title: CV14, GEX

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv14_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: G5-SF18103137-96h

status: Public on Nov 21 2023

type: SRA

city: Nashville

first: Taha

last: Jan

state: TN

address: 2220 Pierce Ave, PRB 752

department: Otolaryngology

country: USA

institute: VUMC

library_source: transcriptomic single cell

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: galGal6
Supplementary files format and content: RDS file with metadata, counts, normcounts, and logcounts in SingleCellExperiment object format for R

molecule: total RNA

organism: Gallus gallus

source_name: basilar papilla

extract_protocol:
FACS sorted into 96-well plates containing RNA lysis buffer
smartseq2

treatment_protocol: in vivo administration of sisomicin with harvesting of cells at indicated timepoints

tag: tissue

value: basilar papilla

tag: treatment


title: CV14, TCRab

city: New York

first: Ellie

last: Ivanova

state: NY

address: 550 First Ave

department: Pathology

institute: NYU Langone

description:
Enriched TCRab fragment
TCRab: Read 1 contains cell barcode and UMI, Read 2 contains enriched VDJ fragment (abT cell receptor)

library_source: transcriptomic

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
PBMCs were isolated form whole blood using ficoll gradient. Cells were encapsulated in Gel-Beads-in emulsion (GEMs) using 10x Controller with a Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1
Gene expression library and VDJ libraries were constructed according to the manufacturer’s protocol (10x Genomics)
The CITE-seq and hashing protocol described by Stoeckius et. al. was used to generate an antibody-derived tag (ADT) sequencing library and hashtag oligo (HTO) library (Stoeckius et. al., 2017). Gene expression library and VDJ libraries were constructed according to the manufacturer’s protocol (10x Genomics)

value: PBMCs

tag: cell type

value: SARS-CoV-2 vaccine

tag: library type

value: TCRab


title: G5-SF18103134-96h


title: CV14, BCR

description:
Enriched BCR fragment
BCR: Read 1 contains cell barcode and UMI, Read 2 contains enriched VDJ fragment

value: BCR


title: G5-SF18103133-96h


title: G4-SF18103137-96h


title: CV14, ADT

description:
Antibody-derived tags (ADT)
ADT: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag

library_source: other

molecule: protein

value: ADT


title: G7-SF18103137-96h


title: CV13, TCRgd

description:
Enriched TCRgd fragment
TCRgd: Read 1 contains cell barcode and UMI, Read 2 contains enriched VDJ fragment (gdT cell receptor)

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv13_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq

value: TCRgd


title: G4-SF18103134-96h


title: CV13, TCRab


title: CV15, BCR

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv15_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: CV13, GEX

description:
Gene expression (GEX)
GEX (5' mRNA): Read 1 contains cell barcode and UMI, Read 2 contains transcript, I1 contains library index

value: GEX


title: CV13, ADT


title: CV14, TCRgd


title: CV13, BCR


title: G3-SF18103137-96h


title: G2-SF19013101-96h


title: CV12, GEX

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv12_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: CV12, TCRab


title: A1-SF18103110-p11control


title: CV12, TCRgd


title: G4-SF18103133-96h


title: G2-SF18103137-96h


title: CV12, BCR


title: G12-SF18103137-96h


title: G2-SF18103134-96h


title: G3-SF18103134-96h


title: G2-SF18103133-96h


title: G11-SF19013101-96h


title: CV11, TCRab

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv11_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: CV12, ADT


title: G3-SF18103133-96h


title: G11-SF18103137-96h


title: CV11, GEX


title: CV11, TCRgd


title: G11-SF18103133-96h


title: CV11, BCR


title: CV10, TCRgd

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv10_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: G10-SF18103137-96h


title: G1-SF18103138-96h


title: CV10, TCRab


title: G1-SF18103137-96h


title: G10-SF18103133-96h


title: CV10, GEX


title: G1-SF18103133-96h


title: F9-SF18103137-96h


title: CV10, BCR


title: F9-SF18103134-96h


title: F9-SF18103138-96h


title: G12-SF18103133-96h


title: CV9, TCRab

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv9_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: F8-SF18103138-96h


title: CV9, BCR


title: CV9, ADT


title: F7-SF18103138-96h


title: F8-SF18103137-96h


title: F8-SF18103133-96h


title: F9-SF18103133-96h


title: F7-SF18103133-96h


title: F8-SF18103134-96h


title: CV7, TCRgd

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv7_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: CV10, ADT


title: CV9, TCRgd


title: F6-SF18103137-96h


title: CV7, HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO: Read 1 contains cell barcode and UMI, Read 2 contains hashtag-derived tag

value: HTO


title: F6-SF18103134-96h


title: F6-SF18103133-96h


title: CV9, HTO


title: CV7, TCRab


title: CV7, BCR


title: CV7, GEX


title: F5-SF18103137-96h


title: CV7, ADT


title: F5-SF18103138-96h


title: CV6, TCRgd

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv6_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: CV6, TCRab


title: F5-SF18103133-96h


title: F4-SF18103137-96h


title: CV6, GEX


title: F7-SF18103137-96h


title: F5-SF18103134-96h


title: F4-SF18103138-96h


title: CV6, HTO


title: F3-SF18103137-96h


title: F3-SF18103138-96h


title: F4-SF18103133-96h


title: CV6, BCR


title: F3-SF18103134-96h


title: CV5, TCRab

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv5_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: CV5, HTO


title: CV5, TCRgd


title: F3-SF18103133-96h


title: CV5, GEX


title: F2-SF18103137-96h


title: F2-SF19013101-96h


title: F2-SF18103138-96h


title: F2-SF18103133-96h


title: F2-SF18103134-96h


title: F12-SF18103138-96h


title: CV5, ADT


title: CV4, GEX

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv4_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: F12-SF19013101-96h


title: F12-SF18103137-96h


title: CV6, ADT


title: CV4, BCR


title: CV4, TCRgd


title: F11-SF18103138-96h


title: F12-SF18103134-96h


title: CV3, TCRgd

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv3_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: F11-SF19013101-96h


title: CV4, ADT


title: CV3, TCRab


title: CV3, HTO


title: CV3, GEX


title: CV5, BCR


title: F10-SF19013101-96h


title: CV4, HTO


title: F11-SF18103134-96h


title: CV4, TCRab


title: CV3, BCR


title: CV3, ADT


title: F10-SF18103138-96h


title: CV2, TCRgd

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv2_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq


title: F10-SF18103137-96h


title: CV2, TCRab


title: F10-SF18103133-96h


title: F10-SF18103134-96h


title: CV2, GEX


title: F1-SF19013101-96h


title: CV2, BCR


title: F1-SF18103134-96h


title: CV2, ADT


title: F1-SF18103138-96h


title: F1-SF18103137-96h


title: CV1, TCRgd (NovaSeq 6000)

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv1_obj.rds. Contains processed data for experiment
Library strategy: CITE-seq


title: CV1, TCRab (NovaSeq 6000)


title: CV1, HTO (NovaSeq 6000)


title: CV1, GEX (NovaSeq 6000)


title: E9-SF19013101-96h


title: E9-SF18103138-96h


title: E9-SF18103137-96h


title: F11-SF18103133-96h


title: E9-SF18103134-96h


title: CV2, HTO


title: CV1, ADT (NovaSeq 6000)


title: E9-SF18103133-96h


title: CV1, BCR (NovaSeq 6000)


title: E8-SF19013101-96h


title: EnP1-3

city: Jinan

first: Jingyu

last: Guan

address: No. 44 Wenhuaxi Road

country: China

institute: Shandong university

data_processing:
software: HiSat2 (http://ccb.jhu.edu/software/hisat2/index.shtml)
software: RSEM (http://deweylab.github.io/RSEM/)
software: DESeq2 (http://bioconductor.org/packages/stats/bioc/DESeq2/)
software: ID mapping (KEGG)
software: KOBAS (http://kobas.cbi.pku.edu.cn/home.do )
Assembly: GRCh38.p13
Supplementary files format and content: Raw data table of EnP1 and GFP gene expression
Supplementary files format and content: Raw data table of total differentially expressed genes in EnP1 and GFP groups
Supplementary files format and content: Raw gene expression matrix table
Supplementary files format and content: EnP1_vs_GFP differentially expressed genes table (include TPM)
Supplementary files format and content: Raw transcript TPM matrix annotation table

growth_protocol: HEK-293T were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% v/v fetal bovine serum (FBS) and 1% v/v penicillin-streptomycin in a 5% CO2 environment.

extract_protocol:
Total RNA from EnP1 and GFP stable cell lines was extracted using TRIzol reagent (Invitrogen).
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following the manufacturer's protocols.

tag: cell line

tag: genotype

value: EnP1 overexpression


title: EnP1-1


title: EnP1-2


title: E8-SF18103138-96h


title: E8-SF18103137-96h


title: GFP-2

value: GFP overexpression


title: GFP-3


title: F1-SF18103133-96h


title: E8-SF18103134-96h


title: E7-SF19013101-96h


title: GFP-1


title: E8-SF18103133-96h


title: E7-SF18103138-96h


title: E7-SF18103133-96h


title: 7.12.I.Das_4_donor3

city: Shinjuku-ku

first: Makoto

last: Ando

state: Tokyo

address: 35 Shinanomachi

department: Department of Microbiology and Immunology

country: Japan

institute: Keio University School of Medicine

data_processing:
Paired-end sequencing was performed on the Illumina NovaSeq 6000 (150bp paired-end reads).
Quality control Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the human reference genome (hg38) using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis Differential expression analysis was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: Microsoft Excel file include read counts for each sample
Supplementary files format and content: Microsoft Excel file include FPKM values for each sample
Supplementary files format and content: Microsoft Excel files include the result of differential expression analysis

source_name: CD8+ anti-HER2 CAR T cells

growth_protocol: T cells were cultured in AIM-V medium supplemented with 5% FBS, 1% penicillin-streptomycin, 2 mmol/L Glutamax, 10 mmol/L HEPES, and 10 ng/mL IL-2 for 4 days. On day 4, 7.12.I CD8+ CAR T cells were cultured in alpha-MEM supplemented with 20% FBS, 1% penicillin-streptomycin, 10 ng/mL IL-7, 100 ng/mL CXCL12, 50 ng/mL IGF-I, and 1% DMSO. 7.12.I.Das CD8+ CAR T cells were cultured in alpha-MEM supplemented with 20% FBS, 1% penicillin-streptomycin, 10 ng/mL IL-7, 100 ng/mL CXCL12, 50 ng/mL IGF-I, and 1 mM Dasatinib. Empty and FOXO1WT CD8+ CAR T cells were cultured in AIM-V medium supplemented with 5% FBS, 1% penicillin-streptomycin, 2 mmol/L Glutamax, 10 mmol/L HEPES, 10 ng/mL IL-2, and 1% DMSO. Cells were cultured at 37℃ and 5% CO2.

