title: SAM24422612_LIB5460999_C3AR1_WT_PBS

description: Library name: SAM24422612_LIB5460999


title: Monocyte derived alveolar macrophages 7 day post infection 1

status: Public on Mar 23 2026

type: SRA

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

country: USA

institute: Rutgers

description: Library name: MoAM-Nb7-1

library_source: transcriptomic

data_processing:
Trimming with cutadapt (v2.5)
Alignment with STAR (vSTAR_2.6.1d)
Hit count extraction with featureCounts (v1.6.4)
Assembly: GRCm38
Supplementary files format and content: tab delimited hit count file

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Qiagen
polyA RNA-seq

tag: tissue

value: Lung

tag: cell type

value: alveolar macrophage

tag: genotype

value: Cx3cr1-CreER x Rosa26-TdT

tag: treatment

value: tamoxifen treated, post-Nb day 14


title: NHLFs

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description: Library name: NHLFs

data_processing:
Following sequencing on a NextSeq 500 (Illumina), single-end reads were mapped to GRCh38 using STAR (v2.7.9a) with ~15-40 million uniquely mapped reads per sample. Gene counts were quantified using featureCounts (v2.0.3). Aggregated counts data was normalized using DESeq2 (v1.40.2) with further analyses for gene differential expression.
Assembly: GRCh38
Supplementary files format and content: VIVOS_bulk_RNAseq_raw_counts_20251219.txt: Combined raw counts for each sample in a tab-delimited text file.
Supplementary files format and content: VIVOS_bulk_RNAseq_DESeq2_normalized_counts_20251219.txt: Combined DESeq2 normalized counts for each sample in a tab-delimited text file.

molecule: total RNA

organism: Homo sapiens

source_name: normal human lung fibroblasts (NHLFs)

growth_protocol: Vascular beds were grown using the VIVOS platform.

extract_protocol:
On the day of collection, vascular beds were excised from microfluidic chips with a scalpel, washed 3 times with warm PBS, minced, and lysed with RLT buffer (Qiagen). The vascular bed compartments of the microfluidic chips were further rinsed with RLT buffer to dislodge remaining vascular bed fragments. Monolayer RFP-labeled BMVECs, NHLFs, and HBVPs were trypsinized, pelleted, and lysed with RLT buffer. RNA extraction was performed using RNeasy (Qiagen).
Samples were processed at the Network Biology Collaborative Centre (NBCC). After TruSeq mRNA library prep (Illumina), Fragment Analyzer (Agilent) assessment showed all RNA quality numbers to be greater than 9.

treatment_protocol: Vascular beds, grown using RFP-labeled BMVECs, were collected on Day 1 (i.e. 24 hrs), Day 2, Day 4, or Day 8 using either low flow or high flow. All samples began with an impeller speed of 300 RPM for the first 18 hrs. Afterwards, devices using low flow were kept at 300 RPM while devices using high flow were increased to 900 RPM.

tag: cell line

value: normal human lung fibroblasts (NHLFs)

tag: impeller speed

tag: day

value: day 0

tag: batch


title: Homo sapiens, WTAP KD_input_1

city: Anhui

first: shan

last: zhang

address: No. 443, Huangshan Road

country: China

institute: University of Science and Technology of China

description: Library name: B1_input

data_processing:
Base calling software: BCL convert
Data filter: fastp(version 0.19.4), remove adapters, repeat sequences and low quality sequences
reads alignment: HISAT2(2.0.4)
Peak calling diffpeak: R package: exomepeak
Peak annotation: ANNOVAR
Transcript assembly and quantification: StringTie(2.1.2)
Differential expression analysis: R package: edgeR(4.1)
Assembly: eq GRCH38
Supplementary files format and content: BVSA_diffPeak_result.xlsx, which contained the result  of differential methylation sites
Supplementary files format and content: BVSA_all_diffPeak_Gene_differential_expression.xlsx contains genes with differential m6A modification and differential expression
Library strategy: MeRIP-Seq

source_name: Cervix

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA concentration and purity were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA). Polyadenylated mRNA was subsequently purified from total RNA using the GenElute mRNA Miniprep Kit (Sigma, cat. no. MRN10-1KT) through two rounds of enrichment.
the polyA RNA was fragmented at 86 °C for 7 minutes using the Magnesium RNA Fragmentation Module (NEB, cat. no. E6150), then incubated for 2 hours at 4 °C with 5 μg of m6A-specific antibody (Synaptic Systems, cat. no. 202003) in immunoprecipitation buffer (50 mM Tris-HCl, 750 mM NaCl, 0.5% Igepal CA-630). Immunoprecipitated RNA  were extracted, purified, and subjected to reverse transcription to generate cDNA.

value: Cervix

value: HeLa

value: Epithelial Cell

value: WTAP Knockdown


title: BMVECs

description: Library name: BMVECs

source_name: brain microvascular endothelial cells (BMVECs)


title: SAM24422611_LIB5460998_C3AR1_WT_LPS

city: Mississauga

first: Justin

middle: JM

last: Wong

address: 7070 Mississauga Road

institute: Hoffmann-La Roche Limited

description: Library name: SAM24422611_LIB5460998

library_source: transcriptomic single cell

data_processing:
FASTQs were processed with the cellranger pipeline from 10X genomics. Transcript counts for a given gene were based on the number of unique UMIs (up to one mismatch) for reads overlapping exons in sense orientation. Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Sample quality was further assessed based on the distribution of per-cell statistics, such as total number of reads, percentage of reads mapping uniquely to the reference genome, percentage of mapped reads overlapping exons, number of detected transcripts (UMIs), number of detected genes, and percentage of mitochondrial transcripts.  After this primary analysis step, cells with less than 1,000 total UMIs or greater than 10% mitochondrial UMIs were discarded. Doublets were identified using Doublet Finder and removed from downstream analyses.
Cell type annotations were determined using markers from: doi:10.1016/j.cell.2018.06.021, doi:10.1016/j.celrep.2017.12.066, doi:10.1016/j.celrep.2022.111189
Assembly: GRCm38
Supplementary files format and content: raw_counts.csv: comma-separated values of annotated gene counts
Supplementary files format and content: cell_info.csv: comma-separated values of mouse identification, biological data, etc.

source_name: mouse hippocampi

growth_protocol: 4~5-month-old WT or C3aRKO mice

extract_protocol:
10x Genomics protocol. Briefly, hippocampi were chopped into small pieces and dissociated with enzyme mixes in a Neural Tissue Dissociation Kit (P) (Miltenyi 130-092-628) in the presence of actinomycin D. After dissociation, cells were resuspended in Hibernate A Low Fluorescence medium (Brainbits) containing 5% FBS, with Calcein Violet AM (Thermo Fisher C34858) and propidium iodide (Thermo Fisher P1304MP). Flow cytometry was used to sort and collect live single-cell suspensions for the single-cell RNAseq study.
Sample processing and library preparation was carried out using the Chromium Next GEM Automated Single Cell 3' Library & Gel Bead Kit v3.1 on the Chromium Connect Instrument according to manufacturer’s instructions. Live cell samples were  prepared to target 10,000 cells per sample and loaded to the instrument. Libraries were sequenced with HiSeq 4000 (Illumina).

treatment_protocol:
1.     WT mice injected with PBS: n = 5
2.     WT mice injected with LPS (1 mg/kg): n = 5
3.     C3aR KO mice injected with PBS: n = 5
4.     C3aR KO mice injected with LPS (1 mg/kg): n = 5

value: mouse hippocampi

value: C3AR1 WT

value: LPS


title: SAM24422609_LIB5460996_C3AR1_WT_PBS

description: Library name: SAM24422609_LIB5460996

value: PBS


title: SAM24422614_LIB5461001_C3AR1_WT_LPS

description: Library name: SAM24422614_LIB5461001


title: Homo sapiens, control_IP_1

description: Library name: A1_IP

value: WT


title: HBVPs

description: Library name: HBVPs

source_name: human brain vascular pericytes (HBVPs)

value: human brain vascular pericytes (HBVPs)


title: Rep2_D8_Low_Flow_2

description: Library name: Rep2_D8_Low_Flow_2

source_name: a mix of brain microvascular endothelial cells (BMVECs), normal human lung fibroblasts (NHLFs), and human brain vascular pericytes (HBVPs)

value: day 8

value: low flow


title: Tissue resident alveolar macrophages 7 day post infection 5

description: Library name: TRAM-Nb7-5

value: Lung

value: alveolar macrophage


title: Day 1 (D1)

description: Library name: Day 1 (D1)

data_processing:
Sequencing reads were processed using Cell Ranger (v7.1.0; 10X Genomics) and aligned to GRCh38, with ~14k-17.5k cells/sample, and ~35-45k mean reads/cell. Prior to creating a merged object in Seurat (v4.4.0) with all samples, velocyto (v0.17.16; Python version) was used to finding spliced and unspliced gene counts, SoupX (v1.6.2) was used to correct for ambient RNA contamination, and Souporcell (v2.5) was used to assign single nucleotide variant (SNV) profiles and remove doublets. All later analyses, with the exception of RNA velocity, were performed on the SoupX corrected counts. Low quality cells were excluded based on a mitochondrial gene percentage greater than 10% or a unique molecular identifier (UMI) count of less than 4000. For more details, please refer to the materials and methods.
Assembly: GRCh38
Supplementary files format and content: VIVOS_all_cells_20260124.rds: Processed Seurat R file containing cells originating from all cell lines and from all conditions.
Supplementary files format and content: VIVOS_BMVECs_20260116.rds: Processed Seurat R file containing cells originating from the BMVEC cell line and from all conditions.
Supplementary files format and content: VIVOS_APLN_APLNR_scatter_20260116.rds: Processed Seurat R file containing a subset of cells originating from the BMVEC cell line and from Day 4 only (both low flow and high flow), with additional metadata information included. Saved UMAP coordinates ("umap" under "reductions") are NOT actually UMAP coordinates. Instead, "UMAP_1" is APLN expression and "UMAP_2" is APLNR expression (both from the "MAGIC_RNA" assay). This was done to facilitate plotting.
Supplementary files format and content: VIVOS_NHLFs_20260126.rds:  Processed Seurat R file containing cells originating from the NHLF cell line and from all conditions.
Supplementary files format and content: VIVOS_HBVPs_20260126.rds:  Processed Seurat R file containing cells originating from the HBVP cell line and from all conditions.

extract_protocol:
On the day of collection, vascular beds were excised from microfluidic devices with a scalpel, washed 3 times with warm PBS, minced, and immersed in Accutase (Gibco) dissolved with 10 mg/ml Nattokinase (Japan Bio Science Laboratory). The vascular bed compartments of the microfluidic devices were further rinsed with Accutase to dislodge remaining vascular bed fragments. Samples from 4 separate devices were combined per condition and were incubated for 20 min on an orbital shaker at 37°C with mixing by pipetting up and down after 10 minutes. Twice, cell suspensions were passed through 35 µm cell strainers (Falcon) followed by centrifuging and resuspension in fresh EGM-2 media.
Samples were processed at the Network Biology Collaborative Centre (NBCC) using the Chromium platform (single cell 3’ v3 chemistry; 10X Genomics), followed by sequencing of cDNA libraries on a NovaSeq 6000 (Illumina).

treatment_protocol: Vascular beds, grown using RFP-labeled BMVECs, were collected on Day 1 (i.e. 24 hrs), Day 4 using low flow, or Day 4 using high flow. The impeller speed for both Day 1 and Day 4 low flow was 300 RPM for the entire duration. For Day 4 high flow, devices began at 300 RPM for the first 18 hrs and then switched to 900 RPM.

