title: aak_PD_2

city: Montreal

first: Sabih

last: Rashid

address: 3611 Rue Sainte Famille, Unit 11

institute: McGill University

description:
Library name: Sample 11
aak_PD_2

data_processing:
Reference genome assembly and DESeq2. Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference C. elegans genome version WBcel235 (gene annotation from Ensembl version 104) using STAR version 2.7.1a. Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression, either in TPM or FPKM values, for these stranded RNA libraries. DESeq2 version 1.48.2 was then used to normalize gene readcounts and obtain pairwise comparisons following filtering of low-readcount genes.
Assembly: WBcel235 (gene annotation from Ensembl version 104)
Supplementary files format and content: "daf2_aak_alg34_normalized_counts.csv" contains read counts, pairwise comparisons in separate files for fold change calculations.

source_name: Whole animal

extract_protocol:
Standard Trizol RNA extraction was carried out, approximately 200 ul per 20 ul packed worms. Freeze-thawing with liquid nitrogen was carried out to separate RNA, followed by heavy centrifugation. Two rounds of chloform extraction were carried out (50 ul per 200 ul Trizol). Samples were washed with isopropanol followed by 70% EtoH, and air-dryed before dissolving in ultrapure water. Sample concentration was measured using Nanodrop, and run on agarose gels to verify integrity of RNA. RNA was stored at -80 °C for up to 3 days before being sent for sequencing. Minimum of 100 ng/ul RNA was sent for sequencing.
mRNA-Seq with PolyA selection, 150 cycles Paired-End (maximum 2x80nt), 400M fragments, using KAPA mRNA Hyper Prep Hyperprep library per manufacturer instructions

value: Whole animal

value: Post-dauer

value: 192 hrs

value: daf-2; aak(0)

value: Trizol


title: aak_Dauer_2

status: Public on Jan 27 2026

type: SRA

state: Quebec

department: Biology

country: Canada

description:
Library name: Sample 8
aak_Dauer_2

library_source: transcriptomic

molecule: total RNA

organism: Caenorhabditis elegans

growth_protocol: Bleach-synchronized worms were put onto large NGM plates and grown at 25 °C. Dauer animals were collected after 96 hours (i.e. Day 2 in dauer) and washed with M9, post-dauer animals collected after 192 hours. Animals were immediately subjected to Trizol RNA extraction after collection.

tag: tissue

tag: developmental stage

value: Dauer

tag: time

value: 96 hrs

tag: genotype

tag: treatment

tag: batch


title: E150009253_L01_C1

city: wenzhou

first: bin

last: zhou

address: Nanbaixiang, Ouhai District, Wenzhou, Zhejiang Province

country: China

institute: Affiliated Hospital of Weifang Medical University

description: Library name: Sample 1

data_processing:
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Read count extraction and normalization were performed using CLC genomic benchwork
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: csv files include RPKM values for each Sample

organism: Mus musculus

source_name: cell line

growth_protocol: Human relapsed and refractory (R/R) AML samples were xenografted into mice to assess the anti-leukemic effects of HF in vivo

extract_protocol:
centrifuge to remove supernatant, add about 2ML PBS (2% FBS), with a total amount of about 2.5mL, Add cells to trizol
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Comparative gene expression profiling analysis of RNA-seq data for stem  cells treated with halofuginone  .

value: cell line

tag: cell line

tag: cell type

value: stem cell

value: adipogenic differentiation

value: Separate ribosomal RNA

value: Day 0


title: aak_PD_1

description:
Library name: Sample 10
aak_PD_1


title: Thymus epithelial cells, NOD.AireWT/WT, 4 to 8 weeks, biol rep 2

city: Aurora

first: Jordan

middle: Keith

last: Abbott

state: CO

department: Allergy and Immunology

country: USA

institute: University of Colorado School of Medicine

description:
Library name: WT/WT 4
1_S2_L005

data_processing:
Reads were demultiplexed into individual FASTQ files. Each FASTQ file was trimmed to remove adaptor sequences, empty reads, and long stretches of homopolymer. Timmed FASTQ files were evaluated with FASTQC for quality control. FASTQ files that passed QC were mapped to mm39 using a pre-built genome index (https://zenodo.org/records/7457660) in HISAT2 with splice-aware setting. Transcriptomes were assembled and quantified using Stringtie using the reference gencode.vM30. Raw counts were extracted in R using txImport.
Assembly: mm39
Supplementary files format and content: gene_count_matrix.csv containing raw gene counts

source_name: Thymus

extract_protocol:
Mouse thymus was surgically harvested and digested into single-cell suspensions. CD45-expressing cells were depleted using magnetic beads. Cells were sorted for EpCAM expression using a Sony MA900 cell sorter. RNA was isolated using the Qiagen RNeasy micro kit.
cDNA libraries were prepared using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1).

value: Thymus

value: Thymus epithelium

value: WT/WT

value: B


title: daf2_PD_1

description:
Library name: Sample 4
daf2_PD_1


title: TAPseq, MEF cells, gRNA enrichment from GEX, biol rep 2

city: Cambridge

first: Stephen

middle: Peter

last: Burr

address: Mitochondrial Biology Unit, Keith Peters Building, Cambridge Biomedical Campus, Hills Road

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

description:
Library name: MitoPerturbSeq_Replicate_2_gRNA_TAPseq
GEX (3' mRNA) library enriched for gRNA sequences: Read 1 file contains cell barcode & UMI, Read 2 file contains transcript
MitoPerturbSeq_Integrated_metadata.tsv

library_source: transcriptomic single cell

data_processing:
RNAseq & ATACseq fastq files were processed using the Cell Ranger ARC (v2.0.1) pipeline using a reference genome with nuclear mitochondrial DNA sequences (NUMTs) masked, as described by Caleb Lareau (https://github.com/caleblareau/mgatk/wiki/Increasing-coverage-from-10x-processing). Additional mtDNA ATAC reads from the ATAC hybridization/capture enrichment experiments were added to the ATACseq fastqs prior to running Cell Ranger ARC
A combined ATAC peaks .bed file was generated with MACS2 (v2.2.9.1) using the individual replicate Cell Ranger ATAC fragment files
Basic QC of RNAseq & ATACseq Cell Ranger outputs was performed in Seurat (v5.1.0), removing cells with < 1,000 or > 60,000 transcript counts, < 1,000 or > 10,000 detected genes, > 10% mitochondrial RNA content, > 30% ribosomal RNA content, < 1,000 or > 150,000 ATAC fragments, < 500 or > 55,000 ATAC accessible regions, > 2 nucleosome signal or < 1 transcription start site enrichment
Following basic QC filtering, RNAseq data was normalised using SCTransform and integrated using the canonical correlation analysis (CCA) method in Seurat. ATAC data was integrated using the reciprocal LSI (RLSI) method in Seurat
mtDNA variants and sequencing depth were analysed with the mgatk software package (v0.7.0, Lareau et al, 2020, https://doi.org/10.1038/s41587-020-0645-6) using the atac_possorted_bam.bam output from Cell Ranger ARC. Following mgatk analysis, per-cell per-base mtDNA sequence data was imported into Seurat and used to calculate variant heteroplasmy burden in each cell. Overall heteroplasmy burdens are reported in the integrated metadata file
gRNA transript reads were identified by aligning GEX fastq files to a custom reference genome containing the guide sequences flanked upstream & downstream by 85bp of the surrounding CROP-RFP plasmid backbone sequence with BWA (v0.7.17), the corresponding cell barcodes of aligned reads were then used to assign each cell with a unique gRNA. Cells with multiple guide alignments were assigned as 'multiple_guides', cells with no guide detected were termed 'unknown'. Guide assignments are reported in the integrated metadata file
Assembly: GRCm38 (mm10)
Supplementary files format and content: Cell Ranger output files RNAseq: Replicate_X_RNAseq_barcodes.tsv, Replicate_X_RNAseq_features.tsv.gz, Replicate_X_RNAseq_matrix.mtx.gz
Supplementary files format and content: Cell Ranger output files ATACseq: Replicate_X_ATACseq_fragments.tsv.gz, Replicate_X_ATACseq_fragments.tsv.gz.tbi, Replicate_X_ATACseq_peaks.bed
Supplementary files format and content: Combined ATAC peaks file generated from Cell Ranger outputs with MACS2: Combined_ATACseq_peaks.bed
Supplementary files format and content: Combined Raw RNAseq counts matrix following intial Seurat QC: Unintegrated_rna_raw_counts.tsv.gz
Supplementary files format and content: Integrated SCT log-normalized RNAseq counts matrix: Integrated_sct_log_counts.tsv.gz
Supplementary files format and content: Integrated normalized ATACseq feature counts matrix: Integrated_ATACseq_normalized_feature_counts.tsv.gz
Supplementary files format and content: Combined mgatk mtdna base call counts: Combined_mgatk_counts.tsv.gz
Supplementary files format and content: Cell-level metadata for integrated QC filtered data: Integrated_metadata.tsv

molecule: polyA RNA

source_name: Mouse Embryonic Fibroblast

growth_protocol: MEFs were cultured in standard high glucose DMEM supplemented with 10% FBS & 50ug/ml uridine

extract_protocol:
CROP-RFP-positive cells were flow sorted, fixed in 0.1% formaldehyde for 5 minutes, permeabilized in 0.1% NP-40 for 5 minutes and resuspended in 10X Genomics Diluted Nuclei Buffer at 3x10e6 cells per ml. 5ul (15,000 cells) of fixed/permeabilized cells was input to the 10X library preparation step.
GEX & ATAC libraries were generated on the 10X Chromium Controller using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit according to the manufacturer's instructions
gRNA enrichment was performed on the GEX cDNA library using the TAPseq protocol (Schraivogel et al, 2020, https://doi.org/10.1038/s41592-020-0837-5)
mtDNA enrichment was performed on the ATAC library by hybridization enrichment with a bespoke panel of mtDNA probes (IDT) using the IDT xGen Hybridization and Wash Kit according to manufacturer's instructions

treatment_protocol: Transduction with CROP-RFP CRISPR library 10 days prior to extraction.

value: Mouse Embryonic Fibroblast

value: m.5024C>T Cas9-Blast

value: CROPseq CRISPR library


title: Cavia porcellus cochlear, with cisplatin treatment, rep1

city: Shanghai

first: Ziwen

last: Gao

address: Fenyang Road

department: ENT Institute and Department of Otorhinolaryngology

institute: Eye & ENT Hospital, Fudan University

description:
Library name: Sample5
Column name in RNAseq_raw data.txt: Treatment1-1

data_processing:
Raw sequencing reads in FASTQ format were processed using Cutadapt (v1.9.1) 1o remove technicalsequences and low-quality bases.
Clean reads were aligned to the reference genome (Species_name, assembly version) using HISAT2(v2.2.1), a splice-aware aligner. The reference genome and annotation files were obtainedfrom ENSEMBL, NCBI or other databases.
Genc-level counts were quanilicd using HTSeq (v0.6.1).
Assembly: mm20
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Cavia porcellus

source_name: cochlear

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1ug of total RNA was used for the construction of sequencing libraries
For mRNA enrichmcnt, poly(A) mRNA isolation was performed using Oligo(dT) beads. Alternatively, when the sample quality or experimental design necessitated, ribosomal RNA was depleted using rRNA removal methods to enrich for coding and non-polyadenylated transcripts. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA synthcsis was carricd out using reverse transcriptase, followed by second-strand cDNA synthesis. For strand-specific library construction, during the second-strand synthesis the standard dTTP was replaced with dUTP; subsequent treatment with USER enzymc selectively degrades the second strand prior to PCR amplification, thereby preserving strand information. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tail in a single reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers, and thc PCR products werc validated. Finally, libraries with different indexes were multiplexed and loaded on an Illumina HiSeg/ Illumina Novaseq/ MG12000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to the manufacturer's instructions.

