title: Sample: B12-61 , Mother: 965 , Day: 27

description: Library name: B12-61


title: Sample: B1-108 , Mother: 965 , Day: 6

status: Public on Nov 14 2025

type: SRA

city: Austin

first: Hans

middle: A

last: Hofmann

state: TX

address: 2415 Speedway

department: Integrative Biology

country: USA

institute: The University of Texas

description: Library name: B1-108

library_source: transcriptomic

data_processing:
sequencing reads were trimmed for adapter sequences and filtered for quality
trimmed reads were aligned using the BWA-MEM algorithm to Flounder_ref_guided_V1.0 (GCF_001970005.1)
read counts were quantified and extracted with htseq-count
Assembly: GCF_001970005.1
Supplementary files format and content: tab delimited text files with raw counts

molecule: total RNA

organism: Paralichthys lethostigma

source_name: Whole fish

extract_protocol:
RNA was extracted using the GeneJET RNA purification kit
The University of Texas Genomic Sequencing and Analysis Facility performed library preparation for 3’ tag-based RNA sequencing (tag-seq), based on prior protocol

tag: tissue

value: Whole fish

tag: time

tag: pooled samples

tag: pigmentation

value: unknown

tag: batch


title: DSP-1001660020370-C-F01

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Library name: DSP-1001660020370-C-F01
spatial transcriptomic sequencing

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

organism: Homo sapiens

source_name: lung

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

tag: slide name

value: lung

tag: panel

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

tag: patient

tag: age

tag: condition

value: COPD GOLD 4

value: COPD

tag: former or_current_smoker

value: former

tag: pack years

tag: gender

value: male

tag: location

value: airway

tag: roi

tag: scan name

value: paraffin


title: Sample: B2-124 , Mother: 94E , Day: 34

description: Library name: B2-124


title: Sample: B11-653 , Mother: FD247 , Day: 48

description: Library name: B11-653


title: DSP-1001660020370-C-F07

description:
Library name: DSP-1001660020370-C-F07
spatial transcriptomic sequencing

value: parenchyma


title: DSP-1001660020370-C-F02

description:
Library name: DSP-1001660020370-C-F02
spatial transcriptomic sequencing


title: Sample: B10-645 , Mother: 94E , Day: 48

description: Library name: B10-645


title: DSP-1001660020370-C-F06

description:
Library name: DSP-1001660020370-C-F06
spatial transcriptomic sequencing


title: DSP-1001660020370-C-G04

description:
Library name: DSP-1001660020370-C-G04
spatial transcriptomic sequencing

value: vessel

value: Copd10LLL_Vessel_003 002


title: Sample: A8-741 , Mother: 965 , Day: 34

description: Library name: A8-741


title: DSP-1001660020370-C-E12

description:
Library name: DSP-1001660020370-C-E12
spatial transcriptomic sequencing


title: Sample: A7-226 , Mother: FD247 , Day: 55

description: Library name: A7-226

value: pseudoalbino


title: Sample: A7-580 , Mother: FD247 , Day: 41

description: Library name: A7-580


title: sbr_7361_liver

city: St. Louis

first: Daniel

middle: Mimbs

last: Alligood

state: Missouri

address: 425 Euclid Ave - BJCIH 7118

department: Pediatric Surgery

institute: Washington University in St. Louis

description: Library name: Sample 6

library_source: transcriptomic single cell

data_processing:
Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a17.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3.2 Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2.3  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0.4
Assembly: Mouse
Supplementary files format and content: tab separated files and matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Single nuclear suspensions were produced in three sham and three SBR samples according to the protocol outlined by Nadelmann et. al. (Nadelmann, E. R. et al. Isolation of Nuclei from Mammalian Cells and Tissues for Single‐Nucleus Molecular Profiling. Current Protocols 1, e132 (2021).) In brief, liver tissue was gently homogenized to release cells. Lysate was added to lyse cells and release nuclei. The nuclei were filtered and stained with NucBlue. They were then sorted with FACS. Single nuclear suspension concentrations were estimated using Countess.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeqX instrument.  Normalized libraries were sequenced on a NovaSeqX Flow Cell using the 151x10x10x151 sequencing recipe according to manufacturer protocol.  Read 1 was trimmed to the 10x Genomics recommendation of 28bp. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

value: liver

tag: treatment

value: sbr


title: Sample: A6-572 , Mother: 94E , Day: 41

description: Library name: A6-572

tag: tissue


title: DSP-1001660020370-C-E10

description:
Library name: DSP-1001660020370-C-E10
spatial transcriptomic sequencing


title: DSP-1001660020370-C-E09

description:
Library name: DSP-1001660020370-C-E09
spatial transcriptomic sequencing


title: Sample: A5-544 , Mother: 965 , Day: 41

description: Library name: A5-544

tag: time


title: DSP-1001660020370-C-E08

description:
Library name: DSP-1001660020370-C-E08
spatial transcriptomic sequencing


title: Sample: A4-334 , Mother: FD247 , Day: 20

description: Library name: A4-334

tag: pooled samples


title: DSP-1001660020370-C-E07

description:
Library name: DSP-1001660020370-C-E07
spatial transcriptomic sequencing

value: SC

value: Smoker

value: female

value: oct


title: Sample: A9-616 , Mother: 965 , Day: 48

description: Library name: A9-616

value: Whole fish

tag: pigmentation

value: unknown


title: Sample: B1-102 , Mother: 965 , Day: 34

description: Library name: B1-102

tag: batch


title: Sample: A5-197 , Mother: 965 , Day: 55

description: Library name: A5-197

value: normal


title: sham_7354_liver

description: Library name: Sample 3

value: sham


title: Sample: A3-248 , Mother: FD247 , Day: 13

description: Library name: A3-248


title: Sample: A4-139 , Mother: FD247 , Day: 34

description: Library name: A4-139


title: DSP-1001660020370-C-E06

description:
Library name: DSP-1001660020370-C-E06
spatial transcriptomic sequencing

tag: slide name

value: lung

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

value: former


title: sham_7353_liver

description: Library name: Sample 2


title: DSP-1001660020370-C-E11

description:
Library name: DSP-1001660020370-C-E11
spatial transcriptomic sequencing

tag: panel

value: COPD GOLD 4

value: COPD

value: male

value: airway

value: paraffin


title: Sample: A8-588 , Mother: FD247 , Day: 41

description: Library name: A8-588


title: DSP-1001660020370-C-E05

description:
Library name: DSP-1001660020370-C-E05
spatial transcriptomic sequencing

tag: patient

value: vessel


title: sham_7352_liver

description: Library name: Sample 1

value: liver


title: Sample: A2-156 , Mother: FD247 , Day: 6

description: Library name: A2-156


title: cerebellar cells, KO male mouse

first: Kyung Pil

last: Ko

state: Tx

address: 1515 Holcombe Blvd

institute: The University of Texas M.D. Anderson Cancer Center

data_processing:
Barcoded processing and gene counting were performed by Cell Ranger. Cells were preprocessed by filtering by number of genes expressed in the count matrix and the percentage of counts in mitochondrial genes are <8000 and <20.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebellum in the brain

extract_protocol:
Cerebellar cells were obtained from mouse cerebella (P5) through the meticulous process of cerebellum dissection, cell straining, and plating. Two to four of cerebella were pooled for each genotype (Kmt2d fl/fl and Atoh1-Cre Kmt2d fl/fl mice) per gender. Single cells were isolated using flow cytometry for library preparation.
Cells were individually isolated and barcoded using droplet-based technique (Chromium Next GEM Single Cell 3ʹ Kit v3.1), and the transcripts were collected.

value: Cerebellum in the brain

tag: cell line

value: primary cell

tag: cell type

value: Cerebellar cell

tag: genotype

value: Atoh1-Cre Kmt2dfl/fl

tag: Sex


title: sbr_7357_liver

description: Library name: Sample 4

value: sbr


title: sbr_7358_liver

description: Library name: Sample 5


title: Sample: A6-218 , Mother: 94E , Day: 55

description: Library name: A6-218

value: Whole fish

value: normal


title: Sample: A2-123 , Mother: 94E , Day: 34

description: Library name: A2-123

value: unknown


title: Sample: A1-107 , Mother: 965 , Day: 6

description: Library name: A1-107


title: Sample: A11-652 , Mother: FD247 , Day: 48

description: Library name: A11-652


title: DSP-1001660020370-C-E03

description:
Library name: DSP-1001660020370-C-E03
spatial transcriptomic sequencing

value: lung

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

tag: age

tag: condition

value: SC

value: Smoker

tag: former or_current_smoker

tag: pack years

tag: gender

value: female

value: parenchyma

value: oct


title: DSP-1001660020370-C-E04

description:
Library name: DSP-1001660020370-C-E04
spatial transcriptomic sequencing

tag: tissue

value: former

tag: location

value: vessel

tag: roi

tag: scan name


title: cerebellar cells, KO female mouse

value: Cerebellum in the brain


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.72 hr^-1 for 48 hours - replicate 2

city: Riverside

first: Thomas

middle: Edward

last: Kuhlman

state: CA

address: 900 University Ave

department: Physics and Astronomy

institute: University of California Riverside

description: Library name: P72-2

data_processing:
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 the read numbers mapped to each gene.
Assembly: hg38 Homo sapiens reference genome downloaded from NCBI
Supplementary files format and content: Excel file includes raw counts for each Sample

growth_protocol: cells were cultured in complete media containing 90% DMEM with high glucose (Gibco), 10% heat-inactivated FBS (Gibco), 200 mM L-glutamine (100X), 10 mM MEM nonessential amino acids (100X), 100 mM MEM sodium pyruvate (100X), and concentrated puromycin (Gibco).

extract_protocol:
Total RNA was extracted from HEK-293T cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions after 48 hours of the indicated treatment
mRNA 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 dTTP for non-strand specific library or dUTP for strand specific library. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries were checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Raw data (raw reads) of fastq format were first 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 downstream analyses were based on the clean data with high quality, with each sample including more than 80 x 106 reads.

value: human embryonic kidney

value: WT

tag: treatment

value: osmotic shock


title: cerebellar cells, WT female mouse

value: primary cell

value: Cerebellar cell


title: Sample: A10-644 , Mother: 94E , Day: 48

description: Library name: A10-644

value: Whole fish

tag: time

tag: pooled samples

tag: pigmentation

tag: batch


title: DSP-1001660020370-C-D12

description:
Library name: DSP-1001660020370-C-D12
spatial transcriptomic sequencing

tag: slide name

tag: panel

tag: patient


title: Sample: A12-60 , Mother: 965 , Day: 27

description: Library name: A12-60

value: unknown


title: EGFP+ BN1 cells, unsorted, normoxia, rep 2

city: pittsburgh

first: Huabo

last: Wang

state: PA

address: 4401 Penn Avenue

institute: Children hospital of pittsburgh

description: Library name: UN2

data_processing:
nf-core 3.12.0
Reads were processed following the nf-core pipeline
Assembly: mm10
Supplementary files format and content: TPM file includes the normalized expression for each sample.

