title: Spleen, PBS mock-infected C57BL/6 mice, Day0, replicate 1, RNAseq

description:
Library name: Mock_1
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 dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution


title: LTR115-POD0-PRE

status: Public on Mar 02 2025

type: SRA

city: Washington

first: Anton

last: Wellstein

state: DC

address: 3970 Reservoir Road, N.W.,

department: Oncology

country: USA

institute: Georgetown University

library_source: genomic

data_processing:
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20 --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10 --retain_unpaired -r1 20 -r2 20” (https://github.com/FelixKrueger/TrimGalore).
Trimmed paired-end FASTQ reads were mapped to the human genome  (GRCh37/hg19 build) using Bismark (V 0.22.3) with parameters “--non-directional” (Kreuger et al. 2011), then converted to BAM files using SAMtools (V 1.12) (Li et al., 2009). BAM files were sorted and indexed using Samtools (V1.12).
Reads were stripped from non-CpG nucleotides and converted to BETA and PAT files using wgbstools (V 0.1.0) (Loyfer and Kaplan, 2023).
Assembly: hg19
Supplementary files format and content: BETA, PAT, and index files were generated using wgbstools bam2pat (https://github.com/nloyfer/wgbs_tools) with default parameters

molecule: genomic DNA

organism: Homo sapiens

source_name: Serum

extract_protocol:
Circulating cell-free DNA was extracted from 4-6 mL human serum, using the QIAamp Circulating Nucleic Acid kit (Qiagen, Cat. No. 55114) according to the manufacturer’s instructions. Cell-free DNA was quantified via Qubit fluorometer using the dsDNA Assay Qubit fluorometer Kits (ThermoFisher Scientific, Cat. No. Q32853 and Q10212 respectively). As a quality control, fragment size distribution of isolated cfDNA was verified based on analysis using a 2100 Bioanalyzer TapeStation using either a High Sensitivity DNA Assay or DNA 1000 Assay (Agilent Technologies, Santa Cruz, CA, USA) dependent on concentration determined via either Qubit dsDNA BR or HS Assay. Additional purification using Beckman Coulter beads was implemented to remove high-molecular weight DNA reflective of cell-lysis and leukocyte contamination (Agencourt AMPure cat#A63880) (Maggi et al. 2018).
Cell-free DNA from serum was subject to bisulfite conversion using the Zymo EZ DNA Methylation Gold kit  (#D5005 Zymo Research, Irvine, CA). Whole Genome Bisulfite Sequencing libraries were generated using the Zymo Research Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research, Irvine, CA). WGBS libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA) and then pooled to meet the required 1ug DNA input necessary for targeted enrichment. Hybridization capture was carried out according to the SeqCap Epi Enrichment System protocol (Roche NimbleGen, Inc.; Pleasanton, CA) using xGen Universal Blocker-TS Mix (Integrated DNA Technologies, USA) as the blocking reagent and SeqCap Epi CpGiant probe pools (human) or SeqCap Epi Developer probe pools (mouse samples). MethylC-Capture Sequencing (MCC-seq) libraries were assessed using Qubit Fluorometer (ThermoFisher) and Agilent Bioanalyzer DNA 1000 assays (Agilent Technologies, Inc., USA). MCC-seq libraries with inclusion of 15-20% spike-in PhiX Control v3 library (Illumina; San Diego, CA) were clustered on a Illumina Novaseq 6000 S4 flow cell followed by 150-bp paired-end sequencing.
MCC-seq (MethylC-capture sequencing)

treatment_protocol: Liver transplant patients were enrolled and provided signed informed consent in this IRB approved study at Medstar Georgetown University Hospital (IRB protocols #2017-0690 and #2017-0365). Serial serum samples were collected from 28 liver transplant patients at predetermined timepoints; pre-transplant (PRE) and post-reperfusion (POST) on post-operative day 0 (POD0), post-operative day 7 (POD0), and post-operative day 30 (POD30). Beyond this, we also collected samples in patients experiencing complications at the time of symptom presentation. Further, we added phenotype-matched samples from an additional 16 patients at the time of for-cause liver biopsy (FC-bx) used to diagnose allograft injury. For serum isolation, peripheral blood (~6-12 mL) was collected in red-top venous puncture tubes and allowed to clot at room temperature for 30 minutes before centrifugation at 1500 x g for 20 min at 4ºC to separate the serum fraction. The serum was aliquoted in 0.5 mL fractions to avoid multiple freeze-thaw cycles and stored at −80ºC until use.

tag: tissue

value: Serum

tag: treatment


title: HumanMonocyte_MDMA1

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
The fastq files of each RNA-seq data sample were aligned to the hg19 human genome.
The raw sequencing reads were quality assessed using fastp (version0.23.2), fastQC(version 0.11.9), and reported using multiqc (version 1.11)
Processed RNA-seq data was filtered, removing genes with low read counts(average counts >0.5)
Feature counts weretabulated with featureCounts (version 2.0.1).
Differential expression analysiswas done using EdgeR(version 3.42.4).
Assembly: hg19
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

molecule: total RNA

source_name: PBMCs

extract_protocol:
RNA was isolated using the Picopure RNA Isolation Kit (Life Technologies) and quantified by the Qubit RNA HS Assay Kit (Thermo Fisher Scientific). 5 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Library Prep Kit according to the manufacturer's protocol.

treatment_protocol: Human monocytes purified from PBMCs were obtained from iQ Biosciences. Cells were plated for 24 hours and then treated for 6-hours with PBS, LPS, Psilocybin, MDMA, Psilocybin+LPS, or MDMA+LPS.

value: PBMCs

tag: cell type

value: Monocyte

value: MDMA


title: HumanMonocyte_MDMA2


title: Neuron, sgNr2f2, 7d Stress3

data_processing:
Duplicate reads were removed with Picard MarkDuplicates (version 2.25.2)
Raw sequencing read quality was assessed using fastp (version 0.23.2), fastQC (version 0.11.9), and reported using multiQC (version 1.11).
Peaks were called by Macs2 (version 2.2.9.1).
Peak differential analysis was done using DiffBind (version 3.10.0)
Motif enrichment and annotation was performed with Homer (version 4.10).
Assembly: mm10
Supplementary files format and content: macs narrowpeaks for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
Nuclei from neurons isolated with the Miltenyi MACS Adult Neuron Isolation Kit were transposed and DNA was amplified.
Libraries were sequenced using paired-end sequencing on an Illumina NextSeq550.

treatment_protocol: AAV-targeting sgRosa or sgNr2f2 were transduced in the amygdala of C57BL/6J mice and allowed to express for >2 weeks. Mice were subsequently exposed to 7D of tube restraint followed by 1 day of fear conditioning and 3 days of fear extinction. The amygdala was digested in 500-uL of Hibernate-A containing 7.5-uL of papain. Tissue was dissociated and processed using the Milentyi MACS Adult Neuron Isolation Kit.

value: Brain

tag: Sex

value: Male

value: Neuron

tag: strain

tag: genotype


title: Neuron, sgRosa, 7d Stress3

value: sgRosa


title: Neuron, sgNr2f2, 7d Stress1


title: LTR117-POD0-PRE


title: LTR115-POD0-POST


title: Neuron, sgRosa, 7d Stress1


title: KP_C271_2

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Library name: KP_C271_2

data_processing:
Raw data were trimmed by Trim Galore (v0.6.6) with default settings. Then, the clean data were mapped to mouse reference genome mm10 using Hisat2 (v2.1.0) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Gene count matrices were calculated by featureCounts (v1.6.4) with the parameters -p -M -O. Differentially expressed gene (DEG) analysis was performed by using DESeq2 package. Only genes with adjusted P value < 0.05 and fold change > 2 were considered to be differentially expressed. DEGs were submitted to DAVID (2021 Update) (https://david.ncifcrf.gov/) for gene ontology (GO) and KEGG pathway enrichment analyses. GSEA was performed using clusterProfiler package.
Assembly: mm10
Supplementary files format and content: comma-separated values file, raw counts for gene expression.

source_name: KP

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

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen).
1 μg total RNA was used for the following library preparation. RNAseq libraries were prepared with VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611). The poly(A) mRNA isolation was performed using Oligo(dT) beads. Using divalent cations and high temperatures, mRNA fragmentation was achieved and the priming process was carried out using random primers. Then first strand cDNA and the second-strand cDNA were synthesized. Once the double-stranded cDNA was purified, adaptors were added to both ends after end repair and dA-tailing. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Libraries were finally subjected to 150 bp paired-end sequencing using the Illumina NovaSeq 6000 platform.

treatment_protocol: KP cells were treated with DMSO or C271 (2.5 μM) for six days.

tag: cell line

value: KP

value: LUAD

value: WT


title: Meninges, 18D Stress, MDMA3

data_processing:
The fastq files of each RNA-seq data sample were aligned to theMus musculusGRCm38 transcriptomeusing STAR (version 2.7.5c)
The raw sequencing reads were quality assessed using fastp (version0.23.2), fastQC(version 0.11.9), and reported using multiqc (version 1.11)
Processed RNA-seq data was filtered, removing genes with low read counts(average counts >0.5)
Feature counts weretabulated with featureCounts (version 2.0.1).
Differential expression analysiswas done using EdgeR(version 3.42.4).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Meninges

treatment_protocol: Monocytes were isolated with the Milentyi MACS Monocyte Isolation Kit from the deep cervical lymph nodes and meninges of mice exposed to 18 days of chronic restraint stress. In cases with psychedelics, mice were exposed to 18 days of chronic restraint stress, administered vehicle, psilocybin, or MDMA, and allowed to sit for 24 hours before tissues were taken for processing.

value: Meninges


title: HumanMonocyte_Psilocybin3

value: Psilocybin


title: KP_C271_1

description: Library name: KP_C271_1


title: LTR115-FC-POD30


title: HumanMonocyte_Psilocybin2


title: KP_DMSO_2

description: Library name: KP_DMSO_2

value: DMSO


title: Meninges, 18D Stress, MDMA2


title: LTR114-POD7


title: LTR114-POD30


title: Meninges, 18D Stress, MDMA1


title: HumanMonocyte_LPS3

value: LPS


title: KP_DMSO_1

description: Library name: KP_DMSO_1


title: UUO operation,Si-based diet,Day14,rep06 [RM706]

city: Suita

first: Ryo

last: Tanaka

state: Osaka

department: Department of Urology

country: Japan

institute: Osaka University Graduate School of Medicine

data_processing:
The sequenced reads were mapped to mouse reference genome sequences (mm10) using TopHat2 v2.1.1
Raw counts were calculated using feature counts v2.0.0.
Fragments per kilobase of exons per million mapped fragments were calculated using Cuffdiff v2.2.1.
Assembly: mm10
Supplementary files format and content: text file includes row counts for each Sample

source_name: kidney

extract_protocol:
Total RNA was extracted from each sample stored in RNAlater (-20 °C) using the RNeasy Kit (QIAGEN, Cat#74104).
Library preparation was performed using a SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech, California, USA) following the manufacturer’s instructions.

