title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to B. pertussis-R (2)

description:
Library name: DICE-TCR_012_Hu_1_15D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the B. pertussis-R peptide megapool (MP)

value: B. pertussis-R-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to B. pertussis-aP (2)

status: Public on Jun 07 2026

type: SRA

city: La Jolla

first: Pandurangan

last: Vijayanand

state: CA

address: 9420 Athena Cir

country: USA

institute: La Jolla Institute for Immunology

description:
Library name: DICE-TCR_012_Hu_2_15D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the B. pertussis-aP peptide megapool (MP)

library_source: transcriptomic single cell

data_processing:
Processing of scRNA-seq libraries: Sequencing reads from single-cell (sc)RNA-seq data were demultiplexed using Cell Ranger (v7.1.0, 10x Genomics) with the mkfastq module and aligned to the GRCh38 reference genome (pre-built reference “2020-A”) with the count module. This generated UMI-collapsed gene expression matrices for 46 single-cell libraries. Independent gene expression libraries were aggregated into combined datasets using the aggr module, yielding a dataset of lung CD3⁺ T cells from 40 donors and a dataset of lung-draining LN CD3⁺ T cells from 8 donors. Aggregated datasets were processed in R (v3.6.1) using Seurat (v3.2.3; Stuart et al., Cell, 2019). Genes expressed in fewer than 0.1% of cells were excluded. To minimize doublets and eliminate low-quality transcriptomes while still allowing for variability in the distribution of UMI and gene counts, we excluded cells that did not meet the following lenient criteria: 500≤ UMI count ≤10,000; 400≤ gene count ≤3,000; and mitochondrial UMI percentage ≤15%. Data normalization was performed using NormalizeData with default parameters. Highly variable genes (HVGs) were identified with the FindVariableFeatures function using the vst method and default settings; selection was restricted to genes with a mean expression >0.01 and contributing 30% of the standardized variance. Gene-wise scaling was performed using ScaleData, with regression of total UMI counts and mitochondrial UMI percentages (vars.to.regress argument), while retaining default settings for other arguments. Dimensionality reduction was performed via principal component analysis (PCA), followed by UMAP embedding using RunUMAP with the top 40 PCs, 15 neighbors (n.neighbors = 15), and a minimum distance of 0.1 (min.dist = 0.1). Unsupervised clustering was conducted with FindNeighbors and FindClusters, with a defined resolution and 30 PCs specified per iteration and all other parameters left unchanged. For the last iteration, 0.2 and 0.3 were chosen as the resolution values for lung and LN T cells, respectively, and irrespective of lineage. Lineage-specific subsets of CD4⁺ and CD8⁺ T cells were defined through iterative rounds of clustering and phenotype-guided filtering. In each round, contaminant clusters were reassigned to the appropriate lineage-specific dataset for further refinement. A total of 16 and 10 rounds of deconvolution were performed for lung and LN T cells, respectively, at which point no lineage contaminating clusters could be discerned.
Processing of hashtag oligonucleotide (HTO)-seq libraries: In the study cohort, hashtag barcoding was used in a subset of libraries to pool cells from multiple donors prior to sequencing. Specifically, 5 coupled scRNA-seq and scTCR-seq libraries included pooled samples and required demultiplexing during analysis. In the resource cohort, all scTCR-seq libraries consisted of pooled, hashtag-barcoded samples that were also demultiplexed during analysis. Reads from hashtag oligonucleotide (HTO) feature barcoding were demultiplexed using Cell Ranger mkfastq (v7.1.0, 10x Genomics) and processed with the count module adapted for feature barcoding (v7.1.0). For each library, cell calling was performed, and barcodes were demultiplexed into separate samples and donor identities with Seurat’s MULTIseqDemux function (v3.2.3; McGinnis et al., Nat. Methods, 2019), as detailed previously (Meckiff et al., Cell, 2020; Kusnadi et al., Science Immunol., 2021). Barcodes classified as doublets were removed from downstream analyses at the initial round of clustering.
Processing of single-cell T-cell receptor (TCR)-seq libraries: Reads from single-cell TCR sequencing (scTCR-seq) data were processed using cellranger vdj (v7.1.0) with the pre-built GCRh38 reference (“vdj-GRCh38-alts-ensembl-7.1.0”) and aggregated following previously described workflows (Meckiff et al., Cell, 2020; Kusnadi et al., Science Immunol., 2021). For the study cohort, one aggregated dataset was generated for lung CD3+ T cells (n=40 libraries, one per donor) and another for lung-draining LN CD3+ T cells (n=6 libraries spanning 8 donors). For the resource cohort, 45 libraries derived from putative pathogen-specific CD4+ T cells were aggregated into a single TCR dataset. For this type of data (single-cell resolution), a clonotype was defined as a unique set of CDR3 α and β sequences and the V and J gene segments encompassing each of them.
Clonotype group-bias assignment problem: Given a clonotype observed across n groups (n>1), let f_g denote its absolute frequency in group g, and let r_g denote its relative frequency in that group, computed as f_g normalized by the total clonotype counts within group g. The task is to classify each clonotype as either biased toward a particular group or unbiased across groups. Proposed solution: First, sort all groups by the clonotype’s relative frequency r_g, identifying the top-ranked group (g_1) and the second-ranked group (g_2). Compute the bias ratio as: bias_ratio=r_(g_1 )/r_(g_2 ) . A clonotype is then assigned as biased to group g_1 if and only if: (i) f_(g_1 )>2 and (ii) bias_ratio>2.
Assignment of uniquely defined antigen specificities to TCR clonotypes: In this study, the ARTE assay was employed to capture antigen-specific T cells, with concomitant TCR repertoires profiled at single-cell resolution. These data have : (i) a readout consisting of CDR3 sequences and the V and J gene segments that encompass them; (ii) clonotypes with an absolute frequency of 1 unit—with cell barcodes as units, referred to as singletons—represented a substantial proportion across the board; (iii) a division of expanded (non-singleton) clonotypes into two classes with regard to antigen specificity—those that were detected with a single peptide MP (unambiguous) and those that were detected with multiple peptide MPs (ambiguous); and (iv) for ambiguous clonotypes, when their associated peptide MPs were ranked by relative frequency and the ratio of the top-to-the-second-highest ranked MP was calculated (reminiscent of the bias_ratio), the resulting distributions were highly similar between assays and data types. Unambiguous clonotypes were directly deemed specific to the antigen corresponding to the peptide MP with which they were detected. In contrast, the assignment of unique specificities to ambiguous clonotypes can be framed as an instance of the clonotype group-bias assignment problem described above. The proposed solution was implemented as a common framework, such that an ambiguous clonotype was defined as specific to antigen g_1 when (i) f_(g_1 )>2, where f_(g_1 ) denotes its absolute frequency for that antigen and (ii) bias_ratio>2.
Assembly: GRCh38 (2020-A reference prebuilt and provided by 10x cellranger).
Supplementary files format and content: This submission includes seurat objects (v3.2.3; Stuart et al., Cell, 2019) created as described above for the sets of CD4+ (HIPC-1_LG-CD4-ALL_SeuratObject.RDS) and CD8+ (HIPC-1_LG-CD8-ALL_SeuratObject.RDS) lung T cells and the sets of CD4+ (HIPC-1_LN-CD4-ALL_SeuratObject.RDS) and CD8+ (HIPC-1_LN-CD8-ALL_SeuratObject.RDS) lung-draining LN T cells.
Supplementary files format and content: TCR clonotype metadata including CDR3 sequences and V and J gene usage, as well as antigen specificity-associated metrics, are provided in file: DICE-TCR_BL-CD4-ALL_ProcessedObject.csv

molecule: total RNA

organism: Homo sapiens

source_name: Blood

growth_protocol: Study cohort samples: A total of 40 individuals undergoing standard-of-care surgical resection for primary lung non-small cell lung cancer (NSCLC) at Liverpool Heart and Chest NHS Foundation Trust Hospital were enrolled. The cohort included 16 men and 24 women, all of White British ethnicity, with a median age of 70 years (range: 61–83). Background lung tissue, along with matched peripheral blood and LLNs, was collected intraoperatively. Background lung samples were obtained from macroscopically uninvolved, non-tumor-bearing regions of the parenchyma, typically distant from the primary tumor. All samples were de-identified and cryopreserved in freezing medium (90% fetal bovine serum (FBS) and 10% DMSO) prior to downstream processing. Reference cohort samples: Peripheral blood mononuclear cells (PBMCs) were obtained from a total of 61 healthy donors through the San Diego Blood Bank (SDBB) between December 2021 and February 2022. Each donor provided approximately 8 mL of LRS-WBC (Leukoreduction System - Whole Blood Collection) material. Donor ages ranged from 27 to 79 years (median of 65). Of the 61 donors, 47 were male, 12 were female, and 2 had unspecified sex information. No clinical or immunological abnormalities were reported for these donors at the time of collection. PBMCs were isolated and cryopreserved according to standard protocols for downstream immunological assays.

extract_protocol:
Single-cell (sc)RNA-seq library preparation was performed alongside TCR repertoire immune profiling (scTCR-seq) and cell surface protein technology to enable hashtag oligonucleotide (HTO) -based sample demultiplexing. Up to 100,000 CD3⁺ T cells from each of 40 lung samples, up to 100,000 CD3+ T cells of 8 LLN samples—from a single- or 2-donor pools—, and up to 120,000 circulating,  pathogen-specific CD4+ T cells—from up to 16 pooled donors—were processed using the 10x Genomics Chromium Next GEM Single Cell 5′ HT Reagent Kit v2 (Dual Index), following the manufacturer’s instructions.
Initial amplification of cDNA (concomitantly, for gene expression library preparation) was carried out with 13 cycles of amplification; scTCR and HTO libraries were both generated with 8 cycles of amplification. All libraries were quantified and pooled according to equivalent molar concentrations. Libraries from lung CD3+ T cells and circulating, pathogen-specific CD4+ T cells were sequenced on an Illumina NovaSeq6000 sequencing instrument (read 1 and read 2 – 100 cycles; i5 and i7 index - 10 cycles). Libraries from LLN CD3+ T cells were sequenced on an Illumina NovaSeq X instrument (150 x 150 cycle paired-end configuration with index reads ).

