title: FL317

description: Library name: FL317

data_processing:
Visium HD libraries were pre-processed using spaceranger v3.0.1.
Assembly: Visium Human Transcriptome Probe Set v2.0
Supplementary files format and content: Visium Spaceranger standard output
Library strategy: Spatial Transcriptomics

extract_protocol:
Tissue sections were deparaffinized and stained with hematoxylin (Sigma Aldrich, cat. GHS232) and eosin (Sigma Aldrich, cat. HT110116-500ML) (H&E) according to manufacturer protocol (Visium CytAssist Protocol CG000520). After H&E staining, slides were coverslipped with VWR Micro Cover Glasses (VWR, cat. 48393-241) and glycerol solution (Sigma Aldrich, cat. 49781) as mounting medium and whole slides were imaged on a Grundium Ocus 40 scanner. Slides were then de-coverslipped according to manufacturer protocol and stored at 4°C with dessicator until being processed on the CytAssist. RNA was extracted from a separate slice of tissue for each case and DV200 was >30% for all used samples. For Visium HD, tissue deparaffinization and H&E staining was done according to the Visium HD manual (CG000684) using the staining solutions recommended by 10x Genomics. Whole Visium HD sections were imaged using a Grundium Ocus 40 scanner in the DFCI Pathology Core Lab.
After assembling two slides with the deparaffinized and stained tissue sections into a Tissue Slide Cassette, sections were de-stained and de-crosslinked, the human whole transcriptome probe panel was added to slides, and probe pair hybridization to their complementary target RNA proceeded overnight. Following washing, hybridized probe pairs were ligated. Following placement of the tissue slides and Visium slide in the Visium CytAssist instrument, probe release and probe capture on Visium slide were performed. The Visium slide was assembled into a Visium Cassette to perform probe extension. Eluted barcoded ligation products were transferred to PCR tubes for subsequent amplification, bead clean-up, and sequencing library preparation. The sequencing libraries were quantified using the Bioanalyzer DNA High Sensitivity Kit (Agilent 5067-4626). The libraries were sequenced on the Illumina NextSeq 1000 using P2-100cycle kits or Illumina NovaSeq SP 100cycle kit. The sequencing parameters for Visium HD libraries were: Read 1: 43nt, Read 2: 50nt, Index 1: 10nt, Index 2: 10nt.

tag: disease

value: admixed FL and tFL


title: Bcell-rich region for tFL-pt8 ROI A48

status: Public on Aug 04 2026

type: SRA

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

state: MA

address: 75 Ames St

country: USA

institute: Broad Institute

description: Library name: tFL_TMA_A_20250520_A48_Bcell

library_source: transcriptomic

data_processing:
Cell segmentation was performed using the MESMER model of DeepCell version 0.12.2(Van Valen et al. 2016; Greenwald et al. 2022), with maxima_threshold set to 0.075 and interior_threshold set to 0.05. The nuclear channel input of MESMER was SYTO13. The membrane channel input of MESMER was a summation of CD3 and CD68. For each marker, the pixel value within the area of each cell, determined by the segmentation mask, was summed and then divided by the area of each cell, and the resulting cell-size scaled sum was set as the expression value for a given marker. Each cell from each core was identified by unique cell label and tissue ID.
Cell phenotyping was performed through iterative rounds of clustering and annotating processes with PhenoGraph based on the phenotyping marker enrichment profiles(Levine et al. 2015). Clustering results were plotted as heatmaps showing the Z-score of each marker within each cluster, and were annotated based on the combination of markers that had the highest Z-score in that cluster. PAX5, CD3 and CD68 were used to annotate the general cell types of B/tumor, T and myeloid cells, respectively. Cells that showed unclear marker enrichment patterns were annotated as “Other” cells.
After an initial round of clustering with PhenoGraph was performed, clusters with clear enrichment patterns were annotated, while clusters with mixed patterns underwent additional rounds of iterative clustering and annotation until all identifiable cells were annotated. To visualize and confirm the assigned annotations, Mantis Viewer(Schiemann et al. 2020) was used to overlay the annotations onto the segmentation mask and the marker image, for visual inspection. A segmentation mask for each annotated cell population was iteratively generated, and these masks were re-uploaded to the GeoMx to guide cell-type specific genome-wide transcriptome extraction.
Assembly: (v1.0) Human NGS Whole Transcriptome Atlas RNA
Supplementary files format and content: Excel containing AOI expression counts and metadata
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Lymph Node

extract_protocol:
FFPE tissue slides were baked in an oven (VWR, 10055-006) at 70°C for 1 hr and thoroughly deparaffinized by immersing in xylenes for 2× 5 minutes. The slides were then rehydrated by a series of graded solutions using a linear stainer (Leica Biosystems, ST4020), with each step proceeding for 3 minutes: 3× xylene, 2× 100% ethanol (EtOH), 2× 95% EtOH, 1× 80% EtOH, 1× 70% EtOH, 3× UltraPure water (Invitrogen 10977-023), and finally left in UltraPure water (Invitrogen 10977-023). Unless otherwise specified, all washes mentioned below were with gentle agitation. Antigen retrieval was performed at 97°C for 20 minutes with pH 9 Target Retrieval Solution (Agilent, S236784-2) using a PT Module (ThermoFisher, A80400012), after which the slides were cooled to room temperature on the benchtop and washed once in 1× PBS for 5 minutes. The RNA probe staining cocktail was prepared according to the Nanostring RNA slide Prep kit (Nanostring, 121300313) using the Nanostring Human Whole Transcriptome Atlas detection probe set (Nanostring, 121401102). The RNA probe cocktail was applied to the tissue slides, covered with a hybridization cover slip (EMS Diasum, 70329-40), and incubated at 37oC for 18 hrs. After hybridization, the tissue slides were first washed twice in Stringent Wash Buffer (mixing 4x SSC (Millipore Sigma, S6639) 1:1 with 100% formamide (Millipore Sigma, 344206-1L-M)) for 5 mins each at 37oC, and twice with 2x SSC for 5 mins each at room temperature (RT) on an orbital shaker .  Tissues were then stained with antibodies against PAX5, CD3 and CD68 for 1 hr at RT, in dark, followed by SYTO13 (100nM) for 10 mins at RT, in dark. The slides were then washed twice in 2x SSC for 2 mins each at RT and scanned on the GeoMx for ROI selection. One 660x660 μm square ROI was drawn in each core, resulting in a total of 72 ROI across the two TMA. Fibrotic areas were excluded from ROI selection for each core. ROIs were selected to achieve the maximum possible coverage of both intra- and inter-follicular regions in cores with distinct follicular structures, while in cores lacking clear follicular structures, ROIs were chosen based on the most representative antibody staining patterns. The spatial coordinates of each ROI were then recorded and used to register the ROI segmentation mask.
After transcriptome capture, unique molecular barcodes for the RNA probes were aspirated from each cell population to 96-well collection plates (Nanostring, 100473). Collection plates were then dried according to Nanostring instructions. Sequencing libraries were prepared by first resuspending each aspirate in 10 µL UltraPure water (Invitrogen 10977-023) and uniquely indexed with the Illumina i5×i7 dual indexing system as part of the Nanostring NGS library preparation kits (Nanostring, 121400201 & 121400202 & 121400203 & 121400204). PCR reactions were performed as follows: 37oC for 30 mins, 50oC for 10 mins, 95oC for 3 mins, followed by 18 cycles of 95oC for 15 s, 65oC for 50 s, 68oC for 30s, followed by a final extension of 68oC for 5 mins and hold indefinitely at 12oC. Next, 4 µL of PCR product from each well of the same plate was pooled and purified with AMPure XP beads (Beckman Coulter A63881) according to Nanostring’s instructions. Finally, QC was performed for the library with the Agilent TapeStation. Equal concentrations of each sub-library were pooled and 5% of PhiX sequencing control (Illumina FC-110-3002) was added to the library. The mixture was then subjected to paired-end sequencing with the NextSeq 2000 platform.

tag: tissue

value: Lymph Node

tag: sample id

tag: patient id

tag: disease binary

value: tFL

tag: disease fine


title: DD597-dedifferentiated-liposarcoma

type: RNA

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

hyb_protocol: cDNA was hybridized to HG U113A oligonucleotide arrays (Affymetrix, Inc.).

scan_protocol: Fluorescence was measured by laser confocal scanner (Agilent) and converted to signal intensity by means of Affymetrix Microarray Suite v5 software.

data_processing: CEL files were processed and normalized using gcrma methods implemented in the BioConductor package gcrma. Citation: Wu J, Gentry RIwcfJMJ (2023). gcrma: Background Adjustment Using Sequence Information. R package version 2.72.0.

label: biotin

source_name: surgical specimen

label_protocol: cDNA was synthesized in the presence of oligo(dT)24-T7 from Genset Corp. cRNA was prepared using biotinylated UTP and CTP.

extract_protocol: Cryomolds were prepared from tissue samples and macrodissected after evaluation by a sarcoma specific pathologist.  After histologic confirmation, RNA was prepared using Rneasy kits from QIAGEN and hybridization to U133A_2.0 gene expression arrays performed per standard protocols

value: dedifferentiated liposarcoma

tag: tumor site

value: retroperitoneal

tag: tumor grade

value: high

tag: treatement

value: surgery


title: MouseLiver_RNA_ImmuneCells_Ctrl_96hr

city: Edinburgh

first: Eleni

last: Papachristoforou

address: Edinburgh BioQuarter 4-5 Little France Drive

department: Institute for Regeneration and Repair

country: United Kingdom

institute: University of Edinburgh

description:
Library name: ML_RNA_Immune_Ctrl_96hr
10X Genomics Single cell 3' gene expression V2

library_source: transcriptomic single cell

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.1.0 Genome_build: mm10 (Ensembl 84)
Assembly: Mouse mm10
Supplementary files format and content: Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

organism: Mus musculus

source_name: liver

extract_protocol:
Enzymatic digestion and FACS 10X Genomics Single cell 3' gene expression V2
ScRNAseq was performed using the ChromiumTM Single Cell 3′ Library and Gel Bead Kit v2 (10X Genomics, PN-120237) and the ChromiumTM Single Cell A Chip Kit (10X Genomics, PN-120236) on the ChromiumTM Single Cell Platform (10X Genomics), according to manufacturer’s protocol. After FACS sorting, cells were washed and counted using the Bio-Rad TC20 cell counter (Bio-Rad). Approximately 12,000 cells were loaded on each lane of the chip. For scATACseq, after FACS sorting, cells were washed and nuclei isolated as described in the 10X Genomics demonstrated protocol (document number CG000169), including modifications for low cell input nuclei isolation. Nuclei were counted using a Countess II automated cell counter and processed for scATACseq using the Chromium™ Single Cell ATAC Library & Gel Bead Kit (10X Genomics, PN-1000111) and the Chromium™ Single Cell ATAC Chip E Kit (10X Genomics, PN-1000086), according to the manufacturers protocol. A nuclei recovery of 7000 per lane was targeted.

value: liver

tag: genotype

value: WT

tag: treatment

value: Healthy

tag: Sex

value: Male


title: DD41-dedifferentiated-liposarcoma


title: FL137

description: Library name: FL137


title: Tcell-rich region for tFL-pt8 ROI A48

description: Library name: tFL_TMA_A_20250520_A48_Tcell


title: LMF-normal-fat

value: normal fat

value: unknown


title: MouseLiver_RNA_ImmuneCells_Ctrl_24hr

description:
Library name: ML_RNA_Immune_Ctrl_24hr
10X Genomics Single cell 3' gene expression V2


title: FL58

description: Library name: FL58


title: Mac-rich region for tFL-pt8 ROI A48

description: Library name: tFL_TMA_A_20250520_A48_Mac


title: ESF1-normal-fat


title: MouseLiver_RNA_ImmuneCells_CCl4_4wk

description:
Library name: ML_RNA_Immune_CCl4_4wk
10X Genomics Single cell 3' gene expression V2


title: DD184-dedifferentiated-liposarcoma


title: DD103-dedifferentiated-liposarcoma


title: Con rep 3

city: Beijing

first: Wentong

last: Ge

address: South Lishi Road

department: Department of Head and Neck Surgery

country: China

institute: Beijing Children's Hospital, Capital Medical University, National Center for Children's Health

data_processing:
After removing adaptor sequence, clean reads were aligned to the  reference genome using HISAT2，and gene expression counts were calculated with HTSeq
Assembly: hg19
Supplementary files format and content: bam.tdf

molecule: polyA RNA

source_name: uncinate process tissue

extract_protocol:
Polyp tissues were obtained from ACP patients by means of functional endoscopic sinus surgery (FESS) performed. Meanwhile, mucosal tissues from the ipsilateral uncinate process (UP) with normal morphology of the same patients were obtained as a control group. Isolated fresh polyp and mucosal samples were quickly placed in an enzyme-free EP tube and immediately sent to RNA sequencing.
Sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the protocal and index codes were added to attribute sequences to each sample.