value: a mix of brain microvascular endothelial cells (BMVECs), normal human lung fibroblasts (NHLFs), and human brain vascular pericytes (HBVPs)

value: Day 1 on VIVOS


title: Rep2_D8_High_Flow_1

description: Library name: Rep2_D8_High_Flow_1

value: high flow


title: Homo sapiens, control_input_1

description: Library name: A1_input

value: Cervix


title: SAM24422606_LIB5460993_C3AR1_KO_PBS

description: Library name: SAM24422606_LIB5460993

value: C3AR1 KO


title: SAM24422608_LIB5460995_C3AR1_WT_LPS

description: Library name: SAM24422608_LIB5460995


title: Day 4 High Flow (D4_HF)

description: Library name: Day 4 High Flow (D4_HF)

value: Day 4 on VIVOS using high flow (900 RPM impeller speed)


title: Naive 4

description: Library name: SA-4

value: Cx3cr1-CreER x Rosa26-TdT

value: tamoxifen treated, Naive


title: Rep2_D8_High_Flow_2

description: Library name: Rep2_D8_High_Flow_2


title: Tissue resident alveolar macrophages 7 day post infection 3

description: Library name: TRAM-Nb7-3

value: tamoxifen treated, post-Nb day 14


title: Day 4 Low Flow (D4_LF)

description: Library name: Day 4 Low Flow (D4_LF)

value: Day 4 on VIVOS using low flow (300 RPM impeller speed)


title: Tissue resident alveolar macrophages 7 day post infection 2

description: Library name: TRAM-Nb7-2


title: Low passage retinoblastoma cell line RB028 with BCOR knockdown, biological replicate 2

city: Miami

first: Jeffim

middle: N

last: Kuznetsoff

state: FL

address: 1501 NW 10th Avenue

department: Ophthalmology

institute: University of Miami

description: Library name: RB028-shBCOR2

data_processing:
FASTQ data were trimmed with TrimGalore and aligned to the genome using STAR
TPMs were generated using TPM-Calculator
Replicate RNA-seq datasets from the same cell line were averaged to produce a representative TPM value.
Assembly: hg19
Supplementary files format and content: CSV format file with normalized counts for each sample of the shBCOR experiment
Supplementary files format and content: CSV format file with average TPM for two samples of each retinoblastoma cell lines.

growth_protocol: All cell lines were cultured as describved in the manuscript.

extract_protocol:
Sequencing was performed using Illumina NovaSeq 6000 with a target of at least 30M raw reads. Sequencing data were processed as follows.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: The cells were transduced with lentiviral particles encoding non-targeting (shSCR) or BCOR specific (shBCOR) small hairpin RNAs, a week later the cells were treated with puromycin for 5 days and RNA isolated for analysis.

value: Retinoblastoma

value: BCOR depleted

value: constitutively expressing shRNA against BCOR


title: Rep2_D4_High_Flow_1

description: Library name: Rep2_D4_High_Flow_1

value: day 4


title: SAM24422607_LIB5460994_C3AR1_KO_LPS

description: Library name: SAM24422607_LIB5460994

value: mouse hippocampi

value: LPS


title: Rat CCI model following PLLA-PCL-RVC treatment 2

city: Chengdu

first: Guihua

last: Wei

address: No.111, North 1st Section, 2nd Ring Rd

institute: Southwest Jiaotong University

description: Library name: H3.R1.fq.gz

data_processing:
Raw paired-end reads (FASTQ) were quality-controlled and adapters were trimmed using fastp. Clean reads were aligned to theRattus norvegicus mRatBN7.2 reference genome using HISAT2. Gene expression levels were quantified as raw read counts using HTSeq-count and as FPKM values. Differential expression analysis between the conduit-treated and control groups was performed using DESeq2 with thresholds of adjusted p-value (q value) < 0.05 and absolute fold-change > 2. Functional enrichment analysis of differentially expressed genes was conducted for Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPkM walues for each sample

organism: Rattus norvegicus

source_name: sciatic nerve tissue

extract_protocol:
Total RNA was extracted from harvested rat sciatic nerve tissues using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. RNA purity and concentration were assessed using a NanoDrop spectrophotometer (Thermo Scientific). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Sequencing libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit (for Illumina) following the manufacturer’s instructions. Briefly, mRNA was enriched, fragmented, and reverse-transcribed into double-stranded cDNA. After end repair, A-tailing, and adapter ligation, the cDNA fragments were PCR-amplified. Final library quality and size distribution were validated.

value: sciatic nerve tissue

value: primary nerve tissue

value: wild type

value: batch 4


title: Low passage retinoblastoma cell line RB028 with BCOR knockdown, biological replicate 1

description: Library name: RB028-shBCOR1


title: Rat CCI model following PLLA-PCL-RVC treatment 3

description: Library name: H4.R1.fq.gz

value: batch 5


title: Low passage retinoblastoma cell line RB028 with BCOR knockdown, biological replicate 3

description: Library name: RB028-shBCOR3


title: Rep2_D8_Low_Flow_1

description: Library name: Rep2_D8_Low_Flow_1

value: a mix of brain microvascular endothelial cells (BMVECs), normal human lung fibroblasts (NHLFs), and human brain vascular pericytes (HBVPs)

value: day 8

value: low flow


title: Tissue resident alveolar macrophages 7 day post infection 4

description: Library name: TRAM-Nb7-4

value: Lung

value: alveolar macrophage

value: Cx3cr1-CreER x Rosa26-TdT


title: Rep2_D4_High_Flow_2

description: Library name: Rep2_D4_High_Flow_2

value: high flow


title: Naive 1

description: Library name: SA-1

value: tamoxifen treated, Naive


title: Naive 3

description: Library name: SA-3


title: Tissue resident alveolar macrophages 7 day post infection 1

description: Library name: TRAM-Nb7-1

value: tamoxifen treated, post-Nb day 14


title: Rep2_D4_Low_Flow_1

description: Library name: Rep2_D4_Low_Flow_1

value: day 4


title: Rat CCI model 3

description: Library name: B3.R1.fq.gz

value: Rat CCI model

value: batch 2


title: Rat CCI model following PLLA-PCL-RVC treatment 1

description: Library name: H2.R1.fq.gz

value: sciatic nerve tissue

value: batch 3


title: Naive 2

description: Library name: SA-2


title: Rep2_D4_Low_Flow_2

description: Library name: Rep2_D4_Low_Flow_2


title: Rep2_D2_High_Flow_1

description: Library name: Rep2_D2_High_Flow_1

value: day 2


title: SAM24422605_LIB5460992_C3AR1_WT_LPS

description: Library name: SAM24422605_LIB5460992

value: mouse hippocampi

value: C3AR1 WT

value: LPS


title: Low passage retinoblastoma cell line RB028, expressing non-specific shRNA biological replicate 3

description: Library name: RB028-shSCR3

value: Retinoblastoma

value: BCOR-WT

value: constitutively expressing non-specific shRNA


title: Low passage retinoblastoma cell line RB028, expressing non-specific shRNA biological replicate 2

description: Library name: RB028-shSCR2


title: Rep2_D2_High_Flow_2

description: Library name: Rep2_D2_High_Flow_2

value: a mix of brain microvascular endothelial cells (BMVECs), normal human lung fibroblasts (NHLFs), and human brain vascular pericytes (HBVPs)


title: Car4fl/fl- CD11cCre 3

description: Library name: B3

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and alignment (Cutadapt v2.5, STAR v2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Assembly: GRCm38
Supplementary files format and content: Tab delimited file (txt) for raw hit counts

extract_protocol:
RNeasy Plus Micro Kit (Qiagen)
polyA capture mRNA-seq

value: Lung

value: Alveolar macrophage

value: Car4flox/flox- CD11c Cre+

value: untreated


title: Car4fl/fl- CD11cCre 1

description: Library name: B1


title: Rat CCI model 2

description: Library name: B2.R1.fq.gz

value: primary nerve tissue

value: wild type

value: batch 1


title: Low passage retinoblastoma cell line RB028, expressing non-specific shRNA biological replicate 1

description: Library name: RB028-shSCR1


title: Rep2_D2_Low_Flow_2

description: Library name: Rep2_D2_Low_Flow_2

value: low flow


title: Low passage retinoblastoma cell line RB006 with BCOR knockdown, biological replicate 3

description: Library name: RB006-shBCOR3

value: BCOR depleted

value: constitutively expressing shRNA against BCOR


title: Rat trigeminal ganglia following CCI-ION and SFM-Gel @NGC-Light groups 2

description:
Library name: TG-2-C.R1.fq.gz
Transcriptomic profiling of rattrigeminal ganglia tissue at day 18 post-injury, comparing the CCI-ION model with a SFM-Gel-light @ NGC treatment group to elucidate mitochondrial function mechanisms.
TG-2-C

data_processing:
Raw paired-end reads (FASTQ) were quality-controlled and adapters were trimmed using fastp. Clean reads were aligned to the reference genome using HISAT2. Gene expression levels were quantified as raw read counts using HTSeq-count and as FPKM values. Differential expression analysis was performed using DESeq2 with thresholds of adjusted p-value (q value) < 0.05 and absolute fold-change > 2. Functional enrichment analysis of differentially expressed genes was conducted for Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Gene Set Enrichment Analysis (GSEA) was also performed. Additionally, transcriptome assembly, novel transcript identification, alternative splicing analysis, and variant calling (SNPs/InDels) were carried out using StringTie2, Cuffcompare, ASprofile, SAMtools/BCFtools, and SnpEff, respectively.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPkM walues for each sample

source_name: trigeminal ganglia

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. RNA purity and concentration were assessed using a NanoDrop 2000 spectrophotometer (Thermo Scientific). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Sequencing libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit (for Illumina) following the manufacturer’s instructions. Briefly, mRNA was purified, fragmented, and reverse-transcribed into cDNA. After end repair, A-tailing, and adapter ligation, cDNA fragments were PCR-amplified. Final library quality and size distribution were validated.

value: trigeminal ganglia

value: SFM-Gel-light @NGC treatment post-CCI-ION

value: batch 3


title: Low passage retinoblastoma cell line RB006 with BCOR knockdown, biological replicate 1

description: Library name: RB006-shBCOR1

value: Retinoblastoma


title: Car4fl/fl 2

description: Library name: A2


title: Rat CCI model 1

description: Library name: B1.R1.fq.gz

value: sciatic nerve tissue

value: Rat CCI model


title: Rep2_D2_Low_Flow_1

description: Library name: Rep2_D2_Low_Flow_1

value: a mix of brain microvascular endothelial cells (BMVECs), normal human lung fibroblasts (NHLFs), and human brain vascular pericytes (HBVPs)

value: day 2


title: Rat trigeminal ganglia following CCI-ION and SFM-Gel @NGC-Light groups 1

description:
Library name: TG-1-C.R1.fq.gz
Transcriptomic profiling of rattrigeminal ganglia tissue at day 17 post-injury, comparing the CCI-ION model with a SFM-Gel-light @ NGC treatment group to elucidate mitochondrial function mechanisms.
TG-1-C

value: batch 2


title: Low passage retinoblastoma cell line RB006, expressing non-specific shRNA biological replicate 2

description: Library name: RB006-shSCR2

value: BCOR-WT

value: constitutively expressing non-specific shRNA


title: Low passage retinoblastoma cell line RB006 with BCOR knockdown, biological replicate 2

description: Library name: RB006-shBCOR2


title: Car4fl/fl 3

description: Library name: A3

value: Lung

value: Alveolar macrophage

value: untreated


title: Low passage retinoblastoma cell line RB006, expressing non-specific shRNA biological replicate 3

description: Library name: RB006-shSCR3


title: Rat trigeminal ganglia following CCI-ION and SFM-Gel @NGC-Light groups 3

description:
Library name: TG5.R1.fq.gz
Transcriptomic profiling of rattrigeminal ganglia tissue at day 19 post-injury, comparing the CCI-ION model with a SFM-Gel-light @ NGC treatment group to elucidate mitochondrial function mechanisms.
TG5

value: primary nerve tissue

value: wild type


title: Car4fl/fl 1

description: Library name: A1


title: Car4fl/fl- CD11cCre 2

description: Library name: B2

value: Car4flox/flox- CD11c Cre+


title: Rep2_D1_High_Flow_2

description: Library name: Rep2_D1_High_Flow_2

value: day 1

value: high flow


title: Rep2_D1_High_Flow_1

description: Library name: Rep2_D1_High_Flow_1


title: Rep2_D1_Low_Flow_2

description: Library name: Rep2_D1_Low_Flow_2

value: low flow


title: scRNAseq of Mus musculus, meningeal dura, APOE4 expressing, PLX5622 diet, male, replicate 2

city: Jacksonville

first: Sandro

last: Da Mesquita

address: 4500 San Pablo Road

institute: Mayo Clinic

description:
Library name: E4PM2
10x Genomics scRNAseq

data_processing:
Cell Ranger v7.1.0, Seurat v5
Assembly: 10x Genomics reference package refdata-gex-mm10-2020-A: mouse reference, mm10 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: 3 output files from Cell Ranger v7.1.0 - cbarcodes.mt.tsv.gz, features.tsv.gz, and matrix.mtx.gz. These 3 files together provide a gene counts matrix for each sample.

