.1-SMAD3-rep2

value: Human prostate cancer cell line

value: control


title: MT.Unique.ID_169

value: 30 min


title: CD45-, sorted from tumor, Abscopal DAY7, Rep1

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: TUM


title: Subject SU025


title: CD45-, sorted from tumor, Control DAY7, Rep2

description:
Total RNA SEQ
RNASeq CD45- D7.csv

value: Sorted Tumor and tumor supporting CD45- cells from tumor

value: Control


title: CD45+, sorted from tumor, Histotripsy DAY7, Rep2

description:
Total RNA SEQ
RNASeq CD45+ D7.csv

value: Sorted Immune CD45+ cells from tumor


title: Subject SU023


title: RGD_HBL1_BiolRep2


title: CD45+, sorted from tumor, Control DAY7, Rep2

description:
Total RNA SEQ
RNASeq CD45+ D7.csv


title: MT.Unique.ID_266

value: Plasma

value: 1 hr


title: RGD_HBL1_BiolRep1


title: REDV_HBL1_CD40L_BiolRep3

value: REDV Matrix; Co-culture with CD40L+ cells


title: MT.Unique.ID_166

value: Healthy Subject

value: Plasma cell


title: Subject SU024

value: ICU Patient from Stanford


title: MT.Unique.ID_264


title: CD45-, sorted from tumor, Control DAY7, Rep1

description:
Total RNA SEQ
RNASeq CD45- D7.csv


title: REDV_HBL1_CD40L_BiolRep1

value: Human diffuse large B-cell lymphoma

value: 4 days organoid culture


title: CD45-, sorted from tumor, Histotripsy DAY3, Rep3

description:
Total RNA SEQ
RNASeq CD45- D3.csv

value: Histotripsy


title: REDV_HBL1_CD40L_BiolRep2


title: MT.Unique.ID_167


title: Subject SU022


title: Subject SU020


title: Subject SU019


title: REDV_HBL1_BiolRep1

value: REDV Matrix; No co-culture


title: CD45-, sorted from tumor, Abscopal DAY3, Rep3

description:
Total RNA SEQ
RNASeq CD45- D3.csv

value: Abscopal


title: CD45+, sorted from tumor, Control DAY7, Rep1

description:
Total RNA SEQ
RNASeq CD45+ D7.csv

value: IMM


title: REDV_HBL1_BiolRep2


title: CD45+, sorted from tumor, Abscopal DAY3, Rep3

description:
Total RNA SEQ
RNASeq CD45+ D3.csv


title: MT.Unique.ID_263


title: MT.Unique.ID_262


title: GFO_HBL1_CD40L_BiolRep3

value: GFO Matrix;Co-culture with CD40L+ cells


title: MT.Unique.ID_261


title: Subject SU018


title: Subject SU016


title: MT.Unique.ID_265


title: Subject SU021


title: GFO_HBL1_CD40L_BiolRep2


title: Subject SU017


title: CD45+, sorted from tumor, Control DAY3, Rep2

description:
Total RNA SEQ
RNASeq CD45+ D3.csv


title: MT.Unique.ID_260


title: REDV_HBL1_BiolRep3


title: MT.Unique.ID_259


title: GFO_HBL1_CD40L_BiolRep1


title: CD45-, sorted from tumor, Control DAY3, Rep1

description:
Total RNA SEQ
RNASeq CD45- D3.csv

value: TUM


title: Subject SU015


title: MT.Unique.ID_258


title: GFO_HBL1_BiolRep3

value: GFO Matrix; No co-culture


title: CD45+, sorted from tumor, Control DAY3, Rep1

description:
Total RNA SEQ
RNASeq CD45+ D3.csv

value: Control


title: MT.Unique.ID_257


title: GFO_HBL1_BiolRep2


title: CD45-, sorted from tumor, Histotripsy DAY3, Rep2

description:
Total RNA SEQ
RNASeq CD45- D3.csv

value: Sorted Tumor and tumor supporting CD45- cells from tumor


title: MT.Unique.ID_256

value: Plasma


title: Subject SU014


title: CD45-, sorted from tumor, Control DAY3, Rep2

description:
Total RNA SEQ
RNASeq CD45- D3.csv


title: Subject SU013


title: GFO_HBL1_BiolRep1


title: CD45+, sorted from tumor, Histotripsy DAY3, Rep2

description:
Total RNA SEQ
RNASeq CD45+ D3.csv

value: Sorted Immune CD45+ cells from tumor


title: MT.Unique.ID_162

value: 30 min


title: Normal-OCTOPUS-d7, replicate 1, scRNAseq

city: Philadelphia

first: Dan Dongeun

last: Huh

state: Pennsylvania

address: 210 South 33rd Street 315S Skirkanich Hall

institute: University of Pennsylvania

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequence reads data were processed using the CellRanger pipeline (10X Genomics, v.5.0.0) for demultiplexing and aligned to the human genome GRCh38 transcriptome. Sample data was aggregated using the CellRanger aggr pipeline and libraries were normalized for sequencing depth across the sample set. A total of 5 organoid sample count matrices were merged together for cell type identification and direct comparisons. For initial filtering, cells with a smaller number (< 200) of uniquely detected genes were excluded. Then, cells with a proportion of unique molecular identifiers (UMIs) count attributable to mitochondrial genes (> 25%) were excluded from the analysis. Finally, highly variable genes were used for dimension reduction, and the results were visualized via UMAP.
Assembly: human genome GRCh38
Supplementary files format and content: barcodes, features, and matrix files