value: kidney

value: UUO operation,Si-based diet,Day14


title: HumanMonocyte_LPS2


title: LTR114-POD0-POST

value: Serum


title: Meninges, 18D Stress, Psilocybin1


title: Meninges, 18D Stress, Psilocybin3


title: UUO operation,Si-based diet,Day14,rep03 [RM403]


title: Meninges, 18D Stress, Psilocybin2


title: Meninges, 18D Stress, Vehicle3

value: Vehicle


title: LTR113-POD7


title: HumanMonocyte_PBS3

value: PBMCs

value: Monocyte

value: PBS


title: UUO operation,Si-based diet,Day14,rep04 [RM404]


title: UUO operation,Si-based diet,Day14,rep05 [RM406]


title: HumanMonocyte_Psilocybin1


title: HumanMonocyte_LPS1


title: LTR114-POD0-PRE


title: LTR113-POD30


title: UUO operation,Si-based diet,Day14,rep02 [RM402]


title: HumanMonocyte_PBS2


title: LTR113-POD0-PRE


title: Amygdala, sgEgfr_3, 7D Stress and Fear Conditioning

source_name: Brain (amygdala)

treatment_protocol: AAV-targeting sgRosa or sgEgfr were transduced in the amygdala of C57BL/6J mice and allowed to express for >2 weeks. Mice were subsequently exposed to 7D of tube restraint followed by 1 day of fear conditioning and 3 days of fear extinction. The amygdala was digested in 500-uL of Hibernate-A containing 7.5-uL of papain. Tissue was dissociated and processed using the Milentyi MACS Anti-Acsa-2 Microbeads Kit.

value: Brain (amygdala)

value: Male

value: Astrocyte

value: sgEgfr


title: UUO operation,Si-based diet,Day14,rep01 [RM401]


title: Meninges, 18D Stress, Vehicle1


title: HumanMonocyte_PBS1


title: LTR112-POD7


title: UUO operation,Normal diet,Day14,rep06 [RM605]

value: UUO operation,Normal diet,Day14


title: UUO operation,Normal diet,Day14,rep05 [RM604]

value: WT


title: HumanAmygdala, MDD

library_source: transcriptomic single cell

data_processing:
The fastq files were processed using the 3' Gene Expression pipeline and cellranger-7.1.0 on the 10x Genomics Cloud CLI.
Intron mode was used to align samples against GRCh38-2020-A. The top 10,000 barcodes were selected for downstream analysis.
Samples were merged using Cell Ranger Aggr v7.1.0, and the Loupe Browser file was output.
Cells were filtered based on UMI between 500-20,000 and <15% mitochondrial reads.
Cell clusters without clearly expressed marker genes were excluded from downstream analysis along with duplicate barcodes between control and MDD samples.
Assembly: GRCh38-2020-A
Supplementary files format and content: Control_filtered_feature_bc_matrix.tar.gz includes barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files.
Supplementary files format and content: MDD_filtered_feature_bc_matrix.tar.gz includes barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files.

extract_protocol:
Nuclei were processed according to the 10x scRNA-seq protocol.
10X Genomics 3' RNA

treatment_protocol: Frozen amygdala samples were processed with the 10x Nuclei Isolation Kit.

tag: disease state

value: MDD


title: LTR112-POD30


title: Stress, Saline, Amygdala, Astrocyte, M2

data_processing:
The fastq files of each RNA-seq data sample were aligned to the Mus musculus GRCm38 transcriptome using STAR (version 2.7.5c)
The raw sequencing reads were quality assessed using fastp (version0.23.2), fastQC(version 0.11.9), and reported using multiqc (version 1.11)
Processed RNA-seq data was filtered, removing genes with low read counts (average counts <0.5)
Feature counts were tabulated with featureCounts (version 2.0.1).
Differential expression analysis was done using EdgeR(version 3.42.4).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

treatment_protocol: The amygdala was dissected from mice exposed to 7 days of restraint injected intravenously with monocytes or saline and was digested in 500-uL of Hibernate-A containing 7.5-uL of papain. Tissue was dissociated and processed using the Milentyi MACS Anti-Acsa-2 Microbeads Kit.

value: Brain

value: exposed to 7-day restraint stress that were transferred intravenously with saline for 7 days


title: Amygdala, sgEgfr_2, 7D Stress and Fear Conditioning


title: UUO operation,Normal diet,Day14,rep04 [RM305]


title: Amygdala, sgEgfr_1, 7D Stress and Fear Conditioning


title: LTR112-POD0-PRE


title: Stress, Saline, Amygdala, Astrocyte, M1


title: Meninges, 18D Stress, Vehicle2

value: Meninges


title: LTR112-POD0-POST


title: Amygdala, sgRosa_4, 7D Stress and Fear Conditioning


title: UUO operation,Normal diet,Day14,rep03 [RM304]

value: kidney


title: LTR113-POD0-POST


title: HumanAmygdala, Control

value: Control


title: UUO operation,Normal diet,Day14,rep02 [RM303]


title: Amygdala, sgRosa_3, 7D Stress and Fear Conditioning


title: Stress, Monocytes, Amygdala, Astrocyte, M2

value: exposed to 7-day restraint stress that were transferred intravenously with monocytes for 7 days


title: Amygdala, sgRosa_2, 7D Stress and Fear Conditioning


title: LTR111-POD7

value: Serum


title: LTR111-POD30


title: UUO operation,Normal diet,Day14,rep01 [RM302]


title: Sham opearation,Normal diet,Day14,rep03 [RM103]

value: Sham opearation,Normal diet,Day14


title: LTR111-POD0-PRE


title: Amygdala, sgRosa_1, 7D Stress and Fear Conditioning


title: LTR111-POD0-POST


title: Sham opearation,Normal diet,Day14,rep02 [RM102]


title: Stress, Monocytes, Amygdala, Astrocyte, M3


title: Stress, anti-IgG, Amygdala, Astrocyte, M3

data_processing:
The fastq files of each RNA-seq data sample were aligned to theMus musculus GRCm38 transcriptome using STAR (version 2.7.5c)
The raw sequencing reads were quality assessed using fastp (version0.23.2), fastQC (version 0.11.9), and reported using multiqc (version 1.11)
Processed RNA-seq data was filtered, removing genes with low read counts (average counts <0.5)
Feature counts were tabulated with featureCounts (version 2.0.1).
Differential expression analysis was done using EdgeR (version 3.42.4).
Assembly: mm10
Supplementary files format and content: feature counts
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

treatment_protocol: The amygdala was dissected from mice and was digested in 500-uL of Hibernate-A containing 7.5-uL of papain. Tissue was dissociated and processed using the Milentyi MACS Anti-Acsa-2 Microbeads Kit. Mice were allowed to sit for 24 hours following the final day of treatment before tissues were taken for processing.

value: exposed to chronic stress and treated ICM with anti-IgG antibody


title: Stress, anti-IgG, Amygdala, Astrocyte, M2


title: Sham opearation,Normal diet,Day14,rep01 [RM101]


title: LTR110-POD30


title: Aldh1l1-tdTomato, chronic stress2

data_processing:
Samples were aligned against the mm10 mouse assembly genome using the DropSeq Resources pipeline.
Cells included in the analysis had 200-3000 genes expressed per cell, at least 2 cells expressing a gene, and <50% mitochondrial reads.
Data were normalized by read counts, highly variable genes extracted, data were then filtered and scaled, followed by PCA.
Differential expression analysis was performed by comparing each cluster to all others using MAST.
Assembly: mm10
Supplementary files format and content: h5ad file includes raw counts for all Samples
Supplementary files format and content: h5ad files include raw counts for each Sample

extract_protocol:
Cells were processed for drop-seq according to the original protocol.
Libraries were sequenced using paired-end sequencing on an Illumina NextSeq550.
Drop-seq

treatment_protocol: Aldh1l1-TdTomato mice were exposed to chronic stress. The brain was digested in 500-uL of Hibernate-A containing 7.5-uL of papain. Tissue was dissociated and TdTomato+ cells were sorted and subsequently processed for drop-seq.

tag: stress

value: Chronic Stress


title: Stress, Monocytes, Amygdala, Astrocyte, M1


title: LTR110-POD0-PRE


title: Aldh1l1-tdTomato, chronic stress1


title: Teff, EKO7, 8A, rep2

city: Shanghai

first: Xiaoxia

last: Wang

state: Shanghai

address: No.280 South Chongqing Road, Room 811, Building No.5 (West Area)

department: Department of Immunology and Microbiology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Low quality reads and sequencing adapters were removed using Trim Galore! (v.0.4.4)
Trimmed reads were aligned to the mouse genome mm10 and quantified using Salmon (0.14.1).
Further analyses were performed with R software (v.4.0.3).
Raw read counts were normalized, and differentially expressed genes were analyzed using the Bioconductor package DESeq2 (v.1.28.1).
Heatmaps were generated with the package pHeatmap (v.1.0.12) using selected gene lists with an adjusted p value less than 0.05.
Genome_build: Mus Musculus genome (version mm10)
Supplementary_files_format_and_content: Comma-Separated Values File with normalized counts of indicated sample.

source_name: spleen

extract_protocol:
Fresh sorted Tregs and Teffs and total RNA was extracted using TRIzol reagent (Invitrogen) according to manual instructions.
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 single end 50 bases reads were generated on DNBSEQ platform(BGI-Shenzhen,China)

value: spleen

value: Teff

value: EAE day7


title: Aldh1l1-tdTomato, chronic stress3


title: Stress, anti-IgG, Amygdala, Astrocyte, M1

value: Male

value: Astrocyte


title: Stress, anti-CCR2, Amygdala, Astrocyte, M3

value: exposed to chronic stress and treated ICM with anti-CCR2 antibody


title: Aldh1l1-tdTomato, ctrl3

value: Ctrl


title: LTR110-POD0-POST


title: Stress, anti-CCR2, Amygdala, Astrocyte, M2

value: Brain


title: Teff, EKO7, 7A, rep1


title: Aldh1l1-tdTomato, ctrl2


title: LTR109-POD30


title: CCR2-DTR, Saline, Amygdala, Astro, M2

data_processing:
The fastq files of each RNA-seq data sample were aligned to the Mus musculus GRCm38 transcriptome using STAR (version 2.7.5c)
The raw sequencing reads were quality assessed using fastp (version0.23.2), fastQC(version 0.11.9), and reported using multiqc (version 1.11)
Processed RNA-seq data was filtered, removing genes with low read counts (average counts <0.5)
Feature counts were tabulated with featureCounts (version 2.0.1).
Differential expression analysis was done using EdgeR(version 3.42.4).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples

treatment_protocol: CCR2-DTR mice were treated with tamoxifen and saline or DTx throughout the course of tube restraint. Mice were exposed to 18D of tube restraint followed by fear conditioning and extinction. The amygdala was digested in 500-uL of Hibernate-A containing 7.5-uL of papain. Tissue was dissociated and processed using the Milentyi MACS Anti-Acsa-2 Microbeads for astrocytes.


