title: B73xNC358_WW_R2

description: Library name: 116

value: WW


title: B73xMs71_WW_R2

status: Public on Apr 16 2025

type: SRA

city: Duesseldorf

first: Thomas

last: Hartwig

address: University Street 1

country: Germany

institute: Heinrich-Heine University

description: Library name: 110

library_source: genomic

data_processing:
library strategy: MNase-defined cistrome-Occupancy Analysis (MOA-seq)
Reads were filtered using SeqPurge (v2022-07-15) with parameters “-min_len 20 -qcut 0” (Sturm et al. 2016).
Due to the short fragment length in MOA, read pairs almost completely overlapped. MOA-seq paired-end reads were merged into single-end reads, including base quality score correction, using NGmerge (v0.3) (Gaspar 2018) with parameters “-p 0.2 -m 15 -d -e 30 -z -v”.
Reads were mapped to the diploid genome (or the separate genomes for inbred data) using STAR (v2.7.7a). As STAR was originally designed to map RNA, we set the flag --alignIntronMax 1 for DNA (no introns allowed) as well as parameters “--outSAMmultNmax 2, --winAnchorMultimapNmax 100, and -outBAMsortingBinsN 5 (Dobin et al. 2013).
Bam files were converted to bed format using bamToBed (Quinlan and Hall 2010).
Format conversion and the calculation of the average mapped fragment length (AMFL) was done using SAMtools (v1.9) (Li et al. 2009).
The effective genome size was calculated using unique-kmers.py (https://github.com/dib-lab/khmer/) with AFML and respective genome fasta as inputs.
The function genomeCoverageBed of Bedtools (v2.29.0) was then used to convert the bed files to bedgraph, scaled by the quotient of the effective genome size and the number of uniquely mapped reads (reads per genome coverage, RPGC).
BigWig files for visualization were generated using bedGraphToBigWig (Kent et al. 2010).
During this study the maize inbred A619 had no reference assembly. Of the inbred maize lines with high quality assemblies, A619 is most closely related to Oh43 (Flint‐Garcia et al.2005). We downloaded approximately 30x coverage of A619 WGS data from NCBI SRA (SRR8997919, SRR10127976, SRR8907067, SRR5725670, SRR5663982, and SRR5663981) and then mapped it to the Oh43 genome using bwa-mem2 (v2.2.1) (Li and Durbin 2009). Only uniquely mapping reads (q30) were retained. The GATK4 pipeline in combination with the “best practices workflow” (https://gatk.broadinstitute.org/hc/en-us/sections/360007226651) was used to identify initial A619/Oh43 SNPs and INDELs with the hard filtering settings: “QD < 2.0”, "QUAL < 100.0", "SOR > 3.0", "FS > 60.0", and "MQ < 40.0". We used these initial variants for base- and variant-recalibration, followed by two additional rounds of training based on convolutional neural networks (CNN) to optimize filtration settings (training input setting: “prior=15.0" and “tranche=99”) and, ultimately selected a refined set of biallelic, homozygous A619/Oh43 SNPs and INDELs. G2Gtools (v. 0.2.7, https://churchill-lab.github.io/g2gtools/) was employed to integrate SNPs and INDELs into the Oh43 genome and generate a A619 pseudo-reference fasta and gff3 file. The average SNP mismatch rate of respective MOA reads from the F1 to the B73xA619 genome was 0.1%, only twice that of the average high-quality B73xNAM genomes (0.04-0.05%), and substantially lower than mapping to either B73 or the A619 psuedo-reference alone (~0.54%).
Assembly: Diploid genomes were created by concatenating the B73 V5 genome with the respective paternal genome (NAM v1 / 2 genomes (Hufford et al. 2021), Mo17 CAU v1, W22 v2 (Springer et al. 2018), A188 v1 (Lin et al. 2021), and A619 see separate entry).
Supplementary files format and content: Bed files containing significantly enriched sites on both parental genomes
Supplementary files format and content: BigWig files containing MOA-seq files on both parental genomes

molecule: genomic DNA

organism: Zea mays

source_name: leaf blade

growth_protocol: Plants were grown at 28C until the V4 stage, which is when treatment began

extract_protocol:
Nuclei extraction and DNase treatment for MOA-seq was performed as decribed in Savadel et al. 2021
Libraries were constructed as decribed in Savadel et al. 2021

treatment_protocol: Plants were subjected to drought treatment or well-watered treatment for 86h

tag: tissue

value: leaf blade

tag: genotype

tag: treatment


title: sample 109_genomic DNA from blood sample C0363

type: genomic

city: Shinjuku-ku, Tokyo

first: Yae

last: Kanai

address: 35, Shinano-machi

department: Pathology

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Initial quality control was performed using GenomeStudio Methylation software. The raw intensity data files were imported into the R environment using the Bioconductor minfi package. Data satisfying detection P-values are 0.05 or more was regarded not applicable. Background correction with dye-bias normalization was performed using the normal-exponential out-of-band preprocessing method.
matrix processed value definition: Normalized Average Beta

label: Cy5 and Cy3

organism: Homo sapiens

source_name: blood sample of control patient

label_protocol: Standard Illumina Protocol

extract_protocol: The genomic DNA was extracted from all blood samples using a Maxwell® 16 Blood DNA Purification Kit (Promega, Madison, WI, USA).

tag: disease state

value: normal

tag: Sex

value: female

tag: age bracket

tag: blood sample id


title: siRNA GSK3A-GM-MØ - Donor B

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

library_source: transcriptomic

data_processing:
BGISEQ-500 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads.Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and FPKM values for each sample

molecule: total RNA

source_name: Monocyte-derived GM-CSF macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 10e6 cells/ml, >95% CD14+ cells) were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 5 days with 1000 U/ml GM-CSF to generate GM-CSF-polarized macrophages (GM-MØ). Cells were then transfected with siRNA control (siCNT), siRNA for GSK3A (siGSK3A), siRNA for GSK3B (siGSK3B) or both (siGSK3A and siGSK3B) and analyzed 72 hours later.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 5 days in RPMI 10% FBS containing GM-CSF. Fully-differentiated macrophages were transfected (HiPerFect, QIAgen) with a human GSK3A-specific siRNA (siGSK3A, Dharmacon), GSK3B-specific siRNA (siGSK3B, Dharmacon) or both (siGSK3A and siGSK3B). Silencer Select Negative Control No. 2 siRNA (siCNT) (Dharmacon) was used as negative control. 72 hours later total RNA was extracted.

tag: cell type

value: Monocyte-derived GM-CSF macrophages

value: siRNA GSK3A (50 nanomolar)


title: Melanocytes (HEM-neo), UVA-irradiated, CPD_CD-seq (UVA vs. UVB)

city: Grand Rapids

first: Gerd

last: Pfeifer

state: Michigan

address: 333 Bostwick Ave. NE., 5352W/Phase2

department: Center for Epigenetics

country: USA

institute: Van Andel Research Institute

description: Library name: 2_HEM-neo_UVA_CPD

data_processing:
Fastq files containing sequencing reads were trimmed from the 3’ end to 2x80 nucleotide length using Trim_Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Trimmed reads were aligned to the hg19 reference genome using BWA-MEM with default parameters.
Duplicate alignments were marked and removed with the ‘removeDups’ SAMBLASTER option.
Only divergently aligned pairs of reads with a single nucleotide gap between reads were selected by selecting SAM records with TLEN of 3 and saved as bam files for downstream analyses. TLEN=3 represents divergently aligned reads with 1 nucleotide between mates.
To visualize the reads, bam files were visualized using the Integrative Genomics Viewer version 2.8.9. The tracks were displayed with a ‘view as pairs’ option to show pairs together with a line joining the ends.
Assembly: hg19
Supplementary files format and content: Chromosome name, position of damaged base, and trinucleotide sequences (5'-N-damaaged base-N) were written to a tab-delimited text file.

source_name: foreskin

growth_protocol: Human primary melanocytes were grown on collagen-coated plates (1.67 μg/ml gelatin) using the MGM-4 melanocyte growth medium Bullet Kit (Lonza, Cat. CC-3249) and incubated in a humidified incubator with 5% CO2 at 37°C

extract_protocol:
Genomic DNAs were isolated using Quick-DNA Miniprep Plus Kit (Zymo Research; Irvine, CA) according to the manufacturer’s instruction manual.
Genomic DNAs were framgmeted to an averge length of 300 bp and circuliarized with T4 DNA ligase at 16°C overnight. Non-circularized linear DNAs were removed with Plasmid-Safe ATP-Dependent DNAse treatment. To generate DNA double-strand breaks at CPD or 8-oxoG lesions, the circularized DNAs were treated with T4-PDG or Fpg and APE1 followed by S1 nuclease to create double-strand breaks with ligatable ends. A-tailed with Klenow fragment exo- (NEB) and then adaptors were ligated with NEBNext Ultra II Ligation Master Mix and followed by incubation with USER enzyme (NEB). The purified DNA libraries were amplified by PCR with NEBNext Ultra II Q5 Master mix and NEBNext i5 and i7 primers and used for DNA sequencing.

treatment_protocol: To induce DNA damage, human primary melanocyte cells were irradiated with several dose of UVA or UVB.

value: foreskin

tag: cell line

value: Primary melanocytes (HEM-neo)

value: Primary human epidermal melanocyte (neonatal)

value: Wild type

value: UVA (72 J/cm2)

tag: batch


title: B73xMs71_WW_R1

description: Library name: 109


title: Melanocytes (HEM-ad), no UV-irradiated control, CPD_CD-seq (UVA vs. UVB)

description: Library name: 2_HEM-ad_NT_CPD

value: Primary melanocytes (HEM-ad)

value: Primary human epidermal melanocyte (adult)


title: siRNA GSK3A+GSK3B-GM-MØ - Donor A

value: siRNA GSK3A (50 nanomolar) and GSK3B (50 nanomolar)


title: sample 108_genomic DNA from blood sample C0333

source_name: blood sample of patient with major depressive disorder

value: major depressive disorder

value: male


title: B73xMs71_DS_R2

description: Library name: 113

value: DS


title: sample 107_genomic DNA from blood sample C0306


title: B73xMo18W_DS_R3

description: Library name: 108


title: B73xMo18W_DS_R2

description: Library name: 107


title: Melanocytes (HEM-neo), no UV-irradiated control, CPD_CD-seq (UVA vs. UVB)

description: Library name: 2_HEM-neo_NT_CPD


title: sample 112_genomic DNA from blood sample C0572


title: siRNA Control-GM-MØ - Donor B

value: siRNA CNT (50 nanomolar)


title: Melanocytes (Hermes-4a), UVA-irradiated (72 J/cm2), CPD_CD-seq

description: Library name: 1_Hermes-4a_UVA_72J_CPD

value: human melanocytes, telomerase immortalized


title: B73xMo18W_DS_R1

description: Library name: 106

value: leaf blade


title: sample 106_genomic DNA from blood sample C0254


title: siRNA Control-GM-MØ - Donor A


title: B73xMs71_WW_R3

description: Library name: 111

value: WW


title: siRNA GSK3A-GM-MØ - Donor C

value: Monocyte-derived GM-CSF macrophages


title: sample 105_genomic DNA from blood sample C0246

value: normal


title: B73xMo18W_WW_R3

description: Library name: 105


title: sample 104_genomic DNA from blood sample C0243

value: female


title: B73xMo18W_WW_R2

description: Library name: 104


title: CHIR99021 treated - AMØ - Donor B

source_name: Alveolar macrophage

growth_protocol: Alveolar macrophages (AMØ) were obtained from patients undergoing bronchoalveolar lavage (BAL) following the Hospital Doce de Octubre Medical Ethics committee procedures and after written informed consent from all subjects, in accordance with the Declaration of Helsinki. BAL procedure was performed with a flexible bronchoscope and a total volume of 200 ml of sterile isotonic saline solution at 37°C. BAL fluid fractions were maintained at 4°C and cellular debris removed using a 40 μm cell strainer. BAL cells were washed with PBS, centrifuged and resuspended in complete medium containing 100 U/mL penicillin and 100 μg/mL streptomycin, 50 μg/ml gentamicin, and 2.5 μg/ml amphotericin B. The cells were seeded at 6–8 × 105 cells per well in 12-well plates for 1 h and washed extensively to remove non-adherent cells. Finally, 2 ml of complete medium with antibiotics was added to each well and the adherent cells incubated for 16–18 h before treatments. More than 95% of adherent BAL cells were identified as macrophages according to morphology and phenotypic analysis.