value: cochlear


title: Cavia porcellus cochlear, without treatment, rep4

description:
Library name: Sample4
Column name in RNAseq_raw data.txt: Control-4


title: Thymus epithelial cells, NOD.AireR249C/R249C, 4 to 8 weeks, biol rep 2

description:
Library name: R249C/R249C 2
8_S22_L001

value: A


title: Cavia porcellus cochlear, with cisplatin treatment, rep2

description:
Library name: Sample6
Column name in RNAseq_raw data.txt: Treatment1-2


title: Thymus epithelial cells, NOD.AireWT/R249C, 4 to 8 weeks, biol rep 3

description:
Library name: WT/R249C 3
6_S20_L001


title: Thymus epithelial cells, NOD.AireWT/R249C, 4 to 8 weeks, biol rep 2

description:
Library name: WT/R249C 2
5_S19_L001


title: TAPseq, MEF cells, gRNA enrichment from GEX, biol rep 1

description:
Library name: MitoPerturbSeq_Replicate_1_gRNA_TAPseq
GEX (3' mRNA) library enriched for gRNA sequences: Read 1 file contains cell barcode & UMI, Read 2 file contains transcript
MitoPerturbSeq_Integrated_metadata.tsv


title: Ryu_13_AGTCAA_L001_R1_001.fastq.gz

city: La Jolla

first: Aishwarya

last: Sundaresan

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institue

description:
Library name: Sample 13
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_13_AGTCAA_L001_R1_001

data_processing:
Adapter trimming was performed using   Cutadapt v5.1 (Python 3.12.10) executed within the Galaxy platform.
Reads were trimmed using Cutadapt v5.1 to remove the Illumina TruSeq Small RNA 3′ adapter sequence (TGGAATTCTCGGGTGCCAAGG). Trimming was performed allowing a maximum error rate of 0.12 and a minimum overlap of 3 nucleotides, irrespective of the adapter position within the read. Low-quality bases were removed using a Phred quality cutoff of 15, and reads containing ambiguous nucleotides (N) were trimmed. Only reads with a minimum length of 15 nucleotides after trimming were retained for downstream analysis.
Trimmed reads were mapped and quantified using MINTmap v1.0 (a dedicated tool for tRNA-derived fragment profiling.) in default mode. Mapping was performed against the human genome using a curated tRNA reference set derived from gtRNAdb release v1.0 and including both nuclear- and mitochondrial-encoded tRNAs, as implemented by default in MINTmap.
Low-abundance features were filtered prior to differential expression analysis using the Thresholdseq R package (v1.1). Differential expression analysis was performed using DESeq2 (R package v1.42.1) applying an experimental design to compare osteoarthritic (OA) and non-osteoarthritic (NORM) cartilage samples
An annotation metadata file was generated to integrate DESeq2 output with additional information on tRNA-derived fragments, including tRF sequence, structural category, and parental tRNA origin. Annotation was derived from MINTmap results and cross-referenced with MINTbase 2.0.
Assembly: gtRNAdb release v1.0
Supplementary files format and content: Cartilage_tRF_OA vs Norm_raw counts.csv File which includes raw counts for all samples
Supplementary files format and content: Cartilage_tRF_OA vs Norm_DESeq2 normalized counts.csv File which includes size factors-adjusted DEseq2 Normalized counts for all samples
Supplementary files format and content: Cartilage_tRF_annotation_MINTmap_MINTbase OA vs Norm.csv Annotation file linking MINTmap license plate identifiers to tRNA-derived fragment sequences, structural categories, parental tRNA origin, and corresponding MINTbase 2.0 unique identifiers.

organism: Homo sapiens

source_name: Cartilage

growth_protocol: Normal human knee cartilage tissues were procured by tissue banks (approved by Scripps Institutional Review Board) from seven donors without history of joint disease or trauma and processed within 24-48 h post mortem. Full thickness cartilage was harvested for RNA isolation from identical locations on the weightbearing regions on medial and lateral femoral condyles. OA-affected cartilage was harvested from the tissue removed during knee replacement surgery from six donors. Cartilage specimens were stored at −20°C in Allprotect Tissue Reagent (Qiagen) immediately after collection.

extract_protocol:
150 mg of frozen cartilage tissue were pulverised using a 6770 Freezer/Mill Cryogenic Grinder (SPEX SamplePrep), homogenised in QIAzol Lysis Reagent (Qiagen) and purified using the miRNeasy Mini Kit (Qiagen)
Small RNA libraries were generated from total RNA using the TruSeq Small RNA Library Preparation Kit (Illumina). Adapters corresponding to the TruSeq index set BC1–BC13 were used to uniquely label each donor sample (OA and normal)

value: Cartilage

value: wild type

value: healthy Control


title: daf2_PD_2

description:
Library name: Sample 5
daf2_PD_2

value: Whole animal

value: Post-dauer

value: 192 hrs

value: Trizol


title: Cavia porcellus cochlear, without treatment, rep2

description:
Library name: Sample2
Column name in RNAseq_raw data.txt: Control-2


title: Ryu_11_GGCTAC_L001_R1_001.fastq.gz

description:
Library name: Sample 11
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_11_GGCTAC_L001_R1_001

value: Osteoarthritic patient


title: daf2_Dauer_2

description:
Library name: Sample 2
daf2_Dauer_2

value: Dauer

value: 96 hrs


title: Ryu_12_CTTGTA_L001_R1_001.fastq.gz

description:
Library name: Sample 12
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_12_CTTGTA_L001_R1_001


title: Thymus epithelial cells, NOD.AireR249C/R249C, 4 to 8 weeks, biol rep 1

description:
Library name: R249C/R249C 1
7_S21_L001

value: Thymus

value: Thymus epithelium


title: Cavia porcellus cochlear, without treatment, rep3

description:
Library name: Sample3
Column name in RNAseq_raw data.txt: Control-3


title: aak_Dauer_1

description:
Library name: Sample 7
aak_Dauer_1

value: daf-2; aak(0)


title: Cavia porcellus cochlear, without treatment, rep1

description:
Library name: Sample1
Column name in RNAseq_raw data.txt: Control-1


title: Cavia porcellus cochlear, with cisplatin treatment, rep3

description:
Library name: Sample7
Column name in RNAseq_raw data.txt: Treatment1-3


title: daf2_Dauer_1

description:
Library name: Sample 1
daf2_Dauer_1


title: Thymus epithelial cells, NOD.AireWT/R249C, 4 to 8 weeks, biol rep 1

description:
Library name: WT/R249C 1
4_S18_L001


title: Ryu_10_TAGCTT_L001_R1_001.fastq.gz

description:
Library name: Sample 10
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_10_TAGCTT_L001_R1_001


title: Thymus epithelial cells, NOD.AireR249C/R249C, 4 to 8 weeks, biol rep 3

description:
Library name: R249C/R249C 3
9_S23_L001


title: Thymus epithelial cells, NOD.AireWT/WT, 4 to 8 weeks, biol rep 1

description:
Library name: WT/WT 3
3_S17_L001

value: WT/WT


title: Bone marrow, aged mouse, replicate 5

first: Ming

last: Cai

address: Yanchang road

institute: Shanghai Tenth People’s Hospital

description:
Library name: WAB5
Aged mouse, 20 months old, biological replicate 5.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
TPM were calculated using protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: The Excel (.xls) files contain TPM values for each Sample …

source_name: bone marrow

extract_protocol:
Total RNA was isolated from mechanically homogenized trabecular bone tissue using TRIzol reagent, in accordance with the manufacturer‘s instructions.
Indexed libraries were prepared and clustered using a cBot cluster generation system with the HiSeq PE Cluster Kit v4-cBot-HS (Illumina), following the manufacturer‘s instructions.

treatment_protocol: Aging

value: bone marrow

value: aged (20-month-old)


title: HighDose-3

city: Guangzhou

first: Zheng

last: Wu

state: Guangdong

address: 601 West Huangpu Road

institute: Jinan University

description: Library name: sample9

data_processing:
step2： RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/transcripts withthe parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts(（contributor：Yaowei Guo)
Assembly: mm10
Supplementary files format and content: raw counts.txt

source_name: brain ctx

extract_protocol: step1：About Bulk RNA-seq: 10 days after virus injection, ice artificial cerebrospinal fluid was reinfused and the virus-infected center was harvested for sequencing（contributor：Yaowei Guo).

treatment_protocol: Stereotaxic viral injection

value: brain ctx

value: WT


title: Ryu_9_GATCAG_L001_R1_001.fastq.gz

description:
Library name: Sample 9
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_9_GATCAG_L001_R1_001

value: Cartilage

value: wild type


title: Hybridization/capture, MEF cells, mtDNA enrichment from ATAC, biol rep 2

description:
Library name: MitoPerturbSeq_Replicate_2_ATACseq_mtDNA
ATAC library enriched for mtDNA sequences, Read 1 & Read 2 files contain ATAC sequences and cell barcode (16bp sequence embedded in sequence identifier line)
MitoPerturbSeq_Combined_mgatk_counts.tsv.gz
MitoPerturbSeq_Integrated_metadata.tsv

library_source: genomic single cell

molecule: genomic DNA

value: Mouse Embryonic Fibroblast

value: m.5024C>T Cas9-Blast

value: CROPseq CRISPR library


title: Bone marrow, aged mouse, replicate 4

description:
Library name: WAB4
Aged mouse, 20 months old, biological replicate 4.


title: HighDose-2

description: Library name: sample8


title: Ryu_8_ACTTGA_L001_R1_001.fastq.gz

description:
Library name: Sample 8
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_8_ACTTGA_L001_R1_001

value: healthy Control


title: Bone marrow, aged mouse, replicate 3

description:
Library name: WAB3
Aged mouse, 20 months old, biological replicate 3.


title: Hybridization/capture, MEF cells, mtDNA enrichment from ATAC, biol rep 1

description:
Library name: MitoPerturbSeq_Replicate_1_ATACseq_mtDNA
ATAC library enriched for mtDNA sequences, Read 1 & Read 2 files contain ATAC sequences and cell barcode (16bp sequence embedded in sequence identifier line)
MitoPerturbSeq_Combined_mgatk_counts.tsv.gz
MitoPerturbSeq_Integrated_metadata.tsv


title: Ryu_6_GCCAAT_L001_R1_001.fastq.gz

description:
Library name: Sample 6
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_6_GCCAAT_L001_R1_001


title: Bone marrow, aged mouse, replicate 2

description:
Library name: WAB2
Aged mouse, 20 months old, biological replicate 2.


title: Ryu_7_CAGATC_L001_R1_001.fastq.gz

description:
Library name: Sample 7
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_7_CAGATC_L001_R1_001

value: Osteoarthritic patient


title: Bulk RNAseq, MEF cells, Tfam gRNA, Day 6, biol rep 2

description:
Library name: Tfam_CRISPR_Replicate_2
Paired end RNAseq

data_processing:
Adapter sequences were trimmed from raw sequencing fastqs using Trimmomatic (v0.39)
Trimmed sequences were aligned to the mouse GRCm38/mm10 reference genome using RUM (v2.0.4)
Aligned Bam files were input to HTSeq-count (v2.0.3) in union mode to generate raw read counts for each sample
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited .txt files include raw read counts, one file per sample

extract_protocol:
Total RNA extracted using the Quick-RNA Microprep Kit (Zymo Research). RNA integrity was checked with High-sensitivity RNA Screen Tape and Reagents (Agilent); RINe values were > 8.5 for all samples
Sequencing libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit (NEB) according to the manufacturer's instructions

treatment_protocol: Transduction with CROP-RFP CRISPR guides 6 days prior to extraction.

value: CRISPR gRNA transduction


title: HighDose-1

description: Library name: sample7


title: Bone marrow, aged mouse, replicate 1

description:
Library name: WAB1
Aged mouse, 20 months old, biological replicate 1.


title: Bulk RNAseq, MEF cells, Tfam gRNA, Day 6, biol rep 1

description:
Library name: Tfam_CRISPR_Replicate_1
Paired end RNAseq


title: Bone marrow, young mouse, replicate 4

description:
Library name: WYB4
Young control mouse, 3 months old, biological replicate 4.

value: none (young)


title: Bulk RNAseq, MEF cells, Opa1 gRNA, Day 6, biol rep 1

description:
Library name: Opa1_CRISPR_Replicate_1
Paired end RNAseq


title: LowDose-3

description: Library name: sample6


title: LowDose-1

description: Library name: sample4


title: Ryu_5_ACAGTG_L001_R1_001.fastq.gz

description:
Library name: Sample 5
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_5_ACAGTG_L001_R1_001


title: Bulk RNAseq, MEF cells, Opa1 gRNA, Day 6, biol rep 2

description:
Library name: Opa1_CRISPR_Replicate_2
Paired end RNAseq


title: Bone marrow, young mouse, replicate 2

description:
Library name: WYB2
Young control mouse, 3 months old, biological replicate 2.


title: PBS-3

description: Library name: sample3


title: LowDose-2

description: Library name: sample5


title: Bone marrow, young mouse, replicate 3

description:
Library name: WYB3
Young control mouse, 3 months old, biological replicate 3.


title: PBS-2

description: Library name: sample2


title: Bulk RNAseq, MEF cells, Nontargeting gRNA, Day 6, biol rep 2

description:
Library name: Nontargeting_CRISPR_Replicate_2
Paired end RNAseq


title: 10 μM valinomycin and Pseudomonas syringae pv. tomato DC3000-treated Arabidopsis thaliana seedlings_3

status: Public on Jan 26 2026

city: Seoul

first: NAYEON

last: YOO

address: 145 Anam-ro, Seongbuk-gu,

country: South Korea

institute: Korea Univ.

