title: iPSC-RPE_H3K4me1,rep2

city: Hangzhou

first: tang

middle: dong

last: mei

address: 866 Yuhangtang Road

institute: Zhejiang University

description: Library name: sample12

data_processing:
The raw reads were trimmed using Trim Galore to remove adapters and the portion of low quality (https://github.com/FelixKrueger/TrimGalore) with default parameters. Trimmed reads were aligned to the human hg38 reference genome using Bowtie2
Duplicated reads were removed with gatk MarkDuplicates (Picard) (https:// github.com/broadinstitute/picard) and uniquely mapped nonredundant reads (MAPQ>30) were passed to MACS2 for peak calling with setting ‘macs2 callpeak -t –nomodel –keep-dup all -q 0.001’.
BigWig file were generated using bamCoverage with the RPKM normalization method.
Assembly: hg38
Supplementary files format and content: bigWig , narrowPeak
Library strategy: CUT&Tag

source_name: induced pluripotent stem cell-derived RPE

extract_protocol:
Human donor eyes, consented for research, were obtained from the Eye hospital and were approved by the Ethics Committee of Optometry Hospital affiliated to Wenzhou Medical University (2022-121-K-92-01). iPSCs were passaged onto Matrigel-coated dish in retinal differentiation medium (RDM, DMEM/F12 with 1% B27 (Gibco, 12587010), 1% N2 (Gibco, 17502048) and 1×NEAA (Gibco, 11140050). 10 mM nicotinamide (Selleck, S1899, Houston, Tx, USA), 10 ng/ml IGF1 (Sino Biological, 10598-HNAE, Beijing, China), 10 ng/ml bFGF (Sino Biological, 10014-HNAE), 1 M A-83-01 (Selleck, S7692) and 1 M IWR-1 (Selleck, S7086) were added to RDM for 0-4 days. 10 mM nicotinamide and 10 ng/ml bFGF were replaced by 100 ng/ml Activin A (Sino Biological, 10429-HNAH) and the concentration of IGF1 increased to 20 ng/ml, and A-83-01 was not added for 4-6 days. IGF1 and IWR-1 were replaced by 1 M SU5402 (Selleck, S7667) for 6-8 days. 1 M CHIR99021 (Selleck, S1263) was added to RDM for 8-14 days. From days 14, cells were maintained in RPE supporting medium (RSM, DMEM/F12 with 15% knockout serum replacement, 5% FBS, 1×NEAA and 10 mM nicotinamide) until they matured and formed pigmented monolayers. iPSC-RPE cells were passaged with EDTA (Gibco, 25200072) and were replaced on the Matrigel-coated dish and at P3 were used in this study.
Histone modifications of ARPE-19, iPSC-RPE, hRPE and iPSC were captured by CUT&Tag using hyperactive universal CUT&Tag assay kit for Illumina (Vazyme, TD903, Nanjing, China). 50,000 viable cells were collected for each library and incubated with concanavalin A-coated magnetic beads. The beads binding cells were captured by H3K4me1 (CST, 5326, Danvers, MA, USA), H3K4me3 (CST, 9751), H3K27ac (CST, 8173), H3K27me3 (CST, 9733) antibodies, then incubated with hyperactive pA/G-Transposon. The tagmented DNA was purified and PCR amplificated for sequencing.


title: iPSC-RPE_H3K27me3,rep1

status: Public on Jul 23 2026

type: SRA

country: China

description: Library name: sample15

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

value: induced pluripotent stem cell-derived RPE


title: Stereotaxic brain tumor biopsy, patient 160, Diffuse glioma

type: genomic

city: Frankfurt

first: Katharina

last: Weber

address: Heinrich-Hoffmann-Straße 7

department: Institute of Neurology

country: Germany

institute: University Hospital Frankfurt

hyb_protocol: Bisulfite-converted DNA was hybridized to Illumina Infinium MethylationEPIC BeadChip (v1) following the manufacturer's standard protocol.

scan_protocol: EPIC array BeadChips were scanned using an iScan system (Illumina, San Diego, California, USA) and raw intensity data (IDAT files) were obtained.

data_processing: IDAT files were uploaded to molecularpathology.org (Heidelberg brain tumor classifier v11b4) to obtain calibrated scores for DNA methylation classes and subclasses, copy number variation profiles and MGMT promoter methylation status. Additional classification was performed using the Bethesda brain tumor classifier (v2) and EpiDiP. IDAT files were processed using R packages RnBeads for quality control and normalization (dasen method from wateRmelon package), and MethylCIBERSORT for reference-based tumor deconvolution. Genome build: hg19.

label: Cy3, Cy5

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_160

label_protocol: DNA was further processed and hybridized to the Illumina Infinium MethylationEPIC BeadChip (v1) following protocols provided by the manufacturer.

growth_protocol: Not applicable (FFPE tissue from stereotaxic brain tumor biopsies)

extract_protocol: Selected FFPE tissue samples were transferred into Eppendorf tubes using biopsy punches.

treatment_protocol: Not applicable (tissue samples)

value: brain

tag: disease state

value: Diffuse glioma

tag: age

tag: Sex

value: male

tag: sample type

value: FFPE stereotaxic biopsy

tag: dna concentration (ng/ul)


title: EVs-EPM1-dCO_2

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped to the human genome (hg38) using STAR (Dobin et al., 2013, PMID: 23104886). Expression of genes in TPM was calculated with RSEM (Li et al., 2011, PMID: 21816040).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

source_name: Neural progenitor cells

growth_protocol: NPCs were cultured in NPM medium according to Boyer et al., 2012. DMEM/F12 , 1× N2 supplement, 1× B27 supplement, Laminin (1 µg/ml), 1x Antibiotic mixture Anti-Anti

extract_protocol:
Trizol and RNA clean and concentrator kit (Zymo research)
Smarter ultra low input-v4 (Clontech 634888) and Microplex-v2 (Diagenode C05010012)

treatment_protocol: Acute treatment (12 hours) with dEVs or vEVs isolated from conditioned media of dorsally or ventrally patterned human spheroids originated from control iPSCs or EPM1 patients-iPSCs. Experiments were performed in biological triplicates.

tag: cell type

value: iPScs-derived neural progenitor cells

tag: treatment

value: NPCs acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of dorsally patterned human spheroids originated from EPM1 patients-iPSCs cells.


title: PolII ChIP 3xFP-NLS EtOH rep3

city: Zurich

first: Shin

last: Ohsawa

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH Zurich

description:
Library name: IP_3225_EtOH_3
Anti-Pol II (8WG16) IP

data_processing:
Raw paired-end sequencing reads were processed using fastp (version 0.23.4) for automated adapter trimming and quality filtering (parameters: -q 30 --length_required 20 --detect_adapter_for_pe).
Cleaned reads were aligned to the standard Saccharomyces cerevisiae reference genome (R64-1-1) using STAR (version 2.7.11b) in basic two-pass mode (parameters: --twopassMode Basic --outFilterMismatchNmax 3 --chimSegmentMin 2 --alignIntronMax 299999 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate).
Gene-level read quantification was performed using featureCounts from the Rsubread package (version 2.16.1). To accurately quantify transcripts from repetitive regions, multi-mapping reads (up to 10 alignments per read) and reads overlapping multiple features were retained and fractionally assigned (parameters: isPairedEnd = TRUE, countReadPairs = TRUE, countMultiMappingReads = TRUE, fraction = TRUE, allowMultiOverlap = TRUE).
Assembly: R64-1-1 (sacCer3)
Supplementary files format and content: raw_counts_Scerevisiae.csv is a comma-separated values (CSV) matrix containing raw read counts for all endogenous S. cerevisiae genes and exogenous constructs across all yeast RNA-seq samples, quantified via featureCounts.
Raw paired-end sequencing reads were trimmed and quality-filtered using fastp (version 0.23.4; parameters: -q 30 --length_required 20).
Cleaned reads were aligned to the human reference genome (GRCh38/hg38) using STAR (version 2.7.11b) in basic two-pass mode. To capture transcription from highly repetitive sequences and transposable elements (TEs), multi-mapping was permitted up to 100 locations per read (parameters: --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100).
Aligned BAM files were name-sorted using multi-threaded samtools (version 1.19.2; samtools sort -n).
Simultaneous quantification of protein-coding genes (GENCODE v44 annotation) and transposable elements (RepeatMasker GTF) was executed using TEcount from the TEtranscripts package (version 2.2.4; in multi-mode: --mode multi).
Assembly: GRCh38 (hg38)
Supplementary files format and content: *.cntTable files (e.g., day2_r1.cntTable) are tab-delimited text tables containing raw read counts for both standard GENCODE protein-coding genes and repetitive transposable elements (TEs), generated via TEcount.
Raw paired-end sequencing reads were processed using fastp (version 0.23.4) for automated adapter trimming and quality filtering (-q 30 --length_required 20 --detect_adapter_for_pe).
leaned paired-end reads were aligned to the Saccharomyces cerevisiae reference genome (R64-1-1/sacCer3) using bowtie2 (version 2.5.2).
Alignments were converted, sorted by coordinate, and indexed using samtools (version 1.19.2). (Note: A single outlier replicate, 3xFP-NES mock replicate 2, exhibiting extreme technical variance on PCA was systematically excluded from downstream analytical quantification).
Genome-wide signal coverage tracks (BigWig format) were generated using bamCoverage from the deepTools suite (version 3.5.6) normalized to Counts Per Million (CPM) (parameters: --normalizeUsing CPM --centerReads --binSize 10).
Assembly: R64-1-1 (sacCer3)
Supplementary files format and content: *_CPM.bw files (e.g., IP_3225_EST_1_CPM.bw) are binary BigWig format tracks representing genome-wide ChIP or input control read coverage normalized to Counts Per Million (CPM), generated via deepTools bamCoverage.

organism: Saccharomyces cerevisiae

source_name: not applicable

growth_protocol:
Yeast cells (Saccharomyces cerevisiae) were cultured in standard growth media to logarithmic phase. For G1 arrest excessive cell expansion experiments, the temperature-sensitive cdc28-13 mutant strain was cultured at the restrictive temperature of 37°C.
Human retinal pigment epithelial (RPE1) cells were cultured under standard growth conditions as previously described (Manohar et al., 2023).
Yeast cells (Saccharomyces cerevisiae) were cultured in standard growth media to logarithmic phase.

