title: DSP-1001660011972-E-H04

city: Houston

address: One Baylor Plaza

description:
Library name: DSP-1001660011972-E-H04
spatial transcriptomic sequencing

data_processing:
Digital count conversion (.dcc) files were produced from fastq files using the GeoMx NGS Pipeline 2.3.3.10 desktop application.  Briefly, reads are trimmed to remove adapter sequences followed by merging paired-end reads. Stitched reads are then aligned to RTS-ID barcodes in the reference assay. PCR duplicates are removed by sorting on UMIs. Supplemental file Hs_R_NGS_WTA_v1.0 contains RTS-ID mapping.
Assembly: GRCh38.p13. Reads are aligned to GeoMx RTS_ID barcodes as part of the GeoMx NGS Pipeline to generate .dcc files
Supplementary files format and content: deduplicated read counts
Library strategy: Spatial Transcriptomics

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

tag: former or_current_smoker

value: former

tag: pack years

tag: gender

value: male

value: vessel

value: COPD_8_LUL:vessel 3

tag: scan name

value: paraffin


title: Normal-fetal-brain-3

status: Public on Nov 14 2025

type: SRA

city: Baltimore

first: Michael

last: Koldobskiy

state: MD

address: 1800 Orleans St., Bloomberg 11379

department: Oncology

country: USA

institute: Johns Hopkins University

description:
Library name: Normal-fetal-brain-3
bigWig

library_source: genomic

data_processing:
base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bismark v0.12.3
InformME
Assembly: hg19
Supplementary files format and content: bigWig format.  Tracks include mean methylation level (MML), normalized methylation entropy (NME), and differential quantities of the above between samples (dMML, dNME) and Jensen Shannon Distance (JSD) to measure epigenetic discordance between samples

molecule: genomic DNA

organism: Homo sapiens

source_name: normal

extract_protocol:
Epicentre DNA extraction kit
Illumina TruSeq, NEBNext

tag: tissue

value: normal

tag: cell line

value: N

tag: cell type

value: normal fetal brain


title: Mock-Con-2

city: Wenzhou

first: Dongqin

last: Zhou

state: Zhejiang

address: Chashan Street

country: China

institute: Wenzhou Medical University

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: Excel files include RPKM values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Bone Marrow Primary Cells

extract_protocol:
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: Bone Marrow Primary Cells

tag: genotype

value: WT

tag: treatment

value: Control


title: Normal-fetal-brain-1

description:
Library name: Normal-fetal-brain-1
bigWig


title: LB4021_TCR

city: Bethesda

first: Seketoulie

last: Keretsu

address: Building 37,

department: Neuro-Oncology Branch

institute: National Institute of Health

description:
Library name: LB4021_TCR
Sample 21_TCR
10x Genomics

data_processing:
Data were demultiplexed and aligned with Cell Ranger version 7.1 (10X Genomics) and aligned to the Genome Reference Consortium Human Build 38 (GRCh38-2020). Transcriptions were quantified using cellranger count with --force-cells: 8000 and --include-introns: true. CellRanger aggr was used to aggregate the samples for downstream analysis. TCR transcripts were quantified using cellranger vdj. The quality-checking reports from Cell Ranger were analyzed to assess sequencing quality and determine cell and gene counts per sample. Single-cell sequencing data were analyzed in R using the Seurat pipeline
Assembly: GRCh38
Supplementary files format and content: Barcodes
Supplementary files format and content: Features
Supplementary files format and content: Count Matrix
Library strategy: TCR-Seq

source_name: Glioblastoma tumor

extract_protocol:
Tumor-infiltrating CD45+ immune cell populations were isolated from GBM tumors of patients undergoing surgical resection at the University of California, Los Angeles.  Resected tumor tissue not needed for diagnosis was digested using the Miltenyi Brain Tumor Dissociation kit (Miltenyi Biotec, cat. 130-095-42) and gentleMACS dissociator (Miltenyi Biotec, cat. 130-093-235).  After treatment with Myelin Removal Beads II (Miltenyi Biotec, cat. 130-096-433), cells were labeled with CD45+ microbeads (Miltenyi Biotec, cat. 130-045-801). CD45+ cells were positively selected from the tumor digest with Miltenyi LS columns (Miltenyi Biotec, cat. 130-042-401) and MidiMACS separator (Miltenyi Biotec, cat. 130-042-302) and immediately frozen for batched analysis in Bambanker (Fisher Scientific, cat. 302-14681) and stored in liquid nitrogen.
On the day of single-cell library preparation, CD45+ cells collected from GBM patient tumors were thawed, counted, and resuspended in PBS with 0.4% BSA (Gemini, cat. 700-101P-100).  Single-cell library construction was performed by the Technology Center for Genomics and Bioinformatics Core, UCLA, utilizing the Chromium single-cell 5′ and VDJ library construction (10x Genomics), per the manufacturer’s protocol.  The constructed single-cell libraries were sequenced on a Novaseq S4 2x100bp flow cell (Illumina).

treatment_protocol: Patients with recurrent GBMs who received neoadjuvant anti-PD1 treatment were given an intravenous infusion of off-label, off-trial pembrolizumab 14 +/- 5 days before surgery, similar to a previously published study

value: Glioblastoma tumor

value: CD45+ cells

value: recurrent GBM neoadjuvant anti-PD-1


title: D21-WT-3

city: Suzhou

first: Li

last: Min

address: 199 Ren-ai Road

department: Institute of Biology and Medical Sciences

institute: Soochow University

data_processing:
Library preparation according to Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® ). Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina novaseq6000. The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina). The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4) . The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization. Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software.
Assembly: mm10
Supplementary files format and content: table-delimited text file includes Raw Reads for each sample

source_name: heart

growth_protocol: All mice were housed at the Soochow University Laboratory Animal Center under a specific-pathogen-free rodent barrier facility.

extract_protocol:
Total RNA was extracted using MJzol animal RNA Extraction Kit(MagBeads) (Cat#T102096)following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
Following the experimental protocol, total RNA purified from the samples will undergo the following steps for mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3' adenylation, adapter ligation, and enrichment, culminating in the construction of a sequencing library.

treatment_protocol: Mice received subcutaneously immunizations on days 0 and 7 of 100 μg/mouse of MyHCα614-629 (Ac-SLKLMATLFSTYASADOH) (Synpeptide, China) emulsified 1:1 with CFA (Sigma-Aldrich, F5881). Control mice were immunized with CFA/phosphate-buffered saline (PBS) only.

value: heart

value: Balb/c

value: Wildtype

value: EAM

tag: time


title: DSP-1001660011972-E-H03

first: Scott

middle: Andrew

last: Ochsner

state: TX

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Library name: DSP-1001660011972-E-H03
spatial transcriptomic sequencing

source_name: lung

extract_protocol:
Sample extraction from tissue slides was performed on the GeoMx Digital Spatial Profiler
Samples were amplified, pooled, purified, and checked for quality control according to the GeoMx NGS Readout NGS Library Preparation and Sequencing protocols

tag: slide name

value: lung

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

tag: age

tag: condition

value: COPD GOLD 4

value: COPD

value: former

value: male

tag: location

tag: roi

value: COPD_8_LUL:vessel 2


title: DSP-1001660011972-E-H02

description:
Library name: DSP-1001660011972-E-H02
spatial transcriptomic sequencing

tag: former or_current_smoker

value: vessel

value: COPD_8_LUL:vessel 1

value: paraffin


title: LB4880_GEX

description:
Library name: LB4880_GEX
Sample 9_GEX
10x Genomics

library_source: transcriptomic single cell

data_processing:
Data were demultiplexed and aligned with Cell Ranger version 7.1 (10X Genomics) and aligned to the Genome Reference Consortium Human Build 38 (GRCh38-2020). Transcriptions were quantified using cellranger count with --force-cells: 8000 and --include-introns: true. CellRanger aggr was used to aggregate the samples for downstream analysis. TCR transcripts were quantified using cellranger vdj. The quality-checking reports from Cell Ranger were analyzed to assess sequencing quality and determine cell and gene counts per sample. Single-cell sequencing data were analyzed in R using the Seurat pipeline
Assembly: GRCh38
Supplementary files format and content: Barcodes
Supplementary files format and content: Features
Supplementary files format and content: Count Matrix

value: Glioblastoma tumor

value: newly diagnosed GBM


title: ATRT-903

description:
Library name: ATRT-903
bigWig

source_name: primary

value: primary

value: N

value: atypical teratoid rhabdoid tumor


title: D21-WT-2

value: heart

value: Balb/c

value: Wildtype


title: LB3914_TCR

description:
Library name: LB3914_TCR
Sample 17_TCR
10x Genomics

value: CD45+ cells

value: recurrent GBM neoadjuvant anti-PD-1


title: ATRT-898

description:
Library name: ATRT-898
bigWig


title: LB4757_GEX

description:
Library name: LB4757_GEX
Sample 11_GEX
10x Genomics

value: recurrent GBM immunotherapy naïve


title: DSP-1001660011972-E-G11

description:
Library name: DSP-1001660011972-E-G11
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

value: former

tag: pack years

value: parenchyma

value: COPD_8_LUL:parenchyma 8


title: DSP-1001660011972-E-G10

description:
Library name: DSP-1001660011972-E-G10
spatial transcriptomic sequencing

tag: gender

value: male

value: COPD_8_LUL:parenchyma 7

value: paraffin


title: DSP-1001660011972-E-H01

description:
Library name: DSP-1001660011972-E-H01
spatial transcriptomic sequencing

value: vessel

value: COPD_8_LUL:vessel 006

tag: scan name


title: ATRT-900

description:
Library name: ATRT-900
bigWig

tag: tissue

value: primary

value: N

value: atypical teratoid rhabdoid tumor


title: D21-TRIM21KO-1

value: heart

value: Balb/c

value: EAM


title: D21-WT-1

value: Wildtype


title: DSP-1001660011972-E-G12

description:
Library name: DSP-1001660011972-E-G12
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4


title: ATRT-895

description:
Library name: ATRT-895
bigWig

tag: cell line


title: DSP-1001660011972-E-G08

description:
Library name: DSP-1001660011972-E-G08
spatial transcriptomic sequencing

value: COPD

value: former

value: parenchyma

value: COPD_8_LUL:parenchyma 5


title: LB4693_GEX

description:
Library name: LB4693_GEX
Sample 1_GEX
10x Genomics

value: Glioblastoma tumor

tag: cell type

value: CD45+ cells

value: newly diagnosed GBM


title: ATRT-894

description:
Library name: ATRT-894
bigWig

value: primary


title: DEX 50

city: UTRECHT

first: PHILIP

last: LIJNZAAD

state: Utrecht

address: HEIDELBERGLAAN 25

department: Single Cell Facility

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

description: 10x genomics

data_processing:
Data were processed into count tables using the 10x Genomics cellranger 6.1 suite of programs
Subsequently, cells with < 500 or > 40,000 transcripts, >= 25% mitochondrial transcripts or >= 5 doublet-calls in 10 runs of scDblFinder were discarded.
Assembly: Mouse mm10 (patch level 6) with gencode M23 (made available by 10x Genomics on 7 July 2020)
Supplementary files format and content: *.h5 files: Cellranger 6.1 hdf5 format
Supplementary files format and content: seurat.rds: normalized, cell-typed Seurat v3 object
Supplementary files format and content: metadata.tsv.gz: gzipped, tab-delimited cell metadata from the seurat object

molecule: polyA RNA

source_name: femur

growth_protocol: Mice were housed in single ventilated IVC cages with a maximum of five animals per cage, and provided with bedding and nesting material, a red dome, and ad libitum supply of water and standard RM3 chow food. Rooms were temperature-controlled (21 ± 0.5°C) and humidity-controlled (45 ± 2%), with a 12:12 light-dark cycle. Humane endpoints were 20% bodyweight loss and/or the animal loses more than 15% of body weight within 2 days; the animal has circulation or breathing problems; the animal shows aberrant behavior/movement Animals were daily monitored and weighed. The experiment study protocol was approved by the ethical committee and animal welfare body under CCD number: AVD3010020198564 Appendix 1 Protocol ID 21.1.10472 and 21.1.10191 and was in compliance with European Community specifications regarding the use of laboratory animals. The study protocol was not (pre)registered in an online preclinical study registry.

