title: ES-2 cells with PBMCs, BTYNB, treatment 3

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

institute: Martin Luther University Halle-Wittenberg

description: Library name: NB_39

data_processing:
Raw fastq files were merged by zcat command, if reads R1/R2 consisted of multiple files.
Sequenced strand specific paired-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 2.8) with parameters -j 0 -q 20 -O 7 -m 20 –trim-n.
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -q --rna-strandness RF --dta -k 5.
Secondary alignments were filtered out using samtools (v 1.10).
Mapped reads were summarized using featureCounts (v 2.0.0) with parameterst -p -s 2 -T 6 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.110).
Assembly: hg38
Supplementary files format and content: Comma-separated text files including raw counts for each sample.

source_name: ES-2 with PMBCs

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: ES-2 with PMBCs

value: ovarian cancer derived cell line with peripheral blood mononuclear cells

value: BTYNB treatment

value: BTYNB


title: DKO-ET247-AR

status: Public on Oct 28 2025

type: SRA

city: Buffalo

first: David

last: Goodrich

state: NY

address: Elm and Carlton Streets

department: Department of Pharmacology & Therapeutics

country: USA

institute: Roswell Park Comprehensive Cancer Center

description:
Library name: DKO-ET247-AR
bigwig file

library_source: genomic

data_processing:
Paired-end sequencing data was assessed for quality using fastqc, aligned with bwa, and deduplicated with picard. Deeptools was used to generate bigwig files for each sample.
Assembly: mm10
Supplementary files format and content: bigwig file

molecule: genomic DNA

organism: Mus musculus

source_name: prostate tissue

extract_protocol:
Mouse prostate tissue was pulverized on dry ice and fixed with 1% formaldehyde. Crosslinked tissue was quenched with glycine, washed, and sonicated. Chromatin was immunoprecipitated with 5ug of antibody and pulled down using Protein A/G beads. Crosslinks were reversed, protein degraded, and column purification was used for DNA extraction.
ChIP-seq libraries were made using Swift DNA Library Prep Kit. 75bp paired end reads were sequenced on a Illumina NextSeq instrument.

treatment_protocol: Endstage prostate tumor tissue from non-castrated (intact) mouse models.

tag: tissue

value: prostate tissue

tag: Sex

value: male

tag: genotype

value: DKO

tag: chip antibody

value: Ar

tag: treatment

value: non-castrated

tag: Stage

value: endpoint tumor


title: myeloid cells from subcutaneous adipose tissue of NCD WT mice, biological rep1

city: La Jolla

first: Yun Sok

last: Lee

state: California

address: 9500 Gilman Dr MC0673

department: Medicine

institute: University of California San Diego

library_source: transcriptomic single cell

data_processing:
Alignment and gene quantification were made using Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Sequences were aligned to reference mm10-2020-A provided by 10X Genomics
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: sorted CD45+ CD11b+ cells from inguinal dipose tissue

extract_protocol:
Trizole
10x genomics kit

value: Wild type


title: DKO_ET166-Input

description:
Library name: DKO_ET166-Input
bigwig file

value: Input DNA


title: myeloid cells from visceral adiposetissue of NCD WT mice, biological rep2

source_name: sorted CD45+ CD11b+ cells from epididymal dipose tissue


title: Human CRC sample 19, CMS4

city: Kyoto-City

first: Kosuke

last: Iwane

address: 54 Shogoin-Kawahara-Cho, Sakyo-Ku

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Kyoto University Graduated School of Medicine

description:
Library name: Tumor19
FFPE spatial transcriptome sequencoing

library_source: transcriptomic

data_processing:
Raw sequencing data was processed using 10x Genomics Space Ranger 1.3.1 to generate FASTQ file.
Sequences were aligned to GRCh38 genome to gene exprtession count using Space Ranger's default setting.
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg: aligned_fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tisssue and spots
Supplementary files format and content: filtered_feature_bc_matrix.h5: H5 archive
Supplementary files format and content: scalefactors_json.json: scalefactors in JSON format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

organism: Homo sapiens

source_name: Colorectal carcinoma

extract_protocol:
ST slides were made from FFPE blocks of surgically resected CRC specimens. Total RNA was extracted using Nucleospin total RNA FFPE or Nucleospin total RNA FFPE XS (MACHEREY-NAGEL) according to manufacture's protocol.
Sequence library of the ST slides was created using Visium Spatial for FFPE Gene Expression Kit and Dual Index Kit TS Set A (10X genomics).

value: Colorectal carcinoma


title: sample 7-3-6 BatchB_water extract of Banhasasim-tang (Low dose)_rep3

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: Human hepatocellular carcinoma cell line, HepG2 (HB-8065) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). HepG2 cells were maintained in DMEM medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 5% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Dulbecco's Modified Eagle Medium (DMEM), phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO) and QIAzol lysis reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Qiagen (Germantown, MD, USA), respectively. The dried medicinal plants, prepared in compliance with the Korean Pharmacopoeia, were supplied from Kwangmyung-dang Medicinal Herbs Co. (Ulsan, Republic of Korea). The samples used in the experiment underwent organoleptic examination by Dr. Choi Goya, an herbal medicine organoleptic examination expert appointed by the Korea Food and Drug Administration, and were additionally identified at the species level by analyzing the DNA barcode region sequences. Voucher specimen were deposited in the Korean Herbarium of Standard Herbal Resources, Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Republic of Korea . All herbs and extracts can be obtained from the Oriental Medicine Resources Research Center (KIOM, https://oasis.kiom.re.kr/herblib). A hot water and 70% ethanol extract of each plant was prepared and supplied by KOC Biotech Co. (Daejeon, Republic of Korea). Briefly, dried plants (1,000 g) were pulverized and extracted in hot distilled water (10 L) for 3 h under a reflux extraction system (MS-DM609; MTOPS, Seoul, Republic of Korea) or in 70% ethanol (15L) for 1 h under ultrasonication system (VCP-20, Lab companion, Dajeon, Republic of Korea) twice. The extract solution was filtered through a 5 µm cartridge filter, concentrated in a rotary evaporator (Ev-1020, SciLab, Seoul, Republic of Korea), and then lyophilized in a freeze dryer (LP-20, Ilshin-Bio-Base, Dongduchen, Republic of Korea) to obtain the final extract. The extract was finely homogenized and packed in a glass bottle containing a desiccant silica gel. The decoction was prepared by mixing each extract, considering the composition ratio and extract yield of a single medicinal herb, and homogenized, according to the Korean Pharmacopoeia. For the in vitro treatment, extracts (100 mg) were vigorously vortexed for 30 min in 10 mL phosphate-buffered saline (PBS; Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 µm membrane to obtain a stock solution (10 mg/mL); the stock solution was aliquoted in small volumes and stored at -80°C until use.

tag: cell line

value: Banhasasim-tang water extract 20 ug/mL

tag: time


title: SKO-T104-AR

description:
Library name: SKO-T104-AR
bigwig file

value: SKO


title: ES-2 cells with PBMCs, BTYNB, treatment 2

country: Germany

description: Library name: NB_38

molecule: polyA RNA

tag: cell type


title: Human CRC sample 24

description:
Library name: Tumor24
Column name in Tumor19202426_counts.csv: Tumor24

data_processing:
Adaptors and low-quality bases were trimmed from the reads using Trimmomatic (version 0.39)  with default parameters.
The reads were aligned to the Homo sapiens reference genome (build hg38) using STAR (version 2.7.3a) and quantified using RSEM (version v1.3.1).
Assembly: GRCh38
Supplementary files format and content: a csv file includes raw counts for each sample

extract_protocol:
Tissues were first homogenized with TRIzol reagent (Thermo Fisher) and a beads homogenizer (Bertin Technologies Precellys 24 tissue homogenizer) and Total RNA was extracted using the RNeasy Mini Kit (QIAGEN). Residual DNA was removed by on-column DNase digestion using the RNase-Free DNase Set (QIAGEN) .
RNA libraries for RNA-seq were prepared with the TruSeq RNA Sample Prep Kit v2.


title: ES-2 cells with PBMCs, BTYNB, treatment 1

description: Library name: NB_37


title: ES-2 cells with PBMCs, CUB, treatment 3

description: Library name: NB_33

value: CUB treatment

value: CUB


title: sample 7-3-4 BatchB_water extract of Banhasasim-tang (High dose)_rep3

value: Banhasasim-tang water extract 500 ug/mL


title: myeloid cells from visceral adiposetissue of NCD WT mice, biological rep1

value: sorted CD45+ CD11b+ cells from epididymal dipose tissue


title: ES-2 cells with PBMCs, CUB, treatment 2

description: Library name: NB_32

value: ES-2 with PMBCs

value: ovarian cancer derived cell line with peripheral blood mononuclear cells


title: sample 7-3-3 BatchB_water extract of Yijung-tang (Low dose)_rep3

value: Yijung-tang water extract 20 ug/mL


title: DKO_ET166-H3K4me3

description:
Library name: DKO_ET166-H3K4me3
bigwig file

value: prostate tissue

value: male


title: Pup5, scRNAseq

city: Los Angeles

first: Jennifer

last: Zieba

state: CA

address: 615 Charles E. Young Dr.

institute: University of California, Los Angeles

description: BD Rhapsody

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the SevenBridges software platform (https://www.sevenbridges.com)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Femoral and tibial growth plate cartilage

extract_protocol:
Proximal tibia and distal femur epiphyses from postnatal day 5 mouse pups were collected and digested with Collagenase I tissue removal solution (1% Collagenase I, 2.5% trypsin w/o EDTA, 30mM Cacl2, in HBSS) at 37ºC for 45 minutes to remove muscle tissue that remained following dissection. Cartilage samples were then incubated at 37ºC in Collagenase II single cell isolation solution (1% Collagenase II, 2.5% trypsin w/o EDTA, 30mM Cacl2, in HBSS) for 2-3 hours with brief vortexing every 10-15 minutes. Single cells were passed through a 40um cell strainer in PBS containing 0.04% BSA.
Library was performed according to the manufacter’s instructions (BD Rhapsody HT Express Single Cell Analysis System).

