title: A5

description:
Library name: A5
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.

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


title: Mac-rich region for tFL-pt6-B ROI B32

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_B_20250520_B32_Mac

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: Control M28 F, replicate 5

city: Singapore

first: Weihan

last: Huai

address: 10 Medical Dr

country: Singapore

institute: NUS

description: Library name: DT_F158S

data_processing:
Sequence data was subjected to quality control FastQC (78) then trimmed using Trimmomatics v0.32 to remove adaptors. Processed/cleaned reads were then mapped with STAR (2.7.11b) and counted via RSEM 1.3.3. The raw count was then imported into R using the R package tximport 1.26.1.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Soleus muscle

extract_protocol:
we collected tissues at different ages and treatments and extracted RNA using Qiagen RNAeasy Mini kit (Qiagen, Hilden, Germany) following the standard protocol.
For library preparation, an amount of 2mg of total RNA per sample was processed using Illumina’s RNA Sample Prep Kit following the manufacturer’s instruction (Illumina, San Diego, CA, USA). Libraries were sequenced using Illumina NovaSeq 6000 sequencing platform (Illumina, San Diego, CA, USA) in a paired end read approach at a read length of 150 nucleotides. Sequence data was extracted in FastQ format.

value: Soleus muscle

tag: genotype

tag: treatment

value: Control

tag: batch


title: IG-CGI (IG-DMR) methylation, heterozygous (maternal Gzf1-KO), adult mouse 4

city: Rehovot

first: Yonatan

last: Stelzer

address: Procurement Division 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description: Library name: HetPup_20_CGI

library_source: genomic

data_processing:
Reads aligned with Bismark v0.24.2 to the reference genome (pre-indexed with bismark_genome_preparation).
CpG methylation extracted with the Bismark methylation extractor.
Per-CpG % methylation = methylated/total reads; sites with coverage < 20 were discarded.
Assembly: mm10
Supplementary files format and content: CpG_OT_<sample>_bismark_bt2.txt.gz: Bismark methylation-extractor output (per-CpG methylation calls), one file per sample.

molecule: genomic DNA

source_name: adult tissue (tail)

extract_protocol:
Genomic DNA was bisulfite-converted with the EZ DNA Methylation-Lightning Kit (Zymo Research, D5031) per manufacturer's instructions.
Bisulfite-converted DNA was amplified by two-round nested, locus-specific PCR (primers in Supplementary Table 8), cleaned with Zymo Clean & Concentrator (D4004), and amplicon-sequenced by Plasmidsaurus (Premium PCR, Oxford Nanopore Technology).

value: adult tissue (tail)

value: heterozygous (maternal Gzf1-KO)

tag: target locus

value: IG-CGI (IG-DMR)

tag: group

value: het pup (F KO x M WT)


title: A4

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: A4
DAP-seq

organism: Klebsiella pneumoniae

source_name: Klebsiella pneumoniae

growth_protocol: LB at 37 °C

tag: cell line

tag: cell type

value: genotype

value: WT

value: ChIP antibody


title: Others-rich region for FL-pt203-B ROI B28

description: Library name: tFL_TMA_B_20250520_B28_Others

value: FL


title: Control M28 F, replicate 4

description: Library name: DT_F157S


title: IG-CGI (IG-DMR) methylation, heterozygous (maternal Gzf1-KO), adult mouse 3

description: Library name: HetPup_5_CGI


title: Control M28 F, replicate 3

description: Library name: DT_F144S


title: A3

description:
Library name: A3
DAP-seq


title: Control M28 F, replicate 2

description: Library name: DT_F143S


title: A2

description:
Library name: A2
DAP-seq


title: Bcell-rich region for FL-pt203-B ROI B28

description: Library name: tFL_TMA_B_20250520_B28_Bcell


title: IG-CGI (IG-DMR) methylation, heterozygous (maternal Gzf1-KO), adult mouse 2

description: Library name: HetPup_3_CGI


title: IG-CGI (IG-DMR) methylation, heterozygous (maternal Gzf1-KO), adult mouse 1

description: Library name: HetPup_1_CGI


title: Tcell-rich region for FL-pt203-B ROI B28

description: Library name: tFL_TMA_B_20250520_B28_Tcell


title: Control M28 F, replicate 1

description: Library name: DT_F142S


title: A19

description:
Library name: A19
DAP-seq


title: IG-CGI (IG-DMR) methylation, Gzf1 knockout, dead pup upon birth

description: Library name: DeadPup_Gzf1KO_CGI

value: Gzf1 knockout

value: dead pup


title: A18

description:
Library name: A18
DAP-seq


title: H3K4me3 CUT&Tag, Gzf1-KO mESC

description:
Library name: Gzf1KO_H3K4me3_CUTandTag
Raw FASTQ provided as reads truncated to 36 nt (Cutadapt v2.8).

data_processing:
Paired-end reads truncated to 36 nt with Cutadapt v2.8 and aligned to GRCm38/mm10 with Bowtie2 v2.5.4 (--very-sensitive-local; properly paired, MAPQ>=30).
CPM-normalized 10-bp bigWig (deepTools bamCoverage v3.3.1; read-centred, 50 bp smoothing), autoscaled to an IgG-control CUT&Tag of the same background.
For differential analysis, reads imported into misha; H3K4me3 peaks called per genotype (sliding +/-1 kb, top 1% signal), merged into a union set, CPM coverage compared (|log2 FC| > 1.5).
Assembly: mm10 (GRCm38)
Supplementary files format and content: *.bw: CPM-normalized bigWig coverage tracks (one per sample).
Library strategy: CUT&Tag

source_name: RGM

growth_protocol: Wild-type and Gzf1-KO mESCs (~1x10^5 cells) were harvested for CUT&Tag.

extract_protocol:
Nuclei were extracted and immobilized on concanavalin A-coated magnetic beads.
CUT&Tag (Kaya-Okur et al. 2019, ref 58): primary anti-H3K4me3 (Cell Signaling #9751, 1:50, overnight 4C); secondary guinea pig anti-rabbit IgG (ABIN101961, 1:100); pA-Tn5 binding; tagmentation with MgCl2 (37C, 1 h). DNA was bead-purified and libraries amplified by PCR; paired-end sequencing on Illumina.

value: RGM

value: embryonic stem cells

value: antibody:primary anti-H3K4me3 (Cell Signaling #9751, 1:50); secondary guinea pig anti-rabbit IgG (ABIN101961, 1:100)


title: Others-rich region for tFL-pt203-A ROI B27

description: Library name: tFL_TMA_B_20250520_B27_Others

value: Lymph Node

value: DLBCL


title: Mac-rich region for FL-pt203-B ROI B28

description: Library name: tFL_TMA_B_20250520_B28_Mac


title: Gtl2-DMR methylation, wild type, Gzf1 knockout, adult mouse

description: Library name: Adult_Gzf1KO_Gtl2

value: adult mouse


title: A17

description:
Library name: A17
DAP-seq

value: Klebsiella pneumoniae

value: strain


title: H3K4me3 CUT&Tag, wild-type mESC

description:
Library name: WT_H3K4me3_CUTandTag
Raw FASTQ provided as reads truncated to 36 nt (Cutadapt v2.8).

value: wild type


title: Bcell-rich region for tFL-pt203-A ROI B27

description: Library name: tFL_TMA_B_20250520_B27_Bcell

value: tFL


title: Gtl2-DMR methylation, wild type, adult mouse

description: Library name: Adult_WT_Gtl2

value: adult tissue (tail)


title: A16

description:
Library name: A16
DAP-seq

value: genotype


title: Gzf1-KO mESC, bulk RNA-seq, replicate 5

description: Library name: Gzf1KO_5

data_processing:
Reads were quality-checked and adapter/quality trimmed.
Reads were aligned to the mouse reference genome (mm10) with STAR (default parameters).
UMI counts per gene were quantified to generate a raw count matrix.
Differential expression between Gzf1-KO (n=5) and WT (n=4) was tested with DESeq2 (default parameters).
Assembly: mm10
Supplementary files format and content: Gzf1_RNAseq_raw_counts.csv: comma-separated matrix of raw UMI counts; rows = genes (MGI symbols), columns = 9 samples (library names).

molecule: polyA RNA

growth_protocol: mESCs were cultured on irradiated mouse embryonic fibroblast (MEF) feeders in standard ESC medium (DMEM, 10% FBS, recombinant LIF, 0.1 mM beta-mercaptoethanol, penicillin/streptomycin, 1 mM L-glutamine, 1% non-essential amino acids); WT and Gzf1-KO cells were harvested after depletion of MEF feeders.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and purified with the Direct-zol RNA Miniprep Kit (Zymo Research).
Bulk RNA-seq libraries were prepared with a standard poly(A)+ selection protocol (MARS-seq2.0; Keren-Shaul et al. 2019). cDNA synthesis, library construction and indexing per manufacturer recommendations.