extract_protocol:
Total RNA were isolated as previously described using RNeasy columns (Qiagen).
For transcriptome sequencing, total RNA was extracted by RNeasy columns (Qiagen), and treated with TURBO DNA-free™ KitThermo Fisher Scientific Inc) . The mRNA was isolated and reverse-transcribed to cDNA and amplified using Illumina® Stranded mRNA Prep from Illumina, Inc (San Diego, CA). The library preparation processes such as adenylation, ligation and amplification were performed following the manual provided by the manufacturer(1, 2). The quantity and quality of the libraries were assessed through Bioanalyzer 2100 and Qubit instruments. The procedure of 150 cycle paired-end sequencing in AVITI sequencer followed the manufacturer’s manual(3).

tag: cell line

tag: cell type

value: immortalized hepatoblastoma cells

tag: genotype

value: Cdkn2a KO

value: unsorted, normoxia


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.18 hr^-1 for 48 hours - replicate 2

description: Library name: P18-2


title: Sample: A1-101 , Mother: 965 , Day: 34

description: Library name: A1-101


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.81 hr^-1 for 48 hours - replicate 2

description: Library name: P81-2


title: DSP-1001660020370-C-E01

description:
Library name: DSP-1001660020370-C-E01
spatial transcriptomic sequencing

value: lung

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

tag: age

tag: condition

value: SC

value: Smoker

tag: former or_current_smoker

tag: pack years


title: cerebellar cells, WT male mouse

tag: tissue

tag: Sex

value: male


title: Sample: A3-131 , Mother: FD247 , Day: 34

description: Library name: A3-131


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.63 hr^-1 for 48 hours - replicate 2

description: Library name: P63-2

tag: treatment


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.45 hr^-1 for 48 hours - replicate 2

description: Library name: P45-2


title: EGFP+ BN1 cells, unsorted, normoxia, rep 1

description: Library name: UN1


title: DSP-1001660020370-C-D11

description:
Library name: DSP-1001660020370-C-D11
spatial transcriptomic sequencing

value: former

tag: gender

value: female

tag: location

value: parenchyma

tag: roi

tag: scan name

value: oct


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.27 hr^-1 for 48 hours - replicate 2

description: Library name: P27-2

value: human embryonic kidney

value: WT

value: osmotic shock


title: DSP-1001660020370-C-D09

description:
Library name: DSP-1001660020370-C-D09
spatial transcriptomic sequencing

tag: slide name

value: airway


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.36 hr^-1 for 48 hours + 10μM SB203580 - replicate 1

description: Library name: P36SB-1


title: EGFP+ BN1 cells, unsorted, hypoxia, rep 2

description: Library name: UH2

value: unsorted, hypoxia


title: DSP-1001660020370-C-D08

description:
Library name: DSP-1001660020370-C-D08
spatial transcriptomic sequencing

tag: panel


title: Hypoxia VCOs, Day 5

city: Oxford

first: Yuqi

last: Shen

state: Oxfordshiore

address: MRC WIMM, University of Oxford

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: Sample 4
snRNA-Seq of D5 hypoxia VCOs

data_processing:
snRNA-seq raw data was processed using the CellRanger pipeline (10x Genomics, v7.0.0), pre-processed using CellBender (v0.3.0), Souporcell (v3.0.0) and analysed using Seurat (v5.1.0). Predicted ligang receptor interaction analysis was perfomed using CellChat (v1.6.1). DIfferential gene expression analysis was carried out using miloR package (v2.0), inetration perfomed using Harmony (v1.2.0) and plotting using the scCustomise package (v2.1.2)
Assembly: GRCh38-2020-A
Supplementary files format and content: R objects containing annotated SingleCellaR objects.

source_name: hiPSC-derived vascularised cardiac organoid

extract_protocol:
Nuclei were isolated from 10 VCO's per experimental batch for every condition before being pooled (30 vCOs in total) for library preparation and sequencing. Samples were digested using homogenisation buffer (250mM Sucrose, 25mM KCL, 5mM MgCl2, 10mM Tris Buffer, pH8, 1µM DTT, 1x EDTA-free Protease Inhibitor, 0.4 U/µl RNAseIn Plus, 0.2 U/µl SUPERraseIn and 0.1% Triton X-100) on ice for 5 minutes. The cell homogenate was passed through a 40µm cell strainer before being centrifuged at 500xg for 5 minutes at 4°C. The supernatant was removed carefully and the nuclei pellet was resuspended in storage buffer (4% BSA, 0.2 U/µl RNAseIn in PBS w/o Ca/Mg). Nuclei were stained with DAPI on ice for 10 minutes prior to being sorted using a BD FACSDiscover S8 Cell Sorter.
Libraries were prepared using the Chromium GEM-X Single Cell 3' Kit, v4 (10X genomics) according to the manufacturers instructions.

value: Cardiomyocytes, endothelial cells, mural cells, stromal cells and immune cells

value: Hypoxia


title: DSP-1001660020370-C-D10

description:
Library name: DSP-1001660020370-C-D10
spatial transcriptomic sequencing

tag: patient


title: DSP-1001660020370-C-D07

description:
Library name: DSP-1001660020370-C-D07
spatial transcriptomic sequencing


title: DSP-1001660020370-C-E02

description:
Library name: DSP-1001660020370-C-E02
spatial transcriptomic sequencing


title: EGFP+ BN1 cells, unsorted, hypoxia, rep 1

description: Library name: UH1

tag: cell line

value: immortalized hepatoblastoma cells

value: Cdkn2a KO


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.36 hr^-1 for 48 hours + 10μM SB203580 - replicate 2

description: Library name: P36SB-2

tag: cell type


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.90 hr^-1 for 48 hours - replicate 2

description: Library name: P90-2

tag: genotype


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.09 hr^-1 for 48 hours - replicate 2

description: Library name: P09-2


title: EGFP+ BN1 cells, unsorted, normoxia, rep 3

description: Library name: UN3

value: unsorted, normoxia


title: DU145CAS9-3

city: Chapel Hill

first: Pengda

last: Liu

state: NC

address: 21-246 Lineberger Building, 450 West Drive, CB7295 450 West Drive, CB7295

department: Biochemistry and Biophysics

institute: The University of North Carolina at Chapel Hill

description: Library name: sample 6

data_processing:
Data 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: Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome.
Quantification of gene expression level: featureCounts (2.0.6) was used to count the reads numbers mapped to each gene.
Differential expression analysis: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package (1.42.0).
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler (4.8.1), in which gene length bias was corrected. KEGG is performed using http://www.genome.jp/kegg/. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independently.
Assembly: hg38
Supplementary files format and content: .txt and .tsv

source_name: prostate

growth_protocol: DU145 cells are cultured in DMEM medium supplemented with 10% FBS,100 units of penicillin and 100 mg/mL streptomycin at 37 oC with 5% CO2.

extract_protocol:
Biobasic EZ-10 DNAaway RNA Miniprep Kit
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 dTTP for non strand specific library or dUTP for strand specific library. 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.

value: prostate

value: prostate cancer cell


title: EGFP+ BN1 cells, sorted, normoxia, rep 3

description: Library name: SN3

value: sorted, normoxia


title: DU145CAS9-2

description: Library name: sample 5


title: DU145CAS9-1

description: Library name: sample 4


title: Uninjured VCOs, Day 5

description:
Library name: Sample 3
snRNA-Seq of D5 uninjured VCOs

value: hiPSC-derived vascularised cardiac organoid

value: Uninjured


title: Hypoxia VCOs, Day 2

description:
Library name: Sample 2
snRNA-Seq of D2 hypoxia VCOs


title: DSP-1001660020370-C-D05

description:
Library name: DSP-1001660020370-C-D05
spatial transcriptomic sequencing

value: lung

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

tag: age

value: SC

value: Smoker

value: former

value: female


title: Uninjured VCOs, Day 2

description:
Library name: Sample 1
snRNA-Seq of D2 uninjured VCOs


title: DSP-1001660020370-C-D06

description:
Library name: DSP-1001660020370-C-D06
spatial transcriptomic sequencing

tag: condition

value: airway

value: oct


title: DU145NC-3

description: Library name: sample 3


title: EGFP+ BN1 cells, sorted, normoxia, rep 2

description: Library name: SN2


title: DU145NC-1

description: Library name: sample 1


title: DU145NC-2

description: Library name: sample 2


title: EGFP+ BN1 cells, unsorted, hypoxia, rep 3

description: Library name: UH3

value: unsorted, hypoxia


title: DSP-1001660020370-C-D04

description:
Library name: DSP-1001660020370-C-D04
spatial transcriptomic sequencing

tag: former or_current_smoker


title: T24 cells, shCCDC137, rep3

city: Shenzhen

first: Haiyu

last: Zhang

country: China

institute: Shenzhen Second People’s Hospital

description:
Library name: Sample6
Column name in Row_counts_all_Samples.txt: Sample6

data_processing:
To get high quality clean reads, reads were further filtered by fastp (https://github.com/OpenGene/fastp,version 0.20.1).
Then, sequences were mapped to the human reference genome (GRCh38) using HISAT2 (https://daehwankimlab.github.io/hisat2/,version 2.2.1).
The mapped reads of each sample were assembled and merged using StringTie (https://github.com/gpertea/stringtie, version 2.0.4).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was harvested using Trizol reagent (5301100，SIMGEN).
RNA libraries for RNA sequencing were prepared using standard IIIumina protocols.

value: bladder cancer cells


title: EGFP+ BN1 cells, sorted, normoxia, rep 1

description: Library name: SN1

value: immortalized hepatoblastoma cells

value: Cdkn2a KO


title: DSP-1001660020370-C-D03

description:
Library name: DSP-1001660020370-C-D03
spatial transcriptomic sequencing

value: COPD GOLD 3

value: COPD

value: current

tag: pack years

value: male

value: vessel


title: EGFP+ BN1 cells, sorted, hypoxia, rep 2

description: Library name: SH2

value: sorted, hypoxia


title: T24 cells, shControl, rep3

description:
Library name: Sample3
Column name in Row_counts_all_Samples.txt: Sample3


title: T24 cells, shCCDC137, rep1

description:
Library name: Sample4
Column name in Row_counts_all_Samples.txt: Sample4


title: EGFP+ BN1 cells, sorted, hypoxia, rep 3

description: Library name: SH3


title: T24 cells, shControl, rep2

description:
Library name: Sample2
Column name in Row_counts_all_Samples.txt: Sample2


title: T24 cells, shCCDC137, rep2

description:
Library name: Sample5
Column name in Row_counts_all_Samples.txt: Sample5


title: T24 cells, shControl, rep1

description:
Library name: Sample1
Column name in Row_counts_all_Samples.txt: Sample1


title: DSP-1001660020370-C-D02

description:
Library name: DSP-1001660020370-C-D02
spatial transcriptomic sequencing

tag: tissue

value: lung

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


title: EGFP+ BN1 cells, sorted, hypoxia, rep 1

description: Library name: SH1


city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description:
Library name: ARPM_ATAC
Airway organoid co-cultured with proinflammatory macrophages (ATAC)