tag: strain

value: Chondrocytes

value: Mutant

tag: age

value: Postnatal day 5


title: sample 7-3-5 BatchB_water extract of Banhasasim-tang (Medium dose)_rep3

value: Banhasasim-tang water extract 100 ug/mL


title: Pup4, scRNAseq

description: BD Rhapsody

value: Femoral and tibial growth plate cartilage


title: DKO_ET166-H3K27ac

description:
Library name: DKO_ET166-H3K27ac
bigwig file

value: DKO

value: non-castrated

value: endpoint tumor


title: DKO_ET166-H3K27me3

description:
Library name: DKO_ET166-H3K27me3
bigwig file


title: ES-2 cells with PBMCs, DMSO, treatment 3

description: Library name: NB_27

value: WT

value: DMSO


title: Pup3, scRNAseq

description: BD Rhapsody


title: ES-2 cells with PBMCs, CUB, treatment 1

description: Library name: NB_31

value: CUB treatment

value: CUB


title: sample 7-3-2 BatchB_water extract of Yijung-tang (Medium dose)_rep3

value: Yijung-tang water extract 100 ug/mL


title: Pup2, scRNAseq

description: BD Rhapsody

value: Wild type


title: ES-2 cells with PBMCs, DMSO, treatment 2

description: Library name: NB_26

value: ES-2 with PMBCs

value: ovarian cancer derived cell line with peripheral blood mononuclear cells


title: DKO_ET166-AR

description:
Library name: DKO_ET166-AR
bigwig file

value: prostate tissue

value: male

value: Ar


title: DKO_E_plus_ET280-Input

description:
Library name: DKO_E_plus_ET280-Input
bigwig file

value: Input DNA


title: sample 7-2-6 BatchB_water extract of Banhasasim-tang (Low dose)_rep2

value: Banhasasim-tang water extract 20 ug/mL


title: Pup1, scRNAseq

description: BD Rhapsody

value: Femoral and tibial growth plate cartilage

value: Chondrocytes

value: Postnatal day 5


title: DKO_E_plus_ET280-H3K4me3

description:
Library name: DKO_E_plus_ET280-H3K4me3
bigwig file

value: non-castrated

value: endpoint tumor


title: ES-2 cells with PBMCs, DMSO, treatment 1

description: Library name: NB_25

value: WT

value: DMSO


title: sample 7-2-5 BatchB_water extract of Banhasasim-tang (Medium dose)_rep2

value: Banhasasim-tang water extract 100 ug/mL


title: KPC-tumor-tissue_Ctsa_KD_obese-VAT-EVs_scRNA-Seq_Rep2

city: Guangzhou

first: Zhou

last: yifan

state: 周一帆

address: 74 Zhongshan Second Road

country: China

institute: Sun Yat-sen University Cancer Center

description: 10 × Genomics

data_processing:
Samples were sequenced with an average depth of 50,000 reads per cell. The quality of cells was assessed based on three metrics including controlling the number of total UMI count per cell (library size) below 30,000, the number of detected genes > 200 and < 6,000 and the percentage of mitochondrial genes < 10%. Subsequently, Seurat (version 4.3.0) was employed to normalize the data to sequencing depth through a LogNormalize approach. Mitochondrial contamination and cell cycle effects were also regressed out. To identify a subset of significant principal components, the PCElbowPlot function of Seurat was utilized. For cell clustering and UMAP visualization, the FindClusters and RunUMAP functions were executed, respectively. The annotations of cell identity on each cluster were defined by the expression of known marker genes.
Assembly: mm10

source_name: KPC tumor tissue

extract_protocol:
Transfer the chopped pieces to a 50 ml centrifuge tube, add Collagenase Type  II and Collagenase Type IV, add 15 ul CaCl2 (100 mg/ml) solution and 1mg/ml DNase I . Mix well and place on a shaker at 37 ℃ for 20-30 min. After the digestion is complete, take it out and filter it through a 70um sieve and then a 40um sieve into a new 50 ml centrifuge tube, and immediately place the filtered supernatant on ice. Centrifuge at 400g for 4 min. And resuspend the pellet with 5 ml RBC Lysis buffer. 5 ml of 0.04% BSA was used to resuspend, and then determine the cell concentration using a Countess II FL Automated Cell Counter. According to the requirements of 10X GENOMICS on the machine, suck out the corresponding volume of cell suspension.
library preparation was performed on  10 × Genomics system.

value: KPC tumor tissue

value: Ctsa KD Obese-VAT-EVs


title: DKO_E_plus_ET280-H3K27me3

description:
Library name: DKO_E_plus_ET280-H3K27me3
bigwig file


title: Organoid_graft_2

city: Shanghai

first: Rulin

last: Huang

state: Shanghai

address: No.639, Manufacturing Bureau Road

department: Department of plastic and reconstructive surgery

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

description: 10x Genomics

data_processing:
The Cell Ranger (Zheng et al., 2017) software was used for sample demultiplexing, barcode processing, and single-cell 3' gene counting. UMI tags and barcodes were extracted and filtered, with corrections applied based on sequencing error probabilities. Read2 was aligned to the reference genome using STAR (Dobin et al., 2012), and PCR duplicates were removed. Cell barcodes were identified via UMI counts and a background RNA model. Data clustering and visualization were performed in Seurat (Butler et al., 2018), using LogNormalize for data scaling, PCA for dimensional reduction, and tSNE/UMAP for visualization. Cluster markers were identified based on differential expression using FindAllMarkers.
Assembly: GRCh38
Supplementary files format and content: tsv and mtx gene expression matrix files which are inputs for Seurat for analysis

source_name: Adipose tissue

extract_protocol:
The tissue samples were washed and digested using collagenase and incubated in a shaking water bath set at 37 °C for 60 minutes to facilitate optimal cell dissociation. Subsequently, debris and dead cell removal was performed to eliminate any remaining tissue fragments and acquire a single-cell suspension with high cell viability. Then, cell count and viability was estimated using fluorescence Cell Analyzer (Countess II, Thermo) with AO/PI reagent. Finally, the harvested cells were washed twice with PBS and then resuspended in PBS with 0.04% BSA at a density of 1 × 106 cells per ml.
Single-cell RNA-Seq libraries were prepared using a 10× Chromium Next Gel Bead-in-Emulsion (GEM) Single Cell 3’ Reagent Kits v3.1 from 10× Genomics as instructions. Briefly, cells were mixed with reverse transcription reagent and then loaded into the sample well in Chromium Next GEM Chip G. Subsequently Gel Beads and Partitioning Oil were dispensed into corresponding wells separately. After emulsion droplet were formed, reverse transcription was performed. The resulting cDNA was then purified, amplified, cleaned, and ligated to sequencing adaptors. Finally, the indexed PCR was employed to amplify the DNA fragments. The indexed sequencing libraries were cleared with SPRI beads, quantified by qPCR, and ultimately sequenced on a NovaSeq 6000 platform (Illumina) with PE150 read length.
The Cell Ranger Single-cell Software Suite61 was used to perform sample demultiplexing, barcode processing, and single-cell 3ʹ gene counting. First, UMI tags and barcode sequences were extracted from Read1, followed by alignment of Read2 (containing the cDNA insert) to a reference genome using STAR62. Next, Barcodes and UMIs were filtered based on quality. Last, PCR duplicates were identified by shared barcode sequences, UMI tags, and gene IDs. Confidently mapped non-PCR duplicates with valid barcodes and UMIs were utilized to generate the gene-barcode matrix. Cell barcodes were determined, distinguishing between cells and empty partitions. Meaningful read counts were calculated based on valid barcodes, UMIs, and mapped reads.

value: Adipose tissue

tag: donor

value: Female


title: KPC-tumor-tissue_Ctsa_KD_obese-VAT-EVs_scRNA-Seq_Rep1

description: 10 × Genomics


title: sample 7-2-4 BatchB_water extract of Banhasasim-tang (High dose)_rep2

value: Banhasasim-tang water extract 500 ug/mL


title: Islet_Organoid_2

description: 10x Genomics


title: sample 7-2-2 BatchB_water extract of Yijung-tang (Medium dose)_rep2

value: Yijung-tang water extract 100 ug/mL


title: sample 7-2-3 BatchB_water extract of Yijung-tang (Low dose)_rep2

value: Yijung-tang water extract 20 ug/mL


title: KPC-tumor-tissue_Obese-VAT-EVs_scRNA-Seq_Rep2

description: 10 × Genomics

value: Obese-VAT-EVs


title: Organoid_graft_1

description: 10x Genomics


title: KPC-tumor-tissue_Obese-VAT-EVs_scRNA-Seq_Rep1

description: 10 × Genomics


title: DKO_E_plus_ET280-H3K27ac

description:
Library name: DKO_E_plus_ET280-H3K27ac
bigwig file

value: prostate tissue

value: male


title: Islet_Organoid_1

description: 10x Genomics


title: DKO_E_plus_ET183-Input

description:
Library name: DKO_E_plus_ET183-Input
bigwig file

value: Input DNA


title: sample 7-3-1 BatchB_water extract of Yijung-tang (High dose)_rep3

value: Yijung-tang water extract 500 ug/mL


title: sample 7-1-6 BatchB_water extract of Banhasasim-tang (Low dose)_rep1

value: Banhasasim-tang water extract 20 ug/mL


title: KPC-tumor-tissue_Normal-VAT-EVs_scRNA-Seq_Rep2

description: 10 × Genomics

value: Normal-VAT-EVs


title: DKO_E_plus_ET183-H3K4me3

description:
Library name: DKO_E_plus_ET183-H3K4me3
bigwig file

value: non-castrated

value: endpoint tumor


title: Expanded_ADSCs_3

description: 10x Genomics


title: sample 7-2-1 BatchB_water extract of Yijung-tang (High dose)_rep2


title: KPC-tumor-tissue_Normal-VAT-EVs_scRNA-Seq_Rep1

description: 10 × Genomics

value: WT


title: DKO_E_plus_ET183-H3K27me3

description:
Library name: DKO_E_plus_ET183-H3K27me3
bigwig file


title: Expanded_ADSCs_2

description: 10x Genomics


title: sample 7-1-5 BatchB_water extract of Banhasasim-tang (Medium dose)_rep1

value: Banhasasim-tang water extract 100 ug/mL


title: MC9-cell_PseudoU_RNA-Seq_Rep5

data_processing:
Fastp software (version 0.12.4)87 was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. We used STAR (version 2.7.1a)88 to map reads to the reference genome of mm10. Read counts were calculated using RSEM (version 1.2.28-0)89. The differentially expressed mRNAs were calculated by R package DESeq290.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
The library preparation was performed on an Illumina Novaseq 6000 sequencing platform (LC-Bio Technology).

value: Murine mast cell

value: PseudoU


title: Expanded_ADSCs_1

description: 10x Genomics

value: Adipose tissue

value: Female


title: sample 7-1-4 BatchB_water extract of Banhasasim-tang (High dose)_rep1

value: Banhasasim-tang water extract 500 ug/mL


title: DKO_E_plus_ET183-H3K27ac

description:
Library name: DKO_E_plus_ET183-H3K27ac
bigwig file


title: DKO_E_plus_ET183-AR

description:
Library name: DKO_E_plus_ET183-AR
bigwig file

value: Ar


title: RMF_pellets_3

description: 10x Genomics


title: MC9-cell_PseudoU_RNA-Seq_Rep4


title: DKO_E_plus_ET280-AR

description:
Library name: DKO_E_plus_ET280-AR
bigwig file


title: sample 7-1-3 BatchB_water extract of Yijung-tang (Low dose)_rep1

value: Yijung-tang water extract 20 ug/mL


title: RMF_pellets_2

description: 10x Genomics


title: DKO_E_E-ET60-Input

description:
Library name: DKO_E_E-ET60-Input
bigwig file

value: prostate tissue


title: MC9-cell_PseudoU_RNA-Seq_Rep3


title: sample 7-1-2 BatchB_water extract of Yijung-tang (Medium dose)_rep1

value: Yijung-tang water extract 100 ug/mL


title: RMF_pellets_1

description: 10x Genomics


title: DKO_E_E-ET60-H3K4me3

description:
Library name: DKO_E_E-ET60-H3K4me3
bigwig file

value: male


title: sample 7-1-1 BatchB_water extract of Yijung-tang (High dose)_rep1

value: Yijung-tang water extract 500 ug/mL


title: MC9-cell_PseudoU_RNA-Seq_Rep1


title: Native_Fat_3

description: 10x Genomics


title: DKO_E_E-ET60-H3K27me3

description:
Library name: DKO_E_E-ET60-H3K27me3
bigwig file


title: sample 6-3-6 BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep3

value: Aconiti Lateralis Radix Preparata water extract 20 ug/mL


title: DKO_E_E-ET60-H3K27ac

description:
Library name: DKO_E_E-ET60-H3K27ac
bigwig file


title: MC9-cell_Vehicle_RNA-Seq_Rep5

value: Vehicle


title: sample 6-3-5 BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep3

value: Aconiti Lateralis Radix Preparata water extract 100 ug/mL


title: MC9-cell_Vehicle_RNA-Seq_Rep4


title: Native_Fat_1

description: 10x Genomics


title: DKO_E_E-ET60-AR

description:
Library name: DKO_E_E-ET60-AR
bigwig file

value: non-castrated

value: endpoint tumor


title: sample 6-3-4 BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep3

value: Aconiti Lateralis Radix Preparata water extract 500 ug/mL


title: MC9-cell_Vehicle_RNA-Seq_Rep3

value: Murine mast cell

value: WT


title: DKO_E_E-ET126-Input

description:
Library name: DKO_E_E-ET126-Input
bigwig file

value: Input DNA


title: RNA-seq iPSC FTD rep3

city: San Francisco

first: Sonia

last: Infante

address: 513 Parnassus Ave

institute: University of California San Francisco

data_processing:
The raw RNA-Seq reads were analyzed by Novogene (Beijing, China). Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample. xls files for processed data with raw counts, fpkm, log fold change, and padj

