title: HBMVEC, Oligomeric amyloid beta, 1hr, 1

description:
Library name: Ab_1h_1
HBMVEC treated with oligomeric Abeta (1 uM) for 1 hour

value: primary HBMVEC

value: brain microvascular endothelial cells

value: Oligomeric amyloid beta (1 uM)


title: Ctrl_bAb_3

status: Public on Jun 11 2026

type: SRA

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

description: Library name: 4WTbAb_MPS12352265_D08

library_source: transcriptomic

data_processing:
The read count matrix was generated using Illumina DRAGEN RNA software. Further analysis was performed using the limma-voom package in R (Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015). "limma powers differential expression analyses for RNA-sequencing and microarray studies." Nucleic Acids Research, 43(7), e47. doi:10.1093/nar/gkv007). The DRAGEN quant.genes.sf file was annotated with the gencode.vM38.basic.annotation.gtf file to obtain gene-level counts from transcript-level data. Differential expression analysis was conducted using the edgeR package (Robinson, M.D., McCarthy, D.J. and Smyth, G.K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), pp. 139-140).
Count data were filtered and normalized using the calcNormFactors function with the TMM (Trimmed Mean of M-values) method. Data were log₂-transformed, and multidimensional scaling (MDS) analysis was performed using the plotMDS function to visualize sample distributions in a 2D scatter plot. Differential gene expression analysis was carried out using the limma-voom pipeline, including the voom, lmFit, contrasts.fit, eBayes, and decideTests functions. Batch correction was performed by design in limma voom function.
Assembly: Mus_musculus:mm10
Supplementary files format and content: quant.genes.sf = output of Salmon (Dragen). quant.genes.sf contains gene expression quantification results in a tab-separated format, where each line corresponds to a gene. This file provides a summary of the expression level for each gene, calculated by summing the expression of all its associated transcripts based on the gene ID in the annotation file.
Supplementary files format and content: quant.sf = output of Salmon (Dragen). quant.sf contains transcript expression quantification results in a tab-separated format, where each line corresponds to a transcript.
Supplementary files format and content: raw_counts_readable_DO_NOT_USE_FOR_ANALYSIS.txt = sample summary of gene counts from tximport(files, type = "salmon", tx2gene = tx2gene) using gencode.vM38.basic.annotation.gtf
Supplementary files format and content: normalized_logCPM_voom_batchcorrected_FOR_VISUALIZATION_ONLY.txt = sample summary of gene counts after normalisation and bacth correction.

molecule: polyA RNA

organism: Mus musculus

source_name: Mouse Brain Endothelial cells

extract_protocol:
Total RNA was extracted and reverse-transcribed into cDNA (polyA-enriched RNA (stranded) - Express NEB)
cDNA (polyA-enriched RNA (stranded) - Express NEB) libraries were sent for sequencing using the Illumina NovaSeq Plus platform (PE100, 25M reads/sample)

treatment_protocol: Mutant mice and littermate controls were injected with a KIT-blocking antibody (500 µg, InVivoMAb anti-mouse c-Kit, BioXCell, BE0293-5MG-A) or an isotype control (500 µg, InVivoMAb rat IgG2b isotype control, BioXCell, BE0090-5MG-A) at P6 and P7. CD31 antibody (BD Pharmingen, 550274) was incubated with Dynabeads (Thermo Fisher, 11035) at 4°C overnight. Beads were then washed with PBS containing 0.1% BSA using a magnetic separator (DynaMag™-15, Thermo Fisher, 12301D) and resuspended in PBS containing 0.01% BSA. At P8, mice were euthanized, and brains were collected, finely chopped, and digested for 1 hour at 37°C in Collagenase/Dispase (Sigma, 11097113001) supplemented with DNase I (50 µg/mL, DN25) and TLCK (0.147 µg/mL, T7254).

tag: tissue

value: Mouse Brain Endothelial cells

tag: genotype

value: Control

tag: treatment

value: Antibody

tag: batch


title: interim_female_low5

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

country: USA

institute: NIEHS

description: Library name: Interim.1522

data_processing:
Reads were aligned to the rn7 reference genome with STAR version 2.6
Read counts for annotated genes were obtained with Rsubread version 2.14
Normalized counts were obtained with DESq2 version 1.42
Assembly: rn7
Supplementary files format and content: DESeq2 normalized counts in tab delimited file

molecule: total RNA

organism: Rattus norvegicus

source_name: heart

extract_protocol:
RNAeasy Kit (Qiagen)
Illumina TruSeq Stranded mRNA

value: heart

value: cART

tag: Sex

value: female


title: interim_female_low4

description: Library name: Interim.1519


title: FVQ-PVBP

city: London

first: Theodoros

last: Xenakis

address: 20 Guilford Street

country: United Kingdom

institute: UCL

description:
Library name: FVQ-sc-AB-gex-1
Control

library_source: transcriptomic single cell

data_processing:
Spatial transcriptomics: Fast files were processed using 10X Genomics' SpaceRanger v2.1.0. Fastq files were generated with `mkfastq`, and processed files with `count`.
Single cell Transcriptomics:Fastq files were processed using 10X Genomics CellRanger 3.1.0 with "cellranger multit".
Assembly: Spatial transcriptomics: 10X Genomics' genome build: GRCh38-2020-A. Single-cell transcriptomics: Pre-built human reference 3.0.0, GRCh38 (Ensembel release 93)
Supplementary files format and content: Spatial transcriptomics: Spaceranger count spatial directory. Paraphrased from https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs: aligned_fiducials.jpg: shows which fiducial spots on the slide were detected by spaceranger; detected_tissue_image.jpg: shows the section of tissue detected by spaceranger; scalefactors_json.json: relative scales of user-supplied images; spatial_enrichment.csv: Moran's I values for each expressed feature; tissue_hires_image.png: high-resolution image of the tissue; tissue_lowres_image.png: low-resolution image of the tissue; tissue_positions.csv: table with information about each spot; barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene expression matrix files.
Supplementary files format and content: Single-cell transcriptomics: CellRanger count output with the files accounting for filtered feature-barcode matrices for each GEM well in "gz" compressed format.

organism: Homo sapiens

source_name: Placenta

extract_protocol:
For spatial transcriptomics: Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat. For single-cell and nuclei transcriptomics: samples were freshly dissociated using custom protocol. Nuclei were isolated using 10X Genomics nuclei isolation kit according to manufacturers recommended protocol.
For spatial transcriptomics: Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction. For single-cell an nuclei transcriptomics: single cell or nuclei suspensions were prepared and processed using the Chromium Single Cell 5’ Reagent Kits v3.1

value: Placenta


title: Mut_Ct_3

description: Library name: 3MutCtrl_MPS12352265_C08

value: IgG-Control


title: term_male_ctrl4

description: Library name: Terminal.1104

value: male


title: HBMVEC, Control, 4

city: Daegu

first: Do-Geun

last: Kim

address: Cheomdan-ro 61

department: Dementia Research Group

country: South Korea

institute: Korea Brain Research Institute

description:
Library name: ctrl_4
HBMVEC, untreated control

data_processing:
Raw reads were quality-checked and adapter-trimmed using Trimmomatic v0.38.
Reads were aligned to the human reference genome (GRCh38, Ensembl release 102) using HISAT2 v2.1.0.
Gene-level counts were obtained using StringTie v2.1.3b.
Assembly: Human genome GRCh38 (Ensembl release 102).
Supplementary files format and content: Tab-delimited text file including gene-level read counts, FPKM, and TPM values for each sample.

source_name: primary HBMVEC

growth_protocol: Primary human brain microvascular endothelial cells (HBMVECs) were cultured in complete classic media with 2% culture boost and 1% penicillin-streptomycin on attachment factor-coated plates at 37°C and 5% CO2 for 2–3 days.

extract_protocol:
After treatment, cells were washed with PBS and total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and integrity were assessed using Quant-IT RiboGreen and TapeStation RNA ScreenTape. Only samples with RIN > 7.0 were used.
0.5 μg of total RNA per sample was used to construct libraries with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina). rRNA was removed using the Ribo-Zero kit, mRNA was fragmented, and cDNA was synthesized with SuperScript II and random primers. Libraries were PCR-enriched, quantified, and quality-checked before sequencing.

treatment_protocol: HBMVECs were treated with Amyloid beta oligomer for 1, 4 or 12 hours.

tag: cell line

tag: cell type

value: WT

value: Untreat


title: 3-months-OSK-rep3

city: Cambridge

first: Yuancheng Ryan

last: Lu

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description: Library name: 17-3m-OSK-C

data_processing:
Paired-end human and mouse reads were mapped to the canonical chromosomes of the GRCh38/hg38 or GRCm38/mm10 genome genomes, respectively, with STAR (v 2.7.1a) using a genome index created using Ensembl 96 gene models (with sjdbOverhang=100). Gene counts were obtained for all genes using featureCounts (v1.6.2) and the same GTF file as for STAR and options "-p -s 1".
Assembly: mm10
Supplementary files format and content: csv; gene feature counts table

source_name: Ear Fibroblasts

extract_protocol:
Total RNA was extracted following the TRIzol Reagent User Guide (Thermo Fisher Scientific). Glycogen (1 μl of 10 mg ml−1 solution) was added to the supernatant to increase RNA recovery. RNA was quantified using a Qubit 2.0 Fluorometer (Life Technologies), and RNA integrity was determined using TapeStation (Agilent Technologies).
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Ear Fibroblasts


title: Mut_bAb_3

description: Library name: 2MutbAb_MPS12352265_B08


title: 24-months-OSK-rep3

description: Library name: 27-24m-OSK-d


title: 3-months-OSK-rep2

description: Library name: 16-3m-OSK-b2


title: Ctrl_Ct_3

description: Library name: 1WTCtrl_MPS12352265_A08


title: Mut_Ct_2

description: Library name: 9MCT_MPS12352056_C05


title: HBMVEC, Control, 3

description:
Library name: ctrl_3
HBMVEC, untreated control


title: interim_female_ctrl6

description: Library name: Interim.1422


title: interim_female_ctrl5

description: Library name: Interim.1420


title: 3-months-OSK-rep1

description: Library name: 15-3m-OSK-b1


title: Ctrl_Ct_2

description: Library name: 7CCT_MPS12352056_B05


title: HBMVEC, Control, 2

description:
Library name: ctrl_2
HBMVEC, untreated control


title: Ctrl_Ct_1

description: Library name: 6CCT_MPS12352074_B01


title: 24-months-OSK-rep2

description: Library name: 25-24m-OSK-b


title: interim_female_ctrl1

description: Library name: Interim.1414


title: 24-months-rep4

description: Library name: 14-24m-e


title: Ctrl_bAb_2

description: Library name: 5CbAb_MPS12352056_H04


title: HBMVEC, Control, 1

description:
Library name: ctrl_1
HBMVEC, untreated control


title: 24-months-rep3

description: Library name: 13-24m-d


title: Ctrl_bAb_1

description: Library name: 4CbAb_MPS12352056_G04


title: Fixed_in-situ_PolyA - Donor1 and 2_2

description:
Library name: SubLib2
scRNA seq

data_processing:
Single cell Transcriptomics:Fastq files were processed using 10X Genomics CellRanger 3.1.0 or Parse Biosciences Split-Pipe.
Assembly: 10X Genomics' genome build: GRCh38-2020-A. Single-cell transcriptomics: Pre-built human reference 3.0.0, GRCh38 (Ensembel release 93)
Supplementary files format and content: Matrix-.mtx, barcodes - .tsv/csv and features - .tsv/.csv

extract_protocol:
Nuclei: Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat. Nuclei were isolated using 10X Genomics nuclei isolation kit according to manufacturers recommended protocol. FFPE: Five 25um sections were collected and dissociated according to 10X Genomics demonstrated protocol CG000632 revD. Viable Cells:  Tissues where dissociated using Accutase and the GentleMACS Octo dissociator
Fresh_droplet_PolyA - Chromium Next GEM Single-cell 5' Kit v2 kit, Nuclei_droplet_PolyA - Chromium Next GEM Single-cell 5' Kit v2 kit, FFPE_droplet_Probe - Chromium Fixed RNA Profiling Reagent Kit, Fixed_droplet_Probe - Chromium Fixed RNA Profiling Reagent Kit, Fixed_in-situ_PolyA -  Evercode WT Mini v2 kit


title: NAC-2

city: Beijing

first: Ming

last: Hao

address: Shuangqing Rd.

