title: Control_None_2

description:
Library name: L2
10x Genomics


title: DSP-1001660014618-B-G05

status: Public on Nov 14 2025

type: SRA

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine

description:
Library name: DSP-1001660014618-B-G05
spatial transcriptomic sequencing

library_source: transcriptomic

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

molecule: total RNA

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

tag: tissue

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: vessel

tag: roi

tag: scan name

value: paraffin


title: DSP-1001660014618-B-F12

description:
Library name: DSP-1001660014618-B-F12
spatial transcriptomic sequencing

value: parenchyma


title: ABCA1/G1 KO_EAE_1

city: Bonn

first: Qian

last: Liu

address: Venusberg Campus 1/Gebäude 99

country: Germany

institute: DZNE

description:
Library name: L7
10x Genomics

library_source: transcriptomic single cell

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

organism: Mus musculus

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

tag: genotype

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

tag: treatment

value: EAE


title: DSP-1001660015818-B-D02

description:
Library name: DSP-1001660015818-B-D02
spatial transcriptomic sequencing

value: NSC

value: Non Smoker

value: never

value: oct


title: DSP-1001660015818-B-D06

description:
Library name: DSP-1001660015818-B-D06
spatial transcriptomic sequencing


title: DSP-1001660014618-B-E12

description:
Library name: DSP-1001660014618-B-E12
spatial transcriptomic sequencing

value: COPD GOLD 2

value: airway


title: DSP-1001660014618-B-G01

description:
Library name: DSP-1001660014618-B-G01
spatial transcriptomic sequencing

value: lung

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


title: DSP-1001660014618-B-G04

description:
Library name: DSP-1001660014618-B-G04
spatial transcriptomic sequencing

value: COPD GOLD 4

value: COPD


title: ABCA1/G1 KO_None_2

description:
Library name: L4
10x Genomics


title: DSP-1001660014618-B-G02

description:
Library name: DSP-1001660014618-B-G02
spatial transcriptomic sequencing

value: former

value: male


title: DSP-1001660014618-B-F10

description:
Library name: DSP-1001660014618-B-F10
spatial transcriptomic sequencing

value: vessel


title: Bone marrow, l-FA HSCs, rep3

city: Chongqing

first: Shuzhen

last: Zhang

address: Gaotanyan zhengjie

country: China

institute: Army Medical University

description: Library name: l_FA3

data_processing:
The first line starts with '@', followed by the Sequence Identifier and an optional description; the second line contains the nucleotide sequence; the third line begins with '+', optionally followed by the Sequence Identifier; the fourth line represents the sequencing quality scores for each base (where the ASCII value of each character minus 33 gives the corresponding quality score)
Paired-end sequence files (fastq) were mapped to the reference genome using  Hisat2   (Hierarchical  Indexing  for  Spliced  Alignment  of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were convertedto BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Differential expression analysis for gene was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis. This choice is motivated by the decision to maximize the sensitivity of this analysis, in order to perform a massive screening and identify candidate genes to be validated with a wider sample population with real-time PCR analysis.
We performed a Gene Ontology (GO) analysis for biological processes, cellular components and molecular function and a KEGG pathway analysis (Kyoto  Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg) via enrich R package.
Assembly: GRCm39.111
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Bone marrow

extract_protocol:
Single-cell    amplification     was     performed     using     SMART-Seq®    HT     Kit(Takara, USA)according to the manufacturer’s instructions. Single cells were lysed in buffer containing free  dNTP and  oligo(dT)  oligonucleotides.  The  RNA fragments  were  copied  into  first  strand cDNA using reverse transcriptase and  several templateless C nucleotides. The oligonucleotide primers  were  then  hybridized  with  poly(C)  to  form  Second  strand  cDNA.  cDNA  was  were purified and enriched by PCR
The  cDNA  librarys  were  constructed  using  the  KAPA Hyper  Prep  Kit（KAPA,  USA） according to the manufacturer’s instructions. Purified libraries were quantified and validated by Qubit® 3.0 Fluorometer and Agilent 2100 bioanalyzer to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).

value: Bone marrow

tag: cell line

value: Hematopoietic stem cells

tag: cell type

value: Stem cells

value: Wild type

value: Isolation of hematopoietic stem cells of l-ferulic acid mice


title: DSP-1001660015818-B-D08

description:
Library name: DSP-1001660015818-B-D08
spatial transcriptomic sequencing

value: NSC

value: Non Smoker


title: DSP-1001660014618-B-F09

description:
Library name: DSP-1001660014618-B-F09
spatial transcriptomic sequencing

value: oct


title: DSP-1001660014618-B-G07

description:
Library name: DSP-1001660014618-B-G07
spatial transcriptomic sequencing

value: paraffin


title: DSP-1001660014618-B-F03

description:
Library name: DSP-1001660014618-B-F03
spatial transcriptomic sequencing

value: COPD GOLD 2


title: DSP-1001660014618-B-F02

description:
Library name: DSP-1001660014618-B-F02
spatial transcriptomic sequencing

value: lung


title: DSP-1001660015818-B-D01

description:
Library name: DSP-1001660015818-B-D01
spatial transcriptomic sequencing

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

value: never

value: parenchyma


title: DSP-1001660014618-B-F01

description:
Library name: DSP-1001660014618-B-F01
spatial transcriptomic sequencing

value: COPD

value: former


title: DSP-1001660014618-B-E10

description:
Library name: DSP-1001660014618-B-E10
spatial transcriptomic sequencing

value: male

value: airway


title: DSP-1001660015818-B-D03

description:
Library name: DSP-1001660015818-B-D03
spatial transcriptomic sequencing


title: DSP-1001660014618-B-E07

description:
Library name: DSP-1001660014618-B-E07
spatial transcriptomic sequencing

value: female

value: vessel


title: DSP-1001660015818-B-C11

description:
Library name: DSP-1001660015818-B-C11
spatial transcriptomic sequencing


title: DSP-1001660015818-B-C10

description:
Library name: DSP-1001660015818-B-C10
spatial transcriptomic sequencing


title: DSP-1001660014618-B-E05

description:
Library name: DSP-1001660014618-B-E05
spatial transcriptomic sequencing


title: Bone marrow, l-FA HSCs, rep1

description: Library name: l_FA1

value: Bone marrow

value: Hematopoietic stem cells

value: Stem cells

value: Wild type


title: Bone marrow, Ctrl HSCs, rep3

description: Library name: Ctrl3

value: Isolation of hematopoietic stem cells of Ctrl mice


title: DSP-1001660015818-B-C09

description:
Library name: DSP-1001660015818-B-C09
spatial transcriptomic sequencing

value: NSC

value: Non Smoker

value: oct


title: DSP-1001660014618-B-E06

description:
Library name: DSP-1001660014618-B-E06
spatial transcriptomic sequencing

value: lung

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


title: DSP-1001660014618-B-E11

description:
Library name: DSP-1001660014618-B-E11
spatial transcriptomic sequencing

value: COPD GOLD 2


title: DSP-1001660014618-B-E08

description:
Library name: DSP-1001660014618-B-E08
spatial transcriptomic sequencing

value: never


title: DSP-1001660015818-B-C08

description:
Library name: DSP-1001660015818-B-C08
spatial transcriptomic sequencing

value: parenchyma


title: Bone marrow, l-FA HSCs, rep2

description: Library name: l_FA2

value: Isolation of hematopoietic stem cells of l-ferulic acid mice


title: DSP-1001660015818-B-C12

description:
Library name: DSP-1001660015818-B-C12
spatial transcriptomic sequencing

value: male

value: airway


title: DSP-1001660014618-B-E02

description:
Library name: DSP-1001660014618-B-E02
spatial transcriptomic sequencing

value: female


title: Control_None_1

description:
Library name: L1
10x Genomics

value: Spinal Cord

value: C57/BL6 background, CX3CR1 +/-


title: Bone marrow, Ctrl HSCs, rep2

description: Library name: Ctrl2

value: Bone marrow

value: Hematopoietic stem cells

value: Stem cells


title: DSP-1001660015818-B-C07

description:
Library name: DSP-1001660015818-B-C07
spatial transcriptomic sequencing

value: COPD GOLD 1

value: COPD

value: former

value: vessel


title: DSP-1001660014618-B-E03

description:
Library name: DSP-1001660014618-B-E03
spatial transcriptomic sequencing

value: lung

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

value: NSC

value: Non Smoker

value: oct


title: DSP-1001660014618-B-E01

description:
Library name: DSP-1001660014618-B-E01
spatial transcriptomic sequencing

value: COPD GOLD 4

value: male

value: paraffin


title: DSP-1001660014618-B-D12

description:
Library name: DSP-1001660014618-B-D12
spatial transcriptomic sequencing


title: DSP-1001660014618-B-E09

description:
Library name: DSP-1001660014618-B-E09
spatial transcriptomic sequencing

value: COPD GOLD 2

value: airway


title: Bone marrow, Ctrl HSCs, rep1

description: Library name: Ctrl1

value: Bone marrow

value: Wild type

value: Isolation of hematopoietic stem cells of Ctrl mice


title: DSP-1001660014618-B-D10

description:
Library name: DSP-1001660014618-B-D10
spatial transcriptomic sequencing

value: parenchyma


title: DSP-1001660014618-B-D11

description:
Library name: DSP-1001660014618-B-D11
spatial transcriptomic sequencing

value: COPD


title: DSP-1001660015818-B-C06

description:
Library name: DSP-1001660015818-B-C06
spatial transcriptomic sequencing

value: COPD GOLD 1

value: former

value: female


title: DSP-1001660014618-B-D09

description:
Library name: DSP-1001660014618-B-D09
spatial transcriptomic sequencing

value: lung

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


title: KE3

city: Suita

first: Sho

last: Matsui

address: Box D11, 2-2 Yamada-oka

department: Nephrology

country: Japan

institute: Osaka University Graduate School of Medicine

description: Library name: Sample 6

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.35 (TRAILING:20 MINLEN:32 SLIDINGWINDOW:10:20 )
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2 v2.1.0
Read counts for each sample were obtained using FeatureCounts v1.4.6
Normalization and significance testing were done using the Bioconductor package, edgeR.
Assembly: Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2 v2.1.0
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

growth_protocol: proximal tubular cells were cultured in DMEM/F-12 medium supplemented wit 10%FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA  Library Prep Kit following manufacturer's protocols.

treatment_protocol: 20uM erastin2 for 24 hours

value: kidney

value: primary

value: proximal tubular epithelial cells

tag: batch


title: DSP-1001660014618-B-E04

description:
Library name: DSP-1001660014618-B-E04
spatial transcriptomic sequencing

tag: slide name

value: NSC

value: Non Smoker

value: never

value: oct


title: DSP-1001660015818-B-C05

description:
Library name: DSP-1001660015818-B-C05
spatial transcriptomic sequencing

tag: tissue


title: DSP-1001660014618-B-D08

description:
Library name: DSP-1001660014618-B-D08
spatial transcriptomic sequencing

tag: panel

value: COPD GOLD 4

value: male

value: paraffin


title: KE2

description: Library name: Sample 5


title: DSP-1001660014618-B-D07

description:
Library name: DSP-1001660014618-B-D07
spatial transcriptomic sequencing

tag: patient

value: vessel


title: DSP-1001660015818-B-C04

description:
Library name: DSP-1001660015818-B-C04
spatial transcriptomic sequencing

tag: age

value: COPD

value: parenchyma


title: DSP-1001660014618-B-D05

description:
Library name: DSP-1001660014618-B-D05
spatial transcriptomic sequencing

tag: condition

value: former


title: KE1

description: Library name: Sample 4


title: DSP-1001660014618-B-D06

description:
Library name: DSP-1001660014618-B-D06
spatial transcriptomic sequencing

tag: former or_current_smoker


title: DSP-1001660014618-B-D04

description:
Library name: DSP-1001660014618-B-D04
spatial transcriptomic sequencing

value: COPD GOLD 1-2

tag: pack years


title: AE3

description: Library name: Sample 3


title: DSP-1001660015818-B-C03

description:
Library name: DSP-1001660015818-B-C03
spatial transcriptomic sequencing

value: lung

value: COPD GOLD 1

tag: gender

value: female


title: DSP-1001660014618-B-D03

description:
Library name: DSP-1001660014618-B-D03
spatial transcriptomic sequencing

