title: granulosa cells, Control, 12h, PGR_ChIP

description: Library name: Sample1_12h_C_PGR

value: Control


title: BEA24P061_GL_24_T2_5_FU_plus_MV_RNA

status: Public on Apr 17 2026

type: SRA

city: Stockholm

first: Gintare

last: Lasaviciute

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences

country: Sweden

institute: Stockholm University

description: Library name: P32606_1024

library_source: transcriptomic

data_processing:
Raw Counts (Aligner: STAR, Ref.genome: Ensembl Homo_sapiens.GRCh38.dna.primary_assembly.fa, Gene quantification method: featureCounts, Gene ref: Ensembl Homo_sapiens.GRCh38.112)
Data was normalized using DeSeq2
R version 4.3.3 was used to perform some data analysis. "dplyr", "biomaRt", "clusterProfiler", "org.Hs.eg.db" and "ggplot2" packages were used for the data analysis.
Assembly: Ensembl Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary files format and content: RNA-Seq raw count matrix as a txt file

molecule: total RNA

organism: Homo sapiens

source_name: Large intestine, colon

growth_protocol: A total of 0.12x106 Caco-2 cells were seeded into 24-well plates containing polyethylene membrane (Stem Cell Technologies). Cells were differentiated for 14 days, changing medium every 3-4 days. DMEM medium was supplemented with 1,15 mg/ml RA (Sigma Aldrich), 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 mg/ml streptomycin. Cells were incubated at 37°C with 5% CO2 throughout the experiments.

extract_protocol:
RNA was isolated using the mirVana miRNA Isolation kit (Ambion by Life Technologies), following the protocol for total RNA extraction.
Total RNA was subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions. To construct libraries suitable for Illumina sequencing, the Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration between 200 ng total RNA. The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries. The yield and quality of the amplified libraries was analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation. The indexed cDNA libraries were normalized and combined, and the pools were sequenced on the Illumina Novaseq Plus 10B flowcell 300 cycles kit sequencing run, generating 150 base paired end reads with dual index 10+10 base pairs. Basecalling and demultiplexing was performed using bcl2fastq (v2.20.0) software with default settings generating Fastq files for further downstream mapping and analysis.

treatment_protocol: Differentiated Caco-2 cells were exposed to 50 µg/ml of 5 FU on the apical and basolateral sides for 24 h or were left unexposed as a control. Following 24 h, cells were washed twice with PBS and then bacterial components were added for 72 h.

tag: tissue

value: Large intestine, colon

tag: cell line

tag: cell type

value: Enterocyte

tag: treatment

value: 24h chemo, then 72h with/without postbiotics


title: granulosa cells, hCG, 12h, PGR_ChIP, Rep2

city: Lexington

first: Hayce

last: Jeon

state: KENTUCKY

address: 800 Rose Street

department: Dept. of OB/GYN

country: USA

institute: University of Kentucky

description: Library name: Sample3_12h_H_PGR

library_source: genomic

data_processing:
FASTQ files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina). Adaptors have been trimmed from the 3' end of the reads, resulting in 760,113,797 filtered reads. Trimmed reads were aligned to the human genome version of GRCh38 from NCBI using BWA (0.7.17-r1188).
Peak calling was performed with MACS2 (2.2.7.1) using default settings and input DNA as a control to identify regions of enriched binding. For the hCG-treated group, peaks from three replicates were merged using MACS2 Consensus to obtain a consensus set of peaks.
Assembly: GRCh38
Supplementary files format and content: BigWig, NarrowPeak (except for Input)

molecule: genomic DNA

source_name: Ovary

growth_protocol: Cells were obatined from IVF patients at the time of oocyte retrieval and subjected to a Percoll gradient to isolate granulosa cells. Isolated granulosa cells were then cultured in Opti-MEM supplemented with 1x antibiotics/antimycotics and 10% fetal bovine serum for 6 days to regain the responsiveness to hCG.

extract_protocol:
Chromatin was extracted from cells fixed with 1.1% formaldehyde and fragmented using sonication.
Libraries from purified DNA from ChIP and input samples were prepared with the UltraLow System V2 DNA-Seq Library Preparation Kit (Tecan; Durham, NC, USA). The libraries were pooled and quantitated by qPCR and sequenced on one 10B lane for 101 cycles from one end of the fragments on a NovaSeq X Plus with V1.0 sequenced kits (Illumina).

treatment_protocol: After the acclimation period, the cells were undergone serum startvation for 1 h and then treated with or without hCG 12 h.

value: Ovary

value: primary human granulosa/lutein cells

value: hCG

tag: time

tag: antibody

value: PGR (Cell Signaling, #8757)


title: granulosa cells, hCG, 12h, Input, Rep3

description: Library name: Sample4_12h_H_Input


title: granulosa cells, Control, 12h, Input

description: Library name: Sample1_12h_C_Input


title: Pg_IFN_3

city: Columbus

first: Juhi

last: Bagaitkar

state: OH

address: 700 Children’s Drive

department: Department of Pediatrics

institute: The Ohio State University

data_processing:
Pair-end reads coming from bulk RNA-seq were aligned with STAR v2.7.0d. Gene counts were derived by featureCount v2.0.0.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file with raw counts

source_name: lung epithelium

extract_protocol:
RNA was collected from IFN primed or unprimed A549 cells infected with P. gingivalis, or left uninfected,  using RNeasy mini kit (Qiagen) according to kit instructions. Approx. 1 ug of RNA was used for construction of the sequencing library.
NEBNext Ultra II RNA Library Prep kit for Illumina

value: lung epithelium

value: IFN- λ primed + P. gingivalis infected


title: Pg_IFN_2


title: Pg_UT_3

value: P. gingivalis infected


title: BEA24P061_GL_30_T3_Chem_RNA

description: Library name: P32606_1030


title: Pg_IFN_4


title: Pg_UT_6


title: Pg_UT_4


title: Pg_IFN_6


title: Pg_UT_2


title: NI_IFN_6

value: IFN-λ primed


title: Pg_UT_1


title: Pg_IFN_1


title: granulosa cells, hCG, 12h, Input, Rep1

description: Library name: Sample2_12h_H_Input


title: NI_IFN_5


title: NI_IFN_3


title: NI_IFN_4


title: NI_UT_5

value: Untreated


title: NI_IFN_2


title: NI_UT_1


title: NI_UT_3


title: NI_UT_2


title: C666-1_Input_A_ChIP

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: C666-1_Input_A_ChIP

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome and human gammaherpesvirus 4 (HHV4) NC_007605.1 genome assembly using bowtie2.
MACS2 software package was used to call peaks in pull-down samples compared to input samples.
Assembly: hg19 and NC_007605.1 version of EBV
Supplementary files format and content: CPM-normalized bigWig files were generated using Deeptools (v3.5.1) for both hg19 and NC_007605.1 version of EBV genome. Score represents the normalized coverage of DNA fragment at a given coordinate.

growth_protocol: RPMI1640 media supplemented with 10% fetal bovine serum, 1X Glutamax, and 100 μg/ml streptomycin, and 100U/ml penicillin, cells were incubated at 37°C with 5% CO2

extract_protocol:
fixed with 1% formaldehyde for 15 min and fragmented using Covaris ME220
Libraries for sequencing were made using the NEBNext Ultra II DNA Library Prep Kit. Libraries were amplified using 10 cycles on the thermocycler. Post amplication libraries were size selected at 250-250bp in length using AMPure XP beads from Beckman Coulter.

value: EBV+ nasopharyngeal carcinoma


title: C666-1_EBNA1_A_ChIP

description: Library name: C666-1_EBNA1_A_ChIP


title: C666-1_Input_B_ChIP

description: Library name: C666-1_Input_B_ChIP


title: Panc-01 wildtype, biol rep 3

city: Uppsala

first: Débora

last: Parrine

state: Uppsala

address: Husargatan 3,

department: NBIS

institute: Scilifelab

description: Library name: Panc-01 wildtype, replicate 3

data_processing:
The sequencing results from the ATAC-seq analysis performed by the NGI platform were analysed by the Nextflow pipeline NF-core/atacseq version 2.1.2 (https://nf-co.re/atacseq) . Briefly, sequence adapters are trimmed by Trim Galore! and aligned by the BWA software. The Picard package marks duplicates and merges alignments from multiple libraries into a single sample. It then filters mitochondrial DNA, duplicates, unmapped regions, and other unwanted sequences using SAMtools, Pysam, and BAMTools. Normalized bigWig files were generated by BEDTools, and bedGraphToBigWig. Genome-wide enrichment was done by deepTools and peaks were called using MACS2. Differential accessibility analysis was performed by DESeq2 and Homer was used to annotate gene features.
Assembly: GRCh38
Supplementary files format and content: Files are in bigWig format. They contain the quantitative values of the sequencing data aligned to the human genome.

growth_protocol: Human pancreatic cancer cell lines Panc-01 and MiaPaCa-2, mouse skeletal muscle cell line C2C12, and human cervical cancer cell line HeLa S3 were used in this study. The HeLa S3 cells were grown in DMEM (Thermo Fisher Scientific) supplemented with 10 % fetal bovine serum (FBS, Thermo Fisher Scientific) and penicillin-streptomycin solution (PEST; Thermo Fisher Scientific).