source_name: meningeal dura

extract_protocol:
Mice were transcardially perfused with a buffered saline solution containing heparin and actinomycin D. Meningeal dural whole mounts were immediately dissected from the skulls of 12-month-old male and female mice expressing APOE3 or APOE4 and digested into a single-cell suspension. Cells were enriched for CD45+, LYVE-1+, and/or CD31+ cells via positive selection using MACS.
5000 cells per sample were used with the 10x Genomics Chromium Next GEM Single Cell 3ʹ Kit

value: meningeal dura

tag: Sex

value: Male

tag: strain

tag: cell sorting

tag: age

value: 12 months

tag: apoe genotype

tag: diet

tag: replicate and pooling

value: biological replicate 2 (pooled from 2 animals)


title: Rat trigeminal ganglia following CCI-ION 3

description:
Library name: CCI-5.R1.fq.gz
Transcriptomic profiling of rattrigeminal ganglia tissue at day 16 post-injury, comparing the CCI-ION model with a SFM-Gel-light @ NGC treatment group to elucidate mitochondrial function mechanisms.
CCI-5

value: trigeminal ganglia

value: chronic constriction injury of the infraorbital nerve (CCI-ION) model


title: Low passage retinoblastoma cell line RB026, biological replicate 2

description: Library name: RB026-Rep2

value: Retinoblastoma

value: BCOR-WT


title: Low passage retinoblastoma cell line RB006, expressing non-specific shRNA biological replicate 1

description: Library name: RB006-shSCR1

value: constitutively expressing non-specific shRNA


title: PRAD-EX019-FU

city: Los Angeles

first: Brandon

last: Tsai

state: California

address: 405 Hilgard Ave

institute: University of California, Los Angeles

description: Library name: PRESTO1PRAD009-T003-P03-P

data_processing:
. RNA-seq FASTQs were aligned using STAR (v2.7.6a) and quantified using RSEM (v1.3.3).
Assembly: GRCh38/GENCODE v36
Supplementary files format and content: tab-delimited text file with TPM for each sample

source_name: PRAD

extract_protocol:
Eight µm-thick representative FFPE tumor sections were subjected to microdissection and RNA extraction, as previously described. FFPE-derived RNA was subjected to paired-end RNA-sequencing [(read-length: PE50; RNA extraction kit: RNeasy FFPE kit (Qiagen)
Library prep kit: TruSeq stranded total (Ribodepletion)] on a HiSeq4000 using validated protocols at MSK’s Integrated Genomics Operation, as previously described.

value: PRAD

tag: patient

tag: time

value: FU


title: Rep2_D1_Low_Flow_1

description: Library name: Rep2_D1_Low_Flow_1

value: a mix of brain microvascular endothelial cells (BMVECs), normal human lung fibroblasts (NHLFs), and human brain vascular pericytes (HBVPs)


title: PRAD-EX019-BL

description: Library name: PRESTO1PRAD009-T001-P01-P

tag: tissue

value: BL


title: Rat trigeminal ganglia following CCI-ION 2

description:
Library name: CCI-4.R1.fg.gz
Transcriptomic profiling of rattrigeminal ganglia tissue at day 15 post-injury, comparing the CCI-ION model with a SFM-Gel-light @ NGC treatment group to elucidate mitochondrial function mechanisms.
CCI-4

tag: cell type

value: primary nerve tissue

value: wild type

value: batch 1


title: Rep1_D8_Low_Flow_1

description: Library name: Rep1_D8_Low_Flow_1

value: day 8

value: low flow


title: PRAD-EX018-BL

description: Library name: PRESTO1PRAD008-T001-P01-P


title: Low passage retinoblastoma cell line WRB06, biological replicate 2

description: Library name: WRB06-Rep2

tag: genotype


title: scRNAseq of Mus musculus, meningeal dura, APOE4 expressing, control diet, male, replicate 2

description:
Library name: E4CM2
10x Genomics scRNAseq

value: meningeal dura

value: Male

value: control


title: scRNAseq of Mus musculus, meningeal dura, APOE4 expressing, PLX5622 diet, female, replicate 1

description:
Library name: E4PF1
10x Genomics scRNAseq

value: Female

value: 12 months

value: biological replicate 1 (pooled from 2 animals)


title: Rat trigeminal ganglia following CCI-ION 1

description:
Library name: CCI.R1.fq.gz
Transcriptomic profiling of rattrigeminal ganglia tissue at day 14 post-injury, comparing the CCI-ION model with a SFM-Gel-light @ NGC treatment group to elucidate mitochondrial function mechanisms.
CCI

value: trigeminal ganglia

tag: treatment

value: chronic constriction injury of the infraorbital nerve (CCI-ION) model


title: Rep1_D8_High_Flow_2

description: Library name: Rep1_D8_High_Flow_2

tag: cell line

value: high flow


title: Low passage retinoblastoma cell line RB018, biological replicate 1

description: Library name: RB018-Rep1

value: Retinoblastoma

value: BCOR-WT


title: scRNAseq of Mus musculus, meningeal dura, APOE4 expressing, control diet, female, replicate 2

description:
Library name: E4CF2
10x Genomics scRNAseq

value: biological replicate 2 (pooled from 2 animals)


title: Low passage retinoblastoma cell line WRB06, biological replicate 1

description: Library name: WRB06-Rep1


title: scRNAseq of Mus musculus, meningeal dura, APOE4 expressing, PLX5622 diet, male, replicate 1

description:
Library name: E4PM1
10x Genomics scRNAseq


title: PRAD-EX017-BL

description: Library name: PRESTO1PRAD007-T001-P01-P

value: PRAD

value: BL


title: PRAD-EX017-FU

description: Library name: PRESTO1PRAD007-T003-P03-P

value: FU


title: Low passage retinoblastoma cell line RB026, biological replicate 1

description: Library name: RB026-Rep1


title: PRAD-EX018-FU

description: Library name: PRESTO1PRAD008-T003-P03-P


title: scRNAseq of Mus musculus, meningeal dura, APOE4 expressing, PLX5622 diet, female, replicate 2

description:
Library name: E4PF2
10x Genomics scRNAseq


title: Rep1_D8_High_Flow_1

description: Library name: Rep1_D8_High_Flow_1

value: a mix of brain microvascular endothelial cells (BMVECs), normal human lung fibroblasts (NHLFs), and human brain vascular pericytes (HBVPs)

tag: impeller speed

value: day 8


title: Rep1_D4_High_Flow_2

description: Library name: Rep1_D4_High_Flow_2

tag: day

value: day 4


title: scRNAseq of Mus musculus, meningeal dura, APOE4 expressing, control diet, male, replicate 1

description:
Library name: E4CM1
10x Genomics scRNAseq

value: meningeal dura

value: Male


title: Rep1_D8_Low_Flow_2

description: Library name: Rep1_D8_Low_Flow_2

value: low flow

tag: batch


title: Low passage retinoblastoma cell line RB016, biological replicate 2

description: Library name: RB016-Rep2


title: scRNAseq of Mus musculus, meningeal dura, APOE4 expressing, control diet, female, replicate 1

description:
Library name: E4CF1
10x Genomics scRNAseq

tag: Sex

value: Female

value: 12 months

value: control


title: Rep1_D4_Low_Flow_2

description: Library name: Rep1_D4_Low_Flow_2


title: Low passage retinoblastoma cell line RB016, biological replicate 1

description: Library name: RB016-Rep1


title: fetal AVN, snRNAseq

first: Stephanie

last: Protze

address: 101 College Street

department: McEwen Stem Cell Institute

institute: University Health Network

description:
Library name: fetal AVN
10x genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using Cell Ranger software v3.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCh38-1.2.0_premrna-
Supplementary files format and content: Tab-separated values files and matrix file

source_name: dissected fetal AVN gestation week 19

extract_protocol:
AVN tissue was dissected from the heart. The tissue was immediately frozen using liquid nitrogen and stored at -80°C. The frozen tissue was retrieved and dissociated using lysis buffer containing: 0.32M sucrose (Sigma, S0389), 5mM CaCl2 (Fluka, 21114), 3mM Mg(AC)2 (Sigma, 228648), 20mM Tris-HCl (ThermoFisher, 15567-027), 0.1%Triton X-100 (MilliporeSigma, X100), 0.1mM EDTA (ThermoFisher, AM9260G) in DNase/RNase free water (Qiagen, 129115). A douncer was used to mechanically homogenize the tissue until single nuclei were obtained. Homogenate was washed twice with PBS containing 1% BSA and 0.2U/ul RNAseOUT (ThermoFisher, 10777019) and filtered through a 40um cell strainer. Nuclei were stained with DAPI (10g/ml) and sorted for DAPI+ single-nuclei on a FACSAria (BD) sorter at the SickKids-UHN Flow Cytometer Facility.
Library construction was performed according to manufacturers instruction (single cell 3' v3 protocol, 10x Genomics)

value: dissected fetal AVN gestation week 19


title: Rep1_D1_High_Flow_1

description: Library name: Rep1_D1_High_Flow_1

value: day 1

value: high flow


title: scRNAseq of Mus musculus, meningeal dura, APOE3 expressing, PLX5622 diet, male, replicate 2

description:
Library name: E3PM2
10x Genomics scRNAseq

tag: strain


title: PRAD-EX015-BL

description: Library name: PRESTO1PRAD005-T001-P01-P


title: scRNAseq of Mus musculus, meningeal dura, APOE3 expressing, control diet, male, replicate 2

description:
Library name: E3CM2
10x Genomics scRNAseq

tag: cell sorting


title: PRAD-EX016-FU

description: Library name: PRESTO1PRAD006-T002-P02-P


title: PRAD-EX016-BL

description: Library name: PRESTO1PRAD006-T001-P01-P


title: scRNAseq of Mus musculus, meningeal dura, APOE3 expressing, control diet, male, replicate 1

description:
Library name: E3CM1
10x Genomics scRNAseq

tag: age

value: biological replicate 1 (pooled from 2 animals)


title: scRNAseq of Mus musculus, meningeal dura, APOE3 expressing, PLX5622 diet, male, replicate 1

description:
Library name: E3PM1
10x Genomics scRNAseq

tag: apoe genotype


title: Rep1_D4_Low_Flow_1

description: Library name: Rep1_D4_Low_Flow_1


title: AVNLPC, scRNAseq

description:
Library name: hPSC AVN
10x genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using Cell Ranger software v6.1.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix file

extract_protocol:
AVNLPCs were dissociated into single cells
Library construction was performed according to manufacturers instruction (single cell 3' v3 protocol, 10x Genomics)

value: AVNLPC differentiation


title: PANC1K siFOSL1-1

city: Sao Paulo

first: Alexandre

middle: Ferro

last: Aissa

state: SP

address: Rua Botucatu 740

country: Brazil

institute: Universidade Federal de São Paulo

description:
Library name: PANC1K siFOSL1-1
X22_02FHNorthwestern_Panc1K.siFOSL1.1_RNA_hs_iG1

data_processing:
The paired-end 150 bp sequencing reads generated by Illumina sequencing were mapped to the genome using the STAR algorithm with default settings. Alignment information for each read was stored in BAM format. The nf-core/rnaseq pipeline was applied to perform the alignment.
Assembly: GRCh38 for human and mm10 for mouse
Supplementary files format and content: Gene-level counts (length-scaled) in TSV format, generated by Salmon after alignment with the nf-core/rnaseq pipeline.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
RNA-seq libraries were prepared by ActiveMotif using their standard RNA library preparation protocols.

