title: TM3_2_18_3_Valinomycin [0.3 µg 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. As the function of valinomycin requires the presence of K+, therefore the treatment with valinomycin was performed in LB medium (Sigma L3522) supplemented with KCl (final concentration 300 mM) and HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) buffer (final concentration 50 mM), following the general growth procedure.

treatment_protocol: The B. subtilis W168 in LB medium at exponential growth phase of OD600 = 0.4 were treated with CCCP (3 µg ml-1) for 10 min at 37°C, 220 rpm. Non-treatment in LB medium were used as control. The B. subtilis W168 in LB medium supplemented with KCl and HEPES buffer at exponential growth phase of OD600 = 0.4 were treated with valinomycin (0.3 µg ml-1), the same amount (volume) of DMSO (Dimethyl sulfoxide) and remained untreated, respectively, for 10 min at 37 °C, 220 rpm, considered as three treatments (corresponding to the sample names 3549_AZ/BA/BB, 3549_BC/BD/BE and 3549_AW/AX/AY, respectively). The treatment with DMSO was to check out the influence of DMSO on the cell stress response as valinomycin was dissolved in DMSO. The untreated cells in LB medium with KCl and HEPES buffer was to rule out any influence of KCl and HEPES buffer on the cell stress response. Each of the treatments and control were prepared in triplicates.

value: Valinomycin [0.3 µg ml-1]


title: 9-Dex_4hr_S33

status: Public on Oct 28 2025

type: SRA

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 9

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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

tag: cell type

tag: treatment

value: Dexamethasone

tag: concentration

tag: concentration unit

value: nM

tag: timepoint

tag: timepoint unit

value: hours


title: N170/92

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children’s Hospital Münster

description:
Library name: KK22-H-258
10x Genomics

library_source: transcriptomic single cell

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

organism: Homo sapiens

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.

tag: tissue

value: tumor


title: Chla02_5

description:
Library name: KK24-H-1446
10x Genomics

tag: cell line


title: sample 14-2-3 BatchD_ethanol extract of Yijung-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

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

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

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

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

value: Yijung-tang ethanol extract 20 ug/mL

tag: time


title: 8-LPS_4hr_S32

description: Library name: Sample 8

value: fetal liver-derived alveolar-like macrophages

value: Lipopolysaccharide

value: ng/ml


title: TM3_2_18_2_Valinomycin [0.3 µg ml-1]

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

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.

tag: strain

value: Bacillus subtilis W168 (BaSysBio)

tag: genotype

value: trp+

tag: growth phase

value: logarithmic phase


title: TM3_2_16_3_Valinomycin [0.3 µg ml-1]


title: Chla02_4

description:
Library name: KK24-H-1445
10x Genomics


title: 7-LPS_4hr_S31

description: Library name: Sample 7


title: sample 14-2-2 BatchD_ethanol extract of Yijung-tang (Medium dose)_rep2

value: Yijung-tang ethanol extract 100 ug/mL


title: TM3_2_17_2_Valinomycin [0.3 µg ml-1]


title: sample 14-2-1 BatchD_ethanol extract of Yijung-tang (High dose)_rep2

value: Yijung-tang ethanol extract 500 ug/mL


title: Chla02_3

description:
Library name: KK24-H-1444
10x Genomics


title: 6-LPS_4hr_S30

description: Library name: Sample 6


title: TM3_2_16_2_Valinomycin [0.3 µg ml-1]


title: Chla02_2

description:
Library name: KK24-H-1443
10x Genomics


title: 5-LPS_4hr_S29

description: Library name: Sample 5


title: Chla02_1

description:
Library name: KK24-H-1442
10x Genomics


title: 4-VEH_S28

description: Library name: Sample 4

value: Vehicle


title: TM3_2_18_1_Valinomycin [0.3 µg ml-1]


title: TM3_2_17_3_Valinomycin [0.3 µg ml-1]


title: TM3_2_17_1_Valinomycin [0.3 µg ml-1]


title: sample 14-1-4 BatchD_ethanol extract of Banhasasim-tang (High dose)_rep1

value: Banhasasim-tang ethanol extract 500 ug/mL


title: SHH310_5

description:
Library name: KK24-H-1441
10x Genomics


title: 3-VEH_S27

description: Library name: Sample 3


title: TM3_2_16_1_Valinomycin [0.3 µg ml-1]


title: sample 14-1-3 BatchD_ethanol extract of Yijung-tang (Low dose)_rep1


title: TM3_2_15_3_CCCP [3 µg ml-1]

value: CCCP [3 µg ml-1]


title: SHH310_3

description:
Library name: KK24-H-1439
10x Genomics


title: SHH310_2

description:
Library name: KK24-H-1438
10x Genomics


title: TM3_2_15_2_CCCP [3 µg ml-1]


title: sample 14-1-2 BatchD_ethanol extract of Yijung-tang (Medium dose)_rep1


title: sample 14-1-1 BatchD_ethanol extract of Yijung-tang (High dose)_rep1


title: DKOE1257

city: Buffalo

first: David

last: Goodrich

state: NY

address: Elm and Carlton Streets

department: Department of Pharmacology & Therapeutics

institute: Roswell Park Comprehensive Cancer Center

description: Library name: DKOE1257

data_processing:
Bulk RNA-seq reads were first assessed for quality using fastqc and then mapped to the mouse GRCm38-mm10 genome using STAR and quantified with RSEM. Batch effect removal was performed using limma. Features not expressed in at least three samples were filtered out. Normalized counts were calculated within DESeq2 with variance stabilization.
Assembly: mm10
Supplementary files format and content: CSV of log2 normalized counts matrix for all samples

source_name: Prostate tumor tissue

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen). RNA yield and purity were assessed using a Qubit Broad Range RNA Kit (Thermo Fisher), and integrity was evaluated via the TapeStation 4200 (Agilent Technologies).
Total RNA (500 ng) was used to prepare sequencing libraries with the RNA HyperPrep Kit with RiboErase.

value: Prostate tumor tissue

tag: age

value: 39 wk

value: Cx


title: sample 14-1-6 BatchD_ethanol extract of Banhasasim-tang (Low dose)_rep1

value: Banhasasim-tang ethanol extract 20 ug/mL


title: TM3_2_05_3_none_treatment

value: non-treatment


title: sample 13-3-5 BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep3

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


title: DKOE858

description: Library name: DKOE858

value: 59 wk


title: DKOE976

description: Library name: DKOE976

value: 46 wk


title: sample 14-1-5 BatchD_ethanol extract of Banhasasim-tang (Medium dose)_rep1

value: Banhasasim-tang ethanol extract 100 ug/mL


title: TM3_2_05_2_none_treatment

value: Bacillus subtilis W168 (BaSysBio)


title: KHSRPi#2-Rep3

city: Boston

first: Qingyu

last: Luo

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description:
Library name: Sample 9
K5.3

data_processing:
The raw FASTQ data were analyzed by the VIPER pipeline to generate gene expression data
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Plus XS (740990.250; Takara Bio) according to the manufacturer’s protocol.
Roche Kapa

value: BPDCN

value: KHSRP knockdown

tag: batch


title: sample 13-3-4 BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (High dose)_rep3

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


title: KHSRPi#2-Rep2

description:
Library name: Sample 8
K5.2


title: DKOE906

description: Library name: DKOE906

value: 40 wk


title: SHH310_4

description:
Library name: KK24-H-1440
10x Genomics


title: sample 13-3-3 BatchD_ethanol extract of Bupleuri Radix (Low dose)_rep3

value: Bupleuri Radix ethanol extract 11.2 ug/mL


title: KHSRPi#2-Rep1

description:
Library name: Sample 7
K5.1


title: TM3_2_05_1_none_treatment

value: trp+

value: logarithmic phase


title: 2-VEH_S26

description: Library name: Sample 2

value: fetal liver-derived alveolar-like macrophages

value: Vehicle

value: nM

value: hours


title: sample 13-3-2 BatchD_ethanol extract of Bupleuri Radix (Medium dose)_rep3

value: Bupleuri Radix ethanol extract 56 ug/mL


title: DKOE878

description: Library name: DKOE878

value: Prostate tumor tissue

value: 35 wk

value: Cx


title: 1-VEH_S25

description: Library name: Sample 1


title: KHSRPi#1-Rep3

description:
Library name: Sample 6
K4.3


title: DKOE1108

description: Library name: DKOE1108

value: 37 wk


title: NOMO-1-Luc-3

first: Sandra

last: Küchler

address: Fetscherstraße 74/PF 64

institute: National Center for Tumor Diseases (NCT) Dresden

description: Library name: Sample 12

data_processing:
Quality control assessment of raw reads was performed using FastQC, followed by Trimmomatic trimming to remove low-quality sequences. The trimmed reads were then aligned to the reference genome using STAR version 2.7.9a. To facilitate the mapping process, a genome reference index was constructed using GRCh38.108.gtf (hg38) as the reference.
Assembly: GRCh38.108.gtf (hg38)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: hematological cells

extract_protocol:
Total RNA from cell lines was isolated using RNAeasy mini kit (Qiagen)
RNA sequencing libraries were prepared using the Stranded mRNA Prep, Ligation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Briefly, mRNA was purified from 1 µg total RNA using oligo(dT) beads, poly(A)+ RNA was fragmented to 150 bp and converted into cDNA, and cDNA fragments were end-repaired, adenylated on the 3’ end, adapter-ligated, and amplified with 12 cycles of PCR. The final libraries were validated using a Qubit 2.0 Fluorometer (Life Technologies) and a Bioanalyzer 2100 system. All barcoded libraries were pooled and sequenced 2x75bp paired-end on an Illumina NextSeq550 platform to obtain a minimum of 10 Mio reads per sample.

value: hematological cells

value: acute myeloid leukemia

value: control


title: sample 13-3-6 BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Low dose)_rep3

