title: Zebrafish brain tissue cells, sertraline exposure

city: Nanjing

first: mengyuan

last: Zhu

address: Xianlin Campus, Nanjing University, No.163 Xianlin Avenue, Qixia District, Nanjing, Jiangsu Province, China

institute: Nanjing university

description: Library name: Sample 4

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CeleScope（https://github.com/singleron-RD/CeleScope）v1.9.0.
Assembly: GRCm38/GRCh38
Supplementary files format and content: Tab separated values files and martrix files

organism: Danio rerio

source_name: Brain

extract_protocol:
Fresh tissues were placed in sCelLive™ tissue preservation solution (Singleron) on ice within 30 minutes after surgery. The specimens were washed three times with Hanks Balanced Salt Solution (HBSS), minced into small pieces, and then incubated with 3 mL of sCelLive™ tissue dissociation solution (Singleron) using the Singleron PythoN™ tissue dissociation system at 37°C for 15 minutes. The cell suspension was collected and filtered through a 40 μm sterile filter. Subsequently, GEXSCOPE® Red Blood Cell Lysis Buffer (RCLB, Singleron Matrix™) was added, and the mixture was incubated at room temperature for 5–8 minutes (following the abovementioned ratio) to remove red blood cells. Afterward, the mixture was centrifuged at 4°C and 300 × g for 5 minutes. The supernatant was discarded, and the pellet was gently resuspended in PBS. Finally, the sample was stained with trypan blue, and cell viability was assessed under a microscope.
The single-cell suspension (2×10⁵ cells/mL, diluted with HyClone PBS) was loaded onto the Singleron Matrix® single-cell processing system’s microfluidic chip. Subsequently, barcoded magnetic beads were collected from the microfluidic chip. mRNA captured by the barcoded magnetic beads was reverse-transcribed to generate cDNA, followed by PCR amplification. The amplified cDNA underwent fragmentation and was ligated to sequencing adapters. The scRNA-seq library was constructed using the GEXSCOPE® single-cell RNA library kit (Singleron) according to the manufacturer’s protocol. The libraries were diluted to 4 nM, pooled, and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

value: Brain

value: Neurons, glial cells, immune cells


title: RB_Xenograft-SJRB063842_X1-frozen

status: Public on Oct 02 2025

type: genomic

city: Memphis

first: Gang

last: Wu

address: 262 Danny Thomas Place

country: USA

institute: St Jude Children's Research Hospital

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina EPIC v1 (850K) array following Illumina standard protocol

scan_protocol: Standard Illumina protocol

data_processing:
Methylation Analysis: Raw data files generated by the iScan array scanner were read and preprocessed by using 'minfi' Bioconductor package.
processed value definition: Average beta value

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Eye

label_protocol: Standard Illumina protocol

extract_protocol: Genomics DNA was extracted from froze tumor tissues using  Qiagen kit (catalog #65904) or FFPE tumors using Promega Maxwell DNA FFPE Kit according to standard instructions recommended by the kit

tag: Sex

value: F

value: RB

tag: tissue

value: Eye

tag: treatment

value: N

tag: sample type

value: Xenograft

tag: tumor group

tag: age at collection (yr)


title: Gene expression library: Pooled tumor samples (n=6 control aCTLA-4-treated and n=6 FLT3L aCTLA-4-treated)

type: SRA

city: Perth

first: Jesse

middle: David

last: Armitage

state: WA

address: 35 Stirling Hwy, Crawley

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

description: Library name: T2-GEX

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files for TCR and GEX libraries were processed using CellRanger (Version 8.0.1, 10x Genomics) and aligned to the mm10 genome assembly. Demixing of MULTIseq FASTQ files was performed using MULTI-seq (v1.0.2). Both pipelines were run using default parameters. GEX, TCR and LMO information was combined in Seurat v5.
Barcode-level LMO count data (MULTIseq libraries) are provided in .txt format.
Assembly: mm10
Supplementary files format and content: Barcode-level count data (GEX libraries) are provided in .h5 format.
Supplementary files format and content: Barcode-level LMO count data (MULTIseq libraries) are provided in .txt format.
Supplementary files format and content: Barcode-level contig annotations (TCR libraries) are provided in .csv format

molecule: total RNA

organism: Mus musculus

source_name: Whole tumor

extract_protocol:
Mice were euthanised for tumor, dLN, BM and spleen collection. Tumors were finely sliced and enzymatically digested in DMEM containing 0.02 mg ml−1 DNase (Sigma Aldrich) and 1 mg ml−1 type IV collagenase (Sigma Aldrich). Digestion was performed in a rocking incubator at 120 r.p.m. for 30 min at 37 °C. Following digestion, cells were filtered through a 70μm filter twice and resuspended in Fc receptor block before being stained with fluorochrome-conjugated antibodies. For tumor-dLNs, samples were processed into single cells through 70-μm filter mesh in FACS buffer containing Fc receptor block.
Single cell suspensions from digested tumors and draining lymph nodes were processed with V3 chemistry using the Chromium GEM-X Gel Bead kits and Chromium GEM-X Single Cell Library Prep Kit (10X Genomics) according to manufacturers' instructions. Samples were sequenced on a NextSeq2000 (Illumina) using a P1 600 cycle flow cell (PN: 20100981) on a paired-end 300 cycle format, according to manufacturer’s protocol.

value: Whole tumor

tag: library type

value: mRNA


title: Mixed sample, replicate II, HTO, B4

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

country: Germany

institute: Leibniz Institute for Immunotherapy

description:
Sequenced on both NovaSeq and NextSeq, two libraries per biological replicate
p123_B4_library_run_1_2_matrix.mtx.gz
p123_B4_library_run_1_2_features.tsv.gz
p123_B4_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-05-04.rds
SeuratObj_clustered_2023-05-04.rds

library_source: other

data_processing:
Sequencing of libraries on NovaSeq 6000 and NextSeq 2000, producing bcl files
Demultiplexing of bcl files with Illumina Dragon bclconvert (v 3.8.4,NextSeq 2000)  and DragonServer (v 2.1 NextSeq 6000)
Mapping to mouse genome with cellranger v.7.0.0 using default parameters
Demultiplexing of treatments using HTOs with Seurat (version 4.0.5), identification of doublets via Cell Hashing and scDblFinder (version 1.8.0)
Normalization, scaling, finding variable features and PCA with Seurat, integration of batches with Harmony (version 0.1.0)
Clustering with Seurat
Annotation with SingleR (version 1.8.1)
Assembly: refdata-gex-mm10-2020-A:ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz, ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.primary_assembly.annotation.gtf.gz
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each library, mRNA and HTO combined
Supplementary files format and content: Seurat objects, raw/unfiltered and filtered/processed (dimensionality reduction, clustering, annotation…)

molecule: protein

source_name: small intestine

growth_protocol: Crypts were suspended in liquefied growth factor reduced Matrigel (Corning) (33% ENR-medium or PBS; 66% growth factor-reduced Matrigel) at 4°C, and were plated in delta-surface Nunc 24-well plates in 30 μL drops, each containing approximately 200 crypts. After the Matrigel drops polymerized, 500 µl complete crypt culture medium was added to small intestine crypt cultures. ENR-medium was prepared as follows: advanced DMEM/F12 (Life technologies), 2 mM L glutamine (Sigma), 10 mM HEPES (Life technologies), 100 U/ml penicillin, 100 μg/ml streptomycin (Life technologies), 1.25 mM N-acetyl cysteine (Sigma), 1x B27 supplement (Life technologies), 1x N2 supplement (Life technologies), 50 ng/ml mEGF (Peprotech), 100 ng/ml rec. mNoggin (Peprotech), 10% human R-spondin-1-conditioned medium of hR spondin-1 transfected HEK 293T cells. All plates were incubated at 37 °C / 5% CO2 and medium was replaced every 2-3 days. After 7 days organoids were passaged by mechanical disruption with a 5 ml syringe and a 18 G needle.

extract_protocol:
Intestinal organoids were washed with PBS, resuspended in TrypLE Express Enzyme and digested for 10 minutes at 37°C. Afterwards the reaction was stopped by adding PBS + 0,5% FBS and passed through a 100µm strainer. The single cells were stained with EpCAM-BUV395 and respective Hashing antibodies (TotalSeq B). Live/dead staining was performed with Propidiumiodid. Single cells were sorted by FACS as live/dead- EpCAM+ single cells and directly processed for scRNA-seq
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and 3’ Feature Barcode Kit (Dual Index)
Oligo-dT priming of full length poly adenylated mRNA, Capture Sequence 1 and 2 for Feature Barcoding library, followed by enzymatic fragmentation, P5,P7 i5,i7 are added via EndRepair, A-tailing and Adaptor Ligation

treatment_protocol: For coculture, allogeneic T cells were added to passaged Balb/c small intestinal organoids with murine IL-2 (30 U/ml, Peprotec) and Dynabeads murine T-activator CD3/CD28 (ThermoFisher, 2 µl per well) respectively. To prevent direct contact between organoids and T cells, plates were kept slightly tilted with the organoid drop above the T cells. T cells were added in concentrations of 100000 cells/well. Blocking antibodies (InVivoMAb anti-mouse IL-10R (CD210), InVivoMAb anti-mouse IFNγ, all Bioxcell) were added in a concentration of 10µg/ml at onset of the coculture. Recombinant IFNγ (Recombinant Murine IFN-γ, Peprotec) was added in a concentration of 0.25ng/ml and rIL-10 (recombinant murine IL-10, Peprotec) in a concentration of 10ng/ml. After 4 days, T cells were removed.

value: small intestine

tag: cell line

value: intestinal organoids

tag: cell type

value: intestinal epithelial cells

tag: genotype

value: WT

value: mixed sample (all treatments)

value: HTO


title: Zebrafish brain tissue cells, citalopram exposure

country: China

description: Library name: Sample 3


title: D70_AOM_DSS_WT_J47

city: Guangzhou

first: Jing

last: Liao

state: Guangdong

address: No.1 Xinzao Road, Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
This data processing pipeline adheres to a standard RNA sequencing analysis workflow: first, Quality Control was performed using fastqc for initial assessment, followed by read cleaning via trimmomatic to remove adapters, trim low-quality bases, and filter by minimum length. Next, the high-quality reads were Aligned to the reference genome, after index construction, using the STAR aligner. Finally, Gene Expression Quantification was completed by employing featureCounts to tally the number of reads mapped to each gene locus, generating the necessary raw count data for downstream differential expression analysis.
This data processing pipeline adheres to a standard TCR repertoire analysis workflow: first, Unique Molecular Barcodes (UMBs) were applied to correct PCR and sequencing errors and to eliminate PCR duplicates, thereby maximizing sequencing accuracy and quantification. This was followed by mapping the sequences against the IMGT® database to define V, D, J, and C segments. Next, the CDR3 regions were extracted and clonotypes were assembled, undergoing a critical quality control step that eliminated sequences with out-of-frame or stop codons. Finally, the abundance of each TRB clonotype was accurately determined by summing the number of individual clones sharing the identical CDR3 nucleotide sequence.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: The tab-delimited text file comprehensively contains all sequencing information for both the TCR alpha (α) chain and the TCR beta (β) chain of the corresponding sample. Specifically, the file details VDJC segment usage, precise CDR3 sequences, and the abundance counts for each unique clonotype after error correction and deduplication.