value: uncinate process tissue

tag: subject id


title: Others-rich region for tFL-pt209 ROI A46

description: Library name: tFL_TMA_A_20250520_A46_Others


title: FL33

description: Library name: FL33


title: Kidney_RNA Hes1 cKO 1 week of inactivation  mutant#3

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

data_processing:
The quality of the reads was verified using FASTQC and  sequences were aligned using STAR.  DESeq2 analysis was performed to determine differentially expressed genes.
Assembly: mm10/Mus_musculus.GRCm38
Supplementary files format and content: cvs files contain raw counts for each sample

source_name: kidney

growth_protocol: Adult mice from matings that produced Pax8->rtTa; TRE->Cre; Hes1 floxed/floxed and control littermates were housed separately based on sex.

extract_protocol:
Whole mouse kidneys were homogenized in lysis buffer (Qiagen) and total RNA was extracted from a portion of the lysate using RNeasy Mini kit (Qiagen).
Total kidney RNA was sequenced at Novogene to generate 150bp paired-end sequences on Illumina NovaSeq platform

treatment_protocol: All mice were provided doxycycline (1mg/mL; Sigma-Aldrich) in drinking water containing 5% sucrose for one week starting at 3 weeks of age and kidnyes collected for RNA extraction.

value: kidney

value: Female

value: Pax8-rtTA;TRE->Cre; Hes1 f/f


title: MouseLiver_ATAC_ImmuneCells_Ctrl_4wk

description:
Library name: ML_ATAC_Immune_Ctrl_4wk
10X Genomics Single cell 3' gene expression V2


title: FL14

description: Library name: FL14

value: admixed FL and tFL


title: MouseLiver_RNA_ImmuneCells_CCl4_96hr

description:
Library name: ML_RNA_Immune_CCl4_96hr
10X Genomics Single cell 3' gene expression V2


title: MouseLiver_RNA_ImmuneCells_CCl4_24hr

description:
Library name: ML_RNA_Immune_CCl4_24hr
10X Genomics Single cell 3' gene expression V2


title: Bcell-rich region for tFL-pt209 ROI A46

description: Library name: tFL_TMA_A_20250520_A46_Bcell

value: Lymph Node


title: RD, sgFANCM Tiling Screen, Tfinal Sample, Rep3

city: Durham

first: Christopher

middle: David

last: Delaney

state: NC

address: 308 Research Drive, LSRC C131

department: Pharmacology and Cancer Biology

institute: Duke University School of Medicine

description:
Library name: Library 51
Column name in FANCM_Tiling_Screen_sgRNA_ReadCounts.txt: RD_sgFANCMtiling_TfinalSample_Rep3

library_source: genomic

data_processing:
Raw FASTQ sequencing files were first quality tested with FastQC (RRID:SCR_014583). Read files were then merged across flow cell lanes when applicable.
The MAGeCK Count function from the MAGeCK pipeline (RRID:SCR_025016) was used to map sequences to sgRNA read counts.
In all MAGeCK analyses, read counts were normalized to a defined list of non-targeting control sgRNAs unique to each library using the Control normalization method. To obtain Beta (essentiality) scores, the MAGeCK maximum likelihood estimation (MLE) function from the MAGeCK VISPR pipeline was used.
For the Genome-scale screens, 2D and 3D Beta scores were obtained from MAGeCK MLE using Time Final samples compared to Plasmid Library samples. For the custom library essentiality screens, the four FP cell lines were merged and Beta scores were obtained from MAGeCK MLE using Time Final samples compared to Plasmid Library samples. The same analysis was performed separately for the two FN cell lines. For the PAX3::FOXO1-based flow screen, the P3F1 Depletion Score was equal to the Beta score from MAGeCK MLE using the sgRNA frequencies from bottom 10% population compared to the top 10% population. For the CKM-based flow screen, the four FP cell lines were merged and the CKM Depletion Score was equal to the Beta score from MAGeCK MLE using the sgRNA frequencies from bottom 10% population compared to the top 10% population. For the FANCM exon tiling screen, control normalized sgRNA counts were obtained from MAGeCK Count for the Rh4 Clone and RD cell lines and the Log10-Fold Change (LFC) of Rh4 Clone / RD normalized read counts was smoothened with a 0.1-weighted moving average in JMP Pro Version 17.0.0. This value was then standardized to compare relative depletion and plotted as Standardized Relative sgRNA Depletion (FP vs FN Cells).
Assembly: sgRNA reads were mapped to sgRNA library files
Supplementary files format and content: Tab-delimited texts files of  mapped sgRNA read counts
Supplementary files format and content: Included for each relevant screen are MACeCK-MLE output files with Beta (essentiality) scores and associated signficance
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: cell line

growth_protocol: All cells were maintained in a humidified incubator at 37C with 5% CO2. Cells were grown in RPMI 1640 (Gibco) medium with 10% fetal bovine serum (FBS, VWR) and 1% penicillin-streptomycin (P/S, Gibco).

extract_protocol:
For flow-based screens, collected cells were subjected to reverse-crosslinking and genomic DNA extraction using the Arcturus PicoPure DNA Extraction Kit (ThermoFisher). For the growth-based screens, Genomic DNA was extracted from cell pellets using the Quick-DNA Midiprep Plus Kit (Zymo Research) or DNeasy Blood & Tissue Kit (Qiagen).
Amplification of the sgRNA barcodes and indexing of each sample was performed via 2-step PCR as previously described using the NEBNext Ultra II Q5 Master Mix (NEB) (12). Amplified libraries were run on a 2% agarose gel and purified by QIAquick Gel Extraction Kit (Qiagen). Each DNA sample was quantified using the Quant-iT dsDNA High Sensitivity Assay Kit (ThermoFisher).

treatment_protocol: Cells were grown as detailed in the manuscript and pellets were harvested for genomic DNA.

value: cell line

tag: cell line

value: RD

tag: cell type

value: Rhabdomyosarcoma

value: Fusion-Negative

tag: screen

value: FANCM Exon Tiling Screen


title: DD112-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: retroperitoneal

value: high

value: surgery


title: DD150-dedifferentiated-liposarcoma


title: Tcell-rich region for tFL-pt209 ROI A46

description: Library name: tFL_TMA_A_20250520_A46_Tcell

value: tFL


title: Irradiated human skin

city: Stanford

last: Januszyk

state: CA

address: 257 Campus Dr

institute: Stanford University

description:
Library name: DA-19227_Irradiated_Human_Skin_b
Irradiated human skin

data_processing:
Single-cell RNA-seq (scRNA-seq) and associated quality control were performed on unsorted cells at the Stanford Functional Genomics Facility using the 10x Chromium Single Cell platform (Single Cell 3′ v3, 10X Genomics, Pleasanton, CA). After scRNA-seq, base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq and then aligned against the Cell Ranger GRCH38 human genome, using Cell Ranger’s count function with SC3Pv3 chemistry and a minimum of 5,000 expected cells per sample [14]. Thereafter, cells were filtered by unique molecular identifiers counts and the mitochondrial content ratio. Only cells with the mitochondrial content below or equal to 10% were retained. Filtering was followed by dimension-reduction and clustering using Seurat v3.1.2. Specifically, the ‘NormalizeData’ and ‘ScaleData’ functions were applied for the normalization and scaling of all gene expression. Next, we performed PCA analysis such that the top 15 principal components were selected to separate cells into clusters using Seurat’s ‘FindClusters’ function and visualized in a two-dimensional space, using a Louvain implementation of Seurat’s UMAP algorithm. SingleR was then applied using the Human Primary Cell Atlas reference dataset to ascribe cell type identities to each cluster.
Assembly: GRCH38
Supplementary files format and content: Both processed samples were submitted as separate .h5 files

source_name: skin

extract_protocol:
Tissue from all 6 paired irradiated and non-irradiated specimens were mechanically digested with scissors followed by Collagenase II (Cat No. 17,101,015; ThermoFisher Scientific) and IV (Cat No. 17,104,019; ThermoFisher Scientific) in DMEM (GIBCO; Fisher Scientific). Samples were added to an orbital shaker at 150 rpm for 90 min at 37oC, resuspended in FACS buffer, and filtered through 70 μm and then 40 μm cell strainers. Cell counts were performed to determine adequate cell survival. Single cell suspenstions were then processed using a 10X Chromium controller, and then underwent GEM generation and barcoding, post GEM incubation cleanup, library consutrction, and qualitative control on an Agilent Bioanalyzer High Sensitivity DNA chip (10x genomics protocol CG000496 Rev B). Libraries were pooled and cDNA libraries sequenced on the Illumina platform.
Single-cell RNA-seq (scRNA-seq) was performed at the Stanford Functional Genomics Facility (SFGF) for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) using the 10x Chromium Single Cell platform (Single Cell 3′ v3, 10X Genomics, Pleasanton, CA, USA). A droplet of the cell suspensions, reverse transcription master mix, and partitioning oil was loaded onto a single cell chip and processed on the Chromium Controller. Reverse Transcription was performed at 53 °C for 45 min. cDNA was amplified for 12 cycles total (BioRad C1000 Touch thermocycler) with cDNA size selected using SpriSelect beads (Beckman Coulter, Indianapolis, IN, USA) and a ratio of SpriSelect reagent volume to sample volume of 0.6. cDNA was analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA was fragmented using the proprietary fragmentation enzyme blend for 5 min at 32 °C, followed by end repair and A-tailing at 65 °C for 30 min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20 °C for 15 min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.

value: skin

value: unsorted

value: Irradiation

tag: batch

value: pooled


title: RD, sgFANCM Tiling Screen, Tfinal Sample, Rep2

description:
Library name: Library 50
Column name in FANCM_Tiling_Screen_sgRNA_ReadCounts.txt: RD_sgFANCMtiling_TfinalSample_Rep2


title: Mac-rich region for tFL-pt209 ROI A46

description: Library name: tFL_TMA_A_20250520_A46_Mac


title: WD844-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low


title: RD, sgFANCM Tiling Screen, Tfinal Sample, Rep1

description:
Library name: Library 49
Column name in FANCM_Tiling_Screen_sgRNA_ReadCounts.txt: RD_sgFANCMtiling_TfinalSample_Rep1


title: Non-irradiated human skin

description:
Library name: DA-19227_Normal_Human_Skin_b
Non-irradiated human skin

value: No treatment


title: Others-rich region for FL-FL34 ROI A42

description: Library name: tFL_TMA_A_20250520_A42_Others

value: Lymph Node

value: FL


title: Kidney_RNA  Hes1 cKO 1 week of inactivation  mutant#2

value: kidney

value: Male

value: Pax8-rtTA;TRE->Cre; Hes1 f/f


title: SCR_Untreated 2

city: chengdu

first: PAN

last: YiTong

address: Wangjiang Street

institute: Sichuan University

description: Library name: LR21E26FV20

data_processing:
Using the 2-pass mapping function of the STAR software, the original data was aligned to the genome.
Assembly: hg19
Supplementary files format and content: Matrix of Percent Spliced In (PSI) values for alternative splicing events across samples,csv format

source_name: lung

extract_protocol:
A549 stably expressing either scramble or shRNAs targeting hnRNP M were treated with 5 ng/ml TGFbeta for 72h or not. Next, cells were harvest in 1ml TRIzol for RNAseq.
Total RNA was extracted and probed to generate Ribo-zero libraries using the Ribo-off rRNA Depletion Kit and Vazyme ssDNA Library Prep kit for Illumina. Libraries were sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

value: lung

value: NSCLC


title: WD824-well-differentiated-liposarcoma

value: retroperitoneal


title: human_rpe_mbr_rna_4

city: Madison

first: Finn

last: Kuusisto

state: WI

address: 1205 University Ave

institute: University of Wisconsin-Madison

description: Library name: human_rpe_mbr_rna_4

data_processing:
Skop Lab - We use fastp (ver 0.23.4) quality filtering, adapter trimming, and quality profiling with default settings for paired-end. We use kallisto (ver 0.46.1) for quantification with an index k-mer size of 31, and otherwise default settings. We build the index against the Ensembl human cDNA FASTA for all genes, release 109.
Iwasaki Lab - Sequencing reads were processed as previously described (Kashiwagi et al. 2021; Mito et al. 2023). fastp (ver. 0.21.0) for the read quality filtering and adapter trimming. cutadapt (ver. 3.7) for demultiplexing by linker barcodes. UMI-tools (ver. 1.1.2) for deduplication based on unique molecule identifier. Alignment to genome with STAR v2.7.0a.
Assembly: hg38
Supplementary files format and content: Skop Lab - text files contain output of kallisto quant, five columns: 1. Ensembl transcript ID; 2. transcript length; 3. adjusted transcript length; 4. read counts; 5. TPM
Supplementary files format and content: Iwasaki Lab - text files contain three columns: 1. transcript name; 2. CDS region used for read counting; 3. read counts

source_name: RPE

extract_protocol:
Skop Lab - Cells were harvested when 80% confluent with Trypsin or Versene, counted, washed with 2 mL PBS and cell pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water. MBRs were isolated by ultracentrifugation of cleared culture media. Cells were cultured until 80% confluent. Culture media was collected and centrifuged at 1,000×g for 10 min to clear cell debris. Cleared culture media was transferred to ultracentrifuge tubes and centrifuged at 10,000×g for 30 min at 4°C. MBR pellets were washed with 2mL sterile PBS, centrifuged at 10,000×g for 30 min at 4°C and MBR pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water.
Iwasaki Lab - Cells were directly lysed in lysis buffer on culture dishes. Purification of desthiobiotinylated ribosomes and RNAs were performed. For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription and PCR amplification.
Skop Lab - For RNA-seq, libraries were prepared by Azenta Life Sciences using standard protocols to assess integrity, remove contaminants, and deplete ribosomal RNA. For RNA sequencing library preparation, the NEBNext Ultra II RNA Library Preparation Kit for Illumina was used according to the manufacturer’s instructions. Detailed steps and reagents are available from Azenta documentation upon request.
Iwasaki Lab - For Ribo-Seq, lysates were used for Thor‑Ribo‑Seq library preparation (Mito et al. 2023).