source_name: terminal ileum

extract_protocol:
Enteroid lines are generated from terminal ileum mucosal biopsies. Briefly, two biopsy tissue fragments were rinsed 3 times in 1 ml cold sterile PBS, then incubated in cold chelation buffer for 30 minutes on a turntable in a cold room, followed by mechanical dis-sociation (scraping) of epithelial layer. The fragments were strained through a 100 μm strainer to deplete the villi and resuspended in 80% Matrigel, then seeded at the density of 50-200 crypts per 30 μl drop. The droplets solidified at 37ºC for 30 minutes, and 500 μl human IntestiCult (STEMCELL Technologies; complete when supplemented with Penicillin-Streptomycin (Gibco)) was added per well. Y-27632 (SelleckChem; final conc. 10 μM) was added to culture medium at seeding only.
Single-cell suspension for each organoid sample was loaded onto a separate channel of a Chromium 10X Genomics Single Cell 3’ Reagent Kit v2 library chip (10X Genomics) according to the manufacturer’s protocol. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed. cDNA sequencing libraries were prepared according to the manufacturer’s protocol (10X user guide for library prep) and sequenced on an Illumina NovaSeq 6000 using an S1 100 cycles flow cell v1.5. Library quality control was done using Agilent TapeStation for sizing (bp) and KAPA qPCR for concentration (nM).

value: terminal ileum

value: intestinal epithelial cells

value: Normal


title: CD45-, sorted from tumor, Abscopal DAY3, Rep2

description:
Total RNA SEQ
RNASeq CD45- D3.csv


title: Subject SU011

value: ICU Patient from Stanford


title: Subject SU012


title: MT.Unique.ID_160

value: Healthy Subject

value: Plasma cell


title: MT.Unique.ID_161


title: Normal-drop-d7, replicate 1, scRNAseq

description: 10X Genomics


title: CD45-, sorted from tumor, Histotripsy DAY3, Rep1

description:
Total RNA SEQ
RNASeq CD45- D3.csv

value: Histotripsy


title: IBD-OCTOPUS-d14, replicate 1, scRNAseq

description: 10X Genomics

value: inflammatory bowel disease (IBD)


title: Subject SU010


title: Subject SU009


title: CD45+, sorted from tumor, Abscopal DAY3, Rep2

description:
Total RNA SEQ
RNASeq CD45+ D3.csv

value: IMM

value: Abscopal


title: Subject SU008


title: MT.Unique.ID_159


title: CD45+, sorted from tumor, Histotripsy DAY3, Rep1

description:
Total RNA SEQ
RNASeq CD45+ D3.csv


title: MT.Unique.ID_158


title: IBD-drop-d7, replicate 1, scRNAseq

description: 10X Genomics


title: Subject SU007


title: Subject SU006


title: MT.Unique.ID_157


title: CD45-, sorted from tumor, Abscopal DAY3, Rep1

description:
Total RNA SEQ
RNASeq CD45- D3.csv

value: TUM


title: MT.Unique.ID_156


title: Patient 873 time point 1 replicate 2

city: Berkeley

first: Iain

middle: Christopher

last: Clark

address: 374 Stanley Hall

institute: University of California, Berkeley

description: Patient 873 time point 1 replicate 2

data_processing:
The sample is aligned to human GRCh38.p13 with Salmon and quantified with alevin v1.2.0
Assembly: GRCh38.p13
Supplementary files format and content: Matrices are zipped folders of 3 files: (1) sparse matrix, (2) barcodes file, (3) genes file. Raw data are gzipped fastqs, most of which have four files per sample: 2 lanes from 2 reads. Two samples were sequenced on a single lane NovaSeq run, and therefore only have the two reads from a single lane.

source_name: Mixed phenotype acute leukemia (MPAL)

growth_protocol: Patient samples

extract_protocol:
Cryopreserved peripheral blood mononuclear cells and peripheral bone marrow mononuclear cell samples
PIP-seq single cell library prep

treatment_protocol: Patients before and after chemotherapy

tag: sample type

value: B/Myeloid diagnosis -

tag: Sex

value: Female

tag: age


title: MT.Unique.ID_155


title: KO Male HFD CellPlex, scRNA seq, CMO IDs- 310, 311, 312

city: Riverside

first: Djurdjica

last: Coss

address: 109 Picnic Hill Rd

department: Biomedical Sciences

institute: University of California Riverside

description:
10x Genomics
KO_Male_matrix.mtx
KO_Male_features.tsv
KO_Male_barcodes.tsv