extract_protocol:
1×10^6 CD8+ CAR T cells were prepared as described above. Total mRNA was isolated using the RNeasy Plus Mini Kit (QIAGEN).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification). For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. Clustering and sequencing The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Pan T cells were activated with Dynabeads Human T-Activator CD3/CD28 (Thermo Fisher) at a bead-to-cell ratio of 2:1. Approximately 24 hours after T cell activation, lentivirus was used to transduce HER2BBz CAR transgenes into pan T cells. The transduction was performed on a Retronectin-coated plate (Takara). On Day 4, the beads were removed from the culture, and then T cells were cultured in the indicated culture medium, following the growth protocol.

tag: donor id

value: CD8+ anti-HER2 CAR T cells

value: WT


title: 7.12.I_4_donor3


title: CV11, ADT


title: 7.12.I_3_donor2


title: 7.12.I.Das_2_donor1


title: E6-SF18103138-96h


title: 7.12.I_2_donor1


title: 7.12.I.Das_3_donor2


title: FOXO1WT_4_donor3

value: FOXO1WT overexpression


title: E6-SF19013101-96h


title: FOXO1WT_3_donor2


title: E6-SF18103137-96h


title: E6-SF18103134-96h


title: FOXO1WT_2_donor1


title: E6-SF18103133-96h


title: Empty_4_donor3


title: E5-SF18103137-96h


title: E5-SF18103138-96h


title: Empty_2_donor1


title: CV9, GEX


title: E7-SF18103137-96h


title: E5-SF18103134-96h


title: 7.12.I.Das_donor3

growth_protocol: T cells were cultured in AIM-V medium supplemented with 5% FBS, 1% penicillin-streptomycin, 2 mmol/L Glutamax, 10 mmol/L HEPES, and 10 ng/mL IL-2 for 4 days. On day 4, 7.12.I CD8+ CAR T cells were cultured in alpha-MEM supplemented with 20% FBS, 1% penicillin-streptomycin, 10 ng/mL IL-7, 100 ng/mL CXCL12, 50 ng/mL IGF-I, and 1% DMSO. 7.12.I.Das CD8+ CAR T cells were cultured in alpha-MEM supplemented with 20% FBS, 1% penicillin-streptomycin, 10 ng/mL IL-7, 100 ng/mL CXCL12, 50 ng/mL IGF-I, and 1 mM Dasatinib. IL2 CD8+ CAR T cells were cultured in AIM-V medium supplemented with 5% FBS, 1% penicillin-streptomycin, 2 mmol/L Glutamax, 10 mmol/L HEPES, 10 ng/mL IL-2, and 1% DMSO. IL2.Das CD8+ CAR T cells were cultured in AIM-V medium supplemented with 5% FBS, 1% penicillin-streptomycin, 2 mmol/L Glutamax, 10 mmol/L HEPES, 10 ng/mL IL-2, and 1 mM Dasatinib. Cells were cultured at 37℃ and 5% CO2.

tag: subject status/id

value: healthy donor 3


title: E5-SF18103133-96h


title: E4-SF18103138-96h


title: skin, lymph node, tumour HASH

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

data_processing:
Sequencing reads were aligned to the reference genome using cellranger (v 7.0.0)
We used the count subcommand to align samples from the EB203 library to the transcriptome and TCR references
We used the multi subcommand to demultiplex hashtags (see EB210_hashtags.csv) and align samples from the EB210 library to the transcriptome.
We used the count command to align TCR sequences for the EB210 library to the VDJ reference.
Assembly: GRCm38-alts-ensembl-5.0.0 (TCR reference)
Assembly: Cellranger 10x genome mm10-2020-A (transcriptome)
Supplementary files format and content: Tar files of VDJ-seq contains CSV files from the cellranger count command
Supplementary files format and content: Tar files of filtered feature barcode matrices from the cellranger count/multi command.
Library strategy: scTCR-seq

organism: Mus musculus

source_name: skin, lymph node, tumour

extract_protocol:
To generate single-cell suspensions, tumour and skin samples were digested in collagenase for 90 minutes, manually digested and filtered through a 70-micron mesh. Lymph nodes were pressed through a wire sieve and filtered through a 70-micron mesh.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index), 10x Genomics)

tag: mixed sample

value: Draining brachial lymph node, day 8 p.i., Tumour-draining brachial lymph node, day 20 p.i., Naive brachial lymph node, Skin, day 8 p.i., Tumour, day 20 p.i.

value: skin, lymph node, tumour

value: CD4+ CD44+, CD4+ CD44negative

tag: gender

value: female

tag: strain

value: noce/ Melanoma inoculation (B16.gD)


title: 7.12.I.Das_donor1

value: healthy donor 1


title: 7.12.I.Das_donor2

value: healthy donor 2


title: E4-SF18103134-96h

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: galGal6
Supplementary files format and content: RDS file with metadata, counts, normcounts, and logcounts in SingleCellExperiment object format for R

value: basilar papilla


title: 7.12.I_donor1


title: 7.12.I_donor3


title: skin, lymph node, tumour scTCR

data_processing:
Sequencing reads were aligned to the reference genome using cellranger (v 7.0.0)
We used the count subcommand to align samples from the EB203 library to the transcriptome and TCR references
We used the multi subcommand to demultiplex hashtags (see EB210_hashtags.csv) and align samples from the EB210 library to the transcriptome.
We used the count command to align TCR sequences for the EB210 library to the VDJ reference.
Assembly: GRCm38-alts-ensembl-5.0.0 (TCR reference)
Assembly: Cellranger 10x genome mm10-2020-A (transcriptome)
Supplementary files format and content: Tar files of VDJ-seq contains CSV files from the cellranger count command
Supplementary files format and content: Tar files of filtered feature barcode matrices from the cellranger count/multi command.


title: 7.12.I_donor2


title: E4-SF18103137-96h


title: Somatic cell samples 1-20

first: Matthew

last: Ritchie

address: 1G Royal Parade

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

description:
Som_0h_F2, Som_0h_F3, Som_0h_F4, Som_0h_F5, Som_0h_M2, Som_0h_M3, Som_0h_M5, Som_0h_M6, Som_24h_DMSO_F4, Som_24h_DMSO_F5, Som_24h_DMSO_F6, Som_24h_DMSO_F9, Som_24h_DMSO_M2, Som_24h_DMSO_M3, Som_24h_DMSO_M4, Som_24h_DMSO_M5, Som_24h_PD500_M1, Som_24h_PD500_M4, Som_24h_PD500_M6
somatic_gene_counts.tsv
somatic_sample_barcodes.tsv

data_processing:
FASTQ files were processed and mapped using scPipe (Tian et al., 2018) and Rsubread (Liao et al., 2019) (Bioconductor) packages in R studio. Briefly, FASTQ files were reformatted with sc_trim_barcode to incorporate barcode information from read 1 into read 2 into the header. Reads were aligned to a reference mouse genome (GENECODE GRCm39) using Rsubread. Reads were assigned to annotated exons with sc_exon_mapping, data were demultiplexed using sc_demultiplex and a gene count matrix was generated with UMI deduplication using sc_gene_counting. Gene count matrices from each set  were combined into a DGEList object for analysis.
Differential gene expression was assessed using the limma (Ritchie et al., 2015), Glimma (Su et al., 2017) and edgeR (Robinson et al., 2009) Bioconductor packages following a previously established workflow (Law et al., 2016).

source_name: Gonadal somatic cells

growth_protocol: Gonad-mesonephros samples were cultured on 30mm Millicell Biopore membranes with 0.4μM pores in media containing 15mM Hepes, 0.1mM non-essential amino acids, 1mg/mL N-acetylcysteine, 1X penicillin/streptomycin, 55nM beta-mercaptoethanol and 10% fetal calf serum in DMEM/F12 with Glutamax supplemented with DMSO or inhibitor. Mesonephros was removed and cells sorted using FACS. Oct4-eGFP transgene was used to isolate the GFP- somatic cells.

extract_protocol:
RNA was extracted using Macherey-Nagel NucleoSpin® RNA XS extraction kit (Scientifix, 740902.50). Libraries were prepared with 30ng of RNA.
Novel RNA-Seq pipeline. Briefly, index is added during initial pA priming and pooled samples amplified using template switching oligo. P5 is added by PCR and P7 by Nextera transposase. I7 indexes were added to the final libraries to enable parsing of sample sets. Sequencing was performed on NextSeq2000 (Illumina) following Illumina protocol 1000000109376 v3.

