title: Adrenalitis (CSP library)

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description: Library name: Adrenalitis_CSP

data_processing:
The BCL files were demultiplexed using Cell Ranger bcl2fastq v5.0.1.
The generated reads were then mapped using 10X Cell Ranger v5.0.1 to the Mus musculus reference genome provided by the Ensembl site (GRCm38, version 102).
Subsequently, the results were processed using Seurat v4.3.0 (Hao et al., 2021) in R v4.2.1. The samples were demultiplexed using hashtag counts. Cells that lacked sufficient hashtag counts or exhibited multiple hashtags were filtered out. Mitochondrial, ribosomal, and T-cell receptor V/J genes were also removed.
Initially, the spleen and adrenal samples were analyzed separately. Each subset underwent normalization, identification of 2,000 variable features, dimensionality reduction, and clustering (with resolutions of 0.8 and 0.9 for the adrenal and spleen subsets, respectively). Contaminating clusters were excluded, and the data subsets were reprocessed using the same pipeline, applying a resolution of 0.8 to both subsets.
The data were then integrated using the CCA integration method (1,050 anchors), following the removal of cells with more than 6% of their transcriptome mapping to mitochondrial genes or those identified as high feature count outliers. The integrated dataset subsequently underwent dimensionality reduction and clustering (resolution of 1).  In total, the final dataset comprised 5,584 cells.
Assembly: GRCm38
Supplementary files format and content: RDS file of finalized scRNA data in Seurat object generated by R, with CSP (HTO) and VDJ (TCR) information in meta data, used directly for manuscript figure generation.
Supplementary files format and content: Standard CSV file formatted according to 10X instructions for CSP mapping with additional column "multiplexed_sample" used to specify samples.
Library strategy: CITE-seq

molecule: protein

source_name: Adrenals or Spleen

extract_protocol:
At day 14 after the immunization, adrenals were isolated, cleaned of surrounded fat and digested in 1.5 ml microtubes containing Collagenase D (0.5 mg/ml) and DNase I (0.1 mg/ml) (both from Sigma-Aldrich) in RPMI medium. Glands were incubated at 37 °C for 5 minutes, then minced with scissors, followed by an additional 20-minute incubation with continuous shaking. During incubation, tissues were gently disrupted at least once by reverse pipetting using wide-bore 1.5 ml tips. Following digestion, samples were transferred to 24-well tissue culture plates, and residual tissue fragments were passed through a 70 µm nylon mesh using syringe plungers. Cells were washed with 1× HBSS supplemented with 2% FBS and 200 mM EDTA and stained with fluorochrome-conjugated primary antibodies (CD11b-BV421, TCRb-FITC, CD4-PE). Each sample was labelled with Totalseq-C Hashtag antibodies for multiplexing (Biolegend, MH1: #155861, MH2: #155863, MH3: #155865, MH4: #155867, MH5: #155869, MH6: #155871, MH7: #155873, MH8: #155875, MH9: #155879, MH10: #155879). CD4+ T cells were sorted as live, CD11b-, TCRb+, CD4+ cells using MoFlo Influx sorter. The viability of the cells pre-loading was validated using TC20 Automated Cell Counter (#1450102, Bio-Rad) and was over 90%. Cells were loaded onto a 10X Chromium machine (10X Genomics).
The libraries were constructed using the Chromium Single Cell 5’ Library & Gel Bead and Chromium Single Cell 5' Feature Barcode Library kits (10X Genomics, #PN-1000014, #PN-1000020, #PN-1000080, #PN-1000009, #PN-1000084, #PN-1000071) following the Feature Barcode technology for Cell Surface Protein protocol (#CG000186 Rev D). The generated cDNA libraries were sequenced on NovaSeq 6000 (Illumina) using the S1 Reagent Kit (100 cycles, Illumina, #20012865).

treatment_protocol: C57BL/6J mice aged 10-12 weeks were subcutaneously immunized with 100 µg of each CYP11A1 peptide emulsified in Complete Freund’s Adjuvant (CFA, Sigma-Aldrich) containing 500 µg of heat-inactivated Mycobacterium tuberculosis H37RA (Difco). For control mice, only CFA without peptides were administrated. Two injection sites were located on the dorsal side of each mouse.

value: Adrenals or Spleen

value: CD4+ T cells

value: No treatment or immunized by CYP11A1

value: HTO

tag: hto

value: TotalSeq-C0301 anti-mouse Hashtag 1 Antibody (immunized Adrenal #1), TotalSeq-C0302 anti-mouse Hashtag 2 Antibody (immunized Adrenal #2), TotalSeq-C0303 anti-mouse Hashtag 3 Antibody (immunized Adrenal #3), TotalSeq-C0304 anti-mouse Hashtag 4 Antibody (immunized Spleen #1), TotalSeq-C0305 anti-mouse Hashtag 5 Antibody (immunized Spleen #2), TotalSeq-C0306 anti-mouse Hashtag 6 Antibody (immunized Spleen #3), TotalSeq-C0307 anti-mouse Hashtag 7 Antibody (CFA Spleen #4), TotalSeq-C0308 anti-mouse Hashtag 8 Antibody (CFA Spleen #5), TotalSeq-C0309 anti-mouse Hashtag 9 Antibody (CFA Spleen #6), TotalSeq-C0310 anti-mouse Hashtag 10 Antibody (CFA Adrenal)


title: Adrenalitis (GEX library)

status: Public on Jul 25 2025

type: SRA

description: Library name: Adrenalitis_GEX

library_source: transcriptomic single cell

data_processing:
The BCL files were demultiplexed using Cell Ranger bcl2fastq v5.0.1.
The generated reads were then mapped using 10X Cell Ranger v5.0.1 to the Mus musculus reference genome provided by the Ensembl site (GRCm38, version 102).
Subsequently, the results were processed using Seurat v4.3.0 (Hao et al., 2021) in R v4.2.1. The samples were demultiplexed using hashtag counts. Cells that lacked sufficient hashtag counts or exhibited multiple hashtags were filtered out. Mitochondrial, ribosomal, and T-cell receptor V/J genes were also removed.
Initially, the spleen and adrenal samples were analyzed separately. Each subset underwent normalization, identification of 2,000 variable features, dimensionality reduction, and clustering (with resolutions of 0.8 and 0.9 for the adrenal and spleen subsets, respectively). Contaminating clusters were excluded, and the data subsets were reprocessed using the same pipeline, applying a resolution of 0.8 to both subsets.
The data were then integrated using the CCA integration method (1,050 anchors), following the removal of cells with more than 6% of their transcriptome mapping to mitochondrial genes or those identified as high feature count outliers. The integrated dataset subsequently underwent dimensionality reduction and clustering (resolution of 1).  In total, the final dataset comprised 5,584 cells.
Assembly: GRCm38
Supplementary files format and content: RDS file of finalized scRNA data in Seurat object generated by R, with CSP (HTO) and VDJ (TCR) information in meta data, used directly for manuscript figure generation.
Supplementary files format and content: Standard CSV file formatted according to 10X instructions for CSP mapping with additional column "multiplexed_sample" used to specify samples.