title: Stress, anti-CCR2, Amygdala, Astrocyte, M1


title: Aldh1l1-tdTomato, ctrl1


title: Teff, F7, 6A, rep2

value: WT


title: Teff, F7, 5A, rep1


title: LTR109-POD7


title: Treg, EKO7, 4A, rep2

value: Treg


title: LTR109-POD0-PRE


title: LTR109-POD0-POST


title: Treg, EKO7, 3A, rep1


title: Bat Liver Marburg virus infected 4

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description: Library name: LIB_05975_01_S12

data_processing:
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt (version 1.12)
Reads were aligned to the Jamaican fruit bat genome assembly version (GCF_021234435.1) using Hisat2
Reads mapping to genes were counted using htseq-count
Differential expression analysis was performed using the Bioconductor package DESeq2
Assembly: CSHL_Ajam (GCF_021234435.1)
Supplementary files format and content: TSV containing gene-level raw counts

molecule: polyA RNA

organism: Artibeus jamaicensis

source_name: Liver

extract_protocol:
Qiagen RNEasy
Two hundred nanograms of RNA was used as input for poly-A pull-out and next-generation sequencing (NGS) library preparation following the Illumina Stranded mRNA prep workflow (Illumina).

value: Liver

value: Marburg virus infected


title: Treg, F7, 2A, rep2


title: Bat Liver Marburg virus infected 3

description: Library name: LIB_05974_01_S11


title: Bat Liver Marburg virus infected 2

description: Library name: LIB_05973_01_S10


title: CCR2-DTR, DTx, Amygdala, Astro, M3


title: LTR108-POD0-POST


title: Treg, F7, 1A, rep1


title: CCR2-DTR, Saline, Amygdala, Astro, M1


title: CCR2-DTR, DTx, Amygdala, Astro, M1


title: Bat Liver Marburg virus infected 1

description: Library name: LIB_05972_01_S9


title: pDC cells, CpG_ATRA 3

city: guangzhou

first: wanli

last: yu

address: 南方医科大学

institute: 南方医科大学

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: peripheral blood

growth_protocol: RPMI medium supplemented with 10% FBS, 1% penicillin G/streptomycin, cells were cultured at 37°C at 5%CO2.

extract_protocol:
Total RNA of pDC cells was prepared using RNAex Pro RNA Reagent(AG,AG21102) after treatment.
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo_x0002_attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle(ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: pDCs were enriched by Human Plasmacytoid DC Enrichment Kit (STEMCELL, Catalog #19062). pDCs were stimulated them with different compounds for 6 hours. ATRA group were treated with 10nM ATRA; CpG group were treated with 1mM CpG; CpG_ATRA group were treated with 10nM ATRA and 1mM CpG and the control group was grown in the same culture conditions without the addition of any drugs.

value: peripheral blood

value: human plasmactoid dendritic cell


title: Bat liver Ebola infected 4

description: Library name: LIB_05971_01_S8

value: Ebola infected


title: LTR108-POD0-PRE

value: Serum


title: Lung, 2 weeks Antibiotic treatment+ 4 weeks Streptococcus mitis treatment + 12 weeks smoke exposure, replicate 3

first: manyi

last: pan

address: Manufacturing Bureau Road, Shanghai

department: Department of Respiratory and Critical Care Medicine

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

description: Library name: SM-3

data_processing:
Total RNA was extracted from the isolated single cells using the Qiagen RNeasy Micro Kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. The quality of RNA was assessed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, USA) to ensure RNA integrity (RIN > 7.0). RNA was used to construct single-cell RNA libraries using the GEXSCOPE® Single-Cell RNA Library Kit and Singleron Matrix® Automated Single-Cell Processing System (Singleron Biotechnologies). After library preparation, the sequencing libraries were pooled, quantified, and sequenced on the Illumina HiSeq X platform to generate paired-end 150 base pair reads.
Assembly: GRCm38 mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
After dissociation, the single-cell suspension was filtered through a 70 µm mesh filter to remove debris and centrifuged to pellet the cells. Red blood cells were removed using a red blood cell lysis buffer. The remaining viable cells were resuspended in PBS and stained with viability dye to exclude dead cells. High-quality, viable cells (≥85% viability) were selected and enriched using a cell sorting technique or manually for further processing.
Single-cell RNA libraries were prepared via the GEXSCOPE® Single-Cell RNA Library Kit and the Singleron Matrix® Automated Single-Cell Processing System (Singleron Biotechnologies) following the manufacturer’s protocol. After library preparation, the sequencing libraries were quantified, diluted to a concentration of 4 ng/μL, and sequenced on the Illumina HiSeq X platform (Illumina, San Diego, USA) to generate paired-end reads of 150 base pairs. The single-cell suspensions were diluted with PBS to a concentration of 1 × 10⁵ cells/mL and loaded onto microfluidic devices for barcoding. Single-cell RNA libraries were constructed via the GEXSCOPE® Single-Cell RNA Library Kit and the Singleron Matrix® Automated Single-Cell Processing System (Singleron Biotechnologies) according to the GEXSCOPE® protocol. The constructed libraries were diluted to 4 ng/μL, pooled, and sequenced on the Illumina HiSeq X platform to generate paired-end reads of 150 base pairs.

value: lung

value: primary cells

value: all cell types


title: Bat liver Ebola infected 3

description: Library name: LIB_05970_01_S7


title: LTR107-POD0-PRE


title: CCR2-DTR, DTx, Amygdala, Astro, M2


title: pDC cells, CpG_ATRA 2


title: LTR107-POD0-POST


title: LTR106-POD0-PRE


title: Bat liver Ebola infected 2

description: Library name: LIB_05969_01_S6


title: pDC cells, CpG_ATRA 1


title: Bat liver Ebola infected 1

description: Library name: LIB_05968_01_S5


title: Bat liver control 4

description: Library name: LIB_05967_01_S4

value: Control


title: pDC cells, CpG 3

value: CpG


title: pDC cells, CpG 2


title: Lung, 2 weeks Antibiotic treatment+ 4 weeks Streptococcus mitis treatment + 12 weeks smoke exposure, replicate 1

description: Library name: SM-1


title: Bat liver control 3

description: Library name: LIB_05966_01_S3


title: LTR105-POD0-POST


title: Lung, Control group, replicate 2

description: Library name: Con-2


title: LTR104-POD0-PRE


title: pDC cells, ATRA 3

value: ATRA


title: pDC cells, CpG 1


title: Lung, 2 weeks Antibiotic treatment+ 4 weeks Streptococcus mitis treatment+ 12 weeks smoke exposure, replicate 2

description: Library name: SM-2


title: Bat liver control 1

description: Library name: LIB_05964_01_S1


title: pDC cells, ATRA 2


title: Lung, Control group, replicate 1

description: Library name: Con-1


title: Lung, 2 weeks Antibiotic treatment+ 12 weeks smoke exposure, replicate 3

description: Library name: ABX-3


title: LTR104-POD0-POST


title: LTR103-POD0-PRE


title: Lung, 2 weeks Antibiotic treatment+ 12 weeks smoke exposure, replicate 2

description: Library name: ABX-2


title: Stress 1

data_processing:
*library strategy: SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq)
Coordinate ID data was mapped to the capture chip and reads with low quality moleculed IDs were removed.
Reads were aligned to GRCh38 using STAR and reads with MAPQ > 10 were annotated to the corresponding genes.
A CID-containing expression profile matrix was obtained by collapsing the UMI with the same CID and gene locus.
Nucleic acid staining images were projected to the Stereo-seq chips and a generated spatial density matrix was converted to an image mapping the DNB and total UMI of the DNB spot.
The nucleic acid staining image was aligned to the transcriptome image and cell segmentation analysis was performed with Scikit-image (V0.18.1).
High cell quality was confirmed (mitochondrial reads < 5% and expressing 500-1200 genes), and cell types were called using ingest. Cells localized to the amygdala were extracted for each tissue section.
Assembly: GRCh38
Supplementary files format and content: h5ad file includes raw counts for all Samples
Supplementary files format and content: h5ad files include raw counts for each Sample
Supplementary files format and content: h5ad files include processed data for each Sample

extract_protocol:
Flash frozen issues were sectioned onto Stereo-seq capture slides
SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq)

treatment_protocol: Mice were perfused and brains were stored in OCT to preserve tissues. STEREO-seq was performed on ctrl (n=3) and 18D stressed (n=3) mice.

value: Male


title: pDC cells, ATRA 1


title: LTR106-POD0-POST


title: Lung, 2 weeks Antibiotic treatment+ 12 weeks smoke exposure, replicate 1

description: Library name: ABX-1


title: LTR103-POD0-POST


title: Bat liver control 2

description: Library name: LIB_05965_01_S2


title: LTR105-POD0-PRE


title: Stress 3


title: Lung, Control group, replicate 3

description: Library name: Con-3


title: LTR102-POD0-POST


title: pDC cells, Ctrl 2


title: Lung, Aged Ventilated

city: London

first: Sean

last: Gill

state: Ontario

address: 1151 Richmond St

department: Physiology and Pharmacology

country: Canada

institute: Western University

description: 10x genomics

data_processing:
Alignment was carried using the mm10 2020-A reference genome and filtering, barcoding, and UMI counting were performed using Cell Ranger 7.0.0 and the 10x Genomics recommended default parameters.
Assembly: mm10 2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung Tissue

growth_protocol: C57BL/6 male mice from Charles River laboratories (Sherbrooke, QC, Canada) were aged to 22 months (aged group) under controlled conditions (standard light-dark cycles, temperature, humidity, and group-housing) within our institutional animal facility. C57BL/6 mice of 2-3 months of age were grown in the same conditions and represented the young group. Mice were fed a food-restricted diet with a gradual reduction to 70% ad libitum, to maintain body weight.