title: Tcell-rich region for tFL-pt203-A ROI B27

description: Library name: tFL_TMA_B_20250520_B27_Tcell


title: IG-CGI (IG-DMR) methylation, Gzf1 knockout, adult mouse

description: Library name: Adult_Gzf1KO_CGI

value: IG-CGI (IG-DMR)

value: adult mose


title: A15

description:
Library name: A15
DAP-seq

value: WT

value: ChIP antibody


title: IG-CGI (IG-DMR) methylation, wildtype,  adult mouse

description: Library name: Adult_WT_CGI


title: Others-rich region for FL-pt13-A ROI B24

description: Library name: tFL_TMA_B_20250520_B24_Others

value: FL


title: Gzf1-KO mESC, bulk RNA-seq, replicate 3

description: Library name: Gzf1KO_3

value: Gzf1 knockout


title: Bcell-rich region for FL-pt13-A ROI B24

description: Library name: tFL_TMA_B_20250520_B24_Bcell


title: A12

description:
Library name: A12
DAP-seq


title: Gzf1-KO mESC, bulk RNA-seq, replicate 4

description: Library name: Gzf1KO_4

value: embryonic stem cells


title: IG-CGI (IG-DMR) methylation, Gzf1 knockout, MII oocyte rep 2

description: Library name: Oocyte_Gzf1KO_CGI_rep2

source_name: oocyte (MII)

value: oocyte (MII)

value: in vivo


title: A11

description:
Library name: A11
DAP-seq


title: Gzf1-KO mESC, bulk RNA-seq, replicate 2

description: Library name: Gzf1KO_2

value: RGM


title: Tcell-rich region for FL-pt13-A ROI B24

description: Library name: tFL_TMA_B_20250520_B24_Tcell

value: Lymph Node


title: IG-CGI (IG-DMR) methylation, Gzf1 knockout, MII oocyte rep 1

description: Library name: Oocyte_Gzf1KO_CGI_rep1


title: A10

description:
Library name: A10
DAP-seq

value: Klebsiella pneumoniae


title: IG-CGI (IG-DMR) methylation, wild type, MII oocyte

description: Library name: Oocyte_WT_CGI


title: Mac-rich region for FL-pt13-A ROI B24

description: Library name: tFL_TMA_B_20250520_B24_Mac


title: Gzf1-KO mESC, bulk RNA-seq, replicate 1

description: Library name: Gzf1KO_1


title: A1

description:
Library name: A1
DAP-seq

value: strain


title: Others-rich region for tFL-pt14-B ROI B232

description: Library name: tFL_TMA_B_20250520_B232_Others

value: DLBCL


title: wild-type mESC, bulk RNA-seq, replicate 4

description: Library name: WT_4

value: wild type


title: CAR_079_FFPE_01

description: Library name: CAR_079_FFPE_01

data_processing:
Raw fastq files were aligned with STAR v2.5.3a to hg19 with a gencode v26 annotation. QC and gene-level quantification were performed using RNA-SeQC2 (Graubert et al. 2021). Only samples with detection with >10k genes were included for analysis. Expression units normalized to transcripts per million were utilized for downstream analysis.
Assembly: hg19 / gencode v26
Supplementary files format and content: gzip csv containing gene expression measurements in transcripts-per-million

extract_protocol:
RNA was extracted from FFPE biopsy samples using standard methods (Qiagen Allprep FFPE kit). RNA extracted from FFPE tissues was assessed for quality using the Agilent Bioanalyzer producing a DV200 metric. Samples with >30% of fragments and >200 base pairs had the highest chance of yielding high quality sequencing data.
100ng of RNA was input for cDNA synthesis using Superscript III reverse transcriptase and then processed with Illumina's TruSeq RNA Access Sample Prep Kit. Synthesis of the second strand of cDNA was followed by indexed adapter ligation with unique molecular index adapters. Subsequent PCR amplification enriched for adapted fragments. Amplified libraries were quantified, normalized, pooled, and hybridized with exome targeting oligos. Following hybridization, a bead-based clean-up was performed, followed by an elution step. PCR was performed to prepare library pools for sequencing on Illumina HiSeq2500 sequencers utilizing sequencing-by-synthesis kits to produce 76bp paired reads.

tag: disease


title: IG-TRE methylation, Gzf1 knockout, E10.5 embryo trunk

description: Library name: EmbTrunk_E105_Gzf1KO_TRE

source_name: embryo trunk (E10.5)

value: embryo trunk (E10.5)

value: IG-TRE


title: wild-type mESC, bulk RNA-seq, replicate 3

description: Library name: WT_3


title: IG-TRE methylation, wild type, E10.5 embryo trunk

description: Library name: EmbTrunk_E105_WT_TRE


title: Tcell-rich region for tFL-pt14-B ROI B232

description: Library name: tFL_TMA_B_20250520_B232_Tcell

value: tFL


title: CAR_078_FFPE_01

description: Library name: CAR_078_FFPE_01


title: wild-type mESC, bulk RNA-seq, replicate 2

description: Library name: WT_2


title: Bcell-rich region for tFL-pt14-B ROI B232

description: Library name: tFL_TMA_B_20250520_B232_Bcell


title: Gtl2-DMR methylation, Gzf1 knockout, E10.5 embryo trunk

description: Library name: EmbTrunk_E105_Gzf1KO_Gtl2


title: wild-type mESC, bulk RNA-seq, replicate 1

description: Library name: WT_1


title: CAR_075_FFPE_01

description: Library name: CAR_075_FFPE_01


title: Mac-rich region for tFL-pt14-B ROI B232

description: Library name: tFL_TMA_B_20250520_B232_Mac


title: Gtl2-DMR methylation, wild type, E10.5 embryo trunk

description: Library name: EmbTrunk_E105_WT_Gtl2


title: CAR_073_FFPE_01

description: Library name: CAR_073_FFPE_01


title: H3K27Ac ChIP, Cas9

description:
Library name: Cas9_HistonePTM
ChIPseq_1kb_signal_matrix.txt.gz

data_processing:
Paired-end reads adapter-trimmed with Cutadapt (min length 20 bp) and aligned to mm10 with Bowtie2 v2.5.4 (--very-sensitive --dovetail -k 1); MAPQ<10 removed; PCR duplicates removed with samtools markdup.
RPGC-normalized 10-bp bigWig (deepTools bamCoverage; effective genome 2,652,783,500); read counts imported into misha and quantified as summed counts per peak; allele assignment with SNPsplit (129S1/SvImJ x CAST/EiJ, dual-hybrid) for RGM F1 samples (allele-split bigWigs).
Assembly: mm10
Supplementary files format and content: *.RPGC.bw: RPGC bigWig (allele-split 129/CAST for RGM F1). ChIPseq_1kb_signal_matrix.txt.gz: genome-wide 1-kb bin x sample summed-count matrix (8 samples incl. H3K27Ac).

source_name: mouse embryonic stem cells

growth_protocol: mESCs (V65, Cas9 and 129xCAST/RGM backgrounds) cultured under standard conditions; Gzf1-Flag introduced by ectopic expression where indicated.

extract_protocol:
Cells were fixed (1% formaldehyde), lysed, and chromatin digested with micrococcal nuclease (MNase).
Chromatin immunoprecipitated with anti-Flag M2 (Sigma F1804) or anti-GZF1 (LSBio LS-C429273) (H3K27Ac: Thermo Fisher MA5-23516); on-bead Illumina library construction.

value: mouse embryonic stem cells

tag: chip antibody

value: anti-H3K27Ac (Thermo Fisher Scientific, MA5-23516)


title: Others-rich region for tFL-pt13-B ROI B231

description: Library name: tFL_TMA_B_20250520_B231_Others


title: IG-CGI (IG-DMR) methylation, Gzf1 knockout, E10.5 embryo trunk

description: Library name: EmbTrunk_E105_Gzf1KO_CGI

value: IG-CGI (IG-DMR)


title: CAR_070_FFPE_01

description: Library name: CAR_070_FFPE_01

tag: subtype

value: nonGCB


title: GZF1-Flag ChIP (anti-FLAG), RGM (129xCAST) Gzf1-Flag OE (clone 56)

description:
Library name: RGM_Gzf1OE_Flag_56
ChIPseq_1kb_signal_matrix.txt.gz

value: Gzf1-Flag overexpression

value: anti-FLAG M2 (Sigma-Aldrich F1804)


title: IG-CGI (IG-DMR) methylation, wild type, E10.5 embryo trunk

description: Library name: EmbTrunk_E105_WT_CGI


title: Bcell-rich region for tFL-pt13-B ROI B231

description: Library name: tFL_TMA_B_20250520_B231_Bcell


title: GZF1-Flag ChIP (anti-FLAG), Cas9 Gzf1-Flag OE (clone 35)

description:
Library name: Cas9_Gzf1OE_Flag_35
ChIPseq_1kb_signal_matrix.txt.gz

value: embryonic stem cells


title: Tcell-rich region for tFL-pt13-B ROI B231

description: Library name: tFL_TMA_B_20250520_B231_Tcell


title: Gtl2-DMR methylation, Gzf1 knockout, mESC

description: Library name: Gzf1KO_Gtl2

value: Gzf1 knockout

value: cells


title: CAR_065_FFPE_01

description: Library name: CAR_065_FFPE_01

value: Lymph Node

value: FL


title: Endogenous GZF1 ChIP (anti-GZF1), RGM (129xCAST)

description:
Library name: RGM_aGZF1
ChIPseq_1kb_signal_matrix.txt.gz

value: RGM

value: anti-GZF1 (LSBio LS-C429273)


title: Mac-rich region for tFL-pt13-B ROI B231

description: Library name: tFL_TMA_B_20250520_B231_Mac

value: DLBCL


title: CAR_055_FFPE_01

description: Library name: CAR_055_FFPE_01

value: GCB


title: Gtl2-DMR methylation, wild type, mESC

description: Library name: WT_Gtl2

value: wild type


title: Others-rich region for FL-pt14-A ROI B222

description: Library name: tFL_TMA_B_20250520_B222_Others


title: Endogenous GZF1 ChIP (anti-GZF1), Cas9

description:
Library name: Cas9_aGZF1
ChIPseq_1kb_signal_matrix.txt.gz


title: Input chromatin, Cas9

description:
Library name: Cas9_Input
ChIPseq_1kb_signal_matrix.txt.gz

value: input

value: input (no antibody)