value: Pancreas cancer cell line

value: siRNA against FOSL1


title: Rep1_D1_Low_Flow_1

description: Library name: Rep1_D1_Low_Flow_1


title: Rep1_D1_High_Flow_2

description: Library name: Rep1_D1_High_Flow_2


title: PANC1K siControl-3

description:
Library name: PANC1K siControl-3
X21_02FHNorthwestern_Panc1K.siControl.3_RNA_hs_iF1

value: Scramble siRNA

value: siControl


title: Rep1_D4_High_Flow_1

description: Library name: Rep1_D4_High_Flow_1

value: a mix of brain microvascular endothelial cells (BMVECs), normal human lung fibroblasts (NHLFs), and human brain vascular pericytes (HBVPs)


title: scRNAseq of Mus musculus, meningeal dura, APOE3 expressing, PLX5622 diet, female, replicate 2

description:
Library name: E3PF2
10x Genomics scRNAseq

tag: diet

value: biological replicate 2 (pooled from 2 animals)


title: PANC1K siFOSL1-3

description:
Library name: PANC1K siFOSL1-3
X24_02FHNorthwestern_Panc1K.siFOSL1.3_RNA_hs_iA2


title: Vhl-Hif1-Hif2_WT_3

city: Madrid

first: Irene

last: Adan-Barrientos

address: Melchor Fernandez Almagro 3

country: Spain

institute: CNIC

description:
Library name: Sample_TKO_WT_3__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv TKO_WT_3__ElenaPriego

data_processing:
Sequencing reads were pre-processed through a pipeline that used FastQC to assess read quality and Cutadapt to trim sequencing reads, eliminate Illumina adaptor remains, and discard reads that were shorter than 30 base pairs. The resulting reads were mapped against the mouse transcriptome (GRCm38.99) with STAR.
Assembly: GRCm38.99
Supplementary files format and content: raw.counts.tsv.gz is a tab-delimited text file contianing raw counts for each sample

source_name: Alveolar Macrophages (AMs)

extract_protocol:
Total RNA was isolated using Rneasy Micro Kit (Qiagen)
Total RNA (100 ng) was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification (~ 13 cycles). The size of the libraries was checked using the Agilent 2100 Bioanalyzer and the concentration was determined using the Qubit® fluorometer (ThermoFisher)

treatment_protocol: Alveolar macrophags were isolated from the bronchoalveolar lavage (BAL) of mice through magnetic positive selection using columns and CD11c Microbeads (Milenyi)

value: Alveolar Macrophages (AMs)

value: Control Vhl-Hif1-Hif2a_flox-flox


title: PRAD-EX015-FU

description: Library name: PRESTO1PRAD005-T003-P03-P

value: PRAD

value: FU


title: scRNAseq of Mus musculus, meningeal dura, APOE3 expressing, PLX5622 diet, female, replicate 1

description:
Library name: E3PF1
10x Genomics scRNAseq

value: meningeal dura

value: Female

value: 12 months

tag: replicate and pooling


title: PANC1K siFOSL1-2

description:
Library name: PANC1K siFOSL1-2
X23_02FHNorthwestern_Panc1K.siFOSL1.2_RNA_hs_iH1


title: PRAD-EX012-FU

description: Library name: PRESTO1PRAD004-T003-P03-P

tag: patient


title: PRAD-EX010-FU

description: Library name: PRESTO1PRAD003-T002-P02-P

tag: time


title: scRNAseq of Mus musculus, meningeal dura, APOE3 expressing, control diet, female, replicate 1

description:
Library name: E3CF1
10x Genomics scRNAseq

tag: tissue

value: control


title: Rep1_D1_Low_Flow_2

description: Library name: Rep1_D1_Low_Flow_2

value: day 1

value: low flow


title: PRAD-EX012-BL

description: Library name: PRESTO1PRAD004-T001-P01-P

value: BL


title: PANC1K siControl-1

description:
Library name: PANC1K siControl-1
X19_02FHNorthwestern_Panc1K.siControl.1_RNA_hs_iD1

tag: cell type

value: Pancreas cancer cell line


title: scRNAseq of Mus musculus, meningeal dura, APOE3 expressing, control diet, female, replicate 2

description:
Library name: E3CF2
10x Genomics scRNAseq


title: PRAD-EX008-FU

description: Library name: PRESTO1PRAD002-T003-P03-P


title: PANC1K OTX-2

description:
Library name: PANC1K OTX-2
X14_02D7Northwestern_PANC1K.OTX.2_RNA_hs_iUDI0014

tag: genotype

value: WT


title: 2138K SGC-2

description:
Library name: 2138K SGC-2
X5_P.02O0Northwestern_s2138K_SGC.2_RNA_mm_iB.H7

tag: treatment


title: PRAD-EX008-BL

description: Library name: PRESTO1PRAD002-T001-P01-P


title: Vhl-Hif1-Hif2_KO_2

description:
Library name: Sample_TKO_KO_2__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv TKO_KO_2__ElenaPriego


title: PRAD-EX010-BL

description: Library name: PRESTO1PRAD003-T001-P01-P


title: Vhl-Hif1-Hif2_WT_2

description:
Library name: Sample_TKO_WT_2__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv TKO_WT_2__ElenaPriego


title: PANC1K siControl-2

description:
Library name: PANC1K siControl-2
X20_02FHNorthwestern_Panc1K.siControl.2_RNA_hs_iE1

tag: cell line

value: Scramble siRNA


title: 2138K SGC-3

description:
Library name: 2138K SGC-3
X6_P.02O0Northwestern_s2138K_SGC.3_RNA_mm_iB.A8


title: Vhl-Hif1-Hif2_WT_1

description:
Library name: Sample_TKO_WT_1__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv TKO_WT_1__ElenaPriego


title: 2138K DMSO-3

description:
Library name: 2138K DMSO-3
X3_P.02O0Northwestern_s2138K_DMSO.3_RNA_mm_iB.F7


title: PANC1K OTX-1

description:
Library name: PANC1K OTX-1
X13_02D7Northwestern_PANC1K.OTX.1_RNA_hs_iUDI0013


title: UCEC-EX004-FU

description: Library name: PRESTO1UCEC001-T002-P02-P

source_name: UCEC

value: UCEC


title: Vhl-Hif2_WT_3

description:
Library name: Sample_DKO2_WT_3__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO2_WT_3__ElenaPriego

value: Control Vhl-Hif2a_flox-flox


title: Vhl-Hif1-Hif2_KO_3

description:
Library name: Sample_TKO_KO_3__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv TKO_KO_3__ElenaPriego


title: PANC1K OTX-3

description:
Library name: PANC1K OTX-3
X15_02D7Northwestern_PANC1K.OTX.3_RNA_hs_iUDI0015V2


title: 2138K SGC-1

description:
Library name: 2138K SGC-1
X4_P.02O0Northwestern_s2138K_SGC.1_RNA_mm_iB.G7


title: UCEC-EX006-FU

description: Library name: PRESTO1UCEC002-T002-P02-P


title: PANC1K JQ1-2

description:
Library name: PANC1K JQ1-2
X11_02D7Northwestern_PANC1K.JQ1.2_RNA_hs_iUDI0011


title: Vhl-Hif2_WT_2

description:
Library name: Sample_DKO2_WT_2__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO2_WT_2__ElenaPriego


title: PANC1K JQ1-3

description:
Library name: PANC1K JQ1-3
X12_02D7Northwestern_PANC1K.JQ1.3_RNA_hs_iUDI0012


title: 2138K-3

description:
Library name: 2138K-3
6_5150NWU_2138K_3_RNA_mm_i6.star.bam


title: UCEC-EX006-BL

description: Library name: PRESTO1UCEC002-T001-P01-P


title: Vhl-Hif1-Hif2_KO_1

description:
Library name: Sample_TKO_KO_1__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv TKO_KO_1__ElenaPriego


title: 2138K DMSO-2

description:
Library name: 2138K DMSO-2
X2_P.02O0Northwestern_s2138K_DMSO.2_RNA_mm_iB.E7


title: 2138K-1

description:
Library name: 2138K-1
4_5150NWU_2138K_1_RNA_mm_i4.star.bam


title: PANC1K JQ1-1

description:
Library name: PANC1K JQ1-1
X10_02D7Northwestern_PANC1K.JQ1.1_RNA_hs_iUDI0010


title: 2138K DMSO-1

description:
Library name: 2138K DMSO-1
X1_P.02O0Northwestern_s2138K_DMSO.1_RNA_mm_iB.D7


title: PANC1K SGC-2

description:
Library name: PANC1K SGC-2
X08_02D7Northwestern_PANC1K.SGC.2_RNA_hs_iUDI0008


title: UCEC-EX004-BL

description: Library name: PRESTO1UCEC001-T001-P01-P


title: Vhl-Hif2_WT_1

description:
Library name: Sample_DKO2_WT_1__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO2_WT_1__ElenaPriego


title: 2138K-2

description:
Library name: 2138K-2
5_5150NWU_2138K_2_RNA_mm_i5.star.bam


title: PANC1K SGC-3

description:
Library name: PANC1K SGC-3
X09_02D7Northwestern_PANC1K.SGC.3_RNA_hs_iUDI0009


title: N5_CD4+_stim_T-SCM

first: Padmini

last: Salgame

state: NJ

department: Medicine

institute: Rutgers New Jersey Medical School

description:
Stem cell memory (CD45RA+CD45RO-CCR7+CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N5_CD4._stim_T.SCM_s39

data_processing:
Sequence Quality control: FastQC_v0.11.5 (default)
Trim adaptors/low quality reads: Cutadapt
Alignment: STAR
Read counts: HTSeq
Normalization: DEseq2 (RLE method)
Genome_build: hg19
Supplementary_files_format_and_content: CSV matrix of normalized expression counts with genes in rows and samples in columns

source_name: Peripheral blood CD4+ T-SCM

extract_protocol:
Qiagen RNeasy Micro Kit (Qiagen #74004)
Illumina TruSeq RNA Sample Preparation Kit v2

tag: individual

value: donor N5

value: stim

value: T-SCM


title: N5_CD4+_stim_T-TM

description:
Transitional memory (CD45RA-CD45RO+CCR7-CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N5_CD4._stim_T.TM_s38

source_name: Peripheral blood CD4+ T-TM

value: T-TM


title: Vhl-Hif2_KO_2

description:
Library name: Sample_DKO2_KO_2__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO2_KO_2__ElenaPriego

value: Alveolar Macrophages (AMs)


title: Vhl-Hif1_WT_3

description:
Library name: Sample_DKO1_WT_3__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO1_WT_3__ElenaPriego