library_source: genomic single cell

data_processing:
Sequencing data were primarily analyzed using the 10X cellranger-arc pipeline v2.0.1
cellranger-arc mkfastq was used to demultiplex the samples and generate FASTQ files
cellranger-arc count aligned the FASTQ data to the 10X pre-built GRCh38-2020-A-2.0.0 human reference genome, producing a gene expression UMI counts matrix for each GEX library and peak and fragment files for each ATAC library
Assembly: GRCh38
Supplementary files format and content: cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: cellranger output files: per_barcode_metrics.csv, atac_peaks.bed, atac_fragments.tsv.gz

molecule: genomic DNA

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

treatment_protocol: organoid co-cultured with unstimulate macrophages or proinflammatory macrophages

value: stem cell derived

value: human

tag: library type

value: ATAC


title: Airway organoid co-cultured with proinflammatory macrophage (RNA)

description:
Library name: ARPM_RNA
Airway organoid co-cultured with proinflammatory macrophages (RNA)

value: mRNA


title: Airway organoid co-cultured with unstimulate macrophages (ATAC)

description:
Library name: ARUM_ATAC
Airway organoid co-cultured with unstimulate macrophage (ATAC)


title: DSP-1001660020370-C-C12

description:
Library name: DSP-1001660020370-C-C12
spatial transcriptomic sequencing

value: oct


description:
Library name: AVPM_ATAC
Alveolar organoid co-cultured with proinflammatory macrophages (ATAC)


title: DSP-1001660020370-C-D01

description:
Library name: DSP-1001660020370-C-D01
spatial transcriptomic sequencing


title: DSP-1001660020370-C-C09

description:
Library name: DSP-1001660020370-C-C09
spatial transcriptomic sequencing

value: parenchyma


title: Alveolar organoid co-cultured with proinflammatory macrophage (RNA)

description:
Library name: AVPM_RNA
Alveolar organoid co-cultured with proinflammatory macrophages (RNA)


title: Alveolar organoid co-cultured with unstimulate macrophages (ATAC)

description:
Library name: AVUM_ATAC
Alveolar organoid co-cultured with unstimulate macrophage (ATAC)


description:
Library name: AVUM_RNA
Alveolar organoid co-cultured with unstimulate macrophage (RNA)


title: DSP-1001660020370-C-C11

description:
Library name: DSP-1001660020370-C-C11
spatial transcriptomic sequencing


title: DSP-1001660020370-C-C10

description:
Library name: DSP-1001660020370-C-C10
spatial transcriptomic sequencing


title: DSP-1001660020370-C-C07

description:
Library name: DSP-1001660020370-C-C07
spatial transcriptomic sequencing


title: DSP-1001660020370-C-C08

description:
Library name: DSP-1001660020370-C-C08
spatial transcriptomic sequencing


title: Crispr-dcas9 SAM screening, Control

city: Guangzhou

first: Binkui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description: Table sam.xlsx

library_source: other

data_processing:
Shalem, O., Sanjana, N.E., Hartenian, E., Shi, X., Scott, D.A., Mikkelson, T., Heckl, D., Ebert, B.L., Root, D.E., Doench, J.G., et al. (2014). Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87.
Supplementary files format and content: Matrix table with  gene foldchange for every gene
Library strategy: CRISPR screen

molecule: other

organism: synthetic construct

growth_protocol: The HCC cells are co-cultured with/without activated CD8+ T cells

extract_protocol: genome-wide crispr library cells are collected,and genome DNA was harvested and sgRNAs were amplified with PCR.

treatment_protocol: A pooled CRISPR genome-wide loss/gain-of-function screen using a lentiviral KO/activation library in PLC-PRF-5/Hep-G2 cells. The cell pools were co-cultured with activated CD8+ T cells for 7 days

value: HCC cells

value: WT

tag: treatment

value: ctrl

tag: time

value: Day 7


title: Crispr-cas9 library screening, Control

description: Table cas9.xlsx


title: Crispr-dcas9 SAM screening,  treatment

description: Table sam.xlsx

value: Treatment

value: co-culture


title: DSP-1001660020370-C-C06

description:
Library name: DSP-1001660020370-C-C06
spatial transcriptomic sequencing

value: COPD GOLD 3

value: COPD

value: current

tag: gender

value: male

tag: location


title: DSP-1001660020370-C-C03

description:
Library name: DSP-1001660020370-C-C03
spatial transcriptomic sequencing

value: lung

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

value: airway

tag: roi

tag: scan name


description:
Library name: ARUM_RNA
Airway organoid co-cultured with unstimulate macrophage (RNA)

value: stem cell derived

value: human


title: cDC2 Flt3L + OP9DL-1 rep3

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Library name: 35-XCR1neg-DL1-Flt3L_S10

data_processing:
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread::align.
Genewise counts were obtained using featureCounts with Rsubread's inbuilt mm10 annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text giving Entrez Gene IDs, gene length (number of bases in union of all exons) and the number of read-pairs assigned to that read.

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: C57/BL6 bone marrow progenitors were cultured in RPMI supplemented with FCS (10%) and antibiotics and were maintained in a humidified incubator with  5% CO2 at 37C

extract_protocol:
RNA from cell pellets was extracted following  Qiagen RNA plus Mini kit instructions
100 ng of total RNA were processed following the instruction of the TrueSeq RNA sample preparation kitC

treatment_protocol: Flt3L 100 ng/ml for 7 days. On day 7 cells were purified according to their cell surface markers by flow cytometry and cell pellets were further processed from RNA extraction

tag: strain

value: Bone marrow

tag: Sex

value: Female

value: Flt3L + OP9DL-1

tag: batch

tag: mouse id


title: cDC2 Flt3L + OP9DL-1 rep1

description: Library name: 31-XCR1neg-DL1-Flt3L_S6

tag: cell type

tag: genotype

value: WT


title: cDC1 Flt3L + OP9DL-1 rep3

description: Library name: 36-XCR1pos-DL1-Flt3L_S11


title: cDC1 Flt3L + OP9DL-1 rep2

description: Library name: 34-XCR1pos-DL1-Flt3L_S9


title: cDC2 Flt3L + OP9DL-1 rep2

description: Library name: 33-XCR1neg-DL1-Flt3L_S8


title: DSP-1001660020370-C-C05

description:
Library name: DSP-1001660020370-C-C05
spatial transcriptomic sequencing

tag: slide name

tag: panel

tag: patient

tag: age

tag: condition

value: oct


title: cDC1 Flt3L + IL-4 + OP9DL-1 rep1

description: Library name: 26-XCR1pos-DL1-IL4_S2

tag: tissue

tag: treatment

value: Flt3L + IL-4 + OP9DL-1


title: cDC2 Flt3L + IL-4 + OP9DL-1 rep1

description: Library name: 25-XCR1neg-DL1-IL4_S1


title: cDC1 Flt3L + OP9DL-1 rep1

description: Library name: 32-XCR1pos-DL1-Flt3L_S7


title: cDC1 Flt3L + IL-4 + OP9DL-1 rep2

description: Library name: 28-XCR1pos-DL1-IL4_S4


title: Crispr-cas9 library screening, treatment

description: Table cas9.xlsx

tag: cell line

value: HCC cells

value: Treatment

tag: time

value: Day 7


title: cDC2 Flt3L + IL-4 + OP9DL-1 rep3

description: Library name: 29-XCR1neg-DL1-IL4_S5


title: cDC2 Flt3L + IL-4 + OP9DL-1 rep2

description: Library name: 27-XCR1neg-DL1-IL4_S3


title: culms under RT treatment for 25 day-3

city: Hangzhou

first: Dan

last: Hou

address: 666 Wusu street, Lin'an District, Hangzhou

institute: A&F university

data_processing:
A cDNA library was sequenced run with Illumina Novaseq 6000 sequence platform.
Firstly, Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
De novo assembly of the transcriptome was performed with Trinity 2.4.0 [2]. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
Salmon [4] was used to perform expression level for Unigenes by calculating TPM
Assembly: clean reads were mapped to the reference genome of P. edulis
Supplementary files format and content: xlsx files include TKM values for each Sample

organism: Phyllostachys nigra

source_name: culms

growth_protocol: growth in greenhouse

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribe™ Reverse Transcriptase reaches the 5’ end of the mRNA, the enzyme’s terminal transferase activity adds a few additional nucleotides to the 3’ end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5’ end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase(NEB, M0348S) by incubate at 37°C for 30min.Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand,indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR.

treatment_protocol: Low temperature 4℃ and Room temperature 25℃

value: culms

value: Room temperature (25℃）


title: cDC2 Flt3L + OP9 rep3

description: Library name: 23-XCR1neg-OP9-Flt3L_S11

value: Flt3L + OP9


title: cDC2 Flt3L + OP9 rep2

description: Library name: 21-XCR1neg-OP9-Flt3L_S9


title: culms under RT treatment for 25 day-1


title: cDC2 Flt3L + OP9 rep1

description: Library name: 19-XCR1neg-OP9-Flt3L_S7


title: DSP-1001660020370-C-C04

description:
Library name: DSP-1001660020370-C-C04
spatial transcriptomic sequencing

value: lung

value: COPD GOLD 3

value: COPD

tag: former or_current_smoker

value: current

tag: pack years

tag: gender

value: male

tag: location

tag: roi


title: DSP-1001660020370-C-C01

description:
Library name: DSP-1001660020370-C-C01
spatial transcriptomic sequencing