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Visceral adipose tissue

extract_protocol:
Visceral adipose tissue was dissected from visceral fat pads, rinsed in ice cold 1X PBS and minced with a razor blade. Fat was digested enzymatically with 3 mg/ml collagenase/dispase at 37 C for 1 hour. Suspension was passed through a 70um strainer and centrifuged to pellet stromal vascular fraction. Cell suspension was resuspended in 1X PBS/0.04% BSA and counted.
Libraries were prepared according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Feature barcode for cell multiplexing oligo label, Unique Molecular Identifier (UMI) and the 10x Barcode. For the gene expression and CellPlex library construction, the pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added to ensure that no sample indices overlapped between different libraries.

value: Visceral adipose tissue

tag: cell type

value: Stromal vascular fraction

value: Knock-out

value: Male

value: high fat diet


title: WT Male HFD CellPlex, scRNA seq, CMO IDs- 304, 306, 309

description:
10x Genomics
WT_Male_matrix.mtx
WT_Male_features.tsv
WT_Male_barcodes.tsv

value: Wildtype


title: KO Female HFD CellPlex, scRNA seq, CMO IDs- 305, 307, 308

description:
10x Genomics
KO_Female_matrix.mtx
KO_Female_features.tsv
KO_Female_barcodes.tsv


title: MT.Unique.ID_153

value: Plasma

value: 30 min


title: Patient 873 time point 1 replicate 1

description: Patient 873 time point 1 replicate 1


title: Subject SU002

description: Antibodies in samples bind to conjugated beads in array. The fluorescence measured as MFI from the secondary antibody was used to determine antibody reactivity.

tag: disease

value: ICU Patient from Stanford


title: MT.Unique.ID_152

value: Healthy Subject

value: Plasma cell


title: Normal-OCTOPUS-d14, replicate 1, scRNAseq

description: 10X Genomics

value: terminal ileum

value: intestinal epithelial cells

value: Normal


title: WT Female HFD CellPlex, scRNA seq, CMO IDs- 301, 302, 303

description:
10x Genomics
WT_Female_matrix.mtx
WT_Female_features.tsv
WT_Female_barcodes.tsv


title: Subject SU003


title: Subject SU004


title: Subject SU005


title: MT.Unique.ID_154


title: Subject HC 22

value: Healthy Control


title: Subject HC 21


title: WT Male HFD GEX, scRNA seq


title: MT.Unique.ID_149


title: KO Male HFD GEX, scRNA seq


title: KO Female HFD GEX, scRNA seq


title: CD45+, sorted from tumor, Abscopal DAY3, Rep1

description:
Total RNA SEQ
RNASeq CD45+ D3.csv

value: IMM

value: Sorted Immune CD45+ cells from tumor

value: Abscopal

tag: time


title: MT.Unique.ID_148


title: MT.Unique.ID_147


title: WT Female HFD GEX, scRNA seq

value: Visceral adipose tissue

value: Stromal vascular fraction

value: Female


title: MT.Unique.ID_146


title: Subject HC 18


title: Graft Periosteal SSCs Day 3, rep3

data_processing:
Original data file from Illumina transformed into sequenced reads by CASAVA base recognition (Base Calling). Raw reads of FASTQ were processed through fastp
Raw reads filtering: remove reads with adaptors, remove reads with N>10%, remove reads with Qscore > 50% bases below 5
Mapped clean reads using STAR software (v2.6.1d); paramaters: mismatch = 2
FeatureCounts (v1.5.0-p3) used to count read numbers mapped of each gene and then RPKM was calculated based on length of gene and reads count mapped to this gene
Assembly: GRCm38
Supplementary files format and content: tab-delimited  file includes FPKM values and gene ID for each sample

value: skeletal stem cells

value: periosteum

value: WT

tag: strain

value: Day 3 after bone transplantation


title: MT.Unique.ID_150

tag: tissue

value: Plasma

value: 30 min


title: MT.Unique.ID_145

value: Healthy Subject

value: Plasma cell


title: Subject SU001

value: ICU Patient from Stanford


title: MT.Unique.ID_143


title: Graft Periosteal SSCs Day 3, rep2


title: MT.Unique.ID_142


title: Periosteal SSCs Day 0, rep3

value: Day 0


title: Subject HC 15

value: Healthy Control


title: MT.Unique.ID_141


title: Graft Periosteal SSCs Day 3, rep1


title: Subject HC 14


title: Subject HC 13


title: Subject HC 20


title: H526-DOXplus_3

city: Bostone

first: Atsushi

last: Fushimi

state: MA

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).

growth_protocol: COR-L279 and NCI-H526 cells were cultured in RPMI 1640 medium (Corning, Corning, NY, USA) supplemented with 10% FBS.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline.

value: small cell lung cancer cells

tag: genotype/variation

value: puromycin resistance

tag: treatment


title: Periosteal SSCs Day 0, rep2


title: Subject HC 12

data_processing: Sample replicate MFI values were averaged for each antigen. The average barebead MFI was then subtracted from the average MFI of each sample and antigen.