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

tag: treatment

tag: library type

value: GEX


title: COLO320-DM cells Lig3-CUT&Tag

city: Tianjin

first: Luning

last: Qin

address: No.38 Tongyan Road, Haihe Education Park, Tianjin, China

country: China

institute: Nankai university

description:
Library name: sample3
CUT&Tag for Lig3 in 200000 COLO320-DM cells

library_source: genomic

data_processing:
For the original image data of sequencing results, the software Bcl2fastq (v2.20.0.422) was used for base calling, preliminary quality analysis, and the original sequencing data were obtained. The results were stored in the FASTQ file format. The quality assessment of the sequencing data was analyzed using the software FastQC (v0.11.4). The software Cutadapt (version 1.9.1) was utilized to preprocess the original data, filter out low-quality data, and remove contaminating and adapter sequences. The filtered clean sequencing data were aligned and statistically analyzed with the reference genome hg38 using the alignment software bowtie2 (Version: 2.2.6).
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Using the Hieff NGS® Multi-Cut &Tag Library Prep Kit for Illumina® (YEASEN), approximately 200,000 cells were collected, counted, and resuspended in 1× Wash Buffer, followed by the addition of ConA Beads. The mixture was incubated at room temperature for 10 minutes. Next, the cell-magnetic bead complex was resuspended in pre-cooled Primary Antibody Buffer containing lig3 (1:50), YY1 (1:50), H3K4me3 (1:50), and H3K27ac (1:50), and incubated at room temperature for 2 hours. After the incubation, a 1× Dig-300 Buffer containing Anti-mouse Tn5 and Anti-rabbit Tn5 was added to facilitate DNA transposition, which was performed at room temperature for 1 hour. Subsequently, transposase was activated, and the reaction was incubated at 37 °C for 60 minutes. Following transposition, a termination solution containing Proteinase K and a DNA spike-in mix was added, and the reaction was incubated at 55 °C for 30 minutes to digest proteins. Genomic DNA was then purified using DNA Extract Beads.
The library was amplified using HiFi Amplification Mix in a PCR program consisting of an initial 3-minute extension at 72 °C, followed by 3 minutes of denaturation at 95 °C. The amplification cycle included 10 seconds of denaturation at 98 °C, 15 seconds of annealing at 60 °C, and a 1-minute extension at 72 °C. After amplification, the library was purified using DNA Selection Beads, and any residual impurities were removed by magnetic bead recovery and ethanol washing. The beads were air-dried and resuspended in ddH₂O to produce a library suitable for sequencing on the Illumina platform. Library quality was assessed using the Agilent 2100 Bioanalyzer.

tag: cell line

value: colorectal cancer

tag: antibody

value: Mouse monoclonal anti-DNA Ligase III, Santa Cruz, Cat# sc-135883;


title: WCM1078_taz_rep3

city: Boston

first: Varadha Balaji

last: Venkadakrishnan

state: MA

address: 450 Brookline Ave

department: Department of Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: Library name: ne1078_taz3

library_source: transcriptomic

data_processing:
STAR RSEM
Assembly: hg38
Supplementary files format and content: tsv

source_name: prostate

extract_protocol:
RNA was extracted using Qiagen column purification kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: prostate

value: patient-derived organoids

value: WT

value: tazemetostat


title: WCM1078_veh_rep3

description: Library name: ne1078_veh3

value: vehicle


title: DTC20317

city: Zurich

first: Mitchell

last: Levesque

address: Wagistrasse 18

country: Switzerland

institute: University of Zurich

description: 10X Chromium Single Cell 3' v3.1 Chemistry Dual Index

data_processing:
The sequenced reads were processed using the Cell Ranger analysis pipeline v.7.0.1 to generate FASTQ files and align sequencing reads to a pre-built human reference transcriptome version GRCh38-3.0.0 by 10x genomics. The raw binary format output with cell barcodes and unique molecular identifier count results were used for the downstream analysis.
Using the Scanpy tookit, the binary data in hierarchical data format (H5) from each sample were combined into an AnnData object. The basic filtering was performed on the number of genes expressed in the count matrix, total counts per cell and the percentage of counts in mitochondrial genes to reduce the number of poor-quality cells present in the data. The highly variable genes were identified using the built-in function from Scanpy. The doublets were identified using Scrublet and to make each cell comparable, the data is normalized to 10,000 reads per cell and corrected by regressing out using total counts, percentage of the mitochondrial genes expressed and the cell cycle scores. Lastly, the cells expressing high levels of immune cells and CD45+ were excluded from the downstream analysis. For embeddings analysis, the data is corrected using Harmony algorithm to reduce the effects of the sample specific effects, and then the mesenchymal and melanocytic marker expressions data is projected in UMAP.
Assembly: cellranger reference GRCh38-3.0.0
Supplementary files format and content: 10x-Genomics-formatted hdf5 file with observations/cells named by their barcode

source_name: dissociated tumor cells

extract_protocol:
Describe the protocols used to extract and prepare the material to be sequenced:  The 10x Genomics Chromium system was used for single-cell RNA sequencing. Cells were loaded onto a 10x Chromium Controller according to the manufacturer’s specifications to achieve a target of approximately 1000 - 3000 cells per sample. First-strand cDNA synthesis was performed in droplets using 10x Genomics reagents, then cDNA was amplified using a 15 cycle PCR to generate sufficient material for library construction.
Describe the library construction protocol: cDNA was fragmented, end-repaired, and A-tailed following the 10x Genomics protocol.  Adapters containing sequencing primers and sample indices were ligated to the prepared fragments. Size selection was performed using SPRIselect reagent (Beckman Coulter) to select fragments of approximately 400 bp. The quality and size distribution of the final library were assessed using an Agilent Tapestation using D5000 High Sensitivity reagents.
Single-cell RNA-seq (scRNA-seq) library prepared using 10x Genomics Chromium Single Cell 3' Solution. The libraries were sequenced on an Illumina NextSeq 2000 system, aiming for a depth of approximately 20,000 reads per cell, using paired-end sequencing.

value: dissociated tumor cells


title: STING_EX-AC01_2

city: Shanghai

first: Zhichao

last: Ai

state: Shanghai

address: 371 Lishizhen Road

department: Oncology

institute: China Innovation Center of Roche (CICoR)

description:
Library name: 9075X
10x Genomics Single Cell 3’ Library Kit V2.

data_processing:
The quality of sequencing reads was evaluated using FastQC and MultiQC. Cell Ranger v2.2.0 was used to align the sequencing reads (fastq) to the mm10 mouse transcriptome and quantify the expression of transcripts in each cell.
Assembly: mm10
Supplementary files format and content: Matrix files

source_name: Tumour

growth_protocol: 5e106 MC38 transplanted to the back of C57

extract_protocol:
Single cell suspensions were filtered through 40 μm cell strainers and resuspended into PBS containing 0.05% BSA following the 10X Genomics protocol.
Isolated tumor single cell suspension (700–1,200 cells/µL in PBS + 0.04% BSA) are loaded onto a microfluidic platform (e.g., 10x Genomics Chromium) for single-cell encapsulation and barcoding. Reverse transcription is performed using template-switching oligos (TSO) to generate cDNA, followed by amplification and fragmentation. Indexed libraries are prepared via end-repair, A-tailing, and adapter ligation, then pooled and quantified (e.g., Bioanalyzer/Qubit). Sequencing is performed on an Illumina platform (e.g., NovaSeq) with recommended read lengths (e.g., 28 bp Read 1, 91 bp Read 2, 8 bp index). Quality control (QC) includes assessing cDNA yield, library size distribution, and doublet rates. Store libraries at –80°C until sequencing. Raw sequencing reads (FASTQ files) are processed using Cell Ranger (10x Genomics) or similar tools (e.g., STARsolo, Alevin) for alignment (to GRCh38/GRCm38), barcode/UMI correction, and gene counting. Low-quality cells are filtered (mitochondrial reads <20%, gene counts 200–6,000/cell, UMI >500). Data normalization (e.g., SCTransform, LogNormalize) and integration (Harmony, Seurat) are applied to correct batch effects. Dimensionality reduction (PCA, UMAP) and clustering (Louvain, Leiden) identify cell populations, followed by differential gene expression analysis (Wilcoxon, MAST). Cell types are annotated using reference databases (SingleR, Azimuth with manual correction). Results are visualized and exported for downstream analysis.

treatment_protocol: 1 mg/kg EX-AC01 at biweekly frequency, i.e. on days 0, 3, 7 before sample collection.

value: Tumour


title: STING_Control_2

description:
Library name: 9656X
10x Genomics Single Cell 3’ Library Kit V2.

value: Vehicle


title: STING_Control_1

description:
Library name: 9165X
10x Genomics Single Cell 3’ Library Kit V2.


title: HiC data for COLO320-DM cells

description:
Library name: sample01
HiCUT in COLO320-DM cells.