extract_protocol:
Approximately 2 x 106 Panc-01WT or Panc-01KO cells were crosslinked in triplicate with 1% paraformaldehyde in PBS buffer for 15 min and stopped by the addition of 1.25 M glycine for 5 minutes at room temperature. Cells were lysed 35 and sonicated using Bioruptor Plus (Diagenode) for 10 min with 5s on and 5s off pulses in low power output at 4ºC. Optimal chromatin fragmentation of 400-300 bp was verified in reversed cross-linked samples on a TapeStation 2200 system (Agilent Technologies).
Library preparation was performed with the Omni-ATAC method. Once the final library was obtained, a purification step using AMPure XP beads was done before concentration and fragment size assessment. A quality control step consistent of size distribution and yield estimation is applied before the library sequencing.

treatment_protocol: Knockout of C16orf87 in Panc-01 cells

value: Human pancreatic carcinoma (duct cells)


title: Panc-01 C16orf87 knockout, biol rep 2

description: Library name: Panc-01 C16orf87 knockout, replicate 2


title: Panc-01 C16orf87 knockout, biol rep 1

description: Library name: Panc-01 C16orf87 knockout, replicate 1


title: Panc-01 C16orf87 knockout, biol rep 3

description: Library name: Panc-01 C16orf87 knockout, replicate 3


title: NI_UT_6


title: C666-1_EBNA1_B_ChIP

description: Library name: C666-1_EBNA1_B_ChIP


title: Panc-01 wildtype, biol rep 2

description: Library name: Panc-01 wildtype, replicate 2


title: FCGS before treatment (D) 3

city: Davis

first: Amir

last: Kol

state: CA

address: One Shields Ave, Davis, CA 95616, USA

institute: UC Davis

description:
Library name: F3
Peripheral blood CD8+ T cells isolated from FCGS (D) cat 3

data_processing:
Raw sequencing reads were processed using HTStream to remove adapters and low-quality bases. Processed reads were aligned to the Felis catus reference genome (F.catus_Fca126_mat1.0, GenBank assembly GCA_018350175.1) using STAR aligner. Unique molecular identifiers (UMIs) were used for deduplication with UMI-tools. Gene-level counts were generated using featureCounts. Downstream analyses were performed in R using the edgeR and limma packages. Lowly expressed genes were filtered using filterByExpr, and normalization was performed using the trimmed mean of M-values (TMM) method. Data were transformed using the voom function prior to linear modeling.
Assembly: Felis_catus_Fca126_mat1.0 (GCA_018350175.1)
Supplementary files format and content: Processed data files are provided as tab-delimited text (.xlsm) files containing normalized gene expression values (log2 counts per million, logCPM) generated using the voom transformation in the limma package. Rows correspond to genes and columns correspond to individual samples. Gene identifiers are based on the Felis catus reference genome (Fca126_mat1.0).

organism: Felis catus

source_name: Blood

extract_protocol:
CD8+ T-cells were lysed in RLT buffer, and RNA was extracted using the RNeasy Mini Kit (Qiagen)
RNA quantity and quality were assessed by NanoDrop spectrophotometry. Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s instructions. This method generates 3′ end-tagged libraries using oligo(dT) priming. Libraries were amplified and prepared for single-end sequencing.

value: Blood

value: CD8 T cells

tag: genotype

value: WT

value: No treatment


title: FCGS after treatment (M) 4

description:
Library name: M4
Peripheral blood CD8+ T cells isolated from FCGS treated (M) cat 4

value: FME and MSC


title: FCGS before treatment (D) 7

description:
Library name: R3
Peripheral blood CD8+ T cells isolated from FCGS (D) cat 7


title: FCGS after treatment (M) 3

description:
Library name: M3
Peripheral blood CD8+ T cells isolated from FCGS treated (M) cat 3


title: FCGS after treatment (M) 1

description:
Library name: M1
Peripheral blood CD8+ T cells isolated from FCGS treated (M) cat 1


title: FCGS after treatment (M) 2

description:
Library name: M2
Peripheral blood CD8+ T cells isolated from FCGS treated (M) cat 2


title: FCGS before treatment (D) 4

description:
Library name: F4
Peripheral blood CD8+ T cells isolated from FCGS (D) cat 4


title: FCGS before treatment (D) 5

description:
Library name: R1
Peripheral blood CD8+ T cells isolated from FCGS (D) cat 5


title: Healthy cat control 5

description:
Library name: C5
Peripheral blood CD8+ T cells isolated from healthy control cat 5


title: FCGS before treatment (D) 2

description:
Library name: F2
Peripheral blood CD8+ T cells isolated from FCGS (D) cat 2


title: FCGS before treatment (D) 1

description:
Library name: F1
Peripheral blood CD8+ T cells isolated from FCGS (D) cat 1


title: Healthy cat control 6

description:
Library name: C6
Peripheral blood CD8+ T cells isolated from healthy control cat 6


title: Healthy cat control 2

description:
Library name: C2
Peripheral blood CD8+ T cells isolated from healthy control cat 2


title: Healthy cat control 1

description:
Library name: C1
Peripheral blood CD8+ T cells isolated from healthy control cat 1


title: Healthy cat control 3

description:
Library name: C3
Peripheral blood CD8+ T cells isolated from healthy control cat 3


title: Healthy cat control 4

description:
Library name: C4
Peripheral blood CD8+ T cells isolated from healthy control cat 4


title: PF3D7, TP5, WR-, RNAseq

city: Nijmegen

first: Martijn

middle: van den

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

description: Library name: RNAseq_TP5-WR-

data_processing:
For RNA sequencing: Reads were mapped against the P. falciparum 3D7 reference transcriptome from PlasmoDB v68, edited to include the hDHFR-GFP transcript instead of the AP2G transcript, using BWA samse (version 0.7.182-r1039r1243). Only uniquely mapping reads with mapping quality ≥15 (samtools SAM tools version 1.21) were used for further analysis. After separating the reads according to the original strand they mapped to (sense strand FLAG16, antisense strand FLAG0), sense transcript abundance was assessed by counting the respective tag for each transcript and saved in the merged in a tab delimited text file.
Assembly: P.falciparum 3D7 reference transcriptome v68 (plasmodb.org)
Supplementary files format and content: For RNA sequencing a tab-delimited text-file is provided with the raw counts of the sense strand for all conditions

molecule: polyA RNA

organism: Plasmodium falciparum

source_name: Infected red blood cells

growth_protocol: P.falciparum F54 tansgenic parasites were cultured in 5% hematocrit in RPMI-1640 medium supplemented with 25 mM HEPES, 100 mM hypoxanthine, 24 mM sodium bicarbonate, 0.5% Albumax II, 2 mM choline and neomycin. Synchronized parasites (to an 8-hour windows: TP1, 8-16h; TP2, 16-24h; TP3, 24-32h; TP4, 32-40h; TP5 40-48h) were obtained by repeated sorbitol treatments.

extract_protocol:
Following standard manufacturer’s instructions, total RNA was extracted using Ribozol, purified and depleted of gDNA by two rounds of purification using the RNeasy Plus Mini Kit and polyA-selected using the Oligotex mRNA Mini Kit. Subsequently RNA was fragmented by alkaline hydrolysis for 1 min 45 sec at 85°C and precipitated with 1 volume of isopropanol, 1/5th volume of 5M ammonium acetate and 2.5 uL of linear acrylamide carrier.
Strand-specific RNA-seq was performed. In short, first-strand cDNA synthesis was performed with AT-corrected random N9 primers (76% AT) in the presence of 0.2 µg Actinomycin D (Thermo Fisher Scientific). Second-strand synthesis was performed by replacing dTTPs with dUTPs to preserve the strand-specific information. The synthetized double-stranded cDNAs were end-repaired, extended with 3’ A-overhangs and ligated to NextFlex adapters. dUTP-containing second strand DNA was degraded using USER enzyme and libraries were subsequently amplified by PCR (98°C for 2 min; 4 cycles of 98°C for 20 sec, 62°C for 3 min; 62°C for 5 min) using KAPA HiFi HotStart ready mix and NEXTflex primer mix. The resulting amplicons were size-selected for 300-400 bp fragments using 2% E-Gel Size Select agarose gels and amplified for another 12 cycles using the same PCR conditions. Library was purified using Agencourt AMPure XP beads in a 1:1 library:beads ratio.

treatment_protocol: To select for parasites with an active AP2G locus, parasites were treated with 4nM WR99210 (WR) and maintained under drug pressure for several generations. WR- parasites are not selected, WR+ are parasites selected under WR pressue for several generations.

value: Infected red blood cells

value: Plasmodium parasite


title: PF3D7, TP4, WR-, RNAseq

description: Library name: RNAseq_TP4-WR-


title: PF3D7, TP4, WR+, RNAseq

description: Library name: RNAseq_TP4-WR+


title: PF3D7, TP5, WR+, RNAseq

description: Library name: RNAseq_TP5-WR+


title: PF3D7, TP3, WR+, RNAseq

description: Library name: RNAseq_TP3-WR+


title: PF3D7, TP3, WR-, RNAseq

description: Library name: RNAseq_TP3-WR-


title: PF3D7, TP2, WR+, RNAseq

description: Library name: RNAseq_TP2-WR+


title: PF3D7, TP1, WR+, RNAseq

description: Library name: RNAseq_TP1-WR+


title: PF3D7, TP1, WR-, RNAseq

description: Library name: RNAseq_TP1-WR-


title: PF3D7, WR+, ChIP-Input

description: Library name: ChIP-Input_WR+

data_processing:
Reads were mapped against the P. falciparum 3D7 reference genome from PlasmoDB v68 (www.plasmodb.org), edited to include the hDHFR-GFP genes instead of the ap2g gene,  using bowtie2 (v2.5.4). Only uniquely mapping reads, not mapping to the mitochondrial or apicoplast genome, with mapping quality ≥30 (SAM tools v1.21) were used for further analysis. Deeptools bamCompare function was used to produce ChIP-over-input ratio tracks for all samples, these ratio tracks were converted to z-scores and provided as bigwig format.
Assembly: P.falciparum 3D7 reference genome v68 (plasmodb.org)
Supplementary files format and content: For ChIP sequencing, bigwig files containing z-score normalized HP1 ChIP-over-input ratio tracks are provided, which were used to produce scatterplots and genome browser screenshots in the manuscript.

