title: Jurkat_Mixture of water extracts of four ingredients_rep3

description: sample 1-3-12

source_name: Jurkat

growth_protocol: Jurkat cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and maintained in the medium recommended by the ATCC with 100 IU penicillin, and 100 µg/mL streptomycin in a humidified incubator. When cells reached 80–90% confluency, the growth medium was replaced every 3~4 days. Mycoplasma contamination was checked using the MycoAlert PLUS mycoplasma detection kit (Lonza, Rockland, ME, USA) and passed all.

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 (500 ng) 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: To determine the maximum concentration, we performed cell cytotoxicity tests and all drugs did not influence cell viability. The highest treatment concentrations (500ug/mL) were selected considering the solubility and clinical application of the drugs. To confirm the influence of concentration, we treated the cells with two concentrations (500 and 125 ug/mL). The cells treated with PBS were used as the vehicle control. Cells were plated at a density of 5 x 105 / well in a 12-well microplate and treated with two concentrations of drugs. After 24 hours, cells were washed two times with ice-cold PBS, and total RNA was isolated using QIAzol RNA Isolation Reagents (Thermo Fisher Scientific) according to the manufacturer's instructions.

value: Jurkat

value: T lymphoblast

value: Total 500ug/mL, 125ug/mL of each of the 4 ingredients mixed


title: Jurkat_Mixture of water extracts of four ingredients_rep2

status: Public on Aug 01 2026

type: SRA

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description: sample 1-3-11

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment

tag: time


title: Jurkat_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep2

description: sample 1-3-8

value: Water extract of Glycyrrhiza uralensis Fisher 125 μg/mL


title: Jurkat_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep1

description: sample 1-3-7


title: Jurkat_Mixture of water extracts of four ingredients_rep1

description: sample 1-3-10


title: Jurkat_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep2

description: sample 1-3-5

value: Water extract of Glycyrrhiza uralensis Fisher 500 μg/mL


title: Jurkat_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep3

description: sample 1-3-3

value: Water extract of Atractylodes japonica Koidzumi 125 μg/mL


title: Jurkat_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep2

description: sample 1-3-2


title: Jurkat_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep1

description: sample 1-3-1


title: Jurkat_Water extract of Atractylodes japonica Koidzumi (High dose)_rep3

description: sample 1-2-12

value: Water extract of Atractylodes japonica Koidzumi 500 μg/mL


title: Jurkat_Water extract of Atractylodes japonica Koidzumi (High dose)_rep2

description: sample 1-2-11


title: Jurkat_Water extract of Astragalus mongholicus Bunge (Low dose)_rep2

description: sample 1-2-8

value: Water extract of Astragalus mongholicus Bunge 125 μg/mL


title: Jurkat_Water extract of Astragalus mongholicus Bunge (Low dose)_rep1

description: sample 1-2-7


title: Jurkat_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep3

description: sample 1-3-9


title: Jurkat_Water extract of Astragalus mongholicus Bunge (High dose)_rep3

description: sample 1-2-6

value: Water extract of Astragalus mongholicus Bunge 500 μg/mL


title: Jurkat_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep3

description: sample 1-3-6


title: Jurkat_Water extract of Astragalus mongholicus Bunge (High dose)_rep2

description: sample 1-2-5


title: Jurkat_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep1

description: sample 1-3-4


title: Mesenteric lnn, day5, PigID_121

city: Copenhagen

first: Malene

middle: Roed

last: Spiegelhauer

address: Dyrlaegevej 68

country: Denmark

institute: University of Copenhagen

data_processing:
The libraries were sequenced on the Illumina Novaseq 6000 instrument A01426, flowcell ID H73WJDSX2. Original data was transformed to raw reads by CASAVA base recognition (base calling).
Quality was checked and adapter trimming performed.
Raw data are stored in FASTQ format files, and contain sequences of reads and corresponding quality
Paired-end clean reads were aligned to the reference genome using HISAT2 v2.0.5
Featurecounts v1.5.0-p3 was used to counts the reads numbers mapped to each gene. Differential expression was analysed with the DESeq2 R package (1.20.0)
Assembly: ncbi_sus_scrofa_gcf_000003025_6_sscrofa11_1
Supplementary files format and content: txt of read counts.
Supplementary files format and content: txt of FPKM counts.

organism: Sus scrofa

source_name: Mesenteric lymph node

growth_protocol: Preterm pigs delivered by C-section were kept in NICU for five days. They were nourished with parenteral nutrition and fed enteral nutrition.

extract_protocol:
Mesenteric lymph nodes were collected immediately after euthanasia and snap-frozen in liquid nitrogen. 20-25 mg of the tissue was homogenized, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Copenhagen, Denmark).
Library was constructed by Novogene NGS RNA Library prep set. Messenger RNA was purified from extracted RNA with poly-T magnetic beads, and cDNA was synthesized using random hexamer primers.

treatment_protocol: On day 1 and 2, piglets received an oral dose of either native fecal virome (nFV), chemostat-propagated virome (cFV), chemostat-propagated virome with oligosaccharides (cFV-OS), or a specific phage cocktail (sPC). The control group received a sterile buffer (SM)

tag: tissue

value: Mesenteric lymph node

tag: animal id

value: cFV-OS


title: Jurkat_Water extract of Astragalus mongholicus Bunge (High dose)_rep1

description: sample 1-2-4


title: Jurkat_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep3

description: sample 1-2-3

value: Water extract of Panax ginseng C. A. Meyer 125 μg/mL


title: Mesenteric lnn, day5, PigID_124

value: cFV


title: Jurkat_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep2

description: sample 1-2-2


title: Mesenteric lnn, day5, PigID_114


title: Mesenteric lnn, day5, PigID_108


title: Mesenteric lnn, day5, PigID_104

value: SM


title: Jurkat_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep1

description: sample 1-2-1


title: Jurkat_Water extract of Panax ginseng C. A. Meyer (High dose)_rep3

description: sample 1-1-12

value: Water extract of Panax ginseng C. A. Meyer 500 μg/mL


title: Jurkat_Water extract of Panax ginseng C. A. Meyer (High dose)_rep2

description: sample 1-1-11


title: Jurkat_Water extract of Panax ginseng C. A. Meyer (High dose)_rep1

description: sample 1-1-10


title: PBMC; SeqWell; Animal T627; Timepoint ART3; Array 3C

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 77 Massachusetts Ave

country: USA

institute: Massachusetts Institute of Technology

description:
Library name: T627_ART3_3C
T627_ART3_3C

library_source: transcriptomic single cell

data_processing:
BCL files were converted to fastQs via Terra cumulus/bcl2fastq/5
For processed data: A custom genome combining  mmul10 and SIVmac251 was created using jgould/dropseq_bundle/10 (Terra). Alignment was performed using cumulus/dropseq_workflow/11 (Terra).
Assembly: custom mmul10 + SIVmac251
Supplementary files format and content: RDS, a seurat object of all cells combined from all samples directly following alignment (untrimmed, filtered)

molecule: polyA RNA

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
PBMC samples from rhesus macaque were processed for single-cell analysis using SeqWellS3 as described in Hughes, et al; Immunity 2020.
scRNAseq libraries were prepared via NexteraXT as described in Hughes, et al; Immunity 2020

value: PBMC

tag: animalid

tag: timepoint

tag: array

tag: assay

value: SeqWell

tag: hassiv

value: yes

tag: onart

tag: weekssinceinfection

tag: weeksonart


title: Jurkat_Water extract of BJIKT (Low dose)_rep3

description: sample 1-1-9

value: Jurkat

value: T lymphoblast

value: Water extract of BJIKT 125 μg/mL


title: Jurkat_Water extract of BJIKT (Low dose)_rep2

description: sample 1-1-8


title: Jurkat_Water extract of Astragalus mongholicus Bunge (Low dose)_rep3

description: sample 1-2-9


title: Jurkat_Water extract of Atractylodes japonica Koidzumi (High dose)_rep1

description: sample 1-2-10


title: Jurkat_Water extract of BJIKT (Low dose)_rep1

description: sample 1-1-7


title: PBMC; SeqWell; Animal T623; Timepoint ART3; Array 6F

description:
Library name: T623_ART3_6F
T623_ART3_6F


title: Jurkat_Water extract of BJIKT (High dose)_rep2

description: sample 1-1-5

value: Water extract of BJIKT 500 μg/mL


title: Jurkat_Water extract of BJIKT (High dose)_rep1

description: sample 1-1-4


title: Jurkat_Vehicle(PBS)_rep3

description: sample 1-1-3

value: PBS


title: Jurkat_Vehicle(PBS)_rep2

description: sample 1-1-2


title: Mature DC_Mixture of water extracts of four ingredients_rep3

description: sample 5-3-12

source_name: Mature DC

growth_protocol: THP-1 cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and maintained in the medium recommended by the ATCC with 100 IU penicillin, and 100 µg/mL streptomycin in a humidified incubator. When cells reached 80–90% confluency, the growth medium was replaced every 3~4 days. Mycoplasma contamination was checked using the MycoAlert PLUS mycoplasma detection kit (Lonza, Rockland, ME, USA) and passed all. Dendritic cells was differentiated using THP-1 according to the protocol. To generate mature dendritic cells, THP-1 cells were incubated with 100ng/mL of GM-CSF (Acrobiosystems, GMF-H4214, Newark, De, USA), 200ng/mL of IL-4 (Acrobiosystems, IL4-H4218), 20ng/mL of TNF-a (Acrobiosystems, TNA-H421) and 200ng/mL of ionomycin (Sigma, I9657) for 3 days

treatment_protocol: To determine the maximum concentration, we performed cell cytotoxicity tests and all drugs did not influence cell viability. The highest treatment concentrations (500ug/mL) were selected considering the solubility and clinical application of the drugs. To confirm the influence of concentration, we treated the cells with two concentrations (500 and 125 ug/mL). The cells treated with PBS were used as the vehicle control. THP-1 cell was plated and differenciated to dendritc cell at a density of 1x106 cells / well in a 12-well microplate and treated with two concentrations of drugs. After 24 hours, cells were washed two times with ice-cold PBS, and total RNA was isolated using QIAzol RNA Isolation Reagents (Thermo Fisher Scientific) according to the manufacturer's instructions.

value: Mature DC

value: dendritic cell

value: Total 500ug/mL, 125ug/mL of each of the 4 ingredients mixed


title: Jurkat_Vehicle(PBS)_rep1

description: sample 1-1-1


title: S010_CD4_CXCR5pos_PD1int

status: Public on Aug 02 2026

first: Vinay

middle: S

last: Mahajan

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

description: Library name: S010_CD4_CXCR5pos_PD1int

library_source: genomic

data_processing:
Sequencing reads were aligned to hg38 using Bowtie2
Accessible peaks / regions were identified using macs2
Assembly: hg38
Supplementary files format and content: narrowPeak.bed (peak file in bed format)
Supplementary files format and content: bw (bigwig files, fraom ATAC-seq alignment to hg38)

molecule: genomic DNA

source_name: tonsil

extract_protocol:
Cells were FACS-sorted, stored on ice, and prompty processed for ATAC-seq
ATAC-seq: nuclei were isolated and tagmented in 10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% IGEPAL CA-630 for 30 min at 37 degrees C as described in Buenrostro et al., 2013 (PMID: 24097267). Tagmented DNA was purified with Qiagen MinElute PCR purification kit, indexed and amplfied for sequencing.