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

value: COPD GOLD 2

value: former

value: female

value: vessel

tag: scan name


title: cDC1 Flt3L + OP9 rep2

description: Library name: 22-XCR1pos-OP9-Flt3L_S10

tag: strain

value: Bone marrow

tag: cell type

tag: Sex

value: Female

value: WT

tag: batch

tag: mouse id


title: cDC1 Flt3L + OP9 rep1

description: Library name: 20-XCR1pos-OP9-Flt3L_S8

tag: genotype


title: cDC2 Flt3L + IL-4+ OP9 rep3

description: Library name: 17-XCR1neg-OP9-IL4_S5

value: Flt3L + IL-4+ OP9


title: cDC1 Flt3L + OP9 rep3

description: Library name: 24-XCR1pos-OP9-Flt3L_S12


title: culms under RT treatment for 15 day-3

value: culms


title: DSP-1001660020370-C-C02

description:
Library name: DSP-1001660020370-C-C02
spatial transcriptomic sequencing

tag: slide name

tag: panel

tag: patient

tag: age

tag: condition

value: parenchyma

value: oct


title: DSP-1001660020370-C-B12

description:
Library name: DSP-1001660020370-C-B12
spatial transcriptomic sequencing

tag: tissue

value: lung

tag: former or_current_smoker


title: DSP-1001660020370-C-B11

description:
Library name: DSP-1001660020370-C-B11
spatial transcriptomic sequencing

tag: pack years

tag: gender


title: cDC1 Flt3L + IL-4+ OP9 rep1

description: Library name: 14-XCR1pos-OP9-IL4_S2

tag: treatment


title: culms under RT treatment for 15 day-1

value: Room temperature (25℃）


title: culms under RT treatment for 25 day-2


title: DSP-1001660020370-C-B10

description:
Library name: DSP-1001660020370-C-B10
spatial transcriptomic sequencing

value: COPD

tag: location

tag: roi

tag: scan name


title: cDC2 Flt3L rep3

description: Library name: 11-XCR1neg-Flt3L_S11

tag: strain

tag: cell type

tag: Sex


title: culms under RT treatment for 1 day-3


title: DSP-1001660020370-C-B09

description:
Library name: DSP-1001660020370-C-B09
spatial transcriptomic sequencing


title: DSP-1001660020370-C-B06

description:
Library name: DSP-1001660020370-C-B06
spatial transcriptomic sequencing


title: cDC1 Flt3L + IL-4+ OP9 rep2

description: Library name: 16-XCR1pos-OP9-IL4_S4

tag: genotype

tag: batch

tag: mouse id


title: culms under RT treatment for 15 day-2


title: culms under RT treatment for 1 day-2


title: cDC2 Flt3L + IL-4+ OP9 rep2

description: Library name: 15-XCR1neg-OP9-IL4_S3


title: DSP-1001660020370-C-B05

description:
Library name: DSP-1001660020370-C-B05
spatial transcriptomic sequencing

tag: slide name

tag: panel

tag: patient

value: airway


title: DSP-1001660020370-C-B07

description:
Library name: DSP-1001660020370-C-B07
spatial transcriptomic sequencing

tag: tissue

tag: age

tag: condition


title: cDC1 Flt3L + IL-4+ OP9 rep3

description: Library name: 18-XCR1pos-OP9-IL4_S6


title: cDC2 Flt3L + IL-4+ OP9 rep1

description: Library name: 13-XCR1neg-OP9-IL4_S1


title: DSP-1001660020370-C-B04

description:
Library name: DSP-1001660020370-C-B04
spatial transcriptomic sequencing

value: SC

value: Smoker

tag: former or_current_smoker

value: current

tag: pack years

tag: gender


title: HBEC26 cigarette smoke transformed

type: genomic

city: Albuquerque

first: Steven

last: Belinsky

state: NM

address: 2425 Ridgecrest Dr SE

department: Lung Cancer Program

institute: Lovelace Respiratory Research Institute

description:
DNA from cigarette smoke transformed HBEC26 cells
H26cst

hyb_protocol: The bisulfite modified DNA was amplified, enzymatically fragmented, precipitated, re-suspended in hybridization buffer, hybridized to the Illumina Infinium MethylationEPICv2.0 Beadchip (EPICv2.0)

scan_protocol: Arrays were imaged using the Illumina iScan System (Illumina, CA, USA), standard Illumina scanning settings, and standard Illumina protocol

data_processing: Minfi package in  R v4.0.2

label: Cy3 and Cy5

source_name: lung epithelial cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and 1.0 µg DNA bisulfite modified using EZ DNA methylation Gold Kit (Zymo Research)

value: lung epithelial cells

tag: cell line

value: bronchial epithelial cells

tag: treatment

value: cigarette smoke exposure

tag: cs treatment time

value: 1x/week for 12 weeks


title: cDC1 Flt3L + IL-4 rep3

description: Library name: 6-XCR1pos-IL4_S6

tag: strain

value: Bone marrow

tag: cell type

value: Female

value: Flt3L + IL-4


title: cDC1 Flt3L + IL-4 rep2

description: Library name: 4-XCR1pos-IL4_S4

tag: Sex

tag: genotype

value: WT


title: cDC2 Flt3L + IL-4 rep2

description: Library name: 3-XCR1neg-IL4_S3

tag: batch

tag: mouse id


title: DSP-1001660020370-C-B03

description:
Library name: DSP-1001660020370-C-B03
spatial transcriptomic sequencing

tag: slide name

tag: panel

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

value: female

tag: location

value: parenchyma

tag: roi

tag: scan name


title: cDC1 Flt3L rep3

description: Library name: 12-XCR1pos-Flt3L_S12

tag: tissue


title: HBEC2 BRG1 + cigarette smoke transformation

description:
DNA from BRG1 knockout + cigarette transformation in HBEC2 cells
H2kocst

value: BRG-KO


title: DSP-1001660020370-C-B02

description:
Library name: DSP-1001660020370-C-B02
spatial transcriptomic sequencing

value: lung

tag: patient

tag: age

tag: condition

tag: former or_current_smoker

tag: pack years

value: oct


title: culms under LT treatment for 25 day-1

value: culms

tag: treatment

value: Low temperature (4℃）


title: cDC2 Flt3L + IL-4 rep1

description: Library name: 1-XCR1neg-IL4_S1

tag: strain

tag: cell type


title: HBEC2 BRG1-knockout

description:
DNA from BRG1 knockout in HBEC2 cells
H2ko

tag: cell line

tag: genotype

tag: cs treatment time


title: culms under LT treatment for 15 day-3


title: DSP-1001660020370-C-B01

description:
Library name: DSP-1001660020370-C-B01
spatial transcriptomic sequencing

tag: slide name

value: SC

value: Smoker

value: current

tag: gender


title: HBEC26 BRG1-knockout

description:
DNA from BRG1 knockout in HBEC26 cells
H26ko

value: lung epithelial cells

value: bronchial epithelial cells


title: HBEC26 control

description:
DNA from wild-type HBEC26 cells
H26cont


title: DSP-1001660020370-C-B08

description:
Library name: DSP-1001660020370-C-B08
spatial transcriptomic sequencing

tag: panel

value: COPD GOLD 2

value: COPD

value: former

tag: location


title: GCP cells, Cerebellum, Control, 4m, replicate 2, RNA-seq

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description: Library name: PLX224818_SD6

data_processing:
Paired-end FASTQ files were processed using the nf-core-rnaseq pipeline (v3.17.0) (auto strandedness).
Adapter sequences were removed with Trim Galore.
Reads were aligned with STAR to GRCm38 (NCBI, p.6, release 108) and quantified to gene counts using RSEM.
Downsteam analysis was performed using Pluto (https://pluto.bio).
Assembly: GRCm38 (NCBI, p.6, release 108)
Supplementary files format and content: comma-delimited text files includes raw counts for each Sample

source_name: Cerebellum

growth_protocol: To enrich cerebellar GCs, murine cerebellar tissues were first processed using the Miltenyi Biotec Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, Germany) according to the manufacturer’s protocol with slight modifications. Briefly, cerebella were dissected from mice, washed in cold phosphate-buffered saline (PBS) supplemented with 0.5% bovine serum albumin (BSA), and transferred into gentleMACS™ C tubes containing the enzyme mix from the dissociation kit. Tissues were mechanically dissociated using the gentleMACS™ Dissociator (Miltenyi Biotec) and incubated at 37°C for 15 minutes with gentle agitation to achieve enzymatic digestion. The tissue suspension was then triturated with fire-polished glass pipettes and further incubated for an additional 10 minutes at 37°C. Following enzymatic dissociation, the cell suspension was passed through a 70 µm cell strainer to remove debris and undissociated tissue fragments. Cells were centrifuged at 300 x g for 10 minutes at 4°C and resuspended in cold PBS containing 0.5% BSA. GC lineage cells were enriched from the dissociated tissue using the Neuron Isolation Kit (Miltenyi Biotec), which removes non-neuronal cells using antibodies specific for non-neuronal cells (e.g., astrocytes, oligodendrocytes, microglia, endothelial cells, and fibroblasts). According to the manufacturer’s data, neurons (including GC lineage cells as the vast majority of neurons) can be enriched to up to 93-99%. Cells were plated at a density of 5 × 105 cells per dish in a Neurobasal medium with B27 supplement, 20 ng/ml Epidermal Growth Factor (EGF), 20 ng/mL basic Fibroblast Growth Factor (bFGF), and 2 μg /mL heparin. Within three to five days, the cells self-organized into neurospheres.

extract_protocol:
Total RNAs were extracted using RNeasy kits (Qiagen), which were used for RNA-seq experiments.
Libraries were prepared for sequencing using standard Illumina protocols (TruSeq RNA Library Prep Kit v2).

value: GCP

value: Cerebellum

value: Control

tag: Sex

value: Male

tag: timepoint


title: culms under LT treatment for 15 day-2

tag: tissue


title: HBEC1 BRG1-knockout + cigarette smoke transformation

description:
DNA from BRG1 knockout + cigarette smoke transformation in HBEC1 cells
H1kocst

value: BRG-KO

value: cigarette smoke exposure

value: 1x/week for 12 weeks


title: cDC2 Flt3L rep2

description: Library name: 9-XCR1neg-Flt3L_S9

value: Bone marrow

value: Female

value: WT

tag: batch

tag: mouse id


title: cDC1 Flt3L rep1

description: Library name: 8-XCR1pos-Flt3L_S8


title: GCP cells, Cerebellum, KO, 30d, replicate 1, RNA-seq

description: Library name: PLX224818_SD3

tag: condition

value: KO


title: cDC1 Flt3L rep2

description: Library name: 10-XCR1pos-Flt3L_S10


title: HBEC2 cigarette smoke transformed

description:
DNA from cigarette transformed HBEC2 cells
H2cst


title: DSP-1001660020370-C-A10

description:
Library name: DSP-1001660020370-C-A10
spatial transcriptomic sequencing

value: lung

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

tag: patient

tag: age

value: SC

value: Smoker

tag: former or_current_smoker

tag: pack years

value: male

value: parenchyma

tag: roi

tag: scan name

value: oct


title: HBEC1 control

description:
DNA from wild-type HBEC1 cells
H1cont

value: lung epithelial cells

tag: cell line

tag: cell type

value: bronchial epithelial cells

tag: genotype

tag: treatment

tag: cs treatment time


title: GCP cells, Cerebellum, Control, 30d, replicate 1, RNA-seq

description: Library name: PLX224818_SD1

value: GCP

value: Cerebellum

value: Control

tag: Sex


title: culms under RT treatment for 1 day-1

value: culms

value: Room temperature (25℃）


title: HBEC1 BRG1-knockout

description:
DNA from BRG1 knockout in HBEC1 cells
H1ko

value: BRG-KO


title: HBEC26 BRG1 + cigarette smoke transformation

description:
DNA from BRG1 knockout + cigarette transformation in HBEC26 cells
H26kocst

value: cigarette smoke exposure

value: 1x/week for 12 weeks


title: cDC2 Flt3L rep1

description: Library name: 7-XCR1neg-Flt3L_S7

tag: strain

value: Bone marrow

value: Female

value: WT


title: culms under LT treatment for 25 day-3

tag: tissue

value: Low temperature (4℃）


title: cDC2 Flt3L + IL-4 rep3

description: Library name: 5-XCR1neg-IL4_S5

value: Flt3L + IL-4

tag: batch


title: GW17

city: Guangdong

first: jing xian

last: huang

state: Guangzhou

address: 暨南大学石牌校区学生宿舍2栋302

institute: jinan university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing , gene counting and aggregation were made using Cell Ranger 3.8.0.
Assembly: 36
Supplementary files format and content: Tab-separated values files and matrix files

source_name: GW17 kidney

extract_protocol:
After isolating tissues from human embryos, they are rapidly frozen in isopentane cooled with liquid nitrogen and then sectioned. The tissue sections are digested at 37°C in 0.25% trypsin solution (Gibco) to prepare a single-cell suspension. The cells are then washed with DPBS and filtered through a 40μm filter (Bel-Art)
Library construction was carried out the GEXSCOPETM Single-Cell RNA Library Kit (Singleron Biotechnologies), adhering to the Singleron GEXSCOPETM protocol.