extract_protocol:
RBC culture pellets were crosslinked with 1% formaldehyde for 10 min at 37ºC followed by quenching with 0.125 M glycine. Parasites were isolated by RBC lysis in 0.05% saponin and preserved at -80°C . Nuclei were obtained by lysing the parasites in cytoplasmic lysis buffer. Chromatin was sheared to 100-600 bp fragment size range by sonication for 20 cycles of 30 sec ON/30 sec OFF in sonication buffer. ChIPs were performed under rotation overnight at 4°C in incubation buffer containing sonicated chromatin and either rabbit α-PfHP1 or  rabbit  IgG negative control antibodies in the presence of 10 μl Dynabeads Protein A and Dynabeads Protein G. Magnetic beads were washed six times and immunoprecipitated chromatin was eluted with 1% SDS, 0.1 M NaHCO3. After de-crosslinking at 45°C in a shaking heat block overnight, DNA fragments were purified using QIAquick MinElute PCR columns.
The purified DNA fragments were end-repaired, extended with 3′ A-overhangs and ligated to barcoded NextFlex adapters. Libraries were amplified using KAPA HiFi HotStart ready mix, NextFlex primer mix and the following PCR program: 98°C for 2 min; four cycles of 98°C for 20 sec, 62°C for 3 min; 62°C for 5 min. Amplified libraries were size-selected for 225-325 bp (mono-nucleosomes + 125 bp NextFlex adapter) using 2% E-Gel Size Select agarose gels and amplified by PCR for ten cycles using the same PCR program. Libraries were purified by Agencourt AMPure XP beads purification using a 1:1 library:beads ratio.

treatment_protocol: To select for parasites with an active AP2G locus, parasites were treated with 4nM WR99210 (WR) and maintained under drug pressure for several generations. WR- parasites are not selected, WR+ are parasites selected under WR pressue for several generations, WR+/- are parasites selected under WR pressure and subsequently released for 42-72 generations before analysis.


title: PF3D7, WR+, HP1-ChIP

description: Library name: ChIP-HP1_WR+


title: PF3D7, WR-, ChIP-Input

description: Library name: ChIP-Input_WR-


title: PF3D7, WR+/-, HP1-ChIP

description: Library name: ChIP-HP1_WR+/-

value: 4 nM WR99210, than off this treatment for >42 generations


title: PF3D7, WR-, HP1-ChIP

description: Library name: ChIP-HP1_WR-


title: hnscc_7.ROI_006.Tumor.buds

city: Heidelberg

first: Jan

last: Budczies

address: Im Neuenheimer Feld 224

department: Institute of Pathology

country: Germany

institute: University Hospital Heidelberg

description:
Library name: DSP-1001660021806-C-G06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling

data_processing:
BCL to FASTQ conversion was performed using DRAGEN and the following command line options: dragen --bcl-conversion-only true --bcl-input-directory /path/to/BCL/directory --output-directory /path/to/FASTQ --sample-sheet /path/to/SeqCodeIndices/SeqCodeIndices.csv FASTQ files were processed using the NanoString GeoMx NGS Pipeline v2.3.3.10 and the following command line options: geomxngspipeline --in=/path/to/FASTQ --out=/path/to/DCC --ini=/path/to/GNP_config.ini The following default options were used: --quality-trim-score=20 (score used for quality trimming), --trim-adapter=true (enable/disable adapter trimming), --adapter-trim-match-length=10 --adapter-trim-max-mismatch=3 , --stitching-max-mismatch=2, --stitch-shift=true, --barcode-max-mismatch=1, --dedup-hd=1. For all downstream analysis, the deduplicated read counts were used. For each segment, additional quality control thresholds were applied. The minimum number of reads per segment was set at 40,000, the minimum number of successfully stitched reads at 80%, and the minimum number of aligned reads at 70%. Additionally, sequencing saturation was required to be at least 50%, while non-template control (NTC) wells were limited to a maximum of 1,000 counts. Each segment (that is a specific ROI-AOI combination) contained a set of negative probes; the geometric mean of the counts of the negative probes was calculated per segment and used to define the limit of quantification (LOQ), according to the formula LOQ = max (2, NegGeoMean × NegGeoSD2), where NegGeoMean is the geometric mean of the counts of the negative probes and NegGeoSD is the geometric standard deviation of the counts of the negative probes for a given segment. Essentially, the LOQ is defined as 2 standard deviations above the negative control mean and at minimum as at least 2 counts. Using the segment-specific LOQ thresholds, segments with exceptionally low signal (fewer than 5% of the genes detected above LOQ) and genes with low detection rates (fewer than 10% of the segments having detected a given gene above LOQ) were filtered out. The final post-QC dataset consisted of 239 segments and 7,795 genes. The raw counts were normalized to upper quartile (UQ or Q3) normalized counts and, for each case, the mean of the normalized counts for each gene was calculated for segments belonging to the same segment type.
Assembly: hg38
Supplementary files format and content: DCC files containing the raw counts for each probe.
Library strategy: Spatial Transcriptomics

source_name: Head and neck squamous cell carcinoma

growth_protocol: FFPE blocks

extract_protocol:
Slides were imaged in three fluorescence channels (FITC/525 nm, Cy3/568 nm, and Texas Red/615 nm) to visualize morphology markers, and regions of interest were segmented based on the expression of the morphology markers. For each tumor, two regions of interest (ROIs) were sampled from the bulk of the tumor and the surrounding stromal tissue. In budding cases, an additional two to three ROIs were sampled, focusing specifically on tumor bud cells and the adjacent stroma. Each ROI is then divided in distinct areas of illumination (AOIs) based on the morphology markers PanCK and CD45. PanCK-negative/CD45-positive cells were assigned the “immune” AOI,  PanCK-negative/CD45-negative cells were assigned the “stroma” AOI, and PanCK-positive/CD45-negative cells were assigned the “tumor” AOI. Each AOI was sequentially illuminated with UV and the UV-cleavable released tags were collected into 96-well plates.
The library preparation was performed according to the GeoMx DSP NGS Readout User Manual. In short, the 96-well plate was dried by being left on the bench top overnight covered by a permeable membrane which was subsequently replaced by another permeable membrane and the plate was then spinned down. The samples were then rehydrated with ten µL nuclease-free water and the plate was pulse-centrifuged to 1000 x g. GeoMx Seq Code primers were used to amplify the WTA tags and add Illumina adaptor sequences and sample demultiplexing barcodes. The GeoMx Seq Code primer plate was thawed and the GeoMx Seq Code primer plate and the GeoMx NGS Master Mix were pulse-centrifuged to 1000 x g. The subsequent PCR reaction was set up on a PCR plate with two μL of GeoMx NGS Master Mix, four μL of GeoMx Seq Code primer mix (added to the corresponding PCR plate well), and four μL of DSP aspirate (added to the corresponding PCR plate well) used per well. The PCR plate was sealed with a PCR plate sticker, pulse centrifuged to 1000 x g, and incubated in the thermocycler with a 100°C heated lid. The cycling conditions were as follows: UDG treatment at 37°C for 30 min, followed by UDG deactivation at 50°C for ten min. Initial denaturation was performed at 95°C for three minutes. Amplification consisted of 18 cycles of denaturation at 95°C for 15 sec, annealing at 65°C for 60 sec, and extension at 68°C for 30 sec. A final extension was carried out at 68°C for five minutes, followed by an indefinite hold at 4°C. The PCR products were pooled using four μL of each PCR product (including the NTC) and the remainder of the NTC PCR product was placed into a separate tube. The tubes with the sample pool and the NTC went through the same AMPure cleanup protocol using the 1.2-fold volume AMPure XP beads and the libraries were sequenced on an Illumina NextSeq 550 with 27x27 paired end reads.

