title: Volunteer 14, photoprotected skin, noon (T12)

description: Library name: 14A


title: Volunteer 14, photoexposed skin, midnight (T00)

status: Public on Apr 04 2026

type: SRA

city: Manchester

first: Qing-Jun

last: Meng

address: A.V. Hill Building, Oxford Road

department: Faculty of Biology, Medicine and Health

country: United Kingdom

institute: The University of Manchester

description: Library name: 14F

library_source: transcriptomic

data_processing:
Raw sequencing data is pre-processed or ‘trimmed’ to remove adapter sequences and low-quality reads.  Cleaned reads were aligned to the Homo sapiens GRCh38 reference genome using STAR aligner v2.5.2b with default parameters.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: raw_counts T00.csv, raw_counts T06.csv, raw_counts T12.csv, raw_counts T18.csv

molecule: total RNA

organism: Homo sapiens

source_name: 3 mm whole thickness skin

extract_protocol:
RNA was extracted and purified using QIAsymphony RNA (Cat no. 931636; Qiagen, Hilden, Germany)
100ng of RNA per sample was used for library preparation, performed by polyA selection-based mRNA enrichment, mRNA fragmentation, and random priming with subsequent first- and second-strand complementary DNA (cDNA) synthesis. Following that, end-repair 5′ phosphorylation and adenine nucleotide (dA)-tailing was performed. Last, adaptor ligation, polymerase chain reaction (PCR) enrichment, and Illumina NovaSeq technology–based sequencing was performed with 20M reads per sample using Trimmomatic v.0.36.

tag: tissue

value: 3 mm whole thickness skin


title: Volunteer 14, photoprotected skin, 6pm (T18)

description: Library name: 14C


title: Volunteer 13, photoprotected skin, 6pm (T18)

description: Library name: 13C


title: Volunteer 14, photoprotected skin, 6am (T06)

description: Library name: 14G


title: Volunteer 13, photoprotected skin, midnight (T00)

description: Library name: 13E


title: Volunteer 12, photoexposed skin, 6am (T06)

description: Library name: 12H


title: Volunteer 13, photoexposed skin, 6pm (T18)

description: Library name: 13D


title: Volunteer 12, photoprotected skin, 6am (T06)

description: Library name: 12G


title: Volunteer 12, photoprotected skin, midnight (T00)

description: Library name: 12E


title: Volunteer 12, photoexposed skin, midnight (T00)

description: Library name: 12F


title: Volunteer 13, photoexposed skin, noon (T12)

description: Library name: 13B


title: Volunteer 13, photoprotected skin, noon (T12)

description: Library name: 13A


title: Volunteer 12, photoexposed skin, 6pm (T18)

description: Library name: 12D


title: Volunteer 12, photoprotected skin, 6pm (T18)

description: Library name: 12C


title: Volunteer 11, photoexposed skin, 6am (T06)

description: Library name: 11H


title: Astrocyte_WT_RNA_Rep1

city: Shanghai

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

country: China

institute: Fudan University

data_processing:
Raw data was first processed by FastQC for quality control, and cleaned using Trim-galore. Clean data were then aligned to the Mouse (mm10) reference genome using default settings of Hisat2 . Then, samtools v1.9 was used to sort and build the alignment file index. Gene expression counts were generated using FeatureCounts v1.6.3. Differential analysis was conducted using DESeq2 and significant genes were selected with p < 0.05.
Assembly: mm10
Supplementary files format and content: COUNT: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: cortex

extract_protocol:
Astrocyte were purified from mice adult cortex by using the Adult Brain Dissociation Kit (Miltenyi Biotec, 130-107-677), Debris Removal Solution (Miltenyi Biotec, 130-109-398) and anti-ACSA-2 (astrocyte cell surface antigen-2) microbeads (Miltenyi Biotec, 130-097-678) according to the manufacturer's instructions. Neuronal nuclei were Isolated from mice adult cortex by FACS using anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated; EMD Millipore Corp., MAB377X). Astrocyte and neuronal nuclei RNA were extracted immediately after purification. Total RNA was extracted by using Direct-zol RNA Microprep kit (Zymoresearch Cat#R2062) following manufactory’s instruction. For cortex RNA: Total RNA was extracted by using RNeasy Lipid Tissue Mini Kit (Qiagen, 74804) following the manufacturer's instructions.
Total RNA from astrocyte was sent to BGI Genomics Co., Ltd., China, for total RNA-seq library preparation and sequenced on an MGISEQ-2000 platform, 50 bp , single-end. Total RNA from neuronal nuclei was also sent to BGI Genomics Co., Ltd. for library preparation, and sequenced on a DNBSEQ platform, 150 bp paired-end. Total RNA from mouse cortex was sent to Novogene Co., Ltd., China, for total library preparation and sequenced on an Illumina NovaSeq platform, 150 bp, paired-end.

value: cortex

tag: cell line

tag: cell type

value: astrocyte

tag: genotype

value: Wildtype

tag: age

value: 3-month-old + 6-month-old

tag: mouseid


title: Volunteer 12, photoexposed skin, noon (T12)

description: Library name: 12B


title: Volunteer 11, photoexposed skin, 6pm (T18)

description: Library name: 11D


title: Astrocyte_KO_RNA_Rep1


title: Astrocyte_WT_RNA_Rep2


title: EpCAM-, DN3 cells 2

city: chongqing

first: Debao

last: Li

address: No. 13, Tianchi Avenue, Mudong Town, Banan District, Chongqing

institute: Chongqing International Institute for Immunology

description: Library name: sample2

library_source: genomic

data_processing:
1. Data Quality Control and Preprocessing Raw sequencing data quality was assessed using FastQC. Adapter sequences and low-quality bases were trimmed using Trim Galore with parameters: quality threshold of 20, minimum read length of 20 bp, and error rate of 0.1. Trimmomatic was subsequently employed to further remove low-quality bases with the following parameters: HEADCROP:15, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:36.
2. Sequence Alignment and Filtering Processed reads were aligned to the mouse reference genome (mm10) using Bowtie2 in --very-sensitive mode with --no-mixed and --no-discordant options, allowing a maximum fragment length of 2000 bp. The resulting alignments were converted to BAM format and filtered using SAMtools to remove reads mapping to mitochondrial DNA and those with mapping quality scores below 30.
3. PCR Duplicate Removal and Blacklist Filtering PCR duplicates were identified and removed using Picard MarkDuplicates. Reads overlapping known blacklisted regions (mm10-blacklist) were excluded using BEDTools. Fragment offset correction specific to ATAC-seq was performed using alignmentSieve from the deepTools suite with the --ATACshift parameter.
4. Peak Calling and Signal Quantification Open chromatin regions were identified using MACS3 with a q-value threshold of 0.05, retaining all replicates for analysis. For genome browser visualization, BAM files were converted to bigWig format using deepTools bamCoverage with counts per million (CPM) normalization and a bin size of 50 bp.
Assembly: GRCm38
Supplementary files format and content: narrowPeak files

molecule: genomic DNA

source_name: Thymus

extract_protocol:
DN3 cells were first gained by flow sorting on BD-FACSAria Fusion. Then, EpCAM-based separation using biotin-conjugated anti-EpCAM antibody and anti-biotin microbeads, according to the manufacturer's protocol (Miltenyi Biotec) on Miltenyi autoMACS® Pro Separator (130-092-545)，where EpCAM⁺ cells were positively selected while the unlabeled fraction constituted EpCAM⁻ cells. Two cell group were then lysised for the ATAC-seq, following DNA fragmentation, purification, amplification, the DNA products were sequencing by HaploX.
Sequencing libraries were constructed using the Vazyme TruePrep DNA Library Prep Kit according to the manufacturer’s instructions for the appropriate input DNA amount (50 ng, 5 ng, or 1 ng). The protocol is based on a tagmentation reaction. Briefly, the starting DNA was mixed with TruePrep Tagment Enzyme Mix (TTE Mix), which contains a transposase and two equimolar adapters (Adapter 1 and Adapter 2), in the presence of 5× TTBL buffer. The mixture was incubated at 55°C for 10 minutes to achieve simultaneous DNA fragmentation and adapter ligation. The tagmentation reaction was immediately stopped by adding 5× TS buffer and incubating at room temperature for 5 minutes. The fragmented DNA was then purified using VAHTS DNA Clean Beads (required for the 50 ng input protocol) or used directly for PCR enrichment. The PCR enrichment reaction was set up with the purified/stopped DNA, 5× TAB buffer, PCR Primer Mix (PPM), N5XX and N7XX indexing primers, and TAE polymerase. Thermal cycling was performed as follows: 72°C for 3 minutes for strand displacement; followed by a cycle of 98°C for 30 seconds; and then 5-15 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 30 seconds; with a final extension at 72°C for 5 minutes. The number of amplification cycles was optimized based on the starting DNA amount (5-9 cycles for 50 ng, 8-12 cycles for 5 ng, and 11-15 cycles for 1 ng). The amplified products were subjected to a two-round size selection and purification using VAHTS DNA Clean Beads. The volumes of beads used in each round were adjusted according to the starting DNA amount to enrich for fragments of the desired length (e.g., for 50 ng input, 0.60× and 0.15× beads were used to select a 300-700 bp library). The final purified library was quality-controlled and stored at -20°C prior to sequencing.

value: Thymus

value: DN3 cells

value: WT mice


title: Volunteer 11, photoexposed skin, midnight (T00)

description: Library name: 11F


title: Volunteer 11, photoprotected skin, 6am (T06)

description: Library name: 11G


title: Volunteer 11, photoprotected skin, midnight (T00)

description: Library name: 11E


title: Astrocyte_KO_RNA_Rep2


title: Volunteer 11, photoprotected skin, 6pm (T18)

description: Library name: 11C


title: EpCAM+, DN3 cells 2

description: Library name: sample4


title: Volunteer 11, photoexposed skin, noon (T12)

description: Library name: 11B


title: Neun_KO_K9_Rep2

description: Library name: sample10

data_processing:
Quality control was conducted with FastQC (version 0.11.9). Reads were trimmed with Trim Galore (version 0.6.7, --quality 20 --phred33 --stringency 1 --length 20 --fastqc --paired). Reads were aligned to mm10 or hg38 with Bowtie2 (version 2.4.1) in default settings. Reads were binarized, sorted, deduplicated and indexed with SAMtools (version 1.6).
Assembly: human:hg38; mouse: mm10
Supplementary files format and content: BW: bigWig file

growth_protocol: 293Tcell line was cultured at 37℃ in 90% DMEM (Gibco, C11995500BT) supplemented with 10% fetal bovine serum((ExCell Biotech, FSP500). The culture medium was replaced every two days.

extract_protocol:
Nuclei of 293T cell line were extracted by using nuclei lysis buffer(0.32 M sucrose, 5 mM CaCl₂, 3 mM MgAc₂, 0.1 mM EDTA, 0.1% NP-40, 10 mM Tris-HCl, pH 8). Neuronal nuclei were Isolated from mice adult cortex by FACS using anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated; EMD Millipore Corp., MAB377X).
For ChIP-seq, ChIP DNA was blunted and A-tailed with VAHTS Universal End preparation Module for Illumina V2 (Vazyme N203-01), ligated with adapter (Vazyme N802-01) using VAHTS Universal Adapter Ligation Module for Illumina V2 (N204-01) and amplified with VAHTS HiFi Universal Amplification Mix for Illumina (Vazyme N618-02). The library was size-selected with SPRIselect beads (Beckman B23318) and sent for sequencing on Illumina NovaSeq 6000 (paired-end, 150 bp).