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

tag: location


title: DSP-1001660014618-B-D02

description:
Library name: DSP-1001660014618-B-D02
spatial transcriptomic sequencing

tag: roi


title: AE2

description: Library name: Sample 2

value: kidney

value: primary

value: proximal tubular epithelial cells


title: DSP-1001660014618-B-D01

description:
Library name: DSP-1001660014618-B-D01
spatial transcriptomic sequencing

value: airway

tag: scan name


title: DSP-1001660015818-B-C01

description:
Library name: DSP-1001660015818-B-C01
spatial transcriptomic sequencing

value: oct


title: AE1

description: Library name: Sample 1

tag: genotype


title: DSP-1001660014618-B-C12

description:
Library name: DSP-1001660014618-B-C12
spatial transcriptomic sequencing


title: DSP-1001660015818-B-B12

description:
Library name: DSP-1001660015818-B-B12
spatial transcriptomic sequencing


title: DSP-1001660014618-B-C10

description:
Library name: DSP-1001660014618-B-C10
spatial transcriptomic sequencing


title: DSP-1001660014618-B-C11

description:
Library name: DSP-1001660014618-B-C11
spatial transcriptomic sequencing


title: PVN cells, saline group 2

city: Jinan

first: E

state: Shandong Province

address: No. 44, West Wenhua Road, Lixia District, Jinan City, Shandong Province, China

institute: Shandong University School of Basic Medicine

description:
Library name: saline 2
microfluidic chip

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Assembly: GRCm38
Supplementary files format and content: matrix files

source_name: brain

extract_protocol:
For optimal nuclei recovery, PVN was microdissected from control mice (n = 6/sample, 2 samples/group) 3 h post-modeling and were immediately placed in ice-cold PBSE buffer (1× PBS containing 2 mM EGTA). Tissue dissociation was performed using gentle mechanical homogenization followed by enzymatic treatment when necessary. Nuclei isolation was carried out using the GEXSCOPE® Nucleus Isolation Kit (Singleron Biotechnologies), with all steps performed on ice to maintain RNA integrity. The homogenate was sequentially filtered through 100 μm and 40 μm cell strainers to remove debris and obtain single nuclei suspensions. Nuclei viability and concentration were assessed using DAPI staining (1:1000 dilution) and automated cell counting with Trypan Blue exclusion. Only intact, single DAPI-positive nuclei with clear nuclear morphology were selected for downstream processing, with final concentrations adjusted to 1×10⁶ nuclei per 400 μL in nuclei preservation buffer.
The concentration of singlenucleus suspension was adjusted to 3-4 × 105 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads.

treatment_protocol: oral gavage of  saline (saline group)

value: brain

value: 6–8 weeks old

value: brain cells

tag: Sex

tag: treatment

value: Oral gavage with saline


title: PVN cells, saline group 1

description:
Library name: saline  1
microfluidic chip

tag: cell type

value: male


title: DSP-1001660014618-B-C07

description:
Library name: DSP-1001660014618-B-C07
spatial transcriptomic sequencing

value: COPD

value: vessel

value: paraffin


title: DSP-1001660015818-B-B10

description:
Library name: DSP-1001660015818-B-B10
spatial transcriptomic sequencing

value: lung

value: former


title: DSP-1001660014618-B-C09

description:
Library name: DSP-1001660014618-B-C09
spatial transcriptomic sequencing

value: COPD GOLD 1-2


title: DSP-1001660015818-B-B11

description:
Library name: DSP-1001660015818-B-B11
spatial transcriptomic sequencing

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

value: COPD GOLD 1

value: female


title: DSP-1001660014618-B-C08

description:
Library name: DSP-1001660014618-B-C08
spatial transcriptomic sequencing


title: DSP-1001660014618-B-C05

description:
Library name: DSP-1001660014618-B-C05
spatial transcriptomic sequencing

value: parenchyma


title: DSP-1001660014618-B-C06

description:
Library name: DSP-1001660014618-B-C06
spatial transcriptomic sequencing


title: DSP-1001660015818-B-B09

description:
Library name: DSP-1001660015818-B-B09
spatial transcriptomic sequencing


title: PVN cells,  IMQ group 2

first: Yaxiao

state: Shandong

address: Wenhuaxi Road 107

institute: Qilu hospital of Shandong University

description:
Library name: Sample  2
microfluidic chip

molecule: nuclear RNA

extract_protocol:
For optimal nuclei recovery, PVN was microdissected from control/gastritis mice (n = 6/sample, 2 samples/group) 3 h post-modeling and were immediately placed in ice-cold PBSE buffer (1× PBS containing 2 mM EGTA). Tissue dissociation was performed using gentle mechanical homogenization followed by enzymatic treatment when necessary. Nuclei isolation was carried out using the GEXSCOPE® Nucleus Isolation Kit (Singleron Biotechnologies), with all steps performed on ice to maintain RNA integrity. The homogenate was sequentially filtered through 100 μm and 40 μm cell strainers to remove debris and obtain single nuclei suspensions. Nuclei viability and concentration were assessed using DAPI staining (1:1000 dilution) and automated cell counting with Trypan Blue exclusion. Only intact, single DAPI-positive nuclei with clear nuclear morphology were selected for downstream processing, with final concentrations adjusted to 1×10⁶ nuclei per 400 μL in nuclei preservation buffer.
The concentration of singlenucleus suspension was adjusted to 3-4 × 105 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads.

treatment_protocol: Apply IMQ on the back (IMQ group).

value: Apply IMQ on the back


title: DSP-1001660014618-B-C04

description:
Library name: DSP-1001660014618-B-C04
spatial transcriptomic sequencing


title: DSP-1001660015818-B-C02

description:
Library name: DSP-1001660015818-B-C02
spatial transcriptomic sequencing

value: oct


title: DSP-1001660014618-B-C03

description:
Library name: DSP-1001660014618-B-C03
spatial transcriptomic sequencing


title: PVN cells,  IMQ group 1

description:
Library name: Sample  1
microfluidic chip

value: brain


title: Long-lived P14 cells, 35 days post-incubation, biol rep 4

city: Cincinnati

first: Yamato

last: Sajiki

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Long_8

data_processing:
Galaxy (version 24.2.1.dev0) and RStudio
Sequence reads were trimmed for adaptor sequence using Cutadapt (Galaxy).
Mapping was performed with HISAT2 (Galaxy) to align the reads with the mm10 genome, and read counts were generated using featureCounts (Galaxy).
Differential gene expression analysis was performed using DESeq2 (RStudio).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes normalized read counts for each sample.

source_name: Spleen

extract_protocol:
RNA was extracted from sorted naïve CD8 T cell populations using Trizol reagent (Life Technologies) and RNA Clean and Concentrator-5 (Zymo Research). 10-100 ng of total RNA was used for the constraction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Standard Total RNA Pep with Ribo-Zero plus kit following manufacturer's protocols.

value: Spleen

value: CD8 T cells


title: DSP-1001660014618-B-B07

description:
Library name: DSP-1001660014618-B-B07
spatial transcriptomic sequencing


title: Long-lived P14 cells, 35 days post-incubation, biol rep 3

description: Library name: Long_7


title: DSP-1001660015818-B-B08

description:
Library name: DSP-1001660015818-B-B08
spatial transcriptomic sequencing


title: DSP-1001660014618-B-B08

description:
Library name: DSP-1001660014618-B-B08
spatial transcriptomic sequencing


title: DSP-1001660015818-B-B07

description:
Library name: DSP-1001660015818-B-B07
spatial transcriptomic sequencing


title: DSP-1001660014618-B-B06

description:
Library name: DSP-1001660014618-B-B06
spatial transcriptomic sequencing


title: DSP-1001660015818-B-B06

description:
Library name: DSP-1001660015818-B-B06
spatial transcriptomic sequencing


title: DSP-1001660014618-B-B04

description:
Library name: DSP-1001660014618-B-B04
spatial transcriptomic sequencing

value: airway


title: DSP-1001660014618-B-B05

description:
Library name: DSP-1001660014618-B-B05
spatial transcriptomic sequencing

value: male


title: DSP-1001660015818-B-B05

description:
Library name: DSP-1001660015818-B-B05
spatial transcriptomic sequencing

value: COPD


title: DSP-1001660014618-B-B02

description:
Library name: DSP-1001660014618-B-B02
spatial transcriptomic sequencing


title: DSP-1001660014618-B-B01

description:
Library name: DSP-1001660014618-B-B01
spatial transcriptomic sequencing


title: DSP-1001660015818-B-B04

description:
Library name: DSP-1001660015818-B-B04
spatial transcriptomic sequencing


title: DSP-1001660014618-B-A12

description:
Library name: DSP-1001660014618-B-A12
spatial transcriptomic sequencing


title: DSP-1001660014618-B-A11

description:
Library name: DSP-1001660014618-B-A11
spatial transcriptomic sequencing


title: DSP-1001660014618-B-A10

description:
Library name: DSP-1001660014618-B-A10
spatial transcriptomic sequencing

value: NSC/SC

value: Non Smoker

value: vessel


title: DSP-1001660015818-B-B03

description:
Library name: DSP-1001660015818-B-B03
spatial transcriptomic sequencing

value: lung

value: former


title: Fresh P14 cells, 1.5 days post-incubation, biol rep 4

description: Library name: Fresh_4


title: Fresh P14 cells, 1.5 days post-incubation, biol rep 3

description: Library name: Fresh_3


title: DSP-1001660014618-B-A09

description:
Library name: DSP-1001660014618-B-A09
spatial transcriptomic sequencing

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

value: paraffin


title: DSP-1001660015818-B-B02

description:
Library name: DSP-1001660015818-B-B02
spatial transcriptomic sequencing

value: COPD GOLD 1-2

value: female


title: DSP-1001660014618-B-A08

description:
Library name: DSP-1001660014618-B-A08
spatial transcriptomic sequencing

value: parenchyma


title: DSP-1001660014618-B-A07

description:
Library name: DSP-1001660014618-B-A07
spatial transcriptomic sequencing


title: Long-lived P14 cells, 35 days post-incubation, biol rep 2

description: Library name: Long_6


title: Fresh P14 cells, 1.5 days post-incubation, biol rep 2

description: Library name: Fresh_2


title: DSP-1001660014618-B-B03

description:
Library name: DSP-1001660014618-B-B03
spatial transcriptomic sequencing

value: COPD GOLD 1


title: DSP-1001660015818-B-B01

description:
Library name: DSP-1001660015818-B-B01
spatial transcriptomic sequencing

value: oct


title: DSP-1001660015818-B-A12

description:
Library name: DSP-1001660015818-B-A12
spatial transcriptomic sequencing

value: COPD GOLD 2

value: never


title: DSP-1001660014618-B-A05

description:
Library name: DSP-1001660014618-B-A05
spatial transcriptomic sequencing


title: Effector P14 cells derived from fresh P14 cells, Day 5 post-infection, Biol Rep 3

description: Library name: Fresh_3

extract_protocol:
RNA was extracted from sorted naïve CD8 T cell populations using Trizol reagent (Life Technologies) and RNA Clean and Concentrator-5 (Zymo Research).
RNA libraries for RNA-seq were prepared using Illumina Nextera XT DNA Library Prep kit following manufacturer's protocols.