source_name: fibroblasts

growth_protocol: iPSCs were maintained at 37°C and 5% CO2 in mTesR+ (#100-0276 STEMCELL Technologies )

extract_protocol:
RNA was extracted from iPSCs plated for 48 h on Matrigel-coated 6 WP with the RNAeasy Micro Kit (Qiagen #74004) according to the manufacturer’s protocol with the following modifications: after disrupting the cells with RLT buffer, cell suspension was transferred into a QIAshredder spin column (Qiagen #79656) and centrifuge. The lysate was pipetted directly, without further dilution, into a QIAshredder spin column and centrifuged for 2 minutes at full speed (13,000 rpm). The RNA concentration and purity were measured using SpectraMax QuickDrop UV-Vis Spectrophotometer (Molecular Devices, #7546).
Libraries were prepared with the RNA Library Prep Kit (Illumina)

value: fibroblasts

value: Induced pluripotent stem cells (iPSCs)

value: Frontotemporal dementia

value: No treatment


title: sample 6-3-3 BatchB_water extract of Bupleuri Radix (Low dose)_rep3

value: Bupleuri Radix water extract 20 ug/mL


title: sample 6-3-2 BatchB_water extract of Bupleuri Radix (Medium dose)_rep3

value: Bupleuri Radix water extract 100 ug/mL


title: RNA-seq iPSC FTD rep2


title: MC9-cell_Vehicle_RNA-Seq_Rep1


title: MC9-cell_PseudoU_RNA-Seq_Rep2

value: PseudoU


title: MC9-cell_Vehicle_RNA-Seq_Rep2


title: RNA-seq iPSC FTD rep1


title: RNA-seq iPSC WT control rep3

value: control


title: DKO_E_E-ET126-H3K27ac

description:
Library name: DKO_E_E-ET126-H3K27ac
bigwig file

value: prostate tissue

value: male


title: DKO_E_E-ET126-H3K27me3

description:
Library name: DKO_E_E-ET126-H3K27me3
bigwig file


title: sample 6-3-1 BatchB_water extract of Bupleuri Radix (High dose)_rep3

value: Bupleuri Radix water extract 500 ug/mL


title: sample 6-2-6 BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep2

value: Aconiti Lateralis Radix Preparata water extract 20 ug/mL


title: CD8T-cell_PseudoU_ATAC-Seq_Rep1

data_processing:
The Diffbind R package (version 3.8.4)92 was used to generate the count matrix of Tn5 insertion site numbers for each consensus peak (peaks that were present in at least two samples). DARs (differentially accessible regions) were identified between conditions using the limma R package (version3.54.2)93 with P < 0.05 and |Log2FC| > 0.58. To visualize ATAC peaks, we use "plotHeatmap" commamd to plot Heatmap and "bamCoverage" command, adding the parameter "normalizeUsingRPKM" to convert bam files to bw format with Deeptools (version 1.9)94.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
The transposition was assessed using the Nextera DNA Library Preparation Kit (Illumina). The nuclei (5 x 104) were pelleted and resuspended with transposase for 30 min at 37 °C. The transposed DNA fragments were then purified instantly with a MinElute PCR Purification Kit (Qiagen) and PCR-amplified using 1 × NEB Next High-Fidelity PCR Master Mix (New England Biolabs).
Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000 using PE150.

value: Murine CD8T-cell


title: RNA-seq iPSC WT control rep2


title: DKO_E_E-ET126-AR

description:
Library name: DKO_E_E-ET126-AR
bigwig file

value: Ar

value: non-castrated

value: endpoint tumor


title: sample 6-2-5 BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep2

value: Aconiti Lateralis Radix Preparata water extract 100 ug/mL


title: Native_Fat_2

description: 10x Genomics

value: Adipose tissue

value: Female


title: CD8T-cell_PseudoU_ATAC-Seq_Rep2

value: WT


title: RNA-seq iPSC WT control rep1

value: fibroblasts

value: Induced pluripotent stem cells (iPSCs)

value: No treatment


title: sample 6-2-4 BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep2

value: Aconiti Lateralis Radix Preparata water extract 500 ug/mL


title: combination treatment

city: Halle

first: Markus

last: Glaß

department: Institute of Molecular Medicine

description:
Library name: COMBI
BD Rhapsody HT

data_processing:
Read processing including demultiplexing, genome mapping and gene counting was performed using the BD Rhapsody Sequence Analysis Pipeline v2.0 at www.sevenbridges.com
Assembly: GRCm39
Supplementary files format and content: 10x compatible tab separated value files and matrix files

source_name: IP xenograft

growth_protocol: ID8-Trp53-/- cells were intraperitoneally injected into C57BL/6 mice and engrafted for  7 days.

extract_protocol:
Mice were sacrificed and ascites was collected, depleted for erytrocytes, filtered and cryopreserved until scRNA-seq was performed. Cells of animals of the same treatment condition were pooled. If applicable, dead cells were removed using the dead cellremoval kit (Miltenyi Biotec).
Single cells were captured using the BD Rhapsody HT Express and the BD Rhapsody Scanner. cDNA synthesis and WTA library constructions was perfomed according to the manufacturer's instructions.

treatment_protocol: Mice were treated twice a week with DMSO, BTYNB (50mg/kg; closed conformation), anti-PD1 (clone RMP1-14; 100ng/dose) or isotype control (IgG2a; 100ng/dose) until reaching the termination criteria (appr. 3 mL ascites)

value: IP xenograft

value: ID8-Trp53 knockout

value: tumor and immune cells

value: BTYNB & PD1 blocking antibody


title: CD8T-cell_Vehicle_ATAC-Seq_Rep2

value: Vehicle


title: CD8T-cell_Vehicle_ATAC-Seq_Rep1

value: Murine CD8T-cell


title: PD1 treatment

description:
Library name: PD1
BD Rhapsody HT

value: DMSO & PD1 blocking antibody


title: sample 6-2-3 BatchB_water extract of Bupleuri Radix (Low dose)_rep2

value: Bupleuri Radix water extract 20 ug/mL


title: DKO_E_E-ET126-H3K4me3

description:
Library name: DKO_E_E-ET126-H3K4me3
bigwig file

value: prostate tissue

value: male

value: non-castrated

value: endpoint tumor


title: KPC-cell_PseudoU_ATAC-Seq_Rep2

source_name: KPC-cell

value: KPC-cell

value: Murine pancreatic cancer cell

value: WT

value: PseudoU


title: BTYNB treatment

description:
Library name: BTYNB
BD Rhapsody HT

value: BTYNB & IgG control antibody


title: HTMCs, DEX-2

first: Yang

last: Zhang

address: 197 Ruijin Er Road

institute: Ruijin Hospital Affiliated Medical School, Shanghai Jiaotong University

data_processing:
Quality control Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast FASTQ preprocessor with useful quality. Clean data (clean reads) were obtained after quality control, adapter trimming, quality filtering and per-read quality cutting. All the downstream analyses were based on the clean data
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0 (hierarchical indexing for spliced alignment of transcripts), which is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT2 uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole genome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments. HISAT2 is the fastest system currently available, with equal or better accuracy than any other method. HISAT2 was run with the default parameters
Quantification of gene expression level Featurecount was used to count the reads numbers mapped to each gene. And then TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene. TPM, Transcripts Per Kilobase of exon model per Million mapped reads, considers the correction of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels .
Differential expression analysis Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with |log2(FoldChange)| > 1 and adjusted Pvalue <0.05 found by DESeq were assigned as differentially expressed.
Assembly: We selected HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) software to align transcriptome sequencing reads to the reference genome. HISAT2 is an improved version of the BWT algorithm, with advantages such as high speed, high sensitivity and accuracy, and low memory consumption. Clean Reads are aligned to the reference genome to obtain alignment feature information and stored in SAM format (Sequence Alignment/Map format). The SAM sequence alignment format standard was developed by Sanger and is mainly used to display the information features of sequencing sequence alignment to the genome. BAM files are the binary format of SAM files, with smaller storage resources and are often used for subsequent calculations. Based on the alignment results, BCFtools is used to sort the BAM files, filter duplicate reads, and finally perform statistics and graphical display on the alignment results of the sequences on the reference genome.
Supplementary files format and content: tab-delimited text file includes read counts for all Sample

source_name: HTMCs

extract_protocol:
After 7 days of culture in the presence or absence of 100 nM dexamethasone, to extract total RNA from HTMCs, begin by lysing the cells with 1 ml of TRIzol Reagent per well of a 6-well plate, ensuring complete lysis by vortexing for 15 seconds. Add 0.2 ml of chloroform per 1 ml of TRIzol, shake vigorously for 15 seconds, and let it sit at room temperature for 2-3 minutes. Centrifuge at 12,000 x g for 15 minutes at 4°C, then carefully transfer the upper aqueous phase to a new tube. Precipitate RNA by adding an equal volume of isopropanol, mix gently, and let it stand at room temperature for 10 minutes. Centrifuge at 12,000 x g for 10 minutes at 4°C, discard the supernatant, and wash the RNA pellet with 1 ml of 75% ethanol. Centrifuge at 7,500 x g for 5 minutes at 4°C, discard the supernatant, and air-dry the pellet for a few minutes. Dissolve the RNA pellet in RNase-free water and incubate at 55-60°C for 10 minutes to ensure complete dissolution.
After the sample is qualified, the sample library is constructed. The specific mRNA capture and library construction process is as follows: Most eukaryotic mRNAs have a polyA structure. Oligo (DT) magnetic beads are used to capture mRNAs with a polyA structure; The fragmented mRNA is used as a template and random oligonucleotides are used as primers to synthesize the first cDNA chain in the M-MuLV reverse transcriptase system; The RNA chain is degraded with RNaseH, and the second cDNA chain is synthesized with dNTPs as raw materials under the DNA polymerase I system; The double-stranded cDNA is purified, and the end is repaired, the A tail is added, and the sequencing adapter is connected; The cDNA of about 200bp is screened with AMPure XP beads, PCR amplification is performed, and the PCR product is purified again with AMPure XP beads to finally obtain the sequencing library.

value: HTMCs

value: DEX


title: sample 6-2-2 BatchB_water extract of Bupleuri Radix (Medium dose)_rep2

value: Bupleuri Radix water extract 100 ug/mL


title: KPC-cell_PseudoU_ATAC-Seq_Rep1


title: control treatment

description:
Library name: DMSO
BD Rhapsody HT

value: IP xenograft

value: ID8-Trp53 knockout

value: tumor and immune cells

value: DMSO & IgG control antibody


title: HTMCs, DEX-1


title: sample 6-2-1 BatchB_water extract of Bupleuri Radix (High dose)_rep2

value: Bupleuri Radix water extract 500 ug/mL


title: KPC-cell_Vehicle_ATAC-Seq_Rep2

value: Vehicle


title: HTMCs, DMSO-3

value: DMSO


title: DKO_EP-DKOE505

type: other

description: Infinium Mouse Methylation MM285 BeadChip

hyb_protocol: Bisulfite-converted DNA was hybridized to the Infinium Mouse Methylation BeadChip (Illumina).