value: neuronal nuclei

tag: chip antibody

value: H3K9me3 abcam #ab8898


title: EpCAM+, DN3 cells 1

description: Library name: sample3


title: Neun_KO_K9_Rep3

description: Library name: sample11


title: Volunteer 11, photoprotected skin, noon (T12)

description: Library name: 11A


title: EpCAM-, DN3 cells 1

description: Library name: sample1


title: Volunteer 10, photoexposed skin, 6am (T06)

description: Library name: 10H


title: Neun_KO_K9_Rep1

description: Library name: sample9


title: Neun_WT_K9_Rep3

description: Library name: sample8


title: Volunteer 10, photoprotected skin, 6am (T06)

description: Library name: 10G


title: Volunteer 10, photoexposed skin, midnight (T00)

description: Library name: 10F


title: Volunteer 12, photoprotected skin, noon (T12)

description: Library name: 12A


title: Neun_WT_K9_Rep2

description: Library name: sample7


title: Volunteer 10, photoprotected skin, midnight (T00)

description: Library name: 10E


title: Neuron_KO_ATAC_Rep3

data_processing:
Quality control of ATAC-seq reads was conducted with FastQC (version 0.11.9). Reads were trimmed with Trim Galore (version 0.6.7, --quality 20 --phred33 --stringency 1 --length 20 --fastqc --paired). Reads were aligned to mm10 with Bowtie2 (version 2.4.1) in default settings. Reads were binarized, sorted, deduplicated and indexed with SAMtools (version 1.6).  Narrow peaks were called with MACS2 (version 2.2.7.1, --shift -100 --extsize 200 --nomodel).
Assembly: mouse: mm10, human: hg38
Supplementary files format and content: NARROWPEAK: Narrow peak text files, tab delimited

extract_protocol:
Astrocyte were purified from mice adult cortex by using the Adult Brain Dissociation Kit (Miltenyi Biotec, 130-107-677), Debris Removal Solution (Miltenyi Biotec, 130-109-398) and anti-ACSA-2 (astrocyte cell surface antigen-2) microbeads (Miltenyi Biotec, 130-097-678) according to the manufacturer's instructions. Neuronal nuclei were Isolated from mice adult cortex by nuclei extraction and FACS using anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated; EMD Millipore Corp., MAB377X). Nuclei of 293T cell line and astrocyte were extracted by using nuclei lysis buffer(0.32 M sucrose, 5 mM CaCl₂, 3 mM MgAc₂, 0.1 mM EDTA, 0.1% NP-40, 10 mM Tris-HCl, pH 8).
For ATAC, 50,000 nuclei were used for each reaction. The library preparation was performed using reagents from the Trueprep DNA Library Prep Kit for Illumina (Vazyme, TD501-02) following the manufacturer’s instructions.


title: Volunteer 10, photoexposed skin, 6pm (T18)

description: Library name: 10D


title: Volunteer 10, photoprotected skin, 6pm (T18)

description: Library name: 10C


title: Neun_WT_K9_Rep1

description: Library name: sample6


title: Volunteer 10, photoexposed skin, noon (T12)

description: Library name: 10B


title: Neuron_KO_ATAC_Rep1


title: Neuron_KO_ATAC_Rep2


title: Neuron_WT_ATAC_Rep3


title: Volunteer 9, photoprotected skin, 6am (T06)

description: Library name: 9G


title: Volunteer 10, photoprotected skin, noon (T12)

description: Library name: 10A


title: iBMDM, 4-1BBL KO-3, IL-4 24 hours

city: Sunnyvale

first: Young

middle: Jun

last: Kang

state: CA

address: 428 Oakmead Pkwy

country: USA

institute: Molecular Medicine Research Institute

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
At the same time, Q20, Q30andGCcontent the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5.
We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM for each sample

source_name: Bone marrow-derived macrophage

growth_protocol: DMEM (high glucose) supplemented with 10% FBS, pyruvate, glutamine and antibiotics.

extract_protocol:
RNeasy mini-prep from Qiagen
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: 5x10^5 cells per ml, IL-4 treatment 10 ng/ml for 24 hours

value: Bone marrow-derived macrophage

value: 4-1BBL KO

tag: treatment


title: Volunteer 9, photoprotected skin, midnight (T00)

description: Library name: 9E


title: iBMDM, 4-1BBL KO-2, IL-4 24 hours

description: Library name: Sample 5


title: Volunteer 9, photoexposed skin, 6am (T06)

description: Library name: 9H


title: iBMDM, WT-1, IL-4 24 hours

description: Library name: Sample 1

value: WT


title: Volunteer 9, photoprotected skin, noon (T12)

description: Library name: 9A


title: Volunteer 9, photoprotected skin, 6pm (T18)

description: Library name: 9C


title: Volunteer 8, photoexposed skin, 6am (T06)

description: Library name: 8H


title: iBMDM, WT-3, IL-4 24 hours

description: Library name: Sample 3


title: Volunteer 8, photoprotected skin, 6am (T06)

description: Library name: 8G


title: iBMDM, 4-1BBL KO-1, IL-4 24 hours

description: Library name: Sample 4


title: Neuron_WT_ATAC_Rep2


title: Volunteer 9, photoexposed skin, noon (T12)

description: Library name: 9B


title: Volunteer 9, photoexposed skin, 6pm (T18)

description: Library name: 9D


title: iBMDM, WT-2, IL-4 24 hours

description: Library name: Sample 2


title: Volunteer 9, photoexposed skin, midnight (T00)

description: Library name: 9F


title: iBMDM, shDRP1-2, IL-4 24 hours

description: Library name: Sample 5

value: DRP1 KD


title: Neuron_WT_ATAC_Rep1


title: iBMDM, shDRP1-3, IL-4 24 hours

description: Library name: Sample 6


title: iBMDM, shPGAM5-3, IL-4 24 hours

description: Library name: Sample 3

value: PGAM5 KD


title: Volunteer 8, photoprotected skin, midnight (T00)

description: Library name: 8E


title: iBMDM, shDRP1-1, IL-4 24 hours

description: Library name: Sample 4


title: Volunteer 8, photoexposed skin, midnight (T00)

description: Library name: 8F


title: iBMDM, shPGAM5-2, IL-4 24 hours

description: Library name: Sample 2


title: Volunteer 8, photoprotected skin, 6pm (T18)

description: Library name: 8C


title: Volunteer 8, photoexposed skin, 6pm (T18)

description: Library name: 8D


title: Volunteer 8, photoexposed skin, noon (T12)

description: Library name: 8B


title: Ctrl 11-A

city: Bonn

first: Georg

last: Sendtner

address: Venusberg Campus 1a

department: Medical Clinic 1, Nephrology Section

country: Germany

institute: University Hospital Bonn

description: Library name: DE72NGSUKBR147093

data_processing:
The nf-core/rnaseq version 3.18.0 pipeline was used for pre-processing the data.  Trimgalore was used for trimming with the extra arguments ‘-a ’AGATCGGAAGAGC -a A{10} -a G{10}".  The alignment was performed with STAR algorithm, version 2.7.11b. Salmon (version 1.10.3) was used for quantification in ‘alignment-based mode’.
Assembly: GRCh38
Supplementary files format and content: tsv file contains raw counts for each sample

source_name: Aorta

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel)
RNA libraries for RNA-seq were prepared using the Lexogen QuantSeq 3'mRNA Library Prep Kit

treatment_protocol: Female Ldlr-/- mice were infected with uropathogenic E. coli strain 536, which was instilled into the bladder twice at a 3-hour interval. One week after infection, mice were placed on high fat diet for three weeks. Kidneys and aorta were harvested four weeks hours after the second infection. Control mice received urethral instillation with PBS.

value: Aorta

tag: agent

value: Ctrl


title: iBMDM, shPGAM5-1, IL-4 24 hours

description: Library name: Sample 1


title: UTI 8-A

description: Library name: DE56NGSUKBR147090

value: UTI


title: Ctrl 6-A

description: Library name: DE13NGSUKBR147088


title: Volunteer 7, photoprotected skin, midnight (T00)

description: Library name: 7E

value: 3 mm whole thickness skin


title: UTI 3-A

description: Library name: DE94NGSUKBR147085


title: Volunteer 8, photoprotected skin, noon (T12)

description: Library name: 8A


title: Ctrl 9-A

description: Library name: DE29NGSUKBR147091


title: Volunteer 7, photoexposed skin, 6am (T06)

description: Library name: 7H


title: Volunteer 7, photoexposed skin, 6pm (T18)

description: Library name: 7D


title: Volunteer 7, photoprotected skin, noon (T12)

description: Library name: 7A


title: UTI 2-A

description: Library name: DE24NGSUKBR147084


title: Ctrl 4-A

description: Library name: DE67NGSUKBR147086


title: Ctrl 10-A

description: Library name: DE02NGSUKBR147092


title: UTI 7-A

description: Library name: DE83NGSUKBR147089


title: Volunteer 7, photoexposed skin, midnight (T00)

description: Library name: 7F


title: Ctrl 5-A

description: Library name: DE40NGSUKBR147087


title: Volunteer 7, photoprotected skin, 6am (T06)

description: Library name: 7G


title: Volunteer 6, photoexposed skin, 6am (T06)

description: Library name: 6H


title: Volunteer 7, photoprotected skin, 6pm (T18)

description: Library name: 7C


title: Volunteer 7, photoexposed skin, noon (T12)

description: Library name: 7B


title: Ctrl 10-N

description: Library name: DE08NGSUKBR147081

source_name: Kidney

value: Kidney


title: Volunteer 6, photoexposed skin, midnight (T00)

description: Library name: 6F


title: Ctrl 11-N

description: Library name: DE78NGSUKBR147082


title: Volunteer 6, photoexposed skin, 6pm (T18)

description: Library name: 6D


title: Volunteer 6, photoprotected skin, 6am (T06)

description: Library name: 6G


title: UTI 8-N

description: Library name: DE62NGSUKBR147079


title: Volunteer 6, photoprotected skin, 6pm (T18)

description: Library name: 6C


title: Volunteer 6, photoexposed skin, noon (T12)

description: Library name: 6B


title: Volunteer 6, photoprotected skin, midnight (T00)

description: Library name: 6E


title: Ctrl 4-N

description: Library name: DE73NGSUKBR147075


title: Volunteer 6, photoprotected skin, noon (T12)

description: Library name: 6A


title: UTI 3-N

description: Library name: DE03NGSUKBR147074


title: Ctrl 6-N

description: Library name: DE19NGSUKBR147077


title: Ctrl 5-N

description: Library name: DE46NGSUKBR147076


title: Volunteer 5, photoexposed skin, 6am (T06)

description: Library name: 5H


title: Ctrl 9-N

description: Library name: DE35NGSUKBR147080


title: Volunteer 5, photoexposed skin, midnight (T00)

description: Library name: 5F


title: UTI 1-N

description: Library name: DE57NGSUKBR147072


title: Volunteer 5, photoprotected skin, 6am (T06)

description: Library name: 5G


title: UTI 1-A

description: Library name: DE51NGSUKBR147083


title: PVN cells,  gastritis group 1

city: Jinan

first: E

last: Liu

state: Shandong Province

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

institute: Shandong University School of Basic Medicine

description:
Library name: gastritis1
microfluidic chip

library_source: transcriptomic single cell

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

source_name: brain

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

treatment_protocol: oral gavage of  HCl/ethanol solution (gastritis group).