title: IG-TRE methylation, Gzf1 knockout, mESC

description: Library name: Gzf1KO_TRE

value: IG-TRE


title: Bcell-rich region for FL-pt14-A ROI B222

description: Library name: tFL_TMA_B_20250520_B222_Bcell


title: CAR_054_FFPE_01

description: Library name: CAR_054_FFPE_01

value: tFL


title: IG-TRE methylation, wild type, mESC

description: Library name: WT_TRE


title: CAR_053_FFPE_01

description: Library name: CAR_053_FFPE_01


title: GZF1-Flag ChIP (anti-FLAG), RGM (129xCAST) control, allele-specific

description: Library name: RGM_ctrl_Flag

value: mouse embryonic stem cells

value: control (no ectopic Flag)


title: Tcell-rich region for FL-pt14-A ROI B222

description: Library name: tFL_TMA_B_20250520_B222_Tcell


title: CAR_052_FFPE_01

description: Library name: CAR_052_FFPE_01


title: Endogenous GZF1 ChIP (anti-GZF1), Cas9 Gzf1-KO

description: Library name: Cas9_Gzf1KO_aGZF1


title: Mac-rich region for FL-pt14-A ROI B222

description: Library name: tFL_TMA_B_20250520_B222_Mac


title: CAR_049_FFPE_01

description: Library name: CAR_049_FFPE_01

value: nonGCB


title: IG-CGI (IG-DMR) methylation, Zfp57 knockout (RGM reporter), mESC reporter

description: Library name: Zfp57KO_reporter_CGI

value: embryonic stem cells

value: Zfp57 knockout (RGM reporter)

value: IG-CGI (IG-DMR)


title: IG-CGI (IG-DMR) methylation, Zfp57/Gzf1 double knockout (RGM reporter), mESC reporter

description: Library name: Zfp57Gzf1dKO_reporter_CGI

value: cells


title: Endogenous GZF1 ChIP (anti-GZF1), Cas9 control

description: Library name: Cas9_ctrl_aGZF1

value: control


title: Others-rich region for FL-pt201-A ROI B21

description: Library name: tFL_TMA_B_20250520_B21_Others

value: Lymph Node

value: FL


title: CAR_044_FFPE_01

description: Library name: CAR_044_FFPE_01

value: DLBCL


title: IG-CGI (IG-DMR) methylation, wild type (RGM reporter), mESC reporter

description: Library name: WT_reporter_CGI

value: RGM

value: wild type (RGM reporter)


title: GZF1-Flag ChIP (anti-FLAG), RGM (129xCAST) Gzf1-Flag OE, allele-specific

description: Library name: RGM_Gzf1OE_Flag

value: Gzf1-Flag overexpression

value: anti-FLAG M2 (Sigma-Aldrich F1804)


title: IG-CGI (IG-DMR) methylation, Tet triple knockout, mESC

description: Library name: TetTKO_CGI

source_name: Tet-TKO

value: Tet-TKO

value: Tet triple knockout


title: CAR_041_FFPE_01

description: Library name: CAR_041_FFPE_01

value: GCB


title: Tcell-rich region for FL-pt201-A ROI B21

description: Library name: tFL_TMA_B_20250520_B21_Tcell


title: GZF1-Flag ChIP (anti-FLAG), V65 Gzf1-Flag OE

description: Library name: V65_Gzf1OE_Flag

value: mouse embryonic stem cells


title: Bcell-rich region for FL-pt201-A ROI B21

description: Library name: tFL_TMA_B_20250520_B21_Bcell


title: IG-CGI (IG-DMR) methylation, Dnmt1 knockout, mESC

description: Library name: Dnmt1KO_CGI

value: Dnmt1 knockout


title: IG-CGI (IG-DMR) methylation, Gzf1 knockout, mESC

description: Library name: Gzf1KO_CGI

value: embryonic stem cells

value: Gzf1 knockout


title: CAR_040_FFPE_01

description: Library name: CAR_040_FFPE_01

value: tFL


title: Mac-rich region for FL-pt201-A ROI B21

description: Library name: tFL_TMA_B_20250520_B21_Mac


title: GZF1-Flag ChIP (anti-FLAG), V65 control (no ectopic Flag)

description: Library name: V65_ctrl_Flag

value: control (no ectopic Flag)


title: CAR_039_FFPE_01

description: Library name: CAR_039_FFPE_01

value: nonGCB


title: CRISPR screen Exp2: sorted Tom-GFP- (MM), P6

description:
Library name: Exp2_MM_TomN_GFPn
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

data_processing:
Amplicons were deep-sequenced on an Illumina NextSeq platform to monitor sgRNA library composition.
sgRNA read counts per sample were quantified with MAGeCK count to produce the sgRNA count matrix.
MAGeCK test was used to identify enriched/depleted sgRNAs and rank candidate genes (PP & MM vs US/PM/T1 controls), excluding genes enriched US-vs-P0 (growth advantage) and PM-vs-US (FACS bias).
Assembly: Mouse Brie sgRNA library (Addgene 73633-LV; 78,637 guides + non-targeting controls)
Supplementary files format and content: CRISPR_screen_sgRNA_counts.txt: tab-delimited sgRNA count matrix (79,633 guides x 11 samples).
Library strategy: CRISPR Screen

growth_protocol: RGM reporter mESCs were transduced with Lenti-Cas9-NeoR and selected, then transduced with the Mouse Brie genome-wide CRISPR-KO library (Addgene 73633-LV; 78,637 sgRNAs; gift of D. Root/J. Doench) at MOI 0.3 (~500x coverage); puromycin-selected for 6 passages.

extract_protocol:
Genomic DNA was extracted from each fraction/timepoint.
Genomic DNA was extracted per fraction/timepoint; the integrated sgRNA cassette was amplified by PCR (Joung et al. 2017). Biological replicates were pooled per sequencing library.

treatment_protocol: At P6, cells were FACS-sorted by tdTomato/GFP fluorescence into Tom+GFP+ (PP), Tom-GFP- (MM), Tom+GFP- (PM, control) and unsorted (US) fractions; T1 = early unsorted baseline.

value: reporter mESC + Cas9 + genome-wide sgRNA library

value: sorted Tom-GFP-; 1.5M cells; passage P6


title: Others-rich region for FL-pt205-A ROI B17

description: Library name: tFL_TMA_B_20250520_B17_Others

value: Lymph Node

value: FL


title: CAR_037_FFPE_01

description: Library name: CAR_037_FFPE_01

value: DLBCL


title: IG-CGI (IG-DMR) methylation, wild type, mESC

description: Library name: WT_noReporter_CGI

value: wild type

value: IG-CGI (IG-DMR)

value: cells


title: CAR_035_FFPE_01

description: Library name: CAR_035_FFPE_01


title: CRISPR screen Exp2: sorted Tom+GFP+ (PP, enriched fraction), P6

description:
Library name: Exp2_PP_TomP_GFPp
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

value: sorted Tom+GFP+ (enriched); 250K cells; passage P6


title: Bcell-rich region for FL-pt205-A ROI B17

description: Library name: tFL_TMA_B_20250520_B17_Bcell


title: CRISPR screen Exp2: sorted Tom+GFP- (PM, FACS control, rep2), P6

description:
Library name: Exp2_PM_TomP_GFPn_rep2
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

value: sorted Tom+GFP- (FACS-bias control); 1M cells; passage P6


title: Tcell-rich region for FL-pt205-A ROI B17

description: Library name: tFL_TMA_B_20250520_B17_Tcell


title: DD226-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: CAR_034_FFPE_01

description: Library name: CAR_034_FFPE_01

tag: tissue


title: CRISPR screen Exp2: sorted Tom+GFP- (PM, FACS control, rep1), P6

description:
Library name: Exp2_PM_TomP_GFPn_rep1
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

value: embryonic stem cells


title: Mac-rich region for FL-pt205-A ROI B17

description: Library name: tFL_TMA_B_20250520_B17_Mac

tag: sample id

tag: patient id


title: CAR_033_FFPE_01

description: Library name: CAR_033_FFPE_01

value: GCB


title: Rh30, ARMS sgRNA Library, Tf Sample, Rep2

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 16
Column name in Custom_Library_Essentiality_Screens_sgRNA_ReadCounts.txt: Rh30_ARMS_Tfinal_Rep2