value: tonsil

value: CD4+ CXCR5pos PD1int


title: R1_ESCs_c3_n2_PCS_R10

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

country: Canada

institute: CHU de Québec - Université Laval

description: Library name: Sample 43

data_processing:
Raw fast5 files from R9 sequencing were converted to the more recent pod5 format using the pod5-file-format software from nanoporetech's github. pod5 files from R9 and R10 libraries files were then basecalled using Guppy v.6.5.7 using the super accurate basecalling settings.
Samples were demultiplexed according to barcodes with the guppy_barcoder software.
The resulting FASTQ reads were aligned to the mm10 mouse reference genome with Minimap2 version 2.24-r1122. Reads with MAPQ<13 were filtered out.
Aligned reads were quality-controlled with the NanoPlot software.
Strand for spliced transcripts were detemined using Minimap2's ts tag ("transcript strand"). As this tag is empty for mono-exonic transcripts, these were oriented with the pychopper software from nanoporetech's github. Stranded BAM files are provided as raw files (..._sup.XS_tag.bam files)
Transcriptome assembly was performed using the Tama software, with the tama_collapse.py script.
Isoform classification was performed on the transcriptome assembly using the SQANTI3 software. SQANTI3 QC was used to classify isoforms. Artifactual isoforms were then filtered using SQANTI3 filter with the "Rules filter" using default rules. Filtered-out isoforms were then rescued using SQANTI3 rescue. A final filter was performed to remove isoforms without a detected polyA as well as isoforms derived from RT-switching events.
Read counts were performed using the Isoquant software, using the previously generated and filtered transcriptome assembly.
Assembly: mm10
Supplementary files format and content: GSE282319_Isoquant.gene_name_id.cpm.txt.gz: Normalized gene-level read counts (in Counts per million, CPM) obtained with the Isoquant software. Annotation file used for this analysis was the "Repro_filter_tst.gtf" file included as a processed data file.
Supplementary files format and content: GSE282319_Isoquant.transcript_name_id.tpm.txt.gz: Normalized transcript-level read counts (in Transcripts per million, TPM) obtained with the Isoquant software. Annotation file used for this analysis was the "Repro_filter_tst.gtf" file included as a processed data file.
Supplementary files format and content: GSE282319_Repro_filter_tst.gtf.gz: Filtered transcriptome annotation file generated with the Tama software from the long-read RNA sequencing data presented here and filtered with the SQANTI3 pipeline.
Supplementary files format and content: GSE282319_Repro_unfiltered_tst.gtf.gz: Transcriptome annotation file generated with the Tama software from the long-read RNA sequencing data presented here (before isoform QC and filtering).
Supplementary files format and content: GSE282319_Repro_unfiltered_tst_classification.txt.gz: SQANTI3 classification file for GSE282319_Repro_unfiltered_tst.gtf.gz transcriptome annotation.

organism: Mus musculus

growth_protocol: Stably transfected Oct4-GFP ESC-derived NPC cell lines were grown in NPC medium on Geltrex™-coated plates (hESC-qualified, growth factor-reduced, ThermoFisher Scientific, #A1413302). NPC medium consists of N2B27 medium with added supplements. N2B27 medium consists of a 1:1 mixture of DMEM/F-12 media mix (ThermoFisher Scientific #11330057) supplemented with 1X N-2 supplement (ThermoFisher Scientific #17502048) and 20μg/mL human recombinant Insulin (ThermoFisher Scientific #12585014), and Neurobasal™ media (ThermoFisher Scientific #21103049) supplemented with 1X B-27™ supplement (ThermoFisher Scientific #17504044), 1mM sodium pyruvate (ThermoFisher Scientific #11360070), 2mM L-glutamine (ThermoFisher Scientific #35050061), 1X MEM Non-Essential Amino Acid solution (ThermoFisher Scientific #11140050) and 10-4M 2-Mercaptoethanol (ThermoFisher Scientific #21985023). Supplements to add for NPC media : 20ng/mL human recombinant EGF, 20ng/mL human recombinant FGF-2 and 500ng/mL heparin sodium salt. Medium was refreshed every other day and NPCs were passaged every 2-3 days. For passaging, cells were washed with DPBS (ThermoFisher Scientific #14190250) and treated with StemPro™ Accutase™ Cell Dissociation Reagent (ThermoFisher Scientific #A1110501) for 5 minutes. Then, StemPro™ Accutase™ Cell Dissociation Reagent was neutralized using DMEM (high glucose, ThermoFisher Scientific #11965118) with 5% KSR (ThermoFisher Scientific #10828-028) and cells were passaged as single-cells (usually 1/6-1/8 ratio). All cell lines were maintained in a humidified incubator at 37°C under 5% CO2 and were negative for mycoplasma.

extract_protocol:
Cell lysates were homogenized with QIAshredder columns (Qiagen #79656) and total RNA was extracted using RNeasy Kit (Qiagen #74106) according to the manufacturer’s instructions. RNA was quantified using a NanoDropTM 2000 Spectrophotometer (ThermoFisher #ND-2000C) and then DNase-treated using TURBOTM DNase (ThermoFisher Scientific #AM2238) according to the manufacturer’s instructions. 300ng of DNase-treated and non-treated RNA were loaded onto a 1% Agarose A (Bio Basic #D0012) gel to verify the RNA integrity and purity. RNA was also quantified using the Qubit™ RNA Broad Range Kit (ThermoFisher Scientific #Q10210) on Qubit™ 4 Fluorometer (ThermoFisher Scientific #Q33238) according to the manufacturer’s instructions. RNA quality was further verified using an RNA 6000 Nano Kit (Agilent Technologies #5067-1511) on a 2100 Bioanalyzer instrument (Agilent Technologies #G2939B) according to the manufacturer’s instructions. Samples all had RNA integrity numbers of 7.8 or more. For samples sequenced on R9 Flow Cells, polyadenylated RNA was enriched from 7.5-20μg of total RNA using NEB®Next Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and a DynaMag™-2 Magnet (ThermoFisher Scientific #12-321-D). PolyA+-enriched RNA was quantified using the Qubit™ RNA High Sensitivity Kit (ThermoFisher Scientific #Q32852) on Qubit™ 4 Fluorometer according to the manufacturer’s instructions and RNA quality was verified using an RNA 6000 Pico Kit (Agilent Technologies #5067-1513) on a 2100 Bioanalyzer instrument according to the manufacturer’s instructions. For samples sequenced on R10 Flow Cells, total RNA was used for RT (Poly(A) enrichment step was omitted).
R9 samples were processed with Oxford Nanopore Technologies' (ONT) SQK-DCS109 kit according to the manufacturer's protocol: "Direct cDNA Native Barcoding (SQK-DCS109 with EXP-NBD104 and EXP-NBD114)" version DCB_9091_v109_revF_04Feb2019. 55-100ng of poly(A)+ RNA were used for each sample's RT reaction. Samples were barcoded with the ONT EXP-NBD104 native barcoding expansion. Barcoded samples were pooled, loaded on a MinION sequencer (ONT) using eight R9.4.1 Flow Cells (ONT #FLO-MIN106D), and sequenced using the MinKNOW (v19) software. Purification of DNA between each step was performed with KAPA Hyperpure Beads (Roche). Flow cells were washed and reloaded with the Flow Cell Wash Kit (ONT #EXP-WSH003) to increase sequencing depth obtained per flow cell. R10 samples were processed with ONT's SQK-NBD114.24 kit using 50ng of total RNA, with each sample assigned to a specific barcode. Briefly, an oligo-dT primer (VNP, sequence: 5'-5phos/ACTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTVN-3' , where V=A, C, or G, and N=A, C, G, or T) was used to reverse-transcribe poly(A) RNA into cDNA with the Maxima H Minus RT (ThermoFisher Scientific). A Strand Switching Primer (SSP 5'-TTTCTGTTGGTGCTGATATTGCTmGmGmG-3' , where mG = 2' O-Methyl RNA bases) was used for strand switching during the RT reaction. Libraries were PCR amplified for 14 cycles with LongAmp Taq polymerase (NEB #M0287) or NEBNext Ultra II Q5 Master Mix (NEB #M0544L). cDNA was quantified using the Qubit™ 1X dsDNA High Sensitivity Kit (ThermoFisher Scientific #Q33230) on Qubit™ 4 Fluorometer according to the manufacturer’s instructions and cDNA smear quality was verified using a DNA 12000 Kit (Agilent Technologies #5067-1508) on a 2100 Bioanalyzer instrument (Agilent Technologies #G2939B) according to the manufacturer’s instructions. The blunt DNA ends were prepared using the NEBNext Ultra II End Repair/dA-Tailing module (NEB), adding a 3' dA tail and phosphorylating the 5' end. Barcodes were ligated to the DNA fragments with a Blunt/TA ligase (NEB), barcoded samples were pooled and motor protein adapters were finally ligated with the NEBNext Quick Ligation Module (NEB). Purification of DNA between each step was performed with KAPA Hyperpure Beads (Roche). Library was loaded on a PromethION 2 Solo (ONT) sequencer using five R10.4.1 Flow Cells (ONT #FLO-PRO114M), and sequenced using the MinKNOW (v23.07.15) software.

treatment_protocol: Stably transfected Oct4-GFP ESC-derived NPC cell lines were seeded at 3 x 103 cells/cm2 on a 0.1% porcine gelatin (Sigma-Aldrich #G1890) coating in NPC medium supplemented with 2%  Fetal Bovine Serum (FBS) to promote adhesion. The following day, medium was replaced with FBS-LIF supplemented with 1µg/mL doxycycline hyclate (Sigma-Aldrich #D9891) to induce overexpression of the reprogramming factors. FBS-LIF medium consists of DMEM (high glucose, ThermoFisher Scientific #11965118) supplemented with 15% FBS, ThermoFisher Scientific #12483020), 1mM sodium pyruvate (ThermoFisher Scientific #11360070), 2mM L-glutamine (ThermoFisher Scientific #35050061), 1X MEM Non-Essential Amino Acid solution (ThermoFisher Scientific #11140050) and 10-4M 2-mercaptoethanol (ThermoFisher Scientific #21985023). Medium was refreshed every other day until D6. From D6, samples noted as "2i-LIF at D6" (D14 and D20) were maintained in 2i-LIF medium and passaged every 2-4 days depending on colonies density. 2i-LIF medium consists of Leukemia Inhibitory Factor (LIF, home-made from pGEX-2T-MLIF, Mereau et al., J. Cell. Biol. 1993) at 20ng/mL, 3μM CHIR-99021 (Selleck Chemicals #S2924) and 1μM PD0325901 (Selleck Chemicals #S1036) in N2B27 media. D10, D14 and D20 samples noted as "FBS-LIF + dox" were instead maintained in FBS-LIF medium supplemented with 1µg/mL doxycycline hyclate. For passaging or collection of time points, cells were washed with DPBS (ThermoFisher Scientific #14190250) and treated with TrypLE Express Enzyme (ThermoFisher Scientific #12604021) for 5 minutes. Then, TrypLE Express Enzyme was neutralized using DMEM (high glucose, ThermoFisher Scientific #11965118) with 5% KSR (ThermoFisher Scientific #10828-028) and cells were passaged as single-cells (1/3-1/30 ratio depending on density). Long-read RNAseq time points were pelletted and flash frozen in liquid nitrogen, then kept in a -80°C Bio-freezer until RNA extraction. Evolution of the proportion of mCherry+ and GFP+ cells was monitored using fluorescence microscopy and flow cytometry with a BD Accuri™ C6 Plus flow cytometer (BD Biosciences). iPSCs could readily be maintained in 2i-LIF medium after 20 days. All cell lines were negative for mycoplasma. Mouse ESC control lines are maintained in 2i-LIF medium. A clonally amplified line from the R1 cell line was also used as an mESC control (R1-Clone3). NPC control lines were maintained in NPC medium.