scan_protocol: Arrays were scanned using the Illumina iScan system.

data_processing:
ChAMP DNA methylation pipeline
File merged_beta_values.csv represents normalized beta values

label: Cy3 and Cy5

molecule: other

source_name: Mouse prostate endstage tumor tissue

label_protocol: 500 ng of high-quality genomic DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit per sample.

extract_protocol: Genomic DNA was extracted from mouse endstage prostate tumor tissue using the QIAamp DNA Mini kit following the manufacturer’s protocol.

value: Mouse prostate endstage tumor tissue

value: intact, non-castrated


title: DKO_EP-ET280


title: KPC-cell_Vehicle_ATAC-Seq_Rep1

value: KPC-cell


title: sample 6-1-6 BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep1

value: Aconiti Lateralis Radix Preparata water extract 20 ug/mL


title: sample 6-1-5 BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep1

value: Aconiti Lateralis Radix Preparata water extract 100 ug/mL


title: HTMCs, DMSO-2


title: HTMCs, DMSO-1


title: DKO_EP-DKOE304


title: sample 6-1-4 BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep1

value: Aconiti Lateralis Radix Preparata water extract 500 ug/mL


title: MC9-cell_PseudoU_ATAC-Seq_Rep1

value: Murine mast cell

value: WT

value: PseudoU


title: MC9-cell_PseudoU_ATAC-Seq_Rep2


title: DKO_EP-ET183


title: DKO_EE-DKOE305


title: sample 6-1-3 BatchB_water extract of Bupleuri Radix (Low dose)_rep1

value: Bupleuri Radix water extract 20 ug/mL


title: HTMCs, DEX-3

value: HTMCs

value: DEX


title: NM66, replicate 1, scRNA-seq, Post

city: dallas

first: Shaheen

last: Khan

state: texas

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: 10X Genomics

data_processing: Data was demultiplexed using Cell ranger by 10X genomics

source_name: PBMCs

extract_protocol:
PBMCs were isolated from blood and frozen in 10% DMSO in liquid Nitrogen tanks. PBMCs were then thawed and RBCs were lysed before preparing the libraries.
Libraries were prepared using 5' prime protocol as per the instructions by 10X Genomics

value: PBMCs

value: Post


title: MC9-cell_Vehicle_ATAC-Seq_Rep2


title: MC9-cell_Vehicle_ATAC-Seq_Rep1


title: NM66, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: BL


title: DKO_EE-ET277


title: sample 6-1-1 BatchB_water extract of Bupleuri Radix (High dose)_rep1

value: Bupleuri Radix water extract 500 ug/mL


title: NM36, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: DKO_EE-ET60


title: Mouse Thymus (APC), Perinatal Day 28, Wild-type, Hashtagged Sample (FB)

city: Nashville

first: Bryan

middle: Robert

last: Helm

state: Tennessee

address: 2525 West End Avenue, Suite 1100

department: Center for Quantitative Science

institute: Vanderbilt University Medical Center

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed with Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files with gene names, cell barcodes, and raw expression counts

source_name: Thymus

extract_protocol:
To sort hematopoietic APCs for scRNA-sequencing, thymi were harvested and enzymatically digested with an enzymatic solution comprising  LiberaseTM (Roche) and DNAse I in PBs at 37 degrees celsius. Isolated cells were spun down and stained with the corresponding panel of antibodies. The sort samples were resuspended in FWB+ EDTA buffer plus propidium iodide (Enzo). Sorted hematopoietic APCsells were then spun down in FWB without EDTA, counted and resuspended at a concentration of 700-1200 cells/µL prior to submission to the sequencing core.
Library prep was performed per the manufacturer's protocol for scRNA-seq samples (Chromium Next GEM Single Cell 3' v3.1).

value: Thymus

value: Antigen Presenting Cells

value: Wild Type


title: NM36, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: sample 5-3-6 BatchB_water extract of  Cimicifugae Rhizoma (Low dose)_rep3

value: Cimicifugae Rhizoma water extract 20 ug/mL


title: Mouse Thymus (APC), Perinatal Day 28, Wild-type, Hashtagged Sample (GEX)


title: DKO_EE-ET58

value: Mouse prostate endstage tumor tissue

value: intact, non-castrated


title: sample 5-3-5 BatchB_water extract of  Cimicifugae Rhizoma (Medium dose)_rep3

value: Cimicifugae Rhizoma water extract 100 ug/mL


title: NM35, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: Mouse Thymus (APC), Perinatal Day 28, Rag2 KO, Sample 2

value: Rag2 KO


title: TKO-T812

value: TKO


title: NM35, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: NM30, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: sample 5-3-4 BatchB_water extract of  Cimicifugae Rhizoma (High dose)_rep3

value: Cimicifugae Rhizoma water extract 500 ug/mL


title: TKO-T209


title: Mouse Thymus (APC), Perinatal Day 28, Rag2 KO, Sample 1


title: TKO-T643


title: Mouse Thymus (APC), Perinatal Day 28, MHCII KO, Sample 2

value: MHCII KO


title: sample 6-1-2 BatchB_water extract of Bupleuri Radix (Medium dose)_rep1

value: Bupleuri Radix water extract 100 ug/mL


title: TKO-T176


title: sample 5-3-3 BatchB_water extract of Citri Unshius Pericarpium (Low dose)_rep3

value: Citri Unshius Pericarpium water extract 20 ug/mL


title: NM30, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: PBMCs


title: sample 5-3-2 BatchB_water extract of Citri Unshius Pericarpium (Medium dose)_rep3

value: Citri Unshius Pericarpium water extract 100 ug/mL


title: NM29, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: Post


title: DKO-T735

value: DKO


title: Mouse Thymus (APC), Perinatal Day 28, B2m KO, Sample 2

value: Thymus

value: B2m KO


title: sample 5-3-1 BatchB_water extract of Citri Unshius Pericarpium (High dose)_rep3

value: Citri Unshius Pericarpium water extract 500 ug/mL


title: NM29, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: BL


title: DKO-T569

value: Mouse prostate endstage tumor tissue


title: sample 5-2-6 BatchB_water extract of  Cimicifugae Rhizoma (Low dose)_rep2

value: Cimicifugae Rhizoma water extract 20 ug/mL


title: Mouse Thymus (APC), Perinatal Day 28, B2m KO, Sample 1

value: Antigen Presenting Cells


title: NM28, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: sample 5-2-5 BatchB_water extract of  Cimicifugae Rhizoma (Medium dose)_rep2

value: Cimicifugae Rhizoma water extract 100 ug/mL


title: DKO-T173

value: intact, non-castrated


title: NM28, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: Mouse Thymus (APC), Perinatal Day 28, Wild-type, Sample 2

value: Wild Type


title: DKO-T57


title: 700 treadwear grades tire wear particles leachate treated group 3

city: Busan

first: Tae Hwan

last: Shin

address: Nakdong-daero 550 beon-gil

department: Health Sciences

institute: Dong-A University

description: Library name: 700-3

data_processing:
Raw sequencing reads were preprocessed to remove adapter sequences and low-quality reads prior to analysis. The cleaned reads were then aligned to the Danio rerio reference genome (GRCz11) using Hierarchical Indexing for Spliced Alignment of Transcripts 2 (HISAT2; v2.1.0).
Following alignment, transcript assembly and quantification were carried out using StringTie (v2.1.3b). DEG analysis was performed using gene-level abundance estimates across samples. Genes with read count values equal to zero in all but one sample were excluded from further analysis. To enable log₂ transformation, a pseudo-count of 1 was added to the read count values of the remaining genes. The data were then log₂-transformed and subjected to relative log expression (RLE) normalization. Statistical significance of differential gene expression was assessed using the nbinomWaldTest function implemented in the DESeq2 package in R, under the null hypothesis that no differences exist between groups. Fold changes were calculated, and p-values were adjusted for multiple testing using the Benjamini–Hochberg procedure to control the false discovery rate (FDR).
Assembly: The Danio rerio reference genome (GRCz11) and its corresponding annotation files were obtained from NCBI.
Supplementary files format and content: processed data.xlsx
Supplementary files format and content: FPKM, TPM, Read Count

organism: Danio rerio

source_name: zebrafish larvae

growth_protocol: Adult wild-type zebrafish were purchased from Gangnam Aquarium (Gyeonggi-do, Korea) and acclimated for at least three months in the breeding facility of the Korea Institute of Toxicology (KIT, Jinju, Korea) before experiments. The breeding conditions were maintained at a temperature of 27 ± 1 °C under a 14 h:10 h (light:dark) photoperiod. Dissolved oxygen concentrations were kept above 6.64 mg/L, and pH was maintained between 7.4 and 7.6. Zebrafish were fed brine shrimp (Artemia franciscana) and tropical flakes (TetraMin®; Spectrum Brands, Blacksburg, VA, USA) twice daily (morning and afternoon). For egg collection, five male and five female zebrafish were placed in mating cages overnight. Eggs were collected the following morning, and those with intact yolk membranes showing no signs of coagulation were carefully selected for subsequent experiments.

extract_protocol:
For each transcriptomic analysis, 80 zebrafish larvae were pooled per sample, with three biological replicates prepared per experimental group. Larvae were rinsed three times with PBS and preserved in RNAlater™ Stabilization Solution (Thermo Fisher) at -20°C until RNA extraction. Total RNA was isolated using a RNeasy Mini Kit (Qiagen, Hilden, Germany), and its concentration was determined with the Quant-iT™ RiboGreen® RNA Assay Kit (Invitrogen, Carlsbad, CA, USA). RNA integrity was evaluated by the Agilent TapeStation system with RNA ScreenTape (#5067-5576, Agilent Technologies).
RNA samples possessing an RNA integrity number (RIN) exceeding 7.0 were utilized for library construction. For each sample, 0.5 μg of total RNA was used to create libraries using a commercial kit (TruSeq Stranded Total RNA Library Prep Gold Kit; Illumina, San Diego, CA, USA). Ribosomal RNA (rRNA) was initially depleted from the total RNA. Isolated mRNAs were fragmented into short pieces, and double-stranded cDNAs were synthesized. The cDNAs were modified through end-repair, poly A addition, and connected with sequencing adapters. Library concentration was measured using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems, Wilmington, MA, USA), and the library size distribution was evaluated with the Agilent D1000 ScreenTape (#5067-5582, Agilent Technologies).

treatment_protocol: To expose zebrafish eggs to leachates, 200 zebrafish eggs were placed in a PYREX® 150×75 mm crystallizing dish (Pyrex, Rosemont, IL, USA) containing 100 mL of medium. Exposure was performed from 4 to 168 h post-fertilization (hpf) The experiment was repeated three times. At 72 hpf, larvae were transferred to clean dishes containing fresh medium with modified conditions (pH 7.2 ± 0.1, dissolved oxygen 8.1 ± 0.1 mg/L), although temperature and photoperiod conditions remained consistent with those of adult zebrafish culture. All experiments related to animal work were approved by the KIT Animal Care and Use Committee (approval #2110-0005).