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

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

value: Rhabdomyosarcoma

value: Fusion-Positive

tag: screen

value: Custom sgRNA Essentiality


title: CRISPR screen Exp2: unsorted (US, rep2), P6

description:
Library name: Exp2_US_unsorted_rep2
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

tag: genotype

value: reporter mESC + Cas9 + genome-wide sgRNA library

value: unsorted; 25M cells; passage P6


title: Others-rich region for FL-pt212 ROI B16

description: Library name: tFL_TMA_B_20250520_B16_Others

value: Lymph Node

tag: disease binary

value: FL

tag: disease fine


title: CAR_031_FFPE_01

description: Library name: CAR_031_FFPE_01

value: DLBCL


title: DD216-dedifferentiated-liposarcoma


title: Bcell-rich region for FL-pt212 ROI B16

description: Library name: tFL_TMA_B_20250520_B16_Bcell


title: CRISPR screen Exp2: unsorted (US, rep1), P6

description:
Library name: Exp2_US_unsorted_rep1
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

tag: treatment

tag: batch


title: DD188-dedifferentiated-liposarcoma


title: CAR_030_FFPE_01

description: Library name: CAR_030_FFPE_01

value: tFL


title: WD183-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low


title: DD176-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: retroperitoneal


title: CRISPR screen Exp1: sorted Tom-GFP- (MM), P6

description:
Library name: Exp1_MM_TomN_GFPn
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

tag: cell line

value: sorted Tom-GFP-; 1.2M cells; passage P6


title: CAR_029_FFPE_01

description: Library name: CAR_029_FFPE_01

value: nonGCB


title: Mac-rich region for FL-pt212 ROI B16

description: Library name: tFL_TMA_B_20250520_B16_Mac


title: CRISPR screen Exp1: sorted Tom+GFP+ (PP, enriched fraction), P6

description:
Library name: Exp1_PP_TomP_GFPp
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

tag: cell type

value: embryonic stem cells

value: sorted Tom+GFP+ (enriched); 200K cells; passage P6


title: Tcell-rich region for FL-pt212 ROI B16

description: Library name: tFL_TMA_B_20250520_B16_Tcell


title: CAR_025_FFPE_01

description: Library name: CAR_025_FFPE_01

tag: disease


title: CRISPR screen Exp1: unsorted (US), P6

description:
Library name: Exp1_US_unsorted
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

value: unsorted; 13M cells; passage P6


title: DD171-dedifferentiated-liposarcoma

value: high

value: surgery


title: Others-rich region for FL-pt32 ROI B14

description: Library name: tFL_TMA_B_20250520_B14_Others


title: WD60-well-differentiated-liposarcoma


title: CAR_023_FFPE_01

description: Library name: CAR_023_FFPE_01

value: GCB


title: CRISPR screen Exp1: sorted Tom+GFP- (PM, FACS control), P6

description:
Library name: Exp1_PM_TomP_GFPn
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

value: reporter mESC + Cas9 + genome-wide sgRNA library

value: sorted Tom+GFP- (FACS-bias control); 1M cells; passage P6


title: Bcell-rich region for FL-pt32 ROI B14

description: Library name: tFL_TMA_B_20250520_B14_Bcell

value: Lymph Node

value: FL


title: CAR_020_FFPE_02

description: Library name: CAR_020_FFPE_02

value: tFL


title: CRISPR screen Exp1: unsorted, 2 passages post-selection (T1, baseline)

description:
Library name: Exp1_T1_unsorted
sgRNA enrichment readout; library composition | cell line: RGM; male mouse ESC, CAST/129 F1 hybrid; Y. Stelzer

value: unsorted (pre-sort baseline); 50M cells; passage P6


title: WD221-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low


title: Tg-KO_Rep1-3

city: Nagoya

first: Ryohei

last: Uenishi

state: Aichi

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku,

department: Neurocognitive Science

country: Japan

institute: Nagoya City University

description: Library name: N109-mix-04

data_processing:
Read1 (10bp of UMI + 9bp of barcode) was assigned to Read2 (insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7).
Reads were mapped to the GRCh38 reference using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRCh38
Supplementary files format and content: compressed tab separated files (.tsv.gz, .txt.gz)

source_name: Brain

extract_protocol:
5–10 mg of hippocampal tissues were lysed in TRIzol reagent (Thermo Fisher Science) and extract RNA by phenol-chloroform extractiont, and then the extracted RNA was further purified using the RNeasy Plus Mini Kit (QIAGEN)
Libraries were prepared by BRB-Seq (Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followed by 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

value: Brain

value: Tau Transgenic; Cxcl10 knock out

tag: time

tag: Sex

value: Male


title: CAR_019_FFPE_01

description: Library name: CAR_019_FFPE_01


title: Tcell-rich region for FL-pt32 ROI B14

description: Library name: tFL_TMA_B_20250520_B14_Tcell


title: WD206-well-differentiated-liposarcoma

tag: tumor site

value: retroperitoneal


title: Mac-rich region for FL-pt32 ROI B14

description: Library name: tFL_TMA_B_20250520_B14_Mac


title: CAR_016_FFPE_01

description: Library name: CAR_016_FFPE_01

value: DLBCL

tag: subtype

value: nonGCB


title: WD203-well-differentiated-liposarcoma

tag: tumor grade

tag: treatement


title: Others-rich region for tFL-pt69-B ROI B13

description: Library name: tFL_TMA_B_20250520_B13_Others

tag: tissue

tag: sample id


title: Tg_Rep1-3

description: Library name: N109-mix-03

value: Tau Transgenic


title: WD200-well-differentiated-liposarcoma

value: surgery


title: CAR_015_FFPE_01

description: Library name: CAR_015_FFPE_01


title: KO_Rep1-3

description: Library name: N109-mix-02

value: Cxcl10 knock out


title: WD199-well-differentiated-liposarcoma


title: Bcell-rich region for tFL-pt69-B ROI B13

description: Library name: tFL_TMA_B_20250520_B13_Bcell

tag: patient id


title: CAR_014_FFPE_01

description: Library name: CAR_014_FFPE_01


title: WT_Rep1-3

description: Library name: N109-mix-01

tag: genotype

value: Wild type


title: WD196-well-differentiated-liposarcoma


title: Mac-rich region for tFL-pt69-B ROI B13

description: Library name: tFL_TMA_B_20250520_B13_Mac

tag: disease binary


title: CAR_013_FFPE_01

description: Library name: CAR_013_FFPE_01


title: Subcutaneous-BCG treated PS19 mice 3

city: Baltimore

first: Somnath

last: Shee

state: MD

address: 1550 Orleans St, CRB2 Building, Room-176

department: Medicine, Infectious diseases

institute: Johns Hopkins University

description: Library name: SC_PS19_3

data_processing:
Raw sequencing quality was assessed using FastQC v0.11.7, and adapter trimming and quality filtering were performed with fastp v0.24.0. The processed reads were aligned to the mouse reference genome (mm39) using RSEM v1.3.3, which generated BAM files along with gene and transcript level expression estimates. Differential expression analysis was conducted using DESeq2 v1.44.0. Gene set enrichment analysis was performed with fgsea v1.30.0, using gene sets obtained from the Molecular Signatures Database (MSigDB).
Genes with an adjusted p-value <0.05 and a log₂ fold change > 1 or <-1 were considered differentially expressed between groups.
Assembly: mm39
Supplementary files format and content: csv file includes TPM counts (transcript per million) for each sample

source_name: hippocampus tissue

extract_protocol:
RNA was extracted from tissue samples using the RNeasy Mini kit (Qiagen) and quantity and quality assessed by Bioanalyzer (Agilent Technologies). Depletion of ribosomal RNA was performed using the Qiagen Fast Select rRNA HMR kit (Qiagen; catalogue number 334387) according to manufacturers instructions.
A stranded mRNA library was prepared using the Illumina TruSeq Stranded Total RNA kit (Illumina; catalogue number 20020596) according to manufacturers instructions. Sequencing was performed using the Novaseq 6000 X platform sequencer and the TruSeq Cluster Kit (Illumina), resulting in approximately 50 million paired reads per sample.

value: hippocampus tissue

value: Hemizygous PS19 mice

value: M. bovis BCG Pasteur AERAS treated

value: Female


title: Tcell-rich region for tFL-pt69-B ROI B13

description: Library name: tFL_TMA_B_20250520_B13_Tcell

value: Lymph Node

value: tFL

tag: disease fine


title: Subcutaneous-BCG treated PS19 mice 2

description: Library name: SC_PS19_2

tag: treatment


title: Others-rich region for FL-pt222 ROI B12

description: Library name: tFL_TMA_B_20250520_B12_Others

value: FL


title: CAR_007_FFPE_01

description: Library name: CAR_007_FFPE_01


title: WD194-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low


title: WD190-well-differentiated-liposarcoma


title: CAR_011_FFPE_01

description: Library name: CAR_011_FFPE_01


title: NFT-well-differentiated-liposarcoma


title: Bcell-rich region for FL-pt222 ROI B12

description: Library name: tFL_TMA_B_20250520_B12_Bcell


title: Subcutaneous-BCG treated PS19 mice 1

description: Library name: SC_PS19_1


title: CAR_006_FFPE_01

description: Library name: CAR_006_FFPE_01


title: Untreated PS19 mice 3

description: Library name: UV_PS19_3

value: sham/PBS-treated


title: NF95-normal-fat

value: normal fat

value: unknown


title: Tcell-rich region for FL-pt222 ROI B12

description: Library name: tFL_TMA_B_20250520_B12_Tcell


title: Mac-rich region for FL-pt222 ROI B12

description: Library name: tFL_TMA_B_20250520_B12_Mac


title: Untreated PS19 mice 2

description: Library name: UV_PS19_2


title: Saliva sample 208234690088_R07C01

type: genomic

city: Yokosuka

first: Takayuki

last: Ishiyama

address: Department of Orthodontics, School of Dentistry, Kanagawa Dental University  82 Inaoka-cho

institute: Kanagawa Dental University

hyb_protocol: Samples were hybridized to Illumina Infinium MethylationEPIC v2 BeadChips following the manufacturer's standard protocol.

scan_protocol: BeadChips were scanned using the Illumina iScan system.

data_processing:
Raw IDAT files were processed using the minfi package in R to obtain beta values.
Beta values representing the proportion of methylation at each CpG site, calculated as M / (M + U + 100).

source_name: mixed dentition; RME; post

label_protocol: DNA was bisulfite converted and processed according to the Illumina Infinium MethylationEPIC v2 protocol.

extract_protocol: Genomic DNA was extracted from saliva samples using a commercial DNA extraction kit according to the manufacturer’s instructions.