title: Bone Marrow MSCs Day 0, rep3

source_name: bone marrow

value: mesenchymal stem cells

value: bone marrow


title: H526-DOXplus_2


title: Subject HC 11

source_name: Serum/Plasma


title: Periosteal SSCs Day 0, rep1


title: H526-DOXplus_1


title: MT.Unique.ID_144

tag: subject id

tag: time point


title: MT.Unique.ID_254

tag: frequency

value: 1 hr

tag: condition


title: MT.Unique.ID_253

tag: anatomical location


title: Subject HC 19


title: Subject HC 16


title: MT.Unique.ID_252


title: H526-DOX-_3

tag: cell line


title: Bone Marrow MSCs Day 0, rep2

tag: genotype


title: MT.Unique.ID_140


title: Subject HC 10


title: MT.Unique.ID_251


title: Subject HC 8


title: MT.Unique.ID_250


title: Subject HC 9


title: Bone Marrow MSCs Day 0, rep1


title: H526-DOX-_2


title: Hypothalamus, TRɑ1+m, Biol Rep2

city: Lübeck

first: Varun

middle: K A

last: Sreenivasan

state: Schleswig Holstein

address: Gebaude 67, BMF, 1.OG Links, Marie-Curie-Strasse,

department: Institute of Human Genetics

country: Germany

description: 10X Genomics

data_processing:
FASTQ files were processed with Cellranger 5.0.1 with include introns option
Seurat was used to analyse the data, including QC, clustering, DE analysis, cell type annotation etc.
Assembly: mm10
Supplementary files format and content: Two tab seperated value files containing gene names and cell barcodes corresponding to the mtx file containing the cell x gene expression count matrix. One set of files per sample (library)

source_name: Hypothalamus

extract_protocol:
Nuclei were isolated from snap frozen hypothalamus tissue with an adapted version of the published sci-RNA-seq3 protocol for nuclei isolation (Cao et al., 2019). The samples were cut into small pieces in 0.5 mL ice cold cell lysis buffer (CLB) (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1%SUPERase In RNase Inhibitor (20 U/μL, Ambion), 2% BSA and 0.1% IGEPAL CA-630) adding another 0.5 mL CLB, the tissue was further singled out by resuspension with a 1 mL pipette. The samples were strained using a 40 µm cell strainer and pooled by genotype (WT or TRα1+m) into respective eppendorf loBind tubes. The nuclei were pelleted (4°C,500g(0.5rcf), 5min) and resuspended in 1 mL nuclei suspension buffer (NSB) (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1%SUPERase In RNase Inhibitor (20 U/μL, Ambion) and 2% BSA). The nuclei were checked for successful lysis under a microscope using a cell counter. After a second cell strainer step into a new loBind tube, the nuclei were again pelleted, resuspended in 1 mL NSB, pooled (across the three biological samples within a genotype) and counted using a cell counter.
In a new loBind tube, the nuclei were diluted into 1.000 nuclei/μL in 20 μL and directly processed for single-cell RNA seq using the 10x protocol (V3.1). The quality of the cDNA was assessed using TapeStation (HighSensitivity D5000 Screen Tape), as recommended by the 10x protocol. Sequencing was performed at the Max Planck Institute Sequencing facility with asynchronous paired end sequencing NovaSeq 6000 (Illumina).
sc-RNA-seq (Chromium 10X)

value: Hypothalamus


title: L279-DOXplus_3


title: Subject HC 6

extract_protocol: Blood was collected from patients and healthy controls. The blood was then processed into serum or plasma which was then run on our arrays.


title: Hypothalamus, TRɑ1+m, Biol Rep1

description: 10X Genomics


title: H526-DOX-_1


title: Subject HC 5


title: Subject HC 7


title: L279-DOXplus_2


title: MT.Unique.ID_248


title: Hypothalamus, WT, Biol Rep2

description: 10X Genomics


title: MT.Unique.ID_247


title: L279-DOXplus_1


title: Hypothalamus, WT, Biol Rep1

description: 10X Genomics


title: Subject HC 4


title: MT.Unique.ID_246


title: Subject HC 3


title: MT.Unique.ID_245


title: L279-DOX-_3


title: MT.Unique.ID_249


title: L279-DOX-_2


title: L279-DOX-_1


title: Subject HC 1


title: Subject HC 2


title: Subject HC 17


title: CsPYL1_5m_5uM_iSB09_rep1

status: Public on Jan 11 2023

city: Valencia

first: Jorge

last: Lozano-Juste

address: Ingeniero Fausto Elio s/n Edificio 8E

country: Spain

institute: IBMCP-UPV-CSIC

data_processing:
TPM
RPKM

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: liquid media 12 days

extract_protocol: none provided by the submitter

tag: background


title: CsPYL1_5m_5uM_iSB09_rep3


title: CsPYL1_5m_DMSO_rep3


title: CsPYL1_5m_5uM_iSB09_rep2


title: CsPYL1_5m_DMSO_rep1


title: wt_5uM_iSB09_rep1

value: wt


title: wt_5uM_iSB09_rep2


title: wt_DMSO_rep3


title: wt_5uM_iSB09_rep3


title: wt_DMSO_rep2


title: wt_DMSO_rep1


title: MT.Unique.ID_244

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.