value: Control Vhl-Hif1a_flox-flox


title: PANC1K DMSO-1

description:
Library name: PANC1K DMSO-1
X04_02D7Northwestern_PANC1K.1_RNA_hs_iUDI0004


title: Vhl-Hif1_WT_2

description:
Library name: Sample_DKO1_WT_2__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO1_WT_2__ElenaPriego


title: N5_CD4+_costim_T-TM

description:
Transitional memory (CD45RA-CD45RO+CCR7-CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N5_CD4._costim_T.TM_s34

value: costim only


title: N5_CD4+_stim_T-EM

description:
Effector memory (CD45RA-CD45RO+CCR7-CD27-CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N5_CD4._stim_T.EM_s40

source_name: Peripheral blood CD4+ T-EM

value: T-EM


title: Vhl-Hif2_KO_1

description:
Library name: Sample_DKO2_KO_1__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO2_KO_1__ElenaPriego


title: PANC1K DMSO-3

description:
Library name: PANC1K DMSO-3
X06_02D7Northwestern_PANC1K.3_RNA_hs_iUDI0006


title: N5_CD4+_costim_T-EM

description:
Effector memory (CD45RA-CD45RO+CCR7-CD27-CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N5_CD4._costim_T.EM_s36


title: N5_CD4+_stim_T-CM

description:
Central memory (CD45RA-CD45RO+CCR7+CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N5_CD4._stim_T.CM_s37

source_name: Peripheral blood CD4+ T-CM

value: T-CM


title: PANC1K DMSO-2

description:
Library name: PANC1K DMSO-2
X05_02D7Northwestern_PANC1K.2_RNA_hs_iUDI0005


title: Endothelial cells isolated from mouse SCLC tumor_rep2

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

description: Library name: Endo_of_SCLC_rep2

data_processing:
Endothelial cells were sorted by flow cytometry and processed using the standard Illumina RNA library preparation protocol. Transcriptome sequencing was conducted on the Illumina NovaSeq 6000 platform. RNA-seq reads were aligned to the reference mouse genome (mm10) using STAR (v2.6.0, RRID:SCR_004463). Raw count data normalization, calculation of significance scores, and log2-fold change values were performed with DESeq2 (RRID:SCR_015687).
Assembly: mm10
Supplementary files format and content: csv files include counts and DESeq2 normalized data

source_name: SCLC tumor tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent (Applied Biosystems, 15596026) according to the manufacturer’s instructions. Reverse transcription was subsequently carried out using M-MLV reverse transcriptase (Invitrogen, 28025013) following the provided protocol.
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

value: SCLC tumor tissue

value: endothelial cells


title: Vhl-Hif1_KO_2

description:
Library name: Sample_DKO1_KO_2__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO1_KO_2__ElenaPriego


title: N5_CD4+_costim_T-CM

description:
Central memory (CD45RA-CD45RO+CCR7+CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N5_CD4._costim_T.CM_s33


title: 2138-3

description:
Library name: 2138-3
3_5150NWU_2138_3_RNA_mm_i3.star.bam

value: Control


title: 2138-2

description:
Library name: 2138-2
2_5150NWU_2138_2_RNA_mm_i2.star.bam

value: Pancreas cancer cell line


title: Vhl-Hif2_KO_3

description:
Library name: Sample_DKO2_KO_3__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO2_KO_3__ElenaPriego


title: N5_CD4+_costim_T-SCM

description:
Stem cell memory (CD45RA+CD45RO-CCR7+CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N5_CD4._costim_T.SCM_s35


title: PANC1K-2

description:
Library name: PANC1K-2
X17_02FHNorthwestern_Panc1K.2_RNA_hs_iB1

value: WT


title: 2138-1

description:
Library name: 2138-1
1_5150NWU_2138_1_RNA_mm_i1.star.bam


title: PANC1K SGC-1

description:
Library name: PANC1K SGC-1
X07_02D7Northwestern_PANC1K.SGC.1_RNA_hs_iUDI0007


title: P14 T cells

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

description: Library name: laneB

data_processing:
Sequencing reads were processed  using cellranger multi (v 7.0.0):
transcriptomic reads (50, 50_topup) were specifiied as GEX and aligned to the reference genome
Hashtag antibody reads (52) were aligned to the hashtag reference file as Antibody Capture
Assembly: Cellranger 10x genome mm10-2020-A (transcriptome)
Supplementary files format and content: From Cellranger: Filtered feature counts for both GEX and Hashtag assays.

source_name: Spleen

extract_protocol:
Cells were barcoded, with RNA extraction and amplification following manufacturer's instructions (10x Genomics)
Libraries processed and constructed following manufacter's instructions (Chromium Next GEM Single Cell 3' Kit v3.1, 10x Genomics)

value: Spleen

value: CD8+ T cells P14

value: ID3 KI/+ P14


title: Vhl-Hif1_WT_1

description:
Library name: Sample_DKO1_WT_1__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO1_WT_1__ElenaPriego


title: Endothelial cells isolated from mouse SCLC tumor_rep1

description: Library name: Endo_of_SCLC_rep1


title: PANC1K-3

description:
Library name: PANC1K-3
X18_02FHNorthwestern_Panc1K.3_RNA_hs_iC1


title: N4_CD4+_stim_T-TM

description:
Transitional memory (CD45RA-CD45RO+CCR7-CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N4_CD4._stim_T.TM_s30

value: donor N4


title: PANC1-3

description:
Library name: PANC1-3
X15_02FHNorthwestern_Panc1.3_RNA_hs_iH12


title: PANC1K-1

description:
Library name: PANC1K-1
X16_02FHNorthwestern_Panc1K.1_RNA_hs_iA1


title: Endothelial cells isolated from mouse NSCLC tumor_rep3

description: Library name: Endo_of_NSCLC_rep3

source_name: NSCLC tumor tissue

value: NSCLC tumor tissue


title: Vhl-Hif1_KO_3

description:
Library name: Sample_DKO1_KO_3__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO1_KO_3__ElenaPriego


title: N4_CD4+_stim_T-SCM

description:
Stem cell memory (CD45RA+CD45RO-CCR7+CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N4_CD4._stim_T.SCM_s31

value: stim

value: T-SCM


title: Vhl-Hif1_KO_1

description:
Library name: Sample_DKO1_KO_1__ElenaPriego_RNA_Seq_Directional
Column name in raw.counts.tsv DKO1_KO_1__ElenaPriego

value: Alveolar Macrophages (AMs)


title: Perivascular cells E14.5-16.5 C

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

library_source: genomic

data_processing:
*library strategy: MeD-seq
Data processing was carried out using custom scripts in Python and MATLAB. Raw FASTQ files were subjected to Illumina adaptor trimming, and reads were filtered based on LpnPI restriction site occurrence between 13 bp and 17 bp from either 5′ or 3′ end of the read. DCM methylation data (CCWGG sites) and CpG methylation data (CCG, CGG and GCGC sites) were separated during filtering and mapped separately to mm10 using bowtie2. Genome-wide individual DCM site scores were used to generate read count scores for all annotated genes from UCSC (GRCm38.p2). BAM files were generated using SAMtools version 0.1.19 for visualization in IGV51,52. Because DCM and CpG methylation can be detected separately using MeD-seq, DCM enrichment was determined by either data normalization using CpG read coverage (for absolute DCM enrichment) or DCM read coverage (for relative DCM enrichment) between samples. For both situations, normalization is done using reads per million (RPM), where absolute DCM levels indicate the level of DCM–Rpol2b induction, and relative DCM levels are used to correct for differences in DCM–Rpol2b induction between mice and/or time points.
Assembly: mm10
Supplementary files format and content: Bigwig with unnormalized DCM signal

molecule: genomic DNA

source_name: Lung

growth_protocol: The DCM–Polr2b:m2rtTA mouse line contains the m2rtTA trans-activator inserted in the Rosa locus and  the DCM-Polr2b in the Col1a1 locus. To generate embryos heterozygous for DCM–Polr2b:m2rtTA, Wild-Type (WT) C57BL/6J females were crossed with homozygous DCM–Polr2b:m2rtTA transgenic males.

extract_protocol:
Embryos were harvested at E18.5 and their lungs were isolated. For each induction, three independent cell preparations were processed. Three to four fetal lungs of male embryos were pooled in 750 µl of DMEM (Lonza) and mechanically dissociated them using dissection scissors. Following the addition of collagenase I, II, and IV (Sigma-Aldrich) at a final concentration of 5 µg/ml, the samples were incubated at 37°C in an Eppendorf shaker at 1000 rpm for 10 minutes.
Subsequent mechanical dissociation involved vigorous resuspension, after which the cell suspensions were filtered through a 40-µm cell strainer. The filters were rinsed with 750 µl of DMEM with 10% FCS, and the resulting cell suspensions were centrifuged at 4°C for 10 minutes at 1000 rpm. After removing the supernatant, the cells were resuspended in 300 µl of 1x red blood cell lysis buffer at 4°C for 1 minute, diluted them in 900 µl of PBS with 10% FCS, and centrifuged them (10 minutes at 4°C, 1000 rpm). The cells were then resuspended in 300 µl of PBS with 5% FCS.
Cells were counted and incubated at 4°C in the dark for 40 minutes with the following antibodies: CD31-PE-Cy7 (1:100, ThermoFisher), CD45-PE-Texas Red (1:100, ThermoFisher), CSPG4-Alexa-488 (1:100, Merck), and PDGFR-β-APC (1:100, ThermoFisher).
Prior to sorting, the cells were concentrated and resuspended in 800 µl of PBS with 5% FCS. DAPI (1:10000, BD Biosciences). CD45- cells were sorted for CD31 and for CSPG4/PDGFRB using a BD FACS Aria III and BD FACSDiva software version 8.0.1. DNA was isolated from the sorted cells using QIAamp DNA micro kit according to the manufacturer’s protocol, and RNA was isolated by Trizol extraction.
At the E8.5-10.10 induction time point, cells were sorted using an unconjugated CSPG4 antibody (1:100, Millipore) for 40 minutes, and subsequently incubated with goat anti-rabbit Alexa 488 secondary antibody (1:200, Jackson) for 30 minutes.
MeD-seq analyses were performed as previously described, with all experimental time points conducted in triplicate (25, 34).

treatment_protocol: The fusion transgene was induced by administering 2.0 mg/ml doxycycline in the drinking water for two days at four different gestational ages: embryonic day (E) 8.5-10.5, E10.5-12.5, E12.5-14.5, and E14.5-16.5 (figure 2).

value: Lung

value: Perivascular cells (CD45- / CSPG4+ / PDGFRB+)

tag: embryonic day

value: DCM-Polr2b:m2rtTA +/-

value: 2.0 mg/ml doxycycline

tag: treatment days


title: Endothelial cells isolated from mouse NSCLC tumor_rep1

description: Library name: Endo_of_NSCLC_rep1


title: PANC1-1

description:
Library name: PANC1-1
X13_02FHNorthwestern_Panc1.1_RNA_hs_iF12


title: Vehicle sample 1

city: Seoul

first: Byoung Chul

last: Cho

address: 501, ABMRC Bldg., 50-1 Yonsei-ro

department: Division of Medical Oncology

country: South Korea

institute: Yonsei Cancer Center

description:
Library name: JLASCRHBO027387
10X Genomics

data_processing:
Sequencing results were aligned to the mm10 and hg19 reference genomes to distinguish human from murine genomic reads. Read quantification and sample merging were performed using Cell Ranger v7.1.0. Mouse and human gene expression data were separated as previously described41. Quality control, normalization, batch correction (using Harmony and BBKNN) and clustering were performed using Scanpy42. Quality control procedures were conducted as previously described41. Pseudotime analysis was conducted using CellOracle30.
Assembly: human, mouse
Supplementary files format and content: Single-cell RNA-seq clustering results in H5AD format, Bulk RNA seq data in csv format

source_name: Lung caner tissue

extract_protocol:
For tumor dissociation, gentle MACS Human Tumor Dissociation Kit (Miltenyi Biotec) was used, and single-cell library preparation was conducted according to the manufacturer’s guidelines (10X Genomics). Gene expression libraries were generated using the Chromium Single Cell 5′ Reagent Kits (10X Genomics), targeting a capture of 8000 to 10,000 cells.
The TruSeq Stranded Total RNA Library Prep Globin Kit (Illumina) was used for RNA sequencing libraries construction and sequenced on the NovaSeq X platform (Illumina). Sequencing reads were performed for quality assessment using FastQC v0.11.7, and adaptor trimming and low-quality read removal were performed using Trimmomatic v0.38. Filtered reads were aligned to the GRCh38 (human) and mm10 (mouse) reference genomes using HISAT2. BAMCMP was utilized to separate human and murine reads, retaining only human-derived reads (GRCh38) for downstream analysis.