data_processing:
The raw image data files obtained from the Illumina sequencing platform are converted into Sequenced Reads through Base Calling analysis, and the results are stored in the FASTQ file format. Referring to the Distiller - nf pipeline, for the clean data obtained from quality control, the bwa software is used to align the data, and the method parameters are selected as bwa mem -SP. Subsequently, pairtools is used to classify the alignment results. The hichipper package is used for correction and then loops are identified, and reads within the range of 5K - 2M are selected for analysis. Subsequently, the diffloop package is used to perform differential analysis on the loop intensities of different samples. The identified loops are filtered for significant loops using FDR < 0.01 and counts > 2.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were first cross-linked with 1% formaldehyde at room temperature for 10 minutes, followed by quenching with 0.125M glycine for 5 minutes. The cells were then subjected to a secondary cross-linking with 3 mM EGS for 40 minutes, and the cross-linking was quenched with 0.4M glycine for 10 minutes. The doubly cross-linked cells were washed with PBS containing 0.05% bovine serum albumin and permeabilized with 0.05% digitonin at room temperature for 15 minutes. They were subsequently treated with 0.1% SDS at 65 °C for 10 minutes, and SDS was neutralized at 37 °C with 1.8% Triton X-100 for 15 minutes. Chromatin DNA was then digested at 37 °C for 2 hours using 50 U each of MboI and DdeI (NEB), followed by DNA end filling with 15 U Klenow (NEB) and dNTPs at 37 °C for 1 hour. DNA ligation was performed at 16 °C for 4 hours using 50 U T4 DNA Ligase (NEB) to ligate adjacent DNA regions. After washing the cells twice in wash buffer, they were incubated overnight with diluted primary antibody in a Dig-wash buffer containing 2 mM EDTA. The next day, the secondary antibody was added and incubated at room temperature for 1 hour. The cells were washed twice in Dig-Wash buffer to remove unbound antibodies. The pG-Tn5 adapter complex was prepared in Dig-300 buffer and incubated with the cells at room temperature for 1 hour, followed by two washes to remove unbound pG-Tn5. The cells were then resuspended in Tagmentation buffer and incubated at 37 °C for 1 hour. Tagmentation was terminated by incubation at 55 °C for 1 hour in a solution containing 16 mM EDTA, 0.1% SDS, and 0.16 mg/mL protease K. DNA was extracted using phenol-chloroform-isoamyl alcohol and ethanol precipitation.
Library amplification was performed by PCR: 3 minutes at 72 °C, 30 seconds at 98 °C, followed by 16 cycles of 15 seconds at 98 °C, 30 seconds at 60 °C, and 30 seconds at 72 °C, with a final 3-minute extension at 72 °C. The amplified DNA was purified using Ampure XP beads, and the libraries were sequenced on the Illumina NovaSeq platform.


title: WTM3

city: Fort Collins

first: Cali

middle: Madison

last: McEntee

state: CO

address: 910 Moby Dr

department: Health and Exercise Science

institute: Colorado State University

description: Library name: WTM3

data_processing:
Reads were mapped to the mouse genome (mm10) with STAR. Differentially expressed genes were analyzed with DESeq2
Assembly: mm10
Supplementary files format and content: APP-v-LM_normalized_counts.csv
Supplementary files format and content: APPnano-v-APP-normalized_counts.csv
Supplementary files format and content: old-v-young-normalized_counts.csv
Supplementary files format and content: oldnano-v-old-normalized_counts.csv

molecule: polyA RNA

source_name: Hippocampus

extract_protocol:
Hippocampal RNA was isolated using the Zymo Direct-zol miniprep kit (Zymo).
PolyA-selected libraries were generated (Illumina TruSeq kits) according to manufacturer's protocols, and libraries were sequenced on an Illumina NovaSeq 6000 plateform.

value: Hippocampus

value: "non-carrier" littermates

value: control

tag: Sex

value: M

tag: age

value: 4 mo


title: Adrenalitis (VDJ library)

description: Library name: Adrenalitis_TCR

library_source: other

data_processing:
The BCL files were demultiplexed using Cell Ranger bcl2fastq v5.0.1.
The generated reads were then mapped using 10X Cell Ranger v5.0.1 to the Mus musculus reference genome provided by the Ensembl site (GRCm38, version 102).
Subsequently, the results were processed using Seurat v4.3.0 (Hao et al., 2021) in R v4.2.1. The samples were demultiplexed using hashtag counts. Cells that lacked sufficient hashtag counts or exhibited multiple hashtags were filtered out. Mitochondrial, ribosomal, and T-cell receptor V/J genes were also removed.
Initially, the spleen and adrenal samples were analyzed separately. Each subset underwent normalization, identification of 2,000 variable features, dimensionality reduction, and clustering (with resolutions of 0.8 and 0.9 for the adrenal and spleen subsets, respectively). Contaminating clusters were excluded, and the data subsets were reprocessed using the same pipeline, applying a resolution of 0.8 to both subsets.
The data were then integrated using the CCA integration method (1,050 anchors), following the removal of cells with more than 6% of their transcriptome mapping to mitochondrial genes or those identified as high feature count outliers. The integrated dataset subsequently underwent dimensionality reduction and clustering (resolution of 1).  In total, the final dataset comprised 5,584 cells.
Assembly: GRCm38
Supplementary files format and content: RDS file of finalized scRNA data in Seurat object generated by R, with CSP (HTO) and VDJ (TCR) information in meta data, used directly for manuscript figure generation.
Supplementary files format and content: Standard CSV file formatted according to 10X instructions for CSP mapping with additional column "multiplexed_sample" used to specify samples.
Library strategy: TCR-Seq

molecule: other

value: Adrenals or Spleen

value: CD4+ T cells

value: No treatment or immunized by CYP11A1

value: TCR


title: WCM1078_veh_rep1

description: Library name: ne1078_veh1

value: prostate


title: WCM1078_taz_rep1

description: Library name: ne1078_taz1

value: patient-derived organoids


title: WTM2

description: Library name: WTM2


title: WCM154_rescue_dT_PROX1_dTAG_48hr_rep3

description: Library name: VBV114


title: WTF2

description: Library name: WTF2

value: F


title: WTF3

description: Library name: WTF3


title: WCM154_rescue_dT_PROX1_dTAG_48hr_rep1

description: Library name: VBV112


title: WCM154_rescue_dT_PROX1_dTAG_8hr_rep3

description: Library name: VBV108


title: MY1

description: Library name: MY1

value: 8 mo


title: MY2

description: Library name: MY2


title: WCM154_rescue_dT_PROX1_veh_rep3

description: Library name: VBV105

value: vehicle


title: MY3

description: Library name: MY3


title: WCM154_rescue_dT_PROX1_veh_rep2

description: Library name: VBV104


title: WCM154_rescue_dT_PROX1_dTAG_48hr_rep2

description: Library name: VBV113


title: MT2

description: Library name: MT2

value: nanoligomer

value: 18 mo


title: WCM1078_taz_rep2

description: Library name: ne1078_taz2

value: WT

value: tazemetostat


title: WCM154_rescue_dT_PROX1_veh_rep1

description: Library name: VBV103


title: WCM154_rescue_dT_PROX1_dTAG_8hr_rep2

description: Library name: VBV107


title: MT1

description: Library name: MT1

value: Hippocampus


title: WCM154_sgPROX1_2_rep2

description: Library name: VBV101


title: WCM154_rescue_dT_PROX1_dTAG_8hr_rep1

description: Library name: VBV106


title: MO3

description: Library name: MO3

value: control


title: 22Rv1_PROX1_OE_rep3

description: Library name: VBV90

value: cell line


title: STING_EX-AC01_1

description:
Library name: 9070X
10x Genomics Single Cell 3’ Library Kit V2.