value: Gonadal somatic cells

value: ASMU Swiss by Oct4(Pou5fl)-eGFP on 129svJT2 background

value: mixed sample (non-demultiplexed)


title: skin, lymph node, tumour scRNA


title: E4-SF18103133-96h


title: Somatic cell samples 21-40

description:
Som_24h_BGJ500_M1, Som_24h_BGJ500_M3,  Som_24h_BGJ500_M4, Som_24h_BGJ500_M5, Som_72h_BGJ500_M2, Som_72h_BGJ500_M4, Som_72h_BGJ500_M5, Som_72h_BGJ500_M6, Som_72h_DMSO_F11, Som_72h_DMSO_F4, Som_72h_DMSO_F7, Som_72h_DMSO_F8, Som_72h_DMSO_M2, Som_72h_DMSO_M4, Som_72h_DMSO_M5, Som_72h_DMSO_M6, Som_72h_PD500_M2, Som_72h_PD500_M3, Som_72h_PD500_M4, Som_72h_PD500_M5
somatic_gene_counts.tsv
somatic_sample_barcodes.tsv


title: E3-SF18103138-96h


title: Empty_3_donor2


title: F6-SF18103138-96h


title: F8-SF19013101-96h


title: IL2.Das_donor3


title: E3-SF18103137-96h


title: FOXO1WT_donor3

library_source: genomic

data_processing:
Paired-end sequencing was performed on the Illumina NextSeq 2000 System (150bp paired-end reads).
Mapping and peak call were conducted by ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). After trimming adapters using Cutadapt, reads were aligned to human reference genome (hg38) using Bowtie2 (ver. 2.3.4.3), and duplicate reads were removed with Picard (ver. 2.20.7) and samtools (ver. 1.9). BAM files were indexed with samtools to visualize tracks in the Integrative Genomics Viewer (Broad Institute).
Peak calling was performed using MACS2 (ver. 2.2.4) with default parameters. After removal of blacklist region, consistency of peaks was tested by Irreproducible Discovery Rate (IDR) using IDR (ver. 2.0.4.2).
Peak annotations were conducted by HOMER (ver. 4.9.1) with default settings. The list of differential accessible peaks was obtained using DEseq2 (Ver. 1.20.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include annotated count data
Supplementary files format and content: tab-delimited text files include differential accessibility between Empty and FOXO1WT or 7/12/I and 7/12/I +Das

molecule: genomic DNA

growth_protocol: T cells were cultured in AIM-V medium supplemented with 5% FBS, 1% penicillin-streptomycin, 2 mmol/L Glutamax, 10 mmol/L HEPES, and 10 ng/mL IL-2 for 4 days. On day 4, 7/12/I CD8+ CAR T cells were cultured in alpha-MEM supplemented with 20% FBS, 1% penicillin-streptomycin, 10 ng/mL IL-7, 100 ng/mL CXCL12, 50 ng/mL IGF-I, and 1% DMSO. 7/12/I +Das CD8+ CAR T cells were cultured in alpha-MEM supplemented with 20% FBS, 1% penicillin-streptomycin, 10 ng/mL IL-7, 100 ng/mL CXCL12, 50 ng/mL IGF-I, and 1 mM Dasatinib. Empty and FOXO1WT-overexpressing CD8+ CAR T cells were cultured in AIM-V medium supplemented with 5% FBS, 1% penicillin-streptomycin, 2 mmol/L Glutamax, 10 mmol/L HEPES, 10 ng/mL IL-2, and 1% DMSO. Cells were cultured at 37℃ and 5% CO2.

extract_protocol:
Approximately 50,000 cells were lysed and transposition reaction was performed with the Tn5 Transposase (Illumina Catalog #FC121-1030) at 37°C for 30 minutes. The reaction liquid was purified with Qiagen MinElute PCR Purification Kit. Then 5 cycles of PCR with custom Nextera PCR primers (from Wu and Buenrostro 2013) were conducted using NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs). Additional number of PCR cycles was determined by qPCR of the partly amplified products, following Wu and Buenrostro 2013. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter: A63881), using double size selection (left ratio: 1.4x, right ratio: 0.5x) according to the manufacturer’s protocol
Fragmentation and amplification of ATAC-seq libraries were conducted according to Buenrostro et al (https://doi.org/10.1002/0471142727.mb2129s109).

treatment_protocol: Pan T cells were activated with Dynabeads Human T-Activator CD3/CD28 (Thermo Fisher) at a bead-to-cell ratio of 2:1. Approximately 24 hours after T cell activation, lentivirus was used to transduce HER2 CAR and HER2 CAR flanked with FOXO1WT transgenes into pan T cells. The transduction was performed on a Retronectin-coated plate (Takara). On Day 4, the beads were removed from the culture, and then T cells were cultured in the indicated culture medium, following the growth protocol.

value: FOXO1-WT overexpression


title: 7/12/I_donor2


title: 7/12/I_donor3


title: E3-SF18103134-96h


title: IL2.Das_donor2


title: FOXO1WT_donor2


title: Empty_donor3


title: 7/12/I+Das_donor3


title: IL2_donor3


title: Empty_donor2


title: 7/12/I+Das_donor2


title: IL2_donor1


title: IL2_donor2


title: E2-SF18103137-96h


title: Col-0, heat, 48hour, rep2

city: Seoul

first: Hongoo

last: Lee

address: Gwan-ak ro 1

country: South Korea

institute: Seoul National University

data_processing:
STAR (v2.7.10a) & RSEM (v1.3.1)
Assembly: TAIR10
Supplementary files format and content: RSEM output file for each sample

organism: Arabidopsis

source_name: 1st and 2nd leaves

extract_protocol:
Total RNA was extracted with a Plant RNA extraction kit (Takara, 9769B) from 1st and 2nd rosette leaves at 1 or 48 h after treatment. Three biological replicates were collected.
Sequencing libraries were constructed with a TruSeq standard mRNA library kit followed by 100-bp paired-end sequencing using the Illumina NovaSeq platform.

value: 1st and 2nd leaves

value: heat

tag: time


title: Col-0, mock, 48hour, rep3

value: mock


title: E2-SF19013101-96h


title: E2-SF18103138-96h


title: Col-0, mock, 48hour, rep2


title: E2-SF18103134-96h


title: F11-SF18103137-96h


title: Col-0, mock, 48hour, rep1


title: IL2.Das_donor1

value: CD8+ anti-HER2 CAR T cells

value: WT


title: Col-0, wound, 1hour, rep3

value: wound


title: Col-0, wound, 1hour, rep2


title: E2-SF18103133-96h


title: MB005, Nuc

city: Cambridge

first: Maxwell

last: Gold

state: MA

address: 21 Ames St

institute: MIT

data_processing:
Data was processed through the standard 10X Genomics pipeline.
Filtered counts matrices were used and uploaded to Seurat for downstream processing.
Assembly: hg38
Supplementary files format and content: counts (h5)

source_name: Tumor Nuclei

extract_protocol:
Nuclei were isolated from fresh, snap frozen tumor tissues as previously described in Nagy et al. 2020. Tumor tissue was mechanically dissociated followed by collagenase-based enzymatic dissociation as previously described in Vladoiu et al. 2019.
Library construction was performed according to 10X Genomics.

value: SHH MB tumors with MBEN histology

tag: assay

value: snRNA-Seq


title: MB009, Nuc


title: Col-0, heat, 48hour, rep1


title: Col-0, mock, 1hour, rep2


title: Col-0, mock, 1hour, rep3


title: MB015, Nuc


title: Col-0, wound, 1hour, rep1


title: E12-SF18103138-96h


title: E3-SF18103133-96h


title: Col-0, heat, 48hour, rep3


title: Col-0, mock, 1hour, rep1


title: 3_9_119095_N2_Day-14_CSE-0% b

city: San Diego

first: John

last: Walker

state: CA

address: 10675 John Jay Hopkins Dr

institute: NIBR

data_processing:
Reads were generated from a NovaSeq instrument with bcl2fastq from Illumina, v 2.20.0.422-2 and were aligned to a combined human/mouse genome provided by 10xGenomics, version 2020-A with STAR aligner v2.7.3a
Gene counts were assessed with RSEM v1.3
Differential gene expression was assessed with DESeq2 v.1.28.0, in R version 4.0 (25)
Assembly: combined human/mouse genome provided by 10xGenomics, version 2020-A
Supplementary files format and content: a single Excel file includes DESEQ2-derived expression values for each Sample

source_name: HBEC

growth_protocol: Bronchospheres were differentiated in 384-well plates on 50% Matrigel for two weeks, after which they were exposed to cigarette smoke extract (CSE) at the indicated percentages (diluted in HBEC differentiation media) for 7, 14, and 21 Days. Then they were lysed directly in the plate with Qiagen buffer RLT

extract_protocol:
RNA was isolated from cell lysis using Qiagen RNEasy kit
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Prep Kit (Illumina 20020595) following manufacturer's protocols.

value: HBEC

value: Human Bronchial Epithelial Cells

value: cigarette smoke extract 0%

tag: time (days)


title: E12-SF18103137-96h


title: MB084, Nuc

data_processing:
Data was processed through the standard 10X genomics pipeline.
Filtered counts matrices were used and uploaded to Seurat for downstream processing.
Assembly: hg38

extract_protocol:
Nuclei were isolated from fresh, snap frozen tumor tissues as previously described in Nagy et al 2020. Tumor tissue was mechanically dissociated followed by collagenase-based enzymatic dissociation as previously described in Vladoiu et al 2019
Library construction was performed according to 10X genomics.

tag: disease state

value: SHH Medulloblastoma

value: snRNA-seq


title: 3_8_119095_N2_Day-7_CSE-3% b

value: cigarette smoke extract 3%


title: 3_7_119095_N2_Day-7_CSE-0% b


title: E11-SF18103138-96h

value: basilar papilla


title: 3_6_119095_N1_Day-21_CSE-3% b


title: MB002, Nuc


title: 3_5_119095_N1_Day-21_CSE-0% b


title: E11-SF18103137-96h


title: 3_4_119095_N1_Day-14_CSE-3% b


title: 3_3_119095_N1_Day-14_CSE-0% b


title: E11-SF18103134-96h


title: E11-SF18103133-96h


title: DSP-1001660020373-D-F12

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Fastq files were automatically generated with the Illumina BaseSpace Sequence Hub
Supplementary files format and content: Digital count conversion (.dcc) files produced from fastq files using the GeoMx NGS Pipeline 2.3.3.10 desktop application.