value: Lung caner tissue

value: Patient-derived xenograft (PDX)


title: N4_CD4+_costim_T-SCM

description:
Stem cell memory (CD45RA+CD45RO-CCR7+CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N4_CD4._costim_T.SCM_s27

value: costim only


title: Perivascular cells E12.5-14.5 B


title: scRNA-seq:E14 ctrl hem

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

data_processing:
CellRanger v7.1.0 was used with default parameters to generate counts matrices. A 2399bp sequence for tdTomato reporter was added to the mm10 reference genome to quantify reporter mRNA.
Assembly: mm10 with tdTomato sequence added
Supplementary files format and content: TSV(tab-separated-values) and MTX (matrix)

source_name: embryonic mouse brain

extract_protocol:
The tissue was dissociated with instructions from Miltenyi Neural Tissue Dissociation Kit (P). Concentration of cells were determined by counting on a haemocytometer (using trypan blue exclusion as an indicator of viability) thrice and averaging the counts. Approximately 14400 cells were loaded on the 10X Genomics Chromium Controller to target recovery of 9000 cells per library.
Libraries were constructed using 10X Chromium Next Gem Single Cell 3’ GEM Kit v3.1, according to manufacturer’s instructions.

value: embryonic mouse brain


title: scRNA-seq:E14 gof hem

value: Lmx1aCre::Ai9::b-cat gof


title: Perivascular cells E14.5-16.5 B


title: N4_CD4+_stim_T-CM

description:
Central memory (CD45RA-CD45RO+CCR7+CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N4_CD4._stim_T.CM_s29

value: T-CM


title: N4_CD4+_costim_T-TM

description:
Transitional memory (CD45RA-CD45RO+CCR7-CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N4_CD4._costim_T.TM_s26

value: T-TM


title: PANC1-2

description:
Library name: PANC1-2
X14_02FHNorthwestern_Panc1.2_RNA_hs_iG12

value: Pancreas cancer cell line

value: WT

value: Control


title: N4_CD4+_stim_T-EM

description:
Effector memory (CD45RA-CD45RO+CCR7-CD27-CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N4_CD4._stim_T.EM_s32

value: donor N4

value: stim

value: T-EM


title: scRNA-seq:E11 ctrl hem


title: Perivascular cells E14.5-16.5 A

value: Lung


title: Internal sample 3

description:
Library name: JLASCRHBO027385
10X Genomics


title: Vehicle sample 2

description:
Library name: JLASCRHBO027393
10X Genomics


title: scRNA-seq:E11 gof hem


title: Vehicle sample 3

description:
Library name: JLASCRHBO027394
10X Genomics


title: Perivascular cells E10.5-12.5 C

value: Perivascular cells (CD45- / CSPG4+ / PDGFRB+)


title: Lung E16.5

description: 10x Genomics

data_processing:
Reads from each batch were processed separately using the 10x Genomics Cell Ranger v6.6.0 pipeline (57)with the mm10 2020-A reference dataset. Cellranger count was run to map the reads to mm10 and generate count matrices based on Ensembl v98 annotation.
The counts were further preprocessed using R v4.0.5 and Seurat v4.3.0 (58). SoupX v1.5.2 (59) was used to remove ambient background RNAs from the datasets. We removed doublets using doubletfinder v2.0.3 (60) with the settings pN = 0.25, pK = 0.09, PCs = 1:10, nExp = number of expected doublets based on each library size. Cells with less 1,000 or more than 9,000 detected genes, more than 70,000 counts or more than 20 percent mitochondrial reads were removed. Furthermore, blood cells were filtered out by excluding cells with over 25% of all reads mapped to hemoglobin genes. Genes expressed in less than 3 cells, Malat1 and Gm42418 were removed for further analysis.
Assembly: mm10
Supplementary files format and content: Tab-delimited file (tsv) with barcodes
Supplementary files format and content: Tab-delimited file (tsv) with genes
Supplementary files format and content: Matrix file (mtx) with expression values

extract_protocol:
WT male fetal mouse lungs were isolated at E10.5, E12.5, E14.5, E16.5, and E18.5 and processed for single cell as described (N=1). For samples isolated at E10.5 and E12.5, duplicates were obtained, one containing only one lung and the other containing three lungs. Samples isolated at later time points consisted of one single lung.
The resulting cell suspensions were processed by the Erasmus Center for Biomics and/or Department for Hematology. Single-cell libraries were prepared using the Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics). Next-generation sequencing (28-8-0-91 cycles) was conducted on an Illumina NovaSeq6000 platform (Illumina). Raw data were processed into FASTQ files, and sequences were quality-checked using FastQC (version v0.11.5).

tag: number of_embryos

tag: Sex

value: Male


title: N4_CD4+_costim_T-EM

description:
Effector memory (CD45RA-CD45RO+CCR7-CD27-CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N4_CD4._costim_T.EM_s28


title: Internal sample 1

description:
Library name: JLASCRHBO026502
10X Genomics


title: Endothelial cells isolated from mouse NSCLC tumor_rep2

description: Library name: Endo_of_NSCLC_rep2

value: NSCLC tumor tissue

value: endothelial cells


title: N3_CD4+_stim_T-EM

description:
Effector memory (CD45RA-CD45RO+CCR7-CD27-CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N3_CD4._stim_T.EM_s24

value: donor N3


title: Perivascular cells E12.5-14.5 C

value: DCM-Polr2b:m2rtTA +/-

value: 2.0 mg/ml doxycycline


title: Lung E12.5 B

description: 10x Genomics


title: Internal sample 2

description:
Library name: JLASCRHBO027381
10X Genomics

value: Lung caner tissue

value: Patient-derived xenograft (PDX)


title: Perivascular cells E12.5-14.5 A


title: N4_CD4+_costim_T-CM

description:
Central memory (CD45RA-CD45RO+CCR7+CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N4_CD4._costim_T.CM_s25

value: costim only

value: T-CM


title: Lung E18.5

description: 10x Genomics

value: WT


title: Lung E12.5 A

description: 10x Genomics


title: Lung E10.5 B

description: 10x Genomics


title: Regrowth sample 1

description:
Library name: JLASCRHBO026114
10X Genomics


title: Perivascular cells E8.5-10.5 B


title: Regrowth sample 3

description:
Library name: JLASCRHBO026122
10X Genomics


title: N3_CD4+_stim_T-CM

description:
Central memory (CD45RA-CD45RO+CCR7+CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N3_CD4._stim_T.CM_s21


title: N3_CD4+_stim_T-TM

description:
Transitional memory (CD45RA-CD45RO+CCR7-CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N3_CD4._stim_T.TM_s22

value: T-TM


title: Perivascular cells E10.5-12.5 B


title: Perivascular cells control C

value: No doxycycline


title: N3_CD4+_stim_T-SCM

description:
Stem cell memory (CD45RA+CD45RO-CCR7+CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N3_CD4._stim_T.SCM_s23

value: stim

value: T-SCM


title: N3_CD4+_costim_T-EM

description:
Effector memory (CD45RA-CD45RO+CCR7-CD27-CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N3_CD4._costim_T.EM_s20

value: T-EM


title: Lung E14.5

description: 10x Genomics

value: Lung


title: Perivascular cells E10.5-12.5 A

value: Perivascular cells (CD45- / CSPG4+ / PDGFRB+)


title: Perivascular cells E8.5-10.5 C


title: Regrowth sample 2

description:
Library name: JLASCRHBO026117
10X Genomics


title: Perivascular cells E8.5-10.5 A


title: N3_CD4+_costim_T-SCM

description:
Stem cell memory (CD45RA+CD45RO-CCR7+CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N3_CD4._costim_T.SCM_s19


title: Lung E10.5 A

description: 10x Genomics

value: Male


title: VLA-4 A2-d35, lin-cells, scRNAseq

city: Shanghai

first: Qiaomei

last: He

address: No. 100 Haining Road, Hongkou District, Shanghai

department: Hematology

institute: Shanghai General Hospital Affiliated to  Shanghai Jiao Tong University

description: BD Rhapsody

data_processing:
Raw sequencing reads of the cDNA library were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline (v1.8), which included filtering by reads quality, annotating reads, annotating molecules, determining putative cells and generating single-cell expression matrix. For 10x Genomics, the demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v7.1.0.
Assembly: GRCH38 for human samples and mm10 for mouse samples.
Supplementary files format and content: Matrix files for 10X Genomics (.mtx, barcodes.tsv, features.tsv).
Supplementary files format and content: For part of the sequencing results of the BD platform, the single-cell expression profile matrix is a tabular file in csv format, which records the number of mRNA molecules corresponding to the expression of each gene, for each cell.

source_name: bone marrow

extract_protocol:
Bone marrow samples obtained from recipients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) or from mice after allo-BMT transplantation were performed by density gradient centrifugation over Lymphoprep (07851, StemCell) to obtain BM mononuclear cells (BMMC). BMMC from VLA-4 A2- and vehicle-treated MDC mice at 2Ws and 5Ws after transplantation were further enriched through EasySep™ Mouse Progenitor Cell Isolation Kit (19856, StemCell) to obtain BM lineage negative cells. Single cell solution were kept on ice before loading to BD Rhapsody cartridge for single cell transcriptome capturation.
Cells were firstly stained with two fluorescent dye, Calcein AM and Draq7, for precisely determination of cell concentration and viability via BD Rhapsody™ Scanner (BD Biosciences). Cells were loaded in one BD Rhapsody micro-well cartridge. Cell capture beads were then loaded excessively to ensure that nearly every micro-well contains one bead, and the excess beads were washed away from the cartridge. After lysing cells with lysis buffer, Cell capture beads were retrieved and washed prior to performing reverse transcription. Microbeads-captured single cell transcriptome were generated into cDNA library containing cell labels and unique molecular identifiers (UMI) information. All procedures were performed with BD Rhapsody cDNA Kit (BD Biosciences, Cat. No. 633773) and BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, Cat No. 633801) strictly following the manufacturers’ protocol. All the libraries were sequenced in a PE150 mode (Pair-End for 150bp read) on the NovaSeq platform (Illumina). For 10x Genomics, library was performed according to the manufacturer's instructions (single cell 3’v2 protocol). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction.

value: bone marrow

value: bone marrow lineage negative cells (lin-cells)

value: 5mg/kg VLA-4 agonist, i.p., from day5 to day35 post allo-BMT

tag: time point

value: 5 weeks


title: MEHP-2

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

description:
Library name: sample8
100 μM  MEHP

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Liver

growth_protocol: Human liver organoids from Elephant Technologies source were used for resuscitation and then inoculated into 48-well plates, cultured for 5 days using proliferation medium (changed every 2 days) for differentiation, and cultured for 5 days using differentiation medium (changed every 2 days) to be considered as mature organoids.