country: China

institute: Tsinghua Univ

description:
Library name: N2
Transcriptom of granulosa cell collected via laser micro dissection

data_processing:
Transcriptom were quantified using Salmon (PMID: 28263959).
Assembly: GRCm38
Supplementary files format and content: Quantified gene expression data using Salmon.

source_name: ovary

extract_protocol:
LCM collected GC were lysised in 50 µl 4M GuSCN at 42 ℃ for 15 min. Lysis were added with 771 µl 80% EtOH with 20 µg glycogen, and incubated in -80 ℃ for 2h, and centrifuged at 12000g, 4℃ for 20 min.
library were constructed as GEO-Seq protocol (PMID: 28207000).

value: ovary

tag: strain

value: Granulosa cell

value: intraperitoneal injected with 150 mg/kg N-acetyl-l-cysteine for 3 consecutive days


title: Mut_Ct_1

description: Library name: 3MCT_MPS12352056_F04


title: Mut_bAb_2

description: Library name: 2MbAb_MPS12352056_E04


title: Mut_bAb_1

description: Library name: 1MbAb_MPS12352056_D04


title: Fixed_in-situ_PolyA - Donor1 and 2_1

description:
Library name: SubLib1
scRNA seq


title: 24-months-rep1

description: Library name: 10-24m-a


title: HEIOC1wt3

city: Lanzhou

first: Chenyang

last: Xu

address: Cuiying 88

institute: Lanzhou University

description: Library name: Sample6

data_processing:
Libraries underwent quality control via Qsep-400 and quantification using Qubit 3.0. Sequencing was performed using the Illumina NovaSeq X Plus platform (San Diego, CA, USA)
Assembly: Clean data were generated using FastQC
Supplementary files format and content: the reads were aligned to the reference genome using HISAT2.

source_name: cochlea

extract_protocol:
Total RNA was extracted from the transfected cells using TRIZOL Reagent (Invitrogen) according to the manufacturer’s instructions. RNA quality was assessed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) with a concentration ≥40 (ng/ul), RIN≥7, and total volume ≥2 (ug), and the integrity was detected using Agient2100.
library preparation utilized the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®

treatment_protocol: For each well, 12ug plasmids were diluted with 1.5ml serum-free medium, 30ul Hieff TransTM reagent was diluted with 1.5ml serum-free medium, and incubated at room temperature for 5min

value: cochlea

value: The cells were incubated in a 5% CO2 incubator at 37 ° C for 6h and then replaced with complete medium


title: Fixed_droplet_Probe - Donor2

description:
Library name: F1958NS-AB-scFixed-GEX
scRNA seq - probes

library_source: other

molecule: other


title: HEIOC1wt1

description: Library name: Sample4


title: HEIOC1wt2

description: Library name: Sample5


title: 3-months-rep4

description: Library name: 4-3m-E


title: Fixed_droplet_Probe - Donor1

description:
Library name: F1950PYI-AB-scFixed-GEX
scRNA seq - probes


title: HEIOC1mut3

description: Library name: Sample3

value: MUT


title: HEIOC1mut1

description: Library name: Sample1


title: HEIOC1mut2

description: Library name: Sample2


title: BMDC_NanoCa_3

first: yujie

last: luo

state: Beijing

address: xueyuan road 38

institute: peking university

description:
Library name: sample3
Column name in raw_counts_All_Samples.excle: BMDC_NanoCa_3

data_processing:
Fastp software
Assembly: Grcm39
Supplementary files format and content: excle file includes raw counts for each Sample
Supplementary files format and content: excle files include FPKM values for each Sample

source_name: cell line

growth_protocol: BMDC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using trizol (TianGEN). 3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: BMDCs were treated with NanoCa at a concentration of 100 μM.

value: cell line

value: BMDC

value: Bone marrow-derived dendritic cells

value: femal_ 4-8 weeks old

value: NanoCa


title: BMDC_Mock_3

description:
Library name: sample6
Column name in raw_counts_All_Samples.excle: Mock_NanoCa_3

value: no treatment


title: FFPE_droplet_Probe - Donor1

description:
Library name: F1950PYI-AB-FFPE-sc-flex
scRNA seq - probes

value: Placenta


title: 3-months-rep1

description: Library name: 1-3m-b1


title: Nuclei_droplet_PolyA - Donor2

description:
Library name: F1958NS-AB-sn-GEX
snRNA seq


title: Old-OSK-rep4

description: Library name: old-OSK-M-1

source_name: RPE

extract_protocol:
Total RNA was extracted following the TRIzol Reagent User Guide (Thermo Fisher Scientific). Glycogen (1 μl of 10 mg ml−1 solution) was added to the supernatant to increase RNA recovery. RNA was quantified using a Qubit 2.0 Fluorometer (Life Technologies), and RNA integrity was determined using TapeStation (Agilent Technologies).
RNA library preparations, sequencing reactions were conducted at Genewiz. A SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech), and Illumina Nextera XT library was used for sequencing library preparation. In brief, cDNA was fragmented and adaptors were added using Transposase, followed by limited-cycle PCR to enrich and add an index to the cDNA fragments. The final library was assessed by a Qubit 2.0 Fluorometer and an Agilent TapeStation.

value: RPE


title: BMDC_NanoCa_2

description:
Library name: sample2
Column name in raw_counts_All_Samples.excle: BMDC_NanoCa_2


title: Old-OSK-rep3

description: Library name: old-OSK-4


title: liver tissues, high-concentration of curcumin (100 mg/kg)-biol rep 3

city: Hangzhou

first: Ling

last: Liu

address: No. 261 Huansha Road

institute: Hangzhou First People's Hospital Affiliated to Medical School of Westlake University

description:
Library name: high_concentration_rep3
H3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp(0.23.4).
Trimmed sequence reads were mapped to mm39 using STAR(2.7.10b).
Transcript-level expression was quantified using StringTie(2.2.1).
Assembly: mm39
Supplementary files format and content: Tab-delimited text file includes raw counts for all sample

source_name: liver

growth_protocol: Six-week-old C57BL/6J mice were utilized to establish an LF model. Before the experiment began, the animals need to be adaptively raised in the new environment for at least three days.  The breeding environment is a specific pathogen-free experimental animal-level barrier environment, providing 12 hours of bright-dark cycle lighting conditions.  The ambient temperatures were respectively controlled at 22±1℃ and 55±10%.  Laboratory animals can obtain laboratory-standard feed and distilled water at any time, with three mice raised in each cage.

extract_protocol:
Total RNA isolation was done by utilizing TRIzol reagent (Thermo Fisher, USA).
RNA libraries were prepared using Hieff RNA Library Prep Kit following the manufacturer's instructions.

treatment_protocol: Each mouse received a 200 μL intraperitoneal injection of a 7.5% carbon tetrachloride (CCl4) olive oil solution twice weekly for six consecutive weeks. Different concentrations of curcumin were administered via gavage, with mice assigned into groups: control (CCl4), low-concentration (25 mg/kg, Low), medium-concentration (50 mg/kg, Med), and high-concentration (100 mg/kg, High), with daily treatments for two weeks.  Subsequently, liver tissues of mice in different treatment groups were obtained.

value: liver

value: WT


title: Fresh_droplet_PolyA - Donor2

description:
Library name: F1958NS-AB-sc-GEX
scRNA seq


title: Nuclei_droplet_PolyA - Donor1

description:
Library name: F1950PYI-AB-sn-GEX
snRNA seq


title: A1_LJ-AB

type: RNA

hyb_protocol: The Human Multi-Tissue and Cancer Xenium gene panel with 100 custom gene add-on was used following standard Xenium V1 protocol

scan_protocol: All scanning and raw data acquisition was performed by the Xenium platform. Instrument software version 1.8.2.1

data_processing: Cell segmentation by 5um heuristic nuclear expansion and all data processing was perfromed using Xenium Ranger (xenium-2.0.0.12).

label: Xenium probe set

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: 8um tissue section was placed onto Xenium slide as per standard Xenium V1 protocol

tag: tissue preservation method

value: Fresh Frozen

value: control


title: liver tissues, high-concentration of curcumin (100 mg/kg)-biol rep 2

description:
Library name: high_concentration_rep2
H2


title: Old-OSK-rep2

description: Library name: old-OSK-3


title: Fresh_droplet_PolyA - Donor1

description:
Library name: F1950PYI-AB-sc-GEX
scRNA seq


title: liver tissues, medium-concentration of curcumin (50 mg/kg)-biol rep 2

description:
Library name: medium_concentration_rep2
M2


title: liver tissues, medium-concentration of curcumin (50 mg/kg)-biol rep 3

description:
Library name: medium_concentration_rep3
M3


title: OSK-2

description: Library name: OSK-mC-b

data_processing:
Paired-end human and mouse reads were mapped to the canonical chromosomes of the GRCh38/hg38 or GRCm38/mm10 genome genomes, respectively, with STAR (v 2.7.1a) using a genome index created using Ensembl 96 gene models (with sjdbOverhang=100). Gene counts were obtained for all genes using featureCounts (v1.6.2) and the same GTF file as for STAR and options "-p -s 1".
Assembly: hg38
Supplementary files format and content: csv; gene feature counts table


title: Old-OSK-rep1

description: Library name: old-OSK-2


title: liver tissues, medium-concentration of curcumin (50 mg/kg)-biol rep 1

description:
Library name: medium_concentration_rep1
M1


title: Old-Control-rep3

description: Library name: old-control-M-2


title: Old-Control-rep2

description: Library name: old-control-M-1


title: liver tissues, low-concentration of curcumin (25 mg/kg)-biol rep 1

description:
Library name: low_concentration_rep1
L1


title: OSK-1

description: Library name: OSK-mC-a


title: liver tissues, low-concentration of curcumin (25 mg/kg)-biol rep 3

description:
Library name: low_concentration_rep3
L3


title: liver tissues, low-concentration of curcumin (25 mg/kg)-biol rep 2

description:
Library name: low_concentration_rep2
L2


title: Klf4-2

description: Library name: Klf4-mC-b


title: Old-Control-rep1

description: Library name: old-control-4


title: liver tissues, control (CCl4)-biol rep 2

description:
Library name: control_rep2
C2

value: control (CCl4)


title: liver tissues, control (CCl4)-biol rep 3

description:
Library name: control_rep3
C3


title: liver tissues, control (CCl4)-biol rep 1

description:
Library name: control_rep1
C1


title: Se_Rt_CC_190_3

city: Richland

first: Predictive Phenomics

last: Initiative

state: WA

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

description:
Library name: Batch 2 Sample 4 Time 3 biol rep 3
mixed co-culture time-series

data_processing:
Rsubread v2.16.1 was used to obtain transcript counts provided in the processed data file.
Assembly: NC_007604.1
Supplementary files format and content: csv, transcript counts

organism:
Synechococcus elongatus PCC 7942 = FACHB-805
Rhodotorula toruloides

source_name: co-culture

growth_protocol: Synechococcus elongatus PCC 7942 CscB/SPS strain, engineered to overexpress sucrose phosphate synthase (SPS) and sucrose permease (CscB), was obtained from Dr. Daniel Ducat. Rhodotorula toruloides NBRC 0880 (Rhodosporidium toruloides IFO0880) was used as the yeast partner. Axenic S. elongatus and co-cultures with R. toruloides were grown at 30 ± 2°C with 2% CO₂ in nitrogen under ~200 µmol photons m⁻² s⁻¹ provided by LED lighting. Cultures were mixed at ~200 rpm using PTFE magnetic stir bars in BG11 medium supplemented with 0.09 g/L yeast nitrogen base (without amino acids and ammonium sulfate), 0.264 g/L ammonium sulfate, 0.174 g/L potassium phosphate dibasic, and 3 g/L HEPES (pH 8.3). Where applicable, 1 mM IPTG was added to induce CscB/SPS expression. Antibiotics (chloramphenicol 25 mg/L and kanamycin 25 mg/L) were used during routine maintenance but removed prior to experiments. Tube perturbation experiments used 25 mL working volume in 50 mL vented tubes supplemented with 100 mg/L sucrose. Bioreactor experiments used membrane-separated (2-chamber mBR) and mixed co-culture configurations in ~600 mL vessels.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus Mini Kit. Samples were homogenized using QiaShredder, then processed following the manufacturer's protocol with 70% ethanol addition. RNA quality and quantity were assessed by NanoDrop One spectrophotometry. A total of 2 µg RNA in 40 µL was submitted for RNA sequencing per sample.
Library construction and sequencing was performed by Azenta Life Sciences. Library preparation used the NEBNext Ultra RNA Library preparation kit with rRNA depletion performed using the QIAGEN FastSelect rRNA depletion kit with dual depletion. Sequencing was performed on the Illumina platform using paired-end 2x150bp with single indexing (~350M PE reads, ~105GB per sample).