value: zebrafish larvae

value: wildtype

value: TWP 700 leachates


title: NM27, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: PBMCs


title: sample 5-2-4 BatchB_water extract of  Cimicifugae Rhizoma (High dose)_rep2

value: Cimicifugae Rhizoma water extract 500 ug/mL


title: SKO-T614

value: SKO


title: 700 treadwear grades tire wear particles leachate treated group 2

description: Library name: 700-2


title: Mouse Thymus (APC), Perinatal Day 28, MHCII KO, Sample 1

value: MHCII KO


title: SKO-T549


title: sample 5-2-3 BatchB_water extract of Citri Unshius Pericarpium (Low dose)_rep2

value: Citri Unshius Pericarpium water extract 20 ug/mL


title: NM27, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: NM26, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: Post


title: NM26, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: Surfactant control group 3

description: Library name: SC-3

value: 0.001% bovine serum albumin (surfactant control)


title: 700 treadwear grades tire wear particles leachate treated group 1

description: Library name: 700-1


title: sample 5-2-1 BatchB_water extract of Citri Unshius Pericarpium (High dose)_rep2

value: Citri Unshius Pericarpium water extract 500 ug/mL


title: SKO-T104

value: Mouse prostate endstage tumor tissue


title: Surfactant control group 2

description: Library name: SC-2


title: NM65, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: sample 5-1-5 BatchB_water extract of  Cimicifugae Rhizoma (Medium dose)_rep1


title: sample 5-1-6 BatchB_water extract of  Cimicifugae Rhizoma (Low dose)_rep1

value: Cimicifugae Rhizoma water extract 20 ug/mL


title: Surfactant control group 1

description: Library name: SC-1


title: J11 crypt like HIO gamma mock-irradiated

city: Houston

first: Sarah

middle: Elizabeth

last: Blutt

state: Texas

address: One Baylor Plaza

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

description: Library name: J11cryptCG

data_processing:
Sequence reads were trimmed for adaptor sequence and low quality reads using Trim Galore version 0.6.6
Trimmed fastq were mapped with HISAT2 version 2.2.1 to the GRCh38.95 homo sapiens reference genome
Read counts were quantified using the featureCounts function in the Subreads package
Assembly: GRCh38.95
Supplementary files format and content: csv file contains raw counts for each sample

source_name: human intestinal organoid

growth_protocol: HIOs are maintained in proliferative media, WRNE, that contains all the known growth factors to support the intestinal stem cell.  HIOs can be maintained and passaged in a proliferative state indefinitely. To allow the HIOs to differentiate into the normal representative cell types of the intestinal epithelium, the HIOs are placed in media in the absence of WNT, Noggin, and R-spondin growth factors for 5 days

extract_protocol:
Total RNA was extracted using the QIAshredder and RNeasy Mini Kit (Qiagen) with the inclusion of the optional DNase digestion following the manufacturer’s instructions.
Total RNA recovered was sent to Novagene Co. (China) for library preparation (poly A enrichment) and sequencing with NovaSeq PE150 (6G raw reads per sample).

value: human intestinal organoid

value: control


title: NM65, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: BL


title: J11 crypt like HIO proton mock-irradiated

description: Library name: J11cryptCPro


title: XTC-2, H3, CnT-BS, biol rep 2

city: New York

first: Rochelle

middle: Makanani

last: Shih

address: 1230 York Ave

institute: Rockefeller University

description: Library name: XTC2_H3_rep2

data_processing:
XTC-2 data downsampled to 30 million reads to match sperm samples using seqtk v1.5-r133. Adapter trimming and dedeuplication of the demultiplexed reads was done using fastp v0.24.0 [--adapter_sequence CTGTCTCTTATACAC --adapter_sequence_r2 CTGTCTCTTATACAC -g --poly_g_min_len 5 -p -l 20 --cut_tail -y -Y 20 -q 20 --dedup]
Processed reads were then aligned to the Xenopus laevis genome (Xenla 10.1) and CpG methylation called using Bismark v0.24.2 [-q --local --score-min G,20,8 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 700]
Reads were then sorted into 1000bp bins of the Xenopus laevis genome. Mitochondrial reads and genomic bins which contained no reads across all samples were then removed. Normalized bigwig files were then generated from bam files using size factors estimated with DESeq2 v1.42.1.
Methylation data for each sample was extracted into a coverage file using Bismark v0.24.0 with a read cutoff of 5 and disregarding the first 9bp of read 2.
H3 methylation bigwigs were generated using a methylRawList object (methylKit v1.28.0) with a minimum read coverage of 2 and CpGs were then counted over 500bp tiles with a 500 bp step size and a minimum of 2 CpG sites for the tile to be counted.
Assembly: Xenla10.1
Supplementary files format and content: bigwig (.bw), Mitochondrial reads removed and sequence depth normalized using DESeq2 estimated size factors
Supplementary files format and content: methylation coverage files (.cov), tab separated with columns as follows: 1. seq-ID; 2. methylation state; 3. chromosome; 4. start position (= end position); 5. methylation call
Supplementary files format and content: peak files (.bed), BED file with columns as follows: 1. chromosome; 2. start coordinate; 3. end coordinate; 4. total signal; 5. max signal; 6. region represented by max signal.

organism: Xenopus laevis

growth_protocol: For sperm pronuclei: demembranated Xenopus laevis sperm was added to Xenopus egg extract at a concentration of 1500 sperm/µl with the addition of CaCl2 to a final concentration of 0.3M and incubated 20 ᵒC 90 min. For XTC-2: Leibovitz's L-15 Medium (Gibco™, Cat# 11415064) (0.7x amphibian strength, diluted with cell culture grade water (Corning®, Cat# 46-000-CV)) supplemented with 500 U/mL each of penicillin and streptomycin (Gibco™, Cat# 15140122), and 10 % FBS (R&D systems, Cat# S11150). XTC-2 cells were cultured in 26 °C incubator without CO2 supply.

extract_protocol:
For sperm pronuclei: Samples were then diluted 1:4 with 1xDB3 buffer [10mM HEPES-KOH pH 8.0, 100mM NaCl, 0.5 mM spermine, 0.5 mM spermidine, 1 mM ASEBF (GoldBio Cat#A-540-1), 1x ROCHE cOmplete™ protease inhibitor cocktail (Cat# 11697498001), 200 mM Sucrose, 0.1% Tween-20], layered onto 1 mL of 60SDB3 [1xDB3 + 60% sucrose] and centrifuged at 4ᵒC, 10,000 rpm for 45 min (Beckman Coulter SX241.5 rotor) to collect nuclei. For XTC-2: Nuclei isolation was performed at 4 ᵒC using the Nuclei EZ Prep kit (Millipore Cat# NUC101-1KT) as per manufacturer’s protocol and resuspended in 1x CnT-WB. For both: unmethylated lambda DNA was added to extracted nuclei at a final concentration of ~1% total DNA mass to assess for bisulfite conversion efficiency.
Libraries were prepared as specified in (Li et al. 2021; https://doi.org/10.1016/j.crmeth.2021.100118) using Illumina Nextra i5/i7 adapter primers. Libraries were amplified using 14 cycles on the thermocycler. Amplified samples were then purified using the MinElute PCR purification kit (Qiagen Cat# 28004), concentration measured using qPCR, pooled, and size selected at 200-1000bp in length on a 2% Agarose E-Gel EX (SYBR Gold II). Libraries were validated using the Agilent High Sensitivity DNA kit.

value: fibroblast


title: sample 5-1-4 BatchB_water extract of  Cimicifugae Rhizoma (High dose)_rep1


title: NM64, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: sample 5-1-3 BatchB_water extract of Citri Unshius Pericarpium (Low dose)_rep1


title: J11 crypt like HIO gamma irradiated

description: Library name: J11cryptRadG

value: 1 Gy gamma irradiation


title: sample 5-2-2 BatchB_water extract of Citri Unshius Pericarpium (Medium dose)_rep2

value: Citri Unshius Pericarpium water extract 100 ug/mL


title: XTC-2, H3, CnT-BS, biol rep 1

description: Library name: XTC2_H3_rep1


title: NM64, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: sample 5-1-2 BatchB_water extract of Citri Unshius Pericarpium (Medium dose)_rep1


title: SKO-T433

value: intact, non-castrated


title: NM4, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: PBMCs


title: J11 villus like HIO gamma mock-irradiated

description: Library name: J11villCG


title: NM4, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: sample B1-3-1 BatchB_Vehicle(DMSO)_rep3

value: 0.1% DMSO


title: NM24, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: Sperm pronuclei, Interphase, H3, CnT-BS, biol rep 1

description: Library name: Sperm_H3_rep1

source_name: sperm pronuclei

value: sperm pronuclei


title: J11 villus like HIO proton mock-irradiated

description: Library name: J11villCPro


title: NM24, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: NM68, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: J11 villus like HIO proton irradiated

description: Library name: J11villRadP

value: 1 Gy low LET proton irradiation


title: J11 villus like HIO gamma irradiated

description: Library name: J11villRadG


title: sample 4-3-6 BatchA_water extract of Zizyphi Fructus (Low dose)_rep3

value: Zizyphi Fructus water extract 20 ug/mL


title: Sperm pronuclei, Interphase, H3, CnT-BS, biol rep 2

description: Library name: Sperm_H3_rep2


title: J2 crypt like HIO gamma mock-irradiated

description: Library name: J2cryptCG


title: Sperm pronuclei, Interphase, H2AZ, CnT-BS, biol rep 1

description: Library name: Sperm_H2AZ_rep1


title: sample B1-2-1 BatchB_Vehicle(DMSO)_rep2


title: sample 4-3-5 BatchA_water extract of Zizyphi Fructus (Medium dose)_rep3

value: Zizyphi Fructus water extract 100 ug/mL


title: Sperm pronuclei, Interphase, H2AZ, CnT-BS, biol rep 2

description: Library name: Sperm_H2AZ_rep2


title: J2 crypt like HIO proton mock-irradiated

description: Library name: J2cryptCPro


title: J11 crypt like HIO proton irradiated

description: Library name: J11cryptRadP


title: lambdaN-Panx_RNA_Dox+

city: Tokyo

first: Kensaku

last: Murano

address: 35 Shinanomachi, Shinjuku

department: Department of Molecular Biology

institute: Keio University School of Medicine

description: Library name: RNA-seq_Sample 28

data_processing:
After adaptor sequence filtering by TrimGalore 0.6.7, RNA-seq reads were mapped to Drosophila melanogaster reference genome (dm6) using STAR 2.7.10a with following options, --outSAMmode NoQS; --alignEndsType Local; --outReadsUnmapped Fastx; --outMultimapperOrder Random; --outFilterMultimapNmax 1000; --winAnchorMultimapNmax 2000; --outFilterMismatchNmax 0; --seedSearchStartLmax 30; --alignSoftClipAtReferenceEnds No; -outFilterType BySJout; --alignSJoverhangMin 15; --alignSJDBoverhangMin 1. Adaptor trimmed ChIP-seq reads were mapped to Drosophila melanogaster reference genome (dm6) and Luc reporter plasmid (pSUb-14Box-Luc) using Bowtie2 2.2.5 with --very-sensitive option.
RNA-seq reads mapped on TE loci were quantified using featureCounts v2.0.1 and multi-mapped reads were counted fractionally for TEs. TE annotation data (RepeatMasker) was obtained from University of California, Santa Cruz (UCSC) Genome Browser.
For visualization of ChIP-seq reads on reference genome, alignment track were generated using bamCoverage program of deepTools 3.5.1 with --normalizeUsing RPKM; -bs 1 parameters.
Assembly: dm6
Supplementary files format and content: Read count data (.txt) from RNA-seq analysis. Read coverage data (.bw) from ChIP-seq analysis.

