title: RS-M MEN_24h_rep.3

city: Warszawa

first: Michal

last: Pawlak

address: Indiry Gandhi 14

department: Department of Experimental Hematology

country: Poland

institute: Institute of Hematology

description: Library name: IHITSAMID000033

data_processing:
RNA-seq reads were aligned to GRCh37 human genome version and gene counts were generated using STAR under nextflow nf-core RNA-seq analysis pipeline.
Assembly: GRCh37
Supplementary files format and content: IHIT_raw_counts_RNAseq.csv contains raw gene counts

source_name: RS-M MEN_24h_rep.3

growth_protocol: THP-1 cells were stimulated with 250nM Phorbol-12-myristate-13-acetate (PMA, Sigma-Aldrich) in RPMI medium for three days, followed by four day resting in PMA-free RPMI medium. To generate MdM, CD14+ monocytes were incubated with 10ng/ml CSF-1 (Biolegend) in TexMACS (Miltenyi Biotec) for 7 days. To generate in vitro cHL-TAMs (RS-M), differentiated THP1-Mϕ and MdM, expressing mature macrophage marker – 25F9, were cocultured with L428 or L1236 RS cells for five days under conditions prohibiting direct contacts, using 0.4µm polycarbonate cell culture inserts (NuncTM, Thermo Fisher Scientific, cat. 140640). For unstimulated, control (M0) macrophages, THP1-Mϕ and MdM were cultured in RPMI only in parallel to the RS cell/ Mϕ cocultures.

extract_protocol:
RNAs were isolated using GeneMATRIX Universal RNA purification kit (EURx). RNA integrity was assessed using TapeStation 4200 Instrument (Agilent) and minimal RINe value of RNA samples subjected to library preparation was ≥9.7
Libraries were generated using SENSE mRNA-Seq Library Prep Kit (Lexogen, cat. 001.96)

value: macrophage


title: UPN827 cells, CHW025BL Local Cohort T1D Baseline plasma

status: Public on Jun 01 2026

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

country: USA

institute: Medical College of Wisconsin

description: Gene expression data from UPN827 cells stimulated with T1D plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: UPN827 cells stimulated with CHW025BL Local Cohort T1D Baseline plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN827 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of participant plasma  that was sampled at baseline or the 3-6 months post-baseline from six TrailNet new-onset T1D intervention trails, or from our local Recent onset T1DM cohort. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN827 cells

tag: sample timepoint

value: Local Cohort T1D Baseline


title: HSC2_cells, C. parapsilosis-treated, low-dose 3, 6 hours

type: SRA

city: Szeged

first: Marton

last: Horvath

state: Csongrád

address: Közép fasor 52.

department: Microbiology

country: Hungary

institute: University of Szeged

description: Library name: H6_CP113

library_source: transcriptomic

data_processing:
Human sequenced reads were trimmed for standard Illumina adaptor sequences / low-quality sequences using trim-galore (v0.6.4) (parameters: -q 20 --paired --illumina), the --length cutoff was set 36 for RNA-seq and 18 for miRNA-seq samples.
Processed RNA reads were aligned using Hisat2 (v2.2.1)  (parameter: --phred33 --dta --non-deterministic --rna-strandness "RF"), sorted and indexed using Samtools (v1.20).
Mapped reads were quantified for genomic features using FeatureCounts (v2.0.6). (parameter: -p --countReadPairs -s 2)
Further analysis steps for RNA-seq samples were conducted in R, inculding differential gene expression analysis using DESeq2 (v1.46.0) packages.
Processed miRNA reads were aligned using mirdeep2 (v2.0.1.3) in two steps: mapped with the mapper.pl script (parameter: -e -h -i -j -m -k AGATCGGAAGAGCACACGTCT -l 18) and quantified with the miRDeep2.pl script.
Assembly: GRCh38 (release 96) from ENSEMBL, further references for the miRNA sequencing were downloaded from miRBase (release 22), including human mature- and hairpin sequences, and mouse and rat mature sequences for contaminant masking.
Supplementary files format and content: total_read_counts.csv
Supplementary files format and content: The 6 column miRNA quantification result tables, including detected mature-, precursor-, and normalized counts.

growth_protocol: HSC-2 cells were grown in EMEM medium supplemented with 10% heat inactivated FBS, 1% PS, and 4 mM L-glutamine. Cells were maintained at 37°C in the presence of 5% CO2.

extract_protocol:
After reaching 85 % confluency, total RNA and total miRNA was extracted using the miRNeasy Mini Kit, following the manufacturer’s instructions.
mRNA and miRNA sequencing libraries were prepared at Novogene (UK) Company Limited, Cambridge, UK, according to the company’s own guidelines. Briefly, mRNA was poly(A)-enriched and sequenced on an Illumina NovaSeq X Plus (2×15 bp, PE150 workflow, ≥20M read pairs/sample). miRNA libraries were sequenced on a NovaSeq 6000 (50 bp single-end, SE50 workflow, ≥10M reads/sample)

treatment_protocol: Host cells were stimulated with yeast cells at the MOI of 1:1 or 5:1 (pathogen: host ratio) in serum-free EMEM medium for 1 or 6 hours at 37C, in the presence of 5% CO2. Yeast cells were cultivated in liquid YPD medium, overnight at 30C, prior to the experiments.

tag: cell line

tag: cell type

value: oral epithelial

tag: treatment

value: C.parapsilosis MOI 1(pathogen):1(host)

tag: time

value: 6 hours


title: Steatosis 10

city: Orlando

first: Daria

last: Igudesman

address: 301 E Princeton St

institute: AdventHealth

description:
Library name: MODIFY21
MODIFY21

data_processing:
Raw counts were generated with the R package salmon.
Assembly: hg38 - Ensembl
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Sigmoid colon

extract_protocol:
Total mRNAs were isolated from colonic tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
cDNA library was prepared using the Invitrogen Collibri Stranded RNA library Prep Kit for Illumina with Collibri H/M/R rRNA Depletion Kit according to the manufacturer’s instructions and starting with 500ng of purified RNAs. Briefly, rRNA were first depleted, and enriched mRNAs subsequently used for fragmentation, adaptors ligation and reverse transcription. After purification, libraries were PCR-enriched, further purified, and quantified and quality-assessed on an Agilent 2100 Bioanalyzer instrument. A master library was generated from the purified products in equimolar ratios. The pooled product was quantified using Qubit and sequenced using an llumina Next-Seq sequencer (paired-end reads, 2x750 bp).

tag: tissue

value: Sigmoid colon


title: Head of MZrlig1 zebrafish embryos, 5 dpf stage, good behaviour 2

city: Konstanz

first: Fiona

middle: Sophie

last: Klusmann

address: Universitätsstrasse 10

country: Germany

institute: University of Konstanz

description:
Library name: KO_good 1
K_G_2

data_processing:
Bioinformatic processing started with the download of the reference genome (Danio_rerio.GRCz11.dna_sm.primary_assembly.fa.gz) and gene annotation file (Danio_rerio.GRCz11.113.gtf.gz) from ENSEMBL (release 113). An index was generated using STAR (v.2.7.10b), and clean paired-end reads were then aligned to the reference genome using the same version of STAR. To reconstruct the transcriptome, the genome FASTA and annotation GTF files were processed with gffread (v.0.12.7). Transcript- and gene-level expression quantification was subsequently performed with Salmon (v.0.14.1) in alignment-based mode, using STAR-generated transcriptome BAM files as input.
Differential gene expression (DGE) analysis was conducted in R using the DESeq2 package (v.1.42.1)71. Transcript-level quantifications from Salmon were imported with the tximport package (v.1.30.0)72, and a DESeqDataSet object was created from the count data and corresponding experimental metadata, with ‘condition’ defined as the main factor of interest. Genes with fewer than 10 reads across all samples were excluded to reduce noise. Counts were normalised using DESeq2’s median-of-ratios method, and p-values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate (FDR).
Assembly: Danio rerio GRCz11 (Ensembl release 113)
Supplementary files format and content: Gene-level count tables (TXT format) containing raw read counts per gene
Supplementary files format and content: Normalised expression values (TXT format) generated with DESeq2.
Supplementary files format and content: Fragments per kilobase of transcript per million fragments mapped  (TXT format).
Supplementary files format and content: Differential expression results (XLSX format) with log₂FoldChange, p-value, adjusted p-value.

organism: Danio rerio

source_name: head

growth_protocol: Embryos used for developmental transcriptome profiling were raised in the dark at 28 °C. Embryos used for behavioural analysis and head transcriptome profiling were raised at 28 °C on a 14 h/10 h light/dark cycle. All embryos were collected by natural spawning and staged according to morphological criteria.

extract_protocol:
Total RNA was extracted from pools of zebrafish embryos or dissected larval heads using TRIzol™ Reagent (Invitrogen) according to the manufacturer’s instructions. For developmental profiling, samples were collected at six stages (4-cell, sphere, shield, bud, 1 dpf, 5 dpf). Per condition, 10 embryos were pooled for the 4-cell, sphere, and shield stages, and 8 embryos for the bud, 1 dpf, and 5 dpf stages. For behavioural profiling, heads from 8 larvae were pooled per sample. RNA integrity was assessed with the Bioanalyzer 2100 system (Agilent).
Poly(A)-enriched libraries were prepared according to Novogene’s standard protocol. mRNA was enriched using oligo(dT) magnetic beads, fragmented, and used for first- and second-strand cDNA synthesis. After end repair, A-tailing, and adapter ligation, fragments were size-selected, PCR amplified, and purified to generate sequencing libraries.