value: RPE

tag: lab

value: Skop


title: Rh4 Clone, sgFANCM Tiling Screen, Tfinal Sample, Rep3

description:
Library name: Library 48
Column name in FANCM_Tiling_Screen_sgRNA_ReadCounts.txt: Rh4Clone_sgFANCMtiling_TfinalSample_Rep3

tag: tissue

value: cell line

value: Rh4 Clone

value: Rhabdomyosarcoma

value: Fusion-Positive

value: FANCM Exon Tiling Screen


title: RNASeq_144 04_24_TDLN_d16

city: Cambridge

first: Richard

middle: Lee

last: Gieseck III

address: 1 Portland St.

institute: Pfizer, Inc.

description:
Library name: 04_24_TDLN_d16
study day=16; RIN=5.7; tumor_volume_mm3=337.59; sample_status=RNAlater

data_processing:
STAR Alignment v020201
bcl2fastq2 v2.20
RSEM v1.3.0
TPM and normalization using Data4Cure Biomedical Intelligence Cloud
Assembly: mm10
Supplementary files format and content: Tab-delimited matrix of log2(TPM) values by gene (HGNC filtered).

source_name: Tumor draining lymph node

growth_protocol: CT26 tumor-bearing BALB/c mouse study; tissue harvested at study day 16 or 23.

extract_protocol:
Total RNA extracted from collected tissues (spleen, tumor, TDLN) using study SOP.
Paired-end stranded mRNA-seq library prep with polyA enrichment.

treatment_protocol: Treatments include Isotype, PD1, CYTO, PD1/CYTO, TS/CYTO, and TS/PD1/CYTO per study design.

value: Tumor draining lymph node

value: BALB/c


title: Bcell-rich region for FL-FL34 ROI A42

description: Library name: tFL_TMA_A_20250520_A42_Bcell

value: Lymph Node

tag: sample id


title: WD780-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low

value: surgery


title: human_rpe_mbr_rna_3

description: Library name: human_rpe_mbr_rna_3


title: Rh4 Clone, sgFANCM Tiling Screen, Tfinal Sample, Rep2

description:
Library name: Library 47
Column name in FANCM_Tiling_Screen_sgRNA_ReadCounts.txt: Rh4Clone_sgFANCMtiling_TfinalSample_Rep2


title: Tcell-rich region for FL-FL34 ROI A42

description: Library name: tFL_TMA_A_20250520_A42_Tcell

tag: patient id

value: FL


title: WD745-well-differentiated-liposarcoma


title: human_rpe_mbr_rna_1

description: Library name: human_rpe_mbr_rna_1


title: WD734-well-differentiated-liposarcoma


title: Rh4 Clone, sgFANCM Tiling Screen, Tfinal Sample, Rep1

description:
Library name: Library 46
Column name in FANCM_Tiling_Screen_sgRNA_ReadCounts.txt: Rh4Clone_sgFANCMtiling_TfinalSample_Rep1


title: Mac-rich region for FL-FL34 ROI A42

description: Library name: tFL_TMA_A_20250520_A42_Mac

tag: disease binary


title: Mac-rich region for tFL-pt88-A ROI A50

description: Library name: tFL_TMA_A_20250520_A50_Mac

value: tFL

tag: disease fine

value: DLBCL


title: human_rpe_cell_rna_3

description: Library name: human_rpe_cell_rna_3


title: sgFANCM Tiling sgRNA Plasmid Library, Rep3

description:
Library name: Library 45
Column name in FANCM_Tiling_Screen_sgRNA_ReadCounts.txt: sgFANCMTiling_PlasmidLibrary_Rep3

source_name: plasmid

value: plasmid


title: WD419-well-differentiated-liposarcoma

tag: tumor site

value: retroperitoneal


title: human_rpe_cell_rna_2

description: Library name: human_rpe_cell_rna_2

value: RPE

value: Skop


title: Others-rich region for FL-pt90 ROI A41

description: Library name: tFL_TMA_A_20250520_A41_Others


title: Kidney_RNA Hes1 cKO 1 week of inactivation  mutant#1

value: kidney

value: Male

value: Pax8-rtTA;TRE->Cre; Hes1 f/f


title: human_rpe_cell_rna_1

description: Library name: human_rpe_cell_rna_1


title: Bcell-rich region for FL-pt90 ROI A41

description: Library name: tFL_TMA_A_20250520_A41_Bcell


title: sgFANCM Tiling sgRNA Plasmid Library, Rep2

description:
Library name: Library 44
Column name in FANCM_Tiling_Screen_sgRNA_ReadCounts.txt: sgFANCMTiling_PlasmidLibrary_Rep2

value: FANCM Exon Tiling Screen


title: WD727-well-differentiated-liposarcoma

tag: tumor grade


title: sgFANCM Tiling sgRNA Plasmid Library, Rep1

description:
Library name: Library 43
Column name in FANCM_Tiling_Screen_sgRNA_ReadCounts.txt: sgFANCMTiling_PlasmidLibrary_Rep1


title: WD724-well-differentiated-liposarcoma

tag: treatement


title: k19

city: Hongkong

first: Xin

last: Deng

state: 九龍

address: Tat Chee Road, City University of Hong Kong, AC1,B2315

department: BMS

country: Hong Kong

institute: City University of Hong Kong

description:
Library name: k19
DAP-seq

data_processing:
Quality-filtered paired reads were mapped to the reference genome, and gene-level quantification was performed using featureCounts (Subread v2.0.1) against annotated features. The resulting count matrix was analyzed using DESeq2 (v1.40.2).
Assembly: Genome assembly ASM585424v1
Supplementary files format and content: The bed file for each DAP-seq displayed the TF binding sites. The counts txt files contained the gene expression counts for each RNA-seq.

organism: Klebsiella pneumoniae

source_name: Klebsiella pneumoniae

growth_protocol: LB at 37 °C

extract_protocol:
Total RNA was extracted using RNAprep Pure Cell/Bacteria Kit (Tiangen, # Gdp430) and depleted of rRNA using NEBNext® rRNA Depletion Kit (Bacteria) (NEB, #E7850).
Libraries were constructed with NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, #E7770L) and sequenced on the Illumina Xten platform.

value: Klebsiella pneumoniae

value: strain

value: genotype

tag: genotype

value: WT

value: ChIP antibody


title: Tcell-rich region for FL-pt90 ROI A41

description: Library name: tFL_TMA_A_20250520_A41_Tcell

value: Lymph Node


title: WD707-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low

value: surgery


title: ARMS (FP-Relevant + Foundation) sgRNA Plasmid Library, Rep3

description:
Library name: Library 8
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: ARMS_PlasmidPool_Rep3

organism: unidentified

value: plasmid

tag: treatment

value: Custom sgRNA Essentiality


title: WD9343-well-differentiated-liposarcoma

value: retroperitoneal


title: human_mcf7_mbr_rna_6

description: Library name: human_mcf7_mbr_rna_6

value: Skop


title: Mac-rich region for FL-pt90 ROI A41

description: Library name: tFL_TMA_A_20250520_A41_Mac

value: FL


title: human_mcf7_mbr_rna_5

description: Library name: human_mcf7_mbr_rna_5


title: Others-rich region for tFL-pt6-B ROI A4

description: Library name: tFL_TMA_A_20250520_A4_Others

value: tFL


title: human_mcf7_mbr_rna_4

description: Library name: human_mcf7_mbr_rna_4


title: Bcell-rich region for tFL-pt6-B ROI A4

description: Library name: tFL_TMA_A_20250520_A4_Bcell


title: ARMS (FP-Relevant + Foundation) sgRNA Plasmid Library, Rep2

description:
Library name: Library 7
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: ARMS_PlasmidPool_Rep2


title: WD726-well-differentiated-liposarcoma


title: human_mcf7_cell_rna_2

description: Library name: human_mcf7_cell_rna_2


title: human_mcf7_cell_rna_3

description: Library name: human_mcf7_cell_rna_3


title: TKOv3 sgRNA Plasmid Library

description:
Library name: Library 1
Column name in Rh4Clone_GenomeScaleScreen_sgRNA_ReadCounts.txt: TKOv3_PlasmidPool

value: Genome-Scale Essentiality


title: Tcell-rich region for tFL-pt6-B ROI A4

description: Library name: tFL_TMA_A_20250520_A4_Tcell


title: ARMS (FP-Relevant + Foundation) sgRNA Plasmid Library, Rep1

description:
Library name: Library 6
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: ARMS_PlasmidPool_Rep1


title: PC3si_DUSP4

city: Clermont-Ferrand

first: Joris

last: Mordier

address: 28 place Henri Dunant Faculté de médecine, BP38

country: France

institute: iGReD

description:
Library name: Sample 6
Column in protein_coding_raw_counts_all_samples.tsv : PC3siDUSP4

data_processing:
Raw data were processed using Doctor Tom pipeline. Quality control, alignment, and expression quantification were performed according to the standard pipeline workflow
Gene-level read counts were generated from BAM files using featureCounts (Subread). Reads were assigned to exons using Ensembl GRCh38 release 116 gene annotation. Paired-end and multi-mapping reads were counted. The resulting count matrix was filtered to retain protein-coding genes only
RPKM values were calculated from the filtered raw count matrix by normalizing for gene length and library size using a custom R script
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with gene name, gene ID and raw counts for each sample
Supplementary files format and content: Tab-delimited text file with RPKM normalized values for each sample

source_name: Prostate

growth_protocol: Seeding 200000 per well , 6 wells plate, 24 H later tranfection

extract_protocol:
Rnas were extracted with Macherey-Nagel Kit
ssCirDNA

treatment_protocol: RNA imax  was  added according to the manufcaturer instruction with 10 µM of siRNAs for 48 H ours

value: Prostate

value: Human prostate cancer cells


title: WD725-well-differentiated-liposarcoma


title: Mac-rich region for tFL-pt6-B ROI A4

description: Library name: tFL_TMA_A_20250520_A4_Mac


title: WD721-well-differentiated-liposarcoma


title: k2

description:
Library name: k2
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: human_mcf7_cell_rna_1

description: Library name: human_mcf7_cell_rna_1


title: PC3si_DUSP3

description:
Library name: Sample 5
Column in protein_coding_raw_counts_all_samples.tsv : PC3siDUSP3


title: WD705-well-differentiated-liposarcoma


title: k18

description:
Library name: k18
DAP-seq

value: genotype

value: WT


title: Others-rich region for FL-pt203-B ROI A38

description: Library name: tFL_TMA_A_20250520_A38_Others

value: Lymph Node


title: WD706-well-differentiated-liposarcoma

value: well-differentiated liposarcoma


title: PC3si_DUSP2

description:
Library name: Sample 4
Column in protein_coding_raw_counts_all_samples.tsv : PC3siDUSP2


title: human_ipsc_mbr_rna_3

description: Library name: human_ipsc_mbr_rna_3

source_name: iPSC

value: iPSC


title: WD702-well-differentiated-liposarcoma

value: low

value: surgery


title: Bcell-rich region for FL-pt203-B ROI A38

description: Library name: tFL_TMA_A_20250520_A38_Bcell


title: PC3si_DUSP1

description:
Library name: Sample 3
Column in protein_coding_raw_counts_all_samples.tsv : PC3siDUSP1