treatment_protocol: Study cohort samples: Human lung tissue and LLN samples were thawed in a 37°C water bath for ~5 minutes until only a small ice fragment remained, followed by washing with FBS and dilution in MACS buffer to reduce DMSO concentration. The thawed tissue suspension was filtered through a 70 µm strainer, with retained tissue pieces collected and finely diced using a scalpel (this step only in case of lung tissue). The minced tissue was transferred to a gentleMACS C tube (Miltenyi Biotec,130-096-334) and supplemented with RPMI, after which enzymatic digestion was initiated by adding DNase I (Sigma, D4527-200K) and Liberase (Sigma, 5401127001). The sample underwent mechanical and enzymatic dissociation using an OctoDissociator (Miltenyi Biotec) set at 37°C for 15 minutes. Following dissociation, the cell suspension was filtered through a MACS SmartStrainer, gently pressing residual tissue to maximize cell yield. The resulting cell suspension was centrifuged, and the pellet resuspended in MACS buffer containing FcR Blocking Reagent, followed by the addition of Cell-hashtag TotalSeq-C antibody (1 μg/condition) to enable hashtag oligonucleotide (HTO)-based sample deconvolution at the analysis stage. Cells were then stained with a panel of antibodies optimized to sort for CD3+ T cells while incubating at 4°C. After washing, the cells were underlaid with FBS and centrifuged again. The final cell pellet was resuspended in cold MACS buffer supplemented with DAPI for viability staining and sorted for CD3+ T cells on a FACSAria Fusion Cell Sorter (Becton Dickinson). Resource cohort samples: The enrichment and FACS sort of pathogen-specific CD4+ memory T cells from the PBMC samples of the resource cohort (n=61 donors) was performed using a modified protocol based on Bacher et al., J Immunol., 2016. PBMCs from donors were thawed, washed, and cultured overnight (5% CO2, 37 °C) in serum-free TexMACS medium at a concentration of 10 × 10^6 cells/mL. The cells were then stimulated with pathogen peptide MPs (1ug/ml) for 6 hours, with a CD40 blocking antibody (1 μg/mL; Miltenyi Biotec) present. To enrich CD154+ cells, a series of staining steps were carried out, including surface antibodies, Cell-hashtag TotalSeq-C antibody (1ug/condition), and a biotin-conjugated CD154 antibody, followed by anti-biotin microbeads. The labeled cells underwent positive selection using MS columns, with the CD154+ cells being eluted for subsequent FACS sorting. The enriched populations were immediately sorted using a FACSAria Fusion Cell Sorter (Becton Dickinson) based on dual expression of CD154 and CD69.

tag: tissue

value: Blood

tag: cell type

value: B. pertussis-aP-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+

tag: treatment

value: Antigen-reactive T cell enrichment (ARTE) assay


title: Vigna radiata T2 0h WGBS rep1

city: Jinan

first: Zhi-Wei

last: Wang

address: No. 23788, Industrial North Road, Licheng District

country: China

institute: Shandong Academy of Agricultural Sciences

description:
Library name: Meth_T2H0_rep1
WGBS of T2 H0 leaf

library_source: genomic

data_processing:
Raw reads were trimmed using fastp (v1.0.1). Clean reads were aligned to the Vigna radiata reference genome using Bismark (v0.25.1, --non_directional). PCR duplicates were removed with samtools (v1.22.1), retaining uniquely mapped reads with ≥ 4× coverage. Cytosine methylation ratios (CpG/CHG/CHH) were calculated using BatMeth2 with sliding-window analysis for DMR detection. Differential methylation analysis was performed using methylKit (v1.34.0), defining DMRs as |Δmeth| ≥ 20% and FDR < 0.05. Methylation levels were integrated with RNA-seq expression profiles by stratifying genes into expression quantiles. Genome-wide methylation landscapes and gene-centric profiles were visualized in R (v4.4.3) using ggplot2 and pheatmap.
Assembly: Vigna radiata (Weilv 9) reference genome
Supplementary files format and content: Methylation_methylation_matrix.txt

molecule: genomic DNA

organism: Vigna radiata

source_name: Leaf

growth_protocol: Mung bean (Vigna radiata cv. Weilv 9) seeds were surface‑sterilized and germinated on moist filter paper for 2 days. Uniform seedlings were transferred to seedling trays and grown for 3 days, then moved to hydroponic containers containing half‑strength Murashige and Skoog (1/2 MS) nutrient solution. Plants were cultivated under controlled conditions: 25°C, 12,000 lux light intensity, 16 h light/8 h dark photoperiod, and 70% relative humidity.

extract_protocol:
Genomic DNA was extracted from frozen leaf tissues using the DNeasy Plant Maxi Kit (Qiagen, USA) following the manufacturer’s protocol. DNA integrity and concentration were assessed using a NanoDrop spectrophotometer and agarose gel electrophoresis. Only samples with A260/280 ratios between 1.8 and 2.0 and high‑molecular‑weight bands were used for library construction.
Whole‑genome bisulfite sequencing (WGBS) libraries were prepared using the TruSeq DNA Methylation Kit (Illumina, USA). Libraries were sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired‑end reads. Library quality and insert size distribution were confirmed using a Bioanalyzer.

treatment_protocol: Two experimental treatments were applied. T1: seedlings were exposed to 100 mM NaCl for 24 h, followed by 48 h recovery in NaCl‑free 1/2 MS solution, then subjected to a second 100 mM NaCl treatment. T2: seedlings were directly exposed to 100 mM NaCl without preconditioning. The first fully expanded true leaves were harvested at 0, 6, and 48 h after the onset of the final salt treatment.

value: Leaf

tag: genotype

value: Weilv 9

value: Direct salt stress


title: nonSMA38

city: Albuquerque

first: Douglas

middle: Jay

last: Perkins

state: NM

address: MSC10 5550, 1 University of New Mexico

department: Center for Global Health

institute: University of New Mexico

description: Library name: s91b

library_source: transcriptomic

data_processing:
Raw data were quality-controlled and filtered using fastp
Sequences were aligned to the Plasmodium falciparum Kenya isolate pfKE01 reference genome using Bowtie 2.
HTSeq v0.6.1 was used to generate read counts mapped to each gene.
Differential expression analysis of the two clinical conditions (non-SMA vs SMA) was performed using EdgeR (3.16.5) package, utilizing a negative binomial (NB) based statistical model
Assembly: GCA_900631975.1
Supplementary files format and content: excel files includes Mapped reads stats for each sample
Supplementary files format and content: excel  files includes raw read counts for each sample
Supplementary files format and content: excel  files includes Quality control summary for each sample

organism: Plasmodium falciparum

source_name: blood

extract_protocol:
Total RNA was batch-isolated using E.Z.N.A® Total RNA Kit (Omega Bio-Tek Inc.), treated with RNase-free DNase I (New England Biolabs Inc.), and further processed using RNA Clean & Concentrator (ZYMO Research Corp.).
Only samples with RNA integrity number (RIN) >8 were used for library preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: blood

tag: time

value: Day 0

tag: sample group

value: nonSMA


title: Vigna radiata T1 48h WGBS rep3

description:
Library name: Meth_T1H48_rep3
WGBS of T1 H48 leaf

value: Pre-conditioned salt stress


title: nonSMA37

description: Library name: s90b


title: Vigna radiata T1 48h WGBS rep2

description:
Library name: Meth_T1H48_rep2
WGBS of T1 H48 leaf


title: Single-cell RNA sequencing of mouse tissue with WT EVs treated, B3

city: Wuhan

first: Zheng

last: Zhang

address: Jiefang Road 1095

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Library name: B3_EmptyDrops_CR_282924_matrix

data_processing:
Raw sequencing data were processed using CeleScope v3.0.1 (Singleron Biotechnologies) with default settings. Cell barcodes and unique molecular identifiers (UMIs) were extracted and corrected from Read 1, while Read 2 was trimmed to remove adapter sequences and poly(A) tails. The trimmed reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR v2.6.1b. Uniquely mapped reads were assigned to exons using FeatureCounts v2.0.1, and UMIs with identical cell barcodes and gene annotations were collapsed to generate the final gene expression matrix.
Assembly: Mus musculus GRCm38 (mm10)
Supplementary files format and content: Each processed data file (.tar) contains the filtered single-cell expression matrix generated by CeleScope, including matrix.mtx, features.tsv, and barcodes.tsv files in Matrix Market format. File names correspond to individual samples.

molecule: polyA RNA

organism: Mus musculus

source_name: epidural scar

extract_protocol:
Fresh tissues were preserved in sCelLiveTM Tissue Preservation Solution (Singleron) on ice within 30 min post-surgery. Specimens were washed with HBSS, minced, and digested with 3 mL sCelLiveTM Dissociation Solution (Singleron) (37°C, 15 min) using Singleron PythoN™ Tissue Dissociation System. After filtration (40 μm strainer), red blood cells were lysed with GEXSCOPE® RCLB (1:2 ratio, 5-8 min, RT). The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant, followed by PBS resuspension. Cell viability was assessed via Trypan Blue staining
Single-cell suspensions (2×105 cells/mL in PBS) were loaded onto a microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads were collected from the chip, and reverse transcription was performed to generate cDNA from captured mRNA, followed by PCR amplification. The amplified cDNA was fragmented, ligated with sequencing adapters, and libraries were constructed using GEXSCOPE® Single Cell RNA Library Kits (Singleron)

value: epidural scar

value: WT EVs


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to EBV (3)

description:
Library name: DICE-TCR_009_Hu_EBV_CD4_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the EBV peptide megapool (MP)

value: EBV-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: nonSMA36

description: Library name: s89b


title: nonSMA35

description: Library name: s88b


title: Vigna radiata T1 48h WGBS rep1

description:
Library name: Meth_T1H48_rep1
WGBS of T1 H48 leaf


title: Vigna radiata T1 6h WGBS rep3

description:
Library name: Meth_T1H6_rep3
WGBS of T1 H6 leaf


title: Vigna radiata T1 6h WGBS rep2

description:
Library name: Meth_T1H6_rep2
WGBS of T1 H6 leaf


title: nonSMA33

description: Library name: s81b


title: nonSMA34

description: Library name: s82b


title: Vigna radiata T1 6h WGBS rep1

description:
Library name: Meth_T1H6_rep1
WGBS of T1 H6 leaf


title: Vigna radiata T1 0h WGBS rep3

description:
Library name: Meth_T1H0_rep3
WGBS of T1 H0 leaf


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to IAV (5)

description:
Library name: DICE-TCR_004_Hu_FLU_CD4_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the IAV peptide megapool (MP)

value: IAV-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: nonSMA32

description: Library name: s7b


title: nonSMA31

description: Library name: s79b


title: nonSMA30

description: Library name: s77b


title: Vigna radiata T1 0h WGBS rep2

description:
Library name: Meth_T1H0_rep2
WGBS of T1 H0 leaf


title: Vigna radiata T1 0h WGBS rep1

description:
Library name: Meth_T1H0_rep1
WGBS of T1 H0 leaf


title: nonSMA28

description: Library name: s72b


title: ATAC-seq T2 H48 rep3

description:
Library name: ATAC_T2_H48_3
ATAC-seq on leaf nuclei from T2 H48 sample