extract_protocol:
After four weeks mice were euthanized, and the hindlimbs were isolated and kept on medium at 4°C until further processing that day. The proximal left femur and the complete right femur were isolated, and muscle was removed. The bone tissue was cut in approximately 1 mm2 pieces, frozen viably and stored at -180°C for scRNA-seq. To obtain sufficient cell numbers for scRNA-seq, the femurs of the mice were pooled per treatment group. To increase the reliability of findings in the downstream analysis, such as differential gene expression and overrepresentation testing, vehicle animals of 2 studies with an identical study protocol were included, resulting in femurs of 20 mice in total pooled in the vehicle group. Next, to obtain a single-cell suspension, bone fragments were digested in two rounds of 30 minutes at 37°C, all centrifugation steps were done for 5 minutes at 300g. Digestion buffer consisted of Optimem (Gibco, cat no. 12634010), 100 U/mL DNase (Stemcell, 7469), 10 mM HEPES buffer (Gibco, 15630056), 1 mM CaCl2, 10 μM ROCK (Y-27632, Biogems, 1293823), and 0.1 mg/mL Liberase DL in the first digestion round (Sigma Aldrich, 5466202001) or 0.1 mg/mL Liberase TM in the second digestion round (Sigma Aldrich, 05401119001). After each digestion bone fragments were strained using a 70 μM cell strainer. Bone fragments were washed extensively at every step to collect cells. Collected cells were centrifuged and resuspended in 5 ml FACS buffer (magnesium-free PBS, 1% (vol/vol) BSA, 1 mM EDTA, 10 μM ROCK) and kept on ice. Red blood cell lysis buffer (Invitrogen) was added for 4 minutes at room temperature. Cells were washed, resuspended in 200 μl FACS buffer, and blocked for 15 minutes with 8 μg anti-CD16/CD32 antibody (Rat anti-mouse BD, 553079). Next, 4 μg CD45-FITC (Stemcell, 60161.2, Clone 2.4G2) incubated in the dark at 4°C for 30 minutes. Cells were washed twice with FACS buffer and resuspended in 1 mL FACS buffer. Sorting was performed with the Sony SH800 Cell Sorter, using a 100 μm nozzle chip. Droplet calibration was performed with Automatic Setup Beads (Sony, Cat. LE-B3001). Live and death cells were determined using 5 μM DRAQ5 (Biolegend) and 2.5 μM DAPI (Biolegend) staining. Gates were set using unstained samples as control, for DRAQ5 positive cells, DAPI negative cells, single cells, and CD45+ and CD45- cells. CD45+ and CD45- cells were sorted and subsequently combined in a 50/50 ratio of CD45+ and CD45- cells, and 45,000 cells per condition were subjected to droplet-based scRNA-seq using the 10x Genomics platform.
The barcoding of individual transcripts from single cells, followed by cDNA amplification and library construction, were performed using 10X Genomics reagents and 10X Chromium Controller, according to the manufacturer’s user guide nr. CG000315 (“Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index), RevC”).

treatment_protocol: The mice received daily intraperitoneal injections of Dexamethasone in 10 ul/g bodyweight according to their respective treatment group for 28 days.

value: femur

value: 6 weeks

tag: Sex

value: male

tag: genotype

value: 50 mg/kg dexametasone (28 days, daily injection)


title: LB4805_GEX

description:
Library name: LB4805_GEX
Sample 3_GEX
10x Genomics

tag: treatment


title: D21-TRIM21KO-3

value: heart

value: Balb/c

value: EAM

tag: time


title: LB4628_GEX

description:
Library name: LB4628_GEX
Sample 22_GEX
10x Genomics

value: recurrent GBM neoadjuvant anti-PD-1


title: ATRT-893

description:
Library name: ATRT-893
bigWig

value: N

value: atypical teratoid rhabdoid tumor


title: D21-TRIM21KO-2


title: ATRT-897

description:
Library name: ATRT-897
bigWig


title: DEX 20

description: 10x genomics

value: 20 mg/kg dexametasone (28 days, daily injection)


title: LB4751_GEX

description:
Library name: LB4751_GEX
Sample 7_GEX
10x Genomics


title: ATRT-891

description:
Library name: ATRT-891
bigWig


title: ATRT-896

description:
Library name: ATRT-896
bigWig


title: DSP-1001660011972-E-G09

description:
Library name: DSP-1001660011972-E-G09
spatial transcriptomic sequencing

tag: slide name

value: lung

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

value: former

value: parenchyma

value: COPD_8_LUL:parenchyma 6

value: paraffin


title: Untreated aged

description: 10x genomics

value: femur

tag: age

value: 58 weeks

value: male

value: 0 mg/kg dexametasone (28 days, daily injection)


title: DSP-1001660011972-E-G06

description:
Library name: DSP-1001660011972-E-G06
spatial transcriptomic sequencing

tag: patient

tag: condition

value: COPD_8_LUL:parenchyma 2


title: LB4477_GEX

description:
Library name: LB4477_GEX
Sample 19_GEX
10x Genomics

value: Glioblastoma tumor

value: CD45+ cells

value: recurrent GBM neoadjuvant anti-PD-1


title: DSP-1001660011972-E-G05

description:
Library name: DSP-1001660011972-E-G05
spatial transcriptomic sequencing

tag: location

tag: roi

value: COPD_8_LUL:parenchyma 1


title: DEX 5

description: 10x genomics

value: 6 weeks

value: 5 mg/kg dexametasone (28 days, daily injection)


title: ATRT-887

description:
Library name: ATRT-887
bigWig

value: primary

value: N

value: atypical teratoid rhabdoid tumor


title: Vehicle2

description: 10x genomics


title: LB4429_GEX

description:
Library name: LB4429_GEX
Sample 12_GEX
10x Genomics

value: recurrent GBM immunotherapy naïve


title: Vehicle1

description: 10x genomics


title: LB4382_GEX

description:
Library name: LB4382_GEX
Sample 2_GEX
10x Genomics

value: newly diagnosed GBM


title: ATRT-889

description:
Library name: ATRT-889
bigWig


title: LB4746_GEX

description:
Library name: LB4746_GEX
Sample 8_GEX
10x Genomics


title: DSP-1001660011972-E-G04

description:
Library name: DSP-1001660011972-E-G04
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

tag: former or_current_smoker

value: former

tag: pack years

value: airway

value: paraffin


title: LB4369_GEX

description:
Library name: LB4369_GEX
Sample 23_GEX
10x Genomics

value: Glioblastoma tumor

value: CD45+ cells


title: condy-nc-4d-3

city: Shanghai

first: Jiahui

last: Du

address: Zhizaoju Road 639

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were trimmed using Cutadapt.
Trimmed reads were aligned with the GRCm39 genome using HISAT2
Read count extraction and normalization were performed using htseq-count.
Assembly: Mus_musculus.GRCm39.
Supplementary files format and content: Excel files include read count and fpkm values for each sample

source_name: mandibular condyle cells

growth_protocol: mandibular condyle cells were harvested from murine mandible of Plagl1 fl/fl mice cultured in α-minimum essential medium containing 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Condyle cells was collected for RNA isolation using TRIzol.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: Cells were infected with adenovirus expressing either Cre or control adenovirus (HBAD-CRE-EGFP with its control adenovirus HBAD-EGFP ) at MOI of 100. For osteoblast induction,  transfected cells were cultured into complete media with  b-glycerophosphate (b-GP) (Sigma G9422, 5 mM), ascorbic acid (Sigma A4403, 50 ug/ml), and dexamethasone (Sigma D4902, 100 nM) .

value: mandibular condyle cells

value: Plagl1 fl/fl

tag: infection

value: control adenovirus HBAD-EGFP

tag: osteoblast induction

value: b-glycerophosphate (b-GP) (5 mM), ascorbic acid (50 ug/ml), and dexamethasone (100 nM)


title: DSP-1001660011972-E-G03

description:
Library name: DSP-1001660011972-E-G03
spatial transcriptomic sequencing

tag: tissue

tag: gender

value: male

tag: scan name


title: LB4372_GEX

description:
Library name: LB4372_GEX
Sample 5_GEX
10x Genomics

tag: cell type


title: condy-nc-4d-2

tag: genotype


title: DSP-1001660011972-E-G07

description:
Library name: DSP-1001660011972-E-G07
spatial transcriptomic sequencing

value: parenchyma

value: COPD_8_LUL:parenchyma 3


title: ATRT-886

description:
Library name: ATRT-886
bigWig

value: primary

tag: cell line

value: N

value: atypical teratoid rhabdoid tumor


title: LB4260_GEX

description:
Library name: LB4260_GEX
Sample 6_GEX
10x Genomics

tag: treatment

value: newly diagnosed GBM


title: ATRT-884

description:
Library name: ATRT-884
bigWig


title: DSP-1001660011972-E-G02

description:
Library name: DSP-1001660011972-E-G02
spatial transcriptomic sequencing

tag: slide name

value: lung

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD


title: ATRT-885

description:
Library name: ATRT-885
bigWig


title: condy-nc-4d-1


title: LB4180_GEX

description:
Library name: LB4180_GEX
Sample 4_GEX
10x Genomics

value: Glioblastoma tumor


title: DSP-1001660011972-E-F11

description:
Library name: DSP-1001660011972-E-F11
spatial transcriptomic sequencing

tag: patient

tag: age

value: former

value: airway

value: paraffin


title: DSP-1001660011972-E-F12

description:
Library name: DSP-1001660011972-E-F12
spatial transcriptomic sequencing

tag: condition

tag: location


title: ATRT-882

description:
Library name: ATRT-882
bigWig


title: LB4177_GEX

description:
Library name: LB4177_GEX
Sample 14_GEX
10x Genomics

value: CD45+ cells

value: recurrent GBM immunotherapy naïve


title: condy-nc-0d-3

value: mandibular condyle cells

value: Plagl1 fl/fl

value: control adenovirus HBAD-EGFP

value: control


title: condy-nc-0d-2


title: DSP-1001660011972-E-F10

description:
Library name: DSP-1001660011972-E-F10
spatial transcriptomic sequencing

tag: former or_current_smoker

value: male

tag: roi


title: ATRT-879

description:
Library name: ATRT-879
bigWig

value: primary

value: N

value: atypical teratoid rhabdoid tumor


title: DSP-1001660011972-E-F09

description:
Library name: DSP-1001660011972-E-F09
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: pack years


title: condy-nc-0d-1

tag: infection

tag: osteoblast induction


title: LB4143_GEX

description:
Library name: LB4143_GEX
Sample 15_GEX
10x Genomics

tag: tissue


title: LB4130_GEX

description:
Library name: LB4130_GEX
Sample 13_GEX
10x Genomics


title: condy-cre-4d-3

value: HBAD-CRE-EGFP adenovirus

value: b-glycerophosphate (b-GP) (5 mM), ascorbic acid (50 ug/ml), and dexamethasone (100 nM)


title: ATRT-880

description:
Library name: ATRT-880
bigWig


title: DSP-1001660011972-E-F08

description:
Library name: DSP-1001660011972-E-F08
spatial transcriptomic sequencing

value: COPD_2_RUL Real

value: COPD GOLD 4

value: COPD

value: former

tag: gender

value: vessel

value: COPD_2_RUL_Vessel 008

tag: scan name


title: ATRT-877

description:
Library name: ATRT-877
bigWig

tag: cell type


title: DSP-1001660011972-E-F07

description:
Library name: DSP-1001660011972-E-F07
spatial transcriptomic sequencing