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


title: DKOE1110

description: Library name: DKOE1110

value: 36 wk


title: sample 13-3-1 BatchD_ethanol extract of Bupleuri Radix (High dose)_rep3

value: Bupleuri Radix ethanol extract 280 ug/mL


title: KHSRPi#1-Rep2

description:
Library name: Sample 5
K4.2

value: BPDCN

value: KHSRP knockdown


title: TM3_2_15_1_CCCP [3 µg ml-1]

value: Bacillus subtilis W168 (BaSysBio)

value: trp+

value: logarithmic phase

value: CCCP [3 µg ml-1]


title: SHH310_1

description:
Library name: KK24-H-1437
10x Genomics


title: NOMO-1-Luc-1

description: Library name: Sample 10


title: NOMO-1-Luc-2

description: Library name: Sample 11


title: DKOE1082

description: Library name: DKOE1082


title: KHSRPi#1-Rep1

description:
Library name: Sample 4
K4.1


title: sample 13-2-6 BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Low dose)_rep2


title: NOMO-1-MYBL2-3

description: Library name: Sample 9


title: NTC-Rep3

description:
Library name: Sample 3
NTC.3

value: WT


title: sample 13-2-5 BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep2

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


title: NOMO-1-MYBL2-2

description: Library name: Sample 8


title: sample 13-2-4 BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (High dose)_rep2

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


title: DKOE1026

description: Library name: DKOE1026

value: Prostate tumor tissue

value: 35 wk

value: Cx


title: DKOE1081

description: Library name: DKOE1081

value: 34 wk


title: NOMO-1-MYBL2-1

description: Library name: Sample 7

value: hematological cells

value: acute myeloid leukemia


title: sample 13-2-3 BatchD_ethanol extract of Bupleuri Radix (Low dose)_rep2

value: Bupleuri Radix ethanol extract 11.2 ug/mL


title: NTC-Rep1

description:
Library name: Sample 1
NTC.1


title: THP-1-Luc-3

description: Library name: Sample 6

value: control


title: DKO82

description: Library name: DKO82

value: 84 wk

value: DKO


title: THP-1-Luc-2

description: Library name: Sample 5


title: sample 13-2-1 BatchD_ethanol extract of Bupleuri Radix (High dose)_rep2

value: Bupleuri Radix ethanol extract 280 ug/mL


title: N1

city: Madrid

first: Silvia

last: Gonzalez-Martinez

address: M-607, Km. 9, 100, Fuencarral-El Pardo

department: Pathological Anatomy

country: Spain

institute: Ramon y Cajal University Hospital

description:
Library name: E10
10x Genomics

data_processing:
Barcoded processing, gene counting and aggregation were made using Cell Ranger software v7.1.0 (10x Genomics)
Assembly: Hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Proliferative endometrium

extract_protocol:
CG000632 from 10X Genomics
CG000477 from 10X Genomics

value: Normal tissue

value: Proliferative endometrium


title: N2

description:
Library name: E11
10x Genomics


title: DKO43

description: Library name: DKO43

value: 99 wk


title: THP-1-Luc-1

description: Library name: Sample 4


title: CS3

description:
Library name: E15
10x Genomics

source_name: Carcinosarcoma

value: Endometrial cancer

value: Carcinosarcoma


title: THP-1-MYBL2-3

description: Library name: Sample 3


title: DKO41

description: Library name: DKO41

value: 39 wk


title: CS4

description:
Library name: E5
10x Genomics


title: T2723

description: Library name: T2723

value: Prostate tumor tissue

value: 18 wk

value: TKO


title: sample 13-1-4 BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (High dose)_rep1

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


title: T2671

description: Library name: T2671

value: 19 wk


title: THP-1-MYBL2-2

description: Library name: Sample 2

value: hematological cells

value: acute myeloid leukemia


title: THP-1-MYBL2-1

description: Library name: Sample 1


title: NTC-Rep2

description:
Library name: Sample 2
NTC.2

value: BPDCN

value: WT


title: DKO124

description: Library name: DKO124

value: 50 wk

value: DKO

value: Cx


title: CS1

description:
Library name: E3
10x Genomics


title: sample 13-2-2 BatchD_ethanol extract of Bupleuri Radix (Medium dose)_rep2

value: Bupleuri Radix ethanol extract 56 ug/mL


title: T2562

description: Library name: T2562


title: sample 13-1-2 BatchD_ethanol extract of Bupleuri Radix (Medium dose)_rep1


title: CS5

description:
Library name: E2
10x Genomics


title: ATRT-Forebrain-Organoid D40 s2

description:
Library name: KK24-H-1321
10x Genomics

molecule: polyA RNA

source_name: organoid

value: organoid

value: hiPSCs + SHH310


title: ATRT-Forebrain-Organoid D40 s1

description:
Library name: KK24-H-1320
10x Genomics

value: hiPSCs + Chla02


title: T2471

description: Library name: T2471


title: sample 13-1-1 BatchD_ethanol extract of Bupleuri Radix (High dose)_rep1

value: Bupleuri Radix ethanol extract 280 ug/mL


title: CS6

description:
Library name: E1
10x Genomics

value: Ovarian cancer

value: Carcinosarcoma


title: FB-Organoid D40 Chla02

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

description: 10x Genomics

data_processing:
Demultiplexing and preprocessing of the scRNA data was conducted with CellRanger v6.0.2.
After converting the raw 10X data to fastq format with CellRanger's mkfastq, the data was aligned against the human reference transcriptome GRCh38 with the CellRanger count function using default values.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cell dissociation using papain/DNAse solution, with incubation for 60min for organoids. Cell dissociation of 2D culture using Accutase.
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 (for sample with a KK21 at the beginning we used single-indexed for all other samples, KK22-KK24 at the beginning, double-indexed libraries). 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).
scRNA-seq with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

tag: treatment time


title: TT-seq_S7A_dTAG_4h_rep2

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: sample58
S7A_dTAG_4h_merged_forward.bw
S7A_dTAG_4h_merged_reverse.bw

data_processing:
TT-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).
Trimmed reads were aligned to concatenated index of  human genome (hg38) and Drosophila melanogaster genome (dm6) with STAR (v.2.7.3a).
Plus- and minus-strand were assigned to uniquely mapped reads using SAMtools, and the final BAM files were converted to bigwig. Dm6 reads and the expression of POLR2A gene were used to calculate spike-in factors.
Assembly: Concatenated index of hg38 and dm6
Supplementary files format and content: bigwig

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:
Nascent RNA samples were prepared as described previously with some modifications (Schwalb et al., 2016). Total RNA was extracted using TRIzol reagent according to the manufactor’s instruction. The RNA was fragmentated with sonication, and the nascent fragmented RNA was biotinylated with MTS-Biotin. Biotinylated RNA was enriched with M280 streptavidin beads following the manufactor's instruction and the enriched RNA was extracted with TRIzol reagent.
The purified nascent RNA was subjected to libray construction following manufactor's instruction (Vazyme, #NR605). Stranded library construction strategy was used.

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% S2 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


title: sample 13-1-5 BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep1

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


title: sample 12-3-6 BatchD_ethanol extract of Cimicifugae Rhizoma (Low dose)_rep3

value: Cimicifugae Rhizoma ethanol extract 20 ug/mL


title: sample 13-1-6 BatchD_ethanol extract of Aconiti Lateralis Radix Preparata (Low dose)_rep1

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


title: TT-seq_S7A_dTAG_4h_rep1

description:
Library name: sample57
S7A_dTAG_4h_merged_forward.bw
S7A_dTAG_4h_merged_reverse.bw


title: sample 12-3-5 BatchD_ethanol extract of Cimicifugae Rhizoma (Medium dose)_rep3

value: Cimicifugae Rhizoma ethanol extract 100 ug/mL


title: T2800

description: Library name: T2800

value: Prostate tumor tissue

value: 17 wk

value: TKO

value: Cx-Veh


title: Chla02

description: 10x Genomics

source_name: cell line

value: cell line

value: Chla02 (ATRT-SHH)


title: T2742

description: Library name: T2742

value: 19 wk


title: CS2

description:
Library name: E4
10x Genomics

value: Endometrial cancer


title: sample 13-1-3 BatchD_ethanol extract of Bupleuri Radix (Low dose)_rep1

value: Bupleuri Radix ethanol extract 11.2 ug/mL


title: TT-seq_S7A_dTAG_0h_rep1

description:
Library name: sample55
S7A_dTAG_0h_merged_forward.bw
S7A_dTAG_0h_merged_reverse.bw

value: Untreated


title: TT-seq_S7A_dTAG_0h_rep2

description:
Library name: sample56
S7A_dTAG_0h_merged_forward.bw
S7A_dTAG_0h_merged_reverse.bw


title: SHH310

description: 10x Genomics

value: SHH310 (ATRT-SHH)


title: sample 12-3-3 BatchD_ethanol extract of Citri Unshius Pericarpium (Low dose)_rep3

value: Citri Unshius Pericarpium ethanol extract 20 ug/mL


title: DKOE719

description: Library name: DKOE719

value: 12 wk

value: Intact


title: TT-seq_S5A_dTAG_4h_rep2

description:
Library name: sample54
S5A_dTAG_4h_merged_forward.bw
S5A_dTAG_4h_merged_reverse.bw

value: RPB1 degron, S5A RPB1 complement

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


title: FB-Organoid D30 BT-183_6

description: 10x Genomics

value: organoid

value: hiPSCs + BT-183


title: DKOE718

description: Library name: DKOE718

value: Prostate tumor tissue


title: sample 12-3-2 BatchD_ethanol extract of Citri Unshius Pericarpium (Medium dose)_rep3

value: Citri Unshius Pericarpium ethanol extract 100 ug/mL


title: sample 12-3-1 BatchD_ethanol extract of Citri Unshius Pericarpium (High dose)_rep3