title: CsPYL1_5m_DMSO_rep2


title: Young_input_rep2

city: San Francisco

first: Xuan

last: Luong

address: 505 Parnassus Ave

institute: UCSF

description:
8-h1_Y2-IN_S8
cpm_input-cpm1.csv

data_processing:
The quality of the raw sequence data was checked via FASTQC. The sequence files were then trimmed using tools in Trimmomatic 0.36 64. The following were removed: Illumina TruSeq3 single-ended adapter sequences, bases with a quality score <3 at the start and end of a read, bases that had an average quality per base of <15 calculated using a sliding window to average four bases, and any reads that were shorter than 36 bases. The reads were single-ended and qualities were ASCII characters equal to the Phred quality plus 33.
HiSat2 65 was used to build indexes from the Reference Consortium Mouse Build 38 (mm10) and to align sequence reads to the genome. The resulting .bam files were sorted and indexed with SAMtools 66. Count files for each group were created with HTSeq using the mouse GENCODE Gene set release M11. The input data were .bam files, the data were not from a strand-specific assay, and the feature type used was ‘gene.’
The Bioconductor packages edgeR 67 and limma 68 were used for statistical analyses. Only reads with greater or equal to 1 count per million (CPM) in at least two samples were kept. Trimmed mean of M-values (TMM) normalization, which accounts for compositional differences among the libraries, was then performed on HA reads and input reads, separately.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TMM-normalized CPM values

source_name: Oocyte

growth_protocol: Female mice were injected with 5 I.U. pregnant mare serum gonadotropin (PMSG; MyBioSource) to induce follicle growth and sacrificed 44 hours after injection. The ovaries were dissected, and COCs were collected in media containing HEPES-modified minimum essential medium Eagle (Sigma-Aldrich, M2645) supplemented with 0.23 mM sodium pyruvate (Gibco, 11360070), penicillin-streptomycin (Genesee Scientific Corporation (GenClone), 25-512), and 3 mg/mL BSA (Sigma-Aldrich, SIAL-A3311), 6 mM sodium bicarbonate (JT-Baker, 3506-1), and a PDE inhibitor (1 µM cilostamide (Calbiochem, 231085) or 2mM milrinone (Enzo ALK-270-083)). Aspiration through a glass pipette allowed for removal of the surrounding cumulus cells. Denuded oocytes were maintained at the GV stage in α-MEM (Gibco, 12561-056) supplemented with 0.23 mM sodium pyruvate, penicillin-streptomicin, and 1 µM cilostamide (or 2 mM milrinone) at 37 °C under 5 % CO2. For the collection of in vivo MII oocytes, female mice were injected with 5 I.U. of PMSG followed by 10 I.U. human chorionic gonadotropin (hCG; Goldline Labs) 48 h after PMSG injection, and after 13 h, sacrificed for ovulated oocytes retrieval from the fallopian tubes.

extract_protocol:
To prepare samples for the IP, the appropriate volume (80 µl per sample) of Dynabeads™ Protein G (Invitrogen, 10004D) was washed two times in 250 µl homogenization buffer (HB: 50 mM Tris–HCl pH 7.4, 100 mM KCl, 12 mM MgCl2 and 1% v/v NP-40) on a rotor at 4 °C for 5 min per wash. Two additional washes were performed with 250 µl supplemented HB (sHB: HB supplemented with 1 mM DTT (sigma 646563), 1× HALT protease inhibitor (Fisher P178441), 200 units/ml RNaseOUT, 200 units/ml RNasin (Promega N2115), 100 µg/ml CHX) on a rotor at 4 °C for 5 min per wash. Following the final wash, the beads were eluted back to the original volume with sHB. Oocyte samples were thawed, pooled to yield a total of 200 oocytes per replicate, and 300 µl sHB was added to each pooled sample. To lyse the cells, samples were vortexed for 30 s and the homogenates were centrifuged for 15 min at 20817 g at 4 °C. Ovaries were homogenized in 300 µl sHB and centrifuged likewise. To pre-clear the samples, the supernatants were transferred to new tubes, 20 µl of washed beads were added to each supernatant, and samples were incubated on a rotor at 4 ◦C for 30 min. A magnetic rack was used to remove the beads, and 30 µl (10 %) of each pre-cleared lysate was collected and added to 250 µl RLT buffer (Qiagen, 74034) supplemented with 1 mM DTT to serve as the input samples. The input samples were frozen and kept at −80 ◦C until RNA extraction. 4 µl (4 µg) anti-HA.11 epitope tag antibody (1/75, Invitrogen, 26183) was added to each of the extracts and all samples were incubated on a rotor at 4 °C for 4 hours. Thirty microliters of washed beads was added to the samples and incubated overnight on a rotor at 4 °C. The beads (now bound by HA-tagged ribosomes and the associated mRNAs) were washed four times in 750 µl urea wash buffer (uWB: 50 mM Tris–HCl pH 7.4, 150 mM KCl, 12 mM MgCl2, 1 % v/v NP-40, 1× protease inhibitors, 1 mM DTT, 40 U RNaseOUT, 40 U RNasin, 100 µg/ml cycloheximide, and 1 M urea) on a rotor at 4 °C for 10 min per wash. The bead slurry was then transferred to fresh tubes, pelleted via magnetic rack, and the uWB removed. To strip the mRNA complex off the beads, 250 µl RLT buffer supplemented with DTT was added to each sample and samples were vortexed for 30 s. Finally, Beads were pelleted and removed before RNA extraction was performed using the Rneasy Plus Micro Kit (Qiagen, 74034). Samples were eluted in 14 µl of RNase-free water and used downstream for RNA-Seq or RT-qPCR analysis.
RiboTag RNA samples were sent to the Gladstone Institutes Genomics Core for quality control using Bioanalyzer (Agilent) and cDNA library preparation. cDNA was prepared with the Ovation RNA-Seq System V2 Kit (NuGEN, 7102), which uses a proprietary combination of enzymes and primers to preferentially prime non-rRNA sequences. First-strand cDNA synthesis is achieved with random hexamer primers and chimeric poly(T) primers, which bind to the region spanning the end of the 3’-UTR and the start of the poly(A) tail. Because stable mRNAs have at least 20 adenosine residues, use of these chimeric poly(T) primers allows for preferential priming of adenylated messages (mRNAs) with minimal bias for messages with longer poly(A) tails. RNA-Seq libraries were constructed using the Ovation Ultralow System V2 (NuGEN, 0344) and analyzed by Bioanalyzer, quantified by qPCR (Kapa Biosystems, KR0405), and sequenced using the HiSeq 4000 system (Illumina).