value: COPD_2_RUL_Vessel 007

value: paraffin


title: LB4117_GEX

description:
Library name: LB4117_GEX
Sample 20_GEX
10x Genomics

value: Glioblastoma tumor

value: CD45+ cells

value: recurrent GBM neoadjuvant anti-PD-1


title: condy-cre-4d-2

value: mandibular condyle cells

tag: genotype

value: Plagl1 fl/fl


title: LB4112_GEX

description:
Library name: LB4112_GEX
Sample 18_GEX
10x Genomics

tag: treatment


title: condy-cre-4d-1


title: ATRT-883

description:
Library name: ATRT-883
bigWig

value: primary

tag: cell line

value: N

value: atypical teratoid rhabdoid tumor


title: condy-Cre-0d-3

value: HBAD-CRE-EGFP adenovirus

value: control


title: LB4102_GEX

description:
Library name: LB4102_GEX
Sample 16_GEX
10x Genomics

value: recurrent GBM immunotherapy naïve


title: ATRT-876

description:
Library name: ATRT-876
bigWig


title: ATRT-875

description:
Library name: ATRT-875
bigWig


title: LB4101_GEX

description:
Library name: LB4101_GEX
Sample 10_GEX
10x Genomics


title: DSP-1001660011972-E-G01

description:
Library name: DSP-1001660011972-E-G01
spatial transcriptomic sequencing

tag: slide name

value: lung

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

value: male

value: airway


title: DSP-1001660011972-E-F05

description:
Library name: DSP-1001660011972-E-F05
spatial transcriptomic sequencing

value: COPD_2_RUL Real

tag: patient

tag: age

value: former

value: vessel

value: COPD_2_RUL_Vessel 005

value: paraffin


title: DSP-1001660011972-E-F04

description:
Library name: DSP-1001660011972-E-F04
spatial transcriptomic sequencing

tag: condition

tag: location

value: COPD_2_RUL_Vessel 004


title: LB4021_GEX

description:
Library name: LB4021_GEX
Sample 21_GEX
10x Genomics

value: Glioblastoma tumor

value: CD45+ cells

value: recurrent GBM neoadjuvant anti-PD-1


title: condy-Cre-0d-2

value: mandibular condyle cells

value: Plagl1 fl/fl

value: HBAD-CRE-EGFP adenovirus

value: control


title: CHLA266-DAC-1

description:
Library name: CHLA266-DAC-1
bigWig

source_name: cell line

value: cell line

value: Y

value: atypical teratoid rhabdoid tumor

value: DAC


title: LB3914_GEX

description:
Library name: LB3914_GEX
Sample 17_GEX
10x Genomics


title: condy-Cre-0d-1


title: DSP-1001660011972-E-F03

description:
Library name: DSP-1001660011972-E-F03
spatial transcriptomic sequencing

value: COPD_2_RUL Real

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

tag: former or_current_smoker

value: male

tag: roi

value: COPD_2_RUL_Vessel 003


title: CHLA266-DMSO-1

description:
Library name: CHLA266-DMSO-1
bigWig

value: DMSO


title: CHLA06-DAC-1

description:
Library name: CHLA06-DAC-1
bigWig


title: DSP-1001660011972-E-F01

description:
Library name: DSP-1001660011972-E-F01
spatial transcriptomic sequencing

value: former

tag: pack years

value: vessel

value: COPD_2_RUL_Vessel 001

value: paraffin


title: DSP-1001660011972-E-F02

description:
Library name: DSP-1001660011972-E-F02
spatial transcriptomic sequencing

value: COPD_2_RUL_Vessel 002


title: WT-Mitotic-Input-2

city: Edinburgh

first: Charles

middle: A C

last: Williams

state: Midlothian

address: 5 Little France Dr, Bioquarter, Scottish Ctr For Regenerative Medicine, Scottish Ctr For Regenerative Medicine

department: Institute for Regeneration and Repair

country: United Kingdom

institute: University of Edinburgh

data_processing:
We aligned paired-end reads (~150 bps and ~100 million reads per replicate, n=3) to the mm10 genome (GCA_000001635.2) using BWA (v0.7.17). All replicates contained >10 million total mapped reads. We removed multi-mapped and supplementary reads and reads overlapping the mm10 blacklisted regions (obtained from https://github.com/Boyle-Lab/Blacklist/tree/master/lists) using samtools (v1.9). We called peaks using macs2 (v2.1.1) with the settings q = 1e-5 for the SOX2 ChIP-seq samples and q=1e-2 for the BL6 ChIP-seq samples. We used Diffbind to analyse differentially bound peaks between the different SOX2 variants and cell cycle phases. To do this, we first merged the peaks from the same technical replicates. For additional control, we subtracted BL6 peaks (twice median width extended) from the SOX2 peaks. We ran Diffbind using the default settings, and annotated the differentially bound peaks using ChIPSeeker. Geneset enrichment was conducted by taking annotated peaks <=3kb from TSS and running GO Term analysis. Motif enrichment was conducted using Homer on differentially bound peak sets57. We generated coverage tracks using bamCoverage (deepTools v3.4.3).
Assembly: Genome_build: mm10
Supplementary files format and content: Merged bigwigs, Individual bigwigs per replicate

source_name: BL6 mNSC

growth_protocol: NSCs were isolated from the young adult 6-8 weeks old SVZ and maintained in vitro in serum-free basal medium supplemented with N2 and B27 (Life Technologies), Laminin-1 (Sigma, 1 μg/ml) and growth factors EGF and FGF2 (Peprotech, 10 ng/ml each). All expoeriments were conducted in early passage cells after p8.

extract_protocol:
SOX2-ChIP analysis was performed as described previously with modifications. Briefly, 10 million cells were crosslinked with 2mM DSG in PBS for 50 min, followed by 1% formaldehyde for 10 min at room temperature, and quenched with 120mM Glycine for 10 min. The crosslinked cells were washed with ice-cold PBS, flash frozen, and stored at -80°C. For nuclear extraction, the cell pellet was thawed on ice, resuspended in lysis buffer (50mM HEPES-KOH [pH7.5], 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, Complete protease inhibitor cocktail) and lysed with a Dounce homogenizer. Nuclei were pelleted by centrifugation (1350g, 5min, 4°C), washed with wash buffer (10mM Tris-HCl [pH 8], 200mM NaCl, 1mM EDTA, 0.5mM EGTA, Complete protease inhibitor cocktail), and resuspended in sonication buffer (10mM Tris-HCl [pH 8], 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, Complete protease inhibitor cocktail). Nuclei were sonicated using a Covaris E220, and chromatin was centrifuged (20,000g, 10min, 4°C). Fragment size distribution and DNA content were assessed using a Nanodrop spectrophotometer and TapeStation. Chromatin and input samples were snap-frozen and stored at -80°C. For immunoprecipitation, 30μl Dyna Protein-G magnetic beads (Thermo Fisher Scientific) were washed with blocking solution (0.5% BSA in PBS-Tween-20), incubated with 10μg antibody (IgG or SOX2) and mixed with 40μg chromatin overnight at 4°C. Beads were washed with wash buffer (50mM HEPES-KOH pH7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and TE buffer (10mM Tris-HCl pH8, 1mM EDTA, 50mM NaCl). Bound chromatin was eluted with elution buffer (50mM Tris-HCl pH8, 10mM EDTA, 1% SDS) at 65°C for 30 min, and crosslinks were reversed by incubation at 65°C for 16 hr. RNA was digested with 0.2mg/ml RNase-A for 2 hr at 37°C, proteins with 0.2mg/ml Proteinase-K for 2 hr at 55°C. DNA was purified using Qiagen Qiaquick PCR cleanup columns, quantified by Qubit Fluorometric Quantitation, and sequenced on the Illumina NovaSeq platform in paired-end mode with 150 bp per read.
NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1)

treatment_protocol: mNSCs were engineered with a piggybac integrated doxycyline inducible expression system, as in (Martella, et. al., (ACS Synth Biol. 2017)) where indicated.  mNSCs were seeded onto 15cm dishes and cultured for 24hrs in NSC medium. SOX2 expression was induced by treating stable cells with 1μg/ml doxycycline for 72hrs

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

tag: time

value: 6 hours

tag: replicate

tag: chip antibody

value: Input


title: DSP-1001660011972-E-F06

description:
Library name: DSP-1001660011972-E-F06
spatial transcriptomic sequencing

value: COPD_2_RUL Real

tag: tissue

value: lung

tag: gender

value: COPD_2_RUL_Vessel 006

tag: scan name


title: WT-Mitotic-Input-3

tag: cell type

tag: treatment


title: ATRT-878

description:
Library name: ATRT-878
bigWig

value: primary

tag: cell line

value: N

value: atypical teratoid rhabdoid tumor


title: DSP-1001660011972-E-E12

description:
Library name: DSP-1001660011972-E-E12
spatial transcriptomic sequencing

tag: slide name

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

value: male

value: parenchyma

value: COPD_2_RUL_Parenchyma 5


title: Human_immune_cells-JN11

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA43077

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: PBMC

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: PBMC

tag: genotype

value: WT


title: CHLA06-DMSO-1

description:
Library name: CHLA06-DMSO-1
bigWig

value: cell line

value: Y

value: DMSO


title: WT-Mitotic-ChIP-3

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

value: 6 hours

value: FLAG


title: CHLA05-DAC-1

description:
Library name: CHLA05-DAC-1
bigWig

value: atypical teratoid rhabdoid tumor

value: DAC


title: DSP-1001660011972-E-E11

description:
Library name: DSP-1001660011972-E-E11
spatial transcriptomic sequencing

value: COPD_2_RUL Real

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

tag: age

tag: condition

value: COPD GOLD 4

value: former

value: COPD_2_RUL_Parenchyma 008

value: paraffin


title: DSP-1001660011972-E-E10

description:
Library name: DSP-1001660011972-E-E10
spatial transcriptomic sequencing

value: COPD

tag: former or_current_smoker

value: male

tag: location

value: parenchyma

tag: roi

value: COPD_2_RUL_Parenchyma 007


title: Human_immune_cells-JN9

description: Library name: GA43075

value: PBMC

value: WT


title: CHLA05-DMSO-1

description:
Library name: CHLA05-DMSO-1
bigWig

value: cell line

value: Y

value: DMSO


title: WT-Mitotic-ChIP-2

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

tag: time

value: 6 hours

tag: replicate

value: FLAG


title: Human_immune_cells-JN8

description: Library name: GA43074

tag: tissue


title: CHLA02-DAC-1

description:
Library name: CHLA02-DAC-1
bigWig

value: atypical teratoid rhabdoid tumor

value: DAC


title: WT-Mitotic-ChIP-1

tag: chip antibody


title: Human_immune_cells-JN7

description: Library name: GA43073


title: Human_immune_cells-JN12

description: Library name: GA43078


title: CHLA02-DMSO-1

description:
Library name: CHLA02-DMSO-1
bigWig


title: DSP-1001660011972-E-E08

description:
Library name: DSP-1001660011972-E-E08
spatial transcriptomic sequencing

value: COPD_2_RUL Real

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: former

tag: pack years

tag: gender

value: COPD_2_RUL_Parenchyma 005

tag: scan name

value: paraffin


title: Human_immune_cells-JN6

description: Library name: GA43072

value: PBMC

tag: cell type

value: WT


title: WT-Interphase-Input-3

tag: cell line

tag: treatment

value: DMSO

value: Input


title: BCH8

city: St. Petersburg

first: JUNKO

last: SAWADA

address: 600 5th Street South

institute: Johns Hopkins All Children's Hispital

data_processing:
All data processing were performed on Partek™ Flow™.  Trimmed read was aligned using STAR 2.7.3a and normalized count has been calculated on DEseq2.
Assembly: hg38
Supplementary files format and content: counts.txt

source_name: Breast cancer tissue FFPE

extract_protocol:
Total RNA was extracted from FFPE slides using QIAGEN RNeasy FFPE kit (standard kit) following Manufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer RNA assay (Invitrogen, Carlsbad, CA, USA) and RNA integrity was checked with Agilent 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). RNA library preparations, sequencing reactions, and initial sequencing data quality analysis were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA).
RNA sequencing library preparation was prepared using TruSeq Stranded Total RNA library Prep kit following manufacturer’s protocol (Illumina, Cat#20020597). Briefly, rRNA was depleted and fragmented for 8 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. Sequencing libraries were validated using DNA Analysis Screen Tape on the Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA).