value: Embryonic stem cells

tag: genotype

value: WT


title: Mature DC_Mixture of water extracts of four ingredients_rep2

description: sample 5-3-11


title: Mature DC_Mixture of water extracts of four ingredients_rep1

description: sample 5-3-10


title: S002_CD4_naive

description: Library name: S002_CD4_naive

value: CD4+ naive


title: Mature DC_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep2

description: sample 5-3-8

value: Water extract of Glycyrrhiza uralensis Fisher 125 μg/mL


title: Mature DC_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep3

description: sample 5-3-6

value: Water extract of Glycyrrhiza uralensis Fisher 500 μg/mL


title: d18_2iL_OKMS_ctrl_PCS_R10

description: Library name: Sample 38

value: Reprogramming timeline to induced pluripotent stem cells

value: OKMS-Luciferase-AS


title: Mature DC_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep2

description: sample 5-3-5


title: Mature DC_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep3

description: sample 5-3-9


title: Mature DC_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep1

description: sample 5-3-4


title: Mature DC_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep3

description: sample 5-3-3

value: Water extract of Atractylodes japonica Koidzumi 125 μg/mL


title: Mature DC_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep1

description: sample 5-3-7


title: Mature DC_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep2

description: sample 5-3-2


title: NPCs_WT_Rep2_PCS_R10

extract_protocol:
Cell lysates were homogenized with QIAshredder columns (Qiagen #79656) and total RNA was extracted using RNeasy Kit (Qiagen #74106) according to the manufacturer’s instructions. RNA was quantified using a NanoDropTM 2000 Spectrophotometer (ThermoFisher #ND-2000C) and then DNase-treated using TURBOTM DNase (ThermoFisher Scientific #AM2238) according to the manufacturer’s instructions. 300ng of DNase-treated and non-treated RNA were loaded onto a 1% Agarose A (Bio Basic #D0012) gel to verify the RNA integrity and purity. RNA was also quantified using the Qubit™ RNA Broad Range Kit (ThermoFisher Scientific #Q10210) on Qubit™ 4 Fluorometer (ThermoFisher Scientific #Q33238) according to the manufacturer’s instructions. RNA quality was further verified using an RNA 6000 Nano Kit (Agilent Technologies #5067-1511) on a 2100 Bioanalyzer instrument (Agilent Technologies #G2939B) according to the manufacturer’s instructions. Samples all had RNA integrity numbers of 7.8 or more. For samples sequenced on R9 Flow Cells, polyadenylated RNA was enriched from 7.5-20μg of total RNA using NEB®Next Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and a DynaMag™-2 Magnet (ThermoFisher Scientific #12-321-D). PolyA+-enriched RNA was quantified using the Qubit™ RNA High Sensitivity Kit (ThermoFisher Scientific #Q32852) on Qubit™ 4 Fluorometer according to the manufacturer’s instructions and RNA quality was verified using an RNA 6000 Pico Kit (Agilent Technologies #5067-1513) on a 2100 Bioanalyzer instrument according to the manufacturer’s instructions. For samples sequenced on R10 Flow Cells, total RNA was used for RT (Poly(A) enrichment step was omitted).
R9 samples were processed with Oxford Nanopore Technologies' (ONT) SQK-DCS109 kit according to the manufacturer's protocol: "Direct cDNA Native Barcoding (SQK-DCS109 with EXP-NBD104 and EXP-NBD114)" version DCB_9091_v109_revF_04Feb2019. 55-100ng of poly(A)+ RNA were used for each sample's RT reaction. Samples were barcoded with the ONT EXP-NBD104 native barcoding expansion. Barcoded samples were pooled, loaded on a MinION sequencer (ONT) using eight R9.4.1 Flow Cells (ONT #FLO-MIN106D), and sequenced using the MinKNOW (v19) software. Purification of DNA between each step was performed with KAPA Hyperpure Beads (Roche). Flow cells were washed and reloaded with the Flow Cell Wash Kit (ONT #EXP-WSH003) to increase sequencing depth obtained per flow cell. R10 samples were processed with ONT's SQK-NBD114.24 kit using 50ng of total RNA, with each sample assigned to a specific barcode. Briefly, an oligo-dT primer (VNP, sequence: 5'-5phos/ACTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTVN-3' , where V=A, C, or G, and N=A, C, G, or T) was used to reverse-transcribe poly(A) RNA into cDNA with the Maxima H Minus RT (ThermoFisher Scientific). A Strand Switching Primer (SSP 5'-TTTCTGTTGGTGCTGATATTGCTmGmGmG-3' , where mG = 2' O-Methyl RNA bases) was used for strand switching during the RT reaction. Libraries were PCR amplified for 14 cycles with LongAmp Taq polymerase (NEB #M0287). cDNA was quantified using the Qubit™ 1X dsDNA High Sensitivity Kit (ThermoFisher Scientific #Q33230) on Qubit™ 4 Fluorometer according to the manufacturer’s instructions and cDNA smear quality was verified using a DNA 12000 Kit (Agilent Technologies #5067-1508) on a 2100 Bioanalyzer instrument (Agilent Technologies #G2939B) according to the manufacturer’s instructions. The blunt DNA ends were prepared using the NEBNext Ultra II End Repair/dA-Tailing module (NEB), adding a 3' dA tail and phosphorylating the 5' end. Barcodes were ligated to the DNA fragments with a Blunt/TA ligase (NEB), barcoded samples were pooled and motor protein adapters were finally ligated with the NEBNext Quick Ligation Module (NEB). Purification of DNA between each step was performed with KAPA Hyperpure Beads (Roche). Library was loaded on a PromethION 2 Solo (ONT) sequencer using two R10.4.1 Flow Cells (ONT #FLO-PRO114M), and sequenced using the MinKNOW (v23.07.15) software.

treatment_protocol: Stably transfected Oct4-GFP ESC-derived NPC cell lines were seeded at 3 x 103 cells/cm2 on a 0.1% porcine gelatin (Sigma-Aldrich #G1890) coating in NPC medium supplemented with 2%  Fetal Bovine Serum (FBS) to promote adhesion. The following day, medium was replaced with FBS-LIF supplemented with 1µg/mL doxycycline hyclate (Sigma-Aldrich #D9891) to induce overexpression of the reprogramming factors. FBS-LIF medium consists of DMEM (high glucose, ThermoFisher Scientific #11965118) supplemented with 15% FBS, ThermoFisher Scientific #12483020), 1mM sodium pyruvate (ThermoFisher Scientific #11360070), 2mM L-glutamine (ThermoFisher Scientific #35050061), 1X MEM Non-Essential Amino Acid solution (ThermoFisher Scientific #11140050) and 10-4M 2-mercaptoethanol (ThermoFisher Scientific #21985023). Medium was refreshed every other day until D6. From D6, samples noted as "2i-LIF at D6" (D14 and D20) were maintained in 2i-LIF medium and passaged every 2-4 days depending on colonies density. 2i-LIF medium consists of Leukemia Inhibitory Factor (LIF, home-made from pGEX-2T-MLIF, Mereau et al., J. Cell. Biol. 1993) at 20ng/mL, 3μM CHIR-99021 (Selleck Chemicals #S2924) and 1μM PD0325901 (Selleck Chemicals #S1036) in N2B27 media. D10, D14 and D20 samples noted as "FBS-LIF + dox" were instead maintained in FBS-LIF medium supplemented with 1µg/mL doxycycline hyclate. For passaging or collection of time points, cells were washed with DPBS (ThermoFisher Scientific #14190250) and treated with TrypLE Express Enzyme (ThermoFisher Scientific #12604021) for 5 minutes. Then, TrypLE Express Enzyme was neutralized using DMEM (high glucose, ThermoFisher Scientific #11965118) with 5% KSR (ThermoFisher Scientific #10828-028) and cells were passaged as single-cells (1/3-1/30 ratio depending on density). Long-read RNAseq time points were pelletted and flash frozen in liquid nitrogen, then kept in a -80°C Bio-freezer until RNA extraction. Evolution of the proportion of mCherry+ and GFP+ cells was monitored using fluorescence microscopy and flow cytometry with a BD Accuri™ C6 Plus flow cytometer (BD Biosciences). iPSCs could readily be maintained in 2i-LIF medium after 20 days. All cell lines were negative for mycoplasma. Mouse ESC control lines are maintained in 2i-LIF medium. NPC control lines were maintained in NPC medium.

value: Neural progenitor cells

value: NPC medium


title: Mature DC_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep1

description: sample 5-3-1


title: Mature DC_Water extract of Atractylodes japonica Koidzumi (High dose)_rep3

description: sample 5-2-12

value: Water extract of Atractylodes japonica Koidzumi 500 μg/mL


title: Mature DC_Water extract of Atractylodes japonica Koidzumi (High dose)_rep2

description: sample 5-2-11


title: d6_OKMS_ctrl_PCS_R10

value: FBS-LIF + dox


title: Mature DC_Water extract of Atractylodes japonica Koidzumi (High dose)_rep1

description: sample 5-2-10

value: Mature DC


title: Mature DC_Water extract of Astragalus mongholicus Bunge (Low dose)_rep2

description: sample 5-2-8

value: dendritic cell

value: Water extract of Astragalus mongholicus Bunge 125 μg/mL


title: Mature DC_Water extract of Astragalus mongholicus Bunge (High dose)_rep3

description: sample 5-2-6

value: Water extract of Astragalus mongholicus Bunge 500 μg/mL


title: Mature DC_Water extract of Astragalus mongholicus Bunge (Low dose)_rep1

description: sample 5-2-7


title: Mature DC_Water extract of Astragalus mongholicus Bunge (Low dose)_rep3

description: sample 5-2-9


title: Mature DC_Water extract of Astragalus mongholicus Bunge (High dose)_rep1

description: sample 5-2-4


title: Mature DC_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep3

description: sample 5-2-3

value: Water extract of Panax ginseng C. A. Meyer 125 μg/mL


title: Mature DC_Water extract of Astragalus mongholicus Bunge (High dose)_rep2

description: sample 5-2-5


title: Mature DC_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep2

description: sample 5-2-2


title: Mature DC_Water extract of Panax ginseng C. A. Meyer (High dose)_rep2

description: sample 5-1-11

value: Water extract of Panax ginseng C. A. Meyer 500 μg/mL


title: Mature DC_Water extract of Panax ginseng C. A. Meyer (High dose)_rep1

description: sample 5-1-10


title: Mature DC_Water extract of Panax ginseng C. A. Meyer (High dose)_rep3

description: sample 5-1-12


title: Mature DC_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep1

description: sample 5-2-1


title: Mature DC_Water extract of BJIKT (Low dose)_rep3

description: sample 5-1-9

value: Water extract of BJIKT 125 μg/mL


title: Mature DC_Water extract of BJIKT (Low dose)_rep2

description: sample 5-1-8


title: Mature DC_Water extract of BJIKT (Low dose)_rep1

description: sample 5-1-7


title: Mature DC_Water extract of BJIKT (High dose)_rep3

description: sample 5-1-6

value: Water extract of BJIKT 500 μg/mL


title: Mature DC_Water extract of BJIKT (High dose)_rep2

description: sample 5-1-5


title: Mature DC_Water extract of BJIKT (High dose)_rep1

description: sample 5-1-4


title: Mature DC_Vehicle(PBS)_rep3

description: sample 5-1-3

value: PBS


title: Mature DC_Vehicle(PBS)_rep2

description: sample 5-1-2


title: M1MO_Mixture of water extracts of four ingredients_rep2

description: sample 4-3-11

growth_protocol: THP-1 cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and maintained in the medium recommended by the ATCC with 100 IU penicillin, and 100 µg/mL streptomycin in a humidified incubator. When cells reached 80–90% confluency, the growth medium was replaced every 3~4 days. Mycoplasma contamination was checked using the MycoAlert PLUS mycoplasma detection kit (Lonza, Rockland, ME, USA) and passed all. Macrophages was differentiated using THP-1 according to the protocol. THP-1 monocyte was differentiated into M0 stage macrophages by 24 h incubation with 150 nM phorbol 12-myristate 13-acetate (PMA, Sigma, P8139). M0 Macrophages differentiated with PMA were polarized in M1 macrophages by incubation with 20 ng/ml of IFN-γ (Sigma, I17001) and 10 pg/ml of LPS (Thermo Fisher Scientific, 00-4976-93) for 48h.

treatment_protocol: To determine the maximum concentration, we performed cell cytotoxicity tests and all drugs did not influence cell viability. The highest treatment concentrations (500ug/mL) were selected considering the solubility and clinical application of the drugs. To confirm the influence of concentration, we treated the cells with two concentrations (500 and 125 ug/mL). The cells treated with PBS were used as the vehicle control. THP-1 cell was plated and differenciated to macrophage at a density of 5x105 cells / well in a 12-well microplate and treated with two concentrations of drugs. After 24 hours, cells were washed two times with ice-cold PBS, and total RNA was isolated using QIAzol RNA Isolation Reagents (Thermo Fisher Scientific) according to the manufacturer's instructions.