treatment_protocol: Isolated alveolar macrophage were cultured in RPMI 10% FBS and were exposed to DMSO or CHIR99021 for 24 hours, total RNA was extracted.

value: Alveolar macrophage


title: Melanocytes (HEM-ad), UVA-irradiated (72 J/cm2), CPD_CD-seq

description: Library name: 1_HEM-ad_UVA_72J_CPD

value: foreskin


title: sample 103_genomic DNA from blood sample C0242


title: Melanocytes (HEM-neo), UVA-irradiated (108 J/cm2), CPD_CD-seq

description: Library name: 1_HEM-neo_UVA_108J_CPD

value: Primary melanocytes (HEM-neo)

value: Primary human epidermal melanocyte (neonatal)

value: Wild type


title: B73xMo18W_WW_R1

description: Library name: 103


title: siRNA Control GM-MØ - Donor C


title: Melanocytes (HEM-neo), UVA-irradiated (72 J/cm2), CPD_CD-seq

description: Library name: 1_HEM-neo_UVA_72J_CPD

value: UVA (72 J/cm2)


title: siRNA GSK3A-GM-MØ - Donor A

value: siRNA GSK3A (50 nanomolar)


title: DMSO treated- AMØ - Donor C

value: DMSO


title: CHIR99021 treated - AMØ - Donor A


title: Melanocytes (HEM-neo), UVA-irradiated (36 J/cm2), CPD_CD-seq

description: Library name: 1_HEM-neo_UVA_36J_CPD

value: UVA (36 J/cm2)


title: DMSO treated- AMØ - Donor B


title: sample 102_genomic DNA from blood sample C0179

value: major depressive disorder


title: sample 100_genomic DNA from blood sample C0155

value: male


title: B73xMo17_DS_R3

description: Library name: 102

value: DS


title: Melanocytes (Hermes-3a), UVA-irradiated (72 J/cm2), CPD_CD-seq

description: Library name: 1_Hermes-3a_UVA_72J_CPD

value: human melanocytes, telomerase immortalized


title: B73xMo17_DS_R2

description: Library name: 101

value: leaf blade


title: sample 99_genomic DNA from blood sample C0123


title: Melanocytes (HEM-neo), no UV-irradiated control, CPD_CD-seq

description: Library name: 1_HEM-neo_NT_CPD


title: B73xMo17_WW_R3

description: Library name: 99

value: WW


title: M-CSF treated- Monocyte - Donor C

source_name: Purified monocytes

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) treated with DMSO (vehicle) or 10 micromolar of GSK3 inhibitor (CHIR99021, Selleckchem) or 10 ng/mL M-CSF (ImmunoTools), for 16 hours.

treatment_protocol: Purified monocytes treated with 10 ng/mL M-CSF (ImmunoTools), DMSO or 10 micromolar of GSK3 inhibitor (CHIR99021, Selleckchem) for 16 hours.

value: Purified monocytes

value: M-CSF (10 ng/ml)


title: B73xMo17_DS_R1

description: Library name: 100


title: CHIR99021 treated - AMØ - Donor C

value: Alveolar macrophage


title: PBMC 58 days after TCR-T infusion

city: Seattle

first: Aude

last: Chapuis

state: WA

address: 1100 Fairview Ave

institute: Fred Hutchinson Cancer Center

description:
Library name: Patient 27 day 58 PB
10x Genomics

library_source: transcriptomic single cell

data_processing:
The 10X Genomics software Cell Ranger (v2.0.0) was used to process the raw data FASTAQ files with default parameters. The “count” function was used to perform alignment, filtering, barcode counting and UMI counting.
Assembly: Reads were aligned to the hg38 human reference genome (Ensembl) and the known transgene codon-optimized sequence using Spliced Transcripts Alignment to a Reference (STAR)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
PBMCs or BMMCs were thawed, washed in PBS and resuspended in 0.04% BSA by volume.
Cells were loaded on a 10x Chromium Controller based on the 3’ Chromium or 5’ Chromium Single Cell V(D)J Reagent Kit manual (10x Genomics). Library preparation was performed as per manufacturer’s protocol with no modifications. Library quality was confirmed by TapeStation High Sensitivity (Agilent, evaluates library size), Qubit (Thermo Fisher, evaluates dsDNA quantity),  and KAPA qPCR analysis (KAPA Biosystems, evaluates quantity of amplifiable transcript). Samples were mixed in equimolar fashion and sequenced on an Illumina HiSeq 2500 rapid run mode according to the standard 10X Genomics protocol. TCR target enrichment, 5’ gene expression library, and TCR library were carried out to the 5’ Chromium Single Cell V(D)J Reagent Kit manual (10x Genomics).

value: Peripheral blood

value: PBMC


title: PBMC 178 days after TCR-T infusion

description:
Library name: Patient 27 day 178 PB
10x Genomics


title: B73xMo17_WW_R2

description: Library name: 98


title: M-CSF treated - Monocyte - Donor B


title: PBMC 21 days after TCR-T infusion

description:
Library name: Patient 27 day 21 PB
10x Genomics


title: sample 98_genomic DNA from blood sample C0047


title: B73xMo17_WW_R1

description: Library name: 97


title: sample 97_genomic DNA from blood sample C0039

value: normal


title: M-CSF treated - Monocyte - Donor A


title: sample 96_genomic DNA from blood sample T04581

value: female


title: sample 101_genomic DNA from blood sample C0172


title: PBMC 28 days after TCR-T infusion

description:
Library name: Patient 26 day 28 PB
10x Genomics


title: DMSO treated - Monocyte - Donor B


title: sample 95_genomic DNA from blood sample T04525


title: B73xM37W_DS_R2

description: Library name: 95


title: DMSO treated - Monocyte - Donor C


title: PBMC 68 days after TCR-T infusion

description:
Library name: Patient 15 day 68 PB
10x Genomics


title: PBMC 7 days after TCR-T infusion

description:
Library name: Patient 26 day 7 PB
10x Genomics


title: B73xM37W_DS_R1

description: Library name: 94


title: sample 93_genomic DNA from blood sample T04062


title: sample 94_genomic DNA from blood sample T04290


title: B73xM37W_WW_R3

description: Library name: 93


title: BMMC 1322 days after TCR-T infusion

description:
Library name: Patient 8 day 1322 BM
10x Genomics

source_name: Bone marrow

value: Bone marrow

value: BMMC


title: sample 92_genomic DNA from blood sample T04013


title: DMSO treated- AMØ - Donor A

value: DMSO


title: DMSO treated - Monocyte - Donor A


title: B73xM37W_WW_R2

description: Library name: 92


title: BMMC 1344 days after TCR-T infusion

description:
Library name: Patient 8 day 1344 BM
10x Genomics


title: CHIR99021 treated - Monocyte - Donor C


title: B73xM37W_WW_R1

description: Library name: 91


title: CHIR99021 treated - Monocyte - Donor B


title: CHIR99021 treated - Monocyte - Donor A


title: PBMC 1343 days after TCR-T infusion

description:
Library name: Patient 8 day 1343 PB
10x Genomics


title: sample 90_genomic DNA from blood sample T03924


title: PBMC 1322 days after TCR-T infusion

description:
Library name: Patient 8 day 1322 PB
10x Genomics


title: B73xM162W_DS_R3

description: Library name: 90


title: PBMC 405 days after TCR-T infusion

description:
Library name: Patient 8 day405 PB
10x Genomics


title: B73xM37W_DS_R3

description: Library name: 96


title: CHIR99021 treated - GM-MØ - Donor C

source_name: Monocyte-derived GM-CSF macrophages (GM-MØ)

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 10e6 cells/ml, >95% CD14+ cells) were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days with 1000 U/ml GM-CSF to generate GM-CSF-polarized macrophages (GM-MØ), and in the presence or absence of 10 micromolar CHIR99021 (GSK3 a/b inhibitor) at day 5 for 48 hours.

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 5 days in RPMI 10% FBS containing GM-CSF. 5 days later, fully-differentiated macrophages were exposed to DMSO and CHIR99021 for 48 hours and total RNA was extracted.

value: Monocyte-derived GM-CSF macrophages


title: sample 89_genomic DNA from blood sample T03906

value: major depressive disorder


title: B73xM162W_DS_R2

description: Library name: 89


title: CHIR99021 treated - GM-MØ - Donor B


title: PBMC 256 days after TCR-T infusion

description:
Library name: Patient 8 day256 PB
10x Genomics


title: sample 87_genomic DNA from blood sample T03855

value: male


title: B73xM162W_DS_R1

description: Library name: 88

value: DS


title: CHIR99021 treated - GM-MØ - Donor A


title: B73xM162W_WW_R3

description: Library name: 87


title: DMSO treated- GM-MØ - Donor C


title: PBMC 581 days after TCR-T infusion

description:
Library name: Patient 4 day581 PB
10x Genomics


title: sample 86_genomic DNA from blood sample T03854


title: sample 85_genomic DNA from blood sample T03825


title: PBMC 100 days after TCR-T infusion

description:
Library name: Patient 4 day100 PB
10x Genomics


title: PBMC 49 days after TCR-T infusion

description:
Library name: Patient 8 day49 PB
10x Genomics


title: B73xM162W_WW_R2

description: Library name: 86


title: B73xM162W_WW_R1

description: Library name: 85


title: DMSO treated- GM-MØ - Donor A


title: sample 84_genomic DNA from blood sample T03786


title: 22RV1 PDCD4-S23D3

city: lexington

first: Jia

last: Peng

address: 760 press ave

institute: University of Kentucky

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. The trimmed reads were then mapped to Ensembl [GRCh38r98] transcripts annotation using RSEM.
Assembly: GRCh38r98
Supplementary files format and content: The processed data include expected counts data and TPM-normalized data, both in tsv format.

source_name: prostate

growth_protocol: 22Rv1 cells were cultured in 100mm2 tissue culture dish with Roswell Park Memorial Institute (RPMI) 1640 medium containing 10% fetal bovine serum, 5% antibiotic-antimycotics under the conditions of 37℃ and 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen))
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

value: prostate

value: epithelial cell


title: 22RV1 PDCD4-S23D2


title: sample 83_genomic DNA from blood sample T03778


title: B73xKy21_DS_R2

description: Library name: 83

value: leaf blade


title: Sorted TTCR37-45 at day 0

description:
Library name: TTCR37-45_D0
Column name in raw counts counts.xlsx: TTCR37-45_D0

data_processing:
Sequencing was performed on a DNBseq T7 machine (MGI) with paired-end 150 bp reads, generating 30M raw reads per sample. Raw sequencing data were filtered and trimmed using the software Soapnuke developed by BGI Genomics.
Assembly: The filtered reads were aligned to the reference transcriptome using Bowtie2 (v2.2.5). Gene read counts were subsequently generated from the alignment results using RSEM (v1.2.8).
Supplementary files format and content: excel file includes raw counts for each sample

source_name: Peripheral Blood

growth_protocol: T cells and K562 cells were cultured in media consisting of IMDM with GlutaMAX (Gibco, Life Technologies, #31980030) with 10% FBS, and 1% of penicillin/streptomycin.

extract_protocol:
total RNA was extracted using the Qiagen RNeasy Micro Kit
For the construction of low input polyA mRNA-seq libraries, the SMARTseq (v4) Package was used

treatment_protocol: T cells were rechallenged with WT1+ K562 tumor cells every 3–4 days; TCR-T cells were sorted at day 13 or day 23 post co-culture initiation.