value: Breast cancer tissue FFPE

value: TLS-rich


title: WT-Mitotic-Input-1

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

value: 6 hours


title: Human_immune_cells-JN5

description: Library name: GA43071

tag: genotype


title: Human_immune_cells-JN10

description: Library name: GA43076


title: WT-Interphase-Input-2


title: Human_immune_cells-JN4

description: Library name: GA43070


title: WT-Interphase-Input-1


title: DSP-1001660011972-E-E06

description:
Library name: DSP-1001660011972-E-E06
spatial transcriptomic sequencing

tag: slide name

value: COPD_2_RUL Real

tag: panel

tag: patient

value: COPD

value: male

value: parenchyma

value: COPD_2_RUL_Parenchyma 003


title: BCH6


title: BCH5


title: WT-Interphase-ChIP-3

value: FLAG


title: Human_immune_cells-JN3

description: Library name: GA43069


title: DSP-1001660011972-E-E05

description:
Library name: DSP-1001660011972-E-E05
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: age

tag: condition

value: COPD GOLD 4

tag: former or_current_smoker

value: former

value: COPD_2_RUL_Parenchyma 002

value: paraffin


title: WT-Interphase-ChIP-2

value: DMSO

tag: time


title: DSP-1001660011972-E-E09

description:
Library name: DSP-1001660011972-E-E09
spatial transcriptomic sequencing

tag: location

tag: roi

value: COPD_2_RUL_Parenchyma 006


title: DSP-1001660011972-E-E04

description:
Library name: DSP-1001660011972-E-E04
spatial transcriptomic sequencing

tag: tissue

value: COPD_2_RUL_Parenchyma 001


title: WT-Interphase-ChIP-1

value: BL6 mNSC

value: Mouse Neural Stem Cell

tag: replicate

tag: chip antibody


title: Human_immune_cells-JN1

description: Library name: GA43067

value: PBMC

value: WT


title: DSP-1001660011972-E-E03

description:
Library name: DSP-1001660011972-E-E03
spatial transcriptomic sequencing

value: COPD_2_RUL Real

value: COPD

tag: pack years

tag: gender

value: male

value: airway

tag: scan name


title: BCH3

value: Breast cancer tissue FFPE

tag: cell type

value: TLS-rich


title: BCH4


title: DSP-1001660011972-E-E02

description:
Library name: DSP-1001660011972-E-E02
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD_2_RUL_Airway 3


title: DSP-1001660011972-E-E07

description:
Library name: DSP-1001660011972-E-E07
spatial transcriptomic sequencing

value: former

value: parenchyma

value: COPD_2_RUL_Parenchyma 004

value: paraffin


title: BCH2


title: DSP-1001660011972-E-E01

description:
Library name: DSP-1001660011972-E-E01
spatial transcriptomic sequencing

value: COPD_2_RUL_Airway 004


title: Human_immune_cells-JW12

description: Library name: GA39178

value: PBMC

tag: genotype


title: Human_immune_cells-JW11

description: Library name: GA39177

value: WT


title: BCH7


title: BCH1


title: Bl6-Mitotic-Input-1

tag: cell line

value: BL6 mNSC

value: Mouse Neural Stem Cell

tag: treatment

value: 50ng/ml Nocodazole (SML1665)

value: 6 hours

value: Input


title: Human_immune_cells-JW10

description: Library name: GA39176


title: DSP-1001660011972-E-D12

description:
Library name: DSP-1001660011972-E-D12
spatial transcriptomic sequencing

tag: slide name

value: COPD_2_RUL Real

tag: panel

tag: patient

value: COPD

value: male

value: airway

value: COPD_2_RUL_Airway 001


title: BC8

value: Breast cancer tissue FFPE

value: TLS-poor


title: Bl6-Mitotic-ChIP-3

value: FLAG


title: DSP-1001660011972-E-D11

description:
Library name: DSP-1001660011972-E-D11
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: age

tag: condition

value: COPD GOLD 4

tag: former or_current_smoker

value: former

value: vessel

value: COPD_8_LLL_Vessel 008

value: paraffin


title: BC7


title: Human_immune_cells-JN2

description: Library name: GA43068

value: PBMC

value: WT


title: Human_immune_cells-JW9

description: Library name: GA39175


title: Bl6-Mitotic-ChIP-2

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

tag: time

value: 6 hours


title: DSP-1001660011972-E-D10

description:
Library name: DSP-1001660011972-E-D10
spatial transcriptomic sequencing

tag: tissue

value: COPD

value: male

tag: location

tag: roi

value: COPD_8_LLL_Vessel 007


title: Bl6-Mitotic-Input-3

tag: replicate

tag: chip antibody

value: Input


title: Human_immune_cells-JW8

description: Library name: GA39174


title: Bl6-Mitotic-ChIP-1

value: FLAG


title: DSP-1001660011972-E-D09

description:
Library name: DSP-1001660011972-E-D09
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: pack years

tag: gender

value: COPD_8_LLL_Vessel 006

tag: scan name


title: BC5

value: Breast cancer tissue FFPE

tag: cell type

value: TLS-poor


title: Human_immune_cells-JW7

description: Library name: GA39173

tag: genotype


title: Bl6-Interphase-Input-3

tag: cell line

tag: treatment

value: DMSO


title: BC4


title: Bl6-Mitotic-Input-2


title: Bl6-Interphase-Input-2


title: DSP-1001660011972-E-D07

description:
Library name: DSP-1001660011972-E-D07
spatial transcriptomic sequencing

tag: slide name

tag: panel

tag: patient

value: COPD GOLD 4

value: former

value: vessel

value: COPD_8_LLL_Vessel 004

value: paraffin


title: Bl6-Interphase-Input-1

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 6 hours


title: BC3


title: DSP-1001660011972-E-D06

description:
Library name: DSP-1001660011972-E-D06
spatial transcriptomic sequencing

tag: age

tag: condition

value: COPD

tag: former or_current_smoker

value: male

value: COPD_8_LLL_Vessel 003


title: Human_immune_cells-JW4

description: Library name: GA39170

tag: tissue

value: PBMC

value: WT


title: Bl6-Interphase-ChIP-3

tag: time

value: FLAG


title: DSP-1001660011972-E-D05

description:
Library name: DSP-1001660011972-E-D05
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: location

tag: roi

value: COPD_8_LLL_Vessel 002


title: BC2

value: Breast cancer tissue FFPE

value: TLS-poor


title: Human_immune_cells-JW3

description: Library name: GA39169


title: Bl6-Interphase-ChIP-2

value: DMSO

tag: replicate

tag: chip antibody


title: Human_immune_cells-JW2

description: Library name: GA39168


title: DSP-1001660011972-E-D04

description:
Library name: DSP-1001660011972-E-D04
spatial transcriptomic sequencing

value: COPD GOLD 4

value: former

tag: pack years

tag: gender

value: vessel

value: COPD_8_LLL_Vessel 001

tag: scan name


title: Bl6-Interphase-ChIP-1

tag: cell line

value: BL6 mNSC

tag: cell type

value: Mouse Neural Stem Cell

value: 6 hours


title: Human_immune_cells-JW1

description: Library name: GA39167

tag: genotype


title: DSP-1001660011972-E-D08

description:
Library name: DSP-1001660011972-E-D08
spatial transcriptomic sequencing

tag: slide name

tag: panel

value: COPD

value: male

value: COPD_8_LLL_Vessel 005

value: paraffin


title: 45P11; DAM45, ENVIRONMENTALLY ENRICHED, LPS, P11

city: New York

first: Jordan

last: Marrocco

state: NY

address: 3 Times Sq, Office 752

department: Biology

institute: Touro University

description: Library name: 45P11

data_processing:
Raw sequence reads were read trimmed to remove low-quality bases and adapter sequences using Trimmomatic (v0.30). Trimmed reads with a length of 18 to 32 bp were retained.
Trimmed reads were compared to, and annotated with, the small RNA database (miRbase 22, www.mirbase.org).
For novel microRNA prediction, sequences were aligned to the corresponding genome and subjected to RNA folding and secondary structure analysis using miRDeep2 (v2_0_0_7).
For quantified miRNAs based on hit counts, Miranda (v3.3a) was used to predict target sites based on microRNA sequences and the corresponding genomic cDNA sequences.
Differential expression analysis was performed using the Bioconductor package edgeR (v3.4.6). Small RNAs with a p<0.01 and fold-change of normalized expression values >2 were considered significant for differential expression.
Assembly: miRbase v22
Supplementary files format and content: txt file includes raw counts and FPKM for each sample

organism: Rattus norvegicus

source_name: Milk

extract_protocol:
RNA was extracted from isolated milk-derived extracellular vesicles using the Exosomal RNA Isolation Kit (58000, Norogen, Biotek).
Small RNA sequencing library was prepared by using NEB Small RNA library Prep Kit (New England Biolabs).

tag: strain

value: Sprague-Dawley

value: Milk

value: Extracellular vesicles derived from milk

value: Wild type

tag: treatment

value: Environmentally Enriched LPS


title: BC1

value: Breast cancer tissue FFPE

value: TLS-poor


title: DSP-1001660011972-E-D02

description:
Library name: DSP-1001660011972-E-D02
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

tag: age

tag: condition

value: COPD GOLD 4

tag: former or_current_smoker

value: former

value: parenchyma

value: COPD_8_LLL_Parenchyma 006


title: 3A-Mitotic-Input-3

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

tag: time

value: 6 hours

value: Input


title: Human_immune_cells-JW6

description: Library name: GA39172

tag: tissue

value: PBMC

value: WT


title: Airway organoid co-cultured with 293T, SARS-CoV-2 infected

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description: Library name: ART+S