extract_protocol:
Total RNA was extracted using a hot TES-phenol method followed by column-based cleanup. Cell pellets (mixed with Candida albicans reference pellets as a spike-in control) were resuspended in TES buffer (10 mM Tris pH 7.5, 10 mM EDTA pH 8.0, 0.5% SDS) and lysed with saturated phenol at 65°C under continuous agitation. After sequential re-extraction with phenol and chloroform, RNA was precipitated using 3 M sodium acetate (pH 5.2) and cold isopropanol at -20°C. Resuspended RNA was treated with DNase I in Buffer RDD (Qiagen, cat. no. 79254) at room temperature to eliminate genomic DNA. RNA was subsequently purified, concentrated, and eluted in RNase-free water using the RNeasy MinElute Cleanup Kit (Qiagen, cat. no. 74204). Quality and concentration were assessed using a Qubit Fluorometer (Thermo Fisher Scientific).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The final cDNA library was completed through end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, cat. no. 74104). Cell pellets were lysed in 400 µL Buffer RLT, vortexed, and homogenized by centrifugation through a QIAshredder spin column (Qiagen, cat. no. 79656). The lysate was mixed with ethanol, applied to an RNeasy spin column, and subjected to on-column DNase I digestion using the RNase-Free DNase Set (Qiagen, cat. no. 79254) to eliminate genomic DNA contamination. Following sequential washes, purified total RNA was eluted in RNase-free water and quantified via Qubit Fluorometer.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The final cDNA library was completed through end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
Harvested cell pellets (250–350 mg) were resuspended in FA lysis buffer (50 mM HEPES-KOH pH 8.0, 150 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate) supplemented with 1 mM PMSF and protease inhibitor cocktail (Thermo Fisher Scientific, cat. no. 78429), and disrupted using ceramic beads in a FastPrep system (MP Biomedicals). Chromatin was sheared by Bioruptor (Diagenode) and clarified by centrifugation. Sheared chromatin was immunoprecipitated overnight at 4°C using Protein G Dynabeads (Thermo Fisher Scientific, cat. no. 10003D) pre-coated with Anti-RNA Polymerase II Antibody (Merck, clone 8WG16). Following sequential washes (FA lysis buffer, high-salt FA buffer, ChIP wash buffer, and TE buffer), chromatin was eluted in 1% SDS buffer at 65°C. Cross-links for both ChIP and input samples were reversed at 65°C overnight, followed by RNase A (Merck, cat. no. 10109169001) and Proteinase K (AppliChem, cat. no. A3830,0100) digestion. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo Research, cat. no. D5201).
ChIP DNA and input control DNA libraries were prepared using the NEBNext Ultra II Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions. Library quality and fragment size distribution were verified using an Agilent TapeStation system with D1000 ScreenTapes (TapeStation Analysis Software v5.2).

treatment_protocol:
For compartment-specific protein accumulation experiments, cells expressing 3xFP-NLS, 3xFP-NES, or control constructs were treated with estradiol (induced condition) or ethanol (mock control) for 6 hours. For G1 arrest time-course experiments (cdc28-13 strain), cells were incubated at 37°C for 2, 4, or 6 hours with estradiol or ethanol mock treatment.
Cells were treated with the CDK4/6 inhibitor palbociclib to induce G1 arrest and excessive cell volume expansion. Cells were harvested at Day 2 (early arrest/reference size, using 1.5 × 10^6 cells) and Day 7 (extended arrest/enlarged size, using 0.5 × 10^6 cells) of palbociclib treatment.
Cells expressing inducible 3xFP-NLS, 3xFP-NES, or control constructs were treated with estradiol (induced) or ethanol (mock control) for 6 hours. Cells were subsequently cross-linked with 1% formaldehyde for 15 minutes at 30°C and quenched with 0.125 M glycine.

value: not applicable

tag: cell line

value: whole cell

tag: genotype

value: 6h ethanol mock

tag: batch


title: EVs-EPM1-dCO_1


title: Stereotaxic brain tumor biopsy, patient 159, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_159

value: Glioblastoma


title: EE_4h_Uterus-21

type: RNA

city: Wuppertal

first: Mira

last: Pavkovic

address: Aprather Weg 18a

institute: Bayer AG

description: OECD-compliant uterotrophic assay using ethinyl estradiol (EE) in juvenile female rats

scan_protocol: fluorescent images of the GeneChips were captured with the Affymetrix GeneChip Scanner 3000

data_processing:
Using Affymetrix MicroarraySuite (MAS)5.0 the raw data image files (dat) were converted in to cel-files in which the scanned data were summarized as one intensity value per unit.
RAE230A.CDF

label: biotin

organism: Rattus norvegicus

source_name: uterus

label_protocol: 5 µg total RNA was processed for Affymetrix RAE230A GenechipsR hybridization according to the manufacturer’s instructions

growth_protocol: OECD uterotrophic assay in immature rats

extract_protocol: total RNA isolation with the RNAeasy Mini kit (Qiagen; Hilden, Germany) according to the manufacturer’s instructions

tag: gender

value: female

tag: development stage

value: immature


title: EVs-EPM1-vCO_3

value: NPCs acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of ventrally patterned human spheroids originated from EPM1 patients-iPSCs cells.


title: PolII ChIP 3xFP-NLS EtOH rep2

description:
Library name: IP_3225_EtOH_2
Anti-Pol II (8WG16) IP


title: Stereotaxic brain tumor biopsy, patient 158, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_158


title: EE_4h_Uterus-20

hyb_protocol: processed for Affymetrix RAE230A GenechipsR hybridization according to the manufacturer’s instructions


title: EE_4h_Uterus-19


title: PolII ChIP 3xFP-NLS EtOH rep1

description:
Library name: IP_3225_EtOH_1
Anti-Pol II (8WG16) IP


title: EVs-EPM1-vCO_2


title: Stereotaxic brain tumor biopsy, patient 157, Circumscribed glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_157

value: Circumscribed glioma


title: PolII ChIP 3xFP-NLS EST rep3

description:
Library name: IP_3225_EST_3
Anti-Pol II (8WG16) IP

value: 6h estradiol


title: EE_2h_Uterus-12


title: EVs-EPM1-vCO_1


title: EE_2h_Uterus-10


title: EE_2h_Uterus-9


title: Stereotaxic brain tumor biopsy, patient 156, Circumscribed glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_156


title: EVs-vCO_3

value: NPCs acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of ventrally patterned human spheroids originated from control-iPSCs cells.


title: PolII ChIP 3xFP-NLS EST rep2

description:
Library name: IP_3225_EST_2
Anti-Pol II (8WG16) IP


title: Stereotaxic brain tumor biopsy, patient 155, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_155


title: EVs-vCO_2


title: EE_2h_Uterus-8


title: PolII ChIP 3xFP-NLS EST rep1

description:
Library name: IP_3225_EST_1
Anti-Pol II (8WG16) IP


title: Stereotaxic brain tumor biopsy, patient 154, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_154


title: EVs-vCO_1


title: Stereotaxic brain tumor biopsy, patient 153, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_153


title: D37 6h EtOH rep3

description:
Library name: D37_6h_EtOH_3
G1 arrest time-course

value: cdc28-13 +3xFP-NES

value: 37C 6h mock


title: D37 6h EtOH rep2

description:
Library name: D37_6h_EtOH_2
G1 arrest time-course


title: Control_72h_Uterus-78


title: EVs-dCO_3

value: NPCs acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of dorsally patterned human spheroids originated from control-iPSCs cells.


title: EE_2h_Uterus-7


title: Stereotaxic brain tumor biopsy, patient 152, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_152

value: brain


title: Control_72h_Uterus-77


title: EVs-dCO_2


title: D37 6h EtOH rep1

description:
Library name: D37_6h_EtOH_1
G1 arrest time-course


title: Stereotaxic brain tumor biopsy, patient 151, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_151

value: male

value: FFPE stereotaxic biopsy


title: D37 6h EST rep3

description:
Library name: D37_6h_EST_3
G1 arrest time-course 3xFP system induced

value: 37C 6h estradiol


title: EVs-dCO_1

value: iPScs-derived neural progenitor cells


title: Control_72h_Uterus-76


title: Stereotaxic brain tumor biopsy, patient 150, Circumscribed glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_150


title: D37 6h EST rep2

description:
Library name: D37_6h_EST_2
G1 arrest time-course 3xFP system induced

value: not applicable

value: whole cell


title: Stereotaxic brain tumor biopsy, patient 149, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_149

value: Glioblastoma


title: D37 6h EST rep1

description:
Library name: D37_6h_EST_1
G1 arrest time-course 3xFP system induced


title: Crt_2

value: NPCs NOT treated


title: Control_72h_Uterus-75

value: female

value: immature


title: Crt_3


title: Stereotaxic brain tumor biopsy, patient 148, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_148


title: D37 4h EtOH rep3

description:
Library name: D37_4h_EtOH_3
G1 arrest time-course

value: 37C 4h mock


title: Control_72h_Uterus-73


title: Stereotaxic brain tumor biopsy, patient 147, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_147

value: Diffuse glioma


title: Ctr_1


title: Control_48h_Uterus-66


title: D37 4h EtOH rep2

description:
Library name: D37_4h_EtOH_2
G1 arrest time-course


title: Control_48h_Uterus-65


title: Jejunum,LNnT,5

city: Shanghai

first: Ru

last: Chen

address: 1665 Kong Jiang Road

department: Department of Pediatric Surgery

institute: Shanghai Institute for Pediatric Research

description: Library name: LNnT5

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: jejunum

value: LNnT


title: Stereotaxic brain tumor biopsy, patient 146, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_146


title: D37 4h EtOH rep1

description:
Library name: D37_4h_EtOH_1
G1 arrest time-course

value: cdc28-13 +3xFP-NES


title: Control_48h_Uterus-63


title: Jejunum,LNnT,4

description: Library name: LNnT4


title: Stereotaxic brain tumor biopsy, patient 145, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_145


title: D37 4h EST rep3

description:
Library name: D37_4h_EST_3
G1 arrest time-course 3xFP system induced

source_name: not applicable

value: 37C 4h estradiol


title: Jejunum,LNnT,3

description: Library name: LNnT3


title: Control_48h_Uterus-62


title: Stereotaxic brain tumor biopsy, patient 144, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_144

value: brain


title: D37 4h EST rep2

description:
Library name: D37_4h_EST_2
G1 arrest time-course 3xFP system induced


title: Jejunum,LNnT,2

description: Library name: LNnT2


title: Stereotaxic brain tumor biopsy, patient 143, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_143


title: Control_48h_Uterus-61

description: OECD-compliant uterotrophic assay using ethinyl estradiol (EE) in juvenile female rats

source_name: uterus


title: D37 4h EST rep1

description:
Library name: D37_4h_EST_1
G1 arrest time-course 3xFP system induced


title: Control_28h_Uterus-53


title: Jejunum,LNnT,1

description: Library name: LNnT1


title: Stereotaxic brain tumor biopsy, patient 142, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_142


title: Stereotaxic brain tumor biopsy, patient 141, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_141


title: D37 2h EtOH rep3

description:
Library name: D37_2h_EtOH_3
G1 arrest time-course

value: 37C 2h mock


title: Control_28h_Uterus-52


title: Jejunum,FL,5

description: Library name: FL5

value: FL


title: D37 2h EtOH rep2

description:
Library name: D37_2h_EtOH_2
G1 arrest time-course


title: Jejunum,FL,4

description: Library name: FL4


title: Control_28h_Uterus-51


title: Stereotaxic brain tumor biopsy, patient 140, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_140

value: male

value: FFPE stereotaxic biopsy


title: Jejunum,FL,3

description: Library name: FL3


title: D37 2h EtOH rep1

description:
Library name: D37_2h_EtOH_1
G1 arrest time-course

value: not applicable


title: Stereotaxic brain tumor biopsy, patient 139, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_139


title: C3xFP EtOH rep3

description:
Library name: C448_EtOH_3
3xFP system mock

value: whole cell

value: 6h ethanol mock


title: Control_28h_Uterus-49


title: Control_28h_Uterus-50


title: Jejunum,FL,2

description: Library name: FL2


title: Stereotaxic brain tumor biopsy, patient 138, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_138


title: C3xFP EtOH rep2

description:
Library name: C448_EtOH_2
3xFP system mock


title: Jejunum,FL,1

description: Library name: FL1


title: Stereotaxic brain tumor biopsy, patient 137, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_137

value: Glioblastoma


title: C3xFP EtOH rep1

description:
Library name: C448_EtOH_1
3xFP system mock


title: Control_24h_Uterus-42

value: female


title: Control_24h_Uterus-41

value: immature


title: Jejunum,HMOs,5

description: Library name: HMOs5

value: HMOs


title: Stereotaxic brain tumor biopsy, patient 136, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_136

value: Diffuse glioma


title: C3xFP EST rep3

description:
Library name: C448_EST_3
3xFP system induced

value: 6h estradiol


title: Jejunum,HMOs,4

description: Library name: HMOs4

value: jejunum


title: Control_24h_Uterus-39


title: Stereotaxic brain tumor biopsy, patient 135, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_135


