title: BatchE_ethanol extract of Yijung-tang (Medium dose)_rep3

description: sample 14-3-2

value: Yijung-tang ethanol extract 100 μg/mL


title: ChIP-seq_YES1_rep2

status: Public on Oct 28 2025

type: SRA

city: Beijing

first: Junyi

last: Zhu

address: Peking University, No.5 YiHeYuan Road, Haidian District

department: School of Life sciences

country: China

institute: Peking University

description:
Library name: sample203
ChIP-seq_YES1_merge.bw

library_source: genomic

data_processing:
ChIP-seq raw data were processed using a custom pipeline that builds on published workflows with minor modifications. Briefly, reads were firstly trimmed for adapter sequences with trim_galore (v.0.6.2).
Then trimmed reads were mapped to the concatenated index of human reference genome (hg38) and mouse reference genome (mm10) using Bowtie2 (v.2.2.3).
The final bam files were converted to bigwig file using bamCoverage method.
Assembly: Concatenated index of hg38 and mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: A549 cells were cultured in basic Dulbecco's modified Eagle's medium (DMEM)-high glucose (SIGMA#D5796-500mL), including 1× penicillin/streptomycin (Gibco#15140-122) and 10% fetal bovine serum (FBS) (VivaCell#C04001-500). The cells were incubated at 37 °C with 5% CO2 in a humidified incubator. The Schneider 2(S2) cells were cultured in complete Schneider’s Drosophila Medium (Invitrogen, Cat#21720024) supplemented with 10% FBS (CellMax, Cat#SA311.02) at room temperature.

extract_protocol:
Sample preparation were similar as standard ChIP-seq protocols with some modifications. Briefly, cells were fixed with 1% formalaldehyde, and chromatin fractions were seperated. After sonication, free chromatin fractions were incubated with corresponding antibodies overnight at 4°C with rotations. Antibody-bound proteins were captured with potein G beads, and after washing, protein-bound genomic DNA was extracted and purified.
Library construction was performed following the VAHTS Universal Pro DNA Library Prep Kit for Illumina (Vazyme #ND608) instructions.

treatment_protocol: TG003 (20 μM) treatment for 4 hours; CH6953755 (10 μM) treatment for 24 hours.

tag: cell line

tag: genotype

value: WT

tag: treatment

value: untreated


title: ChIP-seq_RNAPII_YES1_ctrl_rep2

description:
Library name: sample205
ChIP-seq_RNAPII_YES1_ctrl_merge.bw


title: BatchE_ethanol extract of Banhasasim-tang (Low dose)_rep2

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description: sample 14-2-6

library_source: transcriptomic

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

molecule: total RNA

growth_protocol: Human colorectal adenocarcinoma cell line, HT29 (HTB-38) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). HT29 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.

value: Banhasasim-tang ethanol extract 20 μg/mL

tag: time


title: ChIP-seq_YES1_rep1

description:
Library name: sample202
ChIP-seq_YES1_merge.bw


title: BatchE_ethanol extract of Banhasasim-tang (Medium dose)_rep2

description: sample 14-2-5

value: Banhasasim-tang ethanol extract 100 μg/mL


title: ChIP-seq_pY1_CH6953755_24h_rep2

description:
Library name: sample201
ChIP-seq_pY1_CH6953755_24h_merge.bw


title: BatchE_ethanol extract of Banhasasim-tang (High dose)_rep2

description: sample 14-2-4

value: Banhasasim-tang ethanol extract 500 μg/mL


title: ChIP-seq_RNAPII_YES1_ctrl_rep1

description:
Library name: sample204
ChIP-seq_RNAPII_YES1_ctrl_merge.bw


title: ChIP-seq_pY1_CH6953755_24h_rep1

description:
Library name: sample200
ChIP-seq_pY1_CH6953755_24h_merge.bw


title: BatchE Vehicle(DMSO) rep3

description: sample E1-3-1

value: 0.1% DMSO


title: ChIP-seq_pY1_CH6953755_0h_rep2

description:
Library name: sample199
ChIP-seq_pY1_CH6953755_0h_merge.bw


title: BatchE Vehicle(DMSO) rep2

description: sample E1-2-1


title: BatchE Vehicle(DMSO) rep1

description: sample E1-1-1


title: ChIP-seq_RNAPII_CH6953755_24h_rep2

description:
Library name: sample197
ChIP-seq_RNAPII_CH6953755_24h_merge.bw


title: BatchD_ethanol extract of Yijung-tang (Low dose)_rep2

description: sample 14-2-3

value: Yijung-tang ethanol extract 20 μg/mL


title: ChIP-seq_RNAPII_CH6953755_24h_rep1

description:
Library name: sample196
ChIP-seq_RNAPII_CH6953755_24h_merge.bw


title: BatchD_ethanol extract of Yijung-tang (Medium dose)_rep2

description: sample 14-2-2


title: BatchD_ethanol extract of Yijung-tang (High dose)_rep2

description: sample 14-2-1

value: Yijung-tang ethanol extract 500 μg/mL


title: ChIP-seq_RNAPII_CH6953755_0h_rep1

description:
Library name: sample194
ChIP-seq_RNAPII_CH6953755_0h_merge.bw


title: BatchD_ethanol extract of Banhasasim-tang (Medium dose)_rep1

description: sample 14-1-5


title: ChIP-seq_CLK4_rep2

description:
Library name: sample193
ChIP-seq_CLK4_merge.bw


title: BatchD_ethanol extract of Banhasasim-tang (Low dose)_rep1

description: sample 14-1-6


title: ChIP-seq_CLK4_rep1

description:
Library name: sample192
ChIP-seq_CLK4_merge.bw


title: BatchE_ethanol extract of Yijung-tang (Low dose)_rep3

description: sample 14-3-3


title: ChIP-seq_CLK1_rep2

description:
Library name: sample191
ChIP-seq_CLK1_merge.bw


title: BatchE_ethanol extract of Yijung-tang (High dose)_rep3

description: sample 14-3-1


title: BatchD_ethanol extract of Banhasasim-tang (High dose)_rep1

description: sample 14-1-4


title: ChIP-seq_CLK1_rep1

description:
Library name: sample190
ChIP-seq_CLK1_merge.bw


title: BatchD_ethanol extract of Yijung-tang (Low dose)_rep1

description: sample 14-1-3


title: BatchD_ethanol extract of Yijung-tang (High dose)_rep1

description: sample 14-1-1


title: ChIP-seq_pS7_CLK4_KO_rep2

description:
Library name: sample189
ChIP-seq_pS7_CLK4_KO_merge.bw

value: CLK4 knock-out


title: BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Low dose)_rep3

description: sample 13-3-6

value: Aconiti Lateralis Radix Preparata ethanol extract 20 μg/mL


title: ChIP-seq_RNAPII_CLK4_KO_rep2

description:
Library name: sample187
ChIP-seq_RNAPII_CLK4_KO_merge.bw


title: BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep3

description: sample 13-3-5

value: Aconiti Lateralis Radix Preparata ethanol extract 100 μg/mL


title: ChIP-seq_RNAPII_CLK4_KO_rep1

description:
Library name: sample186
ChIP-seq_RNAPII_CLK4_KO_merge.bw


title: ChIP-seq_pY1_CH6953755_0h_rep1

description:
Library name: sample198
ChIP-seq_pY1_CH6953755_0h_merge.bw


title: BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (High dose)_rep3

description: sample 13-3-4

value: Aconiti Lateralis Radix Preparata ethanol extract 500 μg/mL


title: ChIP-seq_pS7_CLK1_KO_rep2

description:
Library name: sample185
ChIP-seq_pS7_CLK1_KO_merge.bw

value: CLK1 knock-out


title: ChIP-seq_RNAPII_CH6953755_0h_rep2

description:
Library name: sample195
ChIP-seq_RNAPII_CH6953755_0h_merge.bw


title: ChIP-seq_RNAPII_CLK1_KO_rep2

description:
Library name: sample183
ChIP-seq_RNAPII_CLK1_KO_merge.bw


title: BatchD_ethanol extract of Bupleuri Radix (Medium dose)_rep3

description: sample 13-3-2

value: Bupleuri Radix ethanol extract 62 μg/mL


title: BatchD_ethanol extract of Bupleuri Radix (High dose)_rep3

description: sample 13-3-1

value: Bupleuri Radix ethanol extract 310 μg/mL


title: BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Low dose)_rep2

description: sample 13-2-6


title: ChIP-seq_pS7_CLK_ctrl_rep2

description:
Library name: sample181
ChIP-seq_pS7_CLK_ctrl_merge.bw


title: ChIP-seq_pS7_CLK_ctrl_rep1

description:
Library name: sample180
ChIP-seq_pS7_CLK_ctrl_merge.bw


title: BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (High dose)_rep2

description: sample 13-2-4


title: BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep2

description: sample 13-2-5


title: BatchD_ethanol extract of Bupleuri Radix (Low dose)_rep2

description: sample 13-2-3

value: Bupleuri Radix ethanol extract 12.4 μg/mL


title: BatchD_ethanol extract of Yijung-tang (Medium dose)_rep1

description: sample 14-1-2

value: Yijung-tang ethanol extract 100 μg/mL


title: BatchD_ethanol extract of Bupleuri Radix (Medium dose)_rep2

description: sample 13-2-2


title: ChIP-seq_pS7_TG003_4h_rep2

description:
Library name: sample177
ChIP-seq_pS7_TG003_4h_merge.bw

value: WT

value: TG003 (20 μM) for 4 hours


title: BatchD_ethanol extract of Bupleuri Radix (High dose)_rep2

description: sample 13-2-1


title: ChIP-seq_pS7_CLK4_KO_rep1

description:
Library name: sample188
ChIP-seq_pS7_CLK4_KO_merge.bw

value: untreated


title: BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep1

description: sample 13-1-5


title: ChIP-seq_RNAPII_CLK_ctrl_rep1

description:
Library name: sample178
ChIP-seq_RNAPII_CLK_ctrl_merge.bw


title: ChIP-seq_pS7_TG003_0h_rep1

description:
Library name: sample174
ChIP-seq_pS7_TG003_0h_merge.bw


title: BatchD_ethanol extract of Bupleuri Radix (Low dose)_rep3

description: sample 13-3-3


title: BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (High dose)_rep1

description: sample 13-1-4


title: ChIP-seq_RNAPII_TG003_4h_rep2

description:
Library name: sample173
ChIP-seq_RNAPII_TG003_4h_merge.bw


title: ChIP-seq_pS7_CLK1_KO_rep1

description:
Library name: sample184
ChIP-seq_pS7_CLK1_KO_merge.bw


title: BatchD_ethanol extract of Bupleuri Radix (Medium dose)_rep1

description: sample 13-1-2


title: BatchD_ethanol extract of Bupleuri Radix (Low dose)_rep1

description: sample 13-1-3


title: ChIP-seq_RNAPII_TG003_4h_rep1

description:
Library name: sample172
ChIP-seq_RNAPII_TG003_4h_merge.bw


title: BatchD_ethanol extract of Cimicifugae Rhizoma (Low dose)_rep3

description: sample 12-3-6

value: Cimicifugae Rhizoma ethanol extract 20 μg/mL


title: ChIP-seq_RNAPII_TG003_0h_rep1

description:
Library name: sample170
ChIP-seq_RNAPII_TG003_0h_merge.bw


title: ChIP-seq_RNAPII_CLK1_KO_rep1

description:
Library name: sample182
ChIP-seq_RNAPII_CLK1_KO_merge.bw


title: ChIP-seq_S7A_H2AZ.ac_dTAG_4h_rep2

description:
Library name: sample141
ChIP-seq_H2AZAC_S7A_Rawcounts.csv
H2AZAC_S7A_DEseq2_results.csv