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v7.1.0).
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference (GRCh38-2020-A) + the SARS-CoV-2 virus genome and to extract gene expression UMI counts matrix.
Assembly: GRCh38
Supplementary files format and content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

extract_protocol:
Cells were digested by 0.05% trypsin
library was performed according to the instructions (10X Genomics)

treatment_protocol: mock or  SARS-CoV-2 infected

value: stem cell derived

value: virus infected


title: 9P11; DAM9, ENVIRONMENTALLY ENRICHED, LPS, P11

description: Library name: 9P11

value: Sprague-Dawley

value: Milk

value: Extracellular vesicles derived from milk

value: Wild type

value: Environmentally Enriched LPS


title: DSP-1001660011972-E-D03

description:
Library name: DSP-1001660011972-E-D03
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

value: former

value: male

tag: location

tag: roi

value: COPD_8_LLL_Parenchyma 007

value: paraffin


title: BC6

value: Breast cancer tissue FFPE

value: TLS-poor


title: 3A-Mitotic-Input-2

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

value: 6 hours

tag: replicate

tag: chip antibody

value: Input


title: Airway organoid co-cultured with macrophage, SARS-CoV-2 infected

description: Library name: ARM+S

tag: cell line

value: stem cell derived

value: virus infected


title: DSP-1001660011972-E-D01

description:
Library name: DSP-1001660011972-E-D01
spatial transcriptomic sequencing

value: lung

tag: pack years

tag: gender

value: parenchyma

value: COPD_8_LLL_Parenchyma 005

tag: scan name


title: 7P11; DAM7, ENVIRONMENTALLY ENRICHED, LPS, P11

description: Library name: 7P11

value: Sprague-Dawley

value: Milk

tag: cell type

value: Extracellular vesicles derived from milk

tag: genotype

value: Wild type

value: Environmentally Enriched LPS


title: Human_immune_cells-JW5

description: Library name: GA39171

value: PBMC

value: WT


title: 3A-Mitotic-Input-1

value: BL6 mNSC

tag: treatment


title: DSP-1001660011972-E-C12

description:
Library name: DSP-1001660011972-E-C12
spatial transcriptomic sequencing

tag: slide name

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

value: COPD GOLD 4

value: COPD

value: former

value: male

value: COPD_8_LLL_Parenchyma 004

value: paraffin


title: Airway organoid co-cultured with macrophage

description: Library name: ARM+M

value: lung

value: stem cell derived

value: mock


title: 5P11; DAM5, ENVIRONMENTALLY ENRICHED, LPS, P11

description: Library name: 5P11

tag: strain

value: Sprague-Dawley

value: Milk


title: 3A-Mitotic-ChIP-3

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

tag: time

value: 6 hours

value: FLAG


title: 3A-Mitotic-ChIP-2

value: BL6 mNSC


title: DSP-1001660011972-E-C11

description:
Library name: DSP-1001660011972-E-C11
spatial transcriptomic sequencing

tag: tissue

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: age

tag: condition

tag: former or_current_smoker

value: parenchyma

value: COPD_8_LLL_Parenchyma 003


title: 33P11; DAM33, ENVIRONMENTALLY ENRICHED, LPS, P11

description: Library name: 33P11

value: Extracellular vesicles derived from milk

value: Wild type

value: Environmentally Enriched LPS


title: Alveolar organoid co-cultured with 293T, SARS-CoV-2 infected

description: Library name: AVT+S

value: virus infected


title: DSP-1001660011972-E-C10

description:
Library name: DSP-1001660011972-E-C10
spatial transcriptomic sequencing

value: lung

value: COPD GOLD 4

value: COPD

value: former

value: male

tag: location

tag: roi

value: COPD_8_LLL_Parenchyma 002

value: paraffin


title: Alveolar organoid co-cultured with macrophage, SARS-CoV-2 infected

description: Library name: AVM+S

tag: cell line

value: stem cell derived


title: 3A-Mitotic-ChIP-1

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

value: 6 hours

tag: replicate

tag: chip antibody

value: FLAG


title: DSP-1001660011972-E-C07

description:
Library name: DSP-1001660011972-E-C07
spatial transcriptomic sequencing

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: pack years

tag: gender

value: airway

value: COPD_8_LLL_Airway 3

tag: scan name


title: 10P11; DAM10, ENVIRONMENTALLY ENRICHED, SALINE, P11

description: Library name: 10P11

value: Sprague-Dawley

value: Milk

tag: cell type

value: Extracellular vesicles derived from milk

tag: genotype

value: Wild type

tag: treatment

value: Environmentally Enriched Saline


title: 3A-Interphase-Input-3

value: BL6 mNSC

value: DMSO

value: Input


title: 50P11; DAM50, ENVIRONMENTALLY ENRICHED, SALINE, P11

description: Library name: 50P11

tag: strain


title: DSP-1001660011972-E-C09

description:
Library name: DSP-1001660011972-E-C09
spatial transcriptomic sequencing

tag: slide name

value: lung

tag: panel

tag: patient

value: COPD GOLD 4

value: COPD

value: former

value: male

value: parenchyma

value: COPD_8_LLL_Parenchyma 001

value: paraffin


title: Exp10 GEX T cells

city: Rochester

first: Abhinav

last: Jain

address: 200 1st ST SW

institute: Mayo Clinic

description:
Library name: Exp10_GEX
Exp10_feature_reference.csv

data_processing:
The FASTQ files reads were assessed using FastQC v0.11.9. Following quality assessment, the raw reads were aligned to the GRCh38 human genome using Cell Ranger multi v7.1.0 (10x Genomics). The cellranger multi pipeline was employed to quantify libraries of antibody-derived tags (ADT) and identify hashtagged samples from pooled CITE-seq libraries. Seurat v4.2.1 was used for downstream analysis following data preprocessing. Quality control was conducted to exclude low-quality cells based on the following thresholds: cells with fewer than 200 or more than 4000 genes, UMIs > 10% mapping to mitochondrial-encoded transcript, or more than 20,000 ADT UMIs. DoubletFinder was applied to identify and remove cell doublets.
We have identified CD4+ and CD8+ T cells based on their CD4 and CD8 gene and protein expression and processed them separately. For RNA normalization, individual samples were processed using SCTransform PMID:31870423, regressing out mitochondrial gene expression, while ADT counts were normalized using centralized log-ratio (CLR) transformation.
Further samples across experiments were integrated using diagonalized Canonical Correlation Analysis (CCA) to identify mutual nearest neighbors that act as anchors employing the FindTransferAnchors and IntegrateData functions PMID:31178118.
The Integrated RNA and ADT matrices were scaled and PCA were calculated. A weighted nearest-neighbor (WNN) graph was subsequently constructed using the FindMultiModalNeighbors function to integrate the modalities effectively PMID:34062119. The WNN graph is utilized to generate the UMAP embeddings, facilitating the visualization for both the modalities. Clustering was performed based on WNN using a smart local moving algorithm, revealing populations enriched in gE-stimulated versus control cultures.
Assembly: GRCh38
Supplementary files format and content: CellRanger Output Files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

source_name: Blood

extract_protocol:
Forty-two hours after peptide stimulation, cultures were pre-purified with EasySep Human T Cell Isolation Kit (using 20% of the recommended reagents, Stemcell Technologies, # 17951). T cells were stained with hashtag TotalSeq-B antibodies and subjected to FACS. Live, single CD3+ CD8+ or CD3+ CD4+ cells that were CD69hi and/or CD137+ were collected. After FACS, cells were counted and pooled into one sample across T cell subsets and donors at similar cell numbers, if possible. The pooled sample was stained with diluted TotalSeq-B cell surface marker antibodies (BioLegend) in PBS containing 2% FBS for 30 minutes at 4C. Cells were washed twice with PBS containing 2% FBS, and cell viability was determined with Trypan Blue which was consistently >90%.
Cells were subjected to high-throughput single cell capture via the Chromium controller (10x genomics), Chromium Next GEM Single Cell 3' Kit v3.1 (Single Index, 10x genomics, #PN-1000121) and gel beads (10x genomics, #1000376). About 20,000 cells per pooled samples were targeted for cell capture. 3’ gene expression as well as antibody-derived tags (ADT) for TotalSeq-B antibodies including hashtag antibodies and cell surface marker (3' Feature Barcode Library Kit, 10x genomics, #PN-1000079) collective known as CITE-seq, were generated from each captured sample.

treatment_protocol: Lymphoprep was used to purify PBMCs of vaccine recipients by density centrifugation according to the manufacturer’s instructions. Cells were used fresh in all experiments and cultured in RPMI 1640 medium supplemented with 5% filtered human AB serum (Sigma Aldrich, #H4522), 100 U/mL penicillin, and 100 U/mL streptomycin (Sigma Aldrich, #P0781) in an incubator with 5% CO2 and atmospheric O2. We employed activation-induced marker (AIM) assays to collect VZV gE-responsive T cells. Briefly, PBMCs were seeded at 20x10^6 per 12-well and stimulated with 1 ug/ml of a VZV glycoprotein E (gE) peptide pool diluted in 0.2% DMSO (15-mer peptides with 11 amino acids overlap, total of 153 peptides; # PM-VZV-gE, JPT Peptide Technologies). Ultra-LEAF anti-CD28 stimulation antibody was added at 1 ug/ml (clone 28.2, BioLegend, #302943) as well anti-CD40 blocking antibody at 1 ug/ml (clone HB14, Miltenyi, #130-094-133). Parallel control PBMC cultures of the same individuals, received 0.2% DMSO instead of the VZV gE peptide mix. PBMCs were spun in plates at 300×g for 3 min before culturing for 42 hours to allow activation of antigen-specific T cells before further sample processing.

tag: tissue

value: Blood

value: T cell

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

tag: age

value: DMSO_V_Y_IMAG051F_Exp10 (21y) DMSO_V_Y_IMAG052F_Exp10 (20y) DMSO_V_Y_IMAG053M_Exp10 (21y) gE_V_Y_IMAG051F_Exp10 (21y) gE_V_Y_IMAG052F_Exp10 (20y) gE_V_Y_IMAG053M_Exp10 (21y)

tag: t cell_subset

value: VZV gE-responsive CD4 and CD8 T cells, DMSO-reactive CD4 and CD8 T cells


title: 8P11; DAM8, ENVIRONMENTALLY ENRICHED, SALINE, P11

description: Library name: 8P11

value: Sprague-Dawley

value: Milk

value: Extracellular vesicles derived from milk

value: Wild type

value: Environmentally Enriched Saline

tag: time


title: 46P11; DAM46, ENVIRONMENTALLY ENRICHED, SALINE, P11

description: Library name: 46P11


title: Exp10 CSP T cells

description:
Library name: Exp10_CSP
Exp10_feature_reference.csv

library_source: other

molecule: protein


title: Alveolar organoid co-cultured with macrophage

description: Library name: AVM+M

value: lung

tag: cell line

value: stem cell derived

value: mock


title: 3A-Interphase-Input-1

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: DMSO

value: 6 hours

tag: replicate

value: Input


title: 4P11; DAM4, ENVIRONMENTALLY ENRICHED, SALINE, P11

description: Library name: 4P11


title: 3A-Interphase-ChIP-3

tag: chip antibody

value: FLAG


title: DSP-1001660011972-E-C05

description:
Library name: DSP-1001660011972-E-C05
spatial transcriptomic sequencing

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: condition

value: COPD GOLD 4

value: COPD

tag: former or_current_smoker

value: former

tag: pack years

value: male

tag: location

value: airway

tag: roi

value: COPD_8_LLL_Airway 008

value: paraffin


title: DSP-1001660011972-E-C06

description:
Library name: DSP-1001660011972-E-C06
spatial transcriptomic sequencing

value: lung

tag: gender

value: COPD_8_LLL_Airway 2

tag: scan name


title: 3P11; DAM3, ENVIRONMENTALLY ENRICHED, LPS, P11

description: Library name: 3P11

tag: strain

value: Sprague-Dawley

value: Milk

tag: cell type

value: Extracellular vesicles derived from milk

tag: genotype

value: Wild type

tag: treatment

value: Environmentally Enriched LPS


title: Exp09 GEX T cells

description:
Library name: Exp09_GEX
Exp09_feature_reference.csv

tag: tissue

value: Blood

value: T cell

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

tag: age

value: DMSO_V_Y_IMAG001M_Exp09 (29y) DMSO_V_Y_IMAG047F_Exp09 (26y) DMSO_V_Y_IMAG049M_Exp09 (25y) gE_V_Y_IMAG001M_Exp09 (29y) gE_V_Y_IMAG047F_Exp09 (26y) gE_V_Y_IMAG049M_Exp09 (25y)

value: VZV gE-responsive CD4 and CD8 T cells, DMSO-reactive CD4 and CD8 T cells


title: 2P11; DAM2, ENVIRONMENTALLY ENRICHED, SALINE, P11

description: Library name: 2P11

value: Environmentally Enriched Saline

tag: time


title: 65P11; DAM65, STANDARD HOUSED, LPS, P11

description: Library name: 65P11

value: Standard housed LPS


title: DSP-1001660011972-E-C04

description:
Library name: DSP-1001660011972-E-C04
spatial transcriptomic sequencing

tag: slide name

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

value: COPD GOLD 4

value: COPD

value: former

value: male

value: airway

value: COPD_8_LLL_Airway 007


title: 3A-Interphase-ChIP-1

tag: cell line

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: DMSO

value: 6 hours

tag: replicate

tag: chip antibody

value: FLAG


title: 3A-Interphase-ChIP-2


title: DSP-1001660011972-E-C03

description:
Library name: DSP-1001660011972-E-C03
spatial transcriptomic sequencing