value: head

value: 5 dpf

tag: genotype

value: good behaviour


title: Erythroid cells, DZNep  treated 1, Day11, CUT&Tag

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

country: China

institute: zzu

library_source: genomic

data_processing:
Trim Galore version 0.6.6 was used to remove adapter and low-quality reads. Align paired-end reads using Bowtie2 version 2.5.1 with options: “--end-to-end --very-sensitive”. Peak calling uses MACS2 version 2.1.1 with threshold: q<0.01, and the differential binding sites of H3K4me3 were calculated using the DiffBind version 3.8.4 with the parameter log2foldchange >=1 and FDR <0.05 (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind.html). Scatterplots, correlation plots, and heatmaps are displayed using deepTools version 2.5.7. Annotation of peaks is performed using an R package ChIPseeker version 1.34.1(https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/ ChIPseeker.html). The CUT&Tag peak/region <1000bp from the nearest TSS was defined as the promoter. Hypergeometric Optimization of Motif Enrichment (HOMER) version 4.11 (http://homer.ucsd.edu/homer/) was used to search for the binding motif.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Cord blood

growth_protocol: CD34+ cells were puriﬁed from cord blood by positive selection using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’sinstructions. The purity of isolated CD34+ cells was 95% to 98%. The cell culture procedure was comprised of 3 phases. Composition ofthe base culture medium was Iscove’sModiﬁed Dulbecco’s Medium, 2%human peripheral blood plasma, 3% human AB serum, 200 mg/mL Holo-human transferrin, 3 IU/mL heparin, and 10 mg/mL insulin. In the ﬁrst phase(day 0 to day 6), CD34+ cells at a concentration of 105/mL were cultured inthe presence of 10 ng/mL stem cell factor, 1 ng/mL IL-3, and 3 IU/mL erythropoietin. In the second phase (day 7 to day 11), IL-3 was omitted from the culture medium. In the third phase that lasted until day 21, the cell concentration was adjusted to 106/mL on day 11 and to 5 3 106/mL on day 15, respectively, the medium for this phase was the base medium plus 3 IU/mL erythropoietin, and the concentration of transferrin was adjusted to 1mg/mL. The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600×g at room temperature. 1×105 cells were washed twice in 500μL wash buffer by gentle pipetting. Concanavalin A coated magnetic beads were prepared as the kit manual described, 10 µL of activated beads were added per sample and incubated at RT for 10 min. According to the kit instructions, cells were sequentially incubated with ConA Beads, primary antibody (anti-H3K4me3 antibody, secondary antibody (Goat anti-Rabbit IgG) and Hyperactive PG-TN5/PA-TN5 Transposon and then fragmented. The fragmented DNA was extracted from the samples and amplified by PCR.
CUT&Tag libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD901, Vazyme, China) and sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated.

treatment_protocol: Here, we set 0.5μM DZNep dosing which was an inhibitor of AHCY to inhibit AHCY activity. After treated with 0.5μM DZNep for four days, we performed a H3K4me3 CUT&Tag sequencing of DMSO and DZNep treated cells.

value: Cord blood

value: Erythroid cells

value: DZNep 0.5μM


title: Steatosis 9

description:
Library name: MODIFY20
MODIFY20


title: Head of wildtype zebrafish embryos, 5 dpf stage, good behaviour 4

description:
Library name: WT_good 4
W_G_4

value: Wildtype


title: Erythroid cells, Control 3, Day11, CUT&Tag

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

value: DMSO


title: Head of wildtype zebrafish embryos, 5 dpf stage, good behaviour 3

description:
Library name: WT_good 3
W_G_3


title: UPN827 cells, CHW024BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW024BL Local Cohort T1D Baseline plasma


title: Healthy 3

description:
Library name: MODIFY19
MODIFY19


title: UPN827 cells, CHW023BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW023BL Local Cohort T1D Baseline plasma


title: Erythroid cells, Control 2, Day11, CUT&Tag

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: UPN827 cells, CHW022BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW022BL Local Cohort T1D Baseline plasma


title: Steatosis 8

description:
Library name: MODIFY14
MODIFY14


title: Head of wildtype zebrafish embryos, 5 dpf stage, good behaviour 2

description:
Library name: WT_good 2
W_G_2


title: Erythroid cells, Control 1, Day11, CUT&Tag

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: Head of wildtype zebrafish embryos, 5 dpf stage, good behaviour 1

description:
Library name: WT_good 1
W_G_1


title: UPN827 cells, CHW021BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW021BL Local Cohort T1D Baseline plasma


title: Steatosis 7

description:
Library name: MODIFY12
MODIFY12


title: UPN827 cells, CHW020BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW020BL Local Cohort T1D Baseline plasma


title: MZrlig1 zebrafish embryos, 5 dpf stage c

description:
Library name: KO_5dpf 3
K6c

source_name: whole embryo

value: whole embryo


title: Healthy 2

description:
Library name: MODIFY11
MODIFY11


title: Erythroid cells, DZNep  treated 2, Day11, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

data_processing:
The original data were filtered and compared with the reference genome, which can be downloaded from the Ensemble database (http://www.ensembl.org/index.html,human genome build GRCh38.87). Using HISAT2 version 2.2.1 (http://daehwankimlab.github.io/hisat2/) to read the counts for each gene in each sample and gene expression was assessed by StringTie (https://ccb.jhu.edu/software/stringtie/). TPM (Transcripts Per Kilobase of exon model per Million mapped reads) was calculated to evaluate the expression level, and DESeq2 version 1.38.3 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) was packaged to identify differentially expressed genes from the data. Gene ontology (GO) enrichment analysis and visualization of DEGs was performed using the Metascape (www.metascape.org/) online tool with q < 0.05.
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 TPM values for each Sample

extract_protocol:
Experiment procedure before sequencing: 2 million cells were collected and washed twice with PBS. RNA was extracted from cell culture using RNA extract kits (74104, Qiagen) according to the manufacturer’s instruction.
RNA was extracted and used as cDNA input, cDNA library was prepared by VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01,  Vazyme, China), and sequenced on Illumina NovaSeq 6000.

treatment_protocol: Here, we set 0.5μM DZNep dosing which was an inhibitor of AHCY to inhibit AHCY activity. After treated with 0.5μM DZNep for four days, we performed a RNA-seq of DMSO and DZNep treated cells.


title: Steatosis 6

description:
Library name: MODIFY10
MODIFY10


title: MZrlig1 zebrafish embryos, 5 dpf stage b

description:
Library name: KO_5dpf 2
K6b


title: Erythroid cells, DZNep  treated 1, Day11, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: UPN827 cells, CHW018BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW018BL Local Cohort T1D Baseline plasma


title: MZrlig1 zebrafish embryos, 5 dpf stage a

description:
Library name: KO_5dpf 1
K6a


title: Steatosis 5

description:
Library name: MODIFY9
MODIFY9


title: Erythroid cells, Control 3, Day11, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: UPN827 cells, CHW017BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW017BL Local Cohort T1D Baseline plasma


title: Wildtype zebrafish embryos, 5 dpf stage c

description:
Library name: WT_5dpf 3
W6c


title: Steatosis 4

description:
Library name: MODIFY8
MODIFY8


title: UPN827 cells, CHW016BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW016BL Local Cohort T1D Baseline plasma


title: Erythroid cells, Control 2, Day11, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: Steatosis 3

description:
Library name: MODIFY7
MODIFY7


title: Erythroid cells, Control 1, Day11, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: Patient4_techrep3

city: Palo Alto

first: Reema

last: Baskar

address: 3373 Hillview Ave

institute: Stanford University

data_processing:
FASTQ files from Illumina nextseq runs were obtained from primer de-barcoding using the bcl2fastq2 application. Else, they were obtained directly from novogene sequencing service. FASTQ files were input into pepATAC pipeline to check sequencing quality (fastqc), trim (Skewer), and align (bowtie2) to the hg38 genome for cell line data and hg19 for BM and BALL data. Duplicated reads were marked and removed using Picard MarkDuplicates tool. Peaks were called using MACS2 under parameters ‘-q 0.01 ‐‐shift 0 –nomodel’. The signal-to-noise ratio between transcription start sites and flanking regions was calculated and plotted to check data quality. All samples had TSS scores of 10 and above, as well as expected fragment length distributions as plotted for all 3 sequencing experiments with 2 technical and 2 biological replicates each.
Consensus bed file was created for each experiment across technical and biological replicates using Chraccr package. Exact code in github and zenodo as referred to in paper.
Assembly: hg19
Supplementary files format and content: Peak set output from pepATAC pipeline (bed file format)

source_name: Bone marrow

growth_protocol: BALL patient samples of bone marrow or PBMC from blood were thawed and washed before lineage depletion as outlined in paper methods.

extract_protocol:
Lineage-depleted BALL cells were processed using the published Fast-ATAC protocol. Briefly, cells were washed with cold PBS and simultaneously permeabilized and transposed, before DNA purification, PCR amplification, and subsequent Illumina sequencing.
DNA extracted from samples using QIAGEN MiniElute PCR purification columns and subsequent library preparation and next-generation sequencing were carried out as previously described in the ATAC-seq paper.
Fast-ATAC seq

value: Bone marrow

value: B cell acute lymphoblastic leukemia


title: UPN827 cells, CHW014BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW014BL Local Cohort T1D Baseline plasma

value: UPN827 cells


title: Wildtype zebrafish embryos, 5 dpf stage a

description:
Library name: WT_5dpf 1
W6a


title: Wildtype zebrafish embryos, 5 dpf stage b

description:
Library name: WT_5dpf 2
W6b


title: Steatosis 1

description:
Library name: MODIFY2
MODIFY2


title: Steatosis 2

description:
Library name: MODIFY5
MODIFY5


title: 1_473

city: Guangzhou

first: Ximin

last: Hu

address: Department of Burn and Plastic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, Guangdong

description:
Library name: Sample_1
gene_expression_473_DTR.xlsx; sample_473_1_fpkm

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: http://ftp.ensembl.org/pub/release-107/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.toplevel.fa.gz http://ftp.ensembl.org/pub/release-107/gtf/mus_musculus/Mus_musculus.GRCm39.107.gtf.gz http://ftp.ensembl.org/pub/release-107/gtf/mus_musculus_c57bl6nj/Mus_musculus_c57bl6nj.C57BL_6NJ_v1.107.gtf.gz
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

growth_protocol: Male and female mice (8 to 12 weeks old) were housed in individually ventilated cages under a 12-hour light/dark cycle with ad libitum access to food and water. Mice used within each experimental comparison were bred to generate littermates, cohoused under identical conditions, and randomly assigned to experimental groups by lab managers blinded to the study design.