title: C3xFP EST rep2

description:
Library name: C448_EST_2
3xFP system induced


title: Control_24h_Uterus-38


title: Jejunum,HMOs,3

description: Library name: HMOs3


title: Stereotaxic brain tumor biopsy, patient 134, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_134


title: C3xFP EST rep1

description:
Library name: C448_EST_1
3xFP system induced


title: Jejunum,HMOs,2

description: Library name: HMOs2


title: Cempty EtOH rep3

description:
Library name: C3229_EtOH_3
3xFP system mock

value: empty


title: Stereotaxic brain tumor biopsy, patient 133, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_133


title: Control_24h_Uterus-37


title: Jejunum,HMOs,1

description: Library name: HMOs1


title: Control_8h_Uterus-30


title: Stereotaxic brain tumor biopsy, patient 132, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_132


title: Jejunum,Weaned,5

description: Library name: Weaned5

value: Weaned


title: Cempty EtOH rep2

description:
Library name: C3229_EtOH_2
3xFP system mock


title: Cempty EtOH rep1

description:
Library name: C3229_EtOH_1
3xFP system mock


title: Stereotaxic brain tumor biopsy, patient 131, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_131

value: brain


title: Jejunum,Weaned,4

description: Library name: Weaned4


title: Control_8h_Uterus-29


title: Control_8h_Uterus-28


title: Stereotaxic brain tumor biopsy, patient 130, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_130


title: Control_8h_Uterus-27


title: Jejunum,Weaned,3

description: Library name: Weaned3


title: Cempty EST rep3

description:
Library name: C3229_EST_3
3xFP system induced

source_name: not applicable


title: Stereotaxic brain tumor biopsy, patient 129, unclassified brain lesion

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_129

value: unclassified brain lesion


title: Cempty EST rep2

description:
Library name: C3229_EST_2
3xFP system induced


title: Jejunum,Weaned,2

description: Library name: Weaned2


title: Stereotaxic brain tumor biopsy, patient 128, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_128


title: Control_8h_Uterus-25

source_name: uterus


title: Jejunum,Weaned,1

description: Library name: Weaned1


title: Cempty EST rep1

description:
Library name: C3229_EST_1
3xFP system induced


title: Stereotaxic brain tumor biopsy, patient 127, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_127


title: C3xFP-NLS EtOH rep3

description:
Library name: C3225_EtOH_3
3xFP system mock


title: Control_4h_Uterus-18

description: OECD-compliant uterotrophic assay using ethinyl estradiol (EE) in juvenile female rats


title: Jejunum,Control,5

description: Library name: Sucking5

value: Control


title: Stereotaxic brain tumor biopsy, patient 126, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_126

value: male


title: Jejunum,Control,4

description: Library name: Sucking4


title: C3xFP-NLS EtOH rep2

description:
Library name: C3225_EtOH_2
3xFP system mock


title: Control_4h_Uterus-17


title: Stereotaxic brain tumor biopsy, patient 125, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_125

value: FFPE stereotaxic biopsy


title: C3xFP-NLS EtOH rep1

description:
Library name: C3225_EtOH_1
3xFP system mock

value: not applicable


title: Jejunum,Control,3

description: Library name: Sucking3


title: Control_4h_Uterus-16


title: C3xFP-NLS EST rep3

description:
Library name: C3225_EST_3
3xFP system induced

value: whole cell


title: Stereotaxic brain tumor biopsy, patient 124, Pineal tumor

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_124

value: Pineal tumor


title: Control_4h_Uterus-14


title: Control_4h_Uterus-15


title: Jejunum,Control,2

description: Library name: Sucking2


title: Stereotaxic brain tumor biopsy, patient 123, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_123

value: Glioblastoma


title: C3xFP-NLS EST rep2

description:
Library name: C3225_EST_2
3xFP system induced


title: Control_2h_Uterus-6

value: female


title: Stereotaxic brain tumor biopsy, patient 122, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_122


title: Jejunum,Control,1

description: Library name: Sucking1


title: C3xFP-NLS EST rep1

description:
Library name: C3225_EST_1
3xFP system induced


title: BR_L_8_F_R3

city: Bozeman

first: Jennifer

last: Lachowiec

state: MT

address: 119 Plant Biosciences Building

country: USA

institute: Montana State University

description:
Library name: P16-R3-F
Column name in NormalizedCounts: BR_L_8_F_R3

data_processing:
Read quality was checked with FASTQC and MULTIQC software with an average phred score of 36 (Andrews, 2010). RNA sequence trimming, mapping, and read counting was performed with Trimmomatic v.0.36, STAR, and the Rsubread package v.1.5.2 with function featureCounts, respectively using default settings (Bolger et al., 2014; Dobin et al., 2013; Liao et al., 2014). Reads were aligned using the Triticum aestivum cv. Chinese Spring IWGSC RefSeq v2.1 genome assembly (Zhu et al., 2021). Genes with fewer than 10 total reads across all 123 remaining samples were removed were considered non-expressed. Differential gene expression analysis was performed via DESeq2 (Love et al., 2014). Two samples from different treatment groups were removed from analysis as they clustered far from the other biological replicates based on visual assessment of PCA. DESeq2 was additionally used to normalize read counts by length and read depth for data visualization with pheatmap and ggplot2 (Kolde, 2010; Wickham, 2016).
Assembly: Reads were aligned using the Triticum aestivum cv. Chinese Spring IWGSC RefSeq v2.1 genome assembly (Zhu et al., 2021) and STAR R package using default settings (Dobin et al., 2013)
Supplementary files format and content: NormalizedCounts.csv, inlcudes normalized count by length and read depth for each sample

organism: Triticum aestivum

source_name: Floret

growth_protocol: Triticum aestivum  cultivar ‘Vida’ (PI 642366) seeds were germinated in petri plates in a total volume of 0.4 mL water per seed for 48 hours in in the dark. The seed were then planted approximately 2.5 cm deep in untreated Sunshine Mix #1 soil (Sun Gro Horticulture Distribution Inc.), with five seeds per pot. Pots were placed in growth chambers with a 16-hour photoperiod with fluorescent and LED bulbs at 27,000 Lux light intensity, kept at 22°C. Plants were watered as needed and fertilized once a week with a 0.3% solution of 20-20-20 Professional Peters fertilizer. Pot placement followed a randomized complete block design.

extract_protocol:
For RNAseq, 64 plants were grown, with four biological replicates per seed treatment, temperature, and time of sampling combinations. Prior to and at 8, 16, and 24 hours after heat exposure began, the unemerged heads were collected. The unemerged wheat heads were removed from the leaf sheath and dissected into rachis and floret tissues, flash frozen,  and stored at -70°C.  Tissue was ground with 3 mm sterilized glass beads in a bead beater, RNA extraction was performed with the RNeasy Plant Mini Kit (Qiagen, Cat #74903) using Beta-mercaptoethanol, and samples were treated with DNase I (Turbo DNA-free Kit, Invitrogen AM1907). Quality of the samples was confirmed via Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent, 5067-1511). Five total samples were removed for poor or low RNA quality, leaving a minimum of three biological replications per treatment combination.
RNA-seq libraries were prepared using poly(A)-selected mRNA, and RNA-sequencing was performed by Genewiz.

treatment_protocol: Triticum aestivum cultivar ‘Vida’ (PI 642366) (Lanning et al., 2006) seeds were treated with 1 µM dimethyl sulfoxide (DMSO) control or 1 µM 2,4-epibrassinolide (EBR) during germination in petri plates. At the tetrad stage of growth on the Waddington 7.5 scale (booting), half of the pots from each treatment were moved to a 29° C continuous heat stress. The temperature chosen is the average high temperature in major wheat growing regions in Montana during the typical growing season and was previously determined to induce the canonical heat stress (Kothari et al., 2025)

value: Floret

value: Vida

value: 2,4 EBR

tag: temperature

tag: time

tag: replication


title: Stereotaxic brain tumor biopsy, patient 121, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_121

value: Diffuse glioma


title: Control_2h_Uterus-5

value: immature


title: B3xFP-NLS EtOH rep3

description:
Library name: B3225_EtOH_3
3xFP system mock

value: 6h ethanol mock


title: BR_L_8_F_R2

description:
Library name: P16-R2-F
Column name in NormalizedCounts: BR_L_8_F_R2


title: Control_2h_Uterus-4


title: Stereotaxic brain tumor biopsy, patient 120, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_120


title: B3xFP-NLS EtOH rep2

description:
Library name: B3225_EtOH_2
3xFP system mock


title: BR_L_8_F_R1

description:
Library name: P16-R1-F
Column name in NormalizedCounts: BR_L_8_F_R1


title: Stereotaxic brain tumor biopsy, patient 119, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_119


title: DM_L_8_F_R4

description:
Library name: P15-R4-F
Column name in NormalizedCounts: DM_L_8_F_R4

value: DMSO Control


title: B3xFP-NLS EtOH rep1

description:
Library name: B3225_EtOH_1
3xFP system mock


title: WT_H3K27ac

city: Houston

first: Jiexi

last: Li

state: TX

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

description: Library name: Sample 8

data_processing:
The NextSeq RTA (version 2.4.11.0) was used for base calling. Bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files.
Fastq files were aligned to the mouse reference genome (mm9) using Bowtie2 (version 2.5.2)
SAMtools (version 1.18) was used to convert .sam file to .bam file
Deeptools (version 3.5.2) was used to generate .bigwig files
SEACR (version 1.3) was used to call peaks
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: OT-1 CD8+ T cells

growth_protocol: OT-1 CD8+ T cells were cultured in complete T cell culture medium with mouse recombinant IL2.

extract_protocol:
nuclei isolated from ~500,000 mouse OT-1 CD8+ T cells were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories) and permeabilized using wash buffer containing 0.02% digitonin (Promega).  Bead-bound nuclei were incubated with rabbit IgG (Millipore), H3K4me1, H3K4me3, H3K27ac (all from Abcam), H3K4me3 (EpiCypher), and H3K27me3 (Diagenode) antibodies overnight at 4°C. The next day, targeted chromatin digestion was achieved by pAG-MNase (EpiCypher) binding and incubation with CaCl2 at 4°C, followed by CUT&RUN DNA purification using MinElute columns (Qiagen).
Libraries from CUT&RUN DNA were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's instructions.