value: Citri Unshius Pericarpium ethanol extract 500 ug/mL


title: T2813

description: Library name: T2813

value: 17 wk

value: TKO

value: Cx-Veh


title: FB-Organoid D30 BT-183_5

description: 10x Genomics


title: FB-Organoid D30 BT-183_4

description: 10x Genomics


title: FB-Organoid D40 SHH310

description: 10x Genomics

value: hiPSCs + SHH310


title: TT-seq_S5A_dTAG_0h_rep1

description:
Library name: sample51
S5A_dTAG_0h_merged_forward.bw
S5A_dTAG_0h_merged_reverse.bw


title: BT-183_2

description: 10x Genomics

value: cell line

value: BT-183 (human ETMR)


title: DKOE686

description: Library name: DKOE686


title: T2799

description: Library name: T2799

value: 15 wk


title: TT-seq_S5A_dTAG_4h_rep1

description:
Library name: sample53
S5A_dTAG_4h_merged_forward.bw
S5A_dTAG_4h_merged_reverse.bw


title: DKOE674

description: Library name: DKOE674


title: sample 12-3-4 BatchD_ethanol extract of Cimicifugae Rhizoma (High dose)_rep3

value: Cimicifugae Rhizoma ethanol extract 500 ug/mL


title: BT-183_1

description: 10x Genomics


title: sample 12-2-4 BatchD_ethanol extract of Cimicifugae Rhizoma (High dose)_rep2


title: TT-seq_T4V_dTAG_4h_rep2

description:
Library name: sample50
T4V_dTAG_4h_merged_forward.bw
T4V_dTAG_4h_merged_reverse.bw

value: RPB1 degron, T4V RPB1 complement


title: DKOE669

description: Library name: DKOE669

value: 12 wk

value: Intact


title: sample 12-2-5 BatchD_ethanol extract of Cimicifugae Rhizoma (Medium dose)_rep2

value: Cimicifugae Rhizoma ethanol extract 100 ug/mL


title: sample 12-2-3 BatchD_ethanol extract of Citri Unshius Pericarpium (Low dose)_rep2

value: Citri Unshius Pericarpium ethanol extract 20 ug/mL


title: DKOE668

description: Library name: DKOE668


title: Forebrain-Organoid D100_3

description: 10x Genomics

value: organoid

value: hiPSCs


title: TT-seq_T4V_dTAG_4h_rep1

description:
Library name: sample49
T4V_dTAG_4h_merged_forward.bw
T4V_dTAG_4h_merged_reverse.bw

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


title: Forebrain-Organoid D100_2

description: 10x Genomics


title: TT-seq_T4V_dTAG_0h_rep2

description:
Library name: sample48
T4V_dTAG_0h_merged_forward.bw
T4V_dTAG_0h_merged_reverse.bw

value: Untreated


title: Forebrain-Organoid D100_1

description: 10x Genomics


title: TT-seq_T4V_dTAG_0h_rep1

description:
Library name: sample47
T4V_dTAG_0h_merged_forward.bw
T4V_dTAG_0h_merged_reverse.bw


title: DKOE696

description: Library name: DKOE696

value: Prostate tumor tissue


title: sample 12-2-2 BatchD_ethanol extract of Citri Unshius Pericarpium (Medium dose)_rep2

value: Citri Unshius Pericarpium ethanol extract 100 ug/mL


title: sample 12-2-1 BatchD_ethanol extract of Citri Unshius Pericarpium (High dose)_rep2

value: Citri Unshius Pericarpium ethanol extract 500 ug/mL


title: TT-seq_S5A_dTAG_0h_rep2

description:
Library name: sample52
S5A_dTAG_0h_merged_forward.bw
S5A_dTAG_0h_merged_reverse.bw

value: RPB1 degron, S5A RPB1 complement


title: DKOE666

description: Library name: DKOE666

value: DKO


title: DKOE664

description: Library name: DKOE664


title: TT-seq_S2A_dTAG_4h_rep2

description:
Library name: sample46
S2A_dTAG_4h_merged_forward.bw
S2A_dTAG_4h_merged_reverse.bw

value: RPB1 degron, S2A RPB1 complement


title: sample 12-2-6 BatchD_ethanol extract of Cimicifugae Rhizoma (Low dose)_rep2

value: Cimicifugae Rhizoma ethanol extract 20 ug/mL


title: Forebrain-Organoid D60_2

description: 10x Genomics


title: sample 12-1-6 BatchD_ethanol extract of Cimicifugae Rhizoma (Low dose)_rep1


title: T1766

description: Library name: T1766


title: Forebrain-Organoid D60_1

description: 10x Genomics


title: sample 12-1-5 BatchD_ethanol extract of Cimicifugae Rhizoma (Medium dose)_rep1


title: TT-seq_S2A_dTAG_4h_rep1

description:
Library name: sample45
S2A_dTAG_4h_merged_forward.bw
S2A_dTAG_4h_merged_reverse.bw


title: T1765

description: Library name: T1765


title: Forebrain-Organoid D48

description: 10x Genomics


title: TT-seq_S2A_dTAG_0h_rep2

description:
Library name: sample44
S2A_dTAG_0h_merged_forward.bw
S2A_dTAG_0h_merged_reverse.bw


title: sample 12-1-4 BatchD_ethanol extract of Cimicifugae Rhizoma (High dose)_rep1

value: Cimicifugae Rhizoma ethanol extract 500 ug/mL


title: T1762

description: Library name: T1762


title: Forebrain-Organoid D64

description: 10x Genomics


title: TT-seq_S2A_dTAG_0h_rep1

description:
Library name: sample43
S2A_dTAG_0h_merged_forward.bw
S2A_dTAG_0h_merged_reverse.bw


title: sample 12-1-3 BatchD_ethanol extract of Citri Unshius Pericarpium (Low dose)_rep1


title: sample 12-1-2 BatchD_ethanol extract of Citri Unshius Pericarpium (Medium dose)_rep1


title: Forebrain-Organoid D40

description: 10x Genomics


title: TT-seq_Y1F_dTAG_4h_rep2

description:
Library name: sample42
Y1F_dTAG_4h_merged_forward.bw
Y1F_dTAG_4h_merged_reverse.bw

value: RPB1 degron, Y1F RPB1 complement


title: DKOE304-AP

description: Library name: DKOE304.AP

value: 39 wk


title: AsCas12a Plasmid Library, Rep 3

city: Durham

first: Schuyler

last: Melore

state: North Carolina

address: 101 Science Dr

institute: Duke University

description:
Library name: sample54
plasmid library
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta

library_source: other

data_processing:
FastQs were generated using BCLConvert in BaseSpace
Adapter sequences were trimmed using Cutapadapt version 4.4
Reads were aligned to a custom reference using Bowtie2 version 2.5.1.
Read counts were generated using Samtools version 1.17 (idxstats).
Assembly: custom crRNA library reference (see supplementary files)
Supplementary files format and content: tab-delimited text file including raw counts of crRNA sequences for each sample

molecule: other

organism: synthetic construct

source_name: Plasmid

growth_protocol: A549 cells were cultured in F12K media supplemented with 10%FBS (Gibco) and 1%PenStrep. Cells were grown in a humidified incubator at 37C and 5% CO2

extract_protocol:
Plasmid libraries were purified using the Qiagen midi plus kit. Genomic DNA was extracted from cell pellets using a Puregene kit (Qiagen)
crRNA arrays were amplified from genomic or plasmid DNA using KAPA HiFi 2x master mix (Roche). Primers contained Illumina adapter sequences and indexes. Standard Illumina primers were used for sequencing

treatment_protocol: Cells were cultured normally and harvested at 5, 7, 14, and 21 days post-transduction

value: Plasmid


title: DKOE304-DP

description: Library name: DKOE304.DP

value: Intact


title: AsCas12a Plasmid Library, Rep 2

description:
Library name: sample53
plasmid library
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: TT-seq_Y1F_dTAG_0h_rep2

description:
Library name: sample40
Y1F_dTAG_0h_merged_forward.bw
Y1F_dTAG_0h_merged_reverse.bw


title: sample 11-3-6 BatchD_ethanol extract of Zizyphi Fructus (Low dose)_rep3

description: BatchC_ethanol extract of Zizyphi Fructus (Low dose)_rep3

value: Zizyphi Fructus ethanol extract 20 ug/mL


title: TT-seq_Y1F_dTAG_4h_rep1

description:
Library name: sample41
Y1F_dTAG_4h_merged_forward.bw
Y1F_dTAG_4h_merged_reverse.bw


title: sample 12-1-1 BatchD_ethanol extract of Citri Unshius Pericarpium (High dose)_rep1


title: AsCas12a Plasmid Library, Rep 1

description:
Library name: sample52
plasmid library
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: ET183-LP-DP

description: Library name: ET183.LP.DP

value: 42 wk


title: ET183-AP

description: Library name: ET183.AP


title: LbCas12a Plasmid Library, Rep 3

description:
Library name: sample51
plasmid library
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 11-3-5 BatchD_ethanol extract of Zizyphi Fructus (Medium dose)_rep3

description: BatchC_ethanol extract of Zizyphi Fructus (Medium dose)_rep3

value: Zizyphi Fructus ethanol extract 100 ug/mL


title: TT-seq_Y1F_dTAG_0h_rep1

description:
Library name: sample39
Y1F_dTAG_0h_merged_forward.bw
Y1F_dTAG_0h_merged_reverse.bw


title: TT-seq_WT_dTAG_4h_rep2

description:
Library name: sample38
WT_dTAG_4h_merged_forward.bw
WT_dTAG_4h_merged_reverse.bw

value: RPB1 degron, WT RPB1 complement

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


title: sample 11-3-4 BatchD_ethanol extract of Zizyphi Fructus (High dose)_rep3

description: BatchC_ethanol extract of Zizyphi Fructus (High dose)_rep3

value: Zizyphi Fructus ethanol extract 500 ug/mL


title: DKOE366-AP

description: Library name: DKOE366.AP

value: Prostate tumor tissue

value: 31 wk


title: DKOE366-DP-LP

description: Library name: DKOE366.DP.LP


title: sample 11-3-3 BatchD_ethanol extract of Coptidis Rhizoma (Low dose)_rep3

description: BatchC_ethanol extract of Coptidis Rhizoma (Low dose)_rep3

value: Coptidis Rhizoma ethanol extract 11.2 ug/mL


title: LbCas12a Plasmid Library, Rep 2

description:
Library name: sample50
plasmid library
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: TT-seq_WT_dTAG_4h_rep1