data_processing:
ChIP-seq and CUT&Tag raw data were processed using a custom pipeline that builds on published workflows with minor modifications.  Briefly, reads were firstly trimmed for adapter sequences with trim_galore (v.0.6.2).
Then trimmed reads were mapped to human reference genome (hg38) (Endogeneous RNAPII CTD antibody, H3K36me3, H2A.ZAc and H2A.Z) or the concatenated index of human reference genome (hg38) and  mouse reference genome (mm10) (Mutant ChIP-seq) using Bowtie2 (v.2.2.3).
For endogeneous RNAPII CTD antibody ChIP-seq, the final bam files were converted to bigwig file using bamCoverage with RPGC normalize method. For mutant ChIP-seq, bam file were converted to bigwig with normalization of mm10 reads. For H3K36me3, gene body reads were counted with featureCounts (v.2.0.1) and TSS reads were counted for H2A.Zac and H2A.Z.
Differential expression genes were identified with R package DESeq2 (v.1.24.0) with default settings.
Assembly: hg38 or Concatenated index of hg38 and mm10
Supplementary files format and content: bigwig
Supplementary files format and content: Comma-delimited text file includes raw counts and analysis results from deseq2

extract_protocol:
Sample preparation were similar as standard ChIP-seq protocols with some modifications. Briefly, cells were fixed with 1% formalaldehyde, and chromatin fractions were seperated. After sonication, free chromatin fractions were incubated with corresponding antibodies overnight at 4°C with rotations. Antibody-bound proteins were captured with potein G beads, and after washing, protein-bound genomic DNA was extracted and purified. For mutant cells, HA-beads were incubated overnight at 4°C with rotations. For, H2AZ CUT&Tag experiments, samples are collected and performed CUT&Tag assay with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Cat#TD903) following the manufacturers' instruction. Briefly, 0.1% formalaldehyde crosslinked cells were permealization, and incubated with corresponding antibodies overnight at 4℃. After secondary antibody conjugation, samples were mixed with protein A/G-Tnp, and cut DNAs were purified.
Library construction was performed following the VAHTS Universal Pro DNA Library Prep Kit for Illumina (Vazyme #ND608) instructions. For CUT&Tag experiments, library construction was performed following the VAHTS with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Cat#TD903) instructions.

treatment_protocol: Individual cell line were  pretreated with or without 2 μg/ml Doxycycline for 24 h to induce mutant RPB1 expression, then treated with or without 100 nM dTAGV-1 for 4h to induce endogeneous RPB1 degradation. For spike-in, 10% mESCs cells were used. For endogeneous RNAPII CTD antibody ChIP, WT A549 cells were used.

value: RPB1 degron, S7A RPB1 complement

value: Dox (2 μg/mL) for 24 hours followd with dTAGV-1 (100 nM) for 4 hours

tag: chip antibody

value: Acetyl-Histone H2A.Z (Lys4/Lys7) antibody (Cell signaling #75336)


title: BatchD_ethanol extract of Cimicifugae Rhizoma (Medium dose)_rep3

description: sample 12-3-5

value: Cimicifugae Rhizoma ethanol extract 100 μg/mL


title: ChIP-seq_RNAPII_TG003_0h_rep2

description:
Library name: sample171
ChIP-seq_RNAPII_TG003_0h_merge.bw


title: BatchD_ethanol extract of Cimicifugae Rhizoma (High dose)_rep3

description: sample 12-3-4

value: Cimicifugae Rhizoma ethanol extract 500 μg/mL


title: ChIP-seq_S7A_H2AZ.ac_dTAG_0h_rep2

description:
Library name: sample139
ChIP-seq_H2AZAC_S7A_Rawcounts.csv
H2AZAC_S7A_DEseq2_results.csv

value: Untreated


title: BatchD_ethanol extract of Citri Unshius Pericarpium (Low dose)_rep3

description: sample 12-3-3

value: Citri Unshius Pericarpium ethanol extract 20 μg/mL


title: ChIP-seq_RNAPII_CLK_ctrl_rep2

description:
Library name: sample179
ChIP-seq_RNAPII_CLK_ctrl_merge.bw


title: ChIP-seq_S7A_H2AZ.ac_dTAG_4h_rep1

description:
Library name: sample140
ChIP-seq_H2AZAC_S7A_Rawcounts.csv
H2AZAC_S7A_DEseq2_results.csv


title: BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Low dose)_rep1

description: sample 13-1-6

value: Aconiti Lateralis Radix Preparata ethanol extract 20 μg/mL


title: ChIP-seq_T4V_H2AZ.ac_dTAG_4h_rep2

description:
Library name: sample133
ChIP-seq_H2AZAC_T4V_Rawcounts.csv
H2AZAC_T4V_DEseq2_results.csv

value: RPB1 degron, T4V RPB1 complement


title: BatchD_ethanol extract of Cimicifugae Rhizoma (Medium dose)_rep2

description: sample 12-2-5


title: BatchD_ethanol extract of Citri Unshius Pericarpium (Low dose)_rep2

description: sample 12-2-3


title: ChIP-seq_S5A_H2AZ.ac_dTAG_4h_rep1

description:
Library name: sample136
ChIP-seq_H2AZAC_S5A_Rawcounts.csv
H2AZAC_S5A_DEseq2_results.csv

value: RPB1 degron, S5A RPB1 complement


title: ChIP-seq_S7A_H2AZ.ac_dTAG_0h_rep1

description:
Library name: sample138
ChIP-seq_H2AZAC_S7A_Rawcounts.csv
H2AZAC_S7A_DEseq2_results.csv


title: ChIP-seq_S5A_H2AZ.ac_dTAG_4h_rep2

description:
Library name: sample137
ChIP-seq_H2AZAC_S5A_Rawcounts.csv
H2AZAC_S5A_DEseq2_results.csv


title: ChIP-seq_T4V_H2AZ.ac_dTAG_4h_rep1

description:
Library name: sample132
ChIP-seq_H2AZAC_T4V_Rawcounts.csv
H2AZAC_T4V_DEseq2_results.csv


title: ChIP-seq_pS7_TG003_0h_rep2

description:
Library name: sample175
ChIP-seq_pS7_TG003_0h_merge.bw


title: BatchD_ethanol extract of Citri Unshius Pericarpium (High dose)_rep2

description: sample 12-2-1

value: Citri Unshius Pericarpium ethanol extract 500 μg/mL


title: ChIP-seq_S2A_H2AZ.ac_dTAG_4h_rep1

description:
Library name: sample128
ChIP-seq_H2AZAC_S2A_Rawcounts.csv
H2AZAC_S2A_DEseq2_results.csv

value: RPB1 degron, S2A RPB1 complement


title: BatchD_ethanol extract of Citri Unshius Pericarpium (Medium dose)_rep2

description: sample 12-2-2

value: Citri Unshius Pericarpium ethanol extract 100 μg/mL


title: BatchD_ethanol extract of Cimicifugae Rhizoma (Low dose)_rep2

description: sample 12-2-6


title: BatchD_ethanol extract of Citri Unshius Pericarpium (High dose)_rep3

description: sample 12-3-1


title: ChIP-seq_pS7_TG003_4h_rep1

description:
Library name: sample176
ChIP-seq_pS7_TG003_4h_merge.bw

value: WT


title: BatchD_ethanol extract of Citri Unshius Pericarpium (Medium dose)_rep3

description: sample 12-3-2


title: ChIP-seq_S5A_H2AZ.ac_dTAG_0h_rep2

description:
Library name: sample135
ChIP-seq_H2AZAC_S5A_Rawcounts.csv
H2AZAC_S5A_DEseq2_results.csv


title: ChIP-seq_T4V_H2AZ.ac_dTAG_0h_rep2

description:
Library name: sample131
ChIP-seq_H2AZAC_T4V_Rawcounts.csv
H2AZAC_T4V_DEseq2_results.csv


title: BatchD_ethanol extract of Cimicifugae Rhizoma (High dose)_rep2

description: sample 12-2-4


title: ChIP-seq_T4V_H2AZ.ac_dTAG_0h_rep1

description:
Library name: sample130
ChIP-seq_H2AZAC_T4V_Rawcounts.csv
H2AZAC_T4V_DEseq2_results.csv


title: ChIP-seq_S2A_H2AZ.ac_dTAG_0h_rep2

description:
Library name: sample127
ChIP-seq_H2AZAC_S2A_Rawcounts.csv
H2AZAC_S2A_DEseq2_results.csv


title: BatchD_ethanol extract of Citri Unshius Pericarpium (Medium dose)_rep1

description: sample 12-1-2


title: ChIP-seq_S2A_H2AZ.ac_dTAG_4h_rep2

description:
Library name: sample129
ChIP-seq_H2AZAC_S2A_Rawcounts.csv
H2AZAC_S2A_DEseq2_results.csv


title: BatchD_ethanol extract of Bupleuri Radix (High dose)_rep1

description: sample 13-1-1

value: Bupleuri Radix ethanol extract 310 μg/mL


title: BatchD_ethanol extract of Citri Unshius Pericarpium (Low dose)_rep1

description: sample 12-1-3


title: BatchD_ethanol extract of Cimicifugae Rhizoma (High dose)_rep1

description: sample 12-1-4


title: ChIP-seq_S5A_H2AZ.ac_dTAG_0h_rep1

description:
Library name: sample134
ChIP-seq_H2AZAC_S5A_Rawcounts.csv
H2AZAC_S5A_DEseq2_results.csv


title: BatchD_ethanol extract of Cimicifugae Rhizoma (Low dose)_rep1

description: sample 12-1-6


title: BatchD_ethanol extract of Cimicifugae Rhizoma (Medium dose)_rep1

description: sample 12-1-5


title: ChIP-seq_S2A_H2AZ.ac_dTAG_0h_rep1

description:
Library name: sample126
ChIP-seq_H2AZAC_S2A_Rawcounts.csv
H2AZAC_S2A_DEseq2_results.csv


title: ChIP-seq_Y1F_H2AZ.ac_dTAG_4h_rep2

description:
Library name: sample125
ChIP-seq_H2AZAC_Y1F_Rawcounts.csv
H2AZAC_Y1F_DEseq2_results.csv

value: RPB1 degron, Y1F RPB1 complement


title: BatchD_ethanol extract of Zizyphi Fructus (Low dose)_rep3

description: sample 11-3-6

value: Zizyphi Fructus ethanol extract 20 μg/mL


title: BatchD_ethanol extract of Citri Unshius Pericarpium (High dose)_rep1

description: sample 12-1-1


title: ChIP-seq_Y1F_H2AZ.ac_dTAG_0h_rep2

description:
Library name: sample123
ChIP-seq_H2AZAC_Y1F_Rawcounts.csv
H2AZAC_Y1F_DEseq2_results.csv


title: BatchD_ethanol extract of Zizyphi Fructus (Medium dose)_rep3

description: sample 11-3-5

value: Zizyphi Fructus ethanol extract 100 μg/mL


title: ChIP-seq_Y1F_H2AZ.ac_dTAG_0h_rep1

description:
Library name: sample122
ChIP-seq_H2AZAC_Y1F_Rawcounts.csv
H2AZAC_Y1F_DEseq2_results.csv


title: BatchD_ethanol extract of Zizyphi Fructus (High dose)_rep3

description: sample 11-3-4

value: Zizyphi Fructus ethanol extract 500 μg/mL


title: ChIP-seq_WT_H2AZ.ac_dTAG_4h_rep2

description:
Library name: sample121
ChIP-seq_H2AZAC_WT_Rawcounts.csv
H2AZAC_WT_DEseq2_results.csv

value: RPB1 degron, WT RPB1 complement

value: Dox (2 μg/mL) for 24 hours followd with dTAGV-1 (100 nM) for 4 hours

value: Acetyl-Histone H2A.Z (Lys4/Lys7) antibody (Cell signaling #75336)


title: ChIP-seq_WT_H2AZ.ac_dTAG_0h_rep2

description:
Library name: sample119
ChIP-seq_H2AZAC_WT_Rawcounts.csv
H2AZAC_WT_DEseq2_results.csv