title: Tcell-rich region for FL-pt203-B ROI A38

description: Library name: tFL_TMA_A_20250520_A38_Tcell


title: human_ipsc_mbr_rna_2

description: Library name: human_ipsc_mbr_rna_2


title: human_ipsc_mbr_rna_1

description: Library name: human_ipsc_mbr_rna_1


title: PC3si_control2

description:
Library name: Sample 2
Column in protein_coding_raw_counts_all_samples.tsv : PC3si_control2

value: control


title: Mac-rich region for FL-pt203-B ROI A38

description: Library name: tFL_TMA_A_20250520_A38_Mac


title: human_ipsc_cell_rna_3

description: Library name: human_ipsc_cell_rna_3


title: PC3si_control1

description:
Library name: Sample 1
Column in protein_coding_raw_counts_all_samples.tsv : PC3si_control1


title: WD696-well-differentiated-liposarcoma

value: retroperitoneal


title: WD701-well-differentiated-liposarcoma


title: Others-rich region for tFL-pt203-A ROI A37

description: Library name: tFL_TMA_A_20250520_A37_Others

value: DLBCL


title: human_ipsc_cell_rna_2

description: Library name: human_ipsc_cell_rna_2

value: Skop


title: SNP11_56h_IP_dataset3_replicate4

city: Baltimore

first: John

last: Kim

state: MD

address: 3400 Charles Street

department: Department of Biology

institute: Johns Hopkins University

description:
Library name: ChIP2023-012-SNPC11-56h-GN
snpc-1.1::3xflag 56h SNPC-1.1 ChIP-seq 56h IP dataset3 replicate4

data_processing:
Demultiplexed raw data were processed as described previously (Choi et al., 2021).
Global enrichment of SNPC-1.2 ChIP-seq signal at piRNA clusters on chromosome IV was assessed by calculating normalized read coverage across consecutive, non-overlapping 1-kb bins across the C. elegans genome.
Binding profiles and heatmaps for SNPC-1.1, SNPC-1.2, SNPC-1.3, and SNPC-4 at piRNA and snRNA loci were generated using MACS v2.1.2 (Zhang et al., 2008) and deepTools (Ramírez et al., 2016).
Fold-enrichment signal tracks were produced from read count-normalized genome-wide pileup and lambda track outputs using callpeak (bdgcmp in MACS2). Enrichment signal track regions overlapping with regions in the ENCODE ce 11 blacklist (https://github.com/Boyle-Lab/Blacklist/) were removed from further analysis.
Assembly: WBcel235
Supplementary files format and content: narrowPeak, bigWig

organism: Caenorhabditis elegans

source_name: germline nuclei

extract_protocol:
Liquid culture growth at 20°C was performed as described previously (Zanin et al., 2011). Approximately 2.5 million animals were grown per 2-L flask in 500 mL complete S Basal medium. For staged collections at 48 and 72 h post-L1 hatching, animals were harvested at 48 h and remaining animals were transferred to fresh complete S Basal containing HB101. For SNPC-1.2 ChIP, animals were cleaned by sucrose flotation prior to live cross-linking. Cross-linking was performed by nutating animals in 2.6% formaldehyde for 30 min at room temperature and quenched by addition of glycine (final concentration 0.125 M) for 5 min. Animals were then washed 3 times in water, flash-frozen in liquid nitrogen, and stored at -80°C until use.  ChIP was performed as described previously (Weiser et al., 2017), with the addition of proteinase K during de-crosslinking. Extracted DNA was resuspended in 18 µL 1 M Tris-EDTA pH 8 and 2 µL of 20 mg/mL RNase A (Invitrogen). SNPC-1.1 ChIP was performed using germline nuclei isolated from animals as described previously (Kirshner et al., 2025).
ChIP-seq libraries were prepared and multiplexed using the Ovation Ultralow Library Systems v2 kit (NuGEN Technologies) according to the manufacturer’s protocol. Libraries were sequenced as 50-bp paired-end reads on a NovaSeq 6000 platform (Illumina).

value: germline nuclei

tag: age

value: 56h young adult

tag: replicate

value: IP


title: Bcell-rich region for tFL-pt203-A ROI A37

description: Library name: tFL_TMA_A_20250520_A37_Bcell

value: tFL


title: WD691-well-differentiated-liposarcoma


title: human_ipsc_cell_rna_1

description: Library name: human_ipsc_cell_rna_1


title: Tcell-rich region for tFL-pt203-A ROI A37

description: Library name: tFL_TMA_A_20250520_A37_Tcell


title: SNP11_56h_input_dataset3_replicate4

description:
Library name: ChIP2023-011-SNPC11-56h-GN
snpc-1.1::3xflag 56h SNPC-1.1 ChIP-seq 56h input dataset3 replicate4

value: input


title: WD690-well-differentiated-liposarcoma


title: Mac-rich region for tFL-pt203-A ROI A37

description: Library name: tFL_TMA_A_20250520_A37_Mac


title: N2_56h_IP_dataset3_replicate4

description:
Library name: ChIP2023-010-N2-56h-GN
N2 56h SNPC-1.1 ChIP-seq IP dataset3 replicate4


title: WD688-well-differentiated-liposarcoma


title: human_hepg2_mbr_rna_2

description: Library name: human_hepg2_mbr_rna_2


title: SNP11_56h_IP_dataset3_replicate3

description:
Library name: ChIP2023-008-SNPC11-56h-GN
snpc-1.1::3xflag 56h SNPC-1.1 ChIP-seq 56h IP dataset3 replicate3


title: human_hepg2_cell_rna_3

description: Library name: human_hepg2_cell_rna_3


title: human_hepg2_mbr_rna_1

description: Library name: human_hepg2_mbr_rna_1


title: Bcell-rich region for tFL-pt220-A ROI A36

description: Library name: tFL_TMA_A_20250520_A36_Bcell


title: WD5700-well-differentiated-liposarcoma


title: N2_56h_input_dataset3_replicate4

description:
Library name: ChIP2023-009-N2-56h-GN
N2 56h SNPC-1.1 ChIP-seq input dataset3 replicate4


title: N2_56h_IP_dataset3_replicate3

description:
Library name: ChIP2023-006-N2-56h-GN
N2 56h SNPC-1.1 ChIP-seq IP dataset3 replicate3


title: WD602-well-differentiated-liposarcoma


title: human_hepg2_cell_rna_2

description: Library name: human_hepg2_cell_rna_2


title: WD0611-well-differentiated-liposarcoma


title: human_hepg2_cell_rna_1

description: Library name: human_hepg2_cell_rna_1


title: DD718-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: high


title: N2_56h_input_dataset3_replicate3

description:
Library name: ChIP2023-005-N2-56h-GN
N2 56h SNPC-1.1 ChIP-seq input dataset3 replicate3


title: SNP11_56h_IP_dataset3_replicate2

description:
Library name: ChIP2023-004-SNPC11-56h-GN
snpc-1.1::3xflag 56h SNPC-1.1 ChIP-seq IP dataset3 replicate2


title: human_hela_mbr_rna_3

description: Library name: human_hela_mbr_rna_3

source_name: HeLa

value: HeLa


title: Others-rich region for FL-pt206 ROI A35

description: Library name: tFL_TMA_A_20250520_A35_Others

value: Lymph Node

value: FL


title: Bcell-rich region for FL-pt206 ROI A35

description: Library name: tFL_TMA_A_20250520_A35_Bcell


title: DD717-dedifferentiated-liposarcoma


title: DD715-dedifferentiated-liposarcoma


title: Tcell-rich region for FL-pt206 ROI A35

description: Library name: tFL_TMA_A_20250520_A35_Tcell


title: DD714-dedifferentiated-liposarcoma


title: N2_56h_IP_dataset3_replicate2

description:
Library name: ChIP2023-002-N2-56h-GN
N2 56h SNPC-1.2 ChIP-seq IP dataset3 replicate2


title: Mac-rich region for FL-pt206 ROI A35

description: Library name: tFL_TMA_A_20250520_A35_Mac


title: human_hela_mbr_rna_1

description:
Library name: human_hela_mbr_rna_1
[removed from analysis]


title: Others-rich region for tFL-pt220-A ROI A36

description: Library name: tFL_TMA_A_20250520_A36_Others


title: Others-rich region for tFL-pt43 ROI A34

description: Library name: tFL_TMA_A_20250520_A34_Others


title: human_hela_cell_rna_3

description: Library name: human_hela_cell_rna_3


title: human_hela_cell_rna_2

description: Library name: human_hela_cell_rna_2


title: Bcell-rich region for tFL-pt43 ROI A34

description: Library name: tFL_TMA_A_20250520_A34_Bcell


title: SNPC4_SNPC12null_72h_IP_dataset2_replicate3

description:
Library name: ChIP2021-054-SNPC4_SNPC12null-72h-WW
snpc-4::3xflag; snpc-1.2(-) 72h SNPC-4 ChIP-seq IP dataset2 replicate3

source_name: whole worm

value: whole worm

value: 72h gravid adult

value: snpc-4::3xflag; snpc-1.2(-)


title: human_hela_cell_rna_1

description: Library name: human_hela_cell_rna_1


title: DD672-dedifferentiated-liposarcoma

value: surgery


title: human_esc_mbr_rna_6

description: Library name: human_esc_mbr_rna_6


title: Mac-rich region for tFL-pt43 ROI A34

description: Library name: tFL_TMA_A_20250520_A34_Mac

source_name: Lymph Node


title: human_esc_mbr_rna_5

description: Library name: human_esc_mbr_rna_5


title: SNPC4_SNPC13null_48h_IP_dataset2_replicate3

description:
Library name: ChIP2021-051-SNPC4_SNPC13null-48h-WW
snpc-4::3xflag; snpc-1.3(-) 48h SNPC-4 ChIP-seq IP dataset2 replicate3

value: snpc-4::3xflag; snpc-1.3(-)


title: DD621-dedifferentiated-liposarcoma

source_name: surgical specimen

value: retroperitoneal


title: SNPC4_48h_IP_dataset2_replicate3

description:
Library name: ChIP2021-050-SNPC4-48h-WW
snpc-4::3xflag 48h SNPC-4 ChIP-seq IP dataset2 replicate3


title: DD620-dedifferentiated-liposarcoma


title: N2_48h_IP_dataset2_replicate3

description:
Library name: ChIP2021-049-N2-48h-WW
N2 48h SNPC-4 ChIP-seq IP dataset2 replicate3


title: DD616-dedifferentiated-liposarcoma


title: Tcell-rich region for FL-pt58 ROI A33

description: Library name: tFL_TMA_A_20250520_A33_Tcell


title: DD615-dedifferentiated-liposarcoma


title: human_esc_cell_rna_2

description: Library name: human_esc_cell_rna_2

value: Skop


title: SNPC4_SNPC12null_72h_input_dataset2_replicate3

description:
Library name: ChIP2021-048-SNPC4_SNPC12null-72h-WW
snpc-4::3xflag; snpc-1.2(-) 72h SNPC-4 ChIP-seq input dataset2 replicate3


title: Mac-rich region for FL-pt58 ROI A33

description: Library name: tFL_TMA_A_20250520_A33_Mac


title: DD614-dedifferentiated-liposarcoma


title: human_esc_cell_rna_1

description: Library name: human_esc_cell_rna_1


title: Others-rich region for FL-pt83-B ROI A32

description: Library name: tFL_TMA_A_20250520_A32_Others


title: human_hela_mbr_rna_2

description: Library name: human_hela_mbr_rna_2


title: DD613-dedifferentiated-liposarcoma


title: DD712-dedifferentiated-liposarcoma


title: OA-24h

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
Quality of fastq files was assessed with FastQC v0.11.3, MultiQC v1.8.
Alignment and protein-coding gene quantification was performed using 10x cellranger v3.1.0
Normalization of expression was levels was performed with sctransform (Hafemeister and Satija, 2019)
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files of raw and post-QC normalized expression levels

source_name: human induced pluripotent stem cells, primary human cholangiocytes, human immortalised stellate cells line

growth_protocol: hIPSC-derived hepatocytes, macrophages, cholangiocytes and stellate cells were seeded at physiologic ratio and grown in a collagen based 3D system for up to 1week.

extract_protocol:
The single cell solution from each sample was loaded onto the Chromium single cell controller by 10X genomics, a droplet-based single cell capture platform.
Single cells were lysed and tagged by a bead containing unique molecular identifiers (UMIs), and encapsulated in an oil droplet.; this emulsion was amplified through reverse-transcription, and subsequent library preparation was performed following the 10X Genomics manual instructions.

treatment_protocol: 3D co-cultures were treated with free fatty acids (Oleic Acid or Palmitic Acid) for 24hrs up to 1week.