extract_protocol:
Total RNA was extracted from  cultured cells withTRIzol reagent.mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Typical plasticiser metabolite substances were treated: MEHP (100 μM), MBP (100 μM), and 1‰ DMSO was used as a solvent control for the control group, and the transcriptome was harvested after 2 days of treatment.

value: Liver

value: hepatic organoids

value: 100 μM  MEHP


title: N2_CD4+_stim_T-TM

city: Newark

address: 185 South Orange Ave

description:
Transitional memory (CD45RA-CD45RO+CCR7-CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N2_CD4._stim_T.TM_s14

value: donor N2


title: MEHP-3

description:
Library name: sample9
100 μM  MEHP


title: MBP-3

description:
Library name: sample6
100 μM  MBP

value: 100 μM  MBP


title: MEHP-1

description:
Library name: sample7
100 μM  MEHP


title: Perivascular cells control B

value: DCM-Polr2b:m2rtTA +/-


title: Perivascular cells control A

value: No doxycycline


title: Vehicle-d14, lin-cells, scRNAseq

description: 10× Genomics

value: equal amount of DMSO was used as vehicle

value: 2 weeks


title: VLA-4 A2-d14, lin-cells, scRNAseq

description: 10× Genomics

value: 5mg/kg VLA-4 agonist, i.p., from day5 to day14 post allo-BMT


title: MBP-1

description:
Library name: sample4
100 μM  MBP


title: N2_CD4+_stim_T-SCM

description:
Stem cell memory (CD45RA+CD45RO-CCR7+CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N2_CD4._stim_T.SCM_s15

value: stim

value: T-SCM


title: MBP-2

description:
Library name: sample5
100 μM  MBP


title: Endothelial cells E14.5-16.5 C

value: Lung

value: Endothelial cells (CD45- / CD31+)

value: 2.0 mg/ml doxycycline


title: Endothelial cells E14.5-16.5 A


title: Vehicle-d35, lin-cells, scRNAseq

description: BD Rhapsody

value: bone marrow

value: bone marrow lineage negative cells (lin-cells)


title: Endothelial cells E14.5-16.5 B


title: N3_CD4+_costim_T-CM

description:
Central memory (CD45RA-CD45RO+CCR7+CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N3_CD4._costim_T.CM_s17

value: donor N3

value: costim only

value: T-CM


title: D28, FDC, BMMC, replicata2, scRNAseq

description: BD Rhapsody

value: bone marrow mononuclear cells (BMMC)

tag: chimerism

value: full donor (FDC)

value: donor lymphocyte infusion (DLI) at day15 post allo-BMT


title: N2_CD4+_stim_T-EM

description:
Effector memory (CD45RA-CD45RO+CCR7-CD27-CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N2_CD4._stim_T.EM_s16

value: donor N2

value: T-EM


title: DMSO-3

description:
Library name: sample3
DMSO-3

value: Liver

value: hepatic organoids

value: 0.1% DMSO


title: N2_CD4+_stim_T-CM

description:
Central memory (CD45RA-CD45RO+CCR7+CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N2_CD4._stim_T.CM_s13

value: stim


title: Endothelial cells E12.5-14.5 C

value: Lung

value: DCM-Polr2b:m2rtTA +/-


title: DMSO-2

description:
Library name: sample2
DMSO-2


title: N2_CD4+_costim_T-TM

description:
Transitional memory (CD45RA-CD45RO+CCR7-CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N2_CD4._costim_T.TM_s10

value: T-TM


title: Endothelial cells E12.5-14.5 B

value: Endothelial cells (CD45- / CD31+)

value: 2.0 mg/ml doxycycline


title: D28, FDC, BMMC, replicata1, scRNAseq

description: BD Rhapsody

value: bone marrow


title: N2_CD4+_costim_T-SCM

description:
Stem cell memory (CD45RA+CD45RO-CCR7+CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N2_CD4._costim_T.SCM_s11

value: costim only

value: T-SCM


title: Endothelial cells E12.5-14.5 A


title: DMSO-1

description:
Library name: sample1
DMSO-1


title: D15, MDC, BMMC, replicata1, scRNAseq

description: BD Rhapsody

value: bone marrow mononuclear cells (BMMC)

value: mixed donor (MDC)


title: N2_CD4+_costim_T-EM

description:
Effector memory (CD45RA-CD45RO+CCR7-CD27-CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N2_CD4._costim_T.EM_s12


title: Endothelial cells E10.5-12.5 C


title: N2_CD4+_costim_T-CM

description:
Central memory (CD45RA-CD45RO+CCR7+CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N2_CD4._costim_T.CM_s9

value: T-CM


title: D15, MDC, BMMC, replicata2, scRNAseq

description: BD Rhapsody


title: HAP1 cells, untreated, biol rep1

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

description: Library name: HAP1_unt_rep1

library_source: other

data_processing:
Sequencing libraries were demultiplexed and adapter-trimmed with Cutadapt v4.1  using the following command:  -j 40 --no-indels -q 30,30 --trimmed-only -a file:barcodes.fa -m 10.  Reads were further trimmed to remove the two 5′-RN nucleotides introduced by circularization from the RT primer and the five random nucleotides at the 3′ of reads introduced during adapter ligation  (-j 40 -m 10 -u 2 -u -5).
Assembly: hg38
Supplementary files format and content: csv; nucleotide conversion rates for all samples
Library strategy: Ribo-Seq

molecule: other

growth_protocol: HAP1 cells were cultured in IMDM supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin-Glutamine at 37°C and 5% CO2.

extract_protocol:
Cells were lysed with a buffer containing TritonX-100 and cycloheximide to arrest translation. Lysates were treated with RNase I. Ribosomes were then pelleted through a sucrose cushion.  and RNA was isolated by phenol extraction. Ribosome-protected mRNA footprints of 26 - 32 nt were isolated by gel size selection.
Library construction was carried out essentially as described (McGlincy & Ingolia, 2017) with minor modifications. rRNA was depleted with rRNA-tRNA (RiboSeq) riboPOOLs (siTOOLs) following the 3' adapter ligation step.

treatment_protocol: Cells were treated or not with 20 uM azaC for 4 hours.

value: near-haploid derivative of KBM-7

value: WT


title: B-PDL1-03

city: 湖北省 / 武汉市 / 硚口区

first: Yu

last: Xi

state: hubei province

address: 同济医学院附属同济医院

department: Department of Thoracic Surgery

institute: huazhong University of science and technology

data_processing:
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.
Assembly: mm10
Supplementary files format and content: processed data file includes raw counts and FPKM for each sample.

source_name: subcutaneous tumor

growth_protocol: LLC cells were cultured in Dulbecco's modified Eagle's medium (HyClone) supplemented with 10% heat‐inactivated FBS. C57BL/6 mice (male, 6 to 8 were subcutaneously injected with 1 × 10^6 LLC cells in PBS in the right flank. When the tumor volume reaches ≈ 100mm3, the mice were randomized into 3 groups.

extract_protocol:
Total RNA were extracted using MJzol Animal RNA Isolation Kit（Majorivd）according to the manufacturer’s instructions.
VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® was used to construct the RNA library according to the manufacturer’s instructions.

treatment_protocol: C57BL/6 mice in 3 groups were treated with an isotype control (10 mg/kg, i.p.), an anti-PDL1 antibody (10 mg/kg, i.p.), or a combination of the anti-PDL1 antibody and BTZ (0.5 mg/kg, i.p.)

value: subcutaneous tumor

value: LLC

value: lung adenocarcinoma

tag: host strain


title: HAP1 cells, 5-azaC treated, biol rep2

description: Library name: HAP1_azaC_rep2

value: 4h 20uM 5-azaC


title: Endothelial cells E10.5-12.5 B

value: Lung


title: Endothelial cells E10.5-12.5 A

value: DCM-Polr2b:m2rtTA +/-


title: N1_CD4+_stim_T-TM

description:
Transitional memory (CD45RA-CD45RO+CCR7-CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N1_CD4._stim_T.TM_s6

value: donor N1

value: stim

value: T-TM


title: B-PDL1-02

city: 湖北省 / 武汉市 / 硚口区


title: N1_CD4+_stim_T-SCM

description:
Stem cell memory (CD45RA+CD45RO-CCR7+CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N1_CD4._stim_T.SCM_s7


title: HAP1 cells, 5-azaC treated, biol rep1

description: Library name: HAP1_azaC_rep1


title: PDL1-02

city: 湖北省 / 武汉市 / 硚口区


title: B-PDL1-01

city: 湖北省 / 武汉市 / 硚口区


title: LZH28, FDC, BMMC, scRNAseq

description: 10× Genomics

value: bone marrow

value: full donor (FDC)

value: reducing the dose of immunosuppressive agent


title: N1_CD4+_stim_T-CM

description:
Central memory (CD45RA-CD45RO+CCR7+CD27+CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N1_CD4._stim_T.CM_s5


title: Endothelial cells E8.5-10.5 C

value: Endothelial cells (CD45- / CD31+)

value: 2.0 mg/ml doxycycline


title: Senescent_ADT

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Senescent_barcodes.tsv.gz
Senescent_features.tsv.gz
Senescent_matrix.mtx.gz

data_processing:
Pre-processing of sequencing results and generation of count matrices for both RNA and ADT libraries was performed following Feature Barcoding tool pipeline in the Cell Ranger (version 6.1.1; 10X Genomics) with using human GRCh38 reference genome.
Further processing was done with Seurat v 4.1.0
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

growth_protocol: Human diploid WI-38 fibroblasts were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% FBS, 1% antibiotics, and 1% non-essential amino acids (Gibco).  Cell cultures were maintained in an incubator at 37°C and 5% CO2.

extract_protocol:
Cells were detached using TrypLE Express™ (Gibco #12605-010) and 1-2 million cells were resuspended in 50 ul Cell Staining Buffer (Biolegend #420201) with 10% FBS.  Cells were blocked by the addition of 5 ul Human TruStain FcX™ Fc Blocking reagent (Biolegend #422301) for 10 min at 4C and an antibody pool was prepared containing 1 ug of each TotalSeq™ B antibodies (CD112 #337425, HLA-A,B,C #311451, CD44 #103071, CD54 #353135, CD26#302727, CD49a #328323, CD73 #344033, and CD109 #323311, from Biolegend).  After bringing the final volume to 50 ul with Cell Staining Buffer and centrifugation at 14,000 × g for 10 min at 4C, the antibody mixture was added to the cells and incubated at 4C for 30 min.  Cells were then washed with 1 ml of Cell Staining Buffer, centrifuged at 400 × g for 5 min at 4C, and then resuspended in 1 ml of PBS + 5 mM EDTA for a final concentration of 1,000.000 cells/ml.  Antibody-labeled cells were then stained with 2 μg/ml of propidium iodide for 10 min at 25°C in the dark, and 16,000 viable cells were sorted using WOLF G2 (Nanocellect Biomedical, Inc.).  Sorted cells were spun down at 500 × g for 15 min and the resulting cell pellet was resuspended in PBS; the cell suspension was then used for single-cell RNA-sequencing (scRNA-seq) using 10× Genomics.
Single-cell libraries were prepared using Chromium Next GEM Single Cell 3ʹ Kits v3.1 with 3’ Feature Barcode kit using Chip G (10× Genomics) following the manufacturer’s protocol.  Briefly, cells were loaded onto the Chromium Controller Instrument for generation of Gel Beads-in-emulsion (GEMs), the captured cells were lysed, and the RNA was barcoded while reverse-transcribed in each GEM.  GEMs were subsequently broken, and the synthetized cDNA used for library preparation.  cDNA quality was assessed on the Agilent Bioanalyzer with the high-sensitivity DNA kit (Agilent), whereas the final library products were assessed on Agilent TapeStation by using Agilent D1000 ScreenTape assay.