value: Tumour


title: MO1

description: Library name: MO1

value: M


title: WTM1

description: Library name: WTM1

value: "non-carrier" littermates

value: 4 mo


title: WCM154_sgPROX1_2_rep3

description: Library name: VBV102


title: MO2

description: Library name: MO2


title: WTF1

description: Library name: WTF1


title: WCM154_sgPROX1_2_rep1

description: Library name: VBV100


title: MT3

description: Library name: MT3


title: 22Rv1_ctrl_rep3

description: Library name: VBV87


title: FY2

description: Library name: FY2


title: FY1

description: Library name: FY1


title: 22Rv1_ctrl_rep2

description: Library name: VBV86


title: FT3

description: Library name: FT3


title: 22Rv1_ctrl_rep1

description: Library name: VBV85


title: C42_PROX1_OE_rep3

description: Library name: VBV84


title: FT1

description: Library name: FT1


title: FT2

description: Library name: FT2


title: C42_PROX1_OE_rep2

description: Library name: VBV83


title: FO3

description: Library name: FO3


title: C42_PROX1_OE_rep1

description: Library name: VBV82


title: 22Rv1_PROX1_OE_rep2

description: Library name: VBV89


title: FO2

description: Library name: FO2


title: C42_ctrl_rep2

description: Library name: VBV80


title: FO1

description: Library name: FO1


title: C42_ctrl_rep1

description: Library name: VBV79


title: ABTM2

description: Library name: ABTM2


title: FY3

description: Library name: FY3


title: WCM154_sgPROX1_1_rep3

description: Library name: VBV75


title: ABTM1

description: Library name: ABTM1


title: WCM154_sgPROX1_1_rep2

description: Library name: VBV74


title: 22Rv1_PROX1_OE_rep1

description: Library name: VBV88


title: ABTF2

description: Library name: ABTF2


title: ABTF3

description: Library name: ABTF3


title: WCM154_sgPROX1_1_rep1

description: Library name: VBV73


title: WCM154_sgINC_rep3

description: Library name: VBV51


title: ABTF1

description: Library name: ABTF1


title: AMTM3

description: Library name: AMTM3


title: C42_ctrl_rep3

description: Library name: VBV81


title: ABCM2

description: Library name: ABCM2


title: WCM154_sgINC_rep1

description: Library name: VBV49


title: ABCM1

description: Library name: ABCM1


title: WCM154_PROX1_rep1

description: Library name: CR24_005

data_processing:
bowtie2 followied by bamCompare (deepTools)
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

extract_protocol: CUT&RUN Epicypher kit was used.

value: pateint-dervied organoids


title: ABCF3

description: Library name: ABCF3


title: WCM154_IgG_rep2

description: Library name: CR24_002

value: prostate


title: ABCF1

description: Library name: ABCF1


title: WCM1262_H3K27ac_rep2

description: Library name: CR22_096


title: WCM154_IgG_rep1

description: Library name: CR24_001


title: WCM1262_H3K27ac_rep1

description: Library name: CR22_095


title: ABCM3

description: Library name: ABCM3


title: Ex14_Tumor_CD8_R1_2

city: Noda-shi

first: Mikiya

last: Tsunoda

state: Chiba

department: Molecular Preventive Medicine

country: Japan

institute: The University of Tokyo

description: Library name: Sample 32

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5.
In MiXCR, Filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics information system: -starting-material=rna, -5-end=no-v-primers-, -3-end=c-primers, -adapters=no-adapters, vParameters.geneFeatureToAlign=VTranscript, -vjAlignmentOrder=JThenV, then identical sequences were assembled and grouped in clones with PCR and sequencing error correlation with the following parameters: -badQualityThreshold=15, –separateByV=true, –separateByJ=true, -only-productive=true, –region-of-interest=CDR3.
The Variable (V) and Joining (J) segment of TCRs were represented in IMGT gene nomenclature. List of final clones were analyzed by VDJtools-1.2.1. Then, the sequencing reads of sample was normalized to the six times of cell count in each sample by “DownSample” command of VDJtools. T-cell clones were determined as TCR reads with the same TCR V segment, J segment and CDR3 nucleotide sequence.
Assembly: IMGT reference sequences of mouse TRB
Supplementary files format and content: text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

source_name: Tumor

growth_protocol: Lewis lung carcinoma (LLC) cells (5 × 10^5 cells /mouse) were inoculated subcutaneously (s.c.) into the left flank, right flank and the left hip of C57BL/6 mice.

extract_protocol:
Tumors were cut into small fragments and digested for 45 minutes at 37°C with 0.2% collagenase (FUJIFILM Wako) and DNase I (Sigma-Aldrich), except for experiments for single-cell analysis, in which tumors were digested with 0.2% collagenase NB8 (Nordmark Pharma GmbH). The cells were then subjected to two-phase density separation with upper 35% Percoll PLUS (GE Healthcare) (1000g, 10 minutes at room temperature). Leukocytes were recovered, washed and resuspended in preparation medium (PM) [5%FBS, 10mM HEPES (Nacalai), Penicillin-Streptomycin (Nacalai) in RPMI-1640 (Nacalai)]. After RBC lysis with ACK buffer [155mM of NH4Cl (Nacalai), 10mM of KHCO3 (Nacalai), and 0.5mM EDTA pH8.0 (NIPPON GENE)] for 1 minute at room temperature, cells were washed and resuspended in PM, and the cell concentrations were measured using Flow-Count fluorospheres (Beckman Coulter) and a CytoFLEX S flow cytometer (Beckman Coulter).Cells were stained with a mix of Fc Block (anti-mouse CD16/CD32 mAb; clone 2.4G2, BioLegend) and fluorophore-conjugated anti-mouse monoclonal antibodies (Supplementary Table 5). Antibody mixtures were prepared using BD Horizon Brilliant Stain Buffer Plus (BD) diluted 5x with FACS buffer (D-PBS(-) supplemented with 2% FBS, and 0.05% Sodium Azide). Staining was performed for 20 minutes at 4°C. Before sorting, T cells were enriched from tumor suspensions by further staining with BD IMag APC Magnetic Particles-DM (BD Biosciences), then placed on magnetic plate. After washing by MACS buffer (D-PBS(-) supplemented with 10% BSA, and 2 mM EDTA pH8.0), APC and APC-Cy7(CD8, mouse TCRb)-positive cells were collected as positive fraction. Cell sorting was performed using a FACS Aria II or Aria III (BD Biosciences). Cells were stained with 5µg/mL of propidium iodide (PI, Sigma-Aldrich) immediately before sorting. Nonviable cells were excluded from the analysis based on forward and side scatter profiles and PI staining. For bulk TCR repertoire analysis and bulk RNA-seq analysis, cells were sorted into Lysis buffer [1% w/v LiDS, 100 mM Tris-HCl pH7.5, 500 mM LiCl, 5 mM dithiothreitol, and 10 mM EDTA pH8.0] and stored at −80°C. Cells were sorted into D-PBS(-) with 10% FBS.
TCR libraries were prepared on purified T cells lysed in lysis buffer [1% LiDS, 100 mM Tris-HCl (pH 7.5), 500 mM LiCl, and 10 mM EDTA]. PolyA RNAs were isolated according to a previous report with some modifications (GSE110711).To perform reverse transcription and template-swiching, beads were then suspended in 10 µL of RT mix [1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP, 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2, 1 U/µL RNaseIn Plus Rnase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1µM of i5-TSO], and incubated for 60 min at 42ºC and immediately cooled on ice. Beads were washed once with with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with Tris-HCl (pH 8.0). To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed as follows. Beads with containing cDNA was resuspended with the 25 µL of first PCR mixture [0.4 µM of primers (i5, Trac_ex, and Trbc_ex), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, #KK2602)], and the thermal cycling was performed as following condition: denaturation at 95°C for 3 min, 10 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min. Then, 2.5 µL of first PCR product was mixed with the 22.5 µl of second PCR mixture [0.35 µM of primers (i5_2nd, i7-BC_mTrac, and i7-BC_mTrbc), and 1x KAPA Hifi Hotstart ReadyMix], , and the thermal cycling was performed as following condition: denaturation at 95°C for 3 min, 18 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min.. The second-PCR products were purified by an Agencort AM Pure XP kit (Bexkman-Coulter, CA, #A63881) at a 0.7:1 ratio of beads to sample, and eluted with 20 µL of Tris-HCl (pH 8.0).To amplify TCR library and add adaptor sequence for next generation sequencer, the third PCR was performed as follows. 5µL of purified second PCR product was mixed with the 20 µl of third PCR mixture [0.4 µM of primers (i5-BC and i7-BC), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, USA, #KK2602)], and the thermal cycling was performed under the same condition as first PCR, excepted for the number of cycles (23 cycles). The third-PCR products were purified as second PCR. The products were pooled and then purified and subjected to dual size selection using ProNex size-selective purification system (Promega) and eluted with 25 μL of Tris-HCl (pH 8.5). Final TCR libraries, whose lengths were about 600 base pairs were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina, USA). Only read2 contained the sequence regarding the definition of T cell clones.