source_name: Colorectal tumors

growth_protocol: MC38 murine colon cancer cell line were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and 1% L-glutamine under a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from tumor tissue with TRIzol reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
Library construction began with the enrichment of mRNA using Oligo(dT) beads (by binding to the poly-A tail). The enriched mRNA was fragmented and reverse transcribed into cDNA. The resulting cDNA fragments were then processed using the NEBNext Ultra RNA Library Prep Kit for Illumina, which involved end repair, A-tailing, and ligation of Illumina sequencing adapters to finalize the cDNA library.
Library construction utilized the ImmuHub® TCR profiling system, employing a 5' RACE unbiased amplification protocol. Unique molecular barcodes (UMBs) were introduced during first-strand cDNA synthesis, along with a common adaptor and a reverse primer corresponding to the constant (C) regions of the TRB. This method facilitates the high-throughput sequencing of TRB (TCR β) sequences by using UMBs to control bottlenecks and eliminate PCR and sequencing errors.

treatment_protocol:
Six- to eight-week-old immunocompetent wild-type C57BL/6 mice received a single intraperitoneal injection of azoxymethane at 8 mg/kg on day 0. Mice were subsequently given 2.5% dextran sodium sulfate in their drinking water during weeks 1, 4, 7, and 10, with regular water provided at other times. Colorectal tumors were harvested on day 70 for RNA sequencing analysis.
Wild-type C57BL/6J mice were subcutaneously injected with 1 × 10⁶ Ctrl or Galnt7-/- MC38 cells. Tumors were harvested on day 8 for RNA sequencing analysis.
Wild-type C57BL/6J mice were subcutaneously inoculated with 2 × 10⁶ Ctrl or Galnt7-/- MC38 cells. On day 14, CD8⁺ T cells were isolated from the spleens of tumor-bearing mice using magnetic beads for RNA sequencing and T cell receptor sequencing.

value: Colorectal tumors

value: Colorectal tumor tissues from the AOM/DSS-induced tumorigenesis model at day 70


title: D70_AOM_DSS_WT_J48

description: Library name: Sample 3


title: Control_5_RNASeq

city: Okazaki

first: SHOJI

last: TATSUMOTO

address: Myodaiji

country: Japan

institute: The National Institutes of Natural Sciences NINS

description: library 5

data_processing:
The RNA-seq libraries were each sequenced (101 cycles) using the HiSeq 4000 platforms.
Raw sequence reads were aligned to the reference mouse genomes (GRCm38) by TOPHAT2.
Genome-wide expression levels were measured as a unit of FPKM (fragments per kilobase of exon model per million reads mapped) using Cufflinks and the numbers of reads were counted per gene per sample using htseq-count within HTSeq.
Differentially expressed genes (DEGs) were identified by DESeq2.
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: embryonic brain (E16.5)

extract_protocol:
Total RNA was extracted from GFP positive portions of brains of 5 control and 5 Gcm1 overexpressed mice at E16.5 using RNeasy Plus Universal Kit (Qiagen). Quality and quantity measurements of extracted RNA were performed using NanoDrop (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), respectively.
Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for directional libraries (New England BioLabs) and the KAPA HTP Library Preparation Kits (KAPA Biosystems) according to the manufacturer’s instructions. The RNA-seq libraries were each sequenced (101 cycles) using the Illumina HiSeq platforms.

value: embryonic brain (E16.5)

value: control


title: RB_Xenograft-SJRB012408_X1-frozen

source_name: Orbit

value: F

value: Orbit

value: Y


title: D70_AOM_DSS_WT_J46

description: Library name: Sample 1


title: RB_Xenograft-SJRB063841_X1-frozen

value: M

value: RB

value: Eye

value: N


title: Mixed sample, replicate II, HTO, B3

description:
Sequenced on both NovaSeq and NextSeq, two libraries per biological replicate
p123_B3_library_run_1_2_matrix.mtx.gz
p123_B3_library_run_1_2_features.tsv.gz
p123_B3_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-05-04.rds
SeuratObj_clustered_2023-05-04.rds

value: small intestine


title: Zebrafish brain tissue cells, fluoxetine exposure

description: Library name: Sample 2

value: Brain

value: Neurons, glial cells, immune cells


title: Mixed sample, replicate I, HTO, B2

description:
Sequenced on both NovaSeq and NextSeq, two libraries per biological replicate
p123_B2_library_run_1_2_matrix.mtx.gz
p123_B2_library_run_1_2_features.tsv.gz
p123_B2_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-05-04.rds
SeuratObj_clustered_2023-05-04.rds

value: intestinal organoids

value: intestinal epithelial cells

value: WT


title: Gene expression library: Pooled tumor samples (n=6 control non-treated and n=6 FLT3L non-treated)

description: Library name: T1-GEX

value: Whole tumor

value: mRNA


title: D8_Ctrl_C904

description: Library name: Sample 10

source_name: Tumor

value: Tumor

value: Tumor tissues collected on day 8 from wild-type C57BL/6J mice subcutaneously injected with MC38-Ctrl cells


title: Zebrafish brain tissue cells, control group

description: Library name: Sample 1


title: Neurog2_9SA RNA

city: Ann arbor

first: Thanh

last: Hoang

state: Michigan

address: 1000 wall street

institute: University of Michigan ann arbor

description:
Library name: Neurog2_9SA_1week_rna
Single-cell RNA-seq / GEX

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Scanpy was used to perform downstream analysis following the standard pipeline.
Multiomics is analysed by cellranger
Assembly: mm10
Supplementary files format and content: H5 files contain gene- or peak-cell count matrices for scRNA-seq and scATAC-seq.
Supplementary files format and content: TSV files include cell metadata (barcodes, clusters, conditions) and feature annotations (genes or peaks)

source_name: retina

extract_protocol: scRNA-Seq following 10x V3.1 guideline

value: retina

value: GFP+ Muller glia cells and derived neurons

value: 1 week


title: Mixed sample, replicate I, HTO, B1

description:
Sequenced on both NovaSeq and NextSeq, two libraries per biological replicate
p123_B1_library_run_1_2_matrix.mtx.gz
p123_B1_library_run_1_2_features.tsv.gz
p123_B1_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-05-04.rds
SeuratObj_clustered_2023-05-04.rds

value: mixed sample (all treatments)

value: HTO


title: RB_Xenograft-SJRB071790_X1-frozen

value: M

value: RB

value: Eye

value: Xenograft


title: RB_Xenograft-SJRB030281_X1-frozen

value: F

value: Y


title: RB_Xenograft-SJRB063839_X1-frozen

value: N


title: CRC26_T_PBMC

city: Beijing

first: Xinnan

last: Ling

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: BIOPIC

institute: Peking University

description: 10X Genomics

data_processing:
The scRNA-seq data generated were aligned and quantified against the GRCh38 human reference genome, and filtered using the Cell Ranger pipeline (version 3.1). The resulting feature-barcode matrices were used for downstream filtering and analysis. The matched TCR data based on 10x protocol was processed using Cell Ranger software (version 3.1) with the manufacturer-supplied human VDJ reference genome. Bulk RNA-seq data were filtered using Skewer (version 0.2.2). Adapter sequences and low-quality reads (＜30) from the 3’ ends were removed. The bulk RNA expression was quantified by kallisito (version 0.44)60. Gene expression were calculated by aggregating transcript expression (TPM) belonging to the same gene using tximport (version 1.22.0), and the TPM of gene were then logarithmically transformed.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colorectum

extract_protocol:
PBMCs were isolated from peripheral blood by Ficoll density gradient centrifugation. In brief, Ficoll was added into a 15ml centrifuge tube according to the amount of the whole blood, and then the whole blood was slowly added. Centrifuge the tube with acceleration speed 1, and deceleration speed 0 at 800 g for 30 min. After centrifugation, the middle white film layer was taken and washed by PBS containing 2% FBS to remove Ficoll. Red blood cells were removed by Red blood cell lysis solution (Miltenyi Biotec,130-095-929). The number of PBMCs was calculated by Countstar cell counter. Patient tumor tissues were weighed, and dissociated with Tumor Dissociation Kit, human (Miltenyi Biotec,130-095-929). In brief, tumor tissues were cut into small pieces in a C tube (Miltenyi Biotec,130-093-237) and three dissociating enzymes from the kit were added according to the tumor tissue weight. Place the C tube to the gentleMACS™ Octo Dissociator with Heaters and use 37C_h_TDK_1 program for tissue dissociation for 1 h. After dissociation, cells were filtered through a 70 μm filter membrane, and then washed with 10 ml of PBS containing 2% FBS. The suspension was centrifuged at 300g for 10 min. We next collected the cell pellet and counted using Trypan blue staining.
Cell pellets obtained from PBMC and tumor tissue were re-suspended in sorting buffer (PBS with 1% FBS), followed by staining with DAPI, anti-CD45, and anti-CD235a antibodies for FACS with a BD FACSAria™ III instrument (BD Biosciences). Live cells were identified as DAPI-negative. Subsequently, CD235a-negative and CD45-positive single cells from PBMC and CD235a-negative single cells from tumor tissue cell suspension were sorted. 10,000~20,000 cells were loaded for library construction using the 10x Chromium Single cell 5` Library (10X Genomics, PN-1000263), according to the manufacturer’s instructions. Purified libraries were attained through Library Construction Kit (10X Genomics, PN-1000190) according to the manufacturer’s instructions, and then sequenced by BGI MGISEQ-2000 sequencer. TCR sequences were amplified with the Chromium Single Cell Human TCR Amplification Kit (10X Genomics, PN-1000252). V(D)J Libraries were generated with Library Construction Kit (10X Genomics, PN-1000190), and sequenced by Illumina Novaseq6000 sequencer.