value: lung

tag: condition

tag: former or_current_smoker

tag: pack years

tag: location

value: COPD_8_LLL_Airway 006

value: paraffin


title: Exp07 GEX T cells

description:
Library name: Exp07_GEX
Exp07_feature_reference.csv

value: Blood

value: T cell

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

tag: t cell_subset

value: VZV gE-responsive CD4 and CD8 T cells, DMSO-reactive CD4 and CD8 T cells


title: Exp07 CSP T cells

description:
Library name: Exp07_CSP
Exp07_feature_reference.csv

tag: cell type


title: 55P11; DAM55, STANDARD HOUSED, LPS, P11

description: Library name: 55P11

tag: strain

value: Sprague-Dawley

value: Milk

value: Extracellular vesicles derived from milk

tag: genotype

value: Wild type

value: Standard housed LPS


title: F-WT-Noco-ATAC-Seq-REP3

data_processing:
The ATAC-seq pair-end reads were mapped to the Mus musculus genome assembly mm10 and very sensitive parameters
The nf-core/atacseq pipeline (version 2.0; Ewels et al., 2020;10.5281/zenodo.2634132) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/atacseq -r 2.0 --input SampleSheet.csv  --genome GRCm38 -profile eddie, singularity  --email charles.williams@ed.ac.uk --read_length 150".
All data was processed relative to the  UCSC mm10 genome (Karolchik et al., 2004) downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes).
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/atacseq/tree/2.0).
Assembly: Genome_build: mm10
Supplementary files format and content: Merged bigwigs and broadpeak files, Individual bigwigs per replicate

growth_protocol: NSCs were isolated from the young adult 6-8 weeks old SVZ and maintained in vitro in serum-free basal medium supplemented with N2 and B27 (Life Technologies), Laminin-1 (Sigma, 1 μg/ml) and growth factors EGF and FGF2 (Peprotech, 10 ng/ml each). All expoeriments were conducted in early passage cells.

extract_protocol:
50,000 of freshly harvested cells were resuspended in ice-cold RSB buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2). The suspension was centrifuged at 500xg for 3min using a refrigerated centrifuge. The cell pellet was washed once with 50μl ice-cold PBS and centrifuged at 500xg for 3min at 4°C. The cell pellet was resuspended in ice-cold Lysis Buffer (48.5μl RSB buffer supplemented with 0.5μl of 10% NP-40, 0.5μl of 10% Tween-20, 0.5μl of 1% Digitonin) and kept on ice for 3min. Then, 1ml of wash buffer (RSB buffer supplemented with 0.1% Tween-20) was added on the lysed cells. Nuclei were pelleted at 500g for 10min at 4°C and the supernatant (cytoplasm fraction) was carefully discarded. The nuclei were resuspended in the transposition mix (1x Tagment DNA Buffer (Illumina, #20034197), 0.33X PBS, 0.1% Tween-20, 0.01% Digitonin). Next, 2.5μl of Tn5 Transposase (Illumina, #20034197) was added to the reaction mix by pipetting up and down 6 times. The reaction was then incubated at 37°C for 30min on a thermomixer at 1000rpm. Finally, the tagmented DNA was isolated using Qiagen MinElute Reaction Cleanup-Kit (Qiagen, #28204) following the manufacturer’s instructions.
Nextera Index XT Kit v2 (FC-131-2001, Illumina)

value: BL6 mNSC

tag: treatment

value: 50ng/ml Nocodazole (SML1665)


title: DSP-1001660011972-E-C08

description:
Library name: DSP-1001660011972-E-C08
spatial transcriptomic sequencing

tag: tissue

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: age

value: COPD GOLD 4

value: COPD

value: former

tag: gender

value: male

value: airway

tag: roi

tag: scan name


title: 41P11; DAM41, STANDARD HOUSED, LPS, P11

description: Library name: 41P11

tag: time


title: F-WT-Noco-ATAC-Seq-REP2

tag: cell line

value: Mouse Neural Stem Cell

value: 6 hours

tag: replicate


title: 3A-Interphase-Input-2

value: DMSO

tag: chip antibody

value: Input


title: DSP-1001660011972-E-C02

description:
Library name: DSP-1001660011972-E-C02
spatial transcriptomic sequencing

tag: slide name

value: lung

tag: panel

tag: patient

tag: condition

tag: former or_current_smoker

value: COPD_8_LLL_Airway 005

value: paraffin


title: DSP-1001660011972-E-C01

description:
Library name: DSP-1001660011972-E-C01
spatial transcriptomic sequencing

tag: pack years

tag: location

value: COPD_8_LLL_Airway 004


title: Exp06 GEX T cells

description:
Library name: Exp06_GEX
Exp06_feature_reference.csv

value: Blood

tag: cell type

value: T cell

tag: treatment

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

tag: t cell_subset

value: VZV gE-responsive CD4 and CD8 T cells, DMSO-reactive CD4 and CD8 T cells


title: 19P11; DAM19, STANDARD HOUSED, LPS, P11

description: Library name: 19P11

tag: strain

value: Sprague-Dawley

tag: tissue

value: Milk

value: Extracellular vesicles derived from milk

tag: genotype

value: Wild type

value: Standard housed LPS


title: F-WT-Noco-ATAC-Seq-REP1

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

tag: time


title: Exp06 CSP T cells

description:
Library name: Exp06_CSP
Exp06_feature_reference.csv

tag: age


title: F-WT-Async-ATAC-Seq-REP3

tag: cell line

value: DMSO

value: 6 hours

tag: replicate


title: 17P11; DAM17, STANDARD HOUSED, LPS, P11

description: Library name: 17P11


title: Exp05 GEX T cells

description:
Library name: Exp05_GEX
Exp05_feature_reference.csv


title: DSP-1001660011972-E-B12

description:
Library name: DSP-1001660011972-E-B12
spatial transcriptomic sequencing

tag: slide name

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

value: former

tag: gender

value: male

value: vessel

tag: roi

value: COPD10_LLL vessel8

tag: scan name


title: DSP-1001660011972-E-B11

description:
Library name: DSP-1001660011972-E-B11
spatial transcriptomic sequencing

tag: panel

tag: patient

tag: condition

tag: former or_current_smoker

value: COPD10_LLL vessel7

value: paraffin


title: Exp09 CSP T cells

description:
Library name: Exp09_CSP
Exp09_feature_reference.csv

value: Blood

tag: cell type

value: T cell

tag: treatment

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

value: DMSO_V_Y_IMAG001M_Exp09 (29y) DMSO_V_Y_IMAG047F_Exp09 (26y) DMSO_V_Y_IMAG049M_Exp09 (25y) gE_V_Y_IMAG001M_Exp09 (29y) gE_V_Y_IMAG047F_Exp09 (26y) gE_V_Y_IMAG049M_Exp09 (25y)

value: VZV gE-responsive CD4 and CD8 T cells, DMSO-reactive CD4 and CD8 T cells


title: Exp05 CSP T cells

description:
Library name: Exp05_CSP
Exp05_feature_reference.csv

tag: t cell_subset


title: F-WT-Async-ATAC-Seq-REP2

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: DMSO


title: 66P11; DAM66, STANDARD HOUSED, SALINE, P11

description: Library name: 66P11

tag: strain

value: Sprague-Dawley

tag: tissue

value: Milk

value: Extracellular vesicles derived from milk

value: Wild type

value: Standard housed Saline


title: DSP-1001660011972-E-B10

description:
Library name: DSP-1001660011972-E-B10
spatial transcriptomic sequencing

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

value: former

tag: pack years

value: male

tag: location

value: vessel

value: COPD10_LLL vessel6


title: 56P11; DAM56, STANDARD HOUSED, SALINE, P11

description: Library name: 56P11

tag: genotype

tag: time


title: F-WT-Async-ATAC-Seq-REP1

tag: cell line

value: 6 hours

tag: replicate


title: DSP-1001660011972-E-B08

description:
Library name: DSP-1001660011972-E-B08
spatial transcriptomic sequencing

tag: slide name

tag: age

tag: gender

tag: roi

value: COPD10_LLL vessel4

value: paraffin


title: Exp04 CSP T cells

description:
Library name: Exp04_CSP
Exp04_feature_reference.csv

value: Blood

value: T cell

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

value: VZV gE-responsive CD4 and CD8 T cells, DMSO-reactive CD4 and CD8 T cells


title: Exp04 GEX T cells

description:
Library name: Exp04_GEX
Exp04_feature_reference.csv


title: 32P11; DAM32, STANDARD HOUSED, SALINE, P11

description: Library name: 32P11

value: Sprague-Dawley

value: Milk

value: Extracellular vesicles derived from milk

value: Wild type


title: F-3A-Noco-ATAC-Seq-REP3

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)


title: 42P11; DAM42, STANDARD HOUSED, SALINE, P11

description: Library name: 42P11

value: Standard housed Saline


title: DSP-1001660011972-E-B09

description:
Library name: DSP-1001660011972-E-B09
spatial transcriptomic sequencing

value: lung

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

tag: condition

value: COPD GOLD 4

value: COPD

value: former

value: male

value: vessel

value: COPD10_LLL vessel5

tag: scan name


title: DSP-1001660011972-E-B06

description:
Library name: DSP-1001660011972-E-B06
spatial transcriptomic sequencing

tag: former or_current_smoker

value: COPD10_LLL vessel2

value: paraffin


title: DSP-1001660011972-E-B07

description:
Library name: DSP-1001660011972-E-B07
spatial transcriptomic sequencing

value: COPD10_LLL vessel3


title: 45P10; DAM45, ENVIRONMENTALLY ENRICHED, LPS, P10

description: Library name: 45P10

tag: strain

value: Sprague-Dawley

value: Milk

tag: cell type

value: Extracellular vesicles derived from milk

tag: treatment

value: Environmentally Enriched LPS


title: Exp03 GEX T cells

description:
Library name: Exp03_GEX
Exp03_feature_reference.csv

tag: tissue

value: Blood

value: T cell

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

tag: t cell_subset

value: VZV gE-responsive CD4 and CD8 T cells, DMSO-reactive CD4 and CD8 T cells


title: 33P10; DAM33, ENVIRONMENTALLY ENRICHED, LPS, P10

description: Library name: 33P10

tag: genotype

value: Wild type

tag: time


title: Exp01 GEX T cells

description:
Library name: Exp01_GEX
Exp01_feature_reference.csv

value: gE_V_Y_IMAG002F_Exp01 (24y) gE_V_Y_IMAG003F_Exp01 (23y) gE_V_Y_IMAG004M_Exp01 (25y)

value: VZV gE-responsive CD4 and CD8 T cells


title: Exp03 CSP T cells

description:
Library name: Exp03_CSP
Exp03_feature_reference.csv


title: F-3A-Noco-ATAC-Seq-REP2

tag: cell line

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

value: 6 hours

tag: replicate


title: DSP-1001660011972-E-B05

description:
Library name: DSP-1001660011972-E-B05
spatial transcriptomic sequencing

tag: slide name

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: age

value: COPD GOLD 4

value: COPD

value: former

tag: pack years

value: male

tag: location

value: vessel

value: COPD10_LLL vessel1

value: paraffin


title: F-3A-Async-ATAC-Seq-REP2

value: DMSO


title: 16P11; DAM16, STANDARD HOUSED, SALINE, P11

description: Library name: 16P11

value: Sprague-Dawley

value: Milk

value: Extracellular vesicles derived from milk

value: Wild type

value: Standard housed Saline


title: Exp02 GEX T cells

description:
Library name: Exp02_GEX
Exp02_feature_reference.csv

value: Blood

value: T cell

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

value: VZV gE-responsive CD4 and CD8 T cells


title: DSP-1001660011972-E-B04

description:
Library name: DSP-1001660011972-E-B04
spatial transcriptomic sequencing