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 0.2 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306） following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE150) were generated.

treatment_protocol: Optogenetic stimulation was performed using a 473nm 100mW diode-pumped solid-state laser (Laser and Optics Century, Shanghai, China). An optical cannula aimed at the dorsal ear was placed 1 cm from the surface of the skin. Stimulation was at a frequency of 10 Hz for 30 minutes with a power density of 8 mW/mm2 for 11 consecutive days. Both PF4Cre; Ai32 and Ai32 control mice underwent photostimulation of the dorsal ear.

value: PF4 Cre; Ai32

value: Optogenetic stimulation (473nm 100mW, Laser and Optics Century, Shanghai, China)

tag: batch


title: UPN827 cells, CHW011BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW011BL Local Cohort T1D Baseline plasma

value: Local Cohort T1D Baseline


title: MZrlig1 zebrafish embryos, 1 dpf stage b

description:
Library name: KO_1dpf 2
K5b

value: 1 dpf


title: MZrlig1 zebrafish embryos, 1 dpf stage c

description:
Library name: KO_1dpf 3
K5c


title: Healthy 1

description:
Library name: MODIFY1
MODIFY1

value: Sigmoid colon


title: Patient4_techrep1


title: UPN827 cells, CHW012BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW012BL Local Cohort T1D Baseline plasma


title: Patient4_techrep2


title: Naive-like sESCs on MEFs Rep2

city: West Lafayette

first: Shyamkumar

last: TS

state: IN

address: 625 Harrison St

department: Comparative Pathobiology

institute: Purdue University

description: Library name: sESCs_N2_2

data_processing:
Reads were quantified with Salmon using a decoy-aware index built from the Ovis aries reference genome and transcriptome FASTA.
The gentrome was created by concatenating genome and transcriptome FASTAs, with genome identifiers forming the decoy list. Salmon was run with --validateMappings and --gcBias, producing transcript-level TPMs and counts.
Transcript quantifications were imported into R via tximport and summarized to gene-level count matrices.
Assembly: ARS-UI_Ramb_v3.0, RefSeq GCF_016772045.2
Supplementary files format and content: TPM matrix for all samples provided in .xlsx forma

molecule: polyA RNA

organism: Ovis aries

source_name: Inner cell mass of blastocyst

growth_protocol: Cultures were maintained at 37°C in a humidified incubator with 5% CO₂ under ambient oxygen conditions.

extract_protocol:
RNA was extracted with the RNeasy Plus Micro Kit (Qiagen)
PolyA-enriched mRNA libraries (~20 million paired-end reads per sample) were generated on the NovaSeq X Plus platform

treatment_protocol: Primed sheep embryonic stem cells were cultured in NBFR medium containing equal volumes of DMEM/F-12 and Neurobasal medium, supplemented with 1% BSA (MP Biomedicals), N2 supplement and B27 supplement, GlutaMAX™ (Gibco), penicillin-streptomycin, and non-essential amino acids. In addition, the medium was added with 20 ng/mL Activin A (Peprotech, 120-14P), 20 ng/mL bFGF (Peprotech, 100-18B), and 3 µM endo-IWR-1 (Biogems, 1128234). Naive-like cells were cultured in a medium composed of equal volumes of DMEM/F-12 and Neurobasal medium, supplemented with 20 ng/mL human LIF, 20 ng/mL Activin A, 1 µM PD0325901, 2 µM XAV-939, 2 µM Go6983, 1.2 µM CGP77675, and 50 µg/mL ascorbic acid

value: Inner cell mass of blastocyst

value: N sESC

value: Naive-like sheep embryonic stem cells

value: primed to naive converted

value: Naïve media

value: Passage 12


title: Patient3_techrep3

source_name: Peripheral blood mononuclear cells

value: Peripheral blood mononuclear cells


title: Wildtype zebrafish embryos, 1 dpf stage c

description:
Library name: WT_1dpf 3
W5c

value: Wildtype


title: Naive-like sESCs on MEFs Rep1

description: Library name: sESCs_N2_1


title: UPN827 cells, CHW010BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW010BL Local Cohort T1D Baseline plasma


title: Wildtype zebrafish embryos, 1 dpf stage b

description:
Library name: WT_1dpf 2
W5b

value: whole embryo


title: UPN827 cells, CHW009BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW009BL Local Cohort T1D Baseline plasma


title: MZrlig1 zebrafish embryos, 1 dpf stage a

description:
Library name: KO_1dpf 1
K5a


title: Healthy 10

description:
Library name: MODIFY47
MODIFY47

source_name: Sigmoid colon


title: 10-day old male flies, high sucrose diet, rep 1

city: Gießen

first: Sonja

last: Dähn

address: Wilhelmstrasse 20

institute: Justus-Liebig-Universität Gießen

description: Library name: HCMS1

data_processing:
data processing was done by  Novogene Co., Ltd (Beijing, China).
Assembly: NCBI 7227
Supplementary files format and content: csv
Supplementary files format and content: counts and fpkm

organism: Drosophila melanogaster

source_name: whole flie

extract_protocol:
for RNA extraction, the Quick-RNA Tissue/Insect kit (Zymo Research, Freiburg, Germany) was used, according to the manufacturer’s instructions.
polyA enrichment library preparation resulting in the construction of 250-300 bp insert cDNA library, done by Novogene Co., Ltd (Beijing, China).

treatment_protocol: flies were fed 30% sucrose diet with or without 0.25 mM allyl-isothiocyanate for 10 days

value: whole flie

value: high sucrose diet


title: UPN827 cells, CHW006BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW006BL Local Cohort T1D Baseline plasma

value: UPN827 cells


title: MZrlig1 zebrafish embryos, bud stage c

description:
Library name: KO_bud 3
K4c

value: bud stage


title: Patient2_techrep2

value: Bone marrow

value: B cell acute lymphoblastic leukemia


title: Patient3_techrep2


title: Sheep ESCs Line B NBFR Rep2

description: Library name: sESCs_B2

value: sESC B

value: Primed sheep embryonic stem cells

value: WT

value: NBFR

value: Passage 10


title: Naive-like sESCs feeder-free Rep2

description: Library name: sESCs_N1_2

value: Inner cell mass of blastocyst

value: N sESC

value: Naive-like sheep embryonic stem cells

value: primed to naive converted


title: Sheep ESCs Line B NBFR Rep1

description: Library name: sESCs_B1


title: Patient3_techrep1

value: Peripheral blood mononuclear cells


title: Patient2_techrep1


title: Naive-like sESCs feeder-free Rep1

description: Library name: sESCs_N1_1

value: Naïve media

value: Passage 12


title: Wildtype zebrafish embryos, 1 dpf stage a

description:
Library name: WT_1dpf 1
W5a

value: whole embryo

value: 1 dpf

value: Wildtype


title: UPN827 cells, CHW005BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW005BL Local Cohort T1D Baseline plasma

value: UPN827 cells

value: Local Cohort T1D Baseline


title: Patient2_techrep3

value: Bone marrow

value: B cell acute lymphoblastic leukemia


title: Sheep ESCs Line A NBFR Rep2

description: Library name: sESCs_A2

value: sESC A

value: Primed sheep embryonic stem cells

value: WT


title: UPN827 cells, CHW004BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW004BL Local Cohort T1D Baseline plasma


title: MZrlig1 zebrafish embryos, bud stage a

description:
Library name: KO_bud 1
K4a

source_name: whole embryo

value: bud stage


title: Patient1_techrep3


title: UPN827 cells, TN1872 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1872 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: Patient1_techrep2


title: Sheep ESCs Line A NBFR Rep1

description: Library name: sESCs_A1

value: Inner cell mass of blastocyst

value: NBFR

value: Passage 10


title: UPN827 cells, TN1867 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1867 TrailNet 3or6 month T1D plasma


title: Wildtype zebrafish embryos, bud stage c

description:
Library name: WT_bud 3
W4c


title: Wildtype zebrafish embryos, bud stage b

description:
Library name: WT_bud 2
W4b


title: OE-TaCRVP-fed rep3

city: fuzhou

first: 竹君

last: 王

address: cangshan street

institute: fujian agriculture and forestry university

description:
Library name: Sample 12
D3

data_processing:
Illumina Casava software used for basecalling
Raw data of fastp format were firstly processed through in-house perl scripts. In this step,clean fata were obtained by removing reads. At the same time,Q20,Q30 and GCcontent were calculated.All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded  from genome website. Use HISAT2 (2.2.1) to build the index of the  reference genome, and use HISAT2 to align paired-end clean reads to the reference genome. The mapped reads of each sample were assembled by StringTie (v2.2.3) in a reference-based approach. featureCounts (2.0.6) was used to count the reads numbers mapped to  each gene. And then FPKM of each gene was calculated based on the  length of the gene and reads count mapped to this gene.  For DESeq2 with biological replicates: Differential expression analysis for  two conditions/groups was performed using the DESeq2 R package  (1.42.0).
Assembly: sl3.0
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each sample

organism: Solanum lycopersicum

source_name: leaf

extract_protocol:
Total RNA was isolated using TRIzol according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 for Illumina following manufacturer’s instructions

value: leaf

value: OE-TaCRVP

value: fed


title: Patient1_techrep1

source_name: Bone marrow


title: Wildtype zebrafish embryos, bud stage a

description:
Library name: WT_bud 1
W4a

value: whole embryo


title: UPN827 cells, TN1865 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1865 TrailNet 3or6 month T1D plasma


title: OE-TaCRVP-fed rep2

description:
Library name: Sample 11
D2


title: s06_2

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description:
10X genomics
19823X12

library_source: transcriptomic single cell

data_processing:
10x genomics Cell Ranger was used to process raw sequencing data, and produce counts
MEX data were further processed and merged with Seurat (4.1)
The Cell Ranger pipeline was used to generate alignments and counts. Single-cell data in R (4.1.0) processing included dimension reduction and clustering by SCTransformation (0.3.5) using the Gamma-Poisson generalized linear model (glmGamPoi, 1.4.0) method, and were performed using the Seurat (4.3.0) package. Doublet detection was performed with DoubletFinder(2.0.3). Nuclei that were identified as doublets, nuclei with fewer than 500 features, and nuclei associated with more than 15% mitochondrial genes were removed, followed by removal of mitochondrial genes from remaining nuclei.
Assembly: hg38; H_sapiens_Dec_2013; GRCh38
Supplementary files format and content: skin_counts_matrix.csv
Supplementary files format and content: skin_metadata.xlsx

molecule: nuclear RNA

source_name: skin/nevus

extract_protocol:
Excess OCT was removed with a razor blade, and the sample was thawed in ice cold phosphate buffered saline supplemented with an antifungal, free radical spin trapping agent, and inhibitors of histone deacetylases, caspases and RNAses. The samples were minced and transferred into a gentleMACs C tube (Miltenyi, 130096334), with nuclei extraction buffer (Miltenyi Biotec, 130-128-024) supplemented with RNase inhibitor. During protocol optimization we discovered that including RNAse inhibitors in all solutions that touched the tissue after removal from the donor significantly increased the yield of RNA; this included the phosphate buffered saline used to moisten the gauze in the RNAse-free container onto which the tissue was placed after biopsy in the clinic. After agitation, suspensions of nuclei were filtered, and a 10x protocol (10X Genomics Next GEM Single Cell 3’ Gene Expression Library Prep v3.1with UDI) was used to prepare the library which was sequenced on an Illumina NOVAseq 6000 sequencer with an S4 Reagent Kit v1.5 150x150 bp sequencing.
Libraries were prepped according to the 10X Genomics scRNA-seq 3’ v3.1 Next GEM protocol, NovaSeq Reagent Kit v1.5_150x150 bp Sequencing (these six samples were sequenced on a lane of an S4 flowcell).
snRNA-seq

treatment_protocol: A total of 6 volunteers provided 2 nevi each; one irradiated nevus and one control nevus of similar physical location and clinical appearance. At the first clinic visit the participants’ normal skin was treated with 5 graded doses ranging from 100-400 J/M2 of SSR for determination of MED as described in our earlier work (Cassidy, Liu et al. 2017). At the second visit the MED of each patient was determined by visual inspection. Then one clinically normal melanocytic nevus (5 mm or less in diameter) was irradiated with 3 or 4 times the participant’s MED.  At the third visit,  24 hours later, the irradiated nevus as well as one un-irradiated control nevus were collected by 6 mm punch biopsy. A slice (~1.5 mm thick) from the center of each nevus was processed for permanent sections and the remaining pieces of the nevus and surrounding normal skin where frozen in OCT and stored at -80 °C.