value: colorectum


title: Control_1week ATAC

description:
Library name: Control_1week_atac
Single-cell ATAC-seq (chromatin accessibility)

library_source: genomic single cell

value: control


title: RB_Xenograft-SJRB030260_X1-frozen


title: CRC15_T_PBMC

description: 10X Genomics


title: 2 months RNA

description:
Library name: Neurog2_9SA_2mo_rna
Single-cell RNA-seq / GEX

value: 2 months


title: RB_Xenograft-SJRB063838_X1-frozen


title: RB_Xenograft-SJRB063840_X1-frozen


title: Mixed sample, replicate II, GEX, B4

molecule: polyA RNA

value: small intestine

value: intestinal organoids

value: intestinal epithelial cells

value: WT

value: mRNA


title: 5 weeks RNA

description:
Library name: Neurog2_9SA_5weeks_rna
Single-cell RNA-seq / GEX

value: retina

value: GFP+ Muller glia cells and derived neurons

value: 5 weeks


title: Mixed sample, replicate II, GEX, B3

value: mixed sample (all treatments)


title: CRC26_T_tissue

description: 10X Genomics


title: RB_Xenograft-SJRB030135_X1-frozen

value: M

value: RB

value: Eye


title: Mixed sample, replicate III, GEX, B5

description:
Sequenced on both NovaSeq and NextSeq, two libraries per biological replicate
p123_B5_library_run_1_2_matrix.mtx.gz
p123_B5_library_run_1_2_features.tsv.gz
p123_B5_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-05-04.rds
SeuratObj_clustered_2023-05-04.rds


title: CRC23_tissue

description: 10X Genomics


title: CRC23_PBMC

description: 10X Genomics


title: Control_2m RNA

description:
Library name: control_2mo_rna
Single-cell RNA-seq / GEX


title: Neurog2_9SA  ATAC

description:
Library name: Neurog2_9SA_1week_atac
Single-cell ATAC-seq (chromatin accessibility)

value: 1 week


title: RB_Xenograft-SJRB030518_X1-frozen

value: Y

value: Xenograft


title: Control_1week RNA

description:
Library name: Control_1week_rna
Single-cell RNA-seq / GEX

value: control


title: Mixed sample, replicate I, GEX, B1


title: Mixed sample, replicate I, GEX, B2


title: Mixed sample, replicate III, GEX, B6

description:
Sequenced on NextSeq, two libraries per biological replicate
p123_B6_library_run_1_2_matrix.mtx.gz
p123_B6_library_run_1_2_features.tsv.gz
p123_B6_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-05-04.rds


title: CRC23_M_tissue

description: 10X Genomics

value: colorectum


title: RB_Xenograft-SJRB030403_X1-frozen

value: N


title: CRC23_M_PBMC

description: 10X Genomics


title: TCR - Lane C

city: Melbourne

first: Lachlan

last: Dryburgh

state: Victoria

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

institute: The Peter Doherty Institute for Infection and Immunity

description:
Library name: TCR-C
10x Genomics

data_processing:
Cellranger 6.1.2 multi pipline.
Features matrixes load into Seurat 4.3.0.
Filtered for cell quality, merged, harmony integration, clusterd and annotated, non-CD8 cells removed.
VDJ sequences processed with TCRdist3 and merged with seurat object.
Assembly: refdata-gex-GRCh38-2020-A
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: RDS file of seurat object for the filtered CD8+ cells.

source_name: Liver tumour and non-cancerous  tissue

extract_protocol:
Tumour and healthy liver tissues were minced and digested in RPMI 1640 with 10% FCS and 0.5 mg/ml collagenase D at 37 °C for thirty minutes, passed through 70 µm strainers, and lymphocytes were enriched using a 44%:70% isotonic Percoll gradient. PBMCs, when collected, were isolated on Ficoll Paque PLUS. Cells were cryopreserved in CryoStor CS10 (liver samples) or 10% DMSO: 90% FCS. Live, CD3+ T cells were sorted via fluorescence activated cell sorting.
Libraries were made according to the 10x Genomics protocol (Chromium Single Cell 5' v2)

value: Liver tumour and non-cancerous  tissue

value: CD3+ T cells

value: Mixed sample (multiple donors/tissues)

value: TCR


title: Testis,CKO-biol rep1

city: Luoyang

first: Yuqing

last: Jiang

state: China

address: No. 263, Kaiyuan Avenue, Luolong District

institute: The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology

description:
Library name: SAMPLE3
10x Genomics

data_processing:
Bioinformatics analysis Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software （ version5.01 ） . Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline (https://support. 10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell_xFFFE_ranger ， version 3.1.0) and scRNA-seq data were aligned to Ensembl genome GRCm38 reference genome, a total of 45,000 single cell captured from 2 WT and 2 Dhx37-/-  mice were processed using 10X Genomics Chromium Single Cell 3’Solution. The Cell Ranger output was loaded into Seurat(version 3.1.1) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data. Overall, 34,556 cells passed the quality control threshold : all genes expressed in less than three cells （default parameters：1 cell）were removed、number of genes expressed per cell > 500 as low and <5000 as high cut-off, UMI counts less than 500, the percent of mitochondrial-DNA derived gene-expression <25%. To visualize the data, we further reduced the dimensionality of all  cells using Seurat and used t-SNE to project the cells into 2D space. The steps includes:
1. Using the LogNormalize method of the "Normalization" function of the Seurat software to calculated the expression value of genes; 2. PCA (Principal component analysis) analysis was performed using the normalized expression value, Within all the PCs, the top 10 PCs were used to do clustering and t-SNE analysis； 3. To find clusters, selecting weighted Shared Nearest Neighbor (SNN) graph-based clustering method. Marker genes for each cluster were identified with the Wilcoxon rank-sum test （ default parameters is "bimod" : Likelihood-ratio test ） with default parameters via the FindAllMarkers function in Seurat. This selects markers genes which are expressed in more than 10% of the cells in a cluster and average log(Fold Change) of greater than 0.25（default parameters：0.26）.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Testis

extract_protocol:
Single-Nuclei Isolation Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor(5892791001; Roche) and RNase inhibitor(N2615; Promega and AM2696; Life Technologies). 1. Samples were cut into ~1 mm pieces and homogenized using a Dounce homogenizer (885302-0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer. 2. They were incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. 3. Grounded with a dounce(Sigma), resuspended by pipette，gentlely； 4. Incubated on ice for 6 min, then add 2 ml of ice-cold 4% BSA, resuspended by Pasteur pipette, then stop the reaction; 5. Centrifuged at 300g for 5 minutes at 4°C; 6. Add 2 ml of lysis buffer and 4% BSA, resuspended, Incubated on ice for 3 min; 7. De-fragment with Miltenyi (Debris Removal Solution); 8. The pellet was resuspended and washed with 4 ml of the buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation; 9. The pellet was resuspended in Nuclei Suspension Buffer (1x PBS,0.07% BSA, and 0.1% RNase inhibitor); 10. Filtered through a 20-mm cell strainer(43-50020-50; pluriSelect), and counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Chromium 10x Genomics library and sequencing Single-nuclei suspensions were loaded to 10x Chromium to capture 8000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) . The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou,China) at a minimum depth of 20,000 reads per cell.

value: Testis

tag: age

value: 8 weeks old

value: male


title: TCR - Lane B

description:
Library name: TCR-B
10x Genomics


title: Testis,CKO-biol rep2

description:
Library name: SAMPLE4
10x Genomics


title: RB_Xenograft-SJRB030485_X1-frozen


title: CRC15_T_tissue

description: 10X Genomics


title: Testis,WT-biol rep2

description:
Library name: SAMPLE2
10x Genomics

value: WT


title: CRC21_T_tissue

description: 10X Genomics


title: Testis,WT-biol rep1

description:
Library name: SAMPLE1
10x Genomics


title: CRC21_T_PBMC

description: 10X Genomics


title: CRC17_T_tissue

description: 10X Genomics


title: Cell surface protein - Lane C

description:
Library name: CITE-C
10x Genomics

data_processing:
Cellranger 6.1.2 multi pipline.
Features matrixes load into Seurat 4.3.0.
Filtered for cell quality, merged, harmony integration, clusterd and annotated, non-CD8 cells removed.
VDJ sequences processed with TCRdist3 and merged with seurat object.
Assembly: refdata-gex-GRCh38-2020-A
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: RDS file of seurat object for the filtered CD8+ cells.
Library strategy: CITE-seq

value: ADT


title: RB_Xenograft-SJRB063837_X1-frozen

value: M

value: RB


title: RB_Xenograft-SJRB063836_X1-frozen

value: Eye


title: Cell surface protein - Lane B

description:
Library name: CITE-B
10x Genomics


title: RB_Xenograft-SJRB030304_X1-frozen


title: Cell surface protein - Lane A

description:
Library name: CITE-A
10x Genomics


title: CRC26_tissue

description: 10X Genomics


title: CRC17_T_PBMC

description: 10X Genomics


title: RB_Xenograft-SJRB046163_X1-frozen

value: F


title: Tissue array slide 3 well D1 - CHCHD2 PM

city: San Francisco

first: Szu-Chi

state: CA

address: 1600 fourth St

department: Biochemistry and Biophysics

institute: UCSF

description:
Library name: YS-3545_06
Fresh frozen Spatial transcriptome sequencing; processed data file lists median normalized average for each tissue section (MWT946, FWT954, MPM949, FPM932) within regions of interest (SNc, VTA, TH)

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate fastq files.
Sequences were aligned to the mm10 genome to gene expression count using Space Ranger's default settings.
Gene expression level of Refseq coding genese were quantified using space ranger's default settings.
The 10X Loupe Browser software (RRID: SCR_018555) was used to identify six anatomical regions of interest: (1) SN, (2) VTA, and (3) thalamus (TH) in the midbrain, and (4) CP, (5) LSX, and (6) white matter tracts in the striatum. RNA capture areas corresponding to each anatomical region were selected for analysis based on their spatial proximity to the anatomical regions and on the expression of known genetic markers. SN and VTA genetic markers included tyrosine hydroxylase, DAT, and VMAT2; thalamus markers included Prkcd, Ptpn3, and Synpo2; CP was identified with DARPP32; the LSX was identified with PRKCD; white matter was identified with MBP. Capture areas from mice injected with virus (GqCNO, GqVeh) expressed mCherry based on histology. Capture areas that expressed high levels of astrocyte markers (Gfap, Aldh1l1) and microglia markers (Aif1, P2ry12) were excluded. SN and VTA capture areas also had to contain at least one complete DA neuron soma.
Assembly: mm10 2020 A
Supplementary files format and content: barcodes.csv: list of spatial barcodes
Supplementary files format and content: Features.csv: list of gene IDs and gene expression count data
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: scalefactors.json: scalefactors in json format
Supplementary files format and content: lowresimage.png: low-res image of tissue
Supplementary files format and content: highresimage.png: high-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Midbrain tissue

growth_protocol: 3-4mo male GqCNO and GqVeh DATCre mice were bilaterally injected with a conditional AAV-hM3Dq(Gq)-mCherry virus in the midbrain.

extract_protocol:
Fresh frozen tissues were OCT embedded, and 10µm frozen sections were cut with a cryostat. Slides were immunostained for tyrosine hydroxylase (green), mCherry (red), NeuN (magenta), and DAPI (blue).
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression v1 Slides & Reagent kit according to the manufacturer's instruction.

treatment_protocol: GqCNO and CNOAlone mice were administered CNO and 2% sucrose via their drinking water for one week. GqVeh mice were administered 2% sucrose for one week. All mice were single housed and had access to a running wheel during treatment. After treatment, brains were collected and spatial transcriptomics was performed.