value: Untreated


title: BatchD_ethanol extract of Coptidis Rhizoma (Low dose)_rep3

description: sample 11-3-3

value: Coptidis Rhizoma ethanol extract 12.8 μg/mL


title: BatchD_ethanol extract of Coptidis Rhizoma (Medium dose)_rep3

description: sample 11-3-2

value: Coptidis Rhizoma ethanol extract 64 μg/mL


title: BatchD_ethanol extract of Coptidis Rhizoma (High dose)_rep3

description: sample 11-3-1

value: Coptidis Rhizoma ethanol extract 320 μg/mL


title: ChIP-seq_WT_H2AZ.ac_dTAG_0h_rep1

description:
Library name: sample118
ChIP-seq_H2AZAC_WT_Rawcounts.csv
H2AZAC_WT_DEseq2_results.csv


title: ChIP-seq_WT_H2AZ.ac_dTAG_4h_rep1

description:
Library name: sample120
ChIP-seq_H2AZAC_WT_Rawcounts.csv
H2AZAC_WT_DEseq2_results.csv


title: BatchD_ethanol extract of Zizyphi Fructus (Low dose)_rep2

description: sample 11-2-6


title: BatchD_ethanol extract of Zizyphi Fructus (High dose)_rep2

description: sample 11-2-4


title: ChIP-seq_Degron_RPB1_H2AZ.ac_dTAG_0h_rep2

description:
Library name: sample115
ChIP-seq_H2AZAC_Degron_RPB1_Rawcounts.csv
H2AZAC_Degron_RPB1_DEseq2_results.csv

value: RPB1 degron


title: BatchD_ethanol extract of Zizyphi Fructus (Medium dose)_rep2

description: sample 11-2-5


title: BatchD_ethanol extract of Coptidis Rhizoma (Medium dose)_rep2

description: sample 11-2-2


title: ChIP-seq_Degron_RPB1_H2AZ.ac_dTAG_0h_rep1

description:
Library name: sample114
ChIP-seq_H2AZAC_Degron_RPB1_Rawcounts.csv
H2AZAC_Degron_RPB1_DEseq2_results.csv


title: ChIP-seq_Degron_RPB1_H2AZ.ac_dTAG_4h_rep1

description:
Library name: sample116
ChIP-seq_H2AZAC_Degron_RPB1_Rawcounts.csv
H2AZAC_Degron_RPB1_DEseq2_results.csv

value: dTAGV-1 (100 nM) for 4 hours


title: BatchD_ethanol extract of Coptidis Rhizoma (Low dose)_rep2

description: sample 11-2-3


title: BatchD_ethanol extract of Coptidis Rhizoma (High dose)_rep2

description: sample 11-2-1


title: ChIP-seq_Degron_RPB1_H2AZ.ac_dTAG_4h_rep2

description:
Library name: sample117
ChIP-seq_H2AZAC_Degron_RPB1_Rawcounts.csv
H2AZAC_Degron_RPB1_DEseq2_results.csv


title: BatchD Vehicle(DMSO) rep3

description: sample D1-3-1

value: 0.1% DMSO


title: ChIP-seq_S7A_H3K36me3_dTAG_4h_rep1

description:
Library name: sample112
ChIP-seq_H3K36me3_S7A_Rawcounts.csv
H3K36me3_S7A_DEseq2_results.csv

value: RPB1 degron, S7A RPB1 complement

value: H3K36me3 antibody (Abcam #ab9050)


title: ChIP-seq_S7A_H3K36me3_dTAG_4h_rep2

description:
Library name: sample113
ChIP-seq_H3K36me3_S7A_Rawcounts.csv
H3K36me3_S7A_DEseq2_results.csv


title: ChIP-seq_S7A_H3K36me3_dTAG_0h_rep2

description:
Library name: sample111
ChIP-seq_H3K36me3_S7A_Rawcounts.csv
H3K36me3_S7A_DEseq2_results.csv


title: BatchD Vehicle(DMSO) rep2

description: sample D1-2-1


title: ChIP-seq_Y1F_H2AZ.ac_dTAG_4h_rep1

description:
Library name: sample124
ChIP-seq_H2AZAC_Y1F_Rawcounts.csv
H2AZAC_Y1F_DEseq2_results.csv


title: ChIP-seq_S5A_H3K36me3_dTAG_4h_rep2

description:
Library name: sample109
ChIP-seq_H3K36me3_S5A_Rawcounts.csv
H3K36me3_S5A_DEseq2_results.csv

value: RPB1 degron, S5A RPB1 complement


title: ChIP-seq_S5A_H3K36me3_dTAG_4h_rep1

description:
Library name: sample108
ChIP-seq_H3K36me3_S5A_Rawcounts.csv
H3K36me3_S5A_DEseq2_results.csv


title: ChIP-seq_S7A_H3K36me3_dTAG_0h_rep1

description:
Library name: sample110
ChIP-seq_H3K36me3_S7A_Rawcounts.csv
H3K36me3_S7A_DEseq2_results.csv


title: BatchD Vehicle(DMSO) rep1

description: sample D1-1-1


title: ChIP-seq_S5A_H3K36me3_dTAG_0h_rep2

description:
Library name: sample107
ChIP-seq_H3K36me3_S5A_Rawcounts.csv
H3K36me3_S5A_DEseq2_results.csv


title: BatchC_ethanol extract of Zizyphi Fructus (Low dose)_rep1

description: sample 11-1-6


title: BatchC_ethanol extract of Zizyphi Fructus (Medium dose)_rep1

description: sample 11-1-5


title: BatchC_ethanol extract of Zizyphi Fructus (High dose)_rep1

description: sample 11-1-4


title: ChIP-seq_S5A_H3K36me3_dTAG_0h_rep1

description:
Library name: sample106
ChIP-seq_H3K36me3_S5A_Rawcounts.csv
H3K36me3_S5A_DEseq2_results.csv


title: ChIP-seq_T4V_H3K36me3_dTAG_4h_rep1

description:
Library name: sample104
ChIP-seq_H3K36me3_T4V_Rawcounts.csv
H3K36me3_T4V_DEseq2_results.csv

value: RPB1 degron, T4V RPB1 complement


title: BatchC_ethanol extract of Coptidis Rhizoma (Medium dose)_rep1

description: sample 11-1-2


title: BatchC_ethanol extract of Coptidis Rhizoma (Low dose)_rep1

description: sample 11-1-3


title: BatchC_ethanol extract of Coptidis Rhizoma (High dose)_rep1

description: sample 11-1-1


title: ChIP-seq_T4V_H3K36me3_dTAG_0h_rep2

description:
Library name: sample103
ChIP-seq_H3K36me3_T4V_Rawcounts.csv
H3K36me3_T4V_DEseq2_results.csv


title: ChIP-seq_T4V_H3K36me3_dTAG_4h_rep2

description:
Library name: sample105
ChIP-seq_H3K36me3_T4V_Rawcounts.csv
H3K36me3_T4V_DEseq2_results.csv


title: BatchC_ethanol extract of Scutellariae Radix (Low dose)_rep3

description: sample 10-3-6

value: Scutellariae Radix ethanol extract 20 μg/mL


title: ChIP-seq_S2A_H3K36me3_dTAG_4h_rep2

description:
Library name: sample101
ChIP-seq_H3K36me3_S2A_Rawcounts.csv
H3K36me3_S2A_DEseq2_results.csv

value: RPB1 degron, S2A RPB1 complement


title: BatchC_ethanol extract of Scutellariae Radix (High dose)_rep3

description: sample 10-3-4

value: Scutellariae Radix ethanol extract 500 μg/mL


title: BatchC_ethanol extract of Scutellariae Radix (Medium dose)_rep3

description: sample 10-3-5

value: Scutellariae Radix ethanol extract 100 μg/mL


title: ChIP-seq_S2A_H3K36me3_dTAG_0h_rep2

description:
Library name: sample99
ChIP-seq_H3K36me3_S2A_Rawcounts.csv
H3K36me3_S2A_DEseq2_results.csv


title: ChIP-seq_S2A_H3K36me3_dTAG_0h_rep1

description:
Library name: sample98
ChIP-seq_H3K36me3_S2A_Rawcounts.csv
H3K36me3_S2A_DEseq2_results.csv


title: ChIP-seq_T4V_H3K36me3_dTAG_0h_rep1

description:
Library name: sample102
ChIP-seq_H3K36me3_T4V_Rawcounts.csv
H3K36me3_T4V_DEseq2_results.csv


title: BatchC_ethanol extract of Pinelliae Tuber (High dose)_rep3

description: sample 10-3-1

value: Pinelliae Tuber ethanol extract 500 μg/mL


title: BatchC_ethanol extract of Pinelliae Tuber (Low dose)_rep3

description: sample 10-3-3

value: Pinelliae Tuber ethanol extract 20 μg/mL


title: BatchC_ethanol extract of Pinelliae Tuber (Medium dose)_rep3

description: sample 10-3-2

value: Pinelliae Tuber ethanol extract 100 μg/mL


title: ChIP-seq_Y1F_H3K36me3_dTAG_4h_rep1

description:
Library name: sample96
ChIP-seq_H3K36me3_Y1F_Rawcounts.csv
H3K36me3_Y1F_DEseq2_results.csv

value: RPB1 degron, Y1F RPB1 complement

value: Dox (2 μg/mL) for 24 hours followd with dTAGV-1 (100 nM) for 4 hours


title: BatchC_ethanol extract of Scutellariae Radix (Medium dose)_rep2

description: sample 10-2-5


title: ChIP-seq_Y1F_H3K36me3_dTAG_4h_rep2

description:
Library name: sample97
ChIP-seq_H3K36me3_Y1F_Rawcounts.csv
H3K36me3_Y1F_DEseq2_results.csv


title: BatchC_ethanol extract of Scutellariae Radix (High dose)_rep2

description: sample 10-2-4


title: ChIP-seq_Y1F_H3K36me3_dTAG_0h_rep2

description:
Library name: sample95
ChIP-seq_H3K36me3_Y1F_Rawcounts.csv
H3K36me3_Y1F_DEseq2_results.csv

value: Untreated


title: BatchC_ethanol extract of Pinelliae Tuber (Low dose)_rep2

description: sample 10-2-3


title: BatchC_ethanol extract of Pinelliae Tuber (Medium dose)_rep2

description: sample 10-2-2


title: ChIP-seq_Y1F_H3K36me3_dTAG_0h_rep1

description:
Library name: sample94
ChIP-seq_H3K36me3_Y1F_Rawcounts.csv
H3K36me3_Y1F_DEseq2_results.csv


title: ChIP-seq_WT_H3K36me3_dTAG_4h_rep1

description:
Library name: sample92
ChIP-seq_H3K36me3_WT_Rawcounts.csv
H3K36me3_WT_DEseq2_results.csv

value: RPB1 degron, WT RPB1 complement


title: ChIP-seq_WT_H3K36me3_dTAG_4h_rep2

description:
Library name: sample93
ChIP-seq_H3K36me3_WT_Rawcounts.csv
H3K36me3_WT_DEseq2_results.csv


title: BatchC_ethanol extract of Pinelliae Tuber (High dose)_rep2

description: sample 10-2-1


title: BatchC_ethanol extract of Scutellariae Radix (Low dose)_rep1

description: sample 10-1-6


title: ChIP-seq_WT_H3K36me3_dTAG_0h_rep1

description:
Library name: sample90
ChIP-seq_H3K36me3_WT_Rawcounts.csv
H3K36me3_WT_DEseq2_results.csv


title: BatchC_ethanol extract of Scutellariae Radix (High dose)_rep1

description: sample 10-1-4


title: BatchC_ethanol extract of Scutellariae Radix (Medium dose)_rep1

description: sample 10-1-5


title: ChIP-seq_Degron_RPB1_H3K36me3_dTAG_4h_rep2

description:
Library name: sample89
ChIP-seq_H3K36me3_Degron_RPB1_Rawcounts.csv
H3K36me3_Degron_RPB1_DEseq2_results.csv

value: RPB1 degron

value: dTAGV-1 (100 nM) for 4 hours


title: ChIP-seq_Degron_RPB1_H3K36me3_dTAG_4h_rep1

description:
Library name: sample88
ChIP-seq_H3K36me3_Degron_RPB1_Rawcounts.csv
H3K36me3_Degron_RPB1_DEseq2_results.csv