data_processing:
Raw reads were trimmed using fastp (v1.0.1, Q20). Clean reads were aligned to the Vigna radiata reference genome using Bowtie2 (v5.5.4), with discordant/mixed alignments disabled and a 1000 bp insert size limit. PCR duplicates and low-quality reads (MAPQ < 25) were removed using deepTools (v3.5.6) and samtools (v1.22.1). Peaks were called using MACS3 (v3.0.3, q < 0.075) and filtered for reproducibility across replicates using bedtools (v2.28.0, 50% overlap). Peak annotation was performed with UROPA (v1.0.0). BigWig tracks were generated via deepTools bamCoverage (RPKM, 50 bp bins). Transcription factor footprinting and motif analysis were conducted using TOBIAS (v0.14.0) and FIMO/MEME (v5.5.7). Differential accessibility analysis was performed using featureCounts (v2.1.1) and edgeR (v4.0) in R (v4.4.3), defining DARs as FDR < 0.05 and |log2FC| > 0.5. Visualization was performed using ggplot2 and pheatmap.
Assembly: Vigna radiata (Weilv 9) reference genome
Supplementary files format and content: ATACseq_consensus_peaks.bed

source_name: leaf

extract_protocol:
Nuclei were isolated from frozen leaf tissues. Tissue was ground in liquid nitrogen and resuspended in ice‑cold nuclei isolation buffer (25 mM Tris‑HCl pH 7.6, 10 mM MgCl2, 0.44 M sucrose, 0.1% Triton X‑100, 10 mM β‑mercaptoethanol, 2 mM spermidine, 0.1 mM PMSF, 1× protease inhibitor cocktail). The homogenate was filtered through a 40 μm cell strainer. Nuclear integrity was confirmed by DAPI staining. Approximately 50,000 intact nuclei were used for library preparation.
Transposition was performed using Tn5 in a 50 μL reaction system at 37°C for 30 min. DNA fragments were purified using the QIAquick PCR Purification Kit (Qiagen). Libraries were amplified for 11–13 cycles using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, China). Amplified products were purified with VAHTS DNA Clean Beads (Vazyme). Sequencing was performed on the Illumina NovaSeq 6000 platform to generate 150 bp paired‑end reads.

value: leaf

value: protoplast

value: Wild type


title: Breast tumour sample SC9 (tumour cells)

city: Brussels

first: Cedric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

description:
Library name: sc12
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v7.0.1).
Data was processed with Scanpy v1.10.2, soupX v1.6.2, scDBLfinder v3.20 and scVI v1.1.4
Only cells that met the following criteria were included in the subsequent analysis: more than 700 uniquely expressed genes, and less than 20% and 30% of unique molecular identifier counts mapping to mitochondrial and ribosomal sequence. In addition only cells that exhibit enrichment of the YFP transgene, the presence of KrasG12D and Trp53 mutations, and a higher number of copy number aberrations (inferred using inferCNV v1.22.028) were considered for downstream analysis
Assembly: Mouse mm10
Supplementary files format and content: Scanpy processed data for all the samples in Seurat format

source_name: Breast

extract_protocol: 10,000 single cells from the LKPR tumour were loaded onto each channel of the Chromium Single Cell 3′ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was subsequently reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V3-chemistry, PN-120233, 10X Genomics) and sequenced on an Illumina Novaseq 6000 (paired-end 100bp reads).

value: Breast


title: nonSMA27

description: Library name: s67b


title: ATAC-seq T2 H48 rep2

description:
Library name: ATAC_T2_H48_2
ATAC-seq on leaf nuclei from T2 H48 sample


title: MU3

description:
Library name: mu7
10x Genomics

source_name: skin

extract_protocol:
10,000 single cells from the LKPR tumour were loaded onto each channel of the Chromium Single Cell 3′ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was subsequently reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V3-chemistry, PN-120233, 10X Genomics) and sequenced on an Illumina Novaseq 6000 (paired-end 100bp reads).
scRNA-seq

value: skin

value: LKPR tumor cell


title: nonSMA25

description: Library name: s63b


title: ATAC-seq T2 H48 rep1

description:
Library name: ATAC_T2_H48_1
ATAC-seq on leaf nuclei from T2 H48 sample


title: nonSMA26

description: Library name: s64b


title: ATAC-seq T2 H6 rep3

description:
Library name: ATAC_T2_H6_3
ATAC-seq on leaf nuclei from T2 H6 sample


title: nonSMA24

description: Library name: s62b


title: ATAC-seq T2 H6 rep2

description:
Library name: ATAC_T2_H6_2
ATAC-seq on leaf nuclei from T2 H6 sample


title: nonSMA23

description: Library name: s55b


title: ATAC-seq T2 H6 rep1

description:
Library name: ATAC_T2_H6_1
ATAC-seq on leaf nuclei from T2 H6 sample


title: ATAC-seq T2 H0 rep3

description:
Library name: ATAC_T2_H0_3
ATAC-seq on leaf nuclei from T2 H0 sample


title: nonSMA22

description: Library name: s50b


title: nonSMA21

description: Library name: s4b


title: ATAC-seq T2 H0 rep2

description:
Library name: ATAC_T2_H0_2
ATAC-seq on leaf nuclei from T2 H0 sample


title: nonSMA20

description: Library name: s49b


title: nonSMA19

description: Library name: s47b


title: ATAC-seq T1 H48 rep3

description:
Library name: ATAC_T1_H48_3
ATAC-seq on leaf nuclei from T1 H48 sample


title: ATAC-seq T2 H0 rep1

description:
Library name: ATAC_T2_H0_1
ATAC-seq on leaf nuclei from T2 H0 sample


title: nonSMA18

description: Library name: s46b


title: ATAC-seq T1 H48 rep2

description:
Library name: ATAC_T1_H48_2
ATAC-seq on leaf nuclei from T1 H48 sample


title: nonSMA17

description: Library name: s38b


title: SC6

description:
Library name: sc35
10x Genomics


title: nonSMA16

description: Library name: s34b


title: ATAC-seq T1 H48 rep1

description:
Library name: ATAC_T1_H48_1
ATAC-seq on leaf nuclei from T1 H48 sample


title: ATAC-seq T1 H6 rep3

description:
Library name: ATAC_T1_H6_3
ATAC-seq on leaf nuclei from T1 H6 sample


title: nonSMA15

description: Library name: s32b


title: ATAC-seq T1 H6 rep2

description:
Library name: ATAC_T1_H6_2
ATAC-seq on leaf nuclei from T1 H6 sample


title: nonSMA14

description: Library name: s2b


description:
Library name: HIPC-1_LN01_24
10x single-cell library of lung-draining lymph node (LN) sample from donor L024

source_name: lung-draining lymph node (LN)

value: lung-draining lymph node (LN)

value: CD3+ T cells

value: Ex-vivo


title: ATAC-seq T1 H0 rep3

description:
Library name: ATAC_T1_H0_3
ATAC-seq on leaf nuclei from T1 H0 sample


title: ATAC-seq T1 H6 rep1

description:
Library name: ATAC_T1_H6_1
ATAC-seq on leaf nuclei from T1 H6 sample


title: nonSMA13

description: Library name: s29b

value: blood


title: fCLIP Membrane Input_Replicate3

city: Daejeon

first: Jongmin

last: Lim

address: 291 Daehak-ro, Yuseong-gu,

department: Department of Bio and Brain Engineering

country: South Korea

institute: KAIST

data_processing:
For each CLIP-seq library, paired-end reads were trimmed using Cutadapt v.4.0. Trimmed reads were assembled using pear v.0.9.6. 4-nt of the 5′ end and 3′ of each assembled read were used as unique molecular identifiers (UMIs) and extracted by UMI-tools v. 1.1.2. Assembled reads were aligned to the C. sabaeus genome (GCF_015252025.1/ChelSea 2, ENSEMBL release 99) and the SARS-CoV-2 genome (GenBank: NC_045512.2) using STAR v.2.7.9a. PCR duplicates were removed using UMI-tools v.1.1.2. Deduplicated reads were then filtered using samtools v.1.14.  Read coverages were computed using bedtools genomecov v.2.30.0.
Assembly: GCF_015252025.1/ChelSea 2, ENSEMBL release 99
Supplementary files format and content: Strand-specific bedgraph files where the last column represents the number of reads mapped across the SARS-CoV-2 genome.

molecule: nuclear RNA

organism: Chlorocebus aethiops

source_name: Vero cell

extract_protocol:
Vero cells were infected with SARS-CoV-2 at an MOI of 0.05 for 48 hours. Infected cells were washed with cold 1x PBS, treated with 0.1% paraformaldehyde (Pierce, 28906), and added 1.5M glycine quenching solution. After washing with 1x PBS, subcellular fractionation of the cytosol and membrane was performed as described (Thermo Fisher Scientific, 78840). Each fraction was incubated with RNase A (Thermo Fisher Scientific, EN0531) for 10 minutes for RNA fragmentation. Three percent in volume of each subcellular fraction was kept as corresponding input samples. Lysates were incubated with antibodies-conjugated sepharose beads (A/G, GE Healthcare, 17-5138-01/17-0618-02) for immunoprecipitation. Beads were washed stringently, and RNAs were liberated with Proteinase K and 7M urea at 60°C overnight according to the guidelines approved by the International Vaccine Institute (IVI). RNAs were purified followed by DNase I (Takara, 2270A) treatment, and rRNAs were removed by Ribo-Zero kit (Illumina, TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat, 20020596).
RNAs were ligated to the adaptor at 3ʹ-end, resolved on 6% denaturing urea-PAGE gel, and isolated from the corresponding region (50-500nt). RNAs were ligated to the 5′ adapter followed by reverse transcription and PCR amplification. fCLIP-seq libraries were sequenced by paired-end run (151 × 151 cycles) on the Illumina platform (MiSeq) with PhiX control library v.3 (Illumina).

tag: cell line

value: Vero cell

value: Kidney epithelial cell

tag: antibody


title: nonSMA12

description: Library name: s26b

value: Day 0

value: nonSMA


title: ATAC-seq T1 H0 rep2

description:
Library name: ATAC_T1_H0_2
ATAC-seq on leaf nuclei from T1 H0 sample

value: Pre-conditioned salt stress


title: fCLIP Membrane N-IP_Replicate3


title: nonSMA11

description: Library name: s19b


title: fCLIP Cytosol Input_Replicate3

molecule: cytoplasmic RNA


title: fCLIP Cytosol N-IP_Replicate3


title: ATAC-seq T1 H0 rep1

description:
Library name: ATAC_T1_H0_1
ATAC-seq on leaf nuclei from T1 H0 sample


title: nonSMA10

description: Library name: s13b


title: fCLIP Membrane N-IP_Replicate2


title: Vigna radiata T2 48h rep3

description:
Library name: T2H48_rep3
Weilv 9, T2 group, 48h

data_processing:
Raw reads were trimmed with fastp (v1.0.1). Clean reads were aligned to the Vigna radiata (Weilv 9) reference genome using HISAT2 (v2.2.1, --rna-strandness RF). Gene counts and TPM were quantified with FeatureCounts. Differential expression was analyzed using DESeq2 (v1.48.2). Functional annotation and enrichment analyses were performed with eggNOG-mapper (v2) and clusterProfiler (v4.16.0). Co-expression networks were constructed using WGCNA and TO-GCN, and visualized in Cytoscape (v3.10.3).
Assembly: Vigna radiata (Weilv 9) reference genome
Supplementary files format and content: RNAseq_TPM_matrix.txt

growth_protocol: Mung bean (Vigna radiata cv. Weilv 9) seeds were surface‑sterilized and germinated on moist filter paper for 2 days. Uniform seedlings were transferred to seedling trays and grown for 3 days, then moved to hydroponic containers containing half‑strength Murashige and Skoog (1/2 MS) nutrient solution. Plants were cultivated under controlled conditions: 25°C, 12,000 lux light intensity, 16 h light/8 h dark photoperiod, and 70% relative humidity. Nutrient solution was refreshed regularly.