value: brain

value: 6–8 weeks old

value: brain cells

tag: Sex

value: male

value: oral gavage with HCl/ethanol solution


title: PVN cells,  gastritis group 2

description:
Library name: gastritis2
microfluidic chip


title: Volunteer 5, photoprotected skin, 6pm (T18)

description: Library name: 5C


title: Volunteer 5, photoexposed skin, 6pm (T18)

description: Library name: 5D


title: Volunteer 5, photoprotected skin, midnight (T00)

description: Library name: 5E


title: DTX1_KO, replicate 4, scRNA

city: Houston

first: Michael

last: Green

state: Texas

address: 7455 Fannin Street

department: Department of Lymphoma/Myeloma

institute: The University of Texas MD Anderson Cancer Center

description:
Library name: Sample 8 RNA
10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting were done using the Cell Ranger Count software v6.0.0.
Analyses were performed in R (version 4.3.1) using various R packages. FASTQ files were processed using cellranger count (10x genomics). This pipeline aligns reads to the mm10 mouse reference genome, performs barcode error correction, PCR duplicate marking, and gene expression molecule counting to produce expression count matrices.  The filtered gene expression matrices were loaded into R and processed with Seurat (version 4.3.0, https://github.com/satijalab/seurat) for downstream analyses.
Assembly: mm10

source_name: Spleen

extract_protocol:
GC B cells were isolated from mice spleens at day 10 post-immunization using the Germinal Center B Cell (PNA) MicroBead Kit (Miltenyi Biotec, #130-110-479).
Briefly, 10,000 cells/sample were loaded on the Chromium Controller. 10X libraries for scRNA-seq were prepared using chromium Next GEM Chip K Single Cell Kit, (PN-1000287) following the manufacturer’s instructions.

value: Spleen

value: Germinal center B-cell


title: DTX1_KO, replicate 1, scRNA

description:
Library name: Sample 5 RNA
10x Genomics


title: Volunteer 5, photoexposed skin, noon (T12)

description: Library name: 5B


title: DTX1_KO, replicate 3, scRNA

description:
Library name: Sample 7 RNA
10x Genomics


title: Volunteer 4, photoexposed skin, 6am (T06)

description: Library name: 4H


title: Volunteer 5, photoprotected skin, noon (T12)

description: Library name: 5A


title: WT, replicate 3, scRNA

description:
Library name: Sample 3 RNA
10x Genomics


title: WT, replicate 2, scRNA

description:
Library name: Sample 2 RNA
10x Genomics


title: WT, replicate 1, scRNA

description:
Library name: Sample 1 RNA
10x Genomics


title: DTX1_KO, replicate 2, scRNA

description:
Library name: Sample 6 RNA
10x Genomics


title: WT, replicate 4, scRNA

description:
Library name: Sample 4 RNA
10x Genomics


title: Volunteer 4, photoprotected skin, midnight (T00)

description: Library name: 4E


title: Volunteer 4, photoexposed skin, 6pm (T18)

description: Library name: 4D


title: DTX1_KO, replicate 3,  scBCR

description:
Library name: Sample 7 BCR
10x Genomics

data_processing:
Single-cell BCR FASTQ were processed using Cell Ranger VDJ pipeline.
Analyses were performed in R (version 4.3.1) using various R packages. FASTQ files were processed using cellranger VDJ pipeline (10x genomics). scBCR data output from cell ranger were re-annotated for V(D)J gene annotations with IGBLAST (v1.17.0) and IMGT mouse germline sequence databases using AssignGenes.py and MakeDb.py from Immcantation toolbox. Clones were defined by clustering BCR sequences using DefineClones.py.
Assembly: mm10

extract_protocol:
GC B cells were isolated from mice spleens at day 10 post-immunization using the Germinal Center B Cell (PNA) MicroBead Kit (Miltenyi Biotec, #130-110-479).
10X libraries for scBCR-seq were prepared using chromium Next GEM Chip K Single Cell Kit, (PN-1000287), and Chromium Single Cell Mouse BCR Amplification Kit, (PN-1000255) following the manufacturer’s instructions


title: DTX1_KO, replicate 2,  scBCR

description:
Library name: Sample 6 BCR
10x Genomics


title: Volunteer 4, photoprotected skin, 6pm (T18)

description: Library name: 4C


title: WT, replicate 2,  scBCR

description:
Library name: Sample 2 BCR
10x Genomics


title: Volunteer 4, photoprotected skin, noon (T12)

description: Library name: 4A


title: Volunteer 3, photoexposed skin, midnight (T00)

description: Library name: 3F


title: Volunteer 4, photoprotected skin, 6am (T06)

description: Library name: 4G


title: DTX1_KO, replicate 1,  scBCR

description:
Library name: Sample 5 BCR
10x Genomics


title: Volunteer 3, photoexposed skin, 6am (T06)

description: Library name: 3H


title: WT, replicate 3,  scBCR

description:
Library name: Sample 3 BCR
10x Genomics


title: Volunteer 4, photoexposed skin, noon (T12)

description: Library name: 4B


title: Volunteer 3, photoprotected skin, midnight (T00)

description: Library name: 3E


title: Volunteer 3, photoexposed skin, 6pm (T18)

description: Library name: 3D


title: Volunteer 4, photoexposed skin, midnight (T00)

description: Library name: 4F


title: WT, replicate 1, scBCR

description:
Library name: Sample 1 BCR
10x Genomics


title: WT, replicate 4,  scBCR

description:
Library name: Sample 4 BCR
10x Genomics


title: cortex_snRNA_KO_R1

description: 10x Genomics

data_processing:
snRNA-seq data, including barcode, index, and transcript reads, were processed using the CellRanger toolkit (version 7.1.0). The "count" function in CellRanger generated expression matrices for genes and barcodes.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

extract_protocol:
Cortex tissue was dissected and homogenized in lysis buffer (0.32 M sucrose, 5 mM CaCl₂, 3 mM MgAc₂, 0.1 mM EDTA, 0.1% NP-40, 10 mM Tris-HCl, pH 8). A double volume of sucrose solution (1.8 M sucrose, 3 mM MgAc₂, 10 mM Tris-HCl, pH 8) was added to the bottom of the homogenate, and nuclei were purified using sucrose gradient ultracentrifugation at 24,000 rpm for 30 minutes. The nuclei pellet was resuspended, counted, and diluted to 1500 nuclei/μL in Ca²⁺/Mg²⁺-free DPBS with 2% BSA. A concentration of 0.2 U/μL RNAase inhibitor was added to all solutions.
20,000 nuclei were loaded onto 10x Genomics Single Cell 3' ChIP along with the Reverse Transcription Master Mix, following the manufacturer's protocol for the Chromium Single Cell 3’ Library (10x Genomics, PN-1000121) to generate single nuclei gel beads in emulsion (GEM). Subsequently, the cDNA products were amplified, and libraries were constructed. The quality of cDNA products and libraries was assessed using an Agilent 4200. Finally, the libraries were sequenced on an Illumina NovaSeq platform with 150 bp, paired-end

value: cortex

value: female


title: Volunteer 3, photoprotected skin, 6am (T06)

description: Library name: 3G


title: Volunteer 3, photoprotected skin, 6pm (T18)

description: Library name: 3C


title: cortex_snRNA_KO_R2

description: 10x Genomics


title: cortex_snRNA_WT_R2

description: 10x Genomics

value: Wildtype


title: Volunteer 2, photoprotected skin, 6am (T06)

description: Library name: 2G


title: Cortex_DKO_RNA_Rep1

value: Setdb1-CK-cKO/P2rx7 KO


title: Cortex_KO_RNA_Rep3


title: Cortex_WT_RNA_Rep3


title: Volunteer 2, photoprotected skin, 6pm (T18)

description: Library name: 2C


title: Volunteer 2, photoprotected skin, noon (T12)

description: Library name: 2A


title: cortex_snRNA_WT_R1

description: 10x Genomics


title: Volunteer 1, photoexposed skin, 6am (T06)

description: Library name: 1H


title: Volunteer 2, photoexposed skin, 6pm (T18)

description: Library name: 2D


title: Volunteer 2, photoprotected skin, midnight (T00)

description: Library name: 2E


title: Cortex_KO_RNA_Rep1


title: Volunteer 2, photoexposed skin, midnight (T00)

description: Library name: 2F


title: Volunteer 3, photoprotected skin, noon (T12)

description: Library name: 3A


title: Volunteer 3, photoexposed skin, noon (T12)

description: Library name: 3B


title: Cortex_WT_RNA_Rep1


title: Volunteer 2, photoexposed skin, noon (T12)

description: Library name: 2B


title: Volunteer 2, photoexposed skin, 6am (T06)

description: Library name: 2H


title: Cortex_KO_RNA_Rep2


title: Cortex_DKO_RNA_Rep2


title: Astrocyte_KO_H3K9me3_Rep2

data_processing:
Quality control was conducted with FastQC (version 0.11.9). Reads were trimmed with Trim Galore (version 0.6.7, --quality 20 --phred33 --stringency 1 --length 20 --fastqc --paired). Reads were aligned to mm10 with Bowtie2 (version 2.4.1) in default settings. Reads were binarized, sorted, deduplicated and indexed with SAMtools (version 1.6).
Assembly: mouse: mm10
Supplementary files format and content: BW: bigWig file

extract_protocol:
Astrocyte were purified from mice adult cortex by using the Adult Brain Dissociation Kit (Miltenyi Biotec, 130-107-677), Debris Removal Solution (Miltenyi Biotec, 130-109-398) and anti-ACSA-2 (astrocyte cell surface antigen-2) microbeads (Miltenyi Biotec, 130-097-678) according to the manufacturer's instructions. Neuronal nuclei were Isolated from mice adult cortex by nuclei extraction and FACS using anti-NeuN antibody (clone A60, Alexa Fluor 488 conjugated; EMD Millipore Corp., MAB377X). Nuclei of 293T cell line and astrocyte were extracted by using nuclei lysis buffer(0.32 M sucrose, 5 mM CaCl₂, 3 mM MgAc₂, 0.1 mM EDTA, 0.1% NP-40, 10 mM Tris-HCl, pH 8).
For ChIP-seq, ChIP DNA was blunted and A-tailed with VAHTS Universal End preparation Module for Illumina V2 (Vazyme N203-01), ligated with adapter (Vazyme N802-01) using VAHTS Universal Adapter Ligation Module for Illumina V2 (N204-01) and amplified with VAHTS HiFi Universal Amplification Mix for Illumina (Vazyme N618-02). The library was size-selected with SPRIselect beads (Beckman B23318) and sent for sequencing on Illumina NovaSeq 6000 (paired-end, 150 bp).