treatment_protocol: Co-culture perturbation conditions were applied at a single time point and included: oxidative stress (5 mM methyl viologen/5x Fe, 5 mM H₂O₂, 50 µM Cd(NO₃)₂), photosynthesis inhibition (10 µM DCMU), temperature stress (37°C, 14°C), pH stress (pH 6.5, pH 10.5), nutrient limitation (no nitrogen, no phosphorus, no trace elements), alternative nitrogen sources (5x (NH₄)₂SO₄, 5x nitrate), heterotrophic conditions (1–10 g/L sucrose, vented and sealed), vitamin B12 supplementation (0.37 µg/L), vitamin B12 combined with H₂O₂ stress, yeast extract amendment (1 g/L), high salt stress (150 mM NaCl), and reduced gas phase (40 mL in sealed tubes). Membrane bioreactor and mixed co-culture bioreactor samples were collected at ~90, ~140, and ~190 hrs.

value: co-culture

value: cscB+ delta-sps, WT

value: S.e + R.t co-culture day 8


title: Old-rep3

description: Library name: old-RPE-3


title: Se_Rt_CC_190_1

description:
Library name: Batch 2 Sample 4 Time 3 biol rep 1
mixed co-culture time-series


title: Sox2-1

description: Library name: Sox2-mC-a


title: Se_Rt_CC_190_2

description:
Library name: Batch 2 Sample 4 Time 3 biol rep 2
mixed co-culture time-series


title: Se_Rt_CC_140_3

description:
Library name: Batch 2 Sample 4 Time 2 biol rep 3
mixed co-culture time-series

value: S.e + R.t co-culture day 6


title: Old-rep2

description: Library name: old-RPE-2


title: Se_Rt_CC_140_2

description:
Library name: Batch 2 Sample 4 Time 2 biol rep 2
mixed co-culture time-series


title: Oct4-2

description: Library name: Oct4-mC-b


title: Se_Rt_CC_140_1

description:
Library name: Batch 2 Sample 4 Time 2 biol rep 1
mixed co-culture time-series


title: Old-rep1

description: Library name: old-RPE-1


title: Oct4-1

description: Library name: Oct4-mC-a


title: Se_Rt_CC_90_3

description:
Library name: Batch 2 Sample 4 Time 1 biol rep 3
mixed co-culture time-series

value: S.e + R.t co-culture day 4


title: Young-rep7

description: Library name: young-RPE-M-8


title: Control cells

city: Edinburgh

first: Nick

last: Gilbert

address: Crewe Rd

department: MRC Human Genetics Unit

institute: University of Edinburgh

data_processing:
Adaptors were removed using cutadapt
Reads were aligned using bowtie2
MACS was used for peak calling
Peaks were annoted using ChIPseeker
Assembly: hg38
Supplementary files format and content: Table in text format showing genomic annotation of peaks

source_name: FlpIn T-Rex 293 expressing FLAG-SAF-A

growth_protocol: FlpIn T-Rex 293 expressing FLAG-SAF-A were grown in DMEM 10% FCS with P/S

extract_protocol:
Libraries were prepared with a "NEB small RNA library kit". Samples were amplified using NEBNext index 1 and NEBNext SR primer and pair-end sequenced (75 bp)
PAR-CLIP

treatment_protocol: Cells were treated with 4sU to 0.5 mM final concentration for 15 min, washed with PBS, incubated for 1 h in complete medium (without 4sU), washed with PBS and exposed to 365 nm UV for 30 sec (0.15 J/cm2).

value: FlpIn T-Rex 293 expressing FLAG-SAF-A

value: Control + 4sU


title: Se_Rt_CC_90_2

description:
Library name: Batch 2 Sample 4 Time 1 biol rep 2
mixed co-culture time-series


title: GFP-3

description: Library name: Control_GFP-c


title: OCT_4

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw data were checked for quality, adapter content and duplication rates using fastq.gzC.
Trimmomatic version 0.39 was used to trim reads after a drop in quality below a mean value of Q15 in a window of 5 nucleotides. Only reads above 15 nucleotides were released for further analysis.
Trimmed and filtered reads were aligned with STAR 2.7.3a against the Ensembl human genome, version hg38 (ensemble release 99), using STAR 2.7.3a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10 %.
Multi-mapping reads were excluded and duplicate reads were removed using Picard 2.21.7.
The number of reads aligned to genes was counted using featureCounts 1.6.5 from the subread package. Only reads that map at least partially within exons were allowed and aggregated per gene. Reads overlapping with multiple genes or aligned to multiple regions were excluded.
The raw count matrix was normalized with DESeq2 version 1.30.1.
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: Lung cancer cell line

extract_protocol:
RNA was isolated from macrophage and A549 cells using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. The integrity of the RNA and library preparation was checked using the LabChip Gx Touch 24 (Perkin Elmer).
1 µg of total RNA was used as input for the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).

value: Lung cancer cell line

value: cancerous

value: 4-Octyl Itaconate 48 hours


title: Old-rep4

description: Library name: old-RPE-4


title: Klf4-1

description: Library name: Klf4-mC-a


title: Young-rep6

description: Library name: young-RPE-M-7


title: Se_Rt_CC_90_1

description:
Library name: Batch 2 Sample 4 Time 1 biol rep 1
mixed co-culture time-series


title: GFP-2

description: Library name: Control_GFP-b


title: Sox2-2

description: Library name: Sox2-mC-b


title: OCT_3


title: 17_Q_b

description:
Library name: Batch 1 sample 29 biol rep 2
mixed co-culture closed system

value: S.e + R.t co-culture 1 g/L/d fed batch, closed vent, 500 mL


title: Young-rep5

description: Library name: young-RPE-M-6

value: RPE


title: OCT_2


title: GFP-1

description: Library name: Control_GFP-a


title: Young-rep4

description: Library name: young-RPE-5


title: WT-3

description: Library name: WT-c


title: OCT_1


title: Young-rep3

description: Library name: young-RPE-3


title: 17_Q_a

description:
Library name: Batch 1 sample 29 biol rep 1
mixed co-culture closed system


title: 28_BB_c

description:
Library name: Batch 1 sample 28 biol rep 2
mixed co-culture closed system

value: S.e + R.t co-culture 1 g/L sucrose, closed vent, 25 mL


title: WT-2

description: Library name: WT-b


title: CTRL_4

value: DMSO 48 hours


title: Young-rep2

description: Library name: young-RPE-2


title: 28_BB_a

description:
Library name: Batch 1 sample 28 biol rep 1
mixed co-culture closed system


title: CTRL_3


title: WT-1

description: Library name: WT-a


title: Young-rep1

description: Library name: young-RPE-1


title: 14_N_b

description:
Library name: Batch 1 sample 27 biol rep 2
mixed co-culture closed system

value: S.e + R.t co-culture 100 mg/L sucrose, closed vent, 25 mL


title: OSK-3

description: Library name: OSK-c


title: 24-months-OSK-onoff-rep5

description: Library name: 42-24m-OSKonoff-e

library_source: genomic

data_processing:
ATAC-seq data was aligned to the mm10 genome using bowtie2, and duplicate reads were removed using Picard MarkDuplicates. Aligned data was processed using samtools and converted to fragments files with bedtools bamtobed.
Assembly: mm10
Supplementary files format and content: ATAC-seq fragments files (.fastq.gz) : Tab-delimited files with 5 columns corresponding to the chromosome, start, end, sample name, and duplicate count for each paired-end fragment.

molecule: genomic DNA

extract_protocol:
Cells were incubated with custom-loaded Tn5 transposase in high-salt transposition buffer for 30 minutes at 37 °C with agitation. Transposed DNA was purified using the Zymo DNA Clean & Concentrator kit.
Libraries were pre-amplified for 5 cycles, then subjected to qPCR to determine the additional number of cycles needed, minimizing amplification bias. Final libraries were purified, quality-checked by gel electrophoresis, and quantified. Sequencing was performed on an Illumina platform using paired-end reads, targeting ~20 million reads per sample.

value: Ear Fibroblasts


title: CTRL_2


title: 24-months-rep2

description: Library name: 11-24m-b


title: OSK-2

description: Library name: OSK-b


title: 14_N_a

description:
Library name: Batch 1 sample 27 biol rep 1
mixed co-culture closed system


title: CTRL_1


title: 24-months-OSK-onoff-rep4

description: Library name: 41-24m-OSKonoff-d


title: 25_Y_c

description:
Library name: Batch 1 sample 26 biol rep 2
mixed co-culture phosphorus

value: S.e + R.t co-culture 100 mg/L sucrose, phosphorus deplete, 25 mL


title: 3-months-rep3

description: Library name: 3-3m-C


title: FFPE_droplet_Probe - Donor2

description:
Library name: F1958NS-AB-FFPE-sc-flex
scRNA seq - probes

value: Placenta


title: M2-OCT_4

source_name: PBMC-derived macrophages

value: PBMC-derived macrophages

value: Macrophages

value: Healthy

value: IL4 24hour +4-Octyl Itaconate 24 hours


title: 25_Y_b

description:
Library name: Batch 1 sample 26 biol rep 1
mixed co-culture phosphorus

value: co-culture

value: cscB+ delta-sps, WT


title: 24-months-OSK-onoff-rep3

description: Library name: 40-24m-OSKonoff-c


title: OSK-1

description: Library name: OSK-a


title: M2-OCT_3


title: GSTA4-3

description: Library name: GSTA4-c


title: BMDC_Mock_2

description:
Library name: sample5
Column name in raw_counts_All_Samples.excle: Mock_NanoCa_2

value: cell line

value: BMDC

value: Bone marrow-derived dendritic cells

value: femal_ 4-8 weeks old

value: no treatment


title: 3-months-rep2

description: Library name: 2-3m-b2


title: 24-months-OSK-onoff-rep2

description: Library name: 39-24m-OSKonoff-b


title: BMDC_Mock_1

description:
Library name: sample4
Column name in raw_counts_All_Samples.excle: Mock_NanoCa_1


title: 24_X_c

description:
Library name: Batch 1 sample 25 biol rep 2
mixed co-culture nitrogen