value: Macrophage

value: Total 500ug/mL, 125ug/mL of each of the 4 ingredients mixed


title: M1MO_Mixture of water extracts of four ingredients_rep3

description: sample 4-3-12


title: Mature DC_Vehicle(PBS)_rep1

description: sample 5-1-1


title: M1MO_Mixture of water extracts of four ingredients_rep1

description: sample 4-3-10


title: M1MO_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep1

description: sample 4-3-7

value: Water extract of Glycyrrhiza uralensis Fisher 125 μg/mL


title: HUVECs, Ad5-S-3M, 72 h, biol rep 1

city: Kuopio

first: Nihay

last: Laham Karam

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description: Library name: HUVEC_AdS-3M_72h_1

data_processing:
RNA-seq data was trimmed using the following tools: Trimmomatic (v.0.36) for quality trimming the reads (LEADING:5 TRAILING:5 MINLEN:36), HOMER (v.4.10) to trim poly-A ends (-3 AAAAAAAA -mis 1 -min 36).
Reads were aligned using STAR (v.2.7.9) to map to the genome (hg38).
DESeq2  was used for differential gene expression analysis using the commands from HOMER. Reads were counted only if their direction matched the transcript (”-strand +”) and only one identical read was accepted (”-pc 1”).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw read counts that have been transformed with DESeq2's rlog

source_name: primary HUVEC

growth_protocol: HUVECs were maintained in endothelial cell growth medium (ECGM; PromoCell) with the provided SupplementMix (PromoCell) as well as 30 µg/ml gentamicin and 15 ng/ml amphotericin B antibiotic (Lonza). The plates used for culturing HUVECs were coated with a solution of 10 µg/ml fibronectin (Corning) and 0.05 % gelatin (Sigma Aldrich) in PBS at 37 °C for at least 5 min, before removing the solution and plating the cells. Cells were cultured at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen). 5000 ng of RNA was DNase-treated using the TURBO DNA-free kit (Invitrogen) in a total reaction volume of 25 µl. Of Dnase-treated RNA, 500 ng was used for sequencing library construction.
RNA libraries for RNA sequencing were constructed using QuantSeq 3′ mRNA-Seq FWD and Unique Dual Indexing (UDI) 12 nt Kits (Lexogen), according to the manufacturer’s instructions.

treatment_protocol: HUVECs were transduced with multiplicity of infection ratio of 125 viral particles/cell one day after plating, and the Ad5 vectors were incubated on the cells for 4 h, after which the media was changed. RNA extraction followed 72 h after the transduction.

value: primary HUVEC

value: endothelial cell

value: WT

value: Ad5-S-3M transduction

tag: batch


title: zebrafish_FACS_purified_cranial_motor_neurons_48hpf_biorep_01_lane2

city: Seattle

first: Austin

last: Seroka

state: WA

address: 1100 Fairview Ave. North

department: Basic Sciences

institute: Fred Hutchinson Cancer Center

description:
Library name: 48_3_Lane2
10X Genomics Chromium 3' mRNA v3

data_processing:
The demultiplexing, barcoded processing and gene counting were done using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Danio_rerio.GRCz11.dna.primary_assembly
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: FACS purified hindbrain

extract_protocol:
Tg:(isl1:kaede) embryos were raised to 24, 48, 72 or 144hpf respectively prior to anesthetization in 400mg/L MESAB. Hindbrains were dissected in Calcium-Free Ringers / EDTA / 10% MESAB, prior to dissociation to single-cell suspension by pipetting in 0.25% trypsin-EDTA for 5 minutes. Cells were briefly spun down, transferred to dPBS + BSA and passed through a 40uM filter. Prior to FACS, cell health was evaluated using 2pg/mL DAPI. Kaede+ cells were isolated on a BD FACS ARIA II flow cytometer using a 100uM nozzle and collected into dPBS + 2% BSA. Collected cells were concentrated by centrifugation at 300 x g for 5 minutes at 4°C and resuspended to an optimal concentration of 1,200 cells/uL. Cell viability was assessed using a TC20 Automated Cell Counter. Libraries were prepared using the 10X Genomics Chromium 3’ mRNA v3 kit, prior to sequencing on a Novaseq S1 Flowcell
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction.

value: FACS purified hindbrain


title: M1MO_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep1

description: sample 4-3-4

value: Water extract of Glycyrrhiza uralensis Fisher 500 μg/mL


title: M1MO_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep2

description: sample 4-3-5


title: M1MO_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep3

description: sample 4-3-9


title: M1MO_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep2

description: sample 4-3-8


title: M1MO_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep3

description: sample 4-3-3

value: Water extract of Atractylodes japonica Koidzumi 125 μg/mL


title: M1MO_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep3

description: sample 4-3-6


title: M1MO_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep2

description: sample 4-3-2


title: M1MO_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep1

description: sample 4-3-1


title: M1MO_Water extract of Atractylodes japonica Koidzumi (High dose)_rep3

description: sample 4-2-12

value: Water extract of Atractylodes japonica Koidzumi 500 μg/mL


title: M1MO_Water extract of Atractylodes japonica Koidzumi (High dose)_rep2

description: sample 4-2-11


title: M1MO_Water extract of Atractylodes japonica Koidzumi (High dose)_rep1

description: sample 4-2-10


title: M1MO_Water extract of Astragalus mongholicus Bunge (Low dose)_rep2

description: sample 4-2-8

value: Water extract of Astragalus mongholicus Bunge 125 μg/mL


title: M1MO_Water extract of Astragalus mongholicus Bunge (Low dose)_rep3

description: sample 4-2-9


title: M1MO_Water extract of Astragalus mongholicus Bunge (Low dose)_rep1

description: sample 4-2-7


title: M1MO_Water extract of Astragalus mongholicus Bunge (High dose)_rep3

description: sample 4-2-6

value: Water extract of Astragalus mongholicus Bunge 500 μg/mL


title: M1MO_Water extract of Astragalus mongholicus Bunge (High dose)_rep1

description: sample 4-2-4


title: M1MO_Water extract of Astragalus mongholicus Bunge (High dose)_rep2

description: sample 4-2-5


title: M1MO_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep2

description: sample 4-2-2

value: Water extract of Panax ginseng C. A. Meyer 125 μg/mL


title: M1MO_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep3

description: sample 4-2-3


title: M1MO_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep1

description: sample 4-2-1


title: M1MO_Water extract of Panax ginseng C. A. Meyer (High dose)_rep3

description: sample 4-1-12

value: Water extract of Panax ginseng C. A. Meyer 500 μg/mL


title: M1MO_Water extract of Panax ginseng C. A. Meyer (High dose)_rep2

description: sample 4-1-11


title: M1MO_Water extract of BJIKT (High dose)_rep3

description: sample 4-1-6

value: Water extract of BJIKT 500 μg/mL


title: M1MO_Water extract of BJIKT (Low dose)_rep1

description: sample 4-1-7

value: Water extract of BJIKT 125 μg/mL


title: RPMI8226_Water extract of Astragalus mongholicus Bunge (High dose)_rep2

description: sample 2-2-5

growth_protocol: RPMI8226 cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and maintained in the medium recommended by the ATCC with 100 IU penicillin, and 100 µg/mL streptomycin in a humidified incubator. When cells reached 80–90% confluency, the growth medium was replaced every 3~4 days. Mycoplasma contamination was checked using the MycoAlert PLUS mycoplasma detection kit (Lonza, Rockland, ME, USA) and passed all.

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 (500 ng) 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 e MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: To determine the maximum concentration, we performed cell cytotoxicity tests and all drugs did not influence cell viability. The highest treatment concentrations (500ug/mL) were selected considering the solubility and clinical application of the drugs. To confirm the influence of concentration, we treated the cells with two concentrations (500 and 125 ug/mL). The cells treated with PBS were used as the vehicle control. Cells were plated at a density of 5x105 cells / well in a 12-well microplate and treated with two concentrations of drugs. After 24 hours, cells were washed two times with ice-cold PBS, and total RNA was isolated using QIAzol RNA Isolation Reagents (Thermo Fisher Scientific) according to the manufacturer's instructions.

value: B lymphocyte


title: M1MO_Water extract of Panax ginseng C. A. Meyer (High dose)_rep1

description: sample 4-1-10

value: Macrophage


title: M1MO_Water extract of BJIKT (Low dose)_rep2

description: sample 4-1-8


title: M1MO_Vehicle(PBS)_rep1

description: sample 4-1-1

value: PBS


title: NK-92MI_Mixture of water extracts of four ingredients_rep3

description: sample 3-3-12

growth_protocol: NK-92MI cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and maintained in the medium recommended by the ATCC with 100 IU penicillin, and 100 µg/mL streptomycin in a humidified incubator. When cells reached 80–90% confluency, the growth medium was replaced every 3~4 days. Mycoplasma contamination was checked using the MycoAlert PLUS mycoplasma detection kit (Lonza, Rockland, ME, USA) and passed all.

value: natural killer cell

value: Total 500ug/mL, 125ug/mL of each of the 4 ingredients mixed


title: NK-92MI_Mixture of water extracts of four ingredients_rep1

description: sample 3-3-10


title: NK-92MI_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep2

description: sample 3-3-8

value: Water extract of Glycyrrhiza uralensis Fisher 125 μg/mL


title: NK-92MI_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep1

description: sample 3-3-7


title: NK-92MI_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep3

description: sample 3-3-6


title: Piezo1KO_BMDM_D3_rep2

city: Boston

first: Yizhong

last: Hu

address: 190 Longwood Ave.

institute: Harvard School of Dental Medicine

description: Library name: KO2

data_processing:
Sequence alignment were performed using STAR aligner. Paired reads were then counted using ‘featureCounts’ in The Subread software Raw counts were normalized using the edgeR package Assembly: mm10 Supplementary files format and content: csv file includes raw counts for each sample
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files containing gene-level raw read counts and normalized expression values for all samples. Rows correspond to genes and columns correspond to individual biological replicates.

source_name: primary

growth_protocol: Bone marrow-derived monocytes (BMDMs) were isolated from femurs and tibias of 12-week-old female mice. Bone marrow cells were cultured in complete α-MEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Non-adherent cells were collected after 2 days and cultured in the presence of 30 ng/mL M-CSF to generate osteoclast precursors.

extract_protocol:
Total RNA was extracted from differentiated osteoclast precursors using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. Genomic DNA was removed using the RapidOut DNA Removal Kit (Thermo Fisher Scientific). RNA quantity and quality were assessed prior to library preparation.
Poly(A)+ RNA was isolated from 400–1000 ng total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Sequencing libraries were generated using the xGen RNA Library Prep Kit (Integrated DNA Technologies) according to the manufacturer's instructions. Barcoded libraries were sequenced on an Illumina NextSeq platform using paired-end 2 × 45 bp reads.

treatment_protocol: BMDMs were differentiated toward the osteoclast lineage by culture in α-MEM containing 30 ng/mL M-CSF and 50 ng/mL RANKL. Cells were harvested after 3 days of differentiation for RNA sequencing. Samples were obtained from female wild-type (Piezo1fl/fl) and monocyte-specific Piezo1 conditional knockout (Csf1r-iCre;Piezo1fl/fl) mice.

value: bone marrow

value: bone marrow derived monocyte

value: Osteoclast differentiation induced by M-CSF and RANKL,


title: NK-92MI_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep1

description: sample 3-3-4

value: Water extract of Glycyrrhiza uralensis Fisher 500 μg/mL


title: Piezo1KO_BMDM_D3_rep1

description: Library name: KO1


title: NK-92MI_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep2

description: sample 3-3-5


title: WT_BMDM_D3_rep2

description: Library name: CT2


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-NT (rep3)