source_name: lung: lymphoid follicle

extract_protocol:
Default Nanostring GeoMx extraction protocol
Default Nanostring GeoMx library consruction protocol

value: lung

value: lymphoid follicle

tag: slide name

tag: processing date

value: BCM-June

tag: panel

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

tag: patient

tag: %laa950 whole.lung

tag: %laa950 lobe

tag: condition

value: copd

tag: roi

tag: scan name

value: paraffin


title: 3_18_119095_N3_Day-21_CSE-3% b

tag: cell line

tag: cell type

tag: treatment


title: 3_2_119095_N1_Day-7_CSE-3% b


title: 3_16_119095_N3_Day-14_CSE-3% b


title: E10-SF19013101-96h

tag: tissue


title: 3_17_119095_N3_Day-21_CSE-0% b


title: MB019, Nuc


title: 3_12_119095_N2_Day-21_CSE-3% b


title: DSP-1001660020373-D-F10


title: 3_15_119095_N3_Day-14_CSE-0% b


title: DSP-1001660020373-D-F09


title: 3_13_119095_N3_Day-7_CSE-0% b


title: 3_14_119095_N3_Day-7_CSE-3% b


title: DSP-1001660020373-D-D11


title: E10-SF18103137-96h


title: E10-SF18103134-96h


title: 2_9_642823_N2_Day-14_CSE-0% b


title: E10-SF18103138-96h


title: E10-SF18103133-96h


title: 3_10_119095_N2_Day-14_CSE-3% b


title: 3_1_119095_N1_Day-7_CSE-0% b


title: DSP-1001660020373-D-G01


title: DSP-1001660020373-D-D09


title: 2_8_642823_N2_Day-7_CSE-3% b


title: 2_7_642823_N2_Day-7_CSE-0% b


title: E1-SF18103138-96h


title: E1-SF18103137-96h


title: DSP-1001660020373-D-F11


title: DSP-1001660020373-D-C05


title: 2_2_642823_N1_Day-7_CSE-3% b


title: DSP-1001660020373-D-C04


title: E1-SF18103134-96h


title: 2_3_642823_N1_Day-14_CSE-0% b


title: 3_11_119095_N2_Day-21_CSE-0% b


title: 2_17_642823_N3_Day-21_CSE-0% b


title: DSP-1001660020373-D-D10


title: DSP-1001660020373-D-C03


title: D9-SF19013101-96h


title: DSP-1001660020373-D-A11


title: E1-SF18103133-96h


title: 2_15_642823_N3_Day-14_CSE-0% b


title: 2_16_642823_N3_Day-14_CSE-3% b


title: 2_14_642823_N3_Day-7_CSE-3% b


title: 2_13_642823_N3_Day-7_CSE-0% b


title: 2_11_642823_N2_Day-21_CSE-0% b


title: DSP-1001660020373-D-A09


title: DSP-1001660020373-D-A10


title: 2_4_642823_N1_Day-14_CSE-3% b


title: 2_5_642823_N1_Day-21_CSE-0% b


title: D9-SF18103138-96h


title: 2_12_642823_N2_Day-21_CSE-3% b


title: 2_10_642823_N2_Day-14_CSE-3% b


title: D9-SF18103137-96h


title: DSP-1001660020373-D-A08


title: 1_13_646466_N4_Day-7_CSE-0% b


title: D9-SF18103134-96h


title: 2_1_642823_N1_Day-7_CSE-0% b


title: 2_18_642823_N3_Day-21_CSE-3% b


title: DSP-1001660020373-D-A07


title: D9-SF18103133-96h


title: D8-SF19013101-96h


title: DSP-1001660020373-D-A06


title: 1_1_646466_N2_Day-7_CSE-0% b


title: DSP-1001660020373-D-A01

value: No Template Control


title: IL-4_PHNE

first: Hyung-Ju

last: Cho

address: 50-1, Yonsei-ro, Seodaemun-gu,

department: Otorhinolaryngology

institute: Yonsei University College of Medicine

description: 10X Genomics

data_processing:
Single cell RNA-seq matrices were generated using Cell Ranger v3.1.0
Supplementary files format and content: Read count matrix

source_name: nose

extract_protocol:
Primary human nasal epithelial cells of passage 2 were seeded in the culture medium containing a 1:1 mixture of basal epithelial growth medium, Dulbecco’s Modified Eagle’s Medium, and all of the supplements. All cells were maintained in a Transwell®-clear (Costar Co., Cambridge, MA, USA) culture insert. An air-liquid interface (ALI) was then created by removing the apical culture medium. The cells were incubated at 37°C in a humidified atmosphere with 5% CO2. Two weeks after the ALI was established, the fully differentiated HNE cells were incubated with human cytokine IL-4 (10 ng/ml, R&D Systems) for 7 days until day 21. The cells were then gently detached from the Transwells by pipetting, and transferred to a 15-mL tube. Dissociation solution was prepared as 0.5% bovine serum albumin (BSA) in PBS. Finally, the cell suspensions were filtered through a cell strainer with 40-μm pores (Falcon) and centrifuged three times for 3 min at 1,300 rpm. The cells were then resuspended in 0.5% BSA and processed for scRNAseq.
The libraries were prepared using a Chromium Controller according to the 10x Single Cell 3’ v2, v3 protocol (10x Genomics). Briefly, cell suspensions were diluted in nuclease-free water to achieve a cell count of 10,000, mixed with master mix, and loaded with Single Cell 3′ Gel Beads and Partitioning Oil onto a Single Cell 3′ Chip. RNA transcripts from single cells were then uniquely barcoded and reverse-transcribed within droplets on the chip. The resulting cDNA molecules were pooled and subjected to end repair, with the addition of a single “A” base, and adapter ligation. The products were then purified and enriched by PCR to create the final cDNA library. The purified libraries were quantified according to the qPCR Quantification Protocol (KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent Technologies).

value: nose

value: primary cell culture

value: epithelial cells


title: Control_PHNE_2

description: 10X Genomics

value: no treatment


title: Ex_vivo_HNE

description: 10X Genomics

extract_protocol:
Human nasal epithelial (HNE) cells were isolated from three healthy donors for scRNAseq. To obtain single-cell suspensions of epithelial cells directly from nasal turbinate, we harvested turbinate tissues 1.0 cm × 0.5 cm in size, washed and chopped them in HBSS, and incubated them in HBSS for 1 h at 37°C. We then filtered the cell suspension with a 70-μm strainer and then with a 40-μm strainer, centrifuged the filtered cells twice at 260 g f or 3 min, and r e-suspended the cells in HBSS for scRNAseq processing. The epithelial cells from in vivo donors were utilized immediately after harvesting the mucosal tissue.
The libraries were prepared using a Chromium Controller according to the 10x Single Cell 3’ v2, v3 protocol (10x Genomics). Briefly, cell suspensions were diluted in nuclease-free water to achieve a cell count of 10,000, mixed with master mix, and loaded with Single Cell 3′ Gel Beads and Partitioning Oil onto a Single Cell 3′ Chip. RNA transcripts from single cells were then uniquely barcoded and reverse-transcribed within droplets on the chip. The resulting cDNA molecules were pooled and subjected to end repair, with the addition of a single “A” base, and adapter ligation. The products were then purified and enriched by PCR to create the final cDNA library. The purified libraries were quantified according to the qPCR Quantification Protocol (KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent Technologies).

value: ex vivo tissue


title: D8-SF18103138-96h


title: D8-SF18103137-96h


title: DSP-1001660020372-E-F10


title: Control_PHNE_1

description: 10X Genomics


title: Jejunal Mucosa,. GLP-2, Block 5

city: Lexington

first: Ronald

middle: Joseph

last: Trotta

state: KY

address: 808 W.P. Garrigus Bldg.

department: Animal and Food Sciences

institute: University of Kentucky

data_processing:
Raw reads were filtered to remove sequencing adaptors, low-complexity reads, and reads containing low-quality bases.
Paired-end clean reads were aligned to the Bos taurus reference genome (ARS-UCD1.2) using HISAT 2 (version 2.0.5)
Mapped reads of each sample were assembled using StringTie (version 1.3.3b) in a reference-based approach.
Reads per gene were counted using featureCounts (version 1.5.0-p3). Quantification of each gene was calculated as the number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM). Differential gene expression (DEG) analysis was quantified using the DESeq2 R-package (version 1.20). The DEG analysis used the negative binomial generalized linear model to fit gene expression level as a negative binomial distribution and Wald statistics to perform hypothesis testing. Multiple testing adjustment of the P-values was performed using the Benjamini-Hochberg procedure for controlling the false discovery rate (FDR). Genes were identified as differentially expressed if the FDR-adjusted P-value was ≤ 0.05.
Gene ontology and KEGG pathway enrichment analyses of DEGs were conducted using the clusterProfiler R-package. Enrichment analyses were considered significant if the FDR-adjusted P-value was ≤ 0.05. Changes in gene expression were classified as upregulated or downregulated based on the sign of the log2 fold change.
Assembly: ARS-UCD1.2

organism: Bos taurus

source_name: Jejunal mucosa

extract_protocol:
TRIzol
Strand-specific cDNA library preparation was conducted by Novogene Corporation Inc. (Sacramento, CA). Messenger RNA was isolated from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was facilitated using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and Moloney murine leukemia virus reverse transcriptase and second-strand cDNA was synthesized using DNA polymerase I and RNAse H. Remaining overhangs were converted to blunt ends using exonuclease and polymerase activities. Three-prime ends of DNA fragments were adenylated and adaptors with hairpin loop structures were ligated for hybridization preparation. Library fragments were purified with AMPure XP System (Beckman Coulter Inc., Brea, CA) and 370-420 bp cDNA fragments were selected for PCR amplification. Polymerase chain reaction products were purified and assessed with the 2100 Bioanalyzer Instrument (Agilent Technologies Inc.).