title: ChIP-seq_S2A_H3K36me3_dTAG_4h_rep1

description:
Library name: sample100
ChIP-seq_H3K36me3_S2A_Rawcounts.csv
H3K36me3_S2A_DEseq2_results.csv


title: BatchC_ethanol extract of Pinelliae Tuber (Low dose)_rep1

description: sample 10-1-3


title: BatchC_ethanol extract of Pinelliae Tuber (Medium dose)_rep1

description: sample 10-1-2


title: ChIP-seq_Degron_RPB1_H3K36me3_dTAG_0h_rep1

description:
Library name: sample86
ChIP-seq_H3K36me3_Degron_RPB1_Rawcounts.csv
H3K36me3_Degron_RPB1_DEseq2_results.csv


title: ChIP-seq_Degron_RPB1_H3K36me3_dTAG_0h_rep2

description:
Library name: sample87
ChIP-seq_H3K36me3_Degron_RPB1_Rawcounts.csv
H3K36me3_Degron_RPB1_DEseq2_results.csv


title: BatchC_ethanol extract of Pinelliae Tuber (High dose)_rep1

description: sample 10-1-1


title: PBS_Ctrl_3

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

description: Library name: Sample 7

data_processing:
Illumina Casava1.7 software used for basecalling.
The resulting clean reads were saved in FASTQ format and subsequently aligned to the reference genome using HISAT2. The clean reads were aligned against the reference coding gene set using Bowtie2
Genes expression level is quantified through RSEM.
Differential expression analysis was carried out utilizing DESeq2, which identified genes with statistically significant differences at a threshold of Q < 0.05.
Assembly: GRCm38.84
Supplementary files format and content: FPKM ( Fragments Per Kilobase Million) for each Sample

organism: Mus musculus

source_name: Skin

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

tag: tissue

value: Skin

tag: strain

value: PBS


title: BatchC_ethanol extract of Scutellariae Radix (Low dose)_rep2

description: sample 10-2-6


title: PBS_Ctrl_4

description: Library name: Sample 8


title: PBS_Ctrl_2

description: Library name: Sample 6


title: BatchC_ethanol extract of Zingiberis Rhizoma (Low dose)_rep3

description: sample 9-3-6

value: Zingiberis Rhizoma ethanol extract 20 μg/mL


title: BatchC_ethanol extract of Zingiberis Rhizoma (High dose)_rep3

description: sample 9-3-4

value: Zingiberis Rhizoma ethanol extract 500 μg/mL


title: PBS_Ctrl_1

description: Library name: Sample 5


title: ABX_3

description: Library name: Sample 3

value: broad-spectrum antibiotic-treated (ABX)


title: BatchC_ethanol extract of Zingiberis Rhizoma Recens (High dose)_rep3

description: sample 9-3-1

value: Zingiberis Rhizoma Recens ethanol extract 500 μg/mL


title: ABX_4

description: Library name: Sample 4


title: BatchC_ethanol extract of Zingiberis Rhizoma Recens (Medium dose)_rep3

description: sample 9-3-2

value: Zingiberis Rhizoma Recens ethanol extract 100 μg/mL


title: ABX_2

description: Library name: Sample 2


title: BatchC_ethanol extract of Zingiberis Rhizoma (Low dose)_rep2

description: sample 9-2-6


title: ChIP-seq_WT_H3K36me3_dTAG_0h_rep2

description:
Library name: sample91
ChIP-seq_H3K36me3_WT_Rawcounts.csv
H3K36me3_WT_DEseq2_results.csv

value: H3K36me3 antibody (Abcam #ab9050)


title: BatchC_ethanol extract of Zingiberis Rhizoma Recens (Low dose)_rep3

description: sample 9-3-3

value: Zingiberis Rhizoma Recens ethanol extract 20 μg/mL


title: BatchC_ethanol extract of Zingiberis Rhizoma (Medium dose)_rep2

description: sample 9-2-5

value: Zingiberis Rhizoma ethanol extract 100 μg/mL


title: BatchC_ethanol extract of Zingiberis Rhizoma (High dose)_rep2

description: sample 9-2-4


title: BatchC_ethanol extract of Zingiberis Rhizoma Recens (Medium dose)_rep2

description: sample 9-2-2


title: ASPC cells,shCtrl-3

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: sh-Ctrl-3
Column name in gene_sample_FPKM.txt: sh-Ctrl-3

data_processing:
The quality of the RNA-seq data was estimated using RSeQC (version 2.6.4).
Assembly: Mouse mm10
Supplementary files format and content: xls files include FPKM values for each sample

source_name: ASPC cells

growth_protocol: ASPC cells were cultured in DMEM  containing 10% fetal bovine serum  and 1% penicillin/streptomycin.

extract_protocol:
Total RNA from cells was extracted using TRIzol reagent.
RNA libraries were constructed using VAHTS® Universal V6 RNA-seq Library Prep Kit for IlluminaVazyme (Cat.N401-02), and paired-end reads were obtained on the Novaseq 6000 platform.

treatment_protocol: Cells were  infected with lentiviral sh-FBLN7or sh-Ctrl, and  stimulated with human recombinant TGF-β1.

tag: cell type

value: ASPC cells

value: Ctronl


title: ASPC cells,shCtrl-1

description:
Library name: sh-Ctrl-1
Column name in gene_sample_FPKM.txt: sh-Ctrl-1

value: stimulated with human recombinant TGF-β1


title: BatchC_ethanol extract of Zingiberis Rhizoma Recens (Low dose)_rep2

description: sample 9-2-3


title: ASPC cells,shCtrl-2

description:
Library name: sh-Ctrl-2
Column name in gene_sample_FPKM.txt: sh-Ctrl-2


title: ASPC cells,shCtrl-4

description:
Library name: sh-Ctrl-4
Column name in gene_sample_FPKM.txt: sh-Ctrl-4


title: BatchC_ethanol extract of Zingiberis Rhizoma (Medium dose)_rep3

description: sample 9-3-5


title: ASPC cells,shFBLN7-5

description:
Library name: sh-FBLN7-5
Column name in gene_sample_FPKM.txt: sh-FBLN7-5


title: BatchC_ethanol extract of Zingiberis Rhizoma (Low dose)_rep1

description: sample 9-1-6


title: BatchC_ethanol extract of Zingiberis Rhizoma Recens (High dose)_rep2

description: sample 9-2-1


title: BatchC_ethanol extract of Zingiberis Rhizoma (Medium dose)_rep1

description: sample 9-1-5


title: ASPC cells,shFBLN7-4

description:
Library name: sh-FBLN7-4
Column name in gene_sample_FPKM.txt: sh-FBLN7-4


title: ASPC cells,shFBLN7-3

description:
Library name: sh-FBLN7-3
Column name in gene_sample_FPKM.txt: sh-FBLN7-3


title: ASPC cells,shFBLN7-2

description:
Library name: sh-FBLN7-2
Column name in gene_sample_FPKM.txt: sh-FBLN7-2


title: BatchC_ethanol extract of Zingiberis Rhizoma (High dose)_rep1

description: sample 9-1-4


title: BatchC_ethanol extract of Zingiberis Rhizoma Recens (Low dose)_rep1

description: sample 9-1-3


title: BatchC_ethanol extract of Zingiberis Rhizoma Recens (Medium dose)_rep1

description: sample 9-1-2


title: GL261_3

first: Jia

last: Wang

address: No.30 Science Park Road, Zhong-Guan-Cun Life Science Park, Changping District

institute: BeOne Medicines

description: Library name: SS_20_0746

library_source: transcriptomic single cell

data_processing:
Feature-barcode matrices were generated using the Cell Ranger Single Cell Software Suite v3.1.0
Assembly: Mouse mm10
Supplementary files format and content: barcodes.tsv.gz: contains cell barcodes (one per line) identifying individual cells; each barcode corresponds to a column in the expression matrix.
Supplementary files format and content: features.tsv.gz: stores gene metadata (gene ID, name, and feature type) in three tab-separated columns; rows align with the expression matrix.
Supplementary files format and content: matrix.mtx.gz: a sparse matrix in MEX format (Market Exchange Format) with row/column indices and expression values, space-separated, non-zero counts only.

molecule: polyA RNA

source_name: Tumor

extract_protocol:
Tumors were collected, mechanically dissociated, and resuspended in 2.35 mL of RPMI 1640 medium supplemented with 100 µL of Enzyme D, 50 µL of Enzyme R, and 12.5 µL of Enzyme A (Miltenyi Biotec #130-096-730). Tissue dissociation was performed using the gentleMACSTM Octo Dissociator with Heaters (Miltenyi Biotec #130-096-427) according to the manufacturer's program (37C_m_TDK_1). Following dissociation, cell suspensions were filtered through a 70 μm mesh and washed with FACS buffer (1% FBS in PBS). Cells were centrifuged at 500 × g for 5 minutes and resuspended in 500 μL of FACS buffer. For flow cytometry analysis, cells were stained with anti-CD45 antibody (BD, #550994) and Fixable Viability Stain 450 (BD, #562247) to assess viability. CD45+ viable cells were sorted using a BD FACSAria™ III cell sorter, washed in PBS, and resuspended at a concentration of 1 × 10⁶ cells/mL.
Single-cell suspensions were subsequently loaded onto a Chromium Controller (10x Genomics, Pleasanton, CA) using the Single Cell 3’ Library and Gel Bead Kit v3 (10x Genomics) for droplet-based encapsulation and library preparation.

value: Tumor

value: CD45+ immune cells


title: BatchC_ethanol extract of Zingiberis Rhizoma Recens (High dose)_rep1

description: sample 9-1-1


title: BatchC_water extract of Sayeok-tang (Low dose)_rep3

description: sample 8-3-6

value: Sayeok-tang water extract 20 μg/mL


title: GL261_2

description: Library name: SS_20_0745


title: ABX_1

description: Library name: Sample 1


title: BatchC_water extract of Sayeok-tang (Medium dose)_rep3

description: sample 8-3-5

value: Sayeok-tang water extract 100 μg/mL


title: Pan02_3

description: Library name: SS_20_0623


title: BatchC_water extract of Bojungikgi-tang (Low dose)_rep3

description: sample 8-3-3

value: Bojungikgi-tang water extract 20 μg/mL


title: BatchC_water extract of Sayeok-tang (High dose)_rep3

description: sample 8-3-4

value: Sayeok-tang water extract 500 μg/mL


title: GL261_1

description: Library name: SS_20_0744


title: ES-2 cells,PD-L1 3'UTR, Rep 3

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced single-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.18) with parameters -q 20 -O 7 -m 16 --trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using Bowtie2 (v 2.2.6) with parameters -N 1
Mapped reads were summarized using featureCounts (v 1.6.3) with parameterst -p -s 1 -T 6 -t miRNA -g ID and miRBase annotation (22 GRCm 38)
Assembly: hg38
Supplementary files format and content: Comma-separated text files including raw counts for each sample.

extract_protocol:
Total RNA was extracted using phenol-chloroform extraction. Purified RNA was sent for short-read RNA sequencing.
After QC, library was constructed by Small RNA Sample Pre Kit. The final cDNA library was ready after a round of sequencing. Construction was performed at  adaptor ligation, reverse transcription, PCR enrichment, purification and size selection at Novogene (Hong Kong).