value: saliva


title: CAR_004_FFPE_01

description: Library name: CAR_004_FFPE_01


title: CAR_003_FFPE_01

description: Library name: CAR_003_FFPE_01


title: NF92-normal-fat


title: Others-rich region for FL-pt211 ROI B11

description: Library name: tFL_TMA_B_20250520_B11_Others


title: Untreated PS19 mice 1

description: Library name: UV_PS19_1


title: NF90-normal-fat


title: Untreated Age-matched control mice 3

description: Library name: AMC_3

value: Non-carrier age-matched controls of PS19 mice


title: mouse_healthy_liver_2

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: healthy_liver_2
10X Genomics scRNAseq

library_source: transcriptomic single cell

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 7.0.0. Genome build: Mouse mm10-2020-A
Assembly: Mouse mm10-2020-A
Supplementary files format and content: mtx: count matrix in sparse matrix format (CellRanger output)
Supplementary files format and content: barcodes.tsv: barcode ids per sample (CellRanger output)
Supplementary files format and content: genes.tsv: gene ids per sample (CellRanger output)

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

value: Male

tag: strain


title: Bcell-rich region for FL-pt211 ROI B11

description: Library name: tFL_TMA_B_20250520_B11_Bcell


title: NF583-normal-fat

value: surgery


title: mouse_healthy_liver_1

description:
Library name: healthy_liver_1
10X Genomics scRNAseq


title: Tcell-rich region for FL-pt211 ROI B11

description: Library name: tFL_TMA_B_20250520_B11_Tcell


title: NF579-normal-fat


title: Untreated Age-matched control mice 1

description: Library name: AMC_1

value: hippocampus tissue


title: Untreated Age-matched control mice 2

description: Library name: AMC_2


title: Mac-rich region for FL-pt211 ROI B11

description: Library name: tFL_TMA_B_20250520_B11_Mac


title: mouse_healthy_blood_2

description:
Library name: healthy_blood_2
10X Genomics scRNAseq

source_name: Blood

value: Blood


title: Mouse liver, EtOH, female, scRNA-seq

city: Seoul

first: Mingu

last: Kim

address: 222, Banpo-daero

country: South Korea

institute: The Catholic university of Korea

description:
Library name: EtOH_F
Strain: C57BL/6N; Age: 8-10 weeks; Sex: female

data_processing:
Reads were processed using Cell Ranger “count” v8.0.1 to generate filtered gene-by-cell UMI count matrices.
Assembly: Mus musculus GRCm39-2024-A.
Supplementary files format and content: Processed data are provided as per-sample HDF5 files (filtered_feature_bc_matrix.h5) containing the filtered feature-barcode (gene-by-cell UMI count) matrix generated by Cell Ranger.

source_name: liver

growth_protocol: Liver tissue from mice in an NIAAA ethanol-feeding model was dissociated to generate single-cell suspensions for scRNA-seq (Control_M, Control_F, EtOH_M, EtOH_F; n=1 mouse per group).

extract_protocol:
Single-cell suspensions were assessed for cell concentration and viability prior to 10x loading (AO/PI-based viability assessment). Targeted cell input was 10,000 cells per sample.
Libraries were prepared using 10x Genomics Chromium GEM-X Single Cell 3′ RNA library v4 chemistry and sequenced on Illumina NovaSeq 6000 with read structure R1(28)–I1(10)–I2(10)–R2(90).

treatment_protocol: Two-week NIAAA ethanol-feeding model: Control vs EtOH, both sexes (M/F), one mouse per group.

value: liver

value: liver cells (single-cell suspension)

value: female

value: Ethanol feeding (NIAAA model)


title: mouse_healthy_blood_1

description:
Library name: healthy_blood_1
10X Genomics scRNAseq


title: NF117-normal-fat


title: Others-rich region for FL-pt223-B ROI B10

description: Library name: tFL_TMA_B_20250520_B10_Others

source_name: Lymph Node

value: Lymph Node

value: FL


title: NF119-normal-fat


title: Mouse liver, EtOH, male, scRNA-seq

description:
Library name: EtOH_M
Strain: C57BL/6N; Age: 8-10 weeks; Sex: male

value: male


title: Bcell-rich region for FL-pt223-B ROI B10

description: Library name: tFL_TMA_B_20250520_B10_Bcell


title: Tcell-rich region for FL-pt223-B ROI B10

description: Library name: tFL_TMA_B_20250520_B10_Tcell


title: NF108-normal-fat


title: Mouse liver, Control, female, scRNA-seq

description:
Library name: Control_F
Strain: C57BL/6N; Age: 8-10 weeks; Sex: female

value: Control (NIAAA model)


title: Others-rich region for Atonsil ROI Atonsil

description: Library name: tFL_TMA_A_20250520_Atonsil_Others

value: Atonsil


title: DD159-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: extremity

value: high


title: Chip-seq of Tbet with Runx3 KO 3

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road

country: China

institute: Suzhou Institute of Systems Medicine

description: Library name: Sample 30

data_processing:
Library construction and the quality inspection was carried out using Illumina HiSeq 4000 for sequencing
Assembly: T-bet,Runx3
Supplementary files format and content: .txt
Supplementary files format and content: .bw

source_name: CD8+T cells

extract_protocol:
T-bet and Runx3 CUT&RUN:We adopted Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for genome-wide mapping of Runx3 in WT and Tbx21–/–.In brief, FACS-sorted live cells (1 × 105 cells per reaction) were bound to concanavalin A-coated magnetic beads (Bangs Laboratories) and permeabilized with 0.05% (w/v) digitonin and then incubated with anti-Runx3 antibody (Active Motif, 1 µl per reaction) or IgG overnight. After removal of unbounded antibodies with proper washing, the nuclei were incubated with protein A/G-micrococcal nuclease (MNase) fusion protein (plasmid obtained from Addgene) for 1hr at 4 °C. CaCl2 was then added to activate MNase activity and incubated on ice for 30 min. ATAC-seq:WT, Runx3–/–, Tbx21–/–, or Runx3–/–Tbx21–/– cells cells were sorted on 4 dpi. Three biological replicates for each cell type, and 50,000 cells for each replicate were used to prepare ATACseq libraries as previously described71. Briefly, the sorted cell pellets were washed and treated in lysis buffer for 3 min on ice. The extracted nuclei were resuspended in transposition mix containing 2.5 µl Transposase (Illumina) and incubated at 37oC for 30 min. The products were purified with MinElute Reaction Cleanup Kit (Qiagen), and then amplified by PCR for 13 cycles with barcoded Nextera primers (Illumina). DNA fragments in the range of 150-1,000 bp were recovered from 2% E-Gel EX Agarose Gels (Invitrogen/ThermoFisher Scientific). RNA-seq:Total RNA was extracted from the sorted WT, Runx3–/–, Tbx21–/–, or Runx3–/–Tbx21–/– cells on 4 dpi, and triplicates were obtained for each genotype. cDNA synthesis and amplification were performed using SMARTer Ultra Low Input RNA Kit (Clontech).
T-bet and Runx3 CUT&RUN:The reaction was quenched with stopping buffer and the DNA fragments were purified with MinElute Reaction Cleanup kit (QIAGEN) and then amplified by PCR for 10–14 cycles with barcoded Nextera primers (Illumina). ATAC-seq:The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq 4000 sequencing systems in paired end 150 bp reads at the Admera Health. RNA-seq:Libraries were sequenced on Illumina’s HiSeq4000 in paired read mode with the read length of 150 nucleotides. Sequence data in fastq format were generated using CASAVA 1.8.2 processing pipeline from Illumina.

value: CD8+T cells


title: Tcell-rich region for Atonsil ROI Atonsil

description: Library name: tFL_TMA_A_20250520_Atonsil_Tcell


title: mouse_BDL_blood_1

description:
Library name: BDL_blood_1
10X Genomics scRNAseq

value: Male

value: BDL


title: Bcell-rich region for Atonsil ROI Atonsil

description: Library name: tFL_TMA_A_20250520_Atonsil_Bcell


title: DD488-dedifferentiated-liposarcoma

value: retroperitoneal

value: surgery


title: Chip-seq of Tbet with Runx3 KO 2

description: Library name: Sample 29


title: Mac-rich region for Atonsil ROI Atonsil

description: Library name: tFL_TMA_A_20250520_Atonsil_Mac


title: ALT479-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low


title: Chip-seq of Tbet with Runx3 KO 1

description: Library name: Sample 28


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

description: Library name: tFL_TMA_A_20250520_A9_Others


title: PMUC3

city: Shanghai

first: Xudong

last: Zhang

address: 1239 Siping Road

department: Department of Orthopedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University

institute: Tongji University: Shanghai, CN

description: Library name: SAMPLES3

data_processing:
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end read swere generated. About xxxxx raw reads for each sample were generated. Raw reads of fastq form atwere firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads. Then about xxxxxx clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2 . FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4 . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar . Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term. Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis waswww.oebiotech.com used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: After reads ressembled by StringTie210 , gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using Cuffcompare software. ASprofile11 was used to analyse the alternatively splicing of differentially regulated transcripts isoforms or exons. SNPs and InDels were called using SAMtools12 and BCFtools13 , and the details were shown on SAMtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then SnpEff14 annotates and predicts the effects of variants on genes (such as amino acid changes)
Supplementary files format and content: Processed_data.xlsx

source_name: cartilage

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)
The libraries were sequenced on an Illumina NovaSeq 6000 platform, and 150 bp paired-end reads were generated. Approximately 40 million raw reads were obtained for each sample. Raw reads in FASTQ format were first processed using fastp (v0.23.4) to remove low-quality reads, adapters, and poly-N sequences, resulting in clean reads. Subsequently, about 38 million clean reads per sample were retained for downstream analyses. The clean reads were then mapped to the GRCh38/hg38 reference genome using HISAT2 (v2.2.1). The expression level of each gene was quantified as FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and raw read counts for each gene were obtained using HTSeq-count (v0.13.5). Finally, Principal Component Analysis (PCA) was performed using R (v 3.2.0) to evaluate the biological reproducibility among the samples.