description: Library name: VDC_rep 3

data_processing:
Library quality and size distribution were checked using a Fragment Analyzer (Agilent).
Library concentration was quantified using the Qubit dsDNA HS assay kit (Thermo).
Multiplexed libraries were pooled and converted for DNBSEQ platform using MGIEasy Circularization Kit (BGI).
Libraries were sequenced on the DNBSEQ-G400 System (BGI).
Assembly: TAIR10
Supplementary files format and content: Excel file with normalized data

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: 2-3-week-old Arabidopsis thaliana seedlings were used for the experiment.

extract_protocol:
mRNA was extracted using RNeasy Plant Mini kit (QIAGEN).
RNA-seq libraries were prepared from purified mRNA using the CORALL total RNA-seq library prep kit (Lexogen) according to the manufacturer's instructions.

treatment_protocol: Seedlings were vaccum-infiltrated with 10 μM of valinomycin and/or Pseudomonas syringae pv. tomato DC3000.

value: leaf


title: Ryu_3_TTAGGC_L001_R1_001.fastq.gz

description:
Library name: Sample 3
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_3_TTAGGC_L001_R1_001


title: Bone marrow, young mouse, replicate 1

description:
Library name: WYB1
Young control mouse, 3 months old, biological replicate 1.


title: Ryu_2_CGATGT_L001_R1_001.fastq.gz

description:
Library name: Sample 2
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_2_CGATGT_L001_R1_001


title: Ryu_4_TGACCA_L001_R1_001.fastq.gz

description:
Library name: Sample 4
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_4_TGACCA_L001_R1_001


title: Ryu_1_ATCACG_L001_R1_001.fastq.gz

description:
Library name: Sample 1
Column name in "Cartilage_tRF_OA vs Norm_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": Ryu_1_ATCACG_L001_R1_001


title: Pseudomonas syringae pv. tomato DC3000-treated Arabidopsis thaliana seedlings_3

description: Library name: DC_rep 3


title: 10 μM valinomycin and Pseudomonas syringae pv. tomato DC3000-treated Arabidopsis thaliana seedlings_1

description: Library name: VDC_rep 1


title: Pseudomonas syringae pv. tomato DC3000-treated Arabidopsis thaliana seedlings_2

description: Library name: DC_rep 2


title: Pseudomonas syringae pv. tomato DC3000-treated Arabidopsis thaliana seedlings_1

description: Library name: DC_rep 1


title: 10 μM valinomycin-treated Arabidopsis thaliana seedlings_2

description: Library name: V_rep 2


title: 10 μM valinomycin-treated Arabidopsis thaliana seedlings_1

description: Library name: V_rep 1


title: Mock-treated Arabidopsis thaliana seedlings_2

description: Library name: Mock_rep 2


title: Mock-treated Arabidopsis thaliana seedlings_1

description: Library name: Mock_rep 1


title: Pp_rep1, mRNA-seq

first: Jiachen

last: Wang

state: Shanghai

address: No. 2005, Songhu Road

department: Institute of Plant Biology

institute: Fudan University

data_processing:
Raw reads were cleaned by Cutadapt v3.5 to remove low quality bases and sequencing adapters.
Then trimmed reads were mapped to the reference genome Phypa V3 (Ensembl Plants) using HISAT2 v2.1.0.
Samtools v1.17 was used to remove the low mapping quality (MAPQ<20) reads and then featureCounts v2.0.1 was used to count the number of reads that were aligned to exons.
Assembly: Phypa V3 (Ensembl Plants)
Supplementary files format and content: Binary bw files (bigwig)
Supplementary files format and content: Tab-delimited text files including featureCounts value and TPM (Transcripts per million) for each Sample

organism: Physcomitrium patens

source_name: seedlings

growth_protocol: Physcomitrella patens were propagated on BCD or BCDAT media at 25°C  under a 16-hour light and 8-hour dark cycle.

extract_protocol:
RNA was extracted using an RNAprep pure Plant Kit (Tiangen Biotech).
The strand-specific RNA-seq libraries were constructed by following the KAPA stranded mRNA-seq Kit instructions (Illumina® Platforms, KR0960-v5.17), according to the manufacturer’s instructions.

value: seedlings

value: wild-type

value: no treatment


title: Bulk RNAseq, MEF cells, Nontargeting gRNA, Day 6, biol rep 1

description:
Library name: Nontargeting_CRISPR_Replicate_1
Paired end RNAseq


title: Mock-treated Arabidopsis thaliana seedlings_3

description: Library name: Mock_rep 3


title: Pp_Input_rep1, ChIP-seq

library_source: genomic

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using TrimGalore/Cutadapt.
Clean reads were aligned to the Arabidopsis thaliana reference genome Phypa V3 (Ensembl Plants) using Bowtie2.
Reads mapped to the chromosome genome were preserved and tools of SAMtools were used to obtain high quality alignments.
Sequencing signals were normalized by the bamCoverage tool in deepTools. To obtain the enrichment signal around the gene body, TSS and TTS, computeMatrix tool in deepTools was employed.
Assembly: Phypa V3 (Ensembl Plasnts)
Supplementary files format and content: bigwig

extract_protocol:
Seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF. Chromatin was sonicated into DNA fragments around 150~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

tag: chip antibody


title: 10 μM valinomycin-treated Arabidopsis thaliana seedlings_3

description: Library name: V_rep 3


title: PBS-1

description: Library name: sample1


title: Pp_H3K36me3_rep1, ChIP-seq


title: Pp_H3K36me2_rep2, ChIP-seq


title: Pp_H3K4me3_rep2, ChIP-seq


title: Pp_H3K36me2_rep1, ChIP-seq


title: 10 μM valinomycin and Pseudomonas syringae pv. tomato DC3000-treated Arabidopsis thaliana seedlings_2

description: Library name: VDC_rep 2


title: Pp_rep3, mRNA-seq


title: Pp_Input_rep2, ChIP-seq


title: Pp_H3K36me3_rep2, ChIP-seq


title: Pp_H3K4me1_rep1, ChIP-seq


title: Pp_H3K36me1_rep2, ChIP-seq


title: BO58 [207278070123_R02C01]

type: genomic

city: Wantirna South

first: Rust

last: Turakulov

state: Victoria

address: u23 105 Mountain Hwy

department: Bioinformatics

country: Australia

institute: AGRF

description:
207278070123_R02C01
TLL_C

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: T- lymphoblastic leukemia/lymphoma, positive for TCR gamma delta

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: Soft tissue

tag: group

value: Test set

tag: material

value: FFPE

tag: age

tag: Sex

value: M

value: NIH

tag: mcf


title: Pp_H3K4me3_rep1, ChIP-seq


title: MT1131 [206699910165_R03C01]

description:
206699910165_R03C01
JMML

source_name: JMML

value: JMML

value: Blood

value: Frozen


title: DS50 [207278070123_R03C01]

description:
207278070123_R03C01
FTHCL

source_name: Angioimmunoblastic T-cell lymphoma

value: Angioimmunoblastic T-cell lymphoma

value: Lymph node


title: Pp_rep4, mRNA-seq


title: Pp_H3K36me1_rep1, ChIP-seq


title: Pp_rep2, mRNA-seq


title: HP-AH-31 [203726680015_R01C01]

description:
203726680015_R01C01
HS

source_name: Histiocytic sarcoma

value: Histiocytic sarcoma

value: Ref set

value: F


title: Pp_H3K4me1_rep2, ChIP-seq


title: DR40 [206699910050_R07C01]

description:
206699910050_R07C01
TLL_C

source_name: T-cell lymphoblastic leukemia/ lymphoma

value: T-cell lymphoblastic leukemia/ lymphoma


title: HP-AN57 [203723050032_R01C01]

description:
203723050032_R01C01
ETCL_NONSETD2

source_name: Enteropathy-associated T-cell lymphoma

value: Enteropathy-associated T-cell lymphoma

value: Small intestine


title: HP-AN58 [203136010021_R02C01]

description:
203136010021_R02C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: Gastrointestinal


title: Pp_H3K4me2_rep2, ChIP-seq

value: seedlings

value: wild-type

value: no treatment


title: HP-AN-02 [203726680015_R06C01]

description:
203726680015_R06C01
HS

value: GIT

value: FFPE


title: HP-HS-09 [203726680015_R02C01]

description:
203726680015_R02C01
HS

source_name: Histiocytic sarcoma,P

value: Histiocytic sarcoma,P

value: neck mass

value: NIH


title: HP-AN60 [203136010019_R03C01]

description:
203136010019_R03C01
ETCL_SETD2

value: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: M


title: HP-AN59 [203136010021_R03C01]

description:
203136010021_R03C01
ETCL_SETD2


title: MT1132 [206699910165_R04C01]

description:
206699910165_R04C01
JMML

value: JMML

value: Blood

value: Frozen


title: HP-AN52 [203136010019_R01C01]

description:
203136010019_R01C01
ETCL_NONSETD2

source_name: T-cell lymphoma(EATL)

value: T-cell lymphoma(EATL)

value: Ref set


title: Pp_H3K4me2_rep1, ChIP-seq


title: HP-HS-10 [203726680050_R03C01]

description:
203726680050_R03C01
HS

value: Histiocytic sarcoma


title: MX1154 [207019360134_R08C01]

description:
207019360134_R08C01
BL_EBVP

source_name: Burkitt Lymphoma, EBV pos

value: Burkitt Lymphoma, EBV pos

value: Soft tissue

value: Test set

value: F


title: HP-HS-18 [203726680050_R02C01]

description:
203726680050_R02C01
HS

source_name: Malignant histiocytic neoplasm, consistent with histiocytic sarcoma.


title: MX1102 [207019360096_R07C01]

description:
207019360096_R07C01
MCL_SOX11P

value: Lymph node


title: HP-MR327 [206084850024_R05C01]

description:
206084850024_R05C01
FDCS

value: FFPE


title: MX1100 [207019360096_R05C01]

description:
207019360096_R05C01
MCL_SOX11P

source_name: MCL

value: MCL


title: HP-6467 [204551190108_R01C01]

description:
204551190108_R01C01
HCL

source_name: Hairy cell leukemia

value: Hairy cell leukemia

value: Peripheral blood


title: BQ35 [206530740010_R06C01]

description:
206530740010_R06C01
FL_A

source_name: Follicular lymphoma , BCL2R pos

value: Follicular lymphoma , BCL2R pos

value: NIH


title: MX1101 [207019360096_R06C01]

description:
207019360096_R06C01
MCL_SOX11P

value: M


title: HP-8588 [204551190109_R08C01]

description:
204551190109_R08C01
HCL


title: HP-B337 [204809970008_R07C01]

description:
204809970008_R07C01
CLL

source_name: Unknown

value: Unknown


title: HP-HS-22 [203726680050_R04C01]

description:
203726680050_R04C01
HS

source_name: Histiocytic sarcoma, P

value: Histiocytic sarcoma, P

value: Brain


title: MX1099 [207019360096_R04C01]

description:
207019360096_R04C01
MCL_SOX11P


title: HP-D129 [204551190108_R03C01]

description:
204551190108_R03C01
HCL

value: Ref set

value: Frozen


title: HP-MX1113 [206095950110_R06C01]

description:
206095950110_R06C01
LPL

source_name: LPL

value: LPL


title: HP-8081 [204809970008_R02C01]

description:
204809970008_R02C01
HCL

value: Blood


title: HP-MX1106 [206095950110_R05C01]

description:
206095950110_R05C01
LPL

value: Test set


title: HP-E858 [204809970041_R03C01]

description:
204809970041_R03C01
CLL


title: HP-7773 [204551190108_R04C01]

description:
204551190108_R04C01
HCL


title: HP-A652 [204551190108_R08C01]

description:
204551190108_R08C01
HCL


title: HP-D122 [204551190108_R05C01]

description:
204551190108_R05C01
HCL


title: HP-C388 [204551190108_R07C01]

description:
204551190108_R07C01
HCL


title: MX1103 [207019360096_R08C01]

description:
207019360096_R08C01
MCL_SOX11P

value: Soft tissue


title: HP-F040 [204809970041_R04C01]

description:
204809970041_R04C01
CLL

value: F


title: HP-AN-01 [206382220043_R07C01]

description:
206382220043_R07C01
FDCS

source_name: Follicular dendritic cell tumor

value: Follicular dendritic cell tumor

value: FFPE


title: HP-HS03 [205722630144_R02C01]

description:
205722630144_R02C01
HS

value: Histiocytic sarcoma,P

value: Liver


title: MX1078 [207019360143_R08C01]

description:
207019360143_R08C01
DLBCL_EN

source_name: DLBCL, ABC

value: DLBCL, ABC

value: Skin


title: HP-MX1111 [207019370135_R07C01]

description:
207019370135_R07C01
LPL

source_name: Lymphoplasmacytic lymphoma

value: Lymphoplasmacytic lymphoma

value: M

value: NIH


title: HP-MX1110 [207019370135_R06C01]

description:
207019370135_R06C01
LPL


title: HP-E226 [204809970008_R04C01]