value: S.e + R.t co-culture 100 mg/L sucrose, ammonia deplete, 5x nitrate, 25 mL


title: GSTA4-2

description: Library name: GSTA4-b

value: RPE


title: 24-months-OSK-onoff-rep1

description: Library name: 38-24m-OSKonoff-a


title: 24_X_b

description:
Library name: Batch 1 sample 25 biol rep 1
mixed co-culture nitrogen


title: GSTA4-1

description: Library name: GSTA4-a


title: M2-OCT_1


title: 23_W_c

description:
Library name: Batch 1 sample 24 biol rep 2
mixed co-culture nitrogen

value: S.e + R.t co-culture 100 mg/L sucrose, nitrate deplete, 5x [NH4]2SO4, 25 mL


title: 15-months-OSK-onoff-rep5

description: Library name: 37-15m-OSKonoff-f

value: Ear Fibroblasts


title: GFP-3

description: Library name: GFP-c


title: M2-OCT_2


title: M2-DMSO_4

value: IL4 24hour +DMSO 24 hours


title: 15-months-OSK-onoff-rep4

description: Library name: 36-15m-OSKonoff-e


title: 23_W_b

description:
Library name: Batch 1 sample 24 biol rep 1
mixed co-culture nitrogen


title: BMDC_NanoCa_1

description:
Library name: sample1
Column name in raw_counts_All_Samples.excle: BMDC_NanoCa_1

value: NanoCa


title: GFP-2

description: Library name: GFP-b


title: M2-DMSO_3

value: PBMC-derived macrophages


title: 15-months-OSK-onoff-rep3

description: Library name: 35-15m-OSKonoff-d


title: GFP-1

description: Library name: GFP-a


title: 15-months-OSK-onoff-rep2

description: Library name: 34-15m-OSKonoff-c


title: 22_V_c

description:
Library name: Batch 1 sample 23 biol rep 2
mixed co-culture nitrogen

value: S.e + R.t co-culture 100 mg/L sucrose, nitrogen deplete, 25 mL


title: M2-DMSO_2

value: Macrophages

value: Healthy


title: 22_V_a

description:
Library name: Batch 1 sample 23 biol rep 1
mixed co-culture nitrogen

value: co-culture


title: OSK-3

description: Library name: OSK-3


title: 15-months-OSK-onoff-rep1

description: Library name: 33-15m-OSKonoff-a


title: 26_Z_b

description:
Library name: Batch 1 sample 22 biol rep 2
mixed co-culture trace minerals

value: cscB+ delta-sps, WT

value: S.e + R.t co-culture 100 mg/L sucrose, 0X Trace elements, 25 mL


title: liver tissues, high-concentration of curcumin (100 mg/kg)-biol rep 1

description:
Library name: high_concentration_rep1
H1

value: liver

value: WT


title: M2-DMSO_1


title: OSK-2

description: Library name: OSK-2


title: M1_4

value: LPS/IFNy 24hours


title: 3-months-OSK-onoff-rep4

description: Library name: 32-3m-OSKonoff-E


title: 26_Z_a

description:
Library name: Batch 1 sample 22 biol rep 1
mixed co-culture trace minerals


title: OSK-1

description: Library name: OSK-1


title: GFP-3

description: Library name: GFP-3


title: 3-months-OSK-onoff-rep3

description: Library name: 31-3m-OSKonoff-C


title: 6_F_c

description:
Library name: Batch 1 sample 21 biol rep 2
mixed co-culture trace minerals

value: S.e + R.t co-culture 100 mg/L sucrose, 10X Trace elements, 25 mL


title: Healthy M1_2


title: 3-months-OSK-onoff-rep2

description: Library name: 30-3m-OSKonoff-b2


title: 6_F_a

description:
Library name: Batch 1 sample 21 biol rep 1
mixed co-culture trace minerals


title: Healthy M1_1


title: GFP-2

description: Library name: GFP-2


title: Healthy M1_3


title: 3-months-OSK-onoff-rep1

description: Library name: 29-3m-OSKonoff-b1


title: 13_M_b

description:
Library name: Batch 1 sample 20 biol rep 2
mixed co-culture yeast extract supplement

value: S.e + R.t co-culture 100 mg/L sucrose, 1 g/L Yeast extract, 25 mL


title: GFP-1

description: Library name: GFP-1

value: RPE


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse end stage, biol rep 5

city: Rehovot

first: Neta

last: Erez

address: Haim Holtsman St 1

department: Systems Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: sample 19
Endst_peri_5

data_processing:
Reads were trimmed for poly-A/T stretches and Illumina adapters and mapped to the mouse genome. Deduplication was performed based on unique molecular identifiers (UMIs) and quantified gene counts. Differential gene expression (DEG) analysis was conducted using DESeq2, and raw p-values were adjusted for multiple testing. Heatmaps were generated based on gene expression Z-scored per gene derived from DESeq2 analysis results.
Assembly: GRCm39
Supplementary files format and content: The spreadsheet contains one row for each gene, and the following columns: Gene, Raw Counts, Normalized Counts, 7d_peri_vs_Normal_peri, 28d_peri_vs_Normal_peri, Endst_peri_vs_Normal_peri, 28d_peri_vs_7d_peri, Endst_peri_vs_7d_peri, Endst_peri_vs_28d_peri

source_name: peritoneum

growth_protocol: 5×106 tdTomato+ ID8 cells were suspended in 200μL PBS and injected intraperitoneally into C57BL/6;Col1a1-YFP mice. Control mice were injected i.p. with 200μL PBS. Peritoneal dissociation was performed in 20mL of buffer containing Collagenase P (0.75 mg/mL; Merck, 11213865001), 10X Trypsin (Merck,T4174), and DNase. Samples were stirred at 37°C for 40 minutes, filtered through a 70μm strainer, RBCs were lysed, and single-cell suspensions were washed and resuspended in PBS for downstream analysis.

extract_protocol:
RNA from sorted cells was isolated using Qiagen RNeasy Micro Kit (Cat. #74004). Quality samples were run on an Agilent Tapestation 4200 and only samples with RIN scores >8 were used.
MARS-seq protocol.

value: peritoneum

value: fibroblasts

value: Col1a1-YFP transgenic mouse


title: 24-months-OSK-rep5

description: Library name: 28-24m-OSK-e

value: Ear Fibroblasts


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse end stage, biol rep 4

description:
Library name: sample 18
Endst_peri_4


title: 13_M_a

description:
Library name: Batch 1 sample 20 biol rep 1
mixed co-culture yeast extract supplement


title: 7_G_c

description:
Library name: Batch 1 sample 19 biol rep 2
mixed co-culture iron supplement ros stress

value: S.e + R.t co-culture 100 mg/L sucrose, 5X Fe (0.115mM), 5 mM methyl viologen, 25 mL


title: 24-months-OSK-rep4

description: Library name: 27-24m-OSK-d


title: VCaP_p61

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: Library name: VCaP_p61

data_processing:
Sequencing reads were mapped to the hg38 human genome using STAR.v2.7.3a.
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: VCaP

extract_protocol:
Total RNA was prepared with the Qiagen AllPrep Kit (Valencia, CA).
RNA-seq libraries were constructed from total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

value: male

value: VCaP

value: prostate tumor cell line

tag: passage

tag: growth serum

value: DMEM / 10% FBS / Pen-Strep


title: PC3_p11

description: Library name: PC3_p11

value: F-12K / 10% FBS / Pen-Strep


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse end stage, biol rep 3

description:
Library name: sample 17
Endst_peri_3


title: 24-months-OSK-rep3

description: Library name: 26-24m-OSK-c


title: 7_G_b

description:
Library name: Batch 1 sample 19 biol rep 1
mixed co-culture iron supplement ros stress

value: co-culture

value: cscB+ delta-sps, WT


title: DU145_p75_2

description: Library name: DU145_p75_2


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse end stage, biol rep 2

description:
Library name: sample 16
Endst_peri_2


title: 24-months-OSK-rep2

description: Library name: 25-24m-OSK-b


title: DU145_p75_1

description: Library name: DU145_p75_1


title: 8_H_c

description:
Library name: Batch 1 sample 18 biol rep 2
mixed co-culture iron supplement

value: S.e + R.t co-culture 100 mg/L sucrose, 5X Fe (0.115mM), 25 mL


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse day 28, biol rep 5

description:
Library name: sample 15
28d_peri_5


title: 24-months-OSK-rep1

description: Library name: 24-24m-OSK-a


title: 8_H_b

description:
Library name: Batch 1 sample 18 biol rep 1
mixed co-culture iron supplement


title: 22Rv1_p13

description: Library name: 22Rv1_p13

value: RPMI 1640 / 10% FBS / Pen-Strep


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse day 28, biol rep 4

description:
Library name: sample 14
28d_peri_4


title: 15-months-OSK-rep5

description: Library name: 23-15m-OSK-f


title: 32_FF_c

description:
Library name: Batch 1 sample 18 biol rep 3
mixed co-culture B12 supplement ros stress

value: S.e + R.t co-culture 100 mg/L sucrose, 0.37 ug/L Vitamin B12, 5mM H2O2, 25 mL


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse day 28, biol rep 3

description:
Library name: sample 13
28d_peri_3


title: LNCaP_abl_p13_2

description: Library name: LNCaP_abl_p13_2

source_name: LNCaP-abl

value: LNCaP-abl


title: 15-months-OSK-rep4

description: Library name: 22-15m-OSK-e


title: 32_FF_b

description:
Library name: Batch 1 sample 17 biol rep 2
mixed co-culture B12 supplement ros stress


title: LNCaP_abl_p13_1

description: Library name: LNCaP_abl_p13_1


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse day 28, biol rep 2

description:
Library name: sample 12
28d_peri_2


title: 15-months-OSK-rep3

description: Library name: 21-15m-OSK-d


title: 32_FF_a

description:
Library name: Batch 1 sample 17 biol rep 1
mixed co-culture B12 supplement ros stress


title: COPZ1_siRNA_repeat_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Library name: Sample 24
Cells were transfected with COPZ1 siRNA and harvested 72 hours later - replicate 3

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed BBDuk from BBTools (v38.76)
Trimmed FASTQ files were aligned to human reference genome hg38 (Ensembl v104) using STAR software (v2.7.0f_0328).
featureCounts in R package Subread (v2.10.5) was used to generate gene counts
Assembly: hg38 (Ensembl v104)
Supplementary files format and content: text files containing counts

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit (Qiagen) following the manufacturer’s instructions
Libraries were constructed using theTruSeq Stranded Total RNA Library prep kit according to manufacturer’s protocol (Illumina).

value: foreskin fibrohuman fetal lung fibroblastsblasts

value: WT

value: COPZ1 siRNA transfection


title: COPZ1_siRNA_repeat_2

description:
Library name: Sample 23
Cells were transfected with COPZ1 siRNA and harvested 72 hours later - replicate 2


title: 31_EE_b

description:
Library name: Batch 1 sample 16 biol rep 2
mixed co-culture B12 supplement

value: S.e + R.t co-culture 100 mg/L sucrose, 0.37 ug/L Vitamin B12, 25 mL


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse day 28, biol rep 1

description:
Library name: sample 11
28d_peri_1

value: peritoneum

value: fibroblasts

value: Col1a1-YFP transgenic mouse


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse day 7, biol rep 5

description:
Library name: sample 10
7d_peri_5


title: 15-months-OSK-rep2

description: Library name: 20-15m-OSK-c

value: Ear Fibroblasts


title: COPZ1_siRNA_repeat_1

description:
Library name: Sample 22
Cells were transfected with COPZ1 siRNA and harvested 72 hours later - replicate 1


title: 31_EE_a

description:
Library name: Batch 1 sample 16 biol rep 1
mixed co-culture B12 supplement


title: 15-months-OSK-rep1

description: Library name: 19-15m-OSK-a


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse day 7, biol rep 4

description:
Library name: sample 9
7d_peri_4


title: 3-months-OSK-rep4

description: Library name: 18-3m-OSK-E


title: 9_I_b

description:
Library name: Batch 1 sample 15 biol rep 2
mixed co-culture ros stress

value: S.e + R.t co-culture 100 mg/L sucrose, 5mM H2O2, 25 mL


title: COPG1_siRNA_repeat_3

description:
Library name: Sample 21
Cells were transfected with COPG1 siRNA and harvested 72 hours later - replicate 3

value: COPG1 siRNA transfection


title: 3-months-OSK-rep3

description: Library name: 17-3m-OSK-C


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse day 7, biol rep 3

description:
Library name: sample 8
7d_peri_3


title: 9_I_a

description:
Library name: Batch 1 sample 15 biol rep 1
mixed co-culture ros stress