description:
Library name: sample37
WT_dTAG_4h_merged_forward.bw
WT_dTAG_4h_merged_reverse.bw


title: ET280-DP

description: Library name: ET280.DP

value: 52 wk


title: TT-seq_WT_dTAG_0h_rep2

description:
Library name: sample36
WT_dTAG_0h_merged_forward.bw
WT_dTAG_0h_merged_reverse.bw

value: Untreated


title: sample 11-3-2 BatchD_ethanol extract of Coptidis Rhizoma (Medium dose)_rep3

description: BatchC_ethanol extract of Coptidis Rhizoma (Medium dose)_rep3

value: Coptidis Rhizoma ethanol extract 56 ug/mL


title: dEnAsCas12a-4xSID, Day 21, Rep 3

description:
Library name: sample48
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta

library_source: genomic

molecule: genomic DNA

value: lung cancer epithelial


title: TT-seq_WT_dTAG_0h_rep1

description:
Library name: sample35
WT_dTAG_0h_merged_forward.bw
WT_dTAG_0h_merged_reverse.bw


title: DKOE305-DP

description: Library name: DKOE305.DP

value: 35 wk


title: sample 11-3-1 BatchD_ethanol extract of Coptidis Rhizoma (High dose)_rep3

description: BatchC_ethanol extract of Coptidis Rhizoma (High dose)_rep3

value: Coptidis Rhizoma ethanol extract 280 ug/mL


title: DKOE305-LP

description: Library name: DKOE305.LP


title: dEnAsCas12a-4xSID, Day 21, Rep 2

description:
Library name: sample47
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: TT-seq_Degron_RPB1_dTAG_4h_rep2

description:
Library name: sample34
Degron_RPB1_dTAG_4h_merged_forward.bw
Degron_RPB1_dTAG_4h_merged_reverse.bw

value: RPB1 degron

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


title: ET271-AP

description: Library name: ET271.AP

value: Intact


title: sample 11-2-6 BatchD_ethanol extract of Zizyphi Fructus (Low dose)_rep2

description: BatchC_ethanol extract of Zizyphi Fructus (Low dose)_rep2

value: Zizyphi Fructus ethanol extract 20 ug/mL


title: dEnAsCas12a-4xSID, Day 21, Rep 1

description:
Library name: sample46
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: TT-seq_Degron_RPB1_dTAG_4h_rep1

description:
Library name: sample33
Degron_RPB1_dTAG_4h_merged_forward.bw
Degron_RPB1_dTAG_4h_merged_reverse.bw


title: ET271-DP

description: Library name: ET271.DP

value: 42 wk


title: sample 11-2-5 BatchD_ethanol extract of Zizyphi Fructus (Medium dose)_rep2

description: BatchC_ethanol extract of Zizyphi Fructus (Medium dose)_rep2

value: Zizyphi Fructus ethanol extract 100 ug/mL


title: TT-seq_Degron_RPB1_dTAG_0h_rep2

description:
Library name: sample32
Degron_RPB1_dTAG_0h_merged_forward.bw
Degron_RPB1_dTAG_0h_merged_reverse.bw


title: dEnAsCas12a-4xSID, Day 14, Rep 3

description:
Library name: sample45
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 11-2-4 BatchD_ethanol extract of Zizyphi Fructus (High dose)_rep2

description: BatchC_ethanol extract of Zizyphi Fructus (High dose)_rep2


title: dEnAsCas12a-4xSID, Day 14, Rep 2

description:
Library name: sample44
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: ET277-AP

description: Library name: ET277.AP

value: 34 wk


title: TT-seq_Degron_RPB1_dTAG_0h_rep1

description:
Library name: sample31
Degron_RPB1_dTAG_0h_merged_forward.bw
Degron_RPB1_dTAG_0h_merged_reverse.bw


title: sample 11-2-3 BatchD_ethanol extract of Coptidis Rhizoma (Low dose)_rep2

description: BatchC_ethanol extract of Coptidis Rhizoma (Low dose)_rep2


title: LbCas12a Plasmid Library, Rep 1

description:
Library name: sample49
plasmid library
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta

value: Plasmid


title: ET277-DP

description: Library name: ET277.DP

value: Prostate tumor tissue


title: dEnAsCas12a-4xSID, Day 7, Rep 3

description:
Library name: sample42
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: dEnAsCas12a-4xSID, Day 14, Rep 1

description:
Library name: sample43
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 11-2-2 BatchD_ethanol extract of Coptidis Rhizoma (Medium dose)_rep2

description: BatchC_ethanol extract of Coptidis Rhizoma (Medium dose)_rep2


title: DKOE1-PT

description: Library name: DKOE1.PT

value: 28 wk


title: ChIP-seq_S7A_rep2

description:
Library name: sample85
S7A_merged.bw

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: Anti-HA Magnetic Beads (Med Chem Express, #HY-K0201)


title: sample 11-2-1 BatchD_ethanol extract of Coptidis Rhizoma (High dose)_rep2

description: BatchC_ethanol extract of Coptidis Rhizoma (High dose)_rep2


title: ChIP-seq_S7A_rep1

description:
Library name: sample84
S7A_merged.bw


title: ChIP-seq_S5A_rep2

description:
Library name: sample83
S5A_merged.bw

value: RPB1 degron, S5A RPB1 complement


title: dEnAsCas12a-4xSID, Day 7, Rep 2

description:
Library name: sample41
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta

value: lung cancer epithelial


title: sample D1-3-1 BatchD_Vehicle(DMSO)_rep3

value: 0.1% DMSO


title: dEnAsCas12a-4xSID, Day 7, Rep 1

description:
Library name: sample40
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: ET60-PT

description: Library name: ET60.PT

value: 33 wk


title: ChIP-seq_S5A_rep1

description:
Library name: sample82
S5A_merged.bw


title: ET58-PT

description: Library name: ET58.PT

value: 35 wk


title: DKOE478-AP-DP

description: Library name: DKOE478.AP.DP

value: DKO


title: sample D1-1-1 BatchD_Vehicle(DMSO)_rep1


title: dEnAsCas12a-4xSID, Day 5, Rep 3

description:
Library name: sample39
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: dEnAsCas12a-4xSID, Day 5, Rep 2

description:
Library name: sample38
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 11-1-6 BatchC_ethanol extract of Zizyphi Fructus (Low dose)_rep1


title: ET247-DP

description: Library name: ET247.DP

value: 46 wk

value: Intact


title: ChIP-seq_T4V_rep1

description:
Library name: sample80
T4V_merged.bw

value: RPB1 degron, T4V RPB1 complement


title: dEnAsCas12a-4xSID, Day 5, Rep 1

description:
Library name: sample37
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: ChIP-seq_S2A_rep2

description:
Library name: sample79
S2A_merged.bw

value: RPB1 degron, S2A RPB1 complement


title: ET166-PT

description: Library name: ET166.PT

value: 37 wk


title: dEnAsCas12a-KRAB, Day 21, Rep 3

description:
Library name: sample36
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 11-1-4 BatchC_ethanol extract of Zizyphi Fructus (High dose)_rep1

value: Zizyphi Fructus ethanol extract 500 ug/mL


title: sample 11-1-5 BatchC_ethanol extract of Zizyphi Fructus (Medium dose)_rep1

value: Zizyphi Fructus ethanol extract 100 ug/mL


title: ET126-AP

description: Library name: ET126.AP

value: Prostate tumor tissue

value: 30 wk


title: DKO-M218

description: Library name: DKO-M218

data_processing:
10x Cell Ranger Pipeline
aligned with modified mm10 genome with Egfp
Assembly: mm10
Supplementary files format and content: zip of 10x Cell Ranger outs

source_name: prostate tissue

extract_protocol:
Mouse prostates were dissected, and half the prostate was dissociated at 37º C in AdDMEM/F12 containing 5 mg/mL collagenase II, 10 μM Rock inhibitor (Y-27632 dihydrochloride), and 1 nM synthetic androgen R1881. Tissue dissociation was terminated by addition of excess cold AdDMEM/F12, and cells collected by centrifugation at 1000 rpm at 4ºC. Cells were resuspended in warm 0.25% Trypsin, 2.21 mM EDTA containing 10 μM Rock inhibitor and 1 nM R1881 and incubated at 37ºC for 15 minutes with occasional agitation by pipetting. Trypsin digestion reaction was terminated by excess cold AdDMEM/F12 and cells were pelleted by centrifugation at 1000 rpm at 4ºC. The cell pellet was resuspended in 3 mL AdDMEM/F12 and the cell suspension strained through a sterile 40 μm filter. The cell pellet was resuspended in 1x Ammonium-Chloride-Potassium buffer for 10 minutes at room temperature to lyse red blood. The remaining cells were collected by centrifugation at 1000 rpm at 4ºC. Cell suspensions were then used to create single cell libraries. Cells were either used for scRNA-seq directly or after flow sorting for viable cells; flow sorting had no detectable impact on the data based on PCA analysis.
Single-cell transcriptomic libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3' v3.1 platform, following quality assessment. Cells were encapsulated into Gel Beads-in-Emulsion (GEMs), barcoded, and subjected to reverse transcription and library preparation, including cDNA amplification, fragmentation, adaptor ligation, and indexing. Final libraries were quality-checked, pooled, and sequenced on an Illumina NovaSeq 6000 system at an average depth of ~20,000 paired-end reads per cell.