value: Spleen

value: CD8 T cells


title: DSP-1001660014618-B-A06

description:
Library name: DSP-1001660014618-B-A06
spatial transcriptomic sequencing

value: airway


title: DSP-1001660014618-B-A03

description:
Library name: DSP-1001660014618-B-A03
spatial transcriptomic sequencing

value: NSC/SC


title: DSP-1001660014616-A-H10

description:
Library name: DSP-1001660014616-A-H10
spatial transcriptomic sequencing

value: SC

value: Smoker

value: male


title: DSP-1001660014618-B-A04

description:
Library name: DSP-1001660014618-B-A04
spatial transcriptomic sequencing

value: lung

value: Non Smoker

value: former

value: vessel


title: DSP-1001660015818-B-A10

description:
Library name: DSP-1001660015818-B-A10
spatial transcriptomic sequencing

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

value: COPD

value: female


title: Fresh P14 cells, 1.5 days post-incubation, biol rep 1

description: Library name: Fresh_1


title: DSP-1001660014618-B-A02

description:
Library name: DSP-1001660014618-B-A02
spatial transcriptomic sequencing

value: paraffin


title: DSP-1001660015818-B-A11

description:
Library name: DSP-1001660015818-B-A11
spatial transcriptomic sequencing

value: COPD GOLD 2

value: oct


title: DSP-1001660014616-A-H09

description:
Library name: DSP-1001660014616-A-H09
spatial transcriptomic sequencing


title: Long-lived P14 cells, 35 days post-incubation, biol rep 1

description: Library name: Long_5

value: Spleen


title: Effector P14 cells derived from fresh P14 cells, Day 5 post-infection, Biol Rep 2

description: Library name: Fresh_2

value: CD8 T cells


title: Effector P14 cells derived from fresh P14 cells, Day 5 post-infection, Biol Rep 1

description: Library name: Fresh_1


title: DSP-1001660014616-A-H08

description:
Library name: DSP-1001660014616-A-H08
spatial transcriptomic sequencing


title: DSP-1001660015818-B-A09

description:
Library name: DSP-1001660015818-B-A09
spatial transcriptomic sequencing

value: never

value: parenchyma


title: Effector P14 cells derived from long-lived P14 cells, Day 5 post-infection, Biol Rep 3

description: Library name: Long_3


title: DSP-1001660015818-B-A08

description:
Library name: DSP-1001660015818-B-A08
spatial transcriptomic sequencing


title: DSP-1001660014616-A-H06

description:
Library name: DSP-1001660014616-A-H06
spatial transcriptomic sequencing

value: SC


title: DSP-1001660014616-A-H07

description:
Library name: DSP-1001660014616-A-H07
spatial transcriptomic sequencing

value: Smoker


title: Effector P14 cells derived from long-lived P14 cells, Day 5 post-infection, Biol Rep 2

description: Library name: Long_2


title: DSP-1001660014616-A-H03

description:
Library name: DSP-1001660014616-A-H03
spatial transcriptomic sequencing

value: male


title: DSP-1001660014616-A-H05

description:
Library name: DSP-1001660014616-A-H05
spatial transcriptomic sequencing

value: lung


title: DSP-1001660014616-A-H02

description:
Library name: DSP-1001660014616-A-H02
spatial transcriptomic sequencing


title: DSP-1001660015818-B-A06

description:
Library name: DSP-1001660015818-B-A06
spatial transcriptomic sequencing


title: DSP-1001660014616-A-G04

description:
Library name: DSP-1001660014616-A-G04
spatial transcriptomic sequencing


title: DSP-1001660014616-A-H04

description:
Library name: DSP-1001660014616-A-H04
spatial transcriptomic sequencing


title: Effector P14 cells derived from long-lived P14 cells, Day 5 post-infection, Biol Rep 1

description: Library name: Long_1


title: DSP-1001660015818-B-A04

description:
Library name: DSP-1001660015818-B-A04
spatial transcriptomic sequencing

value: airway


title: DSP-1001660015818-B-A05

description:
Library name: DSP-1001660015818-B-A05
spatial transcriptomic sequencing


title: sisox6-2

city: Beijing

first: Xilan

last: Dong

state: Beijing

address: 北京市门头沟区永定镇石龙西路阜外医院西山科研基地

institute: Fuwai hospital

description: Library name: Sample 6

data_processing:
Raw reads were filtered, mapped to the mouse genome (mm10), and analyzed for differential expression using the DESeq2 package in R.
Assembly: mm10
Supplementary files format and content: xlsx file including FPKM values for each Sample

source_name: Primary Vascular smooth muscle cells

extract_protocol:
Total RNA was extracted using TRIzol reagent.
Libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit.

tag: cell line

value: Primary Vascular smooth muscle cells

value: Vascular smooth muscle cells

value: Sox6 knockdown


title: sisox6-4

address: 北京市门头沟区永定镇石龙西路阜外医院西山科研基地

description: Library name: Sample 8


title: DSP-1001660014616-A-G03

description:
Library name: DSP-1001660014616-A-G03
spatial transcriptomic sequencing

tag: slide name

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

value: former

value: vessel


title: DSP-1001660014616-A-G02

description:
Library name: DSP-1001660014616-A-G02
spatial transcriptomic sequencing

tag: tissue

value: female

value: paraffin


title: DSP-1001660014616-A-F11

description:
Library name: DSP-1001660014616-A-F11
spatial transcriptomic sequencing

tag: panel


title: sisox6-3

address: 北京市门头沟区永定镇石龙西路阜外医院西山科研基地

description: Library name: Sample 7


title: sisox6-1

address: 北京市门头沟区永定镇石龙西路阜外医院西山科研基地

description: Library name: Sample 5


title: DSP-1001660014616-A-G01

description:
Library name: DSP-1001660014616-A-G01
spatial transcriptomic sequencing

tag: patient


title: DSP-1001660015818-B-A02

description:
Library name: DSP-1001660015818-B-A02
spatial transcriptomic sequencing

tag: age

value: COPD GOLD 2

value: COPD

value: oct


title: DSP-1001660014616-A-F12

description:
Library name: DSP-1001660014616-A-F12
spatial transcriptomic sequencing

tag: condition


title: DSP-1001660015818-B-A03

description:
Library name: DSP-1001660015818-B-A03
spatial transcriptomic sequencing

tag: former or_current_smoker

value: never


title: DSP-1001660014616-A-F10

description:
Library name: DSP-1001660014616-A-F10
spatial transcriptomic sequencing

value: SC

tag: pack years


title: DSP-1001660014616-A-F09

description:
Library name: DSP-1001660014616-A-F09
spatial transcriptomic sequencing

value: Smoker

tag: gender


title: DSP-1001660014616-A-F08

description:
Library name: DSP-1001660014616-A-F08
spatial transcriptomic sequencing

value: COPD GOLD 1-2

value: male

tag: location


title: nc-4

address: 北京市门头沟区永定镇石龙西路阜外医院西山科研基地

description: Library name: Sample 4

value: WT


title: DSP-1001660015818-B-A07

description:
Library name: DSP-1001660015818-B-A07
spatial transcriptomic sequencing

value: lung

value: parenchyma

tag: roi


title: DSP-1001660014616-A-H01

description:
Library name: DSP-1001660014616-A-H01
spatial transcriptomic sequencing

tag: scan name


title: nc-2

address: 北京市门头沟区永定镇石龙西路阜外医院西山科研基地

description: Library name: Sample 2

value: Primary Vascular smooth muscle cells

value: Vascular smooth muscle cells

tag: genotype


title: 18_0.16uM_1

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

description:
Library name: 8546-AT-2_TGCTCCGT-TCGGTCAA
18_0.16uM_1

data_processing:
Sequencing read quality was assessed via FastQC and MultiQC.
Reads were aligned to a splice junction aware build of the human genome (GRCh38) using STAR.
Aligned reads were assigned to genes using featureCounts, where multimapping and multi-overlapping reads were not counted.
Assembly: GRCh38
Supplementary files format and content: the counts per million reads per sample

growth_protocol: SH-SY5Y cells were cultured and expanded at passage 39 for this experiment. Cells were plated in clear 15cm dishes, one per replicate (Corning) and differentiated according to previsouly published protocols (Shipley, et al., 2016).

extract_protocol:
On days 6, 9, 12, 15, and 18, 3 replicates from each exposure condition were collected. Cells were detached from the dish using Tryp-LE, pelleted, and lysed in Buffer RLT Plus (Qiagen). RNA was extracted from the lysate using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen).
A tagmentation reaction adds the well specific barcode to the cDNA from each well. The tagmented cDNAs are then pooled prior to library preparation, where plate specific barcodes can also be incorporated for ultrahigh sample multiplexing prior to sequencing. For example, 384 wells of treated samples would be processed across 4 custom 96 well plates, where each of the samples receives a well specific barcode and each of the 4 plates receives a plate specific barcode. This leads to each of the 384 samples receiving a unique combination of well and plate barcodes, which can be bioinformatically deconvoluted following sequencing.

treatment_protocol: Cells were exposed to a range of Pb concentrations (0uM, 0.16uM, 1.26uM, or 10uM Pb) beginning on Day 5 of neural differentiation. Exposure continued for the remainder of the 18 day protocol, with fresh Pb added at each media change (i.e., every 2-3 days)

tag: day

value: Human neuroblastoma

tag: replicate


title: DSP-1001660014616-A-F07

description:
Library name: DSP-1001660014616-A-F07
spatial transcriptomic sequencing

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

value: former

value: vessel


title: DSP-1001660014616-A-F04

description:
Library name: DSP-1001660014616-A-F04
spatial transcriptomic sequencing

value: paraffin


title: 18_1.26uM_1

description:
Library name: 8546-AT-2_TCAAGGAT-TCGGTCAA
18_1.26uM_1

tag: cell type

tag: treatment


title: nc-3

address: 北京市门头沟区永定镇石龙西路阜外医院西山科研基地

description: Library name: Sample 3

tag: cell line


title: DSP-1001660014616-A-F05

description:
Library name: DSP-1001660014616-A-F05
spatial transcriptomic sequencing

tag: slide name

tag: tissue

value: COPD


title: DSP-1001660014616-A-F06

description:
Library name: DSP-1001660014616-A-F06
spatial transcriptomic sequencing

tag: panel

tag: patient


title: DSP-1001660014616-A-E10

description:
Library name: DSP-1001660014616-A-E10
spatial transcriptomic sequencing

tag: age

tag: condition


title: DSP-1001660014616-A-E09

description:
Library name: DSP-1001660014616-A-E09
spatial transcriptomic sequencing

tag: former or_current_smoker

tag: pack years


title: nc-1

address: 北京市门头沟区永定镇石龙西路阜外医院西山科研基地

description: Library name: Sample 1


title: 18_10uM_2

description:
Library name: 8546-AT-2_GATGAGAA-TCGGTCAA
18_10uM_2


title: DSP-1001660014616-A-E07

description:
Library name: DSP-1001660014616-A-E07
spatial transcriptomic sequencing

tag: gender

tag: location

value: airway


title: DSP-1001660014616-A-E08

description:
Library name: DSP-1001660014616-A-E08
spatial transcriptomic sequencing

tag: roi

tag: scan name


title: CC030 ILC2 AR420626 Mouse 4 Day 6

city: Nashville

first: Mark

last: Rusznak

state: Tennessee

address: 1161 21st Ave S

department: Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine

institute: Vanderbilt University Medical Center

description: Library name: 10646-MR-19

data_processing:
We conducted RNA-Seq analysis on both C57BL6J and CC030GeniUnc mice. Sequencing data quality was initially assessed using FastQC 87, followed by read trimming with fastp 88. For the C57BL/6J samples, reads were aligned to the mm10 reference genome using STAR 89 with default parameters. For the CC030 samples, reads were aligned to the mm9 reference pseudogenome using STAR with default parameters, after which lapels 90 was used to convert the alignments to mm10 reference coordinates. Gene expression counts were subsequently quantified across all samples using HTSeq 91.
Assembly: C57BL6J samples: mm10, CC030GeniUnc samples: mm9 reference pseudogenome
Supplementary files format and content: CSV files with raw read counts

source_name: Lung

growth_protocol: Experiment 1: (C57BL6J ILC2 1-3, CC030GeniUnc 1-3) cells were not grown. RNA-processing occurred immediately after flow sorting. Experiment 2: ILC2s were isolated by flow cytometry from 5 individual CC030GeniUnc mice. Cells from each biological replicate were kept separate and were grown in media (RPMI w/ 10% FBS, Penicillin/Streptomycin, HEPES, Sodium Pyruvate, and β-mercaptoethanol). Cells were cultured at a density of 3,000 cells per well on a 96-well non-tissue culture plate. IL-33 (10ng/mL), TSLP (10ng/mL) and hIL-2 (100U/mL) were added to all cultures. Either DMSO vehicle or AR420626 (10uM) were added to cells from each biological replicate (for paired analysis). Cells were harvested at Day 2 and Day 6 of culture.