value: cartilage

value: primary mouse chondrocytes

value: PMUC


title: WD472-well-differentiated-liposarcoma


title: ATAC-seq of Tbet and Runx3 KO 3

description: Library name: Sample 21


title: PMUC2

description: Library name: SAMPLES2


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

description: Library name: tFL_TMA_A_20250520_A9_Bcell

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

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: Lymph Node

value: FL


title: DD471-dedifferentiated-liposarcoma


title: ATAC-seq of Tbet and Runx3 KO 2

description: Library name: Sample 20


title: PMUC1

description: Library name: SAMPLES1


title: DD456-dedifferentiated-liposarcoma


title: DD454-dedifferentiated-liposarcoma


title: BMDC (untreated, + 5555 Ptgs+/+, + 5555 Ptgs-/-)

city: Manchester

first: Santiago

last: Zelenay

address: Wilmslow Rd, Manchester M20 4BX

institute: Cancer Research UK Manchester Institute

description:
Library name: SZ20_01_BM_pool_10X_S1
10X Genomics

data_processing:
Pre-processing (quality control (QC), alignment and initial filtering for empty droplets) of raw sequencing files was performed using the CellRanger V.3.0.2 (10x Genomics). Output files (either the filtered_feature_bc_matrix.h5 file or the barcodes.tsv, features.tsv and matrix.mtx files) were imported on Partek Flow software (Single cell Toolkit, build version 11.0.24.0325) for analysis. Hashtag demultiplexing was applied on BMDC counts after CLR normalization to specify culture conditions.
Assembly: mm10
Supplementary files format and content: Comma separated meta data files and space-separated count files.

source_name: Primary bone marrow culture

extract_protocol:
5555 or CT26 tumors were harvested, cut into small pieces with scissors and incubated in RPMI containing 200U/mL Collagenase IV (Worthington Biochemical) and 0.2mg/mL DNase I (Roche) for 30 min at 37oC. Digested tissue was grinded and filtered through a 70μm cell strainer, washed with RPMI and pelleted. BMDCs cultured in the absence or presence of cancer cells were harvested at day 10. For all experiments, cell suspensions were resuspended in PBS and labelled using LIVE/DEAD Fixable Aqua Dead Cell 405nm staining (Invitrogen) to define cell viability. Samples were rinsed in FACS buffer (PBS containing 1-2% FBS and 0.01% sodium azide) and incubated with the anti-mouse CD45 antibody (clone 30-F11) for 30min at 4oC. Live CD45+ cell suspensions were sorted on a BD FACSAria III with ≥98% purity. Sorted single cells were counted, and ≥90% viability was confirmed through Trypan Blue exclusion.
16-18,000 cells + ~3.5% spike-in (of each 5555 tumor sample) or 25,000 cells (of each CT26 tumor sample) were loaded into a channel of the Chromium Chip B (10x Genomics, PN-1000073). Single cell gel beads-in-emulsion (GEMs) were generated using the Chromium Controller and sequencing libraries prepared using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10x Genomics), according to the manufacturer’s protocol. For BMDC cultures, 30,000 cells were loaded into a channel of the Chromium Next GEM Chip G (10x Genomics, PN-1000120), and single cell GEMs were generated using the Chromium Controller and Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics) according to the manufacturer’s protocol. Gene expression and TotalSeq-A HTO libraries were produced according to the BioLegend TotalSeq-A protocol and 10x Genomics user guide. For all experiments, libraries were quality checked using the Agilent Bioanalyzer and quantified by qPCR using a KAPA Library Quantification Kit for Illumina Platforms (Roche). Paired-end sequencing was performed on an Illumina NextSeq 500 in High Output mode with an input of 1.4pM (5555) or 1.6pM (CT26), or on an Illumina NovaSeq 6000 with XP loading and inputs of 0.9 (GEx library) and 1.8pM (HTO library).

value: Primary bone marrow culture

value: Dendritic cells

value: Untreated, Co-culture with 5555 Ptgs+/+ tumor cells, Co-culture with 5555 Ptgs-/- tumor cells


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

description: Library name: tFL_TMA_A_20250520_A9_Tcell


title: ATAC-seq of Tbet and Runx3 KO 1

description: Library name: Sample 19


title: thyroid from mouse injected wtith anti-PD-L1 monoclonal antibody, 2

first: Weijia

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

description: Library name: PDL18

data_processing:
The reads with good quality were firstly aligned to mouse reference databases including mm10 human genome, exon, splicing junction segment and contamination database of ribosome and mitochondria sequences using BWA alignment algorithm. After filtering out reads mapped to contamination database, the reads that were uniquely aligned to the exon and splicing-junction segments with a maximal 2 mismatches for each transcript were then counted as expression level for corresponding transcript. The genes with read count<100 across all samples were excluded. The read counts were log2 transformed, quantile-normalized in order to compare at transcription levels across samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts of all samples.

source_name: thyroid

extract_protocol:
Total RNA from mouse thyroids was extracted using RNeasy Plus Mini Kit (Qiagen).
Library preparation and RNA sequencing were done at Azenta Life Sciences. Briefly, total RNA was first subjected to poly(A)⁺ selection with oligo-dT magnetic beads. The captured transcripts were fragmented and converted to double-stranded cDNA by random-primer-initiated first- and second-strand synthesis. Resulting cDNA fragments underwent end repair, 5′ phosphorylation, and single-adenosine (dA) overhang addition. Illumina sequencing adapters were then ligated, and libraries were amplified by limited-cycle PCR. Final libraries were sequenced on an Illumina NovaSeq platform, generating paired-end 150 bp reads (2 × 150 bp).

value: thyroid

value: anti-PD-L1 Ab treated

value: anti-PD-L1 Ab

tag: batch

value: clone 10F.9G3


title: Others-rich region for FL-pt13-A ROI A7

description: Library name: tFL_TMA_A_20250520_A7_Others


title: thyroid from mouse injected wtith anti-PD-L1 monoclonal antibody, 1

description: Library name: PDL110

value: clone 10F.9G2


title: DD442-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: retroperitoneal

value: high


title: Bcell-rich region for FL-pt13-A ROI A7

description: Library name: tFL_TMA_A_20250520_A7_Bcell


title: ATAC-seq of Runx3 KO 2

description: Library name: Sample 17

tag: cell type

value: CD8+T cells


title: ATAC-seq of Runx3 KO 1

description: Library name: Sample 16


title: WD440-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: low

value: surgery


title: Tcell-rich region for FL-pt13-A ROI A7

description: Library name: tFL_TMA_A_20250520_A7_Tcell

value: Lymph Node


title: thyroid from mouse injected wtith IgG isotype control, 2

description: Library name: CTR2

value: CTR

value: IgG isotype CTR

value: clone LTF3


title: mouse_BDL_liver_1

description:
Library name: BDL_liver_1
10X Genomics scRNAseq

value: Liver

value: Male

value: BDL


title: WD432-well-differentiated-liposarcoma


title: RNA-seq of Tbet KO 3

description: Library name: Sample 12


title: Mac-rich region for FL-pt13-A ROI A7

description: Library name: tFL_TMA_A_20250520_A7_Mac

value: FL


title: RNA-seq of Tbet KO 2

description: Library name: Sample 11


title: Others-rich region for FL-pt211-A ROI A57

description: Library name: tFL_TMA_A_20250520_A57_Others


title: NF428-normal-fat

value: normal fat

value: unknown


title: WD426-well-differentiated-liposarcoma


title: Bcell-rich region for FL-pt211-A ROI A57

description: Library name: tFL_TMA_A_20250520_A57_Bcell


title: RNA-seq of Tbet KO 1

description: Library name: Sample 10


title: RNA-seq of Tbet and Runx3 KO 3

description: Library name: Sample 9


title: Vehicle 2+3

city: Suwon

first: Seunghee

last: Jeong

address: 2066 Seobu-ro, Janna-gu, Suwon, Gyeonggi-do, South Korea

institute: Sunkyunkwan University

description: Spatial transcriptome sequencing of formalin-fixed, paraffin-embedded sample

data_processing:
Raw sequencing reads were processed using Space Ranger software (v2.1.1, 10x Genomics) with default parameters and refdata-gex-mm10-2020-A as the reference genome. Spatial transcriptomics analysis was conducted using R (v4.4.1) with Seurat and STUtility toolkits.
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg:  image of tissue and spots
Supplementary files format and content: scalefactors json.json.gz: scalefactors in json format
Supplementary files format and content: tissue hires image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions.csv.gz: spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

source_name: brain tumor-inoculated model

extract_protocol:
FFPE tissue sections were prepared on slides according to the manufacturer’s instructions (10x Genomics, CG000518). Specific probes hybridized to target RNA molecules within the tissue sections. The probes were designed to bind to specific mRNA targets and were tagged with unique barcodes for spatial resolution. Following hybridization, unbound probes were washed away, and the tissue sections were ready for downstream processing.
fter hybridization of the barcoded probes to the target RNA in the FFPE tissue sections, the bound probes were ligated to form a continuous sequence that includes the spatial barcodes and target-specific sequences. Ligated probes were amplified through PCR to generate sufficient material for sequencing. The amplified products were purified and prepared for library construction using standard protocols (10x Genomics, CG000495). The final libraries were quantified by qPCR and quality-checked using a bioanalyzer.