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Cells were grown at 26 degrees in OSC medium (M3 medium supplemented with fly extract)

extract_protocol:
For RNA-seq, total RNAs were isolated by RNeasy kit (Qiagen). Poly(A)+ RNAs were obtained using oligo-dT beads. For ChIP experiments targeting RNA polymerase II, OSC were fixed in 0.3% formaldehyde (methanol-free, Thermo Fisher) for 10 min at room temperature and quenched with a final concentration of 125 mM glycine for 2 min. After washing twice with PBS (containing 125 mM glycine), nuclei were isolated using 200 µl Low salt lysis buffer (10 mM HEPES-KOH pH 7.4, 10 mM NaCl, 1.5 mM MgCl2, 1% Nonidet P-40) supplemented with cOmplete (Protease inhibitor cocktail, Roche) and PhosSTOP (Phosphatase inhibitor cocktail, Roche). The isolated nuclei were resuspended in 200 µl Sonication buffer (50 mM Tris-HCl pH 7.9, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) supplemented with cOmplete and PhosSTOP, and sonicated using a probe-sonicator (BRANSON, SFX150) at 30% amplitude, with 2 sec pulses and 3 sec intervals, for a total of 2 min, in an ice-cold water bath. After centrifugation, the supernatant was passed through a 0.22-μm syringe filter (Membrane Solutions) and used for immunoprecipitation.To elucidate Pol II occupancy on the reporter gene, we utilized an anti-Pol II ser5-P antibody (Cosmobio, CMA603).The chromatin lysate was incubated with 1 µg of anti-Pol II ser5-P antibody at 4 °C for 3 h with rotation. The antibody was captured using Dynabeads Protein G.The captured chromatin was extracted in 100 µl of Elution buffer (50 mM Tris-HCl pH 7.9, 10 mM EDTA, and 1% SDS) at 65 °C for 10 min. The supernatant was supplemented with 4 µl of 5 M NaCl, and cross-link were reversed at 65 °C overnight in a Thermomixer at 1400 rpm (Eppendorf). DNA was purified using a spin column and eluted in Milli-Q water.
For RNA-seq, Poly(A)+ RNA was isolated from 2 µg total RNA using Dynabeads Oligo (dT)25 (Thermo Fisher), followed by heat-fragmentation at 94ºC for 6 min. cDNA was synthesized from the fragmented RNA by random hexamers and SuperScript III (Thermo Fisher), and then purified by AMPure XP (Beckman). Second strand DNA was synthesized by DNA polymerase I (NEB) in the presence of 1 mM dUTP at 16ºC for 2.5 h, and then purified by AMPure XP. Library preparation was carried out using the NEBNext Ultra II DNA Library Prep kit for illumina (NEB), according to the manufacturer’s instructions. For ChIP-seq, ChIPed DNAs were used for library preparation by NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following the manufacture’s protocol.

value: Ovary

value: OSC

value: Ovarian somatic cell

value: TRE-lambdaN-Panx

value: Doxycycline+


title: NM1, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: Post


title: sample 4-3-4 BatchA_water extract of Zizyphi Fructus (High dose)_rep3

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

value: Zizyphi Fructus water extract 500 ug/mL


title: XTC-2, H2AZ, CnT-BS, biol rep 2

description: Library name: XTC2_H2AZ_rep2

value: fibroblast


title: sample 5-1-1 BatchB_water extract of Citri Unshius Pericarpium (High dose)_rep1

value: Citri Unshius Pericarpium water extract 500 ug/mL


title: J2 crypt like HIO gamma irradiated

description: Library name: J2cryptRadG

value: human intestinal organoid

value: 1 Gy gamma irradiation


title: lambdaN-Panx_RNA_Dox-

description: Library name: RNA-seq_Sample 27

value: Doxycycline-


title: NM1, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: PBMCs

value: BL


title: sample B1-1-1 BatchB_Vehicle(DMSO)_rep1

value: 0.1% DMSO


title: XTC-2, H2AZ, CnT-BS, biol rep 1

description: Library name: XTC2_H2AZ_rep1


title: PNUTS_Setx-KD_RNA_rep2

description: Library name: RNA-seq_Sample 26


title: J2 crypt like HIO proton irradiated

description: Library name: J2cryptRadP

value: 1 Gy low LET proton irradiation


title: NM9, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: sample 4-3-2 BatchA_water extract of Coptidis Rhizoma (Medium dose)_rep3

value: Coptidis Rhizoma water extract 42 ug/mL


title: Setx-KD_RNA_rep2

description: Library name: RNA-seq_Sample 24

value: Ovary

value: Setx-KD


title: NM68, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: NM9, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: sample 4-3-1 BatchA_water extract of Coptidis Rhizoma (High dose)_rep3

value: Coptidis Rhizoma water extract 210 ug/mL


title: J2 villus like HIO proton mock-irradiated

description: Library name: J2villCPro

value: control


title: sample 4-2-6 BatchA_water extract of Zizyphi Fructus (Low dose)_rep2

value: Zizyphi Fructus water extract 20 ug/mL


title: Setx-KD_RNA_rep1

description: Library name: RNA-seq_Sample 23

value: OSC

value: Ovarian somatic cell


title: NM8, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: Post


title: J2 villus like HIO gamma irradiated

description: Library name: J2villRadG


title: sample 4-2-5 BatchA_water extract of Zizyphi Fructus (Medium dose)_rep2

value: Zizyphi Fructus water extract 100 ug/mL


title: NM8, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: J2 villus like HIO proton irradiated

description: Library name: J2villRadP

value: human intestinal organoid


title: J3 crypt like HIO gamma mock-irradiated

description: Library name: J3cryptCG


title: sample 4-2-4 BatchA_water extract of Zizyphi Fructus (High dose)_rep2

value: Zizyphi Fructus water extract 500 ug/mL


title: PNUTS-KD_RNA_rep2

description: Library name: RNA-seq_Sample 22

value: PNUTS-KD


title: sample 4-2-3 BatchA_water extract of Coptidis Rhizoma (Low dose)_rep2

value: Coptidis Rhizoma water extract 8.4 ug/mL


title: NM67, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: PBMCs

value: BL


title: sample 4-3-3 BatchA_water extract of Coptidis Rhizoma (Low dose)_rep3


title: J3 crypt like HIO proton mock-irradiated

description: Library name: J3cryptCPro


title: PNUTS_Setx-KD_RNA_rep1

description: Library name: RNA-seq_Sample 25


title: J2 villus like HIO gamma mock-irradiated

description: Library name: J2villCG


title: sample 4-2-2 BatchA_water extract of Coptidis Rhizoma (Medium dose)_rep2


title: J3 crypt like HIO gamma irradiated

description: Library name: J3cryptRadG

value: 1 Gy gamma irradiation


title: LacZ-KD_3_RNA_rep1

description: Library name: RNA-seq_Sample 19

value: WT


title: NM65, replicate 2, scRNA-seq, BL

description: 10X Genomics


title: NM65, replicate 2, scRNA-seq, Post

description: 10X Genomics


title: Sov-KD_2_RNA_rep2

description: Library name: RNA-seq_Sample 18

value: Ovary

value: Sov-KD


title: sample 4-1-5 BatchA_water extract of Zizyphi Fructus (Medium dose)_rep1


title: NM64, replicate 2, scRNA-seq, BL

description: 10X Genomics


title: Sov-KD_2_RNA_rep1

description: Library name: RNA-seq_Sample 17


title: J3 crypt like HIO proton irradiated

description: Library name: J3cryptRadP

value: 1 Gy low LET proton irradiation


title: NM67, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: PNUTS-KD_RNA_rep1

description: Library name: RNA-seq_Sample 21


title: Piwi-KD_2_RNA_rep2

description: Library name: RNA-seq_Sample 16

value: Piwi-KD


title: LacZ-KD_3_RNA_rep2

description: Library name: RNA-seq_Sample 20


title: J3 villus like HIO gamma irradiated

description: Library name: J3villRadG


title: NM63, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: sample 4-1-4 BatchA_water extract of Zizyphi Fructus (High dose)_rep1


title: Piwi-KD_2_RNA_rep1

description: Library name: RNA-seq_Sample 15


title: J3 villus like HIO proton mock-irradiated

description: Library name: J3villCPro

value: control


title: sample 4-1-3 BatchA_water extract of Coptidis Rhizoma (Low dose)_rep1


title: NM63, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: LacZ-KD_2_RNA_rep2

description: Library name: RNA-seq_Sample 14

value: OSC


title: J3 villus like HIO proton irradiated

description: Library name: J3villRadP


title: sample 4-2-1 BatchA_water extract of Coptidis Rhizoma (High dose)_rep2

value: Coptidis Rhizoma water extract 210 ug/mL


title: sample 4-1-2 BatchA_water extract of Coptidis Rhizoma (Medium dose)_rep1

value: Coptidis Rhizoma water extract 42 ug/mL


title: J6 crypt like HIO gamma mock-irradiated

description: Library name: J6cryptCG


title: sample 4-1-1 BatchA_water extract of Coptidis Rhizoma (High dose)_rep1


title: NM62, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: Post


title: LacZ-KD_2_RNA_rep1

description: Library name: RNA-seq_Sample 13

value: Ovarian somatic cell


title: NCD4

first: Cheng

last: Hu

address: No.600, Yishan Road, Shanghai, China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China

description:
Library name: AT-NCD4
11x Genomics

data_processing:
Raw sequencing data were processed using the Cell Ranger (version 7.1) to align reads to the reference genome (GRCm38) and generate a gene expression matrix.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: adipose tissue

growth_protocol: Animals were housed in groups of 3-5 per cage under specific pathogen-free (SPF) conditions, maintained at 22-24°C with 50–60% relative humidity and a 12-hour light-dark cycle, with unrestricted access to food and water.

extract_protocol:
The eWAT were isolated, minced, and digested in collagenase II. The digest was centrifuged, and the floating adipocytes were subsequently discarded. The SVF cells were filtered through a 40 μm cell strainer, centrifuged, and then re-suspended.
ScRNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3’ Library, following the manufacturer’s instructions. Briefly, GCs were resuspended in the master mikx andloaded together with partitioning oil and gel beads into the chip to generate the gelbead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every singleGEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence.Unigue Molecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiatedsized fragments were selected with SPRlselect reagent for subsequent libraryconstruction. During the library construction llumina R2 primer sequence, paired-endconstructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Seven-week-old mice were fed an NCD or HFD for 16 weeks

value: adipose tissue

value: NCD


title: J3 villus like HIO gamma mock-irradiated

description: Library name: J3villCG

value: human intestinal organoid


title: NM64, replicate 2, scRNA-seq, Post

description: 10X Genomics

value: PBMCs


title: J6 crypt like HIO proton mock-irradiated

description: Library name: J6cryptCPro


title: sample 4-1-6 BatchA_water extract of Zizyphi Fructus (Low dose)_rep1

value: Zizyphi Fructus water extract 20 ug/mL


title: NM59, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: sample 3-3-6 BatchA_water extract of Scutellariae Radix (Low dose)_rep3

value: Scutellariae Radix water extract 20 ug/mL


title: J6 crypt like HIO gamma irradiated

description: Library name: J6cryptRadG

value: 1 Gy gamma irradiation


title: sample 3-3-5 BatchA_water extract of Scutellariae Radix (Medium dose)_rep3