extract_protocol:
Total RNA was extracted from frozen leaf tissues using the FreeZol Reagent Kit (R711, Vazyme, China). RNA quality and concentration were assessed using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA) and agarose gel electrophoresis. Only high‑quality RNA was used for downstream library construction.
Poly(A) mRNA was enriched using Oligo(dT) magnetic beads, fragmented, and reverse‑transcribed into double‑stranded cDNA. After end‑repair, A‑tailing, and ligation of MGI‑specific adapters, the cDNA libraries were amplified, purified, and circularized to form single‑stranded circular DNA (ssCir DNA), which served as templates for DNA nanoball (DNB) preparation. Sequencing was performed on the DNBSEQ platform.

treatment_protocol: Two experimental treatments were applied. T1: seedlings were exposed to 100 mM NaCl for 24 h, followed by 48 h recovery in NaCl‑free 1/2 MS solution, then subjected to a second 100 mM NaCl treatment. T2: seedlings were directly exposed to 100 mM NaCl without preconditioning. For both treatments, the first fully expanded true leaves were harvested at 0, 1, 3, 6, 12, 24, and 48 h after the onset of the final salt treatment.

value: Leaf

value: Direct salt


title: nonSMA9

description: Library name: s12b


title: fCLIP Membrane N-IP_Replicate1


title: Vigna radiata T2 48h rep2

description:
Library name: T2H48_rep2
Weilv 9, T2 group, 48h


description:
Library name: HIPC-1_11_Hu_TL33_6D
10x single-cell library of lung sample from donor L033

source_name: lung

value: lung


title: fCLIP Membrane Input_Replicate1


title: fCLIP Membrane Input_Replicate2


title: nonSMA8

description: Library name: s117b


title: fCLIP Cytosol N-IP_Replicate1


title: fCLIP Cytosol N-IP_Replicate2


title: Vigna radiata T2 48h rep1

description:
Library name: T2H48_rep1
Weilv 9, T2 group, 48h


title: nonSMA7

description: Library name: s115b


title: fCLIP Cytosol Input_Replicate2


title: Vigna radiata T2 24h rep3

description:
Library name: T2H24_rep3
Weilv 9, T2 group, 24h


title: fCLIP Cytosol Input_Replicate1


title: nonSMA6

description: Library name: s114b


title: Vigna radiata T2 24h rep2

description:
Library name: T2H24_rep2
Weilv 9, T2 group, 24h


title: nonSMA5

description: Library name: s112b


title: Neuronal TBPH rescue (RU-486 induced), biological replicate 3

type: RNA

city: Trieste

first: Giulia

last: Romano

address: Padriciano 99

country: Italy

institute: ICGEB

description: FEIGUIN_DROSO_drug_3; fed 5 mM RU-486 (mifepristone) in food for 60 hours post-eclosion

hyb_protocol: Fragmented biotin-labeled cRNA was hybridized to Affymetrix GeneChip Drosophila Genome 2.0 Arrays at GenoSplice technology (Paris, France) following the standard Affymetrix protocol. Hybridization quality was monitored by bacterial spike-in controls (BioB, BioC, BioD, Cre), which showed the expected rank order (BioB < BioC < BioD < Cre) for all 12 samples (QC: PASSED).

scan_protocol: Arrays were washed, stained, and scanned at GenoSplice technology (Paris, France) using the standard Affymetrix GeneChip Scanner / Fluidics Station workflow, generating raw CEL files.

data_processing: Sample-level QC was performed by GenoSplice technology using all_probeset_RLE_mean (all samples < 0.6), 3'/5' ratios on housekeeping genes ACTIN, GAPDH, eIF-4a (all within accepted ranges), %P detection rate (Δ < 10 percentage points within each condition), hybridization spike-in controls (BioB < BioC < BioD < Cre), and labeling spike-in controls (Lys < Phe < Thr < Dap): all 12 arrays PASSED global QC. Raw CEL files were then imported into R/Bioconductor (Huber et al., 2015). Background correction, quantile normalization, and probe-level summarization were performed using the Robust Multi-array Average (RMA) algorithm (Irizarry et al., 2003) to generate log2-transformed expression values. Probe sets were mapped to Drosophila gene symbols using the drosophila2.db annotation package via annotate::getSYMBOL(); probes lacking gene annotation were excluded, and when multiple probe sets mapped to the same gene, expression values were collapsed to gene level by median aggregation. Differential expression analysis was performed with limma (Ritchie et al., 2015), fitting linear models with lmFit() and applying empirical Bayes shrinkage (eBayes). Pairwise contrasts: tbph^Δ23 vs w1118; tbph^Δ142 vs w1118; rescue vs tbph^Δ23; rescue vs tbph^Δ142. Multiple testing correction by Benjamini-Hochberg (FDR < 0.05).

label: biotin

organism: Drosophila melanogaster

source_name: adult Drosophila heads, 60 hours post-eclosion

label_protocol: Labeling was performed at GenoSplice technology (Paris, France) according to the standard Affymetrix GeneChip 3' IVT protocol. Total RNA was reverse-transcribed, amplified, and biotin-labeled to generate cRNA. Labeling quality was monitored by polyA spike-in controls (Lys, Phe, Thr, Dap), which showed the expected rank order (Lys < Phe < Thr < Dap) for all 12 samples (QC: PASSED).

growth_protocol: Stocks were maintained on standard cornmeal medium at 25°C under a 12 h light/dark cycle.

extract_protocol: Total RNA was isolated from whole adult heads using TRIzol reagent (Cat. #15596026, Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Adult flies were collected after eclosion. Heads were dissected on dry ice. The Rescue line carries elav-GeneSwitch-GAL4 (elav-GS) driving UAS-TBPH expression in neurons; Rescue animals were fed standard food supplemented with 5 mM RU-486 (mifepristone) from eclosion for 60 hours to activate neuronal TBPH expression.

value: tbph^23/^23; elav-GS-GAL4/UAS-TBPH


title: Vigna radiata T2 24h rep1

description:
Library name: T2H24_rep1
Weilv 9, T2 group, 24h


title: Neuronal TBPH rescue (RU-486 induced), biological replicate 1

description: FEIGUIN_DROSO_drug_1; fed 5 mM RU-486 (mifepristone) in food for 60 hours post-eclosion to activate UAS-TBPH expression via elav-GS


title: Neuronal TBPH rescue (RU-486 induced), biological replicate 2

description: FEIGUIN_DROSO_drug_2; fed 5 mM RU-486 (mifepristone) in food for 60 hours post-eclosion


title: tbph^Δ142 mutant, biological replicate 3

description: FEIGUIN_DROSO_delta_142_3; on standard food (no RU-486)


title: nonSMA4

description: Library name: s109b


title: Vigna radiata T2 12h rep3

description:
Library name: T2H12_rep3
Weilv 9, T2 group, 12h


title: nonSMA3

description: Library name: s104b


title: tbph^Δ142 mutant, biological replicate 2

description: FEIGUIN_DROSO_delta_142_2; on standard food (no RU-486)


title: Vigna radiata T2 12h rep2

description:
Library name: T2H12_rep2
Weilv 9, T2 group, 12h


title: tbph^Δ23 mutant, biological replicate 2

description: FEIGUIN_DROSO_delta_23_2; on standard food (no RU-486)


title: tbph^Δ23 mutant, biological replicate 3

description: FEIGUIN_DROSO_delta_23_3; on standard food (no RU-486)


title: tbph^Δ142 mutant, biological replicate 1

description: FEIGUIN_DROSO_delta_142_1; on standard food (no RU-486)


title: nonSMA2

description: Library name: s102b


title: tbph^Δ23 mutant, biological replicate 1

description: FEIGUIN_DROSO_delta_23_1; on standard food (no RU-486)


title: Vigna radiata T2 12h rep1

description:
Library name: T2H12_rep1
Weilv 9, T2 group, 12h


title: nonSMA1

description: Library name: s101b


title: Vigna radiata T2 6h rep3

description:
Library name: T2H6_rep3
Weilv 9, T2 group, 6h


title: SMA22

description: Library name: s85b

value: SMA


title: w1118 control, biological replicate 2

description: FEIGUIN_DROSO_H118_2; on standard food (no RU-486)


title: w1118 control, biological replicate 3

description: FEIGUIN_DROSO_H118_3; on standard food (no RU-486)


title: w1118 control, biological replicate 1

description: FEIGUIN_DROSO_H118_1; on standard food (no RU-486)


title: Vigna radiata T2 6h rep2

description:
Library name: T2H6_rep2
Weilv 9, T2 group, 6h


title: SMA21

description: Library name: s84b


title: Vigna radiata T2 6h rep1

description:
Library name: T2H6_rep1
Weilv 9, T2 group, 6h


title: E23T

city: Bunkyo-ku

first: Dai

last: Kubota

country: Japan

institute: The University of Tokyo

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: biopsy,  preESD

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: not provided

value: tumor(early Barrett's adenocarcinoma )

tag: gender

value: male

tag: age


title: E23G

value: gastric epithelium


title: SMA20

description: Library name: s83b


title: E23B

value: Barrett's esophagus


description:
Library name: HIPC-1_04_Hu_TL7_2D
10x single-cell library of lung sample from donor L007