extract_protocol:
Mice were euthanized via intraperitoneal injection of pentobarbital sodium. The pulmonary vasculature was flushed with sterile PBS through the right ventricle of the heart. The lungs were removed and the left lobe was isolated and minced to small pieces (approximately 1-3mm2). The tissue pieces were enzymatically digested for 30 minutes in complete Roswell Park Memorial Institute media (RPMI) containing 10% fetal bovine serum and 1% penicillin/streptomycin, along with 400 µg/mL each of the digestion enzymes, LiberaseTM and DNaseI. The enzymatic reaction was then stopped using 100mM EDTA. Dissociated cells in suspension were passed through a 100μm cell strainer using ice-cold 2mM EDTA in complete Dulbecco’s Modified Eagle Medium (DMEM supplemented with 10% FBS and pen-strep). Centrifugation was performed, and cells were resuspended in ice-cold DMEM with an aliquot being taken to perform cell counts. Centrifugation was performed again, followed by resuspension of the cells in ice-cold DMEM at a concentration of 1 million cells/mL. An additional aliquot was taken for cell counts and cell viability assessments using trypan blue. Centrifugation was performed one last time and cells were resuspended in CryoStor CS10 freezing media at 2 million cells/mL. Cells were transferred to an isopropanol cooling container and placed in a -80°C freezer overnight. The cells were then transferred the following day to a liquid nitrogen storage tank for long-term storage until all samples were collected. Each treatment group yielded n=3 animals pooled per condition.
Mouse lung single cell suspensions were rapidly thawed from cryopreservation. Cell suspensions were washed with ice-cold PBS with 0.5% BSA then counted. Cells were resuspended in PBS with 0.5% BSA. Viability was assessed with trypan blue exclusion. Samples with a viability of less than 80% were excluded. Samples from each treatment group were proportionately pooled to a final count of 5000 cells for each treatment, which were subsequently used for library preparation. The Cells were prepared for cDNA amplification and chromium library construction using the 10x Chromium Next GEM Single Cell 3' Library and Gel Bead Kit v3.1 according to manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA).

treatment_protocol: young (2-3 months) and aged (22 months) mice were randomized to either the non-ventilated control or mechanical ventilation group. Ventilated mice were anesthetized using ketamine hydrochloride (100 mg/kg) and medetomidine (50 mg/kg) and received 1.5 g of buprenorphine subcutaneously for analgesia. Arterial and venous vascular lines were set up for arterial blood gas measurements and a Harvard MidiVent mechanical ventilator (Harvard Apparatus, Holiston, Massachusetts) was connected via an endotracheal tube. Mice were ventilated for 3 hours at a respiratory rate of 150 breaths/minute; a positive end expiratory pressure (PEEP) of 0 cm H2O and a fraction of inspired oxygen (FIO2) at 1.0. The tidal volume was set at 20 mL/ kg up to a maximum of 0.6 mL, such that all the mice weighing 30g and above received a tidal volume related to an estimate of lean body weight. Baseline physiological values were noted and pulmonary blood gases and peak inspiratory pressure (PIP), were measured throughout. Non-ventilated controls were naïve mice that did not undergo the above procedures.

value: Wild Type

tag: age

value: Aged (22 months)

value: Mechanical Ventilation

value: Lung Tissue


title: pDC cells, Ctrl 3

value: WT


title: Control 2

value: Brain


title: pDC cells, Ctrl 1

value: peripheral blood


title: Chrna5-/-

city: Jinan

first: Dianhao

last: Guo

address: 6699 Qingdao Road

department: Institute of Basic Medicine

institute: shandong first medical university

description: 7 days' mouse after Vaseline treatment

data_processing:
The samples of KO and WT mice after IMQ treatment were processed in terms of alignment, barcode assignment, and UMI counting with Cell Ranger, version 3.0.2 (https://github.com/10XGenomics/cellranger) count pipeline.
The cell clustering in primary tissues was performed by the R package Seurat (version 3.0, https://satijalab.org/seurat/) involving normalization.
On acquiring the dataset, each sample contained at least 3 cells, cells which have more than 7,500 or less than 500 unique genes were excluded from the analysis. Only genes which were expressed in 10 or more cells were used for further analysis. Cells with a percentage of mitochondrial genes more than 7%, ribosomal RNA genes more than 40%, and log10GenesPerUMI (the gene numbers of per UMI) less than 0.8 were removed from the dataset.
Anchor strategy was used to integrate these datasets, which were produced across multiple technologies. Finding an accurate set of anchors is the basis for subsequent integration analyses. Thus, these datasets were integrated with 2000 anchors, resulting in a batch corrected expression matrix for all cells.
The new integrated matrix was used for scaling and the principal component analysis (PCA). Non-linear dimensional reduction was performed using the Uniform Manifold Approximation and Projection (UMAP) method, with resolution at 0.6.
The cluster biomarkers were also obtained by FindMarkers. Identification of cell clusters was performed using R package Single R.
The keratinocytes were divided into 5 subclusters. Functional Enrichment Analysis of Cell Clusters-Gene Ontology (GO) enrichment analysis of cell clusters was used to identify the biological significance of keratinocytes subcluster3 in the DAVID portal (https://david.ncifcrf.gov/). To identify sample-specific genes, we calculated the expression difference of each gene between the KO and WT samples using “FindMarkers” function of Seurat. The candidate genes with log2FC >=1 and q-value < 0.05 were used for DAVID analyses.
Genome_build: mm10
Supplementary_files_format_and_content: mtx,barcodes, features

source_name: Skin

growth_protocol: In our laboratory, KO mice have been backcrossed with C57BL/6N mice for more than 10 generations, and they have been crossed with heterozygous knockout mice to breed and maintain this pattern; each mouse has been genotyped . Female C57BL/6N mice (6-8 weeks old) were used for imiquimod (IMQ) modeling and follow-up research.

extract_protocol:
C57BL/6J mice back skin after imiquimod treatment were removed, fat scrapped off, and then skin was minced I nto pieces less than 1 mm in diameter. The minced samples were placed in 15-mL conical tubes and digested with 10 mL of collagenase mix [0.25% collagenase (Sigma; C9891), 0.01M HEPES(Fisher; BP310), 0.001M sodium pyruvate (Fisher; BP356), and 0.1 mg/mL DNase (Sigma; DN25)]. Samples were incubated at 37℃for 2 hours with rotation, and thenfiltered through 70-μm and 40-μm filters, spun down, and resuspended in 2% FBS. Cells were stained with SytoxBlue (Thermo Fisher; S34857) as per manufacturer’s instructions and live cells (SytoxBlue-negative) were sorted using BD FACSAria Fusion Sorter.
RNA libraries were prepared for sequencing using standard llumina protocols

treatment_protocol: IMQ cream (5%; 3M Health Care Limited, England) was used externally in the experimental group. The control group received an external application of the cream base（vaseline）. The experimental groups (n=5) were received 62.5 mg IMQ cream on the backs of the shaved mice for 6 consecutive days, and they were euthanized on the 7th day.

value: dorsal skin

tag: developmental stage

value: control（Vaseline）


title: Control 3


title: LTR101-POD0-POST

data_processing:
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20 --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10 --retain_unpaired -r1 20 -r2 20” (https://github.com/FelixKrueger/TrimGalore).
Trimmed paired-end FASTQ reads were mapped to the human genome  (GRCh37/hg19 build) using Bismark (V 0.22.3) with parameters “--non-directional” (Kreuger et al. 2011), then converted to BAM files using SAMtools (V 1.12) (Li et al., 2009). BAM files were sorted and indexed using Samtools (V1.12).
Reads were stripped from non-CpG nucleotides and converted to BETA and PAT files using wgbstools (V 0.1.0) (Loyfer and Kaplan, 2023).
Assembly: hg19
Supplementary files format and content: BETA, PAT, and index files were generated using wgbstools bam2pat (https://github.com/nloyfer/wgbs_tools) with default parameters

value: Serum


title: Control 1


title: LTR101-POD0-PRE


title: Lung, Aged Non-Ventilated

description: 10x genomics

value: Naive


title: Lung, Young Non-Ventilated

description: 10x genomics

value: Young (2-3 months)


title: Lung, Young Ventilated

description: 10x genomics


title: Stress 2


title: WT

description: 7 days' mouse after Vaseline treatment


title: 13 - KO FFC 1

status: Public on Mar 01 2025

city: Rochester

first: Harmeet

last: malhi

address: 200 First Street SW

institute: Mayo Clinic

description: Library name: 13_-_KO_FFC_1

data_processing:
RNA-seq data were analyzed using the MAP-RSeq pipeline
Assembly: mm10
Supplementary files format and content: Excel file containing gene counts

source_name: Liver tissue

extract_protocol:
Total RNA was extracted using the Quick-RNA MiniPrep Kit (Zymo Research, R1055). RNA quality and yield was assessed by NanoDrop ND1000 (Thermo Scientific, Waltham, MA), then reverse transcribed into cDNA with the iScript cDNA Synthesis Kit (Bio-Rad Laboratories, 1708891)
Bulk RNA sequencing was performed at the Genome Analysis Core of Medical Genome Facility at Mayo Clinic, Rochester. mRNA sequencing libraries were prepared and sequenced on an Ilumina HiSeq 2000 instrument at the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

value: Liver tissue

tag: diet

value: FFC

value: KO


title: 14 - KO FFC 4

description: Library name: 14_-_KO_FFC_4


title: 8 - WT FFC 3

description: Library name: 8_-_WT_FFC_3


title: 9 - WT FFC 4

description: Library name: 9_-_WT_FFC_4


title: 15 - KO FFC 7

description: Library name: 15_-_KO_FFC_7


title: 7 - WT FFC 2

description: Library name: 7_-_WT_FFC_2


title: 4 - KO CD 1

description: Library name: 4_-_KO_CD_1

value: Chow


title: 5- KO CD 2

description: Library name: 5-_KO_CD_2


title: 6 - KO CD 3

description: Library name: 6_-_KO_CD_3


title: 3 - WT CD 4

description: Library name: 3_-_WT_CD_4


title: 2 - WT CD 3

description: Library name: 2_-_WT_CD_3


title: Mm_LT_NPMc_Flt3ITD_rep1

city: Milano

first: Pier Giuseppe

last: Pelicci

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

data_processing:
Basecalls were performed using CASAVA version 1.8
Reads were aligned to the mus musculs  genome build mm9 using tophat (v2.1.0), which uses Bowtie (2.2.4) and Samtools (v0.1.18) using default parameters and --transcriptome Mus Musculus index, UCSC mm9 gtf.
Raw read counts were summarised using HTSeq (v0.6.1p1), then normalized for library size differences using calcNormFactors function from edgeR package (v3.20.7).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TMM normalized expression value expressed as cpm (copy per milion) for each gene for each sample

source_name: bone marrow

extract_protocol:
Bone marrow from from posterior limbs, anterior limbs and sternum were crushed. Recovered cells were stained and LT-HSCs were sorted in RLT lysis buffer. RNA was purified from 3-7,000 LT-HSCs taking advantage of the PicoPureTM RNA Isolation Kit (ThermoFisher)
Libraries of template RNA molecules were prepared with 0.5 μg high quality input RNA using the SMARTseq protocol based on polyA-enrichment (Picelli et al. 2014)