value: Scutellariae Radix water extract 100 ug/mL


title: NM59, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: BL


title: J6 crypt like HIO proton irradiated

description: Library name: J6cryptRadP

value: 1 Gy low LET proton irradiation


title: NCD2

description:
Library name: AT-NCD2
10x Genomics


title: J6 villus like HIO gamma mock-irradiated

description: Library name: J6villCG


title: NCD1

description:
Library name: AT-NCD1
10x Genomics


title: NM4, replicate 2, scRNA-seq, Post

description: 10X Genomics


title: NM4, replicate 2, scRNA-seq, BL

description: 10X Genomics


title: J6 villus like HIO proton mock-irradiated

description: Library name: J6villCPro


title: HFD4

description:
Library name: AT-HFD4
10x Genomics

value: HFD


title: NM34, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: NM62, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: J6 villus like HIO gamma irradiated

description: Library name: J6villRadG


title: NM34, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: sample 3-3-2 BatchA_water extract of Pinelliae Tuber (Medium dose)_rep3

value: Pinelliae Tuber water extract 100 ug/mL


title: HFD3

description:
Library name: AT-HFD3
10x Genomics


title: J6 villus like HIO proton irradiated

description: Library name: J6villRadP


title: HFD2

description:
Library name: AT-HFD2
10x Genomics


title: NM33, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: sample 3-3-1 BatchA_water extract of Pinelliae Tuber (High dose)_rep3

value: Pinelliae Tuber water extract 500 ug/mL


title: HFD1

description:
Library name: AT-HFD1
10x Genomics


title: J8 crypt like HIO gamma mock-irradiated

description: Library name: J8cryptCG

value: control


title: NM33, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: sample 3-2-6 BatchA_water extract of Scutellariae Radix (Low dose)_rep2


title: sample 3-2-5 BatchA_water extract of Scutellariae Radix (Medium dose)_rep2


title: NCD3

description:
Library name: AT-NCD3
10x Genomics


title: J8 crypt like HIO proton mock-irradiated

description: Library name: J8cryptCPro


title: Mouse tumor, EZH2wildtype, biol rep2

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Av des Pins O

department: Biochemistry

country: Canada

institute: McGill University

description: Library name: WT2

data_processing:
Droplet libraries were processed using Cell Ranger (10X Genomics) (Zheng et al., 2017). Sequencing reads were aligned to the mm10 mouse + Cre + human ERBB2 custom reference genome, and transcript counts quantified for each annotated gene within every cell.
Count matrices (genes × cells) were loaded into the R package Seurat (Hao et al., 2021) for quality control and downstream analyses. Low-quality cells were filtered out using the following criteria: (1) the number of detected genes is > 500; (2) percentage of mitochondrial RNA is < 5% per cell. Cell doublets were detected and removed using the R package scDblFinder (Germain et al., 2022).
Assembly: Mouse mm10 and hg38 (human ERBB2 reference genome)
Supplementary files format and content: Matrix files

source_name: Mouse mammary gland tumors

growth_protocol: Tumors were harvested from genetically engineered mice that had been treated with doxycycline (doxycycline inducible breast cancer model) until they reached the experimental endpoint.

extract_protocol:
10x Genome nuclei isolation kit was using to extract nuclei from viably frozen mouse mammary tumor tissues
Library was performed according to ChromiumTM Single Cell 3' v3 library (10x Genomics)

treatment_protocol: Doxycycline water supplied

value: Mouse mammary gland tumors

value: EIC EZH2wildtype

value: Doxycycline induced at age 8-12weeks until tumor reach endpoint


title: sample 3-2-4 BatchA_water extract of Scutellariae Radix (High dose)_rep2

value: Scutellariae Radix water extract 500 ug/mL


title: NM32, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: Post


title: J8 crypt like HIO gamma irradiated

description: Library name: J8cryptRadG

value: human intestinal organoid


title: sample 3-3-4 BatchA_water extract of Scutellariae Radix (High dose)_rep3


title: sample 3-3-3 BatchA_water extract of Pinelliae Tuber (Low dose)_rep3

value: Pinelliae Tuber water extract 20 ug/mL


title: Mouse tumor, EZH2wildtype, biol rep1

description: Library name: WT1


title: NM32, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: PBMCs


title: sample 3-2-2 BatchA_water extract of Pinelliae Tuber (Medium dose)_rep2


title: J8 crypt like HIO proton irradiated

description: Library name: J8cryptRadP


title: Mouse tumor, EZH2knockout, biol rep2

description: Library name: KO2

value: EIC EZH2knockout


title: Mouse tumor, EZH2knockout, biol rep1

description: Library name: KO1


title: sample 3-1-6 BatchA_water extract of Scutellariae Radix (Low dose)_rep1

value: Scutellariae Radix water extract 20 ug/mL


title: J8 villus like HIO gamma mock-irradiated

description: Library name: J8villCG


title: NM31, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: preadipocyte, cgrp, rep3

city: ANN ARBOR

first: Jorge

middle: L

last: Ruas

state: Michigan

address: 2800 Plymouth RD, B025-2681 NCRC - Ruas Lab NCRC B025

institute: University of Michigan

description:
Library name: cgrp_preadipocyte_3
K41_MKRN250005884-1A_22LMNGLT4_L7
res_preadipocyte_cgrp.csv
res.shrink_preadipocyte_cgrp.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.7.3a with extra arguments --outFilterMismatchNmax 33 --alignEndsType Local --alignSJoverhangMin 8 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --seedSearchStartLmax 12
Reads aligning to gene exons (Mus_musculus.GRCm38.94.gtf) were counted using featureCounts v2.0.3 program from Subread package, summarized at gene level.
Differential gene expression at FDR level 0.05 was obtained using DESeq2 R package
Assembly: GRCm38.p6
Supplementary files format and content: .txt file of raw read counts of all samples
Supplementary files format and content: .txt file containing information about samples
Supplementary files format and content: .csv file of normalized counts of all samples
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of CGRP-treated adipocytes vs. control, unshrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of NE-treated adipocytes vs. control, unshrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of NPY-treated adipocytes vs. control, unshrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of SP-treated adipocytes vs. control, unshrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of CGRP-treated preadipocytes vs. control, unshrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of preadipocytes vs. adipocytes, unshrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of CGRP-treated adipocytes vs. control, shrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of NE-treated adipocytes vs. control, shrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of NPY-treated adipocytes vs. control, shrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of SP-treated adipocytes vs. control, shrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of CGRP-treated preadipocytes vs. control, shrunken
Supplementary files format and content: .csv file of differential gene expression analysis output from DESeq2 of preadipocytes vs. adipocytes, shrunken

source_name: Inguinal adipose tissue (iWAT)

growth_protocol: Induction media from day 0 to 4 followed by differentiation media from day 4 to 8 for adipocytes. Preadipocytes maintained in growth media.

extract_protocol:
Total RNA was extracted using TRI reagent (Sigma-Aldrich, T9424) according to the manufacturer's instructions. RNA was further purified, and DNase treated (Zymo, R1013), and integrity confirmed prior to sequencing (Agilent Technologies, 2100 Bioanalyzer), with an RNA integrity number (RIN) greater than 7 as a threshold. Samples were purified by poly-A enrichment before library preparation using the Illumina NovaSeq X Plus Series platform with a paired-end 150 base pair strategy.
Samples were purified by poly-A enrichment before library creation using Illumina TruSeq Stranded mRNA.

treatment_protocol: Vehicle or 100 nM of each treatment.

value: Inguinal adipose tissue (iWAT)

value: CGRP


title: sample 3-2-1 BatchA_water extract of Pinelliae Tuber (High dose)_rep2


title: J8 villus like HIO proton mock-irradiated

description: Library name: J8villCPro


title: sample 3-1-5 BatchA_water extract of Scutellariae Radix (Medium dose)_rep1

value: Scutellariae Radix water extract 100 ug/mL


title: NM25, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: NM31, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: BL


title: preadipocyte, cgrp, rep2

description:
Library name: cgrp_preadipocyte_2
K38_MKRN250005883-1A_22LHHTLT4_L5
res_preadipocyte_cgrp.csv
res.shrink_preadipocyte_cgrp.csv


title: sample 3-1-4 BatchA_water extract of Scutellariae Radix (High dose)_rep1


title: preadipocyte, cgrp, rep1

description:
Library name: cgrp_preadipocyte_1
K37_MKRN250005882-1A_22LMNGLT4_L7
res_preadipocyte_cgrp.csv
res.shrink_preadipocyte_cgrp.csv


title: J8 villus like HIO proton irradiated

description: Library name: J8villRadP

value: 1 Gy low LET proton irradiation


title: J8 villus like HIO gamma irradiated

description: Library name: J8villRadG

value: 1 Gy gamma irradiation


title: NM25, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: sample 3-1-3 BatchA_water extract of Pinelliae Tuber (Low dose)_rep1


title: preadipocyte, control, rep3

description:
Library name: control_preadipocyte_3
K35_MKRN250005881-1A_22LMNGLT4_L7
res_preadipocyte_vs_adipocyte.csv
res.shrink_preadipocyte_vs_adipocyte.csv

value: Control


title: sample 3-1-2 BatchA_water extract of Pinelliae Tuber (Medium dose)_rep1

value: Pinelliae Tuber water extract 100 ug/mL


title: NM24, replicate 2, scRNA-seq, BL

description: 10X Genomics


title: preadipocyte, control, rep2

description:
Library name: control_preadipocyte_2
K33_MKRN250005880-1A_22LMNGLT4_L7
res_preadipocyte_vs_adipocyte.csv
res.shrink_preadipocyte_vs_adipocyte.csv


title: Homo sapiens, Human Corneal Epithelial Cells, experiment CEFFE, biol rep1

city: HONGKONG

first: TSE

last: YUENWAH

state: CHINA

address: JIULONG

institute: Xiangya Hospital of Central South University

description:
Library name: CF2
Column name gene_count.txt: CF2

data_processing:
The raw sequencing data was filtered using the Fastp software to discard sequences containing adapters and low-quality bases. The resulting clean data was then aligned to the human hg19 genome using HISAT2. Transcriptome assembly and gene expression quantification were performed using StringTie.
Differential expression was analyzed with DESeq2 or DEGseq, considering genes with |log2 FC| ≥ 1 and FDR < 0.05 as significant. Functional enrichment, including GO and KEGG pathway analyses, was performed with Bonferroni-corrected P < 0.05 for significance. GO and KEGG analyses were done using Goatools and scipy, respectively.
Assembly: hg19
Supplementary files format and content: Tab separated table count values of genes for each sample

source_name: Human Corneal Epithelial Cells

growth_protocol: Human Corneal Epithelial Cells (HCE-Ts) were purchased from Abiowell (AW-CNH567; Changsha, China). The cell medium used for DMEM/F-12 + 15%FBS + 1%P/S + 5μg/mg insulins + 10ng/ml human epidermal growth factor (EGF). HCE-Ts were cultured in an incubator (temperature: 37℃, CO2 concentration: 5%) until fused to approximately 85% before being digested for passage.

extract_protocol:
Total RNA was extracted using the EasyPure® RNA Kit, quality was assessed using the 5300 Bioanalyzer (Agilent) and quantified with the ND-2000 (NanoDrop Technologies).
RNA purification, reverse transcription, library construction, and sequencing were performed at Shanghai Majorbio Bio-pharm (China) following the manufacturer's guidelines, using 1 μg of total RNA and the Illumina® Stranded mRNA Prep protocol. Briefly, double-stranded cDNAs were synthesized using random hexamer primers and the SuperScript Kit (Invitrogen), then end-repaired, phosphorylated, and adapter-ligated. 300 bp cDNA fragments were amplified by 15 PCR cycles with Phusion DNA polymerase (NEB). After Qubit 4.0 quantification, libraries were loaded onto the NovaSeq X Plus platform (PE150) and sequenced using the NovaSeq Reagent Kit.