treatment_protocol: Tumor sections from formalin-fixed, paraffin-embedded (FFPE) tissue of primary tumors of immunohistochemically p16-negative HNSCC patients were mounted on 24 slides. Tissue microarrays (TMAs) were constructed, incorporating selected tumor regions from two to three representative cases per array. The selected areas measured approximately 25-50 mm². Each slide included a tumor section from a budding case, and on 19 of the 24 slides, an additional section from a non-budding case was also included. Sample preparation was performed as described in the GeoMx DSP Manual Slide Prep User Manual (following the RNA FFPE instructions). In short, five μm thick FFPE tissue sections were mounted on BOND Plus slides. The slides were baked in a 60°C drying oven for 75 minutes and were deparaffinized and rehydrated with three five-minute washes in CitriSolv, two five-minute washes in 100% EtOH, one five-minute wash in 95% EtOH, and one one-minute wash in 1x PBS. The slides were then dipped into DEPC-treated water (at ~99°C) for ten seconds and immediately transferred to a ~99°C 1X Tris-EDTA jar and incubated for 15 minutes for target retrieval. After incubation, the slides were moved to room temperature 1x PBS and were washed for five minutes. The samples were then digested with one µg/mL Proteinase K for 15 minutes at 37°C and washed with 1x PBS for five minutes. The slides were then washed in 10% NBF for five minutes, two times in NBF Stop Buffer for five minutes each time, and one time in 1x PBS for five minutes. The samples were then incubated overnight (16 hours) at 37°C with Buffer R and the Human Whole Transcriptome Atlas (WTA) RNA detection probes in a light-non-permeable humid chamber, ensuring humid conditions by arranging DEPC-treated water-soaked Kimwipes on the bottom of the chamber . The reagent concentrations were adjusted for each run, where 200 μL x n Buffer R, 25 μL x n WTA Probe Mix, and 25 μL x n DEPC-treated water were used for the final solution, with n referring to the number of slides analyzed per run. 200 μL of the final solution was applied on each slide and HybriSlip Hybridization Covers (Grace BioLabs) covered the tissue during incubation. To remove off-target probes, two 25-minute stringent washes were performed in 50% formamide in 2x SSC at 37°C. The slides were then washed twice with 2x SCC for two minutes each time. For the morphology marker staining, the slides were placed in the light-non-permeable humidity chamber, covered with 200 μL Buffer W each at room temperature for 30 minutes. Then the Buffer W was removed and up to 200 μL of morphology marker solution (22 μL x n Syto 13, 5.5 μL x n PanCK, 5.5 μL x n CD45, filling in with Buffer W to reach 220 μL x n final volume, where n is the number of slides per run) was applied on each slide in the humidity chamber. The slides were stained for one hour in the humidity chamber at room temperature. After staining, the solution was removed and the slides were washed in 2x SCC two times for five minutes each time and loaded on the GeoMx DSP instrument.

value: Head and neck squamous cell carcinoma


title: hnscc_7.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021806-C-G03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021806-C-G05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_004.Tumor.budding

description:
Library name: DSP-1001660021806-C-F12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_006.Immune.buds

description:
Library name: DSP-1001660021806-C-G04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: PF3D7, WR+/-, ChIP-Input

description: Library name: ChIP-Input_WR+/-


title: hnscc_7.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021806-C-G02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_005.Immune.buds

description:
Library name: DSP-1001660021806-C-G01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_004.Immune.budding

description:
Library name: DSP-1001660021806-C-F10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_004.Stroma.budding

description:
Library name: DSP-1001660021806-C-F11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_003.Stroma.budding

description:
Library name: DSP-1001660021806-C-F08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: PF3D7, TP2, WR-, RNAseq

description: Library name: RNAseq_TP2-WR-


title: hnscc_7.ROI_003.Tumor.budding

description:
Library name: DSP-1001660021806-C-F09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_002.Tumor.non_budding

description:
Library name: DSP-1001660021806-C-F06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_003.Immune.budding

description:
Library name: DSP-1001660021806-C-F07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_002.Stroma.non_budding

description:
Library name: DSP-1001660021806-C-F05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_001.Tumor.non_budding

description:
Library name: DSP-1001660021806-C-F04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Panc-01 wildtype, biol rep 1

description: Library name: Panc-01 wildtype, replicate 1


title: hnscc_12.ROI_010.Tumor.buds

description:
Library name: DSP-1001660021806-C-F01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_001.Stroma.non_budding

description:
Library name: DSP-1001660021806-C-F03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_010.Stroma.buds

description:
Library name: DSP-1001660021806-C-E12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_009.Tumor.buds

description:
Library name: DSP-1001660021806-C-E11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_004.Tumor.budding

description:
Library name: DSP-1001660021806-C-E09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_004.Stroma.budding

description:
Library name: DSP-1001660021806-C-E08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_003.Tumor.budding

description:
Library name: DSP-1001660021806-C-E07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_002.Stroma.non_budding

description:
Library name: DSP-1001660021806-C-E04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_002.Tumor.non_budding

description:
Library name: DSP-1001660021806-C-E05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_002.Immune.non_budding

description:
Library name: DSP-1001660021806-C-E03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_003.Stroma.budding

description:
Library name: DSP-1001660021806-C-E06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_009.Stroma.buds

description:
Library name: DSP-1001660021806-C-E10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_001.Tumor.non_budding

description:
Library name: DSP-1001660021806-C-E02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_001.Stroma.non_budding

description:
Library name: DSP-1001660021806-C-E01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_9.ROI_007.Tumor.buds

description:
Library name: DSP-1001660021806-C-D11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_9.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021806-C-D09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_9.ROI_007.Stroma.buds

description:
Library name: DSP-1001660021806-C-D10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_9.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021806-C-D08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_9.ROI_003.Tumor.budding

description:
Library name: DSP-1001660021806-C-D07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_9.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021806-C-D05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_9.ROI_001.Tumor.non_budding

description:
Library name: DSP-1001660021806-C-D03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_12.ROI_001.Immune.non_budding

description:
Library name: DSP-1001660021806-C-D12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_20.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021806-C-D01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_20.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021806-C-C12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_7.ROI_001.Immune.non_budding

description:
Library name: DSP-1001660021806-C-F02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_20.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021806-C-C10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_20.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021806-C-C08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_20.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021806-C-C09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_20.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021806-C-C11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_9.ROI_001.Stroma.non_budding

description:
Library name: DSP-1001660021806-C-D02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_20.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021806-C-C07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_9.ROI_003.Stroma.budding

description:
Library name: DSP-1001660021806-C-D06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_23.ROI_007.Stroma.buds

description:
Library name: DSP-1001660021806-C-C04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_23.ROI_003.Tumor.budding

description:
Library name: DSP-1001660021806-C-C01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_23.ROI_003.Stroma.budding

description:
Library name: DSP-1001660021806-C-B12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_23.ROI_007.Tumor.buds

description:
Library name: DSP-1001660021806-C-C05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_23.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021806-C-B11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_23.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021806-C-C02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021806-C-B04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_20.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021806-C-C06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_23.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021806-C-B10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_006.Immune.non_budding

description:
Library name: DSP-1001660021806-C-B05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_23.ROI_001.Stroma.non_budding

description:
Library name: DSP-1001660021806-C-B08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_006.Tumor.non_budding

description:
Library name: DSP-1001660021806-C-B07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_006.Stroma.non_budding

description:
Library name: DSP-1001660021806-C-B06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_004.Tumor.buds

description:
Library name: DSP-1001660021806-C-B01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021806-C-B03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_23.ROI_001.Tumor.non_budding

description:
Library name: DSP-1001660021806-C-B09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_005.Immune.buds

description:
Library name: DSP-1001660021806-C-B02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_004.Stroma.buds

description:
Library name: DSP-1001660021806-C-A12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_003.Stroma.non_budding

description:
Library name: DSP-1001660021806-C-A09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Arsenite stressed (15min), polyA+ RNA, replicate 1

city: Ann Arbor

first: Stephanie

middle: L

last: Moon

state: MI

address: 3734 Med Sci II 1241 E. Catherine St

department: Human Genetics

institute: University of Michigan

description:
Library name: 15min_As_rep1
colname in Time_Course_Counts_File.csv: 15min_rep1

data_processing:
For Biostate (nuc/cyto): Adapter contaminants and low-quality reads trimmed with Cutadapt (v4.2) and aligned to hg38 using HISAT2 (v2.2.1). Gene expression quantified with featureCounts (v2.0.3) using exon level-first strand quantification. Final CPM in Nuc_Cyto_Total_Counts_File.csv.
For plasmidsaurus (time-course): FastQ generation and demux with BCL conver (v4.3.6) and fqtk (v0.3.1). Read-filtering using FastP (v0.24.0) including poly-X tail trimming, 3' quality-based tail trimming, minimum Phred quality of 15 and length of 50 bp. Aligned to hg38 with STAR (v2.7.11) with non-canonical splice junction removal and output of unmapped reads. Coordinate sorting of BAMs with samtools (v1.22.1) and UMI de-duplication with UMICollapse (v1.1.0). Gene-expression quantification using featureCounts (v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons, and 3'UTRs as feature identifeires. Final CPM in Time_Course_Counts_File.csv
Assembly: hg38
Supplementary files format and content: format: csv; content: counts tables

source_name: U-2 OS

growth_protocol: U-2 OS cells were maintained in Dulbecco's modified Eagle medium with 9% FetalGro Ex, 1% penicillin/streptomycin, and 1% Glutamax at 37 °C and 5% CO2

extract_protocol:
Nuc/Cyto fractionation was done as previously described as in Bhatt et al., 2012; Ji et al., 2021; and letswaart et al., 2022 and detailed in accompying manuscript for this submission (Helton et al., 2026). RNA was sent to Biostate.ai for rRNA depletion using Probes for Excess RNA depletion and RNAseq.  For time course RNAseq of PolyA+ RNA, cells were scraped into DNA/RNA Shield (Zymo research) and sent for bulk RNAseq by Plasmidsaurus.
For Biostate (nuc/cyto) library preparation: rRNA depleted RNA was reverse transcribed into cDNA and barcoded using Biostate's Barcode-Integrated Reverse Transcription technology.  For plasmidsaurus (time-course) library prepraration: PolyA+ RNA was converted into cDNA via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.