value: Tumor

value: Lewis lung carcinoma

value: lineage-negative (CD11b, B220, NK1.1  Ter119), TCRb+,  CD4-, CD8+  T cells


title: Ex14_Tumor_CD8_R1_3

description: Library name: Sample 33


title: WCM1262_H3K4me3_rep2

description: Library name: CR22_092


title: Ex14_Tumor_CD8_R2_2

description: Library name: Sample 35


title: Ex14_Tumor_CD8_R2_1

description: Library name: Sample 34


title: WCM1262_H3K27me3_rep1

description: Library name: CR22_093


title: WCM154_sgINC_rep2

description: Library name: VBV50

value: patient-derived organoids


title: WCM1262_IgG_rep2

description: Library name: CR22_090


title: Ex14_Tumor_CD8_R1_1

description: Library name: Sample 31


title: Ex14_Tumor_CD8_L2_3

description: Library name: Sample 30


title: WCM1262_IgG_rep1

description: Library name: CR22_089


title: WCM1262_H3K4me3_rep1

description: Library name: CR22_091


title: WCM154_PROX1_rep2

description: Library name: CR24_006


title: Ex14_Tumor_CD8_L2_2

description: Library name: Sample 29


title: Ex14_Tumor_CD8_L2_1

description: Library name: Sample 28


title: ABCF2

description: Library name: ABCF2

value: F


title: WCM1078_H3K27ac_rep1

description: Library name: CR22_087


title: Ex14_Tumor_CD8_L1_3

description: Library name: Sample 27


title: WCM1262_H3K27me3_rep2

description: Library name: CR22_094


title: WCM1078_H3K27ac_rep2

description: Library name: CR22_088


title: WCM1078_H3K27me3_rep2

description: Library name: CR22_086


title: WCM1078_H3K27me3_rep1

description: Library name: CR22_085


title: WCM1078_H3K4me3_rep2

description: Library name: CR22_084


title: WCM1078_H3K4me3_rep1

description: Library name: CR22_083


title: Ex14_Tumor_CD8_H2_3

description: Library name: Sample 24


title: Ex14_Tumor_CD8_L1_2

description: Library name: Sample 26


title: Ex14_Tumor_CD8_H2_2

description: Library name: Sample 23


title: Ex14_Tumor_CD8_L1_1

description: Library name: Sample 25


title: WCM1078_IgG_rep2

description: Library name: CR22_082


title: Ex14_Tumor_CD8_H1_3

description: Library name: Sample 21


title: Ex14_Tumor_CD8_R2_3

description: Library name: Sample 36


title: Ex14_Tumor_CD8_H1_2

description: Library name: Sample 20


title: Ex14_Tumor_CD8_H2_1

description: Library name: Sample 22


title: WCM155_H3K27me3_rep2

description: Library name: CR22_038


title: Ex14_Tumor_CD4_R2_3

description: Library name: Sample 18

value: lineage-negative (CD11b, B220, NK1.1  Ter119), TCRb+,  CD4+, CD8-  T cells


title: Ex14_Tumor_CD8_H1_1

description: Library name: Sample 19

value: WT


title: WCM155_H3K27ac_rep2

description: Library name: CR22_040


title: WCM155_H3K27ac_rep1

description: Library name: CR22_039


title: Ex14_Tumor_CD4_R2_2

description: Library name: Sample 17


title: WCM1078_IgG_rep1

description: Library name: CR22_081


title: WCM155_H3K27me3_rep1

description: Library name: CR22_037


title: Ex14_Tumor_CD4_R2_1

description: Library name: Sample 16


title: WCM155_H3K4me3_rep2

description: Library name: CR22_036


title: WCM155_IgG_rep2

description: Library name: CR22_034


title: WCM155_IgG_rep1

description: Library name: CR22_033


title: WCM155_H3K4me3_rep1

description: Library name: CR22_035


title: Ex14_Tumor_CD4_L2_3

description: Library name: Sample 12


title: Ex14_Tumor_CD4_R1_1

description: Library name: Sample 13


title: Ex14_Tumor_CD4_R1_3

description: Library name: Sample 15


title: WCM154_H3K27ac_rep2

description: Library name: CR22_024


title: Ex14_Tumor_CD4_L2_2

description: Library name: Sample 11


title: Ex14_Tumor_CD4_L1_3

description: Library name: Sample 9


title: Ex14_Tumor_CD4_L2_1

description: Library name: Sample 10


title: FCPN, Layer3, MCI, 328_L3

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

state: New York

address: 140 Old Orangeburg Road

department: Centre for Dementia Research

institute: Research Foundation for Mental Hygiene

description: Library name: 328_L3

data_processing:
The reads with adapter contamination/ low quality were trimmed using Trimmomatic 0.39.
Trimmed sequence reads were aligned to the reference genome (GRCh38) using STAR Aligner. Gene counts were extracted using RSEM.
Downstream Analysis was performed using R with the gene counts obtained from the RSEM. Genes with over 0.1 counts per million were retained followed by TMM normalization.
Assembly: GRCh38
Supplementary files format and content: tab delimited text files with gene counts of all samples per column
Supplementary files format and content: tab delimited text files with gene counts of one sample per one file

source_name: frontal cortex (BA9)

extract_protocol:
Brain tissues obtained from postmortem autopsy cases (n=20) with an antemortem clinical diagnosis of NCI, MCI, and AD from the NIH NeuroBioBank housed at the University of Miami Brain Endowment Bank (UMBEB) were examined. Frozen unfixed 20 um thick tissue sections from BA9 tissue blocks were cut on a cryostat (CM1860 UV, Leica, Buffalo Grove, IL) in the coronal plane and thaw mounted on polyethylene naphthalate (PEN) membrane slides (Leica). Slides were kept under desiccant at -80 °C until used for LCM. Stringent RNase-free precautions were employed, and solutions were made with RNase-free water (ThermoFisher, Waltham, MA). PEN membranes were equilibrated to room temperature (RT) under desiccant (-20 °C for 10 min, 4 °C for 10 min, RT for 1 min) before the Nissl stain procedure (Alldred et al., 2024). Slides were rinsed in phosphate-buffered saline (PBS, pH 7.4), and immersed in a Nissl stain solution (0.18 M sodium acetate, 0.6% acetic acid, 0.1% thionin; Sigma, St. Louis, MO) for 1 min, then rinsed with PBS twice. Slides were air-dried for 5 min and then immediately utilized for LCM of pyramidal neurons. An LCM system (LMD7000; Leica) was employed to identify and microisolate pyramidal neurons using a 40x objective (PL-Fluotar NA 0.60). Neurons from layer III were outlined using the draw/cut tool (Leica LMD version 8.2.1) and collected by gravity into 50 ul of Qiazol extraction solution (Qiagen, Germantown, MD) (Fig. 1 A-C) (Alldred et al., 2024). Captured cells were counted and frozen at -80 °C until 600-800 cells per region were isolated. An average of 9 tissue sections per subject were required to collect sufficient numbers of Nissl-stained layer III pyramidal neurons.RNA from 600-800 pyramidal neurons was purified using miRNase Micro kit (Qiagen) according to manufacturers’ specifications with the DNase digest performed twice sequentially (Alldred et al., 2024).
RNA quality control was assessed (RNA 6000 pico kit, Agilent, Santa Clara, CA). The SMARTer Stranded Total RNA-Seq Kit v3 Pico Input Mammalian (Takara Bio, Mountain View, CA) was employed with 8 ul of input RNA.
Samples were quantified (2100 HS DNA kit; Agilent) with a minimum of 2 nM required for downstream applications (Alldred et al., 2024). Samples were pooled in equimolar concentrations and assayed on the NovaSeq 6000 using the S1 100 Cycle Flow Cell v1.5 (Illumina, San Diego, CA) at the NYU Grossman School of Medicine Genome Technology Center (NYUGSOM GTC).