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 450 Serra Mall

department: Genetics

institute: Stanford University

description:
Library name: WTC11_NT_WCE_rep3
Whole cell extract (input control) for CTCF ChIP-seq

data_processing:
FASTQ files were processed using the ENCODE ChIP-seq pipeline (v2; https://github.com/ENCODE-DCC/chip-seq-pipeline2). Filtered BAM files generated by the pipeline were converted to bedGraph format using bedtools genomecov67, with the signal scaled by sequencing depth (bedtools genomecov -ibam ~{bam} -bg -scale ~{scale_factor} -pc | sort -k1,1 -k2,2n > ~{sample_name}.bedGraph). The resulting bedGraph files were subsequently converted to bigWig format using the UCSC bedGraphToBigWig utility68. CTCF signal intensity at the regions of interest was quantified using the pyBigWig Python library (source code available on GitHub). CTCF motifs were annotated using the JASPAR track from the UCSC Genome Browser (hg38; https://hgdownload.soe.ucsc.edu/gbdb/hg38/jaspar/JASPAR2024.bb), specifically filtering for the CTCF motif ID MA0139 (source code available on GitHub).
Assembly: human hg38
Supplementary files format and content: bigWig files

growth_protocol: We grew K562 cells harboring dCas9-KRAB  in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA) with 10% heat-inactivated FBS (HIFBS (Thermo Fisher Scientific), 2 mM L-glutamine, and 100 units/ml streptomycin and 100 mg/ml penicillin. We maintained K562 cells at a density between 100K and 1M per mL. We seeded human iPS cells (WTC11) harboring dCas9-KRAB in 6-well plates coated with 1:100 LDEV-Free Reduced Growth Factor Basement Membrane Matrix (Thermo Fisher Scientific). The culture medium used was StemFlex Medium supplemented with 10% StemFlex supplement (SF complete media, Thermo Fisher Scientific), 2 µl of Normacin per ml of media (1:500 final, Invivogen), and 0.4 µl of 10 mM Rock Inhibitor (Y-27632 Dihydrochloride, STEMCELL Technologies). After 24 hours of seeding, we continued to maintain the cells with SF complete media without Rock Inhibitor and passaged them with 1 ml of accutase (STEMCELL Technologies) as necessary, aiming to maintain an 80-90% confluence to prevent stacked cell growth.

extract_protocol:
Cells were harvested for ChIP-seq following ENCODE protocols. All CTCF ChIP-seq protocols are available at the ENCODE portal: https://www.encodeproject.org/chip-seq/transcription_factor/.
Libraries were constructed accroding to ENCODE protocols

tag: individual

value: iPSC

value: WTC11 iPSC clone carrying non-targeting control sgRNA NT1 (OligoID WTC11_Random_Screen_Crop_15807)

tag: chip antibody

value: none (input control)


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-NT (rep2)

description:
Library name: WTC11_NT_WCE_rep2
Whole cell extract (input control) for CTCF ChIP-seq

tag: cell line

tag: cell type


title: RPMI8226_Water extract of BJIKT (Low dose)_rep1

description: sample 2-1-7

tag: treatment

tag: time


title: WT_BMDM_D3_rep1

description: Library name: CT1

tag: tissue


title: NK-92MI_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep1

description: sample 3-3-1

value: Water extract of Atractylodes japonica Koidzumi 125 μg/mL


title: CTCF ChIP-seq in WTC11-NT (rep3)

description:
Library name: WTC11_NT_rep3
CRISPR clonal validation ChIP-seq for CTCF binding

value: CTCF


title: CTCF ChIP-seq in WTC11-NT (rep2)

description:
Library name: WTC11_NT_rep2
CRISPR clonal validation ChIP-seq for CTCF binding


title: NK-92MI_Water extract of Atractylodes japonica Koidzumi (High dose)_rep3

description: sample 3-2-12

value: Water extract of Atractylodes japonica Koidzumi 500 μg/mL


title: Sham bone marrow

city: WINSTON SALEM

first: Yang

last: Yu

state: NC

address: 1 Medical Center Blvd

department: Cancer Biology

institute: Wake Forest University

description:
Library name: Sample 3
10x Genomics

data_processing:
The Cell Ranger Single-Cell Software Suite v7.2 were used to perform sample de‐multiplexing, alignment, filtering, and UMI (i.e., unique molecular identifier) counting. The data for each respective subpopulation were aggregated for direct comparison of single-cell transcriptomes. Low‐quality cells identified as having less than 200 expressed genes were discarded. Cells with low viability were also removed if their proportions of mitochondrial gene expression are larger than 40%.
Assembly: Mouse mm10
Supplementary files format and content: Tab seperated values files and matrix files

source_name: Bone marrow

extract_protocol:
Bone marrow from ipsilateral femurs of male C57BL/6 mice (8–12 weeks of age) were dissected using centrifugation. Tumor dissociation was then performed using Tumor Dissociation Kit (Miltenyi Biotec, Cat. #: 130-096-730) according to the instructions. Briefly, cell pellets were transferred into Miltenyi C tubes containing dissociation buffer. Dissociation was running using the gentleMACS™ Octo Dissociator. Dissociated samples were filtered through 70 μm cell strainer and subjected to RBC removal. RBC removal was performed using Anti-Ter-119 MicroBeads (Miltenyi Biotec, Cat. #: 130-049-901), MS Columns (Miltenyi Biotec, Cat. #: 130-042-201), and QuadroMACS™ Separator (Miltenyi Biotec, Cat. #: 130-091-051). Briefly, cell pellet was incubated with Anti-Ter-119 MicroBeads and passed through MS Columns set on QuadroMACS™ Separator. Cells in flow-through were collected and subjected to sequencing.
Cells with >80% viability were loaded into wells of a 10X Chromium single-cell capture chip targeting a cell recovery rate of 2,000‐4,000 cells. Single‐cell gel beads in emulsion were created on a Chromium Single-Cell Controller and scRNA‐seq libraries were prepared using the Chromium Single-Cell 3’ Library and Gel Bead kit according to the manufacturer's protocol (10X Genomics). Sequencing libraries were loaded at 1.3 PM on an Illumina NextSeq500 with High Output 150 cycle kit for paired‐end sequencing using the following read length: 26 bp Read1, 8 bp i7 Index, 0 bp i5 Index, and 98 bp Read2.

value: Bone marrow


title: NK-92MI_Water extract of Atractylodes japonica Koidzumi (High dose)_rep2

description: sample 3-2-11


title: RPMI8226_Vehicle(PBS)_rep1

description: sample 2-1-1

value: B lymphocyte


title: RM1 Dorsal root ganglion

description:
Library name: Sample 2
10x Genomics

source_name: Dorsal root ganglion

extract_protocol:
Lumbar DRGs (L2-L4) of male C57BL/6 mice (8–12 weeks of age) were dissected and directly placed into a 15 mL conical tube, containing 14 mL of ice-cold HBSS. Isolated DRGs were enzymatically digested in 3 mL of papain solution (30 U/mL papain, 0.1% saturated NaHCO3 solution, 0.3 mg/mL L-Cys) in HBSS for 30 min at 37°C with 5% CO2, and then incubated in 3 mL of collagenase type II and Dispase II solution (4 mg/mL CLS2  and 4.7 mg/mL dispase) in HBSS for 30 min at 37°C with 5% CO2. The resulting DRGs were centrifuged at 200 × g for 2 min and washed with HBSS. The pellet was transferred to a 15 mL conical tube, containing 500 μL of neuronal growth medium with 1% N2, 2% B-27, 2 mM L-glutamine, 1% penicillin-streptomycin, and 0.4% glucose. The DRGs were triturated and filtered through a stainless mesh sieve (40 μm) to obtain single-cell suspensions and remove undigested tissue debris. BSA purification 3.5% (W/V) was performed by centrifugation at 14 × g for 20 min at room temperature to separate sensory neurons and debris.
Cells with >80% viability were loaded into wells of a 10X Chromium single-cell capture chip targeting a cell recovery rate of 2,000‐4,000 cells. Single‐cell gel beads in emulsion were created on a Chromium Single-Cell Controller and scRNA‐seq libraries were prepared using the Chromium Single-Cell 3’ Library and Gel Bead kit according to the manufacturer's protocol (10X Genomics). Sequencing libraries were loaded at 1.3 PM on an Illumina NextSeq500 with High Output 150 cycle kit for paired‐end sequencing using the following read length: 26 bp Read1, 8 bp i7 Index, 0 bp i5 Index, and 98 bp Read2.

value: Dorsal root ganglion

value: dorsal root ganglion


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-NC2 (rep1)

description:
Library name: NC2_WCE_rep1
Whole cell extract (input control) for CTCF ChIP-seq

value: WTC11 iPSC clone carrying legacy non-targeting control guide NC2 (OligoID NC1)


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-NC2 (rep3)

description:
Library name: NC2_WCE_rep3
Whole cell extract (input control) for CTCF ChIP-seq


title: CTCF ChIP-seq in WTC11-NC2 (rep3)

description:
Library name: NC2_rep3
CRISPR clonal validation ChIP-seq for CTCF binding


title: irradiated T cells, 1h after 1 Gy, mouse 4

type: RNA

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The probe-level raw expression data were processed by Illumina Genome Studio v2011.1. The probe average signal intensities were background subtracted, log2 transformed and quantile normalized to adjust for technical variation. Then the data were filtered by detection p-value ≤ 0.01 for at least 19 samples and batch effects among slides were removed by ComBat program. Processed data were imported into Partek Genomics Suite (v6.6) for statistical analysis.

label: biotin

source_name: irradiated T cells, 1h after 1 Gy

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Tumors were established in 8-12 week old female C57BL/6 mice by s.c. injection of 1x106 MC38 cells.

extract_protocol: Intratumoral CD8 T cells were pre-enriched from tumor cell suspensions using Easy Sep mouse CD8a positive selection kit (StemCell). CD8-enriched samples were stained with anti-CD3-PEcy7 and anti-CD8-PE antibodies and CD3+CD8+ cells were sorted in Trizol LS (Invitrogen) using a FACS Aria (BD). RNA was extracted using Trizol method according to the manufacturer’s instructions.

treatment_protocol: When tumors had reached at least 500 mm3, groups of 4 mice were treated with whole body irradiation (WBI) doses of 1 Gy or 5 Gy, or left untreated.

value: CD8+T cells

tag: strain

tag: age

value: 8-12 week

value: Intratumoral T cells


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-FAM111A-CTCF-G3 (rep3)

description:
Library name: FAM111A_CTCF_G3_WCE_rep3
Whole cell extract (input control) for CTCF ChIP-seq

value: WTC11 iPSC clone carrying individual CRISPR sgRNA G3 (OligoID WTC11_Random_Screen_Crop_3866) targeting a candidate CTCF-binding element near FAM111A


title: CTCF ChIP-seq in WTC11-NC2 (rep1)

description:
Library name: NC2_rep1
CRISPR clonal validation ChIP-seq for CTCF binding


title: irradiated T cells, 24h after 1 Gy, mouse 4

description: replicate 4

source_name: irradiated T cells, 24h after 1 Gy


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-FAM111A-CTCF-G3 (rep1)

description:
Library name: FAM111A_CTCF_G3_WCE_rep1
Whole cell extract (input control) for CTCF ChIP-seq


title: irradiated T cells, 6h after 1 Gy, mouse 2

description: replicate 2

source_name: irradiated T cells, 6h after 1 Gy


title: CTCF ChIP-seq in WTC11-FAM111A-CTCF-G3 (rep3)

description:
Library name: FAM111A_CTCF_G3_rep3
CRISPR clonal validation ChIP-seq for CTCF binding


title: NK-92MI_Water extract of Astragalus mongholicus Bunge (Low dose)_rep1

description: sample 3-2-7

value: natural killer cell

value: Water extract of Astragalus mongholicus Bunge 125 μg/mL


title: M1MO_Water extract of BJIKT (High dose)_rep2

description: sample 4-1-5

value: Macrophage

value: Water extract of BJIKT 500 μg/mL


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-FAM111A-CTCF-G2 (rep3)

description:
Library name: FAM111A_CTCF_G2_WCE_rep3
Whole cell extract (input control) for CTCF ChIP-seq