treatment_protocol: To induce senescence by treatment with ionizing radiation (IR), proliferating (PDL24) fibroblasts were exposed to 10 Gray (Gy) and cultured for an additional 10 days.

value: human fetal lung fibroblasts

value: IR-induced senescent (10 days)

tag: library type

value: Antibody-derived oligonucleotide (ADT)

tag: antibodies/tags

value: Anti-CD49a/TotalSeq-B0575; Anti-CD109/TotalSeq-B0817; Anti-CD26/TotalSeq-B0396; Anti-CD73/TotalSeq-B0577; Anti-CD54/TotalSeq-B0217; Anti-CD112/TotalSeq-B0024; Anti-CD44/TotalSeq-B0073; Anti-HLA-A,B,C/TotalSeq-B0058


title: PDL1-01

city: 湖北省 / 武汉市 / 硚口区

value: subcutaneous tumor

value: LLC

value: WT


title: Blank-03

city: 湖北省 / 武汉市 / 硚口区

value: lung adenocarcinoma

value: isotype


title: Endothelial cells E8.5-10.5 B

value: Lung

value: DCM-Polr2b:m2rtTA +/-


title: Endothelial cells E8.5-10.5 A


title: Proliferating_ADT

description:
Proliferating_barcodes.tsv.gz
Proliferating_features.tsv.gz
Proliferating_matrix.mtx.gz

value: Untreated proliferating controls


title: Blank-02

city: 湖北省 / 武汉市 / 硚口区


title: Endothelial cells control C

value: No doxycycline


title: LZH15, MDC, BMMC, scRNAseq

description: 10× Genomics

value: bone marrow

value: bone marrow mononuclear cells (BMMC)

value: mixed donor (MDC)


title: Endothelial cells control B

value: Endothelial cells (CD45- / CD31+)


title: Senescent_RNA

value: human fetal lung fibroblasts

value: poly A RNA


title: N1_CD4+_costim_T-EM

description:
Effector memory (CD45RA-CD45RO+CCR7-CD27-CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N1_CD4._costim_T.EM_s4

value: donor N1

value: costim only

value: T-EM


title: HAP1 cells, untreated, biol rep2

description: Library name: HAP1_unt_rep2

value: near-haploid derivative of KBM-7


title: PDL1-03

city: 湖北省 / 武汉市 / 硚口区

value: subcutaneous tumor

value: LLC

value: WT


title: N1_CD4+_stim_T-EM

description:
Effector memory (CD45RA-CD45RO+CCR7-CD27-CD95+); Mtb antigen stimulation (ESAT-6 and CFP10 peptide pools, Mtb strain H38Rv cell lysate) + Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N1_CD4._stim_T.EM_s8

value: stim


title: N1_CD4+_costim_T-TM

description:
Transitional memory (CD45RA-CD45RO+CCR7-CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N1_CD4._costim_T.TM_s2

value: T-TM


title: N1_CD4+_costim_T-CM

description:
Central memory (CD45RA-CD45RO+CCR7+CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N1_CD4._costim_T.CM_s1

value: T-CM


title: Proliferating_RNA

value: Untreated proliferating controls


title: Blank-01

city: 湖北省 / 武汉市 / 硚口区

value: lung adenocarcinoma

value: isotype


title: A81, RA-/BMS1uM, 26 weeks

status: Public on Mar 22 2026

city: Sydney

first: Carissa

last: Chen

state: NSW

address: 214 Hawkesbury Rd, Westmead

institute: Children's Medical Research Institute

description:
Library name: S1
MGI T7

data_processing:
For each slide, multiple FOVs were manually stitched together into a single panoramic image using the ImageStudio (v3.0.0) software and registered to the gene expression matrix using the SAW registration module (v7.1). Segmentation of the tissue coverage area was performed based on the ssDNA stain.
Assembly: GRCh8
Supplementary files format and content: .rds file containing SpatialExperiment object of single segmented organoids per age
Library strategy: Spatial Transcriptomics

molecule: nuclear RNA

source_name: retinal organoid

extract_protocol:
On collection, organoids were washed with PBS before being cryo-embedded in OCT using liquid nitrogen cooled 2-methylbutane before storage at -80°C. Embedded organoids were sectioned to 10µm using a cryostat, onto transcriptomic chips from the Stereo-seq platform which were then fixed for 10 minutes at -20°C using methanol. Tissue permeabilisation was optimised at 5 minutes of permeabilisation. Slides were then stained with Qubit ssDNA stain.
cDNA synthesis, amplification and library prep were all performed with the manufacturer’s instructions

value: retinal organoid

value: H7 A81.BRN3b.mCherry

value: retinal


title: A81, RA1uM/RA10uM, 26 weeks

description:
Library name: S2
MGI T7


title: A81, RA1uM/RA10uM, 16 weeks

description:
Library name: S4
MGI T7


title: A81, RA-/BMS1uM, 16 weeks

description:
Library name: S3
MGI T7


title: CAGpdCas9het3_Brain_DNA_Tamoxifen

type: genomic

city: Stockholm

first: Maja

last: Jagodic

address: Visionsgatan 18

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, hybridized and imaged

scan_protocol: iScan System

data_processing:
Sesame package in R with additional code from ChatGPT
Average beta value after normalization and signal correction

label: Cy3 and Cy5

source_name: Brain

label_protocol: Infinium HD Methylation

extract_protocol: Approximately 30mg of tissue was used for DNA/RNA extraction with the AllPrep DNA/RNA Mini Kit followed by TissueLyser LT (QIAGEN) homogenization. The DNA was eluted in Elution Buffer and sotred at -20°C until further use.

treatment_protocol: The samples with the prefixes CAGpdCas9het_Brain and CAGndCas9het_Brain were treated with Tamoxifen, and sacrificed 3 weeks after Tamoxifen treatement. All the other samples were treatement naive.

value: Brain

value: Tamoxifen


title: CAGpdCas9het2_Brain_DNA_Tamoxifen


title: Het3_Brain_DNA

value: no


title: WT3_Brain_DNA


title: Het1_Brain_DNA


title: WT2_Brain_DNA


title: CAGndCas9het2_Brain_DNA_Tamoxifen


title: Het2_Brain_DNA


title: CAGndCas9het1_Brain_DNA_Tamoxifen


title: WT1_Brain_DNA


title: CAGpdCas9het1_Brain_DNA_Tamoxifen


title: Endothelial cells control A

value: Lung

value: Endothelial cells (CD45- / CD31+)

value: DCM-Polr2b:m2rtTA +/-

value: No doxycycline


title: CAGndCas9het3_Brain_DNA_Tamoxifen


title: Patient 230

type: protein

first: Jae-ik

last: Oh

address: 101, Daehak-ro, Jongno-gu

department: Translational Medicine

institute: Seoul National University College of Medicine

hyb_protocol: High multiplexed PEATM probes, matched pairs of antibodies with unique DNA oligonucleotides, bind to their respective proteins in the plasma samples. Then oligonucleotides that are brought into proximity hybridize and are extedned using a DNA polymerase. The piece of DNA barcode that is created is then amplified by PCR. Unique sample indexes are added to every sample, to allow pooling of the DNA amplicons for all samples.

scan_protocol: The final DNA amplicons are sequenced by NGS using Illumina platform.

data_processing: The relative concentration of each biomarker, based on matched counts (the number of reads for each specific combination of sample and assay), is calculated using the Olink NPX Explore HT software. As we conducted proteome profiling in two separate batches (one from the discovery cohort and one from the validation cohort), we additionally introduced bridge normalization by eight overlapping samples from each batch. The NPX values from these bridge samples were used to calculate correction factors for each plate, and all protein expression data were bridge normalized for comparative analysis.

source_name: plasma

growth_protocol: The subjects were enrolled in the KORNERSTONE project before their first diagnostic kidney biopsy. On the same day as the biopsy, the first blood samples for the biorepository project were collected and sent to the laboratory in the study hospital. Plasma was separated from EDTA tubes and stored in deep-freezers.

tag: batch

tag: cohort

value: validation

tag: disease group

value: MN

tag: center name

value: DSM

tag: age

value: F

tag: egfr

tag: proteinuria (upcr g/g)

tag: hypertension

value: No

tag: diabetes

tag: immunosuppressant

tag: bridgesample


title: Patient 228

tag: Sex

value: M


title: Patient 229


title: Patient 226

value: BRM

value: Yes


title: Patient 227


title: Patient 231


title: Patient 225

value: KNU


title: N1_CD4+_costim_T-SCM

description:
Stem cell memory (CD45RA+CD45RO-CCR7+CD27+CD95+); Co-stimulation (anti-CD28, anti CD49d)
MemT_normalizedCounts.csv
N1_CD4._costim_T.SCM_s3

tag: individual

value: donor N1

tag: treatment

value: costim only

tag: cell type

value: T-SCM


title: Patient 223


title: Patient 222

value: FSGS

value: SSV


title: Patient 224


title: Patient 219


title: Patient 232


title: Patient 216


title: Patient 217


title: Patient 211


title: Patient 209


title: Patient 213


title: Patient 221


title: Patient 218


title: Patient 215


title: Patient 210


title: Patient 208

value: MCD


title: Patient 214


title: Patient 205


title: Patient 220


title: Patient 204


title: Patient 202


title: Patient 212


title: Patient 199


title: Patient 207


title: Patient 200


title: Patient 197


title: Patient 198


title: Patient 189

value: IgAN


title: Patient 203


title: Patient 206


title: Patient 201


title: Patient 191


title: Patient 193


title: Patient 194


title: Patient 190


title: 1295, Canis lupus familiaris, Ureter,Ureter

status: Public on Mar 25 2026

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

institute: Pfizer

description: Library name: itox001295

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read count mapped to human

organism: Canis lupus familiaris

source_name: Ureter,Ureter

extract_protocol:
RNA was isolated from tissues using the RNeasy mini kit (Qiagen #74534) according to manufacturer’s protocol. RNAseq cDNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq stranded mRNA kit (Cat. No. RS-122-2101) according to the manufacturer's instructions.
After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA Assay Kit (ThermoFisher Scientific, #Q32853).

tag: tissue

value: Ureter,Ureter


title: Patient 182

value: validation


title: Patient 195


title: Patient 188


title: Patient 187


title: Patient 185


title: Patient 186


title: Patient 192


title: Patient 181


title: Patient 184


title: Patient 178


title: Patient 177


title: Patient 183


title: Patient 174


title: Patient 175


title: Patient 167


title: Patient 176


title: Patient 168


title: Patient 173


title: Patient 172


title: Patient 171


title: Patient 170


title: Patient 180


title: Patient 179


title: Patient 165


title: Patient 161

value: discovery

value: Control

value: AJH

value: U/A albumin negative


title: Patient 158

value: F

value: No


title: Patient 162

value: M


title: Patient 159


title: Patient 164

value: KNU


title: Patient 169

value: BRM


title: Patient 163


title: Patient 157


title: Patient 166


title: Patient 154


title: Patient 153


title: Patient 160


title: Patient 150


title: Patient 152


title: Patient 148


title: Patient 155


title: Patient 196


title: Patient 145


title: Patient 151


title: Patient 142


title: Patient 147


title: Patient 146


title: Patient 140


title: Patient 141


title: Patient 143

value: Yes


title: Patient 149


title: Patient 156


title: Patient 144


title: Patient 137


title: Patient 139


title: Patient 135


title: Patient 133


title: Patient 131


title: Patient 134


title: Patient 136


title: Patient 132


title: Patient 128


title: Patient 130


title: Patient 125


title: Patient 138