value: astrocyte


title: Volunteer 1, photoprotected skin, 6am (T06)

description: Library name: 1G


title: Cortex_DKO_RNA_Rep3


title: Volunteer 1, photoexposed skin, midnight (T00)

description: Library name: 1F


title: Cortex_WT_RNA_Rep2


title: Volunteer 1, photoprotected skin, midnight (T00)

description: Library name: 1E


title: Astrocyte_KO_H3K9me3_Rep3


title: Astrocyte_KO_H3K9me3_Rep1


title: Astrocyte_KO_ATAC_Rep2


title: Volunteer 1, photoprotected skin, noon (T12)

description: Library name: 1A


title: Volunteer 1, photoexposed skin, noon (T12)

description: Library name: 1B


title: Volunteer 1, photoexposed skin, 6pm (T18)

description: Library name: 1D


title: Volunteer 1, photoprotected skin, 6pm (T18)

description: Library name: 1C


title: Astrocyte_WT_H3K9me3_Rep1


title: Neuron_KO_RNA_Rep2

value: neuronal nuclei


title: Astrocyte_WT_H3K9me3_Rep2


title: Astrocyte_KO_ATAC_Rep1


title: Astrocyte_WT_ATAC_Rep2


title: Astrocyte_WT_H3K9me3_Rep3


title: 293T_sgSETDB1_H3K9me3_Rep3

description: Library name: sample5

value: SETDB1 knockout

value: H3K9me3 abcam #ab8898


title: Neuron_KO_RNA_Rep1


title: 293T_sgSETDB1_H3K9me3_Rep2

description: Library name: sample4


title: Astrocyte_WT_ATAC_Rep1


title: Neuron_WT_RNA_Rep3


title: 293T_sgSETDB1_H3K9me3_Rep1

description: Library name: sample3


title: Neuron_WT_RNA_Rep2


title: Neuron_KO_RNA_Rep3


title: Neuron_WT_RNA_Rep1


title: sci-RNA-seq3_Arabidopsis_HA_Stress_Biological_Replicate_4_and_5

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: Arabidopsis_HA_Stress_Biological_Replicate_4_and_5
sci-RNA-seq3

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed as described in https://github.com/JunyueC/sci-RNA-seq3_pipeline
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Seurat object

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown on hard agar (HA) stress at different stress levels

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter.
Library construction was performed following the sci-RNA-seq3 workflow

value: leaf

value: seedlings


title: 293T_ctrl_H3K9me3_Rep2

description: Library name: sample2


title: mimics ctrl_rep3

city: Changchun

first: Zhanchuan

last: Ma

state: Jilin

institute: First Hospital of Jilin University

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-  quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version  0.0.13). The short reads less than 16nt were also dropped. After that, clean reads were  aligned to the GRCm39 genome by HISAT2 allowing 4 mismatches.
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped).
The R Bioconductor package DESeq2  was utilized to screen out the differentially expressed genes (DEGs). The P value <0.05 and fold change>1.5 or < 2/3 were set as the cut-off criteria for identifying DEGs.
To sort out functional categories of DEGs, Gene Ontology (GO) terms and KEGG  pathways were identified using KOBAS 2.0 server. Hyper geometric test and Benjamini-Hochberg FDR controlling procedure were used to define the enrichment of each term.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Negative control of miR-200a-3p mimics overexpressed in HL-1  cell (high glucose treated)

extract_protocol:
Total RNAs were extracted from HL-1 cells using TRIeasy™ Total RNA Extraction Reagent TRIeasy™ (YEASEN, China). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. 2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina (Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-  quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version  0.0.13). The short reads less than 16nt were also dropped. After that, clean reads were  aligned to the GRCm39 genome by HISAT2 allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped.

treatment_protocol: The mouse cardiomyocytes HL-1 cells line (Procell Life Science & Technology Co., Ltd., China) were cultured at 37℃ with 5% CO 2 in dulbecco's modified eagle medium with 10% fetal bovine serum, containing 100 µg/mL streptomycin, 100 U/mL penicillin. All miRNA duplexes were purchased from Gemma (Suzhou, China). siRNA transfection was performed using HiPerFect Transfection Reagent (Qiagen, Germany) according to the manufacturer's protocol. Cells were harvested after transfected for 48h for analysis.

value: cardiomyocytes

value: negative control

value: high glucose treated


title: mimics ctrl_rep2


title: EVT derived from bTSC_2

city: Abu Dhabi

first: Satoshi

last: Imamura

address: Saadiyat Campus, C1-L0-RL5-27

department: Science

country: United Arab Emirates

institute: New York University Abu Dhabi

description:
Library name: T0008-651-A02
mRNA-seq data from EVT derived from bTSC cultued in EVT medium, sample 2

data_processing:
BCL to FASTQ conversion using bcl2fastq2 v2.20
Mapping and expression quantification with DRAGEN Bio-IT Platform v4.3.6 (Illumina), using default parameters
Reference genome - GRCh38 primary assembly (GENCODE v39)
Gene annotation - GENCODE v39 GTF
Output - TPM values and read counts at gene and transcript level
Assembly: Genome build - GRCh38; Genome source - GENCODE release 39; Reference FASTA - GRCh38.primary_assembly.genome.fa.gz (GENCODE v39, 2022-03-29); Annotation GTF - gencode.v39.primary_assembly.annotation.gtf.gz (GENCODE v39, 2022-03-29)
Supplementary files format and content: TV0615_gene_expression.csv; Gene-level TPM + read counts with GENCODE/Ensembl/Reactome annotation
Supplementary files format and content: TV0615_transcript_expression.csv; Transcript-level TPM + read counts with annotation

molecule: polyA RNA

growth_protocol: hESCs cultured on Matrigel-coated dishes with a mTeSR-1 medium were harvested with TrypLE Express for 3 min at 37°C and transferred in a 15-mL tube. The dissociated hPSCs were resuspended in mTeSR-1 medium supplemented with 10 µM of Y27632, and then transferred to Aggrewell 400 (Stem Cell Technologies) at 1.5 × 10^5 cells per well. After culturing in an incubator for 24 h at 37°C with 5% (v/v) CO2, the hPSC aggregates were resuspended in the HG solution {DMEM with 10%[w/v] PNIPAAm-β-PEG hydrogel at 4°C. 260 µL of an hPSC aggregate suspension with HG was transferred into the well of a 24-well plate, and then DMEM supplemented with 10%(v/v) FBS was added at 37°C. After 3-day culture, iBlastoid medium was changed on a daily basis, and the cells were maintained at 37°C with 5% (v/v) CO2 in an incubator.

extract_protocol:
RNeasy Micro Kit(QIAGEN)
Illumina - DNA/RNA UD Indexes, Tagmentation

treatment_protocol: Derivation of bTSC, bST and bEVT were performed according to Okae et al.(2018). For deriving bTSCs, after collecting blastoids, dissociated cells were seeded on 5 µg/mL collagen IV (Sigma-Aldrich)-coated plates in iBlastoid medium supplemented with 10 µM Y27632. After 24 hours, the medium was replaced with TSC medium supplemented with 5 µM Y27632. Cells were passaged every 4–6 days at 1:3–1:5 subculture ratios using TrypLE Express on 5 µg/mL collagen IV-coated plates, with medium changes every other day. For derivation of bST, bTSCs were seeded into 6-well plates pre-coated with 2.5 mg/mL collagen IV at a density of 1 × 10^5 cells per well and cultured in 2 mL of ST medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.5% penicillin–streptomycin, 0.3% BSA, 1% ITS-X supplement, 2.5 μM Y-27632, 2 μM forskolin, and 4% KSR). The medium was replaced on day 3, and the cells were analyzed on day 6. For derivation of bEVT, bTSCs were seeded into 6-well plates pre-coated with 1 mg/mL collagen IV at a density of 0.75 × 10^5 cells per well and cultured in 2 mL of EVT medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.5% penicillin–streptomycin, 0.3% BSA, 1% ITS-X supplement, 100 ng/mL NRG1, 7.5 μM A83-01, 2.5 μM Y-27632, and 4% KnockOut Serum Replacement). Matrigel was added shortly after cell suspension to a final concentration of 2%. On day 3, the medium was replaced with EVT medium without NRG1, and Matrigel was added to a final concentration of 0.5%. When the cells reached 80% confluence on day 6, they were dissociated with TrypLE for 15–20 min at 37°C and passaged onto a new collagen IV-coated 6-well plate at a 1:2 split ratio. The cells were then cultured for an additional 2 days in EVT medium without NRG1 or KSR, supplemented with Matrigel at a final concentration of 0.5%.

value: Human embryonic stem cell

value: Extravillous trophoblasts


title: EVT derived from bTSC_1

description:
Library name: T0008-651-H01
mRNA-seq data from EVT derived from bTSC cultued in EVT medium, sample 1


title: 293T_ctrl_H3K9me3_Rep1

description: Library name: sample1


title: mimics ctrl_rep1


title: mimics_rep3

source_name: miR-200a-3p mimics overexpressed in HL-1  cell (high glucose treated)

value: miR-200a-3p mimics overexpressed


title: 293T_sgSET_ATAC_Rep3


title: 0M_3

city: Chengdu

first: Xueji

last: Shi

address: Guoxue Ln, Wuhou District

institute: Sichuan University

description:
Library name: 0M_3
Column in GeneExpression.xlsx: 0M_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Assembly: GRCh38.107
Supplementary files format and content: xlsx files including TPKM, TPM, and raw counts for example

growth_protocol: KYSE150 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Cells were scraped from 6-well plates using cell scrapers, and at least 10^6 cells were collected for each sample. Total RNA was extracted using Trizol and subsequently used for library construction.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: KYSE150 cells were co-cultured with 60 μg/ml FadA or PBS for 2 days.

value: esophageal squamous cell carcinoma cells

value: control

tag: batch


title: mimics_rep2


title: NC_3

description:
Library name: NC_3
Column in GeneExpression.xlsx: NC_3


title: NC_2

description:
Library name: NC_2
Column in GeneExpression.xlsx: NC_2


title: 293T_sgSET_ATAC_Rep2


title: NC_1

description:
Library name: NC_1
Column in GeneExpression.xlsx: NC_1


title: ST derived from bTSC_2

description:
Library name: T0008-651-F01
mRNA-seq data from STB derived from bTSC cultued in STB medium, sample 2

value: Syncytiotrophoblasts


title: TSC derived from PNP blastoid_2

description:
Library name: T0008-651-C01
mRNA-seq data from TSC derived from blastoid cultued in TSC medium, sample 2

value: Trophoblast Stem Cells


title: 293T_sgSET_ATAC_Rep1


title: mimics_rep1


title: 0M_2

description:
Library name: 0M_2
Column in GeneExpression.xlsx: 0M_2


title: inhibitor ctrl_rep3

source_name: Negative control of miR-200a-3p inhibitor overexpressed in HL-1  cell (high glucose treated)


title: ST derived from bTSC_1

description:
Library name: T0008-651-E01
mRNA-seq data from STB derived from bTSC cultued in STB medium, sample 1


title: 293T_Ctrl_ATAC_Rep2

value: Wildtype


title: 293T_Ctrl_ATAC_Rep3


title: TSC derived from PNP blastoid_1

description:
Library name: T0008-651-A01
mRNA-seq data from TSC derived from blastoid cultued in TSC medium, sample 1


title: 0M_1

description:
Library name: 0M_1
Column in GeneExpression.xlsx: 0M_1


title: MSTO_Rx-IR_48hr

city: Los Angeles

first: Frank

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

description:
Library name: Drug_Radiation
10x Genomics

data_processing:
Sequencing reads from the mRNA libraries were mapped to the human genome (hg38) using the Parse Biosciences pipeline (split-pipe vers. 1.1.1) to generate cell by gene counts matrices. Data analysis was performed using the R package Seurat (version 4.3.3). Matrices were filtered for cells with high mitochondrial and ribosomal gene count and doublets were removed using DoubletFinder R package.
Assembly: human genome (hg38)
Supplementary files format and content: matrix files

source_name: Mesothelioma

growth_protocol: MSTO-211H mesothelioma cells were cultured in serum-free conditions in ultra-low adhesion plates in RPMI, supplemented with SM1 Neuronal Supplement, EGF, bFGF and heparin.