value: iPSC

value: WTC11 iPSC clone carrying individual CRISPR sgRNA G2 (OligoID WTC11_Random_Screen_Crop_3864) targeting a candidate CTCF-binding element near FAM111A

value: none (input control)


title: M1MO_Water extract of BJIKT (High dose)_rep1

description: sample 4-1-4


title: M1MO_Vehicle(PBS)_rep2

description: sample 4-1-2

value: PBS


title: irradiated T cells, 6h after 5 Gy, mouse 2

description: replicate 2

source_name: irradiated T cells, 6h after 5 Gy


title: NK-92MI_Mixture of water extracts of four ingredients_rep2

description: sample 3-3-11

value: Total 500ug/mL, 125ug/mL of each of the 4 ingredients mixed


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-FAM111A-CTCF-G2 (rep2)

description:
Library name: FAM111A_CTCF_G2_WCE_rep2
Whole cell extract (input control) for CTCF ChIP-seq


title: NK-92MI_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep2

description: sample 3-3-2

value: Water extract of Atractylodes japonica Koidzumi 125 μg/mL


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-FAM111A-CTCF-G2 (rep1)

description:
Library name: FAM111A_CTCF_G2_WCE_rep1
Whole cell extract (input control) for CTCF ChIP-seq


title: irradiated T cells, 6h after 5 Gy, mouse 1

description: replicate 1


title: CTCF ChIP-seq in WTC11-FAM111A-CTCF-G2 (rep3)

description:
Library name: FAM111A_CTCF_G2_rep3
CRISPR clonal validation ChIP-seq for CTCF binding

value: CTCF


title: CTCF ChIP-seq in WTC11-NT (rep1)

description:
Library name: WTC11_NT_rep1
CRISPR clonal validation ChIP-seq for CTCF binding

value: WTC11 iPSC clone carrying non-targeting control sgRNA NT1 (OligoID WTC11_Random_Screen_Crop_15807)


title: RM1 bone marrow

description:
Library name: Sample 4
10x Genomics

value: Bone marrow


title: NK-92MI_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep3

description: sample 3-3-9

value: Water extract of Glycyrrhiza uralensis Fisher 125 μg/mL


title: CTCF ChIP-seq in WTC11-FAM111A-CTCF-G2 (rep1)

description:
Library name: FAM111A_CTCF_G2_rep1
CRISPR clonal validation ChIP-seq for CTCF binding


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-CDC37-CTCF-G6 (rep3)

description:
Library name: CDC37_CTCF_G6_WCE_rep3
Whole cell extract (input control) for CTCF ChIP-seq

value: WTC11 iPSC clone carrying individual CRISPR sgRNA G6 (OligoID WTC11_Random_Screen_Crop_7498) targeting a candidate CTCF-binding element near CDC37


title: NK-92MI_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep2

description: sample 3-2-2

value: Water extract of Panax ginseng C. A. Meyer 125 μg/mL


title: NK-92MI_Water extract of Astragalus mongholicus Bunge (Low dose)_rep3

description: sample 3-2-9


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-CDC37-CTCF-G6 (rep2)

description:
Library name: CDC37_CTCF_G6_WCE_rep2
Whole cell extract (input control) for CTCF ChIP-seq


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-FAM111A-CTCF-G3 (rep2)

description:
Library name: FAM111A_CTCF_G3_WCE_rep2
Whole cell extract (input control) for CTCF ChIP-seq

value: WTC11 iPSC clone carrying individual CRISPR sgRNA G3 (OligoID WTC11_Random_Screen_Crop_3866) targeting a candidate CTCF-binding element near FAM111A


title: NK-92MI_Water extract of Astragalus mongholicus Bunge (Low dose)_rep2

description: sample 3-2-8

value: natural killer cell


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-CDC37-CTCF-G6 (rep1)

description:
Library name: CDC37_CTCF_G6_WCE_rep1
Whole cell extract (input control) for CTCF ChIP-seq


title: unirradiated T cells, mouse 2

description: replicate 2

source_name: unirradiated T cells

value: CD8+T cells

value: 8-12 week

value: Intratumoral T cells


title: NK-92MI_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep1

description: sample 3-2-1


title: CTCF ChIP-seq in WTC11-FAM111A-CTCF-G3 (rep2)

description:
Library name: FAM111A_CTCF_G3_rep2
CRISPR clonal validation ChIP-seq for CTCF binding

value: iPSC


title: CTCF ChIP-seq in WTC11-CDC37-CTCF-G6 (rep3)

description:
Library name: CDC37_CTCF_G6_rep3
CRISPR clonal validation ChIP-seq for CTCF binding


title: CTCF ChIP-seq in WTC11-CDC37-CTCF-G6 (rep2)

description:
Library name: CDC37_CTCF_G6_rep2
CRISPR clonal validation ChIP-seq for CTCF binding


title: unirradiated T cells, mouse 1

description: replicate 1


title: CTCF ChIP-seq in WTC11-CDC37-CTCF-G6 (rep1)

description:
Library name: CDC37_CTCF_G6_rep1
CRISPR clonal validation ChIP-seq for CTCF binding


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-CDC37-CTCF-G4 (rep3)

description:
Library name: CDC37_CTCF_G4_WCE_rep3
Whole cell extract (input control) for CTCF ChIP-seq

value: WTC11 iPSC clone carrying individual CRISPR sgRNA G4 (OligoID WTC11_Random_Screen_Crop_7494) targeting a candidate CTCF-binding element near CDC37


title: NK-92MI_Water extract of Panax ginseng C. A. Meyer (High dose)_rep1

description: sample 3-1-10

value: Water extract of Panax ginseng C. A. Meyer 500 μg/mL


title: irradiated T cells, 24h after 1 Gy, mouse 2

description: replicate 2


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-CDC37-CTCF-G4 (rep1)

description:
Library name: CDC37_CTCF_G4_WCE_rep1
Whole cell extract (input control) for CTCF ChIP-seq

value: none (input control)


title: irradiated T cells, 24h after 5 Gy, mouse 4

description: replicate 4

source_name: irradiated T cells, 24h after 5 Gy


title: NK-92MI_Water extract of BJIKT (Low dose)_rep2

description: sample 3-1-8

value: Water extract of BJIKT 125 μg/mL


title: CTCF ChIP-seq in WTC11-CDC37-CTCF-G4 (rep3)

description:
Library name: CDC37_CTCF_G4_rep3
CRISPR clonal validation ChIP-seq for CTCF binding


title: CTCF ChIP-seq in WTC11-CDC37-CTCF-G4 (rep2)

description:
Library name: CDC37_CTCF_G4_rep2
CRISPR clonal validation ChIP-seq for CTCF binding


title: irradiated T cells, 1h after 5 Gy, mouse 3

description: replicate 3

source_name: irradiated T cells, 1h after 5 Gy


title: NK-92MI_Water extract of BJIKT (Low dose)_rep1

description: sample 3-1-7


title: CTCF ChIP-seq in WTC11-CDC37-CTCF-G4 (rep1)

description:
Library name: CDC37_CTCF_G4_rep1
CRISPR clonal validation ChIP-seq for CTCF binding


title: irradiated T cells, 24h after 5 Gy, mouse 3

description: replicate 3


title: IPF, mock, SEN, donor 110A, batch2

city: Novato

first: Jun-Wei

middle: Brendan

last: Hughes

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description:
Library name: Sample 27
Donor ID: 110A; disease: IPF; infection: mock; senescence treatment: SEN; batch: batch2
IPF4_SEN_mock

data_processing:
Raw reads were aligned locally using the nf-core/rnaseq salmon pipeline in Windows Subsystem for Linux (WSL), performing pseudo-alignment against a standard reference transcriptome for Homo sapiens (GRCh38 genome).
Assembly: Homo sapiens (GRCh38 genome)
Supplementary files format and content: tab-delimited text file with gene-level count matrices per sample

source_name: lung

growth_protocol: Healthy lung fibroblasts (HLF) and lung fibroblasts from donors diagnosed with idiopathic pulmonary fibrosis (IPF) were obtained from adult donors from collaborators at the University of California, San Francisco, or Cedars-Sinai and isolated at their originating institutions through methods previously described (Hogaboam et al. 2005). A complete list of details for each donor lung fibroblast can be found in “Supplementary Table 1 - Donor Information.” Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS and 1% P/S at 37°C with 5% CO2.

extract_protocol:
Cells were first lysed with RLT buffer before RNA extraction was conducted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Concentration and purity of extracted RNA was assessed with the NanoDrop spectrophotometer ND-1000 (Thermo Fisher Scientific/ PeqLab).
RNA was isolated according to the protocol and sent out to Novogene for sample QC, library preparation, and sequencing. Sequencing was performed at 20M paired-end reads per sample on the NovaSeq X Plus Series (PE150) (Illumina).

treatment_protocol: Senescence in lung fibroblasts was induced by irradiation, in which the cells were exposed to a dose of 15 Gray while maintained in cell culture plates. Immediately after irradiation, the medium was replaced with fresh DMEM containing 10% FCS and 1% P/S. Subsequently, the medium was refreshed every 2-3 days. The induction of senescence was completed after 10 days of culture, and the senescent cells were then utilized for further experiments. As a control, quiescent cells were generated by serum starvation as previously described (Schulz et al. 2023; Neri et al. 2021).  Viral infections were carried out with Influenza A virus/H1N1/Puerto Rico/8/1934 (IAV), which has been propagated in Madin-Darby canine kidney (MDCK) cells cultivated in minimum essential medium (MEM) containing 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin (P/S) (Hornung et al. 2025). Viral titers from both propagated virus and in vitro infections were quantified as plaque-forming units (PFU) per milliliter using a plaque assay, as previously detailed (Deinhardt-Emmer et al. 2021). For viral titers obtained from in vitro experiments, PFU counts were normalized to cell counts and expressed as PFU per 100,000 cells.  HLF and IPF cells were infected with IAV at a multiplicity of infection (MOI) of 1 in Dulbecco's Phosphate Buffered Saline (DPBS) containing 0.2% bovine serum albumin (BSA; Roth, Karlsruhe, Germany), 1 mM MgCl2 (Sigma Aldrich), and 0.9 mM CaCl2 (Sigma Aldrich) for a duration of 30 minutes (min). Following this incubation, the cells were washed and subsequently cultured in DMEM supplemented with 0.2% BSA, 1 mM MgCl2, 0.9 mM CaCl2, and 30 ng/ml of TPCK-treated trypsin (Thermo Fisher Scientific, Waltham, MA, USA) for 24 hours (h) (Schulz et al. 2023).