treatment_protocol: Cells were treated with 250 µM arsenite in complete growth medium or untreated with a change in complete growth medium for unstressed conditions

value: U-2 OS

value: osteosarcoma

value: WT with endogenously tagged G3BP1 with eGFP

value: 250 µM arsenite


title: hnscc_11.ROI_003.Tumor.non_budding

description:
Library name: DSP-1001660021806-C-A10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021806-C-A07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_004.Immune.buds

description:
Library name: DSP-1001660021806-C-A11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021806-C-A06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_002.Immune.budding

description:
Library name: DSP-1001660021806-C-A05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021806-C-A04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021806-C-A03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021758-A-H01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_11.ROI_003.Immune.non_budding

description:
Library name: DSP-1001660021806-C-A08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021758-A-G12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021758-A-G11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021758-A-G10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021758-A-G05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_004.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-G09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021758-A-G01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021758-A-G03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_003.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-G06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_003.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-G07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021758-A-G04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_004.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-G08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_004.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-F09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_003.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-F07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021758-A-F12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021758-A-F05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_004.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-F08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_003.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-F06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021758-A-F01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021758-A-F04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021758-A-F10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021758-A-F11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_6.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021758-A-G02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021758-A-E11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021758-A-E12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021758-A-F02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_004.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-E09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_5.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021758-A-F03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021758-A-E10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_003.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-E07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_003.Immune.non_budding

description:
Library name: DSP-1001660021758-A-E05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021758-A-E04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_004.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-E08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_003.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-E06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_007.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-D11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021758-A-E02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021758-A-E03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_007.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-D10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_005.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-D08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: BEA24P061_GL_23_T2_5_FU_plus_EPS_RNA

description: Library name: P32606_1023

value: Large intestine, colon

value: Enterocyte

value: 24h chemo, then 72h with/without postbiotics


title: hnscc_3.ROI_003.Tumor.budding

description:
Library name: DSP-1001660021758-A-D02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021758-A-E01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_003.Stroma.budding

description:
Library name: DSP-1001660021758-A-D01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_004.Tumor.budding

description:
Library name: DSP-1001660021758-A-D05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_4.ROI_001.Immune.budding

description:
Library name: DSP-1001660021758-A-D12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_004.Immune.budding

description:
Library name: DSP-1001660021758-A-D03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_002.Tumor.buds

description:
Library name: DSP-1001660021758-A-C11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_005.Immune.non_budding

description:
Library name: DSP-1001660021758-A-D06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_005.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-D07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_002.Stroma.buds

description:
Library name: DSP-1001660021758-A-C10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_004.Stroma.budding

description:
Library name: DSP-1001660021758-A-D04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_001.Stroma.buds

description:
Library name: DSP-1001660021758-A-C08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_001.Tumor.buds

description:
Library name: DSP-1001660021758-A-C09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_3.ROI_003.Immune.budding

description:
Library name: DSP-1001660021758-A-C12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_006.Immune.non_budding

description:
Library name: DSP-1001660021758-A-C05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_006.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-C07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_004.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-C01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_006.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-C06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_005.Immune.budding

description:
Library name: DSP-1001660021758-A-C02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_004.Immune.non_budding

description:
Library name: DSP-1001660021758-A-B11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_005.Stroma.budding

description:
Library name: DSP-1001660021758-A-C03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_003.Stroma.budding

description:
Library name: DSP-1001660021758-A-B09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_005.Tumor.budding

description:
Library name: DSP-1001660021758-A-C04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_003.Immune.budding

description:
Library name: DSP-1001660021758-A-B08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_002.Tumor.buds

description:
Library name: DSP-1001660021758-A-B07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_003.Tumor.budding

description:
Library name: DSP-1001660021758-A-B10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_004.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-B12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_006.Tumor.budding

description:
Library name: DSP-1001660021758-A-B03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_001.Tumor.buds

description:
Library name: DSP-1001660021758-A-B05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_001.Stroma.buds

description:
Library name: DSP-1001660021758-A-B04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021758-A-B01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021758-A-A12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_006.Stroma.budding

description:
Library name: DSP-1001660021758-A-B02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_004.Tumor.budding

description:
Library name: DSP-1001660021758-A-A11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_004.Stroma.budding

description:
Library name: DSP-1001660021758-A-A10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_003.Immune.non_budding

description:
Library name: DSP-1001660021758-A-A07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_003.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-A08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_002.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-A06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_2.ROI_002.Stroma.buds

description:
Library name: DSP-1001660021758-A-B06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_001.Stroma.buds

description:
Library name: DSP-1001660021758-A-A02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_001.Tumor.buds

description:
Library name: DSP-1001660021758-A-A03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_002.Stroma.non_budding

description:
Library name: DSP-1001660021758-A-A05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_1.ROI_002.Immune.non_budding

description:
Library name: DSP-1001660021758-A-A04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_009.Tumor.buds

description:
Library name: DSP-1001660021757-D-E11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_008.Tumor.buds

description:
Library name: DSP-1001660021757-D-E09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_008.Stroma.buds

description:
Library name: DSP-1001660021757-D-E08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_007.Stroma.buds

description:
Library name: DSP-1001660021757-D-E06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_003.Tumor.budding

description:
Library name: DSP-1001660021757-D-E03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_004.Tumor.budding

description:
Library name: DSP-1001660021757-D-E05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_002.Tumor.non_budding

description:
Library name: DSP-1001660021757-D-E01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_007.Tumor.buds

description:
Library name: DSP-1001660021757-D-E07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_004.Stroma.budding

description:
Library name: DSP-1001660021757-D-E04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_003.Stroma.budding

description:
Library name: DSP-1001660021757-D-E02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_009.Stroma.buds

description:
Library name: DSP-1001660021757-D-E10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_24.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021757-D-D09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_24.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021757-D-D07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_24.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021757-D-D05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_001.Stroma.non_budding

description:
Library name: DSP-1001660021757-D-D10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_24.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021757-D-D06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_24.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021757-D-D04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_001.Tumor.non_budding

description:
Library name: DSP-1001660021757-D-D11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_24.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021757-D-D03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_15.ROI_002.Stroma.non_budding

description:
Library name: DSP-1001660021757-D-D12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_24.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021757-D-D02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_009.Stroma.budding

description:
Library name: DSP-1001660021757-D-C12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_24.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021757-D-D08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_007.Tumor.buds

description:
Library name: DSP-1001660021757-D-C09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_008.Stroma.buds

description:
Library name: DSP-1001660021757-D-C10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_008.Tumor.buds

description:
Library name: DSP-1001660021757-D-C11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_009.Tumor.budding

description:
Library name: DSP-1001660021757-D-D01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_007.Stroma.buds

description:
Library name: DSP-1001660021757-D-C08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_003.Tumor.budding

description:
Library name: DSP-1001660021757-D-C07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_003.Stroma.budding

description:
Library name: DSP-1001660021757-D-C06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_002.Tumor.non_budding

description:
Library name: DSP-1001660021757-D-C05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_002.Stroma.non_budding

description:
Library name: DSP-1001660021757-D-C04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_001.Tumor.non_budding

description:
Library name: DSP-1001660021757-D-C03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_17.ROI_007.Tumor.budding

description:
Library name: DSP-1001660021757-D-B11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_19.ROI_001.Stroma.non_budding

description:
Library name: DSP-1001660021757-D-C02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_17.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021757-D-B09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_17.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021757-D-B08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_17.ROI_007.Stroma.budding

description:
Library name: DSP-1001660021757-D-B10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_17.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021757-D-B07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_17.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021757-D-B06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-8_S1_sRNA non inoculated rep4

city: České Budějovice

first: Abdoallah

last: Sharaf

address: Branišovská 31

country: Czech Republic

institute: Biology Centre ASCR, v.v.i.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie2
gene counts for every gene and every sample were calculated
Genome_build: IWGSC
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw sRNA counts for every miRNA and every sample

organism: Triticum aestivum

source_name: leaves

extract_protocol:
leaves were collected, flash-frozen on dry ice, and RNA was harvested using Trizol reagent. Lexogen Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Svitava

value: Non inoculated

value: leaves


title: hnscc_1.ROI_003.Tumor.non_budding

description:
Library name: DSP-1001660021758-A-A09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-8_S1_sRNA non inoculated rep2


title: hnscc_16.ROI_008.Tumor.budding

description:
Library name: DSP-1001660021757-D-B05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_16.ROI_007.Stroma.budding

description:
Library name: DSP-1001660021757-D-B02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_16.ROI_007.Tumor.budding

description:
Library name: DSP-1001660021757-D-B03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-8_S1_sRNA non inoculated rep3


title: hnscc_17.ROI_008.Tumor.budding

description:
Library name: DSP-1001660021757-D-C01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-8_S1_sRNA non inoculated rep1


title: hnscc_17.ROI_008.Stroma.budding

description:
Library name: DSP-1001660021757-D-B12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_16.ROI_008.Stroma.budding

description:
Library name: DSP-1001660021757-D-B04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-7_S15_sRNA non inoculated rep4


title: Svitava-7_S15_sRNA non inoculated rep3


title: hnscc_16.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021757-D-B01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_16.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021757-D-A12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-7_S15_sRNA non inoculated rep2


title: Svitava-7_S15_sRNA non inoculated rep1


title: hnscc_16.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021757-D-A10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_16.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021757-D-A11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-6_S17_sRNA non inoculated rep2


title: hnscc_21.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021757-D-A08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-6_S17_sRNA non inoculated rep3


title: hnscc_21.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021757-D-A09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-6_S17_sRNA non inoculated rep4


title: hnscc_21.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021757-D-A07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_21.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021757-D-A05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-3_S10_sRNA WDV infected rep2