value: OT-1 CD8+ T cells

value: CD8+ T cells

value: WT


title: Control_2h_Uterus-3


title: Stereotaxic brain tumor biopsy, patient 118, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_118

value: brain

value: male


title: Control_2h_Uterus-2


title: B3xFP-NLS EST rep3

description:
Library name: B3225_EST_3
3xFP system induced

value: not applicable

value: 6h estradiol


title: DM_L_8_F_R3

description:
Library name: P15-R3-F
Column name in NormalizedCounts: DM_L_8_F_R3


title: Stereotaxic brain tumor biopsy, patient 117, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_117

value: FFPE stereotaxic biopsy


title: B3xFP-NLS EST rep2

description:
Library name: B3225_EST_2
3xFP system induced

source_name: not applicable

value: whole cell


title: WT_H3K4me3

description: Library name: Sample 7


title: DM_L_8_F_R2

description:
Library name: P15-R2-F
Column name in NormalizedCounts: DM_L_8_F_R2


title: WT_H3K4me2

description: Library name: Sample 6


title: Stereotaxic brain tumor biopsy, patient 116, Circumscribed glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_116

value: Circumscribed glioma

value: female


title: B3xFP-NLS EST rep1

description:
Library name: B3225_EST_1
3xFP system induced


title: WT_H3K4me1

description: Library name: Sample 5


title: DM_L_8_F_R1

description:
Library name: P15-R1-F
Column name in NormalizedCounts: DM_L_8_F_R1

value: Floret

value: Vida


title: Stereotaxic brain tumor biopsy, patient 115, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_115

value: Diffuse glioma


title: B1xFP-NLS EtOH rep3

description:
Library name: B1684_EtOH_3
3xFP system mock


title: DM_L_16_F_R4

description:
Library name: P14-R4-F
Column name in NormalizedCounts: DM_L_16_F_R4


title: KD_H3K27ac

description: Library name: Sample 4

value: KD


title: Stereotaxic brain tumor biopsy, patient 114, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_114

value: Glioblastoma


title: B1xFP-NLS EtOH rep2

description:
Library name: B1684_EtOH_2
3xFP system mock

value: 6h ethanol mock


title: Stereotaxic brain tumor biopsy, patient 113, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_113


title: KD_H3K4me3

description: Library name: Sample 3

value: OT-1 CD8+ T cells


title: DM_L_16_F_R3

description:
Library name: P14-R3-F
Column name in NormalizedCounts: DM_L_16_F_R3

value: DMSO Control


title: B1xFP-NLS EtOH rep1

description:
Library name: B1684_EtOH_1
3xFP system mock


title: DM_L_16_F_R2

description:
Library name: P14-R2-F
Column name in NormalizedCounts: DM_L_16_F_R2


title: KD_H3K4me2

description: Library name: Sample 2

value: CD8+ T cells


title: Stereotaxic brain tumor biopsy, patient 112, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_112

value: brain


title: DM_L_16_F_R1

description:
Library name: P14-R1-F
Column name in NormalizedCounts: DM_L_16_F_R1


title: B1xFP-NLS EST rep3

description:
Library name: B1684_EST_3
3xFP system induced


title: KD_H3K4me1

description: Library name: Sample 1


title: B1xFP-NLS EST rep2

description:
Library name: B1684_EST_2
3xFP system induced


title: DM_H_16_F_R4

description:
Library name: P13-R4-F
Column name in NormalizedCounts: DM_H_16_F_R4


title: Stereotaxic brain tumor biopsy, patient 111, unclassified brain lesion

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_111

value: unclassified brain lesion


title: E14.5 WT cortex

city: Tokorozawa-si

first: Noriko

last: Mizota

state: Saitama

address: 2-579-15 Mikajima

department: Faculty of Human Sciences

country: Japan

institute: Waseda University

description: Library name: Sample1

data_processing:
CAGE libraries were sequenced using single-end reads of 75nt on a NextSeq 2000 instrument (Illumina). Obtained reads (CAGE tags) were mapped to the mm10 genome using STAR (version 2.7.9.a). CAGE tag count data were clustered using CAGEr (Haberle et al., Nucleic Acids Research 2015, 30:e51) based on the default parameters of the Paraclu algorithm (Frith et al., Genome Research 2007 18:1-12). Clusters with a count per million (CPM) of less than 0.2 were discarded.
Assembly: mm10
Supplementary files format and content: BigWig files are track objects generated by splitting normalized CAGE tag counts into positive and negative strands. These files can be uploaded to a genome browser for visualization in a genomic context.

source_name: brain

extract_protocol:
The collected cerebral cortex of E14.5 mice was rapidly frozen at -80°C and extracted using Trizol reagent. Subsequently, total RNA from three WT mice was pooled and purified using an RNA purification column.
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5' cap structures of RNAs were oxidized and biotinylated, followed by selection of biotinylated RNA/cDNA using streptavidin beads via cap-trapping. After RNA digestion with RNaseONE/H and adapter ligation at both ends, double-stranded cDNA libraries (CAGE libraries) were constructed.

value: WT


title: Stereotaxic brain tumor biopsy, patient 110, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_110


title: B1xFP-NLS EST rep1

description:
Library name: B1684_EST_1
3xFP system induced

value: not applicable

value: 6h estradiol


title: DM_H_16_F_R3

description:
Library name: P13-R3-F
Column name in NormalizedCounts: DM_H_16_F_R3


title: Stereotaxic brain tumor biopsy, patient 109, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_109

value: male

value: FFPE stereotaxic biopsy


title: Human RPE1 Day7 rep4

description:
Library name: day7_r4
G1 arrest cell expansion

source_name: retina

value: retina

value: epithelial

value: wild type

value: palbociclib 7 days


title: DM_H_16_F_R2

description:
Library name: P13-R2-F
Column name in NormalizedCounts: DM_H_16_F_R2

source_name: Floret

value: Floret

value: Vida


title: Stereotaxic brain tumor biopsy, patient 108, Embryonal tumor

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_108

value: Embryonal tumor

value: female


title: A3xFP-NES EtOH rep2

description:
Library name: A3506_EtOH_2
3xFP system mock

value: whole cell

value: 6h ethanol mock


title: Human RPE1 Day7 rep3

description:
Library name: day7_r3
G1 arrest cell expansion


title: A3xFP-NES EtOH rep3

description:
Library name: A3506_EtOH_3
3xFP system mock


title: DM_H_16_F_R1

description:
Library name: P13-R1-F
Column name in NormalizedCounts: DM_H_16_F_R1

value: DMSO Control


title: Stereotaxic brain tumor biopsy, patient 107, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_107

value: brain

value: Glioblastoma


title: Human RPE1 Day7 rep2

description:
Library name: day7_r2
G1 arrest cell expansion


title: A3xFP-NES EtOH rep1

description:
Library name: A3506_EtOH_1
3xFP system mock

value: not applicable


title: BR_H_0_F_R4

description:
Library name: P12-R4-F
Column name in NormalizedCounts: BR_H_0_F_R4

value: 2,4 EBR


title: Human RPE1 Day7 rep1

description:
Library name: day7_r1
G1 arrest cell expansion


title: Stereotaxic brain tumor biopsy, patient 106, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_106

value: male


title: BR_H_0_F_R3

description:
Library name: P12-R3-F
Column name in NormalizedCounts: BR_H_0_F_R3


title: Human RPE1 Day2 rep4

description:
Library name: day2_r4
G1 arrest cell expansion

value: palbociclib 2 days


title: A3xFP-NES EST rep3

description:
Library name: A3506_EST_3
3xFP system induced

value: 6h estradiol


title: Stereotaxic brain tumor biopsy, patient 105, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_105

value: FFPE stereotaxic biopsy


title: BR_H_0_F_R2

description:
Library name: P12-R2-F
Column name in NormalizedCounts: BR_H_0_F_R2


title: A3xFP-NES EST rep2

description:
Library name: A3506_EST_2
3xFP system induced


title: Human RPE1 Day2 rep3

description:
Library name: day2_r3
G1 arrest cell expansion

value: retina

value: epithelial

value: wild type


title: Stereotaxic brain tumor biopsy, patient 104, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_104

value: Diffuse glioma


title: BR_H_0_F_R1

description:
Library name: P12-R1-F
Column name in NormalizedCounts: BR_H_0_F_R1

value: Floret

value: Vida


title: A3xFP-NES EST rep1

description:
Library name: A3506_EST_1
3xFP system induced

source_name: not applicable

value: whole cell


title: Human RPE1 Day2 rep2

description:
Library name: day2_r2
G1 arrest cell expansion


title: Stereotaxic brain tumor biopsy, patient 103, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_103


title: Aempty EtOH rep3

description:
Library name: A3229_EtOH_3
3xFP system mock

value: empty

value: 6h ethanol mock


title: Human RPE1 Day2 rep1

description:
Library name: day2_r1
G1 arrest cell expansion


title: Aempty EtOH rep2

description:
Library name: A3229_EtOH_2
3xFP system mock


title: BR_H_24_F_R4

description:
Library name: P11-R4-F
Column name in NormalizedCounts: BR_H_24_F_R4


title: Stereotaxic brain tumor biopsy, patient 102, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_102

value: brain


title: BR_H_24_F_R3

description:
Library name: P11-R3-F
Column name in NormalizedCounts: BR_H_24_F_R3


title: siIGF2BP2, DMSO control, 2

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

description: Library name: DMSO_IGF2BP2_2

data_processing:
The quality- and adapter-trimmed reads were aligned to human genome hg38 using GENCODE annotation (release 36) with STAR v2.7.5c allowing up to one or two mismatches. Gene read counts were obtained with featureCounts v2.0.1.
Assembly: hg38
Supplementary files format and content: csv, gene read count table

molecule: polyA RNA

growth_protocol: HCT116 WT cells were a kind gift from Prof. Manuela Baccarini (MPL, University of Vienna). HCT116 cells were cultured in McCoy’s 5A (modified) medium (Sigma, M9309) supplemented with 10% fetal bovine serum (Gibco, 10437028), 2 mM L-Glutamine (Sigmam, G7513), 1% Pen/Step (Sigma, P0781) in a humidified incubator at 37°C and 5% CO2. For siRNA knockdown, cells were transfected with ON-TARGETplus Human IGF2BP2 (Dharmacon, L-017705-00-0005) or IGF2BP3 (Dharmacon, L-003976-00-0005) SMARTpool siRNAs  at 75 nM for 48 hours using DharmaFECT 2 (Dharmacon, T-2002-01). ON-TARGETplus nontargeting siRNA #1 (Dharmacon, D-001810-01-05) was used as a control.

extract_protocol:
One ~80% confluent well of a 6-well plate per condition (three biological replicates per condition) was washed with ice-cold PBS (Sigma) supplemented with 100 mg/mL cycloheximide, lysed on a plate on ice with 350 μL of ice-cold lysis buffer (20 mM HEPES pH 7.3, 150 mM KCl, 5 mM MgCl2, 1% Triton X-100, 100 mg/mL cycloheximide, 1 mM DTT, 1x EDTA-free protease inhibitor cocktail), scraped, and transferred to 1.5 mL RNase-free tube. Cell lysates were passed three times through the 27G needle, incubated on ice for 10 min with intermittent vortexing, and clarified on a table-top centrifuge at maximum speed (20,000 g) for 20 min at 4°C. Total RNA concentration in the lysate was estimated using OD A260 measurement on Nanodrop. The lysate concentrations were brought to 240 ng/μL, 15 μL aliquots were taken for matching RNA-Seq.
RNA-Seq libraries were prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7765L) and sequenced on a NovaSeq SP on SR100 (Illumina) aiming for 30 million reads per sample on average.

treatment_protocol: Endoplasmic reticulum (ER) stress was induced with 5 µg/mL tunicamycin (TM) for 4 hours (1:1000 DMSO was used as a control).

value: human colorectal carcinoma

value: DMSO control


title: ER stress (TM), IGF2BP3 KO, clone D12, 2

description: Library name: TM_IGF2BP3KO_D12_rep2

data_processing:
The quality- and adapter-trimmed reads were aligned to human genome hg38 using GENCODE annotation (release 36) with STAR v2.7.5c allowing up to two mismatches per read.
Assembly: hg38
Supplementary files format and content: csv, gene read count table

growth_protocol: HCT116 conditionally expressing doxycycline-inducible (tetON) OsTIR1 were obtained from the Masato Kanemaki lab (Natsume et al. 2016).  HCT116 cells were cultured in McCoy’s 5A (modified) medium (Sigma, M9309) supplemented with 10% fetal bovine serum (Gibco, 10437028), 2 mM L-Glutamine (Sigmam, G7513), 1% Pen/Step (Sigma, P0781) in a humidified incubator at 37°C and 5% CO2. For knockout cell line generation, gRNA sequences (IGF2BP3 KO clones E4 and A3: 5′TGGCACCGACTGATAGAGCT 3′; clone D12: 5′ACGCGTAGCCAGTCTTCACC 3′; IGF2BP2 KO clones F6 and B7: 5′GAGCTGCCGGAGGTCGTCGG 3′; clone G6: 5′AGGCGTAGCCGGACTTCAGC 3') were cloned into the pSpCas9 (BB)-2A-GFP (PX458) (plasmid #48138; Addgene) (Ran et al. 2013 ). HCT116 tetON OsTIR1 cells were transiently transfected using jetOPTIMUS reagent (Tamar, 101000051), and GFP-positive single-cell clones were FACS sorted at BD FACSAria IIIu at Max Perutz Labs BioOptics FACS Facility.