value: Peripheral Blood

value: TCR-T cells

tag: time

value: Day 0


title: Sorted TTCR37-45 after 23 days of coculture with K562 cell line (replicate 2)

description:
Library name: K562_rep2_D23
Column name in raw counts counts.xlsx: K562_rep2_D23

value: Co-culture with K562 cell line

value: Day 23


title: 22RV1 PDCD4-S23D1


title: DMSO treated- GM-MØ - Donor B


title: sample 88_genomic DNA from blood sample T03861

value: normal


title: B73xKy21_DS_R1

description: Library name: 82


title: sample 82_genomic DNA from blood sample T03708


title: Sorted TTCR37-45 after 13 days of coculture with K562 cell line (replicate 2)

description:
Library name: K562_rep2_D13
Column name in raw counts counts.xlsx: K562_rep2_D13

value: Day 13


title: B73xKy21_DS_R3

description: Library name: 84


title: 22RV1 PDCD4-S239A3


title: Sorted TTCR37-45 after 23 days of coculture with K562 cell line (replicate 1)

description:
Library name: K562_rep1_D23
Column name in raw counts counts.xlsx: K562_rep1_D23


title: B73xKy21_WW_R2

description: Library name: 80

value: WW


title: B73xKy21_WW_R3

description: Library name: 81


title: 22RV1 PDCD4-S239A2


title: 22RV1 PDCD4-S239A1


title: Sorted TTCR37-45 after 13 days of coculture with K562 cell line (replicate 1)

description:
Library name: K562_rep1_D13
Column name in raw counts counts.xlsx: K562_rep1_D13


title: sample 79_genomic DNA from blood sample T03661


title: B73xKy21_WW_R1

description: Library name: 79


title: M1+0.005-2-4

city: Shanghai

first: Ying

last: Xu

address: No. 1755 Hongmeinan Road, Minhang District, Shanghai

country: China

institute: Better Way (Shanghai) Cosmetics Co. Ltd., China

description:
Library name: Sample16
M1+0.005-2-4

data_processing:
The sequencing data were aligned to the genome by Hisat2.
The structure of the transcript was assembled by StringTie according to the alignment results of each sample.
StringTie merge was used to synthesize the assembly results of all samples, combined with official annotation information to merge and optimize the structure of genes and transcripts.
Transcriptional abundance was calculated using StringTie.
Gene and transcript level expression calculations were performed by Ballgown, and Transcript was screened.
Assembly: GRCh37
Supplementary files format and content: Expession _ Gene.xlsx contains all samples FPKM

source_name: human skin fibroblast (HSF)

growth_protocol: HSFcells were maintained in RPMI 1640 supplemented with 10%FBS and 1% antibiotics in humidified atmosphere with 5%CO2 at 37℃

extract_protocol:
The integrity of total RNA was detected by agarose gel electrophoresis, and NanoDrop ND-1000 was used for quantitative and further quality inspection. 1 ~ 2 μg total RNA was selected from each sample for sequencing library construction. The total RNA was first enriched with NEB Next ® Poly (A) mRNA Magnetic Isolation Module (or RiboZero Magnetic Gold Kit for rRNA removal).
The treated product RNA was used to construct the library with KAPA Stranded RNA-Seq Library Prep Kit ( Roche ).

treatment_protocol: HSF cells were treated with 1640 complete medium, M1 type THP-1 cell culture supernatant, Chebulae Fructus extract + M1 type THP-1 cell culture supernatant, supramolecular psoralen + M1 type THP-1 cell culture supernatant for 3 days.

value: human skin fibroblast (HSF)

value: fibroblast

value: M1 type THP-1 supernatant + Terminalia chebula extract intervention for 3 days


title: 22RV1 PDCD4-WT2


title: 22RV1 PDCD4-WT3


title: B73xKi11_DS_R3

description: Library name: 78


title: sample 78_genomic DNA from blood sample T03655

value: major depressive disorder

value: female


title: B73xKi11_DS_R2

description: Library name: 77

value: DS


title: sample 77_genomic DNA from blood sample T03654


title: sample 80_genomic DNA from blood sample T03672


title: sample 76_genomic DNA from blood sample T03626


title: M1+0.005-2-2

description:
Library name: Sample14
M1+0.005-2-2


title: sample 75_genomic DNA from blood sample T03591

value: male


title: M1+0.005-2-1

description:
Library name: Sample13
M1+0.005-2-1


title: T1D.2 enteroid cells, DF

city: Nashik

first: Vishwesh

last: Bharadiya

state: Maharashtra

address: Plot No. 27, Vishwesh Children Hospital, Tidke Colony

country: India

institute: Johns Hopkins University School of Medicine

data_processing:
Raw sequence reads were checked for quality using the FASTQC package ver. 0.11.9; Illumina adapters and low-quality basepairs were trimmed using TrimGalore ver. 0.6.5 with default settings.
Trimmed reads were aligned to human genome build GRCh38.98 using Gencode v40 and a count matrix was generated from the aligned reads using feature Counts. For alignment and counts, the Dragen Bio-IT Platform version 3.10 using specific RNA flags including duplicate marking was employed.
Following count generation, we employed R version 4.1.0 and edgeR for normalization, testing procedures, PCA clustering, and differential expression analysis.
Assembly: GRCh38.98
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: duodenum

growth_protocol: Human enteroids were maintained as cysts embedded in Matrigel in 24-well plates and cultured in Wnt3A, Rspon-1, and Noggin containing growth medium.

extract_protocol:
Total RNA from harvested enteroids was extracted using the PureLink RNA Mini Kit (Life Technologies, Carlsbad, CA) according to the manufacturer’s protocol.
The NEBNext mRNA Library Prep Reagent Set for Illumina was then used to prepare individually bar-coded libraries. Library concentration was assessed using the Quant-iT™ PicoGreen® dsDNA Reagent, and the library quality was estimated by utilizing the Caliper LabChip GX DNA High Sense kit. Accurate quantification for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification Kit. Paired-end sequencing (25 million, 100-bp, paired-end reads) was performed on Illumina NovaSeq 6000 sequencers.

treatment_protocol: For differentiation of enteroids, growth medium was replaced with Wnt3A and Rspon free medium for 5-6 days.

value: duodenum

value: Intestinal enteroid

value: Type 1 diabetes

value: without Wnt and Rspond


title: sample 81_genomic DNA from blood sample T03706


title: B73xKi11_DS_R1

description: Library name: 76

value: leaf blade


title: M1+0.005-2-3

description:
Library name: Sample15
M1+0.005-2-3


title: M1+0.001pct1-4

description:
Library name: Sample12
M1+0.001pct1-4

value: M1 type THP-1 supernatant + Supramolecular bakuchiol intervention for 3 days


title: B73xKi11_WW_R2

description: Library name: 74


title: sample 73_genomic DNA from blood sample T03580


title: M1+0.001pct1-3

description:
Library name: Sample11
M1+0.001pct1-3


title: T1D.1 enteroid cells, DF


title: M1+0.001pct1-2

description:
Library name: Sample10
M1+0.001pct1-2


title: B73xKi11_WW_R1

description: Library name: 73


title: T1D.2 enteroid cells, UD

value: with Wnt and Rspond


title: T1D.1 enteroid cells, UD


title: sample 72_genomic DNA from blood sample T03577

value: normal


title: B73xKi3_DS_R3

description: Library name: 72


title: 22RV1 PDCD4-WT1

value: prostate

value: epithelial cell


title: HS.3 enteroid cells, DF

value: healthy


title: sample 71_genomic DNA from blood sample T03499


title: B73xKi3_DS_R2

description: Library name: 71


title: M1+0.001pct1-1

description:
Library name: Sample9
M1+0.001pct1-1

value: human skin fibroblast (HSF)

value: fibroblast


title: sample 70_genomic DNA from blood sample T03414


title: M1-4

description:
Library name: Sample8
M1-4

value: M1 type THP-1 supernatant was intervened for 3 days


title: HS.3 enteroids cells, UD


title: B73xKi3_DS_R1

description: Library name: 70


title: sample 69_genomic DNA from blood sample T03374

value: major depressive disorder

value: female


title: M1-3

description:
Library name: Sample7
M1-3


title: HS.2 enteroid cells, DF


title: B73xKi3_WW_R3

description: Library name: 69

value: WW


title: sample 74_genomic DNA from blood sample T03587


title: B73xKi11_WW_R3

description: Library name: 75


title: HS.2 enteroids cells, UD

value: duodenum


title: B73xKi3_WW_R2

description: Library name: 68


title: M1-1

description:
Library name: Sample5
M1-1


title: HS.1 enteroid cells, DF

value: Intestinal enteroid


title: 1640-4

description:
Library name: Sample4
1640-4

value: 1640 complete medium intervention for 3 days


title: HS.1 enteroids cells, UD


title: sample 66_genomic DNA from blood sample T03044

value: male


title: B73xKi3_WW_R1

description: Library name: 67

value: leaf blade


title: 1640-3

description:
Library name: Sample3
1640-3


title: B73xIL14H_DS_R3

description: Library name: 66

value: DS


title: M1-2

description:
Library name: Sample6
M1-2


title: sample 65_genomic DNA from blood sample T03043


title: sample 64_genomic DNA from blood sample T02942


title: sample 63_genomic DNA from blood sample T02847


title: sample 62_genomic DNA from blood sample T02844


title: S3 sepsis immunosuppression patient3

type: RNA

city: Beijing

first: Wenjia

last: Zhang

address: Yinghua Road

institute: China-Japan Friendship Hospital

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: After hybridization, the arrays were washed and scanned using the Agilent Scanner G2505C.

data_processing:
Raw data were extracted from array images using Feature Extraction software (version 10.7.1.1, Agilent Technologies).Raw data were normalized using the quantile algorithm.Differentially expressed genes were identified by fold change and P value calculated with t-test (threshold: fold change >= 2.0 and P value <= 0.05).
alldata.csv represents gProcessedSignal(raw) and normalized signals

source_name: sepsis immunosuppression patient

label_protocol: Total RNA was converted to double-stranded cDNA, then to cRNA, and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Blood samples were collected from three patients diagnosed with sepsis-induced immunosuppression and three healthy individuals. PBMCs were isolated from whole blood using standard Ficoll density gradient centrifugation.

tag: condition

value: sepsis-induced immunosuppression

value: human PBMC


title: B73xIL14H_DS_R2

description: Library name: 65


title: B73xIL14H_WW_R3

description: Library name: 63


title: B73xIL14H_WW_R2

description: Library name: 62


title: 1640-1

description:
Library name: Sample1
1640-1


title: sample 60_genomic DNA from blood sample T02819


title: B73xHP301_DS_R3

description: Library name: 60


title: B73xIL14H_WW_R1

description: Library name: 61


title: sample 68_genomic DNA from blood sample T03296

value: normal


title: sample 61_genomic DNA from blood sample T02827


title: C3 healthy person3

source_name: healthy person

value: control


title: sample 67_genomic DNA from blood sample T03052


title: C2 healthy person2


title: B73xHP301_DS_R2

description: Library name: 59


title: EPSC in P2, MeRIP, Replicate 2

city: Ithaca

first: Weiyu

state: NY

address: 215 Tower Rd, Biotechnology Building

department: MBG

institute: Cornell University

data_processing:
Illumina RTA software used for image identification and basecalling.
Raw reads were trimmed using Trim Galore (v0.6.10) , filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs.
Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1).
Samtools view (v1.18) was used to separate stranded reads with “-d XS:+” and “-d XS:-”. Strand-specific genome coverage bigwig files were generated using bamCompare from Deeptools (v3.5.1).
Assembly: hg38
Supplementary files format and content: BigWig files for m6A signal

molecule: polyA RNA

extract_protocol:
Total RNA from P0 and P2 hEPSCs was extracted using TRIzol.
The NEBNext® Ultra™ II RNA Library Prep Kit (NEB, E7770) was used to construct libraries for both the input and IP samples.
MeRIP-seq

value: expanded potential stem cells

value: METTL3 inducible knockout

value: DOX


title: sample 59_genomic DNA from blood sample T02816


title: sample 58_genomic DNA from blood sample T02782


title: B73xIL14H_DS_R1

description: Library name: 64


title: B73xHP301_DS_R1

description: Library name: 58


title: C1 healthy person1


title: EPSC in P2, Input, Replicate 2


title: sample 57_genomic DNA from blood sample T02768


title: B73xHP301_WW_R3

description: Library name: 57


title: 1640-2

description:
Library name: Sample2
1640-2

value: human skin fibroblast (HSF)