value: CD3+ T cells


title: E23S

value: squamous epithelium


title: E22B


title: E22T


title: Vigna radiata T2 3h rep3

description:
Library name: T2H3_rep3
Weilv 9, T2 group, 3h


title: SMA19

description: Library name: s80b

value: blood


title: Vigna radiata T2 3h rep2

description:
Library name: T2H3_rep2
Weilv 9, T2 group, 3h


title: SMA18

description: Library name: s75b


title: E22S


title: E22G


title: Vigna radiata T2 3h rep1

description:
Library name: T2H3_rep1
Weilv 9, T2 group, 3h


title: E21T


title: SMA17

description: Library name: s74b


title: Vigna radiata T2 1h rep3

description:
Library name: T2H1_rep3
Weilv 9, T2 group, 1h


title: E21B


title: E21G


title: E21S


title: SMA16

description: Library name: s71b


title: Vigna radiata T2 1h rep2

description:
Library name: T2H1_rep2
Weilv 9, T2 group, 1h


title: SMA15

description: Library name: s69b


title: E20T


title: Vigna radiata T2 1h rep1

description:
Library name: T2H1_rep1
Weilv 9, T2 group, 1h


title: E20B


title: SMA14

description: Library name: s60b


title: E20G


title: E20S


title: Vigna radiata T2 0h rep3

description:
Library name: T2H0_rep3
Weilv 9, T2 group, 0h


title: E19T


title: SMA13

description: Library name: s5b


title: Vigna radiata T2 0h rep2

description:
Library name: T2H0_rep2
Weilv 9, T2 group, 0h


title: E19B


title: E19G


title: E19S


title: Vigna radiata T2 0h rep1

description:
Library name: T2H0_rep1
Weilv 9, T2 group, 0h


title: SMA12

description: Library name: s43b


title: E17T


title: E17B


title: SMA11

description: Library name: s3b


title: Vigna radiata T1 48h rep3

description:
Library name: T1H48_rep3
Weilv 9, T1 group, 48h

value: Pre-conditioned salt


title: SMA10

description: Library name: s37b


title: E17G


title: E17S


title: SMA9

description: Library name: s35b


title: E12T


title: Vigna radiata T1 48h rep2

description:
Library name: T1H48_rep2
Weilv 9, T1 group, 48h


title: E12S


title: E12B


title: Vigna radiata T1 48h rep1

description:
Library name: T1H48_rep1
Weilv 9, T1 group, 48h


title: E12G


title: SMA8

description: Library name: s30b


title: Vigna radiata T1 24h rep3

description:
Library name: T1H24_rep3
Weilv 9, T1 group, 24h


title: skeletal HC3_P

city: chongqing

first: Jia

last: Luo

state: chongqing

address: tiansheng road

institute: Southwest University

description: Skeletal muscle of HC-P

data_processing:
Total RNA quantity and purity were assessed using a Bioanalyzer 2100 with the RNA 6000 Nano LabChip Kit (Agilent, CA, USA), ensuring an RIN number >7.0. Approximately 1 μg of total RNA was used in preparing small RNA libraries following the protocol provided by the TruSeq Small RNA Sample Prep Kits (Illumina). Single-end sequencing (36 bp) was performed on an Illumina Hiseq 2500 at Novogene Bio (Tianjing, China), adhering to recommended guidelines.
MiRNA differential expression based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test. The significance threshold was set to be 0.01 and 0.05 in each test.
Assembly: Genome database:sus_scrofa_Ensembl_97; miRbase version: V21.0
Supplementary files format and content: identified miRNAs with details (reads,location,length,etc)

organism: Sus scrofa

source_name: Skeletal muscle

growth_protocol: adult HeChuan black pigs (castrated sows)

extract_protocol:
The isolation and preparation process for L-Exo and Y-Exo was conducted as follows: ① The skeletal muscle, devoid of fascia and fat, was minced and homogenized using a tissue homogenizer. It was then dissolved and separated with PBS. ② The resulting solution was filtered through gauze and centrifuged at 2000g for 30 minutes to remove tissue and cell debris. This was followed by another centrifugation at 12000g for 45 minutes to further eliminate cell debris. ③ The supernatant underwent filtration using a 0.2μm filter to eliminate any remaining cell debris or impurities, after which it was subjected to centrifugation at 16000g for two hours. ④ After dissolving the precipitate in PBS, it underwent an additional hour of centrifugation at 12000g, followed by re-dissolution in PBS. Finally, the exosome isolation and purification kit (Ribobio, Guangzhou, China) along with subsequent steps including exosome identification, RNA extraction, and in vitro experiments were employed for further purification.
Approximately 1 μg of total RNA was used to prepare the small RNA library according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina). The extracted RNAs were sent to Novogene Bio (Tianjing, China) for transcriptome sequencing of miRNA and mRNA

treatment_protocol: The HC-L and HC-P samples, as well as the exosomes derived from them (referred to as L-Exo and Y-Exo, respectively), were utilized for the construction of small RNA libraries. MiRNA libraries were constructed separately using skeletal muscle and the corresponding exosomes from HC-L and HC-P. Trizol LS (Thermo Fisher Scientific) was used for extracting total RNA from skeletal muscle exosomes (SKM-Exos), while Trizol (Takara) was employed for extracting skeletal muscle RNA.

value: Skeletal muscle

value: Hechuan black pig

value: tissue


title: SMA7

description: Library name: s1b

value: Day 0


title: Vigna radiata T1 24h rep2

description:
Library name: T1H24_rep2
Weilv 9, T1 group, 24h

value: Leaf


title: skeletal HC2_P

description: Skeletal muscle of HC-P


title: E11T


title: SMA6

description: Library name: s14b


title: skeletal HC1_P

description: Skeletal muscle of HC-P


title: Vigna radiata T1 24h rep1

description:
Library name: T1H24_rep1
Weilv 9, T1 group, 24h


title: E11B


title: SMA5

description: Library name: s113b


title: E11G_2


title: skeletal HC3_L

description: Skeletal muscle of HC-L


title: Vigna radiata T1 12h rep3

description:
Library name: T1H12_rep3
Weilv 9, T1 group, 12h


title: SMA4

description: Library name: s111b


title: E11S


title: skeletal HC2_L

description: Skeletal muscle of HC-L


title: Vigna radiata T1 12h rep2

description:
Library name: T1H12_rep2
Weilv 9, T1 group, 12h


title: E10G_2


title: E10T


title: Mouse scar tissues with lamina excision4

description: Library name: Laminectomy4

data_processing:
After sequencing, raw reads were subjected to quality control to remove adapters and low-quality bases. Clean reads were aligned to the Mus musculus reference genome (mm10) using STAR (v2.6.1b) with default parameters. FeatureCounts (v2.0.1) was used to quantify the number of uniquely mapped reads per gene based on the GENCODE gene annotation. The resulting count matrix was normalized and analyzed for differential expression using DESeq2 (v1.30.1) in R. Differentially expressed genes were defined by an adjusted p-value < 0.05 and |log₂ fold change| > 1. Quantitative real-time PCR was performed to validate selected genes.
Assembly: Mus musculus GRCm38 (mm10)
Supplementary files format and content: Processed data are provided as comma-separated value (.csv) files containing raw read counts for each annotated gene across all sequenced samples. Each row represents one gene (identified by gene symbol or Ensembl ID), and each column corresponds to one biological sample.

source_name: paraspinal soft and scar tissue

extract_protocol:
Total RNA was extracted from the matched tissue samples used for DNA methylation analysis using the RNeasy Mini Kit (Qiagen, catalog no. 75144) according to the manufacturer’s instructions. Extracted RNA was treated with DNase I (Thermo Fisher Scientific, catalog no. AM2222) to remove genomic DNA contamination. RNA integrity and concentration were assessed using agarose gel electrophoresis and spectrophotometry prior to library preparation.
RNA-seq libraries were prepared by Genesky Biotechnologies using the TruSeq Stranded mRNA Library Preparation Kit (Illumina). Polyadenylated RNA (polyA+) was enriched with oligo(dT) magnetic beads and fragmented, followed by first- and second-strand cDNA synthesis. The resulting cDNA was end repaired, A-tailed, and ligated to indexed sequencing adapters according to the Illumina protocol. Adapter-ligated fragments were PCR amplified and purified to generate the final libraries, which were quantified and quality-checked prior to sequencing on the Illumina HiSeq 2000 platform (paired-end 100 bp reads).

value: paraspinal soft and scar tissue

value: Laminectomy


title: HC3_P_ex

description: exosome


title: SMA3

description: Library name: s110b


title: skeletal HC1_L

description: Skeletal muscle of HC-L


title: Vigna radiata T1 12h rep1

description:
Library name: T1H12_rep1
Weilv 9, T1 group, 12h


title: E10B


title: Vigna radiata T1 6h rep3

description:
Library name: T1H6_rep3
Weilv 9, T1 group, 6h


title: Vigna radiata T1 6h rep2

description:
Library name: T1H6_rep2
Weilv 9, T1 group, 6h


title: Mouse scar tissues with lamina excision2

description: Library name: Laminectomy2


title: HC2_P_ex

description: exosome


title: Mouse scar tissues with lamina excision3

description: Library name: Laminectomy3


title: E10S


title: HC1_P_ex

description: exosome


title: Mouse scar tissues with lamina excision1

description: Library name: Laminectomy1


title: Vigna radiata T1 3h rep3

description:
Library name: T1H3_rep3
Weilv 9, T1 group, 3h


title: Vigna radiata T1 6h rep1

description:
Library name: T1H6_rep1
Weilv 9, T1 group, 6h


title: HC2_L_ex

description: exosome


title: E8T


title: HC3_L_ex

description: exosome


title: Mouse scar tissues without lamina excision4

description: Library name: SHAM4

value: SHAM


title: Vigna radiata T1 3h rep2

description:
Library name: T1H3_rep2
Weilv 9, T1 group, 3h


title: E8B


title: E8S


title: Mouse scar tissues without lamina excision3

description: Library name: SHAM3


title: HC1_L_ex

description: exosome


title: Vigna radiata T1 3h rep1

description:
Library name: T1H3_rep1
Weilv 9, T1 group, 3h


title: Mouse scar tissues without lamina excision2

description: Library name: SHAM2


title: HC3_P

description: tissue


title: Mouse scar tissues without lamina excision1

description: Library name: SHAM1


title: Vigna radiata T1 1h rep3

description:
Library name: T1H1_rep3
Weilv 9, T1 group, 1h


title: HC2_P

description: tissue


title: Mouse paraspinal soft tissues with No operation 4

description: Library name: Nooperation4

source_name: paraspinal soft tissue

value: paraspinal soft tissue

value: No operation


title: Vigna radiata T1 1h rep2

description:
Library name: T1H1_rep2
Weilv 9, T1 group, 1h


title: E6T

value: tumor(early Barrett's adenocarcinoma )