value: ovarian cancer derived cell line

value: WT

value: untreated


title: Pan02_2

description: Library name: SS_20_0622


title: BatchC_water extract of Bojungikgi-tang (Medium dose)_rep3

description: sample 8-3-2

value: Bojungikgi-tang water extract 100 μg/mL


title: BatchC_water extract of Bojungikgi-tang (High dose)_rep3

description: sample 8-3-1

value: Bojungikgi-tang water extract 500 μg/mL


title: ES-2 cells,PD-L1 3'UTR, Rep 2


title: Pan02_1

description: Library name: SS_20_0621


title: ES-2 cells,PD-L1 3'UTR, Rep 1


title: BatchC_water extract of Sayeok-tang (Medium dose)_rep2

description: sample 8-2-5


title: BatchC_water extract of Sayeok-tang (Low dose)_rep2

description: sample 8-2-6


title: ASPC cells,shFBLN7-1

description:
Library name: sh-FBLN7-1
Column name in gene_sample_FPKM.txt: sh-FBLN7-1


title: BatchC_water extract of Sayeok-tang (High dose)_rep2

description: sample 8-2-4


title: ES-2 cells,MS2 control RNA, Rep 3


title: BatchC_water extract of Bojungikgi-tang (Low dose)_rep2

description: sample 8-2-3


title: LL2_3

description: Library name: SS_20_0580


title: BatchC_water extract of Bojungikgi-tang (Medium dose)_rep2

description: sample 8-2-2


title: ES-2 cells,MS2 control RNA, Rep 2


title: BatchC_water extract of Sayeok-tang (Low dose)_rep1

description: sample 8-1-6


title: LL2_1

description: Library name: SS_20_0578


title: LL2_2

description: Library name: SS_20_0579


title: BatchC_water extract of Bojungikgi-tang (High dose)_rep2

description: sample 8-2-1


title: ES-2 cells,MS2 control RNA, Rep 1


title: BatchC_water extract of Sayeok-tang (High dose)_rep1

description: sample 8-1-4


title: ES-2 cells, input, Rep 3


title: BatchC Vehicle(DMSO) rep3

description: sample C1-3-1

value: 0.1% DMSO


title: EMT6_2

description: Library name: SS_20_0531


title: BatchC Vehicle(DMSO) rep2

description: sample C1-2-1


title: ES-2 cells, input, Rep 2


title: EMT6_3

description: Library name: SS_20_0532


title: BatchC_water extract of Sayeok-tang (Medium dose)_rep1

description: sample 8-1-5


title: BatchC Vehicle(DMSO) rep1

description: sample C1-1-1


title: BatchB_water extract of Bojungikgi-tang (Low dose)_rep1

description: sample 8-1-3


title: BatchB_water extract of Bojungikgi-tang (Medium dose)_rep1

description: sample 8-1-2


title: EMT6_1

description: Library name: SS_20_0530


title: ES-2 cells, input, Rep 1


title: B16F10_3

description: Library name: SS_20_0529


title: BatchB_water extract of Bojungikgi-tang (High dose)_rep1

description: sample 8-1-1


title: BatchB_water extract of Banhasasim-tang (Low dose)_rep3

description: sample 7-3-6

value: Banhasasim-tang water extract 20 μg/mL


title: B16F10_2

description: Library name: SS_20_0528


title: BatchB_water extract of Banhasasim-tang (Medium dose)_rep3

description: sample 7-3-5

value: Banhasasim-tang water extract 100 μg/mL


title: Pol_II_Ser5-P_ChIP_lambdaN-Setx_Dox-

city: Tokyo

first: Kensaku

last: Murano

address: 35 Shinanomachi, Shinjuku

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

description: Library name: ChIP-seq_Sample 5

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-Setx

value: Doxycycline-

tag: antibody

value: anti-Pol II Ser5-P antibody (Cosmobio, CMA603)


title: Pol_II_Ser5-P_ChIP_lambdaN-Setx_Dox+

description: Library name: ChIP-seq_Sample 6

value: Doxycycline+


title: BatchB_water extract of Banhasasim-tang (High dose)_rep3

description: sample 7-3-4

value: Banhasasim-tang water extract 500 μg/mL


title: B16F10_1

description: Library name: SS_20_0527

value: Tumor

value: CD45+ immune cells


title: BatchB_water extract of Yijung-tang (Medium dose)_rep3

description: sample 7-3-2

value: Yijung-tang water extract 100 μg/mL


title: Pol_II_Ser5-P_ChIP_lambdaN-PNUTS_Dox+

description: Library name: ChIP-seq_Sample 4

value: TRE-lambdaN-PNUTS


title: BatchB_water extract of Yijung-tang (High dose)_rep3

description: sample 7-3-1

value: Yijung-tang water extract 500 μg/mL


title: CT26WT_3

description: Library name: SS_20_0526


title: Pol_II_Ser5-P_ChIP_lambdaN-PNUTS_Dox-

description: Library name: ChIP-seq_Sample 3


title: BatchB_water extract of Banhasasim-tang (Low dose)_rep2

description: sample 7-2-6


title: BatchB_water extract of Banhasasim-tang (Medium dose)_rep2

description: sample 7-2-5


title: BatchB_water extract of Banhasasim-tang (High dose)_rep2

description: sample 7-2-4


title: Pol_II_Ser5-P_ChIP_lambdaN-Panx_Dox+

description: Library name: ChIP-seq_Sample 2

value: TRE-lambdaN-Panx


title: CT26WT_1

description: Library name: SS_20_0524


title: CT26WT_2

description: Library name: SS_20_0525


title: 4T1_3

description: Library name: SS_20_0451


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

description: sample 7-2-2


title: Pol_II_Ser5-P_ChIP_lambdaN-Panx_Dox-

description: Library name: ChIP-seq_Sample 1


title: BatchB_water extract of Banhasasim-tang (Low dose)_rep1

description: sample 7-1-6


title: 4T1_2

description: Library name: SS_20_0450


title: BatchB_water extract of Banhasasim-tang (Medium dose)_rep1

description: sample 7-1-5


title: Airway epithelium, sample60

city: Vancouver

first: Janice

middle: M

last: Leung

state: BC

address: Room 166, 1081 Burrard Street

country: Canada

institute: Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia

description: Library name: sample60

data_processing:
Salmon was used for quantification and quasi-alignment of the sequencing reads to the GENCODE genome reference (assembly GRCh37, release 45). Transcript-level counts were summarised to gene-level using tximport package in R, then filtered and normalized to log2 counts per million (logCPM) with the edgeR package. Batch correction was performed with ComBat. Lowly expressed genes (logCPM < 1 in half of samples) were removed,
Assembly: GRCh37
Supplementary files format and content: text file includes logCPM for each sample

source_name: Airway epithelium

extract_protocol:
Total RNA was extracted from brushes with Qiagen RNeasy Plus Universal Mini Kit (cat. 73404) and were assessed for quality with the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
High quality RNA was sequenced with the Illumina NovaSeq6000 according to the manufacturer’s protocol

value: Airway epithelium

tag: age

tag: Sex

value: Male

tag: cigarette

value: never

tag: vape

value: Yes

tag: cannabis group

value: Non-Cannabis


title: BatchB_water extract of Yijung-tang (Low dose)_rep1

description: sample 7-1-3

value: Yijung-tang water extract 20 μg/mL


title: 4T1_1

description: Library name: SS_20_0449


title: BatchB_water extract of Yijung-tang (Low dose)_rep2

description: sample 7-2-3


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

description: sample 7-3-3


title: Airway epithelium, sample59

description: Library name: sample59

value: Female

value: former


title: MMTV-PyMT_3

description: Library name: SS_20_0370

value: MMTV-PyMT


title: BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep3

description: sample 6-3-6

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


title: MMTV-PyMT_2

description: Library name: SS_20_0369


title: Airway epithelium, sample57

description: Library name: sample57


title: BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep3

description: sample 6-3-4

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


title: MMTV-PyMT_1

description: Library name: SS_20_0368

value: Tumor


title: BatchB_water extract of Bupleuri Radix (Low dose)_rep3

description: sample 6-3-3

value: Bupleuri Radix water extract 20 μg/mL


title: Airway epithelium, sample56

description: Library name: sample56


title: Airway epithelium, sample61

description: Library name: sample61


title: BatchB_water extract of Yijung-tang (High dose)_rep2

description: sample 7-2-1


title: BatchB_water extract of Bupleuri Radix (Medium dose)_rep3

description: sample 6-3-2

value: Bupleuri Radix water extract 100 μg/mL


title: Airway epithelium, sample55

description: Library name: sample55


title: BatchB_water extract of Banhasasim-tang (High dose)_rep1

description: sample 7-1-4

value: Banhasasim-tang water extract 500 μg/mL


title: BatchB_water extract of Bupleuri Radix (High dose)_rep3

description: sample 6-3-1

value: Bupleuri Radix water extract 500 μg/mL


title: BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep2

description: sample 6-2-6


title: BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep2

description: sample 6-2-5

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


title: RENCA_2

description: Library name: SS_20_0336

value: RENCA

value: CD45+ immune cells


title: Airway epithelium, sample54

description: Library name: sample54

value: Airway epithelium

value: Male


title: RENCA_1

description: Library name: SS_20_0335


title: BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep2

description: sample 6-2-4


title: BatchB_water extract of Bupleuri Radix (Low dose)_rep2

description: sample 6-2-3


title: Airway epithelium, sample53

description: Library name: sample53

value: never

value: Yes

value: Non-Cannabis


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

description: sample 7-1-1

value: Yijung-tang water extract 500 μg/mL


title: BatchB_water extract of Bupleuri Radix (Medium dose)_rep2

description: sample 6-2-2


title: MC38 _3

description: Library name: SS_20_0090


title: BatchB_water extract of Yijung-tang (Medium dose)_rep1

description: sample 7-1-2

value: Yijung-tang water extract 100 μg/mL


title: Airway epithelium, sample52

description: Library name: sample52

value: Female


title: BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep3

description: sample 6-3-5


title: Airway epithelium, sample58

description: Library name: sample58

value: former


title: BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep1

description: sample 6-1-6

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


title: BatchB_water extract of Bupleuri Radix (High dose)_rep2

description: sample 6-2-1


title: BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep1

description: sample 6-1-5


title: Airway epithelium, sample51

description: Library name: sample51


title: MC38 _2

description: Library name: SS_20_0089

value: Tumor


title: RENCA_3

description: Library name: SS_20_0337


title: MC38 _1

description: Library name: SS_20_0088


title: BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep1

description: sample 6-1-4

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


title: BatchB_water extract of Bupleuri Radix (Medium dose)_rep1

description: sample 6-1-2

value: Bupleuri Radix water extract 100 μg/mL


title: BatchB_water extract of Bupleuri Radix (Low dose)_rep1

description: sample 6-1-3

value: Bupleuri Radix water extract 20 μg/mL


title: Airway epithelium, sample50

description: Library name: sample50

value: No


title: Airway epithelium, sample49

description: Library name: sample49


title: BatchB_water extract of  Cimicifugae Rhizoma (Medium dose)_rep3

description: sample 5-3-5

value: Cimicifugae Rhizoma water extract 100 μg/mL


title: BatchB_water extract of  Cimicifugae Rhizoma (Low dose)_rep3

description: sample 5-3-6

value: Cimicifugae Rhizoma water extract 20 μg/mL


title: Airway epithelium, sample48

description: Library name: sample48

value: Airway epithelium


title: BatchB_water extract of Bupleuri Radix (High dose)_rep1

description: sample 6-1-1

value: Bupleuri Radix water extract 500 μg/mL


title: KI_P40_testis_biol_rep2

city: Nanjing

first: Yu

last: Zheng

state: Jiangsu Sheng

address: No.1 Wenyuan Road, Xianlin University Town, Qixia District, Nanjing, Jiangsu Province

institute: NANJING NORMAL UNIVERSITY

description:
Library name: Sample38
P40KI-T2

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool, BMKCloud(www.biocloud.net) online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Assembly: GRCm38_release79
Supplementary files format and content: csv files include FPKM values for each Sample
Supplementary files format and content: csv file includes raw counts for each Sample

source_name: testis

growth_protocol: Male C57BL/6J mice (genotypes: WT, INSL3 knock-in, INSL3 knockout) were bred and maintained in a specific pathogen-free facility on a 12 h light/12 h dark cycle at 22–24 °C with 40–60% humidity and ad libitum access to food and water.

extract_protocol:
The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA). RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: No pharmacological or surgical treatments were applied prior to tissue collection. Mice were euthanized by approved methods (e.g., CO₂ inhalation followed by cervical dislocation).

