title: Nonsmoker NS201717, baseline

description: Library name: NS201717

value: female

tag: age


title: P7 PBMC pre-operative, scRNA-seq

status: Public on Feb 05 2026

type: SRA

city: Hidaka-City, Saitama

first: Satoshi

last: Yamasaki

department: Department of Respiratory Medicine

country: Japan

institute: Saitama Medical University

description:
Library name: P7_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files

molecule: polyA RNA

organism: Homo sapiens

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Manufactured protocol of Chromium system (10x genomics)
Library construction was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) protocol (CG000331), 10x Genomics).

tag: tissue

value: Peripheral Blood Mononuclear Cells

tag: disease state

value: Lung cancer

tag: cell type

value: CD3+ T cell

tag: library type

value: mRNA


title: Nonsmoker NS201715, baseline

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

country: USA

institute: Boston University School of Medicine

description: Library name: NS201715

library_source: transcriptomic

data_processing:
Demultiplexing and creation of FASTQ files were automatically performed using the Illumina BaseSpace platform with default parameters.
Reads were aligned to the Genome Reference Consortium human build 38 (GRCh38) using STAR v2.6.0c.
Both gene and transcript level counts were calculated using RSEM v1.3.1 with annotation from Ensembl build 107.
Genes were filtered for analysis based on counts per million (CPM) reads mapped across all samples. Genes with CPM counts greater than 1 in more than 10% of the total number of patients were used in subsequent analyses. CPM was calculated using the calcNormFactors and cpm functions from the edgeR package (version 4.4.1).
Assembly: hg38
Supplementary files format and content: counts.tsv: tab-separated values (TSV) file containing 61860 x 36 matrix of "expected_count" values computed by RSEM

molecule: total RNA

source_name: Bronchial brushing

extract_protocol:
Total RNA was isolated from bronchial brushings using the miRNAs Mini Kit (Qiagen, Valencia, CA).
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit (Illumina, San Diego, CA).

value: Bronchial brushing

tag: subject id

tag: flowcell

value: AAAYGHHHV

tag: median tin

tag: smoking status

value: nonsmoker

tag: visit

value: baseline

tag: race

value: Black or African American

tag: ethnicity

value: Non-Hispanic

tag: Sex


title: P7 TIL, scTCR-seq

description:
Library name: P7_TIL_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files
Library strategy: TCR-Seq

molecule: other

source_name: Tumor-infiltrating lymphocyte (TIL)

value: Tumor-infiltrating lymphocyte (TIL)

value: erythrocyte-removed TIL

value: TCR


title: PB1 knockout Schwann cells, replicate 1

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: PB1-KO-M1

data_processing:
FASTQ file preprocessing, quality control, and alignment to the mouse mm10 genome were done using the NGS-Data-Charmer pipeline. Adaptor trimming was performed with Trim-Galore (v0.6.5), and reads were aligned using Bowtie2 (v2.4.1). Duplicates were removed with SAMtools (v1.10), and gene expression was quantified using Feature Counts with the GENCODE vM25 annotation.
Assembly: mm10
Supplementary files format and content: Tab-separated counts file, "counts_exonic_matrix.txt", contains the non-normalized gene expression values. Tab-separated counts file, "fpkm_exonic_matrix.txt", contains the normalized gene expression values in Fragments Per Kilobase per Million (FPKM).

organism: Mus musculus

source_name: dorsal root ganglion

growth_protocol: For Schwann cell (SC) culture, WT and PB1KO DRGs were isolated from adult mice and placed into DMEM/F12 solution on ice, washed twice with ice-cold HBSS-HEPES buffer, and incubated in 0.6% collagenase at 37°C for 45 minutes. After washing with HBSS-HEPES, mixed cells were plated onto plates coated with poly-L-lysine and laminin. To enrich Schwann cells, the dissociated mixed cell cultures were cultured in SC medium containing 2 µM forskolin, 10 nM neuregulin, 10% FBS, 1% non-essential amino acids, and 4% ascorbic acid in DMEM high glucose Glutamax. Through the use of specialized medium and after passaging, there were almost no neurons remaining in the culture. Fibroblasts were removed by magnetic cell separation using anti-Thy1 antibody, and the medium was changed every 2 days. Cells were passaged at 80% confluence, with purity exceeding 80% at passages 3 to 5.

extract_protocol:
Total RNA from WT and PB1KO SCs was isolated using an RNeasy Micro kit (Qiagen) following instructions for on-column DNase digestion. RNA quality and concentrations were determined using an Agilent Bioanalyzer (Agilent RNA 6000 Pico, 5067-1513).
For library construction using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina), the protocol follows the TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E. This procedure begins with RNA isolation, followed by mRNA enrichment using poly(A) selection. The mRNA is then fragmented, reverse transcribed into cDNA, and adapter-ligated. After amplification, the library is purified, and its quality and quantity are assessed before sequencing.

value: dorsal root ganglion

value: Schwann cell

tag: genotype


title: L. japonicus ASN symbiotic conditions, shoots, biological replicate 3

city: Sevilla

first: MARCO

last: BETTI

state: Sevilla

address: C. Prof. García González 1

department: Bioquímica Vegetal y Biología Molecular

country: Spain

institute: Universidad de Sevilla

description:
Library name: ASNshootNod3
column name in gene_fpkm.txt: ASNshootNod3

data_processing:
Libraries were ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: Lotus japonicus Gifu V 1_2
Supplementary files format and content: FPKM values for all the samples

organism: Lotus japonicus

source_name: shoot

growth_protocol: plants grown in the presence of ammonium nitrate (NN) or nodulated with Mesorhizobium loti (Nod)

extract_protocol:
Tissue was flash-freezed in liquid N2, ground with mortar and pestle and RNA extracted with a modified CTAB protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP.

value: shoot

tag: treatment

value: nodulation


title: Nonsmoker NS201701, baseline

description: Library name: NS201701

value: female


title: L. japonicus ASN symbiotic conditions, shoots, biological replicate 2

description:
Library name: ASNshootNod2
column name in gene_fpkm.txt: ASNshootNod2


title: cont_T6_2

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

institute: National institute of infectious diseases

description: Library name: Sample 4

data_processing:
Read trimming and clipping were done with cutadapt. The resulting trimmed reads were consolidated into FASTA format. Read filtering, read mapping, nucleotide-wise coverage calculations, and genome feature-wise read quantification were performed using READemption2 version2.0.4 and the short-read mapper Segemehl version 0.3.4, applying an accuracy threshold of 95%. The references employed included the Escherichia coli K-12 substr. DH10B genome (accession number NC_010473.1) and the T6 phage that was resequenced in the present study. The uniquely aligned reads were utilized to conduct the coverage calculations.
Assembly: Escherichia coli K-12 substr. DH10B genome (accession number NC_010473.1)
Supplementary files format and content: wiggle

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: Cultures of bacteria expressing either empty vector or Septu EcB88, which were grown overnight, were diluted 100-fold in fresh LB medium with 100 μg/ml of chloramphenicol and 1 mM CaCl₂.

extract_protocol:
Total RNA was extracted using the hot phenol method. The aqueous phase was precipitated with 2 volumes of ice-cold ethanol and 1/30 volume of 3 M NaOAc (pH 6.5) for 2 h at -20°C. The pellet was washed with ice-cold 75% ethanol and resuspended in sterilized water. Then the extracted RNA was treated with DNase followed by phenol:chloroform:isoamyl alcohol extraction. The aqueous phase was precipitated again with 2.5 volumes of ice-cold ethanol and 1/30 volume of 3 M NaOAc (pH 6.5) for 2 h at -20°C. The pellet was washed with 75% ethanol and resuspended in sterilized water.
cDNA library preparation followed by sequencing was conducted by Filgen, Inc. and Arraystar Inc.. RNA samples were pretreated to eliminate specific modifications that might impede the process (deacylation of 3’–aminoacyl RNA, removal of 3’–cP (2’,3’–cyclic phosphate), phosphorylation of 5’–OH, and demethylation of m1A and m3C ). Library preparation was executed using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs). The procedural workflow incorporated 3’–adapter ligation, 5’–adapter ligation, cDNA synthesis, PCR amplification, and size selection of PCR products ranging from 134 to 160 bp.

treatment_protocol: Upon reaching OD600 of 0.5, phages were added into the culture at a multiplicity of infection (MOI) of 10. After 30 min post-infection, a stop solution (95% v/v ethanol and 5% v/v water-saturated phenol (pH > 7.0)) was added to the culture and then immediately stored at -80°C.

value: bacterial cell

tag: strain

tag: infection

value: T6 phage infection


title: AS2

type: RNA

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

hyb_protocol: The tissue sections were processed using the pre-designed Xenium Human Multi-tissue and Cancer Gene Expression panel (377 genes) provided by 10X Genomics.

scan_protocol: GPL33762  - Xenium In Situ Analyzer: Human

data_processing: Image decoding, cell segmentation and transcript assignment were performed using the onboard Xenium analyzer. The resulting data was inputted to Seurat 4.3 (R package) for subsequent analysis including cell clustering and differential expression analysis.

label: Xenium probe set

source_name: Aorta

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: The ascending aorta pieces were immediately embedded and frozen in Optimal cutting temperature (OCT) compound.  OCT blocks were cut into 10 μm sections in a cryostat and then fixed in pre-heated paraformaldehyde.