value: long term hematopoietic stem cell

value: 8-11 weeks


title: Mm_LT_NPMc_Flt3ITD_rep2


title: Mm_LT_Flt3ITD_rep2


title: Mm_LT_Mx_rep1

value: MxCRE


title: Wildtype_unedited_CellscDNA

city: Charlestown

first: Koen

last: Breyne

address: Building 149 149 13th Street

institute: MGH

description: Library name: Wildtype unedited cell cDNA

data_processing:
Data was processed using CRISPResso2 analysis software
Assembly: The reference sequence used for read alignment consisted of the region of the DYT1 mutant allele sequence associated with the appropriate primers used for sequencing.
Supplementary files format and content: the processed data files are jpg images of the CRISPResso2 software's detected allele edits for each sample
Library strategy: CRISPR Screen

source_name: Cell line

extract_protocol:
For RNA isolation, cultured NPCs and EVs from conditioned media were processed using the miRNeasy Micro Kit (Qiagen, #217084, Germantown, MD, USA). For the isolation of exRNA from conditioned media, as little as 500 mL from a confluent 48-well plate to 50 mLs from multiple T75 flasks can be used. Conditioned media should on the cells for 48 hours before isolation. Nanodrop was employed for RNA sample quantification, followed by reverse transcription using the Superscript IV VILO gDNA extraction from cultured hNPCs utilized the remaining sample post-removal of the aqueous layer during RNA isolation. The protocol, adapted with modifications from the TRIzolTM Reagent. Experimental protocol for DNA isolation involved the addition of 300 μL of 100% Isopropanol to the sample. After a 30-min incubation at RT, the sample underwent centrifugation for 5 min at 2000 x g at 4°C to pellet the DNA. The DNA pellet was resuspended in 1 mL of 0.1M Sodium Citrate in 10% ethanol and incubated for 30 min and then spun at 2000 x g for 5 min at 4°C. This step was repeated once. The pellet was then resuspended in 1 mL of 75% ethanol and incubated for 10-20 min. Following a 5-min centrifugation at 2000 x g at 4°C, the pellet was air-dried and resuspended in 8 mM NaOH. pH adjustments were made as needed with HEPES.
Isolated gDNA and cDNA were amplified for NGS analysis using appropriate primers. A portion of the PCR product was run on a gel to check for band size and appropriate amplification. PCR product was cleaned using the QIAquick PCR purification kit (Qiagen, #28106) and eluted in 35 μL of RNAase free water. Samples were sent for Next Generation sequencing (MGH CCIB DNA Core). After sequencing, the results were analyzed using CRISPResso2.

value: Cell line

value: hNPC


title: Mm_LT_Mx_rep2


title: 1 - WT CD  2

description: Library name: 1_-_WT_CD_2

value: WT


title: Wildtype_unedited_cellgDNA

description: Library name: Wildtype unedited cell gDNA


title: gRNA3_exRNA_BiolRep2

description: Library name: gRNA 3 exRNA Biol Rep 2

library_source: other

molecule: other


title: gRNA4_CellgDNA

description: Library name: gRNA 4 Cell gDNA


title: gRNA3_exRNA_BiolRep1

description: Library name: gRNA 3 exRNA Biol Rep 1


title: gRNA3_CellgDNA_BiolRep1

description: Library name: gRNA 3 Cell gDNA Biol Rep 1


title: Mm_LT_Flt3ITD_rep1


title: gRNA3_CellsgDNA_BiolRep2

description: Library name: gRNA 3 Cell gDNA Biol Rep 2


title: gRNA2_CellgDNA_BiolRep2

description: Library name: gRNA 2 cell gDNA Biol Rep 2


title: DYT1_unedited_CellcDNA

description: Library name: DYT1 Cells cDNA


title: gRNA2_CellgDNA_BiolRep1

description: Library name: gRNA 2 cell gDNA Biol Rep 1


title: DYT1_unedited_cellgDNA

description: Library name: DYT1 Cells gDNA


title: gRNA1_CellgDNA_BiolRep2

description: Library name: gRNA 1 cell gDNA Biol Rep 2


title: gRNA1_CellgDNA_BiolRep1

description: Library name: gRNA 1 cell gDNA Biol Rep 1


title: exRNA_noGFP_nucleofected

description: Library name: exRNA from no GFP sorted


title: DYT1_unedited_exRNA

description: Library name: DYT1 exRNA


title: gRNA2_exRNA

description: Library name: gRNA 2 exRNA


title: gRNA1_exRNA

description: Library name: gRNA 1 exRNA


title: Chr13_position_49516018_OffTarget

description: Library name: Off-target gene 6


title: Chr15_position_65426429_OffTarget

description: Library name: Off-target gene 7


title: Chr13_position_31818852_OffTarget

description: Library name: Off-target gene 5


title: Chr8_Position_29786010_OffTarget

description: Library name: Off-target gene 4


title: Chr5_position_92733460_OffTarget

description: Library name: Off-target gene 3


title: Chr5_position_9250094_OffTarget

description: Library name: Off-target gene 2


title: Chr5_position_150025_OffTarget

description: Library name: Off-target gene 1


title: Angel1 IP, rep 2

city: La Jolla

first: Timothy

middle: Luis Cabrera

last: Nicholson-Shaw

state: California

address: 9500 Gilman Dr.

department: Biological Sciences

institute: University of California San Diego

data_processing:
Raw reads were processed using the eCLIP pipeline.
Reads were then trimmed with cutadapt
Reads were then trimmed again with cutadapt to remove double-ligation events.
Trimmed and filtered reads were then mapped with STAR against a repeat element database
Unmapped reads filtered of repeat elements were then mapped with STAR   against a human genome (GRCh37)
Aligned reads were sorted with samtools
Sorted reads were collapsed with umi_tools.
BAM files were used to identify peak clusters with Clipper.
Peak clusters were normalized using BAM files for IP against BAM files for INPUT with overlap_peakfi_with_bam.pl, included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Filtered peak files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR to determine reproducible peaks.
Assembly: hg19
Supplementary files format and content: BigWig files contain RPM-normalized read densities

growth_protocol: HEK293 cells expressing FLAG-Angel1 were maintained in DMEM supplemented with 10% FBS.

extract_protocol: Cell pellets were flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP M2 FLAG antibody. Subsequent protocol was followed exactly as detailed in Blue et al 2021. Sequencing was performed on an Illumina MiSeq platform using single-end reads and data processed through Dr. Yeo's eCLIP pipeline. Libraries were constructed as per the eCLIP protocol using Illumina 50x forward and 70x reverse primers.

treatment_protocol: Cells were induced with 5ng/ml tetracycline 24 hours before harvest to induce FLAG-Angel1 expression. Cells were crosslinked(254 nm; 400 mJ/cm2) and processed through the eCLIP protocol as previously described (van Nostrand et al, 2016).

tag: sample type

value: Angel1 IP


title: Angel1 size matched input, rep 2

value: Angel1 size matched input


title: FLAG-only size matched input

value: FLAG-only size matched input


title: PAO1116 frame-shift deletion in the gacS, stationary growth phase, rep2

city: Norman

first: Justyna

middle: Weronika

last: Adamiak

state: OK

address: 101 Stephenson Parkway

department: Chemistry and Biochemistry

institute: University of Oklahoma

description: Library name: 14_S14

data_processing:
Raw data for each sample was analyzed using CLC Genomics Workbench version 12.0.1 software (QIAGEN Aarhus, Denmark), with default settings, based on their proprietary algorithms.
Assembly: Raw sequence reads were mapped to the Pseudomonas aeruginosa PAO1 genome (Accession# AE004091.2)
Supplementary files format and content: txt files with RPKM values for each sample
Supplementary files format and content: fastq raw data for each sample

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial cell

growth_protocol: Cells were grown in LB broth until mid-exponential phase (OD600 = 0.5-0.6) and stationary phase (OD600 = 2.0)

extract_protocol:
Total RNA was isolated from cells using hot phenol method. High quality total RNA was further processed by removing 23S and 16S rRNAs using the the Illumina Ribo-Zero Plus rRNA Depletion kit (Illumina, USA). Final concentrations and purity grades of the samples were determined using Bioanalyzer 2100 (Agilent, USA). Samples with the amount at least 0.5-1 µg were used for library construction and RNA sequencing.
Libraries of depleted RNA were prepared using the Illumina TruSeq RNA LT v2 kit according to the manufacturer's instructions. RNA libraries were prepared for sequencing using Illumina protocols

value: bacterial cell

value: PAO1116 delmexAB-oprM delmexCD-oprJ delmexEF-oprN delmexJKL delmexXY deltriABC gacS1570del

value: stationary phase


title: Angel1 size matched input, rep 1


title: FLAG-only IP

value: FLAG-only IP


title: PAO1 frame-shift deletion in the gacS, stationary growth phase, rep2

description: Library name: 12_S12

value: PAO1-89 gacS1570del


title: PAO1116 complemented mutant Plac-gacS, stationary growth phase, rep2

description: Library name: 16_S16

value: PAO1116 attTn7::mini-Tn7T-Gmr-LAC-gacS


title: PAO1116 frame-shift deletion in the gacS, stationary growth phase, rep1

description: Library name: 13_S13


title: PAO1 WT, stationary growth phase, rep2

description: Library name: 10_S10

value: Wild Type PAO1-96


title: PAO1 frame-shift deletion in the gacS, stationary growth phase, rep1

description: Library name: 11_S11


title: PAO1116 frame-shift deletion in the gacS, exponential growth phase, rep2

description: Library name: 6_S6

value: exponential phase


title: PAO1 frame-shift deletion in the gacS, exponential growth phase, rep2

description: Library name: 4_S4


title: PAO1116 complemented mutant Plac-gacS, stationary growth phase rep1

description: Library name: 15_S15


title: PAO1 WT, stationary growth phase, rep1

description: Library name: 9_S9


title: PAO1116 frame-shift deletion in the gacS, exponential growth phase, rep1

description: Library name: 5_S5


title: PAO1 frame-shift deletion in the gacS, exponential growth phase, rep1

description: Library name: 3_S3


title: PAO1 WT, exponential growth phase, rep1

description: Library name: 1_S1


title: PAO1 WT, exponential growth phase, rep2

description: Library name: 2_S2


title: A549 with LOC388942-ALK (LA) fusion and sgScr rep2

city: Chengdu

first: Donglin

last: Li

address: Sichuan University, 24 South Section 1, 1st Ring Road

institute: Sichuan University

description: Library name: RNAseq_A549_LAfusion_sgScr_rep2

data_processing:
Transcriptome sequencing was conducted using the Illumina NovaSeq 6000 platform with 150 bp paired-end sequencing. After removing the adapters, ploy-N, and low-quality reads, clean data were aligned against the reference human genome (hg19) using STAR_2.7.10b. Following this, raw counts were normalized and significance scores as well as log2-fold change values were calculated using the DESeq2 (v1.26.0).
Assembly: hg19
Supplementary files format and content: csv files include raw counts of RNAseq

growth_protocol: A545 cell were digested with typsin at 37 °C for 5min, then the remained cell was plated into a 6-well tissue culture plate and cultured at 37°C with 5% CO2 in RPMI medium1640 basic supplemented with 10% (vol/vol) fetal bovine serum (WISENT, Cat#086-150) and penicillin (100 U ml−1)/streptomycin (0.1 mg ml−1).