value: fibroblast


title: S2 sepsis immunosuppression patient2


title: sample 56_genomic DNA from blood sample T02760

value: major depressive disorder

value: female


title: EPSC in P2, MeRIP, Replicate 1


title: B73xHP301_WW_R1

description: Library name: 55

value: WW


title: EPSC in P2, Input, Replicate 1


title: S1 sepsis immunosuppression patient1


title: B73xHP301_WW_R2

description: Library name: 56


title: mock malaria blood infection, plasmo, mRNA Illumina

city: Antwerp

first: Anna

last: Rosanas-Urgell

address: Nationalestraat 155

department: Department of Biomedical Sciences

country: Belgium

institute: Institute of Tropical Medicine Antwerp

description:
Library name: X104974.001.014_S1_L001
no depletion

data_processing:
Raw reads were screened with FastQ Screen v0.15.3 (in bwa mode) against the human (GRCh38.p14 – RefSeq assembly GCF_000001405.40) and P. knowlesi (strain H – RefSeq assembly GCF_000006355.2) reference genomes to assess the proportion of reads derived from each. The nf-core/rnaseq v3.14 Nextflow workflow of the nf-core collection was then used for processing the reads. Briefly, raw reads underwent FastQC (v0.12.1) quality control and were filtered and trimmed by Trim Galore v0.6.7 and cutadapt v3.4. Reads were then competitively aligned to the concatenated human and P. knowlesi reference genomes using STAR v2.7.9a (51) and gene expression was quantified with salmon v1.10.1 (52) in alignment-based mode. A concatenated version of the human (RefSeq Annotation Release GCF_000001405.40-RS_2023_10) and P. knowlesi (GCF_000006355.2 - Apr 3, 2023) annotations was used.
For GEO raw data submission, P. knowlesi paired reads were extracted in fastq format from the human-parasite combined bam alignment files (i.e. after trimming and alignment to the concatenated human and parasite reference genomes) using samtools 1.21 by first filtering the combined bam file on the P. knowlesi H reference's chromosomes/regions (samtools view -L <<Pknowlesi_genome.bed>), and then converting back to fastq files (samtools collate followed by samtools fastq using -s option), while discarding singletons.
Assembly: human genome (GRCh38.p14 – RefSeq assembly GCF_000001405.40); human annotation ((RefSeq Annotation Release GCF_000001405.40-RS_2023_10); P. knowlesi genome (strain H – RefSeq assembly GCF_000006355.2); P. knowlesi annotation (GCF_000006355.2 - Apr 3, 2023)
Supplementary files format and content: *.quant.sf: Salmon transcript-level quantification files per sample for all human and P. knowlesi reads. Plain text tab-separated: Name, Length, EffectiveLength, TPM, NumReads.
Supplementary files format and content: *.quant.genes.sf: Salmon gene-level quantification files per sample for all human and P. knowlesi reads. Plain text tab-separated: Name, Length, EffectiveLength, TPM, NumReads.
Supplementary files format and content: salmon.merged.gene_counts.tsv: Gene-level (aggregated via tximport) salmon raw counts in plain text tab-separated format for all human and P. knowlesi reads merged across all samples. Contains gene name, gene id and 1 count column per sample.
Supplementary files format and content: salmon.merged.gene_tpm.tsv: Gene-level (aggregated via tximport) salmon TPM values in plain text tab-separated format for all human and P. knowlesi reads merged across all samples. Contains gene name, gene id and 1 TPM column per sample.
Supplementary files format and content: salmon.merged.gene_lengths.tsv: Matrix of average within-sample transcript lengths for each human and P. knowlesi gene across all samples.
Supplementary files format and content: salmon.merged.gene_counts.rds: RDS object that can be loaded in R that contains a SummarizedExperiment container with the TPM (abundance), estimated counts (counts) and transcript length (length) in the assays slot for genes, for all human and P. knowlesi reads merged across all samples.

organism: Plasmodium knowlesi

source_name: whole blood

growth_protocol: P. knowlesi A1-H.1 strain parasites were maintained at 3% hematocrit in continuous culture between 0.5 and 10% parasitemia in O+ blood and incubated at 37°C under atmospheric conditions of 90% N2, 5% O2, 5% CO2.

extract_protocol:
RNeasy Qiagen RNA extraction kit (manufacturer's protocol with on-column DNA digestion) and eluted in 30 uL RNase-free water.
Libraries were constructed using an mRNA Qiagen (QIAseq Stranded mRNA Lib Kit), total RNA Qiagen (QIAseq Stranded RNA Lib Kit), or mRNA Illumina kit (Illumina Stranded mRNA Prep, Ligation). FastSelect globin depletion and/or rRNA depletion was applied per sample as noted in the description as per manufacturer's instructions.

treatment_protocol: Different white blood cell (WBC) depletion methods (cent/pip, plasmo, PMACS, cellulose) were applied to aliquots of a P. knowlesi mock natural infection sample and compared to a no filter control. Briefly, the buffy coat was removed using a pipette after centrifugation to separate the plasma from red blood cell pellet (cent/pip). The mock sample was passed through a pre-wet Plasmodipur filter and washed to deplete WBCs (plasmo). Half of an aliquot was passed through a Plasmodipur filter and half through a MACS column to enrich for late life stages (PMACS). A cellulose columns was made with 1 mL packed cellulose, prewet, and the mock sample was allowed to flow through before washing the column. All WBC methods were then centrifuged and 100 uL of RBC pellet was stored in 500 uL RNA protect (Qiagen) Each method (including the no filter) was repeated in triplicate and then pooled before being divided among the three library preparation kits.

value: whole blood

value: blood stage

tag: developmental stage

value: mixed asexual

value: WBC depletion - Plasmodipur filter


title: mock malaria blood infection, cellulose, mRNA Illumina

description:
Library name: X104974.001.016_S1_L001
no depletion

value: WBC depletion - cellulose column


title: sample 55_genomic DNA from blood sample T02749

value: male


title: B73xCML333_DS_R3

description: Library name: 54

source_name: leaf blade

value: leaf blade

value: DS


title: sample 91_genomic DNA from blood sample T04012

source_name: blood sample of control patient

value: normal


title: sample 53_genomic DNA from blood sample T02692


title: EPSC in P0, Input, Replicate 2

value: expanded potential stem cells


title: sample 54_genomic DNA from blood sample T02699


title: B73xCML333_DS_R2

description: Library name: 53


title: sample 52_genomic DNA from blood sample T02686


title: mock malaria blood infection, no filter, mRNA Illumina

description:
Library name: X104974.001.012_S1_L001
no depletion

value: no WBC depletion


title: EPSC in P0, MeRIP, Replicate 2

value: METTL3 inducible knockout

value: DOX


title: B73xCML333_DS_R1

description: Library name: 52


title: mock malaria blood infection, PMACS, mRNA Illumina

description:
Library name: X104974.001.015_S1_L001
no depletion

value: WBC depletion - Plasmodipur filter and MACS column


title: sample 51_genomic DNA from blood sample T02676


title: mock malaria blood infection, cent/pip, mRNA Illumina

description:
Library name: X104974.001.013_S1_L001
no depletion

value: WBC depletion - buffy coat removal (cent/pip)


title: sample 50_genomic DNA from blood sample T02635


title: EPSC in P2, 4C, Replicate 3

data_processing:
Illumina RTA software used for image identification and basecalling.
Raw reads were trimmed using Trim Galore (v0.6.10) , filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs.
Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1).
BWA was used for alignment to the human genome (GRCh38 assembly) to identify chimeric reads. Subsequently, Bowtie2 (v2.4.5) was used to align TE reads and genomic reads. Only uniquely mapped genomic alignments were retained.
Assembly: hg38
Supplementary files format and content: BigWig files LTR5 or SVA_D interating signals.

extract_protocol:
Approximately 1 × 10^7 P2 hEPSCs were cross-linked with 2% formaldehyde for 10 minutes, quenched with 0.13 M glycine, lysed with lysis buffer (0.5% NP40 and 1% TX-100)
The NEBNext® Ultra™ II RNA Library Prep Kit (NEB, E7770) was used to construct libraries for both the input and IP samples.
4C-seq primers carry overhang sequences such that after PCR the amplified products, but not the 3C template itself, are equipped with the up- and downstream (P5/P7) Illumina sequencing adapters and thus require no further library preparation for sequencing.


title: EPSC in P0, MeRIP, Replicate 1


title: B73xCML333_WW_R3

description: Library name: 51


title: B73xCML333_WW_R2

description: Library name: 50


title: mock malaria blood infection, plasmo, total RNA Qiagen, FSglobin/rRNA

description:
Library name: X104974.001.009_S1_L001
FastSelect globin and HMR rRNA depletion


title: EPSC in P2, 4C, Replicate 2


title: B73xCML333_WW_R1

description: Library name: 49


title: sample 48_genomic DNA from blood sample T02467


title: B73xCML322_DS_R3

description: Library name: 48


title: mock malaria blood infection, cent/pip, total RNA Qiagen, FSglobin/rRNA

description:
Library name: X104974.001.008_S1_L001
FastSelect globin and HMR rRNA depletion


title: METTL3 iKO hEPSC Clone 1, 3 Days After Culture in TSC Medium without DOX, Replicate 2

data_processing:
Illumina RTA software used for image identification and basecalling.
Raw reads were trimmed using Trim Galore (v0.6.10) , filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Gene annotation from Ensembl (v107) was used, and featureCounts (v2.0.3) was used to count mapped reads for genomic feature.
FeatureCounts was used to quanlify gene expression
For quantification of transposable elements (TEs), SQuIRE (v 0.9.9.92) was used.
Assembly: hg38
Supplementary files format and content: comma-separated count values for each Sample.

growth_protocol: hEPSCs were maintained on SNL 76/7 feeder layers and enzymatically passaged with TrypLE (Thermo Fisher Scientific, 12604013) at a 4 days interval at a 1:4 to 1:8 ratio. hEPSCM is an N2B27-based media supplement with 4 inhibitors 2.5 μM XAV939, 2.5 μM endo-IWR1 (Tocris, 3532), 1 μM CHIR99021 (Torcris, 4423) and 0.1 μM A419259 (Tocris, 3914). N2B27 basal media consists of a 1:1 mixture of DMEM/F12 (Thermo, Cat.21331020) and Neurobasal Medium (Thermo, Cat. 21103049) with 200x N2 supplement and 100× B27 supplement, 100× ITS-X, 50 μM β-mercaptoethanol, 1% Penicillin-Streptomycin-Glutamine, 100× non-essential amino acid and 50 μg/mL Vitamin C. Primed state hPSCs were maintained in mTESR1 medium on Matrigel (Corning, 354230). Naïve state hPSCs were maintained in PXGL medium on feeder cells. The PXGL medium is prepared by supplementing N2B27 basal medium with 1 μM PD0325901, 2 μM XAV939, 2 μM Go6983, 0.45% BSA and human leukemia inhibitory factor (hLIF, 10 ng/mL). Primed and naïve state hPSCs converted from hEPSCs were cultured in mTESR1 and PXGL medium for more than five passages to achieve stable respective pluripotency state, then perform downstream experiments. hEPSCs  were harvested using TrypLE for 3 mins and seeded in human trophoblast stem cell medium (TSCM) on cell culture plate pre-coated with 1% Matrigel with a cell density of 10000 cells per 6-well plate. Human TSCM is made up of DMEM/F12 containing 0.5x penicillin-streptomycin, 1% fetal bovine serum, 1x ITS-X (Thermo Fisher Scientific, 5150056), 0.3% bovine albumin fraction V (Thermo Fisher Scientific, 15260037), supplemented with 50 μg/mL L-asorbic acid (Sigma, A8960), 50 μg/mL human EGF (Peprotech, AF-100-15), 2 μM CHIR99021 (Torcris, 4423), 0.5 μM A-83-01 (Tocris, 2939), 1 μM SB431542 (Tocris, 1614), 10 μM valproic acid (Tocris, 2815) and 2.5 μM Y27632 (Selleckchem ,S1049).