value: Human epithelium

value: 17 weeks old


title: HBEC2 control

description:
DNA from wild-type HBEC2 cells
H2cont

value: lung epithelial cells


title: GW11

address: 暨南大学石牌校区学生宿舍2栋302

description: 10x Genomics

source_name: GW11 kidney

value: 11 weeks old


title: culms under LT treatment for 25 day-2


title: DSP-1001660020370-C-A08

description:
Library name: DSP-1001660020370-C-A08
spatial transcriptomic sequencing

tag: slide name

value: lung

tag: panel

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

value: SC

value: Smoker

value: former

tag: gender

value: male

tag: location

value: parenchyma

value: oct


title: cDC1 Flt3L + IL-4 rep1

description: Library name: 2-XCR1pos-IL4_S2

value: Bone marrow

tag: mouse id


title: BoMac cells,M.bovis-NX2-EVs,rep3

city: Yinchuan

first: Yiming

last: Wu

state: Ningxia

address: 539, Helanshan West Road

institute: Ningxia university

data_processing:
Sequence reads were filtered for quality, and adapter sequences were trimmed using a custom Perl script that identifies exact string matches to a user-supplied adapter sequence ratio. Clean data were mapped to the reference genome to calculate the alignment using HISAT2.
Assembly: ARS-UCD1.2
Supplementary files format and content: Excel file contains raw counts for each Sample

organism: Bos taurus

source_name: BoMac

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen), 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library Prep Kit.

value: BoMac


title: DSP-1001660020370-C-A07

description:
Library name: DSP-1001660020370-C-A07
spatial transcriptomic sequencing

tag: patient

tag: age

tag: condition

tag: former or_current_smoker

tag: pack years


title: GCP cells, Cerebellum, KO, 4m, replicate 2, RNA-seq

description: Library name: PLX224818_SD8

tag: cell line

value: GCP

value: Cerebellum

value: KO

value: Female

tag: timepoint


title: BoMac cells,M.bovis-NX2-EVs,rep1


title: BoMac cells,Ctrl-EVs,rep3


title: culms before treatment-2

value: culms

tag: treatment


title: BoMac cells,Ctrl-EVs,rep2


title: BoMac cells,Ctrl-EVs,rep1


title: BoMac cells, M.bovisNX2-EVs-24h, rep3

data_processing:
Sequence reads were filtered for quality, and adapter sequences were trimmed using a custom Perl script that identifies exact string matches to a user-supplied adapter sequence ratio. Clean data were mapped to the reference genome to calculate the alignment using HISAT2.
Assembly: ARS-UCD1.2
Supplementary files format and content: raw counts for each Sample


title: GCP cells, Cerebellum, KO, 4m, replicate 1, RNA-seq

description: Library name: PLX224818_SD7

tag: Sex

value: Male


title: BoMac cells, M.bovisNX2-EVs-24h, rep1


title: GCP cells, Cerebellum, Control, 4m, replicate 1, RNA-seq

description: Library name: PLX224818_SD5

value: Control


title: GCP cells, Cerebellum, KO, 30d, replicate 2, RNA-seq

description: Library name: PLX224818_SD4


title: DSP-1001660015818-B-H12

description:
Library name: DSP-1001660015818-B-H12
spatial transcriptomic sequencing

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

value: lung

value: COPD GOLD 3

value: COPD

value: current

value: vessel

tag: roi

tag: scan name


title: BoMac cells, Ctrl-EVs-24h, rep3


title: culms under LT treatment for 15 day-1

tag: tissue

value: Low temperature (4℃）


title: DSP-1001660020370-C-A12

description:
Library name: DSP-1001660020370-C-A12
spatial transcriptomic sequencing

tag: slide name

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

value: SC

value: Smoker

value: female

value: parenchyma


title: DSP-1001660020370-C-A11

description:
Library name: DSP-1001660020370-C-A11
spatial transcriptomic sequencing

tag: panel

value: former

value: male

value: oct


title: L7C

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

description:
Library name: L7C
Liver, neonatal calves (30h after birth)

data_processing:
Sequencing adaptors, low-complexity reads, and reads containing low quality bases were removed in an initial data-filtering step. Reads with a PhredScore lower than 30 were filtered out. Quality control (QC) and read statistics were estimated with FastQC v0.11.8 and MultiQC v1.9 software. After QC, reads were mapped to the Bos taurus reference genome (ARS-UCD 1.3) using the STAR aligner v. 2.7.5. Raw counts per gene were obtained using the –quantMode GeneCounts flag from STAR based on the gene annotation file (release 111, Ensembl). MultiQC, NOISeq, and edgeR software were used to perform the post-mapping quality control. Genes with expression values lower than 10 count per million in 70% of the samples were filtered out using filterbyexpression function from edgeR. After filtering, the genes were analyzed using the DESeq2 v.1.22.1 software to identify DEGs.
Assembly: ARS-UCD1.2, Ensembl (annotation file release 109)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Total RNA isolation was carried out using the RNeasy Kit (Qiagen, Germantown, MA, USA) in conjunction with an on-column DNase digestion step, as per the manufacturer’s guidelines.
Strand-specific libraries were then constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs®, Ipswich, MA, USA).

value: Liver

value: CONTROL


title: GCP cells, Cerebellum, Control, 30d, replicate 2, RNA-seq

description: Library name: PLX224818_SD2

value: GCP

value: Cerebellum

value: Control

value: Male


title: L40V

description:
Library name: L40V
Liver, neonatal calves (30h after birth)

value: VTM


title: culms under LT treatment for 1 day-3

value: culms


title: DSP-1001660015818-B-H10

first: Scott

last: Ochsner

institute: Baylor College of Medicine

description:
Library name: DSP-1001660015818-B-H10
spatial transcriptomic sequencing

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

value: lung

value: COPD GOLD 3

value: COPD

value: current

tag: gender

value: vessel


title: DSP-1001660020370-C-A09

description:
Library name: DSP-1001660020370-C-A09
spatial transcriptomic sequencing

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

value: SC

value: Smoker

tag: location

value: parenchyma


title: culms under LT treatment for 1 day-2

value: Low temperature (4℃）


title: GW10

address: 暨南大学石牌校区学生宿舍2栋302

description: 10x Genomics

source_name: GW10 kidney

value: Human epithelium

value: 10 weeks old


title: culms before treatment-3


title: DSP-1001660020370-C-A04

description:
Library name: DSP-1001660020370-C-A04
spatial transcriptomic sequencing

value: former

value: male

value: airway

value: oct


title: L4V

description:
Library name: L4V
Liver, neonatal calves (30h after birth)

value: Liver

value: VTM


title: BoMac cells, M.bovisNX2-EVs-12h, rep1

value: BoMac


title: L37C

description:
Library name: L37C
Liver, neonatal calves (30h after birth)

value: CONTROL


title: BoMac cells,M.bovis-NX2-EVs,rep2


title: L34V

description:
Library name: L34V
Liver, neonatal calves (30h after birth)


title: DSP-1001660020370-C-A03

description:
Library name: DSP-1001660020370-C-A03
spatial transcriptomic sequencing

value: lung

value: COPD GOLD 3

value: COPD

value: current


title: culms before treatment-1

value: culms


title: DSP-1001660020370-C-A02

description:
Library name: DSP-1001660020370-C-A02
spatial transcriptomic sequencing

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

value: vessel


title: BoMac cells, M.bovisNX2-EVs-24h, rep2


title: culms under LT treatment for 1 day-1

value: Low temperature (4℃）


title: BoMac cells, Ctrl-EVs-24h, rep2


title: DSP-1001660015818-B-H11

description:
Library name: DSP-1001660015818-B-H11
spatial transcriptomic sequencing


title: BoMac cells, Ctrl-EVs-24h, rep1


title: L25C

description:
Library name: L25C
Liver, neonatal calves (30h after birth)


title: DSP-1001660015818-B-H05

description:
Library name: DSP-1001660015818-B-H05
spatial transcriptomic sequencing

value: parenchyma


title: SNU16 cells, DMSO_rep2

city: Boston

first: Yin

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

description: Library name: SNU-16_DMSO_Rep2.fastq.gz

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Assembly: GRCh37.83
Supplementary files format and content: GC_cell line_quants.csv

growth_protocol: YCCEL1 cells were cultured in EMEM medium (ATCC) with 10% fetal Bovine Serum (FBS)  in a humidified chamber at 37 degrees Celcius with 5% CO2. HGC27 cells were cultured in EMEM with 2mM Glutamine, 1% Non Essential Amino Acids (NEAA) and 10% FBS. SNU719, AGS and SNU16 were cultured in RPMI (Gibco) with 10% FBS.

extract_protocol:
Total RNAs were subsequently isolated using the RNeasy Mini kit (Qiagen) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: Cells were treated with DCB for 72 hours or DMSO as the control.

tag: cell type

value: Gastric cancer

tag: genotype

value: wild type

value: treated with DMSO


title: DSP-1001660015818-B-H04

city: Houston

description:
Library name: DSP-1001660015818-B-H04
spatial transcriptomic sequencing

tag: patient

tag: age

value: male

value: oct


title: SNU16 cells, DMSO_rep1

description: Library name: SNU-16_DMSO_Rep1.fastq.gz


title: AGS cells, DCB_rep2

description: Library name: AGS_DCB_Rep2.fastq.gz

source_name: AGS

value: AGS

value: treated with DCB


title: BoMac cells, M.bovis-NX2EVs-12h, rep3

value: BoMac


title: AGS cells, DCB_rep1

description: Library name: AGS_DCB_Rep1.fastq.gz


title: BoMac cells, M.bovis-NX2EVs-12h, rep2


title: AGS cells, DMSO_rep2

description: Library name: AGS_DMSO_Rep2.fastq.gz


title: BoMac cells, Ctrl-EVs-12h, rep3


title: DSP-1001660015818-B-H09

description:
Library name: DSP-1001660015818-B-H09
spatial transcriptomic sequencing

value: lung

tag: condition

tag: former or_current_smoker


title: AGS cells, DMSO_rep1

description: Library name: AGS_DMSO_Rep1.fastq.gz

tag: cell line


title: BoMac cells, Ctrl-EVs-12h, rep2


title: DSP-1001660015818-B-H08

description:
Library name: DSP-1001660015818-B-H08
spatial transcriptomic sequencing

value: COPD GOLD 3

tag: pack years


title: DSP-1001660015818-B-H01

description:
Library name: DSP-1001660015818-B-H01
spatial transcriptomic sequencing

value: COPD GOLD 2-3

value: COPD

value: former


title: SNU719 cells, DCB_rep1

description: Library name: SNU719_DCB_Rep1.fastq.gz

tag: treatment


title: BoMac cells, Ctrl-EVs-12h, rep1


title: HGC27 cells, DCB_rep2

description: Library name: HGC-27_DCB_Rep2.fastq.gz


title: L31C

description:
Library name: L31C
Liver, neonatal calves (30h after birth)

value: Liver

value: CONTROL


title: HGC27 cells, DCB_rep1

description: Library name: HGC-27_DCB_Rep1.fastq.gz


title: SNU719 cells, DMSO_rep1

description: Library name: SNU719_DMSO_Rep1.fastq.gz


title: HGC27 cells, DMSO_rep2

description: Library name: HGC-27_DMSO_Rep2.fastq.gz


title: DSP-1001660015818-B-H07

description:
Library name: DSP-1001660015818-B-H07
spatial transcriptomic sequencing