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse day 7, biol rep 2

description:
Library name: sample 7
7d_peri_2


title: COPG1_siRNA_repeat_2

description:
Library name: Sample 20
Cells were transfected with COPG1 siRNA and harvested 72 hours later - replicate 2


title: 10_J_c

description:
Library name: Batch 1 sample 14 biol rep 2
mixed co-culture ros stress

value: S.e + R.t co-culture 100 mg/L sucrose, 50 uM Cd(NO3)2 25 mL


title: 3-months-OSK-rep2

description: Library name: 16-3m-OSK-b2


title: COPG1_siRNA_repeat_1

description:
Library name: Sample 19
Cells were transfected with COPG1 siRNA and harvested 72 hours later - replicate 1


title: 10_J_a

description:
Library name: Batch 1 sample 14 biol rep 1
mixed co-culture ros stress

value: co-culture


title: peritoneal fibroblasts from normal Col1a1-YFP+ mouse biol rep 5

description:
Library name: sample 5
Normal_peri_5


title: COPE_siRNA_repeat_3

description:
Library name: Sample 18
Cells were transfected with COPE siRNA and harvested 72 hours later - replicate 3

value: COPE siRNA transfection


title: peritoneal fibroblasts from ID8 injected Col1a1-YFP+ mouse day 7, biol rep 1

description:
Library name: sample 6
7d_peri_1


title: 3-months-OSK-rep1

description: Library name: 15-3m-OSK-b1


title: 11_K_b

description:
Library name: Batch 1 sample 13 biol rep 2
mixed co-culture ros stress

value: cscB+ delta-sps, WT

value: S.e + R.t co-culture 100 mg/L sucrose, 10 µM DCMU 25 mL


title: COPE_siRNA_repeat_2

description:
Library name: Sample 17
Cells were transfected with COPE siRNA and harvested 72 hours later - replicate 2


title: COPE_siRNA_repeat_1

description:
Library name: Sample 16
Cells were transfected with COPE siRNA and harvested 72 hours later - replicate 1


title: 11_K_a

description:
Library name: Batch 1 sample 13 biol rep 1
mixed co-culture ros stress


title: peritoneal fibroblasts from normal Col1a1-YFP+ mouse biol rep 3

description:
Library name: sample 3
Normal_peri_3


title: peritoneal fibroblasts from normal Col1a1-YFP+ mouse biol rep 4

description:
Library name: sample 4
Normal_peri_4


title: 24-months-rep3

description: Library name: 12-24m-c


title: 12_L_b

description:
Library name: Batch 1 sample 12 biol rep 2
mixed co-culture osmotic stress

value: S.e + R.t co-culture 100 mg/L sucrose, NaCl stress 150 mM (8.8 g/L) 25 mL


title: peritoneal fibroblasts from normal Col1a1-YFP+ mouse biol rep 2

description:
Library name: sample 2
Normal_peri_2


title: COPD_siRNA_repeat_3

description:
Library name: Sample 15
Cells were transfected with COPD siRNA and harvested 72 hours later - replicate 3

value: COPD siRNA transfection


title: 24-months-rep2

description: Library name: 11-24m-b


title: COPD_siRNA_repeat_2

description:
Library name: Sample 14
Cells were transfected with COPD siRNA and harvested 72 hours later - replicate 2

value: foreskin fibrohuman fetal lung fibroblastsblasts


title: peritoneal fibroblasts from normal Col1a1-YFP+ mouse biol rep 1

description:
Library name: sample 1
Normal_peri_1


title: 24-months-rep1

description: Library name: 10-24m-a


title: COPD_siRNA_repeat_1

description:
Library name: Sample 13
Cells were transfected with COPD siRNA and harvested 72 hours later - replicate 1

value: WT


title: 15-months-rep5

description: Library name: 9-15m-f


title: Notch2_flox_CD11c_Cre_R3_HTO

city: Bethesda

first: Grozdan

last: Cvijetic

address: 30 Convent Dr, Building 30, Room 332

institute: NIH/NIDCR

description:
Library name: Notch2_flox_CD11c_Cre_R3_HTO
10x Genomics

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v4.0.0) to perform quality control and sample de-multiplexing (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). Samples were aligned to the UCSC mouse (mm10) genome using and expression of ensembl genes (v102) was quantified with "STARsolo" (version 2.7.9a) with recommended parameters (-- soloFeatures Gene GeneFull SJ Velocyto, --outSAMattributes NH HI AS nM CR CY UR UY GX GN CB UB, --soloCBwhitelist 3M-february-2018.txt (provided by 10x), --soloCellFilter None) for all 6 samples. Additionally, the expression of Cre was quantified by including these sequences during mapping and quantification step. Similarly, also hashtags-tags (HTO) were quantified with "STARsolo" after aligning the sample data only to HTO barcode sequences (with additional parameter: --clip3pNbases 41). The information obtained from HTO quantification was used only as additional annotation for cells (tissue of origin).
Assembly: Mouse mm10
Supplementary files format and content: Supplementary files format and content: Tab-separated values files and matrix files, RDS file with SingleCellExperiment_B6_N2.Rds The processed_hto.mtx contains UMI counts for HTO, rownanes are stored in processed_hto.tsv. The filtered dataset is stored in SingleCellExperiment_B6_N2.rds, with individual components: processed_counts.mtx (UMI counts), processed_logcounts.mtx (log2 UMI counts), column names in processed_barcodes.tsv and row names in processed_genes.tsv, gene annotation is stored in processed_rowdata.tsv and cell information is in processed_coldata.tsv.

molecule: protein

source_name: spleen, skin-draining lymph node (sLN), mesenteric lymph node (mLN)

extract_protocol:
Sort purified CD11c+ cells derived from C57BL/6 or Notch2fl/fl CD11cCre+ spleens, sLNs and mLNs were multiplexed individually by labeling each sort purified cell suspension with a unique Hashtag (HTO) antibody. 10K sort purified CD11c+ cells from the spleen, sLN and mLN of either C57BL/6 or Notch2fl/fl CD11cCre+ mice were mixed and loaded on a 10x Genomics Chromium Single Cell Controller.
Single cell capture, cDNA and library preparations were performed with the Single Cell 3' v3 Reagent Kit (10x Genomics) according to manufacturer's instructions. GEX sequencing libraries were loaded on an Illumina NovaSeq with high output cycle kits and sequenced paired-end using the following read length: Read1-28 cycles / Read2-8 cycles / Read3-91 cycles. HTO libraries were prepared according to manufacturer instruction and loaded on an Illumina NextSeq 500 with high output cycle kits and sequenced paired-end using the following read length: Read1 28 cycles / Read2 8 cycles / Read3 56 cycles for HTO libraries. The first 15 bases of R3 represented HTO barcode sequence.

value: CD11c+ cells

value: Notch2 flox CD11c Cre

tag: age

value: 6-14 weeks old

tag: replicate

tag: library type

value: HTO -- hash tags


title: COPB2_siRNA_repeat_3

description:
Library name: Sample 12
Cells were transfected with COPB2 siRNA and harvested 72 hours later - replicate 3

value: COPB2 siRNA transfection


title: Notch2_flox_CD11c_Cre_R2_HTO

description:
Library name: Notch2_flox_CD11c_Cre_R2_HTO
10x Genomics

value: spleen, skin-draining lymph node (sLN), mesenteric lymph node (mLN)


title: 15-months-rep4

description: Library name: 8-15m-e

value: Ear Fibroblasts


title: 25_D_b

description:
Library name: Batch 1 sample 10 biol rep 2
mixed co-culture ph stress

value: S.e + R.t co-culture 100 mg/L sucrose, pH 10.5 25 mL


title: Notch2_flox_CD11c_Cre_R1_HTO

description:
Library name: Notch2_flox_CD11c_Cre_R1_HTO
10x Genomics


title: 15-months-rep3

description: Library name: 7-15m-d


title: COPB2_siRNA_repeat_1

description:
Library name: Sample 10
Cells were transfected with COPB2 siRNA and harvested 72 hours later - replicate 1


title: Reamp-EGFP-BC

city: Otsu

first: Shoma

last: Matsumoto

state: Shiga

address: Setatsukinowa-cho

department: Research Center for Animal Life Science

country: Japan

institute: Shiga University of Medical Science

description: Library name: Tg-specific_scRNA-seq_Library

data_processing:
Sequenced reads were mapped on EGFP reference (pNM1419_EGFP_Reference.fa.gz) using the "cellranger multi" function.
Transgene-specific DNA barcode sequences cell barcodes and UMIs were extracted from the bam file.
The dataset was demultiplexed using cell barcode sequences, which were identified by conventional scRNA-seq analysis (Demultiplex_for_CMOlibrary.csv).
The original fastq files for CMO library are available on GSE306203.
To remove error-derived barcodes, all DNA barcode pairs were compared.
For each pairs, we calculated Levenshtein distance (LD) and read count ratio.
If ratio > 10^LD, the lower count barcode was merged into the higher count barcode.
This abundance-weighted clustering, iterated from the most frequent DNA barcode downward until convergence.
After clustering, DNA barcodes supported by fewer than 100 reads were discarded.
To mitigate PCR-recombination artefacts linking 10x barcode for cell to incorrect DNA barcode, read counts were tallied for every DNA barcode-10x barcode-UMI triplet.
Counts were ranked, and elbow point was identified with a custom script that selects the data point with the greatest perpendicular distance from the line connecting the first and last ranked points.
Assembly: pNM1419_EGFP_Reference.fa.gz
Supplementary files format and content: tsv

source_name: E11.5 embryo

extract_protocol:
E11.5 mouse embryos with DNA barcode-linked EGFP were minced and enzymatically into single cell. Four mouse embryos were multiplexed with CellPlex technology (10x Genomics).
Gel-bead-in emulsions (GEMs) were generated by Chromium controller (10x Genomics). cDNA library was condtructed using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) following the manufacturer's protocol. Transgene loci were amplified from scRNA-seq cDNA library using transgene-specific primers with illumina index sequences.

value: E11.5 embryo

value: DNA barcode-linked GFP Tg


title: L-GCK-KO 4

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: 3400 Civic Center Blvd.