value: lung

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

value: COPD GOLD 4

tag: gender

value: parenchyma

tag: roi

value: COPD10_LLL paren7


title: Exp02 CSP T cells

description:
Library name: Exp02_CSP
Exp02_feature_reference.csv


title: 9P10; DAM9, ENVIRONMENTALLY ENRICHED, LPS, P10

description: Library name: 9P10

tag: strain

value: Environmentally Enriched LPS


title: F-3A-Noco-ATAC-Seq-REP1

value: BL6 mNSC

tag: cell type

value: Mouse Neural Stem Cell

value: 50ng/ml Nocodazole (SML1665)

value: 6 hours


title: BL6-Noco-ATAC-Seq-REP2

tag: treatment


title: DSP-1001660011972-E-B01

description:
Library name: DSP-1001660011972-E-B01
spatial transcriptomic sequencing

tag: tissue

tag: condition

value: COPD

tag: former or_current_smoker

value: former

value: male

value: COPD10_LLL paren4

tag: scan name

value: paraffin


title: DSP-1001660011972-E-B03

description:
Library name: DSP-1001660011972-E-B03
spatial transcriptomic sequencing

value: COPD10_LLL paren6


title: 3P10; DAM3, ENVIRONMENTALLY ENRICHED, LPS, P10

description: Library name: 3P10

value: Sprague-Dawley

value: Milk

value: Extracellular vesicles derived from milk

tag: genotype

value: Wild type

tag: time


title: 7P10; DAM7, ENVIRONMENTALLY ENRICHED, LPS, P10

description: Library name: 7P10


title: BL6-Noco-ATAC-Seq-REP3

tag: cell line

tag: replicate


title: BL6-Noco-ATAC-Seq-REP1


title: DSP-1001660011972-E-B02

description:
Library name: DSP-1001660011972-E-B02
spatial transcriptomic sequencing

tag: slide name

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: age

value: COPD GOLD 4

tag: pack years

value: parenchyma

value: COPD10_LLL paren5


title: F-3A-Async-ATAC-Seq-REP3

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: DMSO


title: Exp01 CSP T cells

description:
Library name: Exp01_CSP
Exp01_feature_reference.csv

value: Blood

value: T cell

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

value: gE_V_Y_IMAG002F_Exp01 (24y) gE_V_Y_IMAG003F_Exp01 (23y) gE_V_Y_IMAG004M_Exp01 (25y)

tag: t cell_subset

value: VZV gE-responsive CD4 and CD8 T cells


title: explanted dilated cardiomyopathy ventricular tissue, rep1

first: Xuebing

last: Wu

address: 630 West 168th Street, P&S 10-401

institute: Columbia University

description: Library name: MM031

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format
We perform a pseudoalignment to a kallisto index created from transcriptomes (human MANE select) and generate the abundance.tsv file for each sample
Assembly: hg38 MANE select refseq RNA
Supplementary files format and content: tab-delimited txt file with a header row: target_id       length  eff_length      est_counts      tpm

source_name: heart ventricle

extract_protocol:
Explanted frozen patient heart tissue was homogenized using pestle and mortar under liquid nitrogen. Homogenized tissue was submerged in TRIzol and extracted using Direct-zol kit (Zymo Research). RNA integrity was analyzed with Bioanalyzer electrophoresis.
We use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.Libraries are then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.

value: heart ventricle


title: DSP-1001660011972-E-A12

description:
Library name: DSP-1001660011972-E-A12
spatial transcriptomic sequencing

tag: panel

tag: patient

value: COPD

value: former

tag: gender

value: male

tag: location

value: COPD10_LLL paren3

value: paraffin


title: 5P10; DAM5, ENVIRONMENTALLY ENRICHED, LPS, P10

description: Library name: 5P10

tag: strain

value: Sprague-Dawley

value: Milk

tag: cell type

value: Extracellular vesicles derived from milk

value: Wild type

tag: treatment

value: Environmentally Enriched LPS


title: DSP-1001660011972-E-A11

description:
Library name: DSP-1001660011972-E-A11
spatial transcriptomic sequencing

tag: tissue

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: condition

value: COPD GOLD 4

tag: former or_current_smoker

value: parenchyma

tag: roi

value: COPD10_LLL paren2


title: BL6-Async-ATAC-Seq-REP3

tag: cell line

value: BL6 mNSC

value: Mouse Neural Stem Cell

value: DMSO

tag: time

value: 6 hours


title: Day 26 Human Heart Organoids with Tissue-Resident Macrophages

city: East Lansing

first: Aitor

last: Aguirre

state: MI

address: 775 Woodlot Dr

department: Biomedical Engineering

institute: Michigan State University

description: 10x Genomics

data_processing:
After demultiplexing, reads from each of the sample libraries was further processed using 10x Genomics cellranger count (v7.2.0). This program uses the read 1 data to identify reads from individual cells and remove duplicate reads (based on UMIs) as well as align the corresponding read 2 to the reference transcriptome (H. sapiens GRCh38).
After running cellranger count for each sample, results for each of the projects were aggregated using cellranger aggr.
Assembly: H. sapiens GRCh38
Supplementary files format and content: gzip-compressed tar archive

extract_protocol:
Culture medium was carefully removed and discarded from the hHO. The hHO was washed once with PBS to remove any loosely attached cells. RPMI+B27 with 2% BSA (w/v) was prepared and filtered to make sterile. Cardiomyocyte Dissociation Medium (STEMCELL) was warmed to 37°C prior to dissociation. 500µL of the Cardiomyocyte Dissociation Medium was applied to the organoid and shaken at 37˚C at 250rpm for 5 minutes. The dissociation medium was then collected from the organoid containing RPMI+B27 with 2% BSA. The dissociation medium addition, incubation, and collection was repeated until 20 minutes passed. The collection was filtered with a 40µm filter and then centrifuged at 300g for 5min. The supernatant was decanted, and the pelleted cells were resuspended in a smaller volume of FACS buffer for flow cytometry or RPMI+B27 + 2% BSA for scRNAseq. After the cells were resuspended, the cells were filtered again with a 40µm filter. Libraries were prepared using the 10x Chromium Next GEM Single Cell 3' Kit, v3.1 and associated components.
Libraries were prepared using the 10x Chromium Next GEM Single Cell 3' Kit, v3.1 and associated components. Completed libraries were QC’d and quantified using a combination of Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays. Libraries from each pool were pooled in equimolar proportions and the pool quantified again using the Invitrogen Collibri qPCR assay. These two project pools were then pooled in equal proportions and this final pool again quantified by qPCR. The pool was loaded onto 1 lane of an Illumina NovaSeq 6000 S4 flow cell (v1.5) and sequencing was performed in a 2x150bp paired end format using 300 NovaSeq v1.5 reagent cartridge. Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. For Bcl2fastq only the first 28 bases of read #1 and 100 bases of read #2 were output. The first 28bp of read 1 includes the 10x cell barcodes and UMIs, read 2 is the cDNA read.

value: H9-hESCs (WA09)

value: Multicellular

value: Day 26

value: Macrophages


title: BL6-Async-ATAC-Seq-REP2

tag: replicate


title: explanted dilated cardiomyopathy ventricular tissue, rep2

description: Library name: MM032

value: heart ventricle

tag: genotype


title: 10P10; DAM10, ENVIRONMENTALLY ENRICHED, SALINE, P10

description: Library name: 10P10

value: Sprague-Dawley

value: Milk

value: Extracellular vesicles derived from milk

value: Environmentally Enriched Saline


title: Day 26 Human Heart Organoids

description: 10x Genomics

source_name: Human Heart Organoids

value: Human Heart Organoids

tag: age

value: No Macrophages


title: 50P10; DAM50, ENVIRONMENTALLY ENRICHED, SALINE, P10

description: Library name: 50P10

value: Wild type


title: 8P10; DAM8, ENVIRONMENTALLY ENRICHED, SALINE, P10

description: Library name: 8P10


title: F-3A-Async-ATAC-Seq-REP1


title: Day 15 Human Heart Organoid with Tissue-Resident Macrophages

description: 10x Genomics

source_name: Human Heart Organoids with Tissue-Resident Macrophages

value: Day 15


title: BL6-Async-ATAC-Seq-REP1

value: BL6 mNSC


title: DSP-1001660011972-E-A10

description:
Library name: DSP-1001660011972-E-A10
spatial transcriptomic sequencing

data_processing:
Digital count conversion (.dcc) files were produced from fastq files using the GeoMx NGS Pipeline 2.3.3.10 desktop application.  Briefly, reads are trimmed to remove adapter sequences followed by merging paired-end reads. Stitched reads are then aligned to RTS-ID barcodes in the reference assay. PCR duplicates are removed by sorting on UMIs. Supplemental file Hs_R_NGS_WTA_v1.0 contains RTS-ID mapping.
Assembly: GRCh38.p13. Reads are aligned to GeoMx RTS_ID barcodes as part of the GeoMx NGS Pipeline to generate .dcc files
Supplementary files format and content: deduplicated read counts
Library strategy: Spatial Transcriptomics

tag: slide name

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

value: former

tag: pack years

value: male

value: parenchyma

value: COPD10_LLL paren1

tag: scan name

value: paraffin


title: F-WT-Async-REP3

data_processing:
The RNA-seq pair-end reads were mapped to the Mus musculus genome assembly mm10 and very sensitive parameters
The nf-core/rnaseq pipeline (version 3.10; Ewels et al., 2020;10.5281/zenodo.2634132) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/rnaseq -r 3.10.1 --input samplesheet.csv --outdir /exports/eddie/scratch/cwilli11/RNA-seq --genome GRCm38 -profile eddie,singularity --aligner star_salmon".
All data was processed relative to the  UCSC mm10 genome (Karolchik et al., 2004) downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes).
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/rnaseq/tree/3.10).
Assembly: Genome_build: mm10
Supplementary files format and content: Compiled counts file
Supplementary files format and content: Bigwig read density for Forward and reverse of each replicate

extract_protocol:
All samples were run in triplicate. RNA was extracted from cells using the QIAGEN RNeasy kit. Sample concentration and quality was assessed using the Aligent Tapestation and Nanodrop, only samples with a RIN value of 9.6 or above were used. Library preparation and mRNA sequencing of samples was performed by Azenta (formally, Genewiz).
Illumina, RNA with PolyA selection

value: Mouse Neural Stem Cell


title: Day 15 Human Heart Organoids

description: 10x Genomics

value: H9-hESCs (WA09)

value: Multicellular


title: DSP-1001660011972-E-A09

description:
Library name: DSP-1001660011972-E-A09
spatial transcriptomic sequencing

tag: panel

tag: patient

tag: gender

value: airway

value: COPD10_LLL airway8


title: 4P10; DAM4, ENVIRONMENTALLY ENRICHED, SALINE, P10

description: Library name: 4P10

tag: strain

value: Sprague-Dawley

value: Milk

tag: cell type

value: Extracellular vesicles derived from milk

value: Wild type

value: Environmentally Enriched Saline


title: F-WT-Async-REP2

value: BL6 mNSC


title: DSP-1001660011972-E-A07

description:
Library name: DSP-1001660011972-E-A07
spatial transcriptomic sequencing

tag: tissue

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: COPD GOLD 4

value: COPD

tag: location

value: COPD10_LLL airway6


title: 2P10; DAM2, ENVIRONMENTALLY ENRICHED, SALINE, P10

description: Library name: 2P10

tag: treatment


title: Control skin 5

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
Reads were aligned to the human genome reference index hg38 using STAR 2.7.3a
Gene counts were normalized to counts per million with a 0.0001 offset
Assembly: hg38
Supplementary files format and content: Tab delimited normalized counts file. Column 1 represents gene symbol and each subsequent column is gene counts normalized to counts per million with a 0.0001 offset for each sample

source_name: Control skin

extract_protocol:
Total RNA was extracted using Rneasy Midi Kit (Qiagen)
Total RNA was prepped with the Tecan/Nugen Universal Plus Total RNASeq w/ Human AnyDepleteusing ~60ng via Qubit and 14 cycles PCR. Libraries were sequenced on Illumina Novaseq 6000