extract_protocol:
Total RNA was extracted using Trizol reagent. mRNA was enriched from total RNA using magnetic beads with poly-A oligo attached. Divalent cations were used for fragmentation under elevated temperature with First-strand synthesis reaction buffer from New England Biolabs. Next, the first-strand cDNA was produced using M-MLV reverse transcriptase without RNase H in the presence of random hexamer primer. Subsequently, the second-strand cDNA was synthesized with DNA polymerase I and RNase H. Synthesized DNA fragments were ligated to Next Adaptors from New England Biolabs and amplified by PCR using Phusion high-fidelity DNA polymerase (Vazyme). After purification, assessment of library quality was carried out in Agilent Bioanalyzer 2100 system. Sequencing of the prepared library was performed using Illumina Hiseq platform.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: 5 ng/mL DOX was added to maintain the expression of METTL3 transgenes. DOX was removed to induce METTL3 knockout.


title: mock malaria blood infection, no filter, total RNA Qiagen, FSglobin/rRNA

description:
Library name: X104974.001.007_S1_L001
FastSelect globin and HMR rRNA depletion


title: B73xCML322_DS_R2

description: Library name: 47


title: sample 46_genomic DNA from blood sample T02339

value: female


title: mock malaria blood infection, cellulose, total RNA Qiagen, FSglobin/rRNA

description:
Library name: X104974.001.011_S1_L001
FastSelect globin and HMR rRNA depletion


title: METTL3 iKO hEPSC Clone 1, 3 Days After Culture in TSC Medium without DOX, Replicate 1


title: METTL3 iKO hEPSC Clone 1, 3 Days After Culture in TSC Medium with DOX, Replicate 2


title: mock malaria blood infection, cellulose, mRNA Qiagen, FSglobin

description:
Library name: X104974.001.005_S1_L001
FastSelect globin depletion


title: B73xCML322_DS_R1

description: Library name: 46


title: sample 45_genomic DNA from blood sample T02225


title: mock malaria blood infection, PMACS, mRNA Qiagen, FSglobin

description:
Library name: X104974.001.004_S1_L001
FastSelect globin depletion


title: METTL3 iKO hEPSC Clone 1, 3 Days After Culture in TSC Medium with DOX, Replicate 1


title: EPSC in P0, Input, Replicate 1


title: sample 44_genomic DNA from blood sample T02093


title: B73xCML322_WW_R3

description: Library name: 45

value: WW


title: B73xCML322_WW_R2

description: Library name: 44


title: mock malaria blood infection, plasmo, mRNA Qiagen, FSglobin

description:
Library name: X104974.001.003_S1_L001
FastSelect globin depletion

value: whole blood


title: sample 43_genomic DNA from blood sample T01974


title: METTL3 iKO naïve hESC Clone 2 in Passage 3 without DOX, Replicate 2

value: naive pluripotency stem cells


title: mock malaria blood infection, PMACS, total RNA Qiagen, FSglobin/rRNA

description:
Library name: X104974.001.010_S1_L001
FastSelect globin and HMR rRNA depletion

value: blood stage

value: mixed asexual


title: sample 47_genomic DNA from blood sample T02433


title: METTL3 iKO naïve hESC Clone 2 in Passage 3 without DOX, Replicate 1


title: sample 42_genomic DNA from blood sample T01827


title: sample 49_genomic DNA from blood sample T02629


title: mock malaria blood infection, no filter, mRNA Qiagen, FSglobin

description:
Library name: X104974.001.001_S1_L001
FastSelect globin depletion


title: EPSC in P2,4C, Replicate 1


title: mock malaria blood infection, no filter, mRNA Qiagen, FSglobin/rRNA

description:
Library name: X104974.001.006_S1_L001
FastSelect globin and HMR rRNA depletion


title: METTL3 iKO naïve hESC Clone 2 in Passage 2 without DOX, Replicate 2


title: sample 41_genomic DNA from blood sample T01794


title: WW1_LCL

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

institute: Ulm University and Ulm University Medical Center

description: Lymphoblastoid cell lines (LCL)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 Beadchip using standard Illumina protocol.

scan_protocol: The arrays were scanned using a iScan device.

data_processing: Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction.

label: biotin

source_name: unknown

extract_protocol: genomic DNA was extracted and purified according to commercially available kits from Qiagen according to standard instructions

value: unknown


title: B73xCML322_WW_R1

description: Library name: 43


title: sample 40_genomic DNA from blood sample T01765

value: major depressive disorder

value: male


title: IARC304

description: Lymphoblastoid cell lines (LCL)


title: METTL3 iKO naïve hESC Clone 2 in Passage 2 without DOX, Replicate 1


title: B73xCML277_DS_R1

description: Library name: 40

value: leaf blade

value: DS


title: METTL3 iKO naïve hESC Clone 2 with DOX, Replicate 2


title: AT7BER

description: Lymphoblastoid cell lines (LCL)


title: METTL3 iKO naïve hESC Clone 2 with DOX, Replicate 1


title: sample 38_genomic DNA from blood sample T01380

value: normal


title: B73xCML277_WW_R2

description: Library name: 38


title: METTL3 iKO primed hESC Clone 1 in Passage 3 without DOX, Replicate 2

value: primed pluripotency stem cells


title: sample 37_genomic DNA from blood sample T01308


title: B73xCML277_DS_R2

description: Library name: 41


title: B73xCML277_WW_R3

description: Library name: 39


title: mock malaria blood infection, cent/pip, mRNA Qiagen, FSglobin

description:
Library name: X104974.001.002_S1_L001
FastSelect globin depletion


title: B73xCML277_WW_R1

description: Library name: 37


title: AT17BER

description: Lymphoblastoid cell lines (LCL)


title: METTL3 iKO primed hESC Clone 1 in Passage 3 without DOX, Replicate 1

value: METTL3 inducible knockout


title: METTL3 iKO primed hESC Clone 1 in Passage 2 without DOX, Replicate 2


title: B73xCML247_DS_R3

description: Library name: 36


title: WW1

description: endemic Burkitt lymphoma-derived cell line

source_name: lymph node

value: lymph node


title: sample 35_genomic DNA from blood sample T01284

source_name: blood sample of patient with major depressive disorder


title: B73xCML247_DS_R2

description: Library name: 35


title: METTL3 iKO primed hESC Clone 1 in Passage 2 without DOX, Replicate 1


title: 01P0389

description: Lymphoblastoid cell lines (LCL)


title: GM12878

description: Lymphoblastoid cell lines (LCL)


title: sample 39_genomic DNA from blood sample T01408


title: sample 33_genomic DNA from blood sample T01119


title: Seraphine


title: B73xCML247_WW_R3

description: Library name: 33


title: RAJI


title: B73xCML247_DS_R1

description: Library name: 34


title: sample 32_genomic DNA from blood sample T01111


title: NAMALWA


title: sample 31_genomic DNA from blood sample T01087


title: B73xCML247_WW_R2

description: Library name: 32


title: LY_91


title: sample 30_genomic DNA from blood sample T01053


title: B73xCML247_WW_R1

description: Library name: 31


title: METTL3 iKO hEPSC Clone 2 in Passage 3 without DOX, Replicate 1

value: expanded potential stem cells


title: B73xCML103_DS_R3

description: Library name: 30


title: sample 36_genomic DNA from blood sample T01288


title: EB_3


title: sample 34_genomic DNA from blood sample T01188


title: EB_1


title: sample 29_genomic DNA from blood sample T01008


title: METTL3 iKO hEPSC Clone 2 in Passage 2 without DOX, Replicate 1


title: B73xCML103_DS_R2

description: Library name: 29


title: METTL3 iKO hEPSC Clone 2 in Passage 2 without DOX, Replicate 2


title: sample 28_genomic DNA from blood sample T00965


title: METTL3 iKO primed hESC Clone 1 with DOX, Replicate 2

value: DOX


title: METTL3 iKO hEPSC Clone 2 with DOX, Replicate 2


title: JI

description: sporadic Burkitt lymphoma-derived cell line


title: sample 27_genomic DNA from blood sample T00957


title: METTL3 iKO primed hESC Clone 1 with DOX, Replicate 1


title: DAUDI


title: B73xCML103_WW_R3

description: Library name: 27


title: B73xCML277_DS_R3

description: Library name: 42


title: METTL3 iKO hEPSC Clone 2 in Passage 3 without DOX, Replicate 2


title: Ramos


title: B73xCML103_WW_R2

description: Library name: 26


title: METTL3 iKO hEPSC Clone 1 in Passage 3 without DOX, Replicate 2


title: sample 25_genomic DNA from blood sample T00913

value: female


title: METTL3 iKO hEPSC Clone 1 in Passage 3 without DOX, Replicate 1


title: sample 24_genomic DNA from blood sample T00805


title: B73xCML69_DS_R3

description: Library name: 24


title: CA_46


title: METTL3 iKO hEPSC Clone 1 in Passage 2 without DOX, Replicate 2


title: B73xCML103_DS_R1

description: Library name: 28


title: sample 23_genomic DNA from blood sample T00745


title: BLUE_1


title: METTL3 iKO hEPSC Clone 1 in Passage 2 without DOX, Replicate 1


title: B73xCML69_DS_R2

description: Library name: 23


title: sample 22_genomic DNA from blood sample T00731


title: BL_70


title: sample 26_genomic DNA from blood sample T00916


title: METTL3 iKO hEPSC Clone 2 with DOX, Replicate 1


title: B73xCML69_DS_R1

description: Library name: 22


title: sample 20_genomic DNA from blood sample T00558


title: BL_41


title: B73xCML69_WW_R3

description: Library name: 21

value: WW


title: sample 21_genomic DNA from blood sample T00597


title: B73xCML69_WW_R2

description: Library name: 20


title: BL_30


title: METTL3 iKO hEPSC Clone 1 with DOX, Replicate 1


title: METTL3 iKO hEPSC Clone 1 with DOX, Replicate 2


title: H12

city: Cluj-Napoca

first: Oana

last: Tudoran

address: Str. Republicii 34-36

department: Department of Genetics

country: Romania

institute: The Oncology Institute “Prof. Dr. Ion Chiricuță” in Cluj-Napoca

data_processing:
Fastqc was used for analyzing read quality while trimmomatic was utilized for removing identified low-quality reads and adapters.
Passing reads were further aligned to Hg38 genome and Gencode V35 (hg38) genomic annotation by STAR
Transcriptome was quantified by Salmon (Quasi-mapping mode) using Hg38 reference Gentrome (a combined reference of Hg38 reference genome and Gencode V35 transcriptome)
Quantified read counts were further normalized to transcript-per-million (TPM) on transcript-level and gene-level.
Log2(TPM+1) transformation was conducted to rescale expression levels.
Assembly: HG38
Supplementary files format and content: tab-delimited Log2(TPM+1) transformed whole transcriptome profile

extract_protocol:
MM1S cells treated with NGI-1 were harvested for RNA isolation. 200ng RNA was extracted and sent for sequencing.
Total RNA sequencing and paired-end options were selected. >60 million paired-end reads were obtained from each sample.