treatment_protocol: Oocytes from RiboTagF/F;Zp3-Cre female mice stimulated with 5 I.U. PMSG followed by 10 I.U. hCG, or ovaries from RiboTagF/F;Zp3-Cre female mice stimulated with 5 I.U. PMSG only were used for RiboTag-immunoprecipitation. Oocytes were collected in 10 µl of 1x PBS (Invitrogen, AM9625), supplemented with 0.1% w/v polyvinylpyrrolidone (PVP; Sigma, P0930), 0.1 % v/v Cyclohexamide (CHX; Sigma C7698), and 250 U RNAse OUT (Invitrogen 10777-019), then flash frozen in liquid nitrogen, and stored at −80 °C.

value: Oocyte

value: MII

tag: Sex

value: Female

value: Young

tag: antibody


title: Young_input_rep1

description:
7-g1_Y1-IN_S7
cpm_input-cpm1.csv

tag: cell type


title: Young_HA_rep1

description:
3-c1_Y1-HA_S3
cpm_HA-cpm1.csv

value: HA


title: Young_HA_rep2

description:
4-d1_Y2-HA_S4
cpm_HA-cpm1.csv


title: Old_input_rep2

description:
6-f1_O2-IN_S6
cpm_input-cpm1.csv

value: Old


title: Old_input_rep1

description:
5-e1_O1-IN_S5
cpm_input-cpm1.csv


title: Old_HA_rep1

description:
1-a1_O1-HA_S1
cpm_HA-cpm1.csv


title: ACL non-injured quadricep  Non_B

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: University of Kentucky

description: ACL non-injured quadricep

data_processing:
Sequenced reads were trimmed from the 3' end based on quality score with a minumum Phred score of 20 and a minumum read length of 25 bp
Trimmed reads were alligned to the hg19 reference genome using STAR 2.7.8a aligner with default parameters.
Aligned reads were quantified to the mm10 reference assembly with requrement of junction reads to match introns and strict paired-end compatibility.  Quantified reads went through a noise reduction filter with maximum feature exclusion set less than or equal to 10.
Filtered counts were normalized per million and tested for statistical significance using DESeq2
All steps were performed using the Partek® Flow® Software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Skeletal muscle

extract_protocol:
Human quadricep RNA was isolated using TRIzol and the Zymo MicroPrep Kit and prepared for RNA-sequencing
Conducted at NovoGene

value: Skeletal muscle

value: ACL non-injured quadricep


title: Old_HA_rep2

description:
2-b1_O2-HA_S2
cpm_HA-cpm1.csv


title: ACL non-injured quadricep  Non_C

description: ACL non-injured quadricep


title: control_rep2

type: RNA

city: nanjing

first: yuxi

last: liu

address: Dingjiaqiao Road 87,Nanjing,China

country: China

institute: Southeast university

description: MRNA expression in control cartilage

hyb_protocol: 1.65 ug of Cy3-labeled, linearly amplified cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 2.2ul 25X Fragmentation Buffer and 11ul 10X Blocking Agent following the manufacturer instructions of Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). On completion of the fragmentation reaction, 55ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression 4x44K v2 Microarrays for 17 hours at 65°C in a rotating Agilent Hybridization oven (Agilent p/n G2545A). After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325) and 1 minute with 37°C Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, 5μm scanning mode Single Pass, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: 1.Open the Agilent Feature Extraction (FE) software. 2.Add the images (.tif) to be extracted to the FE Project. 3.Set FE Project Properties. 4. Check the Extraction Set Configuration. 5.Save the FE Project (.fep) by selecting File > Save As and browse for desired location. 6. Select Project > Start Extracting and export data to txt.

source_name: Cartilage, control, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification using RNeasy Mini Kit (Qiagen p/n 74104). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: 1.Homogenization of above pulverized cartilage tissues using the Mini-Bead-Beater-16 (Biospec)v and TRIzol® Reagent (Invitrogen life technologies). 2.Phase separation using chloroform. 3.RNA precipitation using isopropyl alcohol. 4.RNA wash using 75% ethanol. 5.Redissolving the RNA using RNase-free water.