description:
204809970008_R04C01
HCL

value: Hairy cell leukemia


title: HP-MX1104 [207019370135_R01C01]

description:
207019370135_R01C01
LPL

value: Ref set


title: HP-R464 [204809970142_R02C01]

description:
204809970142_R02C01
CLL

value: Unknown

value: Frozen


title: HP-HS20 [205722630144_R05C01]

description:
205722630144_R05C01
HS

source_name: Histiocytic sarcoma

value: Histiocytic sarcoma


title: HP-AN65 [203136010021_R04C01]

description:
203136010021_R04C01
ETCL_SETD2

value: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: colon


title: HP-MX1117 [206100370168_R02C01]

description:
206100370168_R02C01
LPL

value: Lymph node

value: Test set


title: HP-MR0252 [205848670051_R08C01]

description:
205848670051_R08C01
FDCS

source_name: Follicular Dendritic sarcoma

value: Follicular Dendritic sarcoma

value: FFPE

value: F


title: HP-MX1107 [207019370135_R03C01]

description:
207019370135_R03C01
LPL


title: MX1147 [207019360134_R01C01]

description:
207019360134_R01C01
BL_EBVN

source_name: Burkitt Lymphoma

value: Burkitt Lymphoma

value: Soft tissue


title: HP-AN66 [203136010019_R04C01]

description:
203136010019_R04C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: small intestine


title: MX1149 [207019360134_R03C01]

description:
207019360134_R03C01
HG_BCL

value: Colon

value: M


title: HP-MX1112 [207019370135_R08C01]

description:
207019370135_R08C01
LPL

value: Lymphoplasmacytic lymphoma

value: NIH


title: AX35 [206530740078_R03C01]

description:
206530740078_R03C01
FHTCL

source_name: Follicular T-cell lymphoma(AX35) NGS consistent / Follicular T-cell lymphoma

value: Ref set


title: MCL-155 [203546000084_R08C01]

description:
203546000084_R08C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: cMCL, SOX11: Positive, Pre-treatment, MCL_morphology: Conventional

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:Conventional

value: Peripheral Blood

value: Frozen


title: HP-F096 [204809970041_R05C01]

description:
204809970041_R05C01
CLL

value: Unknown


title: HP-MX684 [206535560143_R08C01]

description:
206535560143_R08C01
FDCS


title: HP-MX1105 [207019370135_R02C01]

description:
207019370135_R02C01
LPL


title: MCL-151 [203546000084_R05C01]

description:
203546000084_R05C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: cMCL, SOX11: Positive, Pre-treatment, MCL_morphology:

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:


title: HP-MX1109 [207019370135_R05C01]

description:
207019370135_R05C01
LPL

value: Test set


title: MCL-150 [203546000084_R04C01]

description:
203546000084_R04C01
MCL_SOX11P

value: MG1 :BCN


title: MCL-146 [203545190069_R08C01]

description:
203545190069_R08C01
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: nnMCL, SOX11: Negative, Pre-treatment, MCL_morphology: Small cell

value: Mantle Cell Lymphoma. MCL_WHO_subtype:nnMCL, SOX11:Negative, Pre-treatment, MCL_morphology:Small cell

value: BCN


title: MCL-149 [203546000084_R03C01]

description:
203546000084_R03C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: cMCL, SOX11: Positive, Post-treatment, MCL_morphology: Blastoid

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Post-treatment, MCL_morphology:Blastoid

value: Skin

value: F


title: MCL-148 [203546000084_R02C01]

description:
203546000084_R02C01
MCL_SOX11N_A


title: MX1153 [207019360134_R07C01]

description:
207019360134_R07C01
HG_BCL

value: Burkitt Lymphoma

value: Soft tissue

value: FFPE


title: MCL-153 [203546000084_R07C01]

description:
203546000084_R07C01
MCL_SOX11P

value: M


title: MCL-145 [203545190069_R07C01]

description:
203545190069_R07C01
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: nnMCL, SOX11: Negative, Pre-treatment, MCL_morphology:

value: Mantle Cell Lymphoma. MCL_WHO_subtype:nnMCL, SOX11:Negative, Pre-treatment, MCL_morphology:

value: Ref set


title: MCL-147 [203546000084_R01C01]

description:
203546000084_R01C01
MCL_SOX11N_A

value: Peripheral Blood


title: HP-AN69 [203136010019_R06C01]

description:
203136010019_R06C01
ETCL_SETD2

value: Monomorphic epitheliotropic intestinal T cell lymphoma (MEITL);

value: small intestine

value: NIH


title: MCL-154 [203545190089_R01C01]

description:
203545190089_R01C01
MCL_SOX11P

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:Conventional

value: Lymph node

value: Frozen


title: MX1152 [207019360134_R06C01]

description:
207019360134_R06C01
AGG_BCL


title: MCL-140 [203545190069_R02C01]

description:
203545190069_R02C01
MCL_SOX11P


title: MCL-143 [203545190069_R05C01]

description:
203545190069_R05C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: cMCL, SOX11: Positive, Pre-treatment, MCL_morphology: Small cell

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:Small cell


title: MCL-137 [203545190068_R07C01]

description:
203545190068_R07C01
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: cMCL, SOX11: , Pre-treatment, MCL_morphology: Conventional

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:, Pre-treatment, MCL_morphology:Conventional


title: MCL-141 [203545190069_R03C01]

description:
203545190069_R03C01
MCL_SOX11P


title: MCL-152 [203546000084_R06C01]

description:
203546000084_R06C01
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: nnMCL, SOX11: Negative, Pre-treatment, MCL_morphology: Conventional

value: Mantle Cell Lymphoma. MCL_WHO_subtype:nnMCL, SOX11:Negative, Pre-treatment, MCL_morphology:Conventional


title: MCL-144 [203545190069_R06C01]

description:
203545190069_R06C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: cMCL, SOX11: Positive, Pre-treatment, MCL_morphology: Blastoid

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:Blastoid


title: MCL-138 [203545190068_R08C01]

description:
203545190068_R08C01
MCL_SOX11P


title: MCL-139 [203545190069_R01C01]

description:
203545190069_R01C01
MCL_SOX11P


title: MCL-133 [203545190068_R03C01]

description:
203545190068_R03C01
MCL_SOX11P


title: MCL-142 [203545190069_R04C01]

description:
203545190069_R04C01
MCL_SOX11P

value: F


title: MCL-135 [203545190068_R05C01]

description:
203545190068_R05C01
MCL_SOX11N_A


title: MX1151 [207019360134_R05C01]

description:
207019360134_R05C01
BL_EBVP

source_name: Burkitt Lymphoma, EBV positive

value: Burkitt Lymphoma, EBV positive

value: Testis


title: MCL-136 [203545190068_R06C01]

description:
203545190068_R06C01
MCL_SOX11P

value: M


title: MCL-132 [203545190068_R02C01]

description:
203545190068_R02C01
MCL_SOX11P

value: Test set

value: BCN


title: MCL-130 [203524210064_R08C01]

description:
203524210064_R08C01
MCL_SOX11P

value: Bone marrow

value: Ref set


title: MCL-124 [203524210064_R02C01]

description:
203524210064_R02C01
MCL_SOX11N_A

value: Peripheral Blood


title: MCL-122 [203545190029_R08C01]

description:
203545190029_R08C01
MCL_SOX11P


title: MCL-119 [203545190029_R05C01]

description:
203545190029_R05C01
MCL_SOX11P


title: MCL-123 [203524210064_R01C01]

description:
203524210064_R01C01
MCL_SOX11N_A

value: Mantle Cell Lymphoma. MCL_WHO_subtype:nnMCL, SOX11:Negative, Pre-treatment, MCL_morphology:Small cell


title: MCL-125 [203524210064_R03C01]

description:
203524210064_R03C01
MCL_SOX11P

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:


title: MCL-120 [203545190029_R06C01]

description:
203545190029_R06C01
MCL_SOX11P

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:Conventional


title: MCL-129 [203524210064_R07C01]

description:
203524210064_R07C01
MCL_SOX11P

value: Frozen


title: MCL-116 [203545190029_R02C01]

description:
203545190029_R02C01
MCL_SOX11P


title: MCL-117 [203545190029_R03C01]

description:
203545190029_R03C01
MCL_SOX11P


title: MCL-128 [203524210064_R06C01]

description:
203524210064_R06C01
MCL_SOX11P


title: MCL-131 [203545190068_R01C01]

description:
203545190068_R01C01
MCL_SOX11N_A


title: MCL-115 [203545190029_R01C01]

description:
203545190029_R01C01
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: nnMCL, SOX11: Negative, Post-treatment, MCL_morphology: Small cell

value: Mantle Cell Lymphoma. MCL_WHO_subtype:nnMCL, SOX11:Negative, Post-treatment, MCL_morphology:Small cell


title: MCL-112 [203541700017_R06C01]

description:
203541700017_R06C01
MCL_SOX11N_A


title: MCL-118 [203545190029_R04C01]

description:
203545190029_R04C01
MCL_SOX11P


title: MCL-121 [203545190029_R07C01]

description:
203545190029_R07C01
MCL_SOX11P


title: MCL-105 [203541700013_R07C01]

description:
203541700013_R07C01
MCL_SOX11P


title: MCL-110 [203541700017_R04C01]

description:
203541700017_R04C01
MCL_SOX11P

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Post-treatment, MCL_morphology:Blastoid

value: Lymph node


title: MCL-114 [203541700017_R08C01]

description:
203541700017_R08C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: cMCL, SOX11: Positive, Post-treatment, MCL_morphology: Small cell

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Post-treatment, MCL_morphology:Small cell


title: MCL-134 [203545190068_R04C01]

description:
203545190068_R04C01
MCL_SOX11P

value: F


title: MCL-107 [203541700017_R01C01]

description:
203541700017_R01C01
MCL_SOX11P

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:Blastoid


title: MCL-108 [203541700017_R02C01]

description:
203541700017_R02C01
MCL_SOX11N_A

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:Small cell


title: MCL-106 [203541700013_R08C01]

description:
203541700013_R08C01
MCL_SOX11P


title: MCL-113 [203541700017_R07C01]

description:
203541700017_R07C01
MCL_SOX11N_A

value: M


title: MCL-127 [203524210064_R05C01]

description:
203524210064_R05C01
MCL_SOX11P


title: MCL-126 [203524210064_R04C01]

description:
203524210064_R04C01
MCL_SOX11N_A

value: Mantle Cell Lymphoma. MCL_WHO_subtype:nnMCL, SOX11:Negative, Pre-treatment, MCL_morphology:Conventional


title: MCL-111 [203541700017_R05C01]

description:
203541700017_R05C01
MCL_SOX11P


title: MCL-109 [203541700017_R03C01]

description:
203541700017_R03C01
MCL_SOX11N_A


title: MCL-103 [203541700013_R05C01]

description:
203541700013_R05C01
MCL_SOX11P

value: Test set

value: BCN


title: MCL-097 [203541700109_R07C01]

description:
203541700109_R07C01
MCL_SOX11N_A

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: cMCL, SOX11: Positive, Post-treatment, MCL_morphology: Conventional