value: skin/nevus

tag: donor

value: control


title: MZrlig1 zebrafish embryos, shield stage c

description:
Library name: KO_shield 3
K3c

value: shield stage


title: OE-TaCRVP-fed rep1

description:
Library name: Sample 10
D1


title: UPN827 cells, TN1844 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1844 TrailNet 3or6 month T1D plasma

value: UPN827 cells


title: UPN827 cells, TN1863 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1863 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1842 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1842 TrailNet 3or6 month T1D plasma


title: s06_1

description:
10X genomics
19823X11

value: solar simulator


title: OE-TaCRVP rep3

description:
Library name: Sample 9
C3

value: untreated


title: s05_2

description:
10X genomics
19823X10


title: MZrlig1 zebrafish embryos, shield stage b

description:
Library name: KO_shield 2
K3b


title: MZrlig1 zebrafish embryos, shield stage a

description:
Library name: KO_shield 1
K3a


title: s05_1

description:
10X genomics
19823X9


title: UPN827 cells, TN1839 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1839 TrailNet 3or6 month T1D plasma


title: OE-TaCRVP rep2

description:
Library name: Sample 8
C2


title: OE-TaCRVP rep1

description:
Library name: Sample 7
C1


title: Wildtype zebrafish embryos, shield stage c

description:
Library name: WT_shield 3
W3c

value: Wildtype


title: s04_2

description:
10X genomics
19823X8


title: UPN827 cells, TN1835 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1835 TrailNet 3or6 month T1D plasma


title: Wildtype zebrafish embryos, shield stage b

description:
Library name: WT_shield 2
W3b


title: WT-fed rep3

description:
Library name: Sample 6
B3

value: WT


title: s04_1

description:
10X genomics
19823X7


title: UPN827 cells, TN1828 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1828 TrailNet 3or6 month T1D plasma


title: Wildtype zebrafish embryos, shield stage a

description:
Library name: WT_shield 1
W3a


title: s03_2

description:
10X genomics
19823X6


title: UPN827 cells, TN1822 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1822 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1834 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1834 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1820 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1820 TrailNet 3or6 month T1D plasma


title: MZrlig1 zebrafish embryos, sphere stage f

description:
Library name: KO_sphere 2
K2f

value: sphere stage


title: s03_1

description:
10X genomics
19823X5


title: MZrlig1 zebrafish embryos, sphere stage e

description:
Library name: KO_sphere 1
K2e


title: WT-fed rep1

description:
Library name: Sample 4
B1


title: WT rep3

description:
Library name: Sample 3
A3


title: s02_2

description:
10X genomics
19823X4


title: UPN827 cells, TN1819 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1819 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: Wildtype zebrafish embryos, sphere stage f

description:
Library name: WT_sphere 2
W2f

source_name: whole embryo


title: WT rep2

description:
Library name: Sample 2
A2


title: UPN827 cells, TN1814 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1814 TrailNet 3or6 month T1D plasma


title: Wildtype zebrafish embryos, sphere stage d

description:
Library name: WT_sphere 1
W2d


title: WT rep1

description:
Library name: Sample 1
A1


title: s02_1

description:
10X genomics
19823X3


title: s01_2

description:
10X genomics
19823X2


title: MZrlig1 zebrafish embryos, 4-cell stage f

description:
Library name: KO_4cell 4
K1f

value: 4-cell stage


title: UPN827 cells, TN1811 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1811 TrailNet 3or6 month T1D plasma


title: s01_1

description:
10X genomics
19823X1


title: UPN827 cells, TN1813 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1813 TrailNet 3or6 month T1D plasma


title: N9_induce_168h

city: Shanghai

first: zhengduo

last: wang

institute: east china university of science and technology

description:
Library name: I_168
Column name in GEO-2.xlsx: I_168

data_processing:
Raw data (raw reads) of fastq format were firstly processed throughfastpsoftware. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-Nandlowquality reads from raw data. At the same time, Q20, Q30 and GCcontent the clean data were calculated. All the downstreamanalyses were basedon the clean data with high quality.
Reference genome and gene model annotation files were downloadedfrom genome website. Based on the characteristic of higher genomedensity in bacterial genomes, the software Bowtie2 (2.5.4) was chosentoperform genome mapping on the filtered sequences.
Assembly: GCF_000062885.1
Supplementary files format and content: xlsx file includes raw counts for each Sample.

organism: Saccharopolyspora erythraea

growth_protocol: The strains were cultured in TSB at 30°C for a series of time points (24h, 72h, 120h 168h).

extract_protocol:
The RNA extraction procedure is as follows: Add 1 mL of Trizol to approximately 100 mg of the mycelial powder of the cells, vortex immediately to mix thoroughly, and incubate at room temperature for 10 min. Then add 200 μL of chloroform, vortex for 15 s, and centrifuge at 12,000 rpm and 4°C for 10 min. Transfer 600 μL of the upper aqueous phase to a new tube, add an equal volume of chloroform, vortex for 15 s, and centrifuge again at 12,000 rpm and 4°C for 10 min. Next, transfer 350 μL of the upper aqueous phase to a new tube, add an equal volume of isopropanol, invert to mix, incubate at 4°C for 10 min, and centrifuge at 12,000 rpm and 4°C for 10 min. Discard the supernatant, wash the pellet once with 70% ethanol, air-dry at room temperature, and dissolve in RNase-free water. Prepare the DNase I digestion system (containing 20–50 μg RNA sample, 2 μL DNase I (Takara), 5 μL 10×DNase I buffer, and RNase-free water to a final volume of 50 μL), incubate at 37°C for 1 h, then inactivate DNase I by incubating at 65°C for 10 min. Finally, determine the RNA concentration using a NanoDrop (Thermo Scientific) and store the RNA at −80°C.
For prokaryotic samples, ribosomal RNA was removed fromthe total RNA and then precipitated with ethanol. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Duringthe second strand cDNA synthesis, dUTPs were replaced with dTTPs inthe reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantificationand bioanalyzer for size distribution detection.

treatment_protocol: In the control group, 300 μM cellulose was added to inhibit autoinduction of the hQSCS.

value: bacterial cell

value: Industrial strain N6 carring pKC1139-hQSCS(-)-Thr-Gly-Glc

value: fermentation, 168 h


title: SUBP15_rep2

growth_protocol: BALL cell lines were grown according to general guidelines to a low passage number before washing and counting 50k cells per replicate for transposition.

extract_protocol:
BALL cell lines were processed using the published Fast-ATAC protocol. Briefly, cells were washed with cold PBS and simultaneously permeabilized and transposed, before DNA purification, PCR amplification, and subsequent Illumina sequencing.
DNA extracted from samples using QIAGEN MiniElute PCR purification columns and subsequent library preparation and next-generation sequencing were carried out as previously described in the ATAC-seq paper.

value: B cell precursor leukemia


title: N9_induce_120h

description:
Library name: I_120
Column name in GEO-2.xlsx: I_120

value: Industrial strain N6 carring pKC1138-hQSCS(-)-Thr-Gly-Glc

value: fermentation, 120 h


title: MZrlig1 zebrafish embryos, 4-cell stage d

description:
Library name: KO_4cell 3
K1d

value: whole embryo


title: MZrlig1 zebrafish embryos, 4-cell stage c

description:
Library name: KO_4cell 2
K1c


title: N9_induce_72h

description:
Library name: I_72
Column name in GEO-2.xlsx: I_72

value: Industrial strain N6 carring pKC1137-hQSCS(-)-Thr-Gly-Glc

value: fermentation, 72 h


title: UPN827 cells, TN1808 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1808 TrailNet 3or6 month T1D plasma

value: UPN827 cells


title: MZrlig1 zebrafish embryos, bud stage b

description:
Library name: KO_bud 2
K4b

value: bud stage


title: UPN827 cells, TN1801 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1801 TrailNet 3or6 month T1D plasma


title: N9_induce_24h

description:
Library name: I_24
Column name in GEO-2.xlsx: I_24

value: Industrial strain N6 carring pKC1136-hQSCS(-)-Thr-Gly-Glc

value: fermentation, 24 h


title: SUBP15_rep1


title: REH_rep2

value: REH


title: UPN827 cells, TN1869 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1869 TrailNet 3or6 month T1D plasma


title: MZrlig1 zebrafish embryos, 4-cell stage b

description:
Library name: KO_4cell 1
K1b


title: N9_control_168h

description:
Library name: C_168
Column name in GEO-2.xlsx: C_168

value: Industrial strain N6 carring pKC1135-hQSCS(-)-Thr-Gly-Glc


title: Wildtype zebrafish embryos, 4-cell stage f

description:
Library name: WT_4cell 4
W1f

value: Wildtype


title: N9_control_120h

description:
Library name: C_120
Column name in GEO-2.xlsx: C_120

value: Industrial strain N6 carring pKC1134-hQSCS(-)-Thr-Gly-Glc


title: UPN827 cells, TN1797 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1797 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: N9_control_72h

description:
Library name: C_72
Column name in GEO-2.xlsx: C_72

value: bacterial cell

value: Industrial strain N6 carring pKC1133-hQSCS(-)-Thr-Gly-Glc


title: NALM6_rep1

value: B cell precursor leukemia


title: sw480_lenti-HNF4a3

city: Kunming, China

first: Jianwei

last: Sun

address: Kunming, China

institute: Yunnan University

data_processing:
Novogene company provides both raw data and clean data, and the sequencing quality was assessed using FastQC.
1. The index construction is performed using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), the genome alignment of the clean data is conducted using TopHat2 (https://ccb.jhu.edu/software/tophat/index.shtml), and the transcriptome assembly is performed  using (https://cole-trapnell-lab.github.io/cufflinks/).
2. The expression level of each gene was calculated according to the fragments per kilobase million reads (FPKM) method.
3. The formula for differential analysis calculation is log2(SW480 mean (FPKM)/SW480-HNF4α OE mean (FPKM)). The p-value is calculated using the t-test. , different expressed genes (DEGs) with |log2(foldchange)| ≥ 1, and P-value < 0.05 were considered to be significantly (DEGs).
Assembly: hg38
Supplementary files format and content: The processed data is an expression matrix with a data type of FPKM. The file name is' all-FPKM. xlsx '

source_name: cell line

growth_protocol: Colon cancer cell line SW480 were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Cultivate sw480 andsw480-HNF4α OE cells to a comparable state, collecting 1×107/mL cells in each culture dish with Trizol Reagent. Ensure three biological replicates for each sample.
Subject these samples to Novogene company for transcriptome RNA-sequencing. The paired-end RNA-sequencing library was sequenced (2 × 150 bp read length) using an Illumina NovaSeq 6000 sequencer.