value: Aorta

tag: tissue preservation method

value: Fresh Frozen

tag: gender

value: Male

tag: phenotype

value: Aortic Stenosis


title: L. japonicus ASN symbiotic conditions, shoots, biological replicate 1

description:
Library name: ASNshootNod1
column name in gene_fpkm.txt: ASNshootNod1

tag: tissue


title: AS3

value: Female


title: Nonsmoker NS201711, baseline

description: Library name: NS201711

value: Bronchial brushing

value: AAAYGHHHV

value: nonsmoker

value: baseline

value: Black or African American

tag: age


title: cont_no_1

description: Library name: Sample 1

tag: cell type

value: no infection


title: AS1


title: P7 TIL, scRNA-seq

description:
Library name: P7_TIL_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

value: Tumor-infiltrating lymphocyte (TIL)

tag: disease state

value: Lung cancer

value: erythrocyte-removed TIL

tag: library type

value: mRNA


title: P6 PBMC pre-operative, scTCR-seq

description:
Library name: P6_PBMC1_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell

value: TCR


title: Smoker S201719, follow-up

description: Library name: S201719-2

tag: subject id

tag: flowcell

value: AAATFCTHV

tag: median tin

tag: smoking status

value: smoker

value: follow-up

value: Declined/Not Available

value: Hispanic or Latino

value: male


title: L. japonicus ASN ammonium nitrate, shoots, biological replicate 3

description:
Library name: ASNshootNN3
column name in gene_fpkm.txt: ASNshootNN3

value: shoot

value: ammonium nitrate


title: L. japonicus ASN ammonium nitrate, shoots, biological replicate 2

description:
Library name: ASNshootNN2
column name in gene_fpkm.txt: ASNshootNN2


title: Smoker S201719, baseline

description: Library name: S201719-1

value: Bronchial brushing

tag: visit

value: baseline

tag: race

tag: ethnicity

tag: Sex


title: P6 PBMC pre-operative, Feature Barcoding(ADT)

description:
Library name: P6_PBMC1_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR repertoire analysis were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and comma-separated values files
Library strategy: CITE-seq

molecule: protein

value: ADT

tag: adt

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: P7 TIL, Feature Barcoding(ADT)

description:
Library name: P7_TIL_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

value: Tumor-infiltrating lymphocyte (TIL)

value: Lung cancer

value: erythrocyte-removed TIL


title: GCA3-R2

description: 10X Xenium Human Multi-Tissue and Cancer Gene Expression (Chemistry: RNA V1).

extract_protocol: Control and aortitis samples were resected from the greater curvature of the ascending aorta. The ascending aorta pieces were immediately embedded and frozen in Optimal cutting temperature (OCT) compound.  OCT blocks were cut into 10 μm sections in a cryostat and then fixed in pre-heated paraformaldehyde. The tissue sections were processed using the pre-designed Xenium Human Multi-tissue and Cancer Gene Expression panel (377 genes) provided by 10X Genomics.

value: Female

value: Giant Cell Aortitis


title: P6 PBMC pre-operative, scRNA-seq

description:
Library name: P6_PBMC1_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell

value: mRNA


title: IgG4

value: IgG4-related Aortitis


title: L. japonicus ASN symbiotic conditions, nodulated roots, biological replicate 3

description:
Library name: ASNrootNod3
column name in gene_fpkm.txt: ASNrootNod3

source_name: nodulated root

value: nodulated root

tag: genotype

tag: treatment

value: nodulation


title: Smoker S201716, baseline

description: Library name: S201716-1

value: AAATFCTHV

value: smoker

value: Black or African American

value: Non-Hispanic

value: male


title: P6 TIL, scTCR-seq

description:
Library name: P6_TIL_TCR
Single-cell TCR library generated using the 10x Genomics 5' V(D)J enrichment kit. Derived from cDNA capturing full-length TCRα and TCRβ chains.

value: TCR


title: Smoker S201716, follow-up

description: Library name: S201716-2

value: Bronchial brushing

value: follow-up


title: L. japonicus ASN ammonium nitrate, shoots, biological replicate 1

description:
Library name: ASNshootNN1
column name in gene_fpkm.txt: ASNshootNN1

value: shoot

value: ammonium nitrate


title: GCA2-R2

tag: gender

value: Female

tag: phenotype

value: Giant Cell Aortitis


title: P6 TIL, Feature Barcoding(ADT)

description:
Library name: P6_TIL_FB
Cell surface protein expression profiling using feature barcoding with oligo-conjugated antibodies (TotalSeq-C). Prepared with 10x Genomics Feature Barcoding technology. Processed data is shared with the corresponding gene expression (GEX) library, as ADT counts were extracted from the same filtered_feature_bc_matrix output generated by Cell Ranger with Feature Barcoding support.

tag: tissue

value: Tumor-infiltrating lymphocyte (TIL)

value: Lung cancer

value: erythrocyte-removed TIL

value: ADT

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: Smoker S201710, baseline

description: Library name: S201710-1

value: AAATFCTHV

value: baseline

value: female

tag: age


title: Smoker S201710, follow-up

description: Library name: S201710-2

value: smoker

value: Black or African American

value: Non-Hispanic


title: GCA2-R1


title: GCA1-R2


title: P6 TIL, scRNA-seq

description:
Library name: P6_TIL_GEX
Single-cell RNA-seq library generated using the 10x Genomics Chromium Next GEM Single Cell 5' v2 kit. Captures 5' end of polyA+ transcripts.

tag: disease state

tag: cell type

value: mRNA


title: GCA3-R1


title: Smoker S201708, follow-up

description: Library name: S201708-2

value: Bronchial brushing

tag: subject id

value: follow-up

value: male


title: L. japonicus ASN symbiotic conditions, nodulated roots, biological replicate 1

description:
Library name: ASNrootNod1
column name in gene_fpkm.txt: ASNrootNod1

value: nodulated root

value: nodulation


title: Smoker S201708, baseline

description: Library name: S201708-1

tag: flowcell


title: L. japonicus ASN ammonium nitrate, roots, biological replicate 3

description:
Library name: ASNrootNN3
column name in gene_fpkm.txt: ASNrootNN3

source_name: root

value: root

value: ammonium nitrate


title: HOS NXP800 24h, rep2

city: Nantes

first: Anaïs

last: Postec

address: 1 Rue Gaston Veil

country: France

institute: Nantes University

description: Library name: 6

data_processing:
fastp (version 0.20.1) default parameters “--detect_adapter_for_pe”,  “-q 30”
STAR (version 2.7.5a) default parameters ” --twopassMode Basic”
htseq_count (version 0.12.4) default parameters “--order pos”, “ -s reverse” with GCF_000001405.40_GRCh38.p14 annotation
Assembly: hg38
Supplementary files format and content: Output from htseq_count

source_name: HOS-MNNG

extract_protocol:
NucleoSpin RNA Plus Kit (Macherey-Nagel)
DNBSEQ Eukaryotic Strand-specific mRNA library

tag: cell line

value: HOS-MNNG

value: Osteosarcoma


title: L. japonicus ASN symbiotic conditions, nodulated roots, biological replicate 2

description:
Library name: ASNrootNod2
column name in gene_fpkm.txt: ASNrootNod2


title: Smoker S201705, follow-up

description: Library name: S201705-2

tag: median tin

tag: smoking status

value: White


title: TR-2-24F

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

data_processing: Downstream analysis including CHIKV RNA quantification, gene expression normalization, cell clustering, and cell type annotation were performed using the Seurat R package.

source_name: ankle

extract_protocol: 28 days post infection joint-associated tissue was collected from the ipsilateral ankle and a single cell suspension was generated by mechanical and enzymatic digestion. Cells were assayed using the 10x Genomics Xenium spatial transcriptomics platform according to manufacturer’s instructions.

treatment_protocol: WT C57BL/6J mice were inoculated with the chikungunya virus strain AF15561 or were mock infected

value: CHIKV infected mice


title: TR-2-24E


title: L. japonicus ASN ammonium nitrate, roots, biological replicate 1

description:
Library name: ASNrootNN1
column name in gene_fpkm.txt: ASNrootNN1


title: Smoker S201705, baseline

description: Library name: S201705-1

value: AAATFCTHV

tag: visit

value: baseline

tag: race


title: HOS NXP800 24h, rep3

description: Library name: 9


title: HOS DMSO 24h, rep3

description: Library name: 7

value: DMSO


title: L. japonicus WT symbiotic conditions, shoots, biological replicate 3

description:
Library name: WTshootNod3
column name in gene_fpkm.txt: WTshootNod3

value: shoot

value: WT


title: TR-2-24D


title: HOS DMSO 24h, rep2

description: Library name: 4


title: L. japonicus WT symbiotic conditions, shoots, biological replicate 2

description:
Library name: WTshootNod2
column name in gene_fpkm.txt: WTshootNod2


title: GCA1-R1

value: Female

value: Giant Cell Aortitis


title: TR-2-24C

value: mock infected mice


title: Smoker S201704, baseline

description: Library name: S201704-1

value: Bronchial brushing

value: smoker

tag: ethnicity

value: Non-Hispanic

tag: Sex

value: female


title: L. japonicus WT symbiotic conditions, shoots, biological replicate 1

description:
Library name: WTshootNod1
column name in gene_fpkm.txt: WTshootNod1

tag: genotype

value: nodulation


title: HOS DMSO 24h, rep1

description: Library name: 1

value: HOS-MNNG

tag: treatment


title: L. japonicus WT ammonium nitrate, shoots, biological replicate 3

description:
Library name: WTshootNN3
column name in gene_fpkm.txt: WTshootNN3

value: ammonium nitrate


title: L. japonicus ASN ammonium nitrate, roots, biological replicate 2

description:
Library name: ASNrootNN2
column name in gene_fpkm.txt: ASNrootNN2

value: root


title: P5 PBMC post-operative, scTCRseq

description: 10x genomics

extract_protocol:
Manufactured protocol of Chromium system (10x genomics)
Library was performed according to the manufacter’s instructions (Chromium Single Cell Immune Profiling v2 protocol, 10x Genomics).
scRNAseq+scTCRseq with Feature Barcoding