treatment_protocol: 200 mg of tissue preserved in RNAlater stabilization solution and stored at -80C

tag: animal id

tag: animal type

value: steer

value: Jejunal mucosa

tag: body weight,_kg

tag: block

tag: breed

value: Holstein


title: DSP-1001660020372-E-F09

tag: slide name

tag: processing date


title: Jejunal Mucosa,. GLP-2, Block 4


title: DSP-1001660020372-E-F08

tag: panel

tag: patient


title: Jejunal Mucosa,. GLP-2, Block 6


title: D8-SF18103133-96h


title: Jejunal Mucosa, Control, Block 4

value: Control


title: Jejunal Mucosa,. GLP-2, Block 1


title: Jejunal Mucosa,. GLP-2, Block 3


title: Jejunal Mucosa, Control, Block 5


title: D8-SF18103134-96h

value: basilar papilla


title: Jejunal Mucosa, Control, Block 3


title: DSP-1001660020372-E-F07

value: lung

tag: %laa950 whole.lung

tag: %laa950 lobe


title: Jejunal Mucosa, Control, Block 2


title: D7-SF19013101-96h


title: Jejunal Mucosa, Control, Block 1


title: D7-SF18103138-96h


title: DSP-1001660020372-E-F05

value: lymphoid follicle

tag: condition

tag: roi


title: Jejunal Mucosa, Casein + GLP-2, Block 5

value: Casein + GLP-2


title: Jejunal Mucosa, Casein + GLP-2, Block 2


title: Jejunal Mucosa, Casein + GLP-2, Block 6


title: DSP-1001660020372-E-F03

value: BCM-June

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

tag: scan name


title: DSP-1001660020372-E-F04

tag: cell type

value: paraffin


title: DSP-1001660020372-E-F06


title: Jejunal Mucosa, Casein + GLP-2, Block 3

tag: treatment


title: D7-SF18103134-96h

tag: tissue


title: Jejunal Mucosa, Casein + GLP-2, Block 4

tag: animal id


title: Jejunal Mucosa, Casein, Block 6

tag: animal type

value: Casein


title: DSP-1001660020372-E-F02


title: Jejunal Mucosa, Casein, Block 4

tag: body weight,_kg


title: Jejunal Mucosa, Casein + GLP-2, Block 1

tag: block


title: DSP-1001660020372-E-F01


title: D6-SF18103138-96h


title: Jejunal Mucosa, Casein, Block 2

tag: breed


title: DSP-1001660020372-E-D05

tag: slide name

value: copd


title: D7-SF18103137-96h


title: D7-SF18103133-96h


title: DSP-1001660020372-E-D06

tag: processing date


title: SS3

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
FASTQ files were processed and demultiplexed with CASAVA 1.8.1 (Illumina)
Contaminants were removed with Bowtie 2 v2.2.5
Reads were aligned mm10 using STAR 2.5.3a
Reads were quantified with Ensembl Transcripts release 102
Normalization was done with quantile normalization followed by log2 transformation
Assembly: mm10
Supplementary files format and content: txt files containing Raw counts

molecule: polyA RNA

source_name: Tumor

extract_protocol:
RNA was isolated from control, or SS-treated tumor tissues using an RNA isolation kit (Qiagen) per the manufacturer's protocol.
Paired-end libraries (2 x 75) were prepared using the TruSeq Stranded mRNA Library Prep kit, validated, and normalized following the manufacturer (Illumina, San Diego, CA) protocol. Libraries were sequenced in the NextSeq500 using a High Output Kit v2.5, 150 cycles from Illumina.

treatment_protocol: Tumors were induced by injecting 1 million TNBC C0321 cells into syngeneic mice with 1:1 ratio of Matrigel to PBS into the mammary fat pad of 6-10-weeks old female FVB mice (Jackson Laboratory). Upon detection of a palpable mass, mice were treated with SS alone (60 mg/kg by PO) daily for another 14 days.

value: Tumor

value: Triple-Negative Breast Cancer

value: Sulindac Sulfate (60 mg/kg by PO)


title: SS2


title: D6-SF19013101-96h


title: SS1


title: D6-SF18103134-96h


title: Jejunal Mucosa, Casein, Block 5


title: Jejunal Mucosa, Casein, Block 3


title: D6-SF18103137-96h


title: DSP-1001660020372-E-D04

tag: panel


title: Control3


title: DSP-1001660020372-E-B12

tag: patient


title: Jejunal Mucosa, Casein, Block 1


title: Control1


title: D6-SF18103133-96h


title: D5-SF19013101-96h


title: D5-SF18103138-96h


title: DSP-1001660020372-E-B10

tag: %laa950 whole.lung


title: DSP-1001660020372-E-B11

tag: %laa950 lobe


title: ECs, 95

city: Milano MI

first: Aurora

last: Maurizio

state: Italy

address: Via Olgettina, 60

department: Center for Omics Sciences (COSR)

country: Italy

institute: IRCCS Ospedale San Raffaele

description:
7 days after injury of sciatic nerve
Raw_counts_Tomato.tsv.gz

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v3.0.2).
Single end reads were trimmed with trimmomatic (v0.39) to remove adapters and exclude low-quality reads from the analysis and aligned to the mm10 reference genome using STAR aligner (v2.5.3a).
FeatureCounts (v1.6.4) was used to compute reads mapping on exons as annotated in GENCODE Mus musculus basic gene annotation (version M16) and obtain transcript quantification summarized at the gene level, excluding multimapping reads.
Assembly: mm10, GRCm38, GENCODE Mus musculus basic gene annotation (version M16)
Supplementary files format and content: 1292_all.counts.tsv.gz and 1133_all.counts.tsv.gz: Tab separated files of raw counts.
Supplementary files format and content: counts_Cherry_ComBat-seq.tsv.gz: Only genes with at least 1 CPM (Counts per million) in at least 3 samples were retained. Batch effect correction was performed on counts matrix with SVA’s R package ComBat-seq (v3.35.2).

source_name: sciatic nerve

extract_protocol: Sciatic nerves were freshly harvested in F12medium, pooled, finely chopped and incubated in dissociation buffer (Trypsin 0.2mg/ml, Collegenase Type II 50ul/ml, Hyaluyronidase 1:50, PronaseE 1:10, DNAse 2.5μg/ml) in DMEM and incubated on rotor at 37 C with intermittent mixing for 30 min. Enzymes were inactivated with 5% FBS+ 2mM EDTA in PBS w/o Ca2+, Mg2+. Cell suspension was passed through cell strainer, stained (CD45-APC) and resuspended in 2% BSA PBS w/o Ca2+, Mg2+. Tdtomato+ or Cherry+ (negative for CD45+ myeloid population) were purified by FACS.

tag: genotype

value: Plxnd1 WT

tag: reporter

tag: batch

value: sciatic nerve

value: FACS-isolated peripheral nerve ECs

tag: condition


title: ECs, 98

description:
14 days after injury of sciatic nerve
Raw_counts_Tomato.tsv.gz

tag: cell type


title: ECs, 92

description:
Intact nerve
Raw_counts_Tomato.tsv.gz

tag: tissue

value: intact


title: ECs, 83


title: ECs, 77

description:
Intact nerve
Raw_counts_Tomato.tsv.gz


title: ECs, 80


title: D5-SF18103137-96h

extract_protocol:
FACS sorted into 96-well plates containing RNA lysis buffer
smartseq2

tag: treatment


title: ECs, 74

description:
7 days after injury of sciatic nerve
Raw_counts_Cherry.tsv.gz
Raw_counts_Cherry_corrected_ComBat_Seq.tsv.gz

value: Plxnd1 KO


title: D5-SF18103134-96h

value: basilar papilla


title: DSP-1001660020372-E-B09

value: lung

tag: roi

tag: scan name


title: ECs, 104


title: D5-SF18103133-96h


title: ECs, DB_12_191


title: D4-SF19013101-96h


title: DSP-1001660020372-E-B07

value: lymphoid follicle


title: Control2

value: Control


title: ECs, DB_11_190


title: DSP-1001660020372-E-A06

value: BCM-June


title: ECs, DB_9_154


title: D4-SF18103138-96h


title: ECs, DB_8_153


title: ECs, 101


title: DSP-1001660020372-E-A01

value: No Template Control


title: ECs, DB_10_189

description:
Intact nerve
Raw_counts_Tomato.tsv.gz


title: ECs, DB_7_152

description:
Intact nerve
Raw_counts_Tomato.tsv.gz


title: ECs, DB_6_151


title: D4-SF18103137-96h


title: D4-SF18103134-96h


title: DSP-1001660020371-A-H01

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

value: paraffin


title: ECs, DB_4_133


title: DSP-1001660020371-A-G11

value: copd


title: ECs, DB_1_127


title: ECs, DB_3_131

description:
Intact nerve
Raw_counts_Tomato.tsv.gz


title: D4-SF18103133-96h


title: DSP-1001660020371-A-G12


title: ECs, DB_5_148


title: DSP-1001660020372-E-B08


title: Pelvic replicate 2, scRNAseq

city: Paris

first: Olivier

last: Mirabeau

address: 25-28 rue du Docteur Roux

country: France

institute: Institut Pasteur

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software (v. 6.0.1).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole pelvic ganglion