value: cell line

value: Colorectal cancer

value: overexpressing HNF4a


title: Wildtype zebrafish embryos, 4-cell stage a

description:
Library name: WT_4cell 1
W1a

value: whole embryo

value: 4-cell stage


title: UPN827 cells, TN1780 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1780 TrailNet 3or6 month T1D plasma

value: UPN827 cells


title: sw480_lenti-HNF4a2


title: WT-fed rep2

description:
Library name: Sample 5
B2

source_name: leaf

value: leaf

value: WT

value: fed


title: low grade endometrioid endometrial cancer of patient2

city: Hefei

first: Yifan

last: Feng

state: Anhui

address: Jixi Road 218

institute: The Anhui Medical University

description: 10x Genomics

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Assembly: genome/10xHuman/Ensembl_98
Supplementary files format and content: Tab-separated values files and matrix files

source_name: endometrioid endometrial

extract_protocol:
Briefly, frozen tissue samples were rapidly added to the lysis buffer and homogenized into a liquid state using a tissue homogenizer.  The resulting tissue lysate was filtered through a 40 μm cell sieve to remove impurities and then transferred to a fresh 2 mL EP tube.  The sample was centrifuged at 500 g at 4°C for 5 minutes to collect the precipitate.  Subsequently, PB1, PB2, and PB3 solutions were added to the precipitate, with the nuclei positioned at the interface between PB2 and PB3 solutions.  Finally, the nuclei were resuspended by gentle pipetting into 50 μL of NB solution.  A cell counter was employed to count the nuclei (Thermo Fisher, USA)
Sequencing libraries were prepared following the manufacturer's instructions (10X Genomics, USA) and then sequenced on the NovaSeq 6000 system (Illumina, USA).

tag: pathlogy

value: endometrioid endometrial cancer

tag: age

tag: grade

value: Low

value: endometrioid endometrial


title: N6_72h

description: Library name: N6

source_name: Industrial strain N6

growth_protocol: The strains were cultured in TSB at 30°C for 72 h.

value: Industrial strain N6

value: fermentation, 72 h


title: UPN827 cells, TN1775 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1775 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: PYIII-46

city: Hong Kong

first: Huaping

last: Li

address: 21 Sassoon Rd, Pok Fu Lam

country: Hong Kong

institute: The University of Hong Kong

description: gene expression from FFPE sample

hyb_protocol: The Affymetrix Human U133 GeneChip (Affymetrix, Santa Clara, CA, USA) was used for microarray gene expression analysis

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: locoregionally advanced NPC FFPE sample

label_protocol: RNA integration using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Total RNA was amplified using an Ovation FFPE WTA System (NuGEN, San Carlos, CA, USA), and an Encore Biotin Module (NuGEN) was used for fragmentation and labeling.

growth_protocol: All paraffin was removed from freshly cut FFPE tissue before RNA purification, and the sample was briefly heated in RNeasy lysis bugger

extract_protocol: RNA was extracted from FFPE samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Hilden, Germany).

treatment_protocol: The patients were recruited from seven oncology centers in Hong Kong between September 2006 and September 2012 and were treated with concurrent chemoradiotherapy plus (neo)-adjuvant chemotherapy. The median follow-up time for all patients was 8.4 years. Formalin-fixed paraffin-embedded (FFPE) samples from the nasopharynx were prospectively archived

tag: gender

value: M


title: sw480_lenti3

value: control


title: LSS4

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: hVECs-EVs

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Human valvular endothelial cells (hVECs) and human valvular interstitial cells (hVICs) were co-cultured using a parallel-plate flow system (Ibidi pump system 10902, Ibidi, Munich, Germany). A 0.5 µm pore-size ibiPore SiN membrane (85216-S, Falcon cell culture inserts, Becton Dickinson; 1.6 × 10⁶ pores/cm²) was used to separate the two cell types. hVECs were first seeded on the underside of the membrane and allowed to adhere for 6 hours. The membrane was then inverted and placed into a 6-well plate containing endothelial growth medium-2 (EGM-2, CC-3202, Lonza) supplemented with 2% fetal bovine serum, 100 μg/mL streptomycin, and 100 U/mL penicillin. hVICs were then seeded onto the upper surface of the insert. After firm attachment of both cell types, the inserts were transferred into the parallel-plate flow chamber equipped with a polycarbonate holder.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: To investigate which components in human valvular endothelial cell-derived extracellular vesicles (hVECs-EVs) orchestrate human valvular interstitial cells （hVICs）osteogenic reprogramming, we isolated EVs from hVECs exposed to bi-directional OSS (± 5 dyne/cm² at 1Hz) and laminar shear stress (LSS, 5 dyne/cm²), respectively. We then conducted a two-stage case-control study to investigate circRNAs in hVECs-EVs. The circRNA profiles of these EVs were examined using the Arraystar Human Circular RNA Microarray. extracellular vesicles (EVs) isolated from OSS (hVECsOSS-EVs) and LSS (hVECsLSS-EVs)

value: hVECs

tag: group

value: LSS


title: UPN827 cells, CHW037BL Local Cohort T1D Baseline plasma

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

source_name: UPN827 cells stimulated with CHW037BL Local Cohort T1D Baseline plasma

value: Local Cohort T1D Baseline


title: Fibrosis 2

description:
Library name: MODIFY37
MODIFY37

source_name: Sigmoid colon

value: Sigmoid colon


title: FF_4_WT

department: Department of Burn and Plastic Surgery, Guangzhou First People's Hospital

institute: Guangzhou First People's Hospital, South China University of Technology

description:
Library name: Sample_15
gene_expression_473_DTR.xlsx; sample_FF_4_fpkm

value: iDTR

value: MC903 treatment


title: UPN827 cells, TN1769 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1769 TrailNet 3or6 month T1D plasma

value: UPN827 cells


title: Head of MZrlig1 zebrafish embryos, 5 dpf stage, bad behaviour 4

description:
Library name: KO_bad 4
K_B_4

source_name: head

value: head

value: 5 dpf

value: bad behaviour


title: UPN827 cells, CHW019BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW019BL Local Cohort T1D Baseline plasma


title: Erythroid cells, DZNep  treated 3, Day11, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

source_name: Cord blood

value: Cord blood

value: Erythroid cells

value: DZNep 0.5μM


title: UPN827 cells, TN1767 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1767 TrailNet 3or6 month T1D plasma


title: OSS2

value: OSS


title: sw480_lenti1

value: cell line

value: Colorectal cancer


title: ATAC_J4_rep3

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

country: United Kingdom

institute: Cardiff University

data_processing:
Nextflow (v 23.10.1) was used to run the nf-core/atacseq pipeline.
The command used was: nextflow run nf-core/atacseq -profile singularity -params-file parameters.json --input samples.csv --genome GRCh38 --outdir output
Briefly, fastQ files were aligned to the 'GRCh38/hg38' genome build assembly using Bowtie2 and peak calling was performed using MACS2.
DiffBind was used to identify significant differential peak enrichment between control and experimental samples.
Assembly: hg38
Supplementary files format and content: Indexed Bigwig files (bw).

source_name: Ovarian cancer cell line

growth_protocol: OVCAR-3 cells were grown in 12-well TC plates using RPMI 1640 (20% FBS) media (Thermo Fisher Scientific).

extract_protocol:
After 48h of treatment, cells were lysed, nuclei extracted and DNA tagmented and purified using the ATAC-Seq kit (C01080002, Diagenode) following manufacturer's instructions.
DNA libraries were prepared using the unique dual indexes (UDI) for Tagmeneted libraries kit (C01011034, Diagenode). AMPure XP beads (A63880, Beckman Coulter) were used for library clean up.
DNA libraries were sequenced at Novogene (PE150).

treatment_protocol: OVCAR-3 cells were treated with GSK-J5 (control) and GSK-J4 (2.5µM) for 48h prior to chromatin extraction.

value: Ovarian cancer cell line


title: Lola KD adult midgut, non-stimulated control pool 3, dslola-datab-r3

city: Mexico

first: Veronica

last: Valverde-Garduño

state: Morelos

address: Av Universidad

department: Centro de Investigaciones en Enfermedades Infecciosas

country: Mexico

institute: Instituto Nacional de Salud Pública

description:
Library name: dslola-ctrl-datab-r3
Column name in all.dslola.counts.txt: dslola.dslolabase3

data_processing:
The fastq were subjected to quality check by FastQC
The raw reads were performed using Trimmomatic v0.39
The trimmed reads paired were subjected to mapping using STAR v.2.7.5 mapper
Read count were performed using FeatureCounts
The analysis between sample groups was performed by DEseq2 package
Assembly: Anopheles albimanus STECLA reference genome AalbS3
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Anopheles albimanus

source_name: midgut

growth_protocol: Mosquitoes treated with lola dsRNA and GFP dsRNA were collected 24 h post-injection

extract_protocol:
Total RNA was extracted using TRIzol® reagent
Libraries were pooled and sequenced on the Illumina NextSeq 500.

treatment_protocol: 25 midguts were pooled for each sample

value: midgut

tag: strain

value: Tapachula

value: Lola knockdown

value: non-stimulated control


title: UPN827 cells, TN1766 TrailNet 3or6 month T1D plasma

city: Milwaukee

first: Martin

last: Hessner

institute: Medical College of Wisconsin

source_name: UPN827 cells stimulated with TN1766 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: OSS1

value: hVECs


title: UPN827 cells, TN1765 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1765 TrailNet 3or6 month T1D plasma

value: UPN827 cells


title: ATAC_J4_rep2


title: UPN827 cells, TN1799 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1799 TrailNet 3or6 month T1D plasma


title: Lola KD adult midgut, non-stimulated control pool 1, dslola-datab-r1

description:
Library name: dslola-ctrl-datab-r1
Column name in all.dslola.counts.txt: dslola.dslolabase1


title: Ocy454 cells, FACS-sorted CD61 high, Rep 1

city: Boston

first: Courtney

last: Mazur

state: MA

address: 50 Blossom Street

department: Endocrine Unit

institute: Massachusetts General Hospital

description: Library name: CD61 High 1

data_processing:
For differentiation samples, STAR aligner was used to map sequencing reads to transcripts in reference genome. Read counts for individual transcripts were produced with HTSeq-count.
For FACS-sorted samples, transcript abundances were calculated using Salmon
Assembly: GRCm39
Supplementary files format and content: Tab-delimited file contains counts per million for all 8 differentiation samples.
Supplementary files format and content: Tab-delimited files contain Salmon-calculated transcript abundances for each FACS sample

growth_protocol: Ocy454 cells were grown on standard tissue culture plastic in MEM alpha supplemented with 10% FBS and 1% antibiotic/antimycotic. Cells are cultured at 33C until confluent, then cultured at 37C to induce differentiation.