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell

tag: antibodies/tags


title: HOS NXP800 24h, rep1

description: Library name: 3

value: Osteosarcoma


title: Nonsmoker NS201721, baseline

description: Library name: NS201721

value: AAATFCTHV

value: nonsmoker

value: baseline

value: Black or African American


title: TR-2-24B


title: TR-2-24A


title: Nonsmoker NS201720, baseline

description: Library name: NS201720


title: P5 PBMC post-operative, scRNAseq

description: 10x genomics


title: Nonsmoker NS201718, baseline

description: Library name: NS201718

value: White


title: L. japonicus WT ammonium nitrate, shoots, biological replicate 2

description:
Library name: WTshootNN2
column name in gene_fpkm.txt: WTshootNN2

value: shoot

value: WT


title: L. japonicus WT ammonium nitrate, shoots, biological replicate 1

description:
Library name: WTshootNN1
column name in gene_fpkm.txt: WTshootNN1


title: sh1-3

city: Heverlee

first: Zhi-Xing

last: Lau

address: Willem de Croylaan 42

country: Belgium

institute: KU Leuven

description: Library name: Sample6

data_processing:
RNAseq reads were preprocessed by Trimmomatic v0.39 (Bolger et al., 2014) for adapter removal, where reads shorter than 80bps after trimming were dropped.
Assembly: Clean reads were firstly mapped to the Araport11 transcriptome using Bowtie2 v2.2.6 (Langmead & Salzberg, 2012), where only alignments of read pairs to the same transcripts with identity ≥ 95% were accepted. Rest reads were mapped to the TAIR10 genome using BLAT v34 (Kent, 2002), where alignments were required to be with identity ≥ 95% and alignment blocks at the two ends no short than 8bps. Read counts were computed using the RackJ toolkit (https://rackj.sourceforge.net/). Normalized RPKM values were derived based on read counts normalized by the TMM method (Robinson & Oshlack, 2010).
Supplementary files format and content: csv files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: 16/8 light dark, 100 µmol/m2/s, 22 ºC. Germinated on half-strength MS media with 1% sucrose and 0.7% agar.

extract_protocol:
2 g plant tissue were collected in 2 mL tubes with 3 steel beads, grinded into fine powder with liquid nitrogen using tissue grinder (SH-48, Kurabo).
2 g of total RNA from three biological replicates were used for library construction following Illumina TruSeq stranded mRNA sample preparation kit according to the manufacturers protocol. PolyA RNA was captured by oligodT beads and fragmented after elution from the beads. The first-strand cDNA was synthesized by reverse transcriptase (SuperScript III, 18080-093, Invitrogen) using dNTP and random primers. The second-strand cDNA was generated using a dUTP mix. The double-stranded cDNA was subjected to the addition of a single A base to the 3 end followed by ligation of the barcoded Truseq adapters. Finally, the products were purified and enriched with 11 cycles of PCR to create the final double-stranded cDNA library. For quality check, we used the BioRad QX200 Droplet Digital PCR EvaGreen supermix system (Cat. No. #1864034; BioRad, USA) and Fragment Analyzer 5200 (Agilent) with HS NGS fragment (1-6000bp) kit to estimate the quantity and check size distribution. The prepared library was pooled for paired-end sequencing using Illumina NovSeq 6000 at Genomics Co. (New Taipei City, Taiwan) with 150 bp paired-ended sequence reads.

value: whole seedling

value: sqtl1 RNAi

value: 16/8 light dark


title: Nonsmoker NS201714, baseline

description: Library name: NS201714

value: Bronchial brushing

value: Non-Hispanic

value: male


title: sh1-2

description: Library name: Sample5


title: Smoker S201704, follow-up

description: Library name: S201704-2

value: smoker

value: follow-up

value: female


title: Nonsmoker NS201713, baseline

description: Library name: NS201713


title: sh1-1

description: Library name: Sample4


title: P5 PBMC pre-operative, scTCRseq

description: 10x genomics

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell


title: P5 PBMC post-operative, Feature Barcoding(ADT)

description: 10x genomics

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti CD183/TotalSeq-C0140 ; Anti CD194/TotalSeq-C0071 ; Anti CD196/TotalSeq-C0143 ; Anti IgG1/TotalSeq-C090


title: L. japonicus WT symbiotic conditions, nodulated roots, biological replicate 3

description:
Library name: WTrootNod3
column name in gene_fpkm.txt: WTNod3

value: nodulated root

value: nodulation


title: P5 PBMC pre-operative, Feature Barcoding(ADT)

description: 10x genomics


title: Nonsmoker NS201712, baseline

description: Library name: NS201712

value: AAATFCTHV

value: nonsmoker

value: baseline

value: Black or African American


title: Nonsmoker NS201710, baseline

description: Library name: NS201710


title: Col-0-2

description: Library name: Sample2

value: whole seedling

value: Wild-type


title: P5 TIL, scTCRseq

description: 10x genomics

value: Tumor-infiltrating lymphocyte (TIL)

value: erythrocyte-removed TIL


title: L. japonicus WT ammonium nitrate, roots, biological replicate 3

description:
Library name: WTrootNN3
column name in gene_fpkm.txt: WTrootNN3

value: root

value: WT

value: ammonium nitrate


title: L. japonicus WT symbiotic conditions, nodulated roots, biological replicate 2

description:
Library name: WTrootNod2
column name in gene_fpkm.txt: WTNod2


title: P5 TIL, Feature Barcoding(ADT)

description: 10x genomics

value: Anti-CD4/TotalSeq-C0072 ; Anti-CD8A/TotalSeq-C0080 ; Anti CD62L/TotalSeq-C0147 ; Anti CD45RA/TotalSeq-C0063 ; Anti IgG1/TotalSeq-C090


title: L. japonicus WT symbiotic conditions, nodulated roots, biological replicate 1

description:
Library name: WTrootNod1
column name in gene_fpkm.txt: WTNod1


title: Col-0-1

description: Library name: Sample1

value: 16/8 light dark


title: L. japonicus WT ammonium nitrate, roots, biological replicate 2

description:
Library name: WTrootNN2
column name in gene_fpkm.txt: WTrootNN2


title: P5 PBMC pre-operative, scRNAseq

description: 10x genomics

value: Peripheral Blood Mononuclear Cells

value: CD3+ T cell


title: Col-0-3

description: Library name: Sample3


title: Nonsmoker NS201707, baseline

description: Library name: NS201707

value: Bronchial brushing

value: White

value: Non-Hispanic

value: male


title: ATAC-Seq, BMDM, 2nd Phase, Untrained1

city: Chongqing

first: Tao

last: Chen

address: No.426, Songshi North Road, Yubei District

country: China

institute: Stomatological Hospital of Chongqing Medical University

description: Library name: sample11

library_source: genomic

data_processing:
Raw data was preprocessed using SOAPnuke software to remove adapter sequences and low-quality reads, ensuring high-quality, contaminant-free data for further analysis. Key filtering parameters included stringent quality scores, adapter trimming, and minimum read length specifications.
Sequencing reads longer than 50bp were aligned to the mouse genome (mm10, Genome Reference Consortium Mouse Build 38, GCA_000001635.2) from UCSC (genome.ucsc.edu) using Bowtie2 (version 2.5.4). Subsequently, PCR duplicates were removed using Picard (version 3.2.0), and reads associated with mitochondrial chromatin were discarded post-deduplication. Peak calls for each replicate were made with MACS2 software in BAMPE mode. Deeptools (Version 3.2.1) bamCoverage was used to generate bigwig files for subsequent input into the IGV browser to obtain chromatin accessibility visualization for Acsl1.
As the first step to designate memory and suppressed domains, we used Bedtools (Version 2.28.0) to intersect untrained and diabetic-trained chromatin peaks during the rest phase with primary diabetic stimuli-induced consensus peaks (n=2). The intersected peaks from each rest phase sample were analyzed using the DiffBind package (Version 3.14.0) with the DESeq2 statistical method. Peaks with an FDR < 0.05 were selected, where those with log2FoldChange > 0 were designated as “memory domains”. Motif enrichment of memory domains of Acsl1 chromatin region was performed with HOMER software (Version 5.1) using default settings.
Assembly: mm10, Genome Reference Consortium Mouse Build 38, GCA_000001635.2
Supplementary files format and content: 1stPhase_deseq_sig_annotated.txt
Supplementary files format and content: 2ndPhase_deseq_sig_annotated.txt
Supplementary files format and content: RestPhase_deseq_sig_annotated.txt

molecule: genomic DNA

source_name: Bone Marrow

extract_protocol:
This in vitro model was adapted from Edgar et al.(Edgar et al. 2021) to mimic diabetic-trained and untrained BMDM states. Male C57BL/6J mice (8 weeks old) from the Laboratory Animal Center of National Bioindustry (Chongqing, China) were randomly allocated to control or diabetic groups. For diabetes induction, mice received low-dose streptozotocin (42-45 mg/kg/d; Solarbio, China) via intraperitoneal injection after a 12h fast, repeated daily for 5 days. One week post-final injection, mice with nonfasted blood glucose >16.9 mmol/L were deemed type 1 diabetic. After 6 weeks of hyperglycemia, bone marrow progenitors from both groups were isolated and cultured in 5 mmol/L glucose DMEM with recombinant murine M-CSF for 7 days (rest phase). Cells were then stimulated with 10 ng/mL IFN-γ and 100 ng/mL LPS for 16 hours (2nd phase). The trained BMDMs were analyzed for their epigenetic modifications and metabolic profiles.
(1) Cell Lysis: Lyse the cells and keep the cells on the ice all the time. (2) DNA Transposition and Tagmentation: Add Tn5 transposase to the cell suspension after cell lysis and then purify it with Qiagen MinElute PCR Purification Kit. (3) DNA Fragments Enrichment: Determine PCR cycles based on the DNA concentration and then purify the products with Qiagen MinElute PCR Purification Kit. (4) Size Selecting: Select DNA fragments with agarose gel electrophoresi. Dissolve the products after gel extraction with elution buffer. (5) Library quality control; (6) Library circularization; (7) The library was amplified to make DNA nanoball (DNB); (8) Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: Bone Marrow

value: primary cell

value: bone marrow derived macrophages


title: P5 TIL, scRNAseq

description: 10x genomics


title: Nonsmoker NS201705, baseline

description: Library name: NS201705

value: AAATFCTHV

value: nonsmoker

value: baseline

value: Unknown

value: female


title: L. japonicus WT ammonium nitrate, roots, biological replicate 1

description:
Library name: WTrootNN1
column name in gene_fpkm.txt: WTrootNN1

value: root

value: WT

value: ammonium nitrate


title: ATAC-Seq, BMDM, 2nd Phase, Diabetic-trained2

description: Library name: sample10


title: S3 Th17CD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and TCR clonotyping were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files for scRNA-seq, comma separated values files and protobuf binary files for scTCR-seq.