extract_protocol:
Ganglia were dissected and collected from Phox2bCre;RosatdT P5 pups and placed in artificial cerebrospinal fluid (aCSF) oxygenated with carbogen (4°C).  Fat tissue was carefully removed and nerves emanating from the ganglia were cut. Ganglia were transferred into a 1.5ml Eppendorf tube containing 1ml PBS-Glucose (1mg/ml Glucose), 20 ml Papain solution (Worthington LS003126; 25.4 Units/mg) and 20 ml DNAse (2mg/ml in PBS) and incubated at 37°C for 15min. The ganglia were collected by centrifugation (300g, 1min), the supernatant replaced by 1ml PBS-Glucose supplemented with 50 ml Collagenase/Dispase (Worthington CLS-1 345U/mg; Dispase II Roche 1.2U/mg; 80mg Collagenase and 92mg Dispase II dissolved in 1ml PBs-Glucose) and 20 ml DNAse solution and the ganglia incubated at 37°C for 8min. After collecting the ganglia by centrifugation for 3min at 300g they were dissociated in 1ml PBS-Glucose supplemented with 0.04% bovine serum albumin (BSA) and DNAse (20ml) by trituration, using a fire-polished, siliconized Pasteur pipette. The cell suspension was then filtered through a 40mm cell strainer. To eliminate cell debris, the cell suspension was centrifuged through a density step gradient by overlaying the cell suspension onto 1ml OptiPrep solution (80 ml OptiPrep (Sigma), 900ml PBS supplemented with 0.04%BSA, 20ml DNAse) for 15 min, 100g at 5°C. After removal of the supernatant from the soft cell pellet (rest volume 50ml), the cells were suspended in 100ul PBS-Glucose/0.04%BSA and collected again in 500ml Eppendorf tube for 15 min, 100g at 5°C. The supernatant was carefully removed (under control by fluorescence microscope) (rest volume 10ml). After addition of 40 ml PBS-Glucose/0.04%BSA the cell density was adjusted to 1000 cells/ml and transferred to the 10xGenomics platform.
For samples Coeliac, Lumbar and Pelvic_2: Single cell RNA-seq library preparation Cellular suspensions (around 5300 cells) were loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer's protocol based on the 10X GEMCode proprietary technology. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3' Reagent Kit v3 (10X Genomics) according to manufacturer’s protocol. Briefly, the initial step consisted in performing an emulsion where individual cells were isolated into droplets together with gel beads coated with unique primers bearing 10X cell barcodes, UMI (unique molecular identifiers) and poly(dT) sequences. Reverse transcription reactions were engaged to generate barcoded full length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). Bulk cDNA was amplified using a GeneAmp PCR System 9700 with 96-Well Gold Sample Block Module (Applied Biosystems) (98°C for 3min; 12 cycles : 98°C for 15s, 63°C for 20s, and 72°C for 1min; 72°C for 1min; held at 4°C). Amplified cDNA product was cleaned up with the SPRI select Reagent Kit (Beckman Coulter). Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3' Reagent Kit v3, following these steps: (1) fragmentation, end repair and A-tailing; (2) size selection with SPRI select; (3) adaptor ligation; (4) post ligation cleanup with SPRI select; (5) sample index PCR and cleanup with SPRI select beads (with 12 PCR cycles for sample Sympathetic and 14 for samples Coeliac and Pelvic). Individual library quantification and quality assessment was performed using Qubit fluorometric assay (Invitrogen) with dsDNA HS (High Sensitivity) Assay Kit and Bioanalyzer Agilent 2100 using a High Sensitivity DNA chip (Agilent Genomics). Indexed libraries were then equimolarly pooled and quantified by qPCR using the KAPA library quantification kit (Roche). Sequencing was performed on the NovaSeq 6000 (Illumina), targeting around 400M clusters per sample and using paired-end 28x91bp as sequencing mode.

value: whole pelvic ganglion

tag: strain

tag: age

value: Post-natal day 5 (P5)


title: Coeliac, replicate 1, scRNAseq

description: 10x Genomics

source_name: whole coeliac ganglion

value: whole coeliac ganglion


title: DSP-1001660020371-A-G09

tag: slide name


title: Lumbar replicate 1, scRNAseq

description: 10x Genomics

source_name: whole lumbar ganglion

value: whole lumbar ganglion


title: D3-SF18103138-96h


title: D3-SF18103137-96h


title: Pelvic, replicate 1, scRNAseq

description: 10x Genomics


title: Sphenopalatine, replicate 1, scRNAseq

description: 10x Genomics

source_name: whole sphenopalatine ganglion

value: whole sphenopalatine ganglion


title: DSP-1001660020371-A-F04

tag: processing date


title: PTPMT1 KO_3

city: Atlanta

first: Chao

last: Chen

state: GA

address: 1760 Haygood Drive NE,HSRB E362

department: Pediatrics

institute: Emory University

data_processing:
Raw data of fastq format were firstly processed by TrimGalore to remove bad quality bases, adaptors and short reads.
Reference genome and gene model annotation files were downloaded from https://genome.ucsc.edu. The index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count read numbers mapped to each gene.
FPKM of each gene was then calculated based on the length of the gene and the reads count mapped to this gene. Differential expression genes were identified as those with fold changes > 2 and FDR < 0.05 using DESeq2 (Love et al., 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Spleen and lymph nodes

extract_protocol:
Total RNA was isolated with a Monarch total RNA miniprep kit (New England Biolabs).  Total RNA (50 ug) was used for the construction of sequencing libraries.
RNA sequencing libraries were prepared by TruSeq stranded mRNA sample preparation kit (Illumina).

value: Spleen and lymph nodes

value: CD8 T cells

value: PTPMT1 KO

value: CD3/CD28 antibodies activation


title: DSP-1001660020371-A-F03

value: lung

tag: panel


title: PTPMT1 KO_2


title: DSP-1001660020371-A-G10

value: lymphoid follicle

tag: patient


title: D3-SF19013101-96h

source_name: basilar papilla

value: basilar papilla


title: Stellate, replicate 1, scRNAseq

description: 10x Genomics

source_name: whole stellate ganglion

value: whole stellate ganglion


title: DSP-1001660020371-A-F02

value: BCM-June

tag: %laa950 whole.lung


title: D2-SF19013101-96h


title: PTPMT1 WT_3

value: WT


title: D3-SF18103133-96h


title: PTPMT1 KO_1


title: PTPMT1 WT_2


title: D2-SF18103138-96h


title: DSP-1001660020371-A-F01

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

tag: %laa950 lobe

value: paraffin


title: DSP-1001660020371-A-C08

value: copd


title: PTPMT1 WT_1

tag: genotype


title: X_2

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

institute: Chung-Ang University

data_processing:
Illumina Casava software used for basecalling
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using TrimGalore
Alignment to GRCh38.98 whole genome with STAR 2.5.4b and read feature counting with Rsubread 2.0.1
Normalized by voom function from limma and edgeR 3.28.1
FPKM were calculated using a fpkm function from DESeq2 1.26.0 and differential gene expression by edgeR 3.28.1
Genome_build: GRCm38.99
Supplementary_files_format_and_content: txt files include raw counts, normalized counts(FPKM)

source_name: Bone marrow-derived macrophages (BMDM)

extract_protocol:
Total RNA was extracted using Trizol reagent and mRNA was extracted by mRNA pull-down using poly-A tagged bead.
RNA libraries were prepared for sequencing using standard Truseq RNA Illumina protocols.

value: LPS + HACA treatment


title: X_1


title: P_2

value: LPS treatment


title: DSP-1001660020371-A-C07


title: D2-SF18103137-96h

first: Taha

last: Jan

address: 2220 Pierce Ave, PRB 752

institute: VUMC


title: P_1


title: D2-SF18103134-96h


title: DSP-1001660020371-A-C06


title: D3-SF18103134-96h


title: N_1

value: wild type


title: CV1, TCRgd (NextSeq 500)

first: Ellie

last: Ivanova

address: 550 First Ave

institute: NYU Langone

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv1_obj.rds. Contains processed data for experiment
Library strategy: CITE-seq

source_name: PBMCs

extract_protocol:
PBMCs were isolated form whole blood using ficoll gradient. Cells were encapsulated in Gel-Beads-in emulsion (GEMs) using 10x Controller with a Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1
Gene expression library and VDJ libraries were constructed according to the manufacturer’s protocol (10x Genomics)
The CITE-seq and hashing protocol described by Stoeckius et. al. was used to generate an antibody-derived tag (ADT) sequencing library and hashtag oligo (HTO) library (Stoeckius et. al., 2017). Gene expression library and VDJ libraries were constructed according to the manufacturer’s protocol (10x Genomics)

value: PBMCs

tag: library type

value: TCRgd


title: CV1, HTO (NextSeq 500)

value: HTO


title: DSP-1001660020371-A-B01


title: DSP-1001660020371-A-C05


title: CV1, GEX (NextSeq 500)

value: GEX


title: Donor7_nasal [7N]

city: Utrecht

first: Lisa

last: Rodenburg

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles), and a sequencing depth of 12 million reads per sample. Read 1 was used to identify the Illumina library index and to check for valid CEL-seq sample barcodes that have a maximum Hamming distance of 1. Read 2 was trimmed and aligned to the human GRCh38 reference transcriptome using BWA (version 0.7.15) MEM -t 8 and other parameters were set to default51. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was automated and carried out using the MapAndGo (version 3.0) script
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts of all samples

source_name: Nasal epithelial cells

growth_protocol: Nasal and bronchial epithelial cells were isolated, expanded and ALI-differentiated as previously described (Rodenburg et al., 2023; https://doi.org/10.1016/j.xpro.2023.102337)

extract_protocol:
Total RNA was extracted from ALI-differentiated nasal and bronchial airway epithelial cells using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol
Sequencing libraries were prepared with the Illumina Truseq small RNA library preparation kit.