value: oleic acid 0.25uM

tag: time point

value: 24 hours

tag: disease state

value: NAFLD


title: N2_72h_input_dataset2_replicate3

description:
Library name: ChIP2021-046-N2-72h-WW
N2 72h SNPC-4 ChIP-seq input dataset2 replicate3


title: N2_56h_input_dataset3_replicate2

description:
Library name: ChIP2023-001-N2-56h-GN
N2 56h SNPC-1.2 ChIP-seq input dataset3 replicate2

value: germline nuclei

value: 56h young adult


title: DD711-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma


title: Bcell-rich region for FL-pt83-B ROI A32

description: Library name: tFL_TMA_A_20250520_A32_Bcell


title: SNPC4_SNPC13null_48h_input_dataset2_replicate3

description:
Library name: ChIP2021-045-SNPC4_SNPC13null-48h-WW
snpc-4::3xflag; snpc-1.3(-) 48h SNPC-4 ChIP-seq input dataset2 replicate3

value: input


title: Tcell-rich region for FL-pt83-B ROI A32

description: Library name: tFL_TMA_A_20250520_A32_Tcell


title: DD612-dedifferentiated-liposarcoma

value: high


title: OA-1wk

value: 1 week


title: DD611-dedifferentiated-liposarcoma


title: Mac-rich region for FL-pt83-B ROI A32

description: Library name: tFL_TMA_A_20250520_A32_Mac

value: Lymph Node

value: FL


title: human_esc_mbr_rna_4

description: Library name: human_esc_mbr_rna_4

tag: cell type


title: PA-1wk

value: palmitic acid 0.25uM


title: Others-rich region for FL-pt65-B ROI A31

description: Library name: tFL_TMA_A_20250520_A31_Others


title: CTRL

value: control sample

value: Healthy


title: SNPC4_SNPC12null_72h_IP_dataset2_replicate2

description:
Library name: ChIP2021-042-SNPC4_SNPC12null-72h-WW
snpc-4::3xflag; snpc-1.2(-) 72h SNPC-4 ChIP-seq IP dataset2 replicate2

value: whole worm

value: 72h gravid adult

value: snpc-4::3xflag; snpc-1.2(-)

value: IP


title: Bcell-rich region for FL-pt65-B ROI A31

description: Library name: tFL_TMA_A_20250520_A31_Bcell


title: WD784

type: genomic

hyb_protocol: genomic DNA was hybridized to Agilent 244K or 1M oligonucleotide arrays per manufacturer's instructions in the presence of a DNA reference set (Human Genomic DNA from blood (buffy coat); Roche Applied Science)

scan_protocol: Arrays were scanned using an Agilent Technologies Scanner G2505C at 3 microns per pixel resolution in two-color mode. Images were extracted using Agilent Feature Extraction software version 10.2.1.3.

data_processing:
Array comparative genomic hybridization (aCGH) was performed using Agilent 244K or 1M arrays and analyzed using the RAE pipeline as previously reported.(14, 28).
progV2aCGHMatrixTable_260619_v2__final.csv: Log2 ratio of Cy5 (sample) to Cy3 (reference) signal intensities, background-corrected and dye-normalized by Agilent Feature Extraction software.

source_name: Human Genomic DNA, blood (buffy coat), Roche Applied Science

label_protocol: per Agilent protocols

growth_protocol: not applicable

treatment_protocol: not applicable

value: blood (buffy coat)

tag: tumor class

value: Well-differentiated

value: retroperitoneal


title: Tcell-rich region for FL-pt65-B ROI A31

description: Library name: tFL_TMA_A_20250520_A31_Tcell


title: DD598-dedifferentiated-liposarcoma

value: surgery


title: DD0728-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma


title: WD781


title: N2_72h_IP_dataset2_replicate2

description:
Library name: ChIP2021-040-N2-72h-WW
N2 72h SNPC-4 ChIP-seq IP dataset2 replicate2


title: Mac-rich region for FL-pt65-B ROI A31

description: Library name: tFL_TMA_A_20250520_A31_Mac


title: WD780


title: SNPC4_48h_input_dataset2_replicate3

description:
Library name: ChIP2021-044-SNPC4-48h-WW
snpc-4::3xflag 48h SNPC-4 ChIP-seq input dataset2 replicate3

value: input


title: NF8293-normal-fat

value: normal fat

value: unknown


title: SNPC4_SNPC13null_48h_IP_dataset2_replicate2

description:
Library name: ChIP2021-039-SNPC4_SNPC13null-48h-WW
snpc-4::3xflag; snpc-1.3(-) 48h SNPC-4 ChIP-seq IP dataset2 replicate2

value: snpc-4::3xflag; snpc-1.3(-)


title: N2_48h_input_dataset2_replicate3

description:
Library name: ChIP2021-043-N2-48h-WW
N2 48h SNPC-4 ChIP-seq input dataset2 replicate3


title: Others-rich region for FL-pt204 ROI A30

description: Library name: tFL_TMA_A_20250520_A30_Others

value: Lymph Node

value: FL


title: DD603-dedifferentiated-liposarcoma

value: high


title: WD778


title: WD695-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low


title: NF7583-normal-fat


title: human_hepg2_mbr_rna_3

description: Library name: human_hepg2_mbr_rna_3

tag: lab

value: Skop


title: SNPC4_48h_IP_dataset2_replicate2

description:
Library name: ChIP2021-038-SNPC4-48h-WW
snpc-4::3xflag 48h SNPC-4 ChIP-seq IP dataset2 replicate2

tag: tissue

value: whole worm


title: Bcell-rich region for FL-pt204 ROI A30

description: Library name: tFL_TMA_A_20250520_A30_Bcell

tag: sample id


title: WD756


title: DD2202-dedifferentiated-liposarcoma


title: Tcell-rich region for tFL-pt220-A ROI A36

description: Library name: tFL_TMA_A_20250520_A36_Tcell

tag: patient id

value: tFL

value: DLBCL


title: NF5821-normal-fat


title: N2_48h_IP_dataset2_replicate2

description:
Library name: ChIP2021-037-N2-48h-WW
N2 48h SNPC-4 ChIP-seq IP dataset2 replicate2

value: IP


title: SNP11_56h_input_dataset3_replicate3

description:
Library name: ChIP2023-007-SNPC11-56h-GN
snpc-1.1::3xflag 56h SNPC-1.1 ChIP-seq 56h input dataset3 replicate3

value: germline nuclei

value: 56h young adult


title: Tcell-rich region for FL-pt204 ROI A30

description: Library name: tFL_TMA_A_20250520_A30_Tcell

tag: disease binary


title: Mac-rich region for tFL-pt220-A ROI A36

description: Library name: tFL_TMA_A_20250520_A36_Mac

tag: disease fine


title: RNASeq_144 04_23_TDLN_d16

description:
Library name: 04_23_TDLN_d16
study day=16; RIN=7.9; tumor_volume_mm3=119.492107; sample_status=RNAlater

value: Tumor draining lymph node

tag: cell line

value: BALB/c

tag: batch


title: SNPC4_72h_IP_dataset2_replicate2

description:
Library name: ChIP2021-041-SNPC4-72h-WW
snpc-4::3xflag 72h SNPC-4 ChIP-seq IP dataset2 replicate2

value: 72h gravid adult


title: WD754

value: blood (buffy coat)

value: Well-differentiated

value: retroperitoneal


title: SNPC4_SNPC12null_72h_input_dataset2_replicate2

description:
Library name: ChIP2021-036-SNPC4_SNPC12null-72h-WW
snpc-4::3xflag; snpc-1.2(-) 72h SNPC-4 ChIP-seq input dataset2 replicate2

value: snpc-4::3xflag; snpc-1.2(-)

value: input


title: Mac-rich region for FL-pt204 ROI A30

description: Library name: tFL_TMA_A_20250520_A30_Mac

value: Lymph Node

value: FL


title: NF4640-normal-fat

value: normal fat

tag: tumor site

value: unknown

tag: tumor grade

tag: treatement

value: surgery


title: LysMcre;Nlrp3A350V;Il181r+/- 1

city: La Jolla

first: Rongbo

last: Li

address: 9500 Gilman Drive

department: Pediatrics

institute: UC San DIego

description:
Library name: SAMPLE 11
LysMcre_Nlrp3A350V_Il18r1 Summary.xlsx

data_processing:
FASTQ files were aligned to the GRCm38 mouse reference genome using STAR.
Assembly: mm10
Supplementary files format and content: Excel file with raw count for each sample.

source_name: Lung

extract_protocol:
Samples were homogenized using a tissuelyser (Qiagen) and RNA was RNA was purified using the RNAeasy mini Kit (Qiagen).
cDNA Libraries were constructed using the Illumina mRNA Stranded Prep (Illumina) and sequenced on the Illumina NovaSeq 6000 instrument, with 50 bp paired end reads.

value: Lung

tag: genotype


title: SNP11_56h_input_dataset3_replicate2

description:
Library name: ChIP2023-003-SNPC11-56h-GN
snpc-1.1::3xflag 56h SNPC-1.1 ChIP-seq input dataset3 replicate2

tag: age

tag: replicate

tag: treatment


title: WD753


title: DD670-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: high


title: SNPC4_72h_input_dataset2_replicate2

description:
Library name: ChIP2021-035-SNPC4-72h-WW
snpc-4::3xflag 72h SNPC-4 ChIP-seq input dataset2 replicate2

value: whole worm


title: Others-rich region for tFL-pt210-B ROI A29

description: Library name: tFL_TMA_A_20250520_A29_Others

value: tFL

value: DHL


title: WD736


title: N2_72h_input_dataset2_replicate2

description:
Library name: ChIP2021-034-N2-72h-WW
N2 72h SNPC-4 ChIP-seq input dataset2 replicate2

value: 72h gravid adult


title: Bcell-rich region for tFL-pt210-B ROI A29

description: Library name: tFL_TMA_A_20250520_A29_Bcell


title: WD734

value: blood (buffy coat)


title: SNPC4_SNPC13null_48h_input_dataset2_replicate2

description:
Library name: ChIP2021-033-SNPC4_SNPC13null-48h-WW
snpc-4::3xflag; snpc-1.3(-) 48h SNPC-4 ChIP-seq input dataset2 replicate2

value: snpc-4::3xflag; snpc-1.3(-)


title: Tcell-rich region for tFL-pt210-B ROI A29

description: Library name: tFL_TMA_A_20250520_A29_Tcell


title: DD668-dedifferentiated-liposarcoma

value: retroperitoneal


title: DD6518-dedifferentiated-liposarcoma


title: SNPC4_48h_input_dataset2_replicate2

description:
Library name: ChIP2021-032-SNPC4-48h-WW
snpc-4::3xflag 48h SNPC-4 ChIP-seq input dataset2 replicate2


title: Mac-rich region for tFL-pt210-B ROI A29

description: Library name: tFL_TMA_A_20250520_A29_Mac


title: WD726

value: Well-differentiated


title: N2_48h_input_dataset2_replicate2

description:
Library name: ChIP2021-031-N2-48h-WW
N2 48h SNPC-4 ChIP-seq input dataset2 replicate2

value: input


title: Others-rich region for FL-pt210-A ROI A28

description: Library name: tFL_TMA_A_20250520_A28_Others

value: Lymph Node


title: WD725


title: Tcell-rich region for FL-pt210-A ROI A28

description: Library name: tFL_TMA_A_20250520_A28_Tcell

value: FL


title: DD638-dedifferentiated-liposarcoma


title: SNPC4_72h_IP_dataset2_replicate1

description:
Library name: ChIP2021-029-SNPC4-72h-WW
snpc-4::3xflag 72h SNPC-4 ChIP-seq IP dataset2 replicate1

value: IP


title: WD724


title: Bcell-rich region for FL-pt210-A ROI A28

description: Library name: tFL_TMA_A_20250520_A28_Bcell


title: DD845-dedifferentiated-liposarcoma


title: DD841-dedifferentiated-liposarcoma


title: WD721


title: N2_72h_IP_dataset2_replicate1

description:
Library name: ChIP2021-028-N2-72h-WW
N2 72h SNPC-4 ChIP-seq IP dataset2 replicate1


title: Others-rich region for FL-pt220-A ROI A27

description: Library name: tFL_TMA_A_20250520_A27_Others


title: DD807-dedifferentiated-liposarcoma


title: WD706


title: DD793-dedifferentiated-liposarcoma


title: SNPC4_SNPC13null_48h_IP_dataset2_replicate1

description:
Library name: ChIP2021-027-SNPC4_SNPC13null-48h-WW
snpc-4::3xflag; snpc-1.3(-) 48h SNPC-4 ChIP-seq IP dataset2 replicate1


title: Bcell-rich region for FL-pt220-A ROI A27

description: Library name: tFL_TMA_A_20250520_A27_Bcell


title: Tcell-rich region for FL-pt220-A ROI A27

description: Library name: tFL_TMA_A_20250520_A27_Tcell


title: WD705


title: SNPC4_48h_IP_dataset2_replicate1

description:
Library name: ChIP2021-026-SNPC4-48h-WW
snpc-4::3xflag 48h SNPC-4 ChIP-seq IP dataset2 replicate1


title: WD704


title: DD789-dedifferentiated-liposarcoma


title: N2_48h_IP_dataset2_replicate1

description:
Library name: ChIP2021-025-N2-48h-WW
N2 48h SNPC-4 ChIP-seq IP dataset2 replicate1


title: SNPC4_SNPC12null_72h_input_dataset2_replicate1

description:
Library name: ChIP2021-024-SNPC4_SNPC12null-72h-WW
snpc-4::3xflag; snpc-1.2(-) 72h SNPC-4 ChIP-seq input dataset2 replicate1

value: snpc-4::3xflag; snpc-1.2(-)


title: WD702


title: DD744-dedifferentiated-liposarcoma

value: surgery


title: SNPC4_72h_input_dataset2_replicate1

description:
Library name: ChIP2021-023-SNPC4-72h-WW
snpc-4::3xflag 72h SNPC-4 ChIP-seq input dataset2 replicate1


title: Others-rich region for FL-pt205-A ROI A26

description: Library name: tFL_TMA_A_20250520_A26_Others


title: Bcell-rich region for FL-pt205-A ROI A26

description: Library name: tFL_TMA_A_20250520_A26_Bcell


title: WD703


title: M1-ChIP-seq_dTAG-MED15_HS_DMSO_rep1 (ChIP)