extract_protocol:
Th1, CXCR3±Th7R, Th17 T cells were separated from cultured frozen PBMC according to surface protein expression of CD4, CD62L, CXCR3, CCR4, CCR6 using Dynabeads and SH800Z. These sorted T cells were processed using Chromium controller according to manufacturer's standard protocol (10x genomics).
Library construction was performed according to the manufacturer's instructions (Chromium Single Cell Immune Profiling v2 protocol, 10x Genomics).

value: Peripheral Blood Mononuclear Cells

tag: disease

value: Lung cancer


title: ATAC-Seq, BMDM, 2nd Phase, Untrained2

description: Library name: sample12

tag: tissue


title: bronchiectasis patient 6,  scRNAseq

city: Stockholm

first: Tim

last: Willinger

address: Center for Infectious Medicine (CIM), Alfred Nobels allé 8, level 7

department: Department of Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Assembly: GRCh38
Supplementary files format and content: 10X Genomics .h5 file (gene expression matrices)

source_name: Bronchoalveolar lavage fluid

extract_protocol:
Further processing of sorted immune cells (GEM generation, barcoding, cleanup, cDNA amplification) was done using reagents and protocols from 10X Genomics Single Cell NEXT GEM 3′ Library v3 kit.
Library construction was done using protocol and reagents from 10X Genomics Single Cell NEXT GEM 3′ Library v3 kit.

value: Immune cells

value: Bronchoalveolar lavage fluid

value: bronchiectasis

tag: age


title: S3 CXCR3-Th7RCD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics


title: bronchiectasis patient 5,  scRNAseq

description: 10x Genomics

tag: disease state


title: TRa_mKO_GA_rep2

city: nanjing

first: Yusheng

last: Zhang

address: Nanjing Medical university

institute: Division of Geriatrics

description:
Library name: KO_2
RNA-seq of gastrocnemius muscle from 8-week-old male mice
CRE96 Read Count

data_processing:
Raw sequencing reads in FASTQ format underwent quality control using FastQC (v0.11.9) and MultiQC (v1.12). Adapter contamination and low-quality reads were trimmed using Trimmomatic (v0.39) with parameters: ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36, or processed using SOAPnuke (BGI) with default filtering parameters (quality threshold ≥ 20, minimum length ≥ 36 bp).
Assembly: mm10 (GRCm38.p6), GENCODE Release M25 (or Ensembl 98) gene annotation
Supplementary files format and content: Tab-delimited text file (.txt) containing raw gene-level read counts suitable for differential expression analysis. Columns: Gene ID (Ensembl identifier), Gene Symbol, followed by 6 sample columns (CRE114, CRE87, CRE96, WT64, WT66, WT70) representing biological replicates of TRalpha-mKO (n=3) and Wild-type (n=3) gastrocnemius muscle. Values represent integer counts of uniquely mapped reads per gene (non-normalized, un-transformed raw counts). This matrix corresponds to transcriptomic analysis of 8-week-old male mice comparing skeletal muscle-specific TRalpha knockout versus control to investigate sarcopenia-associated gene expression changes.
Supplementary files format and content: Tab-delimited text file (.txt) containing gene-level raw read counts. Rows: Ensembl Gene IDs (GRCm39); Columns: 6 samples (WT_1-3, mKO_1-3). Values: raw counts (featureCounts). Delimiter: ASCII tab (\t).

source_name: gastrocnemius

growth_protocol: Mice were housed in a specific pathogen-free (SPF) facility with controlled temperature (22±2°C) and 12-hour light/dark cycle, fed standard chow diet ad libitum. TRalpha muscle-specific conditional knockout (TRalpha-mKO) mice were generated by crossing THRA-floxed mice (Thra<fl/fl>) with Myf5-Cre transgenic mice [B6.Cg-Tg(Myf5-cre)1Jme/J] to achieve skeletal muscle-specific ablation of thyroid hormone receptor alpha starting from embryonic myogenesis. Wild-type (WT) littermates (Thra<fl/fl> without Cre recombinase) served as age-matched controls. Genotypes were confirmed by PCR analysis of tail DNA. At 8 weeks of age (young adult), male mice were sacrificed and gastrocnemius muscles were immediately dissected, snap-frozen in liquid nitrogen, and stored at -80°C until RNA extraction. This 8-week time point captures early sarcopenic phenotypes induced by cell-autonomous TRalpha deficiency, preceding chronological aging.

extract_protocol:
Total RNA was extracted from approximately 30-50 mg of frozen gastrocnemius muscle tissue using TRIzol Reagent (Invitrogen, Cat# 15596026) according to the manufacturer's protocol. Tissue was homogenized in 1 mL TRIzol using a bead mill or tissue grinder. Following chloroform phase separation (200 μL), the aqueous phase was collected by centrifugation at 12,000 × g for 15 min at 4°C. RNA was precipitated with isopropanol, washed twice with 75% ethanol, air-dried, and resuspended in 30 μL RNase-free water. RNA quality was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies); only samples with RNA Integrity Number (RIN) ≥ 7.5 were selected for library construction. RNA concentration and purity (A260/A280 ratio 1.9-2.1) were measured using a NanoDrop spectrophotometer.
Stranded mRNA sequencing libraries were prepared using the MGIEasy RNA Library Prep Kit (BGI Genomics) compatible with BGISEQ-500 platform, or equivalent TruSeq-based protocol adapted for DNBSEQ technology. Briefly, 1 μg of total RNA underwent poly(A) selection using oligo(dT) magnetic beads to enrich mRNA. Enriched RNA was fragmented using divalent cations at elevated temperature, followed by first-strand cDNA synthesis using random hexamers and reverse transcriptase. Second-strand cDNA synthesis incorporated dUTP (for strandedness) using DNA polymerase I. Double-stranded cDNA underwent end-repair, 3'-end adenylation, and ligation of BGISEQ-500 adapters with molecular barcodes. Adapter-ligated fragments were purified and amplified by PCR (10-12 cycles). Library quality was verified on an Agilent 2100 Bioanalyzer using DNA High Sensitivity chips, and concentrations were determined by Qubit fluorometry. Paired-end 100 bp (PE100) sequencing was performed on the BGISEQ-500 platform (BGI Genomics) at a depth of ~20-30 million reads per sample.

treatment_protocol: No pharmacological or dietary interventions were applied. Mice were maintained under standard conditions until endpoint. Euthanasia was performed by cervical dislocation following CO₂ inhalation anesthesia. Gastrocnemius skeletal muscles were rapidly excised, trimmed of visible adipose and connective tissue, immediately frozen in liquid nitrogen-cooled isopentane to preserve RNA integrity, and stored at -80°C.

value: gastrocnemius

value: TRalpha-mKO (Myf5-Cre; Thrafl/fl)

tag: batch


title: S3 CXCR3+Th7RCD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics


title: ATAC-Seq, BMDM, 2nd Phase, Diabetic-trained1

description: Library name: sample9

value: Bone Marrow

value: primary cell

tag: cell type


title: TRa_mKO_GA_rep3

description:
Library name: KO_3
RNA-seq of gastrocnemius muscle from 8-week-old male mice
CRE114 Read Count


title: ATAC-Seq, BMDM, Rest Phase, Untrained2

description: Library name: sample8

value: bone marrow derived macrophages


title: Nonsmoker NS201703, baseline

description: Library name: NS201703

value: Bronchial brushing

tag: subject id

tag: flowcell

value: AAATFCTHV

value: nonsmoker

value: Black or African American

value: Non-Hispanic

value: male


title: bronchiectasis patient 4,  scRNAseq

description: 10x Genomics


title: S3 Th1CD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics


title: WT_GA_rep2

description:
Library name: WT_2
RNA-seq of gastrocnemius muscle from 8-week-old male mice
WT66 Read Count

value: Wild-type (Thrafl/fl)


title: ATAC-Seq, BMDM, Rest Phase, Untrained1

description: Library name: sample7

tag: cell line


title: bronchiectasis patient 3,  scRNAseq

description: 10x Genomics


title: ATAC-Seq, BMDM, Rest Phase, Diabetic-trained2

description: Library name: sample6


title: TRa_mKO_GA_rep1

description:
Library name: KO_1
RNA-seq of gastrocnemius muscle from 8-week-old male mice
CRE87 Read Count


title: WT_GA_rep3

description:
Library name: WT_3
RNA-seq of gastrocnemius muscle from 8-week-old male mice
WT70 Read Count


title: S2 CXCR3-Th7RCD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics

value: Peripheral Blood Mononuclear Cells


title: bronchiectasis patient 1,  scRNAseq

description: 10x Genomics


title: S2 CXCR3+Th7RCD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics

value: Lung cancer


title: ATAC-Seq, BMDM, Rest Phase, Diabetic-trained1

description: Library name: sample5


title: Ktx-14d-3

city: yichang

first: huimin

last: Li

state: hubei

address: Wujiagang District, Yichang City, Hubei Province

institute: Yichang Central People's Hospital

data_processing:
Beijing Genomics Institute  conducted an RNA sequencing analysis (Shenzhen, China). DESeq2 was used to examine the genes with variable expression. Gene was considered significant when the adjusted P value.
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: kidney

growth_protocol: All mice were maintained at a constant temperature (19-21℃), with free access to food and water during a 12-hour light/dark cycle.

extract_protocol:
Briefly,Trizolreagent (Invitrogen,  USA) was used to extract the total RNA from the renal cortex following the manufacturer's directions.
A NanoDrop spectrophotometer determined the RNA concentration.

treatment_protocol: A mouse model of diabetes was successfully established by STZ injection,and  AKI  was  induced  in  mice  by  ischemia-reperfusion.