value: frontal cortex (BA9)

value: layer III pyramidal neurons

tag: diagnosis

value: MCI

tag: layer

value: Female


title: FCPN, Layer3, MCI, 326_L3

description: Library name: 326_L3

value: Male


title: FCPN, Layer3, AD, 327_L3

description: Library name: 327_L3

value: AD


title: FCPN, Layer3, AD, 322_L3

description: Library name: 322_L3


title: Ex14_Tumor_CD4_L1_2

description: Library name: Sample 8


title: Ex14_Tumor_CD4_H2_3

description: Library name: Sample 6


title: FCPN, Layer3, AD, 320_L3

description: Library name: 320_L3


title: FCPN, Layer3, MCI, 325_L3

description: Library name: 325_L3


title: FCPN, Layer3, AD, 317_L3

description: Library name: 317_L3


title: FCPN, Layer3, AD, 313_L3

description: Library name: 313_L3


title: Ex14_Tumor_CD4_H2_2

description: Library name: Sample 5


title: Ex14_Tumor_CD4_H1_3

description: Library name: Sample 3


title: Ex14_Tumor_CD4_H2_1

description: Library name: Sample 4


title: Ex14_Tumor_CD4_R1_2

description: Library name: Sample 14


title: FCPN, Layer3, CTR, 291_L3

description: Library name: 291_L3

value: CTR


title: Ex14_Tumor_CD4_H1_1

description: Library name: Sample 1


title: WCM154_H3K27ac_rep1

description: Library name: CR22_023


title: Hippocampus,  sustained hypoxia group (SH) (10% oxygen, 8 hours/day), rep4

city: Tokyo

first: Yuki

last: Uchida

state: Shinagawa

address: 1-5-8 Hatanodai

department: Department of Physiology

institute: Showa University School of Medicine

description: Library name: Sample 13

data_processing:
Quality control using FastQC
RNA-seq analysis performed using Subio Platform
Illumina bcl2fastq2-v2.19 software was used for basecalling.
Transcriptome sequencing (150 bp paired-end sequencing) was performed on a NovaSeq 6000 (Illumina Inc.).
Adapter sequences and low-quality bases in paired-end reads were removed with fastp (version 0.23.4).
Filtered paired-end reads were mapped to the mouse reference genome (GRCm39) by HISAT2 (version 2.2.1) and expression levels were quantified by StringTie (version 2.2.1).
Assembly: GRCm39
Supplementary files format and content: countdata.csv

source_name: hippocampus

extract_protocol:
Total RNA was extracted from the hippocampi using the RNeasyⓇ Plus Universal Mini Kit (QIAGEN, Tokyo, Japan), according to the manufacturer’s protocol. 1 μg of total RNA was used for the construction of sequencing library.
cDNA libraries (150-bp × 2 paired-end reads) were prepared using the NEBNextⓇ Poly(A) mRNA Magnetic Isolation Module kit (Cat No. E7490) and NEBNEXTⓇ UltraTMII Directional RNA Library Prep Kit (Cat No. E7760) (New England Biolabs, MA, USA).

treatment_protocol: Three groups were maintained for 28 days: IH group (oxygen alternating between 10-21% in 2-minute cycles, 8 hours/day), sustained hypoxia group (SH) (10% oxygen, 8 hours/day), and control group (21% oxygen).

value: hippocampus

value: 10% oxygen, 8 hours/day


title: FCPN, Layer3, AD, 288_L3

description: Library name: 288_L3


title: FCPN, Layer3, AD, 289_L3

description: Library name: 289_L3


title: Hippocampus,  sustained hypoxia group (SH) (10% oxygen, 8 hours/day), rep3

description: Library name: Sample 12


title: FCPN, Layer3, MCI, 276_L3

description: Library name: 276_L3


title: Hippocampus,  sustained hypoxia group (SH) (10% oxygen, 8 hours/day), rep1

description: Library name: Sample 10


title: FCPN, Layer3, CTR, 275_L3

description: Library name: 275_L3


title: FCPN, Layer3, CTR, 316_L3

description: Library name: 316_L3


title: Hippocampus,  IH group (oxygen alternating between 10-21% in 2-minute cycles, 8 hours/day), rep5

description: Library name: Sample 9


title: FCPN, Layer3, CTR, 290_L3

description: Library name: 290_L3


title: FCPN, Layer3, MCI, 273_L3

description: Library name: 273_L3


title: FCPN, Layer3, CTR, 274_L3

description: Library name: 274_L3


title: Ex14_Tumor_CD4_L1_1

description: Library name: Sample 7


title: Hippocampus,  IH group (oxygen alternating between 10-21% in 2-minute cycles, 8 hours/day), rep4

description: Library name: Sample 8


title: Ex14_Tumor_CD4_H1_2

description: Library name: Sample 2


title: FCPN, Layer3, CTR, 272_L3

description: Library name: 272_L3


title: Hippocampus,  IH group (oxygen alternating between 10-21% in 2-minute cycles, 8 hours/day), rep3

description: Library name: Sample 7


title: Hippocampus, control group (21% oxygen, 28 days), rep3

description: Library name: Sample 3

value: 21% oxygen, 28 days


title: NK cells, GFP+, week 3, replicate 2

city: Tübingen

first: Morgana

last: Barroso Oquendo

address: Otfried-Müller-Straße 37

department: Quantitative Biology Center (QBiC)

country: Germany

institute: University of Tuebingen

description:
Library name: QNKC2035AG
QNKC2035AG_17_GFP_plus_NKw3.2

data_processing:
Raw data analysis was performed with the Nextflow-based nf-core/rnaseq (version 1.4.2, https://github.com/nf-core/rnaseq) pipeline. In short, quality control of the FASTQ files was performed using FastQC (version 0.11.8). Adapter trimming was conducted with Trim Galore (version 0.6.4). Reads that passed the quality control were mapped to the reference genome using the STAR aligner (version 2.6.1d). The RNA-seq data quality control was performed with RSeQC (version 3.0.1). Quantification of raw gene expression was performed with featureCounts (version 1.6.4).
Due to signs of significant DNA contamination, a snakemake workflow was established to parallelize the removal of this contamination in all samples simultaneously. The reads were filtered based on gapped alignments (N in CIGAR string of SAM/BAM files), in addition to standard QC filtering (e.g. removal of duplicates, etc). Further filtering was applied to maintain only those gapped mapping reads, that matched with an exon at the start and end of the read, excluding potential DNA derived reads covering exon-intron, intron-exon or intron-intron regions. The filtered reads were extracted from BAM files and converted into FASTQ files using the nf-core/bamtofastq. The new generated FASTQ files were re-run with nf-core/rnaseq (version 1.4.2) and the output used for downstream analysis.
Differential expression analysis was performed using the featureCounts raw read count table as input for the rnadeseq (version 2.2) pipeline, used with the R package (version 4.3.1). The integrated DESeq2 tool (version 1.40.2) utilized the normalized counts to calculate the log2 fold change and assess its statistical significance using the Wald test, reported as p-value. The adjusted p-values (padj) were calculated using the Benjamini-Hochberg correction for multiple testing. Genes with padj≤0.05 were considered differentially expressed.
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: iPSC

growth_protocol: The human iPSC line Nuff C.3 was differentiated into HSPCs using STEMdiff (STEMCELL Technologies) and NK cells on murine OP9-DL1 stroma cells as previously reported (Euchner, Front Immunol, 2020).

extract_protocol:
GFP+ and GFP- NK cell progenitors were sorted using FACS.
RNA libraries were prepared using an input of 500 cells and following the manufacture's protocol for the NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs).

treatment_protocol: RAG-fate mapping reporter consisting of an inverted EGFP flanked by RSS were introduced into the AAVS1 locus of human iPSC using CRISPR/Cas9.