extract_protocol:
48hr post-irradiation, mesothelioma cells in the suspension culture were collected and dissociated with TrypLE (no phenol red). The cells were then pooled and filtered through a 40-µm strainer and fixed with PIPseq V T2 3’ Single Cell RNA Kit following the User Guide (Fluent Biosciences)
Library was performed according to the manufacter's instructions for the  PIPseq V T2 3’ Single Cell RNA Kit (Fluent Biosciences)

treatment_protocol: MSTO-211H mesothelioma cells were seeded into T25 flasks, then treated with QTP and irradiated with 4 Gy the next day. 48 hours after the irradiation, the cells were collected.

value: Mesothelioma

value: WT

tag: group


title: MSTO_Rx_48hr

description:
Library name: Drug
10x Genomics

value: Drug


title: inhibitor ctrl_rep1


title: FadA_3

description:
Library name: FadA_3
Column in GeneExpression.xlsx: FadA_3


title: OX-lung-2

type: RNA

city: Xi'an

first: Yiwei

last: Cao

address: Hanguang Road

institute: Xi'an Physical Education University

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
log2-transformed and quantile normalized

label: biotin

source_name: mice lung

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit

growth_protocol: Specific pathogen‑free conditions with regular health monitoring

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment

tag: strain


title: FadA_2

description:
Library name: FadA_2
Column in GeneExpression.xlsx: FadA_2


title: OX-lung-1

description: replicate 3


title: 293T_Ctrl_ATAC_Rep1


title: inhibitor ctrl_rep2


title: KO-lung-3

description: replicate 2


title: inhibitor_rep3

source_name: miR-200a-3p inhibitor overexpressed in HL-1  cell (high glucose treated)

value: miR-200a-3p inhibitor overexpressed


title: MSTO_IR_48hr

description:
Library name: Radiation
10x Genomics

value: Radiation


title: FadA_1

description:
Library name: FadA_1
Column in GeneExpression.xlsx: FadA_1


title: inhibitor_rep1


title: inhibitor_rep2


title: MSTO_CTRL_48hr

description:
Library name: Control
10x Genomics

value: Control


title: mCherry cells, late-HSPCs_TLN

city: Bronx

first: Teresa

last: Bowman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description:
Library name: late-HSPC trace TLN
3dTL

data_processing:
For all adult tissues, CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples.
Assembly: Danie rerio GRCz11
Supplementary files format and content: Matrix files (CellRanger output filtered_feature_bc_matrix)

organism: Danio rerio

source_name: Hematopoietic & Immune Cells

growth_protocol: Larvae were maintained in standard conditions, at 28C and adult fish were maintained under the standard established protocols for Zebrafish maintenance.

extract_protocol:
Kidney marrows, TLN, thymus and intestines were dissected from the adult fish and dissociated according to eastablished protocols for each tissues. For intestine, the tissue was digested with collagenase. For kidney, TLN and thymus, tissue was triturated gently to release the hematopoietic cells. The mCherry expressing cells were isolated from each tissue using FACS.
Libraries were prepared according to manufacturer's instructions of the kits. For all adult tissues, the Chromium Next GEM Single Cell 3' Kit v4 was used.

value: Hematopoietic & Immune Cells

value: late-HSPCs


title: HaCaT VitD,TSA

city: Iwaki

first: Takahiro

last: Sawada

state: Fukushima

address: Jobankamiyunagayamachi Kaminodai57

country: Japan

institute: Research Institute of Innovative Medicine

description: Library name: Sample8

data_processing:
Obtained reads (CAGE tags) were mapped to the human hg38※ genome using STAR (version 2.7.9a).CAGE tag count data were clustered using the CAGEr using Paraclu algorithm with default parameters. Clusters with count per million (CPM) < 0.2 were discarded.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0). For motif analysis, the genomic DNA sequence of the region from 200bp upstream to 50bp downstream of differentially expressed CAGE peaks were subjected to de novo motif discovery tools: AMD, GLAM2, DREME and Weeder. The occurrences of the motifs were examined by FIMO. The similarity of consensus motifs and the motifs in database JASPAR CORE 2016 vertebrates were evaluated by Tomtom.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each sample.
Supplementary files format and content: The mapping were performed bigwig. (plus means sense, minus means anti-sense)

source_name: HaCaT

extract_protocol:
A 100-μl aliquot of cell lysate was mixed with 700μl of QIAzol (Qiagen) and used for total RNA extraction. The remaining lysate was incubated on ice for 10min and centrifuged at 800g for 5min at 4 °C. The pellets were washed once with 200μl of Buffer A.
The cDNAs were synthesized from nascent RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

value: HaCaT

value: Human keratinocyte cell line


title: KO-lung-2

description: replicate 2


title: HaCaT TSA

description: Library name: Sample7

value: 1 µM TSA 4 h


title: KO-lung-1

description: replicate 2


title: mCherry cells, late-HSPCs_Thymus

description:
Library name: late-HSPC trace Thymus
3dTh


title: HG_rep3

source_name: HL-1  cell (high glucose treated)

value: cardiomyocytes

value: high glucose treated


title: HaCaT VitD

description: Library name: Sample6


title: mCherry cells, late-HSPCs_Intestine

description:
Library name: late-HSPC trace Intestine
3dInt


title: HG_rep2

value: control


title: WT-lung-3

description: replicate 1


title: HaCaT EtOH

description: Library name: Sample5

value: EtOH 4 h


title: WT-lung-2

description: replicate 1


title: HG_rep1


title: Ctrl_rep2

source_name: HL-1  cell (vehicle)

value: vehicle


title: WT-lung-1

description: replicate 1


title: genome-wide paternal uniparental heterodisomy patient oral swab

type: genomic

city: Saga

last: Hara

address: 5-1-1 Nabeshima

institute: Saga University

description:
Hybridized to CytoScan 750K array
CytoScan HD Array
GWpUPhD patient oral swab

hyb_protocol: Labeled DNA was hybridized to the CytoScan 750K Array at 50°C for 18 hours in a GeneChip Hybridization Oven 645 with rotation at 60 rpm. Arrays were washed and stained using the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G. Image acquisition was performed using GeneChip Data Collection (GCDC) software version 1.0.1.

data_processing:
Raw CEL files were analyzed using Chromosome Analysis Suite (ChAS) software version 4.5.0.34 with the NA36.r1 library files. Copy number analysis was performed using the reference model included in the ChAS software. Segmentation was conducted using the Hidden Markov Model (HMM) algorithm. Log2 ratio and allele difference values were calculated for each probe. CNV and LOH regions were called based on the default ChAS thresholds (minimum 25 markers, 50 kb for CNV; 3 Mb for LOH).
[primary data description] CHP files generated by ChAS software (version 4.5.0.34) are provided. Each CHP file contains segment data including Copy Number Gain/Loss, Loss of Heterozygosity (LOH), and Mosaic Gain/Loss segments, as well as graph data including Copy Number State, Log2 Ratio, Weighted Log2 Ratio, Smooth Signal, Loss of Heterozygosity (LOH), Allele Difference, B-allele Frequency, and Genotype calls.

source_name: genome-wide paternal uniparental disomy patient oral swab DNA

label_protocol: Genomic DNA was digested with NspI restriction enzyme, ligated to adaptors, and amplified by PCR. The PCR product was purified, quantified, and fragmented. Fragmented DNA was labeled with biotin using terminal deoxynucleotidyl transferase (TdT).

extract_protocol: Genomic DNA was extracted from peripheral blood or oral swab using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

value: oral swab


title: mCherry cells, early-HSPCs_Thymus

description:
Library name: early-HSPC trace Thymus
1dTh

value: early-HSPCs


title: HCT116 TSA

description: Library name: Sample3

value: an adherent cell line isolated from the colon of a patient with colon cancer.


title: Ctrl_rep1


title: Ctrl_rep3


title: HCT116 VitD

description: Library name: Sample2


title: HCT116 VitD,TSA

description: Library name: Sample4


title: mCherry cells, late-HSPCs_Kidney Marrow

description:
Library name: late-HSPC trace Kidney Marrow
3dK


title: mCherry cells, early-HSPCs_TLN

description:
Library name: early-HSPC trace TLN
1dTL


title: HCT116 EtOH

description: Library name: Sample1


title: mCherry cells, early-HSPCs_Intestine

description:
Library name: early-HSPC trace Intestine
1dInt


title: genome-wide paternal uniparental heterodisomy patient peripheral blood

description:
Hybridized to CytoScan 750K array
CytoScan HD Array
GWpUPhD patient blood

source_name: genome-wide paternal uniparental disomy patient peripheral blood DNA

value: peripheral blood


title: PBMC from COVID-19 patient 5

status: Public on Apr 03 2026

city: shenzhen

first: huang

last: peiming

state: Guangdong

address: xinhu

institute: Sun Yat-sen University

description: Library name: COVID_PBMC5

data_processing:
Quality Control: Raw reads were quality-filtered to remove low-quality data and adapters.
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: A tab-delimited text file (matrix) containing the raw read counts for each sample.

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
To isolate PBMCs, first centrifuge the anticoagulated whole blood to remove the plasma layer, then resuspend the remaining cell pellet in PBS. Carefully layer this suspension over the human lymphocyte separation medium and centrifuge with the brake off to create a density gradient. Finally, collect the white cloudy interface (the PBMC layer), treat it with RBC lysis buffer to remove contaminating red cells, and wash the resulting pellet with PBS for downstream use.
Libraries were prepared using BGI/MGI standard protocols. This included mRNA enrichment, fragmentation, double-stranded cDNA synthesis, and adapter ligation for DNBSEQ sequencing.

treatment_protocol: Samples were collected from hospitalized patients diagnosed with COVID-19.All procedures were approved by the Ethics Committee.

value: Peripheral Blood Mononuclear Cells

value: Mixed


title: PBMC from COVID-19 patient 4

description: Library name: COVID_PBMC4


title: mCherry cells, early-HSPCs_Kidney Marrow

description:
Library name: early-HSPC trace Kidney Marrow
1dK


title: PBMC from COVID-19 patient 1

description: Library name: COVID_PBMC1


title: Ad/BCKDHA2

city: Guangzhou

first: Liyun

last: Feng

address: 253 Industrial Avenue, Guangzhou, Guangdong province

institute: Zhujiang Hospital, Southern Medical University

description: Library name: Sample 5

data_processing:
The sequencing data was filtered with SOAPnuke by removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%
Removing reads whose unknown base ratio is more than 5%，afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the
Bowtie2(v2.2.5) was applied to align the clean reads to the reference coding gene set
The expression level of gene was calculated by RSEM (v1.2.12).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: xls file includes FPKM, TPM values and read counts for each sample

source_name: artery

growth_protocol: Human vascular smooth muscle cells were cultured in calcifying medium (CM)

extract_protocol:
Total RNA of human vascular smooth muscle cells were extracted using TRIzol reagents and RNA quality and quantity were assessed using a Nano Drop and Agilent 2100 bioanalyzer.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on MGIseq2000 platform.