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

value: current


title: DSP-1001660015818-B-H06

description:
Library name: DSP-1001660015818-B-H06
spatial transcriptomic sequencing

value: parenchyma


title: L28V

description:
Library name: L28V
Liver, neonatal calves (30h after birth)

value: VTM


title: HGC27 cells, DMSO_rep1

description: Library name: HGC-27_DMSO_Rep1.fastq.gz

value: Gastric cancer

value: wild type

value: treated with DMSO


title: DSP-1001660015818-B-H02

description:
Library name: DSP-1001660015818-B-H02
spatial transcriptomic sequencing

value: male

value: vessel

value: oct


title: SNU16 cells, DCB_rep1

description: Library name: SNU-16_DCB_Rep1.fastq.gz

value: treated with DCB


title: SNU16 cells, DCB_rep2

description: Library name: SNU-16_DCB_Rep2.fastq.gz


title: L22V

description:
Library name: L22V
Liver, neonatal calves (30h after birth)


title: L10V

description:
Library name: L10V
Liver, neonatal calves (30h after birth)


title: DSP-1001660015818-B-H03

description:
Library name: DSP-1001660015818-B-H03
spatial transcriptomic sequencing

value: lung

value: COPD GOLD 3


title: YCCEL1 cells, DCB_rep1

description: Library name: YCCEL1_DCB_Rep1.fastq.gz


title: L1C

description:
Library name: L1C
Liver, neonatal calves (30h after birth)


title: DSP-1001660015818-B-G11

description:
Library name: DSP-1001660015818-B-G11
spatial transcriptomic sequencing

value: COPD GOLD 2-3

value: COPD


title: YCCEL1 cells, DCB_rep2

description: Library name: YCCEL1_DCB_Rep2.fastq.gz


title: L19C

description:
Library name: L19C
Liver, neonatal calves (30h after birth)

value: Liver


title: NC-2

city: Luoyang

first: Yuqing

last: Jiang

state: China

address: No. 263, Kaiyuan Avenue, Luolong District

institute: The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology

description: Library name: SAMPLE5

data_processing:
Fastp was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was also verified using fastp We used Bowtie2 and Tophat2 to map reads to the genome of GRCm39. The mapped reads of each sample were assembled using StringTie. Then, all transcriptome from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the ﬁnal transcriptome was generated, StringTie was used to estimate the expression levels of all transcripts. Transcripts were annotated with known mRNAs, known long non-coding RNAs (lncRNAs) and transcripts shorter than 200 nt were discarded. Then we utilized CPC and CNCI to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts with class code (I, j, o, u, x) were considered as lncRNAs. StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM (FPKM = [total_exon_fragments/mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Approximately 2μg of total RNA was used to remove ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the ribo-minus RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: NC

value: Sertoli


title: YCCEL1 cells, DMSO_rep1

description: Library name: YCCEL1_DMSO_Rep1.fastq.gz


title: L16V

description:
Library name: L16V
Liver, neonatal calves (30h after birth)


title: DSP-1001660015818-B-G12

address: One Baylor Plaza

description:
Library name: DSP-1001660015818-B-G12
spatial transcriptomic sequencing

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

value: former


title: SNU719 cells, DMSO_rep2

description: Library name: SNU719_DMSO_Rep2.fastq.gz


title: L13C

description:
Library name: L13C
Liver, neonatal calves (30h after birth)

value: CONTROL


title: SNU719 cells, DCB_rep2

description: Library name: SNU719_DCB_Rep2.fastq.gz

value: Gastric cancer


title: YCCEL1 cells, DMSO_rep2

description: Library name: YCCEL1_DMSO_Rep2.fastq.gz

value: wild type


title: DSP-1001660015818-B-G08

description:
Library name: DSP-1001660015818-B-G08
spatial transcriptomic sequencing

value: COPD GOLD 2

value: current


title: DSP-1001660015818-B-G10

description:
Library name: DSP-1001660015818-B-G10
spatial transcriptomic sequencing

value: male

value: parenchyma


title: DSP-1001660015818-B-G07

description:
Library name: DSP-1001660015818-B-G07
spatial transcriptomic sequencing

value: oct


title: DSP-1001660015818-B-G09

description:
Library name: DSP-1001660015818-B-G09
spatial transcriptomic sequencing

value: lung

value: vessel


title: DSP-1001660014619-C-G05

description:
Library name: DSP-1001660014619-C-G05
spatial transcriptomic sequencing

value: female

value: airway

value: paraffin


title: DSP-1001660014619-C-G03

description:
Library name: DSP-1001660014619-C-G03
spatial transcriptomic sequencing

value: COPD


title: DSP-1001660014619-C-G04

description:
Library name: DSP-1001660014619-C-G04
spatial transcriptomic sequencing


title: SI-3

description: Library name: SAMPLE3

value: Sertoli


title: NC-1

description: Library name: SAMPLE4

value: NC


title: DSP-1001660015818-B-G06

description:
Library name: DSP-1001660015818-B-G06
spatial transcriptomic sequencing

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


title: SI-1

description: Library name: SAMPLE1


title: SI-2

description: Library name: SAMPLE2


title: DSP-1001660014619-C-G06

description:
Library name: DSP-1001660014619-C-G06
spatial transcriptomic sequencing


title: DSP-1001660014619-C-G07

description:
Library name: DSP-1001660014619-C-G07
spatial transcriptomic sequencing


title: DSP-1001660014619-C-G01

description:
Library name: DSP-1001660014619-C-G01
spatial transcriptomic sequencing

value: COPD GOLD 1-2

value: former


title: DSP-1001660014619-C-G02

description:
Library name: DSP-1001660014619-C-G02
spatial transcriptomic sequencing


title: Pancreatic islets, WT, ADT

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades, INSERM U1151

description:
Library name: WT_adt
Antibody-derived oligonucleotide (ADT)

data_processing:
TOTAL-seq files were demultiplexed using Cellranger mkfastq. Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: CellRanger output files.
Library strategy: CITE-seq

molecule: protein

source_name: Pancreatic islets

extract_protocol:
Single cell solutions were obtained from pancreatic islets isolated from 6-8 C57BL/6J males as previously described. Immune cells were sort-purified as live DAPI-Epcam-CD45+ cells with a FACS ARIA III cell sorter (BD Biosciences) using FACS Diva software (BD Biosciences) and lysed for mRNA extraction. Sorted cells were then centrifuged at 300 rcf for 5 minutes and resuspended in PBS containing 0.04% of Ultrapure BSA (Invitrogen Cat# AM2616).
Isolated cells were then stained with DNA barcoded antibodies (CD9, CD206) TotalSeq-B antibodies.

value: Pancreatic islets

value: CD45+ cells

value: WT

tag: library type

value: ADT


title: DSP-1001660015818-B-G05

description:
Library name: DSP-1001660015818-B-G05
spatial transcriptomic sequencing

value: COPD GOLD 2

value: current

value: male

tag: roi


title: DSP-1001660014619-C-F11

description:
Library name: DSP-1001660014619-C-F11
spatial transcriptomic sequencing

value: lung

value: parenchyma

tag: scan name


title: DSP-1001660014619-C-F12

description:
Library name: DSP-1001660014619-C-F12
spatial transcriptomic sequencing

tag: tissue

value: vessel


title: DSP-1001660014619-C-G09

description:
Library name: DSP-1001660014619-C-G09
spatial transcriptomic sequencing

tag: slide name

value: female

value: paraffin


title: DSP-1001660014619-C-G08

description:
Library name: DSP-1001660014619-C-G08
spatial transcriptomic sequencing

tag: panel

value: COPD


title: DSP-1001660015818-B-G03

description:
Library name: DSP-1001660015818-B-G03
spatial transcriptomic sequencing

tag: gender

value: airway

value: oct


title: DSP-1001660015818-B-G04

description:
Library name: DSP-1001660015818-B-G04
spatial transcriptomic sequencing

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

tag: location


title: DSP-1001660014619-C-F09

description:
Library name: DSP-1001660014619-C-F09
spatial transcriptomic sequencing

value: COPD GOLD 1-2

value: former


title: DSP-1001660014619-C-F10

description:
Library name: DSP-1001660014619-C-F10
spatial transcriptomic sequencing


title: DSP-1001660014619-C-F08

description:
Library name: DSP-1001660014619-C-F08
spatial transcriptomic sequencing


title: Pancreatic islets, WT, mRNA

description:
Library name: WT_mrna
polyA RNA

value: Pancreatic islets

tag: cell type

value: CD45+ cells

value: mRNA


title: DSP-1001660014619-C-F07

description:
Library name: DSP-1001660014619-C-F07
spatial transcriptomic sequencing


title: DSP-1001660014619-C-F05

description:
Library name: DSP-1001660014619-C-F05
spatial transcriptomic sequencing

value: SC

value: Smoker


title: Pancreatic islets, Slc7a11-MacKO

description: Library name: islets_slc7a11_ko

data_processing:
CellRanger mkfastq and count (10x Genomics) were used to align to the mouse genome (mm10) and generate gene-barcode matrices.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix output from CellRanger count

extract_protocol:
Single cell solutions were obtained from pancreatic islets isolated from 6-8 C57BL/6J males as previously described. Immune cells were sort-purified as live DAPI-Epcam-CD45+ cells with a FACS ARIA III cell sorter (BD Biosciences) using FACS Diva software (BD Biosciences) and lysed for mRNA extraction. Sorted cells were then centrifuged at 300 rcf for 5 minutes and resuspended in PBS containing 0.04% of Ultrapure BSA (Invitrogen Cat# AM2616).
Cells were loaded on a Chromium Controller (10x Genomics) with a target output of 3000-4000 cells per condition and RNA-seq libraries were prepared with the Chromium Single Cell 3’ Reagents Kit v3 Library protocol (10x Genomics) according to manufacturer’s guidelines at the CurieCoreTech Next Generation Sequencing (ICGex, Paris, France). After individual qualification and quantification, the libraries were then equimolarly pooled and quantified using a qPCR method (KAPA library quantification kit, Roche). The sequencing was carried out on an Illumina Novaseq 6000 instrument, using paired-end 28x91bp as sequencing mode, at the Curie Genomic Platform (Paris, France). The sequencing configuration was set to reach an average of 50,000 reads per cell.