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Post-treatment, MCL_morphology:Conventional


title: MCL-098 [203541700109_R08C01]

description:
203541700109_R08C01
MCL_SOX11P


title: MCL-104 [203541700013_R06C01]

description:
203541700013_R06C01
MCL_SOX11N_A

value: Peripheral Blood

value: Ref set


title: MCL-099 [203541700013_R01C01]

description:
203541700013_R01C01
MCL_SOX11P


title: MCL-100 [203541700013_R02C01]

description:
203541700013_R02C01
MCL_SOX11N_A

value: Mantle Cell Lymphoma. MCL_WHO_subtype:nnMCL, SOX11:Negative, Pre-treatment, MCL_morphology:Small cell


title: MCL-092 [203541700109_R02C01]

description:
203541700109_R02C01
MCL_SOX11P

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:Conventional


title: MCL-091 [203541700109_R01C01]

description:
203541700109_R01C01
MCL_SOX11P

value: Frozen


title: MCL-094 [203541700109_R04C01]

description:
203541700109_R04C01
MCL_SOX11P


title: MCL-090 [203541700106_R08C01]

description:
203541700106_R08C01
MCL_SOX11P


title: MCL-101 [203541700013_R03C01]

description:
203541700013_R03C01
MCL_SOX11P


title: MCL-093 [203541700109_R03C01]

description:
203541700109_R03C01
MCL_SOX11P


title: MCL-086 [203541700106_R04C01]

description:
203541700106_R04C01
MCL_SOX11N_A


title: MCL-083 [203541700106_R01C01]

description:
203541700106_R01C01
MCL_SOX11P


title: MCL-087 [203541700106_R05C01]

description:
203541700106_R05C01
MCL_SOX11P


title: MCL-089 [203541700106_R07C01]

description:
203541700106_R07C01
MCL_SOX11N_A

value: Mantle Cell Lymphoma. MCL_WHO_subtype:nnMCL, SOX11:Negative, Post-treatment, MCL_morphology:Small cell


title: MCL-084 [203541700106_R02C01]

description:
203541700106_R02C01
MCL_SOX11P

value: Tonsil


title: MCL-096 [203541700109_R06C01]

description:
203541700109_R06C01
MCL_SOX11N_B


title: CH2_H1465-19 [204958100064_R02C01]

description:
204958100064_R02C01
ALCL_A

source_name: Primary cutaneous anaplastic large cell lymphoma

value: Skin

value: FFPE


title: CH2_H2697-18 [204958100011_R07C01]

description:
204958100011_R07C01
ALCL_A

value: Primary cutaneous anaplastic large cell lymphoma

value: F


title: MCL-102 [203541700013_R04C01]

description:
203541700013_R04C01
MCL_SOX11P

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:Positive, Pre-treatment, MCL_morphology:Blastoid

value: Lymph node


title: MCL-085 [203541700106_R03C01]

description:
203541700106_R03C01
MCL_SOX11N_A

value: M


title: CH2_H10390-18 [204958100011_R08C01]

description:
204958100011_R08C01
ALCL_A


title: MCL-088 [203541700106_R06C01]

description:
203541700106_R06C01
MCL_SOX11P

source_name: Mantle Cell Lymphoma. MCL_WHO_subtype: cMCL, SOX11: PositiveMCL_morphology: Conventional

value: Mantle Cell Lymphoma. MCL_WHO_subtype:cMCL, SOX11:PositiveMCL_morphology:Conventional


title: CH2_cALCL_Wu3 [205617080163_R04C01]

description:
205617080163_R04C01
ALCL_A


title: CH2_cALCL_Wu1 [205617080163_R02C01]

description:
205617080163_R02C01
ALCL_A


title: CH2_cALCL_Wu4 [206152230116_R02C01]

description:
206152230116_R02C01
ALCL_B

value: unknown


title: CH2_H2704-20 [204958100064_R05C01]

description:
204958100064_R05C01
ALCL_B


title: CH2_cALCL_Wu5 [206152230116_R03C01]

description:
206152230116_R03C01
ALCL_A


title: CH2_cALCL_Wu6 [206152230116_R04C01]

description:
206152230116_R04C01
ALCL_A


title: MCL-095 [203541700109_R05C01]

description:
203541700109_R05C01
MCL_SOX11N_B


title: CH2_H7676-18 [204958100011_R06C01]

description:
204958100011_R06C01
FHTCL

source_name: Nodal Peripheral T-Cell Lymphoma TFH

value: Nodal Peripheral T-Cell Lymphoma TFH


title: CH2_H3081-20 [205310760157_R08C01]

description:
205310760157_R08C01
FHTCL


title: CH2_H3524-20 [205310760157_R07C01]

description:
205310760157_R07C01
FTHCL

value: Test set


title: CH2_H1134-19 [204792780094_R04C01]

description:
204792780094_R04C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T cell lymphoma


title: CH2_H9751-17 [205096370115_R08C01]

description:
205096370115_R08C01
ETCL_SETD2

value: Monomorphic epitheliotropic intestinal T cell lymphoma


title: CH2_E08-044265 [203810690111_R01C01]

description:
203810690111_R01C01
HSTCL_GD

source_name: Hepatosplenic T cell lymphoma

value: Hepatosplenic T cell lymphoma

value: Spleen

value: Ref set


title: CH2_R.2012.081964 [205624890115_R04C01]

description:
205624890115_R04C01
ETCL_SETD2

source_name: Hepatosplenic T-cell lymphoma

value: Hepatosplenic T-cell lymphoma


title: CH2_H11136-18 [204958100011_R05C01]

description:
204958100011_R05C01
FHTCL


title: CH2_H434-20 [204792780094_R05C01]

description:
204792780094_R05C01
FHTCL


title: CH2_E19-026342 [203810690111_R04C01]

description:
203810690111_R04C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T-cell lymphoma

value: Stomach


title: CH2_H9208-18_3 [204958100011_R04C01]

description:
204958100011_R04C01
FHTCL


title: CH2_H9748-17 [205096370115_R07C01]

description:
205096370115_R07C01
ETCL_SETD2


title: CH2_B18300064 [203293640003_R04C01]

description:
203293640003_R04C01
ETCL_SETD2

value: Frozen


title: CH2_E12-016572_1 [203668660049_R06C01]

description:
203668660049_R06C01
ENKTL

source_name: Extranodal NK/T-cell lymphoma, nasal type

value: Skin

value: FFPE


title: CH2_E18-050427 [203145740111_R06C01]

description:
203145740111_R06C01
ENKTL

value: Extranodal NK/T-cell lymphoma, nasal type

value: F


title: CH2_H4241-20 [204792780094_R01C01]

description:
204792780094_R01C01
ENKTL


title: CH2_H3289-20_2 [204964480104_R06C01]

description:
204964480104_R06C01
ENKTL


title: CH2_H2911-17_4 [205096370115_R06C01]

description:
205096370115_R06C01
ETCL_SETD2


title: CH2_R.2020.083830 [205854140075_R08C01]

description:
205854140075_R08C01
ENKTL

source_name: Extranodal NK/T cell lymphoma, nasal type

value: Soft tissue


title: CH2_R.2011.081316 [205624890115_R03C01]

description:
205624890115_R03C01
HSTCL_GD

value: Lymph node


title: CH2_H8381-19_1 [204964480104_R05C01]

description:
204964480104_R05C01
ENKTL


title: CH2_R.2018.082655 [205689140047_R01C01]

description:
205689140047_R01C01
ENKTL

value: Extranodal NK/T cell lymphoma, nasal type

value: M


title: CH2_H4107-20 [204964480104_R01C01]

description:
204964480104_R01C01
ETCL_SETD2


title: CH2_R.2021.080928 [205624890115_R05C01]

description:
205624890115_R05C01
HSTCL_GD


title: CH2_H4832-20 [204964480104_R04C01]

description:
204964480104_R04C01
ENKTL


title: CH2_R.2017.082647 [205689130040_R08C01]

description:
205689130040_R08C01
ENKTL


title: CH2_H4587-20_2 [204964480104_R03C01]

description:
204964480104_R03C01
ENKTL


title: CH2_R.2016.080379 [205689130040_R06C01]

description:
205689130040_R06C01
ENKTL


title: CH2_R.2015.081605 [205689130040_R05C01]

description:
205689130040_R05C01
ENKTL


title: CH2_H6659-19 [204958100011_R02C01]

description:
204958100011_R02C01
FHTCL

value: Nodal Peripheral T-Cell Lymphoma TFH


title: CH2_R.2018.082946 [206065910157_R06C01]

description:
206065910157_R06C01
ENKTL

value: Test set


title: CH2_E13-016605 [203668660049_R04C01]

description:
203668660049_R04C01
ENKTL


title: CH2_R.2019.086141 [206065910157_R04C01]

description:
206065910157_R04C01
ENKTL


title: CH2_002-006-6 [203866300080_R07C01]

description:
203866300080_R07C01
ETCL_NONSETD2

source_name: Enteropathy-associated T-cell lymphoma

value: Enteropathy-associated T-cell lymphoma


title: CH2_E19-043877_1A [203810690111_R06C01]

description:
203810690111_R06C01
ETCL_NONSETD2


title: CH2_E16-038669_2A [203175700067_R05C01]

description:
203175700067_R05C01
ETCL_NONSETD2


title: CH2_H8918-19_2 [204964480104_R08C01]

description:
204964480104_R08C01
ENKTL


title: CH2_R.2013.080981 [205689130040_R02C01]

description:
205689130040_R02C01
ENKTL


title: CH2_H6385-18_1 [205055470056_R05C01]

description:
205055470056_R05C01
ETCL_NONSETD2

value: unknown


title: CH2_H4780-20_2 [205041750163_R07C01]

description:
205041750163_R07C01
ETCL_NONSETD2


title: CH2_R.2013.085026 [205689130040_R04C01]

description:
205689130040_R04C01
ENKTL


title: CH2_B18345048 [203941510022_R05C01]

description:
203941510022_R05C01
FHTCL

source_name: Angioimmunoblastic T-cell lymphoma

value: Angioimmunoblastic T-cell lymphoma


title: CH2_R.2013.084631 [205689130040_R03C01]

description:
205689130040_R03C01
ENKTL

value: Ref set


title: CH2_B1213060 [203952880039_R06C01]

description:
203952880039_R06C01
FTHCL


title: CH2_B18325104 [203952880039_R01C01]

description:
203952880039_R01C01
FHTCL


title: CH2_B18325105 [203941510022_R02C01]

description:
203941510022_R02C01
FTHCL


title: CH2_B17352814 [203952880039_R05C01]

description:
203952880039_R05C01
FHTCL


title: CH2_B18358925 [203941510022_R06C01]

description:
203941510022_R06C01
FHTCL


title: CH2_81533-16 [203810640131_R03C01]

description:
203810640131_R03C01
FTHCL


title: CH2_R.2016.083047 [205689130040_R07C01]

description:
205689130040_R07C01
ENKTL


title: CH2_401-006-1 [203866300136_R05C01]

description:
203866300136_R05C01
FHTCL


title: CH2_301-012-3 [203866300138_R02C01]

description:
203866300138_R02C01
FHTCL


title: CH2_80004-16 [203810640131_R07C01]

description:
203810640131_R07C01
FHTCL


title: CH2_EC-TC-0007 [203808720157_R02C01]

description:
203808720157_R02C01
FTHCL


title: CH2_81274-16 [203810640131_R08C01]

description:
203810640131_R08C01
FTHCL


title: CH2_B16338146 [203941510022_R01C01]

description:
203941510022_R01C01
FHTCL


title: CH2_H1392-20 [205046550054_R07C01]

description:
205046550054_R07C01
ETCL_NONSETD2


title: CH2_701-013-2 [203810640147_R03C01]

description:
203810640147_R03C01
FHTCL


title: CH2_81937-16 [203810640131_R01C01]

description:
203810640131_R01C01
FHTCL


title: CH2_EC-TC-0006 [203808720130_R02C01]

description:
203808720130_R02C01
FHTCL


title: CH2_B16328641 [203941510022_R07C01]

description:
203941510022_R07C01
FHTCL


title: CH2_301-006-8 [203866300080_R05C01]

description:
203866300080_R05C01
FHTCL


title: CH2_419-021-3 [203927450073_R07C01]

description:
203927450073_R07C01
ETCL_NONSETD2

value: small intestine


title: CH2_EC-TC-0004 [203808720149_R01C01]

description:
203808720149_R01C01
FHTCL


title: CH2_EC-TC-0018 [203808720149_R05C01]

description:
203808720149_R05C01
FHTCL


title: CH2_EC-TC-0003 [203808720116_R02C01]

description:
203808720116_R02C01
FHTCL


title: CH2_EC-TC-0013 [203808720157_R08C01]

description:
203808720157_R08C01
FHTCL


title: CH2_EC-TC-0011 [203808720116_R04C01]

description:
203808720116_R04C01
FHTCL


title: CH2_B18344552 [203952880039_R08C01]

description:
203952880039_R08C01
FTHCL


title: CH2_EC-TC-0017 [203808720116_R08C01]

description:
203808720116_R08C01
FTHCL


title: CH2_EC-TC-0002 [203808720151_R04C01]

description:
203808720151_R04C01
FHTCL


title: CH2_EC-TC-0026 [203808720094_R08C01]

description:
203808720094_R08C01
FTHCL


title: CH2_EC-TC-0005 [203808720151_R02C01]

description:
203808720151_R02C01
FHTCL


title: CH2_EC-TC-0009 [203808720094_R01C01]

description:
203808720094_R01C01
FHTCL


title: CH2_EC-TC-0012 [203808720151_R08C01]

description:
203808720151_R08C01
FHTCL


title: CH2_EC-TC-0019 [203808720148_R05C01]

description:
203808720148_R05C01
FTHCL


title: CH2_EC-TC-0021 [203808720085_R08C01]

description:
203808720085_R08C01
FHTCL


title: CH2_EC-TC-0008 [203808720085_R04C01]

description:
203808720085_R04C01
FHTCL


title: CH2_EC-TC-0025 [203808720085_R01C01]

description:
203808720085_R01C01
FHTCL


title: CH2_EC-TC-0016 [203808720094_R05C01]

description:
203808720094_R05C01
FHTCL


title: CH2_EC-TC-0001 [203808720148_R01C01]

description:
203808720148_R01C01
FHTCL


title: CH2_R.2019.083741 [204068280104_R04C01]

description:
204068280104_R04C01
FHTCL


title: CH2_R.2019.083159 [203927450065_R01C01]

description:
203927450065_R01C01
FHTCL


title: CH2_R.2019.082130 [203927450061_R07C01]