value: brain tumor-inoculated model

value: Day 11 Vehicle


title: WD418-well-differentiated-liposarcoma

value: retroperitoneal


title: RNA-seq of Tbet and Runx3 KO 2

description: Library name: Sample 8

value: CD8+T cells


title: Vehicle 1+4


title: thyroid from mouse injected wtith IgG isotype control,1

description: Library name: CTR1

value: thyroid

value: clone LTF2


title: Mac-rich region for FL-pt211-A ROI A57

description: Library name: tFL_TMA_A_20250520_A57_Mac


title: TREAT 2+3

value: Day 11 TREAT


title: RNA-seq of Tbet and Runx3 KO 1

description: Library name: Sample 7


title: Kidney_RNA Control  wild type#9

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: Wild type control littermate


title: NF400-normal-fat

value: surgery


title: TREAT 1+4


title: Others-rich region for tFL-pt215 ROI A55

first: Nicholas

address: 75 Ames St

institute: Broad Institute

description: Library name: tFL_TMA_A_20250520_A55_Others

value: Lymph Node

value: tFL


title: RNA-seq of Runx3 KO 3

description: Library name: Sample 6


title: Kidney_RNA Control  wild type#8

value: Male


title: DD391-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: high


title: Tcell-rich region for tFL-pt215 ROI A55

description: Library name: tFL_TMA_A_20250520_A55_Tcell


title: RNA-seq of Runx3 KO 2

description: Library name: Sample 5


title: Tcell-rich region for FL-pt211-A ROI A57

description: Library name: tFL_TMA_A_20250520_A57_Tcell

value: FL


title: Kidney_RNA Control  wild type#7


title: NF387-normal-fat

value: normal fat

value: unknown


title: 32D-LV-H19 cells expressing empty vector, replicate 2

city: Tianjin

first: Shuangshuang

last: Pu

state: China

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood Diseases Institute of Hematology

description:
Library name: Sample 2
Column name in 32D_H19_Adar_gene_count_matrix.tsv.gz: 32D_H19_Ctrl-2

data_processing:
Raw paired-end reads were processed using fastp v0.23.1. Read pairs were removed when either read contained adapter contamination, more than 10% undetermined bases, or more than 50% bases with Phred quality scores below 5. Clean reads were aligned to the Mus musculus GRCm38/mm10 reference genome using HISAT2. Alignment files were converted to BAM format, name-sorted, and filtered to remove unmapped reads using SAMtools. Gene-level unnormalized read counts were generated using HTSeq-count with the Ensembl Mus musculus GRCm38.101 annotation.
Raw single-end reads were processed to remove reads containing adapter contamination, poly-N sequences, homopolymeric sequences, low-quality bases, or reads lacking the expected 3′ adapter or insert sequence. Clean reads within the selected small-RNA length range were retained for downstream analysis. Clean reads were mapped to the Mus musculus GRCm38/mm10 reference genome using Bowtie. Seed-based alignment was performed using a 20-nt seed, allowing no more than one mismatch within the seed region. Mapped reads were annotated against known mouse miRNA sequences in miRGeneDB 2.1 and used to quantify known miRNAs.
Assembly: GRCm38/mm10
Supplementary files format and content: 32D_H19_Adar_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for nine bulk RNA-seq libraries generated from 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A.
Supplementary files format and content: ckit_h19_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for 12 bulk RNA-seq libraries generated from primary mouse c-Kit-positive cells expressing empty vector, wild-type editable H19-A, the H19-G edited mimic, or the editing-resistant H19-T mutant.
Supplementary files format and content: AN_GN_TN_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for nine bulk RNA-seq libraries generated from poly(I)-treated Ki67-eGFP-negative LT-HSCs carrying H19-A, H19-G, or H19-T alleles.
Supplementary files format and content: miRNA_pulldown_raw_counts.tsv.gz contains gene-level unnormalized read counts for 12 RNA-seq libraries generated from input and biotinylated miRNA pulldown fractions of 32D cells transfected with scrambled-control, unedited wild-type miR-675-3p, or edited miR-675-3p mimics.
Supplementary files format and content: ki67_eGFP_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for six bulk RNA-seq libraries generated from steady-state Ki67-eGFP-negative and Ki67-eGFP-positive LT-HSCs.
Supplementary files format and content: miRNA_RCadj_libraryRPM.tsv.gz contains reverse-complement-adjusted miRNA abundance values for 21 small RNA-seq libraries. The matrix includes 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A, and primary mouse c-Kit-positive cells expressing empty vector, H19-A, H19-G, or H19-T.

growth_protocol: 32D and 32D-LV-H19 mouse myeloid progenitor cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 10 ng/mL recombinant mouse interleukin-3, penicillin, and streptomycin at 37°C in a humidified incubator containing 5% CO₂. Primary mouse c-Kit-positive hematopoietic progenitor cells were isolated from bone marrow by magnetic enrichment using CD117 MicroBeads (Miltenyi Biotec). Cells were cultured in serum-free expansion medium supplemented with 100 ng/mL stem cell factor, 100 ng/mL thrombopoietin, penicillin, and streptomycin at 37°C in a humidified incubator containing 5% CO₂. Mice were maintained under specific-pathogen-free conditions. Bone marrow cells were collected from 8- to 10-week-old female mice. LT-HSCs were identified and purified by fluorescence-activated cell sorting using the Lin⁻Sca-1⁺c-Kit⁺CD34⁻Flt3⁻ phenotype. In Ki67-eGFP reporter mice, Ki67-eGFP-negative LT-HSCs were defined as quiescent cells, whereas Ki67-eGFP-positive LT-HSCs were defined as cycling cells.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. Samples were treated with DNase I to remove residual genomic DNA. For miRNA pulldown experiments, RNA was extracted separately from the input lysate and the streptavidin-enriched pulldown fraction using TRIzol reagent. RNA concentration was determined using a Qubit fluorometer or NanoDrop spectrophotometer. RNA integrity was evaluated using an Agilent RNA analysis system when sample yield permitted.
For conventional bulk RNA-seq, libraries were prepared from 200 ng total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L). Poly(A)-positive RNA was enriched using poly-T oligo-attached magnetic beads, fragmented, reverse-transcribed, adapter-ligated, and PCR-amplified according to the manufacturer’s instructions. For miRNA pulldown RNA-seq, libraries were prepared from RNA recovered from the corresponding input and pulldown fractions using the NEBNext Ultra RNA Library Prep Kit for Illumina. Libraries were generated using the same poly(A) enrichment, fragmentation, reverse-transcription, adapter-ligation, and PCR-amplification workflow. Conventional bulk RNA-seq and miRNA pulldown RNA-seq libraries were sequenced using a paired-end 150-bp strategy on an Illumina NovaSeq 6000 or DNBSEQ-T7 platform, as specified for each sample. For small RNA-seq, libraries were prepared from total RNA using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300L). Following sequential 3′- and 5′-adapter ligation, reverse transcription, and PCR amplification, library fragments containing 18–40-nt inserts were size-selected. Qualified libraries were sequenced using a single-end 50-bp strategy on an Illumina NovaSeq 6000.

treatment_protocol: For ADAR1-dependent experiments, 32D-LV-H19 cells were transduced with lentiviral vectors expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A. Cells were collected 48 h after transduction. For H19 allele-dependent experiments, primary mouse c-Kit-positive cells were transduced with lentiviral vectors expressing empty vector, wild-type editable H19-A, the H19-G edited mimic, or the editing-resistant H19-T mutant. GFP-positive transduced cells were purified by fluorescence-activated cell sorting before RNA extraction. For inflammatory-stress experiments, H19-A, H19-G, and H19-T mice carrying the Ki67-eGFP reporter were administered polyinosinic acid [poly(I)] at 10 mg/kg. Bone marrow was collected 24 h after treatment, and Ki67-eGFP-negative LT-HSCs were purified by fluorescence-activated cell sorting. For miRNA pulldown experiments, 32D cells were transfected with a biotinylated scrambled-control miRNA mimic, biotinylated unedited wild-type miR-675-3p mimic, or biotinylated edited miR-675-3p mimic. Cells were harvested 48 h after transfection. An aliquot of each cell lysate was retained as the input fraction, and biotinylated miRNA-associated RNA complexes were isolated using streptavidin-coated beads. Steady-state Ki67-eGFP-negative and Ki67-eGFP-positive LT-HSCs were isolated without additional experimental treatment.

tag: cell line

value: myeloid progenitor cell line

value: wild type

value: lentiviral transduction


title: Bcell-rich region for tFL-pt215 ROI A55

city: CAMBRIDGE

last: Haradhvala

description: Library name: tFL_TMA_A_20250520_A55_Bcell


title: mouse_BDL_liver_2

description:
Library name: BDL_liver_2
10X Genomics scRNAseq

value: Liver

value: BDL


title: DD382-dedifferentiated-liposarcoma

value: retroperitoneal


title: RNA-seq of Runx3 KO 1

description: Library name: Sample 4

value: CD8+T cells


title: Mouse liver, Control, male, scRNA-seq

description:
Library name: Control_M
Strain: C57BL/6N; Age: 8-10 weeks; Sex: male

value: liver

value: liver cells (single-cell suspension)

value: male

value: Control (NIAAA model)