value: Midbrain tissue

value: CHCHD2 T61I homozygote


title: Gene expression - Lane C

description:
Library name: GEX-C
10x Genomics

value: mRNA


title: Tissue array slide 3 well B1 - CHCHD2 PM

description:
Library name: YS-3545_04
Fresh frozen Spatial transcriptome sequencing; processed data file lists median normalized average for each tissue section (MWT964, FWT956, MPM937, FPM935) within regions of interest (SNc, VTA, TH)


title: Tissue array slide 3 well C1 - CHCHD2 PM

description:
Library name: YS-3545_05
Fresh frozen Spatial transcriptome sequencing; processed data file lists median normalized average for each tissue section (MWT968, FWT933, MPM936, FPM934) within regions of interest (SNc, VTA, TH)


title: CRC26_M_tissue

description: 10X Genomics

value: colorectum


title: RB_Xenograft-SJRB030402_X1-frozen

value: N

value: Xenograft


title: RB_Xenograft-SJRB030241_X1-frozen


title: CRC25_T_tissue

description: 10X Genomics


title: Gene expression - Lane B

description:
Library name: GEX-B
10x Genomics

value: Liver tumour and non-cancerous  tissue

value: CD3+ T cells

value: Mixed sample (multiple donors/tissues)


title: Tissue array slide 3 well A1 - CHCHD2 PM

description:
Library name: YS-3545_03
Fresh frozen Spatial transcriptome sequencing; processed data file lists median normalized average for each tissue section (FWT958, FWT959, MPM939, FPM955) within regions of interest (SNc, VTA, TH)


title: RB_Xenograft-SJRB046160_X1-frozen


title: Tissue array slide 2 well A1 - CHCHD2 KO

description:
Library name: YS-3545_02
Fresh frozen Spatial transcriptome sequencing; processed data file lists median normalized average for each tissue section (FWT894, FWT00, FKO623, FKO662) within regions of interest (SNc, VTA, TH)

value: CHCHD2 KO homozygote


title: Gene expression - Lane A

description:
Library name: GEX-A
10x Genomics


title: TCR - Lane A

description:
Library name: TCR-A
10x Genomics

value: TCR


title: RB_Xenograft-SJRB046154_X1-frozen

value: Orbit


title: CRC25_T_PBMC

description: 10X Genomics


title: Tissue array slide 1 well A1 - CHCHD2 KO

description:
Library name: YS-3545_01
Fresh frozen Spatial transcriptome sequencing; processed data file lists median normalized average for each tissue section (FWT352, FWT624, MKO625, FKO660) within regions of interest (SNc, VTA, TH)


title: PF5_C

city: Brescia

first: Paolo

last: Martini

address: viale Europa 11

department: Department of Molecular and Translational Medicine

country: Italy

institute: University of Brescia

description: Library name: PF5_C_S23

data_processing:
Transcript quantification was done using Salmon (v1.9.0) with transcripts defined in Human Ensembl v106
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file with raw counts for each Sample (gene symbol)
Supplementary files format and content: tab-delimited text file with TPM and  raw counts for each Sample (salmon format - transcripts)

source_name: hiPSCs

extract_protocol:
Total RNA extraction was performed using the ZymoResearchTM kit (Irvine, CA, USA), according to the manufacturer’s instructions.
Libraries were prepared starting from 100 ng, using the Illumina cDNA synthesis and the Illumina Stranded mRNA Prep Ligation Kit following the manufacturer's instruction

treatment_protocol: LRRK2 kinase inhibitors (MLi-2 and PF) were used at 200 nM in DMSO. Glial cells were exposed to LRRK2 inhibitors for 90 min and successively treated with Aβ fibrils or α-syn pffs at 2 µM or 1 µM, respectively for 16 hours. Inflammation was induced by exposing hiPSC-derived cholinergic neurons (CHOL) to inflamed glial medium for 3 days and hiPSC-derived dopaminergic neurons (DA) for 7 days.

value: hiPSCs

value: AB + PF


title: CRC25_tissue

description: 10X Genomics


title: RB_Xenograft-SJRB046150_X1-frozen

value: RB


title: PF4_C

description: Library name: PF4_C_S37


title: KD2

city: Honolulu

first: Xue

last: Wang

state: Hawaii

address: 701 Ilalo Street

institute: University of Hawaii Cancer Center

description:
Library name: KD2
Column name in Processed data_fpkm.txt: KD2

data_processing:
Poor quality reads were trimmed using the fastq-mcf (v1.05). Reads quality was checked using the fastqc (v0.11.7).
Gene read counts were in Ensembl Gene ID and converted to Entrez Gene ID.
Corresponding Symbol annotations and full gene names were added using the “org.Mm.eg.db” library. NA (Not Annotated), duplicate Entrez IDs and genes without symbols were removed.
After removing the duplicated genes, the fragments per kilobase of transcript per million mapped reads (FPKM) were calculated.
Assembly: GRCm38
Supplementary files format and content: The tab-delimited text file includes FPKM values for each sample

source_name: HCC3-4 liver cancer cells

growth_protocol: The mouse liver tumor cell line HCC3-4 was derived from MYC transgenic mice. HCC3-4 cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM; Biological Industries) containing 10% FBS and 1% P/S. Cells were incubated at 37°C in a humidified atmosphere with 5% CO₂. Cell viability was more than 90% according to trypan blue exclusion analysis.

extract_protocol:
Total RNA was extracted from PLKO (n=3) and KD (n=3) groups using RNAiso Plus according to the manufacturer’s protocol.
RNA-seq libraries were prepared by poly(A) capture, followed by reverse transcription into cDNA.

treatment_protocol: HCC3-4 cells were stably transfected with either shSf3b3 (KD) or negative control pLKO.1-TRC (PLKO).

value: HCC3-4 liver cancer cells

value: KD

value: total RNA


title: KD3

description:
Library name: KD3
Column name in Processed data_fpkm.txt: KD3


title: RB_Patient tumor-SJRB071796_D1-FFPE

value: M

value: Eye

value: Patient tumor


title: RB_Patient tumor-SJRB071793_D1-FFPE

value: N


title: PF3_C

description: Library name: PF3_C_S22


title: KD1

description:
Library name: KD1
Column name in Processed data_fpkm.txt: KD1


title: CRC24_T_tissue

description: 10X Genomics

value: colorectum


title: PF2_C

description: Library name: PF2_C_S36


title: PF1_C

description: Library name: PF1_C_S7


title: CRC24_tissue

description: 10X Genomics


title: RB_Patient tumor-SJRB030178_D3-FFPE

value: F


title: RB_Patient tumor-SJRB013765_D2-FFPE


title: PLKO1

description:
Library name: PLKO1
Column name in Processed data_fpkm.txt: PLKO1

value: PLKO


title: CRC24_PBMC

description: 10X Genomics


title: NT5_C

description: Library name: NT5_C_S17


title: CRC24_M_tissue

description: 10X Genomics


title: NT3_C

description: Library name: NT3_C_S4


title: NT4_C

description: Library name: NT4_C_S16


title: BAT-DHM_HFD-3

city: Tianjin

first: shuran

last: yang

address: No. 10, Poyanghu Road, West District of Tuanbo New Town, Jinghai District, Tianjin

institute: Tianjin University of Traditional Chinese Medicine

description:
Library name: Sample9
10x Chromium

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0（https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome）
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: brown adipose tissue

extract_protocol:
For single-nucleus isolation, tissues were minced into 1-mm pieces in 1 mL of pre-chilled lysate, then homogenized with an additional 2 mL of lysate using a tissue homogenizer (5 slow strokes). After incubation on ice for 5 min, 4 mL of pre-cooled 2% BSA was added to terminate the reaction. Samples were filtered through a 30-μm cell strainer, and the filtrate was centrifuged (300 ×g, 5 min, 4°C). Pellets were resuspended in 5 mL of 2% BSA and centrifuged again under the same conditions. Nuclei were resuspended in 500 μL of resuspension buffer (1× PBS, 2% BSA, 0.1% RNase inhibitor), stained with propidium iodide (PI), and sorted on a BD FACSAria II flow cytometer to exclude debris
For snRNA-seq, nuclei were loaded onto a 10x Chromium chip (10X Genomics Chromium Single-Cell 3' Kit v3) targeting 8,000 cells per sample. cDNA amplification and library preparation followed the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq 6000 (LC-Bio Technology, China) with paired-end 150-bp reads (minimum depth: 20,000 reads/cell).

treatment_protocol: The normal-diet (ND) group served as the negative control, the high-fat-diet (HFD) group as the positive control, and the HFD plus dihydromyricetin (DHM, 200 mg/kg) group as the intervention group.

value: brown adipose tissue

value: adipocytes (Ads), adipocyte progenitor cells (APCs), endothelial cells (ECs), lymphatic endothelial cells (LECs), adipose-endothelial hybrid cells (LipECs), smooth muscle cells (SMCs), pericytes (PCs), Schwann cells (SCs), macrophages (MACs), lymphocytes (LYMs), and skeletal muscle cells(SkMCs).


title: BAT-DHM_HFD-2

description:
Library name: Sample8
10x Chromium


title: CRC24_M_PBMC

description: 10X Genomics


title: CRC25_PBMC

description: 10X Genomics


title: RB_Xenograft-SJRB012408_X2-frozen

value: Y

value: Xenograft


title: BAT-DHM_HFD-1

description:
Library name: Sample7
10x Chromium


title: CRC22_T_tissue

description: 10X Genomics


title: CRC24_T_PBMC

description: 10X Genomics


title: PLKO3

description:
Library name: PLKO3
Column name in Processed data_fpkm.txt: PLKO3


title: RB_Xenograft-SJRB030240_X1-frozen


title: CRC22_T_PBMC

description: 10X Genomics


title: NT1_C

description: Library name: NT1_C_S30

value: hiPSCs


title: RB_Xenograft-SJRB049187_X1-frozen_rep3


title: RB_Patient tumor-SJRB071789_D1-FFPE


title: MLI2_5_C

description: Library name: MLI2_5_C_S35

value: AB + MLi2


title: BAT-HFD-2

description:
Library name: Sample5
10x Chromium


title: CRC22_tissue

description: 10X Genomics


title: PLKO2

description:
Library name: PLKO2
Column name in Processed data_fpkm.txt: PLKO2


title: MLI2_4_C

description: Library name: MLI2_4_C_S34


title: RB_Patient tumor-SJRB012408_R1-FFPE

value: RB

value: Orbit


title: CRC22_PBMC

description: 10X Genomics


title: RB_Xenograft-SJRB030199_X1-frozen_rep3


title: RB_Xenograft-SJRB030188_X1-frozen


title: MLI2_3_C

description: Library name: MLI2_3_C_S21


title: CRC22_M_tissue

description: 10X Genomics


title: MLI2_2_C

description: Library name: MLI2_2_C_S20


title: RB_Xenograft-SJRB030289_X1-frozen_rep2


title: NT2_C

description: Library name: NT2_C_S31


title: BAT-ND-3

description:
Library name: Sample3
10x Chromium


title: BAT-ND-2

description:
Library name: Sample2
10x Chromium


title: RB_Xenograft-SJRB030197_X1-frozen_rep3


title: BAT-HFD-3

description:
Library name: Sample6
10x Chromium


title: MLI2_1_C

description: Library name: MLI2_1_C_S6


title: BAT-ND-1

description:
Library name: Sample1
10x Chromium


title: CRC21_M_tissue

description: 10X Genomics


title: RB_Xenograft-SJRB049186_X1-frozen_rep3


title: CRC21_tissue

description: 10X Genomics


title: AB5

description: Library name: AB5_C_S19

value: AB


title: AB4

description: Library name: AB4_C_S18


title: BAT-HFD-1

description:
Library name: Sample4
10x Chromium


title: 24JK-FLT3L Tumors (Day16) rep 4

description: Library name: MJ_157

data_processing:
Raw FASTQ files were processed using CellRanger (Version 7.1.0, 10x Genomics) and aligned to the mm10 genome assembly. The CellRanger count pipeline was run with default parameters.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz

source_name: Whole Tumor

extract_protocol:
Tumors were finely sliced and enzymatically digested in DMEM containing 0.02 mg ml−1 DNase (Sigma Aldrich) and 1 mg ml−1 type IV collagenase (Sigma Aldrich). Digestion was performed in a rocking incubator at 120 r.p.m. for 30 min at 37 °C. Following digestion, cells were filtered through a 70μm filter twice and resuspended in Fc receptor block before being stained with fluorochrome-conjugated antibodies.
Single cell suspensions from digested tumors were processed with V3 chemistry using the Chromium Next GEM Single Cell 3’ Gel Bead Kit v3.1 (10X Genomics) and Chromium Next GEM Single Cell Library Prep Kit (10X Genomics), according to manufacturer’s protocol.

value: Whole Tumor


title: RB_Xenograft-SJRB030317_X1-frozen

value: M


title: AB3

description: Library name: AB3_C_S5


title: 24JK-FLT3L Tumors (Day16) rep 3

description: Library name: MJ_156


title: CRC20_T_tissue

description: 10X Genomics


title: RB_Xenograft-SJRB030240_X2-frozen_rep2

value: Eye


title: RB_Xenograft-SJRB030252_X1-frozen


title: 24JK-FLT3L Tumors (Day16) rep 2

description: Library name: MJ_155


title: AB2

description: Library name: AB2_C_S33


title: AB1

description: Library name: AB1_C_S32


title: CRC20_T_PBMC

description: 10X Genomics


title: CRC22_M_PBMC

description: 10X Genomics


title: 24JK-FLT3L Tumors (Day16) rep 1

description: Library name: MJ_154


title: RB_Xenograft-SJRB049187_X1-frozen_rep2


title: PF5

description: Library name: PF5_D_S15

value: ASYN + PF


title: 24JK Tumors (Day16) rep 5

description: Library name: K_11


title: RB_Xenograft-SJRB030199_X1-frozen_rep2

value: N


title: CRC21_PBMC

description: 10X Genomics

value: colorectum


title: CRC20_tissue

description: 10X Genomics


title: RB_Xenograft-SJRB049185_X1-frozen


title: 24JK Tumors (Day16) rep 4

description: Library name: K_10


title: CRC20_PBMC

description: 10X Genomics


title: CRC19_tissue

description: 10X Genomics


title: PF3

description: Library name: PF3_D_S29


title: PF2

description: Library name: PF2_D_S14


title: CRC21_M_PBMC

description: 10X Genomics


title: 24JK Tumors (Day16) rep 2

description: Library name: K_08


title: 24JK-FLT3L Tumors (Day16) rep 5

description: Library name: MJ_158


title: RB_Xenograft-SJRB030289_X1-frozen_rep1

value: F


title: RB_Xenograft-SJRB049186_X1-frozen_rep2


title: RB_Xenograft-SJRB030197_X1-frozen_rep2


title: 24JK Tumors (Day16) rep 1

description: Library name: K_07


title: CRC18_tissue

description: 10X Genomics


title: PF1

description: Library name: PF1_D_S28


title: RB_Xenograft-SJRB030149_X1-frozen


title: NT5

description: Library name: NT5_D_S24


title: CRC18_PBMC

description: 10X Genomics


title: 24JK Tumors (Day16) rep 3

description: Library name: K_09


title: NT4

description: Library name: NT4_D_S9


title: CRC17_tissue

description: 10X Genomics


title: RB_Xenograft-SJRB046161_X1-frozen_rep2


title: CRC19_PBMC

description: 10X Genomics


title: scRNA-seq library of Tet+ T cells deficient for Tbx21

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

country: Spain

institute: IDIBAPS

description:
Library name: Tbx21
Tetramer-sorted CD4 T cells deficient for Tbx21

data_processing:
Cellranger count v7
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5. Detected cell-associated barcodes in MEX format

source_name: Spleen

growth_protocol: Sorting by tetramer of CD4 T cells from spleen.

extract_protocol:
10x Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead kit (PN-1000121)
10x Chromium Next GEM Chip G Single Cell Kit (PN-1000120)

treatment_protocol: Mice were treated with BDC2.5/IAg7-NPs at 30ug/dose, 2 times a week for 5 weeks.

value: Spleen

value: CD4+ Tet+ T cells

tag: batch

value: A


title: RB_Xenograft-SJRB071788_X1-frozen_rep2

source_name: Eye


title: scRNA-seq library of Tet+ T cells deficient for Stat4

description:
Library name: Stat4
Tetramer-sorted CD4 T cells deficient for Stat4

value: C


title: PF4

description: Library name: PF4_D_S3


title: scRNA-seq library of Tet+ T cells deficient for Stat3

description:
Library name: Stat3
Tetramer-sorted CD4 T cells deficient for Stat3


title: NT1

description: Library name: NT1_D_S8


title: CRC16_T_tissue

description: 10X Genomics


title: CRC17_PBMC

description: 10X Genomics


title: scRNA-seq library of Tet+ T cells deficient for Prdm1

description:
Library name: Prdm1
Tetramer-sorted CD4 T cells deficient for Prdm1


title: RB_Patient tumor-SJRB071805_R2-FFPE

value: Y

value: Patient tumor


title: NT2

description: Library name: NT2_D_S1

value: hiPSCs


title: MLI2_5

description: Library name: MLI2_5_D_S13

value: ASYN + MLi2


title: CRC16_T_PBMC

description: 10X Genomics


title: RB_Patient tumor-SJRB030135_R1-FFPE

value: RB


title: RB_Patient tumor-SJRB049185_D2-FFPE


title: CRC16_tissue

description: 10X Genomics


title: scRNA-seq library of Tet+ T cells deficient for Irf4

description:
Library name: Irf4
Tetramer-sorted CD4 T cells deficient for Irf4

value: B


title: RB_Xenograft-SJRB049187_X1-frozen_rep1

value: Xenograft


title: scRNA-seq library of Tet+ T cells deficient for Maf

description:
Library name: Maf
Tetramer-sorted CD4 T cells deficient for Maf

value: Maf-/-


title: MLI2_4

description: Library name: MLI2_4_D_S27


title: RB_Xenograft-SJRB013765_X2-frozen

value: Eye


title: CRC16_PBMC

description: 10X Genomics


title: scRNA-seq library of Tet+ T cells deficient for Elk4

description:
Library name: Elk4
Tetramer-sorted CD4 T cells deficient for Elk4


title: MLI2_2

description: Library name: MLI2_2_D_S26


title: MLI2_1

description: Library name: MLI2_1_D_S12


title: CRC15_PBMC

description: 10X Genomics


title: scRNA-seq library of Tet+ T cells from Control_cd4cre mice

description:
Library name: Control_cd4cre
Tetramer-sorted CD4 T cells from  Control_cd4cre mice


title: RB_Xenograft-SJRB071808_X1-frozen


title: RB_Xenograft-SJRB071805_X1-frozen

value: M


title: CRC15_tissue

description: 10X Genomics


title: ASYN5

description: Library name: ASYN5_D_S25

value: ASYN


title: scRNA-seq library of Tet+ T cells from Control_Blimp1 mice

description:
Library name: Control_Blimp1
Tetramer-sorted CD4 T cells from  Control_Blimp1 mice


title: ASYN4

description: Library name: ASYN4_D_S11


title: scRNA-seq library of Tet+ T cells from Control2_cd4cre mice

description:
Library name: Control2_cd4cre
Tetramer-sorted CD4 T cells from  Control2_cd4cre mice


title: CRC14_tissue

description: 10X Genomics

value: colorectum


title: CRC14_PBMC

description: 10X Genomics


title: scRNA-seq library of Tet+ T cells from Control3_cd4cre mice

description:
Library name: Control3_cd4cre
Tetramer-sorted CD4 T cells from  Control3_cd4cre mice

value: D


title: RB_Xenograft-SJRB071804_X1-frozen_rep1

value: N


title: ASYN3

description: Library name: ASYN3_D_S2


title: CRC13_PBMC

description: 10X Genomics


title: RB_Xenograft-SJRB071801_X1-frozen


title: RB_Xenograft-SJRB071802_X1-frozen

value: F


title: ASYN2

description: Library name: ASYN2_D_S10


title: CRC12_T_PBMC

description: 10X Genomics


title: CRC02_tissue

description: 10X Genomics


title: scRNA-seq library of Tet+ T cells deficient for Bhlhe40

description:
Library name: Bhlhe40
Tetramer-sorted CD4 T cells deficient for Bhlhe40

value: Spleen

value: CD4+ Tet+ T cells


title: RB_Xenograft-SJRB071799_X1-frozen


title: CRC01_tissue

description: 10X Genomics


title: scRNA-seq library of Tet+ T cells deficient for Batf

description:
Library name: Batf
Tetramer-sorted CD4 T cells deficient for Batf

value: Batf-/-


title: Hashtags

city: Brooklyn

first: Ngoc

middle: Bao

last: Luu

state: NY

address: 6 Metrotech Center, RH 621

institute: New York University

description:
Library name: CAR-T_pool_HTO
10X Genomics

data_processing:
Cell Ranger Single Cell Software was used to perform de-multiplexing, barcode and UMI processing, and single-cell 3′ gene counting, Seurat package was used for quality control, data filtering, dimensionality reduction, differential gene expression analysis, and uniform manifold approximation.
Assembly: Homo Sapien
Supplementary files format and content: Matrix and fastq files

source_name: Blood

growth_protocol: T Cells were cultured in ImmunoCult-XF T Cell Expansion Medium (Cat#10981, StemCell Technologies) supplemented with IL-2 (200 IU/mL, Cat#200-02, Peprotech) in a 37 °C, 5% CO2 incubator.