value: kidney

value: RPTCs

value: Rat kidney proximal tubular cells

value: WT

value: cold storage-associated kidney transplantation,After transplantation, grafts were harvested at 14days


title: bronchiectasis patient 2,  scRNAseq

description: 10x Genomics

value: Immune cells

value: Bronchoalveolar lavage fluid

value: bronchiectasis


title: WT_GA_rep1

description:
Library name: WT_1
RNA-seq of gastrocnemius muscle from 8-week-old male mice
WT64 Read Count

value: gastrocnemius


title: S2 Th1CD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics


title: S2 Th17CD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics


title: S1 Th17CD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics


title: ATAC-Seq, BMDM, 1st Phase, Healthy1

description: Library name: sample3

value: Bone Marrow

value: primary cell

value: bone marrow derived macrophages


title: ATAC-Seq, BMDM, 1st Phase, Healthy2

description: Library name: sample4


title: Ktx-14d-1


title: ATAC-Seq, BMDM, 1st Phase, Diabetic2

description: Library name: sample2


title: S1 CXCR3-Th7RCD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics


title: patient5: T2D - pre SGLT2i

first: Jennifer

middle: A.

last: Schaub

address: 1500 Medical Center Dr

department: Internal Medicine

description:
Library name: patient5
Formalin fixed paraffin embedded (FFPE) biopsy cores processed with VisiumHD 8 um bins

data_processing:
Probes covering nearly the entire transcriptome (Visium Human Transcriptome Probe Set v2.0) are then applied to the tissue to pair transcript expression with the spatial barcode identifier for each molecule. Thus, each measured transcript can be mapped to specific tissue coordinates allowing for an exploration of RNA expression in native tissue context.
After sequencing of the transcripts and accompanying barcodes, transcript based reads were aligned against the h38 genome (GRCh38-2020-A) within spaceranger (v3.1.1) to build count matrices of gene expression for each 8 um x 8 um spot.
Spots with low counts (<20) were removed using Seurat v5.
Then the filtered matrices were normalized, scaled, reduced to low dimensional embeddings, and subsequently integrated using the Harmony algorithm to create a unified representation of the data.
The integrated dataset was then clustered and highly upregulated genes in each cluster (identified by the Wilcoxon rank sum test in Seurat) along with spatial context of the cluster’s location in situ were used to annotate the predominant cell type in each spot.
Assembly: GRCh38-2020-A
Supplementary files format and content: Harmony integrated rds object
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol: Formalin fixed paraffin embedded (FFPE) biopsy cores from four individuals with type 2 diabetes (T2D) not treated with SGLT2i were sectioned, placed on a slide, and run through the VisiumHD platform (v1; 10x). Each slide is comprised of a grid of 8 um by 8 um squares and each square or spot is covered in a lawn of one unique barcode identifier that anneals to any RNA within that grid space.

value: Kidney

value: Kidney and immune cells


title: Sham-14d-3

value: sham


title: Ktx-14d-2


title: patient7: T2D - pre SGLT2i

description:
Library name: patient7
Formalin fixed paraffin embedded (FFPE) biopsy cores processed with VisiumHD 8 um bins


title: ATAC-Seq, BMDM, 1st Phase, Diabetic1

description: Library name: sample1


title: Sham-14d-2


title: S1 CXCR3+Th7RCD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics

source_name: Peripheral Blood Mononuclear Cells

value: Peripheral Blood Mononuclear Cells


title: patient1: T2D - pre SGLT2i

description:
Library name: patient1
Formalin fixed paraffin embedded (FFPE) biopsy cores processed with VisiumHD 8 um bins


title: Sham-14d-1


title: patient9: T2D - pre SGLT2i

description:
Library name: patient9
Formalin fixed paraffin embedded (FFPE) biopsy cores processed with VisiumHD 8 um bins


title: BMDM, 2nd Phase, Untrained2

description: Library name: sample13

data_processing:
The sequencing data was filtered with SOAPnuke (1 by (1) Removing reads containingsequencing adapter; (2) Removing reads whose low-quality base ratio (base quality lessthan or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N'base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQformat. The subsequent analysis and data mining were performed on Dr. Tom Multi-omicsData mining system (https://biosys.bgi.com).
The clean data were aligned to the reference genome (https://hgdownload.soe.ucsc.edu/goldenPath/mm10/) using HISTA2 software (v2.1.0). Subsequently, gene fusion detection was performed using Ericscript (v0.5.5), and alternative splicing and differential alternative splicing analysis were conducted using rMATS (V3.2.5).
Assembly: GRCm38/mm10
Supplementary files format and content: RestPhaseCounts.txt/1stPhaseExpression.txt

extract_protocol:
This in vitro model was adapted from Edgar et al.(Edgar et al. 2021) to mimic diabetic-trained and untrained BMDM states. Male C57BL/6J mice (8 weeks old) from the Laboratory Animal Center of National Bioindustry (Chongqing, China) were randomly allocated to control or diabetic groups. For diabetes induction, mice received low-dose streptozotocin (42-45 mg/kg/d; Solarbio, China) via intraperitoneal injection after a 12h fast, repeated daily for 5 days. One week post-final injection, mice with nonfasted blood glucose >16.9 mmol/L were deemed type 1 diabetic. After 6 weeks of hyperglycemia, bone marrow progenitors from both groups were isolated and cultured in 5 mmol/L glucose DMEM with recombinant murine M-CSF for 7 days (rest phase). Total RNA was extracted from tissues using TRlzol (Invitrogen, Carlsbad, California,USA) according to manual instruction. For cell samples, the TRlzol was directly added to the cell sample with the amount 1mL per 1x10^6 cells, followed by vortex mixing and standing for 5-minute. Themixture was centrifuged at 4°C at 12,000xg for 5 minutes, and the supernatant wastransferred to a new EP tube for extraction. 300ul of chloroform/isoamyl alcohol(24:1) was added into the transferred supernatant and the mixture was vigorouslyvortexed to ensure thorough mixing. Then the mixture was centrifuged at 4°C and12,000xg for 8 minutes. Take the clear upper aqueous layer and repeat the aboveprocess one time. After centrifugation, the final upper aqueous layer was carefully transferred to a new 1.5ml EP tube with a 2/3 supernatant volume of isopropanol(for low amount of tissues/ cell, 2ul 5mg/mL glycogen can be added forprecipitation), gently inverted to mix well, placed in a -20°C refrigerator for 2 hours.Next, the precipitation mixture was centrifuged with 17500xg at 4°C for 25 minutes.The supernatant was discarded, and the precipitation was washed with 0.9ml of 75%ethanol. The precipitation was suspended by inverting the tube up and downseveral times. Then the precipitation was collected by centrifuging at 17500g for 3minutes at 4°C and discarding the supernatant. Repeat the centrifugation to removesupernatant completely and the precipitation was dried in the biosafety cabinet for3-5 minutes. Finally, 20uL~200ul of DEPC-treated or RNase-free water was added todissolve the RNA. Subsequently, total RNA was qualified and quantified using Qseq-400(Bioptic, Taiwan, China).
(1) Cell Lysis: Lyse the cells and keep the cells on the ice all the time. (2) DNA Transposition and Tagmentation: Add Tn5 transposase to the cell suspension after cell lysis and then purify it with Qiagen MinElute PCR Purification Kit. (3) DNA Fragments Enrichment: Determine PCR cycles based on the DNA concentration and then purify the products with Qiagen MinElute PCR Purification Kit. (4) Size Selecting: Select DNA fragments with agarose gel electrophoresi. Dissolve the products after gel extraction with elution buffer. (5) Library quality control; (6) Library circularization; (7) The library was amplified to make DNA nanoball (DNB); (8) Sequencing on DNBSEQ (DNBSEQ Technology) platform.


title: BMDM, 2nd Phase, Untrained3

description: Library name: sample14


title: S1 Th1CD62LlowCD4+ T cell, scTCR-seq

description: 10x genomics

value: Lung cancer


title: S3 Th17CD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: BMDM, 2nd Phase, Untrained1

description: Library name: sample12


title: S3 CXCR3-Th7RCD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: Ktx-7d-2

value: kidney

value: cold storage-associated kidney transplantation,After transplantation, grafts were harvested at 7days


title: Ktx-7d-3

value: RPTCs

value: Rat kidney proximal tubular cells


title: BMDM, 2nd Phase, Diabetic-trained3

description: Library name: sample11


title: PBT707IL15_1

city: Duarte

first: Guihua

last: Sun

state: CA

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

description:
Library name: Sample7
2x150, 40M paired end reads (20M in each direction) per sample

data_processing:
bbduk to remove primer in fastq.gz files
subread for alignment using hg38 genmoe, output bam files
featurecounts generate gene read count table
Assembly: human hg38
Supplementary files format and content: featurecounts generate gene read count table .txtx file

source_name: Human peripheral blood mononuclear cells (PBMCs)

growth_protocol: Generation of CAR-T cells  Fresh PBMCs were stimulated with Dynabeads Human T-Expander CD3/CD28 (Fisher Scientific, Cat# 11131D) at a ratio of 1:3 (cell:bead) in RPMI 1640 medium (Gibco, Cat# 11875085) containing 10% FBS, 25 U/mL rhIL-2. Cells were transduced with lentivirus to express BiCAR with 5 µg/ml polybrene following a published procedure (Prommersberger et al., 2020). Cultures were then maintained under the same medium and cytokine conditions. Fresh cytokines were supplied every other day. On day 9 after transduction, the CD3/CD28 Dynabeads were removed from the culture using the DynaMag-50 magnet (Fisher Scientific, Cat# 12321D). The cells were expanded in culture until harvest at day 17 or as indicated.The PBMC-derived CAR-T cells were sorted by flow cytometry. The sorted CAR-T cells were cultured on 50 × 106 γ-irradiated (35 Gy) PBMCs and 10 × 106 γ-irradiated K562-mIL21 cells (80 Gy) in 50 mL RPMI 1640 medium containing 10% FBS, 20 ng/mL anti-CD3 (Miltenyi Biotec, Cat# 130-093-377), 50 U/mL rhIL-2 and 10 ng/mL rhIL-7. The cultures were maintained for 14 days with half-volume medium changes every 2 days.