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

country: Japan

institute: Yokohama City University

description: Library name: Sample 39, ChIP

data_processing:
Raw paired-end sequence reads were subjected to quality control using FastQC (v0.12.1). For ChIP-seq data, Adapter sequences were trimmed and reads were quality filtered using fastp (fastp 0.23.2). Processed reads were mapped to the human genome (GRCh38) using Bowtie2 (version 2.4.2 64-bit) with default parameters. Mapped reads were converted to sorted BAM files and indexed using SAMtools (1.16.1). Normalized genome coverage tracks were generated using bamCoverage with CPM normalization. Peaks were identified using MACS2 (macs2 2.2.7.1), followed by peak annotation and motif analysis using HOMER.
For RNA-seq data, Raw paired-end RNA-seq reads were first subjected to quality control using FastQC (v0.12.1). Adapter trimming and quality filtering were performed with fastp, generating trimmed paired-end FASTQ files. Cleaned reads were aligned to the human reference genome (GRCh38) using STAR (2.7.8a) with default parameters. The STAR index was generated based on the Homo sapiens GRCh38 primary assembly and the corresponding Ensembl gene annotation (release 112). Aligned reads were output as coordinate-sorted BAM files, which were subsequently indexed using SAMtools (samtools 1.16.1). Genome-wide coverage tracks were generated from the sorted BAM files using bamCoverage with CPM normalizationto produce bigWig files for visualization. Transcript and gene expression levels were quantified using RSEM (v1.3.1) based on the STAR transcriptome-aligned BAM files.
Assembly: GRCh38
Supplementary files format and content: BigWig

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovin serum (FBS) and penicillin/streptomycin under 5% CO2 at 37 °C.

extract_protocol:
Total RNA was harvested using sepasol Sepasol-RNA I Super G and purified by phenol-chloroform extraction and ethanol precipitation method.
For ChIP, Cells were fixed with DSG for 30min and 1%PFA for 15min, after quenching and cell lysis, chromatin was sonimated using a Bioruptor Sonicator (30×30 s at maximum power, Diagenode, Denville, NJ).
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (rRNA Depletion Kit v2) (NEB#E7400L). 1µg of total RNA was used for the construction of sequencing libraries.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB#E7645L).

treatment_protocol: HCT116 cells were incubated at 43℃, 1hr for the HS treatment

tag: cell type

value: colon cancer cells

value: WT

value: HS

tag: chip antibody

value: MED1 (Abcam, #Ab64965)


title: WD701

tag: tumor class


title: DD671-dedifferentiated-liposarcoma

tag: tissue

value: dedifferentiated liposarcoma

value: high


title: N2_72h_input_dataset2_replicate1

description:
Library name: ChIP2021-022-N2-72h-WW
N2 72h SNPC-4 ChIP-seq input dataset2 replicate1

value: whole worm

value: 72h gravid adult


title: Tcell-rich region for FL-pt205-A ROI A26

description: Library name: tFL_TMA_A_20250520_A26_Tcell

data_processing:
Cell segmentation was performed using the MESMER model of DeepCell version 0.12.2(Van Valen et al. 2016; Greenwald et al. 2022), with maxima_threshold set to 0.075 and interior_threshold set to 0.05. The nuclear channel input of MESMER was SYTO13. The membrane channel input of MESMER was a summation of CD3 and CD68. For each marker, the pixel value within the area of each cell, determined by the segmentation mask, was summed and then divided by the area of each cell, and the resulting cell-size scaled sum was set as the expression value for a given marker. Each cell from each core was identified by unique cell label and tissue ID.
Cell phenotyping was performed through iterative rounds of clustering and annotating processes with PhenoGraph based on the phenotyping marker enrichment profiles(Levine et al. 2015). Clustering results were plotted as heatmaps showing the Z-score of each marker within each cluster, and were annotated based on the combination of markers that had the highest Z-score in that cluster. PAX5, CD3 and CD68 were used to annotate the general cell types of B/tumor, T and myeloid cells, respectively. Cells that showed unclear marker enrichment patterns were annotated as “Other” cells.
After an initial round of clustering with PhenoGraph was performed, clusters with clear enrichment patterns were annotated, while clusters with mixed patterns underwent additional rounds of iterative clustering and annotation until all identifiable cells were annotated. To visualize and confirm the assigned annotations, Mantis Viewer(Schiemann et al. 2020) was used to overlay the annotations onto the segmentation mask and the marker image, for visual inspection. A segmentation mask for each annotated cell population was iteratively generated, and these masks were re-uploaded to the GeoMx to guide cell-type specific genome-wide transcriptome extraction.
Assembly: (v1.0) Human NGS Whole Transcriptome Atlas RNA
Supplementary files format and content: Excel containing AOI expression counts and metadata
Library strategy: Spatial Transcriptomics

tag: sample id


title: SNPC4_SNPC13null_48h_input_dataset2_replicate1

description:
Library name: ChIP2021-021-SNPC4_SNPC13null-48h-WW
snpc-4::3xflag; snpc-1.3(-) 48h SNPC-4 ChIP-seq input dataset2 replicate1

value: snpc-4::3xflag; snpc-1.3(-)


title: Mac-rich region for FL-pt205-A ROI A26

description: Library name: tFL_TMA_A_20250520_A26_Mac

tag: patient id


title: WD698

value: blood (buffy coat)

value: retroperitoneal


title: WD696

value: Well-differentiated


title: SNPC4_48h_input_dataset2_replicate1

description:
Library name: ChIP2021-020-SNPC4-48h-WW
snpc-4::3xflag 48h SNPC-4 ChIP-seq input dataset2 replicate1

value: input


title: DD172-dedifferentiated-liposarcoma

data_processing: CEL files were processed and normalized using gcrma methods implemented in the BioConductor package gcrma. Citation: Wu J, Gentry RIwcfJMJ (2023). gcrma: Background Adjustment Using Sequence Information. R package version 2.72.0.


title: Others-rich region for FL-pt37 ROI A25

description: Library name: tFL_TMA_A_20250520_A25_Others

value: Lymph Node

tag: disease binary

value: FL


title: WD690


title: N2_48h_input_dataset2_replicate1

description:
Library name: ChIP2021-019-N2-48h-WW
N2  48h SNPC-4 ChIP-seq SNPC-4 ChIP-seq input dataset2 replicate1


title: WD685


title: WD828-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low


title: DD795-dedifferentiated-liposarcoma

value: surgery


title: Bcell-rich region for FL-pt37 ROI A25

description: Library name: tFL_TMA_A_20250520_A25_Bcell

tag: disease fine


title: SNPC12_SNPC4AID_72h_IP_dataset1_replicate3

description:
Library name: ChIP2021-018-SNPC12_SNPC4AID-72h-WW
snpc-1.2::3xflag; snpc-4::aid; Psun-1::tir1 72h SNPC-1.2 ChIP-seq IP dataset1 replicate3

value: IP


title: WD472


title: Mac-rich region for FL-pt37 ROI A25

description: Library name: tFL_TMA_A_20250520_A25_Mac


title: SNPC12_72h_IP_dataset1_replicate3

description:
Library name: ChIP2021-017-SNPC12-72h-WW
snpc-1.2::3xflag 72h SNPC-1.2 ChIP-seq IP dataset1 replicate3


title: WD1336-well-differentiated-liposarcoma


title: WD450


title: Others-rich region for FL-pt89 ROI A24

description: Library name: tFL_TMA_A_20250520_A24_Others


title: N2_72h_IP_dataset1_replicate3

description:
Library name: ChIP2021-016-N2-72h-WW
N2 72h SNPC-1.2 ChIP-seq IP dataset1 replicate3


title: DD783-dedifferentiated-liposarcoma


title: WD440


title: WD821_791-well-differentiated-liposarcoma


title: Bcell-rich region for FL-pt89 ROI A24

description: Library name: tFL_TMA_A_20250520_A24_Bcell


title: DD788-dedifferentiated-liposarcoma


title: SNPC12_SNPC4AID_72h_input_dataset1_replicate3

description:
Library name: ChIP2021-015-SNPC12_SNPC4AID-72h-WW
snpc-1.2::3xflag; snpc-4::aid; Psun-1::tir1 72h SNPC-1.2 ChIP-seq input dataset1 replicate3


title: WD368

value: extremity


title: SNPC12_72h_input_dataset1_replicate3

description:
Library name: ChIP2021-014-SNPC12-72h-WW
snpc-1.2::3xflag 72h SNPC-1.2 ChIP-seq input dataset1 replicate3


title: Tcell-rich region for FL-pt89 ROI A24

description: Library name: tFL_TMA_A_20250520_A24_Tcell


title: Mac-rich region for FL-pt220-A ROI A27

description: Library name: tFL_TMA_A_20250520_A27_Mac


title: WD3031


title: N2_72h_input_dataset1_replicate3

description:
Library name: ChIP2021-013-N2-72h-WW
N2 72h SNPC-1.2 ChIP-seq input dataset1 replicate3


title: WD1298-well-differentiated-liposarcoma


title: DD719-dedifferentiated-liposarcoma


title: Mac-rich region for FL-pt89 ROI A24

description: Library name: tFL_TMA_A_20250520_A24_Mac


title: WD286


title: NF1300-normal-fat

value: normal fat


title: SNPC12_SNPC4AID_72h_IP_dataset1_replicate2

description:
Library name: ChIP2021-012-SNPC12_SNPC4AID-72h-WW
snpc-1.2::3xflag; snpc-4::aid; Psun-1::tir1 72h SNPC-1.2 ChIP-seq IP dataset1 replicate2


title: Others-rich region for tFL-pt14-B ROI A23

description: Library name: tFL_TMA_A_20250520_A23_Others

value: tFL

value: DLBCL


title: NF1312-normal-fat


title: WD221


title: SNPC12_72h_IP_dataset1_replicate2

description:
Library name: ChIP2021-011-SNPC12-72h-WW
snpc-1.2::3xflag 72h SNPC-1.2 ChIP-seq IP dataset1 replicate2

value: whole worm


title: Bcell-rich region for tFL-pt14-B ROI A23

description: Library name: tFL_TMA_A_20250520_A23_Bcell


title: NF1311-normal-fat


title: WD200


title: N2_72h_IP_dataset1_replicate2

description:
Library name: ChIP2021-010-N2-72h-WW
N2 72h SNPC-1.2 ChIP-seq IP dataset1 replicate2

value: 72h gravid adult


title: WD190


title: NF1310-normal-fat


title: DD3516-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: high


title: Tcell-rich region for tFL-pt14-B ROI A23

description: Library name: tFL_TMA_A_20250520_A23_Tcell


title: SNPC12_SNPC4AID_72h_input_dataset1_replicate2

description:
Library name: ChIP2021-009-SNPC12_SNPC4AID-72h-WW
snpc-1.2::3xflag; snpc-4::aid; Psun-1::tir1 72h SNPC-1.2 ChIP-seq input dataset1 replicate2


title: WD1309-well-differentiated-liposarcoma

value: retroperitoneal


title: Mac-rich region for tFL-pt14-B ROI A23

description: Library name: tFL_TMA_A_20250520_A23_Mac


title: WD183

value: blood (buffy coat)