extract_protocol:
Total RNA was isolated using peqGOLD TriFast (Peqlab, VWR), treated with RNase-free DNase I (NEB), and re-purified with peqGOLD TriFast (Peqlab, VWR). RNA precipitation was done using isopropanol method.
Total RNA sequencing libraries were prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7765L) by Vienna BioCenter NGS facility sequenced on a NovaSeq S4 on PE100 (Illumina) with 55 million reads per sample on average.

treatment_protocol: HCT116 tetON OsTIR1 IGF2BP3 KO clones E4, A3, and D12 (in duplicates) and parental cells (four replicates) were treated with 5 µg/mL tunicamycin (TM) for 4 hours (1:1000 DMSO was used as a control).

value: IGF2BP3 KO, clone D12, Tet-OsTIR1-PURO

value: Tunicamycin (TM)


title: ER stress (TM), IGF2BP2 KO, clone G6, 2

description: Library name: TM_IGF2BP2KO_G6_rep2

value: IGF2BP2 KO, clone G6, Tet-OsTIR1-PURO


title: iEPDCs_TGFβ3_MD3

city: Bielefeld

first: Katja

last: Nowak

address: Universitätstraße 25

department: Faculty of Biology, Cell Biology

institute: University of Bielefeld

description:
Library name: iEPDCs_TGFB3_MD3
Column name in iEPDCs_readcounts_all.txt: iEPDCs_TGFB3_MD3

data_processing:
Low-quality bases were trimmed and adapter clipping was performed with Trimmomatic-0.39. The following settings were applied: PE; -phred33; ILLUMI-NACLIP:TruSeq3-PE.fa:2:30:10; LEADING:6; TRAILING:6; SLIDINGWINDOW:4:15; MINLEN:36.
Trimmed sequence were mapped to homo sapiens reference genome sequence (GRCh38.p14) was conducted utilizing HiSat2 [version 2.1.0]
For quantifying the read numbers after mapping Feature counts (version 2.0.0) was used with the subsequent parameters: -T 4; -t gene; -g gene_id; -a Ho-mo_sapiens.GRCh38.78.gtf.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes readcounts for each sample

source_name: immortalized epicardium-derived cells

growth_protocol: iEPDCs were maintained in DMEM low-glucose and M199 (1:1) suplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin and and 10 µM SB431542.

extract_protocol:
RNA was harvested with NucleoSpin RNA Kit (Macherey-Nagel GmbH)
mRNA libraries were prepared using poly(A) enrichment by Novogene GmbH.

treatment_protocol: Treatment was perfomed for five days with these three different conditions:  For SB431542: DMEM low-glucose and M199 (1:1) suplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin and 10 µM SB431542; NoAdditive: DMEM low-glucose and M199 (1:1) suplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin and corresponding amount of DMSO; TGFB3: DMEM low-glucose and M199 (1:1) suplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin and corresponding amount of DMSO and 1ng/mL TGFB3.

value: immortalized epicardium-derived cells

value: male


title: Stereotaxic brain tumor biopsy, patient 101, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_101

value: Glioblastoma

value: FFPE stereotaxic biopsy


title: Aempty EtOH rep1

description:
Library name: A3229_EtOH_1
3xFP system mock

value: not applicable


title: iEPDCs_NoAdditive_MD3

description:
Library name: iEPDCs_NoAdditive_MD3
Column name in iEPDCs_readcounts_all.txt: iEPDCs_NoAdditive_MD3

value: NoAdditive


title: BR_H_24_F_R2

description:
Library name: P11-R2-F
Column name in NormalizedCounts: BR_H_24_F_R2

value: Floret

value: 2,4 EBR


title: Stereotaxic brain tumor biopsy, patient 100, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_100


title: BR_H_24_F_R1

description:
Library name: P11-R1-F
Column name in NormalizedCounts: BR_H_24_F_R1

value: Vida


title: Aempty EST rep3

description:
Library name: A3229_EST_3
3xFP system induced

value: whole cell

value: empty

value: 6h estradiol


title: iEPDCs_SB431542_MD3

description:
Library name: iEPDCs_SB431542_MD3
Column name in iEPDCs_readcounts_all.txt: iEPDCs_SB431542_MD3


title: Stereotaxic brain tumor biopsy, patient 99, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_99

value: brain


title: Aempty EST rep2

description:
Library name: A3229_EST_2
3xFP system induced


title: BR_L_0_F_R4

description:
Library name: P10-R4-F
Column name in NormalizedCounts: BR_L_0_F_R4


title: iEPDCs_TGFβ3_MD2

description:
Library name: iEPDCs_TGFB3_MD2
Column name in iEPDCs_readcounts_all.txt: iEPDCs_TGFB3_MD2


title: Stereotaxic brain tumor biopsy, patient 98, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_98


title: Stereotaxic brain tumor biopsy, patient 97, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_97

value: female


title: BR_L_0_F_R3

description:
Library name: P10-R3-F
Column name in NormalizedCounts: BR_L_0_F_R3


title: BR_L_0_F_R2

description:
Library name: P10-R2-F
Column name in NormalizedCounts: BR_L_0_F_R2


title: iEPDCs_SB431542_MD2

description:
Library name: iEPDCs_SB431542_MD2
Column name in iEPDCs_readcounts_all.txt: iEPDCs_SB431542_MD2


title: A3xFP-NLS EtOH rep3

description:
Library name: A3225_EtOH_3
3xFP system mock

value: 6h ethanol mock


title: A3xFP-NLS EtOH rep2

description:
Library name: A3225_EtOH_2
3xFP system mock


title: Stereotaxic brain tumor biopsy, patient 96, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_96


title: BR_L_0_F_R1

description:
Library name: P10-R1-F
Column name in NormalizedCounts: BR_L_0_F_R1


title: iEPDCs_TGFβ3_FD5

description:
Library name: iEPDCs_TGFB3_FD5
Column name in iEPDCs_readcounts_all.txt: iEPDCs_TGFB3_FD5


title: Stereotaxic brain tumor biopsy, patient 95, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_95


title: A3xFP-NLS EtOH rep1

description:
Library name: A3225_EtOH_1
3xFP system mock


title: BR_H_16_F_R3

description:
Library name: P9-R3-F
Column name in NormalizedCounts: BR_H_16_F_R3

source_name: Floret


title: Stereotaxic brain tumor biopsy, patient 94, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_94


title: A3xFP-NLS EST rep3

description:
Library name: A3225_EST_3
3xFP system induced


title: BR_H_16_F_R2

description:
Library name: P9-R2-F
Column name in NormalizedCounts: BR_H_16_F_R2


title: iEPDCs_SB431542_FD5

description:
Library name: iEPDCs_SB431542_FD5
Column name in iEPDCs_readcounts_all.txt: iEPDCs_SB431542_FD5


title: A3xFP-NLS EST rep2

description:
Library name: A3225_EST_2
3xFP system induced


title: BR_H_16_F_R1

description:
Library name: P9-R1-F
Column name in NormalizedCounts: BR_H_16_F_R1


title: iEPDCs_TGFβ3_FD4

description:
Library name: iEPDCs_TGFB3_FD4
Column name in iEPDCs_readcounts_all.txt: iEPDCs_TGFB3_FD4


title: A3xFP-NLS EST rep1

description:
Library name: A3225_EST_1
3xFP system induced


title: Stereotaxic brain tumor biopsy, patient 90, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_90


title: Stereotaxic brain tumor biopsy, patient 89, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_89

value: Diffuse glioma


title: iEPDCs_TGFβ3_MD1

description:
Library name: iEPDCs_TGFB3_MD1
Column name in iEPDCs_readcounts_all.txt: iEPDCs_TGFB3_MD1


title: 4 week, infected, synovium, bio rep 1

city: Grand Forks

first: Archana

last: Dhasarathy

state: ND

address: 1301 N. Columbia Road, STOP 9061, STOP 9037

department: Biomedical Sciences

institute: UNIVERSITY OF NORTH DAKOTA

description:
Library name: 4Av4B_infected_28
028

data_processing:
Initial quality control (QC) was performed at the AOI (segment) level using the dataset tech_signal_2. The following thresholds were applied: ≥1,000 raw reads; ≥80 aligned reads; ≥80 stitched reads; and ≥80 trimmed reads. Sequencing saturation was required to be ≥50 to ensure adequate library complexity. Background signal was assessed using negative control probes (geometric mean ≥2), and No Template Control (NTC) counts were required to be ≤1,000. AOIs were required to have a minimum surface area of 16,000 image-derived units to ensure adequate tissue coverage, and a nuclei count ≥95 to ensure sufficient cellular content. All thresholds were required to be met for AOI retention.
Probe QC was conducted on the probe_qc dataset derived from segment-QC–filtered data. Failed segments were not removed prior to probe QC. Probes were excluded if the ratio of probe geometric mean across all AOIs was <0.1. Probes were also excluded if they failed a Grubbs outlier test in ≥20% of AOIs. Local segment outlier exclusion was not applied. The limit of quantification (LOQ) was defined as 2 standard deviations above background.
Expression filtering was performed at the target level using the dataset filter_.10. Targets were retained using the higher of LOQ or user-defined threshold method, in which the minimum expression threshold was defined as the greater of the calculated LOQ or a user-defined count value of 2. Targets were required to meet this threshold in at least 10 AOIs to be retained for downstream analysis.
Normalization was performed using third quartile (Q3) normalization within the GeoMx DSP Analysis Suite. Segment filtering was not applied at this stage; however, target filtering remained enabled. The resulting normalized dataset (Q3 after filter) was used for all downstream statistical analyses.
Differential expression analysis was performed using paired t-tests within the GeoMx DSP Analysis Suite. Three independent paired comparisons were conducted. P-values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate (FDR) correction. Pathway enrichment analysis was performed using Reactome (Build 78 + NCBI_08122021) within the GeoMx DSP Analysis Suite. Pathways were required to meet the following criteria: minimum gene coverage of 20%, minimum of 5 genes detected per pathway, pathway size between 15 and 500 genes, and 10,000 permutations for significance testing. Pathway analysis was conducted separately for each statistical comparison.
Assembly: mm10
Supplementary files format and content: Heatmaps.xlsx contain normalized probe intensities per gene for each ROI
Supplementary files format and content: Pathway.xlsx contain pathway enrichment stats for each comparison
Library strategy: Spatial Transcriptomics

source_name: Synovium

growth_protocol: All animal infections were carried out in accordance with approved protocols from the Institutional Animal Care and Use Committee (IACUC) of the University of North Dakota. C3H mice were purchased from The Jackson Laboratory. For all experiments, 6–8-week-old female mice were used and housed in groups.