extract_protocol:
Total RNA isolated using Trizol reagent (Ambion)
NEBNext Ultra II (Directional) with Poly A selection

treatment_protocol: GBM cells as the target cells were infected with an oncolytic virus encoding truncated CD19 and EGFRvIII antigens at a multiplicity of infection (MOI) of 1 for 4 hours, together with an oncolytic virus encoding membrane-bound IL-15 and membrane-bound IL-21 (mIL15/mIL21) or a control virus encoding GFP. After infection, Bi-specific CAR-T cells were added at a 1:1 effector-to-target (E:T) ratio. Following 48 hours of co-culture, cells were collected for RNA extraction using TRIzol reagent. The purified RNA samples were subsequently submitted to the vendor for bulk RNA sequencing (RNA-seq) analysis.

value: Cocultured with oncolytic virus and PBT cells


title: S3 CXCR3+Th7RCD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: Ktx-7d-1

value: WT


title: BMDM, 2nd Phase, Diabetic-trained2

description: Library name: sample10


title: PBT707GFP_2

description:
Library name: Sample6
2x150, 40M paired end reads (20M in each direction) per sample

value: Human peripheral blood mononuclear cells (PBMCs)


title: PBT003IL15_2

description:
Library name: Sample4
2x150, 40M paired end reads (20M in each direction) per sample


title: PBT707GFP_1

description:
Library name: Sample5
2x150, 40M paired end reads (20M in each direction) per sample


title: PBT707IL15_2

description:
Library name: Sample8
2x150, 40M paired end reads (20M in each direction) per sample


title: BMDM, 2nd Phase, Diabetic-trained1

description: Library name: sample9


title: Sham-7d-3


title: PBT003IL15_1

description:
Library name: Sample3
2x150, 40M paired end reads (20M in each direction) per sample


title: S3 Th1CD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: Sham-7d-1


title: PBT003GFP_2

description:
Library name: Sample2
2x150, 40M paired end reads (20M in each direction) per sample


title: S2 Th17CD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: BMDM, 1st Phase, Healthy3

description: Library name: sample7


title: BMDM, 1st Phase, Healthy4

description: Library name: sample8


title: S2 CXCR3+Th7RCD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: PBT003GFP_1

description:
Library name: Sample1
2x150, 40M paired end reads (20M in each direction) per sample


title: BMDM, 1st Phase, Healthy2

description: Library name: sample6


title: S2 Th1CD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: BMDM, 1st Phase, Healthy1

description: Library name: sample5


title: Ktx-1d-2

value: cold storage-associated kidney transplantation,After transplantation, grafts were harvested at 24h


title: S1 Th17CD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: Ktx-1d-1


title: Sham-7d-2


title: Neural organoid control

city: Leeds

first: Heiko

last: Wurdak

address: Worsley Building, University of Leeds, Woodhouse

country: United Kingdom

institute: Leeds Institute of Medical Research (LIMR)

description:
Library name: Sample 12
Never cocultured with GB cells

data_processing:
For bioinformatic analysis of the GB-FUCCI cells, FASTQ files were delivered via the sequencing provider (Novogene) cloud-based platform. Following data integrity verification using a Message-digest algorithm 5 (MD5) checker to ensure complete cloud delivery, sequencing data were concatenated and aligned to the human genome reference GRCh38 (Hg38) using the PARSE bioinformatics pipeline (https://www.biomage.net/blog/converting-parsebio-output-for-cellenics). The organoids were preprocessed and filtered using the following parameters: filtered to retain cells with more than 5000 UMIs, normalisation using LogNormalize and scale factor kept at 10000. The resulting outputs was formatted for compatibility with 10x Genomics analytical workflows and analysed using the BioTuring ‘BBrowser’ platform (https://bioturing.com/).
Assembly: Human/ Homo sapiens GRCh38 (Hg38)
Supplementary files format and content: tab-separated value files and matrix files

source_name: Hoik_1 cells

extract_protocol:
GB-FUCCI (FUCCI_GBM1) cells were enzymatically dissociated from adherent cultures using TrypLE™ Express Enzyme (Thermo Fisher Scientific, Cat# 12604013). Cell suspensions were centrifuged at 300 × g and resuspended in NB medium. Samples were fixed using the Evercode™ Cell Fixation v2 kit (Parse Biosciences, ECF2001/ECF2101) following the manufacturer’s instructions. Fixed cells were stored at –80 °C for up to 1 month prior to barcoding. GB spheroids were co-cultured with either neural-like organoids, or foregut-like organoids. A few days were given for the GB cells to invade into the neigbouring organoid/ environment. The now “assembloid” was dissociated and the GB cells and environment cells separated by Fluorescence-Activated Cell Sorting through the means of GFP expressing GB cells. The cells were then pooled again at a 1:1 ratio.
Library preparation was performed for the GB-FUCCI cells according to manufacturer instructions using the EvercodeTM WT Mini v2 kit (Parse Biosciences, ECW02010/ECW02110). Fixed single-cell suspensions underwent a series of intracellular, instrument-free reverse transcription barcoding reactions. Resulting barcoded libraries were divided into sublibraries as required, with an additional sublibrary-specific barcode introduced. Final sublibraries were lysed, and barcoded cDNA was amplified by PCR and prepared for Illumina sequencing. Satisfactory sublibrary quality control was checked and confirmed on a Tapestation 4200 (Agilent). Sequencing was performed using the NovaSeq 6000 platform with a resultant 100% clean reads.Library preparation for the pooled assembloid cells was performed using the 10x Genomics GEM-X 3′ v4 assay, and the libraries were processed and sequenced on an Illumina NovaSeq X Plus at 50,000 reads per cell using the 10x Genomics 3′ Single Cell Gene Expression Service provided by Single Cell Discoveries.

value: Hoik_1 cells


title: BMDM, 1st Phase, Diabetic3

description: Library name: sample3

value: Bone Marrow


title: S1 CXCR3+Th7RCD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: BMDM, 1st Phase, Diabetic4

description: Library name: sample4

value: primary cell


title: Ktx-1d-3


title: BMDM, 1st Phase, Diabetic2

description: Library name: sample2

value: bone marrow derived macrophages


title: sham-1d-2


title: S2 CXCR3-Th7RCD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: Foregut organoid control

description:
Library name: Sample 7
Never cocultured with GB cells


title: S1 CXCR3-Th7RCD62LlowCD4+ T cell, scRNA-seq

description: 10x genomics


title: GB cells pooled with associated Neural-like organoid

description:
Library name: Sample 14
Pooled at a 1:1 ratio


title: sham-1d-3


title: Non-fluorescent late L4-stage cells other than DTC, Sample 3

status: Public on Feb 04 2026

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

description: Library name: NL43

data_processing:
Quality control - FastQC
Adapter trimming - CutAdapt
Alignment - bowtie2
Feature counting - HTseq_count
Assembly: WS235/ce11
Supplementary files format and content: Raw count matrix (comma-separated values)

organism: Caenorhabditis elegans

source_name: Other worm tissue except DTC

growth_protocol: Worms expressing Venus-labelled DTC were grown on the plates containing nematode growth media (NGM) seeded with OP50, an E. coli strain, at 20°C

extract_protocol:
The miRNeasy Mini Kit (Qiagen, Cat no. 217004) was used for RNA extraction. We obtained approximately 5-9 ng/μl of RNA from 30,000 to 60, 000 cells.
One ng of cDNA was used as input for preparation of sequencing libraries using the Nextera XT DNA Sequencing kit (Illumina). Libraries were prepared according to the manufacturer's instructions.

value: Other worm tissue except DTC

value: Other cells

value: Wild-type


title: GB cells

description:
Library name: Sample 8
GB cells from a flask


title: GB cells pooled with associated Foregut-like organoid

description:
Library name: Sample 6
Pooled at a 1:1 ratio


title: Non-fluorescent late L4-stage cells other than DTC, Sample 2

description: Library name: NL42


title: BMDM, 1st Phase, Diabetic1

description: Library name: sample1


title: sham-1d-1

value: sham


title: Non-fluorescent early L4-stage cells other than DTC, Sample 1

description: Library name: NL31


title: Non-fluorescent late L4-stage cells other than DTC, Sample 1

description: Library name: NL41


title: Non-fluorescent early L4-stage cells other than DTC, Sample 3

description: Library name: NL33


title: Non-fluorescent early L4-stage cells other than DTC, Sample 2

description: Library name: NL32


title: Non-fluorescent late L3-stage cells other than DTC, Sample 2

description: Library name: NL22


title: Non-fluorescent adult-stage cells other than DTC, Sample 3

description: Library name: NA3


title: S1 Th1CD62LlowCD4+ T cell, scRNA-seq

first: Satoshi

last: Yamasaki

description: 10x genomics

value: Peripheral Blood Mononuclear Cells

value: Lung cancer


title: Non-fluorescent late L3-stage cells other than DTC, Sample 1

description: Library name: NL21


title: Non-fluorescent adult-stage cells other than DTC, Sample 2

description: Library name: NA2


title: Venus-positive early L4-stage DTCs, Sample 3

description: Library name: GL33

source_name: Somatic gonad (DTC)

value: Somatic gonad (DTC)

value: Distal tip cell (DTC)


title: Venus-positive early L4-stage DTCs, Sample 2

description: Library name: GL32


title: Venus-positive late L4-stage DTCs, Sample 3

description: Library name: GL43


title: Non-fluorescent late L3-stage cells other than DTC, Sample 3

description: Library name: NL23


title: Venus-positive late L4-stage DTCs, Sample 2

description: Library name: GL42


title: Venus-positive late L4-stage DTCs, Sample 1

description: Library name: GL41


title: Venus-positive early L4-stage DTCs, Sample 1

description: Library name: GL31


title: Venus-positive late L3-stage DTCs, Sample 2

description: Library name: GL22


title: Venus-positive late L3-stage DTCs, Sample 3

description: Library name: GL23


title: Non-fluorescent adult-stage cells other than DTC, Sample 1

description: Library name: NA1


title: Venus-positive late L3-stage DTCs, Sample 1

description: Library name: GL21


title: Venus-positive adult-stage DTCs, Sample 3

description: Library name: GA3


title: daf-16(lf); daf-2(lf), all cells, rep 1

city: Toronto

first: Shifei

last: Wu

state: Ontario

address: 1 King's College Cir

country: Canada

institute: University of Toronto

description: Library name: Sample22

data_processing:
Salmon 1.4.0 was used to quantify transcript abundance
Assembly: WBcel235
Supplementary files format and content: csv file includes TPM values for all samples

source_name: all

extract_protocol:
RNA was extracted from sorted cells using TRIzol LS followed by chloroform and cleaned up using Zymo RNA Clean & Concentrator-5.
For single-end samples, RNA was assessed by Fragment Analyzer, and high quality total RNA was subjected to library preparation using the Illumina TruSeq Stranded mRNA Library Preparation Kit (Cat# 20020594) according to the manufacturer’s instructions. For paired-end samples, RNA quality was assessed by Agilent Bioanalyzer 2100. The full length cDNA library was first generated from high quality total RNA using TaKaRa SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Cat# 634890) according to manufacturer protocol. The final barcoded sequencing libraries were prepared from the full length cDNA using Illumina Nextera Flex according to manufacturer protocol.