value: WDV infected


title: hnscc_21.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021757-D-A04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-3_S10_sRNA WDV infected rep3


title: hnscc_21.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021757-D-A06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_21.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021757-D-A03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_33.ROI_012.Tumor.buds

description:
Library name: DSP-1001660021755-B-G03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-6_S17_sRNA non inoculated rep1


title: Svitava-3_S10_sRNA WDV infected rep4


title: Svitava-3_S10_sRNA WDV infected rep1


title: Svitava-2_S8_sRNA WDV infected rep3


title: Svitava-2_S8_sRNA WDV infected rep2


title: Svitava-2_S8_sRNA WDV infected rep4


title: hnscc_33.ROI_012.Stroma.buds

description:
Library name: DSP-1001660021755-B-G02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-2_S8_sRNA WDV infected rep1


title: hnscc_33.ROI_011.Tumor.buds

description:
Library name: DSP-1001660021755-B-G01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_33.ROI_011.Stroma.buds

description:
Library name: DSP-1001660021755-B-F12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-1_S9_sRNA WDV infected rep4


title: hnscc_33.ROI_004.Tumor.budding

description:
Library name: DSP-1001660021755-B-F11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_21.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021757-D-A02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-1_S9_sRNA WDV infected rep3


title: hnscc_33.ROI_004.Stroma.budding

description:
Library name: DSP-1001660021755-B-F10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Svitava-1_S9_sRNA WDV infected rep1


title: Svitava-1_S9_sRNA WDV infected rep2


title: hnscc_33.ROI_003.Stroma.budding

description:
Library name: DSP-1001660021755-B-F08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Fengyou-9_S4_sRNA non inoculated rep1

value: Fengyou


title: ACL_PKCi2

city: Miami

first: xiaomin

last: cai

state: Florida

address: Rosenstiel Medical Science Building 1600 NW, 10th Ave.

institute: University of Miami

description: Library name: C2

data_processing:
Libraries were prepared following rRNA depletion and sequenced using the DNBSEQ-G400 platform, generating paired-end 100 bp reads. Sequencing reads were aligned to the mouse reference genome (mm10) using HISAT2, and gene-level quantification was performed using featureCounts.
Assembly: mm10
Supplementary files format and content: raw gene count matrix (raw_counts.txt)

organism: Mus musculus

source_name: mouse knee joint tissue

extract_protocol:
Total RNA was extracted from mouse knee joint tissues using TRIzol reagent according to the manufacturer’s protocol.
Libraries were prepared following rRNA depletion and sequenced using the DNBSEQ-G400 platform, generating paired-end 100 bp reads.

value: mouse knee joint tissue


title: ACL_PKCi3

description: Library name: C3


title: Fengyou-9_S4_sRNA non inoculated rep3


title: Fengyou-9_S4_sRNA non inoculated rep2


title: hnscc_33.ROI_002.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-F07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Fengyou-9_S4_sRNA non inoculated rep4


title: ACL_PKCi1

description: Library name: C1


title: hnscc_33.ROI_003.Tumor.budding

description:
Library name: DSP-1001660021755-B-F09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_33.ROI_002.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-F06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Fengyou-5_S11_sRNA WDV infected rep4


title: Fengyou-5_S11_sRNA WDV infected rep2


title: Fengyou-5_S11_sRNA WDV infected rep1


title: Fengyou-5_S11_sRNA WDV infected rep3


title: hnscc_33.ROI_001.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-F04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: ACL3

description: Library name: B3


title: Fengyou-3_S13_sRNA WDV infected rep4


title: Fengyou-3_S13_sRNA WDV infected rep3


title: ACL2

description: Library name: B2


title: hnscc_33.ROI_001.Immune.non_budding

description:
Library name: DSP-1001660021755-B-F03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: ACL1

description: Library name: B1


title: hnscc_33.ROI_001.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-F05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Fengyou-3_S13_sRNA WDV infected rep1


title: Fengyou-3_S13_sRNA WDV infected rep2


title: BN1_iLS_Day14_1

status: Public on Apr 22 2026

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

country: Japan

institute: Graduate School of Medicine, The University of Osaka

description:
Library name: Smaple 13
0716_BRD9

data_processing:
The FASTQ-sequenced reads were mapped to the mm10 genome using STAR.
Raw gene counts were calculated by RSEM.
Batch corrected data counts by ComBat were normalized and differentially expressed genes were identified with Adjusted p value < 0.05 by DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Bone marrow

extract_protocol:
FACS sorted cells were proceeded to RNA extraction using RNeasy columns (Qiagen).
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit.

value: Bone marrow

tag: strain

value: CD45.2+ bone marrow cells


title: hnscc_31.ROI_006.Tumor.buds

description:
Library name: DSP-1001660021755-B-F02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Fengyou-1_S16_sRNA WDV infected rep4


title: Sham3

description: Library name: A3


title: Sham2

description: Library name: A2


title: hnscc_31.ROI_006.Stroma.buds

description:
Library name: DSP-1001660021755-B-F01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Fengyou-1_S16_sRNA WDV infected rep3


title: hnscc_31.ROI_005.Tumor.buds

description:
Library name: DSP-1001660021755-B-E12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Fengyou-11_S18_sRNA non inoculated rep2


title: Fengyou-11_S18_sRNA non inoculated rep4


title: Fengyou-11_S18_sRNA non inoculated rep3


title: Fengyou-1_S16_sRNA WDV infected rep1


title: hnscc_31.ROI_005.Stroma.buds

description:
Library name: DSP-1001660021755-B-E11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Fengyou-10_S6_sRNA non inoculated rep4


title: Fengyou-11_S18_sRNA non inoculated rep1


title: Sham1

description: Library name: A1


title: Fengyou-10_S6_sRNA non inoculated rep3


title: hnscc_31.ROI_004.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-E09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Fengyou-10_S6_sRNA non inoculated rep2


title: Fengyou-1_S16_sRNA WDV infected rep2


title: Akteur-9_S3_sRNA non inoculated rep4

value: Akteur


title: SHAPE-MaP of Ymu1 TnpB 127-nt reRNA (wild-type scaffold)

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

description:
Library name: HS_RNA_7_WT
SHAPE-MaP chemical probing; N = DMSO untreated, S = 1M7 modified

data_processing:
Small RNA-seq: Paired-end reads were trimmed and merged with fastp (v0.23.2).
Small RNA-seq: Merged reads of 100-150 nucleotides were extracted using fastq-filter (v0.3.0) and mapped to TnpB loci with BWA (v0.7.17).
Small RNA-seq: Alignments were sorted with SAMTools (v1.17) and converted to BigWig format with deepTools2 (v3.5.1) for visualization in IGV.
SHAPE-MaP: Reads were processed with ShapeMapper2 using the command: shapemapper --name <run_name> --target <target.fasta> --modified --folder <modified_fastqs_dir> --untreated --folder <untreated_fastqs_dir>. SHAPE reactivities were visualized in VARNA on the Ymu1 reRNA 2D structure.
Assembly: Ymu1 TnpB reRNA reference sequences (pHS607 200-nt scaffold for small RNA-seq; pHS610 127-nt and pHS612 short scaffold for SHAPE-MaP)
Supplementary files format and content: Small RNA-seq: BigWig files containing normalized read coverage mapped to the TnpB reRNA reference sequence. SHAPE-MaP: Tab-delimited ShapeMapper2 profile.txt files containing per-nucleotide SHAPE reactivity, standard error, mutation rates, and read depth.

organism: Escherichia coli

source_name: E. coli

growth_protocol: Escherichia coli BL21-AI cells harboring the indicated plasmid were grown in LB medium supplemented with appropriate antibiotics at 37 °C to mid-log phase (OD600 ≈ 0.6).

extract_protocol:
For small RNA-seq: Purified reRNA was isolated directly from assembled TnpB RNP complexes using the RNA Clean & Concentrator-5 Kit (Zymo Research). Approximately 20 ng of purified RNA was end-repaired with QuickCIP (NEB, M0525S) and T4 PNK (NEB, M0201S). For SHAPE-MaP: 1 µg purified RNP was mixed with folding buffer (333 mM HEPES pH 8.0, 333 mM NaCl), combined with 10 mM MgCl2, and incubated at 37 °C. RNA was modified with 100 mM 1M7 in DMSO (modified) or DMSO alone (untreated control), then purified using the Qiagen RNeasy Micro Kit.
For small RNA-seq: End-repaired RNA was used for library preparation with the Collibri Stranded RNA Library Prep Kit for Illumina Systems (Invitrogen, A38994024). Libraries were amplified with KAPA HiFi DNA Polymerase at 65 °C annealing temperature and size-selected by gel extraction on E-Gel EX 4% Agarose Gels. For SHAPE-MaP: Modified RNA was reverse-transcribed with SuperScript II using random primers and a transcript-specific primer in MaP buffer containing MnCl2 (25 °C 10 min, 42 °C 3 h, 70 °C 15 min). cDNA was purified, second-strand synthesis was performed with the NEBNext Second Strand Synthesis Module, and libraries were prepared with the Illumina Nextera XT kit (tagmentation at 55 °C, 14-cycle indexed PCR) and purified with AMPure XP beads (1.8×).

treatment_protocol: Gene expression was induced by addition of arabinose to the growth medium, followed by overnight incubation at 16 °C.