description:
203927450061_R07C01
FHTCL


title: CH2_R.2019.084374 [204068280104_R05C01]

description:
204068280104_R05C01
FTHCL


title: CH2_R.2019.083233 [204068280104_R01C01]

description:
204068280104_R01C01
FTHCL


title: CH2_R.2019.085541 [204294120088_R02C01]

description:
204294120088_R02C01
FHTCL


title: CH2_R.2019.081843 [203927450061_R08C01]

description:
203927450061_R08C01
NMZL


title: CH2_R.2019.086100 [204339300051_R07C01]

description:
204339300051_R07C01
FHTCL


title: CH2_R.2019.083469 [204229180134_R06C01]

description:
204229180134_R06C01
FHTCL


title: CH2_R.2019.087600 [204229180134_R07C01]

description:
204229180134_R07C01
FHTCL


title: CH2_R.2019.084704 [204339300051_R08C01]

description:
204339300051_R08C01
FHTCL


title: CH2_R.2019.084527 [204229190135_R08C01]

description:
204229190135_R08C01
FHTCL


title: CH2_82500-14 [203810640128_R03C01]

description:
203810640128_R03C01
ALCL_A

source_name: Anaplastic large cell lymphoma, ALK-positive


title: CH2_N900-19 [203668660049_R05C01]

description:
203668660049_R05C01
ALCL_A

value: Anaplastic large cell lymphoma, ALK-positive

value: Brain


title: CH2_E08-039476 [204073520007_R08C01]

description:
204073520007_R08C01
ALCL_A


title: CH2_R.2019.086232 [204339300051_R06C01]

description:
204339300051_R06C01
FHTCL


title: CH2_E15-068377 [203197470019_R03C01]

description:
203197470019_R03C01
ALCL_B

source_name: Anaplastic large cell lymphoma, ALK-negative

value: soft tissue


title: CH2_303-019-6 [203866300136_R08C01]

description:
203866300136_R08C01
ALCL_B

value: FFPE


title: dkfz_hem188 [203989100139_R07C01]

description:
203989100139_R07C01
BLL_NONKMT2A

source_name: B-ALL

value: B-ALL


title: CH2_80008-12 [204294120090_R04C01]

description:
204294120090_R04C01
ALCL_A


title: CH2_R.2019.081737 [204068280047_R07C01]

description:
204068280047_R07C01
FHTCL


title: CH2_E16-055396_1A [203175700067_R04C01]

description:
203175700067_R04C01
ALCL_A

value: Anaplastic large cell lymphoma, ALK-negative


title: dkfz_hem179 [203949840120_R03C01]

description:
203949840120_R03C01
BLL_NONKMT2A


title: dkfz_hem176 [203734290022_R04C01]

description:
203734290022_R04C01
BLL_KMT2A

value: F


title: dkfz_hem177 [203734290022_R05C01]

description:
203734290022_R05C01
BLL_KMT2A


title: dkfz_hem173 [203734290002_R05C01]

description:
203734290002_R05C01
BLL_NONKMT2A


title: dkfz_hem175 [203734290002_R07C01]

description:
203734290002_R07C01
BLL_NONKMT2A


title: dkfz_hem186 [203989100054_R08C01]

description:
203989100054_R08C01
BLL_KMT2A


title: dkfz_hem167 [203717910069_R03C01]

description:
203717910069_R03C01
LPL

source_name: Lymphoplasmocytic Lymphoma

value: Lymphoplasmocytic Lymphoma


title: dkfz_hem174 [203734290002_R06C01]

description:
203734290002_R06C01
BLL_NONKMT2A


title: dkfz_hem170 [203717910104_R05C01]

description:
203717910104_R05C01
BLL_NONKMT2A


title: dkfz_hem166 [203717910069_R02C01]

description:
203717910069_R02C01
LPL


title: dkfz_hem161 [203712390048_R05C01]

description:
203712390048_R05C01
LPL


title: CH2_R.2019.083214 [204068280088_R08C01]

description:
204068280088_R08C01
FHTCL

value: Lymph node


title: CH2_R.2019.084693 [204229180134_R03C01]

description:
204229180134_R03C01
FHTCL

value: M


title: dkfz_hem164 [203712390048_R08C01]

description:
203712390048_R08C01
LPL


title: dkfz_hem144 [203259190135_R03C01]

description:
203259190135_R03C01
BLL_NONKMT2A


title: dkfz_hem165 [203717910069_R01C01]

description:
203717910069_R01C01
LPL


title: dkfz_hem148 [203533830077_R06C01]

description:
203533830077_R06C01
BLL_NONKMT2A


title: dkfz_hem147 [203533820084_R01C01]

description:
203533820084_R01C01
BLL_NONKMT2A


title: dkfz_hem146 [203511880085_R01C01]

description:
203511880085_R01C01
BLL_KMT2A


title: dkfz_hem140 [203259190057_R03C01]

description:
203259190057_R03C01
DLBCL_EN

source_name: DLBCL-Testes

value: DLBCL-Testes

value: Testes


title: dkfz_hem163 [203712390048_R07C01]

description:
203712390048_R07C01
LPL


title: dkfz_hem139 [203259190057_R02C01]

description:
203259190057_R02C01
DLBCL_EN

value: Test set


title: dkfz_hem141 [203259190057_R04C01]

description:
203259190057_R04C01
DLBCL_EN


title: dkfz_hem145 [203504430037_R08C01]

description:
203504430037_R08C01
BLL_NONKMT2A


title: dkfz_hem137 [203259190050_R08C01]

description:
203259190050_R08C01
DLBCL_EN


title: dkfz_hem138 [203259190057_R01C01]

description:
203259190057_R01C01
DLBCL_EN


title: dkfz_hem143 [203259190057_R06C01]

description:
203259190057_R06C01
DLBCL_EN


title: dkfz_hem135 [203259190050_R06C01]

description:
203259190050_R06C01
DLBCL_EN


title: dkfz_hem142 [203259190057_R05C01]

description:
203259190057_R05C01
DLBCL_EN


title: dkfz_hem131 [203259190050_R02C01]

description:
203259190050_R02C01
DLBCL_EN

source_name: DLBCL-Brain

value: DLBCL-Brain


title: dkfz_hem130 [203259190050_R01C01]

description:
203259190050_R01C01
DLBCL_EN


title: dkfz_hem134 [203259190050_R05C01]

description:
203259190050_R05C01
DLBCL_EN


title: dkfz_hem133 [203259190050_R04C01]

description:
203259190050_R04C01
DLBCL_EN


title: dkfz_hem128 [203259190042_R07C01]

description:
203259190042_R07C01
DLBCL_EN


title: dkfz_hem129 [203259190042_R08C01]

description:
203259190042_R08C01
DLBCL_EN


title: dkfz_hem092 [203175830024_R03C01]

description:
203175830024_R03C01
CLL

source_name: Chronic lymphocytic leukaemia

value: Chronic lymphocytic leukaemia


title: dkfz_hem126 [203259190042_R05C01]

description:
203259190042_R05C01
DLBCL_EN


title: dkfz_hem117 [203175830101_R02C01]

description:
203175830101_R02C01
BLL_KMT2A


title: dkfz_hem136 [203259190050_R07C01]

description:
203259190050_R07C01
DLBCL_EN


title: dkfz_hem125 [203259190042_R04C01]

description:
203259190042_R04C01
DLBCL_EN


title: dkfz_hem090 [203175830024_R01C01]

description:
203175830024_R01C01
CLL


title: dkfz_hem087 [203175830023_R06C01]

description:
203175830023_R06C01
CLL


title: dkfz_hem118 [203197470211_R01C01]

description:
203197470211_R01C01
BLL_KMT2A


title: dkfz_hem091 [203175830024_R02C01]

description:
203175830024_R02C01
CLL


title: dkfz_hem088 [203175830023_R07C01]

description:
203175830023_R07C01
CLL


title: dkfz_hem089 [203175830023_R08C01]

description:
203175830023_R08C01
CLL


title: dkfz_hem085 [203175830023_R04C01]

description:
203175830023_R04C01
CLL


title: dkfz_hem081 [203175830015_R08C01]

description:
203175830015_R08C01
CLL


title: dkfz_hem083 [203175830023_R02C01]

description:
203175830023_R02C01
CLL


title: dkfz_hem080 [203175830015_R07C01]

description:
203175830015_R07C01
CLL


title: dkfz_hem132 [203259190050_R03C01]

description:
203259190050_R03C01
DLBCL_EN


title: dkfz_hem127 [203259190042_R06C01]

description:
203259190042_R06C01
DLBCL_EN


title: dkfz_hem084 [203175830023_R03C01]

description:
203175830023_R03C01
CLL


title: dkfz_hem065 [203049640010_R01C01]

description:
203049640010_R01C01
MCL_SOX11P

source_name: Mantle cell lymphoma

value: Mantle cell lymphoma


title: dkfz_hem121 [203239580055_R03C01]

description:
203239580055_R03C01
MCL_SOX11P


title: dkfz_hem066 [203049640010_R02C01]

description:
203049640010_R02C01
MCL_SOX11P


title: dkfz_hem061 [203049640003_R04C01]

description:
203049640003_R04C01
DLBCL_EN


title: dkfz_hem082 [203175830023_R01C01]

description:
203175830023_R01C01
CLL


title: dkfz_hem057 [203049640002_R08C01]

description:
203049640002_R08C01
DLBCL_EN


title: dkfz_hem086 [203175830023_R05C01]

description:
203175830023_R05C01
CLL


title: dkfz_hem064 [203049640003_R07C01]

description:
203049640003_R07C01
DLBCL_EN


title: dkfz_hem124 [203259190042_R03C01]

description:
203259190042_R03C01
DLBCL_EN


title: dkfz_hem060 [203049640003_R03C01]

description:
203049640003_R03C01
DLBCL_EN


title: dkfz_hem049 [203049640001_R08C01]

description:
203049640001_R08C01
DLBCL_EN


title: dkfz_hem063 [203049640003_R06C01]

description:
203049640003_R06C01
DLBCL_EN


title: dkfz_hem058 [203049640003_R01C01]

description:
203049640003_R01C01
DLBCL_EN


title: dkfz_hem056 [203049640002_R07C01]

description:
203049640002_R07C01
DLBCL_EN


title: dkfz_hem045 [203049640001_R04C01]

description:
203049640001_R04C01
DLBCL_EN


title: dkfz_hem059 [203049640003_R02C01]

description:
203049640003_R02C01
DLBCL_EN


title: dkfz_hem053 [203049640002_R04C01]

description:
203049640002_R04C01
DLBCL_EN


title: dkfz_hem042 [203045470176_R06C01]

description:
203045470176_R06C01
MCL_SOX11P


title: dkfz_hem055 [203049640002_R06C01]

description:
203049640002_R06C01
DLBCL_EN


title: dkfz_hem051 [203049640002_R02C01]

description:
203049640002_R02C01
DLBCL_EN


title: dkfz_hem052 [203049640002_R03C01]

description:
203049640002_R03C01
DLBCL_EN


title: dkfz_hem078 [203049640048_R05C01]

description:
203049640048_R05C01
BLL_NONKMT2A


title: Heart, SIC+AAVGata4, rep3

city: Xi’an

first: He

last: Sun

state: Shaanxi

address: Changle West Road

institute: Air Force Medical University

description: Library name: Sample 9

data_processing:
In this study, raw reads were filtered using Cutadapt software (v1.9) with the following criteria: removing reads containing adapters, polyA/polyG sequences, over 5% unknown nucleotides (N), or over 20% low-quality bases (Q ≤ 20). Subsequently, sequencing quality was validated via FastQC software (v0.11.9), with Q20, Q30 and GC content as the evaluation metrics.
Assembly: GRCm38
Supplementary files format and content: csv files include Count values for each Sample

source_name: Heart

extract_protocol:
Total RNA from the samples was isolated and purified using TRIzol (Thermo Fisher, Cat. No. 15596018) following the manufacturer’s protocol. Subsequently, the quantity and purity of the total RNA were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA), and RNA integrity was examined with a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Only RNA samples meeting the following criteria were used for downstream experiments: concentration > 50 ng/μL, RNA Integrity Number (RIN) > 7.0, and total RNA yield > 1 μg.
PolyA-tailed mRNA was captured via two-round purification using oligo(dT) magnetic beads. The captured mRNA was fragmented by magnesium ion fragmentation kit at 94℃ for 5–7 minutes, followed by cDNA synthesis with reverse transcriptase. Double-stranded DNA was synthesized using E. coli DNA polymerase I and RNase H with dUTP incorporation, and then subjected to end-repair, dA-tailing, adapter ligation and magnetic bead-based purification. After double-stranded DNA digestion with UDG enzyme, the product was amplified by PCR for 8 cycles, generating a strand-specific library with an insert size of 300 bp ± 50 bp.