tag: genotype


title: DSP-1001660014619-C-F06

description:
Library name: DSP-1001660014619-C-F06
spatial transcriptomic sequencing

tag: patient

value: male


title: DSP-1001660014619-C-F04

description:
Library name: DSP-1001660014619-C-F04
spatial transcriptomic sequencing

value: lung

tag: age


title: DSP-1001660015818-B-G01

description:
Library name: DSP-1001660015818-B-G01
spatial transcriptomic sequencing

tag: condition

value: COPD GOLD 2-3

value: never


title: DSP-1001660015818-B-G02

description:
Library name: DSP-1001660015818-B-G02
spatial transcriptomic sequencing

tag: former or_current_smoker

value: female

value: vessel


title: NC-3

description: Library name: SAMPLE6

value: NC

tag: cell line

value: Sertoli


title: DSP-1001660014619-C-E11

description:
Library name: DSP-1001660014619-C-E11
spatial transcriptomic sequencing

tag: pack years

value: paraffin


title: brain tissue, 6-OHG_4

city: xi'an

first: linlin

last: jing

state: Shaanxi

address: NO.277 Yanta West Road, Yanta District

institute: The first affiliated hospital of xi'an jiaotong university

description:
Library name: Sample 13
6_OHG_4

data_processing:
To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced.
We aligned reads of all samples to the reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes.
Assembly: GRCm38/mm10
Supplementary files format and content: FPKMs_allSamples.txt

source_name: brain

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
The libraries were established with RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) and sequenced on a illumina Novaseq 6000 platform, producing a total of millon 2 x 150 bp paired-end reads

value: brain

tag: strain

value: Balb/c

value: 6~8 weeks

tag: Sex

tag: stress

tag: treatment


title: DSP-1001660014619-C-E12

description:
Library name: DSP-1001660014619-C-E12
spatial transcriptomic sequencing

source_name: lung

tag: tissue

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

value: former

tag: roi

tag: scan name


title: brain tissue, 6-OHG_3

description:
Library name: Sample 12
6_OHG_3


title: DSP-1001660015818-B-F12

description:
Library name: DSP-1001660015818-B-F12
spatial transcriptomic sequencing

tag: slide name

tag: panel

value: COPD

tag: gender

value: parenchyma

value: oct


title: DSP-1001660014619-C-E10

description:
Library name: DSP-1001660014619-C-E10
spatial transcriptomic sequencing

value: SC

value: Smoker

value: male

tag: location


title: DSP-1001660014619-C-F03

description:
Library name: DSP-1001660014619-C-F03
spatial transcriptomic sequencing

value: lung

tag: patient


title: brain tissue, 6-OHG_2

description:
Library name: Sample 11
6_OHG_2

tag: age


title: DSP-1001660014619-C-E07

description:
Library name: DSP-1001660014619-C-E07
spatial transcriptomic sequencing

tag: condition

value: airway


title: brain tissue, 6-OHG_1

description:
Library name: Sample 10
6_OHG_1


title: DSP-1001660015818-B-F09

description:
Library name: DSP-1001660015818-B-F09
spatial transcriptomic sequencing

value: COPD GOLD 2-3

tag: former or_current_smoker

value: never

value: female


title: brain tissue, Mod_5

description:
Library name: Sample 9
Mod_5

value: no 6-OHG


title: DSP-1001660014619-C-E08

description:
Library name: DSP-1001660014619-C-E08
spatial transcriptomic sequencing

value: paraffin


title: DSP-1001660015818-B-F08

description:
Library name: DSP-1001660015818-B-F08
spatial transcriptomic sequencing


title: DSP-1001660015818-B-F10

description:
Library name: DSP-1001660015818-B-F10
spatial transcriptomic sequencing


title: DSP-1001660015818-B-F11

description:
Library name: DSP-1001660015818-B-F11
spatial transcriptomic sequencing


title: DSP-1001660014619-C-E05

description:
Library name: DSP-1001660014619-C-E05
spatial transcriptomic sequencing

value: vessel


title: DSP-1001660014619-C-E09

description:
Library name: DSP-1001660014619-C-E09
spatial transcriptomic sequencing


title: DSP-1001660014619-C-E03

description:
Library name: DSP-1001660014619-C-E03
spatial transcriptomic sequencing


title: brain tissue, Mod_4

description:
Library name: Sample 8
Mod_4

value: brain

value: Balb/c

value: 6~8 weeks


title: Pancreatic islets, Slc7a11-MacWT

description: Library name: islets_slc7a11_wt

value: Pancreatic islets

tag: cell type

value: CD45+ cells

tag: genotype


title: DSP-1001660014619-C-D08

description:
Library name: DSP-1001660014619-C-D08
spatial transcriptomic sequencing

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

value: former

tag: pack years


title: brain tissue, Mod_3

description:
Library name: Sample 7
Mod_3

tag: strain

tag: Sex


title: DSP-1001660014619-C-D07

description:
Library name: DSP-1001660014619-C-D07
spatial transcriptomic sequencing

value: SC

value: Smoker


title: DSP-1001660014619-C-E04

description:
Library name: DSP-1001660014619-C-E04
spatial transcriptomic sequencing

value: lung

value: male


title: DSP-1001660015818-B-F05

description:
Library name: DSP-1001660015818-B-F05
spatial transcriptomic sequencing

value: COPD GOLD 2

value: COPD

value: current

value: oct


title: DSP-1001660015818-B-F07

description:
Library name: DSP-1001660015818-B-F07
spatial transcriptomic sequencing

value: COPD GOLD 2-3

value: never

value: female

value: parenchyma


title: DSP-1001660014619-C-D04

description:
Library name: DSP-1001660014619-C-D04
spatial transcriptomic sequencing

value: airway

value: paraffin


title: brain tissue, Mod_2

description:
Library name: Sample 6
Mod_2

value: brain

value: Balb/c

value: 6~8 weeks

tag: stress

tag: treatment

value: no 6-OHG


title: brain tissue, Mod_1

description:
Library name: Sample 5
Mod_1

tag: tissue


title: DSP-1001660014619-C-D06

description:
Library name: DSP-1001660014619-C-D06
spatial transcriptomic sequencing

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

value: SC

value: Smoker

value: former

value: vessel

tag: roi

tag: scan name


title: DSP-1001660015818-B-F03

description:
Library name: DSP-1001660015818-B-F03
spatial transcriptomic sequencing

tag: slide name

value: lung

tag: panel

value: COPD GOLD 2

value: COPD

value: current

value: male


title: DSP-1001660014619-C-D05

description:
Library name: DSP-1001660014619-C-D05
spatial transcriptomic sequencing

tag: gender

tag: location


title: DSP-1001660015818-B-F04

description:
Library name: DSP-1001660015818-B-F04
spatial transcriptomic sequencing

tag: patient

tag: age

value: oct


title: DSP-1001660014619-C-D01

description:
Library name: DSP-1001660014619-C-D01
spatial transcriptomic sequencing

tag: condition

tag: former or_current_smoker

value: airway


title: DSP-1001660014619-C-C11

description:
Library name: DSP-1001660014619-C-C11
spatial transcriptomic sequencing

value: paraffin


title: DSP-1001660015818-B-F02

description:
Library name: DSP-1001660015818-B-F02
spatial transcriptomic sequencing

value: parenchyma


title: DSP-1001660014619-C-C10

description:
Library name: DSP-1001660014619-C-C10
spatial transcriptomic sequencing


title: DSP-1001660014619-C-C12

description:
Library name: DSP-1001660014619-C-C12
spatial transcriptomic sequencing


title: DSP-1001660015818-B-F01

description:
Library name: DSP-1001660015818-B-F01
spatial transcriptomic sequencing


title: brain tissue, Con_3

description:
Library name: Sample 3
Con_3

value: brain

value: Balb/c

value: normal condition


title: DSP-1001660014619-C-C09

description:
Library name: DSP-1001660014619-C-C09
spatial transcriptomic sequencing

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


title: brain tissue, Con_1

description:
Library name: Sample 1
Con_1

value: 6~8 weeks

value: no 6-OHG


title: DSP-1001660014619-C-C07

description:
Library name: DSP-1001660014619-C-C07
spatial transcriptomic sequencing

value: COPD GOLD 4

value: former


title: DSP-1001660015818-B-E12

description:
Library name: DSP-1001660015818-B-E12
spatial transcriptomic sequencing

value: lung


title: DSP-1001660014619-C-B12

description:
Library name: DSP-1001660014619-C-B12
spatial transcriptomic sequencing

value: vessel


title: DSP-1001660014619-C-C06

description:
Library name: DSP-1001660014619-C-C06
spatial transcriptomic sequencing

value: COPD


title: DSP-1001660015818-B-E10

description:
Library name: DSP-1001660015818-B-E10
spatial transcriptomic sequencing

value: COPD GOLD 2

value: current


title: DSP-1001660014619-C-B11

description:
Library name: DSP-1001660014619-C-B11
spatial transcriptomic sequencing

value: male


title: DSP-1001660014619-C-D03

description:
Library name: DSP-1001660014619-C-D03
spatial transcriptomic sequencing

value: SC

value: Smoker

value: airway


title: DSP-1001660014619-C-B10

description:
Library name: DSP-1001660014619-C-B10
spatial transcriptomic sequencing

value: paraffin


title: DSP-1001660014619-C-D02

description:
Library name: DSP-1001660014619-C-D02
spatial transcriptomic sequencing


title: Spinal cord, P15, CNP KO, replicate 2

first: Barbara

last: Delaunay-Piednoir

address: 11 Place Marcelin Berthelot

department: CIRB

institute: INSERM

description: Library name: 12

data_processing:
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting counts, TPM of genes

source_name: Spinal cord

extract_protocol:
RNA was harvest using TRI Reagent® Solution (ThermoFisher)
mRNA library preparation was realized following manufacturers recommendations (KAPA mRNA HyperPrep Kit from Roche). Final samples pooled library prep were sequenced on ILLUMINA Novaseq 6000, corresponding to 2x31Millions of 100bases reads per sample after demultiplexing.

value: Spinal cord

tag: developmental stage

tag: genotype

value: CNP KO


title: DSP-1001660014619-C-B09

description:
Library name: DSP-1001660014619-C-B09
spatial transcriptomic sequencing