value: male


title: E6B

value: Barrett's esophagus


title: HC1_P

description: tissue


title: Vigna radiata T1 1h rep1

description:
Library name: T1H1_rep1
Weilv 9, T1 group, 1h


title: E2T


title: E6S


title: E2S


title: Mouse paraspinal soft tissues with No operation 3

description: Library name: Nooperation3


title: HC3_L

description: tissue


title: Vigna radiata T1 0h rep3

description:
Library name: T1H0_rep3
Weilv 9, T1 group, 0h


title: HC2_L

description: tissue


title: Mouse paraspinal soft tissues with No operation 2

description: Library name: Nooperation2


title: Vigna radiata T1 0h rep2

description:
Library name: T1H0_rep2
Weilv 9, T1 group, 0h


title: Mouse paraspinal soft tissues with No operation 1

description: Library name: Nooperation1


title: HC1_L

description: tissue


title: E1T


title: Vigna radiata T1 0h rep1

description:
Library name: T1H0_rep1
Weilv 9, T1 group, 0h


title: WF_CONNECTED_replicate4

status: Public on Jun 06 2026

city: Riga

first: Ayman

last: Osman

address: Riga

country: Latvia

institute: University of Latvia

description: Library name: Sample 15

data_processing:
Read filtering and adapter removal was performed with fastp 0.20.0 (default parameters; read trimming >100 bp). STAR 2.7.10a (Dobin & Gingeras, 2015) was used to map the reads against Medicago truncatula R108 reference genome available in https://medicago.toulouse.inrae.fr/MtrunR108_HiC (INRA, Toulouse). SortMeRNA version 4.3.6 (Kopylova et al., 2012) was used to quantify and filter rRNS using smr_v4.3_default_db database. DEG analysis was performed with limma (Bioconductor) (Ritchie et al., 2015).
Supplementary files format and content: log2(fold changes)

organism: Medicago truncatula

extract_protocol: Three separate trifoliate leaves from 8-weeks old receiver plants were harvested in liquid N2, homogenized with pestle and mortar for RNA extraction using ReliaPrepTM RNA Miniprep System (Promega, cat. Z6012). RNA quantification was performed with Qubit™ RNA BR Assay Kit and Agilent Bioanalyzer RNA 6000 Pico Kit. Samples from 4 different plants were processed as biological replicates for each treatment. Total 400ng of each RNA sample (RIN≥7, OD260/280 between 1.9-2.1, OD260/230 between 1.5-2.0) was processed for library preparation using MGIEasy RNA Directional Library Prep Set following manufacturer’s instructions. QIAseq FastSelect –rRNA Plant Kit (QIAGEN) was used to deplete rRNA prior to the library fragmentation step. Qubit® dsDNA HS Assay and Agilent HS DNA Kit was used to determine library concentration and length (average 326 nt) prior to multiplexing and circularization. The final pooled libraries (1.94 ng/µL) were sequenced on DNB G400RS high throughput sequencing machine (MGI) using FLC PE150 flowcell.

value: leaf

value: wild type


title: WF_CUT_replicate3

description: Library name: Sample 14


title: WF_CUT_replicate1

description: Library name: Sample 12


title: E1S

value: squamous epithelium


title: WF_CONNECTED_replicate3

description: Library name: Sample 11


title: E1G

value: gastric epithelium


title: WF_CONNECTED_replicate2

description: Library name: Sample 10


title: WF_CONNECTED_replicate1

description: Library name: Sample 9


title: H2O_CUT_replicate4

description: Library name: Sample 8


title: H2O_CUT_replicate3

description: Library name: Sample 7


title: H20_CONNECTED_replicate4

description: Library name: Sample 4


title: H20_CONNECTED_replicate3

description: Library name: Sample 3


title: H20_CONNECTED_replicate2

description: Library name: Sample 2


title: H2O_CUT_replicate2

description: Library name: Sample 6


title: H2O_CUT_replicate1

description: Library name: Sample 5


title: H20_CONNECTED_replicate1

description: Library name: Sample 1


title: HK,Day7,replicate 1

first: Peng

last: Yang

address: No. 7 Donghu South Road

institute: Institute of Hydrology, Chinese Academy of Sciences

description: Library name: HK_7d_1

data_processing:
Reads were processed using the Cell Ranger 7.0.0 pipeline with default and recommended parameters.
Assembly: GCF_018340385.1_GCF_000850305.1_BT
Supplementary files format and content: Tab-separated values files and matrix files

organism: Cyprinus carpio

source_name: Head kidney

extract_protocol:
Cyprinus carpio head kidney and gut tissue were transported in In sterile culture dish with 10 ml 1× DPBS solution (Solarbio, cat. no. D1040) on ice to remove the residual MACS Tissue Storage Solution (Miltenyi Biotec, cat. no. 130-100-008), then minced on ice. We used dissociation enzyme 0.25% Trypsin (Hyclone, cat. no. SH30042.01) and 10 ug/mL Recombinant DNase I (RNase-free) (TaKaRa, cat. no. 2270B) dissolved in DPBS with 5% Fetal Bovine Serum (FBS, Thermo Fisher Scientific, cat. no. SV30087.02) to digest the tissues.Head kidney and gut  tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 μm nylon cell strainer and red blood cells were removed by 1× Red Blood Cell Lysis buffer (Thermo Fisher Scientific, cat. no. 00-4333-57) . Dissociated cells were washed with 1× DPBS containing 2% FBS. Cells were stained with AO/PI, and viability was assessed using a Countstar Fluorescence Cell Analyzer (Aber Instruments).
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification.Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3.1). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina), and 150 bp paired-end reads were generated. The sequencing and bioinformatics analysis were performed by Majorbio Co., Ltd (Shanghai, China).

value: Head kidney

value: cells

tag: collection date

tag: geo loc_name

value: Wuhan,China


title: HK,Day7,replicate 2

description: Library name: HK_7d_2


title: HK,Day35,replicate 2

description: Library name: HK_35d_2


title: WF_CUT_replicate2

description: Library name: Sample 13


title: HK,Day35,replicate 1

description: Library name: HK_35d_1


title: HK,Day28,replicate 1

description: Library name: HK_28d_1


title: HK,Day28,replicate 2

description: Library name: HK_28d_2


title: gut,Day7,replicate 2

description: Library name: gut_7d_2

source_name: gut

value: gut


title: gut,Day7,replicate 1

description: Library name: gut_7d_1


title: gut,Day35,replicate 2

description: Library name: gut35d_2


title: gut,Day35,replicate 1

description: Library name: gut35d_1


title: gut,Day28,replicate 2

description: Library name: gut28d_2


title: gut,Day28,replicate 1

description: Library name: gut28d_1


title: HK,control group,replicate 2

description: Library name: Con_HK2


title: HK,control group,replicate 1

description: Library name: Con_HK1


title: gut,control group,replicate 2

description: Library name: Con_gut2


title: gut,control group,replicate 1

description: Library name: Con_gut1


title: whole larval P. promelas, DMSO, sample51

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

description:
Treated_QA_P4_B12
FHM QAs_counts_matrix.txt

data_processing:
*library strategy: TempO-Seq (Templated Oligo-Sequencing)
Sample-specific TempO-Seq libraries were pooled together and sequenced on an Illumina sequencer (NextSeq 500), 2 × 50 bp, single-end reads, NovaSeq X 10B reagent kits.
Sequence reads were then demultiplexed based on sample-specific barcodes, and a FASTQ file was generated for each sample using Illumina's bcl2fastq conversion software. Resulting TempO-Seq data were analyzed by Biospyder using TempO-SeqR software implemented in R.
The FASTQ files were aligned to the known transcript composition of the reduced transcriptome, and a count table (columns = samples, genes = rows) was generated.
Assembly: GCA_016745375.1
Supplementary files format and content: count matrices with rows as gene features and columns as samples

organism: Pimephales promelas

source_name: whole body

growth_protocol: not applicable

extract_protocol:
Samples were prepared for transcriptomics analysis by homogenization in a protease lysis buffer as directed by BioSpyder Technologies, Inc. Pimephales promelas were homogenized in 75 µL/well with a 2.3 mm stainless steel bead (BioSpec) at 30 Hz for 2 min using a well plate homogenizer (Bead Ruptor 96, OMNI International). Plates were centrifuged for 3 min at 1000 rpm. Homogenates were pooled (excluding any mortalities) by treatment concentration within each plate, resulting in n=3 replicates per treatment, each containing five pooled organisms (Supplementary Figure 2B). The final plates containing pool homogenates were stored at -80ºC until shipped on dry ice to BioSpyder Technologies, Inc. (Carlsbad, CA) for TempO-seq analysis. Test acceptability criteria were met if control survival was >90 %.
TempO-Seq libraries were prepared by ligating detector oligos to corresponding transcripts present in the whole-body homogenates. Quality control and sample quantification were performed with a DeNovix UV-visible spectrophotometer (DeNovix). Ligated transcripts were subjected to polymerase chain reaction amplification, which also introduces adaptors for sequencing and a sample-specific barcode.

treatment_protocol: High-throughput in vivo exposures were conducted in 1 mL 96-well deep well plates (NEST, Catalog #502162) for 24 h. Each exposure consisted of two chemicals tested in a 1/2 log dilution series with five replicates per treatment concentration on each of three plates (15 organisms exposed per concentration). Final exposure concentrations ranged from 66.67 – 0.021 µM for all data poor chemicals, except fipronil amide (56.43- 0.018 µM) and fexofenadine hydrochloride (32.2 – 0.011 µM). All chemical stocks were prepared in DMSO and had purities > 95%. For each exposure, a Tecan D300e Bioprinter (Corvallis, OR, USA) was used to prepare an initial chemical dosing plate containing 1800 µL/well of test solution diluted in UV-treated, filtered Lake Superior Water in a 2 mL 96-well deep well plate (NEST, Catalog #503162). The concentration of DMSO was normalized across all wells to match those of the highest % DMSO obtained with the chemical delivery (i.e., the highest exposure concentration; generally 0.34% DMSO). Using the bioprinter, the dosing solutions were arranged to evenly distribute replicate exposure groups along the edges of the plate to avoid confounding any edge effects, if present, with treatment. For each exposure, one organism was loaded with 150 µL of control water (UV-treated, filtered Lake Superior Water) to each well of the three 96-well plates. A multi-channel pipette was used to deliver 550 µL of dosing solution to each well for a final volume of 700 µL per well. Each assay included DMSO controls, with final in-well DMSO concentrations never exceeding 0.34% in the exposure plate wells.