value: iPSC

value: iPSCs generated from human newborn foreskin fbroblasts (NuFF)

value: NK progenitor cells derived from RSS-EGFP+/+

value: GFP+

value: NK cell differentiation

tag: time

value: Week 3


title: NK cells, GFP+, week 3, replicate 3

description:
Library name: QNKC2036AO
QNKC2036AO_18_GFP_plus_NK3.3


title: FCPN, Layer3, CTR, 271_L3

description: Library name: 271_L3


title: Hippocampus, control group (21% oxygen, 28 days), rep4

description: Library name: Sample 4

value: WT


title: Hippocampus,  sustained hypoxia group (SH) (10% oxygen, 8 hours/day), rep5

description: Library name: Sample 14


title: Hippocampus,  IH group (oxygen alternating between 10-21% in 2-minute cycles, 8 hours/day), rep1

description: Library name: Sample 5


title: FCPN, Layer3, CTR, 270_L3

description: Library name: 270_L3

value: frontal cortex (BA9)


title: Hippocampus,  IH group (oxygen alternating between 10-21% in 2-minute cycles, 8 hours/day), rep2

description: Library name: Sample 6


title: NK cells, GFP+, week 3, replicate 1

description:
Library name: QNKC2034A8
QNKC2034A8_16_GFP_plus_NKw3.1


title: Tumor microenvironment Lysm WT

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

country: Spain

institute: CNAG

data_processing:
Pre-processing was done with Cellranger v6.0.1 except for fibroblast data, v4.0.0
Assembly: Mm10
Supplementary files format and content: comma-separated files, count matrices
Supplementary files format and content: comma-separated files, TCR contig information
Supplementary files format and content: comma-separated files, hashing information

source_name: liver metastasis

growth_protocol: C57BL/6J mice, were purchased from Janvier Labs at six weeks of age, and injected at 7-8 weeks. Intrasplenic injections were used for liver colonization by the introduction of dissociated organoids (small 3-4 cell clusters) into the portal circulation.

extract_protocol:
Microdissected liver metastases were chopped with scalpels. Subsequent enzymatic digestion was performed with LiberaseTM (Roche, 5401119001), 10mg/ml DNase I (Roche, 10104159001) in DMEM (Invitrogen, 41966-029) for 90 min at 37 °C, in a shaking water bath. Digested tissue fragments were quenched, filtered through 70μm cell strainer and subsequently, washed with FACS Buffer (PBS with 1% BSA (Roche, 10735086001), 2mM EDTA (Sigma, E5134-500G), 0.05% NaN3 (Sigma, S2002-25G)).  Dead cells were stained with either LIVE/DEAD™ Fixable Dead Cell Stain Kit Yellow, Aqua (ThermoFisher, L34959 & L34957) or Zombie Violet™ Fixable Viability Kit (BioLegend, 423113) or DAPI (Sigma Aldrich, D9542). Samples were Fc-blocked with anti-CD16/32, and then cells were stained for the extracellular markers for 25 min at 4°C.
10x Genomics 3-prime v3.0 (TME and CAFs) and 5-prime v1.0 (T cells)

treatment_protocol: Galunisertib (also known as LY2157299) was synthesized in house and prepared as previously described (Tauriello et al, 2018). Galunisertib or vehicle control was administered by oral gavage in a 0.15 ml volume, twice per day, starting 12-15 days after cell injection for metastasis-initiation experiments, unless otherwise indicated. An 800 mg/kg dose per treatment was used for all experiments. For checkpoint immunotherapy or dual immunotherapy, we used rat anti-PD-L1 (10F.9G2; BioXCell BE0101) or rat anti-IgG2b (LTF-2; BioXCell BE0090) isotype-control antibodies.

value: liver metastasis

value: tumor microenvironment

tag: strain


title: Hippocampus, control group (21% oxygen, 28 days), rep2

description: Library name: Sample 2


title: NK cells, GFP-, week 3, replicate 3

description:
Library name: QNKC2033A0
QNKC2033A0_15_GFP_minus__NKw3.3

value: GFP-


title: NK cells, GFP-, week 3, replicate 2

description:
Library name: QNKC2032AQ
QNKC2032AQ_14_GFP_minus__NKw3.2


title: NK cells, GFP+, week 2, replicate 2

description:
Library name: QNKC2029A7
QNKC2029A7_11_GFP_plus_NKw2.2

value: Week 2


title: ADCKO female mice, DAPI+ NeuN-, replicate 3

city: San Francisco

first: Xianhua

last: Piao

state: CA

institute: University of California, San Francisco

description: 10X Genomics Chromium Single Cell 3' Reagent Kits  v3.1

data_processing:
The demultiplexing, barcoded processing, gene counting were made using Cell Ranger v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: neocortex

extract_protocol:
Flash-frozen mouse neocortex brain tissues were minced on dry ice and transferred to a Dounce homogenizer. The tissues were homogenized in 1.5 mL of Nuclei-Pure Lysis Buffer (Sigma) supplemented with 0.2 U/μL RNase inhibitor (Takara) on ice. The homogenate was filtered through a 40 µm cell strainer to remove large debris and centrifuged at 600g for 5 minutes at 4°C to pellet the nuclei. The pelleted nuclei were washed thrice with 1 mL of nuclei wash buffer, composed of 1% BSA in PBS, 20 mM DTT, and RNase inhibitor, with centrifugation between each wash. The washed nuclei were resuspended in 0.04% BSA in PBS containing RNase inhibitor and incubated with anti-NeuN-Alexa 488 conjugated antibody (1:500) for 40 minutes on ice. Subsequently, the nuclei were stained with DAPI (1:100) for 5 minutes on ice. Nuclei were washed and passed through a 35 µm cell strainer cap of Falcon round-bottom polystyrene test tubes. Using flow cytometry, DAPI+ and DAPI+ NeuN- nuclei were gated and collected from each animal. The nuclei were then pelleted again at 600g for 5 minutes at 4°C and resuspended in 0.04% BSA in PBS. The nuclei were counted for downstream library preparation procedures.
Following nuclei isolation, the snRNA-seq library was prepared using Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 according to the manufacturer’s protocol (10X Genomics).

value: neocortex

value: DAPI+ NeuN- nuclei

value: 6 months old


title: NK cells, GFP-, week 3, replicate 1

description:
Library name: QNKC2031AI
QNKC2031AI_13_GFP_minus__NKw3.1


title: ADCKO female mice, DAPI+ NeuN-, replicate 2


title: SH2_0pt5mM_2

city: Bethesda

first: Jonathan

last: Hernandez

state: MD

address: Building 37

institute: NCI/NIH

description: Library name: SH2_0pt5mM_2

data_processing:
8 mRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using Illumina® Stranded mRNA Prep and paired-end sequencing
Basecalling was performed by RTA (version 3.10.30).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.20) allowing 1 mismatch.
Reads were filtered to retain reads with base quality Q30 and above (~92% retained)
Trimming of adapters and low-quality bases was performed using CutAdapt (v1.18).
STAR (version 2.5.2b) is run in twopass basic mode to align trimmed reads to mm10 genome
Gene-level expression quantificiation  was performed using RSEM (version 1.3.3) and the mm10 (Gencode M12)
differential expression was performed using DESeq2
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains RSEM gene-level counts output.