value: all

value: daf-16(lf); daf-2(lf)


title: daf-2(lf), all cells, rep 1

description: Library name: Sample19


title: daf-16(lf); daf-2(lf), all cells, rep 2

description: Library name: Sample23


title: daf-2(lf), all cells, rep 2

description: Library name: Sample20


title: daf-16(lf); daf-2(lf), muscle cells, rep 3

description: Library name: Sample14

source_name: muscle

value: muscle


title: Venus-positive adult-stage DTCs, Sample 1

description: Library name: GA1


title: Venus-positive adult-stage DTCs, Sample 2

description: Library name: GA2


title: daf-2(lf), all cells, rep 3

description: Library name: Sample21


title: daf-16(lf); daf-2(lf), muscle cells, rep 2

description: Library name: Sample13


title: daf-2(lf), muscle cells, rep 3

description: Library name: Sample11


title: daf-2(lf), muscle cells, rep 1

description: Library name: Sample9


title: daf-16(lf); daf-2(lf), all cells, rep 3

description: Library name: Sample24


title: Week 9 male rat venticle heart muscle, Vegfb KO diabetes 3

city: Vancouver

first: Hualin

last: Wang

state: BC

address: 2405 Wesbrook Mall

department: Faculty of Pharmaceutical Sciences

institute: University of British Columbia

description: Library name: KOD3

data_processing:
First, I processed the raw FASTQ data to generate count matrices with Kallisto for transcript quantification, then I used tximport package to generate count data based on transcription abundance files from Kallisto. Then I created DGEList object containing the count matrix, sample information, and gene annotations. Duplicate annotations were removed and keep only the first occurrence of each ENSEMBL gene ID for simplicity. The entire with missing symbol was also be removed. The low-count genes will be filtered out. Then I normalized the data by EdgeR using trimmed mean of M values method and DESeq2 based on median of ratios normalization. I will also perform quality control using multi-dimensional scaling (MDS) plots and PCA plot to evaluate sample clustering and identify potential outliers.
Assembly: mRatBN7.2
Supplementary files format and content: The processed RNA-seq data are stored in a plain text file (.txt) in tab-delimited matrix format. This file contains raw counts for each sample

organism: Rattus norvegicus

source_name: venticle heart muscle

growth_protocol: VegfbKO and Wildtype (WT) littermate male rats 9 weeks old were used for various studies. All animals had free access to food (LabDiet PicoLab Rodent 20 No. 5053) and reverse osmosis water and were housed in standard cages with 12 h of light/dark cycles.

extract_protocol:
Total RNA was extracted from frozen ventricular tissue using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. The concentration and purity of the RNA samples were checked by Qubit fluorometer. The RNA integrity of the RNA samples was checked by Bioanalyzer. Then, we sent our qualified RNA sample to Sequencing Core Facility for library preparation and sequencing.
The sequencing library was prepared using NEBNext Ultra II Directional RNA library Prep Kit and sequenced using Illumina Nextseq 500 platform to generate paired-end reads.

treatment_protocol: Diabetes was induced by intravenous administration of streptozotocin (Sigma) (55 mg/kg) to kill the insulin-producing beta cells.  All animals injected with STZ developed hyperglycemia and hypoinsulinemia within 24 hours. Animals were monitored for 4 days. On day 4 of diabetes, ventricular tissue was collected from diabetic rats and their littermate-matched controls.

value: venticle heart muscle

value: Vegfb KO

value: 4 day 55mg/kg STZ


title: Week 9 male rat venticle heart muscle, Vegfb KO diabetes 5

description: Library name: KOD5


title: Week 9 male rat venticle heart muscle, Vegfb KO diabetes 4

description: Library name: KOD4


title: Week 9 male rat venticle heart muscle, Vegfb KO diabetes 2

description: Library name: KOD2


title: daf-2(lf), muscle cells, rep 2

description: Library name: Sample10


title: daf-16(lf); daf-2(lf), muscle cells, rep 1

description: Library name: Sample12


title: Week 9 male rat venticle heart muscle, Vegfb KO control 4

description: Library name: KOC4

value: control


title: Week 9 male rat venticle heart muscle, Vegfb KO control 5

description: Library name: KOC5


title: Week 9 male rat venticle heart muscle, Vegfb KO diabetes 1

description: Library name: KOD1


title: Week 9 male rat venticle heart muscle, Vegfb KO control 3

description: Library name: KOC3


title: Week 9 male rat venticle heart muscle, Vegfb KO control 2

description: Library name: KOC2


title: Week 9 male rat venticle heart muscle, Vegfb KO control 1

description: Library name: KOC1


title: Week 9 male rat venticle heart muscle, Wildtype diabetes 5

description: Library name: WTD5

value: WT


title: Week 9 male rat venticle heart muscle, Wildtype diabetes 4

description: Library name: WTD4


title: Week 9 male rat venticle heart muscle, Wildtype control 5

description: Library name: WTC5


title: Week 9 male rat venticle heart muscle, Wildtype diabetes 3

description: Library name: WTD3


title: Week 9 male rat venticle heart muscle, Wildtype control 2

description: Library name: WTC2


title: Week 9 male rat venticle heart muscle, Wildtype control 3

description: Library name: WTC3


title: Week 9 male rat venticle heart muscle, Wildtype diabetes 2

description: Library name: WTD2


title: whole_blood_203810640100_R04C01

type: genomic

city: Oslo

first: Lasse

last: Pihlstrøm

address: Sognsvannsveien 20

department: Department of Neurology

country: Norway

institute: Oslo University Hospital

description: Human whole blood

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using and Illumina array scanner with standard recommended Illumina settings

data_processing:
Raw signal intensity data were imported into R using the minfi package. CpG sites with a beadcount < 3 in 5% of samples or detection p-value > 0.05 in 1% of samples were filtered out using the pfilter function in the wateRmelon package. Samples failing sex-checks, samples with low median signal intensities as flagged by the minfi getQC function and samples flagged as outliers by the wateRmelon outlyx function were filtered out. The wateRmelon dasen method was used for normalization. After mapping of methylation data to the genome we removed probes on sex chromosomes, probes  overlapping loci with known single-nucleotide polymophisms (SNPs) and probes previously reported  as cross-reactive. We removed probes showing predominantly  technical variation (ICC < 0.1), leaving 502,261 CpGs in the dataset.
Normalized average Beta using the dasen method implemented in the wateRmelon R package

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted by a commercial provider using a standard method, exact protocol unknown