value: multiple myeloma

tag: time point

value: 5 day


title: B73xCML103_WW_R1

description: Library name: 25


title: BL_2


title: sample 19_genomic DNA from blood sample T00511


title: B73xCML69_WW_R1

description: Library name: 19


title: H11


title: DG_75


title: sample 18_genomic DNA from blood sample T00488


title: MPI_895

description: sporadic Burkitt lymphoma, cryo-preserved, EBV-positive


title: B73xB97_DS_R3

description: Library name: 18


title: H10


title: sample 17_genomic DNA from blood sample T00429


title: B73xB97_DS_R2

description: Library name: 17


title: MPI_680

description: sporadic Burkitt lymphoma, cryo-preserved, EBV-negative


title: sample 16_genomic DNA from blood sample T00337


title: H9

value: 3 day


title: B73xB97_DS_R1

description: Library name: 16


title: MPI_623

description: sporadic Burkitt lymphoma, cryo-preserved, EBV-unknown


title: sample 15_genomic DNA from blood sample T00317


title: MPI_622


title: B73xB97_WW_R3

description: Library name: 15


title: sample 14_genomic DNA from blood sample T00138


title: MPI_619


title: H7


title: MPI_618


title: H6

value: 2 day


title: B73xB97_WW_R1

description: Library name: 13


title: H5


title: MPI_593


title: sample 12_genomic DNA from blood sample C1150


title: B73xA619_DS_R3

description: Library name: 12


title: B73xA619_DS_R2

description: Library name: 11


title: H4


title: MPI_589


title: sample 11_genomic DNA from blood sample C1122


title: H3

value: 0 day


title: B73xA619_DS_R1

description: Library name: 10


title: sample 10_genomic DNA from blood sample C1056

value: major depressive disorder


title: H2


title: sample 9_genomic DNA from blood sample C0971

value: male


title: MPI_588


title: B73xA619_WW_R3

description: Library name: 9

value: leaf blade


title: MPI_580


title: H8


title: sample 8_genomic DNA from blood sample C0897


title: B73xA619_WW_R2

description: Library name: 8


title: MPI_579


title: B73xB97_WW_R2

description: Library name: 14


title: H1


title: sample 7_genomic DNA from blood sample C0869


title: MPI_576


title: B73xA619_WW_R1

description: Library name: 7


title: sample 13_genomic DNA from blood sample C1257


title: MPI_568


title: B73xA188_DS_R3

description: Library name: 6

value: DS


title: MPI_532


title: B73xA188_DS_R2

description: Library name: 5


title: sample 4_genomic DNA from blood sample C0814


title: sample 5_genomic DNA from blood sample C0835


title: MPI_528


title: sample 3_genomic DNA from blood sample C0747


title: B73xA188_DS_R1

description: Library name: 4


title: MPI_527


title: B73xA188_WW_R3

description: Library name: 3


title: sample 2_genomic DNA from blood sample C0310


title: B73xA188_WW_R2

description: Library name: 2


title: MPI_323


title: sample 1_genomic DNA from blood sample C0171


title: B73xA188_WW_R1

description: Library name: 1


title: Pt8Site B_T3

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

hyb_protocol: Hybridization was performed at 45°C for 16 hours in a GeneChip Hybridization Oven. Arrays were washed and stained using a GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000, following the Affymetrix protocol.

data_processing:
Raw data were normalized using the Robust Multi-Chip Average (RMA) method in Partek. Probe sets were aggregated into genes and log2-transformed. Gene annotations were matched using the "hugene10sttranscriptcluster.db" R library.
Processed data file contains: the normalized log2-transformed intensity values from the Affymetrix GeneChip Human Gene 1.0 ST Arrays, representing relative gene expression levels.

source_name: tumor biopsy

label_protocol: First- and second-strand cDNA were synthesized from 30 ng of total RNA using the NuGEN Ovation Pico WTA System V2. cDNAs were fragmented, biotinylated with the NuGEN Encore Biotin Module, and hybridized to GeneChip Human Gene 1.0 ST Arrays (Affymetrix).

growth_protocol: Patients with metastatic breast cancer were enrolled and tumor tissue was collected via fine-needle aspiration (FNA) biopsy. Tumors were maintained in a sterile environment until processed for RNA extraction.

extract_protocol: Total RNA was extracted from tumor FNA samples using Qiagen RNA extraction kits (Catalog numbers: 217004/74104). RNA quality was verified using a Nanodrop spectrophotometer and an Agilent 2100 Bioanalyzer.

treatment_protocol: Patients received topical Imiquimod (IMQ) 5% cream, applied 5 days per week for 8 weeks to designated areas. Radiotherapy (RT) was administered to specific tumor regions (30 Gy over five fractions). Cyclophosphamide (200 mg/m²) was given intravenously one week prior to treatment in designated cohorts.

tag: local response

value: PR

tag: site

value: Site B

tag: tumor

value: YES

value: SD


title: MPI_172

tag: tissue

value: lymph node


title: sample 6_genomic DNA from blood sample C0852


title: Pt8Site A_T3

value: Site A


title: MPI_171


title: HMEC_donor1_YDAC(-) 48H

city: Nagakute

first: Akihito

last: Inoko

state: Aichi

address: 1-1 Yazakokarimata

institute: Aichi Medical University School of Medicine

description: Gene expression in HMEC after YDAC removal for 48 hr

hyb_protocol: Gene Expression Wash Pack (5188-5327 : Agilent) was used, and both hybridazation and the wash were performed according to Agilent's standard manuals.The Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was finally hybridized to Agilent SurePrint G3 Human GE Microarray 8 x 60K Ver3.0.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner according to the manufacturer’s protocol.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) according to the manufacturer’s protocol.  Background was subtracted according to the manufacturer’s protocol.

source_name: HMEC,YDAC(-) 48H

label_protocol: Following processes were supported by DNA Chip Research Inc. (Tokyo, Japan). Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA and processed using the Low Input Quick Amp Labeling Kit (5190-2305 : Agilent), RNA Spike in kit (5188-5282 : Agilent), Qiagen RNeasy mini kit (74104 : Qiagen), and Gene Expression Hybridization Kit (5188-5242 : Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the Agilent 2100 Bioanalyzer.

growth_protocol: HMEC were purchased from Lonza (Basel, Switzerland). Long-term expansion of epithelial stem/progenitor cells without feeder cells was achieved by using F medium (Liu et al., 2012) and our new combination of four inhibitors named “YDAC”. F medium was composed of 3:1 (v/v) Ham’s F-12 (087-08335, Wako, Tokyo, Japan) and DMEM (043-30085, Wako), 5% fetal bovine serum, 0.4 µg/ml hydrocortisone (086-10191, Wako), 5 µg/ml insulin (I9278, Sigma, St. Louis, MO, USA), 8.4 ng/ml cholera toxin (030-20621, Wako), 10 ng/mL epidermal growth factor (059-07873, Wako), 24 µg/ml adenine (A2786, Wako), 100 ug/ml streptomycin (Meiji Seika, Tokyo, Japan), 100 U/ml penicillin (Meiji Seika), 250 ng/ml Amphotericin B (A2942, Sigma), and 10 µg/ml gentamicin (078-06061, Wako). YDAC is a combination of 10 µM Y-27632 (1000583, Cayman Chemical, Ann Arbor, MI, USA), 1 µM DMH1 (041-33881, Wako), 1 µM A-83-01 (039-24111, Wako), and 1 µM CHIR99021 (038-23101, Wako).

extract_protocol: RNA was prepared using the mirVana™ miRNA Isolation Kit, with phenol (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Differentiation into mammary epithelium at 2D condition was achieved by cultivating the stem/progenitor cells in F medium without YDAC for 2-3 days.

value: Mammary gland

tag: gender

value: Female

tag: age


title: MPI_144


title: Pt6Site B_T3


title: PrEC_donor1_YDAC(-) 48H

hyb_protocol: Gene Expression Wash Pack (5188-5327 : Agilent) was used, and both hybridization and the wash were performed according to Agilent's standard manuals.The Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was finally hybridized to Agilent SurePrint G3 Human GE Microarray 8 x 60K Ver3.0.

source_name: PrEC,YDAC(-) 48H

growth_protocol: PrEC were purchased from Lonza (Basel, Switzerland). Long-term expansion of epithelial basal cells without feeder cells was achieved by using F medium (Liu et al., 2012) and our new combination of four inhibitors named “YDAC”. F medium was composed of 3:1 (v/v) Ham’s F-12 (087-08335, Wako, Tokyo, Japan) and DMEM (043-30085, Wako), 5% fetal bovine serum, 0.4 µg/ml hydrocortisone (086-10191, Wako), 5 µg/ml insulin (I9278, Sigma, St. Louis, MO, USA), 8.4 ng/ml cholera toxin (030-20621, Wako), 10 ng/mL epidermal growth factor (059-07873, Wako), 24 µg/ml adenine (A2786, Wako), 100 ug/ml streptomycin (Meiji Seika, Tokyo, Japan), 100 U/ml penicillin (Meiji Seika), 250 ng/ml Amphotericin B (A2942, Sigma), and 10 µg/ml gentamicin (078-06061, Wako). YDAC is a combination of 10 µM Y-27632 (1000583, Cayman Chemical, Ann Arbor, MI, USA), 1 µM DMH1 (041-33881, Wako), 1 µM A-83-01 (039-24111, Wako), and 1 µM CHIR99021 (038-23101, Wako).

treatment_protocol: Differentiation into epithelium in 2D condition was achieved by cultivating the basal cells in F medium without YDAC for 2-3 days.

value: Prostate gland

value: Male


title: HMEC_donor1_YDAC(+)

description: Gene expression in HMEC before YDAC removal

source_name: HMEC,YDAC(+)


title: MPI_114


title: PrEC_donor1_YDAC(+)

source_name: PrEC,YDAC(+)


title: Pt5Site B_T3


title: PDAC-PDX 14 - p2

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: For every sample, 600 ng of labeled specimens were hybridized on the Agilent Human Gene Expression v3 8x60K microarrays.

scan_protocol: After17 hours, slides were washed and scanned using the Agilent Scanner version C (G2505C, Agilent Technologies).

data_processing: Images were analyzed using the Feature Extraction software v10.7.3.1 (Agilent Technologies). Raw data elaboration was carried out with Bioconductor (www.bioconductor.org), using The LIMMA (LInear Models for Microarray Analysis) R package. Background correction was performed with the normexp method with an offset of 50, and quantile was used for the between-array normalization. The empirical Bayes method was used to compute a moderated t-statistics for class comparison.

source_name: pancreatic ductal adenocarcinoma PDX

label_protocol: mRNA from 100 ng of totRNA was amplified, labeled with Cy3 and purified with columns.

extract_protocol: RNA was extracted following standard procedures (PureLink RNA Mini Kit, Ambion).

tag: passage

value: p2 passage

value: PDAC-PDX orthotopically engrafted in the pancreas of immunodeficient mice


title: MPI_085


title: PDAC-PDX 11 - p4

value: p4 passage


title: MPI_084


title: PDAC-PDX 8 - p4


title: PDAC-PDX 11 - p2 [murine array]

hyb_protocol: For every sample, 600 ng of labeled specimens were hybridized on the Agilent Mouse Gene Expression v2 8x60K microarrays.

organism: Mus musculus

value: PDAC-PDX orthotopically engrafted  in the pancreas of immunodeficient mice


title: PDAC-PDX 13 - p2


title: PDAC-PDX 11 - p2


title: Pt31Site B_T3

value: PD


title: Lipus-7

city: Wuhan

first: Xiaojian

last: Cao

state: Hubei

address: No.1095 Jiefang Avenue

department: Department of Rehabilination Medicne

institute: Tongji Hospital

description: Library name: LIPUS7

data_processing:
Trimmomatic (version 0.38)
Read Alignment HISAT2 (version 2.0.5)
Bam sort  SAMtools
Read count StringTie
Assembly: RGSC Rnor_6.0 (Rat Genome Sequence Consortium, version 6.0)
Supplementary files format and content: Merged.txt
Supplementary files format and content: Raw counts matrix

organism: Rattus norvegicus

source_name: Whole Brain

extract_protocol:
TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA)
First, total RNA is extracted from the tissue ( rat sciatic nerve), and mRNA is isolated using magnetic beads with Poly-T oligo. The isolated mRNA is fragmented into smaller pieces, followed by complementary DNA (cDNA) synthesis through reverse transcription. The cDNA ends are repaired, and sequencing adapters are ligated to both ends of the cDNA fragments. PCR amplification enriches the library for the desired fragments. The quality and quantity of the library are assessed using a Qubit Fluorometer and an Agilent Bioanalyzer 2100. Finally, the prepared library is sequenced using the Illumina NovaSeq 6000 platform

value: Whole Brain

tag: genotype

tag: treatment

value: sciatic nerve crushed and treated with low intensity pulsed ultrasound therapy (250 mW/cm², 1 MHz) was applied unilaterally in vivo, 20% duty cycle, 5 minutes/day, 5 days/week, for 4 weeks.