department: Institute of Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

description:
Library name: Sample 7
Column name in AllSamples_RawCounts_GENENAME and AllSamples_Log2CP_TMM_GENENAME: RFGK4

data_processing:
The raw fastq files were first analyzed with FastQC (version 0.11.9) for quality control checks. The paired-end reads were mapped to the GRCm39.
Ensembl reference transcriptome for Mus musculus using kallisto (version 0.44.0).
The abundance.tsv files generated by kallisto were read into R (version 4.3.0) at the gene level using the tximport package (version 1.28.0).
Limma (version 3.56.2) was used for differential gene expression analysis.
Assembly: GRCm39
Supplementary files format and content: Raw counts as a comma-separated value file
Supplementary files format and content: Log2 counts per million expression with a trimmed-mean of M-values normalization as a comma-separated value file

source_name: Liver

extract_protocol:
RNA was purified from liver samples using the Qiagen RNeasy Mini Kit. 5 µg of RNA for each sample were given to Novogene for processing.
Library construction was performed by Novogene

value: Liver

value: Liver GCK knockout

value: High Carbohydrate Diet:overnight fasted & 6 hour refed


title: FLR-Myometrium-Spatial-2

description:
Library name: FLR-sp-CD-gex
Control

data_processing:
Spatial transcriptomics: Fast files were processed using 10X Genomics' SpaceRanger v2.1.0. Fastq files were generated with `mkfastq`, and processed files with `count`.
Single cell Transcriptomics:Fastq files were processed using 10X Genomics CellRanger 3.1.0 with "cellranger multit".
Assembly: Spatial transcriptomics: 10X Genomics' genome build: GRCh38-2020-A. Single-cell transcriptomics: Pre-built human reference 3.0.0, GRCh38 (Ensembel release 93)
Supplementary files format and content: Spatial transcriptomics: Spaceranger count spatial directory. Paraphrased from https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs: aligned_fiducials.jpg: shows which fiducial spots on the slide were detected by spaceranger; detected_tissue_image.jpg: shows the section of tissue detected by spaceranger; scalefactors_json.json: relative scales of user-supplied images; spatial_enrichment.csv: Moran's I values for each expressed feature; tissue_hires_image.png: high-resolution image of the tissue; tissue_lowres_image.png: low-resolution image of the tissue; tissue_positions.csv: table with information about each spot; barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene expression matrix files.
Supplementary files format and content: Single-cell transcriptomics: CellRanger count output with the files accounting for filtered feature-barcode matrices for each GEM well in "gz" compressed format.
Library strategy: Spatial Transcriptomics

source_name: Myometrium

extract_protocol:
For spatial transcriptomics: Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat. For single-cell and nuclei transcriptomics: samples were freshly dissociated using custom protocol. Nuclei were isolated using 10X Genomics nuclei isolation kit according to manufacturers recommended protocol.
For spatial transcriptomics: Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction. For single-cell an nuclei transcriptomics: single cell or nuclei suspensions were prepared and processed using the Chromium Single Cell 5’ Reagent Kits v3.1

value: Myometrium


title: ND-PVBP-Spatial

description:
Library name: FND-sp-AB-gex
Preeclamptic

source_name: Placenta

value: Placenta


title: 15-months-rep2

description: Library name: 6-15m-c

source_name: Ear Fibroblasts


title: 3_C_c

description:
Library name: Batch 1 sample 9 biol rep 2
mixed co-culture temperature stress

value: co-culture

value: cscB+ delta-sps, WT

value: S.e + R.t co-culture 100 mg/L sucrose, 14°C 25 mL


title: COPB1_siRNA_repeat_3

description:
Library name: Sample 9
Cells were transfected with COPB1 siRNA and harvested 72 hours later - replicate 3

value: foreskin fibrohuman fetal lung fibroblastsblasts

value: WT

value: COPB1 siRNA transfection


title: 15-months-rep1

description: Library name: 5-15m-a


title: 3-months-rep4

description: Library name: 4-3m-E


title: 2_B_c

description:
Library name: Batch 1 sample 8 biol rep 2
mixed co-culture temperature stress

value: S.e + R.t co-culture 100 mg/L sucrose, 37°C, 25 mL flask


title: Splenic_cDC1_Notch2cKO_R3

description:
Library name: Splenic_cDC1_Notch2cKO_R3
G6_P5

data_processing:
After sequencing, the base-called demultiplexed (fastq) read qualities were determined using the “FastQC” software, aligned to the mouse genome (UCSC version mm10) and gene counts were generated using the package “STAR” (v2.7.3a). The function “quantMode” of the “STAR” aligner was used for read counting. Genes with less that 5 reads in at least 1 sample were removed.
Assembly: Mouse mm10
Supplementary files format and content: Supplementary files format and content: Bulk_RawCountFile_filtered.txt: Tab-separated text file with raw counts for Ensembl genes. Column 1 is Ensembl GeneID, Column 2 and remaining columns contain raw counts.

source_name: spleen

extract_protocol:
Total RNA was isolated from the indicated sort-purified cell subsets using the Qiagen RNeasy Mini Kit according to the manufacturers instructions and including the optional DNase digestion. RNA quality was assessed using a Fragment Analyzer.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit (Illumina) following manufacturer's protocols. Samples were run on an Illumina NextSeq 2000 configured for 55 paired-end reads.

value: spleen

value: Notch2 flox CD11c Cre

value: 9 weeks old


title: 2_B_a

description:
Library name: Batch 1 sample 8 biol rep 1
mixed co-culture temperature stress


title: COPB1_siRNA_repeat_1

description:
Library name: Sample 7
Cells were transfected with COPB1 siRNA and harvested 72 hours later - replicate 1


title: Splenic_cDC1_Notch2cKO_R2

description:
Library name: Splenic_cDC1_Notch2cKO_R2
G4_P5


title: 27_AA_b

description:
Library name: Batch 1 sample 7 biol rep 2
mixed co-culture heterotrophy

value: S.e + R.t co-culture 10 g/L sucrose, 25 mL


title: Splenic_cDC1_Notch2cKO_R1

description:
Library name: Splenic_cDC1_Notch2cKO_R1
G2_P5


title: COPA_siRNA_repeat_2

description:
Library name: Sample 5
Cells were transfected with COPA siRNA and harvested 72 hours later - replicate 2

value: COPA siRNA transfection


title: 3-months-rep1

description: Library name: 1-3m-b1

value: Ear Fibroblasts


title: 27_AA_a

description:
Library name: Batch 1 sample 7 biol rep 1
mixed co-culture heterotrophy


title: COPA_siRNA_repeat_1

description:
Library name: Sample 4
Cells were transfected with COPA siRNA and harvested 72 hours later - replicate 1


title: Splenic_DC3_Notch2cKO_R2

description:
Library name: Splenic_DC3_Notch2cKO_R2
G6_P3


title: SW1 sh Polr1a biol rep 3

city: Hershey

first: Vladimir

last: Spiegelman

address: 500 University Drive Hershey, Pennsylvania

department: Pediatrics

institute: Penn State University

description:
Library name: Sample 6
Columns name in SW1_Polr1a_KD_RNA_seq_counts.xls: K6_count; K6_fpkm

data_processing:
Low-quality reads were filtered by fastp.Adapter sequences were trimmed.
The reference genome index was created by the build-index function in HISAT2 software package with default options. Then the filtered clean reads were mapped to the reference genome by HISAT2, and the position and gene characteristics information were acquired. After the alignment, the generated SAM files were sorted to BAM files using samtools. The featureCounts software of the subread package to quantify transcripts and gene expression levels using mapped reads positional information on the gene. The gene expression level was normalized by using FPKM (fragment per kilobase of transcript per million mapped reads) method.
Assembly: Mus musculus mm10
Supplementary files format and content: xls file include raw counts and fpkm values for each sample

growth_protocol: SW1 cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin in the humidified incubator at 37°C, 5% CO2.

extract_protocol:
RNA was isolated using the Rneasy kit (Qiagen). Magnetic beads with Oligo (dT) were used to isolate mRNA from the total RNA.
The mRNA was fragmented randomly by adding the fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer after adding dNTPs, RNase H, and DNA polymerase I. Short fragments were purified and resolved with EB buffer for end repair and single-nucleotide A (adenine) addition. After that, the short fragments were connected with sequencing adapters. The double-stranded cDNA library was completed through size selection and PCR enrichment. During the QC steps, the Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System was used in quantification and qualification of the sample library. Lastly, the qualified RNA-seq libraries are sequenced using Illumina NovaSeq6000.

value: melanoma cell line

value: Polr1a knockdown


title: 20_T_b

description:
Library name: Batch 1 sample 6 biol rep 2
mixed co-culture heterotrophy

value: S.e + R.t co-culture 1 g/L sucrose, 25 mL


title: Splenic_DC3_Notch2cKO_R1

description:
Library name: Splenic_DC3_Notch2cKO_R1
G4_P3


title: Control_siRNA_repeat_3

description:
Library name: Sample 3
Cells were transfected with Control siRNA and harvested 72 hours later - replicate 3

value: Control siRNA transfection


title: SW1 sh Polr1a biol rep 2

description:
Library name: Sample 5
Columns name in SW1_Polr1a_KD_RNA_seq_counts.xls: K5_count; K5_fpkm


title: Control_siRNA_repeat_2

description:
Library name: Sample 2
Cells were transfected with Control siRNA and harvested 72 hours later - replicate 2


title: Splenic_cDC1_Notch2FL_R3

description:
Library name: Splenic_cDC1_Notch2FL_R3
G5_P5

value: Notch2 flox


title: TTchemSeq h2o2 Treated replicate 3 exp1

status: Public on Jun 12 2026

city: København

first: Lea

middle: Haarup

last: Gregersen

address: Blegdamsvej 3B,

department: ICMM

country: Denmark

institute: University of Copenhagen

description: Library name: TT1_H2O2_no_recovery_r3

data_processing:
Raw fastq files for Read 1 were labelled with appropriate UMI reads using UMItools
adapter trimming with cutadapt (v4.5) within trim_galore (v0.6.10) and read length filtering > 19nt
samples were mapped with STAR75 (v2.7.11b) against a merged human-yeast genome assemblies (Homo sapiens GRCh38 and Saccharomyces cerevisiae sacCer, Ensembl release 108)
Genome alignments BAM files were filtered for multimapped reads with samtools (v1.21) view function (-q 10)
UMI duplicates were then removed with UMItools dedup function. A yeast gene-level count matrix was generated with Subread (v2.0.6) featureCounts76 and used to calculate yeast size-factors with DEseq277 (v1.42.0) “estimateSizeFactors” function. Strand specific and spike-in normalised BigWig files were generated from strand-specific bam files using Deeptools78 (v3.5.5) bamCoverage function (--scaleFactor = 1/ yeast size-factor) with bin size of 25 nt (-bs 25)
Assembly: (Homo sapiens GRCh38 and Saccharomyces cerevisiae sacCer, Ensembl release 108)
Supplementary files format and content: bigwig forward and reverse strands

molecule: nuclear RNA

source_name: HEK293 Flp-in T-Rex

growth_protocol: Flp-InTM T-REx HEK293 cells (HEK293, R78007, ThermoFisher Scientific, human embryonic kidney epithelial, female origin) were cultured at 37C with 5% CO2 in high glucose DMEM (Biowest, Cat#L0104) supplemented with 10% v/v FBS (Gibco, Cat#10270106), 100 U/mL penicillin, 100 μg/mL streptomycin (Gibco, 10378016) 2 mM L-glutamine.

extract_protocol:
80% confluent cells RNA were labelled in vivo for 15 min with 4sU by adding it directly to the tissue culture media to a final concentration of 1 mM. Per samples 80-100 μg of total RNA resuspended in 100 μL RNAse-free H2O was complemented with 1 % (relative to total RNA concentration) of S. cerevisiae 4tU-labelled RNA spike-in. Total RNA was fragmented by adding 20 μL of freshly prepared 1 M NaOH per sample, thoroughly mixed and incubated for 40 min on ice to < 400 nt fragments. Resuspended and purified 4sU labelled RNA in RNAse-free water was biotinylated in 10 mM Tris-HCl pH = 7.4; 1 mM EDTA complemented with 0.5 mg/ μL MTSEA biotin-XX linker (Biotum, Cat# BT90066) for 30 min in the dark at room temperature. Biotinylated RNA was immediately purified by ROTI®Aqua-P/C/I extraction and isopropanol precipitation and resuspended in 50 μL RNAse-free water. and isolated with μMACS Streptavidin Kit (Miltenyi, Cat#130-074-101). A total of 100uL μMACS Streptavidin MicroBeads were added to denatured 4sU total RNA and incubated for 15 min at room temperature with agitation. Beads bound to 4sU biotinylated RNA were applied to magnetic μColumns and transferred to the magnetic field of the μMACS magnetic separator (Miltenyi).
Approx. 30 ng of purified 4sU biotinylated RNA was used to prepare libraries with NEBNext® Ultra™ II RNA library prep kit (NEB, Cat#E7760) according to manufacturer’s protocol (protocol 5 for fragmented RNA) with ligation of two barcodes of 8 nt and 11 nt UMIs (NEB, Cat#E7416).

treatment_protocol: Inhibitors treatments were carried out by direct addition to the cell culture media with the following concentration 100 μM DRB (Sigma, D1916) or/and 10 μM Olaparib (PARPi, MedchemExpress, Cat#HY-10162) or/and 10 μM TH5487 (OGG1i, MedchemExpress, Cat#HY-125276). Oxidative stress induction treatments were carried out for 15 min (or 30 min for EU-labelling) with direct addition of freshly prepare 1000x concentrate to cell culture media, fresh H2O2 (maximum 3 month old kept at 4CC) to final concentration of 1 mM H2O2 (Sigma, H1009) or freshly resuspended Menadione sodium bisulfite (MND, Sigma, M5750) in water to final concentration of 0.25 mM.

value: HEK293 Flp-in T-Rex


title: SW1 sh Polr1a biol rep 1

description:
Library name: Sample 4
Columns name in SW1_Polr1a_KD_RNA_seq_counts.xls: K4_count; K4_fpkm


title: 33_GG_c

description:
Library name: Batch 1 sample 5 biol rep 2
mixed co-culture heterotrophy

value: co-culture

value: cscB+ delta-sps, WT

value: S.e + R.t co-culture 100 mg/L sucrose, 50 mL flask


title: Control_siRNA_repeat_1

description:
Library name: Sample 1
Cells were transfected with Control siRNA and harvested 72 hours later - replicate 1

value: foreskin fibrohuman fetal lung fibroblastsblasts

value: WT


title: SW1 sh ctrl biol rep 3

description:
Library name: Sample 3
Columns name in SW1_Polr1a_KD_RNA_seq_counts.xls: C3_count; C3_fpkm


title: 33_GG_a

description:
Library name: Batch 1 sample 5 biol rep 1
mixed co-culture heterotrophy


title: Degos13_CSF_TCR

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

source_name: CSF

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. Peripheral blood mononuclear cells (PBMCs) from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell capturing. cDNA was generated using 5' 10X kit and subsequenctly used for gene expression library and single cell TCR library preparation.
Single cell TCR library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).

value: CSF


title: Splenic_cDC1_Notch2FL_R1

description:
Library name: Splenic_cDC1_Notch2FL_R1
G1_P5

value: spleen


title: SW1 sh ctrl biol rep 2

description:
Library name: Sample 2
Columns name in SW1_Polr1a_KD_RNA_seq_counts.xls: C2_count; C2_fpkm


title: Degos5_CSF_TCR

description: 10x Genomics


title: SW1 sh ctrl biol rep 1

description:
Library name: Sample 1
Columns names in SW1_Polr1a_KD_RNA_seq_counts.xls: C1_count; C1_fpkm


title: 20_T_a

description:
Library name: Batch 1 sample 6 biol rep 1
mixed co-culture heterotrophy


title: 1_A_a

description:
Library name: Batch 1 sample 4 biol rep 1
mixed co-culture no sucrose supplement

value: S.e + R.t co-culture, 50 mL flask


title: Degos3_CSF_TCR

description: 10x Genomics


title: Splenic_cDC1_Notch2FL_R2

description:
Library name: Splenic_cDC1_Notch2FL_R2
G3_P5

value: 9 weeks old


title: Splenic_DC3_Notch2FL_R2

description:
Library name: Splenic_DC3_Notch2FL_R2
G3_P3


title: 24-months-rep5

first: Yuancheng Ryan

last: Lu

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description: Library name: 14-24m-e


title: Notch2_flox_CD11c_Cre_R3_GEX

description:
Library name: Notch2_flox_CD11c_Cre_R3_GEX
10x Genomics

value: spleen, skin-draining lymph node (sLN), mesenteric lymph node (mLN)

value: CD11c+ cells

value: Notch2 flox CD11c Cre

value: 6-14 weeks old

value: GEX -- gene expression


title: 24-months-rep4

description: Library name: 13-24m-d

value: Ear Fibroblasts


title: 15_O_c

description:
Library name: Batch 1 sample 3 biol rep 2
mixed co-culture no sucrose supplement

value: S.e + R.t co-culture, 25 mL flask


title: Degos_4_PBMC_TCR

description: 10x Genomics

source_name: PBMC

value: PBMC


title: 12_L_a

description:
Library name: Batch 1 sample 12 biol rep 1
mixed co-culture osmotic stress

source_name: co-culture

value: co-culture

value: S.e + R.t co-culture 100 mg/L sucrose, NaCl stress 150 mM (8.8 g/L) 25 mL


title: Splenic_DC3_Notch2FL_R1

description:
Library name: Splenic_DC3_Notch2FL_R1
G1_P3

value: Notch2 flox


title: Notch2_flox_CD11c_Cre_R2_GEX

description:
Library name: Notch2_flox_CD11c_Cre_R2_GEX
10x Genomics


title: 1_A_c

description:
Library name: Batch 1 sample 4 biol rep 2
mixed co-culture no sucrose supplement

value: cscB+ delta-sps, WT


title: 5_E_b

description:
Library name: Batch 1 sample 11 biol rep 2
mixed co-culture ph stress

value: S.e + R.t co-culture 100 mg/L sucrose, pH 6.5 25 mL


title: 15_O_a

description:
Library name: Batch 1 sample 3 biol rep 1
mixed co-culture no sucrose supplement


title: Degos_3_PBMC_TCR

description: 10x Genomics


title: Splenic_cDC2a_Notch2FL_R3

description:
Library name: Splenic_cDC2a_Notch2FL_R3
G5_P1


title: Notch2_flox_CD11c_Cre_R1_GEX

description:
Library name: Notch2_flox_CD11c_Cre_R1_GEX
10x Genomics


title: SW1 sh Polr1a biol rep 3

description:
Library name: Sample 6
Columns name in SW1_Polr1a_KD_RNA_seq_counts.xls: CHX_K6_count; CHX_K6_fpkm

data_processing:
Low-quality reads were filtered by fastp. Raw reads containing over 50% of low-quality bases or over 10% of N bases were removed. Adapter sequences were trimmed. Reads with lengths between 20-40bp were retained for subsequent analysis. Short reads alignment tool Bowtie2 was used for mapping reads to the ribosome RNA (rRNA) database, GenBank, Rfam database. The reads mapped to rRNAs, transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), and miRNA were removed.
Reads counts in the open reading frame of coding genes was calculated by the software RSEM,and the gene expression level was normalized by using FPKM (fragment per kilobase of transcript per million mapped reads) method.
Assembly: Processed RNA-seq reads were aligned to the genome using whole-genome alignment by STAR with a 2-pass setting enabled.
Supplementary files format and content: xls file include raw counts and fpkm values for each sample
Library strategy: Ribo-Seq

extract_protocol:
To prepare RFs, 10μL of RNase I and 6μL of DNase I were added to 400μL of lysate， which was then incubated for 45 min at room temperature with gentle mixing on a Nutator mixer. Nuclease digestion was stopped by adding 10μL of SUPERase·In RNase inhibitor. Size exclusion columns (illustra MicroSpin S-400 HR Columns; GE Healthcare; catalog no. 27- 5140-01) were equilibrated with 3 mL of polysome buffer by gravity flow and centrifuged at 600g for 4 min at room temperature. 100μL of digested RFs were added to the column and centrifuged at 600g for 2 min. Next, 10μL 10% (wt/vol) SDS was added to the elution, and RFs with a size greater than 17nt was isolated according to the RNA Clean and Concentrator-25 kit (Zymo Research;R1017). rRNA was removed using short (50–80 bases) antisense DNA probes complementary to rRNA sequences were added to the solution containing RFs, then RNase H and DNase Iwas added to digest rRNA and residual DNA probes. Finally, RFs were further purified using magnet beads.
Ribo-seq libraries were prepared using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM X10.

treatment_protocol: Cells were treated with 0.1 mg/mL of cycloheximide for 2 min, then collected in ice-cold PBS with 0.1 mg/mL of cycloheximide.

value: melanoma cell line

value: Polr1a knockdown

value: Cycloheximide 100 μg/mL


title: Degos_2_PBMC_TCR

description: 10x Genomics


title: 5_E_a

description:
Library name: Batch 1 sample 11 biol rep 1
mixed co-culture ph stress


title: Splenic_DC3_Notch2FL_R3

description:
Library name: Splenic_DC3_Notch2FL_R3
G5_P3

value: spleen

value: 9 weeks old


title: COPB2_siRNA_repeat_2

description:
Library name: Sample 11
Cells were transfected with COPB2 siRNA and harvested 72 hours later - replicate 2

value: foreskin fibrohuman fetal lung fibroblastsblasts

value: WT

value: COPB2 siRNA transfection


title: Splenic_cDC2a_Notch2FL_R2

description:
Library name: Splenic_cDC2a_Notch2FL_R2
G3_P1


title: Pnvp Mutant EC enriched P8

city: Montréal

first: Gael

last: Cagnone

address: 3175 Chemin de la Côte-Sainte-Catherine

institute: CHU Sainte Justine

description:
Library name: PnvpMut
10X Genomics

data_processing:
Libraries were sequenced  on Illumina NovaSeq6000 S4 , followed by de-multiplexing and mapping to the mouse genome (Mus_musculus:GRCm38) using CellRanger (pipeline cellranger-6.1.1) (10x Genomics). Count matrices were analyzed using Seurat V5. Following quality control and dimensionality reduction , endothelial cells were then analyzed separately. Briefly, ECs from the 4 four datasets (CTL PNVP = 1195 cells, CTL BRAIN = 3221 cells, mutant PNVP = 2193 cells, mutant BRAIN = 1904 cells) were merged together, normalised using SCTranform (vars.to.regress = c("nFeature_RNA", "percent.mt")) then dimensionality reduction was performed using runUMAP based on the first 20 PCs from PCA analysis on 3000 variable genes (SCT assay). Clustering was then performed on UMAP first and second dimensions (dims=1:2, reduction = “umap”) at a resolution of 1.2, followed by differential marker expression analysis between clusters based on normalised RNA count (RNA assay). Normalised RNA counts were then scaled (vars.to.regress = c("nFeature_RNA", "percent.mt")) for data visualization. Clusters were finally annotated based on known endothelial subtype marker genes.
Assembly: Mus_musculus:GRCm38
Supplementary files format and content: h5 files (filtered_feature_bc_matrix.h5)

source_name: Pnvp

extract_protocol:
The cell suspension was washed with a FACS buffer (PBS containing 1% FBS and 0.2% EDTA). Cells were stained for 30 minutes at room temperature with PE anti-mouse CD140b Antibody (Biolegend, 136006); APC-conjugated anti-mouse CD31 antibody (BD Biosciences, 551262) and FITC-conjugated anti-mouse CD45 antibody (BioLegend, 103108) in Fc block solution (5 µg/mL CD16/CD32 Fc Block, eBioscience, 16-0161-82). After washing, cells were stained with Live/Dead Fixable Aqua Dead Cell Stain (ThermoFisher Scientific, L34957) for 20 minutes at room temperature. Stained cells were washed and resuspended in PBS. The gating strategy was defined using unstained and single-stained controls. Dead cells and doublets were excluded, and endothelial cells (CD45⁻ CD31⁺) were sorted using a BD FACS Aria Fusion. Cells were resuspended in PBS containing 0.04% BSA. Cells from WT PNVP/brain and mutant PNVP/brain sample were then subjected to single-cell RNAseq aiming at a yield of 5 000 cells per condition.
Four libraries (CTL PNVP, CTL BRAIN, mutant PNVP, mutant BRAIN) were generated using the Chromium  Single Cell 3’ Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA).

value: Pnvp

value: Endothelial enriched


title: SW1 sh Polr1a biol rep 2

description:
Library name: Sample 5
Columns name in SW1_Polr1a_KD_RNA_seq_counts.xls: CHX_K5_count; CHX_K5_fpkm


title: Degos_1_PBMC_TCR

description: 10x Genomics


title: Splenic_cDC2a_Notch2FL_R1

description:
Library name: Splenic_cDC2a_Notch2FL_R1
G1_P1


title: 25_D_a

description:
Library name: Batch 1 sample 10 biol rep 1
mixed co-culture ph stress

data_processing:
Rsubread v2.16.1 was used to obtain transcript counts provided in the processed data file.
Assembly: NC_007604.1
Supplementary files format and content: csv, transcript counts

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus Mini Kit. Samples were homogenized using QiaShredder, then processed following the manufacturer's protocol with 70% ethanol addition. RNA quality and quantity were assessed by NanoDrop One spectrophotometry. A total of 2 µg RNA in 40 µL was submitted for RNA sequencing per sample.
Library construction and sequencing was performed by Azenta Life Sciences. Library preparation used the NEBNext Ultra RNA Library preparation kit with rRNA depletion performed using the QIAGEN FastSelect rRNA depletion kit with dual depletion. Sequencing was performed on the Illumina platform using paired-end 2x150bp with single indexing (~350M PE reads, ~105GB per sample).

value: S.e + R.t co-culture 100 mg/L sucrose, pH 10.5 25 mL


title: Brain Mutant EC enriched P8

description:
Library name: BrainMut
10X Genomics

source_name: Brain

value: Brain


title: SW1 sh Polr1a biol rep 1

description:
Library name: Sample 4
Columns name in SW1_Polr1a_KD_RNA_seq_counts.xls: CHX_K4_count; CHX_K4_fpkm


title: Degos_4_Skin_L2_TCR

description: 10x Genomics

source_name: Skin

value: Skin


title: perR mutant S. aureus, iron-replete, biol rep 3

city: London

first: Alexander

last: Sheikh

state: Ontario

address: 1400 Western Road

department: Microbiology and Immunology

institute: Western University

description:
Library name: Sample 12
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.

data_processing:
Sequencing reads were mapped to the reference S. aureus USA300 FPR3757 genome in Geneious Prime 2025.1 (https://www.geneious.com)
Demultiplexing, quality control, and adapter trimming was performed by the Microbial Genome Sequencing Center in Pittsburgh, PA \with bcl-convert (v4.2.4)
Assembly: Staphylococcus aureus USA300_FPR3757
Supplementary files format and content: xlsx file format, contains TPM values and calculated differential expression and p-values for every transcript

organism: Staphylococcus aureus

growth_protocol: Overnight precultures grown in tryptic soy broth (TSB) with 100µM EDDHA were subcultured in technical duplicate at a starting OD600 of 0.1 in fresh TSB + EDDHA and left to grow for 3 hours at 37 °C with shaking to an OD600 of ~1.0.

extract_protocol:
Cells were normalized to an OD600 equivalent of 3.0, pelleted, lysed, and RNA extraction performed with Trizol (Invitrogen) according to manufacturer’s instructions. Extracted RNA was then subject to rigorous DNAse treatment (Invitrogen) and phenol chloroform extraction to inactivate and remove DNAse.
RNA samples were processed by the Microbial Genome Sequencing Center in Pittsburgh, PA. Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI). Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads.

treatment_protocol: One of each technical duplicate in above protocol was spiked with 50µM ferric chloride following 3 hours of growth and then all tubes were left to grow for another hour at 37 °C with shaking.

value: 100 µM EDDHA, 50 µM ferric chloride


title: Pnvp Control EC enriched P8

description:
Library name: PnvpCT
10X Genomics


title: SW1 sh ctrl biol rep 3

description:
Library name: Sample 3
Columns name in SW1_Polr1a_KD_RNA_seq_counts.xls: CHX_C3_count; CHX_C3_fpkm


title: Degos_4_Skin_L1_TCR

description: 10x Genomics


title: Gene_Expression_Group1

description: Library name: Gene_Expression_Group1

data_processing:
Merged fastq file was mapped and aligned to the custom mouse genome (mm10) with EGFP sequence via demultiplexing by cellranger multi.
The read counts derived from ambient RNA were corrected using SoupX.
Doublets were estimated and removed using DoubletFinder.
RECODE was used to reduce the noises of scRNA-seq data.
Downstream analyses and visualization were performed in R with Seurat.
Assembly: mm10
Supplementary files format and content: tsv, mtx, csv

extract_protocol:
E11.5 mouse embryos with DNA barcode-linked EGFP were minced and enzymatically into single cell. Four mouse embryos were multiplexed with CellPlex technology (10x Genomics).
Gel-bead-in emulsions (GEMs) were generated by Chromium controller (10x Genomics). cDNA library was condtructed using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) following the manufacturer's protocol.

value: E11.5 embryo

value: DNA barcode-linked GFP Tg


title: 3_C_b

description:
Library name: Batch 1 sample 9 biol rep 1
mixed co-culture temperature stress

value: co-culture

value: cscB+ delta-sps, WT

value: S.e + R.t co-culture 100 mg/L sucrose, 14°C 25 mL


title: perR mutant S. aureus, iron-deplete, biol rep 3

description:
Library name: Sample 11
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.

value: 100 µM EDDHA


title: SW1 sh ctrl biol rep 2

description:
Library name: Sample 2
Columns name in SW1_Polr1a_KD_RNA_seq_counts.xls: CHX_C2_count; CHX_C2_fpkm

value: melanoma cell line

value: Cycloheximide 100 μg/mL


title: Degos_2_Skin_L2_TCR

description: 10x Genomics


title: COPB1_siRNA_repeat_2

description:
Library name: Sample 8
Cells were transfected with COPB1 siRNA and harvested 72 hours later - replicate 2

value: foreskin fibrohuman fetal lung fibroblastsblasts

value: COPB1 siRNA transfection


title: Brain Control EC enriched P8

description:
Library name: BrainCT
10X Genomics


title: CellPlex_Group1

description: Library name: CellPlex_Group1


title: Wild-type S. aureus, iron-replete, biol rep 3

description:
Library name: Sample 10
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.

value: wild-type


title: KP_sgBACH1_siFEM1B_3

city: Marseille

first: Luca

last: Lignitto

address: 27 Boulevard Leï Roure

country: France

institute: CNRS

description: Library name: SAMPLE_12

data_processing:
RNA-seq reads were aligned to the reference genome using Subread-align (v1.6.4) with default parameters.
Mapped reads were filtered using samtools (v1.9) with --exclude-flags 4.
Gene counts were obtained with featureCounts (v1.6.4).
Differential expression analysis was performed using DESeq2 (v1.26.0).
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts for each sample

source_name: lung

growth_protocol: KP cells were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37 C

extract_protocol:
RNA extraction kit qiagen
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: knockout by CRISPR/Cas9 and knockdown by siRNA

value: lung

value: KP

value: lung adenocarcinoma

value: KrasLSL-G12D/+; Trp53flox/flox


title: SW1 sh ctrl biol rep 1

description:
Library name: Sample 1
Columns names in SW1_Polr1a_KD_RNA_seq_counts.xls: CHX_C1_count; CHX_C1_fpkm

value: WT


title: Wild-type S. aureus, iron-deplete, biol rep 3

description:
Library name: Sample 9
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.


title: Degos_1_Skin_L2_TCR

description: 10x Genomics

value: Skin


title: UMUC3_FASN_KD_Smoke_4

city: Houston

first: Karthik Reddy

last: Kami Reddy

email: karthikr@bcm.edu, amara@bcm.edu, putluri@bcm.edu, piyarath@bcm.edu

state: Texas

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Library name: Sample 14

data_processing:
Fastq files were run through fastqc for primary qc
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt (parameter- Default settings)
Trimmed sequence reads were mapped to GRCh38 using Salmon
with ‘libType A’ and ‘validateMapping’ options
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Feature counts

source_name: Xenograft Tissue

growth_protocol: UMUC3 control and FASN KD cells were grown in regular media and CSM media before engraftment.

extract_protocol:
For transcriptomics analysis from mouse xenografts, RNA was isolated from frozen tissues using the QIAGEN RNAeasy microkit.
Libraries were created from the cDNA by attaching an adenosine to the 3’ end and ligating adapters to the ends

treatment_protocol: Cells are pre-exposed to 10%CSM before engraftment

value: Xenograft Tissue

value: Human

value: KD + Smoke


title: perR mutant S. aureus, iron-replete, biol rep 2

description:
Library name: Sample 8
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.

value: 100 µM EDDHA, 50 µM ferric chloride


title: KP_sgBACH1_siFEM1B_2

description: Library name: SAMPLE_11


title: KP_sgBACH1_siFEM1B_1

description: Library name: SAMPLE_10


title: UMUC3_FASN_KD_Smoke_3

description: Library name: Sample 13


title: KP_sgCTRL_siFEM1B_3

description: Library name: SAMPLE_9


title: perR mutant S. aureus, iron-deplete, biol rep 2

description:
Library name: Sample 7
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.


title: UMUC3_FASN_KD_Smoke_2

description: Library name: Sample 12


title: Degos_1_Skin_L1_TCR

description: 10x Genomics


title: Degos_3_CSF_PostRuxo_Wk_0_Rep2

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. PBMCs from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell RNA-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).

value: CSF


title: Wild-type S. aureus, iron-replete, biol rep 2

description:
Library name: Sample 6
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.


title: Degos_3_CSF_PostRuxo_Wk_0_Rep1

description: 10x Genomics


title: UMUC3_FASN_KD_Smoke_1

description: Library name: Sample 11


title: KP_sgCTRL_siFEM1B_1

description: Library name: SAMPLE_7


title: Wild-type S. aureus, iron-deplete, biol rep 2

description:
Library name: Sample 5
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.

value: 100 µM EDDHA


title: FFM-PBMCs

first: Theodoros

last: Xenakis

address: 20 Guilford Street

institute: UCL

description:
Library name: FFM-sc-E-gex
Preeclamptic

data_processing:
Spatial transcriptomics: Fast files were processed using 10X Genomics' SpaceRanger v2.1.0. Fastq files were generated with `mkfastq`, and processed files with `count`.
Single cell Transcriptomics:Fastq files were processed using 10X Genomics CellRanger 3.1.0 with "cellranger multit".
Assembly: Spatial transcriptomics: 10X Genomics' genome build: GRCh38-2020-A. Single-cell transcriptomics: Pre-built human reference 3.0.0, GRCh38 (Ensembel release 93)
Supplementary files format and content: Spatial transcriptomics: Spaceranger count spatial directory. Paraphrased from https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs: aligned_fiducials.jpg: shows which fiducial spots on the slide were detected by spaceranger; detected_tissue_image.jpg: shows the section of tissue detected by spaceranger; scalefactors_json.json: relative scales of user-supplied images; spatial_enrichment.csv: Moran's I values for each expressed feature; tissue_hires_image.png: high-resolution image of the tissue; tissue_lowres_image.png: low-resolution image of the tissue; tissue_positions.csv: table with information about each spot; barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene expression matrix files.
Supplementary files format and content: Single-cell transcriptomics: CellRanger count output with the files accounting for filtered feature-barcode matrices for each GEM well in "gz" compressed format.

source_name: PBMCs

value: PBMCs