value: whole body

tag: developmental stage

value: larval

value: Caffeine


title: whole larval P. promelas, DMSO, sample52

description:
Treated_QA_P4_H01
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample50

description:
Treated_QA_P3_H01
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample49

description:
Treated_QA_P3_D12
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample47

description:
Treated_QA_P2_B12
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample45

description:
Treated_QA_P1_D12
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample46

description:
Treated_QA_P1_H01
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample44

description:
PC_C9C10_C_B12
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample43

description:
PC_C9C10_B_F10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample41

description:
PC_C7C8_C_H10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample42

description:
PC_C9C10_A_B10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample40

description:
PC_C7C8_B_H10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample37

description:
PC_C5C6_B_F10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample38

description:
PC_C5C6_C_F10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample39

description:
PC_C7C8_A_H10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample36

description:
PC_C5C6_A_F10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample35

description:
PC_C3C4_C_D10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample34

description:
PC_C3C4_B_D10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample33

description:
PC_C3C4_A_D10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample32

description:
PC_C1C2_C_B10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample31

description:
PC_C1C2_B_B10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample28

description:
PC_C11C12_B_H10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample30

description:
PC_C1C2_A_B10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample26

description:
Control_QA_P4_G01
FHM QAs_counts_matrix.txt

value: DMSO


title: whole larval P. promelas, DMSO, sample23

description:
Control_QA_P3_C12
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample22

description:
Control_QA_P2_G01
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample21

description:
Control_QA_P2_A12
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample20

description:
Control_QA_P1_G01
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample24

description:
Control_QA_P3_G01
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample19

description:
Control_QA_P1_C12
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample18

description:
CON_C9C10_C_A12
FHM Controls_counts_matrix.txt
Chem9_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample15

description:
CON_C7C8_C_G10
FHM Controls_counts_matrix.txt
Chem7_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample25

description:
Control_QA_P4_A12
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample17

description:
CON_C9C10_B_E10
FHM Controls_counts_matrix.txt
Chem9_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample16

description:
CON_C9C10_A_A10
FHM Controls_counts_matrix.txt
Chem9_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample14

description:
CON_C7C8_B_G10
FHM Controls_counts_matrix.txt
Chem7_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample13

description:
CON_C7C8_A_G10
FHM Controls_counts_matrix.txt
Chem7_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample12

description:
CON_C5C6_C_E10
FHM Controls_counts_matrix.txt
Chem5_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample9

description:
CON_C3C4_C_C10
FHM Controls_counts_matrix.txt
Chem3_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample8

description:
CON_C3C4_B_C10
FHM Controls_counts_matrix.txt
Chem3_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample10

description:
CON_C5C6_A_E10
FHM Controls_counts_matrix.txt
Chem5_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample7

description:
CON_C3C4_A_C10
FHM Controls_counts_matrix.txt
Chem3_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample6

description:
CON_C1C2_C_A10
FHM Controls_counts_matrix.txt
Chem1_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample5

description:
CON_C1C2_B_A10
FHM Controls_counts_matrix.txt
Chem1_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample2

description:
CON_C11C12_B_G10
FHM Controls_counts_matrix.txt
Chem11_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample4

description:
CON_C1C2_A_A10
FHM Controls_counts_matrix.txt
Chem1_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample3

description:
CON_C11C12_C_A12
FHM Controls_counts_matrix.txt
Chem11_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample1

description:
CON_C11C12_A_C10
FHM Controls_counts_matrix.txt
Chem11_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample24

description:
Chem9_C_D8_H11
Chem9_counts_matrix.txt

value: Cetirizine


title: whole larval P. promelas, Cetirizine, sample22

description:
Chem9_C_D6_F11
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample20

description:
Chem9_C_D4_D11
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample21

description:
Chem9_C_D5_E11
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample18

description:
Chem9_C_D2_B11
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample14

description:
Chem9_B_D6_F06
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample13

description:
Chem9_B_D5_E06
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample15

description:
Chem9_B_D7_G06
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample10

description:
Chem9_B_D2_B06
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample9

description:
Chem9_B_D1_A06
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample7

description:
Chem9_A_D7_G02
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample5

description:
Chem9_A_D5_E02
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample6

description:
Chem9_A_D6_F02
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample8

description:
Chem9_A_D8_H02
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample4

description:
Chem9_A_D4_D02
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample3

description:
Chem9_A_D3_C02
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample2

description:
Chem9_A_D2_B02
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample1

description:
Chem9_A_D1_A02
Chem9_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample24

description:
Chem8_C_D8_H09
Chem8_counts_matrix.txt

value: 4-Chlorophenyl methyl sulfoxide


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample23

description:
Chem8_C_D7_G09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample22

description:
Chem8_C_D6_F09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample21

description:
Chem8_C_D5_E09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample19

description:
Chem8_C_D3_C09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample18

description:
Chem8_C_D2_B09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample17

description:
Chem8_C_D1_A09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample16

description:
Chem8_B_D8_H09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample15

description:
Chem8_B_D7_G09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample14

description:
Chem8_B_D6_F09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample13

description:
Chem8_B_D5_E09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample9

description:
Chem8_B_D1_A09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample8

description:
Chem8_A_D8_H09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample7

description:
Chem8_A_D7_G09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample6

description:
Chem8_A_D6_F09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample5

description:
Chem8_A_D5_E09
Chem8_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample2

description:
Chem8_A_D2_B09
Chem8_counts_matrix.txt


title: 4863, LOW RFI

status: Public on Jun 08 2026

city: Guelph

first: Victoria

last: Asselstine

state: Ontario

address: 553 Gordon St #501

country: Canada

institute: University of Guelph

description: Library name: Sample 39

data_processing:
Data was processed using CLC genomics workbench
the raw sequence data was trimmed using the automatic trimmer function of CLC Genomics Workbench (CLC Bio, Aarhus, Denmark) using a quality trimming score = 0.05.
After the reads were trimmed, quality control was performed using the NGS quality control tool of CLC Genomics Workbench
The trimmed sequence reads were then aligned to the annotated ARS_UCD1.2 bovine reference genome using the CLC Genomics Workbench
Alignment parameters included a length fraction of 0.8 and a similarity of 0.8, mismatch cost = 2, deletion cost = 3, insert cost = 3, minimum contig length = 200 base pairs (bp) were allowed
Read cound and normalization was performed using CLC genomics workbench
Assembly: ARS_UCD1.2
Supplementary files format and content: csv file with raw counts per gene and sample

organism: Bos taurus

source_name: Milk Somatic Cells

extract_protocol:
Milk samples were collected using a 3 cm plastic cannula to ensure no bacteria contaminated the sample. Milk was kept on ice and immediately processed for RNA extraction using Trizol reagent to preserve the integrity of RNA.
Library construction was performed using the TruSeq RNA sample preparation kit

value: Milk Somatic Cells

tag: breed

value: Holstein dairy


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample1

description:
Chem8_A_D1_A09
Chem8_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample24

description:
Chem7_C_D8_H08
Chem7_counts_matrix.txt

value: Hydrochlorothiazide


title: whole larval P. promelas, Hydrochlorothiazide, sample22

description:
Chem7_C_D6_F08
Chem7_counts_matrix.txt


title: 4833, HIGH RFI

description: Library name: Sample 34


title: whole larval P. promelas, Hydrochlorothiazide, sample21

description:
Chem7_C_D5_E08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample20

description:
Chem7_C_D4_D08
Chem7_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample4

description:
Chem8_A_D4_D09
Chem8_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample19

description:
Chem7_C_D3_C08
Chem7_counts_matrix.txt


title: GRA knockin, PBS, biol rep5

city: RTP

first: Thomas

last: Randall

state: NC

address: 101 TW Alexander

institute: NIEHS

description: Library name: Sample 15

data_processing:
Alignment using STAR (V 2.5.1).
Read count was produced with featureCount (subread, Version 1.5.1)
Statistical analysis done with DEseq2 (v 1.38.3)
DEG was obtained using adjusted pvalue <0.05
Assembly: mm39/genecode_vM34
Supplementary files format and content: readcounts in txt format

source_name: hippocampus

extract_protocol:
The hippocampus was collected after the 6 hour PBS or Dex treatment.  Total RNA was isolated from the hippocampus using Qiagen RNeasy mini kit.
The integrity of the total RNA was determined using the TapeStation (Agilent Technologies), and RNA concentration was assessed using a Qubit (ThermoFisher Scientific).  A TruSeq RNA kit (Illumina, San Diego, CA) was utilized to prepare the poly(A)-enriched RNA-seq libraries that were sequenced on the Illumina NovaSeq 6000 in a 75-base paired-end mode according to the manufacturer’s protocol.

treatment_protocol: Adrenalectomized wild-type and homozygous GRA knockin mice were injected IP with PBS (vehicle) or dexamethasone (Dex) (1mg/kg).  After a 6-hour treatment time, mice were euthanized and the hippocampus removed.

value: hippocampus

tag: Sex

value: male

tag: strain

value: GRA knockin

value: PBS


title: whole larval P. promelas, DMSO, sample48

description:
Treated_QA_P2_H01
FHM QAs_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample3

description:
Chem8_A_D3_C09
Chem8_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample17

description:
Chem7_C_D1_A08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample16

description:
Chem7_B_D8_H08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample15

description:
Chem7_B_D7_G08
Chem7_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample29

description:
PC_C11C12_C_B12
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample13

description:
Chem7_B_D5_E08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample14

description:
Chem7_B_D6_F08
Chem7_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample27

description:
PC_C11C12_A_D10
FHM Controls_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample12

description:
Chem7_B_D4_D08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample11

description:
Chem7_B_D3_C08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample10

description:
Chem7_B_D2_B08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample9

description:
Chem7_B_D1_A08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample8

description:
Chem7_A_D8_H08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample7

description:
Chem7_A_D7_G08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample23

description:
Chem7_C_D7_G08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample6

description:
Chem7_A_D6_F08
Chem7_counts_matrix.txt


title: whole larval P. promelas, DMSO, sample11

description:
CON_C5C6_B_E10
FHM Controls_counts_matrix.txt
Chem5_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample18

description:
Chem7_C_D2_B08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample4

description:
Chem7_A_D4_D08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample5

description:
Chem7_A_D5_E08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample3

description:
Chem7_A_D3_C08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample2

description:
Chem7_A_D2_B08
Chem7_counts_matrix.txt


title: whole larval P. promelas, Hydrochlorothiazide, sample1

description:
Chem7_A_D1_A08
Chem7_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample22

description:
Chem6_C_D8_H07
Chem6_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample23

description:
Chem9_C_D7_G11
Chem9_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample21

description:
Chem6_C_D7_G07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample20

description:
Chem6_C_D6_F07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample18

description:
Chem6_C_D4_D07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample19

description:
Chem6_C_D5_E07
Chem6_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample16

description:
Chem9_B_D8_H06
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample17

description:
Chem9_C_D1_A11
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample19

description:
Chem9_C_D3_C11
Chem9_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample17

description:
Chem6_C_D3_C07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample16

description:
Chem6_C_D2_B07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample15

description:
Chem6_B_D8_H07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample14

description:
Chem6_B_D7_G07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample13

description:
Chem6_B_D6_F07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample12

description:
Chem6_B_D5_E07
Chem6_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample12

description:
Chem9_B_D4_D06
Chem9_counts_matrix.txt


title: whole larval P. promelas, Cetirizine, sample11

description:
Chem9_B_D3_C06
Chem9_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample11

description:
Chem6_B_D4_D07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample10