extract_protocol:
ILC2s were suspended in Single Cell Lysis Buffer (Takara), ILC2 were sorted into Single Cell Lysis Buffer (Takara), and subsequent library preparation and sequencing was performed at the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core lab. The SMART-Seq v4 Ultra Low Input RNA Kit (Takara) was used to isolate RNA.
The SMART-Seq v4 Ultra Low Input RNA Kit (Takara) was used to isolate RNA. cDNA was generated from extracted RNA through reverse transcription. cDNA was fragmented, blunt-ended, and adenylated for adaptor ligation and subsequently PCR amplified. Amplified cDNA libraries were quality controlled by bioanalyzer.

value: Lung

value: primary cells

tag: genotype

value: WT CC030GeniUnc


title: 18_0uM_2

description:
Library name: 8546-AT-2_CTCTCAGG-TCGGTCAA
18_0uM_2

tag: day

tag: replicate


title: CC030 ILC2 AR420626 Mouse 5 Day 6

description: Library name: 10646-MR-20

tag: cell type

tag: treatment


title: 18_0.16uM_2

description:
Library name: 8546-AT-2_CGAGCATT-TCGGTCAA
18_0.16uM_2

tag: cell line


title: DSP-1001660014616-A-E06

description:
Library name: DSP-1001660014616-A-E06
spatial transcriptomic sequencing

tag: slide name

tag: tissue

value: COPD GOLD 1-2


title: DSP-1001660014616-A-E05

description:
Library name: DSP-1001660014616-A-E05
spatial transcriptomic sequencing

tag: panel

tag: patient

value: male


title: DSP-1001660014616-A-E04

description:
Library name: DSP-1001660014616-A-E04
spatial transcriptomic sequencing

tag: age

tag: condition


title: 18_1.26uM_3

description:
Library name: 8546-AT-2_CAGAGTGG-TCGGTCAA
18_1.26uM_3

value: WT


title: CC030 ILC2 AR420626 Mouse 3 Day 6

description: Library name: 10646-MR-18


title: DSP-1001660014616-A-E02

description:
Library name: DSP-1001660014616-A-E02
spatial transcriptomic sequencing

value: lung

value: NSC

value: Non Smoker

tag: former or_current_smoker

value: never

tag: pack years


title: CC030 ILC2 AR420626 Mouse 2 Day 6

description: Library name: 10646-MR-17


title: DSP-1001660014616-A-E03

description:
Library name: DSP-1001660014616-A-E03
spatial transcriptomic sequencing

tag: gender

tag: location


title: DSP-1001660014616-A-E01

description:
Library name: DSP-1001660014616-A-E01
spatial transcriptomic sequencing

value: parenchyma

tag: roi

tag: scan name


title: 18_0uM_3

description:
Library name: 8546-AT-2_CACCGCAA-TCGGTCAA
18_0uM_3

tag: day

value: Human neuroblastoma

tag: genotype


title: 18_10uM_1

description:
Library name: 8546-AT-2_TTGGCTGC-TCGGTCAA
18_10uM_1

tag: cell type

tag: replicate


title: DSP-1001660014616-A-D12

description:
Library name: DSP-1001660014616-A-D12
spatial transcriptomic sequencing

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


title: CC030 ILC2 AR420626 Mouse 1 Day 6

description: Library name: 10646-MR-16

tag: cell line

tag: treatment


title: DSP-1001660014616-A-D11

description:
Library name: DSP-1001660014616-A-D11
spatial transcriptomic sequencing

tag: slide name

tag: tissue


title: 18_1.26uM_2

description:
Library name: 8546-AT-2_CAAGTGAC-TCGGTCAA
18_1.26uM_2


title: DSP-1001660014616-A-D08

description:
Library name: DSP-1001660014616-A-D08
spatial transcriptomic sequencing

tag: panel

tag: patient

value: vessel


title: DSP-1001660014616-A-D07

description:
Library name: DSP-1001660014616-A-D07
spatial transcriptomic sequencing

tag: age

tag: condition

value: paraffin


title: DSP-1001660014616-A-D09

description:
Library name: DSP-1001660014616-A-D09
spatial transcriptomic sequencing

tag: former or_current_smoker

tag: pack years


title: CC030 ILC2 Vehicle Mouse 4 Day 6

description: Library name: 10646-MR-14

value: IL-33, TSLP, IL-2 + DMSO Vehicle


title: 18_10uM_3

description:
Library name: 8546-AT-2_ATGACACC-TCGGTCAA
18_10uM_3


title: CC030 ILC2 Vehicle Mouse 3 Day 6

description: Library name: 10646-MR-13


title: 12_0uM_2

description:
Library name: 8546-AT-1_TTCACACT-TCGGTCAA
12_0uM_2


title: CC030 ILC2 Vehicle Mouse 2 Day 6

description: Library name: 10646-MR-12


title: DSP-1001660014616-A-D05

description:
Library name: DSP-1001660014616-A-D05
spatial transcriptomic sequencing

tag: gender

tag: location

value: airway


title: DSP-1001660014616-A-D03

description:
Library name: DSP-1001660014616-A-D03
spatial transcriptomic sequencing

value: SC

value: Smoker

value: former

tag: roi

tag: scan name


title: DSP-1001660014616-A-D10

description:
Library name: DSP-1001660014616-A-D10
spatial transcriptomic sequencing


title: DSP-1001660014616-A-D02

description:
Library name: DSP-1001660014616-A-D02
spatial transcriptomic sequencing


title: DSP-1001660014616-A-D04

description:
Library name: DSP-1001660014616-A-D04
spatial transcriptomic sequencing


title: CC030 ILC2 AR420626 Mouse 5 Day 2

description: Library name: 10646-MR-10

value: Lung

value: primary cells

tag: genotype

value: WT CC030GeniUnc


title: DSP-1001660014616-A-D01

description:
Library name: DSP-1001660014616-A-D01
spatial transcriptomic sequencing

value: lung

value: male


title: 18_0uM_1

description:
Library name: 8546-AT-2_ACGAAGCG-TCGGTCAA
18_0uM_1

tag: day

tag: cell type

value: WT


title: DSP-1001660014616-A-C10

description:
Library name: DSP-1001660014616-A-C10
spatial transcriptomic sequencing


title: 6_1.26uM_1

description:
Library name: 8546-AT-1_TGGTGGAA-TCGGTCAA
6_1.26uM_1

tag: cell line

tag: replicate


title: CC030 ILC2 Vehicle Mouse 1 Day 6

description: Library name: 10646-MR-11

tag: treatment


title: CC030 ILC2 AR420626 Mouse 4 Day 2

description: Library name: 10646-MR-09

tag: tissue


title: DSP-1001660014616-A-D06

description:
Library name: DSP-1001660014616-A-D06
spatial transcriptomic sequencing

tag: slide name

tag: panel

value: NSC

value: Non Smoker

value: never


title: 6_0.16uM_2

description:
Library name: 8546-AT-1_TGGTGACT-TCGGTCAA
6_0.16uM_2

value: Human neuroblastoma


title: CC030 ILC2 AR420626 Mouse 3 Day 2

description: Library name: 10646-MR-08


title: DSP-1001660014616-A-C08

description:
Library name: DSP-1001660014616-A-C08
spatial transcriptomic sequencing

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

tag: patient

tag: age

value: vessel


title: 15_1.26uM_2

description:
Library name: 8546-AT-1_TGGTACAG-TCGGTCAA
15_1.26uM_2


title: DSP-1001660014616-A-C05

description:
Library name: DSP-1001660014616-A-C05
spatial transcriptomic sequencing

tag: condition

tag: former or_current_smoker

value: paraffin


title: CC030 ILC2 Vehicle Mouse 5 Day 6

description: Library name: 10646-MR-15

value: IL-33, TSLP, IL-2 + DMSO Vehicle


title: DSP-1001660014616-A-C03

description:
Library name: DSP-1001660014616-A-C03
spatial transcriptomic sequencing

value: SC

tag: pack years

tag: gender

value: airway


title: 9_10uM_3

description:
Library name: 8546-AT-1_TGAATGTG-TCGGTCAA
9_10uM_3


title: DSP-1001660014616-A-C01

description:
Library name: DSP-1001660014616-A-C01
spatial transcriptomic sequencing

value: Smoker

value: former

tag: location

tag: roi


title: CC030 ILC2 Vehicle Mouse 5 Day 2

description: Library name: 10646-MR-05

value: Lung

value: primary cells

tag: genotype


title: CC030 ILC2 AR420626 Mouse 2 Day 2

description: Library name: 10646-MR-07

value: WT CC030GeniUnc


title: CC030 ILC2 AR420626 Mouse 1 Day 2

description: Library name: 10646-MR-06


title: 12_10uM_2

description:
Library name: 8546-AT-1_TGTAAGAC-TCGGTCAA
12_10uM_2

tag: day


title: 9_10uM_2

description:
Library name: 8546-AT-1_TCTATTGG-TCGGTCAA
9_10uM_2

tag: cell type


title: DSP-1001660014616-A-B12

description:
Library name: DSP-1001660014616-A-B12
spatial transcriptomic sequencing

value: lung

value: male

tag: scan name

value: oct


title: DSP-1001660014616-A-B11

description:
Library name: DSP-1001660014616-A-B11
spatial transcriptomic sequencing


title: 12_0.16uM_1

description:
Library name: 8546-AT-1_TCCTATCT-TCGGTCAA
12_0.16uM_1

tag: cell line

value: WT

tag: replicate


title: DSP-1001660014616-A-C04

description:
Library name: DSP-1001660014616-A-C04
spatial transcriptomic sequencing

tag: tissue


title: CC030 ILC2 Vehicle Mouse 3 Day 2

description: Library name: 10646-MR-03

tag: treatment


title: CC030 ILC2 Vehicle Mouse 4 Day 2

description: Library name: 10646-MR-04


title: DSP-1001660014616-A-B10

description:
Library name: DSP-1001660014616-A-B10
spatial transcriptomic sequencing

tag: slide name

tag: panel


title: DSP-1001660014616-A-C02

description:
Library name: DSP-1001660014616-A-C02
spatial transcriptomic sequencing

tag: patient

tag: age


title: DSP-1001660014616-A-B09

description:
Library name: DSP-1001660014616-A-B09
spatial transcriptomic sequencing

tag: condition

value: COPD GOLD 2

value: COPD

tag: former or_current_smoker


title: DSP-1001660014616-A-B08

description:
Library name: DSP-1001660014616-A-B08
spatial transcriptomic sequencing

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

tag: pack years

tag: gender


title: DSP-1001660014616-A-A10

description:
Library name: DSP-1001660014616-A-A10
spatial transcriptomic sequencing

tag: location

tag: roi


title: CC030 ILC2 Vehicle Mouse 2 Day 2

description: Library name: 10646-MR-02

tag: genotype


title: 15_10uM_3

description:
Library name: 8546-AT-1_TGAACTCT-TCGGTCAA
15_10uM_3

tag: day

tag: cell type

value: Human neuroblastoma


title: DSP-1001660014616-A-A09

description:
Library name: DSP-1001660014616-A-A09
spatial transcriptomic sequencing

tag: scan name


title: DSP-1001660014616-A-A08

description:
Library name: DSP-1001660014616-A-A08
spatial transcriptomic sequencing


title: CC030 ILC2 Vehicle Mouse 1 Day 2

description: Library name: 10646-MR-01

tag: cell line


title: 9_0.16uM_2

description:
Library name: 8546-AT-1_GTTGACAG-TCGGTCAA
9_0.16uM_2

tag: replicate


title: DSP-1001660014616-A-A06

description:
Library name: DSP-1001660014616-A-A06
spatial transcriptomic sequencing

tag: tissue


title: DSP-1001660014616-A-A07

description:
Library name: DSP-1001660014616-A-A07
spatial transcriptomic sequencing

tag: slide name


title: CC030GeniUnc 3

description: Library name: 9537-MR-0006

tag: treatment


title: DSP-1001660014616-A-A05

description:
Library name: DSP-1001660014616-A-A05
spatial transcriptomic sequencing

tag: panel

tag: patient


title: CC030GeniUnc 2

description: Library name: 9537-MR-0005


title: 15_0.16uM_2

description:
Library name: 8546-AT-1_GTTCGTCT-TCGGTCAA
15_0.16uM_2


title: DSP-1001660014616-A-A04

description:
Library name: DSP-1001660014616-A-A04
spatial transcriptomic sequencing

tag: age

tag: condition


title: DSP-1001660014616-A-A03

description:
Library name: DSP-1001660014616-A-A03
spatial transcriptomic sequencing

tag: former or_current_smoker

tag: pack years

value: UA22_AIRWAY LF 004


title: 9_1.26uM_3

description:
Library name: 8546-AT-1_GTTAAGCA-TCGGTCAA
9_1.26uM_3


title: 12_1.26uM_2

description:
Library name: 8546-AT-1_TCAGATAC-TCGGTCAA
12_1.26uM_2


title: CC030GeniUnc 1

description: Library name: 9537-MR-0004


title: DSP-1001660014616-A-A02

description:
Library name: DSP-1001660014616-A-A02
spatial transcriptomic sequencing

tag: gender

tag: location

value: parenchyma


title: DSP-1001660011973-F-H09

description:
Library name: DSP-1001660011973-F-H09
spatial transcriptomic sequencing

value: COPD GOLD 4

value: vessel

tag: roi

value: paraffin


title: 9_0uM_2

description:
Library name: 8546-AT-1_GTACCAGC-TCGGTCAA
9_0uM_2

tag: day

tag: genotype


title: C57BL6J ILC2 3

description: Library name: 9537-MR-0003

tag: cell type

value: WT C57BL6J


title: 12_0.16uM_3

description:
Library name: 8546-AT-1_GGTGTGAC-TCGGTCAA
12_0.16uM_3

tag: cell line


title: DSP-1001660011973-F-H06

description:
Library name: DSP-1001660011973-F-H06
spatial transcriptomic sequencing

value: former

tag: scan name


title: 12_1.26uM_3

description:
Library name: 8546-AT-1_TACAGAGT-TCGGTCAA
12_1.26uM_3

tag: replicate


title: C57BL6J ILC2 2

description: Library name: 9537-MR-0002

tag: tissue

value: Lung

value: primary cells


title: DSP-1001660011973-F-H05

description:
Library name: DSP-1001660011973-F-H05
spatial transcriptomic sequencing

tag: slide name

value: lung


title: 6_1.26uM_3

description:
Library name: 8546-AT-1_GGCTCCTA-TCGGTCAA
6_1.26uM_3

tag: treatment


title: DSP-1001660011973-F-H04

description:
Library name: DSP-1001660011973-F-H04
spatial transcriptomic sequencing

tag: panel

tag: patient

value: male


title: GCKR mutation carried sHLOs treated with TLC-2716_3

city: Lausanne

first: Xiaoxu

last: Li

address: Station 15 - CH

country: Switzerland

institute: EPFL

description: Library name: sample12

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads
For the human liver organoid samples, sequenced reads were mapped to the GRCh38 assembly of the human genome using ensembl release 113 gene annotation with STAR aligner version 2.7.3a
Read counts were generated using STAR aligner
Assembly: GRCh38, v113
Supplementary files format and content: tab-delimited excel file includes raw counts per samples

source_name: Human liver organoids

extract_protocol:
RNA was extracted in Trizol and purified using NucleoSpin RNA purification kit (MACHEREY-NAGEL). mRNA concentration was measured for all samples. All samples passed a quality check of purity (NanoDrop) and fragmentation (FragmentAnalyzer).
BGISEQ-500 library construction was performed by BGI

value: Human liver organoids

value: GCKR rs1260326 TT


title: DSP-1001660011973-F-H03

description:
Library name: DSP-1001660011973-F-H03
spatial transcriptomic sequencing

tag: age

tag: condition


title: 18_0.16uM_3

description:
Library name: 8546-AT-2_ACCGTTCC-TCGGTCAA
18_0.16uM_3

value: WT


title: DSP-1001660011973-F-H02

description:
Library name: DSP-1001660011973-F-H02
spatial transcriptomic sequencing

value: COPD

tag: former or_current_smoker

tag: pack years


title: GCKR mutation carried sHLOs treated with TLC-2716_2

description: Library name: sample11


title: DSP-1001660011973-F-H01

description:
Library name: DSP-1001660011973-F-H01
spatial transcriptomic sequencing

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

tag: gender

tag: location


title: DSP-1001660011973-F-G12

description:
Library name: DSP-1001660011973-F-G12
spatial transcriptomic sequencing

tag: roi


title: 12_10uM_1

description:
Library name: 8546-AT-1_CTTGTTGG-TCGGTCAA
12_10uM_1

tag: day

value: Human neuroblastoma

tag: genotype


title: GCKR mutation carried sHLOs treated with TLC-2716_1

description: Library name: sample10


title: DSP-1001660011973-F-H08

description:
Library name: DSP-1001660011973-F-H08
spatial transcriptomic sequencing


title: 6_1.26uM_2

description:
Library name: 8546-AT-1_CTGTACGC-TCGGTCAA
6_1.26uM_2

tag: cell line

tag: cell type


title: DSP-1001660011973-F-H07

description:
Library name: DSP-1001660011973-F-H07
spatial transcriptomic sequencing

tag: scan name


title: GCKR mutation carried sHLOs treated with vehicle_3

description: Library name: sample9

tag: tissue

value: DMSO


title: DSP-1001660011973-F-G10

description:
Library name: DSP-1001660011973-F-G10
spatial transcriptomic sequencing

tag: slide name

value: parenchyma


title: 12_10uM_3

description:
Library name: 8546-AT-1_CTGGTCGT-TCGGTCAA
12_10uM_3

tag: treatment

tag: replicate


title: DSP-1001660011973-F-G09

description:
Library name: DSP-1001660011973-F-G09
spatial transcriptomic sequencing

tag: panel

tag: patient

value: COPD GOLD 4


title: DSP-1001660011973-F-G08

description:
Library name: DSP-1001660011973-F-G08
spatial transcriptomic sequencing

tag: age

tag: condition


title: DSP-1001660011973-F-G07

description:
Library name: DSP-1001660011973-F-G07
spatial transcriptomic sequencing

tag: former or_current_smoker

tag: pack years


title: 15_0uM_1

description:
Library name: 8546-AT-1_CTCGTACA-TCGGTCAA
15_0uM_1


title: DSP-1001660011973-F-G06

description:
Library name: DSP-1001660011973-F-G06
spatial transcriptomic sequencing

tag: gender

tag: location


title: 6_0.16uM_1

description:
Library name: 8546-AT-1_GGAGCTAT-TCGGTCAA
6_0.16uM_1

tag: day


title: Wild-type sHLO treated with TLC-2716_3

description: Library name: sample6

tag: genotype

value: GCKR rs1260326 CC


title: DSP-1001660011973-F-G04

description:
Library name: DSP-1001660011973-F-G04
spatial transcriptomic sequencing

value: airway

tag: roi

value: paraffin


title: DSP-1001660011973-F-G03

description:
Library name: DSP-1001660011973-F-G03
spatial transcriptomic sequencing

value: former


title: DSP-1001660011973-F-G11

description:
Library name: DSP-1001660011973-F-G11
spatial transcriptomic sequencing


title: Wild-type sHLO treated with TLC-2716_2

description: Library name: sample5


title: 15_10uM_2

description:
Library name: 8546-AT-1_CGCTCTTG-TCGGTCAA
15_10uM_2

tag: cell line

tag: cell type


title: DSP-1001660011973-F-F12

description:
Library name: DSP-1001660011973-F-F12
spatial transcriptomic sequencing

tag: tissue

tag: scan name


title: GCKR mutation carried sHLOs treated with vehicle_2

description: Library name: sample8

tag: treatment


title: 9_1.26uM_2

description:
Library name: 8546-AT-1_CGACTAGC-TCGGTCAA
9_1.26uM_2

tag: replicate


title: DSP-1001660011973-F-F10

description:
Library name: DSP-1001660011973-F-F10
spatial transcriptomic sequencing

tag: slide name

tag: panel


title: DSP-1001660011973-F-F11

description:
Library name: DSP-1001660011973-F-F11
spatial transcriptomic sequencing

tag: patient

tag: age


title: Wild-type sHLO treated with vehicle_3

description: Library name: sample3


title: 6_0uM_2

description:
Library name: 8546-AT-1_CCTTATGT-TCGGTCAA
6_0uM_2


title: Wild-type sHLO treated with TLC-2716_1

description: Library name: sample4


title: DSP-1001660011973-F-F09

description:
Library name: DSP-1001660011973-F-F09
spatial transcriptomic sequencing

tag: condition

value: COPD GOLD 2

tag: former or_current_smoker

value: vessel


title: Wild-type sHLO treated with vehicle_2

description: Library name: sample2


title: DSP-1001660011973-F-F08

description:
Library name: DSP-1001660011973-F-F08
spatial transcriptomic sequencing

value: lung

tag: pack years

tag: gender


title: GCKR mutation carried sHLOs treated with vehicle_1

description: Library name: sample7


title: DSP-1001660011973-F-F07

description:
Library name: DSP-1001660011973-F-F07
spatial transcriptomic sequencing

value: male

tag: location


title: 9_0.16uM_1

description:
Library name: 8546-AT-1_CCTGTTAC-TCGGTCAA
9_0.16uM_1

tag: day

tag: genotype


title: 6_10uM_3

description:
Library name: 8546-AT-1_CGTCTGAA-TCGGTCAA
6_10uM_3

tag: cell line


title: 15_0uM_2

description:
Library name: 8546-AT-1_CGTAATTC-TCGGTCAA
15_0uM_2

tag: cell type


title: Wild-type sHLO treated with vehicle_1

description: Library name: sample1

tag: tissue

value: Human liver organoids


title: 6_0.16uM_3

description:
Library name: 8546-AT-1_CCGAGTTA-TCGGTCAA
6_0.16uM_3


title: DSP-1001660011973-F-F05

description:
Library name: DSP-1001660011973-F-F05
spatial transcriptomic sequencing

tag: roi

tag: scan name


title: DSP-1001660011973-F-F06

description:
Library name: DSP-1001660011973-F-F06
spatial transcriptomic sequencing


title: DSP-1001660011973-F-G01

description:
Library name: DSP-1001660011973-F-G01
spatial transcriptomic sequencing


title: DSP-1001660011973-F-G02

description:
Library name: DSP-1001660011973-F-G02
spatial transcriptomic sequencing


title: DSP-1001660011973-F-F04

description:
Library name: DSP-1001660011973-F-F04
spatial transcriptomic sequencing


title: DSP-1001660011973-F-F02

description:
Library name: DSP-1001660011973-F-F02
spatial transcriptomic sequencing


title: Cardiac-specific YY1 KO mouse 3

city: Pittsburgh

first: Shuchang

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: Sample 7
Cardiac-specific YY1 KO mouse 3

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic
Reads were aligned to mouse reference genome mm10 by STAR aligner
Gene counts were quantified by STRA
Assembly: mm10
Supplementary files format and content: TAB

molecule: polyA RNA

source_name: Heart

extract_protocol:
Using snap frozen heart tissue, RNA was isolated using the Trizol reagent
RNA libraries were prepared for sequencing using standard BGI protocols

value: Heart

tag: strain

tag: treatment

value: Transaortic constriction


title: 15_0.16uM_3

description:
Library name: 8546-AT-1_CCAGGTAA-TCGGTCAA
15_0.16uM_3

value: WT

tag: replicate


title: DSP-1001660011973-F-F03

description:
Library name: DSP-1001660011973-F-F03
spatial transcriptomic sequencing

tag: slide name

tag: panel

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

tag: patient

value: COPD


title: DSP-1001660011973-F-E11

description:
Library name: DSP-1001660011973-F-E11
spatial transcriptomic sequencing

tag: age

tag: condition

tag: former or_current_smoker


title: DSP-1001660014616-A-C07

description:
Library name: DSP-1001660014616-A-C07
spatial transcriptomic sequencing

value: SC

value: Smoker

tag: pack years

tag: gender

tag: location


title: 12_1.26uM_1

description:
Library name: 8546-AT-1_CCACAATG-TCGGTCAA
12_1.26uM_1

tag: day

tag: cell line

value: Human neuroblastoma

tag: genotype


title: DSP-1001660011973-F-E10

description:
Library name: DSP-1001660011973-F-E10
spatial transcriptomic sequencing

tag: tissue

value: parenchyma

tag: roi


title: Cardiac-specific YY1 KO mouse 2

description:
Library name: Sample 6
Cardiac-specific YY1 KO mouse 2

tag: strain


title: DSP-1001660011973-F-E12

description:
Library name: DSP-1001660011973-F-E12
spatial transcriptomic sequencing

tag: scan name


title: DSP-1001660011973-F-E09

description:
Library name: DSP-1001660011973-F-E09
spatial transcriptomic sequencing


title: 6_10uM_2

description:
Library name: 8546-AT-1_CAGGAAGG-TCGGTCAA
6_10uM_2

tag: cell type

tag: treatment

tag: replicate


title: DSP-1001660011973-F-E08

description:
Library name: DSP-1001660011973-F-E08
spatial transcriptomic sequencing

tag: slide name

tag: panel

tag: patient


title: MerCreMer control mouse 4

description:
Library name: Sample 4
MerCreMer control mouse 4


title: 6_10uM_1

description:
Library name: 8546-AT-1_CAGAAGAA-TCGGTCAA
6_10uM_1


title: DSP-1001660011973-F-E07

description:
Library name: DSP-1001660011973-F-E07
spatial transcriptomic sequencing

tag: age

tag: condition

tag: former or_current_smoker


title: DSP-1001660011973-F-G05

description:
Library name: DSP-1001660011973-F-G05
spatial transcriptomic sequencing

value: COPD GOLD 4

tag: pack years

tag: gender

tag: location

value: airway


title: MerCreMer control mouse 3

description:
Library name: Sample 3
MerCreMer control mouse 3


title: DSP-1001660011973-F-E05

description:
Library name: DSP-1001660011973-F-E05
spatial transcriptomic sequencing

value: former

value: paraffin


title: 12_0.16uM_2

description:
Library name: 8546-AT-1_CACATGGT-TCGGTCAA
12_0.16uM_2

tag: day

tag: cell line

tag: genotype


title: DSP-1001660011973-F-F01

description:
Library name: DSP-1001660011973-F-F01
spatial transcriptomic sequencing

tag: tissue

value: COPD GOLD 2

tag: roi


title: DSP-1001660011973-F-E04

description:
Library name: DSP-1001660011973-F-E04
spatial transcriptomic sequencing

value: lung

tag: scan name


title: MerCreMer control mouse 2

description:
Library name: Sample 2
MerCreMer control mouse 2

tag: strain

tag: treatment


title: 12_0uM_1

description:
Library name: 8546-AT-1_CCATTGCG-TCGGTCAA
12_0uM_1

tag: cell type

tag: replicate


title: DSP-1001660011973-F-E03

description:
Library name: DSP-1001660011973-F-E03
spatial transcriptomic sequencing

tag: slide name

tag: panel

tag: patient

value: male


title: 15_1.26uM_1

description:
Library name: 8546-AT-1_CACAGTCT-TCGGTCAA
15_1.26uM_1


title: DSP-1001660011973-F-E02

description:
Library name: DSP-1001660011973-F-E02
spatial transcriptomic sequencing

tag: age

tag: condition

tag: former or_current_smoker


title: MerCreMer control mouse 1

description:
Library name: Sample 1
MerCreMer control mouse 1


title: 15_0uM_3

description:
Library name: 8546-AT-1_ATTCGCAG-TCGGTCAA
15_0uM_3


title: DSP-1001660011973-F-E01

description:
Library name: DSP-1001660011973-F-E01
spatial transcriptomic sequencing

tag: pack years

tag: gender

tag: location


title: 15_10uM_1

description:
Library name: 8546-AT-1_ATTCCGTA-TCGGTCAA
15_10uM_1

tag: day

tag: cell line

tag: genotype


title: DSP-1001660011973-F-D12

description:
Library name: DSP-1001660011973-F-D12
spatial transcriptomic sequencing

tag: tissue

tag: roi

tag: scan name


title: DSP-1001660011973-F-D10

description:
Library name: DSP-1001660011973-F-D10
spatial transcriptomic sequencing

value: NSC

value: Non Smoker

value: never

value: vessel

value: UA_35_LLL  Vessel_6

value: oct


title: CKO6

city: Wenzhou

first: Dongqin

last: Zhou

state: Zhejiang

address: Chashan Street

institute: Wenzhou Medical University

description: Library name: Sample 28

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

source_name: Bone Marrow Primary Cells

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

tag: cell type

value: Bone Marrow Primary Cells

tag: treatment

value: Control


title: DSP-1001660011973-F-D09

description:
Library name: DSP-1001660011973-F-D09
spatial transcriptomic sequencing

tag: slide name

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

value: UA_35_LLL  Vessel_5


title: DSP-1001660011973-F-E06

description:
Library name: DSP-1001660011973-F-E06
spatial transcriptomic sequencing

tag: panel

value: COPD


title: 12_0uM_3

description:
Library name: 8546-AT-1_ATGGTCCG-TCGGTCAA
12_0uM_3

value: Human neuroblastoma

value: WT

tag: replicate


title: DSP-1001660011973-F-D08

description:
Library name: DSP-1001660011973-F-D08
spatial transcriptomic sequencing

tag: patient

tag: age

value: UA_35_LLL  Vessel_4


title: 6_0uM_3

description:
Library name: 8546-AT-1_ATAGATCC-TCGGTCAA
6_0uM_3


title: DSP-1001660011973-F-D07

description:
Library name: DSP-1001660011973-F-D07
spatial transcriptomic sequencing

tag: condition

tag: former or_current_smoker

value: UA_35_LLL  Vessel_3


title: CKO5

description: Library name: Sample 27


title: CKO3

description: Library name: Sample 26


title: DSP-1001660011973-F-D06

description:
Library name: DSP-1001660011973-F-D06
spatial transcriptomic sequencing

value: lung

tag: pack years

tag: gender

value: UA_35_LLL  Vessel_2


title: 9_0uM_3

description:
Library name: 8546-AT-1_ACTTCAAC-TCGGTCAA
9_0uM_3

tag: day


title: DSP-1001660011973-F-D04

description:
Library name: DSP-1001660011973-F-D04
spatial transcriptomic sequencing

value: NSC

value: male

tag: location

value: parenchyma

value: UA_35_LLL  Parenchyma_8


title: DSP-1001660011973-F-D05

description:
Library name: DSP-1001660011973-F-D05
spatial transcriptomic sequencing

value: Non Smoker

value: never

value: vessel

value: UA_35_LLL  Vessel_1


title: Cardiac-specific YY1 KO mouse 1

description:
Library name: Sample 5
Cardiac-specific YY1 KO mouse 1

value: Heart

tag: strain

value: Transaortic constriction


title: DSP-1001660011973-F-D11

description:
Library name: DSP-1001660011973-F-D11
spatial transcriptomic sequencing

tag: tissue

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

value: UA_35_LLL  Vessel_7

value: oct


title: CKO1

description: Library name: Sample 25

value: Bone Marrow Primary Cells

tag: genotype

value: Control


title: 9_0uM_1

description:
Library name: 8546-AT-1_ACTCGAAT-TCGGTCAA
9_0uM_1

tag: cell line

value: Human neuroblastoma

value: WT


title: C57BL6J ILC2 1

description: Library name: 9537-MR-0001

value: Lung

value: primary cells

tag: cell type

value: WT C57BL6J


title: DSP-1001660011973-F-D02

description:
Library name: DSP-1001660011973-F-D02
spatial transcriptomic sequencing

value: lung

value: NSC

value: male

value: parenchyma

tag: roi

value: UA_35_LLL  Parenchyma_6

tag: scan name


title: DSP-1001660011973-F-D03

description:
Library name: DSP-1001660011973-F-D03
spatial transcriptomic sequencing

tag: slide name

tag: panel

value: Non Smoker

value: never

value: UA_35_LLL  Parenchyma_7


title: DSP-1001660011973-F-D01

description:
Library name: DSP-1001660011973-F-D01
spatial transcriptomic sequencing