title: PDAC-PDX 13 - p2 [murine array]


title: MPI_081


title: PDAC-PDX 4 - p4


title: Pt31Site A_T3

value: PR


title: PDAC-PDX 8 - p2


title: Lipus-6

description: Library name: LIPUS6


title: PDAC-PDX 4 - p2


title: PDAC-PDX 8 - p4 [murine array]


title: MPI_080


title: PDAC-PDX 11 - p4 [murine array]


title: Lipus-2

description: Library name: LIPUS2


title: PDAC-PDX 8 - p2 [murine array]


title: PDAC-PDX 4 - p4 [murine array]


title: Expsome-5

description: Library name: EXO5

value: sciatic nerve crushed and treated with 10 μL of 105 μg/mL of iPSC-Exosomes.


title: Pt30Site A_T3

value: YES


title: ETMR-PC culture1

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

description: 10x Genomics

data_processing:
Demultiplexing and preprocessing of the scRNA data was conducted with CellRanger v2.0.2 for KK21-M-074 to KK21-M-077. Similarly, CellRanger v3.0.2 was used for the cell line data (KK21-M-005 to KK21-M-009), and CellRanger v6.0.2 for the E18.5 samples KK22-M-198, KK22-M-199, KK22-M-200, KK22-M-273, KK22-M-274 and KK22-M-278.
After converting the raw 10X data to fastq format with CellRanger's mkfastq, the data was aligned against the murine reference transcriptome mm10 with the CellRanger count function using default values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cell lines

extract_protocol:
Cell dissociation using papain/DNAse solution, with incubation for 30min for primary tumors. Cell dissociation of 2D culture using Accutase and Trypsin EDTA for all conditions. All primary tumor samples were FACS sorted for live cells before taken for scRNA-seq.
Approximately 10,000 vital single-cells of each sample were processed for single-cell RNA sequencing using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, the Chromium Next GEM Chip G and the Single Index Kit T Set A (10X Genomics) according to the manufacturer's instructions. In brief, single-cell GEM (Gel Beads-in-Emulsion) were generated by the Chromium Controller, followed by GEM-RT (reverse transcription), Dynabeads cleanup, cDNA amplification, SPRIselect beads cleanup and Library construction. Quality, purity, size and concentrations of cDNA and libraries were assured by measurement on a Tapestation 2200 (Agilent Technologies). Indexed libraries were sequenced separately by the Illumina NextSeq500 sequencing platform.
scRNA-seq with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

value: cell lines

value: murine ETMR1 + and brain vascular pericyte (RBVP) from ScienCell Cat n. M1200


title: ETMR-PC culture2

description: 10x Genomics

value: murine ETMR2 + and brain vascular pericyte (RBVP) from ScienCell Cat n. M1201


title: MPI_077

value: lymph node


title: PDAC-PDX 4 - p2 [murine array]


title: Pt5Site A_T3

value: Site A

value: SD


title: Expsome-3

description: Library name: EXO3

value: sciatic nerve crushed and treated with 10 μL of 104 μg/mL of iPSC-Exosomes.


title: Pt27Site B_T3

value: Site B


title: MPI_067


title: ETMR-monoculture 2

description: 10x Genomics

value: murine ETMR2 cell line

tag: strain

value: hGFAP-cre; Ctnnb1(ex3)Fl/+SmoM2Fl/+


title: Pt30Site B_T3


title: Expsome-2

description: Library name: EXO2

value: sciatic nerve crushed and treated with 10 μL of 103 μg/mL of iPSC-Exosomes.


title: Pt27Site A_T3

value: CR

value: PD


title: Pt26Site B_T3


title: MPI_055


title: MPI_079


title: MPI_048


title: Pt26Site A_T3


title: Murine E16.5 cre -_2

description: 10x Genomics

source_name: fore-/midbrain

value: fore-/midbrain

value: cre-


title: Exosome+Lipus-3

description: Library name: EXO+LIPUS3

value: Whole Brain

value: sciatic nerve crushed and treated with 10 μL of 100 μg/mL of iPSC-Exosomes and low intensity pulsed ultrasound therapy (250 mW/cm², 1 MHz) was applied unilaterally in vivo, 20% duty cycle, 5 minutes/day, 5 days/week, for 4 weeks..


title: Exosome+Lipus-2

description: Library name: EXO+LIPUS2


title: ETMR-monoculture 1

description: 10x Genomics

value: cell lines

value: murine ETMR1 cell line


title: Exosome+Lipus-1

description: Library name: EXO+LIPUS1


title: Pt25Site B_T3

value: YES


title: MPI_043

value: lymph node


title: MPI_005


title: Murine E16.5 cre -_1

description: 10x Genomics


title: Control-9

description: Library name: CTRL9

value: sciatic nerve crushed


title: Pt25Site A_T3

value: Site A


title: D15_1596_R3A


title: Control-4

description: Library name: CTRL4

value: SD


title: Pt23Site B_T3

value: Site B


title: D15_1426_R6A


title: Pt23Site A_T3

value: NO


title: EPSC in P2, H3K27ac, Replicate 2, ChIP

data_processing:
Illumina RTA software used for image identification and basecalling.
Raw reads were trimmed using Trim Galore (v0.6.10) , filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs.
Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v 2.4.5)
Bigwig files were generated by bamCompare from Deeptools (v3.5.1).
Assembly: hg38
Supplementary files format and content: BigWig files normalized by IP signal minus input signal

extract_protocol:
Cells were harvested after feeder layer removal and fixed with 1% formaldehyde. Then cells were lysed and sonicated using Diagenode BioruptorPico UltraSonication System so that length of the majority of DNA fragments is between 100 to 500bp.
ChIP-seq library will be generated using NEBNext® UltraTM IIDNA Library Prep Kit

tag: cell type

value: expanded potential stem cells

value: METTL3 inducible knockout


title: D15_1423_R2A

description: sporadic Burkitt lymphoma, FFPE, EBV-negative


title: Pt22Site B_T3


title: EPSC in P2, H3K27ac, Replicate 1, ChIP

tag: cell line


title: D15_1405_R1A


title: D14_1463

description: sporadic Burkitt lymphoma, FFPE, EBV-positive


title: Pt22Site A_T3

value: CR


title: Pt20Site B_T3

value: PD


title: spy4, seedling, rep4

city: Palo Alto

first: Shouling

state: CA

address: 260 Panama St

department: Department of Plant Biology

institute: Carnegie Institution at Stanford

description: Library name: SPY_D1

data_processing:
Cutadapt v 2.6, STAR v 2.7.10b, RACKJ v 0.99a
Raw sequence was trimmed using cutadapt (Parameters: Quality cut: 20 and Minimum length: 50.
Trimmed reads were mapped to the Tair10/Araport11 using STAR. (parameters: outFilterMultimapNmax: 20, outSAMattributes: NH HI AS nM MD, quantmode: GeneCounts )
Alignment files were processed using RACKj’s tools.
Genecount files from the STAR alignment were processed using R’s deseq2 plugin.
Assembly: TAIR10 Araport11
Supplementary files format and content: tab delimited files that contain raw gene counts from STAR for each sample
Supplementary files format and content: tab delimited files that contain EXON, SPLICE, RPKM, INTRON counts from RACKJ for each sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: For seedlings grown on the medium in petri dishes, all the sterilized seeds were stratified at 4°C for 2-3 days and grown on on ½ Murashige and Skoog medium supplemented with 0.8% (w/v) phytoagar under constant light (24 h light, 22°C). Wild-type (WT), acinus pinin, spy-4 were grown on ½ MS for 8 days before harvesting. shSEC RNAi spy-4 were grown on ½ MS plates for 5 days and transferred to mock (DMSO) or Dex treated plates for 3 days before harvesting.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plant Mini Kit (Hilden, Germany). Harvested tissues collected above for  WT, spy-4, shSEC RNAi spy-4 (Dex and mock treated) and acinus pnn (n=4) were ground in 2mL tubes with liquid nitrogen. For each sample, 30μl RNase free water was used and incubated on the column for 5 minutes prior to elution. The eluate was run through the column a second time to maximize concentration.
Libraries were generated by Novogene using poly A enrichment (UofC, California)

treatment_protocol: shSEC RNAi spy-4 were grown on ½ MS plates for 5 days and transferred to mock (DMSO) or Dex (10µM in DMSO) supplemented plates for 3 days before harvesting.

value: seedling

tag: ecotype


title: spy4, seedling, rep2

description: Library name: SPY_B1


title: EPSC in P2, H3K9me3, Replicate 2, ChIP


title: 4198478


title: Pt20Site A_T3

tag: time


title: EPSC in P0, Input

description:
EPSC_P0_H3K9me3.bw
EPSC_P0_H3K27ac.bw and EPSC_P0_METTL3.bw

value: DOX


title: spy4, seedling, rep1

description: Library name: SPY_A1


title: Murine E16.5 cre +_2

description: 10x Genomics

value: fore-/midbrain

value: hGFAP-cre; Ctnnb1(ex3)Fl/+SmoM2Fl/+

value: cre+


title: 4194891


title: Pt17Site B_T3


title: Murine E16.5 cre +_1

description: 10x Genomics


title: Control-1

description: Library name: CTRL1

value: Whole Brain

tag: batch


title: spy4_secRNAi, seedling, DMSO, rep4

description: Library name: DMSO_D1

value: DMSO


title: EPSC in P0, H3K27ac, Replicate 2, ChIP


title: EPSC in P2, Input

description:
EPSC_P2_H3K9me3.bw
EPSC_P2_H3K27ac.bw


title: Pt17Site A_T3

value: PR


title: EPSC in P0, H3K27ac, Replicate 1, ChIP


title: spy4_secRNAi, seedling, DMSO, rep3

description: Library name: DMSO_C1


title: 4193278

value: lymph node


title: 4194218


title: Pt16Site A_T3

value: Site A

value: YES


title: EPSC in P0, H3K9me3, Replicate 2, ChIP


title: spy4_secRNAi, seedling, DMSO, rep2

description: Library name: DMSO_B1


title: 4190784


title: EPSC in P2, H3K9me3, Replicate 1, ChIP


title: spy4_secRNAi, seedling, DMSO, rep1

description: Library name: DMSO_A1


title: 4190495


title: Pt15Site A_T3


title: spy4, seedling, rep3

description: Library name: SPY_C1


title: EPSC in P0, H3K9me3, Replicate 1, ChIP


title: Pt15Site B_T3

value: SD

value: Site B


title: spy4_secRNAi, seedling, DEX, rep4

description: Library name: DEX_G_Backup

value: DEX


title: Pt11Site B_T3


title: EPSC in P0, METTL3, Replicate 2, ChIP

value: expanded potential stem cells

value: METTL3 inducible knockout


title: EPSC in P0, METTL3, Replicate 1, ChIP


title: Pt11Site A_T3


title: HDF, Input

source_name: Primary Human Dermal Fibroblasts

value: Primary Human Dermal Fibroblasts

value: wildtype


title: spy4_secRNAi, seedling, DEX, rep2

description: Library name: DEX_D_Backup

value: seedling


title: 4190231


title: Pt8Site B_T2


title: spy4_secRNAi, seedling, DEX, rep3

description: Library name: DEX_E_Backup


title: HDF, METTL3, Replicate 2, ChIP


title: spy4_secRNAi, seedling, DEX, rep1

description: Library name: DEX_C_Backup


title: 4189998


title: Pt8Site A_T2


title: 4186812


title: 4182393


title: col0, seedling, rep4

description: Library name: Col0_E1

value: wild-type


title: Pt6Site B_T2


title: col0, seedling, rep3

description: Library name: Col0_D1


title: Pt6Site A_T2

value: CR

value: NO


title: TSC, Input

source_name: trophoblast stem cells

value: trophoblast stem cells


title: HDF, METTL3, Replicate 1, ChIP


title: 4190316


title: 4178310


title: Pt5Site B_T2


title: col0, seedling, rep2

description: Library name: Col0_C1


title: TSC, METTL3, Replicate 2, ChIP


title: 4178518


title: col0, seedling, rep1

description: Library name: Col0_B1


title: TSC, METTL3, Replicate 1, ChIP


title: 4177856


title: 4177434


title: acinuspnn, seedling, rep4

description: Library name: AP_D1

value: acinus-2 pnn


title: H9 hESC Input

value: embryonic stem cells


title: Pt5Site A_T2

value: PR


title: H9 hESC METTL3 Replicate 2


title: Pt31Site B_T2

value: PD


title: 4174742

value: lymph node


title: Pt31Site A_T2

value: Site A

value: YES


title: acinuspnn, seedling, rep2

description: Library name: AP_B1


title: 4170844


title: acinuspnn, seedling, rep3

description: Library name: AP_C1


title: 4164943


title: Pt30Site B_T2

value: SD

value: Site B


title: Pt30Site A_T2


title: 171-10

city: Bangkok

first: Supanat

last: Lumbikanada

address: Thanon Henri Dunant

country: Thailand

institute: Chulalongkorn University

data_processing:
Data were aligned to reference genome via software Hisat2 (v2.2.1). Differential expression analysis used the DESeq2 Bioconductor package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: Human Periodontal ligament tissue

growth_protocol: hPDLSCs were maintained in complete growth medium (GM) containing Dulbecco's Modified Eagle Medium (DMEM) (Gibco, USA), with 10% fetal bovine serum (FBS, cat. no.10270, Gibco, USA), 1% Antibiotic-Antimycotic (Gibco, USA), and 1% Glutamax (Gibco, USA). The isolated cells were incubated at 37 °C with 5% CO2 in humidified atmosphere.