extract_protocol:
CAR T cells were oligo-tagged using TotalSeq A anti-human antibodies (BioLegend): Hashtag 5- AAGTATCGTTTCGCA (CAT#394609), Hashtag 6- GGTTGCCAGATGTCA (CAT#394611), Hashtag 7- TGTCTTTCCTGCCAG (CAT#394613), Hashtag 8- CTCCTCTGCAATTAC (CAT#394615) and combined into a single suspension.
Single Cell RNA-seq and Cell Surface Protein libraries were constructed using the Chromium Single Cell 3′ v3.1 Reagent Kit (10x Genomics, PN-1000268) according to the manufacturer’s protocol (manual part number CG000204 Rev D). Reverse transcription and library preparation were performed on a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad).  cDNA was amplified 12 cycles and evaluated on a Agilent BioAnalyzer 2100 using a High Sensitivity DNA Kit (Agilent Technologies).  Final Gene Expression and Cell Surface Protein libraries were amplified 12 and 10 cycles respectively and visualized on an Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies).  Individual libraries were diluted to 2nM and pooled for sequencing.

treatment_protocol: CAR T cells were pre-treated with GsMTx4 for 30 minutes and then acitvated by anti-FMC63 Antibody μBeads for 24 hours.

value: Blood

value: T cell

value: CAR T cell

value: pretreament with GsMTx4


title: scRNA-seq library of Tet+ T cells deficient for Atf6

description:
Library name: Atf6
Tetramer-sorted CD4 T cells deficient for Atf6


title: RB_Xenograft-SJRB071798_X1-frozen

data_processing:
Methylation Analysis: Raw data files generated by the iScan array scanner were read and preprocessed by using 'minfi' Bioconductor package.
processed value definition: Average beta value

value: RB


title: RB_Xenograft-SJRB071796_X1-frozen

value: Xenograft


title: CRC11_PBMC

description: 10X Genomics


title: RB_Xenograft-SJRB071795_X1-frozen


title: CAR T cells

description:
Library name: CAR-T_pool_GEX
10X Genomics


title: Fabp4Knockout

city: Shatin

first: Karl Kam Hei

last: So

state: New Territories

address: 608A, Lo Kwee-Seong Integrated Biomedical Sciences Building, The Chinese University of Hong Kong

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: KO

data_processing:
For each sample, there is an average throughout of 24.2Gb and a total throughput of 96.9Gb. An average of 94% of the bases achieved a quality score of Q30 where Q30 denotes the accuracy of a base call to be 99.9%. STAR 2.5.2, RSEM 1.2.31 and EBSeq 1.18.0 were used to proceed alignment, expression estimation and tests for differential expression.
Assembly: mm10
Supplementary files format and content: Processed.xlsx

source_name: liver tumor

extract_protocol:
Total RNA was harvested from mouse liver tumors by using the RNease Plus Mini Kit (QIAGEN).
The qualified RNA was subjected to Illumina NovaSeq 6000 sequencer, indexed library construction
Illumina sequencing run (pair-end sequencing of 151bp)

value: liver tumor


title: Wildtype

description: Library name: WT


title: CRC10_T_PBMC

description: 10X Genomics


title: TIM3–Prdm1+TCF1–, d22, mouse 37

city: SAINT LOUIS

first: Takeshi

last: Egawa

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Library name: DN 37

library_source: genomic

data_processing:
Reads were mapped to the mm9 genome using the package Bowtie2.
HOMER was used to find peaks and generate bedGraphs of the data. BedGraphs were visualized in the UCSC genome browser.
Assembly: mm9
Supplementary files format and content: bed graphs of each of the samples

extract_protocol:
Nuclei were isolated for tagmentation according to the OmniATAC pipeline using the using the Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit (Illumina, Cat # 20034197). Tagmented nuclear DNA was purified using the Qiagen MinElute Reaction Cleanup Kit.
The libraries were indexed with a custom set of barcoded primers described in the associated manuscript. Amplified libraries were cleaned up using  the Qiagen MinElute Reaction Cleanup Kit. Library concentrations were determined by Qubit prior to pooling, and the pooled library was sequenced for a target of 500 million read pairs on an Illumina HiSeq 2500.

treatment_protocol: TPEX were sorted from spleens of LCMV-c13 infected mice on 22 dpi.

value: CD8+ T cell

tag: cell population


title: RB_Xenograft-SJRB071794_X1-frozen

city: Memphis

first: Gang

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

extract_protocol: Genomics DNA was extracted from froze tumor tissues using  Qiagen kit (catalog #65904) or FFPE tumors using Promega Maxwell DNA FFPE Kit according to standard instructions recommended by the kit

value: M

value: Eye


title: RB_Xenograft-SJRB071793_X1-frozen


title: CRC10_PBMC

description: 10X Genomics

value: colorectum


title: TIM3–Prdm1–TCF1+, d22, mouse 31

description: Library name: TCF 31


title: RB_Xenograft-SJRB071792_X1-frozen


title: metastatic liver tumors in mice with SCLC

first: Yujie

last: Hao

address: 22 Qixiangtai Road

institute: Tianjin Medical University

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

source_name: tumor tissues from mice with spontaneous tumor formation

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTM Reverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM 6000 at the (LC Sceiences, USA) following the vendor's recommended protocol.

value: mouse-derived SCLC tumor cells

value: liver metastatic nodules harvested from the CMV-Cre induced RP mouse model


title: spontaneously developed primary lung tumors in mice with SCLC rep2

value: tumor tissues from mice with spontaneous tumor formation

value: lung tumor nodules harvested from CMV-Cre induced RP mouse model；rep2


title: scRNA-seq library of Tet+ T cells deficient for Bcl6

description:
Library name: Bcl6
Tetramer-sorted CD4 T cells deficient for Bcl6

value: Spleen

value: CD4+ Tet+ T cells

value: C


title: TIM3–Prdm1–TCF1+, d22, mouse 37

description: Library name: TCF 37


title: CRC09_PBMC

description: 10X Genomics


title: spontaneously developed primary lung tumors in mice with SCLC rep1

value: lung tumor nodules harvested from CMV-Cre induced RP mouse model；rep1


title: RB_Xenograft-SJRB071788_X1-frozen_rep1

last: Wu

value: N


title: TIM3–Prdm1–TCF1+, d22, mouse 40

description: Library name: TCF 40


title: CRC08_T_PBMC

description: 10X Genomics


title: CRC12_PBMC

description: 10X Genomics


title: TIM3–Prdm1+TCF1–, d22, mouse 40

description: Library name: DN 40


title: mouse-derived SCLC tumor cells; subpopulation with low autophagic flux; rep2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

tag: cell subtype


title: CRC11_T_PBMC

description: 10X Genomics


title: TIM3+Prdm1+TCF1–, d22, mouse 31

description: Library name: TIM 31


title: RB_Xenograft-SJRB030240_X2-frozen_rep1

value: F


title: CRC08_PBMC

description: 10X Genomics


title: mouse-derived SCLC tumor cells; subpopulation with low autophagic flux; rep1


title: CRC07_T_PBMC

description: 10X Genomics


title: CRC07_PBMC

description: 10X Genomics


title: mouse-derived SCLC tumor cells; subpopulation with high autophagic flux; rep2


title: RB_Xenograft-SJRB030197_X1-frozen_rep1

value: RB


title: TIM3+Prdm1+TCF1–, d22, mouse 37

description: Library name: TIM 37


title: mouse-derived SCLC tumor cells; subpopulation with high autophagic flux; rep1


title: CRC06_T_PBMC

description: 10X Genomics


title: RB_Xenograft-SJRB049186_X1-frozen_rep1

value: Y

value: Xenograft


title: SAS-3 [S_283]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

data_processing:
Reads were aligned to the human reference genome (hg38) using STAR (version_2.7.5c) in two-pass mode following STAR best practices and recommendations [Dobin et al]. The quality of the data was evaluated using STAR (version 2.7.5c) [Dobin et al] and samtools (version 1.15) [Danecek et al and Bonfield et al]. PCR duplicates were removed from aligned bam files using samtools (version 1.15) [Bonfield et al]. Read counts were extracted from the aligned bam files using subread’s FeatureCounts (version 2.0.3) [Liao et al]. Normalisation of read counts for analysis was done according to EdgeR recommendations using the Ratio of the Variance method which accounts for inter-sample variance and the differential expression analysis of the normalised read counts between the sample groups was performed following best practices and recommendations of EdgeR [Robinson et al, McCarthy et al, Chen et al] and Limma [Ritchie et al] on R environment (version 3.6.0).
Transcription factor motif enrichment analysis for motif discovery was performed with HOMER (Heinz, et al, 2010), using the findMotifs.pl function for 8, 10, and 12 nt motif lengths. Analysis included findings for gene ontology biological processes (GO-BP) pathways.
Assembly: mm10
Supplementary files format and content: Tab separated raw reads values

source_name: Bone marrow

extract_protocol:
Single cells were obtained by cell sorting, staining for lineage markers (Lin), cKit/CD117, and Annexin V.  Prior to sorting, DAPI was added for viability.  Cells stained as Lin-cKit+Annexin V-DAPI- were sorted and stored at -80ºC until processing. RNA was isolated using a Total RNA Purification Kit (Norgen Biotek Corp). The quantity and quality of the RNAs were evaluated using Agilent RNA 6000 Pico Chips (Agilent Technologies, Cat.# 5067-1513).
Sequencing libraries were prepared using “NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®” (New England Biolabs, Cat # E6420S) and “NEBNext Multiplex Oligos for Illumina (Index Primers 1-12)” (New England Biolabs, Cat # E7335S), following the corresponding Instruction manual (Version 5.0_5/20)

value: Bone marrow

value: Hematopoietic stem and progenitor cells

value: SAS


title: RB_Xenograft-SJRB046161_X1-frozen_rep1

value: M

value: Eye


title: CRC06_PBMC

description: 10X Genomics

data_processing:
The scRNA-seq data generated were aligned and quantified against the GRCh38 human reference genome, and filtered using the Cell Ranger pipeline (version 3.1). The resulting feature-barcode matrices were used for downstream filtering and analysis. The matched TCR data based on 10x protocol was processed using Cell Ranger software (version 3.1) with the manufacturer-supplied human VDJ reference genome. Bulk RNA-seq data were filtered using Skewer (version 0.2.2). Adapter sequences and low-quality reads (＜30) from the 3’ ends were removed. The bulk RNA expression was quantified by kallisito (version 0.44)60. Gene expression were calculated by aggregating transcript expression (TPM) belonging to the same gene using tximport (version 1.22.0), and the TPM of gene were then logarithmically transformed.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

value: colorectum


title: SAS-2 [S_282]


title: RB_Patient tumor-SJRB071808_D1-FFPE

value: Patient tumor


title: TIM3+Prdm1+TCF1–, d22, mouse 40

description: Library name: TIM 40

value: CD8+ T cell


title: LG oligodendrocyte progenitors rep4

city: New York

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
High-quality reads were aligned to the mouse reference genome (mm10) using the STAR package toolset (RRID:SCR_004463, Dobin et al., 2013). The featureCounts program (RRID:SCR_012919, Liao et al., 2014) was used to count mapped reads, and DESeq2 (RRID: SCR_015687, Love et al., 2014) was used for differential gene expression analysis. We used a cut-off of FDR < 0.05 and |foldchange|>1 to identify differentially expressed genes and for the GSEA.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each biological replicate

source_name: PDGFRa+ oligodendrocyte progenitor cells

growth_protocol: Oligodendrocyte progenitors were isolated from WT neonatal pups aged postnatal day 6-8 as previously described. Cortices from neonates of either sex were dissected, and the meninges were removed. The cortices were dissociated in papain buffer supplemented with DNAse I with gentle rotation at 37°C to generate single cell suspensions. Cell suspensions were transferred onto two consecutive rounds of negative-selection dishes coated with lectins derived from Griffonia simplicifolia to adhere microglia and endothelial cells (L-1100-5, Vector Labs). The remaining cell suspension was then transferred to a positive selection dish coated with rat anti-mouse CD140α (clone APA5, BD Pharmingen) tandemly bound to goat-anti rat IgG. Positive selection dishes were washed thoroughly to remove non antibody-captured cells. PDGFRα OPCs were released from positive selection dishes by trypsin digest and mild trituration before seeding in poly-d-lysine (Sigma) coated dishes in defined culture medium in 25 mM glucose supplemented with mitogens (10 ng/mL recombinant human PDGF-AA; 20 ng/mL recombinant human bFGF; Peprotech). Cultures were maintained in humidified CO2 incubators at 37°C. bFGF was washed out prior to commencement of in vitro assays with 10 ng/mL PDGF-AA maintained until completion.