value: E. coli

value: 1M7 and DMSO control


title: hnscc_31.ROI_003.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-E08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling

value: Head and neck squamous cell carcinoma


title: SHAPE-MaP of Ymu1 TnpB short reRNA scaffold

description:
Library name: HS_RNA_7_mut
SHAPE-MaP chemical probing; N = DMSO untreated, S = 1M7 modified


title: hnscc_31.ROI_004.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-E10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Fengyou-10_S6_sRNA non inoculated rep1


title: Akteur-9_S3_sRNA non inoculated rep3


title: Ymu1 TnpB reRNA expression from 200-nt scaffold, small RNA-seq

description: Library name: HS_RNA_4


title: Akteur-9_S3_sRNA non inoculated rep2


title: Akteur-9_S3_sRNA non inoculated rep1


title: Vav1CreTet2KO PD-1+CD8+ TILs, biol rep 2

city: Tsukuba

first: AI NHAN THI

last: LE

state: Ibaraki Prefecture

address: 2-1-1 Amakubo, University of Tsukuba Global Village, 305-8575

department: Department of Hematology

institute: Graduate School of Comprehensive Human Sciences, University of Tsukuba

description:
Library name: KO46_CD8
PBAT WGBS library

data_processing:
Raw sequencing reads were trimmed and aligned to the Mus musculus reference genome (GRCm39) using the Bismark pipeline with PBAT mode enabled.
Duplicate reads were removed using Bismark's deduplication function. Per-CpG methylation calls were extracted using bismark2bedGraph and coverage2cytosine to generate bedGraph and coverage files.
Differentially methylated region (DMR) analysis was performed using the methylKit package (v1.30.0, Bioconductor, RRID: SCR_005177), scanning non-overlapping 1000 bp windows across the genome with q-value < 0.01 and |methylation difference| ≥ 20% as thresholds.
DMRs were annotated using the annotatePeakInBatch function from the ChIPpeakAnno package (v3.38, Bioconductor, RRID: SCR_012828) with Gencode vM35 primary assembly and ENCODE Registry of cCREs (v3, 2021) as reference.
Assembly: GRCm39
Supplementary files format and content: Per-sample Bismark coverage files (bismark.cov.gz): tab-delimited, genome-wide CpG methylation values including chromosome, position, methylation percentage, count methylated, and count unmethylated.
Supplementary files format and content: Per-sample bedGraph files (bedGraph.gz): UCSC bedGraph format containing CpG methylation percentages across the genome, suitable for visualization in genome browsers.

source_name: liver metastatic tumor

extract_protocol:
PD-1+CD8+ tumor-infiltrating lymphocytes (TILs) were isolated from liver metastatic tumors by enzymatic digestion and density gradient centrifugation. CD45+ cells were enriched by MACS separation, and PD-1+CD8+ TILs were sorted by flow cytometry using anti-CD45, anti-CD3ε, anti-CD8α, and anti-PD-1 antibodies on a BD FACSAria III cell sorter (BD Biosciences, RRID: SCR_016695). Genomic DNA was extracted from sorted cells using the QIAamp DNA Blood Mini Kit (Qiagen, Cat#51106).
WGBS libraries were prepared using the post-bisulfite adaptor tagging (PBAT) protocol. Library yields were quantified using the Library Quantification Kit (Takara Bio Inc.) and amplified using PrimeStar Max DNA polymerase (Takara Bio, Cat#R045A).

value: liver metastatic tumor


title: hnscc_31.ROI_003.Immune.non_budding

description:
Library name: DSP-1001660021755-B-E06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Vav1CreTet2KO PD-1+CD8+ TILs, biol rep 3

description:
Library name: KO55_CD8
PBAT WGBS library


title: Akteur-8_S5_sRNA non inoculated rep2


title: hnscc_31.ROI_002.Tumor.budding

description:
Library name: DSP-1001660021755-B-E05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_31.ROI_003.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-E07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Vav1CreTet2KO PD-1+CD8+ TILs, biol rep 1

description:
Library name: KO45_CD8
PBAT WGBS library


title: Akteur-8_S5_sRNA non inoculated rep3


title: hnscc_31.ROI_001.Tumor.budding

description:
Library name: DSP-1001660021755-B-E03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Akteur-3_S14_sRNA WDV infected rep4


title: Akteur-8_S5_sRNA non inoculated rep4


title: Akteur-3_S14_sRNA WDV infected rep3


title: Tet2fl/fl PD-1+CD8+ TILs, biol rep 2

description:
Library name: WT49_CD8
PBAT WGBS library


title: Akteur-3_S14_sRNA WDV infected rep1


title: Tet2fl/fl PD-1+CD8+ TILs, biol rep 1

description:
Library name: WT25_CD8
PBAT WGBS library


title: Akteur-3_S14_sRNA WDV infected rep2


title: Tet2fl/fl PD-1+CD8+ TILs, biol rep 3

description:
Library name: WT50_CD8
PBAT WGBS library


title: Akteur-2_S12_sRNA WDV infected rep3


title: Akteur-2_S12_sRNA WDV infected rep2


title: Akteur-2_S12_sRNA WDV infected rep4


title: ovEn_3

city: shenyang

first: Wei

last: Wang

address: No. 155 Nanjing North Street

country: China

institute: China Medical University Affiliated First Hospital

description:
Library name: sample 6
ovEn_3.fpkm

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
RNAseq reads were aligned to the hg38 genome using STAR.
Read counts for individual gene of each sample were produced with HTSeq-count
Assembly: En1
Supplementary files format and content: txt(gene expression of all sample)

organism: Rattus norvegicus

extract_protocol:
RNA was extracted using Trizol following the manufacturer's protocol.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Pheochromocytoma cells

value: WT

value: Glucose-free DMEM, 1% O2 + 5% CO2 + 94% N2, 6 h; followed by high-glucose DMEM + 10% FBS + 1% P/S, 24 h.


title: hnscc_31.ROI_002.Stroma.budding

description:
Library name: DSP-1001660021755-B-E04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Akteur-2_S12_sRNA WDV infected rep1


title: Akteur-8_S5_sRNA non inoculated rep1


title: hnscc_31.ROI_001.Stroma.budding

description:
Library name: DSP-1001660021755-B-E02
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_27.ROI_010.Tumor.buds

description:
Library name: DSP-1001660021755-B-E01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_27.ROI_010.Stroma.buds

description:
Library name: DSP-1001660021755-B-D12
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Akteur-1_S2_sRNA WDV infected rep4


title: Control_3

description:
Library name: sample 3
Control_3.fpkm


title: ovEn_2

description:
Library name: sample 5
ovEn_2.fpkm


title: Akteur-1_S2_sRNA WDV infected rep1


title: ovEn_1

description:
Library name: sample 4
ovEn_1.fpkm


title: Akteur-1_S2_sRNA WDV infected rep3


title: Akteur-1_S2_sRNA WDV infected rep2


title: hnscc_27.ROI_009.Tumor.buds

description:
Library name: DSP-1001660021755-B-D11
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_27.ROI_009.Stroma.buds

description:
Library name: DSP-1001660021755-B-D10
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Akteur-10_S7_sRNA non inoculated rep4


title: hnscc_27.ROI_004.Tumor.budding

description:
Library name: DSP-1001660021755-B-D09
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Akteur-10_S7_sRNA non inoculated rep3


title: Akteur-10_S7_sRNA non inoculated rep2


title: Control_1

description:
Library name: sample 1
Control_1.fpkm


title: OZ60PBMC

type: genomic

city: La Jolla

first: Michael

last: Corley

address: 9575 Gilman Drive

department: Department of Medicine, Division of Geriatrics, Gerontology and Palliative Care The Sam and Rose Stein Institute for Research on Aging and Center for Healthy Aging

institute: University of California San Diego

description:
DNABlood
OZ60
208126150034_R06C01

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC V2.0 BeadChip (Illumina) protocol.

scan_protocol: Illumina Infinium HumanMethylationEPIC protocol. Scanned using Illumina HiScan System.

data_processing:
IDAT Data loaded into R using Sesame and normalized using BMIQ method.
[processed value definition] Normalized average beta

label: Cy5 and Cy3

label_protocol: Illumina Infinium protocol. Cy5 and Cy3

extract_protocol: Genomic DNA was extracted using a Qiagen kit according to manufacturer's instructions. DNA was bisulfite converted using the Zymo EZ DNA methylation kit.

tag: Sex

value: Female

value: PBMC

tag: disease state

value: HIV

tag: chronological age


title: Control_2

description:
Library name: sample 2
Control_2.fpkm


title: hnscc_27.ROI_004.Stroma.budding

description:
Library name: DSP-1001660021755-B-D08
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: En1-3

description:
Library name: sample 6
En1-3_FPKM

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to rat genome assembly Rnor6 (https://ftp.ensembl.org/pub/release-104/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.104.gtf.gz.
Assembly: En1
Supplementary files format and content: txt(gene expression of all sample)

extract_protocol:
Chondrocytes were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Hyclone, UT) containing 10% fetal bovine serum (FB-1058, Biosera) and 1% penicillin-streptomycin(ST488S, Beyotime).control cells were cultured in a high-glucose DMEM medium containing 10% FBS for 24 h, while cells in the RA group were cultured in the same medium with 1 μM retinoic acid(S1653, Bimake) for 24 h.
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Control cells were cultured in a high-glucose DMEM medium containing 10% FBS for 24 h, while cells in the RA group were cultured in the same medium with 1 μM retinoic acid(S1653, Bimake) for 24 h.