value: testis

value: KI


title: KI_P40_testis_biol_rep3

description:
Library name: Sample39
P40KI-T3


title: BatchB_water extract of Citri Unshius Pericarpium (Medium dose)_rep3

description: sample 5-3-2

value: Citri Unshius Pericarpium water extract 100 μg/mL


title: BatchB_water extract of  Cimicifugae Rhizoma (Low dose)_rep2

description: sample 5-2-6


title: WT_P40_testis_biol_rep2

description:
Library name: Sample35
P40WT-T2

value: WT


title: BatchB_water extract of Citri Unshius Pericarpium (High dose)_rep3

description: sample 5-3-1

value: Citri Unshius Pericarpium water extract 500 μg/mL


title: Airway epithelium, sample46

description: Library name: sample46

value: Female

value: never

value: Cannabis


title: WT_P40_testis_biol_rep3

description:
Library name: Sample36
P40WT-T3


title: Airway epithelium, sample45

description: Library name: sample45

value: former

value: Non-Cannabis


title: BatchB_water extract of  Cimicifugae Rhizoma (Medium dose)_rep2

description: sample 5-2-5


title: BatchB_water extract of  Cimicifugae Rhizoma (High dose)_rep2

description: sample 5-2-4

value: Cimicifugae Rhizoma water extract 500 μg/mL


title: BatchB_water extract of Citri Unshius Pericarpium (Low dose)_rep2

description: sample 5-2-3

value: Citri Unshius Pericarpium water extract 20 μg/mL


title: Airway epithelium, sample44

description: Library name: sample44

value: Yes


title: WT_P40_testis_biol_rep1

description:
Library name: Sample34
P40WT-T1


title: BatchB_water extract of Citri Unshius Pericarpium (Medium dose)_rep2

description: sample 5-2-2


title: KO_P23_testis_biol_rep3

description:
Library name: Sample33
P23KO-T3

value: KO


title: Airway epithelium, sample43

description: Library name: sample43

value: Male

value: No


title: KO_P23_testis_biol_rep2

description:
Library name: Sample32
P23KO-T2


title: BatchB_water extract of  Cimicifugae Rhizoma (Low dose)_rep1

description: sample 5-1-6

value: Cimicifugae Rhizoma water extract 20 μg/mL


title: BatchB_water extract of  Cimicifugae Rhizoma (High dose)_rep3

description: sample 5-3-4


title: KI_P40_testis_biol_rep1

description:
Library name: Sample37
P40KI-T1

value: testis


title: BatchB_water extract of Citri Unshius Pericarpium (Low dose)_rep3

description: sample 5-3-3


title: BatchB_water extract of  Cimicifugae Rhizoma (Medium dose)_rep1

description: sample 5-1-5

value: Cimicifugae Rhizoma water extract 100 μg/mL


title: BatchB_water extract of  Cimicifugae Rhizoma (High dose)_rep1

description: sample 5-1-4


title: Airway epithelium, sample47

description: Library name: sample47

value: Airway epithelium


title: Airway epithelium, sample42

description: Library name: sample42


title: KO_P23_testis_biol_rep1

description:
Library name: Sample31
P23KO-T1


title: KI_P23_testis_biol_rep3

description:
Library name: Sample30
P23KI-T3

value: KI


title: BatchB_water extract of Citri Unshius Pericarpium (Low dose)_rep1

description: sample 5-1-3


title: BatchB_water extract of Citri Unshius Pericarpium (High dose)_rep1

description: sample 5-1-1

value: Citri Unshius Pericarpium water extract 500 μg/mL


title: Airway epithelium, sample40

description: Library name: sample40


title: KI_P23_testis_biol_rep2

description:
Library name: Sample29
P23KI-T2


title: BatchB Vehicle(DMSO) rep3

description: sample B1-3-1

value: 0.1% DMSO


title: BatchB Vehicle(DMSO) rep1

description: sample B1-1-1


title: BatchB Vehicle(DMSO) rep2

description: sample B1-2-1


title: Airway epithelium, sample39

description: Library name: sample39

value: never


title: KI_P23_testis_biol_rep1

description:
Library name: Sample28
P23KI-T1


title: BatchA_water extract of Zizyphi Fructus (Medium dose)_rep3

description: sample 4-3-5

value: Zizyphi Fructus water extract 100 μg/mL


title: BatchB_water extract of Citri Unshius Pericarpium (High dose)_rep2

description: sample 5-2-1


title: WT_P23_testis_biol_rep3

description:
Library name: Sample27
P23WT-T3

value: WT


title: Airway epithelium, sample37

description: Library name: sample37

value: former

value: Cannabis


title: BatchA_water extract of Coptidis Rhizoma (Medium dose)_rep3

description: sample 4-3-2

value: Coptidis Rhizoma water extract 58 μg/mL


title: Airway epithelium, sample41

description: Library name: sample41

value: Non-Cannabis


title: BatchB_water extract of Citri Unshius Pericarpium (Medium dose)_rep1

description: sample 5-1-2

value: Citri Unshius Pericarpium water extract 100 μg/mL


title: BatchA_water extract of Coptidis Rhizoma (Low dose)_rep3

description: sample 4-3-3

value: Coptidis Rhizoma water extract 11.6 μg/mL


title: Airway epithelium, sample35

description: Library name: sample35

value: Male

value: No


title: WT_P23_testis_biol_rep1

description:
Library name: Sample25
P23WT-T1

value: testis


title: BatchA_water extract of Zizyphi Fructus (Medium dose)_rep2

description: sample 4-2-5


title: Airway epithelium, sample36

description: Library name: sample36

value: current

value: Yes


title: BatchA_water extract of Coptidis Rhizoma (High dose)_rep3

description: sample 4-3-1

value: Coptidis Rhizoma water extract 290 μg/mL


title: KO_P8_testis_biol_rep3

description:
Library name: Sample24
P8KO-T3

value: KO


title: Airway epithelium, sample34

description: Library name: sample34

value: Airway epithelium


title: BatchA_water extract of Coptidis Rhizoma (Low dose)_rep2

description: sample 4-2-3


title: BatchA_water extract of Zizyphi Fructus (High dose)_rep2

description: sample 4-2-4

value: Zizyphi Fructus water extract 500 μg/mL


title: BatchA_water extract of Zizyphi Fructus (Low dose)_rep3

description: sample 4-3-6

value: Zizyphi Fructus water extract 20 μg/mL


title: BatchA_water extract of Zizyphi Fructus (Low dose)_rep1

description: sample 4-1-6


title: KO_P8_testis_biol_rep1

description:
Library name: Sample22
P8KO-T1


title: Airway epithelium, sample32

description: Library name: sample32


title: Airway epithelium, sample38

description: Library name: sample38

value: never


title: BatchA_water extract of Zizyphi Fructus (High dose)_rep3

description: sample 4-3-4


title: BatchA_water extract of Zizyphi Fructus (Medium dose)_rep1

description: sample 4-1-5

value: Zizyphi Fructus water extract 100 μg/mL


title: KO_P8_testis_biol_rep2

description:
Library name: Sample23
P8KO-T2


title: BatchA_water extract of Coptidis Rhizoma (Medium dose)_rep2

description: sample 4-2-2


title: BatchA_water extract of Zizyphi Fructus (High dose)_rep1

description: sample 4-1-4


title: Airway epithelium, sample31

description: Library name: sample31


title: BatchA_water extract of Coptidis Rhizoma (Low dose)_rep1

description: sample 4-1-3


title: WT_P23_testis_biol_rep2

description:
Library name: Sample26
P23WT-T2

value: WT


title: BatchA_water extract of Zizyphi Fructus (Low dose)_rep2

description: sample 4-2-6


title: KI_P8_testis_biol_rep2

description:
Library name: Sample20
P8KI-T2

value: KI


title: BatchA_water extract of Coptidis Rhizoma (High dose)_rep1

description: sample 4-1-1


title: BatchA_water extract of Coptidis Rhizoma (Medium dose)_rep1

description: sample 4-1-2

value: Coptidis Rhizoma water extract 58 μg/mL


title: KI_P8_testis_biol_rep1

description:
Library name: Sample19
P8KI-T1


title: Airway epithelium, sample29

description: Library name: sample29

value: Female

value: former

value: Cannabis


title: BatchA_water extract of Scutellariae Radix (Low dose)_rep3

description: sample 3-3-6

value: Scutellariae Radix water extract 20 μg/mL


title: BatchA_water extract of Scutellariae Radix (Medium dose)_rep3

description: sample 3-3-5

value: Scutellariae Radix water extract 100 μg/mL


title: Airway epithelium, sample30

description: Library name: sample30

value: current


title: WT_P8_testis_biol_rep3

description:
Library name: Sample18
P8WT-T3

value: testis


title: Airway epithelium, sample28

description: Library name: sample28

value: Male

value: Yes


title: BatchA_water extract of Scutellariae Radix (High dose)_rep3

description: sample 3-3-4

value: Scutellariae Radix water extract 500 μg/mL


title: WT_P8_testis_biol_rep2

description:
Library name: Sample17
P8WT-T2


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

description: sample 3-3-3

value: Pinelliae Tuber water extract 20 μg/mL


title: Airway epithelium, sample33

description: Library name: sample33

value: Airway epithelium


title: BatchA_water extract of Coptidis Rhizoma (High dose)_rep2

description: sample 4-2-1

value: Coptidis Rhizoma water extract 290 μg/mL


title: BatchA_water extract of Pinelliae Tuber (Medium dose)_rep3

description: sample 3-3-2

value: Pinelliae Tuber water extract 100 μg/mL


title: BatchA_water extract of Scutellariae Radix (Low dose)_rep2

description: sample 3-2-6


title: WT_P8_testis_biol_rep1

description:
Library name: Sample16
P8WT-T1

value: WT


title: KI_P8_testis_biol_rep3

description:
Library name: Sample21
P8KI-T3

value: KI


title: BatchA_water extract of Scutellariae Radix (Medium dose)_rep2

description: sample 3-2-5


title: Airway epithelium, sample27

description: Library name: sample27

value: No


title: BatchA_water extract of Pinelliae Tuber (High dose)_rep3

description: sample 3-3-1

value: Pinelliae Tuber water extract 500 μg/mL


title: Airway epithelium, sample26

description: Library name: sample26

value: never


title: Airway epithelium, sample25

description: Library name: sample25

value: Female

value: former

value: Cannabis


title: BatchA_water extract of Pinelliae Tuber (Low dose)_rep2

description: sample 3-2-3


title: KI_P23_gubernaculum_biol_rep3

description:
Library name: Sample15
P23KI-G3

source_name: gubernaculum

value: gubernaculum


title: KI_P23_gubernaculum_biol_rep2

description:
Library name: Sample14
P23KI-G2


title: BatchA_water extract of Pinelliae Tuber (Medium dose)_rep2

description: sample 3-2-2


title: BatchA_water extract of Scutellariae Radix (High dose)_rep2

description: sample 3-2-4


title: Airway epithelium, sample24

description: Library name: sample24

value: current


title: BatchA_water extract of Pinelliae Tuber (High dose)_rep2

description: sample 3-2-1


title: Airway epithelium, sample23

description: Library name: sample23

value: Male


title: KI_P23_gubernaculum_biol_rep1

description:
Library name: Sample13
P23KI-G1


title: WT_P23_gubernaculum_biol_rep3

description:
Library name: Sample12
P23WT-G3


title: BatchA_water extract of Scutellariae Radix (Medium dose)_rep1

description: sample 3-1-5

value: Scutellariae Radix water extract 100 μg/mL


title: BatchA_water extract of Scutellariae Radix (High dose)_rep1

description: sample 3-1-4

value: Scutellariae Radix water extract 500 μg/mL


title: Airway epithelium, sample22

description: Library name: sample22

value: Non-Cannabis


title: BatchA_water extract of Scutellariae Radix (Low dose)_rep1

description: sample 3-1-6

value: Scutellariae Radix water extract 20 μg/mL


title: WT_P23_gubernaculum_biol_rep2

description:
Library name: Sample11
P23WT-G2


title: BatchA_water extract of Pinelliae Tuber (Medium dose)_rep1

description: sample 3-1-2


title: BatchA_water extract of Pinelliae Tuber (High dose)_rep1

description: sample 3-1-1


title: BatchA_water extract of Zingiberis Rhizoma (Low dose)_rep3