value: prostate tissue

tag: Sex

value: male

value: non-castrated

tag: Stage

value: endpoint tumor


title: ChIP-seq_S2A_rep1

description:
Library name: sample78
S2A_merged.bw

tag: treatment

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

value: Anti-HA Magnetic Beads (Med Chem Express, #HY-K0201)


title: ChIP-seq_Y1F_rep2

description:
Library name: sample77
Y1F_merged.bw

value: RPB1 degron, Y1F RPB1 complement


title: dEnAsCas12a-KRAB, Day 21, Rep 2

description:
Library name: sample35
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta

tag: cell type

value: lung cancer epithelial


title: DKO-M169

description: Library name: DKO-M169

value: DKO


title: sample 11-1-3 BatchC_ethanol extract of Coptidis Rhizoma (Low dose)_rep1

value: Coptidis Rhizoma ethanol extract 11.2 ug/mL


title: ChIP-seq_Y1F_rep1

description:
Library name: sample76
Y1F_merged.bw


title: dEnAsCas12a-KRAB, Day 14, Rep 3

description:
Library name: sample33
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: dEnAsCas12a-KRAB, Day 21, Rep 1

description:
Library name: sample34
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample D1-2-1 BatchD_Vehicle(DMSO)_rep2

value: 0.1% DMSO


title: sample 11-1-2 BatchC_ethanol extract of Coptidis Rhizoma (Medium dose)_rep1

value: Coptidis Rhizoma ethanol extract 56 ug/mL


title: ChIP-seq_T4V_rep2

description:
Library name: sample81
T4V_merged.bw

value: RPB1 degron, T4V RPB1 complement


title: ChIP-seq_WT_rep2

description:
Library name: sample75
WT_merged.bw

value: RPB1 degron, WT RPB1 complement


title: sample 10-3-6 BatchC_ethanol extract of Scutellariae Radix (Low dose)_rep3

value: Scutellariae Radix ethanol extract 20 ug/mL


title: TKO-T1918

description: Library name: TKO-T1918

value: TKO


title: sample 10-3-5 BatchC_ethanol extract of Scutellariae Radix (Medium dose)_rep3

value: Scutellariae Radix ethanol extract 100 ug/mL


title: DKO-M361

description: Library name: DKO-M361

value: prostate tissue


title: ChIP-seq_Mock_rep2

description:
Library name: sample73
Mock_merge.bw

value: RPB1 degron

value: Untreated


title: ChIP-seq_WT_rep1

description:
Library name: sample74
WT_merged.bw


title: dEnAsCas12a-KRAB, Day 14, Rep 1

description:
Library name: sample31
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 10-3-4 BatchC_ethanol extract of Scutellariae Radix (High dose)_rep3

value: Scutellariae Radix ethanol extract 500 ug/mL


title: SKO-159

description: Library name: SKO-159

value: male

value: SKO

value: non-castrated

value: endpoint tumor


title: TKO-T2579

description: Library name: TKO-T2579


title: dEnAsCas12a-KRAB, Day 7, Rep 3

description:
Library name: sample30
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta

value: lung cancer epithelial


title: sample 10-3-3 BatchC_ethanol extract of Pinelliae Tuber (Low dose)_rep3

value: Pinelliae Tuber ethanol extract 20 ug/mL


title: ChIP-seq_Mock_rep1

description:
Library name: sample72
Mock_merge.bw

value: Anti-HA Magnetic Beads (Med Chem Express, #HY-K0201)


title: sample 10-3-2 BatchC_ethanol extract of Pinelliae Tuber (Medium dose)_rep3

value: Pinelliae Tuber ethanol extract 100 ug/mL


title: SKO-143

description: Library name: SKO-143


title: dEnAsCas12a-KRAB, Day 7, Rep 2

description:
Library name: sample29
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: SKO-134

description: Library name: SKO-134


title: ChIP-seq_pS7_rep2

description:
Library name: sample71
pS7_merged.bw

value: WT

value: Phospho-Rpb1 CTD (Ser7) antibody (Cell signaling #13780)


title: dEnAsCas12a-KRAB, Day 7, Rep 1

description:
Library name: sample28
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: ChIP-seq_pS7_rep1

description:
Library name: sample70
pS7_merged.bw


title: sample 10-3-1 BatchC_ethanol extract of Pinelliae Tuber (High dose)_rep3

value: Pinelliae Tuber ethanol extract 500 ug/mL


title: dEnAsCas12a-KRAB, Day 5, Rep 3

description:
Library name: sample27
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: DKO-M671

description: Library name: DKO-M671

value: DKO


title: ChIP-seq_pS5_rep2

description:
Library name: sample69
pS5_merged.bw

value: Phospho-Rpb1 CTD (Ser5) antibody (Cell signaling#13523)


title: sample 10-2-6 BatchC_ethanol extract of Scutellariae Radix (Low dose)_rep2

value: Scutellariae Radix ethanol extract 20 ug/mL


title: DKO-4113

description: Library name: DKO-4113

value: prostate tissue


title: sample 10-2-5 BatchC_ethanol extract of Scutellariae Radix (Medium dose)_rep2

value: Scutellariae Radix ethanol extract 100 ug/mL


title: dEnAsCas12a-KRAB, Day 5, Rep 2

description:
Library name: sample26
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: ChIP-seq_pS5_rep1

description:
Library name: sample68
pS5_merged.bw

value: Untreated


title: dEnAsCas12a-KRAB, Day 14, Rep 2

description:
Library name: sample32
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: DKO-EP-DKOE1562

description: Library name: DKO-EP-DKOE1562

value: male


title: dEnAsCas12a-KRAB, Day 5, Rep 1

description:
Library name: sample25
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 10-2-4 BatchC_ethanol extract of Scutellariae Radix (High dose)_rep2

value: Scutellariae Radix ethanol extract 500 ug/mL


title: ChIP-seq_pT4_rep2

description:
Library name: sample67
pT4_merged.bw

value: Phospho-Rpb1 CTD (Thr4) Antibody (Cell signaling #14934)


title: sample 10-2-3 BatchC_ethanol extract of Pinelliae Tuber (Low dose)_rep2


title: dHyperLbCas12a-4xSID, Day 21, Rep 3

description:
Library name: sample24
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: dHyperLbCas12a-4xSID, Day 21, Rep 2

description:
Library name: sample23
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: ChIP-seq_pS2_rep2

description:
Library name: sample65
pS2_merged.bw

value: Phospho-Rpb1 CTD (Ser2) antibody (Cell signaling #13499)


title: DKO-EP-DKOE1221

description: Library name: DKO-EP-DKOE1221

value: non-castrated

value: endpoint tumor


title: ChIP-seq_pT4_rep1

description:
Library name: sample66
pT4_merged.bw


title: sample 10-2-2 BatchC_ethanol extract of Pinelliae Tuber (Medium dose)_rep2


title: sample 10-2-1 BatchC_ethanol extract of Pinelliae Tuber (High dose)_rep2


title: dHyperLbCas12a-4xSID, Day 21, Rep 1

description:
Library name: sample22
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta

value: lung cancer epithelial


title: DKO-EP-DKOE1219

description: Library name: DKO-EP-DKOE1219


title: dHyperLbCas12a-4xSID, Day 14, Rep 3

description:
Library name: sample21
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: ChIP-seq_pY1_rep2

description:
Library name: sample63
pY1_merged.bw

value: Phospho-Rpb1 CTD (Tyr1) antibody (Merck Millipore #MABE350)


title: ChIP-seq_pS2_rep1

description:
Library name: sample64
pS2_merged.bw

value: WT


title: sample 10-1-6 BatchC_ethanol extract of Scutellariae Radix (Low dose)_rep1


title: DKO-EE-DKOE1232

description: Library name: DKO-EE-DKOE1232


title: DKO-EE-DKOE1223

description: Library name: DKO-EE-DKOE1223


title: sample 10-1-5 BatchC_ethanol extract of Scutellariae Radix (Medium dose)_rep1


title: dHyperLbCas12a-4xSID, Day 14, Rep 2

description:
Library name: sample20
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: ChIP-seq_pY1_rep1

description:
Library name: sample62
pY1_merged.bw


title: ChIP-seq_RNAPII_rep2

description:
Library name: sample61
RNAPII_merged.bw

value: RNPII antibody (Santa #sc-55492)


title: dHyperLbCas12a-4xSID, Day 14, Rep 1

description:
Library name: sample19
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: DKO-EE-DKOE1393

description: Library name: DKO-EE-DKOE1393


title: Tumor, Thbs2KO, rep3

city: Kyoto-City

first: Kosuke

last: Iwane

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

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Kyoto University Graduated School of Medicine

description:
Library name: KO13
Column name in WTvsTSP2KO_tumor_count.csv: KO13

data_processing:
Adaptors and low-quality bases were trimmed from the reads using Trimmomatic (version 0.39)  with default parameters.
The reads were aligned to the Mus musculus reference genome (build mm10) using STAR (version 2.7.3a) and quantified using RSEM (version v1.3.1).
Assembly: mm10
Supplementary files format and content: a csv file includes raw counts for each sample

source_name: orthotopic implanted tumor in the rectum of the mice

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


title: sample 10-1-4 BatchC_ethanol extract of Scutellariae Radix (High dose)_rep1


title: dHyperLbCas12a-4xSID, Day 7, Rep 3

description:
Library name: sample18
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: ChIP-seq_RNAPII_rep1

description:
Library name: sample60
RNAPII_merged.bw


title: DKO-EP-DKOE1546

description: Library name: DKO-EP-DKOE1546


title: Tumor, Thbs2KO, rep2

description:
Library name: KO12
Column name in WTvsTSP2KO_tumor_count.csv: KO12

value: orthotopic implanted tumor in the rectum of the mice


title: dHyperLbCas12a-4xSID, Day 7, Rep 2

description:
Library name: sample17
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: Tumor, Thbs2KO, rep1

description:
Library name: KO10
Column name in WTvsTSP2KO_tumor_count.csv: KO10


title: ChIP-seq_Input

description:
Library name: sample59
Input.bw


title: RNA-seq_S7A_dTAG_12h_rep2

description:
Library name: sample30
RNA-seq_S7A_Rawcounts_and_TPM.csv
RNA-seq_S7A_DEseq2_results.csv

data_processing:
RNA-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).
Trimmed reads were aligned to concatenated index of  human genome (hg38) and Drosophila melanogaster genome (dm6) with STAR (v.2.7.3a) with default settings.
Then featureCounts (v.2.0.1) was used to summarize gene-level read counts per sample from the GENCODE annotation.
Differential expression genes were identified with R package DESeq2 (v.1.24.0). hg38 read counts were normalized with size factors estimated on the corresponding reads mapped to the dm6 genome as spike-in normalization.
Assembly: Concatenated index of hg38 and dm6
Supplementary files format and content: Comma-delimited text file includes raw counts and analysis results from deseq2

extract_protocol:
Total RNA were extracted with TRIzol reagent following the manufacturers' instruction.
After sample qualification, 1–3 μg of total RNA from each sample served as the initial material for constructing a transcriptome sequencing library. Following the protocols of the VAHTS Universal V6 RNA-seq Library Prepkit for Illumina (Vazyme #NR 604), various index tags were selected to establish the database. Following library qualification, sample pooling was performed based on the effective concentration of the library and the targeted data volume. Sequencing was conducted using the Illumina platform, employing the PE150 sequencing strategy to generate 150-bp paired-end sequencing reads.