treatment_protocol: Human vascular smooth muscle cells were transfected with either Ad/GFP or Ad/BCKDHA

value: artery

value: vascular smooth muscle cells

value: human vascular smooth muscle cells transfected with Ad/BCKDHA


title: Ad/BCKDHA1

description: Library name: Sample 4


title: Ad/GFP2

description: Library name: Sample 2

value: human vascular smooth muscle cells transfected with Ad/GFP


title: PBMC from COVID-19 patient 2

description: Library name: COVID_PBMC2


title: PBMC from COVID-19 patient 3

description: Library name: COVID_PBMC3


title: Ad/BCKDHA3

description: Library name: Sample 6


title: Treg cells, ChimeraWT4,H3K27ac,Control rep3

city: YI WU

first: Yage

last: Zhang

state: Zhejiang Province

address: No. 1575, Chouzhou North Road, Yiwu City, Zhejiang Province

institute: International Institutes of Medicine Zhejiang University

description: Library name: 4-Cre27ac2

data_processing:
Bioinformatics data analysis was provided by NewCore BioTechnology (Shanghai, China). Briefly, Fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. Clean reads were aligned to mouse mm39 reference genome using bowtie2 software (v2.2.4). Deeptools software (v3.5.1) was used to calculate and plot the correlations. MACS2 soft ware (v2.2.7.1) was used for peak calling and peaks within ENCODE blacklist regions were removed. ChIPSeeker R package (v1.30.3) was used for peak annotation. Homer software (v4.11) was used to identify motifs. MANorm2 softwre (v1.2.0) was used to identify differentially enriched regions be tween two samples and/or two groups of samples. The enriched peaks were visualized in IGV (v2.4.10) software. GO and KEGG Pathway analysis were performed based on the promoter enriched peaks (or promoter enriched differentially enriched regions) associated genes by ClusterProfiler R packages (v3.18.1).
Assembly: mm39
Supplementary files format and content: narrowPeak (except for IgG samples)
Library strategy: CUT&Tag

source_name: Regulatory T cells

extract_protocol:
For CUT&Tag-seq, FACS-sorted TREG cells isolated from Foxp3YFPcre;wt and Foxp3YFP-Slc31a1△;wt mice (as described in the “Cell sorting and FACS sorting”) underwent library preparation using the CUT&Tag 4.0 High-Sensitivity Kit (Novoprotein, N259-YH01) according to the manufacturer’s instructions. Initially, a total of 1.4 × 105 cells from each sample were resuspended in 90 μL of wash buffer and enriched with 10 μL of conA beads at RT for 10 min, and the supernatant was removed via magnet adsorption.
After being resuspended in 50 μl of antibody buffer, the cells were treated with primary antibodies directed against H3k27ac (CST, 8173S), H3k27me3 (CST, 9733S) and IgG control (CST, 2729S) at 4°C overnight. The next day, the supernatant was removed, and the beads were washed before 1 h of incubation with secondary antibody (Novoprotein; N269). Following incubation and washing, the beads were resuspended in 50 μL of tagmentation buffer and incubated at 37°C for 1 h, followed by a stop reaction step with 10% SDS at 55°C for 10 min. Subsequently, the DNA fragments were extracted and amplified via PCR via the i5 and i7 primers. Finally, NovoNGS® DNA Clean Beads were used to purify the PCR libraries, and the final libraries were sent to Annoroad Gene Technology (Beijing, China) to perform CUT&Tag-seq on an Illumina NovaSeq 6000 platform.

value: Regulatory T cells


title: Treg cells, ChimeraWT3,IgG,Control rep3

description: Library name: 3-CreIgG


title: Treg cells, ChimeraKO2,IgG,Exp rep1

description: Library name: 2-KOIgG


title: Treg cells, ChimeraKO4,H3K27ac,Exp rep3

description: Library name: 4-KO27ac2


title: Treg cells, ChimeraKO3,H3K27ac,Exp rep2

description: Library name: 3-KO27ac1


title: Ad/GFP1

description: Library name: Sample 1


title: Ad/GFP3

description: Library name: Sample 3


title: Hypothalamus, CCK1/2-KO, male, rep1

city: Wuhan

first: Hangyu

last: Li

state: 湖北省

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

description: Library name: OES246593

data_processing:
Raw reads generated from high-throughput sequencing were sequenced in fastq format. The CellRanger software package (version. 5.0.0, 10x Genomics, California, USA) was used to perform data quality statistics on the original data and to quantify the high-throughput single-cell transcriptome against the reference genome to obtain quality control statistics such as the number of high-quality cells. The Seurat software package (version. 4.1.0) was then used for further quality control and processing based on the CellRanger preliminary quality control results. The principal component analysis (PCA) was performed using gene expression levels, and the results were visualised in two-dimensional space using tSNE. The FindAllMarkers function in Seurat was used to identify marker genes and to identify genes that are differentially up-regulated in each cell category compared to other cell groups. The marker genes were visualised using the VlnPlot and FeaturePlot functions.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hypothalamus

extract_protocol:
Hypothalamus  tissues were dissected, washed in ice-cold minimal essential medium, and dissociated using trypsin, EDTA, and DNase II. After cell counting, cells were washed twice in NeuroGro medium (T710KJ, BasalMedia, Shanghai, China) and resuspended in PBS at a concentration of 1 × 10⁶ cells per mL
The 10X Genomics was used to generate single-cell Gel Beads-in-emulsion (GEMs). Immediately after GEM generation, the gel bead was dissolved, primers including an Illumina TruSeq Read 1 (read 1 sequencing primer), 16 nt 10x barcode, 12 nt unique molecular identifier (UMI), 30 nt poly(dT) sequence were released and mixed with cell lysate and a master mix containing reverse transcription (RT) reagents. Silane magnetic beads were used to purify first-strand cDNA from the post-GEM-RT reaction mixture, which contained residual biochemical reagents and primers. Barcoded full length cDNA was amplified by PCR to generate sufficient mass for library construction.

value: hypothalamus

value: male


title: Treg cells, ChimeraKO2,H3K27me3,Exp rep2

description: Library name: 2-KO27me3


title: Hypothalamus, WT, male, rep1

description: Library name: OES246591

value: WT


title: Pituitary, WT, male, rep1

description: Library name: OES246592

source_name: Pituitary

extract_protocol:
Pituitary  tissues were dissected, washed in ice-cold minimal essential medium, and dissociated using trypsin, EDTA, and DNase II. After cell counting, cells were washed twice in NeuroGro medium (T710KJ, BasalMedia, Shanghai, China) and resuspended in PBS at a concentration of 1 × 10⁶ cells per mL
The 10X Genomics was used to generate single-cell Gel Beads-in-emulsion (GEMs). Immediately after GEM generation, the gel bead was dissolved, primers including an Illumina TruSeq Read 1 (read 1 sequencing primer), 16 nt 10x barcode, 12 nt unique molecular identifier (UMI), 30 nt poly(dT) sequence were released and mixed with cell lysate and a master mix containing reverse transcription (RT) reagents. Silane magnetic beads were used to purify first-strand cDNA from the post-GEM-RT reaction mixture, which contained residual biochemical reagents and primers. Barcoded full length cDNA was amplified by PCR to generate sufficient mass for library construction.

value: Pituitary


title: Treg cells, ChimeraKO2,H3K27ac,Exp rep1

description: Library name: 2-KO27ac


title: Treg cells, ChimeraWT3,H3K27ac,Control rep2

description: Library name: 3-Cre27ac1


title: Treg cells, ChimeraWT2,H3K27ac,Control rep1

description: Library name: 2-Cre27ac


title: Treg cells, ChimeraWT2,H3K27me3,Control rep2

description: Library name: 2-Cre27me3


title: Pituitary, CCK1/2-KO, male, rep1

description: Library name: OES246594


title: Treg cells, ChimeraKO1,H3K27me3,Exp rep1

description: Library name: 1-KO27me3


title: Treg cells, ChimeraWT4

description: Library name: CY31

data_processing:
Reverse transcription (first-strand synthesis) was performed using Oligo(dT) primers to target polyadenylated mRNA. The MMLV reverse transcriptase added three cytosine (C) residues to the 3' end of the cDNA. Subsequently, template-switching oligonucleotide (TSO) primers facilitated second-strand cDNA synthesis, replacing the RNA template. The cDNA was then pre-amplified by PCR. The amplified cDNA was fragmented and tagged with adapters using a modified, highly active Tn5 transposase. Following a final PCR amplification, the resulting libraries were quantified using Qubit 4.0. The sequencing library was performed on NovaSeq X Plus platform (PE150) using NovaSeq Reagent Kit. The raw paired-end reads were processed for quality control and adapter trimming using fastp [12] with default parameters. Cleaned reads were then separately aligned to the reference genome using HISAT2 [13] software. Transcript assembly was performed from the aligned reads using StringTie [14]. Transcript abundances were quantified as TPM (transcripts per million) using RSEM [15]. Differential expression analysis was performed using DESeq2 [9], with significantly differentially expressed genes (DEGs) defined by |log2<FC| ≥ 1 and an FDR < 0.05.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
Treg cells were lysed in ice-cold TRIzol Reagent (Thermo Fisher Scientific) by vortexing and incubated at room temperature. After centrifugation, the supernatant was mixed with ice-cold chloroform, vortexed, and re-incubated. Following centrifugation, the aqueous phase was carefully transferred (avoiding interphase) and combined with ice-cold isopropanol. Post-incubation, RNA was pelleted by centrifugation. The pellet was washed with ice-cold 75% ethanol, repelleted, and residual ethanol removed by brief centrifugation and aspiration. After air-drying (avoiding overdrying), RNA was dissolved in RNase-free DEPC-treated water.
RNA-seq transcriptome library was prepared using the SMART-Seq V4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, Inc., San Jose, CA[12]) with 10 ng of total RNA.


title: Treg cells, ChimeraWT1

description: Library name: CY2


title: Treg cells, ChimeraKO1

description: Library name: CY94


title: Mito-Low

description:
Library name: Sample2
10x Genomics

data_processing:
The raw scRNA-seq data in this study were processed with Cell Ranger (v.7.1.0) for barcode processing and single-cell 3′ gene counting and aligned to the Ensembl mouse reference genome (mm10). Subsequent analysis with the Seurat R (v.4.3.0.1) package [6] included quality control filtering, dimension reduction, and clustering.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
Following sorting, cells were pelleted by centrifugation, washed with PBS, counted, and resuspended in 50 µL of PBS containing 0.04% FBS. scRNA-seq library preparation was performed by Annoroad Gene Technology (Beijing, China). cell viability and concentration were assessed using a Luna-FL cell counter (Logos Biosystems, Korea), and cell suspensions were adjusted to 700-1,200 cells/µL.
Single-cell libraries were generated from 1.2 × 10⁴ sorted Mitohigh Treg cells and 1.2 × 10⁴ Mitolow Treg cells per group using the Chromium Single Cell 5’ Kit V2 (PN-1000263, 10X Genomics, USA) according to the manufacturer's instructions.


title: Treg cells, ChimeraKO3

description: Library name: CY3


title: Treg cells, ChimeraWT1,IgG,Control rep1

description: Library name: 1-CreIgG


title: Treg cells, ChimeraWT1,H3K27me3,Control rep1

description: Library name: 1-Cre27me3


title: Mito-High

description:
Library name: Sample1
10x Genomics


title: Treg cells, ChimeraWT2

description: Library name: FY8


title: Treg cells, ChimeraWT5

description: Library name: CY32


title: Treg cells, ChimeraWT2,IgG,Control rep2

description: Library name: 2-CreIgG


title: Treg cells, ChimeraKO2

description: Library name: CY97


title: tomatidine treatment

city: Rochester

first: Dominik

last: Saul

state: Minnesota

address: 200 First Street SW Rochester

institute: Mayo Clinic

description: Library name: Treated_S2

data_processing:
Raw sequencing data from scRNA-seq samples were processed using cellranger multi from 10X Genomics Cellranger v8.0.0 using mouse mm10 reference genome (refdata-gex-mm10-2020-A) and mouse transcriptome probe set v1.0 (mm10-2020-A).
Assembly: mm10
Supplementary files format and content: Tab-delimited aggregated cell barcodes, features, and counts matrix

source_name: Hippocampus

extract_protocol:
Fixed, single cell suspension was prepared from flash frozen hippocampus using the Chromium Next GEM Single Cell Fixed RNA Preparation kit (10x Genomics) according to the user guide (CG000553, Rev B). Cell dissociation was performed using the gentleMACS Octo Dissociator (Miltenyi).
Libraries were constructed using the single-plex Chromium Fixed RNA Profiling kit (CG000477, Rev C). Libraries were sequenced with the Element Biosciences AVITI Sequencing platform using the AVITI 2x75 High Output Cloudbreak Freestyle Kit (Element Biosciences).