description: sample 2-3-6

value: Zingiberis Rhizoma water extract 20 μg/mL


title: BatchA_water extract of Pinelliae Tuber (Low dose)_rep1

description: sample 3-1-3

value: Pinelliae Tuber water extract 20 μg/mL


title: KO_P8_gubernaculum_biol_rep3

description:
Library name: Sample9
P8KO-G3

value: KO


title: WT_P23_gubernaculum_biol_rep1

description:
Library name: Sample10
P23WT-G1

value: WT


title: Airway epithelium, sample20

description: Library name: sample20

value: Airway epithelium

value: Yes


title: BatchA_water extract of Zingiberis Rhizoma Recens (Low dose)_rep3

description: sample 2-3-3

value: Zingiberis Rhizoma Recens water extract 20 μg/mL


title: Airway epithelium, sample19

description: Library name: sample19

value: Female

value: No


title: BatchA_water extract of Zingiberis Rhizoma (High dose)_rep3

description: sample 2-3-4

value: Zingiberis Rhizoma water extract 500 μg/mL


title: KO_P8_gubernaculum_biol_rep1

description:
Library name: Sample7
P8KO-G1

value: gubernaculum


title: Airway epithelium, sample18

description: Library name: sample18

value: current

value: Cannabis


title: BatchA_water extract of Zingiberis Rhizoma (Medium dose)_rep3

description: sample 2-3-5

value: Zingiberis Rhizoma water extract 100 μg/mL


title: KO_P8_gubernaculum_biol_rep2

description:
Library name: Sample8
P8KO-G2


title: BatchA_water extract of Zingiberis Rhizoma (Medium dose)_rep2

description: sample 2-2-5


title: BatchA_water extract of Zingiberis Rhizoma Recens (Medium dose)_rep3

description: sample 2-3-2

value: Zingiberis Rhizoma Recens water extract 100 μg/mL


title: Airway epithelium, sample17

description: Library name: sample17

value: never


title: BatchA_water extract of Zingiberis Rhizoma Recens (High dose)_rep3

description: sample 2-3-1

value: Zingiberis Rhizoma Recens water extract 500 μg/mL


title: BatchA_water extract of Zingiberis Rhizoma (High dose)_rep2

description: sample 2-2-4


title: BatchA_water extract of Zingiberis Rhizoma (Low dose)_rep2

description: sample 2-2-6

value: Zingiberis Rhizoma water extract 20 μg/mL


title: KI_P8_gubernaculum_biol_rep3

description:
Library name: Sample6
P8KI-G3

value: KI


title: BatchA_water extract of Zingiberis Rhizoma Recens (Low dose)_rep2

description: sample 2-2-3


title: KI_P8_gubernaculum_biol_rep2

description:
Library name: Sample5
P8KI-G2


title: BatchA_water extract of Zingiberis Rhizoma Recens (Medium dose)_rep2

description: sample 2-2-2


title: BatchA_water extract of Zingiberis Rhizoma Recens (High dose)_rep2

description: sample 2-2-1


title: KI_P8_gubernaculum_biol_rep1

description:
Library name: Sample4
P8KI-G1


title: Airway epithelium, sample21

description: Library name: sample21

value: Male


title: Airway epithelium, sample15

description: Library name: sample15


title: Airway epithelium, sample14

description: Library name: sample14


title: BatchA_water extract of Zingiberis Rhizoma (Medium dose)_rep1

description: sample 2-1-5


title: BatchA_water extract of Zingiberis Rhizoma (Low dose)_rep1

description: sample 2-1-6


title: BatchA_water extract of Zingiberis Rhizoma (High dose)_rep1

description: sample 2-1-4


title: WT_P8_gubernaculum_biol_rep3

description:
Library name: Sample3
P8WT-G3

value: WT


title: WT_P8_gubernaculum_biol_rep2

description:
Library name: Sample2
P8WT-G2


title: Airway epithelium, sample13

description: Library name: sample13

value: Airway epithelium


title: BatchA_water extract of Zingiberis Rhizoma Recens (Low dose)_rep1

description: sample 2-1-3


title: Airway epithelium, sample12

description: Library name: sample12

value: former

value: Yes


title: BatchA_water extract of Zingiberis Rhizoma Recens (Medium dose)_rep1

description: sample 2-1-2


title: BatchA Wortmannin rep2

description: sample 1-2-4

value: wortmannin 10 uM


title: WT_P8_gubernaculum_biol_rep1

description:
Library name: Sample1
P8WT-G1


title: BatchA_water extract of Zingiberis Rhizoma Recens (High dose)_rep1

description: sample 2-1-1


title: Airway epithelium, sample11

description: Library name: sample11

value: Female


title: BatchA Wortmannin rep3

description: sample 1-3-4


title: BatchA Vehicle(DMSO) rep3

description: sample A1-3-1

value: 0.1% DMSO


title: Airway epithelium, sample10

description: Library name: sample10


title: BatchA Vehicle(DMSO) rep2

description: sample A1-2-1


title: 36-DHA_Dex_8hr_S60

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

country: USA

institute: Michigan State University

description: Library name: Sample 36

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.
. Following quality control using FastQC, reads were aligned to the mouse reference genome GRCm39 (release 107) using STAR  (v2.3.7a).
Differential expression analysis was performed using DESeq2 in R (version 4.1.2).
Assembly: GRCm39 (release 107)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file of normalized counts using DESeq2

source_name: fetal liver-derived alveolar-like macrophages

extract_protocol:
Cells were then lysed using RLT lysis buffer (Qiagen) and RNA was isolated from cells using RNeasy Mini Kits (Qiagen). RNA was quantified with Qubit (Thermo Fisher Scientific) and integrity was verified with TapeStation (Agilent Technologies).
Ligation Kit with IDT for Illumina Unique Dual Index adapters following the manufacturer’s recommendations except that half volume reactions were used. Libraries were pooled in equimolar proportions and quantified using the Invitrogen Collibri Quantification qPCR kit

value: Dexamethasone; docosahexaenoic acid

tag: concentration

tag: concentration unit

value: nM; uM

tag: timepoint

tag: timepoint unit

value: hours


title: 35-DHA_Dex_8hr_S59

description: Library name: Sample 35

value: fetal liver-derived alveolar-like macrophages


title: BatchA Wortmannin rep1

description: sample 1-1-4

tag: cell line


title: Airway epithelium, sample16

description: Library name: sample16

value: Cannabis


title: Airway epithelium, sample9

description: Library name: sample9

value: never

value: No

value: Non-Cannabis


title: 34-DHA_Dex_8hr_S58

description: Library name: Sample 34

tag: treatment


title: sample 15-3-5 BatchE_ethanol extract of Sayeok-tang (Medium dose)_rep3

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.

value: Sayeok-tang ethanol extract 100 ug/mL

tag: time


title: Airway epithelium, sample8

description: Library name: sample8


title: sample 15-3-4 BatchE_ethanol extract of Sayeok-tang (High dose)_rep3

value: Sayeok-tang ethanol extract 500 ug/mL


title: sample 15-3-6 BatchE_ethanol extract of Sayeok-tang (Low dose)_rep3

value: Sayeok-tang ethanol extract 20 ug/mL


title: Airway epithelium, sample7

description: Library name: sample7

value: Airway epithelium


title: 33-DHA_Dex_8hr_S57

description: Library name: Sample 33


title: 32-DHA_8hr_S56

description: Library name: Sample 32

value: Docosahexaenoic acid

value: uM


title: sample 15-3-2 BatchE_ethanol extract of Bojungikgi-tang (Medium dose)_rep3

value: Bojungikgi-tang ethanol extract 100 ug/mL


title: Airway epithelium, sample6

description: Library name: sample6

value: Male

value: Yes


title: sample 15-3-1 BatchE_ethanol extract of Bojungikgi-tang (High dose)_rep3

value: Bojungikgi-tang ethanol extract 500 ug/mL


title: sample 15-2-6 BatchE_ethanol extract of Sayeok-tang (Low dose)_rep2


title: 31-DHA_8hr_S55

description: Library name: Sample 31


title: sample 15-2-5 BatchE_ethanol extract of Sayeok-tang (Medium dose)_rep2


title: Airway epithelium, sample5

description: Library name: sample5


title: 30-DHA_8hr_S54

description: Library name: Sample 30


title: sample 15-2-3 BatchE_ethanol extract of Bojungikgi-tang (Low dose)_rep2

value: Bojungikgi-tang ethanol extract 20 ug/mL


title: Airway epithelium, sample4

description: Library name: sample4

value: Female


title: 29-DHA_8hr_S53

description: Library name: Sample 29

value: fetal liver-derived alveolar-like macrophages

value: hours


title: Airway epithelium, sample3

description: Library name: sample3

value: never

value: Cannabis


title: Airway epithelium, sample2

description: Library name: sample2

value: No


title: 28-Dex_8hr_S52

description: Library name: Sample 28

value: Dexamethasone

value: nM


title: sample 15-2-1 BatchE_ethanol extract of Bojungikgi-tang (High dose)_rep2


title: sample 15-2-2 BatchE_ethanol extract of Bojungikgi-tang (Medium dose)_rep2


title: 27-Dex_8hr_S51

description: Library name: Sample 27


title: BatchA Vehicle(DMSO) rep1

description: sample A1-1-1

value: 0.1% DMSO


title: Airway epithelium, sample1

description: Library name: sample1

value: Airway epithelium


title: 26-Dex_8hr_S50

description: Library name: Sample 26


title: sample 15-3-3 BatchE_ethanol extract of Bojungikgi-tang (Low dose)_rep3


title: sample 15-1-5 BatchE_ethanol extract of Sayeok-tang (Medium dose)_rep1

value: Sayeok-tang ethanol extract 100 ug/mL


title: 4010/07

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

institute: University Children’s Hospital Münster

description:
Library name: KK23-H-680
10x Genomics

data_processing:
NovaSeq 6000 binary base call (bcl) files were demultiplexed into individual library fastq files using the mkfastq program from the Cellranger v7.2.0  Suite (10X Genomics). Feature-barcode matrices were obtained for each sample by aligning the raw fastq files to the GRCh38 reference genome using the cellranger count and cellranger multi pipeline (10X Genomics).
Assembly: Human GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: tumor

extract_protocol:
For scRNAseq of organoids: cell dissociation using papain/DNAse solution, with incubation for 60min for organoids. Fixed snRNAseq: Sample preparation for deparafinization and isolation of cells from FFPE tissue sections following 10x Genomics for Fixed RNA seq - protocol CGO000632_RevB, using gentleMACS Octo dissociator with heaters (Miltenyi, Cat n. 140-004-386.06).
For scRNAseq of organoids: Approximately 10,000 vital single-cells of each sample were processed for single-cell RNA sequencing using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, the Chromium Next GEM Chip G and the Single Index Kit T Set A (10X Genomics) according to the manufacturer's instructions. In brief, single-cell GEM (Gel Beads-in-Emulsion) were generated by the Chromium Controller, followed by GEM-RT (reverse transcription), Dynabeads cleanup, cDNA amplification, SPRIselect beads cleanup and Library construction. Quality, purity, size and concentrations of cDNA and libraries were assured by measurement on a Tapestation 2200 (Agilent Technologies). Indexed libraries were sequenced separately by either the Illumina NextSeq 500 platform or the NextSeq2000 sequencing platform (please refer to "instrument model" in the sample description section). Fixed snRNAseq: Protocol for probe hybridization, GEM generation and barcoding, amplification and library construction as per 10x Genomics Fixed RNA seq protocol CG000527_RevE, for multiplexed library (16 rxns x 16 BC): 1Mio cells per sample taken for probe hibridization; strategy washing -> pooling for pool preparation; targeted 80.000 cells per library.
For scRNAseq of organoids: scRNA-seq with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1. Fixed snRNAseq: Chromium Fixed RNA Profiling for Multiplexed Samples.