value: Nasal epithelial cells

tag: donor number

tag: subject status

value: cystic fibrosis (CF)


title: CV1, BCR (NextSeq 500)

tag: cell type

value: BCR


title: D12-SF19013101-96h

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: galGal6
Supplementary files format and content: RDS file with metadata, counts, normcounts, and logcounts in SingleCellExperiment object format for R

tag: tissue

value: basilar papilla


title: Donor7_bronchial [7B]

source_name: Bronchial epithelial cells

value: Bronchial epithelial cells


title: CV1, TCRab (NextSeq 500)

tag: treatment

value: TCRab


title: DSP-1001660020371-A-A12

value: lung

value: lymphoid follicle

value: BCM-June

tag: condition

tag: roi


title: DSP-1001660020371-A-A11

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

value: copd

tag: scan name

value: paraffin


title: Donor6_nasal [6N]


title: D12-SF18103134-96h


title: CV1, ADT (NextSeq 500)

value: ADT


title: N_2

value: wild type


title: DSP-1001660020371-A-A10


title: Donor6_bronchial [6B]


title: Donor4_nasal [4N]


title: Donor4_bronchial [4B]


title: D2-SF18103133-96h


title: Donor3_bronchial [3B]


title: D11-SF19013101-96h


title: DSP-1001660020371-A-A09


title: Donor3_nasal [3N]


title: Donor2_nasal [2N]


title: Donor2_bronchial [2B]


title: DSP-1001660020371-A-A02


title: D12-SF18103137-96h


title: D12-SF18103133-96h


title: D11-SF18103138-96h


title: DSP-1001660014619-C-F02

value: BCM-August


title: DSP-1001660020371-A-A01

value: No Template Control


title: DSP-1001660020370-C-H02


title: D12-SF18103138-96h


title: D11-SF18103134-96h


title: DSP-1001660020370-C-H01


title: DSP-1001660014619-C-E06


title: D11-SF18103137-96h


title: D11-SF18103133-96h


title: DSP-1001660014619-C-E01


title: DSP-1001660014619-C-E02


title: DSP-1001660014619-C-F01


title: DSP-1001660020370-C-G12


title: D10-SF19013101-96h


title: DSP-1001660014619-C-D11


title: D10-SF18103138-96h


title: DSP-1001660020370-C-F05


title: DSP-1001660014619-C-D10


title: DSP-1001660020370-C-F04


title: D10-SF18103137-96h


title: DSP-1001660014619-C-D09


title: DSP-1001660014619-C-C04


title: DSP-1001660014619-C-C03


title: DSP-1001660014619-C-C05


title: DSP-1001660014619-C-C02


title: DSP-1001660020370-C-F03


title: DSP-1001660020370-C-A06

value: oct


title: D10-SF18103133-96h


title: DSP-1001660014619-C-C01


title: DSP-1001660014619-C-B02

value: COPD3rul_LF 003


title: DSP-1001660014619-C-D12


title: DSP-1001660014619-C-B04

value: COPD3rul_LF 005


title: DSP-1001660014619-C-B03

value: COPD3rul_LF 004


title: D1-SF18103138-96h

value: basilar papilla


title: D10-SF18103134-96h


title: DSP-1001660020370-C-A05


title: DSP-1001660015818-B-F06


title: D1-SF19013101-96h


title: DSP-1001660014619-C-A01


title: DSP-1001660014619-C-B01

value: COPD3rul_LF 002


title: DSP-1001660014618-B-H04


title: DSP-1001660015818-B-A01


title: D1-SF18103137-96h


title: DSP-1001660014618-B-H02


title: D1-SF18103133-96h


title: DSP-1001660014618-B-H01


title: DSP-1001660014618-B-F08


title: DSP-1001660014618-B-G12


title: PANC-1, 10mM Lactate, input

first: Yong Jin

last: An

address: 1, Gwanak-ro, Gwanak-gu

data_processing:
For data processing, Macrogen, Inc. (Seoul, Korea) service was used.
Assembly: hg38
Supplementary files format and content: bigWing, bedGraph

source_name: Pancreas

growth_protocol: DMEM, 10% FBS, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were cross-linked using formaldehyde (final 1%) for 10min at RT and quenched with glycine (final 100 mM) for 5 min at RT. The cell pellet was then resuspended in lysis buffer and sonicated (10 sec pulse and 10 sec rest, 60 cycles at 60% amplification).
TruSeq DNA Sample prep Kit was used through Macrogen, Inc. (Seoul, Korea).

treatment_protocol: 0 or 10 mM lactate, for overnight.

value: Pancreas

tag: cell line

value: Human Caucasian pancreas

tag: chip antibody


title: DSP-1001660014618-B-F07

source_name: lung: lymphoid follicle

value: lung

value: lymphoid follicle

tag: slide name

tag: processing date


title: PANC-1, 10mM Lactate, ChIP

value: histone acetyl H4 antibody (#06-866, Merck)


title: C9-SF19013101-96h


title: DSP-1001660020370-C-A01


title: DSP-1001660014618-B-F06

tag: panel

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

tag: patient

value: copd


title: C9-SF18103138-96h


title: DSP-1001660014618-B-F05

tag: %laa950 whole.lung

tag: %laa950 lobe


title: PANC-1, 0mM Lactate, input


title: DSP-1001660014619-C-A12

value: COPD3rul_ LF_001

value: paraffin


title: PANC-1, 0mM Lactate, ChIP


title: C9-SF18103137-96h


title: DSP-1001660014618-B-F04

value: BCM-August


title: DSP-1001660014618-B-C01


title: DSP-1001660014618-B-B12


title: C9-SF18103133-96h


title: DSP-1001660014618-B-B11


title: D1-SF18103134-96h


title: iPSC-derived neurons (Patient #4, Clone #3), EOAD

city: La Jolla

first: Shankar

last: Subramaniam

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
Preprocessing of both paired-end and single-end RNA-seq data was conducted using the Trimgalore! package v0.6.4 by removing adapters and low quality reads using CutAdapt v1.18.
Trimmed RNA-seq reads were then mapped to the GRCh38.104 human transcriptome using Kallisto v0.46.1 with the following options: -bias -rf-stranded -b 100 for the paired-end RNA-seq data
Transcript abundances from Kallisto were imported and summarized to the gene level using tximport v1.22.0.
A DGEList object was created from gene-level read counts using the DGEList function from edgeR v3.36.0.
Lowly expressed genes were filtered out using filterByExpr function in edgeR.
Then gene-level counts were normalized using the weighted mean trimmed of M values (TMM) in the calcNormFactors R package
Assembly: GRCh38.104 human transcriptome
Supplementary files format and content: comma-separated value (.csv) file includes unfiltered, raw counts matrix for all samples

source_name: skin

growth_protocol: Patient and subject fibroblasts that were grown on a Trevigen Reduced Growth Factor Basement Membrane Extract (Trevigen Cat. No. 3433-005-01) with Stem Cell mTeSR-1 media (STEMCELL Technologies Cat. No. 05851) were then reprogrammed into iPSCs using Sendai Virus at the Salk Institute. Direct differentiation of iPSCs to a population of neurons was performed as previously described. Briefly, iPSCs were differentiated into neurons using two stages: First, iPSCs were differentiated into pluripotent neuronal cells (NPCs) using dual Suppressor of Mothers Against Decapentaplegic (SMAD) inhibitors SB431542 (StemRD No. 50176030; Final concentration = 10 uM), LDN193189 (BioVision No. 1995-5; Final concentration = 0.5 uM), and the recombinant protein Noggin (R&D Systems No. 1967-NG/CF; Final concentration = 0.5 ug/ml)) in 500ml of Neural Maintenance Media (NMM) based on previous methods. Next, NPCs were differentiated into mixed neuronal cell populations by basic-Fibroblast Growth Factor (bFGF) (Millipore Cat. No. GF003AF; Final concentration = 20 ng/ml) withdrawal for 3-4 weeks.

extract_protocol:
Total RNA was extracted from previously-harvested EOAD and NDC frozen neuron pellets (replicates, n=3) with cell counts ranging from 500,000 – 2 million cells using the RNeasy Plus Micro Kit protocol (Qiagen, catalog no. 74034) as previously described. Concentrations of total RNA were determined using the Nanodrop 2000c according to the manufacturer’s guidelines. QC measurements were performed at the UC San Diego IGM sequencing core to evaluate the RNA Integrity Numbers (RIN) using TapeStation (Agilent Technologies), which ranged from 7.8-9.8.
Libraries were generated for RNA-seq using the Illumina Ribo-Zero Plus rRNA Depletion kit with IDT for Illumina RNA UD Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions. Resulting libraries were multiplexed and sequenced on an Illumina NovaSeq 6000 generating paired-end, 100-bp (PE100) to a depth of approximately 25 million reads per sample at the UC San Diego IGM sequencing core. In addition, samples were demultiplexed using the bcl2fastq v.2.20 Conversion Software (Illumina, San Diego, CA).

value: skin

value: induced pluripotent stem cells

tag: genotype

value: Early-onset Alzheimer's disease (EOAD)

tag: age at_onset

tag: age at_skin_biopsy

tag: Sex

value: Female

tag: clinical diagnosis

value: EOAD

tag: mri or_other_imaging

value: Diffuse atrophy

tag: csf biomarkers_for_ad

tag: cognition at_time_of_skin_biopsy

value: MMSE 4/30

tag: apoe status

tag: rna rin_score

value: SMAD inhibition and bFGF withdrawal


title: C9-SF18103134-96h

tag: tissue

value: basilar papilla

tag: treatment


title: DSP-1001660014618-B-B10

value: lung

tag: cell type

tag: slide name

tag: processing date

tag: condition

tag: roi

tag: scan name


title: iPSC-derived neurons (Patient #4, Clone #1), EOAD

tag: genotype

tag: age at_onset


title: DSP-1001660014618-B-B09

value: lymphoid follicle

tag: panel

tag: patient

tag: %laa950 whole.lung

tag: %laa950 lobe


title: DSP-1001660014618-B-H03

value: oct


title: DSP-1001660014618-B-A01

value: No Template Control


title: C8-SF18103138-96h


title: DSP-1001660014616-A-F03

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

value: copd


title: iPSC-derived neurons (Patient #3, Clone #2), EOAD

tag: age at_skin_biopsy

tag: Sex

value: Male

tag: clinical diagnosis

tag: mri or_other_imaging

value: atrophy including hippocampus

tag: csf biomarkers_for_ad

tag: cognition at_time_of_skin_biopsy


title: DSP-1001660014616-A-F02

tag: tissue

tag: cell type

tag: slide name

value: BCM-August

value: paraffin


title: C8-SF19013101-96h

tag: treatment


title: DSP-1001660014618-B-C02

tag: processing date

tag: condition

tag: roi

tag: scan name


title: C8-SF18103137-96h


title: DSP-1001660014616-A-E12

tag: panel

tag: patient


title: C8-SF18103134-96h


title: DSP-1001660014616-A-C06

tag: %laa950 whole.lung

tag: %laa950 lobe

value: UA100_ARTERY AND LN_001


title: iPSC-derived neurons (Patient #2, Clone #3), EOAD

value: skin

value: induced pluripotent stem cells

tag: genotype

value: Early-onset Alzheimer's disease (EOAD)