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 12h to induce endogeneous RPB1 degradation. For spike-in, 10% S2 cells were used.

value: RPB1 degron, S7A RPB1 complement

value: Dox (2 μg/mL) for 24 hours followd with dTAGV-1 (100 nM) for 12 hours


title: dHyperLbCas12a-4xSID, Day 7, Rep 1

description:
Library name: sample16
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 10-1-2 BatchC_ethanol extract of Pinelliae Tuber (Medium dose)_rep1

value: Pinelliae Tuber ethanol extract 100 ug/mL


title: sample 10-1-1 BatchC_ethanol extract of Pinelliae Tuber (High dose)_rep1

value: Pinelliae Tuber ethanol extract 500 ug/mL


title: Tumor, WT, rep3

description:
Library name: WT10
Column name in WTvsTSP2KO_tumor_count.csv: WT10


title: sample 9-3-6 BatchC_ethanol extract of Zingiberis Rhizoma (Low dose)_rep3

value: Zingiberis Rhizoma ethanol extract 20 ug/mL


title: RNA-seq_S7A_dTAG_12h_rep1

description:
Library name: sample29
RNA-seq_S7A_Rawcounts_and_TPM.csv
RNA-seq_S7A_DEseq2_results.csv


title: Tumor, WT, rep2

description:
Library name: WT9
Column name in WTvsTSP2KO_tumor_count.csv: WT9


title: dHyperLbCas12a-4xSID, Day 5, Rep 3

description:
Library name: sample15
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: dHyperLbCas12a-4xSID, Day 5, Rep 2

description:
Library name: sample14
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: RNA-seq_S7A_dTAG_0h_rep2

description:
Library name: sample28
RNA-seq_S7A_Rawcounts_and_TPM.csv
RNA-seq_S7A_DEseq2_results.csv

value: Untreated


title: sample 9-3-5 BatchC_ethanol extract of Zingiberis Rhizoma (Medium dose)_rep3

value: Zingiberis Rhizoma ethanol extract 100 ug/mL


title: Tumor, WT, rep1

description:
Library name: WT8
Column name in WTvsTSP2KO_tumor_count.csv: WT8


title: RNA-seq_S7A_dTAG_0h_rep1

description:
Library name: sample27
RNA-seq_S7A_Rawcounts_and_TPM.csv
RNA-seq_S7A_DEseq2_results.csv


title: CAF, WT, rep3

description:
Library name: WTCAF7
Column name in CAF_WTvsTSP2KO_count.csv: WTCAF7

source_name: CAF isolated from orthotopic implanted tumor generated by injection of MTO in the rectum of mice

growth_protocol: Isolated CAFs were seeded on fibronectin-coated multiwell plate and cultured in DMEM supplemented with 10%FBS, 1% L-glutamine  and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN). Residual DNA was removed by on-column DNase digestion using the RNase-Free DNase Set (QIAGEN) .
RNA libraries for RNA-seq were prepared with the TruSeq RNA Sample Prep Kit v2.


title: sample 9-3-3 BatchC_ethanol extract of Zingiberis Rhizoma Recens (Low dose)_rep3

value: Zingiberis Rhizoma Recens ethanol extract 20 ug/mL


title: sample 10-1-3 BatchC_ethanol extract of Pinelliae Tuber (Low dose)_rep1

value: Pinelliae Tuber ethanol extract 20 ug/mL


title: sample 9-3-2 BatchC_ethanol extract of Zingiberis Rhizoma Recens (Medium dose)_rep3

value: Zingiberis Rhizoma Recens ethanol extract 100 ug/mL


title: RNA-seq_S5A_dTAG_12h_rep2

description:
Library name: sample26
RNA-seq_S5A_Rawcounts_and_TPM.csv
RNA-seq_S5A_DEseq2_results.csv

value: RPB1 degron, S5A RPB1 complement


title: CAF, WT, rep2

description:
Library name: WTCAF6
Column name in CAF_WTvsTSP2KO_count.csv: WTCAF6

value: CAF isolated from orthotopic implanted tumor generated by injection of MTO in the rectum of mice


title: RNA-seq_S5A_dTAG_12h_rep1

description:
Library name: sample25
RNA-seq_S5A_Rawcounts_and_TPM.csv
RNA-seq_S5A_DEseq2_results.csv


title: sample 9-3-1 BatchC_ethanol extract of Zingiberis Rhizoma Recens (High dose)_rep3

value: Zingiberis Rhizoma Recens ethanol extract 500 ug/mL


title: CAF, WT, rep1

description:
Library name: WTCAF5
Column name in CAF_WTvsTSP2KO_count.csv: WTCAF5


title: dHyperLbCas12a-KRAB, Day 21, Rep 2

description:
Library name: sample11
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta

value: lung cancer epithelial


title: dHyperLbCas12a-KRAB, Day 21, Rep 1

description:
Library name: sample10
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: RNA-seq_S5A_dTAG_0h_rep2

description:
Library name: sample24
RNA-seq_S5A_Rawcounts_and_TPM.csv
RNA-seq_S5A_DEseq2_results.csv


title: CAF, Thbs2KO, rep3

description:
Library name: TSP2KOCAF7
Column name in CAF_WTvsTSP2KO_count.csv: TSP2KOCAF7


title: dHyperLbCas12a-KRAB, Day 14, Rep 3

description:
Library name: sample9
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: CAF, Thbs2KO, rep2

description:
Library name: TSP2KOCAF6
Column name in CAF_WTvsTSP2KO_count.csv: TSP2KOCAF6


title: RNA-seq_S5A_dTAG_0h_rep1

description:
Library name: sample23
RNA-seq_S5A_Rawcounts_and_TPM.csv
RNA-seq_S5A_DEseq2_results.csv


title: sample 9-2-5 BatchC_ethanol extract of Zingiberis Rhizoma (Medium dose)_rep2


title: RNA-seq_T4V_dTAG_12h_rep2

description:
Library name: sample22
RNA-seq_T4V_Rawcounts_and_TPM.csv
RNA-seq_T4V_DEseq2_results.csv

value: RPB1 degron, T4V RPB1 complement


title: dHyperLbCas12a-KRAB, Day 14, Rep 2

description:
Library name: sample8
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 9-2-4 BatchC_ethanol extract of Zingiberis Rhizoma (High dose)_rep2

value: Zingiberis Rhizoma ethanol extract 500 ug/mL


title: CAF, Thbs2KO, rep1

description:
Library name: TSP2KOCAF5
Column name in CAF_WTvsTSP2KO_count.csv: TSP2KOCAF5


title: dHyperLbCas12a-4xSID, Day 5, Rep 1

description:
Library name: sample13
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: RNA-seq_T4V_dTAG_12h_rep1

description:
Library name: sample21
RNA-seq_T4V_Rawcounts_and_TPM.csv
RNA-seq_T4V_DEseq2_results.csv


title: sample 9-2-2 BatchC_ethanol extract of Zingiberis Rhizoma Recens (Medium dose)_rep2


title: RNA-seq_T4V_dTAG_0h_rep2

description:
Library name: sample20
RNA-seq_T4V_Rawcounts_and_TPM.csv
RNA-seq_T4V_DEseq2_results.csv


title: dHyperLbCas12a-KRAB, Day 21, Rep 3

description:
Library name: sample12
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: 3_KO_F_Library_410518_1

city: Zurich

first: Burkhard

last: Becher

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

data_processing:
Gene expression matrix was computed using CellRanger v7.0.0 with the option '--include-introns=true'
Assembly: GRCm39 with the annotation Annotation Release 106 from ENSEMBL, downloaded 2022-07-05
Supplementary files format and content: Filtered count matrix from cellranger count is stored in three files: barcodes.tsv.gz, genes.tsv,gz and matrix.mtx.gz

source_name: Salivary Gland

extract_protocol:
Cell extraction from tissue according to study design.
Library construction was performed according to the 10x Chromium Single Cell 3' Reagent Kit v2.