extract_protocol:
RNA from cells were extracted from at least three biological replicates for each condition using TRIzol (Invitrogen) extraction and isopropanol precipitation. RNA samples were resuspended in nuclease-free H2O and further purified with RNeasy Mini Kit (Qiagen,  74106) with on-column DNase treatment. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop.
100 ng of total RNA per sample was used for library construction using KAPA mRNA Hyperprep kit (Roche). The libraries were sequenced on an Illumina Novaseq X Plus platform according to the manufacturer’s instructions. Depths of 15-30 million paired-end 150 bp reads were generated for each sample.

treatment_protocol: For high or low glucose experiments, independent biological preparations were seeded in defined culture medium with DMEM no glucose supplemented with 25 mM glucose (Day 0) and 10 ng/mL PDGF-AA (maintained throughout). On Day 1, 50% of the culture medium was replaced with media containing 25 mM (HG) or no glucose (LG, remaining effective concentration 12.5 mM). On Day 2, 60% of the culture medium was replaced with media containing 25 mM (HG) or no glucose (LG, remaining effective concentration 5 mM). On Day 3, 50% of the culture medium was replaced with media containing 25 mM (HG) or no glucose (LG, remaining effective concentration 2.5 mM). On Day 4 50% of the culture medium was replenished to maintain 25 mM (HG) or 2.5 mM (LG) culture. On Day 5, OPCs in HG or LG were washed with cold EBSS and harvested in TriZol for nucleic acid.

tag: strain

value: WT

value: postnatal day 6-8

value: low glucose (2.5 mM)


title: HG oligodendrocyte progenitors rep4

value: PDGFRa+ oligodendrocyte progenitor cells

value: high glucose (25 mM)


title: CRC05_PBMC

description: 10X Genomics


title: PBS-3 [S_278]

value: PBS


title: RB_Patient tumor-SJRB071806_D1-FFPE

value: RB

value: N


title: CRC04_T_PBMC

description: 10X Genomics


title: SAS-1 [S_281]


title: LG oligodendrocyte progenitors rep3


title: RB_Patient tumor-SJRB071807_D1-FFPE

value: F


title: HG oligodendrocyte progenitors rep3


title: PBS-2 [S_276]

value: Bone marrow


title: RB_Xenograft-SJRB030199_X1-frozen_rep1

value: Xenograft


title: RB_Patient tumor-SJRB071804_D1-FFPE


title: TIM3–Prdm1+TCF1–, d22, mouse 31

description: Library name: DN 31

value: Spleen


title: CRC04_PBMC

description: 10X Genomics


title: LG oligodendrocyte progenitors rep2


title: CRC03_PBMC

description: 10X Genomics


title: RB_Patient tumor-SJRB071802_D1-FFPE


title: PBS-1 [S_274]

value: Hematopoietic stem and progenitor cells


title: CRC13_tissue

description: 10X Genomics


title: SAS_scRNA-seq

description: single cell transcriptome sequencing

data_processing:
Sequences were aligned to the mm10  reference genome, the counts separated by cell, the data filtered and processed using Cell Ranger version 6.1.2 according to manufacturer recommendations
To analyze the data, processed 10x files were uploaded into RStudio (version 2023.06.0+421) and processed with Seurat (version 4.3.0), following default, standard, and generally recommended settings. Quality control was performed using filtration criteria to allow for cells containing at least 1,000 genes per cell and fewer than 5% mitochondrial genes for analysis.  To account for variations due to cell cycle effects, cell cycle scaling was applied as described in the Seurat manual for murine hematopoiesis, by predicting cell cycle phase using canonical markers and regressing out the difference between assigned G2M and S phase scores.
Integration of the datasets was accomplished by using 3000 variable features as anchors for integration, which was accomplished using the SelectIntegrationFeatures, FindIntegrationAnchors, and IntegrateData functions.  Data underwent scaling and principal component analysis (PCA), and 50 PCA dimensions were utilized to generate a uniform manifold approximation and projection (UMAP).  To achieve clusters, the FindNeighbors (using 50 PCAs) and FindClusters (with resolution 1.0) functions were performed.  The UMAP was further fitted to a three-dimensional model.  Differential gene expression analysis was performed using the FindMarkers function under default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format

extract_protocol:
Single cells were obtained by cell sorting, staining for lineage markers (Lin), cKit/CD117, and Annexin V.  Prior to sorting, DAPI was added for viability.  Cells stained as Lin-cKit+Annexin V-DAPI- were sorted, pooled from each group, and added to the 10X chip.
Single cell library was prepared using “Chromium Next GEM Chip G Single Cell Kit”, 16 rxns PN-1000127 and “Chromium Next GEM Single Cell 3ʹ Kit v3.1”, 4 rxns PN-1000269 and “Dual Index Kit TT Set A”, 96 rxns PN-1000215, following “Chromium Next GEM Single Cell 3’ Reagent Kits v3.1(Dual Index) User Guide” (Document number CG000315).
single-cell 3' mRNA Transcriptomics

value: SAS


title: LG oligodendrocyte progenitors rep1


title: CRC05_T_PBMC

description: 10X Genomics

extract_protocol:
PBMCs were isolated from peripheral blood by Ficoll density gradient centrifugation. In brief, Ficoll was added into a 15ml centrifuge tube according to the amount of the whole blood, and then the whole blood was slowly added. Centrifuge the tube with acceleration speed 1, and deceleration speed 0 at 800 g for 30 min. After centrifugation, the middle white film layer was taken and washed by PBS containing 2% FBS to remove Ficoll. Red blood cells were removed by Red blood cell lysis solution (Miltenyi Biotec,130-095-929). The number of PBMCs was calculated by Countstar cell counter. Patient tumor tissues were weighed, and dissociated with Tumor Dissociation Kit, human (Miltenyi Biotec,130-095-929). In brief, tumor tissues were cut into small pieces in a C tube (Miltenyi Biotec,130-093-237) and three dissociating enzymes from the kit were added according to the tumor tissue weight. Place the C tube to the gentleMACS™ Octo Dissociator with Heaters and use 37C_h_TDK_1 program for tissue dissociation for 1 h. After dissociation, cells were filtered through a 70 μm filter membrane, and then washed with 10 ml of PBS containing 2% FBS. The suspension was centrifuged at 300g for 10 min. We next collected the cell pellet and counted using Trypan blue staining.
Cell pellets obtained from PBMC and tumor tissue were re-suspended in sorting buffer (PBS with 1% FBS), followed by staining with DAPI, anti-CD45, and anti-CD235a antibodies for FACS with a BD FACSAria™ III instrument (BD Biosciences). Live cells were identified as DAPI-negative. Subsequently, CD235a-negative and CD45-positive single cells from PBMC and CD235a-negative single cells from tumor tissue cell suspension were sorted. 10,000~20,000 cells were loaded for library construction using the 10x Chromium Single cell 5` Library (10X Genomics, PN-1000263), according to the manufacturer’s instructions. Purified libraries were attained through Library Construction Kit (10X Genomics, PN-1000190) according to the manufacturer’s instructions, and then sequenced by BGI MGISEQ-2000 sequencer. TCR sequences were amplified with the Chromium Single Cell Human TCR Amplification Kit (10X Genomics, PN-1000252). V(D)J Libraries were generated with Library Construction Kit (10X Genomics, PN-1000190), and sequenced by Illumina Novaseq6000 sequencer.

value: colorectum


title: HG oligodendrocyte progenitors rep1


title: RB_Patient tumor-SJRB071798_D1-FFPE

value: M

value: Eye

value: Patient tumor


title: RB_Patient tumor-SJRB071799_D1-FFPE


title: KPC3

city: Cardiff

first: Beatriz

last: Salvador-Barbero

state: Wales

address: Hadyn Ellis Building, Maindy road

department: ECSCRI-BIOSI

country: United Kingdom

institute: Cardiff University

data_processing:
sequencing was performed using Sanger sequencing Illumina 1.9. Sequenced
reads Fastq files were quality-checked using FastQC
Reads were aligned to the mouse genome (Ensembl-GRCm38 Mus musculus) using the STAR package
duplicates were removed using MarkDuplicates from GATK
reads were counted using the FeatureCounts package
Assembly: Reads were aligned to the mouse genome (Ensembl-GRCm38 Mus musculus) using the STAR package
Supplementary files format and content: featurecounts files obtained after removing duplicates

source_name: pancreas

growth_protocol: Animals were housed in conventional pathogen-free animal facilities and experiments were conducted in accordance with UK Home Office regulations (ASPA 1986 & EU Directive 2010) under the guidelines of Cardiff University Animal Welfare and Ethics Committee.

extract_protocol:
RNA was extracted using the RNeasy Micro kit (Qiagen) following the manufacturer’s recommendations.
Libraries were prepared using the Protocol for Low Input RNA: cDNA Synthesis, Amplification and Library Generation (NEB #E6420) following manufacturer's protocol.

treatment_protocol: Both male and female 6-8-week-old experimental and control mice were injected with intraperitoneal injection of tamoxifen in corn oil 1µg/40g bodyweight once. Pancreata were harvested at 35-days post tamoxifen induction.