value: tumor


title: sample 15-1-6 BatchE_ethanol extract of Sayeok-tang (Low dose)_rep1

value: Sayeok-tang ethanol extract 20 ug/mL


title: TM3_2_20_2_Hermetia illucens larvae extract [0.5 %]

city: Dresden

first: Thorsten

last: Mascher

address: Zellescher Weg 20b

department: Institute of Microbiology

institute: Technische Universität Dresden

data_processing:
mapping was done with bowtie 2 (bowtie 2: 2.4.1)
unmapped reads were filtered with samtools (samtools: 1.10).
Mapped reads were sorted, and converted to bam with samtools (samtools: 1.10)
counting features with FeatureCounts on the opposite strand (subread: 2.0.1)
counts were normalized using DESeq2 and a differential gene expression was calculated (DESeq2: 1.28.0, r-base: 4.0.2)
The DESeq 2 comparisons were combined and enriched to an Excel sheet using in-house scripts(, which can be accessed on request). Condition TM3_2_05 was used as the reference point.
With bamCoverage from Deeptools, bam files were normalized and converted to BigWig files for forward and reverse strand (deeptools: 3.4.3)
Genome_build: Assembly ASM904v1 (RefSeq: GCF_000009045.1); Genome annotation (in GFF format) was gathered from BSGatlas (Version 1.0)
Supplementary_files_format_and_content: Counts and normalized counts in tab separated files. A differential gene expression xlsx sheet containing all genes with p-values, adjusted p-values, log2 fold-changes, and information extracted from the GFF file. BigWig files contain coverages for either forward or reverse strand

organism: Bacillus subtilis

source_name: whole cells

growth_protocol: Overnight culture of B. subtilis W168 was prepared in LB medium (Sigma L3522) at 37 °C, 220 rpm overnight. On the next day, 10 ml LB medium (Sigma L3522) was inoculated with overnight culture in a 100 ml flask 1:100 and grown at 37 °C, 220 rpm until OD600 = 0.4-0.5 as day culture 1. Subsequently, 200 ml LB (Sigma L3522) in a 2000 ml flask was inoculated with appropriate amount of day culture 1 to an OD600 of 0.01, and incubated at 37 °C, 220 rpm until OD600 reached to around 0.4 as day culture 2. Then, day culture 2 was split into 25 ml aliquots and either exposed to H. illucens larvae extract or remained untreated for 10 min under shaking. After that, cells were immediately transferred into pre-cooled 50 ml falcon tubes in ice/NaCl bath (ice:NaCl=3:1) to stop induction and then centrifuged at 4 °C, 8000 rcf for 3 min. The falcons containing the cell pellets were then frozen in liquid nitrogen and kept at -80 °C until further use.

extract_protocol:
B. subtilis cells were disrupted using a micro-dismembrator. Total RNA isolation was performed with a phenol-chloroform isoamyl-alcohol (25:24:1, pH 5.5) extraction method.
rRNA was subtracted from the samples with the Illumina Ribo-Zero rRNA removal Kit (Bacteria) according to manufacturer instructions. The cDNA library was prepared using the NEB Ultra directional RNA library prep kit for Illumina according to instructions and sequencing was performed on an Illumina HiSeq3000 system.

treatment_protocol: The B. subtilis W168 at exponential growth phase of OD600 = 0.4 were treated with H. illucens larvae extract (final concentration in culture, 0.5 % (V/V)) for 10 min at 37 °C, 220 rpm. Non-treated samples were used as control. Each of the treatment and control were prepared in triplicates.

value: Bacillus subtilis W168 (BaSysBio)

tag: genotype

value: trp+

tag: growth phase

value: logarithmic phase


title: TM3_2_20_1_Hermetia illucens larvae extract [0.5 %]

tag: strain


title: TM3_2_20_3_Hermetia illucens larvae extract [0.5 %]


title: TM3_2_05_3  non-treatment

value: non-treatment


title: N1676/21 Block A

description:
Library name: KK23-H-675
10x Genomics

tag: tissue


title: TM3_2_05_2  non-treatment


title: sample 15-2-4 BatchE_ethanol extract of Sayeok-tang (High dose)_rep2

value: Sayeok-tang ethanol extract 500 ug/mL


title: sample 15-1-4 BatchE_ethanol extract of Sayeok-tang (High dose)_rep1


title: 24-LPS_8hr_S48

description: Library name: Sample 24

tag: cell type

value: fetal liver-derived alveolar-like macrophages

value: Lipopolysaccharide

value: ng/ml


title: TM3_2_05_1  non-treatment


title: N3462/22 Block B

description:
Library name: KK23-H-671
10x Genomics


title: sample 15-1-3 BatchE_ethanol extract of Bojungikgi-tang (Low dose)_rep1

value: Bojungikgi-tang ethanol extract 20 ug/mL


title: 23-LPS_8hr_S47

description: Library name: Sample 23

value: hours


title: TM4_3_22_3_Tunicamycin (50 ng ml-1)

growth_protocol: Overnight culture of B. subtilis W168 was prepared in LB medium (Sigma L3522) at 37 °C, 220 rpm overnight. On the next day, 10 ml LB medium (Sigma L3522) was inoculated with overnight culture in a 100 ml flask 1:100 and grown at 37 °C, 220 rpm until OD600 = 0.4-0.5 as day culture 1. Subsequently, 200 ml LB (Sigma L3522) in a 2000 ml flask was inoculated with appropriate amount of day culture 1 to an OD600 of 0.01, and incubated at 37 °C, 220 rpm until OD600 reached to around 0.4 as day culture 2. Then, day culture 2 was split into 25 ml aliquots and either exposed to corresponding antibiotics or remained untreated for 10 min under shaking. After that, cells were immediately transferred into pre-cooled 50 ml falcon tubes in ice/NaCl bath (ice:NaCl=3:1) to stop induction and then centrifuged at 4 °C, 8000 rcf for 3 min. The falcons containing the cell pellets were then frozen in liquid nitrogen and kept at -80 °C until further use.

treatment_protocol: The B. subtilis 168 Δ7ECF mutant at exponential growth phase of OD600 = 0.4 were treated with vancomycin (250 ng ml-1) and tunicamycin (50 ng ml-1), respectively, or remained untreated, for 10 min at 37 °C, 220 rpm. Non-treated B. subtilis W168 wild type undergoing the same growth procedure were used as control. Each of the treatments and control were prepared in triplicates.

tag: strain/genotype

value: Bacillus subtilis 168 delta-ecf7 (Marburg)

value: trp-

value: Tunicamycin (50 ng ml-1)


title: N/2013/000032

description:
Library name: KK23-H-584
10x Genomics


title: sample 15-1-2 BatchE_ethanol extract of Bojungikgi-tang (Medium dose)_rep1

value: Bojungikgi-tang ethanol extract 100 ug/mL


title: 22-LPS_8hr_S46

description: Library name: Sample 22


title: TM4_3_22_2_Tunicamycin (50 ng ml-1)


title: 21-LPS_8hr_S45

description: Library name: Sample 21


title: sample 15-1-1 BatchE_ethanol extract of Bojungikgi-tang (High dose)_rep1

value: Bojungikgi-tang ethanol extract 500 ug/mL


title: N/2018/002132

description:
Library name: KK23-H-578
10x Genomics

value: tumor


title: sample 14-3-6 BatchE_ethanol extract of Banhasasim-tang (Low dose)_rep3

description: BatchD_ethanol extract of Banhasasim-tang (Low dose)_rep3

value: Banhasasim-tang ethanol extract 20 ug/mL


title: TM4_3_22_1_Tunicamycin (50 ng ml-1)


title: N/2020/000053

description:
Library name: KK23-H-577
10x Genomics


title: TM4_3_21_3_Vancomycin (250 ng ml-1)

value: Vancomycin (250 ng ml-1)


title: sample 14-3-5 BatchE_ethanol extract of Banhasasim-tang (Medium dose)_rep3

description: BatchD_ethanol extract of Banhasasim-tang (Medium dose)_rep3

value: Banhasasim-tang ethanol extract 100 ug/mL


title: N/2020/000259

description:
Library name: KK23-H-576
10x Genomics


title: 25-Dex_8hr_S49

description: Library name: Sample 25

value: Dexamethasone

value: nM


title: TM4_3_21_2_Vancomycin (250 ng ml-1)

value: logarithmic phase


title: 19-DHA_Dex_4hr_S43

description: Library name: Sample 19

value: fetal liver-derived alveolar-like macrophages

value: Dexamethasone; docosahexaenoic acid

value: nM; uM


title: 18-DHA_Dex_4hr_S42

description: Library name: Sample 18


title: 20-DHA_Dex_4hr_S44

description: Library name: Sample 20


title: TM4_3_21_1_Vancomycin (250 ng ml-1)


title: sample 14-3-3 BatchE_ethanol extract of Yijung-tang (Low dose)_rep3

description: BatchD_ethanol extract of Yijung-tang (Low dose)_rep3

value: Yijung-tang ethanol extract 20 ug/mL


title: N/1361/2022

description:
Library name: KK23-H-528
10x Genomics


title: 17-DHA_Dex_4hr_S41

description: Library name: Sample 17

value: hours


title: sample 14-3-2 BatchE_ethanol extract of Yijung-tang (Medium dose)_rep3

description: BatchD_ethanol extract of Yijung-tang (Medium dose)_rep3

value: Yijung-tang ethanol extract 100 ug/mL


title: TM4_3_05_3_non-treatment

value: Bacillus subtilis 168 delta-ecf7 (Marburg)

value: trp-

value: non-treatment


title: N232/18 (Prag 18311/15)

description:
Library name: KK23-H-520
10x Genomics


title: 16-DHA_4hr_S40

description: Library name: Sample 16

value: Docosahexaenoic acid

value: uM


title: N/2023/000797

description:
Library name: KK23-H-573
10x Genomics

value: tumor


title: sample 14-3-1 BatchE_ethanol extract of Yijung-tang (High dose)_rep3

description: BatchD_ethanol extract of Yijung-tang (High dose)_rep3

value: Yijung-tang ethanol extract 500 ug/mL


title: N229/18 (Prag 20137/15)

description:
Library name: KK23-H-518
10x Genomics


title: TM4_3_05_2_non-treatment


title: 15-DHA_4hr_S39

description: Library name: Sample 15


title: 14-DHA_4hr_S38

description: Library name: Sample 14


title: sample 14-2-6 BatchE_ethanol extract of Banhasasim-tang (Low dose)_rep2

value: Banhasasim-tang ethanol extract 20 ug/mL


title: NP 1296/10

description:
Library name: KK23-H-504
10x Genomics


title: TM3_2_05_3 non-treatment

value: Bacillus subtilis W168 (BaSysBio)

value: trp+


title: TM4_3_05_1_non-treatment

value: logarithmic phase


title: sample 14-2-5 BatchE_ethanol extract of Banhasasim-tang (Medium dose)_rep2

value: Banhasasim-tang ethanol extract 100 ug/mL


title: N 1126/09

description:
Library name: KK23-H-503
10x Genomics


title: 13-DHA_4hr_S37

description: Library name: Sample 13

value: fetal liver-derived alveolar-like macrophages


title: TM3_2_05_2 non-treatment


title: H25919-08

description:
Library name: KK23-H-502
10x Genomics


title: sample 14-2-4 BatchE_ethanol extract of Banhasasim-tang (High dose)_rep2

value: Banhasasim-tang ethanol extract 500 ug/mL


title: sample E1-3-1 BatchE_Vehicle(DMSO)_rep3

value: 0.1% DMSO


title: sample 14-3-4 BatchE_ethanol extract of Banhasasim-tang (High dose)_rep3

description: BatchD_ethanol extract of Banhasasim-tang (High dose)_rep3


title: TM3_2_05_1 non-treatment


title: N 2011/1696

description:
Library name: KK23-H-499
10x Genomics


title: sample E1-2-1 BatchE_Vehicle(DMSO)_rep2


title: N4413/14

description:
Library name: KK22-H-335
10x Genomics


title: 12-Dex_4hr_S36

description: Library name: Sample 12

value: Dexamethasone

value: nM

value: hours


title: 11-Dex_hr_S35

description: Library name: Sample 11


title: 10-Dex_hr_S34

description: Library name: Sample 10


title: sample E1-1-1 BatchE_Vehicle(DMSO)_rep1