value: lung

value: primary

value: fibroblast

tag: Sex

value: Female

tag: infection

value: mock

value: SEN

tag: disease

value: IPF


title: NK-92MI_Water extract of BJIKT (High dose)_rep3

description: sample 3-1-6

value: Water extract of BJIKT 500 μg/mL


title: IPF, IAV, QUI, donor 110A, batch2

description:
Library name: Sample 25
Donor ID: 110A; disease: IPF; infection: IAV; senescence treatment: QUI; batch: batch2
IPF4_QUI_IAV

value: IAV

value: QUI


title: irradiated T cells, 24h after 5 Gy, mouse 2

description: replicate 2

value: CD8+T cells

value: 8-12 week


title: NK-92MI_Water extract of BJIKT (High dose)_rep2

description: sample 3-1-5

value: natural killer cell


title: irradiated T cells, 6h after 1 Gy, mouse 1

description: replicate 1

value: Intratumoral T cells


title: IPF, IAV, SEN, donor 83A, batch2

description:
Library name: Sample 23
Donor ID: 83A; disease: IPF; infection: IAV; senescence treatment: SEN; batch: batch2
IPF3_SEN_IAV

value: Male


title: IPF, mock, QUI, donor 83A, batch2

description:
Library name: Sample 22
Donor ID: 83A; disease: IPF; infection: mock; senescence treatment: QUI; batch: batch2
IPF3_QUI_mock


title: irradiated T cells, 1h after 1 Gy, mouse 3

description: replicate 3


title: NK-92MI_Water extract of BJIKT (High dose)_rep1

description: sample 3-1-4


title: IPF, IAV, QUI, donor 83A, batch2

description:
Library name: Sample 21
Donor ID: 83A; disease: IPF; infection: IAV; senescence treatment: QUI; batch: batch2
IPF3_QUI_IAV


title: NK-92MI_Vehicle(PBS)_rep3

description: sample 3-1-3

value: PBS


title: IPF, mock, SEN, donor 155B, batch1

description:
Library name: Sample 20
Donor ID: 155B; disease: IPF; infection: mock; senescence treatment: SEN; batch: batch1
IPF2_SEN_mock


title: IPF, IAV, SEN, donor 155B, batch1

description:
Library name: Sample 19
Donor ID: 155B; disease: IPF; infection: IAV; senescence treatment: SEN; batch: batch1
IPF2_SEN_IAV


title: irradiated T cells, 1h after 1 Gy, mouse 2

description: replicate 2


title: IPF, mock, QUI, donor 155B, batch1

description:
Library name: Sample 18
Donor ID: 155B; disease: IPF; infection: mock; senescence treatment: QUI; batch: batch1
IPF2_QUI_mock


title: irradiated T cells, 24h after 1 Gy, mouse 1

description: replicate 1


title: NK-92MI_Vehicle(PBS)_rep1

description: sample 3-1-1


title: IPF, mock, SEN, donor 86A, batch1

description:
Library name: Sample 16
Donor ID: 86A; disease: IPF; infection: mock; senescence treatment: SEN; batch: batch1
IPF1_SEN_mock


title: IPF, IAV, SEN, donor 86A, batch1

description:
Library name: Sample 15
Donor ID: 86A; disease: IPF; infection: IAV; senescence treatment: SEN; batch: batch1
IPF1_SEN_IAV


title: irradiated T cells, 1h after 5 Gy, mouse 2

description: replicate 2


title: RPMI8226_Mixture of water extracts of four ingredients_rep3

description: sample 2-3-12

value: B lymphocyte

value: Total 500ug/mL, 125ug/mL of each of the 4 ingredients mixed


title: IPF, mock, QUI, donor 86A, batch1

description:
Library name: Sample 14
Donor ID: 86A; disease: IPF; infection: mock; senescence treatment: QUI; batch: batch1
IPF1_QUI_mock

value: lung

value: primary


title: IPF, IAV, QUI, donor 86A, batch1

description:
Library name: Sample 13
Donor ID: 86A; disease: IPF; infection: IAV; senescence treatment: QUI; batch: batch1
IPF1_QUI_IAV

value: fibroblast

value: Female


title: RPMI8226_Mixture of water extracts of four ingredients_rep2

description: sample 2-3-11


title: IPF, IAV, SEN, donor 110A, batch2

description:
Library name: Sample 26
Donor ID: 110A; disease: IPF; infection: IAV; senescence treatment: SEN; batch: batch2
IPF4_SEN_IAV

value: SEN


title: healthy, mock, SEN, donor AJDL, batch2

description:
Library name: Sample 12
Donor ID: AJDL; disease: healthy; infection: mock; senescence treatment: SEN; batch: batch2
HLF3_SEN_mock

value: not provided

value: mock

value: healthy


title: 9OC

status: Public on Aug 03 2026

city: Pisa

first: Francesca

last: Scebba

address: Piazza martiri della libertà 33

country: Italy

institute: Scuola Superiore Sant'Anna

description: Library name: 30804-007

data_processing:
Analysis was performed using CLC Genomics Server 21.0.4 with the QIAseq miRNA Quantification workflow and standard parameters. Reads were mapped to miRBase v22 after trimming of common sequences, UMIs, and adapters, followed by filtering of reads shorter than 15 nt or longer than 55 nt. Reads were then deduplicated based on their UMIs by grouping reads with the same start position, strand, and identical UMI. Singleton UMI groups were merged into non-singleton groups when their UMI differed by a single nucleotide (SNP), with assignment to the largest matching group.
All reads that don’t map to miRBase, neither with perfect matches nor as isomiRs (maximum 2 mismatches and/or alternative start/end position of 2 nt), are mapped the human genome GRCh38 with ENSEMBL GRCh38 version 97 annotation. This is carried out using the “RNA-Seq Analysis” workflow of CLC Genomics Server with standard parameters.
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.4 was used for differential expression analysis with default settings.
Assembly: miRBase version 22
Supplementary files format and content: excel file with total miRNa count for each miRNA and each sample

source_name: saliva

extract_protocol:
RNA was isolated from 200 μl using the miRNeasy Serum/Plasma Kit (QIAGEN) according to manufacturer’s instructions
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 5 μl total RNA was converted into miRNA NGS libraries. After adapter ligation, UMIs were introduced in the reverse transcription step. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation was quality controlled using capillary electrophoresis (Agilent DNA 1000 Chip)

value: saliva

tag: gender

value: female

value: ovarian cancer


title: IPF, mock, SEN, donor 83A, batch2

description:
Library name: Sample 24
Donor ID: 83A; disease: IPF; infection: mock; senescence treatment: SEN; batch: batch2
IPF3_SEN_mock

value: IPF


title: irradiated T cells, 1h after 1 Gy, mouse 1

description: replicate 1

value: CD8+T cells

value: 8-12 week

value: Intratumoral T cells


title: healthy, IAV, SEN, donor AJDL, batch2

description:
Library name: Sample 11
Donor ID: AJDL; disease: healthy; infection: IAV; senescence treatment: SEN; batch: batch2
HLF3_SEN_IAV

value: IAV


title: RPMI8226_Mixture of water extracts of four ingredients_rep1

description: sample 2-3-10

value: B lymphocyte

value: Total 500ug/mL, 125ug/mL of each of the 4 ingredients mixed


title: healthy, mock, QUI, donor AJDL, batch2

description:
Library name: Sample 10
Donor ID: AJDL; disease: healthy; infection: mock; senescence treatment: QUI; batch: batch2
HLF3_QUI_mock

value: lung

value: primary

value: QUI


title: healthy, IAV, QUI, donor AJDL, batch2

description:
Library name: Sample 9
Donor ID: AJDL; disease: healthy; infection: IAV; senescence treatment: QUI; batch: batch2
HLF3_QUI_IAV

value: fibroblast


title: RPMI8226_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep3

description: sample 2-3-9

value: Water extract of Glycyrrhiza uralensis Fisher 125 μg/mL


title: NK-92MI_Vehicle(PBS)_rep2

description: sample 3-1-2

value: natural killer cell

value: PBS


title: irradiated T cells, 24h after 5 Gy, mouse 1

description: replicate 1


title: healthy, mock, SEN, donor HLF250, batch2

description:
Library name: Sample 8
Donor ID: HLF250; disease: healthy; infection: mock; senescence treatment: SEN; batch: batch2
HLF2_SEN_mock

value: Male

value: mock

value: SEN

value: healthy


title: Huh7 cells, VPS72, ATAC-seq

city: Hong Kong

first: Qinglin

last: Zhang

address: Room 7N07, Kadoorie Biological Sciences Building, The University of Hong Kong, Sai Ying Pun

country: China

institute: The University of Hong Kong

description: Library name: VPS72-ATAC

data_processing:
fastq was QC and trimmed by fastqc and TRIMMOMATIC then aligned to hg19 genome by bwa mem
duplicated reads, low-quality mapping (mapq<47), encode blacklist regions were removed from the bam file
Density of fragments length was estimated to make sure there were two peaks around 100bp and 200bp
All reads aligning to the positive strand are offset by +4bp, and all reads aligning to the negative strand are offset by -5bp because of Tn5 transposase
The shifted reads were splitted into different bins, namely nucleosome-free, mononucleosome, dinucleosome, and trinucleosome
Assembly: hg38
Supplementary files format and content: text file document includes nucleosomefree and mononucleosome counts for each samples

growth_protocol: All cells were cultured in Dulbecco’s  modified Eagle medium (DMEM, Gibco). 10% fetal bovine serum (FBS,  Gibco) and antibiotic-antimycotic mixture (Gibco) were added into the  culture media. Cells were maintained at 37 °C in a CO2 incubator with  5% CO2.

extract_protocol:
50000 of nucleuses were incubated with Tagment Enzyme A50 from the Rapid DNA Lib Prep Kit (ABclonal) for DNA end preparation.
The library was prepared by following PCR condition (65 °C, 5 min; 98 °C,  30 sec; 98 °C, 10 sec; 65 °C, 75 sec). Repeat steps 3–4, cycle rounds to be  determined by parallel real-time PCR.

treatment_protocol: For lentivirus packaging, psPAX2, pMD2.G to gether with the carrier plasmid were co-transfected into HEK293T cells in  a 2:1:2 mass ratio. Lentivirus was harvested 48 and 72h after transfection  by centrifuging at 500g for 5 min and filtering through a 0.45 um filter and preserved at -80 ℃.For infection, lentivirus was added into cell media and maintained for 24h.

value: human hepato cellular carcinoma cell line

value: VPS72 overexpression

value: lentivirus infection


title: healthy, IAV, SEN, donor HLF250, batch2

description:
Library name: Sample 7
Donor ID: HLF250; disease: healthy; infection: IAV; senescence treatment: SEN; batch: batch2
HLF2_SEN_IAV

value: IAV


title: RPMI8226_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep2

description: sample 2-3-8

value: B lymphocyte


title: healthy, mock, QUI, donor HLF250, batch2

description:
Library name: Sample 6
Donor ID: HLF250; disease: healthy; infection: mock; senescence treatment: QUI; batch: batch2
HLF2_QUI_mock


title: Huh7 cells, FLAG, ATAC-seq

description: Library name: FLAG-ATAC

value: WT


title: IPF, IAV, QUI, donor 155B, batch1

description:
Library name: Sample 17
Donor ID: 155B; disease: IPF; infection: IAV; senescence treatment: QUI; batch: batch1
IPF2_QUI_IAV

value: lung

value: IPF


title: healthy, IAV, QUI, donor HLF250, batch2

description:
Library name: Sample 5
Donor ID: HLF250; disease: healthy; infection: IAV; senescence treatment: QUI; batch: batch2
HLF2_QUI_IAV

value: primary

value: QUI


title: RPMI8226_Water extract of Glycyrrhiza uralensis Fisher (Low dose)_rep1

description: sample 2-3-7

value: Water extract of Glycyrrhiza uralensis Fisher 125 μg/mL


title: healthy, mock, SEN, donor AJAZ, batch2

description:
Library name: Sample 4
Donor ID: AJAZ; disease: healthy; infection: mock; senescence treatment: SEN; batch: batch2
HLF1_SEN_mock

value: fibroblast

value: not provided


title: healthy, IAV, SEN, donor AJAZ, batch2

description:
Library name: Sample 3
Donor ID: AJAZ; disease: healthy; infection: IAV; senescence treatment: SEN; batch: batch2
HLF1_SEN_IAV


title: RPMI8226_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep3

description: sample 2-3-6

value: Water extract of Glycyrrhiza uralensis Fisher 500 μg/mL


title: HepG2, 10uM 5-azacytidine, rep2, ATAC-seq

city: 강남구

first: Wonjin

last: Woo

state: 서울 — Seoul

address: 서울시 강남구 도곡로237 강남세브란스 의생명연구센터 1층 김락균 교수님 실험실

institute: Yonsei University

description:
Library name: HepG2_10uM_rep2_ATAC
HepG2 cells treated with 10 μM 5-azacytidine for 4 days (ATAC-seq)

data_processing:
ATAC-seq raw FASTQ files were processed using PEPATAC pipeline (v0.10.2) for quality control, alignment, and peak calling.
ATAC-seq consensus peak sets were generated using iterative peak merging approach.
ATAC-seq read counts were quantified and differential accessibility analysis was performed using DiffBind (v3.12.0) with DESeq2 normalization.
RNA-seq raw FASTQ files were aligned to hg38 genome using HISAT2 (v2.2.1).
RNA-seq gene-level read counts were generated using HTSeq (v2.0.4).
RNA-seq differential expression analysis was performed using DESeq2 (v1.42.1).
RNA-seq variance-stabilized transformation was applied for data visualization.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing normalized count matrices for RNA-seq and peak count matrices for ATAC-seq with gene/peak annotations.
Supplementary files format and content: BED format file containing consensus peak coordinates for ATAC-seq analysis.