value: pancreas

tag: mouse strain

value: KPC

value: acinar and ductal cells

value: Pdx1-CreERT; LSL-KrasG12D/+; p53R172H; Rosa26LSL-tdRFP

value: Tamoxifen low dose


title: CRC12_T_tissue

description: 10X Genomics


title: HG oligodendrocyte progenitors rep2

value: PDGFRa+ oligodendrocyte progenitor cells

value: WT

value: postnatal day 6-8

value: high glucose (25 mM)


title: KPC2


title: RB_Patient tumor-SJRB030065_D4-FFPE

value: F

value: RB

value: N


title: CRC11_tissue

description: 10X Genomics


title: PBS_scRNA-seq

description: single cell transcriptome sequencing

value: Bone marrow

value: Hematopoietic stem and progenitor cells

value: PBS


title: Control_Cap

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

institute: Cornell University

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Normalized read density was calculated by custom python scripts.
Assembly: GRCh39.p13
Supplementary files format and content: comma-delimited text files including sense and antisense peak positions for trans-RNA-seq samples.
Supplementary files format and content: comma-delimited text files including normalized read density around start and stop codons for Ribo-seq samples.

molecule: other

extract_protocol:
For Ribo-seq, RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. To enrich capped small RNAs, 50 μg of total cellular RNA was fractionated using the RNA Clean & Concentrator kit (Zymo research). Briefly, adjusted RNA Binding Buffer was prepared by mixing an equal volume of buffer and 100% ethanol. Total RNA sample were mixed with 2 volumes of the adjusted buffer and transferred to the column. The mix was then centrifuged at 16,000 g for 30 s, and the flow-through was collected. 1 volume of ethanol were mixed with flow-through and transferred to a new column. The mix were centrifuged at 16,000 g for 30 s, and the flow-through was discarded. The column was washed by RNA Prep Buffer and Wash buffer, and the bound RNA was eluted with 50 μl DNase/RNase-Free water.  The eluted RNAs were dephosphorylated with 50 U of CIP (NEB) in a 100 μl reaction containing 1 × rCutSmart Buffer and 0.5 U/μl SUPERase·In at 37 °C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. Three-fourths of resulting RNAs were decapped with 0.75 μl of 5 U/μl Cap-Clip Acid Pyrophosphatase (Cellscript) in 1 × Cap-Clip Acid Pyrophosphatase Buffer at 37 °C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. The remaining one-fourth RNAs were phosphorylated with 20 U of T4 PNK in a 20 μl reaction containing 0.5 U/μl SUPERase·In, 2 mM ATP and 1 × T4 PNK Buffer at 37 °C for 1 h, followed by ethanol precipitation.
For Ribo-seq and trans-RNA-seq, 14 μl RNAs (10~200 ng) were mixed with 1 μl T4 PNK (NEB), 20 U SUPERase·In in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 65 °C for 20 min. After ethanol precipitation, 10 μl dissolved RNA were mixed with 1 μl homemade Ezra enzyme, 1 μl Poly(A) Polymerase (NEB) and 20 U SUPERase·In in 7 μl Ezra buffer. After incubation at 37 °C for 30 min followed by 65 °C for 20 min, 1 μl of 1 μM 5’ end adaptor, 1 μl of 1 μM biotinylated reverse transcription primer, 20 U SUPERase·In were added and incubated at 70 °C for 3 min followed by slowly cooling down (3 °C/min) to 25 °C. The hybridized RNA sample was mixed with 10 μl of pre-washed streptavidin beads and incubated at room temperature for 10 min. Beads were washed and re-suspended in 10 μl nuclease-free water. Ligation was performed for 60 min at 25 °C by mixing beads with a 10 μl reaction mixture (1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). After washing once with 2 × SSC, beads were re-suspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, RNaseOUT and SuperScript III) followed by incubation at 50 °C for 30 min. After washing once with 2 × SSC, beads were resuspended in 10 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR 5primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 68 °C, 15 s; 72 °C, 10 s) for 12 cycles; 72 °C, 3 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA).


title: KPC1


title: PC3


title: Control_Total


title: CRC10_T_tissue

first: Xinnan

address: Haidian District, Beijing Summer Palace Road No. 5

institute: Peking University

description: 10X Genomics

value: colorectum


title: CRC10_tissue

description: 10X Genomics


title: Ribo_starvation_trans2

data_processing:
Library strategy: Ribo-seq
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Normalized read density was calculated by custom python scripts.
Assembly: GRCh39.p13;GRCm39
Supplementary files format and content:
comma-delimited text files including sense and antisense peak positions for trans-RNA-seq samples
comma-delimited text files including normalized read density around start and stop codons for Ribo-seq samples
comma-delimited text files including RPKM and TPM of RNA-seq samples
tab-delimited text files including identified ORF results by PRICE of Ribo-seq samples

value: starvation, transfection with trans-RNA against ATF4


title: PC2

value: pancreas


title: RB_Patient tumor-SJRB071797_D1-FFPE

value: Eye

value: Patient tumor


title: RB_Patient tumor-SJRB071800_D1-FFPE

value: M


title: Ribo_starvation_trans1


title: Ribo_starvation

value: starvation


title: PC1

value: KPC

value: acinar and ductal cells

value: Tamoxifen low dose


title: RB_Patient tumor-SJRB071794_D1-FFPE


title: CRC08_T_tissue

description: 10X Genomics


title: CRC12_tissue

description: 10X Genomics


title: Ribo_control

value: WT

value: control


title: CRC09_tissue

description: 10X Genomics


title: KC4


title: Normal_Controls-4

first: Dong

last: Han

address: 28 Fuxing street

institute: Chinese PLA general hospital

data_processing:
Sequencing quality was examined by FastQC software and trimmed reads (pass Illumina quality filter, trimmed 3'-adaptor bases by cutadapt) were aligned to the piRBase (a manually curated resource of piRNAs) using NovoAlign software (v2.07.11). The maximum mismatch <= 2 reads are kept.
The expression profiling and differential expression of piRNAs were calculated based on normalized TPM.
Hierarchical clustering, scatter plots and classification analysis were performed with the differentially expressed piRNAs in R or Perl environment for statistical computing and graphics.
Assembly: piRBase
Supplementary files format and content: Excel table files include raw count for each Sample

source_name: aortic valve

extract_protocol:
Agarose electrophoresis was used to check the integrality of total RNA samples, and then the samples were quantified on the NanoDrop ND-1000 instrument.
1~2μg total RNA was used to prepare the sequencing library in the following steps: 1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of 142~153bp PCR amplified fragments (corresponding to 24~35nt small RNA size range). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as sequencing clusters and sequenced for 50 cycles on Illumina NextSeq500 system per the manufacturer's instructions.

value: aortic valve

tag: disease state

value: healthy control


title: RB_Patient tumor-SJRB071792_D1-FFPE

tag: Sex

value: F

value: RB

value: N


title: CRC11_T_tissue

last: Ling

description: 10X Genomics

source_name: colorectum

tag: tissue

value: colorectum


title: KC3

tag: treatment


title: RB_Patient tumor-SJRB046160_D2-FFPE

tag: sample type


title: Normal_Controls-3


title: CRC08_tissue

description: 10X Genomics


title: CRC07_tissue

description: 10X Genomics


title: RB_Patient tumor-SJRB071795_D2-FFPE

tag: tumor group


title: RB_Patient tumor-SJRB071790_D1-FFPE

tag: age at collection (yr)


title: KC2


title: Normal_Controls-2


title: WT3

value: Pdx1-CreERT; Rosa26LSL-tdRFP


title: RB_Patient tumor-SJRB030281_D1-FFPE


title: RB_Patient tumor-SJRB030402_D2-FFPE


title: WT2

value: pancreas


title: Calcific_Valves-4

value: calcific aortic valve disease


title: CRC06_tissue

description: 10X Genomics


title: RB_Patient tumor-SJRB030485_D2-FFPE

value: Eye

value: Patient tumor


title: Normal_Controls-1


title: WT1


title: RB_Patient tumor-SJRB063835_D3-FFPE


title: Calcific_Valves-3


title: CRC05_T_tissue

description: 10X Genomics


title: Calcific_Valves-2


title: CRC05_tissue

description: 10X Genomics


title: CRC07_T_tissue

description: 10X Genomics


title: RB_Patient tumor-SJRB030317_D2-FFPE

value: M


title: Calcific_Valves-1


title: CRC04_T_tissue

description: 10X Genomics


title: RB_Patient tumor-SJRB030252_D2-FFPE


title: D14_KO_CD8T_3

city: Guangzhou

first: Jing

last: Liao

address: No.1 Xinzao Road, Xinzao, Panyu District

institute: Guangzhou Medical University

description: Library name: Sample 19

data_processing:
This data processing pipeline adheres to a standard RNA sequencing analysis workflow: first, Quality Control was performed using fastqc for initial assessment, followed by read cleaning via trimmomatic to remove adapters, trim low-quality bases, and filter by minimum length. Next, the high-quality reads were Aligned to the reference genome, after index construction, using the STAR aligner. Finally, Gene Expression Quantification was completed by employing featureCounts to tally the number of reads mapped to each gene locus, generating the necessary raw count data for downstream differential expression analysis.
This data processing pipeline adheres to a standard TCR repertoire analysis workflow: first, Unique Molecular Barcodes (UMBs) were applied to correct PCR and sequencing errors and to eliminate PCR duplicates, thereby maximizing sequencing accuracy and quantification. This was followed by mapping the sequences against the IMGT® database to define V, D, J, and C segments. Next, the CDR3 regions were extracted and clonotypes were assembled, undergoing a critical quality control step that eliminated sequences with out-of-frame or stop codons. Finally, the abundance of each TRB clonotype was accurately determined by summing the number of individual clones sharing the identical CDR3 nucleotide sequence.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: The tab-delimited text file comprehensively contains all sequencing information for both the TCR alpha (α) chain and the TCR beta (β) chain of the corresponding sample. Specifically, the file details VDJC segment usage, precise CDR3 sequences, and the abundance counts for each unique clonotype after error correction and deduplication.

source_name: Splenic CD8+ T

extract_protocol:
Total RNA was extracted from tumor tissue with TRIzol reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
Library construction began with the enrichment of mRNA using Oligo(dT) beads (by binding to the poly-A tail). The enriched mRNA was fragmented and reverse transcribed into cDNA. The resulting cDNA fragments were then processed using the NEBNext Ultra RNA Library Prep Kit for Illumina, which involved end repair, A-tailing, and ligation of Illumina sequencing adapters to finalize the cDNA library.
Library construction utilized the ImmuHub® TCR profiling system, employing a 5' RACE unbiased amplification protocol. Unique molecular barcodes (UMBs) were introduced during first-strand cDNA synthesis, along with a common adaptor and a reverse primer corresponding to the constant (C) regions of the TRB. This method facilitates the high-throughput sequencing of TRB (TCR β) sequences by using UMBs to control bottlenecks and eliminate PCR and sequencing errors.

value: Splenic CD8+ T

value: CD8⁺ T cells isolated on day 14 from the spleens of C57BL/6J mice inoculated with MC38-Ctrl or MC38-Galnt7⁻/⁻ cells