value: Salivary Gland

value: Whole CD45 positive

value: female

value: 20 days


title: RNA-seq_T4V_dTAG_0h_rep1

description:
Library name: sample19
RNA-seq_T4V_Rawcounts_and_TPM.csv
RNA-seq_T4V_DEseq2_results.csv


title: sample 9-2-1 BatchC_ethanol extract of Zingiberis Rhizoma Recens (High dose)_rep2


title: dHyperLbCas12a-KRAB, Day 7, Rep 2

description:
Library name: sample5
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: RNA-seq_S2A_dTAG_12h_rep2

description:
Library name: sample18
RNA-seq_S2A_Rawcounts_and_TPM.csv
RNA-seq_S2A_DEseq2_results.csv

value: RPB1 degron, S2A RPB1 complement

value: Dox (2 μg/mL) for 24 hours followd with dTAGV-1 (100 nM) for 12 hours


title: sample 9-1-6 BatchC_ethanol extract of Zingiberis Rhizoma (Low dose)_rep1

value: Zingiberis Rhizoma ethanol extract 20 ug/mL


title: dHyperLbCas12a-KRAB, Day 7, Rep 1

description:
Library name: sample4
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: dHyperLbCas12a-KRAB, Day 5, Rep 3

description:
Library name: sample3
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 9-2-6 BatchC_ethanol extract of Zingiberis Rhizoma (Low dose)_rep2


title: sample 9-1-5 BatchC_ethanol extract of Zingiberis Rhizoma (Medium dose)_rep1

value: Zingiberis Rhizoma ethanol extract 100 ug/mL


title: 2_Het_M_Library_410517_1

value: male


title: sample 9-1-4 BatchC_ethanol extract of Zingiberis Rhizoma (High dose)_rep1


title: RNA-seq_S2A_dTAG_0h_rep2

description:
Library name: sample16
RNA-seq_S2A_Rawcounts_and_TPM.csv
RNA-seq_S2A_DEseq2_results.csv

value: Untreated


title: dHyperLbCas12a-KRAB, Day 5, Rep 2

description:
Library name: sample2
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: tumor_TNFR2_Tcells_1

city: Creteil

first: Caroline

last: Pilon

address: 51 avenue du Mal de Lattre de Tassigny

country: France

institute: INSERM U955 Eq21, Hopital Henri Mondor

description: 10X genomics

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

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

value: tumor

value: FVB/n

value: 10-14 weeks old


title: tumor_TNFR2_Tcells_2

description: 10X genomics


title: RNA-seq_S2A_dTAG_0h_rep1

description:
Library name: sample15
RNA-seq_S2A_Rawcounts_and_TPM.csv
RNA-seq_S2A_DEseq2_results.csv


title: dHyperLbCas12a-KRAB, Day 14, Rep 1

description:
Library name: sample7
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: dHyperLbCas12a-KRAB, Day 5, Rep 1

description:
Library name: sample1
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta


title: sample 9-1-3 BatchC_ethanol extract of Zingiberis Rhizoma Recens (Low dose)_rep1

value: Zingiberis Rhizoma Recens ethanol extract 20 ug/mL


title: 4_KO_M_Library_410519_1


title: RNA-seq_S2A_dTAG_12h_rep1

description:
Library name: sample17
RNA-seq_S2A_Rawcounts_and_TPM.csv
RNA-seq_S2A_DEseq2_results.csv


title: dHyperLbCas12a-KRAB, Day 7, Rep 3

description:
Library name: sample6
crRNA array amplified from gDNA
As.CRISPRi.crRNA.ref.fasta
Lb.CRISPRi.crRNA.ref.fasta

value: lung cancer epithelial


title: tumor_ctrl_Tcells_2

description: 10X genomics

value: ctrl


title: sample 9-2-3 BatchC_ethanol extract of Zingiberis Rhizoma Recens (Low dose)_rep2


title: A549 cells, Bulk

description: crRNA amplified from gDNA

data_processing:
FastQs were generated using BCLConvert in BaseSpace
To compare the barcode sequence with its associated array in the plasmid and input samples, Umi Tools version 1.1.4 was used to extract the barcode sequence from reads.
Adapter sequences were trimmed using Cutapadapt version 4.4
Reads were aligned to a custom reference using Bowtie2 version 2.5.1.
Read counts were generated using Samtools version 1.17 (idxstats).
Assembly: custom crRNA library reference (see supplementary files)
Supplementary files format and content: tab-delimited text file including raw counts of crRNA barcode for each sample
Supplementary files format and content: tab-delimited text file including raw counts of crRNA arrays and their associated barcode (for bulk and plasmid libraries)
Library strategy: DNA amplicon sequencing

extract_protocol:
Plasmid libraries were purified using the Qiagen midi plus kit. A549 cells were subject to hybridization chain reaction (HCR) Flow-FISH as in. (https://pubmed.ncbi.nlm.nih.gov/34326544/). Briefly, cells were fixed in 4% formaldehyde, permeabilized using 70% ethanol, FISH targeting PER1 were hybridized, and then the signal was amplified using the B3 amplifier (molecular instruments). Cells were washed and then top and bottom 12% PER1 cells were sorted based on PER1 expression (FITC). Genomic DNA was extracted from these cells using the FFPE miniprep kit (Zymo). Genomic DNA was also extracted from a bulk unsorted cell population using a Puregene kit (Qiagen)
crRNA arrays were amplified from genomic or plasmid DNA using Q5 Hotstart 2x master mix. Primers contained Illumina adapter sequences and indexes

treatment_protocol: Cells were treated for three hours with vehicle, 200pM dexamethasone, or 100nM dexamethasone before harvesting


title: RNA-seq_Y1F_dTAG_12h_rep2

description:
Library name: sample14
RNA-seq_Y1F_Rawcounts_and_TPM.csv
RNA-seq_Y1F_DEseq2_results.csv

value: RPB1 degron, Y1F RPB1 complement


title: sample 9-1-2 BatchC_ethanol extract of Zingiberis Rhizoma Recens (Medium dose)_rep1

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

value: Zingiberis Rhizoma Recens ethanol extract 100 ug/mL


title: tumor_ctrl_Tcells_1

description: 10X genomics


title: sample 9-1-1 BatchC_ethanol extract of Zingiberis Rhizoma Recens (High dose)_rep1

value: Zingiberis Rhizoma Recens ethanol extract 500 ug/mL


title: LPS replicate2, scRNA-seq

city: Shanghai

first: Jian

last: Xu

address: 180 Fenglin Road

institute: Zhongshan hospital

description: 10x Genomics

data_processing:
High quality Clean Reads were processed, evaluated and mapped to the reference genome through Cell Ranger count module; a gene expression matrix was prepared for the sequenced samples. Cell Ranger and Seurat (version: 4.1.0) were applied for subsequent downstream analysis, such as data normalization, scaling, principal component analysis (PCA), uniform manifold approximation and projection (UMAP) dimension reduction, and gene expression visualization
Assembly: mm10
Supplementary files format and content: Tab-separated value and matrix files

source_name: Lung

extract_protocol:
Mouse lung tissue samples from two ALI and control mice each were minced and digested by collagenase II and trypsin for single cell suspensions, which were loaded onto ChromiumTM microfluidic chips (viability ≥80%, fragmentation rate ≤5%, group rate ≤5%).
The released mRNA was reverse-transcribed into complementary deoxyribonucleic acid (cDNA) with barcode. Subsequently, the commercial 10x Genomics platform (10x Genomics, Pleasanton, USA) was used for the establishment of cDNA libraries. Following the 10x Genomics’s instructions, technician generated the scRNA sequencing libraries by Single-Cell 3’ Library Kit v3 which were sequenced on a NovaSeq 6000 system (Illumina, San Diego, US) to obtain 150 bp at each end.

value: Lung

tag: strain background

value: Lipopolysaccharide (LPS)-induced acute lung injury (ALI) mouse model


title: RNA-seq_Y1F_dTAG_12h_rep1

description:
Library name: sample13
RNA-seq_Y1F_Rawcounts_and_TPM.csv
RNA-seq_Y1F_DEseq2_results.csv


title: 1_Het_F_Library_410516_1

value: Salivary Gland

value: Whole CD45 positive

value: female

value: 20 days


title: RNA-seq_Y1F_dTAG_0h_rep2

description:
Library name: sample12
RNA-seq_Y1F_Rawcounts_and_TPM.csv
RNA-seq_Y1F_DEseq2_results.csv


title: sample 8-3-6 BatchC_water extract of Sayeok-tang (Low dose)_rep3

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

value: Sayeok-tang water extract 20 ug/mL


title: LPS, replicate1, scRNA-seq

description: 10x Genomics


title: sample 8-3-5 BatchC_water extract of Sayeok-tang (Medium dose)_rep3

value: Sayeok-tang water extract 100 ug/mL


title: A549 cells, 200pM Dex, Low Bin

description: crRNA amplified from gDNA

value: 200pM dexamethasone


title: A549 cells, 200pM Dex, High Bin

description: crRNA amplified from gDNA


title: control, replicate2, scRNA-seq

description: 10x Genomics

value: control


title: RNA-seq_WT_dTAG_12h_rep2

description:
Library name: sample10
RNA-seq_WT_Rawcounts_and_TPM.csv
RNA-seq_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 12 hours


title: control, replicate1, scRNA-seq

description: 10x Genomics


title: RNA-seq_WT_dTAG_12h_rep1

description:
Library name: sample9
RNA-seq_WT_Rawcounts_and_TPM.csv
RNA-seq_WT_DEseq2_results.csv


title: RNA-seq_WT_dTAG_0h_rep2

description:
Library name: sample8
RNA-seq_WT_Rawcounts_and_TPM.csv
RNA-seq_WT_DEseq2_results.csv

value: Untreated


title: PseudoU-H3K7me3-Rep2

city: Guangzhou

first: Zhou

last: yifan

state: 周一帆

address: 74 Zhongshan Second Road

institute: Sun Yat-sen University Cancer Center

description: 10 × Genomics

data_processing:
FASTQ files were trimmed with Fastp software (Fastp version 0.12.4), and the filtered, pair-ended reads were aligned to mm10 with Bowtie2(Bowtie2 version 2.3.5.1)
Peaks were called over input using MACS2 (version 2.2.7.1)84 and only peaks with a q-value < 0.05 were kept , and then annotated by HOMER(version 4.11.1)
The Diffbind R package (version 3.8.4) was used to generate the count matrix for each consensus peak. DARs(differentially accessible regions) were identified between conditions using the limma R package with P < 0.05 and |fold change|>0.58. To visualize peaks , we use “plotHeatmap” commamd to plot Heatmap and "bamCoverage" command, adding the parameter "--normalizeUsingRPKM" to convert bam files to bw format with Deeptools (version 1.9). CUT&Tag signals of H3K27ac and Chd4 were calculated by BEDTools
Visualization of the depositions along genomic regions was using IGV (2.6.3)
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: Cut&Tag

growth_protocol: RPMI 1640,10% fetal bovine serum, 1x pen:illin/streptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
Genomic DNA was extracted using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
Sequencing libraries were prepared according to the manufacturer's protocol and cleaned-up using XP beads (Beckman Coulter). Sequencing was conducted on the Illumina NovaSeq 6000 platform using PE150.