treatment_protocol: All cartilage samples were immediately frozen in liquid nitrogen before RNA isolation. Cryo pulverization of fresh cartilage tissues using the Biopulverizer (Biospec).

value: Cartilage

tag: disease state

value: traumatic fracture


title: OA_rep4

description: MRNA expression in OA cartilage

source_name: Cartilage, OA, replicate 4

value: osteoarthritis


title: OA_rep1

description: MRNA expression in OA cartilage

source_name: Cartilage, OA, replicate 1


title: control_rep1

description: MRNA expression in control cartilage

source_name: Cartilage, control, replicate 1


title: control_rep4

description: MRNA expression in control cartilage

source_name: Cartilage, control, replicate 4


title: OA_rep3

description: MRNA expression in OA cartilage

source_name: Cartilage, OA, replicate 3


title: control_rep3

description: MRNA expression in control cartilage

source_name: Cartilage, control, replicate 3


title: Ahr_CD8cre_IEL_CD8_R2

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

data_processing:
FastQC was used to ensure high per-base sequence quality of reads.
[RNA-seq] Sequenced reads were mapped and raw count values quantified with STAR (v2.7.4a) to the Mus musculus genome (GRCm38/mm10 assembly) and filtered for uniquely mapped reads. Quantitated mRNA expression levels, FPKM aligned reads, were calculated based on exon regions using RSEM (v1.2.25)
[ChIP-seq] ChIP-seq reads were mapped to the mouse genome (mm10) with bowtie2 (Langmead and Salzberg, 2012). The mapped reads were filtered using samtools (Li et al., 2009), keeping only the uniquely aligned reads, and bedgraph files (scaled to 10 million reads) were made with bedtools (Quinlan and Hall, 2010).  CHIP-seq peak locations were identified using Homer (Heinz et al., 2010)
[scRNA-seq] Alignment, quantification, and quality control were performed using the Cell Ranger Software (v3.1.0) and default parameters. After quality control and removal of dead cells, doublets, and contaminating melanoma cells (Pmel mRNA count > 0) a total of 9726 cells remained for downstream analysis. Normalization, cell clustering (resolution = 2), dimensionality reduction, differential expression, visualization, and pseudotime analysis were performed using the R packages Seurat (Butler et al., 2018) and Monocle (Trapnell et al., 2014). The 3000 most variable features identified with the variance-stabilizing transformation (vst)-method were used for principal component analysis (PCA). Upon inspection of elbowplot and jackstraw plot, the first 20 principal components (PCs) were used for further analysis. Cell type annotation was performed manually by assessment of cluster marker genes.
Assembly: GRCm38/mm10
Supplementary files format and content: [RNA-seq] text file of raw counts for all samples, [ChIP-seq] bedgraph files for each sample, [scRNAseq] single cell barcodes, features, and matrix files for each sample

source_name: Small Intestine IEL CD8+ T cell

extract_protocol:
RNA was extracted using RNAeasy Micro Kit, followed by cDNA generation with SMART-Seq® HT Kit (TaKaRa).
cDNA generation was performed with SMART-Seq® HT Kit (Takara). Sequencing libraries were generated with Nextera® XT DNA Library Preparation Kit (Illumina).

value: Small Intestine IEL

value: CD8+ T cell


title: ACL non-injured quadricep  Non_A

description: ACL non-injured quadricep


title: Ahr_KO_CD8_Ahr_ChIP

source_name: Isolated from spleen then in vitro cultured

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 15 min. Chromatin was sheared by sonication with Bioruptor Pico (30” on and 30” off for 25 cycles) and immunoprecipitated with anti-Ahr (Enzo Life Science) using iDeal ChIP-Seq Kit for transcription factors or True MicroChIP kit (Diagenode).
Eluted DNA was made into indexed library according to the manual of NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The library was cleaned up with 1.2x SPRIselect beads (Beckman Coulter) before sequencing.

treatment_protocol: Naive CD8+ T cells were purified from splenocytes using mouse naive CD8+ T cell isolation kit (Stemcell Technologies) then cultured in RPMI-1640 medium (plus β-mercaptoethanol) supplemented with 10% fetal bovine serum, 1% L-glutamine, 1% penicillin-streptomycin (cRPMI). 100 ng/ml IL-2 and anti-CD3/CD28 coated Dynabeads (Thermo Fisher) at 1:1 cell to bead ratio were added and cells incubated for 48 hours. Then media volume was doubled, each well split into a second, and 5 ng/ml TGF-β and 100 ng/ml IL-33 were added and incubated for another 48 hours, then just before harvest, cells were treated with FICZ (200 nM) for 4 hours.

value: in vitro cultured

value: Ahr-/-


title: CTRL_IEL_CD8_R2

value: Ahrf/f


title: Ahr_CD8cre_IEL_CD8_R1


title: B16_TIL_Ahr_WT1

source_name: B16F10 TIL

extract_protocol:
Live CD45+ total TILs were isolated and purified by FACS before being loaded on the chromium controller (10x Genomics) aiming for a recovery of 10,000 cells.
Single Cell 30 reagent kit v3.1 was used for reverse transcription, cDNA amplification, and library construction of gene expression libraries (10x Genomics) according to the manufacturer.