extract_protocol:
Differentiated cells were lysed in RLT buffer. Lysates were passed through QIAshredder columns, then total RNA was isolated using the PureLink RNA Mini Kit with on-column DNase. FACS-sorted cells were pelleted and lysed in RLT buffer. Lysates were passed through QIAshredder columns, then total RNA was isolated using the Arcturus PicoPure RNA isolation kit with on-column DNase treatment.
mRNA molecules were purified from total RNA using oligo(dT)-magnetic beads. After fragmentation and reverse transcription, adapters were ligated and products amplified by PCR. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The ssCir DNA was formatted as the final library.

treatment_protocol: Differentiation samples were collected after the indicated days at 37C. CD61-sorted samples were prepared for flow cytometry after 17 days of differentiation by labeling with CD61-PE antibody and DAPI. The top 10% and bottom 10% of live cells were collected based on CD61-PE fluorescence intensity. Sorted cells were collected into PBS with 2% FBS and RNase inhibitor.


title: UPN827 cells, TN1758 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1758 TrailNet 3or6 month T1D plasma


title: Wildtype zebrafish embryos, 4-cell stage b

city: Konstanz

first: Fiona

last: Klusmann

institute: University of Konstanz

description:
Library name: WT_4cell 2
W1b

data_processing:
Bioinformatic processing started with the download of the reference genome (Danio_rerio.GRCz11.dna_sm.primary_assembly.fa.gz) and gene annotation file (Danio_rerio.GRCz11.113.gtf.gz) from ENSEMBL (release 113). An index was generated using STAR (v.2.7.10b), and clean paired-end reads were then aligned to the reference genome using the same version of STAR. To reconstruct the transcriptome, the genome FASTA and annotation GTF files were processed with gffread (v.0.12.7). Transcript- and gene-level expression quantification was subsequently performed with Salmon (v.0.14.1) in alignment-based mode, using STAR-generated transcriptome BAM files as input.
Differential gene expression (DGE) analysis was conducted in R using the DESeq2 package (v.1.42.1)71. Transcript-level quantifications from Salmon were imported with the tximport package (v.1.30.0)72, and a DESeqDataSet object was created from the count data and corresponding experimental metadata, with ‘condition’ defined as the main factor of interest. Genes with fewer than 10 reads across all samples were excluded to reduce noise. Counts were normalised using DESeq2’s median-of-ratios method, and p-values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate (FDR).
Assembly: Danio rerio GRCz11 (Ensembl release 113)
Supplementary files format and content: Gene-level count tables (TXT format) containing raw read counts per gene
Supplementary files format and content: Normalised expression values (TXT format) generated with DESeq2.
Supplementary files format and content: Fragments per kilobase of transcript per million fragments mapped  (TXT format).
Supplementary files format and content: Differential expression results (XLSX format) with log₂FoldChange, p-value, adjusted p-value.

source_name: whole embryo

extract_protocol:
Total RNA was extracted from pools of zebrafish embryos or dissected larval heads using TRIzol™ Reagent (Invitrogen) according to the manufacturer’s instructions. For developmental profiling, samples were collected at six stages (4-cell, sphere, shield, bud, 1 dpf, 5 dpf). Per condition, 10 embryos were pooled for the 4-cell, sphere, and shield stages, and 8 embryos for the bud, 1 dpf, and 5 dpf stages. For behavioural profiling, heads from 8 larvae were pooled per sample. RNA integrity was assessed with the Bioanalyzer 2100 system (Agilent).
Poly(A)-enriched libraries were prepared according to Novogene’s standard protocol. mRNA was enriched using oligo(dT) magnetic beads, fragmented, and used for first- and second-strand cDNA synthesis. After end repair, A-tailing, and adapter ligation, fragments were size-selected, PCR amplified, and purified to generate sequencing libraries.

value: whole embryo

value: 4-cell stage

value: Wildtype


title: Mock KD adult midgut, microbial challenge pool 3, dsGFP-mch-datab-r3

description:
Library name: dsGFP-chall-datab-r3
Column name in all.dsgfp.counts.txt: dsGFP.dsgfpreto3

value: WT, mock silenced

value: microbial challenge


title: Ocy454 cells, FACS-sorted CD61 high, Rep 2

description: Library name: CD61 High 2


title: ATAC_J5_rep3


title: UPN827 cells, TN1787 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1787 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1756 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1756 TrailNet 3or6 month T1D plasma


title: UPN827 cells, CHW034BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW034BL Local Cohort T1D Baseline plasma

value: Local Cohort T1D Baseline


title: Mock KD adult midgut, microbial challenge pool 2, dsGFP-mch-datab-r2

description:
Library name: dsGFP-chall-datab-r2
Column name in all.dsgfp.counts.txt: dsGFP.dsgfpreto2


title: Ocy454 cells, FACS-sorted CD61 low, Rep 3

description: Library name: CD61 Low 3


title: ATAC_J5_rep2


title: Lola KD adult midgut, microbial challenge pool-3, dslola-mch-datab-r3

description:
Library name: dslola-chall-datab-r3
Column name in all.dslola.counts.txt: dslola.dslolareto3


title: ATAC_J5_rep1


title: Ocy454 cells, FACS-sorted CD61 low, Rep 1

description: Library name: CD61 Low 1


title: Mock KD adult midgut, non-stimulated control pool 3, dsGFP-datab-r3

description:
Library name: dsGFP-ctrl-datab-r3
Column name in all.dsgfp.counts.txt: dsGFP.gfpbase3


title: UPN827 cells, TN1753 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1753 TrailNet 3or6 month T1D plasma


title: hESC cells, PI4KAP1-KD rep2

city: Beijing

first: Liu

last: He

address: No. 5, Dongdan Sanjo, Dongcheng District

institute: Peking Union Medical College

data_processing:
Clean reads were mapped to human genome version hg19 by STAR(v2.4.0j) with default settings.
Uniquely aligned reads were then quantified using RSEM(v1.3.1) with parameter ‘--paired-end’ and ‘--forward-prob 0’.
Normalization and differential expression analysis were performed using DESeq2
Assembly: hg19
Supplementary files format and content: .txt files of raw counts, TPM , FPKM for RNA-seq

source_name: hESC

extract_protocol:
hESC was digested into single-cell using accutase and centrifuged at 1000 r.p.m. for 5 min. 1mL Trizol was added to mix the cell pellets, and 200μL chloroform was added for shaking violently. After centrifuging at 12000 r.p.m., 4 ° C for 15min, the upper water phase was absorbed, and added with equal volume isopropyl alcohol. RNA was precipitated by centrifugation at 12000 r.p.m., 4 ° C for 15min and cleaned with 75% ethanol then dissolved in RNase-free water. RNA concentration was measured using nanodrop.
Stranded sequencing library preparation by VAHTS Universal V6 RNA-seq Library Prep Kit for  Illumina(NR604-01/02) according to manufacturer's instructions.

value: hESC

value: PI4KAP2 knock down


title: UPN827 cells, TN1749 TrailNet 3or6 month T1D plasma

address: 8701 Watertown Plank Road

source_name: UPN827 cells stimulated with TN1749 TrailNet 3or6 month T1D plasma


title: sw480_lenti2

source_name: cell line

value: cell line

value: Colorectal cancer

value: control


title: sh-dlx3 rep5

first: Fang

address: No.22 Zhongguancun South Avenue

institute: Peking University

data_processing:
The raw sequence data was trimmed and quality assessed using SOAPnuke. Next, the acquired sequences were aligned to the reference genome using HISAT2 software. The expression levels of each transcript were normalized to fragments per kilobase of exon model (FPKM) per million mapped reads using RSEM tool. KEGG pathway enrichment analysis and Gene Ontology analysis of DEGs were subsequently conducted.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files included FPKM values for each sample

source_name: alveolar bone

extract_protocol:
The alveolar bone was collected. RNA was harvested using Trizol reagent. 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols.

value: alveolar bone

value: Dlx3 inhibition


title: UPN827 cells, TN1754 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1754 TrailNet 3or6 month T1D plasma


title: Lola KD adult midgut, non-stimulated control pool 2, dslola-datab-r2

description:
Library name: dslola-ctrl-datab-r2
Column name in all.dslola.counts.txt: dslola.dslolabase2

value: midgut

value: Tapachula

value: Lola knockdown

value: non-stimulated control


title: Mock KD adult midgut, non-stimulated control pool 2, dsGFP-datab-r2

description:
Library name: dsGFP-ctrl-datab-r2
Column name in all.dsgfp.counts.txt: dsGFP.gfpbase2


title: LSS6

source_name: hVECs-EVs

value: hVECs

value: LSS


title: hESC cells, PI4KAP1-KD rep1

value: PI4KAP1 knock down


title: sh-dlx3 rep4


title: Mock KD adult midgut, non-stimulated control pool 1, dsGFP-datab-r1

description:
Library name: dsGFP-ctrl-datab-r1
Column name in all.dsgfp.counts.txt: dsGFP.gfpbase1

value: WT, mock silenced


title: hESC cells, FBXW4P1-KD rep2

value: FBXW4P1 knock down


title: UPN827 cells, TN1747 TrailNet 3or6 month T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN1747 TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: sh-dlx3 rep3


title: RNA-seq, flagleaf, Nijinokirameki, green manure, Year 2024, rep3

city: Tsukuba

first: Hirofunmi

last: Fukuda

state: Ibaraki

address: 1-31-1 Kannondai

country: Japan

institute: National Agriculture and Food Research Organization (NARO)

description:
Library name: rna_Niji_flagleaf_GM_2024_rep3
column name in Niji_flagleaf_5DAF_CF_GM_RNA_rawdata_UniqueExonReads_2024.csv: 2024_GM_rep3

data_processing:
The libraries were sequenced using the Illumina NovaSeq X Plus. Sequencing was performed on the 25B flow cell with paired-end 150-bp and unique dual-index reads. The reads were preprocessed by CLC Genomics Workbench version 25.0 (Qiagen). Reads were first trimmed using the following parameters: quality limit of 0.05, maximum number of ambiguities 2. Next, raw reads were mapped to the genome assembly and gene sets of Os-Nipponbare-IRGSP-1.0 with the following parameters: mismatch cost of 2, insertion–deletion cost of 3, length fraction of 0.8, similarity fraction of 0.8, and maximum number of hits of a read of 10. Then, uniquely mapped read counts were quantified. Genes with at least one raw read count in all of the library samples for each comparison were analyzed.
Assembly: Os-Nipponbare-IRGSP-1.0
Supplementary files format and content: csv file includes RNA-seq raw count on whole transcripts for each sample.

organism: Oryza sativa

source_name: flag leaf

growth_protocol: Hairy vetch (Vicia villosa), a legume species, was grown as a cover crop in paddy fields in Kannondai, Tsukuba City, Ibaraki Prefecture, Japan (36°01′29″N, 140°06′25″E, 21 m a.s.l.). Nutrient element contents in the field soils were analyzed by Tokachi Federation of Agricultural Cooperatives (https://www.nokyoren.or.jp/; Obihiro, Japan). The seeds (Fujiemon [Massa], Snow Brand Seed Co., Ltd.) were sown in field by hand on October 31 and again on November 15, 2023 (i.e., 60 kg/ha in total) since the germination rate of the first-sown seeds was low. The plants were grown for 5 months until April in 2024 and then directly plowed into the soil in the Kannondai paddy fields.  Seeds of rice plants were soaked in water at 30 °C for 2 d, sown in trays filled with synthetic granular soil (Sumitomo Chemical Company Co., Ltd., Tokyo, Japan), and incubated at 30 °C in the dark for 2 d. The seeds were sown on April 22, 2024. Those trays placed in a field for nearly 3 weeks to 1 month and then transplanted by hand or with a rice planter (18 cm apart × 30 cm apart, planting density 18.5 hills/m2) into the desired field conditions and grown for approximately 5 more months from mid-May to September. A normal paddy field condition (fertilization with 56:176:56 kg/ha of N:PO4:K) was set as the control condition. No chemical fertilizers were added to the green manure–treated soil.

extract_protocol:
For both flag leaves and caryopses sampling, spikelets in our field were marked on the day of flowering and collected at five days after flowering (DAF) (i.e., six days after heading) in rice plants cultivated for approximately 15 weeks after sowing. More than ten spikelets were taken from the upper third of three panicles collected from the same plant from 9:00 to 10:00 am, immediately frozen in liquid nitrogen, combined as one biological replicate of endosperms, and stored in a deep freezer. Husk was removed from frozen caryopses. Endosperms were sampled separately from embryonic bud on the cold base and then stored  in a deep freezer until sample crushing. Frozen samples were crushed by a multi-specimen cell disruption device (BMS-A20TP; BMS) just before RNA extraction. Total RNA from each sample was extracted using an RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol.
RNA-sequencing (RNA-seq) libraries were prepared using the NEBNext Ultra II Directional mRNA-seq kit for Illumina (New England Biolabs), following the manufacturer’s protocols.

treatment_protocol: Chemical fertilizer was applied as a basal dressing at 56:176:56 kg/ha (N:PO4:K). Green-manure treatment consisted of hairy vetch–derived nutrients with no additional chemical fertilizer.

value: flag leaf

value: WT

value: GM


title: hESC cells, FBXW4P1-KD rep1

value: hESC


title: UPN827 cells, TN1743 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1743 TrailNet 3or6 month T1D plasma

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN827 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).


title: sh-dlx3 rep2

value: alveolar bone


title: RNA-seq, flagleaf, Nijinokirameki, green manure, Year 2024, rep2

description:
Library name: rna_Niji_flagleaf_GM_2024_rep2
column name in Niji_flagleaf_5DAF_CF_GM_RNA_rawdata_UniqueExonReads_2024.csv: 2024_GM_rep2


title: UPN827 cells, TN1741 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1741 TrailNet 3or6 month T1D plasma


title: sh-dlx3 rep1

value: Dlx3 inhibition


title: RNA-seq, flagleaf, Nijinokirameki, green manure, Year 2024, rep1

description:
Library name: rna_Niji_flagleaf_GM_2024_rep1
column name in Niji_flagleaf_5DAF_CF_GM_RNA_rawdata_UniqueExonReads_2024.csv: 2024_GM_rep1


title: hESC cells, TMED10P1-KD rep1

value: TMED10P1 knock down


title: control rep3


title: hESC cells, WT rep 2


title: RNA-seq, flagleaf, Nijinokirameki, chemical fertilizer, Year 2024, rep3

description:
Library name: rna_Niji_flagleaf_CF_2024_rep3
column name in Niji_flagleaf_5DAF_CF_GM_RNA_rawdata_UniqueExonReads_2024.csv: 2024_CF_rep3

value: CF


title: UPN827 cells, TN1736 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1736 TrailNet 3or6 month T1D plasma


title: 10-day old female flies, high sucrose diet, rep 2

institute: Justus-Liebig-Universität Gießen

description: Library name: HCFS2

source_name: whole flie

value: whole flie

value: high sucrose diet


title: UPN827 cells, TN1735 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1735 TrailNet 3or6 month T1D plasma


title: control rep2


title: RNA-seq, flagleaf, Nijinokirameki, chemical fertilizer, Year 2024, rep2

description:
Library name: rna_Niji_flagleaf_CF_2024_rep2
column name in Niji_flagleaf_5DAF_CF_GM_RNA_rawdata_UniqueExonReads_2024.csv: 2024_CF_rep2


title: hESC cells, WT rep 1


title: control rep1


title: MC_mLN_replicate3

city: Guangzhou

first: Qidong

last: Xia

state: Guangdong

address: No.107, Yangjiangxi Road, Guangzhou

department: Breast Tumor Center

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

description:
mast cells
MC_mLN3

data_processing:
Sequence reads were trimmed for adaptor/low quality sequence using the Cutadapt package. Filtering was performed using the quality parameter q 25 and the minimum length of the reading m 15. Quality reports were generated using FASTQC software. The reads were mapped with TopHat to the reference genome of Mus musculus sapiens in the version GRCm38.91.
Assembly: GRCm38.91
Supplementary files format and content: csv files include count values for each Sample

source_name: lymph node

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the DNBSEQ mRNA library kit (BGI Genomics) following the manufacturer's protocol.

value: lymph node

value: metastatic lymph node


title: Ocy454 cells, FACS-sorted CD61 low, Rep 2

description: Library name: CD61 Low 2


title: SK_GSK5_72h rep3

data_processing:
FastQ files that contained high quality RNA sequencing reads were aligned to the 'GRCh38/hg38' genome build assembly using STAR.
Gene count tables were generated using the --quantMode GeneCounts argument in STAR.
DESeq2 was used to identify significant differential expression between control and experimental samples.
Assembly: hg38
Supplementary files format and content: Processed_OVCAR3.txt: Tab-delimited text file including Ensembl gene ID and total counts per sample
Supplementary files format and content: Processed_CAOV3.txt: Tab-delimited text file including Ensembl gene ID and total counts per sample
Supplementary files format and content: Processed_SKOV3.txt: Tab-delimited text file including Ensembl gene ID and total counts per sample

source_name: Cell line

growth_protocol: OVCAR-3, CAOV3 and SKOV3 cells were grown in 12-well TC plates using RPMI 1640 (20% FBS), DMEM/F12 (10% FBS) and McCoys 5A (10%) media respectively (Thermo Fisher Scientific).

extract_protocol:
Following 48-72h of treatment, total RNA samples were extracted using the Qiagen RNeasy Plus kit (74134).
cDNA libraries were prepared using the polyA enrichment mRNA library preparation following manufacturer's instructions (Novogene).

treatment_protocol: OVCAR-3, CAOV3 and SKOV3 cells were treated with GSK-J5 (control) and GSK-J4 (2.5µM) for 48-72h prior to RNA extraction.

value: Cell line

value: GSKJ5 72h 2.5uM


title: MC_mLN_replicate2

description:
mast cells
MC_mLN2


title: Mock KD adult midgut, microbial challenge pool 1, dsGFP-mch-datab-r1

description:
Library name: dsGFP-chall-datab-r1
Column name in all.dsgfp.counts.txt: dsGFP.dsgfpreto1

source_name: midgut

value: midgut

value: Tapachula

value: WT, mock silenced

value: microbial challenge


title: UPN827 cells, TN1723 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1723 TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: RNA-seq, endosperm, Nijinokirameki, green manure, Year 2024, rep1

description:
Library name: rna_Niji_endosperm_GM_2024_rep1
column name in Niji_endosperm_5DAF_CF_GM_RNA_rawdata_UniqueExonReads_2024.csv: 2024_GM_rep1

source_name: endosperm

value: endosperm

value: WT

value: GM


title: CA_GSKJ4_72h rep3

value: GSKJ4 72h 2.5uM


title: NALM6_rep2

city: Palo Alto

first: Reema

last: Baskar

address: 3373 Hillview Ave

institute: Stanford University

data_processing:
FASTQ files from Illumina nextseq runs were obtained from primer de-barcoding using the bcl2fastq2 application. Else, they were obtained directly from novogene sequencing service. FASTQ files were input into pepATAC pipeline to check sequencing quality (fastqc), trim (Skewer), and align (bowtie2) to the hg38 genome for cell line data and hg19 for BM and BALL data. Duplicated reads were marked and removed using Picard MarkDuplicates tool. Peaks were called using MACS2 under parameters ‘-q 0.01 ‐‐shift 0 –nomodel’. The signal-to-noise ratio between transcription start sites and flanking regions was calculated and plotted to check data quality. All samples had TSS scores of 10 and above, as well as expected fragment length distributions as plotted for all 3 sequencing experiments with 2 technical and 2 biological replicates each.
Consensus bed file was created for each experiment across technical and biological replicates using Chraccr package. Exact code in github and zenodo as referred to in paper.
Assembly: hg19
Supplementary files format and content: Peak set output from pepATAC pipeline (bed file format)

value: B cell precursor leukemia


title: MC_mLN_replicate1

description:
mast cells
MC_mLN1


title: UPN827 cells, TN1719 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1719 TrailNet 3or6 month T1D plasma


title: RNA-seq, endosperm, Nijinokirameki, chemical fertilizer, Year 2024, rep2

description:
Library name: rna_Niji_endosperm_CF_2024_rep2
column name in Niji_endosperm_5DAF_CF_GM_RNA_rawdata_UniqueExonReads_2024.csv: 2024_CF_rep2

value: CF


title: CA_GSK5_72h rep3


title: MC_uLN_replicate3

description:
mast cells
MC_uLN3

value: uninvolved lympn nodes


title: RNA-seq, endosperm, Nijinokirameki, chemical fertilizer, Year 2024, rep1

description:
Library name: rna_Niji_endosperm_CF_2024_rep1
column name in Niji_endosperm_5DAF_CF_GM_RNA_rawdata_UniqueExonReads_2024.csv: 2024_CF_rep1


title: UPN827 cells, TN1717 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1717 TrailNet 3or6 month T1D plasma


title: OV_GSKJ4_72h rep3


title: MC_uLN_replicate2

description:
mast cells
MC_uLN2

value: lymph node


title: OV_GSK5_72h rep3


title: Vehicle 5

city: Annandale

first: Thomas

last: Conrads

state: VA

address: 3289 Woodburn Rd, Suite 375

institute: Women’s Health Integrated Research Center

description: Library name: V5

data_processing:
Quality controlled sequencing reads was aligned to the mouse reference genome (GRCm39/mm39, Ensembl release 104) using the STAR algorithm (v2.7.1) within the RSEM workflow (v1.3.3) generating of both raw read counts and Transcripts Per Million (TPM) expression values for each transcript. TPM values were normalized using the formula log₂(TPM + 1) to stabilize variance and approximate a normal distribution for downstream statistical analyses
Assembly: GRCm39/mm39, Ensembl release 104
Supplementary files format and content: tab-delimited text file includes raw count for all samples

source_name: GP33+ CD8+ T cells

extract_protocol:
RNA was “harvested” by sorting cells directly into lysis buffer: live GP33-specific (GP33⁺) CD8⁺ T cells were FACS-sorted (500–1,000 cells/well) into a 96‑well plate containing cell lysis buffer. Lysates were stored: the plate was stored at −80 °C.
RNA libraries for RNA-seq were prepared using the SMART-seq HT Ultra Low input protocol

treatment_protocol: Female C57BL/6 mice were purchased from The Jackson Laboratory and were 6-8 weeks old at the time of infection with 1.5 x 106 PFU LCMV Armstrong (in 150 µL), administered intraperitoneally on day 0. Mice received 75 mg/kg ATRi (ceralasertib) or Vehicle (10% DMSO, 40% Propylene Glycol, 50% dH2O) via oral gavage on days 5, 6, and 7 post LCMV Armstrong infection. Spleens were harvested at 6 weeks after infection for sorting of GP33+ memory CD8+ T cells.

value: GP33+ CD8+ T cells

value: vehicle on days 5, 6, and 7


title: UPN827 cells, TN1715 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1715 TrailNet 3or6 month T1D plasma

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of participant plasma  that was sampled at baseline or the 3-6 months post-baseline from six TrailNet new-onset T1D intervention trails, or from our local Recent onset T1DM cohort. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).


title: hESC cells, TMED10P1-KD rep2

source_name: hESC

value: hESC

value: TMED10P1 knock down


title: UPN827 cells, TN1714 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1714 TrailNet 3or6 month T1D plasma


title: MC_uLN_replicate1

description:
mast cells
MC_uLN1


title: Vehicle 4

description: Library name: V4


title: UPN827 cells, TN1740 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1740 TrailNet 3or6 month T1D plasma


title: Patient-rep09

city: New York

first: Bettina

last: Nadorp

state: NY

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg19. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Deduplication: Duplicated reads were excluded using picard-tools version 2.6.0.
Read counting: Reads were counted on a stranded gene-basis within annotated exons downloaded from Ensembl Genes V75 using the ngsutils tool bamutils count (special paramters: -uniq, -multiple complete, -library RF).
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V75 was used to calculate FPKM values for filtered genes.
Assembly: hg19
Supplementary files format and content: xlsx file with containing FPKM values for each sample

source_name: bone marrow

extract_protocol:
RNA was extracted using the RNEasy micro kit following manufacturer's guidelines
RNA libraries for RNA-seq were prepared using Truseq library prep protocol

value: bone marrow

value: whole BM


title: REH_rep1

value: REH


title: Wildtype zebrafish embryos, 4-cell stage c

address: Universitätsstrasse 10

description:
Library name: WT_4cell 3
W1c

source_name: whole embryo

growth_protocol: Embryos used for developmental transcriptome profiling were raised in the dark at 28 °C. Embryos used for behavioural analysis and head transcriptome profiling were raised at 28 °C on a 14 h/10 h light/dark cycle. All embryos were collected by natural spawning and staged according to morphological criteria.

value: whole embryo

value: 4-cell stage

value: Wildtype


title: Vehicle 3

description: Library name: V3


title: Cochlear outer sulcus , Hypothyroid rep5

first: zhifang

last: xie

address: 1665 Kongjiang Road

department: Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

data_processing:
The sequencing data was filtered with SOAPnuke(V1.5.2) by removing reads containing adaptors, removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%, removing reads whose unknown base ratio is more than 5%.
The clean reads were mapped to the reference genome (Mus musculus, GCF_000001635.26_GRCm38.p6) with HISAT2 (v2.0.4) program and aligned to reference coding gene set with Bowtie2 (v2.2.5).
Expression levels of gene was calculated by RSEM (v1.2.12)
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Excel files include read counts and FPKM, tpm, read count values for each Sample

source_name: Cochlear outer sulcus

extract_protocol:
Articular cartilage total RNA was extracted from bilateral femoral heads of each mouse at P22 using Trizol combined with Qiagen RNeasy Micro kit.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Timed-pregnant C57BL/6J mice were treated with either antithyroid agents (0.05% methimazole, 1.0% sodium perchlorate monohydrate, and 5.0% sucrose in drinking water) or vehicle from embryonic day 17. The treatment was continued during lactation and stopped at P10.

value: Cochlear outer sulcus

value: Hypothyroid


title: Patient-rep08


title: UPN827 cells, TN1796 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1796 TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: UPN827 cells, TN1708 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1708 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1788 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1788 TrailNet 3or6 month T1D plasma


title: Cochlear outer sulcus , Hypothyroid rep4


title: N9_control_24h

first: zhengduo

last: wang

institute: east china university of science and technology

description:
Library name: C_24
Column name in GEO-2.xlsx: C_24

data_processing:
Raw data (raw reads) of fastq format were firstly processed throughfastpsoftware. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-Nandlowquality reads from raw data. At the same time, Q20, Q30 and GCcontent the clean data were calculated. All the downstreamanalyses were basedon the clean data with high quality.
Reference genome and gene model annotation files were downloadedfrom genome website. Based on the characteristic of higher genomedensity in bacterial genomes, the software Bowtie2 (2.5.4) was chosentoperform genome mapping on the filtered sequences.
Assembly: GCF_000062885.1
Supplementary files format and content: xlsx file includes raw counts for each Sample.

extract_protocol:
The RNA extraction procedure is as follows: Add 1 mL of Trizol to approximately 100 mg of the mycelial powder of the cells, vortex immediately to mix thoroughly, and incubate at room temperature for 10 min. Then add 200 μL of chloroform, vortex for 15 s, and centrifuge at 12,000 rpm and 4°C for 10 min. Transfer 600 μL of the upper aqueous phase to a new tube, add an equal volume of chloroform, vortex for 15 s, and centrifuge again at 12,000 rpm and 4°C for 10 min. Next, transfer 350 μL of the upper aqueous phase to a new tube, add an equal volume of isopropanol, invert to mix, incubate at 4°C for 10 min, and centrifuge at 12,000 rpm and 4°C for 10 min. Discard the supernatant, wash the pellet once with 70% ethanol, air-dry at room temperature, and dissolve in RNase-free water. Prepare the DNase I digestion system (containing 20–50 μg RNA sample, 2 μL DNase I (Takara), 5 μL 10×DNase I buffer, and RNase-free water to a final volume of 50 μL), incubate at 37°C for 1 h, then inactivate DNase I by incubating at 65°C for 10 min. Finally, determine the RNA concentration using a NanoDrop (Thermo Scientific) and store the RNA at −80°C.
For prokaryotic samples, ribosomal RNA was removed fromthe total RNA and then precipitated with ethanol. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Duringthe second strand cDNA synthesis, dUTPs were replaced with dTTPs inthe reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantificationand bioanalyzer for size distribution detection.

value: bacterial cell

value: Industrial strain N6 carring pKC1132-hQSCS(-)-Thr-Gly-Glc

value: fermentation, 24 h


title: Vehicle 2

description: Library name: V2

value: GP33+ CD8+ T cells


title: UPN827 cells, TN1707 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1707 TrailNet 3or6 month T1D plasma


title: Patient-rep07


title: Cochlear outer sulcus , Hypothyroid rep3


title: Q7_72h

description: Library name: Q7

value: Q7 (N6_hQSCS)

value: fermentation, 72 h


title: Vehicle 1

description: Library name: V1

value: vehicle on days 5, 6, and 7


title: Patient-rep06

value: bone marrow


title: Patient-rep05

value: whole BM


title: LSS5

institute: The Second Xiangya Hospital of Central South University

source_name: hVECs-EVs

value: hVECs

value: LSS


title: Cochlear outer sulcus , Hypothyroid rep1


title: ATRi 4

description: Library name: A4

value: ATRi (75 mg/kg ceralasertib) on days 5, 6, and 7


title: Patient-rep04


title: UPN827 cells, TN1724 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1724 TrailNet 3or6 month T1D plasma


title: Cochlear outer sulcus , Euthyroid rep5

value: Euthyroid


title: sw480_lenti-HNF4a1

first: Jianwei

last: Sun

address: Kunming, China

institute: Yunnan University

data_processing:
Novogene company provides both raw data and clean data, and the sequencing quality was assessed using FastQC.
1. The index construction is performed using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), the genome alignment of the clean data is conducted using TopHat2 (https://ccb.jhu.edu/software/tophat/index.shtml), and the transcriptome assembly is performed  using (https://cole-trapnell-lab.github.io/cufflinks/).
2. The expression level of each gene was calculated according to the fragments per kilobase million reads (FPKM) method.
3. The formula for differential analysis calculation is log2(SW480 mean (FPKM)/SW480-HNF4α OE mean (FPKM)). The p-value is calculated using the t-test. , different expressed genes (DEGs) with |log2(foldchange)| ≥ 1, and P-value < 0.05 were considered to be significantly (DEGs).
Assembly: hg38
Supplementary files format and content: The processed data is an expression matrix with a data type of FPKM. The file name is' all-FPKM. xlsx '

source_name: cell line

extract_protocol:
Cultivate sw480 andsw480-HNF4α OE cells to a comparable state, collecting 1×107/mL cells in each culture dish with Trizol Reagent. Ensure three biological replicates for each sample.
Subject these samples to Novogene company for transcriptome RNA-sequencing. The paired-end RNA-sequencing library was sequenced (2 × 150 bp read length) using an Illumina NovaSeq 6000 sequencer.

value: cell line

value: Colorectal cancer

value: overexpressing HNF4a


title: ATRi 3

description: Library name: A3


title: UPN827 cells, TN1774 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1774 TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: Cochlear outer sulcus , Euthyroid rep4

value: Cochlear outer sulcus


title: Patient-rep03


title: ATRi 2

description: Library name: A2


title: UPN827 cells, TN1690 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1690 TrailNet 3or6 month T1D plasma


title: Patient-rep02