treatment_protocol: Vehicle or PseudoU treatment (10 μM)

value: mast cell

value: WT

value: PseudoU

tag: antibody


title: A549 cells, Vehicle, High Bin

description: crRNA amplified from gDNA

value: lung cancer epithelial

value: Ethanol


title: A549 cells, Vehicle, Low Bin

description: crRNA amplified from gDNA


title: PseudoU-H3K7me3-Rep1

description: 10 × Genomics


title: sample 8-3-2 BatchC_water extract of Bojungikgi-tang (Medium dose)_rep3

value: Bojungikgi-tang water extract 100 ug/mL


title: sample 8-3-3 BatchC_water extract of Bojungikgi-tang (Low dose)_rep3

value: Bojungikgi-tang water extract 20 ug/mL


title: Non-targeting plasmid library

description: plasmid library

source_name: Non-targeting plasmid library

tag: sample type

value: Non-targeting plasmid library


title: sample 8-3-1 BatchC_water extract of Bojungikgi-tang (High dose)_rep3

value: Bojungikgi-tang water extract 500 ug/mL


title: A549 cells, 100nM Dex, High Bin

description: crRNA amplified from gDNA

value: 100nM dexamethasone


title: PER1-Targeting plasmid library

description: plasmid library

source_name: PER1-Targeting plasmid library

value: PER1-Targeting plasmid library


title: A549 cells, 100nM Dex, Low Bin

description: crRNA amplified from gDNA


title: RNA-seq_Degron_RPB1_dTAG_12h_rep2

description:
Library name: sample6
RNA-seq_Degron_RPB1_Rawcounts_and_TPM.csv
RNA-seq_Degron_RPB1_DEseq2_results.csv

value: RPB1 degron

value: dTAGV-1 (100 nM) for 12 hours


title: sample 8-2-6 BatchC_water extract of Sayeok-tang (Low dose)_rep2

value: Sayeok-tang water extract 20 ug/mL


title: Vehicle-H3K27me3-Rep1

description: 10 × Genomics

value: Vehicle


title: RNA-seq_Degron_RPB1_dTAG_12h_rep1

description:
Library name: sample5
RNA-seq_Degron_RPB1_Rawcounts_and_TPM.csv
RNA-seq_Degron_RPB1_DEseq2_results.csv


title: sample 8-2-5 BatchC_water extract of Sayeok-tang (Medium dose)_rep2

value: Sayeok-tang water extract 100 ug/mL


title: RNA-seq_Y1F_dTAG_0h_rep1

description:
Library name: sample11
RNA-seq_Y1F_Rawcounts_and_TPM.csv
RNA-seq_Y1F_DEseq2_results.csv

value: RPB1 degron, Y1F RPB1 complement

value: Untreated


title: SKO-T433-Input

description:
Library name: SKO-T433-Input
bigwig file

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

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

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

tag: tissue

value: prostate tissue

value: male

value: SKO

value: Input DNA

value: non-castrated

value: endpoint tumor


title: sample 8-3-4 BatchC_water extract of Sayeok-tang (High dose)_rep3

tag: cell line

value: Sayeok-tang water extract 500 ug/mL


title: SKO-T433-H3K4me3

description:
Library name: SKO-T433-H3K4me3
bigwig file


title: sample 8-2-4 BatchC_water extract of Sayeok-tang (High dose)_rep2

tag: time


title: myeloid cells from subcutaneous adipose tissue of HFD WT mice after the treatment with rosiglitazone, biological rep1

city: La Jolla

first: Yun Sok

last: Lee

state: California

address: 9500 Gilman Dr MC0673

department: Medicine

institute: University of California San Diego

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

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

extract_protocol:
Trizole
10x genomics kit

value: Wild type


title: sample 8-2-3 BatchC_water extract of Bojungikgi-tang (Low dose)_rep2

value: Bojungikgi-tang water extract 20 ug/mL


title: RNA-seq_WT_dTAG_0h_rep1

description:
Library name: sample7
RNA-seq_WT_Rawcounts_and_TPM.csv
RNA-seq_WT_DEseq2_results.csv

value: RPB1 degron, WT RPB1 complement


title: myeloid cells from visceral adiposetissue of HFD WT mice after the treatment with rosiglitazone, biological rep2

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


title: SKO-T433-H3K27ac

description:
Library name: SKO-T433-H3K27ac
bigwig file


title: Vehicle-H3K27me3-Rep2

description: 10 × Genomics

value: mast cell

value: WT


title: sample 8-2-2 BatchC_water extract of Bojungikgi-tang (Medium dose)_rep2

value: Bojungikgi-tang water extract 100 ug/mL


title: myeloid cells from visceral adiposetissue of HFD WT mice after the treatment with rosiglitazone, biological rep1

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


title: RNA-seq_Degron_RPB1_dTAG_0h_rep1

description:
Library name: sample3
RNA-seq_Degron_RPB1_Rawcounts_and_TPM.csv
RNA-seq_Degron_RPB1_DEseq2_results.csv

value: RPB1 degron


title: SKO-T433-AR

description:
Library name: SKO-T433-AR
bigwig file

value: Ar


title: RNA-seq_Mock_rep1

description:
Library name: sample1
RNA-seq_Mock_Rawcounts_and_TPM.csv

value: Untreated


title: SKO-T104-Input

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

value: prostate tissue


title: sample 8-1-6 BatchC_water extract of Sayeok-tang (Low dose)_rep1

value: Sayeok-tang water extract 20 ug/mL


title: sample 8-2-1 BatchC_water extract of Bojungikgi-tang (High dose)_rep2

value: Bojungikgi-tang water extract 500 ug/mL


title: Human CRC sample 26, CMS2

description:
Library name: Tumor26
FFPE spatial transcriptome sequencoing

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

source_name: Colorectal carcinoma

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

value: Colorectal carcinoma


title: sample 8-1-5 BatchC_water extract of Sayeok-tang (Medium dose)_rep1

value: Sayeok-tang water extract 100 ug/mL


title: myeloid cells from subcutaneous adipose tissue of HFD WT mice after the diet switch to NCD, biological rep1

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


title: SKO-T104-H3K4me3

description:
Library name: SKO-T104-H3K4me3
bigwig file

value: male

value: SKO

value: non-castrated

value: endpoint tumor


title: Human CRC sample 24, CMS1

description:
Library name: Tumor24
FFPE spatial transcriptome sequencoing


title: myeloid cells from visceral adiposetissue of HFD WT mice after the diet switch to NCD, biological rep2

value: Wild type


title: myeloid cells from subcutaneous adipose tissue of HFD WT mice after the treatment with rosiglitazone, biological rep2


title: SKO-T104-H3K27me3

description:
Library name: SKO-T104-H3K27me3
bigwig file


title: Human CRC sample 20, CMS4

description:
Library name: Tumor20
FFPE spatial transcriptome sequencoing


title: RNA-seq_Degron_RPB1_dTAG_0h_rep2

description:
Library name: sample4
RNA-seq_Degron_RPB1_Rawcounts_and_TPM.csv
RNA-seq_Degron_RPB1_DEseq2_results.csv


title: sample 8-1-4 BatchC_water extract of Sayeok-tang (High dose)_rep1

value: Sayeok-tang water extract 500 ug/mL


title: myeloid cells from visceral adiposetissue of HFD WT mice after the diet switch to NCD, biological rep1


title: RNA-seq_Mock_rep2

description:
Library name: sample2
RNA-seq_Mock_Rawcounts_and_TPM.csv

value: WT


title: SKO-T433-H3K27me3

description:
Library name: SKO-T433-H3K27me3
bigwig file


title: SKO-T104-H3K27ac

description:
Library name: SKO-T104-H3K27ac
bigwig file


title: sample C1-3-1 BatchC_Vehicle(DMSO)_rep3

value: 0.1% DMSO


title: Human CRC sample 26

description:
Library name: Tumor26
Column name in Tumor19202426_counts.csv: Tumor26

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

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


title: myeloid cells from subcutaneous adipose tissue of HFD WT mice, biological rep2


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


title: sample C1-2-1 BatchC_Vehicle(DMSO)_rep2


title: sample C1-1-1 BatchC_Vehicle(DMSO)_rep1


title: myeloid cells from subcutaneous adipose tissue of HFD WT mice after the diet switch to NCD, biological rep2


title: DKO-ET247-Input

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

value: DKO

value: Input DNA


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

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


title: DKO-ET247-H3K4me3

description:
Library name: DKO-ET247-H3K4me3
bigwig file

value: prostate tissue


title: Human CRC sample 20

description:
Library name: Tumor20
Column name in Tumor19202426_counts.csv: Tumor20


title: sample 8-1-3 BatchB_water extract of Bojungikgi-tang (Low dose)_rep1

value: Bojungikgi-tang water extract 20 ug/mL


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


title: Human CRC sample 19

description:
Library name: Tumor19
Column name in Tumor19202426_counts.csv: Tumor19


title: DKO-ET247-H3K27me3

description:
Library name: DKO-ET247-H3K27me3
bigwig file


title: sample 8-1-2 BatchB_water extract of Bojungikgi-tang (Medium dose)_rep1

value: Bojungikgi-tang water extract 100 ug/mL


title: myeloid cells from subcutaneous adipose tissue of NCD WT mice, biological rep2


title: DKO-ET247-H3K27ac

description:
Library name: DKO-ET247-H3K27ac
bigwig file


title: sample 8-1-1 BatchB_water extract of Bojungikgi-tang (High dose)_rep1

value: Bojungikgi-tang water extract 500 ug/mL