extract_protocol:
Total RNA extraction used TRIzol reagent (Applied Biosystems, Cat# 15596026) according to the instructions.
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

value: tumor cells

value: sgScr; sgLOC388942; sgALK


title: A549 with LOC388942-ALK (LA) fusion and sgScr rep1

description: Library name: RNAseq_A549_LAfusion_sgScr_rep1


title: A549 with LOC388942-ALK (LA) fusion and sgScr rep3

description: Library name: RNAseq_A549_LAfusion_sgScr_rep3


title: A549 with LOC388942-ALK (LA) fusion and sgFOS rep1

description: Library name: RNAseq_A549_LAfusion_sgFOS_rep1

value: sgFOS; sgLOC388942; sgALK


title: A549 with LOC388942-ALK (LA) fusion and sgFOS rep2

description: Library name: RNAseq_A549_LAfusion_sgFOS_rep2


title: A549 rep2

description: Library name: RNAseq_A549_rep2


title: A549 rep1

description: Library name: RNAseq_A549_rep1


title: A549 with LOC388942-ALK (LA) fusion rep2

description: Library name: RNAseq_A549_LAfusion_rep2

value: sgLOC388942; sgALK


title: Plasma -Z_Z11

city: TIANJIN

first: JIYU

last: SHI

address: Heping District,No.22 Qixiangtai Road

institute: Tianjin Medical University

data_processing:
Remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A; remove tags shorter than 18 nt.
After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2 .
Particularly, cmsearch was performed for Rfam mapping. The software miRDeep2  was used to predict novel miRNA by exploring the secondary structure, and Piano was used to predict piRNAs.
Genome_build: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include expression and read_count values for each Sample

source_name: Plasma

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to adenylated 3’ adapters annealed to unique molecular identifiers (UMI), followed by the ligation of 5’adapters. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 110~130 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, V alencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).

value: plasma

tag: bmi

tag: diagnosis

value: Acute Pancreatitis


title: PAO1116 complemented mutant Plac-gacS, exponential growth phase, rep2

description: Library name: 8_S8


title: Angel1 IP, rep 1

value: Angel1 IP


title: HCT8 cells, OE1

city: Guangzhou

first: Tanxing

last: Cai

state: Guangdong

address: 26 Erheng Road, Yuancun, Tianhe District

department: Department of General Surgery

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

description:
Library name: HCT8-OE-1
Column name in raw_counts_All_Samples.txt:HCT8-OE-1

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads.
The clean reads were then aligned to human genome (GRCh38_Ensembl104) using the Hisat2.
HTseq was used to get gene counts and RPKM method was used to determine the gene expression.
Assembly: GRCh38
Supplementary files format and content: XLSX file contain counts for each sample

growth_protocol: HCT8 cells were mainteined in DMEM supplemented with 10 fetal bovine serum(FBS) and antibodics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT8 cells transfected with control plasmid or KDM4A overexpression plasmid

value: colorectal cancer

value: HCT8 cells transfected with KDM4A overexpression plasmid

tag: batch


title: A549 with LOC388942-ALK (LA) fusion rep1

description: Library name: RNAseq_A549_LAfusion_rep1


title: Plasma -Z_Z04


title: HCT8 cells, Con2

description:
Library name: HCT8-CON-2
Column name in raw_counts_All_Samples.txt:HCT8-CON-2

value: WT

value: HCT8 cells transfected with control plasmid


title: Plasma -Z_Z03


title: HCT8 cells, OE2

description:
Library name: HCT8-OE-2
Column name in raw_counts_All_Samples.txt:HCT8-OE-2


title: HCT8 cells, Con1

description:
Library name: HCT8-CON-1
Column name in raw_counts_All_Samples.txt:HCT8-CON-1


title: Plasma -Z_N42


title: Plasma -Z_M04


title: HCT8 cells, Con3

description:
Library name: HCT8-CON-3
Column name in raw_counts_All_Samples.txt:HCT8-CON-3


title: HT29 cells, shFITM2_2

city: Nanjing

first: Lingyan

last: Xu

address: Guzhou Road

department: Department of Oncology and Cancer Rehabilitation Centre

institute: The First Affiliated Hospital of Nanjing Medical University

description: Library name: Sample 5

data_processing:
Hisat2 v2.0.5 was used as the mapping  tool for the reference genome.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: Hg19
Supplementary files format and content: tab-delimiyed text include gene counts for each sample

growth_protocol: HT29 colon cancer cells were cultivated in McCoy’s 5A supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 mg/ml) under a humidified 5% CO2 atmosphere at 37 ℃.

extract_protocol:
RNA was harvested using Trizol reagent (TaKaRa, Japan)  and  1.5 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: We knocked down FITM2 in HT29 human colon cancer cells.

value: colon cancer cells

value: FITM2 knockdown

value: untreated


title: Plasma -Z_Z04_3


title: HT29 cells, shCTRL_3

description: Library name: Sample 3


title: Plasma -S_S12


title: Plasma -S_S10


title: HT29 cells, shCTRL_2

description: Library name: Sample 2


title: HT29 cells, shCTRL_1

description: Library name: Sample 1


title: Plasma -Z_D01


title: Plasma -M_N33


title: HCT8 cells, OE3

description:
Library name: HCT8-OE-3
Column name in raw_counts_All_Samples.txt:HCT8-OE-3


title: Plasma -M_N130


title: HT29 cells, shFITM2_3

description: Library name: Sample 6


title: K_280L

city: torrance

first: Omid

last: Khorram

state: CA

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

description: Library name: Sample 38

data_processing:
FastQC was used to check quality of reads
Hisat2 and featureCounts was used to align and count reads.
DeSeq2 was used for differential expression analysis.
Assembly: hg18

source_name: Leiomyoma

extract_protocol:
TRIzol
Performed by Novogene Corporation Inc.
QiaSeq miRNA small RNA

value: Leiomyoma

value: Mutant

tag: race

value: Caucasian


title: Plasma -M_M13

tag: tissue


title: K_221L

description: Library name: Sample 36

value: African American


title: K_280M

description: Library name: Sample 37

source_name: Myometrium

value: Myometrium


title: Plasma -M_M01


title: K_214M

description: Library name: Sample 33


title: Plasma -S_N101


title: Plasma -M_M12


title: K_221M

description: Library name: Sample 35


title: Plasma -H_H04

value: HEALTH


title: Plasma -M_M15


title: K_214L

description: Library name: Sample 34


title: K_233L

description: Library name: Sample 32


title: Plasma -H_H03


title: Plasma -H_H01


title: K_263L

description: Library name: Sample 30


title: Plasma -H_A31


title: Plasma -H_A25


title: Plasma -H_A22


title: K_97L

description: Library name: Sample 28


title: K_97M

description: Library name: Sample 27


title: K_263M

description: Library name: Sample 29


title: K_121M

description: Library name: Sample 25


title: K_121L

description: Library name: Sample 26


title: K_233M

description: Library name: Sample 31


title: Ovary fresh, slice 1 & 2, 28 yo donor

city: HK

first: Kun

last: MA

state: Hong Kong

address: No 12 Kam Ling Court Whitty Street Sai Wan HK Island

country: Hong Kong

institute: The University of Hong Kong

description: Library name: A03390D2

data_processing:
We used STOmics Analysis Workflow (SAW), the official data processing pipeline to perform read quality control, genome mapping and gene expression quantification. Prior to genome mapping, we employed the ST_BarcodeMap module for filtering and mapping of chip identifiers (CID) from sequenced reads to their corresponding chip locations, and FastP for quality control and trimming of the reads. The reads were then mapped to the GRCh38 reference genome with STAR and counted for each spot with Bam2Gem.
Assembly: GRCh38
Supplementary files format and content: bin50.rds - bin50 spots of all samples with preprocessed meta data after preprocessing
Supplementary files format and content: fresh.gem.gz - SAW pipeline output gem file (fresh)
Supplementary files format and content: slow.gem.gz - SAW pipeline output gem file (slow)
Supplementary files format and content: vitri.gem.gz - SAW pipeline output gem file (vitri)
Library strategy: Stereo-seq

source_name: ovary

extract_protocol:
Human ovarian tissues were donated from one patient aged 35 years who underwent oophorectomy due to cervical cancer. The ovarian tissues were removed using scissors rather than electrocoagulation. Obtained ovarian tissues were directly placed in sterile transport medium (Leibovitz抯 L-15 Medium supplemented with 1% HSA) and transported on ice to the laboratory. In the laboratory, the ovarian tissues were transferred to 10 cm sterile dishes containing chilled sterile normal saline. The saline was changed several times during the process. After most of the medulla was removed with scalpels, the tissues were cut into 10?? mm pieces and divided into fresh and two cryopreservation groups. According to the Stereo-Seq protocol, one piece of fresh group tissues was fixed in O.C.T. compound (Tissue Tek) for subsequent sequencing, tissues of the two cryopreservation groups were processed after freezing and thawing. The tissue capture area was approximately 10? mm. 10?m tissue sections were cut using cryo-microtome (CM1950, Leica) with head temperature set at -16 癈 and adhered to the Stereo-seq chip (BGI) surface. The sections were then performed histomorphology detection, staining in hematoxylin for 3 min, 10 s in bluing agent, and 1 min in eosin. To release mRNA from the cells, the sections were permeabilized, the optimal time was 22 min. After in situ reverse transcription, the resulting cDNAs were amplified.
PCR products were purified for DNA nanoball (DNB) generation and finally sequenced on MGI DNBSEQ-Tx sequencer; detailed protocols are available on the BGI Stereo-seq website (https://en.stomics.tech/).

value: ovary

tag: treatment

value: slice 1:fresh; slice 2:fresh


title: Ovary slow-frozen and vitrified, slice 1 & 2, 28 yo donor

description: Library name: A03390D6

value: slice 1:slow-frozen; slice 2:vitrified


title: Ovary fresh, slice 1 & 2, 43 yo donor

description: Library name: A03494G3


title: K_90L

description: Library name: Sample 24


title: MNGIE-2

first: Jixiang

last: Du

state: Shandong

address: Wenhua Xi road

institute: Shandong university

data_processing:
DNBSEQ-T7 platform used for sequence
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence
using HISAT2 and StringTie to mapping reads to human genome and to reconstruct transcirpts
using bowtie2 and RSEM to mapping reads to gene and to calculate gene expression
Functional enrichment analyses including Gene Ontology (GO) and KEGG were performed to identify which DEGs were signifcantly enriched in GO terms or metabolic pathways
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Primary skin fibroblasts