source_name: liver

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2. Cells were seeded at 70-80% confluence.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104) according to manufacturer's protocol. For ATAC-seq, nuclei were extracted and processed according to standard ATAC-seq protocol using Nextera DNA Library Prep Kit.
RNA libraries were prepared with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina). ATAC-seq libraries were prepared using the Nextera DNA Library Prep Kit (Illumina).

treatment_protocol: DNA methyltransferase inhibition was induced using 5-azacytidine (Sigma-Aldrich) at concentrations of 0, 2, or 10 μM for 4 days, with daily medium replacement.

value: liver

value: hepatocyte

value: 10 μM 5-azacytidine for 4 days


title: healthy, mock, QUI, donor AJAZ, batch2

description:
Library name: Sample 2
Donor ID: AJAZ; disease: healthy; infection: mock; senescence treatment: QUI; batch: batch2
HLF1_QUI_mock

value: mock

value: healthy


title: HepG2, 10uM 5-azacytidine, rep1, ATAC-seq

description:
Library name: HepG2_10uM_rep1_ATAC
HepG2 cells treated with 10 μM 5-azacytidine for 4 days (ATAC-seq)


title: healthy, IAV, QUI, donor AJAZ, batch2

description:
Library name: Sample 1
Donor ID: AJAZ; disease: healthy; infection: IAV; senescence treatment: QUI; batch: batch2
HLF1_QUI_IAV


title: iMGL, LACTBKO, clone C, differentiation 1

city: New York

first: Tulsi

last: Patel

state: NY

address: Icahn School Of Medicine At Mount Sinai, 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: BKOC1
PIP-seq chemistry V

data_processing:
The demultiplexing, barcoded processing and gene counting were performed using pipseeker software v3.3.0
Paired-end FASTQ files were processed with pipseeker (v3.3.0) for read trimming, alignment, and quantification to generate gene count matrices at multiple sensitivity levels. Sensitivity 3 was used for downstream analyses.
Count matrices were imported into Seurat v5.0.2 for quality control and further analysis.
Assembly: GRCh38
Supplementary files format and content: Cell barcodes tsv, features tsv and gene expression matrix file

source_name: Cell line

growth_protocol: We CRISPR-edited the WTC11 line to generate control (WT) and LACTB KO isogenic clonal lines (3 independent clones per genotype) at the Stem Cell Core at Ichan School of Medicine at Mount Sinai. iPSC lines were differentiated to hematopoietic precursor cells (HPCs) using StemDiff kit (StemCell Technologies). HPCs were plated and differentiated for 24 days to microglia (iMGL) in iMGL media (DMEM/F12, B27, 0.5xN2, 2xITSG, 400uM monothioglycerol, 5ug/ml insulin, 1xNEAA, 1xGlutaMax) supplemented with three factors (IL34 (100ng/ml), TGFb (50ng/ml), and MCSF (25ng/ml). iMGLs were fed Monday, Wednesday and Friday with 1ml of iMGL media with three factors. Cells were splitted in 1:2 ratio if too confluent. At day 24 iMGLs were lifted with gentle pipetting and Accutase and plated in fresh media iMGL media with three factors supplemented additionally with two factors (CX3CL1 and CD200 100ng/ml each) for 3 additional days (day 25, day 26, day 27). At day 26 of iMGL differentiation. Cells were collected at day 27.

extract_protocol:
iMGLs were dissociated and processed through the PIP-seq workflow, which captures individual cells and barcodes RNA transcripts to generate single cell transcriptomes for sequencing
PIP-seq

treatment_protocol: No additional treatments were added

value: Cell line

value: iPSC-derived microglia

value: LACTBKO

value: No treatment


title: HepG2, 2uM 5-azacytidine, rep3, ATAC-seq

description:
Library name: HepG2_2uM_rep3_ATAC
HepG2 cells treated with 2 μM 5-azacytidine for 4 days (ATAC-seq)

value: WT

value: 2 μM 5-azacytidine for 4 days


title: RPMI8226_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep2

description: sample 2-3-5

value: B lymphocyte


title: RPMI8226_Water extract of Glycyrrhiza uralensis Fisher (High dose)_rep1

description: sample 2-3-4


title: iMGL, LACTBKO, clone B, differentiation 2

description:
Library name: BKOB2
PIP-seq chemistry V


title: iMGL, LACTBKO, clone A, differentiation 1

description:
Library name: BKOA1
PIP-seq chemistry V


title: HepG2, 2uM 5-azacytidine, rep2, ATAC-seq

description:
Library name: HepG2_2uM_rep2_ATAC
HepG2 cells treated with 2 μM 5-azacytidine for 4 days (ATAC-seq)


title: RPMI8226_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep3

description: sample 2-3-3

value: Water extract of Atractylodes japonica Koidzumi 125 μg/mL


title: iMGL, LACTBKO, clone B, differentiation 1

description:
Library name: BKOB1
PIP-seq chemistry v4


title: RPMI8226_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep2

description: sample 2-3-2


title: HepG2, 2uM 5-azacytidine, rep1, ATAC-seq

description:
Library name: HepG2_2uM_rep1_ATAC
HepG2 cells treated with 2 μM 5-azacytidine for 4 days (ATAC-seq)


title: iMGL, WT, clone L, differentiation 1

description:
Library name: SCRL1
PIP-seq chemistry V


title: irradiated T cells, 1h after 5 Gy, mouse 1

description: replicate 1

value: CD8+T cells

value: 8-12 week

value: Intratumoral T cells


title: iMGL, WT, clone J, differentiation 1

description:
Library name: SCRJ1
PIP-seq chemistry V


title: iMGL, WT, clone K, differentiation 2

description:
Library name: SCRK2
PIP-seq chemistry V


title: HepG2, 0uM 5-azacytidine, rep3, ATAC-seq

description:
Library name: HepG2_0uM_rep3_ATAC
HepG2 cells treated with 0 μM 5-azacytidine for 4 days (ATAC-seq)

value: 0 μM 5-azacytidine for 4 days


title: NK-92MI_Water extract of Atractylodes japonica Koidzumi (High dose)_rep1

description: sample 3-2-10

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 (500 ng) 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: natural killer cell

value: Water extract of Atractylodes japonica Koidzumi 500 μg/mL


title: iMGL, WT, clone K, differentiation 1

description:
Library name: SCRK1
PIP-seq chemistry v4


title: STIL_6__STIL_Epithelium_sample275

description: Library name: DSP-1001660012748-E-E05

data_processing:
Sequencing files were processed into DCC format using the GeoMx NGS Pipeline software v1.0. GeoMx counts were log2 transformed in preparation for statistic data analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files include raw read counts along with RTS_IDs for each ROI
Supplementary files format and content: PKC file includes probe metadata describing the targets and is needed to interpret RTS_IDs in the DCC files

source_name: Fallopian tube, dysplastic lesion or invasive cancer

extract_protocol:
Tissue processing began with sectioning FFPE samples to a 5 μm thickness following the Nanostring GeoMx user manual (MAN-10132-04). After deparaffinization and rehydration, protein target retrieval was performed using Tris-EDTA antigen retrieval buffer for 20 minutes in a pressure cooker. RNA targets were retrieved through proteinase K digestion for 15 minutes at 37 °C. Tissues were then post-fixed in 10% NBF and hybridized overnight at 37 °C with RNA probes (Human Whole Transcriptome Atlas, containing 18,000 protein-coding genes coupled to UV-cleavable oligonucleotide barcodes). Following hybridization, excess probes were removed by stringent washing at 37 °C and incubated in blocking buffer W (Nanostring LOT#:2-23020032). The tissue sections were subsequently stained with conjugated primary antibodies targeting pan-cytokeratin (mouse monoclonal antibody, Novus NBP2-33200AF488) and p53 (Dako primary and secondary antibodies), along with CAPS (primary and secondary antibodies) and SYTO13 nuclear stain (ThermoFisher Scientific, S7575) for one hour at room temperature. For transcriptomic data acquisition, slides were analyzed on the GeoMx Digital Spatial Profiler (DSP) at 20× magnification. Regions of interest (ROIs) were identified based on immunofluorescence images with a pathologist's (AB) supervision and matched to regions selected in DVP. Following ROI selection, RNA probes were photocleaved using UV illumination within each ROI, and oligonucleotide barcodes were collected into a 96-well plate, allowing precise separation of tissue compartments.
Sequencing libraries were prepared using Illumina TruSeq technology for adaptor ligation and amplification. The amplified libraries underwent two rounds of Ampure XP magnetic bead cleanup (1.2:1 beads ratio) (HighPrep PCR from MAGBIO, Cat#: AC-60500). Purified libraries were sequenced on an Illumina NovaSeq flowcell PE50 at a depth of 100× per μm².

value: Epithelium

tag: cohort

value: STIL


title: HepG2, 0uM 5-azacytidine, rep2, ATAC-seq

description:
Library name: HepG2_0uM_rep2_ATAC
HepG2 cells treated with 0 μM 5-azacytidine for 4 days (ATAC-seq)

value: liver

value: hepatocyte


title: RPMI8226_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep1

description: sample 2-3-1

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


title: STIL_6__STIL_Epithelium_sample273

description: Library name: DSP-1001660012748-E-E03

value: Fallopian tube, dysplastic lesion or invasive cancer


title: RPMI8226_Water extract of Atractylodes japonica Koidzumi (High dose)_rep3

description: sample 2-2-12


title: STIL_6__STIL_Epithelium_sample274

description: Library name: DSP-1001660012748-E-E04


title: HepG2, 0uM 5-azacytidine, rep1, ATAC-seq

description:
Library name: HepG2_0uM_rep1_ATAC
HepG2 cells treated with 0 μM 5-azacytidine for 4 days (ATAC-seq)


title: p53_1__P53_Stroma_sample272

description: Library name: DSP-1001660012748-E-E02

value: Stroma


title: p53_1__FOXJ1neg_Epithelium_sample271

description: Library name: DSP-1001660012748-E-E01


title: RPMI8226_Water extract of Atractylodes japonica Koidzumi (High dose)_rep2

description: sample 2-2-11


title: HGC27_CAF2_3

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

data_processing:
Processed and selected high-quality reads using FastQC (v0.11.8), excluding any reads with low base quality
Aligned to the GRCh37 human reference genome provided by GENCODE, employing STAR v2.74a
Gene and transcript expression levels were then quantified using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: tab-delimited txt file include TPM value for each sample

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Epithelial cell

value: humangastric cancer

value: Co-colture with CAF


title: RPMI8226_Water extract of Atractylodes japonica Koidzumi (High dose)_rep1

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

description: sample 2-2-10

value: B lymphocyte


title: p53_1__FOXJ1neg_Epithelium_sample269

description: Library name: DSP-1001660012748-E-D11


title: p53_1__FOXJ1pos_Epithelium_sample270

description: Library name: DSP-1001660012748-E-D12


title: HGC27_CAF2_2


title: RPMI8226_Water extract of Astragalus mongholicus Bunge (Low dose)_rep3

description: sample 2-2-9

value: Water extract of Astragalus mongholicus Bunge 125 μg/mL


title: NK-92MI_Water extract of Astragalus mongholicus Bunge (High dose)_rep3

description: sample 3-2-6

value: Water extract of Astragalus mongholicus Bunge 500 μg/mL


title: p53_1__FOXJ1pos_Epithelium_sample268

description: Library name: DSP-1001660012748-E-D10


title: RPMI8226_Water extract of Astragalus mongholicus Bunge (Low dose)_rep2

description: sample 2-2-8


title: p53_1__FOXJ1neg_Epithelium_sample267

description: Library name: DSP-1001660012748-E-D09


title: p53_1__P53_Epithelium_sample265

description: Library name: DSP-1001660012748-E-D07