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

tag: patient

value: UA_35_LLL  Parenchyma_5


title: 6_0uM_1

description:
Library name: 8546-AT-1_ACTCACCG-TCGGTCAA
6_0uM_1

tag: treatment

tag: replicate


title: WT6

description: Library name: Sample 24

value: Bone Marrow Primary Cells


title: WT4

description: Library name: Sample 23

value: Control


title: DSP-1001660011973-F-C11

description:
Library name: DSP-1001660011973-F-C11
spatial transcriptomic sequencing

tag: age

tag: condition

tag: former or_current_smoker

value: UA_35_LLL  Parenchyma_3

value: oct


title: DSP-1001660011973-F-C12

description:
Library name: DSP-1001660011973-F-C12
spatial transcriptomic sequencing

tag: pack years

tag: gender

value: UA_35_LLL  Parenchyma_4


title: 15_0.16uM_1

description:
Library name: 8546-AT-1_ACCTGAGC-TCGGTCAA
15_0.16uM_1

tag: day

value: Human neuroblastoma

value: WT


title: DSP-1001660011973-F-C10

description:
Library name: DSP-1001660011973-F-C10
spatial transcriptomic sequencing

tag: tissue

value: lung

tag: location

value: UA_35_LLL  Parenchyma_2


title: WT3

description: Library name: Sample 22

tag: genotype


title: DSP-1001660011973-F-C09

description:
Library name: DSP-1001660011973-F-C09
spatial transcriptomic sequencing

value: NSC

value: male

value: UA_35_LLL  Parenchyma_1


title: Cardiac-specific YY1 KO mouse 4

description:
Library name: Sample 8
Cardiac-specific YY1 KO mouse 4

value: Heart

tag: strain

value: Transaortic constriction


title: DSP-1001660011973-F-C07

description:
Library name: DSP-1001660011973-F-C07
spatial transcriptomic sequencing

value: Non Smoker

value: never

value: airway

tag: roi

value: UA_35_LLL  Bronch 009


title: 9_1.26uM_1

description:
Library name: 8546-AT-1_AAGTACCT-TCGGTCAA
9_1.26uM_1

tag: cell line

tag: cell type


title: DSP-1001660011973-F-C06

description:
Library name: DSP-1001660011973-F-C06
spatial transcriptomic sequencing

tag: slide name

tag: panel

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

value: UA_35_LLL  Bronch 008

tag: scan name


title: DSP-1001660014616-A-C09

description:
Library name: DSP-1001660014616-A-C09
spatial transcriptomic sequencing

tag: patient

value: SC

value: Smoker

value: former

value: vessel

value: paraffin


title: TCM-25HC-5

description: Library name: Sample 20

value: Bone Marrow Primary Cells

value: WT

tag: treatment


title: 15_1.26uM_3

description:
Library name: 8546-AT-1_AACGCTTG-TCGGTCAA
15_1.26uM_3

value: Human neuroblastoma

tag: replicate


title: DSP-1001660011973-F-C05

description:
Library name: DSP-1001660011973-F-C05
spatial transcriptomic sequencing

value: lung

tag: age

tag: condition

value: NSC

tag: former or_current_smoker

value: male

value: UA_35_LLL  Bronch 007

value: oct


title: 9_10uM_1

description:
Library name: 8546-AT-1_AACCAATC-TCGGTCAA
9_10uM_1

tag: day


title: TCM-25HC-3

description: Library name: Sample 18


title: DSP-1001660011973-F-C02

description:
Library name: DSP-1001660011973-F-C02
spatial transcriptomic sequencing

tag: tissue

value: Non Smoker

value: never

tag: pack years

tag: gender

value: airway

value: UA_35_LLL  Bronch 004


title: TCM-25HC-4

description: Library name: Sample 19

tag: genotype


title: DSP-1001660014616-A-C12

description:
Library name: DSP-1001660014616-A-C12
spatial transcriptomic sequencing

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

value: SC

tag: location

value: parenchyma

tag: roi


title: DSP-1001660014616-A-C11

description:
Library name: DSP-1001660014616-A-C11
spatial transcriptomic sequencing

value: Smoker

value: former


title: DSP-1001660011973-F-C03

description:
Library name: DSP-1001660011973-F-C03
spatial transcriptomic sequencing

value: UA_35_LLL  Bronch 005


title: DSP-1001660011973-F-C04

description:
Library name: DSP-1001660011973-F-C04
spatial transcriptomic sequencing

value: UA_35_LLL  Bronch 006


title: DSP-1001660011973-F-B12

description:
Library name: DSP-1001660011973-F-B12
spatial transcriptomic sequencing

value: UA_35_LLL  Bronch 002


title: TCM-25HC-2

description: Library name: Sample 17

tag: cell type

value: Bone Marrow Primary Cells

value: WT


title: DSP-1001660011973-F-C01

description:
Library name: DSP-1001660011973-F-C01
spatial transcriptomic sequencing

tag: slide name

value: lung

value: NSC

value: male

value: UA_35_LLL  Bronch 003


title: LB4880_TCR

city: Bethesda

first: Seketoulie

last: Keretsu

state: MD

address: Building 37,

department: Neuro-Oncology Branch

institute: National Institute of Health

description:
Library name: LB4880_TCR
Sample 9_TCR
10x Genomics

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

source_name: Glioblastoma tumor

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

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

value: Glioblastoma tumor

value: CD45+ cells

value: newly diagnosed GBM


title: DSP-1001660011973-F-B11

description:
Library name: DSP-1001660011973-F-B11
spatial transcriptomic sequencing

tag: panel

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

value: Non Smoker

value: never

value: airway

value: UA_35_LLL  Bronch 001

value: oct


title: DSP-1001660011973-F-B10

description:
Library name: DSP-1001660011973-F-B10
spatial transcriptomic sequencing

value: COPD GOLD 1-2

value: COPD

value: former

value: female

value: vessel

tag: scan name


title: LB4805_TCR

description:
Library name: LB4805_TCR
Sample 3_TCR
10x Genomics


title: DSP-1001660011973-F-B09

description:
Library name: DSP-1001660011973-F-B09
spatial transcriptomic sequencing

value: lung

tag: patient


title: TCM-25HC-1

description: Library name: Sample 16

value: Bone Marrow Primary Cells

value: WT

tag: treatment


title: DSP-1001660011973-F-B08

description:
Library name: DSP-1001660011973-F-B08
spatial transcriptomic sequencing


title: WT1

description: Library name: Sample 21

value: Control


title: DSP-1001660011973-F-C08

description:
Library name: DSP-1001660011973-F-C08
spatial transcriptomic sequencing

value: NSC

value: male

value: UA_35_LLL  Bronch 010


title: LB4757_TCR

description:
Library name: LB4757_TCR
Sample 11_TCR
10x Genomics

value: Glioblastoma tumor

value: CD45+ cells

value: recurrent GBM immunotherapy naïve


title: 9_0.16uM_3

description:
Library name: 8546-AT-1_AATGTGCC-TCGGTCAA
9_0.16uM_3

tag: cell line

value: Human neuroblastoma

tag: replicate


title: TCM-Con-5

description: Library name: Sample 15


title: DSP-1001660011973-F-B07

description:
Library name: DSP-1001660011973-F-B07
spatial transcriptomic sequencing

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

tag: age

tag: condition

value: oct


title: DSP-1001660011973-F-B06

description:
Library name: DSP-1001660011973-F-B06
spatial transcriptomic sequencing

value: COPD GOLD 1-2

value: COPD

tag: former or_current_smoker


title: TCM-Con-4

description: Library name: Sample 14


title: LB4746_TCR

description:
Library name: LB4746_TCR
Sample 8_TCR
10x Genomics

tag: tissue

value: newly diagnosed GBM


title: DSP-1001660011973-F-B05

description:
Library name: DSP-1001660011973-F-B05
spatial transcriptomic sequencing

value: former

tag: pack years

value: female

value: vessel

value: UA_45_RLL Vessel 006


title: DSP-1001660011973-F-B04

description:
Library name: DSP-1001660011973-F-B04
spatial transcriptomic sequencing

value: lung

tag: gender

value: parenchyma

value: UA_45_RLL Parenchyma 008


title: LB4751_TCR

description:
Library name: LB4751_TCR
Sample 7_TCR
10x Genomics


title: TCM-Con-3

description: Library name: Sample 13

value: Bone Marrow Primary Cells

tag: genotype

value: WT


title: TCM-Con-2

description: Library name: Sample 12


title: DSP-1001660011973-F-B03

description:
Library name: DSP-1001660011973-F-B03
spatial transcriptomic sequencing

tag: location

value: UA_45_RLL Parenchyma 007


title: DSP-1001660011973-F-A12

description:
Library name: DSP-1001660011973-F-A12
spatial transcriptomic sequencing

tag: roi

value: UA_45_RLL Parenchyma 004


title: DSP-1001660011973-F-B01

description:
Library name: DSP-1001660011973-F-B01
spatial transcriptomic sequencing

value: UA_45_RLL Parenchyma 005


title: LB4693_TCR

description:
Library name: LB4693_TCR
Sample 1_TCR
10x Genomics

value: Glioblastoma tumor

tag: cell type

value: CD45+ cells


title: LB4628_TCR

description:
Library name: LB4628_TCR
Sample 22_TCR
10x Genomics

value: recurrent GBM neoadjuvant anti-PD-1


title: DSP-1001660011973-F-A11

description:
Library name: DSP-1001660011973-F-A11
spatial transcriptomic sequencing

tag: slide name

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

value: COPD GOLD 1-2

value: COPD

value: UA_45_RLL Parenchyma 003

value: oct


title: LB4477_TCR

description:
Library name: LB4477_TCR
Sample 19_TCR
10x Genomics


title: DSP-1001660011973-F-A10

description:
Library name: DSP-1001660011973-F-A10
spatial transcriptomic sequencing

tag: panel

value: former

value: female

value: UA_45_RLL Parenchyma 002


title: TCM-Con-1

description: Library name: Sample 11


title: GCP-CB cells, KMT2D, KO, replicate 2, SD6, CUT&RUN

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description: Library name: PLX292020_SD6_KMT2D_KO_rep2

library_source: genomic

data_processing:
Paired-end FASTQ files were processed using the nf-core-cutandrun pipeline (v3.0).
Adapter sequences were removed with Trim Galore.
Reads were aligned with Bowtie2 to GRCm38 (NCBI, p.6, release 108) and duplicates were removed for only control samples using picard.
Peaks were called with MACS2 (normalization mode: CPM).
Peaks were defined as regions where at least one of the target samples significantly exceeds its matched IgG control for a given genomic region.
Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER.
Peak counts were generated using featureCounts.
Downsteam analysis was performed using Pluto (https://pluto.bio).
Assembly: GRCm38 (NCBI, p.6, release 108)
Supplementary files format and content: bigWig
Supplementary files format and content: comma-delimited text files includes consensus peak counts for each Sample
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: GCP-CB

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:
CUT&RUN assays were performed with CUTANATM ChIC/CUT&RUN kit according to the manufacturer’s protocol (EpiCypher, #14-1048). Briefly, fresh 500,000 cells were collected with a cell lifter (Corning, #3008) and resuspended in wash buffer (Pre-wash buffer (EpiCypher, #21-1002), protease inhibitor, and 0.5 mM spermidine and bound to activated Concanavalin A beads. Cells conjugated with beads were incubated with Antibody buffer (Cell permeabilization buffer and 2 mM EDTA) and antibodies at 4°C overnight. After extensive washing with Cell permeabilization buffer (Wash buffer and 0.01% digitonin), the cells were incubated with pAG-MNase (EpiCypher, #15-1016) for 10 min at room temperature, and then chromatin digestion was performed with calcium chloride for 2 h at 4°C. SNAP CUTANA™ Spike-in Controls for CUT&RUN (Cat: SKU-19-1002) panels of modified DNA-barcoded Designer Nucleosomes (dNucs™) carrying an array of widely studied histone post-translational modifications (PTMs) were used. After chromatin digestion, the stop buffer and E. coli spike-in DNA (EpiCypher, #18-1401) were added and incubated for 10 min at 37°C. Chromatin fragments were purified with DNA cleanup columns.
Library preparation on samples was conducted using manufacturer’s protocols for NEBNext Ultra II Dna Library Prep Kit (New England BioLabs, CAT#E7645) and NEB Multiplex Dual Index oligos (New England BioLabs, CAT#E7600, #E7780) with the following modifications. We input approximately 10ng of sample for half reactions, we diluted the NEBNext Illumina adaptor 1:25, we used the following PCR cycling conditions: 1 cycle of Initial Denaturation at 98C for 30 seconds, 12+ cycles of Denaturation at 98C for 10 seconds then Annealing/Extension at 65C for 10 seconds, and 1 final cycle of extension at 65C for 5 minutes. Following library preparation, double size selection was performed using Ampure beads and quality and concentration of libraries were determined by an Agilent 4200 Tapestation with High-Sensitivity D1000 reagents before pooling for sequencing.