value: Heart


title: Whole skeletal muscle sample of a mouse-APM chimera in the Pax7Cre/ERT2; Rosa26lsl-DTA host

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description:
Library name: C1_018
10x Genomics

data_processing:
CellRanger used for custom reference genome building + read mapping + barcode assignment + UMI counting
R package Seurat used for quality control + normalization + dimensionality reduction + clustering + visualization
Assembly: GRCm39 + SA-H2B-mCherry-bGHpolyA
Supplementary files format and content: Filtered count matrices from CellRanger

source_name: Skeletal muscle

growth_protocol: All animals were housed in Allentown cages, at room temperature (RT), at relative humidity of 50-60%, with ad libitum available food and water in a 12h light-dark cycle. Furthermore, the following mouse strains were purchased from the Jackson Laboratory and were mated in our animal facility to produce blastocysts: B6.129P2-Gt(ROSA)26Sortm1(DTA)Lky/J (Stock No 009669, here referred to as Rosa26lsl-DTA) and B6.Cg-Pax7tm1(cre/ERT2)Gaka/J (Stock No: 017763 here referred to as Pax7Cre/ERT2).

extract_protocol:
Single cell RNA sequencing (scRNA-Seq) was performed as previously described (Lenardic et al., 2024). Skeletal muscles were isolated, and 1g of muscle was homogenized, resuspended and digested in HBSS (Thermo Fisher Scientific, 14025050), containing 1.5% bovine serum albumin (BSA; AppliChem, A1391) and 0.2% Collagenase II (Thermo Fisher Scientific, 17101015) for 60-90min at 37°C in a shaking water bath. After digestion, medium consisting of low glucose DMEM (Thermo Fisher Scientific, 31885049) supplemented with 10% FBS was added to the sample. The sample was vortexed and filtered through a 100μm cell strainer. After straining, the sample was centrifuged at 350g for 5min and subsequently resuspended in 2ml ACK lysis buffer (Thermo Fisher Scientific, A1049201) and incubated on ice for 1min. After incubation, cold PBS was added to a final volume of 25ml, after the sample was strained through a 40μm cell strainer and centrifuged for 8min at 650 x g. The pellet was resuspended in FACS buffer containing 0.5% BSA and placed on ice until a live staining was performed with eBioscience™ Calcein Violet 450 AM Viability Dye (1:10000, Thermo Fisher Scientific, 65-0854-39). Live cells were sorted, and 20K cells were used for the library preparation according to the manufacturer’s instruction of the Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index, 10X Genomics platform). Single cell sequencing of the libraries was performed by Novogene GmbH (Germany).
According to the manufacture's protocol of the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index, 10X Genomics platform, PN-1000268)

treatment_protocol: The mouse-APM chimera was postnatally injected with Tamoxifen from day 3 to 5, and then once per week for a total duration of 10 weeks. At this time point, the chimeras were sacrificed and the tissue isolated.

value: Skeletal muscle


title: dkfz_hem048 [203049640001_R07C01]

description:
203049640001_R07C01
DLBCL_EN

value: Brain


title: Heart, SIC+AAVGata4, rep2

description: Library name: Sample 8


title: dkfz_hem054 [203049640002_R05C01]

description:
203049640002_R05C01
DLBCL_EN


title: Heart, SIC+AAVGata4, rep1

description: Library name: Sample 7


title: dkfz_hem047 [203049640001_R06C01]

description:
203049640001_R06C01
DLBCL_EN


title: dkfz_hem037 [203045470175_R07C01]

description:
203045470175_R07C01
MCL_SOX11P


title: dkfz_hem044 [203045470176_R08C01]

description:
203045470176_R08C01
MCL_SOX11P


title: dkfz_hem046 [203049640001_R05C01]

description:
203049640001_R05C01
DLBCL_EN


title: snATAC-seq of nuclei isolated from cropreserved endosteal cells

city: SYDNEY

first: Peter

last: Croucher

state: NSW

address: 384 VICTORIA ST, DARLINGHURST NSW 2010

institute: Garvan Institute of Medical Research

description: Library name: 9w_endosteal_cryo

data_processing:
Raw data were processed with Cell Ranger ATAC (v2.1.0) and analysed using Signac (v1.15.0) and Seurat. Low-quality nuclei were filtered. Data was normalised (TF-IDF), reduced (SVD), and clustered (SNN/UMAP). Gene activity scores were computed and integrated with scRNA-seq via CCA. Differential accessibility was assessed using logistic regression and enriched transcription factor binding motifs identified using FindMotifs.
Assembly: Mouse GRCm39
Supplementary files format and content: Filtered peak matrix file, Per-barcode fragment metrics file and Barcoded alignment fragment file generated from Cell Ranger ATAC
Supplementary files format and content: Seurat object saved as Rds format

source_name: Femora and tibiae

extract_protocol:
Endosteal cells were isolated from femora and tibiae of 9-week-old male C57BL/6J mice as described above. Single-cell suspensions were washed with PBS containing 1% BSA and pelleted (500 × g, 5 min, 4 °C). Cells were lysed in 100 µL custom lysis buffer (0.0075% digitonin, 0.05 mg/mL protease inhibitor [Millipore Sigma, 114298668001], 20 mM Tris-HCl [pH 7.4], 150 mM NaCl, 3 mM MgCl₂, 2% BSA) on ice for 1–2 min with gentle pipetting to facilitate lysis. Nuclei were washed with washing buffer (0.025 mg/mL protease inhibitor, 20 mM Tris-HCl [pH 7.4], 150 mM NaCl, 3 mM MgCl₂, 1% BSA) and pelleted (300 × g, 8 min, 4°C).
Single-nucleus ATAC-seq (snATAC-seq) was performed using the 10x Genomics Chromium Single Cell ATAC v2 platform, following the manufacturer’s protocol. Briefly, nuclei were counted using a LUNA counter and haemocytometer to assess concentration and nuclear integrity. Nuclei were diluted to the recommended loading concentration and transposed using the Tn5 transposase in the ATAC transposition mix. Following transposition, gel bead-in-emulsions (GEMs) were generated using the Chromium Controller, enabling barcoding of accessible chromatin fragments in individual nuclei. Post-GEM amplification and library construction were carried out according to the 10x Genomics protocol. Final libraries were quantified using Qubit and assessed for fragment distribution using the Agilent Bioanalyzer or Tapestation.

value: Femora and tibiae

tag: sample preparation

value: Tissue digested with collagenase A and dispase

value: male

tag: strain


title: Heart, SIC, rep1

description: Library name: Sample 4

value: SIC


title: dkfz_hem033 [202292310027_R01C01]

description:
202292310027_R01C01
BLL_NONKMT2A

value: B-ALL

value: FFPE

value: F


title: Heart, SIC, rep3

description: Library name: Sample 6


title: dkfz_hem038 [203045470175_R08C01]

description:
203045470175_R08C01
MCL_SOX11P

value: M


title: dkfz_hem034 [203034110090_R06C01]

description:
203034110090_R06C01
BLL_NONKMT2A


title: dkfz_hem035 [203045470175_R05C01]

description:
203045470175_R05C01
MCL_SOX11P


title: dkfz_hem040 [203045470176_R04C01]

description:
203045470176_R04C01
MCL_SOX11P


title: dkfz_hem039 [203045470176_R03C01]

description:
203045470176_R03C01
MCL_SOX11P


title: dkfz_hem062 [203049640003_R05C01]

description:
203049640003_R05C01
DLBCL_EN

value: DLBCL-Testes


title: Heart, Sham, rep1

description: Library name: Sample 1

value: Sham


title: dkfz_hem032 [202292310026_R06C01]

description:
202292310026_R06C01
BLL_NONKMT2A

value: Test set


title: dkfz_hem030 [202279130017_R07C01]

description:
202279130017_R07C01
BLL_NONKMT2A


title: microdisected facial tissue, E11.5, control

first: Hong

last: Li

department: Craniofacial Biology

institute: University of Colorado Denver Anschutz Medical Campus

description:
Library name: NotchGOF_Control
10XGenomics

data_processing:
Cell Ranger v4.0.0 software (10xGenomics) was using for barcode processing and gene counting.
Assembly: mouse mm10-2020-A
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: embryonic facial tissue

extract_protocol:
Following microdissection, lambdoidal junction tissues from 2 embryos were pooled together and treated with 750µl of 0.25% trypsin-EDTA at 37°C for 10 mins with gentle agitation. The reaction was stopped by adding 750µl of DMEM with 10% FBS. The mixture was then pipetted up and down 20 times with wide orifice tips to assist in cell dispersion, and the cells were collected by centrifugation at 300 g for 3 mins. Cells were washed in PBS with 0.4% BSA twice, and then filtered through Flowmi 40µM cell strainer before proceeded for single cell RNA-seq.
Libraries were prepared uing the 10xGenomics Chromium Next GEM 3′ v3.1 kit following the manufacturer’s protocol.

value: embryonic facial tissue


title: dkfz_hem036 [203045470175_R06C01]

description:
203045470175_R06C01
MCL_SOX11P


title: dkfz_hem043 [203045470176_R07C01]

description:
203045470176_R07C01
MCL_SOX11P


title: dkfz_hem023 [202176290151_R01C01]

description:
202176290151_R01C01
BLL_KMT2A


title: dkfz_hem022 [202176290120_R01C01]

description:
202176290120_R01C01
BLL_NONKMT2A


title: dkfz_hem050 [203049640002_R01C01]

description:
203049640002_R01C01
DLBCL_EN

value: DLBCL-Brain


title: dkfz_hem024 [202176290151_R02C01]

description:
202176290151_R02C01
BLL_KMT2A


title: dkfz_hem041 [203045470176_R05C01]

description:
203045470176_R05C01
MCL_SOX11P

value: Mantle cell lymphoma


title: dkfz_hem021 [202163530139_R07C01]

description:
202163530139_R07C01
BLL_NONKMT2A


title: Heart, Sham, rep3

description: Library name: Sample 3

value: Heart


title: dkfz_hem031 [202279130017_R08C01]

description:
202279130017_R08C01
BLL_NONKMT2A


title: dkfz_hem018 [202073190097_R07C01]

description:
202073190097_R07C01
BLL_KMT2A


title: dkfz_hem017 [202073190096_R08C01]

description:
202073190096_R08C01
BLL_KMT2A


title: BMDMs, Smyd5-KO, IL4 treatment, rep2

city: Xiamen

first: dang

last: buyun

state: Fujian

address: Xiang 'an District Xiang Annan Road

institute: xiamen university

description: Library name: Smyd5-IL4_rep2

data_processing:
ATAC-seq reads trimmed for adaptor sequence/low-quality using trim_galore. Discarding reads left with < 50bp
ATAC-seq reads were aligned to the mm10 genome by bowtie2  using the default settings
Coverage profiles represent Reads Per Kilobase Million (RPKM) values, calculated using deeptools2 bamCoverage
Peaks were called by MACS2
Assembly: mm10
Supplementary files format and content: bigwig

source_name: BMDMs

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin, Cells were cultured at 37°C at 5% CO2

extract_protocol:
BMDMs were spun at 500 g for 5 min and then lysed for 10 min at 4°C with pre-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630)
ATAC-seq was carried out using the TruePrep DNA Library Prep Kit V2 (Vazyme) for Illumina following manufacturer's protocols.

value: BMDMs

value: Bone marrow-derived macrophages

value: Smyd5 knockout


title: MHCII-CD86-，rep2

description: Library name: Library-2MHCII-CD86-

data_processing:
Reads trimmed for adaptor sequence/low-quality using trim_galore
Reads were aligned to the mm10 genome by BWA  using the default settings
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CRISPR Screen

extract_protocol:
MHCII+CD86+ and MHCII-CD86- BMDMs  were isolated by FACS.Meanwhile, genomic DNA was extracted.
Library construction by TruePrep DNA Library Prep Kit V2 (Vazyme) following manufacturer's protocols.