description:
Chem6_B_D3_C07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample9

description:
Chem6_B_D2_B07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample8

description:
Chem6_A_D8_H07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample7

description:
Chem6_A_D7_G07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample5

description:
Chem6_A_D5_E07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample4

description:
Chem6_A_D4_D07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample2

description:
Chem6_A_D2_B07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample3

description:
Chem6_A_D3_C07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample6

description:
Chem6_A_D6_F07
Chem6_counts_matrix.txt


title: whole larval P. promelas, 2-tert-Butyl-4-methoxyphenol, sample1

description:
Chem6_A_D1_A07
Chem6_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample24

description:
Chem5_C_D8_H06
Chem5_counts_matrix.txt

value: Metribuzin-DA


title: whole larval P. promelas, Metribuzin-DA, sample23

description:
Chem5_C_D7_G06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample20

description:
Chem5_C_D4_D06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample21

description:
Chem5_C_D5_E06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample22

description:
Chem5_C_D6_F06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample18

description:
Chem5_C_D2_B06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample17

description:
Chem5_C_D1_A06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample19

description:
Chem5_C_D3_C06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample16

description:
Chem5_B_D8_H06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample15

description:
Chem5_B_D7_G06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample14

description:
Chem5_B_D6_F06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample13

description:
Chem5_B_D5_E06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample11

description:
Chem5_B_D3_C06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample12

description:
Chem5_B_D4_D06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample10

description:
Chem5_B_D2_B06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample8

description:
Chem5_A_D8_H06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample9

description:
Chem5_B_D1_A06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample7

description:
Chem5_A_D7_G06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample6

description:
Chem5_A_D6_F06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample4

description:
Chem5_A_D4_D06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample3

description:
Chem5_A_D3_C06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample2

description:
Chem5_A_D2_B06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample5

description:
Chem5_A_D5_E06
Chem5_counts_matrix.txt


title: whole larval P. promelas, Metribuzin-DA, sample1

description:
Chem5_A_D1_A06
Chem5_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample20

description:
Chem8_C_D4_D09
Chem8_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample24

description:
Chem4_C_D8_H05
Chem4_counts_matrix.txt

value: Gabapentin


title: whole larval P. promelas, Gabapentin, sample23

description:
Chem4_C_D7_G05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample22

description:
Chem4_C_D6_F05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample18

description:
Chem4_C_D2_B05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample19

description:
Chem4_C_D3_C05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample15

description:
Chem4_B_D7_G05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample17

description:
Chem4_C_D1_A05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample13

description:
Chem4_B_D5_E05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample14

description:
Chem4_B_D6_F05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample12

description:
Chem4_B_D4_D05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample10

description:
Chem4_B_D2_B05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample8

description:
Chem4_A_D8_H05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample9

description:
Chem4_B_D1_A05
Chem4_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample7

description:
Chem4_A_D7_G05
Chem4_counts_matrix.txt


title: ESC-derived Lin-Sca-1+c-Kit-  rep3

city: Hangzhou

first: Wei

last: Shan

state: Zhejiang

address: Bone Marrow Transplantation Center, The First Afﬁliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, Zhejiang, PR China.

institute: Zhejiang University

data_processing:
The predefined gene sets representing the comprehensive biological processes are from the Molecular Signatures Database (MSigDB v7.0)
The sequencing data were compared with the reference genome using Hisat software
StringTie was used to determine the expression levels for mRNAs by calculating fragments per kilobase of transcript per million mapped reads (FPKM)
The differentially expressed mRNAs and genes were selected with log2 (fold change) > 1 or log2 (fold change) < − 1 and with statistical significance (P value < 0.05) by Ballgown
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow

extract_protocol:
RNA was extracted from 2000 isolated single cells (Lin-Sca-1+c-Kit- cells from bone marrow of primary recipient transplanted with sorted CD144+ cell and Lin-Sca-1+c-Kit+ cells (LSK) from bone marrow of 6-8 weeks C57BL/6 mice) and reverse transcribed using the SMART-Seq v4 Ultra Low Input RNA kit
libraries were generated with the cDNAs using the Nextera XT DNA Library Preparation Kit (FC-131-1024, Illumina, San Diego, CA), and sequenced using the Illumina Hiseq XTEN platform at Novogene Co.Ltd  (Beijing,  China).

value: Bone marrow

value: ESC-derived Lin-Sca-1+c-Kit-

value: hematopoietic cells

value: Wild type

value: ESCs differentiation


title: whole larval P. promelas, Gabapentin, sample6

description:
Chem4_A_D6_F05
Chem4_counts_matrix.txt

value: whole body

value: larval


title: whole larval P. promelas, Gabapentin, sample5

description:
Chem4_A_D5_E05
Chem4_counts_matrix.txt


title: ESC-derived Lin-Sca-1+c-Kit-  rep2


title: whole larval P. promelas, Gabapentin, sample4

description:
Chem4_A_D4_D05
Chem4_counts_matrix.txt


title: ESC-derived Lin-Sca-1+c-Kit-  rep1


title: bone marrow-derived Lin-Sca-1+c-Kit+  rep3

value: primary cell

value: untreated


title: whole larval P. promelas, Gabapentin, sample2

description:
Chem4_A_D2_B05
Chem4_counts_matrix.txt


title: bone marrow-derived Lin-Sca-1+c-Kit+  rep1


title: whole larval P. promelas, Gabapentin, sample1

description:
Chem4_A_D1_A05
Chem4_counts_matrix.txt


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample24

description:
Chem3_C_D8_H04
Chem3_counts_matrix.txt


title: mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 4h), H4K8ac, rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Library name: dtag_4h_mNPC_G0_1_H4K8ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz

data_processing:
The data were processed using the snakePipes DNA-mapping (v2.1.2) (Bhardwaj et al. 2019). Illumina adaptors were removed using cutadapt (v2.8) (Martin 2011) with default settings. Reads were then mapped to the mm10 genome with Bowtie2 (v2.3.5.1) (Langmead and Salzberg 2012), using the modified options –local –very-sensitive-local –no-mixed –no-discordant –phred33 -I 60 -X 700. Reads mapping to blacklisted regions from the Encode Consortium (Amemiya, Kundaje, and Boyle 2019) were discarded. Finally, only properly paired mapped reads and reads with a mapping quality over 3 were retained for further analysis
Assembly: mm10
Supplementary files format and content: bigwig files from sequencing-depth normalized counts
Library strategy: CUT&Tag

source_name: mNPC

growth_protocol: NPCs were cultured in N2B27 medium supplemented with EGF and FGF on gelatin-coated plates.

extract_protocol:
DNA fragments were isolated using the ChIP DNA Clean & Concentrator kit (Zymo Research) and eluted with 15 l elution buffer (provided by the kit). The library was prepared using 13 l DNA solution, mixed with 1 l of 10 M barcoded i5 and i7 primers separately, and 15 l NEBNext HiFi 2x PCR Master Mix. The PCR program included 72 °C for 5 minutes, 98 °C for 30 seconds, followed by 13 to 16 cycles of 98 °C for 10 seconds and 72 °C for 10 seconds, ending with 72 °C for 1 minute and holding at 8 °C. Ampure beads (39 l) were used for DNA purification.
CUT&Tag

treatment_protocol: MOF-dTAG cells were treated with dTAG13 (5 mg, Tocris) at 500nM, or with TSA at 330nM at different time points before proceeding the downstream experiments.

value: mNPC

value: MOF-dTAG

tag: cut&tag antibody


title: mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 4h), H4K8ac, rep1

description:
Library name: dtag_4h_mNPC_G0_1_H4K8ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: mNPC ES, MOF-dTAG, dTAG13 (500 nM, 4h), H4K5ac, rep1

description:
Library name: dtag_4h_mNPC_ES_H4K5ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample23

description:
Chem3_C_D7_G04
Chem3_counts_matrix.txt

tag: tissue


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample22

description:
Chem3_C_D6_F04
Chem3_counts_matrix.txt


title: mNPC ES, MOF-dTAG, dTAG13 (500 nM, 4h), H4K5ac, rep2

description:
Library name: dtag_4h_mNPC_ES_H4K5ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz

tag: cell type


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample21

description:
Chem3_C_D5_E04
Chem3_counts_matrix.txt

tag: treatment


title: mNPC G2_M, MOF-dTAG, dTAG13 (500 nM, 4h), H4K8ac, rep2

description:
Library name: dtag_4h_mNPC_G2_M_H4K8ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz

tag: genotype


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample20

description:
Chem3_C_D4_D04
Chem3_counts_matrix.txt


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample19

description:
Chem3_C_D3_C04
Chem3_counts_matrix.txt


title: mNPC LS, MOF-dTAG, negative control, H4K5ac, rep1

description:
Library name: neg_4h_mNPC_LS_H4K5ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz

value: negative control


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample18

description:
Chem3_C_D2_B04
Chem3_counts_matrix.txt


title: mNPC LS, MOF-dTAG, negative control, H4K5ac, rep2

description:
Library name: neg_4h_mNPC_LS_H4K5ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample17

description:
Chem3_C_D1_A04
Chem3_counts_matrix.txt


title: mNPC LS, MOF-dTAG, dTAG13 (500 nM, 4h), H4K5ac, rep1

description:
Library name: dtag_4h_mNPC_LS_H4K5ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample16

description:
Chem3_B_D8_H04
Chem3_counts_matrix.txt


title: mNPC LS, MOF-dTAG, dTAG13 (500 nM, 4h), H4K5ac, rep2

description:
Library name: dtag_4h_mNPC_LS_H4K5ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: mNPC G0_1, MOF-dTAG, negative control, H4K5ac, rep1

description:
Library name: neg_4h_mNPC_G0_1_H4K5ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample14

description:
Chem3_B_D6_F04
Chem3_counts_matrix.txt


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample13

description:
Chem3_B_D5_E04
Chem3_counts_matrix.txt


title: mNPC G0_1, MOF-dTAG, negative control, H4K5ac, rep2

description:
Library name: neg_4h_mNPC_G0_1_H4K5ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: mNPC G2_M, MOF-dTAG, negative control, H4K5ac, rep2

description:
Library name: neg_4h_mNPC_G2_M_H4K5ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample12

description:
Chem3_B_D4_D04
Chem3_counts_matrix.txt


title: mNPC G2_M, MOF-dTAG, negative control, H4K5ac, rep1

description:
Library name: neg_4h_mNPC_G2_M_H4K5ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample11

description:
Chem3_B_D3_C04
Chem3_counts_matrix.txt


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample10

description:
Chem3_B_D2_B04
Chem3_counts_matrix.txt


title: mNPC ES, MOF-dTAG, negative control, H4K5ac, rep1

description:
Library name: neg_4h_mNPC_ES_H4K5ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz