title: wt BMDMs, IL-4, K5

city: Shanghai

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

data_processing:
For Novaseq output, basecalls were performed using bcl2fastq v2.17.
Fastx v0.0.13 was used to trim CUT&Tag readings from the 3' end until the last base had a quality score greater than 20, removing reads with fewer than 20 bp.
Using Bowtie2 version v2.2.6, CUT&Tag reads were aligned to the UCSC mm10 genome. Only readings that uniquely mapped and had no more than two mismatches were kept.
The positions of the mapped ChIP-Seq reads were expanded to 150 bp to represent sequenced segments, renormalized (to reads per million, rpm), and reformatted in the bigWig file format in order to construct CUT&Tag coverage graphs. Peaks were identified using MACS v2.2.7.1 with a p-value cutoff of =0.01.
BamCoverage was used to create bigWig files. The normalized coverage of DNA fragments at a specific genomic coordinate is represented by score. MACS v2 was used to create the narrowPeak files, and the default settings were used.
Assembly: mm10
Supplementary files format and content: narrowPeak files for the following 6 samples: wt cMa, sham, npm1; wt cMa, mi, npm1;  wt BMDM,UT,npm1; wt BMDMs, IL-4, npm1; wt cMa, mi, h3k4me3; ko cMa, mi, h3k4me3
Supplementary files format and content: bw files for the following 4 samples: wt BMDMs, IL-4, h3k4me3; ko BMDMs, IL-4, h3k4me3; wt BMDMs, IL-4, K5; ko BMDMs, IL-4, K5

source_name: bone marrow

growth_protocol: Bone marrow-derived cells were isolated from wt and ko mice and cultured in vitro using RPMI 1640 medium added with M-CSF 50 ng/ml for 7 days to induce their development into macrophages.

extract_protocol:
Using the indicated antibodies against NPM1(A302-403A) from Bethyl, or H3K4me3(SAB5600123) from Merck, or KDM5b(A301-813A)  from Bethyl, CUT&Tag was carried out using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) in accordance with the manufacturer's instructions.
Library construction was perfromed using TruePrep® DNA Library Prep Kit V2 for Illumina(Vazyme) and TruePrep® Index Kit V2 for Illumina(Vazyme).

treatment_protocol: 20ng/ml IL-4 stimulation for 12 hours

value: bone marrow

value: bone marrow derived macrophage

tag: disease state

value: IL-4 stimulation

tag: time

value: 12 hours


title: Col-0 PEP3 rep2

status: Public on Jan 26 2026

type: SRA

city: Marburg

first: Timo

last: Engelsdorf

address: Karl-von-Frisch-Str. 8

country: Germany

institute: Marburg University

description: Library name: Sample 8

library_source: transcriptomic

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing poly-N and low-quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Assembly: Index of the TAIR10 reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: xls file includes FPKM data for all samples

molecule: total RNA

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Surface-sterilized seeds were grown in half-strength Murashige and Skoog liquid medium [Murashige and Skoog Basal Medium (2.1 g/liter), MES salt (0.5g/liter), and 1% sucrose, pH 5.7]. Seedling cultures were established in a 24-well plate with 6 seeds per well. Seedlings were grown under a 16-hour light (22°C) / 8-hour dark (20°C) cycle and a photon flux density of 110μmol m−2 s−1.

extract_protocol:
Total RNA was isolated using a NucleoSpin Plant and Fungi RNA Mini Kit (Macherey-Nagel). One microgram of total RNA was treated with RNase-Free DNase (Thermo Scientific) and used for complementary DNA (cDNA) synthesis with a RevertUP II Reverse Transcriptase Kit (Biotechrabbit).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: 10-day-old seedlings were subjected to the following treatments in fresh liquid growth medium at the indicated final concentrations: 600 nM isoxaben (ISX; Supelco 36138), 10 nM AtPEP3 (EIKARGKNKTKPTPSSGKGGKHN), 600 nM ISX + 10 nM AtPEP3 (combined treatment of ISX and AtPEP3). Equal amounts of DMSO were present in all treatments, including mock treatments.

tag: tissue

value: whole seedlings

tag: genotype

tag: treatment


title: BRCA_18_3_1

type: genomic

city: Melbourne

first: Dale

last: Garsed

state: Victoria

address: 305 Grattan St

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina Infinium HD Methylation protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner settings.

data_processing:
Methylation data quality control assessment and processing were performed using the R package minfi (v1.32.0). Probes failing detection (P > 0.01), SNP positions, and cross reactive probes (as collected in https://github.com/sirselim/illumina450k_filtering) were excluded. Data was normalized using the minfi function "preprocessFunnorm" and beta values were generated. Probes were annotated to the Ensembl release GRCh37.92 GTF annotation and output file "betaVals.all.txt.gz" was generated. Beta values for samples from EPIC and 450k arrays were combined to contain shared probes and batch corrected for platform differences using the "ComBat" function in the R package sva (v3.34.0) to generate output file "betaVals.platform_corrected_by_combat.txt.gz".
Beta value

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary Tumour

label_protocol: Illumina Infinium HD Methylation Assay

extract_protocol: DNA was isolated from frozen tissue sections using either the Gentra Puregene Tissue Kit (Qiagen), DNeasy Blood and Tissue Kit (Qiagen), or AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)

value: Primary Tumour

tag: case id


title: Col-0 PEP3 rep3

description: Library name: Sample 9


title: Col-0 PEP3 rep1

description: Library name: Sample 7


title: BRCA_22_3_8


title: BRCA_2_3_6


title: Mut E12.5 fetal liver, Lin- cells, ChIP-seq

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

description: Library name: Mut1_E12.5FL

library_source: genomic

data_processing:
Raw paired-end ChIP-seq reads were trimmed for adapters and filtered for quality using Cutadapt. Trimmed reads were aligned to the mouse genome (mm10 or CNS11mut-modified mm10) with Bowtie2 (v2.2.5). Non-uniquely mapping reads and reads that aligned to the mitochondrial genome were filtered out using Samtools. Normalized coverage tracks (bigWig) were generated with deepTools bamCoverage using CPM normalization.
Assembly: mm10
Supplementary files format and content: bigWig

organism: Mus musculus

source_name: 12.5 fetal liver

extract_protocol:
Fetal liver were separated under a stereo microscope, and single-cell suspension was generated by robustly pipetting with a 1000-μl pipette. Lineage-negative cells were isolated by negative selection with the MojoSort magnetic cell separation system.
Sequence libraries were constructed with NEBNext Ultra II DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina (New England Biolabs).

value: 12.5 fetal liver

tag: cell type

value: Lin-

tag: antibody

value: CBFβ


title: BRCA_19_3_0


title: Vaccine bioreps 1-3, Naive bioreps 1-3

city: Aurora

first: Tonya

last: Brunetti

state: CO

address: 12800 East 19th Avenue

department: Immunology and Microbiology

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
Library name: all_samples_GEX_TCR_mutliplexed
BD Rhapsody sample multiplexed of single cell Whole Transcriptome Analysis (WTA) and TCR sequencing

library_source: transcriptomic single cell

data_processing:
FASTQ reads were demultiplexed and aligned using the BD Rhapsody WTA Analysis Pipeline (v. 1.11.1) with the mm10 genome reference.
Data were imported into RStudio (v. 2022.07.2+576) and analyzed using Seurat (v. 4.3.0). Low-quality cells were removed by filtering out those with <100 or >3000 detected genes or >15% mitochondrial content. Genes expressed in fewer than 10 cells were excluded, resulting in 2,623 cells and 14,370 genes for downstream analyses. Data were normalized (NormalizeData), scaled (ScaleData), and subjected to principial component analysis (RunPCA). Nearest neighbors were determined using FindNeighbors() (dims 1:6), and clustering was performed with FindClusters (resolution = 0.18), and UMAP was computed using the same six dimensions. WTA and V(D)J libraries included cDNA from A20 and EL4 lymphoma cells for unrelated studies/internal controls, so any cells with EL4 TCR-B sequences (TRBV12, TRBJ2-3, CDR3: CASSTGTETLYF) were excluded from these analyses.
TCR data was filtered using the following criteria: 1) exclusion of any A20/EL4 contamination, 2) exclusion of g/d TCR sequences, 3) selected only cells with paired a/b sequences, and 4) excluded cells with CDR3 sequences containing a stop codon (“non-productive”):
Assembly: mm10
Supplementary files format and content: *RSEC_MolsPerCell.csv: unnormalized counts matrices in csv format demultiplexed per sample generated by BD Rhapsody WTA Analysis Pipeline (v. 1.11.1)
Supplementary files format and content: TCR_data_WTA_df.csv: csv file of TCR sequencing for all samples generated by BD Rhapsody WTA Analysis Pipeline (v. 1.11.1)
Supplementary files format and content: top10.csv: csv file containing all the data used to generated heatmap in the publication
Supplementary files format and content: filtered_seurat_08_08_25.RDS: RDS file of Seurat object to be loaded into R.  Contains the final processed Seurat anlaysis for all cells, samples, and metadata
Supplementary files format and content: final_cell_metadata_with_embeddings.csv: csv file of final analyzed seurat metadata including UMAP and PCA embeddings

source_name: spleen

extract_protocol:
To generate effector H2-Kb:VVLSFELL-specific CD8 T cells for sequencing, C57BL/6 mice were immunized intravenously with 150 μg RBD protein, 40 μg poly(I:C) and 40 μg anti-CD40. Seven days later, splenocytes from three mice were incubated with H2-Kb:VVLSFELL-APC tetramer (NIH Tetramer Core) in RPMI 1640 containing 10% FBS, 10 mM HEPES, 0.1 mM beta mercaptoethanol, 0.1 mM non-essential amino acids, 0.1 mM sodium pyruvate, 2 mM l-glutamine, and penicillin-streptomycin (complete media), for 30 mins at 37°C. Cells were labeled with anti-APC microbeads (Miltenyi) and enriched via magnetic column separation. Tetramer-enriched cells were stained and flow-sorted as live CD44highB220−CD8+ dual tetramer+ (APC/BV421) live cells using a BDFACSAria (BD Biosciences). As a comparator, splenocytes from 3 unmanipulated mice magnetically enriched for CD8 T cells (Bio-Legend) and sorted as live CD44lowB220−CD8+ cells. Post-sort purities exceeded 99% for both populations.
Each sorted population was stained with a unique oligo-labeled sample tag (BD Biosciences) before library preparation. Whole transcriptome (WTA) and V(D)J libraries were prepared using the BD Rhapsody Single-Cell Analysis System with the “early-access” mouse VDJ reagents now sold as the BD Rhapsody Mouse TCR/BCR Next Amplification Kit following the manufacturer’s protocol. Libraries pooled in equimolar ratios and sequenced on an Illumina NextSeq 500-series platform by BD Biosciences.

value: spleen

value: CD8+ T cells

value: C57BL/6 mice

tag: library type

value: mRNA, VDJ-T, sample tag


title: ko BMDMs, IL-4, h3k4me3

country: China

value: NPM1 knockout


title: sEVs from ApoE ko western diet ischemic muscle

city: Montreal

first: Alain

last: Rivard

state: Qc

address: 900 rue St-Denis

country: Canada

institute: CRCHUM

description:
Library name: sEVs ApoE
Column name in sEVs_Processed_DATA.csv: sEVs_ApoE_READs and sEVs_ApoE_CPM
sEVs_Processed_DATA.csv

data_processing:
Sequenced fragments (R1 read only when appplicable) were trimmed in 3' for sequencing adapters and candidates longer than 20bp where mapped to the reference genome GRCh38 using STAR version 2.7.1a and ENCODE alignment parameters for smallRNA analysis. Known miRNA extracted from miRBase version 22 were then quantified by counting the number of reads that fall into each of their location on the genome, discriminating between 3p and 5p portion of the hairpin miRNA.
Assembly: GRCm38:mm10
Supplementary files format and content: csv files include raw counts and CPM values

source_name: sEVs from Hind limb muscle

extract_protocol:
Muscle : RNA extraction with the mirVana miRNA Isolation Kit (Thermo) Evs : RNA extraction with the miRNeasy Mini kit (Qiagen)
Muscle : Truseq Small RNA
sEVs : Qiaseq small RNA
lEVs : TriLink SmallRNA

treatment_protocol: ApoE-/- (Jax#2052) mice on Western diet (TD.88137)for 4 weeks prior to hind limb ischemia induction vs C57Bl/6 mice on regular chow

value: sEVs from Hind limb muscle

value: ApoE ko

tag: diet

value: Western Diet

value: hind limb ischemia


title: ko BMDMs, IL-4, K5

value: bone marrow

value: bone marrow derived macrophage


title: Col-0 ISX rep3

description: Library name: Sample 6

value: isoxaben


title: sEVs from C57Bl/6 control ischemic muscle

description:
Library name: sEVs C57
Column name in sEVs_Processed_DATA.csv: sEVs_C57_READs and sEVs_C57_CPM
sEVs_Processed_DATA.csv

value: Regular diet


title: wt BMDMs, IL-4, h3k4me3

value: WT

value: IL-4 stimulation

value: 12 hours


title: ko cMa, mi, h3k4me3

source_name: heart

value: heart

value: cardiac macrophage

value: myocardial infarction

value: Day 3


title: BRCA_13_3_6

value: Primary Tumour


title: BRCA_16_3_3


title: BRCA_17_3_2


title: BRCA_15_3_4


title: MHC-IIlow3

city: Leuven

first: Eleonora

last: Leucci

address: Herestraat 49, bus 818 room 06.423

department: Oncology

country: Belgium

institute: KU Leuven

description: Library name: 20

data_processing:
Libraries were sequenced on an Illumina NextSeq platform. Paired-end reads of 75bp length were produced.
Quality control of raw reads was performed using FastQC [65].  FASTQ files were cleaned up with Groomer[66].
Adapter sequences were removed with Trimmomatic [67]. Reads shorter than 20 nucleotides and or with a quality less than 20 were discarded. Splice-aware alignment was performed with STAR [68] against the mus musculus reference genome using the default parameters.
Quantification of reads per gene was performed with HT-seq Count[69]. Differential expression analysis was performed with the R [70].
Bioconductor package DESeq2 [71]. Reported p-values were adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).
Assembly: mus musculus GRCm38
Supplementary files format and content: HTSeq count files

source_name: macrophage

growth_protocol: Lewis Lung Carcinoma cells were cultured in 5% CO2 at 37 °C in DMEM (Gibco) supplemented with 10% Fetal Calf Serum (FCS) (Gibco), 1% Penicillin-Streptomycin (Gibco), and 1% L-Glutamine (Gibco). C57BL/6 mice were injected subcutaneously in the right flank with 1E6 cells suspended in HBSS (Gibco). After 15-17 days, the mice were euthanized and the tumours were extracted.

extract_protocol:
Cells were lysed using Trizol (Invitrogen) and vortexed. For each 1 ml of Trizol, 200 μl of chloroform (Sigma) was added, followed by vortexing. The samples were incubated at room temperature (RT) for 3 minutes and centrifuged at 12,000 rcf for 15 minutes at 4°C. The aqueous phase was collected, and an equal volume of 100% isopropanol was added. After tapping and vortexing, the samples were incubated for 40 minutes at RT. The samples were then centrifuged at 12,000 rcf for 30 minutes at 4°C. The supernatant was removed, and the pellet was washed with cold (-20°C) 75% ethanol (Acros Organics). The samples were centrifuged again at 12,000 rcf for 20 minutes at 4°C. The RNA pellets were dried in a fume hood for up to 10 minutes. The pellets were resuspended in ultrapure DEPC water (Thermo Fisher) and gently vortexed. RNA concentration was determined using the Qubit RNA HS assay (Thermo Fisher), and RNA integrity was assessed using the Agilent RNA 6000 Nano kit (Agilent Technologies).
The RiboMinus Eukaryote Kit (Thermo Fisher)  for RNA-Seq was used to deplete ribosomal RNA.The TruSeq Stranded Total RNA kit (Illumina) was used to construct the library for RNA sequencing. The low sample protocol was used and the following adjustments were made to the standard protocol. The first step was cleaning up the RNA with RNAClean XP beads (Beckman Coulter). Then the first strand was synthesized followed by the second strand. CTE for end pair control was not added. The 3’ ends were adenylated, the adapter ligated and the DNA fragments were enriched. The library concentration and size was determined with Qubit and Bioanalyzer. The libraries were normalized and pooled.

treatment_protocol: The tumours were dissociated into single-cell suspensions using 10 U/mL Collagenase I (Worthington Biochemical), 400 U/mL Collagenase IV (Worthington Biochemical), and 30 U/mL DNase I (Worthington Biochemical) diluted in HBSS (Gibco). The plates were incubated for 20–25 min at 37°C. The cell suspension was filtered through 70 μm nylon filters, then centrifuged at 450 rcf for 6 min at 4°C. Red blood cells were lysed using a buffer containing 8.26 g/L NH4Cl (Merck KgaA), 1 g/L KHCO3 (Merck KgaA) and 37.2 mg/L EDTA (Duchefa Biochemie), pH 7.2. Mononuclear cells were isolated using a Lymphoprep gradient (Axis-shield), and CD11b-positive cells were enriched using magnetic-activated cell sorting (MACS) (Miltenyi Biotec). Fc block (rat anti-mouse CD16/CD32) was added, and the samples were incubated on ice for 15 min at 4˚C. The following antibodies were then added: Alexa Fluor® 647 anti-mouse Ly-6C (BioLegend); PE-Cy7-conjugated anti-CD11b antibody (clone M1/70, BD Biosciences); PE Rat Anti-Mouse Ly-6G (BD Pharmingen™); PerCP-Cy5.5-conjugated anti-I-A/I-E (MHC-II) antibody (clone M5/114.15.2, BioLegend); and Alexa Fluor® 488 Rat Anti-Mouse F4/80 (BioRad). The cells were incubated for 20 min at 4˚C protected from light. After incubation, the samples were washed and sorted for CD11b⁺, Ly6C⁻, Ly-6G⁻, F4/80⁺, MHC-II (high and low) cells. The sorted cells were washed and prepared for RNA extraction.

value: macrophage

tag: batch


title: wt BMDMs, IL-4, npm1


title: MHC-IIlow1

description: Library name: 15


title: BRCA_14_3_5


title: Col-0 ISX rep2

description: Library name: Sample 5

value: whole seedlings


title: MHC-IIlow2

description: Library name: 18


title: Col-0 DMSO rep3

description: Library name: Sample 3

value: control


title: BRCA_10_3_9


title: BRCA_12_3_7


title: MHC-IIhigh2

description: Library name: 17


title: Col-0 DMSO rep2

description: Library name: Sample 2


title: BRCA_11_3_8


title: wt cMa, mi, h3k4me3


title: MHC-IIhigh1

description: Library name: 14


title: wt cMa, mi, npm1


title: Col-0 ISX rep1

description: Library name: Sample 4


title: Col-0 DMSO rep1

description: Library name: Sample 1


title: wt cMa, sham, npm1

value: sham operation


title: MHC-IIhigh3

description: Library name: 19


title: BRCA_1_3_7


title: Neuron, 18weeks, 2div, rep224

status: Public on Jan 25 2026

city: Toronto

first: Shreejoy

last: Tripathy

state: Ontario

address: 250 College st.

institute: CAMH

data_processing:
Raw sequencing data were demultiplexed and converted into fastq format using bcl2fastq2 v2.20.
Assembly: Sus scrofa 11.1 (Ensembl release 104)
Supplementary files format and content: csv files of counts per sample and metadata

organism: Sus scrofa

source_name: dorsal root ganglion

extract_protocol:
Given the large size of pig DRG neurons, the sample collection followed a procedure using two separate pipettes as follows: First, the recording pipette was retracted under slightly negative pressure from the cell and immutably broken into in PCR-tube containing 4 µl of lysis buffer (40 mM Guanidine hydrochloride, 0.1 mM Smart dT30VN primer, 5 mM dNTPs), secondly a second bigger pipette with diameter customized for cell diameter of cell to collect (resistance ~0.7 Mohm, size adapted for patched cell for ideal harvesting result) was used to collect the entire cell. After collection, this pipette was broken into the same PCR-tube. Samples were immediately frozen on dry ice.
Individual lysed cells were treated according to the Smart-Seq2 library preparation protocol

value: dorsal root ganglion

value: neuron


title: Neuron, 18weeks, 2div, rep221


title: Neuron, 18weeks, 2div, rep222


title: Neuron, 18weeks, 2div, rep218


title: Neuron, 18weeks, 2div, rep223


title: Neuron, 18weeks, 2div, rep226


title: Neuron, 18weeks, 1div, rep214


title: wt BMDM,UT,npm1

value: bone marrow

value: bone marrow derived macrophage

value: untreated

value: 0 hours


title: Neuron, 18weeks, 2div, rep217

value: WT


title: Neuron, 18weeks, 1div, rep212


title: Neuron, 18weeks, 1div, rep215


title: Neuron, 18weeks, 1div, rep216


title: Neuron, 18weeks, 1div, rep213


title: Neuron, 17weeks, 2div, rep210


title: Neuron, 18weeks, 2div, rep220


title: Neuron, 18weeks, 2div, rep219


title: Neuron, 17weeks, 2div, rep207


title: Neuron, 18weeks, 2div, rep225


title: Neuron, 17weeks, 2div, rep209


title: Neuron, 18weeks, 1div, rep211


title: Neuron, 17weeks, 2div, rep206


title: Neuron, 17weeks, 2div, rep201


title: Neuron, 17weeks, 2div, rep203


title: Neuron, 17weeks, 2div, rep200


title: Neuron, 17weeks, 2div, rep202


title: Neuron, 17weeks, 2div, rep208


title: Neuron, 17weeks, 1div, rep194


title: Neuron, 17weeks, 1div, rep199


title: Neuron, 17weeks, 1div, rep198


title: Neuron, 17weeks, 1div, rep196


title: Neuron, 17weeks, 1div, rep191


title: Neuron, 17weeks, 2div, rep204


title: Neuron, 17weeks, 1div, rep184


title: Neuron, 17weeks, 1div, rep197


title: Neuron, 17weeks, 1div, rep185


title: Neuron, 17weeks, 2div, rep205


title: Neuron, 17weeks, 1div, rep189


title: Neuron, 17weeks, 1div, rep190


title: Neuron, 17weeks, 1div, rep179


title: Neuron, 17weeks, 1div, rep193


title: Neuron, 17weeks, 1div, rep182


title: Neuron, 17weeks, 1div, rep195


title: Neuron, 18weeks, 3div, rep173


title: Neuron, 18weeks, 3div, rep174


title: Neuron, 18weeks, 3div, rep175


title: Neuron, 20weeks, 2div, rep172


title: Neuron, 17weeks, 1div, rep180


title: Neuron, 18weeks, 3div, rep176


title: Neuron, 17weeks, 1div, rep177


title: Neuron, 17weeks, 1div, rep192


title: Neuron, 17weeks, 1div, rep188


title: Neuron, 18weeks, 3div, rep164


title: Neuron, 17weeks, 1div, rep186


title: Neuron, 18weeks, 3div, rep166


title: Neuron, 18weeks, 2div, rep161


title: Neuron, 18weeks, 3div, rep163


title: Neuron, 18weeks, 2div, rep158


title: Neuron, 17weeks, 1div, rep178


title: Neuron, 17weeks, 1div, rep187


title: Neuron, 18weeks, 2div, rep156


title: Neuron, 20weeks, 2div, rep170


title: Neuron, 17weeks, 1div, rep181


title: Neuron, 18weeks, 3div, rep168


title: Neuron, 20weeks, 1div, rep150


title: Neuron, 18weeks, 2div, rep152


title: Neuron, 20weeks, 2div, rep171


title: Neuron, 20weeks, 1div, rep149


title: Neuron, 18weeks, 2div, rep160


title: Neuron, 18weeks, 2div, rep155


title: Neuron, 18weeks, 1div, rep145


title: Neuron, 18weeks, 1div, rep147


title: Neuron, 18weeks, 1div, rep143


title: Neuron, 17weeks, 1div, rep183


title: Neuron, 18weeks, 3div, rep162


title: Neuron, 15weeks, 2div, rep140


title: Neuron, 18weeks, 1div, rep142


title: Neuron, 15weeks, 2div, rep138


title: Neuron, 15weeks, 2div, rep137


title: Neuron, 18weeks, 2div, rep159


title: Neuron, 15weeks, 2div, rep135


title: Neuron, 18weeks, 2div, rep157


title: Neuron, 15weeks, 1div, rep130


title: Neuron, 18weeks, 3div, rep167


title: Neuron, 20weeks, 2div, rep169


title: Neuron, 18weeks, 1div, rep144


title: Neuron, 18weeks, 3div, rep165


title: Neuron, 18weeks, 2div, rep151


title: Neuron, 15weeks, 1div, rep126


title: Neuron, 15weeks, 2div, rep139


title: Neuron, 15weeks, 1div, rep127


title: Neuron, 18weeks, 1div, rep141


title: Neuron, 18weeks, 1div, rep148


title: Neuron, 18weeks, 2div, rep153


title: Neuron, 18weeks, 2div, rep154


title: Neuron, 15weeks, 1div, rep122


title: Neuron, 15weeks, 1div, rep123


title: Neuron, 15weeks, 1div, rep110


title: Neuron, 15weeks, 1div, rep115


title: Neuron, 15weeks, 2div, rep136


title: Neuron, 15weeks, 1div, rep113


title: Neuron, 15weeks, 2div, rep109


title: Neuron, 15weeks, 1div, rep131


title: Neuron, 15weeks, 1div, rep134


title: Neuron, 18weeks, 1div, rep146


title: Neuron, 15weeks, 1div, rep132


title: Neuron, 15weeks, 2div, rep108


title: Neuron, 15weeks, 1div, rep124


title: Neuron, 15weeks, 1div, rep128


title: Neuron, 15weeks, 1div, rep125


title: Neuron, 15weeks, 1div, rep129


title: Neuron, 15weeks, 2div, rep105


title: Neuron, 15weeks, 2div, rep104


title: Neuron, 15weeks, 1div, rep133


title: Neuron, 15weeks, 1div, rep117


title: Neuron, 15weeks, 2div, rep103


title: Neuron, 15weeks, 1div, rep111


title: Neuron, 15weeks, 1div, rep112


title: Neuron, 15weeks, 2div, rep107


title: Neuron, 15weeks, 2div, rep100


title: Neuron, 15weeks, 1div, rep116


title: Neuron, 15weeks, 1div, rep120


title: Neuron, 15weeks, 1div, rep121


title: Neuron, 15weeks, 1div, rep118


title: Neuron, 15weeks, 1div, rep119


title: Neuron, 15weeks, 2div, rep102


title: Neuron, 15weeks, 1div, rep91


title: Neuron, 15weeks, 1div, rep92


title: Neuron, 15weeks, 1div, rep88


title: Neuron, 15weeks, 2div, rep99


title: Neuron, 15weeks, 2div, rep106


title: Neuron, 15weeks, 1div, rep114


title: Neuron, 15weeks, 1div, rep89


title: Neuron, 14weeks, 3div, rep81


title: Neuron, 15weeks, 1div, rep96


title: Neuron, 15weeks, 1div, rep90


title: Neuron, 15weeks, 1div, rep93


title: Neuron, 15weeks, 1div, rep95


title: Neuron, 14weeks, 2div, rep76


title: Neuron, 15weeks, 2div, rep98


title: Neuron, 15weeks, 1div, rep94


title: Neuron, 14weeks, 2div, rep73


title: Neuron, 14weeks, 2div, rep70


title: Neuron, 14weeks, 2div, rep69


title: Neuron, 14weeks, 2div, rep68


title: Neuron, 15weeks, 1div, rep85


title: Neuron, 14weeks, 2div, rep66


title: Neuron, 14weeks, 3div, rep79


title: Neuron, 14weeks, 2div, rep63


title: Neuron, 15weeks, 1div, rep87


title: Neuron, 14weeks, 3div, rep83


title: Neuron, 14weeks, 2div, rep61


title: Neuron, 14weeks, 3div, rep80


title: Neuron, 14weeks, 2div, rep72


title: Neuron, 14weeks, 1div, rep55


title: Neuron, 14weeks, 2div, rep71


title: Neuron, 15weeks, 2div, rep101


title: Neuron, 14weeks, 3div, rep82


title: Neuron, 14weeks, 2div, rep75


title: Neuron, 15weeks, 1div, rep86


title: Neuron, 14weeks, 1div, rep53


title: db/db3

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

description: Library name: Sample6

data_processing:
The raw sequencing data (raw reads) were first subjected to quality control and filtering using the fastp software to obtain clean reads suitable for downstream analysis. The filtering criteria included: removing reads containing sequencing adapters, discarding reads with the proportion of unknown nucleotides (N) exceeding 10%, and excluding low-quality reads with more than 50% of bases having a Phred quality score < 20. The quality of clean reads was further validated using FastQC software, with key metrics including Q20 (≥ 99.29%), Q30 (≥ 97.74%), and GC content (≈ 49%). The clean reads were then aligned to the reference mouse genome using HISAT2 software, and the alignment efficiency was evaluated by statistics of total mapped reads, uniquely mapped reads, and multiple mapped reads (with total mapped rate ≥ 97.46%). Based on the alignment results, subsequent bioinformatics analyses were performed, including alternative splicing analysis (using rMATs), SNP/InDel detection (using samtools and bcftools), novel transcript prediction and gene structure optimization (using StringTie and gffcompare), gene expression level quantification (calculating FPKM values via StringTie), differential gene expression analysis (using DESeq2 with the threshold of |FoldChange| ≥ 2 and padj ≤ 0.05), functional enrichment analysis (GO and KEGG enrichment via clusterProfiler), gene set enrichment analysis (GSEA), and protein-protein interaction (PPI) network construction (using STRING database and R package).
Processed RNA-seq data were organized by analytical modules with standardized file formats. Key formats and their core contents are as follows: (1) Fastq format: Stores filtered clean reads and corresponding sequencing quality scores, serving as input for genome alignment. (2) BAM/SAM format: Records clean read alignment information against the reference genome, including mapping positions, strand orientation and mapping quality. (3) Text/csv format: Compiles statistical data and analytical results, such as sequencing yield, alignment metrics, differential gene lists, GO/KEGG enrichment outcomes and SNP/InDel detection results, providing quantifiable data for further analysis. (4) PNG format: Presents visualized results, including quality control plots, sample correlation heatmaps, PCA plots, differential gene volcano plots and PPI network diagrams. (5) GTF/GFF format: Documents annotation information of novel transcripts and optimized gene structures. A detailed file description is available in the readme document.
Assembly: The reference genome used for all bioinformatics analyses was the mouse (Mus musculus) genome assembly GCF_000001635.27, which was downloaded from the National Center for Biotechnology Information (NCBI) database. This assembly corresponds to a high-quality, well-annotated genome version, providing comprehensive genomic sequences and gene annotation information including exons, introns, and intergenic regions. The clean reads were aligned to this reference genome using HISAT2, a fast and efficient spliced aligner designed for RNA-seq data, which can accurately map reads spanning splice junctions. The alignment results showed that the total mapped rate of clean reads for all samples was above 97.46%, with uniquely mapped reads accounting for 86.18%–87.72% of the total clean reads, indicating that the selected reference genome was highly suitable for this study and ensured the reliability of subsequent gene expression and variation analyses.
Supplementary files format and content: gene_count_matrix.txt

source_name: whole kidney

extract_protocol:
Total RNA was isolated from mouse tissue samples using a commercially available RNA extraction kit (e.g., Trizol reagent or column-based RNA purification kit) following the manufacturer’s standard protocols. Briefly, the collected samples were homogenized in lysis buffer to fully release intracellular RNA, followed by phase separation with chloroform to remove protein and genomic DNA contaminants. The aqueous phase containing RNA was then precipitated with isopropanol, and the RNA pellet was washed with 75% ethanol, air-dried, and resuspended in RNase-free water. The quality and integrity of the extracted total RNA were evaluated using a NanoDrop spectrophotometer (to assess the A260/A280 ratio, with an optimal range of 1.8–2.1) and an Agilent 2100 Bioanalyzer (to determine the RNA Integrity Number, RIN ≥ 7.0). Only high-quality RNA samples that passed the above quality control criteria were subjected to subsequent mRNA enrichment and library construction.
A strand-specific mRNA-seq library was constructed using the enriched mRNA from total RNA samples. First, eukaryotic mRNA was purified and enriched from total RNA using magnetic beads conjugated with Oligo(dT) to specifically bind the poly(A) tails of mRNA molecules. The purified mRNA was fragmented into short fragments (approximately 200–300 bp) by adding fragmentation buffer under thermostatic conditions. Using these fragmented mRNAs as templates, the first strand of cDNA was synthesized with random hexamer primers, followed by the synthesis of the second strand of cDNA using DNA polymerase I, RNase H, dNTPs, and buffer. The double-stranded cDNA products were then subjected to end repair, 3' end adenylation, and ligation of sequencing adapters. After adapter ligation, the cDNA fragments of target size were selected by magnetic bead purification, and the resulting cDNA library was amplified by PCR with limited cycles to enhance library yield. Finally, the constructed library was quantified using a Qubit fluorometer and its insert size was verified using an Agilent 2100 Bioanalyzer. Qualified libraries with consistent insert size and sufficient concentration were used for high-throughput sequencing.

value: whole kidney

value: db/db

value: mice fed with normal chow


title: Neuron, 15weeks, 1div, rep97


title: db/db2

description: Library name: Sample5


title: db/db1

description: Library name: Sample4


title: Neuron, 14weeks, 2div, rep77


title: Neuron, 14weeks, 2div, rep60


title: Neuron, 14weeks, 1div, rep59


title: Neuron, 14weeks, 2div, rep74


title: Neuron, 14weeks, 1div, rep56


title: db/m2

description: Library name: Sample2

value: db/m


title: Neuron, 14weeks, 2div, rep64


title: Neuron, 14weeks, 3div, rep84


title: Neuron, 12weeks, 1div, rep48


title: Neuron, 14weeks, 1div, rep58


title: Neuron, 14weeks, 3div, rep78


title: Neuron, 14weeks, 2div, rep67


title: Neuron, 12weeks, 1div, rep43


title: Neuron, 14weeks, 2div, rep62


title: Neuron, 14weeks, 2div, rep65


title: trampc_tumor_sot101_5

type: RNA

city: Prague 9

first: Lenka

last: Palova Jelinkova

address: Ceskomoravska 2532/19b

country: Czech Republic

institute: Sotio Biotech a.c.

description: Two probes were used to detect each transcript: a reporter probe that carries the fluorescent barcode, and a biotinylated capture probe that immobilizes the complex for data collection. The code set contained 770 probe pairs, each pair specific to a particular nucleic acid target

scan_protocol: nCounter Mouse PanCancer Immune Profiling Panel - 20 housekeeping genes, 8 negative controls, 6 positive controls

data_processing: nSolver Advanced Analysis and R NanoStringDiff package

label: Fluorescent barcode, unique to each probe

source_name: tumor from SOT101-treated TRAMP-C mice

extract_protocol: The total RNA was extracted via RNeasy Mini Kit.

treatment_protocol: TC-1 and TRAMP-C2 mice bearing tumor were treated with SOT101 at 40 µg/mouse at Day 1-4 and collected at Day 7.

tag: strain

value: TRAMP-C

value: tumor


title: Neuron, 14weeks, 1div, rep57


title: Neuron, 14weeks, 1div, rep54


title: trampc_tumor_sot101_1


title: Neuron, 12weeks, 1div, rep41


title: Neuron, 12weeks, 1div, rep49


title: db/m3

description: Library name: Sample3


title: Neuron, 14weeks, 1div, rep52


title: db/m1

description: Library name: Sample1


title: Neuron, 14weeks, 1div, rep50


title: Neuron, 14weeks, 1div, rep51


title: Neuron, 12weeks, 1div, rep45


title: Neuron, 12weeks, 1div, rep46


title: Neuron, 11weeks, 3div, rep38


title: Neuron, 12weeks, 1div, rep40


title: Neuron, 12weeks, 1div, rep44


title: Neuron, 11weeks, 3div, rep37


title: trampc_tumor_sot101_2


title: Neuron, 12weeks, 1div, rep42


title: Neuron, 12weeks, 1div, rep39


title: trampc_tumor_nt_2

source_name: tumor from non-treated TRAMP-C mice

value: Non-treated


title: trampc_tumor_sot101_3


title: Neuron, 12weeks, 1div, rep47


title: Neuron, 11weeks, 3div, rep35


title: trampc_tumor_nt_5


title: trampc_tumor_sot101_4


title: trampc_tumor_nt_3


title: Neuron, 11weeks, 3div, rep36


title: trampc_tumor_nt_1


title: trampc_tumor_nt_4


title: trampc_ln_sot101_4

source_name: LN from SOT101-treated TRAMP-C mice

value: lymph node


title: trampc_ln_sot101_5


title: Neuron, 11weeks, 3div, rep34


title: Neuron, 11weeks, 1div, rep28


title: Neuron, 11weeks, 1div, rep27


title: trampc_ln_sot101_3


title: Neuron, 11weeks, 2div, rep30


title: trampc_ln_sot101_1


title: Neuron, 11weeks, 2div, rep31


title: Neuron, 11weeks, 2div, rep32


title: trampc_ln_nt_4

source_name: LN from non-treated TRAMP-C mice


title: Neuron, 11weeks, 1div, rep26


title: Neuron, 11weeks, 2div, rep29


title: trampc_ln_nt_3


title: trampc_spleen_sot101_5

source_name: spleen from SOT101-treated TRAMP-C mice

value: spleen


title: trampc_ln_nt_2


title: trampc_ln_nt_5


title: trampc_spleen_sot101_4


title: trampc_spleen_sot101_2


title: trampc_ln_sot101_2


title: Neuron, 11weeks, 3div, rep33


title: trampc_ln_nt_1


title: trampc_spleen_nt_5

source_name: spleen from non-treated TRAMP-C mice


title: Neuron, 11weeks, 1div, rep23


title: trampc_spleen_nt_4


title: Neuron, 11weeks, 1div, rep19


title: trampc_spleen_sot101_3


title: Neuron, 11weeks, 1div, rep18


title: Neuron, 11weeks, 1div, rep24


title: Neuron, 11weeks, 1div, rep22


title: Neuron, 11weeks, 1div, rep16


title: trampc_spleen_nt_1


title: Neuron, 11weeks, 1div, rep21


title: tc1_tumor_sot101_6

source_name: tumor from SOT101-treated TC-1 mice


title: Neuron, 11weeks, 1div, rep11


title: Neuron, 11weeks, 2div, rep13


title: tc1_tumor_sot101_1


title: Neuron, 11weeks, 1div, rep8


title: Neuron, 11weeks, 1div, rep25


title: tc1_tumor_sot101_2


title: Neuron, 11weeks, 1div, rep20


title: Neuron, 11weeks, 1div, rep17


title: tc1_tumor_nt_6

source_name: tumor from non-treated TC-1 mice


title: trampc_spleen_sot101_1


title: Neuron, 11weeks, 1div, rep14


title: tc1_tumor_sot101_4


title: trampc_spleen_nt_3


title: Neuron, 11weeks, 1div, rep4


title: Neuron, 11weeks, 2div, rep12


title: tc1_tumor_nt_4


title: tc1_tumor_sot101_3


title: trampc_spleen_nt_2


title: tc1_tumor_nt_1


title: tc1_tumor_nt_5


title: Neuron, 11weeks, 1div, rep5


title: Neuron, 11weeks, 1div, rep6


title: tc1_ln_sot101_6

source_name: LN from SOT101-treated TC-1 mice


title: Neuron, 11weeks, 1div, rep7


title: DRG, round3, s8

data_processing:
The generated Illumina BCL files were processed with the 10XGenomics pipeline (Space Ranger v1.1). This pipeline allowed the alignment of the FASTQ files with bright-field microscope images and the pig reference transcriptome
Assembly: Sscrofa11
Supplementary files format and content: RDS Seurat file of raw and transformed counts, including metadata
Library strategy: Spatial Transcriptomics

extract_protocol:
Methanol fixation and Eosin and Haematoxylin staining for an initial tissue quality control analysis was performed as described in the 10XGenomics Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (Demonstrated Protocol CG000160). We stained a total of 60 sections, each 10 µm in thickness, from 22 fresh frozen DRG obtained from 7 female pigs. Different permeabilization times (3, 6, 12, 18, 24 and 30 minutes) were evaluated following the 10XGenomics Visium Spatial Gene Expression Reagent Kits - Tissue Optimization User Guide CG000238 Rev E. This protocol required the reagents from the Visium Spatial Tissue Optimization Reagent Kit, PN-1000192 (stored at −20°C) and the Visium Spatial Tissue Optimization Slide Kit PN-1000191 (stored at ambient temperature). The exposure time of the permeabilization enzyme was 18 minutes based on the analysis of the tissue optimization experiment.
We used the spatial sequencing protocol Visium Spatial Gene Expression Reagent Kits, 16 rxns PN-1000186 and Library Construction Kits, 16 rxns PN-1000190. All reagents were stored at -20°C. Additionally, Visium Spatial Gene Expression Slide Kits, 16 rxns PN-1000185 were acquired and stored at ambient temperature. The protocol was performed exactly as stated in the Visium Spatial Gene Expression Reagents Kits User Guide CG000239 Rev F.


title: Neuron, 11weeks, 1div, rep10


title: DRG, round3, s7


title: Neuron, 11weeks, 1div, rep15


title: Neuron, 11weeks, 1div, rep9


title: tc1_tumor_sot101_5


title: tc1_tumor_nt_2


title: tc1_tumor_nt_3


title: tc1_ln_nt_6

source_name: LN from non-treated TC-1 mice


title: tc1_ln_sot101_5


title: Neuron, 11weeks, 1div, rep2


title: DRG, round3, s6


title: DRG, round3, s4


title: tc1_ln_sot101_1


title: tc1_ln_sot101_2


title: Neuron, 11weeks, 1div, rep1


title: tc1_ln_nt_5


title: tc1_ln_sot101_4


title: tc1_ln_sot101_3


title: tc1_ln_nt_3


title: DRG, round3, s2


title: DRG, round3, s5


title: Neuron, 11weeks, 1div, rep3


title: tc1_ln_nt_2


title: tc1_spleen_sot101_5

source_name: spleens from SOT101-treated TC-1 mice


title: DRG, round2, s7


title: DRG, round3, s3


title: DRG, round2, s3


title: DRG, round3, s1


title: DRG, round2, s6


title: tc1_spleen_sot101_2


title: tc1_ln_nt_4


title: tc1_spleen_nt_6

source_name: spleen from non-treated TC-1 mice


title: DRG, round2, s4


title: DRG, round2, s2


title: tc1_spleen_sot101_3


title: tc1_spleen_nt_4


title: DRG, round1, s12


title: tc1_spleen_sot101_6


title: tc1_spleen_nt_5


title: tc1_spleen_nt_2


title: DRG, round1, s9


title: calumenin KD2

city: Jinan

first: Huirui

last: Wang

state: -- None selected --

address: 44 Wenhuaxi Road

institute: Shandong University

description:
Library name: KD2
KO2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: mouse primary lung fibroblasts

extract_protocol:
Cells were lysed in TRIzol reagent, and total RNA was extracted by using a Rapid RNA Extraction Kit per the manufacturer’s protocol. The integrity of the RNA was verified via agarose gel electrophoresis, and the RNA concentrations were quantified with a NanoDrop spectrophotometer.
RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq 6000. The index of the reference genome was built by using HISAT2 (v2.0.5), and paired-end clean reads were aligned to the reference genome.

tag: cell line

value: mouse primary lung fibroblasts

value: KD


title: DRG, round1, s8

value: dorsal root ganglion


title: erf96_RBF_3

city: Kurashiki

first: Yoji

last: Kawano

state: Okayama

department: Institute of Plant Science and Resources

institute: Okayama University

description: Library name: Sample 18

data_processing:
Base calling and demultiplexing were performed by the sequencing provider using DNBSEQ built-in software.
Assembly: Cleaned reads were aligned to a combined reference genome incorporating gene models from both RAP-DB (IRGSP-1.0) and MSU (RGAP 7.0) databases
Supplementary files format and content: csv file include TPM values for each sample

organism: Oryza sativa Japonica Group

source_name: plant leave

extract_protocol:
RNA was harvested using TRIzol, 2 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared by Azenta Life Sciences (Japan) following their standard eukaryotic mRNA-seq protocol. Total RNA was enriched for mRNA using oligo(dT) beads (PolyA selection). The libraries were constructed for the DNBSEQ platform using MGI-compatible adaptors. Sequencing was performed on a DNBSEQ instrument. Data quality control and adapter trimming were performed using fastp v.0.20.0.

value: plant leave

value: OsERF96.2 knockout

value: Magnaporthe oryzae


title: tc1_spleen_nt_1


title: tc1_ln_nt_1


title: calumenin KD1

description:
Library name: KD1
KO1


title: DRG, round1, s11


title: tc1_spleen_sot101_1


title: DRG, round1, s7


title: NC2

description:
Library name: NC2
WT2

value: NC


title: tc1_spleen_nt_3


title: DRG, round2, s1


title: calumenin KD3

description:
Library name: KD3
KO3


title: NC1

description:
Library name: NC1
WT1


title: Primary CD8+ T, 25uM Hemin treatment 4

city: Tianjin

first: Yingxi

last: Xu

address: 288 Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: Female_Hemin_4

data_processing:
Conversion and demultiplexing: IlluminaBasecallsToMultiplexSam to generate one bam file per lane from the data on the Illumina machine, IlluminaSamDemux to demultiplex the bam file into multiple samples
Trimming: Sequencing adapters were removed and low-quality reads were filtered by fastp (0.20.1).
Alignment: Bowtie2 (version 2.4.1) with the ‘very-sensitive-local’ parameter, later duplicate reads were removed using samblaster (version 0.1.24).
Peak calling: Peaks were called using MACS2 (2.2.7.1) on each individual sample using the function callpeak with narrow peak setting.
Assembly: mm10
Supplementary files format and content: The format is bed.

source_name: spleen

growth_protocol: Primary CD8+ T cells were isolated from the spleens of wild-type mice. The isolated CD8+ T cells were stimulated with CD3/CD28 beads for 72 hours, after which the beads were removed and the cells were rested for an additional 72 hours. The T cells were cultured and maintained in RPMI-1640 medium supplemented with 10% FBS, 1% sodium pyruvate, 1% NEAA, 1% glutamine, 1% penicillin–streptomycin, and 50 μM β-mercaptoethanol.

extract_protocol:
DNA were collected by Qiagen MinElute kit
50,000 cells were harvested and further processed with Illumina tagment DNA kit. Samples were purify with Qiagen MinElute kit with EB buffer.

treatment_protocol: At day 6, collect the cell and restimulated with 5ng/ml anti-CD3 coated 48-well plat for 48h with or without 25uM Hemin.

value: CD8+ T

value: wild-type

value: Hemin


title: NC3

description:
Library name: NC3
WT3


title: Primary CD8+ T, 25uM Hemin treatment 3

description: Library name: Female_Hemin_3


title: DRG, round1, s5

source_name: dorsal root ganglion


title: DRG, round2, s8


title: Primary CD8+ T, 25uM Hemin treatment 2

description: Library name: Female_Hemin_2


title: DRG, round1, s4


title: DRG, round1, s2


title: Primary CD8+ T, treatment control 1

description: Library name: Female_Ctrl_1

value: control


title: DRG, round2, s5


title: DRG, round1, s1


title: Primary CD8+ T, treatment control 2

description: Library name: Female_Ctrl_2


title: OGT-KO, No Recovery

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

data_processing:
STAR Alignment using default arguments.
Reads were aligned to the mouse genome GRCm39
Counts were taken using the argument within the STAR software.
Read count extraction and normalization were performed using DESeq2 in Rstudio.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include DESeq2 normalzied values for each Sample

source_name: liver

extract_protocol:
Total RNA was isolated using the TRIzol method from ~ 60mg of liver tissue.
mRNA libraries were prepared for sequencing using Tecan universal plus mRNA-seq following manufacturer's protocols.

value: CDE

tag: type of mice

value: OGT-Floxed

tag: background

tag: virus

value: No Recovery

value: liver

value: OGT-KO


title: Control, 7 Day Recovery

value: 7 Day

value: Control


title: NP_RBF_1

description: Library name: Sample 10

value: WT


title: erf96_RBF_1

description: Library name: Sample 16


title: erf96_RBF_2

description: Library name: Sample 17


title: Model_3,INPUT

city: Harbin

first: Sun

middle: Hong

last: Hong

state: Heilongjiang

address: Network Information Center all rights reserved 157 Nangang District, Harbin health care road

department: Department of Pharmacology

institute: Harbin Medical University

description: Library name: Model_3,INPUT

data_processing:
Fastqc evaluation of the quality of the original data,Trim-galore was used to trim the sequences;
bowtie2 was used to map reads against the reference genome,Aligned SAM files were sorted and deduplicated using Samtools;
Signal distribution (peak calling) was identified by MACS2, using input as control if input exists;
BAM coverage computation, heatmap and profile of peak coverage were made using deeptools;
Peak and motif annotation results were generated by HOMER,Statistical analyses and function enrichment analyses were condcuted using respective R packages.
Assembly: rn6
Supplementary files format and content: bw,narrowPeak

organism: Rattus norvegicus

source_name: Myocardial

growth_protocol: The rats were placed in a colony room with controlled temperature and humidity, where food and water were freely available in a 12-h light/dark cycle.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Male Wistar rats were exposed to abdominal aorta constriction (AAC). Briefly, the rats were anesthetized via isoflurane gas inhalation and positioned supine. Under aseptic conditions, a midline incision was made to access the abdomen. A 1 cm segment of the abdominal aorta, located above the bifurcation of the renal arteries, was isolated and positioned with a 0.7 mm thick wire on its exterior. The wire and aorta were then tightly ligated using surgical silk, constricting the abdominal aorta.

value: Myocardial

value: input


title: DRG, round1, s10

value: dorsal root ganglion


title: App NL-G-F/NL-G-F, high fat diet, #561

city: Nagoya

first: Noe

last: Kawade

address: Furo-cho, Chikusa-ku

institute: Nagoya university

description: Library name: Sample 16

data_processing:
Adapter sequences and low quality bases (quality score < 20) were trimmed from the 3’-ends of the sequencing reads using fastp v0.23.2. Reads were quality checked with fastpv0.23.2 before and after trimming. The trimmed reads were aligned to the mouse genome version mm10 assembly using HISAT2 v2.2.1, with strand specificity information employed for reads prepared using the standard kit. Alignments to rDNA regions were excluded using the standard kit. Alignments to rDNA regions were excluded using BEDTools v2.25.0. Expression levels of individual annotated genes were quantified from the mapping data using StringTie v2.2.1.
Assembly: mm10
Supplementary files format and content: csv file include count data for each sample

source_name: oligodendrocyte isolated from brain

growth_protocol: Heterozygous App+/NL-G-F mice (C57BL/6-App <tm3 (NL-G-F) Tcs>), carrying the App gene with humanized Aβ sequence (G676R, F681Y, R684H), Swedish (KM670/671NL), Beyreuther/Iberian (I716F), and Arctic (E693G) mutations, were previously established using a knock-in strategy. Homozygous AppNL-G-F/NL-G-F (App) mice were obtained by crossbreeding and were maintained as inbred lines. Mice were maintained in a temperature-, humidity-, and light-controlled room (12-hour light/dark cycle). They were given free access to water and a normal control diet (NCD) (CE-2; 345.0 kcal/100 g, 12.5% energy as fat; CLEA Japan Inc., Tokyo, Japan).

extract_protocol:
Total RNA was extracted from oligodendrocyte lineage cells isolated from brain using the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. 0.05~0.17 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Biolabs, MA, USA) for mRNA isolation and the MGI Easy RNA Directional Library Prep Set (MGI, Shenzhen, China).

treatment_protocol: Male App mice at 2 months of age were fed NCD (App-NCD group) or a high-fat diet (HFD) (D12492; 524 kcal per 100 g, 60.0% energy as fat; Research Diets, New Brunswick, NJ, USA) (App-HFD group) for 6 months. Male C57BL/6J Jcl (WT) mice, purchased from CLEA Japan Inc., at 2 months of age were also maintained on NCD (WT-NCD group) or HFD (WT-HFD group) for the same period as the control. At 8 months of age, mice were deeply anesthetized by an overdose of three types of mixed anesthesia (medetomidine, midazolam, and butorphanol) and transcardially perfused with phosphate-buffered saline (PBS) for 5 min, and the brain was dissected. Isolation of oligodendrocytes from brain was conducted by magnetic activated cell sorting (MACS).

value: oligodendrocyte isolated from brain

value: App NL-G-F/NL-G-F

value: fed high fat diet


title: tc1_spleen_sot101_4

value: spleen


title: T cells, scRNA-seq

description: Library name: Pool1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V2.1.1
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz

molecule: polyA RNA

source_name: tumor

extract_protocol:
Tumors were digested, cell mixtures were washed and stained with flow cytometry antibodies. Live transferred cells were then sorted by FACS based on their CD8, CD44 and CD45 markers
Library was performed according to the manufacturer's instructions (single cell 3' V2 protocol, 10x Genomics)

treatment_protocol: P14 cells were transfected with Bach2WT or Bach2MUT.

value: tumor

value: T cell

value: overexpressed with Bach2WT or Bach2MUT


title: LLC cells transfected with mimics control_2

city: Xining City

first: Guowei

last: Liu

state: Qinghai Province

address: No. 2, Gonghe Road, Chengdong District

department: Department of Thoracic Surgery

institute: Qinghai Provincial People's Hospital

description: Library name: Sample5

data_processing:
Raw reads with more than 2-N bases were discarded, and adaptors and low-quality bases were trimmed using FASTX-Toolkit (Version 0.0.13). Additionally, reads shorter than 16nt were removed.
Clean reads were then aligned to the GRCm39 genome using HISAT2, allowing for 4 mismatches. Uniquely mapped reads were utilized for gene read number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped).
The R Bioconductor package DESeq2 was employed to identify differentially expressed genes (DEGs), with a significance threshold set at a FDR < 0.05 and a fold change > 2 or < 0.5.
Alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between samples were defined and quantified using the ABLas pipeline as described previously[18]. Ten types of ASEs, including exon skipping (ES), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), mutually exclusive 5'UTRs (5pMXE), mutually exclusive 3'UTRs (3pMXE), cassette exon, A3SS&ES, and A5SS&ES, were detected based on splice junction reads. To assess lncRNA-regulated ASEs, Student’s t-test was applied, and events significant at a p-value cutoff corresponding to a false discovery rate cutoff of 5% were considered lncRNA-regulated ASEs.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes FPKM value for each Sample.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

source_name: LLC cells

extract_protocol:
Total RNA was extracted using TRIzol Reagent and then treated with RQ1 DNase to remove DNA, followed by assessing its quality and quantity using a smartspec plus spectrophotometer (BioRad) and confirming integrity through 1.5% agarose gel electrophoresis. Each sample underwent mRNA capture using VAHTS mRNA capture Beads (Vazyme, N401), with an additional round of RQ1 DNase treatment.
Directional library preparation with the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (NR605) involved purifying, fragmenting, and converting polyadenylated mRNAs into double-stranded cDNA. This was followed by end repair, A tailing, and adaptor ligation (N323), with subsequent purification and size fractionation (300 - 500bps). Ligated products were then amplified, purified, quantified, and stored at -80℃ prior to sequencing, with strand-specific sequencing achieved by excluding amplification of the dUTP-marked strand. High-throughput sequencing was performed on an Illumina NovaSeq X Plus  system using 150nt paired-end sequencing, as per the manufacturer's instructions.

value: LLC cells

value: Lewis lung cancer cell


title: erf65_RBF_3

description: Library name: Sample 15

value: plant leave

value: OsERF65 knockout

value: Magnaporthe oryzae


title: DRG, round1, s6


title: erf65_RBF_1

description: Library name: Sample 13


title: Primary CD8+ T, treatment control 4

description: Library name: Female_Ctrl_4

value: CD8+ T

value: wild-type

value: control


title: erf96_mock_1

description: Library name: Sample 7

value: OsERF96.2 knockout

value: mock


title: T cells, CMO

description: Library name: Pool1 CMO


title: Primary CD8+ T, 25uM Hemin treatment 1

description: Library name: Female_Hemin_1

value: Hemin


title: NP_RBF_3

description: Library name: Sample 12

value: WT


title: LLC cells transfected with miR-291-3 mimics_2

description: Library name: Sample2


title: erf65_RBF_2

description: Library name: Sample 14


title: LLC cells transfected with miR-291-3 mimics_1

description: Library name: Sample1


title: App NL-G-F/NL-G-F, high fat diet, #559

description: Library name: Sample 14

value: oligodendrocyte isolated from brain

value: App NL-G-F/NL-G-F

value: fed high fat diet


title: NP_RBF_2

description: Library name: Sample 11


title: mouse TILs, treated with mono-IL10, Hashtag Oligo Library

city: Boston

first: Jiao

last: Shen

state: MA

address: 450 Brookline Ave, SM-552A

department: Cancer Immunology and Virology

institute: Dana-Farber Cancer Institute (DFCI)

description: Library name: PDAC-monoIL10-HTO

data_processing:
For the PDAC tumor model, the filtered barcode matrix was processed and analyzed using Seurat (v5.1.0). For quality control, we excluded cells with fewer than 1,000 detected genes and those with >10% mitochondrial reads. Counts from each sample were log-normalized, scaled, and subjected to dimensionality reduction by Principal Component Analysis (PCA). To minimize batch effects across mice, we used Harmony (v1.2.1) for integration, and generated Uniform Manifold Approximation and Projection (UMAP) embeddings from the top 50 Harmony dimensions. For T cell sub-clustering, variable features were re-identified for each sample, excluding TCR and Ig variable region genes, and clusters were manually annotated. Core STAT5 targets list (Gzmb, Prf1, Nkg7, Gzma, Klrd1, Klrb1c, Klra7, Ccr5, Ly6a, Thy1) was found from the literatures (PMID: 24006458; 16585578; 28916644; 33326784). Differential expression (DE) analysis between clusters and between treatment groups was performed by summing gene counts across all cells and using the DESeq2 (v1.46.0) package. Gene set enrichment analysis (GSEA) was conducted using log₂ fold-change–ranked DE genes between treatment groups (all clusters combined) with the fgsea (1.32.4) package. Mouse Hallmark gene sets were obtained from MSigDB.
Assembly: GRCm39
Supplementary files format and content: Processed data for each sample includes a filtered barcode matrix (matrix.mtx) with features.tsv and barcodes.tsv annotation files. A separate CSV matadata file contains cell-level metadata including sample identity, cell type annotation, and clustering results.

source_name: tumor-infiltrating lymphocytes

extract_protocol:
10x Genomics Chromium GEM-X Single Cell 5’ Reagent Kits
10x Genomics Chromium GEM-X Single Cell 5’ Reagent Kits

value: tumor-infiltrating lymphocytes

value: primary cells

value: CD45+ TILs


title: Control, No Recovery

value: CDE

value: OGT-Floxed

value: No Recovery

value: liver

value: Control


title: mouse TILs, treated with PBS, Hashtag Oligo Library

description: Library name: PDAC-PBS-HTO

value: PBS


title: App NL-G-F/NL-G-F, normal control diet, #553

description: Library name: Sample 12

value: fed normal control diet


title: Primary CD8+ T, treatment control 5

description: Library name: Female_Ctrl_5

value: spleen

value: CD8+ T

value: wild-type

value: control


title: erf65_mock_3

description: Library name: Sample 6

value: plant leave

value: OsERF65 knockout

value: mock


title: OGT-KO, 7 Day Recovery

value: 7 Day

value: OGT-KO


title: erf96_mock_3

description: Library name: Sample 9

value: OsERF96.2 knockout


title: erf96_mock_2

description: Library name: Sample 8


title: App NL-G-F/NL-G-F, high fat diet, #547

description: Library name: Sample 13

value: oligodendrocyte isolated from brain

value: App NL-G-F/NL-G-F

value: fed high fat diet


title: LLC cells transfected with mimics control_3

description: Library name: Sample6

value: LLC cells

value: Lewis lung cancer cell


title: mouse TILs, treated with IL10/2-Trikine, Hashtag Oligo Library

description: Library name: PDAC-IL10/2-Trikine-HTO

value: tumor-infiltrating lymphocytes

value: primary cells

value: CD45+ TILs


title: App NL-G-F/NL-G-F, normal control diet, #545

description: Library name: Sample 11

value: fed normal control diet


title: erf65_mock_1

description: Library name: Sample 4


title: LLC cells transfected with mimics control_1

description: Library name: Sample4


title: Model_3,ChIP

description: Library name: Model_3,ChIP

value: Myocardial

value: ChIP (PTM BIO, Cat. PTM-1427RM)


title: WT RPE1 TP53 null ERCC6L2 KO, 12 h gMulti, anti-MRE11 ChIP

city: Zurich

first: Eric

middle: J

last: Aird

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

description: Library name: KO_gMulti

data_processing:
Reads were demultiplexed, aligned with Bowtie2, and MRE11 peak pile up / gMulti target sites called with Blender2.
Assembly: hg38
Supplementary files format and content: Bigwig file of aligned reads from Bowtie2

growth_protocol: 10 million RPE1 cells were grown in DMEM supplemented with 10 % FBS and 100 µg / mL penicillin / streptomycin. Cells were incubated at 37 °C and 5 % CO2.

extract_protocol:
Cells were detached, washed, fixed in 1 % PFA for 15 min at RT, and quenched with 50 mM glycine. Cell pellets were washed, and flash frozen in liquid nitrogen. Pellets were lysed in 3 sequential lysis buffers to remove cytoplasm and obtain isolated nuclei according to a previously published protocol71. Nuclei were sonicated with a Covaris S220 to obtain a desired fragment length of 300 bp. Lysates were then incubated overnight at 4 °C with 10 µg of prebound anti-MRE11 or rabbit IgG isotype control protein A dynabeads (Thermo Fisher). The next morning, beads were washed in 6x RIPA buffer followed by 1x TBS and eluted in 50 mM Tris-HCl, pH 8, 1 mM EDTA, 1 % SDS by incubating at 65 °C overnight to reserve crosslinks. The following day, the dynabeads were collected on a magnetic stand and the supernatant was collected. The supernatant was then incubated with RNase A and proteinase K (Qiagen). DNA was purified (MinElute kit, Qiagen) and analyzed on a TapeStation (Agilent).
The NEBNextII kit (New England Biolabs) was used to prepare the sequencing library, and the indexed library was sequenced on a NovaSeq 6000 (Illumina) with 150 bp paired end reads

treatment_protocol: Cells were edited with Cas12a RNP + gMulti and incubated for 12 h.

value: ERCC6L2 KO

tag: grna

value: gMulti


title: WT RPE1 TP53 null, 12 h gNT, anti-MRE11 ChIP

description: Library name: WT_ctrl

value: WT

value: gNT


title: NP_mock_3

description: Library name: Sample 3

value: plant leave

value: mock


title: erf65_mock_2

description: Library name: Sample 5

value: OsERF65 knockout


title: mouse TILs, treated with IL10/2-Trikine, Gene Expression Library

description: Library name: PDAC-IL10/2-Trikine-GEX


title: App NL-G-F/NL-G-F, normal control diet, #537

description: Library name: Sample 9

value: oligodendrocyte isolated from brain

value: App NL-G-F/NL-G-F


title: WT RPE1 TP53 null, 12 h gMulti, anti-MRE11 ChIP

description: Library name: WT_gMulti


title: NP_mock_1

description: Library name: Sample 1


title: App NL-G-F/NL-G-F, high fat diet, #560

description: Library name: Sample 15

value: fed high fat diet


title: LLC cells transfected with miR-291-3 mimics_3

description: Library name: Sample3

value: LLC cells

value: Lewis lung cancer cell


title: NP_mock_2

description: Library name: Sample 2


title: DRG, round1, s3

value: dorsal root ganglion


title: Primary CD8+ T, 25uM Hemin treatment 4

description:
Library name: FH4
Column name in YX_RNAseq_normalized_count_FemaleSample.txt: FH4

data_processing:
Raw reads were trimmed using TrimGalore (v.0.6.6) according to quality from FastQC and adaptor.
The trimmed reads were mapped to the mm10 using STAR (v.2.7.9a).
The summarizeOverlaps function from the GenomicAlignments package (v.1.30.0) in R/Bioconductor (v.3.13) was used to define gene expression level by counting the alignments to exons
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: normalized counts from DEseq2

extract_protocol:
RNA were collected by Qiagen RNeasy Kits
The sequencing library was prepared by illumine Truseq Stranded RNA kit

value: spleen

value: CD8+ T

value: wild-type

value: Hemin


title: mouse TILs, treated with mono-IL10, Gene Expression Library

description: Library name: PDAC-monoIL10-GEX

value: tumor-infiltrating lymphocytes

value: primary cells

value: CD45+ TILs


title: App NL-G-F/NL-G-F, normal control diet, #538

description: Library name: Sample 10

value: fed normal control diet


title: C57BL/6J Jcl, high fat diet, #16

description: Library name: Sample 8

value: wild tiype


title: Primary CD8+ T, 25uM Hemin treatment 5

description:
Library name: FH5
Column name in YX_RNAseq_normalized_count_FemaleSample.txt: FH5


title: mouse TILs, treated with PBS, Gene Expression Library

description: Library name: PDAC-PBS-GEX

value: PBS


title: C57BL/6J Jcl, high fat diet, #15

description: Library name: Sample 7


title: PPA_6h_2

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
sequences (fastq files) were aligned to mm10 using Hisat2 (v2.1.0) with parameters --dta-cufflinks
SAM files were converted to BAM files using Samtools (v0.1.18-r580)
BAM files were further processed for sorting and duplicate removal using Samtools (v0.1.18-r580)
FPKM were calculated using cuffdiff v2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: an excel file (RPKM.xlsx) contains RPKM values for each gene.

source_name: Liver

extract_protocol:
Total RNA was extracted from mouse liver tissues using Trizol reagent (Thermo, 15596018). Afterwards, mRNA was extracted from total RNA using  NEBNext® Poly(A) mRNA Magnetic Isolation Module, 24 rxns (NEB, E7490S)
RNA libraries were prepared for sequencing using ThruPLEX-FD-12 kit (Rubicon Genomics)

treatment_protocol: C57BL/6 mice were treated with PPA in drinking water (or normal water as a control). After 4 weeks of PPA treatment, mice were overnight fasted (16 h), injected with APAP (i.p, 300 mg/kg). Mice were sacrificed and liver tissues were collected at 0 or 6 h after APAP administration.

value: C57BL/6 (from Taconic Bioscience)

value: Liver


title: Primary CD8+ T, 25uM Hemin treatment 2

description:
Library name: FH2
Column name in YX_RNAseq_normalized_count_FemaleSample.txt: FH2


title: SP110 KO RPE1, 6h IFNB, anti-IgG ChIP

description: Library name: ChIPseq_SP110KO_antiIgG

data_processing:
Reads were demultiplexed, aligned with Bowtie2, and peaks called with MACS3. Graphics were generated using deepTools and ChIPseeker (v1.32.1).
Assembly: hg38
Supplementary files format and content: Bigwig file of aligned reads from Bowtie2
Supplementary files format and content: Bed files of called peaks comparing anti-SP100 to anti-IgG control using MACS3 filtered against a blacklist.

growth_protocol: 10 million RPE1 WT or SP110 KO cells were grown in DMEM supplemented with 10 % FBS and 100 µg / mL penicillin / streptomycin. Cells were incubated at 37 °C and 5 % CO2.

extract_protocol:
Cells were detached, washed, fixed in 1 % PFA for 15 min at RT, and quenched with 50 mM glycine. Cell pellets were washed, and flash frozen in liquid nitrogen. Pellets were lysed in 3 sequential lysis buffers to remove cytoplasm and obtain isolated nuclei according to a previously published protocol71. Nuclei were sonicated with a Covaris S220 to obtain a desired fragment length of 300 bp. Lysates were then incubated overnight at 4 °C with 5 µg of prebound anti-SP100 or rabbit IgG isotype control protein A dynabeads (Thermo Fisher). The next morning, beads were washed in 6x RIPA buffer followed by 1x TBS and eluted in 50 mM Tris-HCl, pH 8, 1 mM EDTA, 1 % SDS by incubating at 65 °C overnight to reserve crosslinks. The following day, the dynabeads were collected on a magnetic stand and the supernatant was collected. The supernatant was then incubated with RNase A and proteinase K (Qiagen). DNA was purified (MinElute kit, Qiagen) and analyzed on a TapeStation (Agilent).
The NEBNextII kit (New England Biolabs) was used to prepare the sequencing library, and the indexed library was sequenced on a NovaSeq 6000 (Illumina) with 150 bp paired end reads

treatment_protocol: Cells incubated with 10 ng / mL interferon beta for 6 h.

value: SP110 KO

tag: chip antibody

value: IgG control


title: SP110 KO RPE1, 6h IFNB, anti-SP100 ChIP

description: Library name: ChIPseq_SP110KO_antiSP100


title: Primary CD8+ T, 25uM Hemin treatment 3

description:
Library name: FH3
Column name in YX_RNAseq_normalized_count_FemaleSample.txt: FH3


title: PPA_6h_5


title: PPA_6h_1


title: C57BL/6J Jcl, high fat diet, #3

description: Library name: Sample 6

value: oligodendrocyte isolated from brain

value: fed high fat diet


title: CTL_6h_4


title: Primary CD8+ T, treatment control 4

description:
Library name: FC4
Column name in YX_RNAseq_normalized_count_FemaleSample.txt: FC4

value: control


title: WT RPE1, 6h IFNB, anti-SP100 ChIP

description: Library name: ChIPseq_WT_antiSP100

value: WT


title: CTL_6h_3


title: WT RPE1, 6h IFNB, anti-IgG ChIP

description: Library name: ChIPseq_WT_antiIgG


title: C57BL/6J Jcl, normal control diet, #11

description: Library name: Sample 3


title: Cell-free DNA from stage IV mPDAC patient 5

city: Cordoba

first: María Victoria

last: García-Ortiz

state: Cordoba

address: Av. Menéndez Pidal

country: Spain

institute: Maimonides Institute for Biomedical Research in Cordoba

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system and standard recommended Illumina scanner setting

data_processing: ChAMP Bioconductor package in R environment (v4.3.3)

source_name: plasma cell-free DNA

label_protocol: Standard Illumina Protocol

extract_protocol: cell-free DNA was extracted from plasma samples using QIAamp Circulating Nucleic Acid Kit (Qiagen) according to standard instructions

tag: Sex

value: Male

tag: disease state

value: Stage IV mPDAC

value: plasma cell-free DNA


title: C57BL/6J Jcl, high fat diet, #2

description: Library name: Sample 5

tag: tissue

tag: genotype


title: C57BL/6J Jcl, normal control diet, #12

description: Library name: Sample 4

tag: treatment


title: Primary CD8+ T, treatment control 3

description:
Library name: FC3
Column name in YX_RNAseq_normalized_count_FemaleSample.txt: FC3

value: spleen

tag: cell type

value: CD8+ T

value: wild-type


title: Cell-free DNA from stage IV mPDAC patient 6


title: Primary CD8+ T, treatment control 5

description:
Library name: FC5
Column name in YX_RNAseq_normalized_count_FemaleSample.txt: FC5


title: Primary CD8+ T, 25uM Hemin treatment 1

description:
Library name: FH1
Column name in YX_RNAseq_normalized_count_FemaleSample.txt: FH1

value: Hemin


title: Cell-free DNA from stage IV mPDAC patient 4


title: C57BL/6J Jcl, normal control diet, #5

description: Library name: Sample 2

value: wild tiype

value: fed normal control diet


title: Pig 5, snRNAseq

data_processing:
Sequencer output files were converted into fastq-files using Cellranger 6.0.1 mkfastq. Using Cellranger 6.0.1 reads were then mapped to the pig genome (Sscrofa11.1 with Ensembl 105 annotation) on the bwForcluster Helix high-performance computing system. Reads uniquely mapping in sense to the transcriptome (exon and intron) were then used to quantify transcript abundances using unique molecular identifiers (UMI).
Assembly: Sus scrofa 11.1 (Ensembl release 105)
Supplementary files format and content: csv file of counts per sample
Supplementary files format and content: RDS Seurat object with metadata

molecule: nuclear RNA

extract_protocol:
Nuclei were isolated from 80 mg thoracic and lumbar DRG tissue per sample employing previously published protocols (Ernst et al., 2020; Nguyen et al., 2021; Yang et al., 2021) that differ with respect to tissue lysis conditions (Triton X-100 or IGEPAL CA-630) and strategies employed for separation of debris and nuclei (40 µm filtration plus iodixanol density gradient centrifugation or 40 µm filtration plus magnetic-assisted enrichment of neurons using rabbit polyclonal anti-NeuN antibody (Millipore, cat# ABN78, dilution 1:5,000) and anti-rabbit IgG microbeads (Miltenyi Biotech, cat# 130-048-602, dilution 1:5)). The protocol by Ernst et al. that only relies on 40 µm filtration was modified to include an additional step of fluorescence-assisted enrichment of neuronal nuclei after the final two nuclei washing steps of the protocol. For this purpose, the nuclei were stained with Anti-NeuN-Alexa Fluor 555 (Millipore, cat# MAB377A5, dilution 1:100) for 30 minutes at 4°C on a rotator and subsequently with DAPI for 5 minutes on ice. At the FlowCore Mannheim, double-positive singlets were sorted into PBS/1% BSA using a BD FACSAria IIu equipped with a 100 µm nozzle.
Single-nucleus solutions were subjected to barcoding, reverse transcription and gene expression library construction using the 10XGenomics microfluidics platform (Chromium controller and Next GEM Single Cell 3' Kit v3.1) according to the manufacturer’s instructions.

value: dorsal root ganglion

value: neuron


title: Primary CD8+ T, treatment control 2

description:
Library name: FC2
Column name in YX_RNAseq_normalized_count_FemaleSample.txt: FC2


title: CTL_6h_2

value: C57BL/6 (from Taconic Bioscience)

value: Liver


title: Cell-free DNA from stage IV mPDAC patient 3


title: C57BL/6J Jcl, normal control diet, #4

description: Library name: Sample 1

value: oligodendrocyte isolated from brain


title: PPA_0h_4


title: PPA_0h_2


title: Pig 3, snRNAseq


title: PPA_0h_5


title: Cell-free DNA from stage IV mPDAC patient 1


title: deletion hutC gene

city: Auckland

first: Xue-Xian

last: Zhang

address: 3a Symonds Street

country: New Zealand

institute: University of Auckland

description:
Library name: PAO1_hutC
del-hutC

data_processing:
After removing adaptor sequences, rRNA reads and low-quality reads, the clean reads were mapped to the reference genome (NC_002516.2) using Bowtie2
Assembly: Assembly was performed using the Rockhopper software. DEGs identified using edgeR with FDR < 0.05, log2(FC) > 1. DEGs identified using edgeR with FDR < 0.05, log2(FC) > 1. KEGG enrichments were evaluated with padj < 0.05 as the significance cutoff.
Supplementary files format and content: An excel file showing results of DEGs with the calculated log2foldchange, pvalue, padj, FPKM etc, for each of the three hutC mutants relative to the wild-type strain PAO1

organism: Pseudomonas aeruginosa

source_name: bacterial cell

growth_protocol: Bacteria were exponentially grown in triplicate in the M9 mininmal salt medium summplemented with histidine (10 mM)

extract_protocol:
Total RNA samples preparated using standard method were subjected quantity control using the Agilent 2100 bioanalyzer.
RNA libraries were prepared for sequencing by Novogene Technology Co. Ltd, using the standard Illumina protocols

value: bacterial cell

value: PAO1 devoid of hutC


title: Cell-free DNA from stage IV mPDAC patient 2

value: Female


title: pME6010-hutC with hutC being overexpressed under a strong constitutive promoter (hutC overexpression mutant)

description:
Library name: PAO1_hutC_OE
PAO1 carrying pME6010-hutC with hutC being overexpressed under a strong constitutive promoter

value: PAO1 derived mutant with hutC overexpression


title: Pig 4, snRNAseq


title: Cell-free DNA Healthy control 1

description: Cell-free DNA Healthy control

value: Male

value: Healthy


title: MDA_MB_231 cells , No Gluc,-+ Gln_C

status: Public on Jan 24 2026

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: College of Pharmacy and Pharmaceutical Sciences, 241 Fred Humphries Science Research Facility, 1515 MLK Blvd, Tallahassee , Florida 32307

institute: FAMU College of Pharmacy

description: Library name: Sample_17

data_processing:
Instrument Platform was Singular G4
Demux fastq files to trimmed cut adapt 0 fastq , QC verification fastqc
MutliQC tx to jason Alighned with Hisat2 to reference genome
SAM to BAM / SAM Tools /feature counts Subread
DESeq2
Assembly: GRCh38.p14
Supplementary files format and content: Normalized_Counts_9-20.txt

source_name: Breast, Mammary Gland

growth_protocol: Human breast adenocarcinoma MDA-MB-231 cells (ATCC HTB-26) were cultured at 37 °C in high-glucose Hanks’ balanced salt solution (HBSS) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin under humidified conditions with 5% CO₂.

extract_protocol:
RNA was isolated using Direct-Zol MiniPrep Plus (Zymo) with DNASE1
RNA-seq libraries were prepared from using the SEQuoia Complete Stranded RNA Library Prep Kit (Bio-Rad)/SEQuoia RiboDepletion Kit (Bio-Rad)

treatment_protocol: Cells were then incubated in one of four defined glucose-deficient media conditions, each containing 3% FBS : (1) full medium (25 mM glucose, 4 mM glutamine), (2) nutrient-deficient medium lacking both glucose and glutamine, (3) glucose-only medium (25 mM glucose, no glutamine), or (4) glutamine-only medium (4 mM glutamine, no glucose). Cultures were maintained under standard conditions for 36 h and monitored microscopically to confirm cellular integrity and the absence of overt cell death

value: Breast, Mammary Gland

value: MDA-MB_231 HTB-26

value: Epithelial

value: No Gluc,-+ Gln_C


title: CTL_0h_1


title: CTL_0h_3


title: Cell-free DNA Healthy control 2

description: Cell-free DNA Healthy control

value: plasma cell-free DNA


title: Primary CD8+ T, treatment control 1

description:
Library name: FC1
Column name in YX_RNAseq_normalized_count_FemaleSample.txt: FC1

value: spleen

value: CD8+ T

value: wild-type

value: control


title: WT_RNAseq

description:
Library name: PAO1_WT
WT_RNAseq

value: wild type


title: MDA_MB_231 cells , No Gluc,-+ Gln_A

description: Library name: Sample_15

value: No Gluc,-+ Gln_A


title: MDA_MB_231 cells , Full_+ Gluc,-+ Gln_A

description: Library name: Sample_18

value: Full_+ Gluc,-+ Gln_A


title: MDA_MB_231 cells , Full_+ Gluc,-+ Gln_B

description: Library name: Sample_19

value: Full_+ Gluc,-+ Gln_B


title: Pig 2, snRNAseq

value: dorsal root ganglion

value: neuron


title: MDA_MB_231 cells , +Gluc,-No Gln_B

description: Library name: Sample_13

value: +Gluc,-No Gln_B


title: MDA_MB_231 cells , Full + Gluc,-+ Gln_C

description: Library name: Sample_20

value: Full + Gluc,-+ Gln_C


title: MDA_MB_231 cells , Deficient _No Glu, No Gln_C

description: Library name: Sample_11

value: Breast, Mammary Gland

value: Deficient _No Glu, No Gln_C


title: Pig 1, snRNAseq


title: MDA_MB_231 cells , +Gluc,-No Gln_A

description: Library name: Sample_12

value: MDA-MB_231 HTB-26

value: Epithelial

value: +Gluc,-No Gln_A


title: CTL_0h_4

value: C57BL/6 (from Taconic Bioscience)

value: Liver


title: MDA_MB_231 cells , +Gluc,-No Gln_C

description: Library name: Sample_14

value: +Gluc,-No Gln_C


title: MDA_MB_231 cells , Deficient _No Glu, No Gln_B

description: Library name: Sample_10

value: Deficient _No Glu, No Gln_B


title: ScRNA-seq data of NTM_MAB-PD_03

city: Shanghai

first: Guoling

address: No. 507 Zhengmin Road

department: Department of Tuberculosis

institute: Shanghai Pulmonary Hospital

description:
Library name: TS008
10x genomics

data_processing:
Seurat [43] v3.1.2 was used for quality control, dimensionality reduction and clustering. For each sample dataset, we filtered expression matrix by the following criteria: 1) cells with gene count less than 200; 2) cells with top 2 % UMI count were excluded; 3) cells with mitochondrial content >10 % were excluded; 4) genes expressed in less than 5 cells were excluded.
Assembly: human GRCh38
Supplementary files format and content: Gzip-compressed 10X Genomics MTX files: barcodes (cells), features (genes), and sparse raw UMI count matrix.

source_name: Peripheral blood

extract_protocol:
Cells were isolated from whole-blood samples, and BD Pharm Lyse™ (BD, USA) lysing solution was used in this study. Blood cells were isolated within 2 h after blood collection. The steps of adding red cell lysate were as follows: (1)Peripheral blood collection: For both NTM-PD patients and healthy controls, 5 ml of fresh peripheral blood from each participant were collected and stored in EDTA anticoagulated blood collection tubes. (2)Preparation of 1× lysing solution: BD Pharm Lyse™ (BD, USA) lysing solution is concentrated (10×) reagent. Dilute the 10× concentrate 1:10 with distilled water. The pH of the 1× solution should fall within the range of pH 7.1–7.4. (3)Plasma removal: The blood was centrifuged at 500g for 5 min to remove the plasma; Then 15 ml BD Pharm Lyse™ red blood cell lysate was added into the blood cells and inverted gently several times for adequate mixing. 15 ml BD Pharm Lyse™ red blood cell lysate for each sample. The mixed blood was kept at room temperature for 10 min. Next, 5 ml Dulbecco's Phosphate-Buffered Saline and 0.2 % Bovine Serum Albumin (BSA) were added. The mixed blood was centrifuged at 500g for 5 min to remove the supernatant. Cells were washed twice and lysed with BD Pharm Lyse™ to completely remove red blood cells. (4)Cell quality inspection: Cell viability and counting were evaluated with Trypan Blue by microscopy. 10ul 0.4 % Trypan Blue was mixed 1:1 with 10ul cell suspension, 10ul of the mixed liquid was added to the blood cell counting plate, and the counting was observed under the microscope. The samples with viabilities > 80 % were used for sequencing.
The prepared cell suspensions were subjected to 10× Chromium Single Cell 3′ library with Chromium Single Cell 30 v3 reagent (10× Genomics) according to the manufacturer’s instructions.

value: Peripheral blood


title: ScRNA-seq data of NTM_MAB-PD_02

description:
Library name: TS005
10x genomics


title: ScRNA-seq data of NTM_MAC-PD_03

description:
Library name: TS004
10x genomics


title: ScRNA-seq data of Healthy control_02

description:
Library name: TS007
10x genomics


title: ScRNA-seq data of NTM_MAB-PD_01

description:
Library name: TS003
10x genomics


title: MDA_MB_231 cells , Deficient _No Glu, No Gln_A

description: Library name: Sample_9

value: Deficient _No Glu, No Gln_A


title: ScRNA-seq data of NTM_MAC-PD_02

description:
Library name: TS002
10x genomics


title: 101-002 (Follow-up)

city: Houston

first: Sanjay

last: Singh

state: TX

address: 6767 Bertner St

department: Neurosurgery

institute: MD Anderson Cancer Center

description:
Library name: SC260_6
10X Genomics

data_processing:
Pipeline version: cellranger-6.1.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab separated values files and matrix files

source_name: PBMC

growth_protocol: Cryopreserved peripheral blood mononuclear cells obtained from patients enrolled in the study were thawed overnight in interleukin-2 containing culture media.

extract_protocol:
After overnight stimulation cells were resuspended in PBS with 0.04% BSA and viability of the samples was determined by Trypan Blue Stain (0.4%) for use with the Countess™ II FL.
Cells were diluted or concentrated to the recommended range 500-1000 cells/μl) for loaded at a volume to recover 7000 to 10000 cells for single cell RNA-sequencing (scRNA-seq). Single cell capture, barcoding and library preparation were performed by following the 10X Genomics Single Cell Chromium 3’ protocols (CG000315 Rev E). Ten libraries were pooled to give a final concentration of 10 nM, Pooled samples were further qPCR for final concentration before submission for sequencing with the NovaSeq6000 sequencer using the S2 100 cycles flowcell and sequence with 28 cycles for read1, 8 cycles for i7 index, and 91 cycles for read 2 through the ATGC core at MD Anderson.

treatment_protocol: Viable CD3+ T-cells within peripheral blood mononuclear cells were sorted using magnetic assorted cell sorting. CD3+ T-cells were then stimulated overnight using anti-CD3/anti-CD28 co-stimulation.

value: PBMC

value: anti-CD3/anti-CD28 co-stimulation


title: ScRNA-seq data of NTM_MAC-PD_01

description:
Library name: TS001
10x genomics


title: MDA_MB_231 cells , No Gluc,-+ Gln_B

description: Library name: Sample_16

value: No Gluc,-+ Gln_B


title: 101-004 (Follow-up)

description:
Library name: SC260_8
10X Genomics


title: 101-004 (Baseline)

description:
Library name: SC260_7
10X Genomics


title: ScRNA-seq data of Healthy control_01

description:
Library name: TS006
10x genomics


title: 104-010 (Follow-up)

description:
Library name: SC299_4
10X Genomics


title: 101-002 (Baseline)

description:
Library name: SC260_5
10X Genomics


title: 104-010 (Baseline)

description:
Library name: SC299_3
10X Genomics


title: 104-004 (Follow-up)

description:
Library name: SC260_10
10X Genomics


title: 104-006 (Baseline)

description:
Library name: SC299_1
10X Genomics


title: 101-005 (Follow-up)

description:
Library name: SC260_4
10X Genomics


title: 104-006 (Follow-up)

description:
Library name: SC299_2
10X Genomics


title: 101-009 (Baseline)

description:
Library name: SC299_9
10X Genomics


title: hPSC-derived HIO, Day 35, biol rep 1, diff 3

first: Daniel

middle: O.

last: Kechele

state: OH

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

description:
Library name: Sample 6
10x Genomics

data_processing:
Standard 10x Genomics Cell Ranger hAGO, hAGO+SM, hAGO+SM+NCC (v3.0.2), HIO and hAGO+SM TXP (v6.1.2) pipeline to generate FASTQ and generate filtered matrices.
Assembly: hg38
Supplementary files format and content: tab seperated value files and matrix files

source_name: hPSC-derived intestinal organoids

extract_protocol:
For in vitro Day 37 HAGOs and Day 35 HIOs: Organoid were washed with cold Cell Recovery solution and minced in HBSS with Mg2+ and Ca2+ 1% BSA. Organoids were mechanically and enzymatically digested enzymes from Neural Tissue Dissociation Kit as recommended by Manufacturer's instructions for 45-60 minutes at 37C. Samples were shaken and fluxed through a P1000 then P200 tip every 10 mins. Dissociated cells were washed and filtered through a BSA coated 70um follow 40um cell strainer, centrifuged at 300 RPM for 5 minutes, and resuspended in HBSS with Y-27632 and 1% BSA.
For hAGO+SM TXP: Organoid was removed from mouse kidney capsule after 10 weeks in vivo growth. The organoid was separated from surrounding kidney and mechanically minced into small pieces using scapel in HBSS with Mg2+ and Ca2+. HAGO TXP were mechanically and enzymatically digested enzymes from Neural Tissue Dissociation Kit as recommended by Manufacturer's instructions for 45-60 minutes at 37C. Samples were shaken and fluxed through a P1000 then P200 tip every 10 mins. 400 ul of 10x TrypLE was added for the last 20 min of enzymatic digestion. Dissociated cells were washed and filtered through a BSA coated 70um follow 40um cell strainer, centrifuged at 300 RPM for 5 minutes, and resuspended in HBSS with Y-27632 and 1% BSA.
The scRNA-seq assay was performed according to the manufacter’s instructions (single cell Chromium 3’ v3.1 GEM protocol, single or dual indexed, 10x Genomics) loading 12,800 cell for approximately 8,000 captured cells on either a Chromium or Chromium X instrument. Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads and amplified using 14 cycles by PCR.  Full-length, barcoded cDNA was then enzymatically fragmented, sized-selected using SPRIselect reagent, adapter-ligated, and amplified for library construction. During the library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and sample indexes were added. Samples were pooled and run on the NovaSeq 6000 with S4 flow cells using the following sequencing parameters:  R1: 28 cycles, i7: 8 cycles, i5: 0 cycles, R2: 91 cycles (HAGO 1, HAGO+SM, HAGO+SM+NCC 1, HAGO+SM+NCC 2) or R1: 28 cycles, i7: 10 cycles, i5: 10 cycles, R2: 90 cycles (HAGO 2, HIO, HAGO+SM TXP).

value: hPSC-derived intestinal organoids

value: WA01 hESC

value: epithelial, mesenchymal, few endothelial & hematopoietic

tag: age

value: 35 days post-hPSC


title: hPSC-derived HAGO+SM+NCC, Day 37, biol rep 1, diff 1

description:
Library name: Sample 3
10x Genomics

source_name: hPSC-derived gastric organoids

value: hPSC-derived gastric organoids

value: epithelial, mesenchymal, few neural

value: 37 days post-hPSC


title: 101-005 (Baseline)

description:
Library name: SC260_3
10X Genomics


title: 101-009 (Follow-up)

description:
Library name: SC299_10
10X Genomics


title: 104-004 (Baseline)

description:
Library name: SC260_9
10X Genomics


title: SF9427

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: Library name: SF9427

data_processing:
trimmed reads to hg19 (patch 13) (genome.ucsc.edu/ENCODE/releaseLog.html) using RNA STAR v2.5 and counted using HTSeq.
Assembly: Hg19
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: fpkm normalized counts for each sample

source_name: Brain-derived

extract_protocol:
RNeasy Plus micro kit (QIAGEN)
NEBNext UltraTM RNA Library Prep Kit for Illumina (New
AMPure XP magnetic beads (Beckman Coulter)

value: Brain-derived

value: Patient-derived

value: Primary cell line


title: hPSC-derived HAGO, Day 37, biol rep 1, diff 1

description:
Library name: Sample 1
10x Genomics


title: SF8628

description: Library name: SF8628


title: hPSC-derived HAGO+SM+NCC, Day 37, biol rep 2, diff 1

description:
Library name: Sample 4
10x Genomics

value: epithelial, mesenchymal, neural


title: SF7761

description: Library name: SF7761


title: PED36

description: Library name: PED36


title: PED40

description: Library name: PED40


title: PED8

description: Library name: PED8


title: GBM36t

description: Library name: GBM36t


title: DIPGXIII

description: Library name: DIPGXIII


title: KNS42

description: Library name: KNS42


title: PCGBM2

description: Library name: PCGBM2


title: SF9402

description: Library name: SF9402


title: DIPGXIX

description: Library name: DIPGXIX


title: hutC gene deletion, complementation at attTn7 site

description:
Library name: PAO1_hutC_hutC
del-hutC-hutC

value: bacterial cell

value: PAO1 carrying hutC deletion, and hutC at the attTn7 site


title: PED17

description: Library name: PED17


title: DIPGXVII

description: Library name: DIPGXVII


title: hPSC-derived HAGO+SM, TXP 10 wks, biol rep 1, diff 2

description:
Library name: Sample 5
10x Genomics

value: epithelial, mesenchymal

value: 10 wk TXP 112 days post-hPSC


title: GBM36n5

description: Library name: GBM36n5


title: DJD14

description: Library name: DJD14


title: hPSC-derived HAGO+SM, Day 37, biol rep 1, diff 1

description:
Library name: Sample 2
10x Genomics