tag: age at_onset

tag: age at_skin_biopsy

tag: Sex

value: Positive

tag: apoe status

tag: rna rin_score


title: iPSC-derived neurons (Patient #3, Clone #1), EOAD

tag: tissue

tag: cell type

tag: clinical diagnosis

value: EOAD

tag: mri or_other_imaging

tag: csf biomarkers_for_ad

tag: cognition at_time_of_skin_biopsy

value: SMAD inhibition and bFGF withdrawal


title: C8-SF18103133-96h

value: basilar papilla

tag: treatment


title: iPSC-derived neurons (Patient #4, Clone #2), EOAD

value: Female

value: Diffuse atrophy

value: MMSE 4/30


title: DSP-1001660014616-A-B06

value: lung

value: lymphoid follicle

tag: slide name

tag: processing date

tag: panel

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

tag: condition

tag: roi

tag: scan name

value: oct


title: DSP-1001660014616-A-B07

value: BCM-August

tag: patient

tag: %laa950 whole.lung

tag: %laa950 lobe

value: copd


title: C7-SF19013101-96h


title: DSP-1001660014616-A-B05


title: iPSC-derived neurons (Patient #3, Clone #3), EOAD

tag: genotype

tag: age at_onset

tag: age at_skin_biopsy

tag: Sex

value: Male

value: atrophy including hippocampus

tag: apoe status

tag: rna rin_score


title: DSP-1001660014616-A-B04

tag: tissue

tag: cell type


title: iPSC-derived neurons (Patient #2, Clone #2), EOAD

value: skin

value: induced pluripotent stem cells

tag: clinical diagnosis

tag: mri or_other_imaging

tag: csf biomarkers_for_ad

tag: cognition at_time_of_skin_biopsy

tag: treatment


title: DSP-1001660014616-A-F01

tag: slide name

tag: processing date

tag: panel

tag: condition

tag: roi

tag: scan name

value: paraffin


title: C7-SF18103138-96h


title: iPSC-derived neurons (Patient #2, Clone #1), EOAD

tag: genotype

value: Early-onset Alzheimer's disease (EOAD)

tag: age at_onset

tag: age at_skin_biopsy

value: EOAD

value: Positive


title: iPSC-derived neurons (Patient #1, Clone #3), EOAD

tag: Sex

value: Female

value: MMSE 8/30

tag: apoe status

tag: rna rin_score

value: SMAD inhibition and bFGF withdrawal


title: THP1, PHF6

city: Cleveland

first: Yasuo

last: Kubota

state: Ohio

address: 9500 Euclid Ave

department: Translational Hematology & Oncology

institute: Cleveland Clinic

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.39, discarding reads left with < 30 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing HOMER v4.11.
bigWig files were generated using the deeptools v3.5.1.
Assembly: hg19
Supplementary files format and content: bigWig, bed

extract_protocol:
Cells were fixed with 1% formaldehyde for 7 minutes. After quenching and cell lysis, chromatin was sonicated using Fisher Scientific 550 Sonic Dismembrator.
ChIP-seq libraries were prepared using QIAseq FX DNA Library Kits according to the manufacturer's protocol. Post amplification libraries were purified using Agencourt AMPure XP beads.

tag: cell line

tag: cell type

value: Acute monocytic leukemia

tag: chip antibody

value: PHF6 (SCBT, sc-365237AC)


title: C7-SF18103137-96h

city: Nashville

tag: tissue

value: basilar papilla


title: DSP-1001660014616-A-B01

value: lung

value: lymphoid follicle

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

tag: patient

tag: %laa950 whole.lung

tag: %laa950 lobe

value: oct


title: iPSC-derived neurons (Patient #1, Clone #2), EOAD

tag: clinical diagnosis

tag: mri or_other_imaging

value: Diffuse atrophy

tag: csf biomarkers_for_ad

tag: cognition at_time_of_skin_biopsy

tag: treatment


title: C7-SF18103134-96h


title: DSP-1001660014616-A-A12

tag: slide name

tag: processing date

value: BCM-August

tag: panel

tag: condition

value: copd

tag: roi

tag: scan name


title: TMSC-blastocyst-14h-3

city: Macau

first: Ren-He

last: Xu

state: Macau

address: N22 Research Building, University of Macau, Taipa

department: Faculty of Health Sciences

institute: University of Macau

data_processing:
Bulk RNA sequenced reads were trimmed for short or low-quality sequence, then mapped to hg38 whole genome using hisat2 with defalut parameters
Single-cell squenced reads were analyzed using Drop-seq pipeline with parameters NUM_CORE_BARCODES=10000
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample of bulk RNA-seq,

organism:
Homo sapiens
Mus musculus

source_name: Mouse blastocysts injected with T-MSCs for 14 h-3

growth_protocol: MSCs were cultured in α-MEM with 20%FBS.

extract_protocol:
Bulk mRNA was extracted using RNeasy mini kit (QIAGEN). Smart-seq samples were lysed in lysis buffer containing Triton X-100, RNase inhibitor, dNTPs and miliQ H2O preparing for expansion. Single cell mRNA was captured in Nadia platform (Dolomite) using ChemGenes Barcoded beads for Drop-seq (Macosko-2011-10)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Mouse blastocysts injected with T-MSCs

tag: strain

value: ENVY cell line and C57/BL6J mouse blastocyst

tag: genotype

value: Wildtype


title: TMSC-blastocyst-14h-1

source_name: Mouse blastocysts injected with T-MSCs for 14 h-1


title: iPSC-derived neurons (Subject #4, Clone #3), NDC

tag: tissue

value: skin

value: induced pluripotent stem cells

value: Non-demented control (NDC)

tag: age at_onset

tag: age at_skin_biopsy

tag: Sex

value: Negative (2013)

value: Normal

tag: apoe status

tag: rna rin_score


title: iPSC-derived neurons (Subject #4, Clone #2), NDC

value: Female

tag: clinical diagnosis

tag: mri or_other_imaging

tag: csf biomarkers_for_ad

tag: cognition at_time_of_skin_biopsy

value: SMAD inhibition and bFGF withdrawal


title: TMSC-blastocyst-14h-2

source_name: Mouse blastocysts injected with T-MSCs for 14 h-2


title: C6-SF19013101-96h

value: basilar papilla

tag: treatment


title: iPSC-derived neurons (Patient #1, Clone #1), EOAD

value: Early-onset Alzheimer's disease (EOAD)

value: EOAD

value: Positive

value: MMSE 8/30


title: Fpt1-TAP ChIP-exo 5.0 NKI5632-1 Replicate 2

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

data_processing:
High-throughput DNA sequencing in paired-end mode was performed with Illumina NextSeq 500.
Sequence reads were aligned to the yeast genome (sacCer3) using bwa-mem (v0.7.9a). Reference: https://arxiv.org/pdf/1303.3997.pdf
Aligned reads obtained were filtered to remove PCR duplicates and non-unique alignments.
Assembly: sacCer3
Supplementary files format and content: Bedgraph, de-duplicated BAM files aligned to sacCer3
Library strategy: ChIP-exo

organism: Saccharomyces cerevisiae

source_name: Fpt1-TAP yeast

growth_protocol: Yeast strains were grown to an O.D600 of ~0.8 at 25°C.

extract_protocol:
Cells were crosslinked with formaldehyde to a final concentration of 1.0%. Lysates were clarified from sonicated nuclei and protein-DNA complexes were purified using appropriate antibody.
Libraries were prepared as described in PMID: 33692541
ChIP-exo 5.0

tag: chip antibody

value: IgG (Sigma i5006, Lot#SLBM2617V)

value: Fpt1-TAP yeast

value: MATa his3d1 leu2d0 ura3d0 met15d0 YKR011C-TAP-KanMX


title: DSP-1001660014616-A-B03

extract_protocol:
Default Nanostring GeoMx extraction protocol
Default Nanostring GeoMx library consruction protocol

value: lung

value: lymphoid follicle

tag: slide name

tag: processing date

value: BCM-August

tag: panel

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

tag: patient

tag: %laa950 whole.lung

tag: %laa950 lobe

tag: condition

value: copd

tag: roi

value: oct


title: iPSC-derived neurons (Subject #4, Clone #1), NDC

tag: tissue

value: skin

tag: cell type

value: induced pluripotent stem cells

tag: genotype

value: Non-demented control (NDC)

tag: age at_onset

tag: age at_skin_biopsy

tag: Sex

value: Negative (2013)

value: Normal


title: iPSC-derived neurons (Subject #3, Clone #3), NDC

value: Female

tag: clinical diagnosis

tag: mri or_other_imaging

value: Negative amyloid PET scan (2019)

tag: csf biomarkers_for_ad

value: Low A-beta42, normal tau and P-tau (2014)

tag: cognition at_time_of_skin_biopsy

tag: apoe status

tag: rna rin_score

value: SMAD inhibition and bFGF withdrawal


title: DSP-1001660014616-A-A11

tag: slide name

tag: processing date

tag: panel

tag: patient

tag: scan name


title: TMSC-blastocyst-6h

source_name: Mouse blastocysts injected with T-MSCs for 6 h

value: Mouse blastocysts injected with T-MSCs

tag: strain

value: ENVY cell line and C57/BL6J mouse blastocyst

value: Wildtype


title: C6-SF18103137-96h

tag: tissue

value: basilar papilla

tag: treatment


title: C7-SF18103133-96h


title: C6-SF18103134-96h


title: DSP-1001660014616-A-A01

value: lung

tag: cell type

value: lymphoid follicle

value: No Template Control


title: C6-SF18103138-96h