value: Control skin


title: Control skin 2


title: Control skin 4


title: F-WT-Async-REP1

value: Mouse Neural Stem Cell


title: 46P10; DAM46, ENVIRONMENTALLY ENRICHED, SALINE, P10

description: Library name: 46P10


title: DSP-1001660011972-E-A06

description:
Library name: DSP-1001660011972-E-A06
spatial transcriptomic sequencing

tag: condition

tag: former or_current_smoker

value: former

value: male

tag: roi

value: COPD10_LLL airway5

value: paraffin


title: Control skin 1


title: 65P10; DAM65, STANDARD HOUSED, LPS, P10

description: Library name: 65P10

value: Sprague-Dawley

value: Standard housed LPS

tag: time


title: DSP-1001660011972-E-A05

description:
Library name: DSP-1001660011972-E-A05
spatial transcriptomic sequencing

value: airway

value: COPD10_LLL airway4


title: 55P10; DAM55, STANDARD HOUSED, LPS, P10

description: Library name: 55P10

value: Milk

value: Extracellular vesicles derived from milk

tag: genotype

value: Wild type


title: F-3A-Async-REP2

tag: cell line

value: BL6 mNSC

tag: replicate


title: F-3A-Async-REP3


title: F-3A-Async-REP1


title: Control skin 3


title: DSP-1001660011972-E-A04

description:
Library name: DSP-1001660011972-E-A04
spatial transcriptomic sequencing

tag: slide name

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: age

value: COPD GOLD 4

tag: pack years

value: COPD10_LLL airway3


title: 41P10; DAM41, STANDARD HOUSED, LPS, P10

description: Library name: 41P10


title: VLU11

source_name: Non-healing ulcer

value: Non-healing ulcer


title: DSP-1001660011972-E-A03

description:
Library name: DSP-1001660011972-E-A03
spatial transcriptomic sequencing

tag: panel

tag: patient

value: COPD

value: former

value: COPD10_LLL airway2

tag: scan name


title: VLU10


title: 15P10; DAM15, STANDARD HOUSED, LPS, P10

description: Library name: 15P10

tag: strain

tag: cell type


title: DSP-1001660011972-E-A02

description:
Library name: DSP-1001660011972-E-A02
spatial transcriptomic sequencing

tag: tissue

tag: gender

value: male

tag: location

value: COPD10_LLL airway1 006

value: paraffin


title: BL6-Async-REP2

value: Mouse Neural Stem Cell


title: DSP-1001660011972-E-A08

description:
Library name: DSP-1001660011972-E-A08
spatial transcriptomic sequencing

tag: condition

tag: former or_current_smoker

value: airway

value: COPD10_LLL airway7


title: BL6-Async-REP3


title: Muscle, DM1 patient, classic5

city: San José

first: Fernando

last: Morales

address: San Pedro de Montes de Oca

country: Costa Rica

institute: Universidad de Costa Rica

description:
Library name: CR99_SM
DM1 patient living in Costa Rica

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 for basecalling and demultiplexing
Raw sequence quality was assessed using FASTQC.
Reads passing quality control were mapped to the hg19 genome using Hisat2.
Percent splice in (PSI or Ψ) values were computed using MISO with hg19 v2.0 MISO annotations.
TPM were calculated using Kallisto
Assembly: hg19
Supplementary files format and content: txt format, TPM counts for all samples

source_name: Muscle

extract_protocol:
RNA samples used in this study were previously purified using TRIzol reagent (Thermo-Scientific, USA) from three different tissues (blood, skeletal muscle [tibialis anterior-TA], and skin) of the same DM1 patients.
RNA-seq libraries were constructed using the NEBNext Ultra II RNA library prep kit for Illumina (New England Biolabs, USA) with ribosomal RNA depletion (NEBNext rRNA depletion kit, New England Biolabs). Strand-specific RNA-seq libraries were sequenced using Illumina NextSeq 500 v2 with 75 nucleotide paired-end reads.

value: Muscle


title: VLU9


title: 17P10; DAM17, STANDARD HOUSED, LPS, P10

description: Library name: 17P10

value: Sprague-Dawley

value: Milk

value: Extracellular vesicles derived from milk

value: Wild type

tag: treatment

value: Standard housed LPS

tag: time


title: 66P10; DAM66, STANDARD HOUSED, SALINE, P10

description: Library name: 66P10

tag: genotype

value: Standard housed Saline


title: Skin, DM1 patient, classic5

description:
Library name: CR99_SK
DM1 patient living in Costa Rica

source_name: Skin

value: Skin


title: BL6-Async-REP1

tag: cell line

value: BL6 mNSC

tag: replicate


title: 56P10; DAM56, STANDARD HOUSED, SALINE, P10

description: Library name: 56P10


title: VLU7

value: Non-healing ulcer


title: Blood, DM1 patient, classic5

description:
Library name: CR99_BL
DM1 patient living in Costa Rica

value: Blood


title: 42P10; DAM42, STANDARD HOUSED, SALINE, P10

description: Library name: 42P10


title: Cured LN 20,BCR

first: Mi

last: Liu

state: Jiangsu

address: 1435 of Yunxuan Lou, Du Shu Hu Xiao Qu,, Gong Ye Yuan Qu

department: Pharmaceutics

description: BD Rhapsody,BCR

data_processing:
Basecalls performed using CASAVA version 1.8
We applied BD Genomics Rhapsody Analysis pipeline(https://bitbucket.org/CRSwDev/cwl/src/master/,V1.10.1)with default parameter toanalyzesingle-cellGEX,TCR/BCRsequencingdata,assemblecontigscorrespondingtorearrangedTCR/BCRchainmRNA.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files;filtered contig for TCR and BCR sequencing.

source_name: Draning lymph nodes

extract_protocol:
Healthy mice, tumor-bearing mice treated with PBS, non-cured mice or cured mice were sacrifaced. Blood,Spleen and drainining lymph nodes were collected. PBMC, single cell suspension of splenocytes or single cell suspension of draining lymph node cells were prepared for single cell sequencing analysis
BD Rhapsody system and BD RhapsodyTM TCR/BCR Amplification kit(Cat.NO.633773) were used to capture the single cells and construct the scRNA-Seq libraries and V(D)J libraries.
scRNA-seq; scTCR-seq; scBCR-seq

treatment_protocol: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then these tumor-bearing mice were treated with nanovaccines or PBS. After nanovaccine treatment, non-cured mice were sacrificed and cured mice were sacrificed at different time (Freshly, 3 months or 8 months). In terms of cured mice sacrificed at 8 months, they were rechallenged with nanovaccines or cancer cells.

value: Draning lymph nodes

value: Draning lymph node cells

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with nanovaccines


title: 32P10; DAM32, STANDARD HOUSED, SALINE, P10

description: Library name: 32P10


title: VLU6


title: Skin, DM1 patient, classic4

description:
Library name: CR94_SK
DM1 patient living in Costa Rica


title: Cured LN 19,BCR

description: BD Rhapsody,BCR


title: VLU5

source_name: Healing ulcer

value: Healing ulcer


title: 16P10; DAM16, STANDARD HOUSED, SALINE, P10

description: Library name: 16P10


title: VLU4


title: 14P10; DAM14, STANDARD HOUSED, SALINE, P10

description: Library name: 14P10


title: Cured LN 18,BCR

description: BD Rhapsody,BCR


title: Blood, DM1 patient, classic4

description:
Library name: CR94_BL
DM1 patient living in Costa Rica


title: Muscle, DM1 patient, classic4

description:
Library name: CR94_SM
DM1 patient living in Costa Rica


title: Treated not cured LN 17,BCR

description: BD Rhapsody,BCR


title: Muscle, DM1 patient, classic3

description:
Library name: CR70_SM
DM1 patient living in Costa Rica


title: VLU3


title: Fascia_dysentery_scRNA2

city: Nanjing

first: ZhenWei

last: Zhang

address: No. 1 Weigang

department: veterinarian

institute: Nanjing Agricultural University

description:
Fascia_CT_2
10x Genomics

data_processing:
The reads were processed using the Cell Ranger V6.0.1 pipeline with default and recommended parameters. FASTQ files generated from Illumina sequencing output were aligned to the rat/human genome (version mRatBN7.2/GRCh38.p13) using the STAR algorithm. Subsequently, Gene-Barcode matrices were generated for each individual sample by counting Unique Molecular Identifiers (UMIs) and filtering non-cell associated barcodes. This resulted in a gene-barcode matrix containing the barcoded cells and gene expression counts.
Assembly: mRatBN7.2
Supplementary files format and content: 10X expression matrix generated by CellRanger V6.0.1

source_name: subcutaneous fascia

extract_protocol:
The process of tissue dissociation and cell purification for single-cell RNA sequencing and fascia primary cell extraction was meticulously executed. The fascia was placed in a sterile culture dish containing 10 ml of 1x Dulbecco’s Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to eliminate the residual blood and adipose, followed by mincing on ice.We employed a specially formulated dissociation solution, composed of the collagenase type 4 (sigma-Aldrich, Cat. no. C5138), elastase (sigma-aldrich, Cat. no. e1250), and 10 ug/mL DNase I (Thermo Fisher, Cat. no. en0523) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02), to digest the fascia. The fascia was dissociated at 37℃ with a shaking speed of 50 rpm for approximately 40 minutes. We collected the dissociated cells at 20-minute intervals to maximize cell yield and viability.Cell suspensions were filtered by the sequence of nylon cell strainer from 100μm to 40 μm, and residual red blood cells were eliminated using 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57). The dissociated cells were then washed with 1x DPBS containing 2% FBS. Cell viability was assessed using 0.4% Trypan blue staining and the Countess® II Automated Cell Counter (Thermo Fisher), all samples of suspension cells were filtered by Dead Cell Removal Kit (Miltenyi Biotec, Cat. No. 130-090-101), and only samples with >95 % living cells were used for next steps.Suspension cells were prepared for 10X library construction and 3’ sequencing, water-in-oil solution was prepared by the Chromium™ Single Cell Controller (10X Genomics).
The process of tissue dissociation and cell purification for single-cell RNA sequencing and fascia primary cell extraction was meticulously executed. The fascia was placed in a sterile culture dish containing 10 ml of 1x Dulbecco’s Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to eliminate the residual blood and adipose, followed by mincing on ice.We employed a specially formulated dissociation solution, composed of the collagenase type 4 (sigma-Aldrich, Cat. no. C5138), elastase (sigma-aldrich, Cat. no. e1250), and 10 ug/mL DNase I (Thermo Fisher, Cat. no. en0523) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02), to digest the fascia. The fascia was dissociated at 37℃ with a shaking speed of 50 rpm for approximately 40 minutes. We collected the dissociated cells at 20-minute intervals to maximize cell yield and viability.Cell suspensions were filtered by the sequence of nylon cell strainer from 100μm to 40 μm, and residual red blood cells were eliminated using 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57). The dissociated cells were then washed with 1x DPBS containing 2% FBS. Cell viability was assessed using 0.4% Trypan blue staining and the Countess® II Automated Cell Counter (Thermo Fisher), all samples of suspension cells were filtered by Dead Cell Removal Kit (Miltenyi Biotec, Cat. No. 130-090-101), and only samples with >95 % living cells were used for next steps.Suspension cells were prepared for 10X library construction and 3’ sequencing, water-in-oil solution was prepared by the Chromium™ Single Cell Controller (10X Genomics).

value: subcutaneous fascia

value: acupuncture


title: Skin, DM1 patient, classic3

description:
Library name: CR70_SK
DM1 patient living in Costa Rica


title: PBS treated LN 16,BCR

description: BD Rhapsody,BCR

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with PBS


title: VLU2


title: Fascia_dysentery_scRNA1

description:
Fascia_CT_1
10x Genomics


title: VLU8