value: Well-differentiated


title: Others-rich region for FL-pt14-A ROI A22

description: Library name: tFL_TMA_A_20250520_A22_Others

value: Lymph Node


title: SNPC12_72h_input_dataset1_replicate2

description:
Library name: ChIP2021-008-SNPC12-72h-WW
snpc-1.2::3xflag 72h SNPC-1.2 ChIP-seq input dataset1 replicate2

value: input


title: WD1306-well-differentiated-liposarcoma

value: well-differentiated liposarcoma


title: DD783

value: Dedifferentiated


title: N2_72h_input_dataset1_replicate2

description:
Library name: ChIP2021-007-N2-72h-WW
N2 72h SNPC-1.2 ChIP-seq input dataset1 replicate2


title: Bcell-rich region for FL-pt14-A ROI A22

description: Library name: tFL_TMA_A_20250520_A22_Bcell

value: FL


title: DD1304-dedifferentiated-liposarcoma

value: surgery


title: DD779


title: SNPC12_SNPC4AID_72h_IP_dataset1_replicate1

description:
Library name: ChIP2021-006-SNPC12_SNPC4AID-72h-WW
snpc-1.2::3xflag; snpc-4::aid; Psun-1::tir1 72h SNPC-1.2 ChIP-seq IP dataset1 replicate1

value: IP


title: Tcell-rich region for FL-pt14-A ROI A22

description: Library name: tFL_TMA_A_20250520_A22_Tcell


title: Tcell-rich region for FL-pt37 ROI A25

description: Library name: tFL_TMA_A_20250520_A25_Tcell


title: WD1303-well-differentiated-liposarcoma

value: low


title: DD757


title: SNPC12_72h_IP_dataset1_replicate1

description:
Library name: ChIP2021-005-SNPC12-72h-WW
snpc-1.2::3xflag 72h SNPC-1.2 ChIP-seq IP dataset1 replicate1


title: DD1299-dedifferentiated-liposarcoma


title: Mac-rich region for FL-pt14-A ROI A22

description: Library name: tFL_TMA_A_20250520_A22_Mac


title: DD744


title: NF1246-normal-fat

value: normal fat


title: N2_72h_IP_dataset1_replicate1

description:
Library name: ChIP2021-004-N2-72h-WW
N2 72h SNPC-1.2 ChIP-seq IP dataset1 replicate1


title: Others-rich region for tFL-pt201-B ROI A21

description: Library name: tFL_TMA_A_20250520_A21_Others

value: tFL

value: DLBCL


title: SNPC12_SNPC4AID_72h_input_dataset1_replicate1

description:
Library name: ChIP2021-003-SNPC12_SNPC4AID-72h-WW
snpc-1.2::3xflag; snpc-4::aid; Psun-1::tir1 72h SNPC-1.2 ChIP-seq input dataset1 replicate1

value: whole worm

value: 72h gravid adult


title: DD733


title: Bcell-rich region for tFL-pt201-B ROI A21

description: Library name: tFL_TMA_A_20250520_A21_Bcell


title: DD720


title: WD1216-well-differentiated-liposarcoma


title: SNPC12_72h_input_dataset1_replicate1

description:
Library name: ChIP2021-002-SNPC12-72h-WW
snpc-1.2::3xflag 72h SNPC-1.2 ChIP-seq input dataset1 replicate1


title: DD719


title: Tcell-rich region for tFL-pt201-B ROI A21

description: Library name: tFL_TMA_A_20250520_A21_Tcell


title: N2_72h_input_dataset1_replicate1

description:
Library name: ChIP2021-001-N2-72h-WW
N2 72h SNPC-1.2 ChIP-seq input dataset1 replicate1


title: DD677-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: high


title: WD1210-well-differentiated-liposarcoma

value: retroperitoneal


title: Others-rich region for FL-pt201-A ROI A20

description: Library name: tFL_TMA_A_20250520_A20_Others


title: DD718

value: blood (buffy coat)


title: Tcell-rich region for FL-pt201-A ROI A20

description: Library name: tFL_TMA_A_20250520_A20_Tcell

value: Lymph Node


title: BaP-lineage adult male F1 whole brain, biological replicate 3

city: Corpus Christi

first: Nonnie

last: Cook

state: Texas

address: 6300 Ocean Drive

department: Life Sciences

institute: Texas A&M University-Corpus Christi

description:
Library name: TAM6
Whole-brain nuclei from a 6-month-old adult male F1 Japanese medaka. This fish was not directly exposed to benzo[a]pyrene and was derived from parents exposed to 1 µg/L benzo[a]pyrene for 21 days.

data_processing:
FASTQ reads were assessed for mean and per-base sequence quality, nucleotide composition, GC content, and the percentage of bases with Phred quality scores greater than Q30 using the provider-generated FASTQ quality report.
Reads were processed with 10x Genomics Cell Ranger and aligned to the Oryzias latipes reference assembly GCA_004347445.1. Gene-expression matrices were generated for TAM1-TAM6 and aggregated for downstream analysis.
Low-quality nuclei and genes with minimal expression were removed. Dimensionality reduction was performed using t-distributed stochastic neighbor embedding, and unsupervised clustering identified 14 transcriptionally distinct cell populations.
Cluster marker genes were identified by comparing expression in each cluster with all other clusters. Cell identities were assigned using cross-species reference mapping and hypergeometric overlap with published zebrafish and mouse single-cell datasets, followed by manual evaluation of biological plausibility.
Within each cluster, expression in BaP-lineage samples (TAM4-TAM6) was compared with control-lineage samples (TAM1-TAM3). Processed tables contain GeneSymbol, ratio_Treatment_vs_Control, pval_Treatment_vs_Control, and FDR_Treatment_vs_Control.
Assembly: Oryzias latipes reference assembly GCA_004347445.1
Supplementary files format and content: Fourteen tab-delimited text files are provided, one for each transcriptional cluster (clusters 0-13). Each file contains the complete cluster-level treatment-versus-control differential-expression results.
Supplementary files format and content: Each cluster file contains GeneSymbol, ratio_Treatment_vs_Control, pval_Treatment_vs_Control, and FDR_Treatment_vs_Control.

organism: Oryzias latipes

source_name: whole brain

growth_protocol: Parental breeding pairs and F1 offspring were maintained under standard Japanese medaka husbandry conditions. After parental exposure, eggs were collected daily, rinsed, and F1 offspring were reared in clean system water without further chemical exposure until adulthood.

extract_protocol:
Whole brains were rapidly dissected from 6-month-old adult male F1 medaka and frozen. Frozen tissue was immersed in nuclei isolation buffer, dispersed with a plastic pestle, transferred to a Dounce homogenizer, and filtered through a 30 µm filter. Recovered nuclei were counted using a Countess FLII automated cell counter.
Single-nucleus RNA-seq libraries were prepared from individual brain nuclei using the 10x Chromium Next GEM Single Cell 3' Gene Expression v3.1 Dual Index protocol, Rev. E (10x Genomics document CG000315). Libraries were prepared with a target of 8,000 nuclei per sample and sequenced at approximately 40,000 reads per nucleus using an Illumina sequencer.

treatment_protocol: At 6 months of age, adult parental breeding pairs were assigned to solvent-control or 1 µg/L benzo[a]pyrene (BaP) exposure groups and exposed for 21 days. Following exposure, eggs were collected daily and F1 offspring were reared in clean water. TAM1-TAM3 were derived from solvent-control parents; TAM4-TAM6 were derived from BaP-exposed parents. F1 fish were not directly exposed to BaP.

value: whole brain

value: mixed brain cell populations (nuclei)

value: 6 months

tag: parental exposure

tag: Sex

value: male

tag: generation

tag: direct exposure

value: none; F1 offspring were reared in clean water

value: single sequencing batch


title: DD717

value: Dedifferentiated


title: Bcell-rich region for FL-pt201-A ROI A20

last: Haradhvala

address: 75 Ames St

institute: Broad Institute

description: Library name: tFL_TMA_A_20250520_A20_Bcell

extract_protocol:
FFPE tissue slides were baked in an oven (VWR, 10055-006) at 70°C for 1 hr and thoroughly deparaffinized by immersing in xylenes for 2× 5 minutes. The slides were then rehydrated by a series of graded solutions using a linear stainer (Leica Biosystems, ST4020), with each step proceeding for 3 minutes: 3× xylene, 2× 100% ethanol (EtOH), 2× 95% EtOH, 1× 80% EtOH, 1× 70% EtOH, 3× UltraPure water (Invitrogen 10977-023), and finally left in UltraPure water (Invitrogen 10977-023). Unless otherwise specified, all washes mentioned below were with gentle agitation. Antigen retrieval was performed at 97°C for 20 minutes with pH 9 Target Retrieval Solution (Agilent, S236784-2) using a PT Module (ThermoFisher, A80400012), after which the slides were cooled to room temperature on the benchtop and washed once in 1× PBS for 5 minutes. The RNA probe staining cocktail was prepared according to the Nanostring RNA slide Prep kit (Nanostring, 121300313) using the Nanostring Human Whole Transcriptome Atlas detection probe set (Nanostring, 121401102). The RNA probe cocktail was applied to the tissue slides, covered with a hybridization cover slip (EMS Diasum, 70329-40), and incubated at 37oC for 18 hrs. After hybridization, the tissue slides were first washed twice in Stringent Wash Buffer (mixing 4x SSC (Millipore Sigma, S6639) 1:1 with 100% formamide (Millipore Sigma, 344206-1L-M)) for 5 mins each at 37oC, and twice with 2x SSC for 5 mins each at room temperature (RT) on an orbital shaker .  Tissues were then stained with antibodies against PAX5, CD3 and CD68 for 1 hr at RT, in dark, followed by SYTO13 (100nM) for 10 mins at RT, in dark. The slides were then washed twice in 2x SSC for 2 mins each at RT and scanned on the GeoMx for ROI selection. One 660x660 μm square ROI was drawn in each core, resulting in a total of 72 ROI across the two TMA. Fibrotic areas were excluded from ROI selection for each core. ROIs were selected to achieve the maximum possible coverage of both intra- and inter-follicular regions in cores with distinct follicular structures, while in cores lacking clear follicular structures, ROIs were chosen based on the most representative antibody staining patterns. The spatial coordinates of each ROI were then recorded and used to register the ROI segmentation mask.
After transcriptome capture, unique molecular barcodes for the RNA probes were aspirated from each cell population to 96-well collection plates (Nanostring, 100473). Collection plates were then dried according to Nanostring instructions. Sequencing libraries were prepared by first resuspending each aspirate in 10 µL UltraPure water (Invitrogen 10977-023) and uniquely indexed with the Illumina i5×i7 dual indexing system as part of the Nanostring NGS library preparation kits (Nanostring, 121400201 & 121400202 & 121400203 & 121400204). PCR reactions were performed as follows: 37oC for 30 mins, 50oC for 10 mins, 95oC for 3 mins, followed by 18 cycles of 95oC for 15 s, 65oC for 50 s, 68oC for 30s, followed by a final extension of 68oC for 5 mins and hold indefinitely at 12oC. Next, 4 µL of PCR product from each well of the same plate was pooled and purified with AMPure XP beads (Beckman Coulter A63881) according to Nanostring’s instructions. Finally, QC was performed for the library with the Agilent TapeStation. Equal concentrations of each sub-library were pooled and 5% of PhiX sequencing control (Illumina FC-110-3002) was added to the library. The mixture was then subjected to paired-end sequencing with the NextSeq 2000 platform.

value: FL


title: BaP-lineage adult male F1 whole brain, biological replicate 2

description:
Library name: TAM5
Whole-brain nuclei from a 6-month-old adult male F1 Japanese medaka. This fish was not directly exposed to benzo[a]pyrene and was derived from parents exposed to 1 µg/L benzo[a]pyrene for 21 days.

tag: batch


title: BaP-lineage adult male F1 whole brain, biological replicate 1

description:
Library name: TAM4
Whole-brain nuclei from a 6-month-old adult male F1 Japanese medaka. This fish was not directly exposed to benzo[a]pyrene and was derived from parents exposed to 1 µg/L benzo[a]pyrene for 21 days.


title: DD715

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

extract_protocol: Cryomolds were prepared from tissue samples and macrodissected after evaluation by a sarcoma specific pathologist.  After histologic confirmation, RNA was prepared using Rneasy kits from QIAGEN and hybridization to U133A_2.0 gene expression arrays performed per standard protocols


title: Mac-rich region for FL-pt201-A ROI A20

description: Library name: tFL_TMA_A_20250520_A20_Mac


title: DD1405-dedifferentiated-liposarcoma

tag: tumor site

tag: tumor grade

tag: treatement

value: surgery


title: DD1055-dedifferentiated-liposarcoma


title: DD714


title: control-lineage adult male F1 whole brain, biological replicate 3

description:
Library name: TAM3
Whole-brain nuclei from a 6-month-old adult male F1 Japanese medaka. This fish was not directly exposed to benzo[a]pyrene and was derived from solvent-control parents.