value: B16F10 tumor

value: Tumor Infiltrating Leukocyte

value: Ahr+/+


title: B16_TIL_Ahr_KO2


title: B16_TIL_Ahr_WT2


title: B16_TIL_Ahr_KO1


title: ACL injured quadricep  Inj_B

description: ACL injured quadricep

value: ACL injured quadricep


title: ACL injured quadricep  Inj_C

description: ACL injured quadricep


title: ACL injured quadricep  Inj_A

description: ACL injured quadricep


title: Ahr_WT_CD8_Ahr_ChIP


title: sham 3

city: Shanghai

first: Xiaohui

address: No.150 Jimo Road,Pudong district

department: Shanghai Heart Failure Research Center

institute: Shanghai East Hospital, Tongji University School of Medicine, Shanghai

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer.
The BioAnalyzer 2100 system (Agilent Technologies, Inc., Richardson, TX, USA) was used for library quality assessment.
The low quality reads removing by cutadapt software (v1.9.3).
The high quality reads were aligned to the mouse reference genome (UCSC mm10) with hisat2 software
Genome_build: mm10
Supplementary_files_format_and_content: Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA

source_name: sham 3

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, MA, USA).The concentration and purity of RNAs were determined by a NanoDrop® ND-2000 spectrophotometer (Thermo, Waltham, MA, USA). After rRNA depletion with the Ribo-Zero Magnetic Gold Kit (Epicentre, Inc., Madison, WI, USA), the RNA libraries were constructed using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cardiac EVs from 4 sham and 4 I45minR24h mice were isolated for RNA sequencing.

value: Cardiac EVs

value: sham

tag: age

value: 10 weeks


title: CTRL_IEL_CD8_R1

tag: strain


title: sham 1

source_name: sham 1

tag: tissue


title: OA_rep2

description: MRNA expression in OA cartilage

source_name: Cartilage, OA, replicate 2


title: sham 2

source_name: sham 2


title: sham 4

source_name: sham 4


title: IR 3

source_name: IR 3

value: IR


title: IR 4

source_name: IR 4


title: IR 1

source_name: IR 1


title: IR 2

source_name: IR 2


title: CD4_lean_3

first: Shumeng

last: Hao

address: Yue Yang Road 320

institute: Chinese Academy of Sciences

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (GRCm38/mm10) using Bowtie.
Gene expression levels were quantified using the RSEM software package.
Differentially expressed genes were subsequently analyzed using the DAVID bioinformatics platformand IPA and GraphPad.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.

source_name: CD4+ T cells from lean mice

growth_protocol: Mice were fed with either a normal diet (referred to lean mice) or a high-fat diet (HFD, 60 kcal% fat, referred to obese mice) generally from 6-8 weeks of age, for up to 4 months. Lean and obese mice were sacrified,and primary CD4+ T cells were purified by  flow cytometry.

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: diet

value: normal diet

tag: state

value: lean

value: spleen

value: CD4+ T cells


title: CD4_obese_1

source_name: CD4+ T cells from obese mice

value: high fat diet

value: obese


title: CD4_lean_1


title: CD4_obese_2


title: CD4_lean_2


title: Patient 120_lh 187

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 187

hyb_protocol: RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a propierty flourescent barcode system specific for each transcript.

scan_protocol: Scaning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 3 HK genes (SF3A3, GUSB, G6PD). Raw values are the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the forty available in the panel based on the lowest coefficients of variation (CV= ratio between mean counts and standard deviations across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls. After completion of normalization processes, counts were log2 transformed.

label: Molecular barcode on reporter probe

source_name: Classical Hodgkin Lymphoma

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tumor diagnostic biopsies of classical Hodgkin Lymphoma were reviewed by three different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 773 genes by NanoString using the PanCancer Immune Profiling Panel (NanoString Technologies).

treatment_protocol: Pretreatment diagnostic biopsies from ABVD-treated classical Hodgkin Lymphoma patients

value: tumor

tag: patient diagnosis

value: Classical Hodgkin Lymphoma

tag: gender

value: F

tag: Stage

value: IV

value: no


title: Patient 114_lh 171

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 171

value: M


title: Patient 116_lh 177

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 177

value: yes


title: Patient 110_lh 156

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 156


title: Patient 115_lh 172

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 172

value: III


title: Patient 122_lh 193

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 193


title: Patient 118_lh 182

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 182

value: II


title: Patient 124_lh 199

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 199


title: Patient 112_lh 165

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 165


title: Patient 113_lh 167

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 167


title: Patient 111_lh 164

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 164


title: Patient 121_lh 191

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 191


title: Patient 123_lh 194

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 194


title: Patient 119_lh 183

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 183


title: CD4_obese_3


title: Patient 106_lh 147

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 147


title: Patient 108_lh 151

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 151


title: Patient 125_lh 201

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 201


title: Patient 126_lh 209

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
lh 209