extract_protocol:
Total RNA of hPDLSCs treated with 10mM MgCl2 for 3 days were extracted using a RNeasy kit (Qiagen, USA)
Total RNA was used for the library preparation. The libraries with different indices were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/MGI2000 instrument

treatment_protocol: hPDLSCs were maintained in OM medium. In the treatment group, MgCl2  was added to an OM medium at final concentrations of 10 mM.

value: Human Periodontal ligament tissue

value: 10mM MgCl2 Treated


title: 171-om

value: Control


title: 4162611


title: Pt27Site B_T2


title: Pt27Site A_T2


title: 4158769


title: DMSO_6h, repeat2

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

institute: VIB

data_processing:
Illumina CASAVA software used for basecalling.
Single-end reads were trimmed for adaptor sequences and aligned to the TAIR10 genome using GSNAP
The HTSeq python tool was used to summarize read counts
R package edgeR was used for statistical analysis
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files generated from HTSeq quantification, contain number of reads

source_name: root meristem

growth_protocol: Col-0 seeds were bleach sterilized and stratified for 24h at 4°C. Seeds were sown on ½ MS medium containing 0.8% agar without sucrose and grown vertically in a growth room at 22°C in continuous light conditions.

extract_protocol:
300 individual root tips were sampled per sample and three biological repeats per time point were used. Root tips were harvested directly into liquid nitrogen, RNA was extracted using the RNeasy kit (QIAGEN).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® Stranded mRNA Sample Prep Kit.

treatment_protocol: 5 DAG Col-0 plants were transferred to ½ MS plates containing 50μM coral7 and solvent control plates and were sampled at the following time points: 0h, 6h, 12h and 24h.

value: root meristem

value: DMSO


title: DMSO_6h, repeat1


title: 4142267


title: 387-10


title: Compound7_6h, repeat2


title: Pt26Site B_T2


title: Compound7_6h, repeat3


title: 4133511


title: Pt25Site B_T2


title: 387-om


title: Compound7_6h, repeat1


title: DMSO_6h, repeat3


title: H9 hESC, METTL3, Replicate 1, ChIP

value: wildtype


title: 4130003


title: acinuspnn, seedling, rep1

description: Library name: AP_A1

value: seedling


title: Compound7_24h, repeat3


title: Pt25Site A_T2


title: 4127766


title: ATN4_EMS-b

city: Bologna

first: Gloria

last: Ravegnini

address: via Zamboni 33

institute: Alma Mater Studiorum - Università di Bologna

description:
Library name: ATN.4_S3.UMIs
small non-coding RNA

library_source: other

data_processing:
The data  was analyzed using the Qiagen GeneGlobe miRNA sequencing pipelines. Briefly, the pipeline performs sample demultiplexing, adapter and low quality read trimming, mapping to the human transcriptome to identify the sequenced miRNA and counting the number of Unique Molecular Identifiers (UMIs) per miRNA to obtain the raw expression values in each sample.
analysis was done in R using DESeq2 package
Assembly: miRBase_v22
Supplementary files format and content: xlsx with batch corrected reads

molecule: other

source_name: endometriosis benign

extract_protocol:
QIAseq miRNA Library Kit (Illumina)
according to manual

value: endometriosis benign


title: ATN3_ECOC

description:
Library name: ATN.3_S2.UMIs
small non-coding RNA

source_name: endometriosis-correlated ovarian cancer

value: endometriosis-correlated ovarian cancer


title: Pt23Site B_T2


title: Compound7_24h, repeat2


title: 924-10


title: ATN1_EMS-b

description:
Library name: ATN.1_S1.UMIs
small non-coding RNA


title: Pt23Site A_T2

value: NO


title: 4125240

source_name: lymph node


title: 924-om


title: 4144633


title: Co-culture HUVECs and Pericytes Donor 3

city: Aachen

first: Julian

last: Gonzalez-Rubio

address: Forckenbeckstraße 55

department: BioTex

institute: RWTH University Aachen

description: Library name: Sample 6

data_processing:
FASTQ files were generated using the bcl2fastq software (Illumina) and processed using Nextflow 23.10.0 with the nf-core/RNA-seq pipeline (Version 3.12). Lane-level reads were trimmed with Trim Galore 0.6.7 and aligned to the human genome (GRCh39) with STAR 2.7.9a. Gene-level and transcript-level quantification was performed by Salmon v1.10.1 (Patro et al. 2017) and all the posterior analysis was done using custom scripts in R version 4.3.2 with the DESeq2 v.1.32.0 framework. Gene Set Enrichment Analysis (GSEA) was performed using clusterProfiler version 4.6.2, employing hallmark gene sets from MSigDB. Pre-ranked gene lists, generated from differential gene expression analysis, were added to clusterProfiler to identify enriched biological pathways. Results were corrected for multiple testing, and FDR q-values below 0.05 were considered significant.
Assembly: GRCh39
Supplementary files format and content: DGEA_ASCs_vs_Pericytes_res.xlsx

source_name: Fibrin co-culture

growth_protocol: The fibrin gels were cultured with EGM MV2 media for ten days.

extract_protocol:
First, 1 mL TRIzol (Invitrogen, Waltham, USA) was added to the samples and incubated for 5 minutes. The gels were pipetted up and down vigorously until completely dissociated in the TRIzol solution and were then frozen at -20 ºC. On the day of isolation, the samples were thawed, mixed with 0.2 mL of chloroform, and thoroughly shaken. This mixture was separated into two phases by centrifugation for 15 minutes at 12,000 g at 4ºC. The aqueous phase was removed and added to 0.5 mL isopropanol to precipitate the RNA. The mixture was incubated for 10 minutes at 4°C, followed by centrifugation at 12,000 g for 10 minutes at 4°C. A white, gel-like RNA pellet was formed at the bottom of the tube and the supernatant was carefully removed using a pipette. To further purify the RNA, the pellet was resuspended in 1 mL of 75% ethanol. The sample was briefly vortexed and then centrifuged at 7,500 g for 5 minutes at 4°C. The supernatant was discarded and the RNA pellet was air-dried for 10-15 minutes until no liquid was left which was then resuspended in RNase-free water.
The 3’mRNA-Seq libraries were generated using the QuantSeq 3’mRNA-Seq v2 Library Prep Kit FWD with UDIs (Lexogen, Vienna, Austria), following the protocol provided by the manufacturer.

value: Fibrin co-culture

value: Pericytes + HUVECs


title: 4119027

value: lymph node


title: 4112512


title: Pt26Site A_T2

source_name: tumor biopsy

value: PR

value: Site A

value: PD


title: Pt22Site B_T2

value: SD

value: Site B

value: YES


title: Pt22Site A_T2

value: CR


title: 4110996


title: Co-culture HUVECs and Pericytes Donor 2

description: Library name: Sample 5


title: Co-culture HUVECs and Pericytes Donor 1

description: Library name: Sample 4


title: Compound7_12h, repeat1

value: root meristem


title: 4110498


title: Co-culture HUVECs and ASCs Donor 3

description: Library name: Sample 3

value: ASCs + HUVECs


title: Pt20Site A_T2


title: Pt20Site B_T2


title: Mfap2-/- mouse, CCl4 treatment for 8 weeks, scRNA-seq

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

data_processing:
The raw scRNA-seq data underwent preprocessing using 10× Genomics software CellRanger (version 3.1.0), encompassing sample demultiplexing, alignment to the reference genome (mm10), filtering, and gene-level unique molecular identifier (UMI) counting. Subsequently, the Seurat package was employed for quality control.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: liver

growth_protocol: Mfap2+/+ and Mfap2-/- mice

extract_protocol:
Liver nonparenchymal cells were freshly isolated from livers of Mfap2+/+ and Mfap2-/- mice with intraperitoneal injection of CCl4 for 8 weeks.
RNA libraries for scRNA-seq were constructed using Chromium Single Cell 3' Library & Single Cell 3' v3 Gel Beads, DynaBeads® MyOneTM Silane Beads, SPRIselect Reagent Kit, Qubit dsDNA Assay Kit, and Agilent High Sensitivity DNA Kit.

treatment_protocol: Intraperitoneal injection of CCl4 for 8 weeks

value: liver

value: non-parenchymal liver cells (NPCs)

value: KO

value: Intraperitoneal injection of CCl4


title: 4108627


title: Co-culture HUVECs and ASCs Donor 2

description: Library name: Sample 2


title: Pt17Site A_T2


title: Co-culture HUVECs and ASCs Donor 1

description: Library name: Sample 1


title: Compound7_24h, repeat1


title: 4100314


title: Fracture callus, ADO material, 7 d #2

city: Durham

first: Shyni

last: Varghese

state: NC

address: 203 Research Drive

department: Department of Biomedical Engineering

institute: Duke University

description: Calluses harvested 7 days post-treatment

data_processing:
10X Genomics reads were converted to FASTQ files using bcl2fastq command-line tool. FASTQ files were aligned to the mm10 reference transcriptome, filtered, and counted using the CellRanger 7.0.0 pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
To obtain single-cell suspensions from calluses of tibiae, mice were euthanized, and calluses were minced using a scalpel in 100 U ml−1DNase I (Millipore Sigma, 10104159001), 1% bovine serum albumin (Sigma-Aldrich) and PBS for 20 min at 37 °C. The cell suspension was filtered using 40-μm cell strainers and centrifuged at 300 g for 5 min and treated with RBC lysis buffer (Millipore Sigma, 11814389001) for 10 min. Cells were stained with propidium iodide and viable cells were sorted using DiVa cell sorter (BD Biosciences) for scRNA-seq preparation.
Cell suspensions harvested from calluses of tibiae were loaded onto a 10x Genomics Chromium Controller Single-Cell Instrument (10x Genomics) mixed with reverse transcription (RT) reagents, gel beads, and oil to generate single-cell gel bead-in emulsions (GEMs). GEM–RT was performed using an Eppendorf Mastercycler Pro using the following program: 53 °C for 45 min, 85 °C for 5 min. After RT, GEMs were broken, and the single-strand cDNA was purified using DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). cDNA was then amplified using the Eppendorf Mastercycler Pro using the following program: 98 °C for 3 min, 11–13 cycles of 98 °C for 15 s, 67 °C for 20 s and 72 °C for 1 min, 72 °C for 1 min. The amplified cDNA product was then purified using the SPRIselect Reagent Kit (0.6 × SPRI; Beckman Coulter). Indexed sequencing libraries were constructed using the reagents in the Chromium Single-Cell Library Kit 3´ v2 using the following steps: 1) fragmentation, end repair and A-tailing, 2) SPRIselect cleanup, 3) adapter ligation, 4) post-ligation cleanup with SPRIselect, 5) sample index PCR, and 6) post-index PCR cleanup. Sequencing libraries were transferred to BGI and were loaded onto a MGISEQ-2000 platform (MGI Tech) for sequencing.

value: Bone marrow

tag: Sex

value: Male

value: 20 months

value: adenosine microgel


title: Compound7_12h, repeat3


title: Mfap2+/+ mouse, CCl4 treatment for 8 weeks, scRNA-seq

value: WT