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

extract_protocol:
Total RNA was extracted from cell sample tube using Trizol reagent according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard MGI protocols

value: Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE)

value: Primary skin fibroblasts

tag: cell type

value: fibroblasts


title: K_131M

description: Library name: Sample 21

value: WT


title: K_295L

description: Library name: Sample 20


title: K_131L

description: Library name: Sample 22


title: MELAS-3

value: Mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS)


title: K_90M

description: Library name: Sample 23


title: MELAS-2


title: K_295M

description: Library name: Sample 19


title: MELAS-1


title: MNGIE-1


title: K_259L

description: Library name: Sample 18


title: HC-3

value: healthy control


title: K_259M

description: Library name: Sample 17


title: HC-2


title: HC-1


title: K_8L

description: Library name: Sample 16


title: PAO1116 complemented mutant Plac-gacS, exponential growth phase rep1

description: Library name: 7_S7

value: bacterial cell

value: PAO1116 attTn7::mini-Tn7T-Gmr-LAC-gacS

value: exponential phase


title: Pancreas-Model-M59M_miRNA

data_processing:
Remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A; remove tags shorter than 18 nt.
After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2 .
Particularly, cmsearch was performed for Rfam mapping. The software miRDeep2  was used to predict novel miRNA by exploring the secondary structure, and Piano was used to predict piRNAs.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include expression and read_count values for each Sample

source_name: Pancreas

tag: weight

value: caerulein+LPS, saline

value: pancreas


title: K_289M

description: Library name: Sample 11

value: Caucasian


title: Pancreas-Control-C45M_miRNA

tag: strain

value: saline, saline


title: K_32M

description: Library name: Sample 13

value: Myometrium

tag: genotype


title: Pancreas-Model-M56M_miRNA


title: K_289L

description: Library name: Sample 12

value: Leiomyoma


title: HT29 cells, shFITM2_1

description: Library name: Sample 4

tag: cell line

value: colon cancer cells

value: FITM2 knockdown

value: untreated


title: Pancreas-Control-C44M_miRNA


title: K_276L

description: Library name: Sample 10

value: Mutant


title: Pancreas-Control-C43M_miRNA


title: K_228L

description: Library name: Sample 8

value: African American


title: Pancreas-QYD-Q68

data_processing:
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 ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2(v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM(v1.2.12).
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
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 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Pancreas

value: caerulein+LPS, QTD


title: K_276M

description: Library name: Sample 9

value: WT


title: K_314L

description: Library name: Sample 6


title: Pancreas-QYD-Q65


title: Pancreas-Model-M59M


title: K_32L

description: Library name: Sample 14


title: Pancreas-Model-M57M_miRNA


title: K_314M

description: Library name: Sample 5


title: K_8M

description: Library name: Sample 15


title: Pancreas-Model-M57M


title: Pancreas-Model-M56M


title: K_293M

description: Library name: Sample 3


title: Pancreas-Control-C45M


title: Pancreas-Control-C43M


title: K_293L

description: Library name: Sample 4


title: K_228M

description: Library name: Sample 7


title: Pancreas-Control-C44M


title: F2

city: Chongqing

first: Shan

last: Wang

address: No. 136 Zhongshan 2nd Road, Yuzhong District, Chongqing

institute: Children’s Hospital of Chongqing Medical University

description: Library name: F2

data_processing: Raw reads were processed with fastQC and fastp to remove low-quality reads. Unique molecular identiﬁers  (UMI) and cell  barcodes  were  extracted  after  ﬁltering  out  reads without  poly-A  tails.  Poly-A  tails  and  adapter  sequences were then trimmed by cutadapt, and the reads that met quality control standards were matched to the reference genome  GRCh38   (ensembl  version  92  annotation)   using STAR. Gene counts and UMI counts were grouped by fea- tureCounts software to generate expression matrix ﬁles for downstream analyses.

source_name: Neuroblastoma liver metastasis(family)

extract_protocol:
Fresh tumor samples were transported expeditiously to the Singleron lab. The tumor tissues were washed three times with Hanks Balanced Salt Solution (HBSS), cut into 1e2 mm pieces, and digested in 2 ml GEXSCOPE® Tissue Dissociation Solution (Singleron) at 37 。C for 15 min with constant but gentle agitation. The digested samples were ﬁltered using 40-micron  sterile  strainers  and  centrifuged  at  800×g for 5   min.  The   pellets  were   then   resuspended   in   1   ml phosphate-buffered saline  (PBS;  HyClone, United States), and 2 ml GEXSCOPE® red blood cell lysis buffer (Singleron) was added at 25 。C for  10 min to  remove the  red blood cells. The tumor cell-containing solution was centrifuged at 500×g for 5 min, and the cells were resuspended in PBS. The samples were stained with trypan blue (Sigma, United States) to verify cell viability.
Single-cell suspensions with 1  × 105  cells/mL in  PBS were prepared. Then, the suspensions were loaded onto micro- ﬂuidic devices, and scRNA-seq libraries were constructed according  to  the  Singleron  GEXSCOPEⅢ  protocol  in  the GEXSCOPEⅢ  Single-Cell  RNA  Library  Kit  (Singleron  Bio- technologies).21   Individual  libraries were diluted to 4  nM and  pooled for sequencing.  Pools were sequenced on an Illumina HiSeq X with 150 bp paired-end reads.

value: Neuroblastoma liver metastasis

tag: Sex

value: female


title: F1

description: Library name: F1

source_name: neurablastoma(family)

value: neurablastoma


title: K_296L

description: Library name: Sample 2


title: 2 hours after training, N.S. treatment, PL PFC, sample 3

city: Wuhan

first: Feiyang

last: Zhang

state: Hubei

address: Bayi Road #299

institute: 武汉大学

description: Library name: 2H-nsPL3

data_processing:
Illumina high-throughput sequencing data was dealt with bcl2fastq and converted into sequenced reads (raw reads). Fastq files were filted by TrimGalore(https://github.com/FelixKrueger/TrimGalore) with the criteria of phred quality score of 30 and minimum length of 25. Hisat2 [ref] were used to mapping fastq files to mouse genome. Index for mapping were downloaded from the official website of Hisat2. We used samtools (version:1.8) (http://www.htslib.org/) to convert sam files to bam files along with sorting, which was dealt with FeatureCounts to create gene expression matrix with parameters “-t exon -g gene_id”.
Assembly: mm39
Supplementary files format and content: csv file. Raw count of fragments with column names correspondent to the library names.

growth_protocol: Male C57BL/6 mice (10–12 weeks old) were housed four per cage, maintained on a 12 h light/dark time schedule and allowed free access to food and water. Efforts were made to minimize the number of animals used. The mice were allowed one week to acclimatize the laboratory environment before the experiment.

extract_protocol:
Tissue derived from PLPFC of fear conditioning trained mice was homogenized using a Dounce tissue grinder in 500 μL of cold 1X PBS (Servicebio, China).
100 μL of homogenate was used for RNA extraction. RNA was extracted using Trizol (Invitrogen). Both extraction protocols were followed according to the manufacturer’s instructions. The concentration of RNA was measured by Qubit assay (Invitrogen).

treatment_protocol: Two contexts (A and B) were used for all behavioral testing as described previous study. Both conditioning chambers (AniLab Scientific Instruments Co., Ltd., China) had a metal grid floor (3.2 mm in diameter, 8 mm center). However, the floors in context B were covered with a flat white plastic nontransparent surface with two white LED lights used to minimize context generalization. Individual digital cameras were mounted on the ceiling of each chamber and automated scoring of freezing behavior (FreezeFrame). Fear conditioning was performed in context A with spray of lemon (10% lemon essence extract and 10% ethanol) using a 120 s pre-fear conditioning period, followed by three pairings of a 120 s, 80dB, 16kHZ pure tone conditioned stimulus (CS) co-terminating with a 1 s (2 min intervals), 0.7 mA foot shock (US). Mice that did not reach 50% freezing behavior during the last conditioned stimulus were excluded. For extinction (EXT), conducted in context B with a stimulus light on and spray of vinegar (10% vinegar extract and 10% ethanol), mice were placed in a transparent cylinder that did not restrict their movement. The mice were first acclimated for 2 min. Extinction training then comprised 30 non-reinforced 120 s CS presentations (at 5-s intervals). For the retention test, all mice were returned to context B and following a 2 min acclimation (used to minimize context generalization), freezing was assessed during three 120 s CS presentations (120 s intertrial interval). Memory was calculated as the percentage of time spent freezing during the test. Animals that had off-target injections or ineffective gene knockdowns were excluded from the study.1 ml of dexmedetomidine hydrochloride injection (Jiangsu Hengrui Pharmaceuticals Co., Ltd.) was diluted with normal saline (0.9% NaCl) to a total volume of 25 ml, resulting in a final concentration of 4 μg ml-1. The mice were given an intraperitoneally injection at a dose of 40μg Kg-1（10ml Kg-1）, while an equal volume of normal saline was given in the control group. Drug administration was performed immediately after FC in the mice.

value: Brain

value: Brain Cells

value: male


title: Pancreas-QYD-Q66


title: 2 hours after training, N.S. treatment, PL PFC, sample 2

description: Library name: 2H-nsPL2


title: K_296M

description: Library name: Sample 1

value: Caucasian


title: A45

description: Library name: A45

source_name: adrenal gland

value: adrenal gland


title: 2 hours after training, N.S. treatment, PL PFC, sample 1

description: Library name: 2H-nsPL1


title: 2 hours after training, N.S. treatment, IL PFC, sample 3

description: Library name: 2H-nsIL3


title: A41

description: Library name: A41


title: 2 hours after training, Dex. treatment, PL PFC, sample 3

description: Library name: 2H-dexPL3

value: Dex.