extract_protocol:
H&E staining was performed at the University of North Dakota Histology core using standard protocols. To determine arthritis severity scores, a histological analysis of the tibiotarsal joint from each mouse was performed. The sections were evaluated based on arthritis severity on a scale of 0 to 4. Score 0 is given with no inflammation in the tissue. Score 1 with minimal inflammation affecting <5% of tissue. Score 2 with multiple focally extensive areas of inflammation involving 5 % to 25 % of tissue. Score 3 with confluent inflammation involving 25% to 50% of tissue and multiple structures (>3) affected. Score 4 with confluent inflammation in all structures involving >50% of sample.
Spatial transcriptomic profiling was performed using the NanoString GeoMx® Digital Spatial Profiler (DSP) platform. Following UV-photocleavage of oligo-tagged probes and collection of region-of-interest (ROI/AOI) material, libraries were prepared according to the manufacturer’s protocol and sequenced on an Illumina platform. FASTQ files were processed using NanoString GeoMx DSP Analysis Suite software (v2.5.1.166). The final normalized dataset used for downstream analysis was designated Q3 after filter.

treatment_protocol: For infections, animals were placed under anesthesia using isoflurane inhalation, followed by subdermal inoculation in the dorsal thoracic midline with 100 uL of BSK-II medium containing  Borrelia B. Two and four weeks following challenge by needle inoculation, mice were assayed for infectivity by culturing ear biopsy specimens for B. burgdorferi in BSK-II media(Sinsky & Piesman, 1989). Ear biopsy cultures were observed microscopically after a 7 day incubation for the presence of spirochetes and negative culture samples were maintained and observed for about 4 weeks before being discarded.  Mice were euthanized at both 2 and 4 weeks post-infection for collection of the tibiotarsal joint, which was immediately snap frozen in liquid nitrogen for later imaging. Measurements of the tibiotarsal joint were taken every week over the course of 4 weeks.

value: Synovium

tag: strain

value: 4 weeks

value: infected


title: DM_L_24_F_R1

description:
Library name: P8-R1-F
Column name in NormalizedCounts: DM_L_24_F_R1

tag: tissue

value: DMSO Control


title: iEPDCs_NoAdditive_MD1

description:
Library name: iEPDCs_NoAdditive_MD1
Column name in iEPDCs_readcounts_all.txt: iEPDCs_NoAdditive_MD1

value: immortalized epicardium-derived cells

value: male


title: Stereotaxic brain tumor biopsy, patient 88, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_88

tag: disease state

value: FFPE stereotaxic biopsy


title: DM_H_0_F_R3

description:
Library name: P7-R3-F
Column name in NormalizedCounts: DM_H_0_F_R3

value: Floret


title: Stereotaxic brain tumor biopsy, patient 87, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_87

value: Glioblastoma

tag: age


title: DM_H_0_F_R2

description:
Library name: P7-R2-F
Column name in NormalizedCounts: DM_H_0_F_R2

value: Vida


title: A2058 cells, KIT-K642E, DMSO, 24h, rep3

city: Chengdu

first: Jing

last: Yu

state: Sichuan

address: No.17, Section 3, Renmin South Road

institute: Sichuan university

description: Library name: A58-4-3

data_processing:
Raw sequencing data underwent standardized quality control using trim_galore (v0.6.4) to remove low-quality bases and adapter sequences. Quality-verified clean reads were subsequently aligned to the reference genome (GRCh38) with HISAT2 (v2.1.0). Resultant SAM files were sorted and converted to BAM format via samtools (v1.15.1), followed by gene expression quantification with featureCounts (v2.0.0) based on Ensembl gene annotations.
Assembly: GRCh38
Supplementary files format and content: Excel fle includes TPM for each Sample

source_name: skin

growth_protocol: The human-derived melanoma cell lines M21 and A2058 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
1） Samples were ground under liquid nitrogen in a mortar and pestle, and the resulting powder dissolved in TRIzol™ Reagent (Invitrogen, Carlsbad, CA, USA), then extracted total RNA. 2） The quality and purity of RNA were examined by a NanoDrop™ One/OneC spectrophotometer (Thermo Scientific, Waltham, MA, USA) and Life Invitrogen Qubit RNA BR (Broad-Range) Assay Kit. RNA integrity was analyzed using Agilent 4200 TapeStation system (Agilent, Santa Clara, CA, USA).
1）0.1-1 μg of total RNA per sample was prepared for library preparation. The ABclonal Poly(A)mRNA Capture Module and ABclonal Fast RNA-seq Lib Prep Kit V2 were used for mRNA isolation and library construction following the manufacturers’ protocols. 2）As for the quality control of library, Qubit dsDNA HS Assay Kit was used to measure the concentration of library, then Agilent 4200 was used to examine the distribution of segments in library. Finally, library molar concentration was determined using the KAPA Library Quant kit (illumina) universal qPCR Mix. 3）High-throughput transcriptome sequencing was performed on an Illumina NovaSeq xplus platform according to the manufacturer’ s instructions.

value: skin

value: melanoma epithelial cells

value: DMSO


title: Stereotaxic brain tumor biopsy, patient 86, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_86

value: brain

tag: Sex


title: 4 week, uninfected, synovium, bio rep 1

description:
Library name: 4Av4B_uninfected_17
017

value: uninfected


title: Stereotaxic brain tumor biopsy, patient 92, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_92

tag: sample type


title: DM_H_0_F_R1

description:
Library name: P7-R1-F
Column name in NormalizedCounts: DM_H_0_F_R1


title: iEPDCs_NoAdditive_FD4

description:
Library name: iEPDCs_NoAdditive_FD4
Column name in iEPDCs_readcounts_all.txt: iEPDCs_NoAdditive_FD4

source_name: immortalized epicardium-derived cells

value: NoAdditive

value: female


title: 4 week, infected, synovium, bio rep 3

description:
Library name: 4Av4B_infected_26
026

value: Synovium


title: Stereotaxic brain tumor biopsy, patient 91, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_91

value: Diffuse glioma

tag: dna concentration (ng/ul)


title: DM_L_24_F_R3

description:
Library name: P8-R3-F
Column name in NormalizedCounts: DM_L_24_F_R3


title: A2058 cells, KIT-K642E, DMSO, 24h, rep2

description: Library name: A58-4-2

tag: cell type


title: Stereotaxic brain tumor biopsy, patient 85, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_85


title: 2 week, infected, lateral synovium, bio rep 3

description:
Library name: 2Av2B_infected_15
015

source_name: Lateral synovium

value: Lateral synovium

value: 2 weeks

tag: treatment

value: infected


title: A2058 cells, KIT-K642E, DMSO, 24h, rep1

description: Library name: A58-4-1

tag: cell line


title: Stereotaxic brain tumor biopsy, patient 84, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_84


title: BR_H_8_F_R3

description:
Library name: P6-R3-F
Column name in NormalizedCounts: BR_H_8_F_R3

tag: genotype

value: 2,4 EBR


title: 4 week, uninfected, synovium, bio rep 3

description:
Library name: 4Av4B_uninfected_20
020

value: 4 weeks


title: A2058 cells, KIT-K642E, 100nM imatinib, 24h, rep3

description: Library name: A58-4+3

value: imatinib, 100nM, 24h


title: iEPDCs_SB431542_MD1

description:
Library name: iEPDCs_SB431542_MD1
Column name in iEPDCs_readcounts_all.txt: iEPDCs_SB431542_MD1

value: immortalized epicardium-derived cells

value: male


title: Stereotaxic brain tumor biopsy, patient 83, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_83

value: Glioblastoma

value: FFPE stereotaxic biopsy


title: 2 week, infected, lateral synovium, bio rep 1

description:
Library name: 2Av2B_infected_11
011


title: BR_H_8_F_R2

description:
Library name: P6-R2-F
Column name in NormalizedCounts: BR_H_8_F_R2

value: Floret

value: Vida


title: A2058 cells, KIT-K642E, 100nM imatinib, 24h, rep2

description: Library name: A58-4+2

value: skin

value: melanoma epithelial cells


title: Stereotaxic brain tumor biopsy, patient 82, Circumscribed glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_82

value: brain

value: Circumscribed glioma


title: 2 week, uninfected, lateral synovium, bio rep 2

description:
Library name: 2Av2B_uninfected_8
008

value: uninfected


title: A2058 cells, KIT-K642E, 100nM imatinib, 24h, rep1

description: Library name: A58-4+1


title: BR_H_8_F_R1

description:
Library name: P6-R1-F
Column name in NormalizedCounts: BR_H_8_F_R1

source_name: Floret


title: Stereotaxic brain tumor biopsy, patient 81, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_81


title: BR_L_24_F_R4

description:
Library name: P5-R4-F
Column name in NormalizedCounts: BR_L_24_F_R4


title: A2058 cells, KIT-L576P, DMSO, 24h, rep3

description: Library name: A58-3-3

value: DMSO


title: BR_L_24_F_R3

description:
Library name: P5-R3-F
Column name in NormalizedCounts: BR_L_24_F_R3


title: A2058 cells, KIT-L576P, DMSO, 24h, rep2

description: Library name: A58-3-2


title: Stereotaxic brain tumor biopsy, patient 79, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_79


title: 2 week, post-infection, medial synovium, bio rep 2

description:
Library name: 2Av2B_infected_10
010

source_name: Medial synovium

value: Medial synovium

value: 2 weeks


title: BR_L_24_F_R2

description:
Library name: P5-R2-F
Column name in NormalizedCounts: BR_L_24_F_R2

value: 2,4 EBR


title: A2058 cells, KIT-L576P, DMSO, 24h, rep1

description: Library name: A58-3-1


title: Stereotaxic brain tumor biopsy, patient 78, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_78

value: Diffuse glioma


title: 2 week, post-infection, medial synovium, bio rep 1

description:
Library name: 2Av2B_infected_9
009

value: infected


title: BR_L_24_F_R1

description:
Library name: P5-R1-F
Column name in NormalizedCounts: BR_L_24_F_R1


title: BR_H_8_F_R4

description:
Library name: P6-R4-F
Column name in NormalizedCounts: BR_H_8_F_R4


title: A2058 cells, KIT-L576P, 100nM imatinib, 24h, rep3

description: Library name: A58-3+3

value: imatinib, 100nM, 24h


title: 2 week, infected, lateral synovium, bio rep 2

description:
Library name: 2Av2B_infected_12
012

value: Lateral synovium


title: Stereotaxic brain tumor biopsy, patient 77, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_77

value: Glioblastoma

value: female


title: DM_H_24_F_R4

description:
Library name: P4-R4-F
Column name in NormalizedCounts: DM_H_24_F_R4

value: Floret

value: DMSO Control


title: 2 week, uninfected, medial synovium, bio rep 3

description:
Library name: 2Av2B_uninfected_7
007


title: A2058 cells, KIT-L576P, 100nM imatinib, 24h, rep2

description: Library name: A58-3+2

value: skin


title: Stereotaxic brain tumor biopsy, patient 76, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_76

value: male

value: FFPE stereotaxic biopsy


title: 2 week, uninfected, medial synovium, bio rep 2

description:
Library name: 2Av2B_uninfected_2
002


title: DM_H_24_F_R3

description:
Library name: P4-R3-F
Column name in NormalizedCounts: DM_H_24_F_R3

value: Vida


title: Stereotaxic brain tumor biopsy, patient 75, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_75

value: brain


title: A2058 cells, KIT-L576P, 100nM imatinib, 24h, rep1

description: Library name: A58-3+1

source_name: skin

value: melanoma epithelial cells


title: 2 week, uninfected, medial synovium, bio rep 1

description:
Library name: 2Av2B_uninfected_1
001

value: Medial synovium

value: uninfected


title: DM_H_24_F_R2

description:
Library name: P4-R2-F
Column name in NormalizedCounts: DM_H_24_F_R2


title: A2058 cells, KIT-Amplification, DMSO, 24h, rep3

description: Library name: A58-2-3

value: KIT-Amplification

value: DMSO


title: Stereotaxic brain tumor biopsy, patient 74, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_74