value: Highglucose DMEM (Hyclone) + 10% FBS (FB1058, Biosera) + 1% penicillinstreptomycin (ST488S)  24 h


title: Akteur-10_S7_sRNA non inoculated rep1

value: Non inoculated

value: leaves


title: hnscc_27.ROI_003.Tumor.budding

description:
Library name: DSP-1001660021755-B-D07
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: OZ14PBMC

description:
DNABlood
OZ14
208125100077_R02C01


title: s40K1

city: Fukuoka

first: Takanori

last: Shinjo

state: fukuoka

address: Maidashi 3-1-1

department: Section of Periodontology

institute: Kyushu University

description: Library name: Sample 19

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: Epididymal adipose tissue

extract_protocol:
The total RNA was isolated from eWAT using TRIzol Reagent (nitrogen) and purified using PureLink Mini Prep kit (Thermo Scientific) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

value: Epididymal adipose tissue

value: 40%HFD feeding for 10 weeks


title: RNA-seq of Mus musculus: WT_D_IgG1_GC_LZ

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

description: Library name: WT_D_IgG1_GC_LZ

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl GRCm39.113 primary assembly with STAR version 2.7.11b.
Gene counts were derived from the number of uniquely aligned unambiguous fragments by Subread:featureCount version 2.0.8.
Assembly: GRCm39
Supplementary files format and content: Excel spreadsheet file includes raw counts for each Sample

source_name: spleen and draining lymph node

extract_protocol:
RNA and DNA were isolated with the AllPrep DNA/RNA kit (Qiagen Cat#80204) according to manufacturer instructions and stored at -80°C.
Library preparation was performed with 3-10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt-ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus using paired-end reads extending 150 bases.

value: spleen and draining lymph node

value: GC B cells


title: RNA-seq of Mus musculus: WT_D_IgG1_GC_DZ

description: Library name: WT_D_IgG1_GC_DZ


title: En1-2

description:
Library name: sample 5
En1-2_FPKM

growth_protocol: Chondrocytes were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Hyclone, UT) containing 10% fetal bovine serum (FB-1058, Biosera) and 1% penicillin-streptomycin(ST488S, Beyotime).control cells were cultured in a high-glucose DMEM medium containing 10% FBS for 24 h, while cells in the RA group were cultured in the same medium with 1 μM retinoic acid(S1653, Bimake) for 24 h.


title: RNA-seq of Mus musculus: WT_C_IgG1_GC_LZ

description: Library name: WT_C_IgG1_GC_LZ


title: RNA-seq of Mus musculus: WT_C_IgG1_GC_DZ

description: Library name: WT_C_IgG1_GC_DZ


title: hnscc_27.ROI_003.Stroma.budding

description:
Library name: DSP-1001660021755-B-D06
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: RNA-seq of Mus musculus: WT_A_IgG1_GC_LZ

description: Library name: WT_A_IgG1_GC_LZ


title: RNA-seq of Mus musculus: WT_A_IgG1_GC_DZ

description: Library name: WT_A_IgG1_GC_DZ


title: Control-3

description:
Library name: sample 3
Control-3_FPKM


title: hnscc_27.ROI_002.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-D05
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: hnscc_27.ROI_002.Stroma.non_budding

description:
Library name: DSP-1001660021755-B-D04
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Control-2

description:
Library name: sample 2
Control-2_FPKM


title: RNA-seq of Mus musculus: FL_D_IgG1_GC_DZ

description: Library name: FL_D_IgG1_GC_DZ


title: RNA-seq of Mus musculus: FL_D_IgG1_GC_LZ

description: Library name: FL_D_IgG1_GC_LZ


title: En1-1

description:
Library name: sample 4
En1-1_FPKM


title: hnscc_27.ROI_001.Tumor.non_budding

description:
Library name: DSP-1001660021755-B-D03
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Control-1

description:
Library name: sample 1
Control-1_FPKM


title: hnscc_30.ROI_011.Tumor.buds

description:
Library name: DSP-1001660021755-B-D01
Nanostring GeoMx DSP Whole Transcriptome Atlas profiling


title: Tet2fl/fl CD45+ TILs, TCR, biol rep 2

description:
Library name: TCR_WT_89
10x Genomics TCR V(D)J enriched library

data_processing:
Raw sequencing data were demultiplexed and mapped to the mouse reference genome (GRCm39) using Cell Ranger v8.0.1 (10x Genomics, RRID: SCR_017344) with default parameters.
For GEX libraries, gene expression count matrices were generated using the Cell Ranger count pipeline.
For TCR libraries, V(D)J contig annotations were generated using the Cell Ranger vdj pipeline. Filtered contig annotations were used for downstream TCR repertoire analysis.
Downstream analysis including quality control, clustering, dimensionality reduction, differential gene expression, trajectory inference, and TCR repertoire analysis was performed using Seurat (v5.0.1), Monocle3 (v1.3.7), AUCell (v1.26.0), and scRepertoire (v2.3.0) in R (v4.4.1).
Assembly: GRCm39
Supplementary files format and content: Per-sample Cell Ranger output: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene IDs and names), matrix.mtx.gz (UMI count matrix in Matrix Market Exchange Format).
Supplementary files format and content: Per-sample filtered_contig_annotations.csv: Cell Ranger V(D)J output containing TCR contig annotations, V(D)J gene assignments, CDR3 sequences, and clonotype information for each cell barcode.

extract_protocol:
Tumor-infiltrating leukocytes were isolated from liver metastatic tumors by enzymatic digestion with collagenase A (0.75 mg/ml) and DNase I (50 µg/ml) followed by density gradient centrifugation using Histopaque-1083. Cells were washed and resuspended in PBS supplemented with 1% BSA, stained with BV421 anti-mouse CD45.2 antibody (clone 104, BioLegend, Cat#109832) and 7-AAD viability solution (ThermoFisher Scientific, Cat#00-6993-50), and CD45+ live cells were sorted using BD FACSAria III (BD Biosciences, RRID: SCR_016695).
Sorted CD45+ live cells were processed to generate barcoded 5' gene expression (GEX) libraries and TCR V(D)J-enriched libraries using the Chromium Next GEM Single Cell 5' Kit v1.1 (10x Genomics, Cat#1000165) and GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics, Cat#1000181), targeting 10,000 cells per library, following the manufacturer's instructions (CG000208 Rev G). Library quality and concentration were assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies, Cat#5067-4626) and KAPA Library Quantification Kit (Kapa Biosystems, Cat#KK4873).

value: CD45+ tumor-infiltrating leukocytes


title: 20251218_SBI_MK

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

institute: Oklahoma Medical Research Foundation

description:
Library name: 20251218_SBI_MK
MK‑1775 (1 µM) for 40 min prior to labeling and during EdU/BrdU pulses; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.

data_processing:
Basecalling and alignment: Dorado v0.8.1 high-accuracy mode; alignments to hg38/GRCh38.
Replication tract detection and fork calling: DNAscent v4.0.3 (forkSense), minimum read length 20 kb.
Pipeline: ReplisomeTracer v1.0.2 used to orchestrate basecalling/alignment, DNAscent analyses, and output formatting.
Assembly: hg38 / GRCh38
Supplementary files format and content: Processed data include DNAscent detect BAM files and forkSense output archives. forkSense archives contain BED/TSV-style segmentations of EdU- and BrdU-labeled tracts and calls for leftward/rightward forks, initiation (origin) sites, and termination sites, along with per-read tract length summaries.

growth_protocol: HCT116 TICRR gene-trap (mClover) cell lines were maintained under standard mammalian cell culture conditions and plated in 6‑cm dishes for labeling experiments.

extract_protocol:
High–molecular weight genomic DNA was extracted from 1×10^6 cells per sample using the Monarch HMW DNA Extraction Kit for Cells and Blood (NEB #T3050S).
Sequencing libraries were prepared from 400 ng HMW genomic DNA using the Oxford Nanopore Rapid Barcoding Kit 96 V14 (SQK‑RBK114.96) per manufacturer instructions and sequenced on a PromethION flow cell (FLO‑PRO114M) using a PromethION 2 Solo device.

treatment_protocol: Where indicated, cells were treated with the WEE1 inhibitor MK‑1775 (1 µM) for 40 min prior to labeling and maintained in MK‑1775 during EdU and BrdU labeling (total MK‑1775 exposure 1 h). Cells were sequentially pulse-labeled with EdU (50 µM, 10 min) followed by BrdU (50 µM, 10 min), then chased with thymidine (250 µM, 40 min). Vehicle controls were processed identically without MK‑1775.

value: TICRR-GT[SA-mClover- ex20-22(DeltaSBI)]

tag: batch


title: RNA-seq of Mus musculus: FL_A_IgG1_GC_LZ

description: Library name: FL_A_IgG1_GC_LZ


title: RNA-seq of Mus musculus: FL_A_IgG1_GC_DZ

description: Library name: FL_A_IgG1_GC_DZ


title: Tet2fl/fl CD45+ TILs, TCR, biol rep 1

description:
Library name: TCR_WT_75
10x Genomics TCR V(D)J enriched library


title: 20251218_SBI

description:
Library name: 20251218_SBI
Vehicle control; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.

value: vehicle


title: 20251218_WT_MK

description:
Library name: 20251218_WT_MK
MK‑1775 (1 µM) for 40 min prior to labeling and during EdU/BrdU pulses; Sequential EdU (50 µM, 10 min) → BrdU (50 µM, 10 min) pulse labeling followed by thymidine chase (250 µM, 40 min); HMW genomic DNA extracted and sequenced by Oxford Nanopore WGS.

value: TICRR-GT[SA-mClover- ex20-22(WT)]