title: 2 hours after training, N.S. treatment, IL PFC, sample 1

description: Library name: 2H-nsIL1


title: A44

description: Library name: A44


title: 2 hours after training, Dex. treatment, PL PFC, sample 2

description: Library name: 2H-dexPL2


title: A32

description: Library name: A32

source_name: Ganglioneuroma

value: Ganglioneuroma


title: 2 hours after training, Dex. treatment, PL PFC, sample 1

description: Library name: 2H-dexPL1


title: S1

description: Library name: S1

source_name: ganglioneuroblastoma

value: ganglioneuroblastoma


title: 2 hours after training, N.S. treatment, IL PFC, sample 2

description: Library name: 2H-nsIL2


title: 2 hours after training, Dex. treatment, IL PFC, sample 3

description: Library name: 2H-dexIL3


title: A49

description: Library name: A49


title: A48

description: Library name: A48


title: A12

description: Library name: A12


title: 2 hours after training, Dex. treatment, IL PFC, sample 2

description: Library name: 2H-dexIL2


title: A53

description: Library name: A53

source_name: neurablastoma


title: 2 hours after training, Dex. treatment, IL PFC, sample 1

description: Library name: 2H-dexIL1


title: A51

description: Library name: A51


title: A8

description: Library name: A8


title: B16, sgNcor1-2-rep1

city: Beijing

first: Xuejiao

last: Ren

address: Beijing

institute: Nanjing Medical university

description: Library name: Sample 16

data_processing:
The quality of raw sequencing reads was evaluated using FastQC (v0.12.1).
Adaptor sequences and low-quality score bases were trimmed using TrimGalore (v.0.6.7).
These reads were then aligned to the mm10 reference mouse genomes using Bowtie2 (v.2.2.5).
The fragments per kilobase of exon per million mapped reads (FPKM) and gene counts were computed using RSEM (v.1.2.8).
Assembly: mm10
Supplementary files format and content: xls files include count values for all Sample

extract_protocol:
RNA was extracted from mouse Hepa1-6 and B16 cell lines using the Quick-RNA column purification kit (Zymo, USA).
RNA-seq libraries were constructed using the VAHTS mRNA-seq v2 Library Prep Kit (Illumina, USA) according to the manufacturer’s protocol. The libraries were sequenced using Novaseq 6000 (Illumina, USA) at Bioguoke Corporation (Beijing, China).

value: B16 (Mouse Melanoma)

value: Ncor1 knockout


title: B16, sgNcor1-1-rep3

description: Library name: Sample 15


title: A50

description: Library name: A50


title: A24

description: Library name: A24


title: B16, sgNcor1-2-rep2

description: Library name: Sample 17


title: A52

description: Library name: A52


title: B16, sgNcor1-1-rep1

description: Library name: Sample 13


title: B16, sgNcor1-2-rep3

description: Library name: Sample 18


title: B16, sgCtrl-rep2

description: Library name: Sample 11


title: A5

description: Library name: A5


title: A16

description: Library name: A16


title: B16, sgCtrl-rep1

description: Library name: Sample 10


title: Hepa1-6, sgNcor1-2-rep3

description: Library name: Sample 9

value: Hepa1-6 (Mouse Liver Cancer)


title: LYG1206-2

description: Library name: LYG1206-2


title: B16, sgNcor1-1-rep2

description: Library name: Sample 14


title: OE6

first: James

last: Pittaway

address: Charterhouse Square

department: Centre for Endocrinology

country: United Kingdom

institute: Queen Mary University of London

description: Library name: Sample 12

data_processing:
Primary bioinformatic analysis was completed using the DNAnexus platform. FastQC Reads Quality Control version 3.0.1 was used for quality control on reads data. HISAT2 version 1.03 was used for read alignment, subread_featureCounts  version v1.5.2 and DESeq2 (R.3.2) for differential gene expression analysis.
Assembly: GRCh38
Supplementary files format and content: featurecounts.xlsx

extract_protocol:
RNA was extracted from H295R grown when 70% confluent using Rneasy spin columns according to the manufacturer’s instructions (Qiagen).
Strand specific cDNA library, genome sequencer Illumina Hiseq, Novaseq 6000 S4 model. PE 150 XP

value: Adrenocortical carcinoma

value: OE


title: A21

description: Library name: A21


title: OE5

description: Library name: Sample 11


title: OE4

description: Library name: Sample 10


title: A17

description: Library name: A17


title: Hepa1-6, sgNcor1-2-rep1

description: Library name: Sample 7


title: KD6

description: Library name: Sample 8

value: KD


title: B16, sgCtrl-rep3

description: Library name: Sample 12

value: WT


title: Hepa1-6, sgNcor1-2-rep2

description: Library name: Sample 8


title: KD5

description: Library name: Sample 7


title: OE3

description: Library name: Sample 9


title: Hepa1-6, sgCtrl-rep2

description: Library name: Sample 2


title: KD3

description: Library name: Sample 5


title: MNGIE-3

tag: disease state

value: Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE)

value: Primary skin fibroblasts

value: fibroblasts


title: WT6

description: Library name: Sample 4


title: Hepa1-6, sgCtrl-rep1

description: Library name: Sample 1


title: ChATBKO (mb1Cre+/-Chatfl/fl) 24h post-infection

city: Baltimore

first: Antonio

last: Cembellin-Prieto

address: 1742 Fleet St, Apt. 102

institute: Johns Hopkins University

description:
Library name: S7
10X GENOMICS

data_processing:
For single cell analysis, automatically called cells were further filtered to ensure usage of high-quality droplets with captured cells. RNA barcodes were filtered on Total UMI Count ( > 500 UMIs), feature count ( > 250 features), and percentage of mitochondrial genes ( < 25%).  Signac v1.9.0129 was used to determine nucleosome signaling and transcription start site enrichment scores. ATAC barcodes were filtered on number of fragments mapping to peak regions ( > 3,000 and < 20,000), percentage of fragments mapping to peak regions ( > 15%), nucleosome signal scores ( < 4) and transcription start site scores (> 1).
Assembly: Mus musculus mm10 C57BL/6J
Supplementary files format and content: raw counts given

source_name: Lung homogenate

extract_protocol:
lungs were harvested after left ventricle perfusion of the heart and then mechanically and chemically digested. The lungs were placed in 3 mL of DMEM F12 1X with 10% NCS in gentleMACS™ M Tubes (Milenty, # 130-093-236) and processed using a gentleMACS dissociator m_Lung_02 twice (Milteny). Following this, the lungs were incubated with DNAse I (50 U/mL) (Worthington-Biochem # LS002139) and Collagenase, Type I (250 U/mL) (Worthington-Biochem # LS004196) for 25 minutes at 37°C at 220 rpm shaking. After incubation, the lungs underwent another round of processing using the m_lung_02 program. The resulting cells were passed through a 50 μm nylon filter and diluted for staining and sorting. Prior to sorting, 0.5uL of Propidium Iodide (PI) was addeed to disitinguish between live and dead cells and live cells were immediately submitted for sequencing.
Barcoded 3’ single cell libraries were prepared from single cell suspensions using the Chromium Next GEM Single Cell 3’ kit v3.1(10X Genomics, Pleasanton, California) for sequencing according to the recommendations of the manufacturer.  The cDNA and library fragment size distribution were verified on a Bioanalyzer 2100 (Agilent, Santa Clara, CA). The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies, Carlsbad, CA) and by qPCR with a Kapa Library Quant kit (Kapa Biosystems-Roche) prior to sequencing. The libraries were sequenced on a NovaSeq 6000 sequencer (Illumina, San Diego, CA) with paired-end 100 bp reads.

treatment_protocol: Intranasal influenza infection

value: Lung homogenate

value: Primary mouse lung cells

value: 24h after intranasal infection with influenza A/Puerto Rico 8/34 infected

value: Batch 1


title: Hepa1-6, sgNcor1-1-rep1

description: Library name: Sample 4


title: Hepa1-6, sgNcor1-1-rep3

description: Library name: Sample 6


title: Hepa1-6, sgCtrl-rep3

description: Library name: Sample 3


title: Hepa1-6, sgNcor1-1-rep2

description: Library name: Sample 5


title: A22

description: Library name: A22

value: neurablastoma

value: male


title: KD4

city: London

description: Library name: Sample 6


title: WT5

description: Library name: Sample 3


title: WT3

description: Library name: Sample 1


title: ChATBKO (mb1Cre+/-Chatfl/fl) non-infected

description:
Library name: S3
10X GENOMICS

value: No treatment


title: WT (mb1Cre-/-Chatfl/fl) 24h post-infection

description:
Library name: S5
10X GENOMICS


title: WT4

description: Library name: Sample 2


title: WT (mb1Cre-/-Chatfl/fl) non-infected

description:
Library name: S1
10X GENOMICS


title: hCOs, Normoxia-48h

city: shanghai

first: quanlong

last: jiang

institute: PICB

description: Library name: Normoxia-48h

data_processing:
Raw sequencing reads were evaluated using quality metrics and analyzed with Cell Ranger software (v3.1.0). Cells deemed low quality—characterized by fewer than 200 unique detected genes, fewer than 500 UMIs, or mitochondrial content exceeding 15%—were filtered out. Additionally, genes expressed in fewer than 100 cells were removed. Subsequently, the UMIs were normalized and logarithmically transformed.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hCOs

extract_protocol:
Hypoxic and normoxic hCOs were collected and dissociated into single-cell suspensions using papain (Sigma, 9001-73-4), resulting in a concentration of 2 × 10⁵ cells/mL in ice-cold D-PBS.
Single cells were barcoded, and mRNA was captured using the GEXSCOPE Single Cell RNA Library Kit (Singleron Biotechnologies, Nanjing, China), followed by cDNA library generation for scRNA-seq. The individual libraries were then diluted to 4 ng/mL and pooled for sequencing on a NovaSeq 6000 platform (Illumina, San Diego, CA, USA) with 150-bp paired-end reads.

value: hCOs


title: C.aero group

city: Wenzhou

first: Chenghao

state: Zhejiang

address: Wenzhou Medical University, Xueyuan Xi Road

institute: Wenzhou Medical University

description: Library name: 2406101_G1_3_Case

data_processing:
Raw data were processed with the seeksoultools (v1.2.2)
Assembly: mm10
Supplementary files format and content: Matrix file (mtx) includes sparse matrix of read counts, unique cell barcode files (tsv), and feature file (tsv)

source_name: Liver

extract_protocol:
The nuclei from mouse liver tissues were isolated using the Nucleus Isolation Kit (SHBIO, 52009-10) according to the manufacturer’s instructions. Nucleus count and viability was assessed using Fluorescence Cell Analyzer (Countstar Rigel S2) or SeekMate Tinitan Fluorescence Cell Counter (SeekGene M002C) with AO/PI reagent. After staining with 0.4% trypan blue (Sangon Biotech, E607320-0001), the nuclei were observed under a 40X microscope (Jiangnan Novel Optics, XD-202). Subsequent experiments were conducted if the nuclear envelope was intact, and their impurities were minimal.
Single Nuclei RNA (snRNA-seq) libraries were prepared using SeekOne Digital Droplet Single Cell 3' library preparation kit (SeekGene, Catalog No. K00202).

value: Liver

value: C.aero treated


title: control group

description: Library name: 2406101_G1_1_Control

value: blank control