title: Kidney_RNA Control  wild type#6

value: kidney

value: Male

value: Wild type control littermate


title: mouse_BDL_blood_2

description:
Library name: BDL_blood_2
10X Genomics scRNAseq

value: Blood


title: NF115-normal-fat

value: normal fat

value: surgery


title: Mac-rich region for tFL-pt215 ROI A55

description: Library name: tFL_TMA_A_20250520_A55_Mac

value: Lymph Node

value: tFL


title: RNA-seq of Cpntrol 3

description: Library name: Sample 3


title: Kidney_RNA Hes1 cKO 1 week of inactivation  mutant#7

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


title: DD370-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: high


title: DD506-dedifferentiated-liposarcoma

value: retroperitoneal


title: Con3

description: Library name: SAMPLES6

value: cartilage

value: primary mouse chondrocytes

value: PBS control


title: Con2

description: Library name: SAMPLES5


title: Others-rich region for FL-pt88-C ROI A52

description: Library name: tFL_TMA_A_20250520_A52_Others

value: FL


title: Con1

description: Library name: SAMPLES4


title: Kidney_RNA Hes1 cKO 1 week of inactivation  mutant#6

value: Female


title: Tcell-rich region for FL-pt88-C ROI A52

description: Library name: tFL_TMA_A_20250520_A52_Tcell


title: Kidney_RNA  Hes1 cKO 1 week of inactivation  mutant#5

value: kidney


title: Bcell-rich region for FL-pt88-C ROI A52

description: Library name: tFL_TMA_A_20250520_A52_Bcell


title: RNA-seq of Cpntrol 2

description: Library name: Sample 2

value: CD8+T cells


title: RNA-seq of Cpntrol 1

description: Library name: Sample 1


title: WD368-well-differentiated-liposarcoma

value: well-differentiated liposarcoma

value: extremity

value: low


title: DD330-dedifferentiated-liposarcoma

value: unknown

value: surgery


title: WD326-well-differentiated-liposarcoma


title: Kidney_RNA Control  wild type#5

value: Wild type control littermate


title: Bcell-rich region for FL-pt88-B ROI A51

description: Library name: tFL_TMA_A_20250520_A51_Bcell

value: Lymph Node


title: MouseBlood_ATAC_ImmuneCells_Ctrl_4wk

description:
Library name: MB_ATAC_Immune_Ctrl_4wk
10X Genomics Single cell 3' gene expression V2

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

source_name: blood

value: blood

value: WT

value: Healthy

value: Male


title: Kidney_RNA Control  wild type#4


title: Kidney_RNA Control  wild type#3


title: WD286-well-differentiated-liposarcoma

value: retroperitoneal


title: Tcell-rich region for FL-pt88-B ROI A51

description: Library name: tFL_TMA_A_20250520_A51_Tcell


title: NF313-normal-fat

value: normal fat


title: MouseLiver_ATAC_ImmuneCells_CCl4_4wk

description:
Library name: ML_ATAC_Immune_CCl4_4wk
10X Genomics Single cell 3' gene expression V2

value: liver


title: Mac-rich region for FL-pt88-B ROI A51

description: Library name: tFL_TMA_A_20250520_A51_Mac

value: FL


title: Kidney_RNA Control  wild type#2

value: kidney


title: MouseLiver_ATAC_ImmuneCells_CCl4_24hr

description:
Library name: ML_ATAC_Immune_CCl4_24hr
10X Genomics Single cell 3' gene expression V2


title: Kidney_RNA Control  wild type#1


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

description: Library name: tFL_TMA_A_20250520_A50_Others

value: tFL

value: DLBCL


title: ELF-normal-fat


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

description: Library name: tFL_TMA_A_20250520_A50_Tcell


title: MouseLiver_ATAC_ImmuneCells_Ctrl_24hr

description:
Library name: ML_ATAC_Immune_Ctrl_24hr
10X Genomics Single cell 3' gene expression V2


title: FRPBiopsy_12_Female_MASLD

description:
Library name: FRPBiopsy_12
10X Genomics scRNAseq FLEX

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs was performed using 'cellranger multi' (Cell Ranger 7.0.0), and a csv specifying the probe barcode. Genome build: Human GRCh38-2020-A
Conversion of per-sample BAM files from CellRanger to per-sample fastq files using  'cellranger bamtofastq' Cell Ranger 7.0.0
Assembly: Human GRCh38-2020-A
Supplementary files format and content: mtx: count matrix in sparse matrix format (CellRanger output)
Supplementary files format and content: barcodes.tsv: barcode ids per sample (CellRanger output)
Supplementary files format and content: genes.tsv: gene ids per sample (CellRanger output)

extract_protocol:
Liver needle biopsies were taken from patients and immediately snap-frozen. Samples were fixed and cells isolated using the ChromiumTM Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics, 1000414) according to the 10X Genomics demonstrated protocol (document number CG000553).
scRNA-seq and library preparation was performed using ChromiumTM Next GEM Single Cell Fixed RNA Hybridization & Library Kit (10X Genomics, PN-1000415), ChromiumTM Single Cell Fixed RNA Human Transcriptome Probe Kit and Chromium Next GEM Chip Q Kit (10X Genomics, PN-2000518) on the ChromiumTM X Single Cell Platform (10X Genomics), according to manufacturer’s protocol.

value: Liver

value: Female

tag: disease state

value: MASLD

tag: probe barcode


title: DMT-well-differentiated-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.

value: well-differentiated liposarcoma

tag: tumor site

value: low

value: surgery


title: FRPBiopsy_08_Male_MASLD

description:
Library name: FRPBiopsy_08
10X Genomics scRNAseq FLEX

tag: Sex


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

description: Library name: tFL_TMA_A_20250520_A50_Bcell

value: Lymph Node


title: DD88-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

tag: tumor grade

value: high


title: MouseBlood_RNA_ImmuneCells_Ctrl_4wk

description:
Library name: MB_RNA_Immune_Ctrl_4wk
10X Genomics Single cell 3' gene expression V2

value: blood

value: WT

value: Healthy

value: Male


title: DD8379-dedifferentiated-liposarcoma

value: retroperitoneal

tag: treatement


title: mpkCCDc14, Input, Batch2,  Repeat 2

data_processing:
Fastq files were assessed with fastqc and aligned using bowtie2 (2.4.0) and peaks called using macs2 (v2.2.6).
Assembly: mm10
Supplementary files format and content: bed

extract_protocol:
Cells were incubated with 1% formaldehyde (Fisher Scientific, BP531-25) for 10 minutes at room temperature with rocking. The formaldehyde was quenched with glycine to a final concentration of 125mM for 5 minutes at room temperature. Cell were lysed to isolate nuclei which were lysed to release chromatin. The chromatin was sonicated using  ME220 focused ultrasonicator (Covaris).
Libraries were prepared by Novogene through the processes of end reparining, adding A to tils, purificaton and PCR amplification.

value: mouse primary kidney cortical collecting duct

tag: chip antibody


title: Others-rich region for tFL-pt221 ROI A49

description: Library name: tFL_TMA_A_20250520_A49_Others

tag: tissue

tag: sample id

value: tFL


title: WD72-well-differentiated-liposarcoma

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: MouseBlood_RNA_ImmuneCells_Ctrl_24hr

description:
Library name: MB_RNA_Immune_Ctrl_24hr
10X Genomics Single cell 3' gene expression V2

tag: genotype


title: mpkCCDc14, FLAG ChIP, Batch2, Repeat 3

value: FLAG (Sigma, F1804)


title: Bcell-rich region for tFL-pt221 ROI A49

description: Library name: tFL_TMA_A_20250520_A49_Bcell

tag: patient id

tag: disease binary

value: DLBCL


title: DD69-dedifferentiated-liposarcoma


title: mpkCCDc14, FLAG ChIP, Batch 2, Repeat 2


title: MouseBlood_RNA_ImmuneCells_Ctrl_96hr

description:
Library name: MB_RNA_Immune_Ctrl_96hr
10X Genomics Single cell 3' gene expression V2

tag: treatment


title: Tcell-rich region for tFL-pt221 ROI A49

description: Library name: tFL_TMA_A_20250520_A49_Tcell

tag: disease fine


title: DD606-dedifferentiated-liposarcoma


title: MouseBlood_RNA_ImmuneCells_CCl4_96hr

description:
Library name: MB_RNA_Immune_CCl4_96hr
10X Genomics Single cell 3' gene expression V2


title: mpkCCDc14, Input, Batch1, Repeat 1


title: Mac-rich region for tFL-pt221 ROI A49

description: Library name: tFL_TMA_A_20250520_A49_Mac


title: MouseBlood_RNA_ImmuneCells_CCl4_4wk

description:
Library name: MB_RNA_Immune_CCl4_4wk
10X Genomics Single cell 3' gene expression V2


title: MouseBlood_RNA_ImmuneCells_CCl4_24hr

description:
Library name: MB_RNA_Immune_CCl4_24hr
10X Genomics Single cell 3' gene expression V2


title: Kidney_RNA Hes1 cKO 1 week of inactivation  mutant#4

value: kidney

value: Female

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


title: Mac-rich region for FL-pt88-C ROI A52

description: Library name: tFL_TMA_A_20250520_A52_Mac

value: FL


title: MouseBlood_ATAC_ImmuneCells_CCl4_4wk

description:
Library name: MB_ATAC_Immune_CCl4_4wk
10X Genomics Single cell 3' gene expression V2


title: DD604-dedifferentiated-liposarcoma

value: surgery


title: MouseBlood_ATAC_ImmuneCells_CCl4_24hr

description:
Library name: MB_ATAC_Immune_CCl4_24hr
10X Genomics Single cell 3' gene expression V2


title: PL324-dedifferentiated-liposarcoma

value: unknown


title: Others-rich region for FL-pt88-B ROI A51

description: Library name: tFL_TMA_A_20250520_A51_Others

value: Lymph Node


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

description: Library name: tFL_TMA_A_20250520_A48_Others


title: mpkCCDc14, FLAG ChIP, Batch1, Repeat 1


title: MouseBlood_ATAC_ImmuneCells_Ctrl_24hr

description:
Library name: MB_ATAC_Immune_Ctrl_24hr
10X Genomics Single cell 3' gene expression V2


title: MouseLiver_RNA_ImmuneCells_Ctrl_4wk

description:
Library name: ML_RNA_Immune_Ctrl_4wk
10X Genomics Single cell 3' gene expression V2

value: liver