title: 2 week, uninfected, lateral synovium, bio rep 1

description:
Library name: 2Av2B_uninfected_4
004

value: 2 weeks


title: Aempty EST rep1

description:
Library name: A3229_EST_1
3xFP system induced

source_name: not applicable

value: not applicable

value: whole cell

value: empty

value: 6h estradiol

tag: batch


title: iEPDCs_NoAdditive_MD2

description:
Library name: iEPDCs_NoAdditive_MD2
Column name in iEPDCs_readcounts_all.txt: iEPDCs_NoAdditive_MD2

source_name: immortalized epicardium-derived cells

value: immortalized epicardium-derived cells

value: NoAdditive


title: Stereotaxic brain tumor biopsy, patient 80, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_80

value: Glioblastoma


title: 2 week, post-infection, medial synovium, bio rep 3

description:
Library name: 2Av2B_infected_16
016

value: infected


title: DM_H_24_F_R1

description:
Library name: P4-R1-F
Column name in NormalizedCounts: DM_H_24_F_R1

value: Floret

value: DMSO Control


title: Skin, CD45+TCR-, PC61-IL-2mutein 24, ADT

city: South San Francisco

first: Weiwen

last: Deng

address: 750 Gateway Blvd

institute: Amgen

description:
Library name: km5_ADT
10x Genomics

library_source: other

data_processing:
Raw fastq data of GEX and HTO libraries was demultiplexed using a custom workflow of Cell Ranger (v7.1.0) multi
Demultiplexed bam files were convert to fastq using Cellranger bamtofastq
Converted fastq files of the GEX library as well as raw fastq files of TCR and ADT libraries were aligned on the mouse reference genome mm10 and GRCm38 V(D)J using Cellranger multi. Force-cell value set to the number detected by demultiplexing.
RDS files were generated with output of GEX and ADT libraries using Seurat R package (version 4.3.0)
Assembly: mm10
Assembly: GRCm38 V(D)J
Supplementary files format and content: GEX library: sample.rds files
Supplementary files format and content: ADT library: sample_ADT.rds files (GEX embedded)
Supplementary files format and content: TCR library: sample_HTO_filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

source_name: Skin

extract_protocol:
Skin cell suspensions were enriched with Percoll density gradient centrifugation using Ficoll-Paque™ PLUS density gradient media gradient. The interphase containing the enriched leukocytes was collected for downstream processing. Before staining, cells were preincubated for 20 min with anti-mouse CD16/32. For sample multiplexing, each individual sample from mice within the same treatment group were incubated with a cocktail of TotalSeq™-C Mouse Universal Cocktail, V1.0 plus one TotalSeq™-C Hashtag antibodies (Hashtags C0306, C0307, C0308, C0309, and C0310). Sample were washed with BD Pharmingen™ Stain Buffer (BSA) and were stained for CD45-BV786, TCRβ -PE and LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit. Within each treatment group, samples were pooled and sorted on a FACS Aria into three single cell fractions: CD45+ TCRβ+ GFP+, CD45+ TCRβ + GFP-, CD45+ TCRβ-.
Libraries were prepared according to the manufacter's instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) User Guide with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping). Briefly, sorted cells were captured in droplet emulsions using Chromium X and libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 5' Kit v2 and Chromium Next GEM Single Cell 5' Gel Bead Kit v2. Amplified 5' Gene Expression, V(D)J and Cell Surface Protein libraries were profiled using the Agilent 4200 TapeStation System and pooled at 10:1:1 ratio. Pooled samples were sequenced on Illumina NovaSeq X using a 28-10-10-90 asymmetric read configuration. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

value: Skin

value: PC61-IL-2mutein 24, s.c.

tag: library

value: ADT+HTO

tag: hto

value: TotalSeq-C0306, TotalSeq-C0307, TotalSeq-C0308, TotalSeq-C0309, TotalSeq-C0310 (biological replicates)


title: A2058 cells, KIT-Amplification, DMSO, 24h, rep2

description: Library name: A58-2-2

value: skin

value: melanoma epithelial cells

value: KIT-Amplification


title: Stereotaxic brain tumor biopsy, patient 73, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_73

value: brain

value: male

value: FFPE stereotaxic biopsy


title: DM_H_8_F_R4

description:
Library name: P3-R4-F
Column name in NormalizedCounts: DM_H_8_F_R4

value: Vida

tag: temperature


title: iEPDCs_NoAdditive_FD5

description:
Library name: iEPDCs_NoAdditive_FD5
Column name in iEPDCs_readcounts_all.txt: iEPDCs_NoAdditive_FD5

value: immortalized epicardium-derived cells

value: female


title: Stereotaxic brain tumor biopsy, patient 72, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_72

value: Glioblastoma


title: A2058 cells, KIT-Amplification, DMSO, 24h, rep1

description: Library name: A58-2-1

value: DMSO


title: Skin, CD45+TCR-, Isotype Control, ADT

description:
Library name: km1_ADT
10x Genomics

value: Isotype Control, s.c.


title: Stereotaxic brain tumor biopsy, patient 93, Circumscribed glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_93

value: Circumscribed glioma


title: DM_H_8_F_R3

description:
Library name: P3-R3-F
Column name in NormalizedCounts: DM_H_8_F_R3

source_name: Floret

value: Floret

value: DMSO Control

tag: time


title: DM_L_24_F_R4

description:
Library name: P8-R4-F
Column name in NormalizedCounts: DM_L_24_F_R4

tag: replication


title: A2058 cells, KIT-Amplification, 100nM imatinib, 24h, rep3

description: Library name: A58-2+3

value: imatinib, 100nM, 24h


title: Stereotaxic brain tumor biopsy, patient 71, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_71


title: Skin, TCR+GFP-, PC61-IL-2mutein 24, ADT

description:
Library name: kTc5_ADT
10x Genomics

value: Skin

tag: strain

value: Conventional T cell

value: PC61-IL-2mutein 24, s.c.

value: ADT+HTO

value: TotalSeq-C0306, TotalSeq-C0307, TotalSeq-C0308, TotalSeq-C0309, TotalSeq-C0310 (biological replicates)


title: Skin, CD45+TCR-, Fc-IL-2 mutein 24, ADT

description:
Library name: km2_ADT
10x Genomics

tag: tissue

value: Fc-IL-2 mutein 24, s.c.


title: DM_H_8_F_R2

description:
Library name: P3-R2-F
Column name in NormalizedCounts: DM_H_8_F_R2


title: A2058 cells, KIT-Amplification, 100nM imatinib, 24h, rep2

description: Library name: A58-2+2

value: skin

value: melanoma epithelial cells

value: KIT-Amplification


title: iEPDCs_SB431542_FD4

description:
Library name: iEPDCs_SB431542_FD4
Column name in iEPDCs_readcounts_all.txt: iEPDCs_SB431542_FD4

value: immortalized epicardium-derived cells

value: female


title: Stereotaxic brain tumor biopsy, patient 70, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_70

value: brain

tag: disease state

value: Glioblastoma

value: male

value: FFPE stereotaxic biopsy


title: 4 week, infected, synovium, bio rep 2

description:
Library name: 4Av4B_infected_32
032

source_name: Synovium

value: Synovium

value: 4 weeks

value: infected


title: DM_H_8_F_R1

description:
Library name: P3-R1-F
Column name in NormalizedCounts: DM_H_8_F_R1

value: Floret

value: Vida

value: DMSO Control


title: A2058 cells, KIT-Amplification, 100nM imatinib, 24h, rep1

description: Library name: A58-2+1

value: imatinib, 100nM, 24h


title: Skin, TCR+GFP-, Fc-IL-2 mutein 24, ADT

description:
Library name: kTc2_ADT
10x Genomics

value: Skin

value: Conventional T cell

value: Fc-IL-2 mutein 24, s.c.

value: ADT+HTO

value: TotalSeq-C0306, TotalSeq-C0307, TotalSeq-C0308, TotalSeq-C0309, TotalSeq-C0310 (biological replicates)


title: DM_L_24_F_R2

description:
Library name: P8-R2-F
Column name in NormalizedCounts: DM_L_24_F_R2


title: Stereotaxic brain tumor biopsy, patient 68, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_68

tag: age


title: A2058 cells, CTR, DMSO, 24h, rep3

description: Library name: A58-1-3

value: skin

value: melanoma epithelial cells

value: WT (Control)

value: DMSO


title: Stereotaxic brain tumor biopsy, patient 69, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_69

value: brain

value: Diffuse glioma

tag: Sex

value: male

value: FFPE stereotaxic biopsy


title: Skin, TCR+GFP-, Isotype Control, ADT

description:
Library name: kTc1_ADT
10x Genomics

value: Isotype Control, s.c.


title: Skin, TCR+GFP+, PC61-IL-2mutein 24, ADT

description:
Library name: kTr5_ADT
10x Genomics

value: Treg

value: PC61-IL-2mutein 24, s.c.


title: A2058 cells, CTR, DMSO, 24h, rep2

description: Library name: A58-1-2


title: BR_L_16_F_R4

description:
Library name: P2-R4-F
Column name in NormalizedCounts: BR_L_16_F_R4

value: Floret

value: Vida

value: 2,4 EBR


title: BR_L_16_F_R3

description:
Library name: P2-R3-F
Column name in NormalizedCounts: BR_L_16_F_R3


title: Stereotaxic brain tumor biopsy, patient 67, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_67

value: Glioblastoma

tag: sample type


title: Skin, TCR+GFP+, Fc-IL-2 mutein 24, ADT

description:
Library name: kTr2_ADT
10x Genomics

value: Skin

value: Fc-IL-2 mutein 24, s.c.

value: ADT+HTO


title: A2058 cells, CTR, DMSO, 24h, rep1

description: Library name: A58-1-1

value: skin

value: melanoma epithelial cells


title: BR_L_16_F_R1

description:
Library name: P2-R1-F
Column name in NormalizedCounts: BR_L_16_F_R1


title: BR_L_16_F_R2

description:
Library name: P2-R2-F
Column name in NormalizedCounts: BR_L_16_F_R2


title: Stereotaxic brain tumor biopsy, patient 66, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_66

value: female

tag: dna concentration (ng/ul)


title: A2058 cells, CTR, 100nM imatinib, 24h, rep3

description: Library name: A58-1+3

source_name: skin

tag: cell type

value: WT (Control)

value: imatinib, 100nM, 24h


title: Skin, TCR+GFP+, Isotype Control, ADT

description:
Library name: kTr1_ADT
10x Genomics

tag: treatment

value: TotalSeq-C0306, TotalSeq-C0307, TotalSeq-C0308, TotalSeq-C0309, TotalSeq-C0310 (biological replicates)


title: Stereotaxic brain tumor biopsy, patient 65, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_65

value: brain

value: male

value: FFPE stereotaxic biopsy


title: Skin, TCR+GFP-, PC61-IL-2mutein 24, TCR

description:
Library name: kTc5_TCR
10x Genomics

value: Conventional T cell

value: PC61-IL-2mutein 24, s.c.

value: VDJ-T


title: DM_L_0_F_R4

description:
Library name: P1-R4-F
Column name in NormalizedCounts: DM_L_0_F_R4

value: Floret

value: Vida

value: DMSO Control


title: Stereotaxic brain tumor biopsy, patient 64, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_64

value: Glioblastoma


title: Skin, TCR+GFP-, Fc-IL-2 mutein 24, TCR

description:
Library name: kTc2_TCR
10x Genomics

value: Skin

value: Fc-IL-2 mutein 24, s.c.