value: GCP-CB

tag: cut&run antibody

value: KMT2D (Genscript, Homemade)

value: KO

tag: internal id


title: LB4429_TCR

description:
Library name: LB4429_TCR
Sample 12_TCR
10x Genomics

tag: treatment

value: recurrent GBM immunotherapy naïve


title: Mock-25HC-4

description: Library name: Sample 9

value: Bone Marrow Primary Cells

value: WT


title: DSP-1001660011973-F-A09

description:
Library name: DSP-1001660011973-F-A09
spatial transcriptomic sequencing

value: lung

tag: patient

value: parenchyma

value: UA_45_RLL Parenchyma 001

tag: scan name


title: DSP-1001660011973-F-A08

description:
Library name: DSP-1001660011973-F-A08
spatial transcriptomic sequencing

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

tag: age

value: airway

value: UA_45_RLL Bronch 005


title: GCP-CB cells, KMT2D, KO, replicate 1, SD5, CUT&RUN

description: Library name: PLX292020_SD5_KMT2D_KO_rep1

tag: cell line

tag: condition


title: Mock-25HC-3

description: Library name: Sample 8


title: LB4382_TCR

description:
Library name: LB4382_TCR
Sample 2_TCR
10x Genomics

tag: tissue

value: Glioblastoma tumor

value: CD45+ cells

value: newly diagnosed GBM


title: LB4372_TCR

description:
Library name: LB4372_TCR
Sample 5_TCR
10x Genomics


title: GCP-CB cells, KMT2D, Control, replicate 2, SD3, CUT&RUN

description: Library name: PLX292020_SD3_KMT2D_control_rep2

value: Control


title: DSP-1001660011973-F-A07

description:
Library name: DSP-1001660011973-F-A07
spatial transcriptomic sequencing

value: COPD GOLD 1-2

value: COPD

tag: former or_current_smoker

value: former

tag: pack years

value: female

value: UA_45_RLL Bronch 004

value: oct


title: Mock-25HC-2

description: Library name: Sample 7

value: Bone Marrow Primary Cells

tag: genotype

value: WT


title: DSP-1001660011973-F-A06

description:
Library name: DSP-1001660011973-F-A06
spatial transcriptomic sequencing

value: lung

tag: gender

tag: location

value: UA_45_RLL Bronch 003


title: LB4369_TCR

description:
Library name: LB4369_TCR
Sample 23_TCR
10x Genomics

tag: cell type

value: recurrent GBM neoadjuvant anti-PD-1


title: DSP-1001660011973-F-A05

description:
Library name: DSP-1001660011973-F-A05
spatial transcriptomic sequencing

tag: slide name

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

value: airway

tag: roi

value: UA_45_RLL Bronch 002


title: GCP-CB cells, KMT2D, Control, replicate 1, SD2, CUT&RUN

description: Library name: PLX292020_SD2_KMT2D_control_rep1

value: GCP-CB

tag: cut&run antibody

value: KMT2D (Genscript, Homemade)


title: LB4260_TCR

description:
Library name: LB4260_TCR
Sample 6_TCR
10x Genomics

value: Glioblastoma tumor

value: CD45+ cells

value: newly diagnosed GBM


title: DSP-1001660011973-F-A04

description:
Library name: DSP-1001660011973-F-A04
spatial transcriptomic sequencing

tag: panel

value: COPD GOLD 1-2

value: COPD

value: former

value: UA_45_RLL Bronch 001


title: GCP-CB cells, H3K27ac, KO, replicate 1, SD5, CUT&RUN

description: Library name: PLX176399_SD5_H3K27ac_KO_rep1

value: KO

tag: internal id


title: Mock-Con-5

description: Library name: Sample 5

value: Bone Marrow Primary Cells

value: WT

tag: treatment

value: Control


title: DSP-1001660011973-F-B02

description:
Library name: DSP-1001660011973-F-B02
spatial transcriptomic sequencing

value: lung

tag: patient

value: female

value: parenchyma

value: UA_45_RLL Parenchyma 006

tag: scan name

value: oct


title: Mock-25HC-1

description: Library name: Sample 6


title: Mock-25HC-5

description: Library name: Sample 10


title: DSP-1001660011973-F-A03

description:
Library name: DSP-1001660011973-F-A03
spatial transcriptomic sequencing

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

tag: age

value: vessel

value: UA_45_RLL  Vessel 008


title: LB4177_TCR

description:
Library name: LB4177_TCR
Sample 14_TCR
10x Genomics

value: Glioblastoma tumor

value: CD45+ cells

value: recurrent GBM immunotherapy naïve


title: Mock-Con-4

description: Library name: Sample 4


title: Mock-Con-3

description: Library name: Sample 3


title: DSP-1001660011973-F-A02

description:
Library name: DSP-1001660011973-F-A02
spatial transcriptomic sequencing

tag: condition

value: COPD GOLD 1-2

value: COPD

value: former

value: UA_45_RLL  Vessel 007


title: GCP-CB cells, H3K27ac, Control, replicate 2, SD3, CUT&RUN

description: Library name: PLX176399_SD3_H3K27ac_control_rep2

tag: cell line

value: GCP-CB


title: LB4130_TCR

description:
Library name: LB4130_TCR
Sample 13_TCR
10x Genomics

tag: tissue


title: LB4143_TCR

description:
Library name: LB4143_TCR
Sample 15_TCR
10x Genomics


title: GCP-CB cells, H3K27ac, Control, replicate 1, SD2, CUT&RUN

description: Library name: PLX176399_SD2_H3K27ac_control_rep1

value: Control


title: DSP-1001660011972-E-H08

description:
Library name: DSP-1001660011972-E-H08
spatial transcriptomic sequencing

value: lung

value: COPD GOLD 4

tag: former or_current_smoker

tag: pack years

value: male

value: COPD_8_LUL:vessel 8

value: paraffin


title: Mock-Con-1

description: Library name: Sample 1

value: Bone Marrow Primary Cells

tag: genotype

value: WT


title: LB4117_TCR

description:
Library name: LB4117_TCR
Sample 20_TCR
10x Genomics

value: recurrent GBM neoadjuvant anti-PD-1


title: DSP-1001660011972-E-H07

description:
Library name: DSP-1001660011972-E-H07
spatial transcriptomic sequencing

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

tag: gender

tag: location

value: vessel

value: COPD_8_LUL:vessel 7


title: GCP-CB cells, IgG, Control,  replicate 1, SD1, Input

description: Library name: PLX176399_SD1_IgG_control_rep1


title: HSPC OP-HU

city: Xi'an

first: Chen

address: Xinsi road

department: Department of hematology

institute: Tangdu Hospital

description: GEXSCOPE

data_processing:
Raw reads were processed to generate gene expression profiles using CeleScope v1.12.0 (Singleron Biotechnologies) with default parameters. Scanpy v1.8.1 was used for quality control, dimensionality reduction and clustering under Python 3.7.
Assembly: mm10
Supplementary files format and content: Tab-seprated values files and matrix files.

extract_protocol:
BM cells were obtained by crushing or flushing femurs and tibia in staining media composed of PBS containing 2% heat-inactivated FBS. Red blood cells were removed with RBC Lysis buffer (eBioscience™, 00-4300-54). BM cells were furthered enriched by combination of lineage depletion kit (Miltenyi Biotech, 130-090-858) and CD117 MicroBeads (Miltenyi Biotech, 130-091-224).
Library was prepared according to GEXSCOPE Single Cell RNA Library Kit (high density). Briefly, Lin- CD117+ enriched HSPCs (90,000 cells) were dispelled into single cell for further single-cell RNA sequencing using high density microwell chip (containing 250,0000 wells/chip for capturing 20,000-50,000 single cells, Singleron Biotech Co., Ltd, Nanjing, China) for each sample. The GEXSCOPE microchip integrates single cell capture, cell lysis, capture of the cellular mRNA and molecular labeling. The barcoded cDNA is then amplified and used for the construction of single cell NGS libraries.

value: Bone marrow

value: Hematopoietic stem and progenitor cells

value: OP-HU

tag: strain

value: 12 weeks


title: LB4112_TCR

description:
Library name: LB4112_TCR
Sample 18_TCR
10x Genomics

value: Glioblastoma tumor

tag: cell type

value: CD45+ cells


title: DSP-1001660011972-E-H06

description:
Library name: DSP-1001660011972-E-H06
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

tag: slide name

value: lung

value: COPD

value: former

tag: roi

value: COPD_8_LUL:vessel 5


title: LB4180_TCR

description:
Library name: LB4180_TCR
Sample 4_TCR
10x Genomics

value: newly diagnosed GBM


title: GCP-CB cells, H3K7ac, KO, replicate 2, SD6, CUT&RUN

description: Library name: PLX176399_SD6_H3K27ac_KO_rep2

value: GCP-CB

tag: cut&run antibody

value: KO

tag: internal id


title: Normal-fetal-brain-4

city: Baltimore

first: Michael

last: Koldobskiy

address: 1800 Orleans St., Bloomberg 11379

department: Oncology

institute: Johns Hopkins University

description:
Library name: Normal-fetal-brain-4
bigWig

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

source_name: normal

extract_protocol:
Epicentre DNA extraction kit
Illumina TruSeq, NEBNext

value: normal

value: N

value: normal fetal brain


title: DSP-1001660011972-E-H05

first: Scott

institute: Baylor College of Medicine

description:
Library name: DSP-1001660011972-E-H05
spatial transcriptomic sequencing

tag: panel

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

tag: patient

value: COPD GOLD 4

value: male

value: vessel

value: COPD_8_LUL:vessel 4

value: paraffin


title: LB4102_TCR

description:
Library name: LB4102_TCR
Sample 16_TCR
10x Genomics

value: Glioblastoma tumor

value: CD45+ cells

tag: treatment

value: recurrent GBM immunotherapy naïve


title: HSPC control

description: GEXSCOPE

value: Bone marrow

value: Hematopoietic stem and progenitor cells

tag: condition

value: control

tag: age

value: 12 weeks


title: D0-2

city: Suzhou

first: Li

last: Min

address: 199 Ren-ai Road

department: Institute of Biology and Medical Sciences

institute: Soochow University

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

source_name: heart

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

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

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

tag: tissue

value: heart

value: Balb/c

value: Wildtype

value: Control

tag: time


title: LB4101_TCR

description:
Library name: LB4101_TCR
Sample 10_TCR
10x Genomics


title: GCP-CB cells, IgG, KO, replicate 1, SD4, Input

description: Library name: PLX176399_SD4_IgG_KO_rep1

tag: cell line

value: GCP-CB

value: KO


title: D0-1

tag: genotype


title: Normal-fetal-brain-2

description:
Library name: Normal-fetal-brain-2
bigWig

value: normal

value: N

value: normal fetal brain