tag: age

value: parents exposed to solvent control for 21 days


title: WD698-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low


title: Others-rich region for FL-pt65-B ROI A19

description: Library name: tFL_TMA_A_20250520_A19_Others


title: DD712


title: WD804-well-differentiated-liposarcoma


title: DD1193-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma


title: control-lineage adult male F1 whole brain, biological replicate 2

description:
Library name: TAM2
Whole-brain nuclei from a 6-month-old adult male F1 Japanese medaka. This fish was not directly exposed to benzo[a]pyrene and was derived from solvent-control parents.

tag: cell type


title: Bcell-rich region for FL-pt65-B ROI A19

description: Library name: tFL_TMA_A_20250520_A19_Bcell


title: control-lineage adult male F1 whole brain, biological replicate 1

description:
Library name: TAM1
Whole-brain nuclei from a 6-month-old adult male F1 Japanese medaka. This fish was not directly exposed to benzo[a]pyrene and was derived from solvent-control parents.


title: Tcell-rich region for FL-pt65-B ROI A19

description: Library name: tFL_TMA_A_20250520_A19_Tcell


title: DD711


title: DD699


title: FTY720-L3_Visium Spatial Gene Expression (FFPE)

city: Seoul

first: Mingu

address: 222, Banpo-daero

country: South Korea

institute: The Catholic university of Korea

description: Library name: FTY720-L3

data_processing:
Demultiplexing and FASTQ generation were performed using Illumina BCL Convert (v4.3.6).
Raw read QC was assessed using FastQC.
Space Ranger (v4.0.1) “spaceranger count” was run using the mm10-2020-A reference and the matched tissue image to generate spatial gene-by-spot count matrices and QC metrics.
Space Ranger outputs (filtered matrices and QC summaries) were used for downstream clustering and differential expression as needed.
Assembly: Mus musculus mm10 (10x reference: mm10-2020-A)
Supplementary files format and content: Space Ranger (v4.0.1) filtered feature-barcode matrix provided as HDF5: (sample name)_filtered_feature_bc_matrix.h5 (spatial spot/barcode-by-gene UMI count matrix for each sample).
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
FFPE tissue sections were deparaffinized, stained/imaged, and processed using the Visium CytAssist Spatial Gene Expression for FFPE workflow. CytAssist-enabled RNA digestion and probe release enabled capture of released products on spatially barcoded oligonucleotides on the Visium slide.
Whole-transcriptome probe pairs were hybridized to target RNA in decrosslinked FFPE sections, followed by ligation to form probe products. Ligation products were released by RNase treatment and captured on the Visium slide. Captured products were extended to add UMI, spatial barcode, and partial Read 1, then harvested for qPCR to determine indexing PCR cycles. Libraries were generated by sample index PCR, cleaned up, QC’d, quantified, and sequenced on an Illumina platform.

treatment_protocol: Mice were subjected to a chronic-plus-binge ethanol feeding model (NIAAA) with or without daily fingolimod (FTY720, 1mg/kg/day) administration.

value: Liver

tag: genotype

value: wild-type

tag: treatment

value: Ethanol feeding+FTY720 (NIAAA model)

tag: strain

value: 8-10 weeks


title: Mac-rich region for FL-pt65-B ROI A19

city: CAMBRIDGE

first: Nicholas

description: Library name: tFL_TMA_A_20250520_A19_Mac

tag: tissue

value: Lymph Node

tag: sample id


title: DD693

city: New York

first: Bic

value: blood (buffy coat)

tag: tumor class

value: retroperitoneal


title: WD1158-well-differentiated-liposarcoma


title: FTY720-L2_Visium Spatial Gene Expression (FFPE)

description: Library name: FTY720-L2


title: DD1192-dedifferentiated-liposarcoma

value: high


title: DD1194-dedifferentiated-liposarcoma


title: WD727

value: Well-differentiated


title: Others-rich region for FL-pt65-A ROI A18

description: Library name: tFL_TMA_A_20250520_A18_Others

tag: patient id

tag: disease binary

tag: disease fine


title: DD639-dedifferentiated-liposarcoma


title: DD69


title: FTY720-I2_Visium Spatial Gene Expression (FFPE)

description: Library name: FTY720-I2

source_name: Intestine

value: Intestine


title: DD677

value: Dedifferentiated


title: Tcell-rich region for FL-pt65-A ROI A18

description: Library name: tFL_TMA_A_20250520_A18_Tcell

value: FL


title: Bcell-rich region for FL-pt65-A ROI A18

description: Library name: tFL_TMA_A_20250520_A18_Bcell


title: EtOH-L3_Visium Spatial Gene Expression (FFPE)

description: Library name: EtOH-L3

value: Ethanol feeding (NIAAA model)


title: WD1568-well-differentiated-liposarcoma

value: surgery


title: DD1196-dedifferentiated-liposarcoma


title: DD673


title: SNPC4_SNPC12null_72h_IP_dataset2_replicate1

description:
Library name: ChIP2021-030-SNPC4_SNPC12null-72h-WW
snpc-4::3xflag; snpc-1.2(-) 72h SNPC-4 ChIP-seq IP dataset2 replicate1

value: whole worm

value: 72h gravid adult

tag: replicate

value: snpc-4::3xflag; snpc-1.2(-)

value: IP


title: Mac-rich region for FL-pt65-A ROI A18

description: Library name: tFL_TMA_A_20250520_A18_Mac


title: DD672


title: EtOH-L2_Visium Spatial Gene Expression (FFPE)

description: Library name: EtOH-L2

value: Liver

value: wild-type


title: DD1195-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma


title: Others-rich region for tFL-pt69-A ROI A17

description: Library name: tFL_TMA_A_20250520_A17_Others

value: Lymph Node

value: tFL

value: DLBCL


title: EtOH-I2_Visium Spatial Gene Expression (FFPE)

description: Library name: EtOH-I2

value: 8-10 weeks


title: WD3031-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: retroperitoneal

value: low


title: Control-L3_Visium Spatial Gene Expression (FFPE)

description: Library name: Control-L3

value: Control (NIAAA model)


title: DD671

value: blood (buffy coat)

value: Dedifferentiated


title: Bcell-rich region for tFL-pt69-A ROI A17

description: Library name: tFL_TMA_A_20250520_A17_Bcell


title: DD670


title: Mac-rich region for tFL-pt69-A ROI A17

description: Library name: tFL_TMA_A_20250520_A17_Mac


title: Control-L2_Visium Spatial Gene Expression (FFPE)

description: Library name: Control-L2


title: DD668


title: DD1159-dedifferentiated-liposarcoma

value: high

value: surgery


title: DD786-dedifferentiated-liposarcoma


title: DD1129-dedifferentiated-liposarcoma


title: Control-I2_Visium Spatial Gene Expression (FFPE)

description: Library name: Control-I2

value: Intestine


title: Tcell-rich region for tFL-pt69-A ROI A17

description: Library name: tFL_TMA_A_20250520_A17_Tcell


title: DD639


title: Others-rich region for FL-pt85 ROI A16

description: Library name: tFL_TMA_A_20250520_A16_Others

value: FL


title: WD1362-well-differentiated-liposarcoma


title: FTY720-L_Visium Spatial Gene Expression (FFPE)

description:
Library name: FTY720-L
Strain: C57BL/6N; Age: 8-10 weeks

value: Liver

value: Ethanol feeding+FTY720 (NIAAA model)


title: DD638


title: Bcell-rich region for FL-pt85 ROI A16

description: Library name: tFL_TMA_A_20250520_A16_Bcell


title: FTY720-I_Visium Spatial Gene Expression (FFPE)

description:
Library name: FTY720-I
Strain: C57BL/6N; Age: 8-10 weeks

value: wild-type


title: DD6213


title: WD778-well-differentiated-liposarcoma


title: EtOH-L_Visium Spatial Gene Expression (FFPE)

description:
Library name: EtOH-L
Strain: C57BL/6N; Age: 8-10 weeks

value: Ethanol feeding (NIAAA model)


title: Tcell-rich region for FL-pt85 ROI A16

description: Library name: tFL_TMA_A_20250520_A16_Tcell

value: Lymph Node


title: DD606


title: Mac-rich region for FL-pt85 ROI A16

description: Library name: tFL_TMA_A_20250520_A16_Mac


title: EtOH-I_Visium Spatial Gene Expression (FFPE)

description:
Library name: EtOH-I
Strain: C57BL/6N; Age: 8-10 weeks


title: Control-L_Visium Spatial Gene Expression (FFPE)

description:
Library name: Control-L
Strain: C57BL/6N; Age: 8-10 weeks


title: DD597


title: WD1344-well-differentiated-liposarcoma


title: DD454


title: DD1346-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma


title: Tcell-rich region for FL-pt9 ROI A15

description: Library name: tFL_TMA_A_20250520_A15_Tcell


title: Control-I_Visium Spatial Gene Expression (FFPE)

description:
Library name: Control-I
Strain: C57BL/6N; Age: 8-10 weeks


title: NF1347-normal-fat

value: normal fat


title: DD442


title: spf3

city: Providence

first: Geongoo

last: Han

address: 171 Meeting St.

institute: Brown University

description: Library name: lkb_gh_dirty_spln_9

data_processing:
Adapter and low-quality sequences were trimmed from the raw sequence reads using Trimmomatic (v0.39)
Trimmed sequences were aligned to the mm10 mouse genome and reads per gene was counted using STAR (v2.7.10b)
Gene count was normalized in DESeq2 v1.38.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file raw counts for all samples
Supplementary files format and content: tab-delimited text file normalized counts by DESeq2 for all samples

source_name: Spleen

extract_protocol:
Small pieces of the spleen were stored in RNAlater (Invitrogen) and stored at −70 °C until RNA extraction. Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Spleen

tag: group

value: SPF

value: WT


title: Mac-rich region for FL-pt9 ROI A15

description: Library name: tFL_TMA_A_20250520_A15_Mac


title: WD1296-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: retroperitoneal

value: low


title: DD391

value: blood (buffy coat)

value: Dedifferentiated


title: spf2

description: Library name: lkb_gh_dirty_spln_8


title: Others-rich region for FL-pt11-B ROI A11

description: Library name: tFL_TMA_A_20250520_A11_Others


title: DD3516


title: spf1

description: Library name: lkb_gh_dirty_spln_7


title: Mac-rich region for FL-pt26 ROI A9

description: Library name: tFL_TMA_A_20250520_A9_Mac


title: WD825-well-differentiated-liposarcoma

value: surgery


title: Bcell-rich region for FL-pt11-B ROI A11

description: Library name: tFL_TMA_A_20250520_A11_Bcell

value: FL


title: gaf3

description: Library name: lkb_gh_dirty_spln_6

value: gavage-fomite (GaF)


title: DD2586


title: Tcell-rich region for FL-pt11-B ROI A11

description: Library name: tFL_TMA_A_20250520_A11_Tcell


title: DD2213


title: gaf2

description: Library name: lkb_gh_dirty_spln_5


title: Mac-rich region for FL-pt11-B ROI A11

description: Library name: tFL_TMA_A_20250520_A11_Mac


title: WD1352-well-differentiated-liposarcoma


title: NF1350-normal-fat

value: unknown


title: DD1135-dedifferentiated-liposarcoma

value: high


title: SNPC4_72h_IP_dataset2_replicate3

description:
Library name: ChIP2021-053-SNPC4-72h-WW
snpc-4::3xflag 72h SNPC-4 ChIP-seq IP dataset2 replicate3

value: whole worm

value: 72h gravid adult

value: IP


title: Tcell-rich region for tFL-pt43 ROI A34

description: Library name: tFL_TMA_A_20250520_A34_Tcell

value: Lymph Node

value: tFL

value: DLBCL


title: gaf1

description: Library name: lkb_gh_dirty_spln_4

value: Spleen

value: WT


title: DD184

value: retroperitoneal


title: N2_72h_IP_dataset2_replicate3

description:
Library name: ChIP2021-052-N2-72h-WW
N2 72h SNPC-4 ChIP-seq IP dataset2 replicate3


title: DD1213-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma


title: gav3

description: Library name: lkb_gh_dirty_spln_3

value: gavage


title: DD176

value: blood (buffy coat)

value: Dedifferentiated


title: Bcell-rich region for FL-pt11-A ROI A10

description: Library name: tFL_TMA_A_20250520_A10_Bcell

value: FL


title: DD172


title: WD1342-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low

value: surgery


title: Tcell-rich region for FL-pt11-A ROI A10

description: Library name: tFL_TMA_A_20250520_A10_Tcell


title: gav2

description: Library name: lkb_gh_dirty_spln_2


title: DD171


title: DD103


title: gav1

description: Library name: lkb_gh_dirty_spln_1


title: NF1341-normal-fat

value: normal fat

value: unknown