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

tag: pack years


title: DSP-1001660015818-B-E09

description:
Library name: DSP-1001660015818-B-E09
spatial transcriptomic sequencing

value: oct


title: DSP-1001660014619-C-B08

description:
Library name: DSP-1001660014619-C-B08
spatial transcriptomic sequencing


title: brain tissue, Con_4

description:
Library name: Sample 4
Con_4

value: brain

tag: strain

value: Balb/c

value: 6~8 weeks

tag: Sex

value: normal condition

value: no 6-OHG


title: Spinal cord, P15, CNP KO, replicate 1

description: Library name: 11


title: DSP-1001660014619-C-B07

description:
Library name: DSP-1001660014619-C-B07
spatial transcriptomic sequencing

value: lung

value: COPD GOLD 4

value: COPD

value: former


title: DSP-1001660015818-B-E08

description:
Library name: DSP-1001660015818-B-E08
spatial transcriptomic sequencing

value: COPD GOLD 2

value: current

value: male


title: DSP-1001660014619-C-B06

description:
Library name: DSP-1001660014619-C-B06
spatial transcriptomic sequencing

value: airway

value: paraffin


title: brain tissue, Con_2

description:
Library name: Sample 2
Con_2

tag: stress

tag: treatment


title: Spinal cord, P15, CNP WT, replicate 3

description: Library name: 200

tag: tissue

value: Spinal cord

value: CNP WT


title: DSP-1001660014619-C-C08

description:
Library name: DSP-1001660014619-C-C08
spatial transcriptomic sequencing

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

value: vessel

tag: roi

tag: scan name


title: DSP-1001660014619-C-A10

description:
Library name: DSP-1001660014619-C-A10
spatial transcriptomic sequencing

tag: slide name

tag: panel

value: COPD3rul_ Arway_ 005


title: DSP-1001660014619-C-B05

description:
Library name: DSP-1001660014619-C-B05
spatial transcriptomic sequencing

tag: gender

tag: location


title: DSP-1001660015818-B-E07

description:
Library name: DSP-1001660015818-B-E07
spatial transcriptomic sequencing

tag: patient

tag: age

value: oct


title: DSP-1001660014619-C-A11

description:
Library name: DSP-1001660014619-C-A11
spatial transcriptomic sequencing

tag: condition

tag: former or_current_smoker

value: COPD3rul_ Arway_ 006


title: Spinal cord, P15, CNP WT, replicate 2

description: Library name: 199

tag: developmental stage

tag: genotype


title: DSP-1001660014619-C-A09

description:
Library name: DSP-1001660014619-C-A09
spatial transcriptomic sequencing

tag: pack years

value: COPD3rul_ Arway_ 004


title: Spinal cord, P15, CNP WT, replicate 1

description: Library name: 197


title: DSP-1001660014619-C-A08

description:
Library name: DSP-1001660014619-C-A08
spatial transcriptomic sequencing

value: lung

value: COPD3rul_ Arway_ 003


title: DSP-1001660015818-B-E06

description:
Library name: DSP-1001660015818-B-E06
spatial transcriptomic sequencing

value: COPD


title: DSP-1001660015818-B-E11

description:
Library name: DSP-1001660015818-B-E11
spatial transcriptomic sequencing

value: parenchyma


title: Spinal cord, P15, CNP KO, replicate 3

description: Library name: 13

value: CNP KO


title: DSP-1001660015818-B-E05

description:
Library name: DSP-1001660015818-B-E05
spatial transcriptomic sequencing

value: COPD GOLD 2

value: current


title: DSP-1001660014619-C-A07

description:
Library name: DSP-1001660014619-C-A07
spatial transcriptomic sequencing

value: COPD GOLD 4

value: former

value: male

value: airway

value: COPD3rul_ Arway_ 002


title: DSP-1001660015818-B-E04

description:
Library name: DSP-1001660015818-B-E04
spatial transcriptomic sequencing

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

value: NSC

value: Non Smoker

value: never

value: vessel


title: DSP-1001660014619-C-A05

description:
Library name: DSP-1001660014619-C-A05
spatial transcriptomic sequencing

value: lung

value: COPD3rul_ Artery _ 004

value: paraffin


title: Spinal cord, P60, replicate 2

description: Library name: 108

value: Spinal cord

value: WT


title: DSP-1001660015818-B-E03

description:
Library name: DSP-1001660015818-B-E03
spatial transcriptomic sequencing

value: parenchyma

value: oct


title: DSP-1001660014619-C-A06

description:
Library name: DSP-1001660014619-C-A06
spatial transcriptomic sequencing

value: COPD GOLD 4

value: COPD

value: COPD3rul_ Arway_ 001


title: Spinal cord, P60, replicate 3

description: Library name: 109


title: DSP-1001660014619-C-A04

description:
Library name: DSP-1001660014619-C-A04
spatial transcriptomic sequencing

value: former

value: male

value: COPD3rul_ Artery _ 003


title: DSP-1001660014619-C-A02

description:
Library name: DSP-1001660014619-C-A02
spatial transcriptomic sequencing

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

value: COPD3rul_ Artery _ 001


title: DSP-1001660014618-B-H10

description:
Library name: DSP-1001660014618-B-H10
spatial transcriptomic sequencing

value: SC

value: Smoker

value: current


title: DSP-1001660015818-B-E01

description:
Library name: DSP-1001660015818-B-E01
spatial transcriptomic sequencing

value: lung

value: NSC

value: Non Smoker

value: never


title: Spinal cord, P15, replicate 2

description: Library name: 134

value: Spinal cord

value: WT


title: DSP-1001660014618-B-H08

description:
Library name: DSP-1001660014618-B-H08
spatial transcriptomic sequencing

value: parenchyma

value: oct


title: DSP-1001660015818-B-D12

description:
Library name: DSP-1001660015818-B-D12
spatial transcriptomic sequencing


title: DSP-1001660015818-B-E02

description:
Library name: DSP-1001660015818-B-E02
spatial transcriptomic sequencing


title: DSP-1001660014618-B-H12

description:
Library name: DSP-1001660014618-B-H12
spatial transcriptomic sequencing

value: vessel


title: DSP-1001660014618-B-H07

description:
Library name: DSP-1001660014618-B-H07
spatial transcriptomic sequencing


title: Spinal cord, P15, replicate 1

description: Library name: 133


title: DSP-1001660015818-B-D11

description:
Library name: DSP-1001660015818-B-D11
spatial transcriptomic sequencing


title: DSP-1001660014618-B-H06

description:
Library name: DSP-1001660014618-B-H06
spatial transcriptomic sequencing


title: Spinal cord, P3, replicate 3

description: Library name: 190


title: DSP-1001660014618-B-H05

description:
Library name: DSP-1001660014618-B-H05
spatial transcriptomic sequencing


title: Spinal cord, P3, replicate 2

description: Library name: 189


title: DSP-1001660014618-B-G10

description:
Library name: DSP-1001660014618-B-G10
spatial transcriptomic sequencing

value: airway


title: DSP-1001660015818-B-D09

description:
Library name: DSP-1001660015818-B-D09
spatial transcriptomic sequencing

value: male


title: DSP-1001660014618-B-G09

description:
Library name: DSP-1001660014618-B-G09
spatial transcriptomic sequencing


title: Spinal cord, P3, replicate 1

description: Library name: 188


title: DSP-1001660015818-B-D10

description:
Library name: DSP-1001660015818-B-D10
spatial transcriptomic sequencing


title: DSP-1001660014618-B-G11

description:
Library name: DSP-1001660014618-B-G11
spatial transcriptomic sequencing


title: Spinal cord, P60, replicate 1

description: Library name: 107


title: DSP-1001660014619-C-A03

description:
Library name: DSP-1001660014619-C-A03
spatial transcriptomic sequencing

value: COPD GOLD 4

value: COPD

value: former

value: COPD3rul_ Artery _ 002

value: paraffin


title: Spinal cord, P15, replicate 3

description: Library name: 135


title: DSP-1001660014618-B-H11

description:
Library name: DSP-1001660014618-B-H11
spatial transcriptomic sequencing

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

value: SC

value: Smoker

value: current


title: DSP-1001660015818-B-D07

description:
Library name: DSP-1001660015818-B-D07
spatial transcriptomic sequencing

value: lung

value: NSC

value: Non Smoker

value: never


title: DSP-1001660015818-B-D05

description:
Library name: DSP-1001660015818-B-D05
spatial transcriptomic sequencing

value: oct


title: DSP-1001660014618-B-G08

description:
Library name: DSP-1001660014618-B-G08
spatial transcriptomic sequencing

value: vessel


title: DSP-1001660014618-B-G03

description:
Library name: DSP-1001660014618-B-G03
spatial transcriptomic sequencing

value: parenchyma


title: DSP-1001660015818-B-D04

description:
Library name: DSP-1001660015818-B-D04
spatial transcriptomic sequencing

value: male


title: Control_EAE_1

city: Bonn

first: Qian

address: Venusberg Campus 1/Gebäude 99

country: Germany

institute: DZNE

description:
Library name: L5
10x Genomics

data_processing:
For the scRNA-seq data, the raw sequencing data for each library were processed using Cell Ranger (10x Genomics, v7.0.0) to generate the gene-by-cell unique molecular identifier (UMI) count matrix. Initially, the FASTQ files generated from the sequencing run were input into the Cell Ranger pipeline. The pipeline was configured to align the reads to the mouse reference genome (GRCm39), which was downloaded from the 10x Genomics website and pre-indexed for compatibility.
Assembly: Mouse mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Spinal Cord

extract_protocol:
The spinal cord was removed from vertebrae and cervical and thoracal parts (C1-Th10) of the spinal cord were used for scRNA-seq experiments. Cells were isolated with a previously established isolation protocol using gentleMACS with the Papain Neural Tissue Dissociation Kit (Miltenyi Biotec) and actinomycin D (catalogue no. A1410, Sigma-Aldrich) at a final concentration of 45 mM. After dissociation, myelin debris was removed from the cell suspension using Myelin Removal Beads II (Miltenyi Biotec). Cells were resuspended in 0.04% BSA + PBS and counted using an automated cell counter (TC20, Bio-Rad).
Chromium Single Cell 3′ Library & Gel Bead Kit v.3.1 (10X Genomics) Single-cell suspensions were loaded on to the Chromium Single Cell Controller using the Chromium Single Cell 3′ Library & Gel Bead Kit v.3.1 (10X Genomics) chemistry following the manufacturer’s instructions. Sample processing and library preparation were performed according to the manufacturer’s instructions using AMPure beads (Beckman-Coulter). Libraries were sequenced on the DNBSEQ Sequencing System (Dresden).

value: Spinal Cord

value: C57/BL6 background, CX3CR1 +/-

value: EAE


title: DSP-1001660014618-B-F11

description:
Library name: DSP-1001660014618-B-F11
spatial transcriptomic sequencing

value: COPD GOLD 2

value: COPD

value: former


title: ABCA1/G1 KO_EAE_2

description:
Library name: L8
10x Genomics

value: C57/BL6 background, CX3CR1 +/-  x  Abca1/g1 flox/flox


title: DSP-1001660014618-B-G06

description:
Library name: DSP-1001660014618-B-G06
spatial transcriptomic sequencing

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

value: COPD GOLD 4

value: paraffin


title: ABCA1/G1 KO_None_1

description:
Library name: L3
10x Genomics


title: DSP-1001660014618-B-H09

description:
Library name: DSP-1001660014618-B-H09
spatial transcriptomic sequencing

value: lung

value: SC

value: Smoker

value: current


title: Control_EAE_2

description:
Library name: L6
10x Genomics