title: A2058 cells, CTR, 100nM imatinib, 24h, rep2

description: Library name: A58-1+2

value: skin

tag: cell line

value: melanoma epithelial cells


title: Stereotaxic brain tumor biopsy, patient 63, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_63

value: female


title: A2058 cells, CTR, 100nM imatinib, 24h, rep1

description: Library name: A58-1+1

tag: genotype

value: WT (Control)

value: imatinib, 100nM, 24h


title: DM_L_0_F_R3

description:
Library name: P1-R3-F
Column name in NormalizedCounts: DM_L_0_F_R3


title: Skin, TCR+GFP-, Isotype Control, TCR

description:
Library name: kTc1_TCR
10x Genomics

value: Isotype Control, s.c.


title: DM_L_0_F_R2

description:
Library name: P1-R2-F
Column name in NormalizedCounts: DM_L_0_F_R2


title: M21 cells, KIT-K642E, DMSO, 24h, rep3

description: Library name: A21-4-3

value: DMSO


title: Stereotaxic brain tumor biopsy, patient 62, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_62

value: brain

value: FFPE stereotaxic biopsy


title: DM_L_0_F_R1

description:
Library name: P1-R1-F
Column name in NormalizedCounts: DM_L_0_F_R1


title: M21 cells, KIT-K642E, DMSO, 24h, rep2

description: Library name: A21-4-2


title: Stereotaxic brain tumor biopsy, patient 61, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_61

value: male


title: 4 week, uninfected, synovium, bio rep 2

description:
Library name: 4Av4B_uninfected_19
019

value: Synovium

value: 4 weeks

value: uninfected


title: Skin, TCR+GFP+, PC61-IL-2mutein 24, TCR

description:
Library name: kTr5_TCR
10x Genomics

source_name: Skin

value: Treg

value: PC61-IL-2mutein 24, s.c.

value: VDJ-T


title: BR_L_8_R_R3

description:
Library name: P16-R3-R
Column name in NormalizedCounts: BR_L_8_R_R3

source_name: Rachis

value: Rachis

value: Vida

value: 2,4 EBR


title: M21 cells, KIT-K642E, DMSO, 24h, rep1

description: Library name: A21-4-1

value: skin

value: melanoma epithelial cells


title: Skin, TCR+GFP+, Isotype Control, TCR

description:
Library name: kTr1_TCR
10x Genomics

value: Skin


title: M21 cells, KIT-K642E, 100nM imatinib, 24h, rep3

description: Library name: A21-4+3

value: imatinib, 100nM, 24h


title: Stereotaxic brain tumor biopsy, patient 59, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_59

value: Glioblastoma


title: Stereotaxic brain tumor biopsy, patient 60, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_60

value: brain


title: Skin, CD45+TCR-, PC61-IL-2mutein 24, GEX

description:
Library name: km5_GEX
10x Genomics

value: GEX


title: M21 cells, KIT-K642E, 100nM imatinib, 24h, rep2

description: Library name: A21-4+2


title: BR_L_8_R_R1

description:
Library name: P16-R1-R
Sample removed from final analysis


title: Stereotaxic brain tumor biopsy, patient 58, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_58

value: female

value: FFPE stereotaxic biopsy


title: DM_L_8_R_R4

description:
Library name: P15-R4-R
Column name in NormalizedCounts: DM_L_8_R_R4

value: DMSO Control


title: Skin, CD45+TCR-, Fc-IL-2 mutein 24, GEX

description:
Library name: km2_GEX
10x Genomics

value: Fc-IL-2 mutein 24, s.c.


title: Stereotaxic brain tumor biopsy, patient 57, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_57

value: male


title: M21 cells, KIT-K642E, 100nM imatinib, 24h, rep1

description: Library name: A21-4+1


title: Skin, CD45+TCR-, Isotype Control, GEX

description:
Library name: km1_GEX
10x Genomics

value: Isotype Control, s.c.


title: DM_L_8_R_R3

description:
Library name: P15-R3-R
Column name in NormalizedCounts: DM_L_8_R_R3


title: Stereotaxic brain tumor biopsy, patient 56, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_56


title: M21 cells, KIT-L576P, DMSO, 24h, rep3

description: Library name: A21-3-3

value: DMSO


title: DM_L_8_R_R2

description:
Library name: P15-R2-R
Column name in NormalizedCounts: DM_L_8_R_R2

value: Rachis


title: M21 cells, KIT-L576P, DMSO, 24h, rep2

description: Library name: A21-3-2


title: Skin, TCR+GFP-, Fc-IL-2 mutein 24, GEX

description:
Library name: kTc2_GEX
10x Genomics

value: Conventional T cell


title: Stereotaxic brain tumor biopsy, patient 55, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_55

value: Diffuse glioma


title: Skin, TCR+GFP-, PC61-IL-2mutein 24, GEX

description:
Library name: kTc5_GEX
10x Genomics

value: PC61-IL-2mutein 24, s.c.


title: DM_L_8_R_R1

description:
Library name: P15-R1-R
Column name in NormalizedCounts: DM_L_8_R_R1

value: Vida


title: M21 cells, KIT-L576P, DMSO, 24h, rep1

description: Library name: A21-3-1

value: skin

value: melanoma epithelial cells


title: Stereotaxic brain tumor biopsy, patient 54, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_54

value: Glioblastoma


title: Skin, TCR+GFP-, Isotype Control, GEX

description:
Library name: kTc1_GEX
10x Genomics

value: Skin


title: DM_L_16_R_R4

description:
Library name: P14-R4-R
Column name in NormalizedCounts: DM_L_16_R_R4


title: M21 cells, KIT-L576P, 100nM imatinib, 24h, rep3

description: Library name: A21-3+3

value: imatinib, 100nM, 24h


title: Stereotaxic brain tumor biopsy, patient 53, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_53

value: brain

value: female


title: Skin, TCR+GFP+, PC61-IL-2mutein 24, GEX

description:
Library name: kTr5_GEX
10x Genomics

value: Treg

value: GEX


title: M21 cells, KIT-L576P, 100nM imatinib, 24h, rep2

description: Library name: A21-3+2


title: Stereotaxic brain tumor biopsy, patient 52, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_52

value: male

value: FFPE stereotaxic biopsy


title: DM_L_16_R_R3

description:
Library name: P14-R3-R
Column name in NormalizedCounts: DM_L_16_R_R3

value: DMSO Control


title: Skin, TCR+GFP+, Fc-IL-2 mutein 24, GEX

description:
Library name: kTr2_GEX
10x Genomics

value: Fc-IL-2 mutein 24, s.c.


title: M21 cells, KIT-L576P, 100nM imatinib, 24h, rep1

description: Library name: A21-3+1

source_name: skin


title: DM_L_16_R_R2

description:
Library name: P14-R2-R
Column name in NormalizedCounts: DM_L_16_R_R2

value: Rachis


title: Stereotaxic brain tumor biopsy, patient 51, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_51


title: DM_L_16_R_R1

description:
Library name: P14-R1-R
Column name in NormalizedCounts: DM_L_16_R_R1


title: M21 cells, KIT-Amplification, DMSO, 24h, rep3

description: Library name: A21-2-3

value: KIT-Amplification

value: DMSO


title: Stereotaxic brain tumor biopsy, patient 50, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_50

value: Diffuse glioma


title: Illumina-PHD1-KD-IAA48h_R3

city: La Tronche

first: Christopher

last: Swale

address: Batiment Jean Roger

department: U1209 - Institute of Advanced Biosciences

country: France

institute: INSERM

description: Library name: Sample 18

data_processing:
The quality of the raw sequencing reads was assessed using FastQC (www.bioinformatics. babraham.ac.uk/projects/fastqc/) and MultiQC. For the expression data quantification and normalization, the FASTQ reads were aligned  T. gondii ME49 genome using Subread version 2.0.1 with the following options ‘subread-align -d 50 -D 600 --sortReadsByCoordinates’. Read counts for each gene were calculated using featureCounts from the Subread package.
Assembly: TGME49 version 67
Supplementary files format and content: Count file or normalized TPM values in a .csv format

organism: Toxoplasma gondii

source_name: RH

growth_protocol: HFF cells were grown to confluence and infected with RHKU80 GCN5b or PHD1 mAID HA strains. For every library, a T180 plate was infected with 2ml of freshly egressed tachyzoites. At the time of harvest, the cells were scrapped and washed in fresh DPBS.

extract_protocol:
Total RNA was prepared using TRIzol extraction followed by RNAeasy column cleaning (Qiagen).
Messenger RNAs (mRNA) were purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, strand-specific sequencing) and generated ~40 million paired-end reads for each sample.

treatment_protocol: Cells were left untreated or supplemented with indole-3-acetic acid (IAA).

value: RH

value: Intracellular tachyzoites

value: IAA treated for 48h


title: DM_H_16_R_R4

description:
Library name: P13-R4-R
Column name in NormalizedCounts: DM_H_16_R_R4

value: Vida


title: M21 cells, KIT-Amplification, DMSO, 24h, rep2

description: Library name: A21-2-2

value: skin

value: melanoma epithelial cells


title: Stereotaxic brain tumor biopsy, patient 49, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_49

value: brain


title: Illumina-PHD1-KD-IAA48h_R2

description: Library name: Sample 17


title: M21 cells, KIT-Amplification, DMSO, 24h, rep1

description: Library name: A21-2-1


title: Stereotaxic brain tumor biopsy, patient 48, Glioblastoma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_48

value: Glioblastoma


title: DM_H_16_R_R3

description:
Library name: P13-R3-R
Column name in NormalizedCounts: DM_H_16_R_R3


title: DM_H_16_R_R2

description:
Library name: P13-R2-R
Column name in NormalizedCounts: DM_H_16_R_R2


title: M21 cells, KIT-Amplification, 100nM imatinib, 24h, rep3

description: Library name: A21-2+3

value: imatinib, 100nM, 24h


title: Stereotaxic brain tumor biopsy, patient 47, unclassified brain lesion

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_47

value: unclassified brain lesion

value: male


title: DM_H_16_R_R1

description:
Library name: P13-R1-R
Column name in NormalizedCounts: DM_H_16_R_R1

source_name: Rachis

value: DMSO Control


title: M21 cells, KIT-Amplification, 100nM imatinib, 24h, rep2

description: Library name: A21-2+2


title: Stereotaxic brain tumor biopsy, patient 46, Diffuse glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_46

value: female

value: FFPE stereotaxic biopsy


title: BR_H_0_R_R4

description:
Library name: P12-R4-R
Column name in NormalizedCounts: BR_H_0_R_R4

value: Rachis

value: 2,4 EBR


title: M21 cells, KIT-Amplification, 100nM imatinib, 24h, rep1

description: Library name: A21-2+1

value: KIT-Amplification


title: Illumina-PHD1-KD-IAA24h_R2

description: Library name: Sample 14

value: RH

value: IAA treated for 24h


title: Stereotaxic brain tumor biopsy, patient 45, Circumscribed glioma

source_name: FFPE stereotaxic brain tumor biopsy, patient STX_45

value: Circumscribed glioma


title: Illumina-PHD1-KD-IAA24h_R1

description: Library name: Sample 13

value: Intracellular tachyzoites


title: BR_H_0_R_R3

description:
Library name: P12-R3-R
Column name in NormalizedCounts: BR_H_0_R_R3

value: Vida


title: M21 cells, CTR, DMSO, 24h, rep3

description: Library name: A21-1-3

value: skin

value: melanoma epithelial cells

value: WT (Control)

value: DMSO


title: BR_H_0_R_R2

description:
Library name: P12-R2-R
Column name in NormalizedCounts: BR_H_0_R_R2


title: Illumina-PHD1-KD-UT_R3

description: Library name: Sample 12

value: untreated sample


title: M21 cells, CTR, DMSO, 24h, rep2

description: Library name: A21-1-2