treatment_protocol: Firstly,  BMDMs were treated with or without IL-4 for 24 hours, then BMDMs were stimulated with or without LPS for another 24 hours


title: CD45-positive immune cells in B16F10 tumor tissue

description:
Library name: scRNA-seq_Control_B16F10
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
CD45-positive immune cells in B16F10 tumor were isolated by FACS.Meanwhile, 10x Genomics was performed
10x Genomics scRNA-seq library construction  was performed by AZENTA company  for Illumina sequencing

treatment_protocol: Transfer IL4-treatment BMDMs

value: Tumor

value: CD45-positve immune cells

value: WT

value: Transfer non-treatment BMDMs


title: Heart, SIC, rep2

description: Library name: Sample 5

value: SIC


title: Heart, Sham, rep2

description: Library name: Sample 2


title: dkfz_hem013 [201876940215_R08C01]

description:
201876940215_R08C01
BLL_KMT2A

value: B-ALL

value: FFPE

value: F


title: MHCII+CD86+，rep2

description: Library name: Library-2MHCII+CD86+


title: BMDMs, Smyd5-KO, rep1

description: Library name: Smyd5_rep1

value: non-treatment


title: BMDMs, Smyd5-KO, rep2

description: Library name: Smyd5_rep2


title: dkfz_hem004 [200790260041_R02C01]

description:
200790260041_R02C01
BLL_NONKMT2A

value: Test set

value: M


title: dkfz_hem006 [201465960038_R02C01]

description:
201465960038_R02C01
BLL_KMT2A


title: MHCII+CD86+，rep1

description: Library name: Library-1MHCII+CD86+


title: CD45-positive immune cells in B16F10 tumor tissue, IL4 treatment

description:
Library name: scRNA-seq_IL-4_B16F10
10x Genomics

value: Transfer IL4-treatment BMDMs


title: microdisected facial tissue, E11.5, mutant

description:
Library name: NotchGOF_mutant
10XGenomics

value: embryonic facial tissue

value: Crect+/-; RosaN1-IC+/-


title: ISS-46 [206359150189_R04C01]

description:
206359150189_R04C01
MDS_HR

source_name: subdural tumor growth pattern  suggests a hematological tumor but all makers are negative

value: Brain


title: HP-MR320 [206084850030_R04C01]

description:
206084850030_R04C01
FDCS

source_name: Castleman's disease, hyaline vascular variant, with overgrowth of a dysplastic follicular dendritic cell component, consistent with progression to follicular dendritic cell tumor

value: Soft tissue

value: Ref set

value: NIH


title: MHCII-CD86-，rep1

description: Library name: Library-1MHCII-CD86-

value: BMDMs

value: Bone marrow-derived macrophages


title: dkfz_hem007 [201465960038_R07C01]

description:
201465960038_R07C01
BLL_NONKMT2A


title: dkfz_hem003 [200784530009_R08C01]

description:
200784530009_R08C01
BLL_NONKMT2A


title: BMDMs, IL4 treatment, rep2

description: Library name: NTC-IL4_rep2

value: WT


title: CY10 [206699910067_R06C01]

description:
206699910067_R06C01
FTHCL

source_name: Follicular helper T-cell lymphoma, angioimmunoblastic type

value: Lymph node


title: dkfz_hem019 [202093110007_R08C01]

description:
202093110007_R08C01
BLL_NONKMT2A

value: B-ALL


title: BMDMs, non-treatment and IL4-treatment, WT or Smyd5 KO

description: Library name: Mix pool library_RNA-seq

data_processing:
We used the iPrimer-seq protocol for sequencing, so there was only one raw data file. In the subsequent analysis process, we divided the raw data files through labels and calculate the counts of each different sample in the file respectively.
The raw data were filtered by bbduk2.sh.
Using the picard merge the forward and reverse sequence
Using the dropseq and STAR to mapping counting the gene count according to different barcode.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
BMDMs were  lysed for 1 min at 4°C with pre-cold lysis buffer (100 mM Tris-HCl, pH 7.5, 1% SDS, 500mM LiCl, 10mM EDTA, 5mM dithiothreitol). Then, total polyA RNA was extracted by oligodT-beads
Using the primer-seq protocols build the Mix RNA-seq library. Briefly, after marking each sample with a barcode, the samples are mixed to form a mix library and then sequenced simultaneously.

treatment_protocol: Firstly, WT or Smyd5 knockout BMDMs were treated with or without IL-4 for 24 hours, then BMDMs were stimulated with or without LPS for another 4 hours

value: WT and Smyd5 KO

value: non-treatment and IL4-treatment


title: dkfz_hem020 [202163110014_R02C01]

description:
202163110014_R02C01
BLL_NONKMT2A

value: FFPE


title: C57BL/6_K18-hACE2, Retina, 1

city: Wuxi

first: Xiaolu

state: China

address: 299 Qingyang Road

institute: The Affiliated Wuxi People's Hospital of Nanjing Medical University

description:
Library name: K18hACE2_Retina
10x Genomics

data_processing:
Raw FASTQ files were mapped to the Reference genome (human, mouse et al) using Cell Ranger 3.0(10x Genomics). To create Cell Ranger-compatible reference genomes, the references were rebuilt according to instructions from 10x Genomics (https://support.10xgenomics.com/single-cell-gene expression/ software/ pipelines/ latest/ advanced/references). which performs alignment, filtering, barcode counting and UMI counting. Following alignment, digital gene expression (DGE) matrices were generated for each sample and for all samples. Merged 10x Genomics DGE files were generated using the aggregation function of the Cell Ranger pipeline. All the cells in different batches were merged together normalized by equalizing the read depth among libraries. The final result was the matrix of all cells and their global gene expressions.
Assembly: Mouse mm10
Supplementary files format and content: Processed data files are provided in HDF5 (.h5) format. The H5 file contains an AnnData object storing processed single-cell RNA-seq data. The file includes a normalized gene expression matrix, cell-level metadata, gene annotations, and dimensionality reduction results used for downstream analysis. The data can be accessed using standard HDF5-compatible tools or single-cell analysis packages such as Scanpy

source_name: C57BL/6_K18-hACE2, Retina

extract_protocol:
Samples were obtained during surgery，the tissue were washed twice with 1× PBS and minced into approximately 1 mm3 fragments with sharp scissors and digested with collagenase Ⅱ (sigma V900892, 2 mg/mL) and DNase I (sigma DN25-100MG10 μg/mL) at 37℃ for 1h. Then, the single cell suspensions were collected through a 40 μm strainer (MACS® SmartStrainer 40μm, Miltenyi Biotec, Germany), and centrifuged at 500 g for 5 min, the supernatant was completely aspirated and cells were resuspended with 1ml 1 × PBS containing 0.04% weight/volume BSA. Finally, the cell number and viability were assessed by an automatic cell counter.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V2 following the manufacture’s introduction. Finally sequencing was performed on an Illumina Novaseq6000 with a sequencing depth of at least 100,000 reads per cell and pair end 150bp (PE150).

value: Retina


title: dkfz_hem016 [202073190042_R04C01]

description:
202073190042_R04C01
BLL_KMT2A

value: Test set

value: M


title: BMDMs, Smyd5-KO, IL4 treatment, rep1

description: Library name: Smyd5-IL4_rep1

value: Smyd5 knockout


title: dkfz_hem187 [203989100129_R06C01]

description:
203989100129_R06C01
BLL_NONKMT2A


title: 50_CLP+a_ACBP_24h

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

country: France

institute: Centre de Recherche des Cordeliers

description: Library name: 50

data_processing:
Fastq verification by FastQC
Fastq is align on assemble genome by HISAT2 results are write in SAM file
Count is done HTSeq-count
Assembly: mm10
Supplementary files format and content: Result  are present in a tabulate text file, with ensembl ID and gene name associate, raw count gene for each sample.

source_name: Lung

extract_protocol:
For RNA-sequencing library preparation, RNA was extracted from mouse lungs using RNA Plus Mini Kit (Qiagen) according to manufacturer’s instructions. The concentration and integrity of total RNA was analysed using electrophoretic separation on microfabricated chips in Agilent 2100 Bioanalyzer System (Agilent, CA, USA).
mRNA-sequencing library preparation (1.5 µg total RNA per sample) was carried out on NovaSeq 6000 PE150 instrument (2 x 150 bp, 40 million reads per sample).

treatment_protocol: Eight-week-old male C57Bl/6J mice were randomly assigned to treatment groups and administered either a monoclonal antibody against ACBP/DBI (α-ACBP; 4h and 1h prior to surgery) or its isotype control (IgG), administered 1h before surgery. Sepsis was induced by cecal ligation and puncture (CLP) under isoflurane anesthesia. Briefly, the cecum was exteriorized, ligated at 75% of its length using non-absorbable 4-0 silk suture, and punctured once through-and-through with a 21-gauge needle. A small amount of fecal content was gently extruded, and the cecum was returned to the abdominal cavity. Sham-operated mice underwent the same procedure, including treatment injections, but without ligation or puncture. Mice that died within the first 24h post-surgery were considered to have succumbed to perioperative complications and were excluded from further analysis. For molecular analyses, organs were collected on the day of euthanasia (6h and 24h post-CLP) and immediately snap-frozen in liquid nitrogen.

value: Lung

value: CLP+a-ACBP

tag: time point


title: C57BL/6_WT, Lung, 1

description:
Library name: C57_WT_Lung
10x Genomics

source_name: C57BL/6_WT, Lung,

tag: tissue


title: UPN2015 [202292320092_R03C01]

description:
202292320092_R03C01
JMML

source_name: Juvenile Myelomonocytic Leukemia

value: Juvenile Myelomonocytic Leukemia

value: PB


title: CW49 [206699910123_R04C01]

description:
206699910123_R04C01
BL_EBVN

source_name: High grade B-cell lymphoma consistent with Burkitt lymphoma

value: Soft tissue

value: F

value: NIH


title: BMDMs, IL4 treatment, rep1

description: Library name: NTC-IL4_rep1

value: BMDMs

value: Bone marrow-derived macrophages

value: WT


title: C57BL/6_WT, Retina, 1

description:
Library name: C57_WT_Retina
10x Genomics

source_name: C57BL/6_WT, Retina


title: BMDMs, non-treatment, rep1

description: Library name: NTC_rep1

value: non-treatment


title: UPN1199 [202292320091_R01C01]

description:
202292320091_R01C01
JMML


title: UPN1333 [202292320091_R02C01]

description:
202292320091_R02C01
JMML


title: HP-MR0235 [205848670066_R01C01]

description:
205848670066_R01C01
FDCS

source_name: Follicular Dendritic sarcoma

value: Follicular Dendritic sarcoma

value: Lymph node

value: Ref set


title: Z827 [206530740161_R06C01]

description:
206530740161_R06C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T-cell lymphoma(JAKSTAT, PPM1D, BCOR) / Monomorphic epitheliotropic intestinal T-cell lymphoma

value: Jejunum

value: Test set

value: FFPE


title: MX1155 [206699910050_R01C01]

description:
206699910050_R01C01
BL_EBVP

source_name: High-grade B-cell lymphoma consistent with Burkitt lymphoma

value: M


title: 42_CLP+a_ACBP_24h

description: Library name: 42

value: Lung

value: CLP+a-ACBP


title: C57BL/6_K18-hACE2, Lung, 1

description:
Library name: K18hACE2_Lung
10x Genomics

source_name: C57BL/6_K18-hACE2, Lung


title: BMDMs, non-treatment, rep2

description: Library name: NTC_rep2


title: CZ27 [206699910114_R01C01]

description:
206699910114_R01C01
FTHCL

source_name: Follicular helper T-cell lymphoma, NOS

value: Follicular helper T-cell lymphoma, NOS


title: UPN1383 [202292320091_R04C01]

description:
202292320091_R04C01
JMML

value: Juvenile Myelomonocytic Leukemia

value: BM

value: PB


title: 49_CLP+a_ACBP_24h

description: Library name: 49


title: 41_CLP+a_ACBP_24h

description: Library name: 41


title: HP-MR321 [206084850030_R05C01]

description:
206084850030_R05C01
FDCS

source_name: Follicular dendritic cell sarcoma arising in Castleman disease, hyaline-vascular type

value: Neck

value: NIH


title: 47_CLP+a_ACBP_24h

description: Library name: 47


title: 45_CLP+a_ACBP_24h

description: Library name: 45


title: Z850 [206530740134_R07C01]

description:
206530740134_R07C01
ETCL_SETD2

source_name: Monomorphic epitheliotropic intestinal T-cell lymphoma

value: Small bowel


title: 39_CLP+IgG_24h

description: Library name: 39

value: CLP+IgG


title: MX1156 [206699910050_R02C01]

description:
206699910050_R02C01
AGG_BCL

source_name: Burkitt lymphoma,

value: Burkitt lymphoma,


title: 48_CLP+a_ACBP_24h

description: Library name: 48


title: 38_CLP+IgG_24h

description: Library name: 38


title: 43_CLP+a_ACBP_24h

description: Library name: 43


title: HP-JS-04 [203136010021_R06C01]

description:
203136010021_R06C01
ETCL_SETD2

source_name: Intestinal Peripheral T-cell lymphoma with cytotoxic phenotype of probable gamma delta derivation,

value: small bowel


title: AY13 [206530740105_R03C01]

description:
206530740105_R03C01
DLBCL_EN

source_name: Diffuse Large B-Cell Lymphoma, CD5 positive,  Non-GCB by the Hans algorithm

value: Scrotum


title: UPN1711 [202292320092_R02C01]

description:
202292320092_R02C01
JMML


title: 37_CLP+IgG_24h

description: Library name: 37


title: dkfz_hem184 [203989100032_R03C01]

description:
203989100032_R03C01
BLL_NONKMT2A

source_name: B-ALL

value: B-ALL