value: Hippocampus


title: Treg cells, ChimeraWT3

description: Library name: FY10


title: Vehicle-treated DVC, GEM-X chemistry, replicate 3

city: Iowa City

first: Jon

last: Resch

state: Iowa

address: 51 Newton Rd

institute: University of Iowa

description:
Library name: Veh_GEMX_rep3
10X GEM-X

data_processing:
Raw sequencing reads were processed into count matrices using Cell Ranger (10x Genomics; version 9.0.1) and using the mm10-2020-A mouse assembly.
Assembly: mm10-2020-A mouse assembly
Supplementary files format and content: Cell Ranger output files: *filtered_feature_bc_matrix.h5

source_name: Dorsal Vagal Complex

extract_protocol:
Hsd11b2-IRES-Cre mice aged 5-10 weeks received bilateral stereotaxic injections of Cre-dependent AAV-H2b-mCherry into the NTS. After 2 weeks of recovery, mice were sacrificed between 9:00 am – 12:00 pm by rapid decapitation immediately after removal from the home cage. Brains were extracted and chilled in DMEM/F12 media slush (Thermo Fisher Scientific). Brains were then placed dorsal side up in a chilled stainless steel brain matrix (Stoelting, Wood Dale, IL) and 1 mm coronal sections of the caudal medulla were collected. Tissue from the caudal medulla was placed in chilled RNAprotect solution (QIAGEN, Aarhus, Denmark) and then the Dorsal Vagal Complex was microdissected under a fluorescent stereoscope. During dissections, tissue was pooled according to treatment (vehicle or aldosterone). All pooled samples were incubated overnight at 4°C in RNAprotect®. RNAprotect solution was then removed from sample tubes the following day before storing samples at -80°C.
Each sample underwent nuclear dissociation and purification procedures before being incubated with NucBlue (Thermo fisher scientific). After incubation, nuclei were flow sorted together into RT Reagent B (10x Genomics) using a Cytek Aurora CS cell sorter with a 70 μm nozzle to remove poor quality nuclei, enrich for mCherry positive nuclei, and count the number of nuclei per sample. Sorted nuclei were immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol. Single Cell 3’ GEM-X chemistry was used to process all samples. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). Gene expression libraries for 'Rep 2' were sequenced on an Illumina NovaSeq 6000 sequencer (Read1 - 28, i7 = 10, i5 = 10, Read2 = 90). Gene expression libraries for 'Rep 3' were sequenced on an AVITI24 (Element Biosciences) (Rep 2) sequencer using a 150-cycle kit with the following sequencing configuration: i7 = 10, i5 = 10, Read1 = 29, Read2 =91.

treatment_protocol: Mice were treated with either vehicle or aldosterone for 24 hours before tissue collection

value: Dorsal Vagal Complex

value: 24hr vehicle

value: mixed


title: Aldosterone-treated DVC, GEM-X chemistry, replicate 3

description:
Library name: ALDO_GEMX_rep3
10X GEM-X

value: 24hr ALDO


title: control treatment

description: Library name: Control_S1

value: ctrl


title: HSR_T1D_NEU_4

city: Monza

first: Jacopo

last: Ronchi

state: MB

address: Via Cadore 48

department: School of Medicine and Surgery

country: Italy

institute: University of Milano-Bicocca

description: neutrophils from Female T1D patient

hyb_protocol: The labeled RNA was hybridized to the Affymetrix GeneChip miRNA 4.1 microarrays.

scan_protocol: Microarrays were scanned using the GeneAtlas™ Imaging Station.

data_processing: Raw CEL files were imported into the R environment and underwent normalization using the RMA algorithm, as implemented in the oligo R/Bioconductor package.

source_name: Peripheral Blood

label_protocol: 1µg of total RNA was tagged with biotin using the FlashTag™ HSR RNA Labeling Kit for Affymetrix miRNA arrays (Genisphere LLC., Hatfield, PA, USA).

extract_protocol: The mirVana RNA isolation kit (Ambion, Inc., Austin, TX, USA) was used to extract total RNA from CD14+ monocytes, CD8+ T cells, and neutrophils, including small non-coding RNAs, in accordance with the manufacturer's protocol.

value: Peripheral Blood

value: F

tag: condition

value: Type 1 Diabetes

value: neutrophils

tag: hospital

value: HSR


title: HSR_T1D_NEU_14

description: neutrophils from Female T1D patient


title: HSR_T1D_NEU_1

description: neutrophils from MaleT1D patient

value: M


title: HSR_T1D_NEU_21

description: neutrophils from MaleT1D patient


title: HSR_T1D_NEU_8

description: neutrophils from Female T1D patient


title: HSR_T1D_NEU_20

description: neutrophils from MaleT1D patient


title: HSR_T1D_CD8_20

description: lymphocytes from Male T1D patient

value: CD8+ cells


title: HSR_T1D_CD8_14

description: lymphocytes from T1D patient


title: HSR_T1D_NEU_9

description: neutrophils from MaleT1D patient


title: HSR_T1D_CD8_4

description: lymphocytes from Female T1D patient


title: HSR_T1D_NEU_3

description: neutrophils from Female T1D patient


title: HSR_T1D_NEU_11

description: neutrophils from Female T1D patient


title: HSR_T1D_CD8_21

description: lymphocytes from Male T1D patient


title: HSR_T1D_CD8_8

description: lymphocytes from Female T1D patient


title: HSR_T1D_CD8_11

description: lymphocytes from Female T1D patient


title: HSR_T1D_CD8_17

description: lymphocytes from T1D patient


title: HSR_T1D_CD8_3

description: lymphocytes from Female T1D patient


title: HSR_T1D_CD14_9

description: monocytes from Male T1D patient

value: CD14+ monocytes


title: HSR_T1D_CD14_4

description: monocytes from Female T1D patient


title: HSR_T1D_NEU_10

description: neutrophils from MaleT1D patient


title: HSR_T1D_NEU_26

description: neutrophils from MaleT1D patient


title: HSR_T1D_CD8_1

description: lymphocytes from Male T1D patient


title: HSR_T1D_CD8_26

description: lymphocytes from Male T1D patient


title: DTX1_KO, replicate 4,  scBCR

city: Houston

last: Green

institute: The University of Texas MD Anderson Cancer Center

description:
Library name: Sample 8 BCR
10x Genomics

data_processing:
Single-cell BCR FASTQ were processed using Cell Ranger VDJ pipeline.
Analyses were performed in R (version 4.3.1) using various R packages. FASTQ files were processed using cellranger VDJ pipeline (10x genomics). scBCR data output from cell ranger were re-annotated for V(D)J gene annotations with IGBLAST (v1.17.0) and IMGT mouse germline sequence databases using AssignGenes.py and MakeDb.py from Immcantation toolbox. Clones were defined by clustering BCR sequences using DefineClones.py.
Assembly: mm10

source_name: Spleen

extract_protocol:
GC B cells were isolated from mice spleens at day 10 post-immunization using the Germinal Center B Cell (PNA) MicroBead Kit (Miltenyi Biotec, #130-110-479).
10X libraries for scBCR-seq were prepared using chromium Next GEM Chip K Single Cell Kit, (PN-1000287), and Chromium Single Cell Mouse BCR Amplification Kit, (PN-1000255) following the manufacturer’s instructions