value: Human Corneal Epithelial Cells

value: Experiment group CEFFE


title: sample 3-1-1 BatchA_water extract of Pinelliae Tuber (High dose)_rep1

first: Musun

last: Park

value: Pinelliae Tuber water extract 500 ug/mL


title: Homo sapiens, Human Corneal Epithelial Cells, experiment CEFFE, biol rep2

description:
Library name: CF3
Column name gene_count.txt: CF3


title: NM23, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: Post


title: NM23, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: sample 2-3-6 BatchA_water extract of Zingiberis Rhizoma (Low dose)_rep3

value: Zingiberis Rhizoma water extract 20 ug/mL


title: preadipocyte, control, rep1

description:
Library name: control_preadipocyte_1
K32_MKRN250005879-1A_22LMNGLT4_L7
res_preadipocyte_vs_adipocyte.csv
res.shrink_preadipocyte_vs_adipocyte.csv


title: adipocyte, ne rep3

description:
Library name: ne_adipocyte_3
K27_MKRN250005878-1A_22LHHTLT4_L8
res_adipocyte_ne.csv
res.shrink_adipocyte_ne.csv

value: NE


title: NM22, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: PBMCs


title: adipocyte, ne, rep2

description:
Library name: ne_adipocyte_2
K26_MKRN250005877-1A_22LHHTLT4_L8
res_adipocyte_ne.csv
res.shrink_adipocyte_ne.csv


title: sample 2-3-4 BatchA_water extract of Zingiberis Rhizoma (High dose)_rep3

value: Zingiberis Rhizoma water extract 500 ug/mL


title: adipocyte, ne, rep1

description:
Library name: ne_adipocyte_1
K25_MKRN250005876-1A_22LHHTLT4_L4
res_adipocyte_ne.csv
res.shrink_adipocyte_ne.csv


title: Homo sapiens, Human Corneal Epithelial Cells, control blank, biol rep1

description:
Library name: CON1
Column name gene_count.txt: CON1

value: Control blank


title: tumor_TNFR2_VDJ_1

city: Creteil

first: Caroline

last: Pilon

address: 51 avenue du Mal de Lattre de Tassigny

country: France

institute: INSERM U955 Eq21, Hopital Henri Mondor

description: 10X genomics

data_processing:
For scRNA-seq, demultiplexing, barcoded processing, quality control, alignment and gene counting were made using Cell Ranger Cell Software (V3.1.0)
For scTCR-seq, demultiplexing, barcoded processing, quality control, alignment and vdj cdr3 counting were made using Cell Ranger Cell Software (V3.1.0)
Assembly: For scRNA-seq : mm10-3.0.0 / For scTCR-seq : vdj_GRCm38_alts_ensembl-3.1.0.gz-3.1.0
Supplementary files format and content: Count Matrix of sc-RNAseq (with Barcodes and Features information)
Supplementary files format and content: VDJ CDR3 count matrix

source_name: tumor

extract_protocol:
Murine pancreatic cancer cells mPDAC were injected in syngenic immunocompetent FVB/n mice. Mice were treated with anti-TNFR2 mAb or untreated. After 18 days, mice were euthanized, and tumors were processed with Collagenase IV and DNase I. Cells were stained with DAPI, CD45, CD4, CD8, CD11c, Ly6G, Ly6C, CD19, NK1.1, F4/80 and T cells were sorted on a FACSAria III (BD) by gating on live cells, CD45+, lineage (CD11c, Ly6G, Ly6C, CD19, NK1.1, F4/80) negative cells, CD4+ and CD8+ cells. CD4 and CD8 isolated T cells were mixed. Sorted T cells samples were used for scRNA-seq analysis.
Indexed libraries were tested for quality, equimolarly pooled and sequenced on an Illumina HiSeq2500 using paired-end 26 × 98bp as sequencing mode. By using a full Rapid flow cell, coverage was around 100M reads per sample corresponding to 100,000 reads per cell.

value: tumor

value: FVB/n

value: 10-14 weeks old


title: NM24, replicate 2, scRNA-seq, Post

description: 10X Genomics


title: NM22, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: BL


title: sample 2-3-5 BatchA_water extract of Zingiberis Rhizoma (Medium dose)_rep3

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

value: Zingiberis Rhizoma water extract 100 ug/mL


title: tumor_TNFR2_VDJ_2

description: 10X genomics


title: NM21, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: adipocyte, npy, rep3

description:
Library name: npy_adipocyte_3
K24_MKRN250005875-1A_22LMNGLT4_L7
res_adipocyte_npy.csv
res.shrink_adipocyte_npy.csv

value: Inguinal adipose tissue (iWAT)

value: NPY


title: NM21, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: tumor_ctrl_VDJ_2

description: 10X genomics

value: ctrl


title: sample 2-3-2 BatchA_water extract of Zingiberis Rhizoma Recens (Medium dose)_rep3

value: Zingiberis Rhizoma Recens water extract 100 ug/mL


title: adipocyte, npy, rep2

description:
Library name: npy_adipocyte_2
K22_MKRN250005874-1A_22LHHTLT4_L7
res_adipocyte_npy.csv
res.shrink_adipocyte_npy.csv


title: sample 2-3-3 BatchA_water extract of Zingiberis Rhizoma Recens (Low dose)_rep3

value: Zingiberis Rhizoma Recens water extract 20 ug/mL


title: Homo sapiens, Human Corneal Epithelial Cells, control blank, biol rep2

description:
Library name: CON3
Column name gene_count.txt: CON3

value: Human Corneal Epithelial Cells


title: NM161, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: adipocyte, npy, rep1

description:
Library name: npy_adipocyte_1
K21_MKRN250005873-1A_22LHHTLT4_L8
res_adipocyte_npy.csv
res.shrink_adipocyte_npy.csv


title: sample 2-3-1 BatchA_water extract of Zingiberis Rhizoma Recens (High dose)_rep3

value: Zingiberis Rhizoma Recens water extract 500 ug/mL


title: MCF10A cells, sgMETTL3-4, rep2 (ChIP-seq)

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA mem.
For peak calling MACS2 was used.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: breast

growth_protocol: The MCF10A cells were cultured in DMEM/F12 mediaum  supplementing with horse serum,  EGF, hydrocortisone, cholera toxin, insulin  and penicillin-streptomycin

extract_protocol:
Control or METTL3 KO MCF10A cells were grown to 80% confluence on 15 cm dishes and crosslinked by 2mM DSG (Pierce) for 45 minutes at room temperature and then fixed in 1% methanol-free formaldehyde for 10 minutes. Cells were then lysed in 1% SDS lysis buffer and sonicated for 10 min on ice. Sonicated chromatin was diluted and immunoprecipitated with GATA3 antibodies overnight, followed by incubating with Protein A/G beads for 1 hour. Chip precipitates were sequentially washed with 2 × RIPA 0 buffer (0.1% SDS, 1% Triton-X100, 10 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.1% sodium deoxycholate), 2 × RIPA 0.3 buffer (0. 1% SDS, 1% Triton-X-100, 10 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.1% sodium deoxycholate, 0.3 M NaCL) and 2 × LiCL buffer (250 mM LiCl, 5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl).
library was prepared using the Smarter Thruplex DNAseq Kit (Takara Bio Inc.)

treatment_protocol: Vector expressing CAS9 and sgRNAs targeting either AACS1 or METTL3 was lentivirally transduced into MCF10A cells.

value: breast

value: mammary epithelial cells

value: METTL3 KO


title: sample 2-2-6 BatchA_water extract of Zingiberis Rhizoma (Low dose)_rep2

city: Daejeon

value: Zingiberis Rhizoma water extract 20 ug/mL


title: NM161, replicate 1, scRNA-seq, Post

description: 10X Genomics

value: PBMCs

value: Post


title: adipocyte, sp rep3

description:
Library name: sp_adipocyte_3
K16_MKRN250005872-1A_22LMNGLT4_L7
res_adipocyte_sp.csv
res.shrink_adipocyte_sp.csv

value: SP


title: MCF10A cells, sgMETTL3-2, rep2 (ChIP-seq)


title: sample 2-2-5 BatchA_water extract of Zingiberis Rhizoma (Medium dose)_rep2


title: NM155, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: adipocyte, sp, rep2

description:
Library name: sp_adipocyte_2
K14_MKRN250005871-1A_22LMNGLT4_L7
res_adipocyte_sp.csv
res.shrink_adipocyte_sp.csv


title: adipocyte, sp, rep1

description:
Library name: sp_adipocyte_1
K13_MKRN250005870-1A_22LMNGLT4_L7
res_adipocyte_sp.csv
res.shrink_adipocyte_sp.csv


title: NM155, replicate 1, scRNA-seq, BL

description: 10X Genomics


title: MCF10A cells, sg control, rep2 (ChIP-seq)

value: AAVS1 KO


title: MCF10A cells, sgMETTL3-4, rep1 (ChIP-seq)


title: sample 2-2-4 BatchA_water extract of Zingiberis Rhizoma (High dose)_rep2

value: Zingiberis Rhizoma water extract 500 ug/mL


title: sample 2-2-3 BatchA_water extract of Zingiberis Rhizoma Recens (Low dose)_rep2


title: NM146, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: adipocyte, cgrp rep3

description:
Library name: cgrp_adipocyte_3
K12_MKRN250005869-1A_22LMNGLT4_L7
res_adipocyte_cgrp.csv
res.shrink_adipocyte_cgrp.csv

value: CGRP


title: MCF10A cells, sgMETTL3-2, rep1 (ChIP-seq)


title: tumor_ctrl_VDJ_1

description: 10X genomics

value: tumor

value: FVB/n

value: 10-14 weeks old


title: MCF10A cells, sg control, rep1 (ChIP-seq)


title: NM145, replicate 1, scRNA-seq, Post

description: 10X Genomics


title: NM146, replicate 1, scRNA-seq, BL

description: 10X Genomics

value: BL


title: adipocyte, cgrp, rep1

description:
Library name: cgrp_adipocyte_1
K7_MKRN250005867-1A_22LMNGLT4_L7
res_adipocyte_cgrp.csv
res.shrink_adipocyte_cgrp.csv

value: Inguinal adipose tissue (iWAT)


title: adipocyte, cgrp, rep2

description:
Library name: cgrp_adipocyte_2
K9_MKRN250005868-1A_22LMNGLT4_L7
res_adipocyte_cgrp.csv
res.shrink_adipocyte_cgrp.csv


title: sample 2-2-1 BatchA_water extract of Zingiberis Rhizoma Recens (High dose)_rep2


title: MCF10A cells, sgMETTL3-4, rep2 (ATAC-seq)

extract_protocol:
1 × 105 control or METTL3 KO MCF10A cells were trypsinised and suspended in 50 ul of ATAC resuspension buffer (10mM Tris-HCl pH 7.4, 10mM NaCl and 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin) on ice for 3 mins. After addition of 1 ml ATAC- resuspension buffer containing 0.1% Tween-20, cells were centrifuged at maximum speed for 10 min at 4°C. The supernatant was removed, and nuclei were resuspended in 50 μL transposition mix: 2.5 μL transposase (100 nM final), 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20 and 5 μL water. The transposition reactions were carried out at 37 °C for 30 minutes in a thermomixer with shaking at 100 x g followed by sequencing library preparation.
Library concentrations were quantified using the NEBNext Library Quant Kit. 1 µL of the pre-amplified sample is diluted with 99 µL of 1× NEB Dilution Buffer, followed by the creation of qPCR reactions in a 384-well plate. After completing the qPCR, DNA concentration is determined using tape station. The amplified samples are then processed with DNA Binding Buffer, transferred to Zymo-Spin Columns, washed, and finally eluted to obtain the DNA product.