tag: slide

value: N

value: Female

value: CONTR


title: whole_blood_203810640100_R05C01

description: Human whole blood

value: Male

value: PD


title: whole_blood_203810640100_R02C01

description: Human whole blood


title: Week 9 male rat venticle heart muscle, Wildtype control 4

description: Library name: WTC4


title: whole_blood_203810640100_R08C01

description: Human whole blood


title: whole_blood_203810640098_R07C01

description: Human whole blood


title: Week 9 male rat venticle heart muscle, Wildtype control 1

description: Library name: WTC1


title: Week 9 male rat venticle heart muscle, Wildtype diabetes 1

description: Library name: WTD1


title: whole_blood_203810640100_R07C01

description: Human whole blood


title: whole_blood_203810640100_R06C01

description: Human whole blood


title: whole_blood_203810640100_R03C01

description: Human whole blood


title: whole_blood_203810640100_R01C01

description: Human whole blood


title: whole_blood_203810640098_R04C01

description: Human whole blood


title: whole_blood_203810640098_R08C01

description: Human whole blood


title: whole_blood_203810640098_R06C01

description: Human whole blood


title: whole_blood_203810640091_R07C01

description: Human whole blood


title: whole_blood_203810640091_R08C01

description: Human whole blood


title: whole_blood_203810640098_R03C01

description: Human whole blood


title: whole_blood_203810640098_R05C01

description: Human whole blood


title: whole_blood_203810640098_R02C01

description: Human whole blood


title: whole_blood_203810640091_R05C01

description: Human whole blood


title: whole_blood_203810640098_R01C01

description: Human whole blood


title: whole_blood_203810640091_R06C01

description: Human whole blood


title: whole_blood_203810640091_R04C01

description: Human whole blood


title: whole_blood_203810640091_R01C01

description: Human whole blood


title: whole_blood_203821710075_R08C01

description: Human whole blood


title: whole_blood_203821710075_R07C01

description: Human whole blood


title: whole_blood_203810640091_R03C01

description: Human whole blood


title: whole_blood_203821710075_R06C01

description: Human whole blood


title: whole_blood_203821710075_R03C01

description: Human whole blood


title: whole_blood_203821710075_R05C01

description: Human whole blood


title: whole_blood_203810640156_R08C01

description: Human whole blood


title: whole_blood_203810640156_R07C01

description: Human whole blood


title: whole_blood_203821710075_R04C01

description: Human whole blood


title: whole_blood_203810640156_R05C01

description: Human whole blood


title: whole_blood_203821710075_R02C01

description: Human whole blood


title: whole_blood_203810640156_R01C01

description: Human whole blood


title: whole_blood_203810640156_R06C01

description: Human whole blood


title: whole_blood_203810640156_R02C01

description: Human whole blood


title: whole_blood_203821710054_R07C01

description: Human whole blood


title: whole_blood_203810640091_R02C01

description: Human whole blood


title: whole_blood_203821710054_R08C01

description: Human whole blood


title: whole_blood_203821710054_R03C01

description: Human whole blood


title: whole_blood_203821710054_R04C01

description: Human whole blood


title: whole_blood_203821710054_R05C01

description: Human whole blood


title: whole_blood_203821710054_R02C01

description: Human whole blood


title: whole_blood_203810640156_R03C01

description: Human whole blood


title: whole_blood_203821710054_R06C01

description: Human whole blood


title: whole_blood_203821710075_R01C01

description: Human whole blood


title: whole_blood_203824900047_R08C01

description: Human whole blood


title: whole_blood_203824900047_R07C01

description: Human whole blood


title: whole_blood_203821710054_R01C01

description: Human whole blood


title: whole_blood_203824900047_R06C01

description: Human whole blood


title: whole_blood_203810640156_R04C01

description: Human whole blood


title: whole_blood_203824900047_R05C01

description: Human whole blood


title: whole_blood_203824900047_R02C01

description: Human whole blood


title: whole_blood_203824900047_R04C01

description: Human whole blood


title: whole_blood_203824900047_R01C01

description: Human whole blood


title: whole_blood_203829800038_R07C01

description: Human whole blood


title: whole_blood_203829800038_R06C01

description: Human whole blood


title: whole_blood_203824900047_R03C01

description: Human whole blood


title: whole_blood_203829800038_R05C01

description: Human whole blood


title: whole_blood_203829800038_R01C01

description: Human whole blood


title: whole_blood_203829800038_R02C01

description: Human whole blood


title: whole_blood_203821710030_R08C01

description: Human whole blood


title: whole_blood_203829800038_R04C01

description: Human whole blood


title: whole_blood_203821710030_R06C01

description: Human whole blood


title: whole_blood_203821710030_R02C01

description: Human whole blood


title: whole_blood_203821710030_R07C01

description: Human whole blood


title: whole_blood_203821710030_R03C01

description: Human whole blood


title: whole_blood_203821710030_R04C01

description: Human whole blood


title: whole_blood_203821710027_R04C01

description: Human whole blood


title: whole_blood_203821710027_R01C01

description: Human whole blood


title: whole_blood_203829800038_R08C01

description: Human whole blood


title: whole_blood_203821710027_R07C01

description: Human whole blood


title: whole_blood_203821710027_R02C01

description: Human whole blood


title: whole_blood_203821710027_R08C01

description: Human whole blood


title: whole_blood_203821710027_R06C01

description: Human whole blood


title: whole_blood_203821710030_R05C01

description: Human whole blood


title: whole_blood_203829800038_R03C01

description: Human whole blood


title: whole_blood_203821710027_R05C01

description: Human whole blood


title: whole_blood_203821710030_R01C01

description: Human whole blood


title: whole_blood_203821710027_R03C01

description: Human whole blood


title: whole_blood_203829800012_R08C01

description: Human whole blood


title: whole_blood_203829800012_R07C01

description: Human whole blood


title: whole_blood_203829800012_R06C01

description: Human whole blood


title: whole_blood_203829800012_R03C01

description: Human whole blood


title: whole_blood_203829800012_R04C01

description: Human whole blood


title: whole_blood_203829800010_R08C01

description: Human whole blood


title: whole_blood_203829800012_R02C01

description: Human whole blood


title: whole_blood_203829800012_R01C01

description: Human whole blood


title: whole_blood_203829800010_R07C01

description: Human whole blood


title: whole_blood_203829800012_R05C01

description: Human whole blood


title: whole_blood_203829800010_R06C01

description: Human whole blood


title: whole_blood_203829800010_R02C01

description: Human whole blood


title: whole_blood_203810640086_R08C01

description: Human whole blood


title: whole_blood_203829800010_R03C01

description: Human whole blood


title: whole_blood_203810640086_R04C01

description: Human whole blood


title: whole_blood_203810640086_R05C01

description: Human whole blood


title: whole_blood_203821710076_R06C01

description: Human whole blood


title: whole_blood_203821710076_R07C01

description: Human whole blood


title: whole_blood_203810640086_R03C01

description: Human whole blood


title: whole_blood_203829800010_R01C01

description: Human whole blood


title: whole_blood_203810640086_R01C01

description: Human whole blood


title: whole_blood_203810640086_R07C01

description: Human whole blood


title: whole_blood_203810640086_R06C01

description: Human whole blood


title: whole_blood_203821710076_R04C01

description: Human whole blood


title: whole_blood_203821710076_R02C01

description: Human whole blood


title: whole_blood_203821710076_R08C01

description: Human whole blood


title: whole_blood_203821710076_R05C01

description: Human whole blood


title: whole_blood_203829800010_R05C01

description: Human whole blood


title: whole_blood_203829800010_R04C01

description: Human whole blood


title: whole_blood_203821710076_R01C01

description: Human whole blood


title: whole_blood_203821710069_R06C01

description: Human whole blood


title: whole_blood_203821710076_R03C01

description: Human whole blood


title: whole_blood_203821710069_R07C01

description: Human whole blood


title: whole_blood_203810640086_R02C01

description: Human whole blood


title: whole_blood_203821710069_R02C01

description: Human whole blood


title: whole_blood_203821710069_R05C01

description: Human whole blood


title: whole_blood_203821710069_R01C01

description: Human whole blood


title: whole_blood_203810640064_R07C01

description: Human whole blood


title: whole_blood_203810640064_R06C01

description: Human whole blood


title: whole_blood_203810640064_R05C01

description: Human whole blood


title: whole_blood_203821710069_R03C01

description: Human whole blood


title: whole_blood_203810640064_R04C01

description: Human whole blood


title: whole_blood_203821710069_R04C01

description: Human whole blood


title: whole_blood_203810640064_R02C01

description: Human whole blood


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description: Human whole blood


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city: Beijing

first: fengzhi

last: li

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District,

institute: Chinese Institute for Brain Research, Beijing

description:
Library name: AD60_1
RNA-seq of mus musculus: mouse brain cortex,Ast_12month_AD60_1

data_processing:
RNA-seq raw data were initially filtered with “FastQC” to obtain clean data after quality control. Clean data were aligned to the reference genome (Version: GRCm38) downloaded from Gencode by HISAT. Raw counts for each gene were calculated by FeatureCounts.
The expression level of detected genes was estimated by DESeq2.A volcano plot was generated by ggplot2 in R, with a cutoff of p-value less than 0.01 and the absolute value of log2 (Foldchange) more than 4, measured by DESeq2.
The heat map was generated by heatmap with the z-score of each gene. Gene Set Enrichment Analysis (GSEA) was performed using the ClusterProfiler package in R, with an adjusted p-value less than 0.05
Assembly: Hisat2 GRCm38
Supplementary files format and content: p30 cell mRNA counts.csv
Supplementary files format and content: gpx1_5fad_Mg12m_RNA.csv
Supplementary files format and content: Ast-12month mRNA counts.csv

source_name: Brain, P360

extract_protocol:
Total RNA was extracted from microglia, astrocytes or neurons using RNeasy Micro Kit (Qiagen, 74004) following the manufacturer's protocol
DNA library for sequencing was prepared following the protocol of TruePrep DNA Library Prep Kit V2

value: Brain, P360

value: astrocyte


description:
Library name: AD60_2
RNA-seq of mus musculus: mouse brain cortex,Ast_12month_AD60_2


title: whole_blood_203810690117_R05C01

description: Human whole blood


title: whole_blood_203808720139_R06C01

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title: whole_blood_203810690117_R04C01

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description:
Library name: M12
RNA-seq of mus musculus: mouse brain cortex,mg_fad_3

value: microglia


title: whole_blood_203810690117_R03C01

description: Human whole blood


description:
Library name: M10
RNA-seq of mus musculus: mouse brain cortex,mg_fad_2


title: whole_blood_203808720139_R03C01

description: Human whole blood


title: whole_blood_203810690117_R02C01

description: Human whole blood


title: whole_blood_203810640076_R06C01

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description:
Library name: M4
RNA-seq of mus musculus: mouse brain cortex, mg_gpx1_4

source_name: Brain, P40

value: Brain, P40


title: whole_blood_203810640076_R04C01

description: Human whole blood


title: whole_blood_203810640076_R02C01

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description:
Library name: AD59
RNA-seq of mus musculus: mouse brain cortex,Ast_12month_AD59


description:
Library name: M3
RNA-seq of mus musculus: mouse brain cortex, mg_gpx1_3


title: whole_blood_203824800064_R08C01

description: Human whole blood


description:
Library name: M2
RNA-seq of mus musculus: mouse brain cortex, mg_gpx1_2


title: whole_blood_203824800064_R04C01

description: Human whole blood


description:
Library name: M1
RNA-seq of mus musculus: mouse brain cortex, mg_gpx1_1


title: whole_blood_203824800064_R02C01

description: Human whole blood


description:
Library name: M53-2
RNA-seq of mus musculus: mouse brain cortex, Microglia_1y_4


title: whole_blood_203824800056_R08C01

description: Human whole blood


description:
Library name: M53-1
RNA-seq of mus musculus: mouse brain cortex, Microglia_1y_3


description:
Library name: M5
RNA-seq of mus musculus: mouse brain cortex,mg_fad_1


description:
Library name: AD58
RNA-seq of mus musculus: mouse brain cortex, Ast_12month_AD58


description:
Library name: M52-2
RNA-seq of mus musculus: mouse brain cortex, Microglia_1y_2


title: whole_blood_203824800056_R04C01

description: Human whole blood


description:
Library name: M52-1
RNA-seq of mus musculus: mouse brain cortex, Microglia_1y_1


title: whole_blood_203824800056_R02C01

description: Human whole blood