value: Spleen

value: Germinal center B-cell


title: HSR_T1D_CD8_10

description: lymphocytes from Male T1D patient


title: HSR_T1D_CD14_8

description: monocytes from Female T1D patient


title: HSR_T1D_CD14_3

description: monocytes from Female T1D patient


title: HSR_T1D_CD14_20

description: monocytes from Male T1D patient


title: HSR_T1D_CD14_21

description: monocytes from Male T1D patient


title: HSR_T1D_CD14_10

description: monocytes from Male T1D patient


title: HSR_T1D_CD14_1

description: monocytes from Male T1D patient


title: HSR_T1D_CD14_14

description: monocytes from Female T1D patient


title: HSR_HC_NEU_5

description: neutrophils from Male healty control

value: HC

value: Healthy Control


title: HSR_T1D_CD14_26

description: monocytes from Male T1D patient


title: HSR_HC_NEU_22

description: neutrophils from Female healty control


title: HSR_HC_NEU_7

description: neutrophils from Male healty control


title: HSR_T1D_CD14_17

description: monocytes from Female T1D patient


title: HSR_HC_CD8_5

description: lymphocytes fromMale  healty control


title: HSR_T1D_CD14_11

description: monocytes from Female T1D patient


title: HSR_HC_NEU_18

description: neutrophils from Female healty control


title: HSR_HC_CD8_23

description: lymphocytes from Female healty control


title: HSR_HC_NEU_25

description: neutrophils from Male healty control


title: HSR_HC_NEU_6

description: neutrophils from Male healty control


title: HSR_HC_NEU_24

description: neutrophils from Female healty control


title: HSR_HC_CD8_19

description: lymphocytes fromMale  healty control


title: HSR_HC_NEU_2

description: neutrophils from Female healty control


title: HSR_HC_NEU_16

description: neutrophils from Female healty control


title: HSR_HC_NEU_12

description: neutrophils from Female healty control


title: HSR_HC_NEU_19

description: neutrophils from Male healty control


title: HSR_HC_NEU_15

description: neutrophils from Female healty control


title: HSR_HC_CD8_24

description: lymphocytes from Female healty control


title: HSR_HC_CD8_13

description: lymphocytes from Female healty control


title: HSR_HC_NEU_23

description: neutrophils from Female healty control


title: HSR_HC_CD8_16

description: lymphocytes from Female healty control


title: HSR_HC_NEU_13

description: neutrophils from Female T1D patient


title: HSR_HC_CD8_15

description: lymphocytes from Female healty control


title: HSR_HC_CD14_6

description: monocytes from Male healty control


title: HSR_HC_CD8_25

description: lymphocytes fromMale  healty control


title: HSR_HC_CD8_6

description: lymphocytes fromMale  healty control


title: HSR_HC_CD8_18

description: lymphocytes from Female healty control


title: HSR_HC_CD8_2

description: lymphocytes from Female healty control


title: HSR_HC_CD14_22

description: monocytes from Female healty control


title: HSR_HC_CD8_22

description: lymphocytes from Female healty control


title: HSR_HC_CD14_5

description: monocytes from Male healty control


title: HSR_HC_CD8_7

description: lymphocytes fromMale  healty control


title: HSR_HC_CD14_7

description: monocytes from Male healty control


title: HSR_HC_CD14_25

description: monocytes from Male healty control


title: HSR_HC_CD14_13

description: monocytes from Female T1D patient


title: HSR_HC_CD14_12

description: monocytes from Female healty control


title: HSR_HC_CD14_19

description: monocytes from Male healty control


title: HSG_RR_NEU_8

description: neutrophils from Female RR-MS patient

value: RR

value: Relapsing-Remitting Multiple Sclerosis

value: HSG


title: HSR_HC_CD14_2

description: monocytes from Female healty control


title: HSR_HC_CD14_16

description: monocytes from Female healty control


title: HSG_RRA_NEU_20

description: neutrophils from Female ACUTE RR-MS patient


title: HSR_HC_CD14_15

description: monocytes from Female healty control


title: HSG_RR_NEU_9

description: neutrophils from Male RR-MS patient


title: HSG_RRA_NEU_2

description: neutrophils from Male RR-MS patient


title: HSR_HC_CD14_18

description: monocytes from Female healty control


title: HSG_RR_NEU_15

description: neutrophils from Female RR-MS patient


title: HSG_RR_NEU_11

description: neutrophils from Female RR-MS patient


title: HSG_RR_NEU_6

description: neutrophils from Female RR-MS patient


title: HSG_RR_NEU_23

description: neutrophils from Female RR-MS patient


title: HSG_RR_NEU_21

description: neutrophils from Female RR-MS patient


title: HSG_RR_CD8_23

description: lymphocytes from Female RR-MS patient


title: HSG_RR_NEU_12

description: neutrophils from Female RR-MS patient


title: HSG_RR_CD8_5

description: lymphocytes from Female RR-MS patient


title: HSG_RR_CD8_6

description: lymphocytes from Female RR-MS patient


title: HSG_RR_CD8_8

description: lymphocytes from Female RR-MS patient


title: HSG_RR_CD8_19

description: lymphocytes from Female RR-MS patient


title: C6706 AKI, ::PompU-OueS-GBE1116, replicate 2

city: Memphis

first: Deepak

last: Balasubramanian

state: TN

address: 262 Danny Thomas Pl Rm D2037

department: Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

data_processing:
Demultiplexing, quality control and adapter trimming was performed with bcl-convert (v3.9.3). CLC Genomics Workbench (Qiagen) was used for subsequent data processing. Briefly, paired Illumina reads were mapped to the El Tor reference genome (GenBank AE003852.1- Chromosome I; AE003853.1- chromosome II) using the following settings to generate the transcripts per million bases (TPM) values: mismatch cost 2, insertion / deletion cost 3, length / similarity fraction 0.8, global strand specific alignment. Subsequent pairwise analysis between two datasets of interest (absolute fold change ≥ 2.0 filtered on average expression for FDR correction ≤ 0.01) were used for downstream analysis.
Assembly: Vibrio cholerae El Tor reference genome (GenBank AE003852.1- Chromosome I; AE003853.1- chromosome II)
Supplementary files format and content: Excel files containing read counts
Supplementary files format and content: Excel files containing TPM data

organism: Vibrio cholerae O1 biovar El Tor

source_name: bacterial cell

growth_protocol: AKI broth was used for virulence-inducing conditions (15 g l-1 BactoTM peptone, 4 g l-1 yeast extract, 5 g l-1 NaCl, 0.03% w/v sodium bicarbonate). Cells were grown for at 37 ˚C, initially static for 3.5 hrs followed by 4 hrs at 200 RPM before RNA isolation.

extract_protocol:
Total RNA was extracted using the DirectZol RNA miniprep kit, Zymo Research, following manufacturer instructions
DNase treatment, rRNA depletion, library preparation and Illumina NovaSeq 6000 sequencing (2x51 bp reads) was performed at SeqCenter, LLC (Pittsburgh, PA).

value: Strain C6706

value: bacterial cell

value: AKI growth


title: HSG_RR_NEU_17

description: neutrophils from Female RR-MS patient

value: Peripheral Blood

value: F


title: HSG_RR_NEU_10

description: neutrophils from Male RR-MS patient

value: neutrophils


title: HSG_RR_CD8_7

description: lymphocytes from Female RR-MS patient


title: HSG_RR_NEU_7

description: neutrophils from Female RR-MS patient


title: HSG_RR_CD8_9

description: lymphocytes from Male RR-MS patient


title: HSG_RR_NEU_18

description: neutrophils from Male RR-MS patient


title: HSG_RR_NEU_14

description: neutrophils from Male RR-MS patient


title: HSG_RR_CD8_16

description: lymphocytes from Female RR-MS patient


title: HSG_RR_CD8_21

description: lymphocytes from Female RR-MS patient


title: HSG_RR_CD8_17

description: lymphocytes from Female RR-MS patient


title: HSG_RR_CD8_15

description: lymphocytes from Female RR-MS patient


title: HSG_RR_CD8_22

description: lymphocytes from Male RR-MS patient


title: C6706 AKI, ::PompU-OueS-GBE1116, replicate 1


title: C6706 AKI, ::PompU-OueS-GBE1194, replicate 1


title: C6706 AKI, ::PompU-OueS-GBE1114, replicate 1


title: C6706 AKI, ::PompU-OueS-GBE1114, replicate 2


title: HSG_RR_NEU_22

description: neutrophils from Male RR-MS patient


title: C6706 AKI, ::PompU-OueS-C6706, replicate 2

value: WT


title: HSG_RR_CD8_14

description: lymphocytes from Male RR-MS patient

value: M


title: 40-day exposed, 10-day cessation, 5 µM Mn

city: West Lafayette

first: Aaron

middle: B

state: IN

address: 700 Mitch Daniels Blvd

department: School of Health Sciences

institute: Purdue University

description: Library name: CD10-T40_10_5

data_processing:
FastQ raw reads went through quality control using FastQC, CellRanger (v6.1.2) pipeline, and empty droplet removal with DropletQC (0.0.0.9000) to create Seurat objects.
Assembly: hg38
Supplementary files format and content: Seurat object

source_name: hiPSC-derived cortical culture

growth_protocol: An hiPSC line from a de-identified neurotypical male control (CD10) was maintained in mTeSR1 (Stem Cell Technologies, Cat# 85857, 85850) on Matrigel (Corning, Cat# 354277) coated 6-well plates. Before differentiation, hiPSCs were disassociated with Accutase (Innovative Cell Technologies, Inc., Cat# AT-104) and were subcultured into Matrigel coated plates with mTeSR1 supplied with 10 µM ROCK inhibitor Y-27632 (Selleckchem, Cat# S1049, dissolved in culture graded water, stock concentration 10 mM). Once the hiPSC culture reached 100% confluence, cortical neural induction was performed following a modified dual SMAD inhibition protocol as described previously (Joshi et al., 2019). Neural induction was initiated by switching from mTeSR1 to neuralization medium containing SMAD inhibitors SB431542 (Reprocell, Cat# 04-0010, dissolved in DMSO, stock concentration 20 mM, final concentration 10 µM) and LDN-193189 (Reprocell, Cat# 04-0074, dissolved in DMSO, stock concentration 2 mM, final concentration 0.4 µM). The neuralization medium is based on knockout DMEM/F12 (Gibco, Cat# 12660012) supplied with 15% v/v knockout serum replacement (Gibco, Cat# 10828028), 1X GlutaMAX (Gibco, Cat# 35050061), 1% (v/v) penicillin-streptomycin (Gibco, Cat# 15140122), 1X MEM non-essential amino acids (Gibco, Cat# 11140050), and 55 µM 2-mercaptoethanol (Sigma, Cat# M3148). During the 10-day induction phase, neuralization medium was gradually replaced by N2 medium while the concentration of SB431542 and LDN-193189 were maintained. The medium switch happened on induction Day 5, Day 7, and Day 9, when the ratio of neuralization medium and N2 medium moved from 3:1, to 1:1, and 1:3, respectively. N2 medium composed of DMEM/F-12 with GlutaMAX supplement (Gibco, Cat# 10565042), 4.5 g/L D-(+)-glucose (Thermo Scientific Chemicals, Cat# A16828), and 1X N2 supplement (Gibco, Cat# 17502048). On day 11, the culture medium was fully shifted to maintenance medium composed of 1:1 mixture of B27 neurobasal medium (Neurobasal medium (Gibco, Cat. #: 21103049) supplied with 1X B27 (Gibco, Cat. #: 17504044) and 1X GlutaMax (Gibco, Cat. #: 35050061)) and N-2 DMEM/F-12 medium (DMEM/F-12 with GlutaMax supplied with 1X N-2 (Gibco, Cat. #: 17502048), 1X MEM non-essential amino acid solution (Gibco, Cat. #: 11140050), 2% penicillin-streptomycin, and 100 µM 2-mecaptoethanol (CAS 60-24-2, Sigma-Aldrich, Cat. #: M3148) (Shi et al., 2012). The culture was maintained in this medium from day 11 onwards and replated by disassociating with Accutase (Innovative Cell Technologies, AT104) as needed.

extract_protocol:
Upon termination of either the exposure or the recovery phase, cultured cells were disassociated with Accutase and collected with DMEM/F12 (Gibco, Cat. #11320033) with 10% (v/v) fetal bovine serum (R&D Systems, Cat. #S11150) and 10 µM ROCK inhibitor Y-27632. Collected cell pellets were transferred into 50 mL conical tubes and gently triturated to ensure full disassociation. Cell suspensions were then centrifuged at 300 xg for 5 min and resuspended in DMEM/F12 with GlutaMax supplement (Gibco, Cat. #10565042) with 0.04% bovine serum albumin (BSA, Invitrogen, Cat. # AM2616) and 10 µM ROCK inhibitor Y-27632. A 70-µm strainer was used to remove clumps and cell counts were determined with Nexcelom Cellometer aiming for a final concentration of 1,000 cells/µL. Single cell suspension was transferred into low-binding Eppendorf tubes for 10X Chromium droplet preparation.
Libraries were prepared following instructions from 10X Genomics Chromium Gel Single Cell 3' protocol.

treatment_protocol: The day of neuralization initiation was counted as differentiation day 0 and Mn exposure was started upon full maturation of cortical neurons on differentiation day 110. MnCl2 was added to the culture media to achieve final concentrations of 0.05, 0.5, and 5 µM. An additional well with no MnCl2 was included as non-exposed control. The exposure was conducted for 40 consecutive days with medium refreshment interval of 72 hours. Upon exposure day 40, cultured cells either directly went into sample collections or switched into maintenance medium without Mn to recover for another 10 days before further assessments.

value: hiPSC-derived cortical culture


title: 40-day exposed, 10-day cessation, 0.05 µM Mn

description: Library name: CD10-T40_10_005


title: HSG_RR_CD8_11

description: lymphocytes from Female RR-MS patient

value: CD8+ cells


title: 40-day exposed, 10-day cessation, 0.5 µM Mn

description: Library name: CD10-T40_10_05


title: HSG_RR_CD8_12

description: lymphocytes from Female RR-MS patient


title: C6706 AKI, ::PompU-OueS-C6706, replicate 1


title: HSG_RR_CD14_9

description: monocytes from Male RR-MS patient

value: CD14+ monocytes


title: HSG_RR_CD8_10

description: monocytes from Male RR-MS patient


title: 40-day exposed, 10-day cessation, 0 µM Mn control

description: Library name: CD10-T40_10_0


title: HSG_RR_CD14_7

description: monocytes from Female RR-MS patient


title: HSG_RR_CD8_13

description: lymphocytes from Female RR-MS patient


title: 40-day exposed, 5 µM Mn

description: Library name: CD10-T40_5


title: HSG_RR_CD14_8

description: monocytes from Female RR-MS patient


title: 40-day exposed, 0.5 µM Mn

description: Library name: CD10-T40_05


title: HSG_RR_CD14_6

description: monocytes from Female RR-MS patient