growth_protocol: KPC177669 cells were grown in DMEM medium containing 10% FBS and antibiotics

extract_protocol:
Total RNA was isolated using RNeasy kit (QIAGEN) according to the manufacturers protocol.
Illumina Stranded mRNA prep

treatment_protocol: KPC177669 cells were grown in DMEM containing either 4mM or 0.5 mM glutamine

value: mouse pancreatic

value: GCN1 knockdown KRASG12D, TP53R172H

value: 0.5 mM Glutamine


title: ADCKO female mice, DAPI+ NeuN-, replicate 1


title: NK cells, GFP+, week 2, replicate 3

description:
Library name: QNKC2030AA
QNKC2030AA_12_GFP_plus_NKw2.3

value: iPSC

value: iPSCs generated from human newborn foreskin fbroblasts (NuFF)


title: Tumor microenvironment Lysm KO


title: SH1_0pt5mM_2

description: Library name: SH1_0pt5mM_2


title: SH1_0pt5mM_1

description: Library name: SH1_0pt5mM_1


title: ADCKO female mice, DAPI+, replicate 3

value: DAPI+ nuclei


title: SCR_4mM_2

description: Library name: SCR_4mM_2

value: Wild Type, KRASG12D, TP53R172H

value: 4mM Glutamine


title: NK cells, GFP-, week 2, replicate 3

description:
Library name: QNKC2027AP
QNKC2027AP_9_GFP_minus__NKw2.3

value: NK progenitor cells derived from RSS-EGFP+/+

value: NK cell differentiation


title: SCR_4mM_1

description: Library name: SCR_4mM_1


title: SCR_0pt5mM_1

description: Library name: SCR_0pt5mM_1


title: ADCKO female mice, DAPI+, replicate 2


title: SCR_0pt5mM_2

description: Library name: SCR_0pt5mM_2


title: ADCKO female mice, DAPI+, replicate 1


title: NK cells, GFP+, week 1, replicate 2

description:
Library name: QNKC2023AR
QNKC2023AR_5_GFP_plus_NKw1.2

value: GFP+

value: Week 1


title: NK cells, GFP-, week 2, replicate 1

description:
Library name: QNKC2025A9
QNKC2025A9_7_GFP_minus__NKw2.1

value: GFP-


title: Hippocampus, control group (21% oxygen, 28 days), rep1

description: Library name: Sample 1

value: hippocampus

value: WT

value: 21% oxygen, 28 days


title: pooled_S5i+10w_S5i+14w_10w+S5i6w_16w+S5i12w

city: Vienna

first: Laura

last: Boccuni

address: Währinger Gürtel 18-20

department: Cardiology

country: Austria

institute: Ludwig Boltzmann Institute for Cardiovascular Research

description: Library name: LB0602

data_processing:
Sequencing data were demultiplexed and mapped with Cell Ranger software version 8.0.1 (10x Genomics) (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Cell Ranger outputs (sample_filtered_feature_bc_matrix) were loaded in R (v.4.4.1), pre-processed and analyzed using Seurat (v.5.1.0) (Hao et al., 2021).
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the homepage (https://satijalab.org/seurat/)
For pseudo-bulk differential expression analysis the package DElegate was used (https://github.com/cancerbits/DElegate) (Hafemaister 2023).
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files
Supplementary files format and content: Comma-separated value (csv) files from hematopoietic cell clusters and aortic mononuclear phagocyte clusters (MPCs) obtain with FindAllMarkers function from Seurat package (https://satijalab.org/seurat/reference/findallmarkers)
Supplementary files format and content: Comma-separated value (csv) files from down-regulated genes in Trem2hiGpnbmhi and Trem2hiSlamf9hi clusters from comparison of S5i16w vs 16w HFD obtained from the findDE() function of the DElegate package.

source_name: Aorta

extract_protocol:
Whole aorta was isolated from ApoE-/- mice and digested with HBSS (Thermo Fischer Scientific), 2 mg/ml Collagenase IV (Aigma-Aldrich) + 50 U/ml DNase I (Sigma-Aldrich) at 37°C for 1h. The resulting suspension was filtered through a 70 mm cell strainer. Red blood cells were lysed with 150 mM NH4Cl, 10 mM KHCO3, and 0.1 mM Na2EDTA and the resulting cell suspension was resuspended in FBS+2% FBS and processed for sc-RNAseq.
Freshly isolated whole aortic cells from a pool of n = 6 mice were fixed with the Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling kit (Cat # CG000478; 10x Genomics) according to manufacturer’s instructions and cryoconserved at -80 °C, until the last sample was processed. All samples had viability ≥ 70%. Libraries were prepared by the NGS facility of the Medical University of Vienna (https://corefacilities.meduniwien.ac.at/en/our-units/genomics-rna/). In brief, libraries were prepared using 10x Chromium Fixed RNA kit, Mouse Transcriptome (Cat #BC PN-1000496; 10x Genomics) according to the manufacturer’s instructions. We employed Chromium Next GEM Chip Q Single Cell Kit (Cat # PN-1000422; 10x Genomics) for Gel beads in emulsion (GEMs) generation. All libraries were quantified by a Qubit 3.0 Fluorometer using Qubit dsDNA HS Assay kit (Thermo Fisher Scientific), and quality was checked using a Bioanalyzer 2100 with High Sensitivity DNA Kit (Agilent).

treatment_protocol: We fed the mice with HFD  [21 % fat and 0.20 % cholesterol (TD88137, ssniff)]. For S5I adminitsration, the inhibitor was dissolved in 5% DMSO and administered at 10mg/kg in a mixture of Nutella and soy milk. The inhibitor was administered either for the whole duration of the HFD or 4 weeks after HFD initiation. 5% DMSO + milk and Nutella were administered in HFD control mice.

value: Aorta

value: Whole aortic cells without red blood cells

value: ApoE-/-

value: pooled male and female

value: 8-12 weeks

value: S5i 10 weeks HFD; S5i 16 weeks HFD; 10 weeks + S5i 6 weeks; 16 weeks + S5i 12 weeks


title: pooled_4w_10w_14w_S5i+4w

description:
Library name: LB0601
.fastq files are generated by lane (2 flowcell lanes per run) resulting in 2 files for each sample for the 2 lanes of the flowcell, which have to be used all together for any downstream analysis. 4 samples have been pooled into one chip: LB06001, LB06002, LB06003, LB06004 belong to raw file LB0601*; LB06005, LB06006, LB06007, LB06008 belong to raw file LB0602*

value: 4 weeks HFD; 10 weeks HFD; 16 weeks HFD; S5i 4 weeks


title: NK cells, GFP+, week 1, replicate 3

description:
Library name: QNKC2024A1
QNKC2024A1_6_GFP_plus_NKw1.3

value: iPSC

value: iPSCs generated from human newborn foreskin fbroblasts (NuFF)


title: NK cells, GFP+, week 2, replicate 1

description:
Library name: QNKC2028AX
QNKC2028AX_10_GFP_plus_NKw2.1

value: NK progenitor cells derived from RSS-EGFP+/+

value: Week 2


title: 1025_2024-Veh + PDL1

city: Barcelon

first: Lidia

last: Mateo

address: C/ Baldiri Reixac 10

institute: Institute for Research in Biomedicine (IRB Barcelona)

data_processing:
Single-end reads were aligned to the mouse genome ENSEMBLE_mmusculus_GRCm38.102.primary_assembly using STAR (v2.7.10a).
SAM files were converted to BAM files and sorted using sambamba-0.8.2.
The count matrix was generated with Rsubread with ENSEMBLE_mmusculus_GRCm38 annotation.
Assembly: GRCm38 (mm10)
Supplementary files format and content: featureCounts.tsv is a tab-delimited text file that contains the number of reads mapped to each gene (rows) for each sample (columns).

extract_protocol:
Whole individual metastases were excised from livers ex vivo and mechanically disaggregat¬ed in 1 ml of Trizol (Life Technologies, 15596018) using a tissue disruptor. Disaggregat¬ed tissues in Trizol were stored in -80ºC until processing. For RNA extraction, samples in Trizol were thawed. 200μl of chloroform (Sigma, 372978) was then added and samples were vigorously mixed for 15 seconds. Mixed samples were centrifuged at 12.000 g for 15 minutes at 4ºC, after which a colorless upper phase containing the RNA was transferred into a new Eppendorf, and mixed with one volume of 70% ethanol. The mix was then processed using a PureLink® RNA Mini Kit (Life Technologies, 12183025) following the manufacturer’s specifications. RNA was eluted using distilled water (Invitrogen, 10977-035) and the concentration was determined using the Nanodrop 1000 spectrophotometer (ThermoFisher).
RNA libraries were prepared for sequencing using the kits Illumina® Stranded mRNA Prep, Ligation (20040534) and IDT® for Illumina® RNA UD Indexes Set A, Ligation (20040553), following manufacturer´s instructions and 10 cycles of amplification.

value: liver metastasis

value: liver metastatic cell originated from colorectal primary tumor

value: MTO129 cells are APKT (Apc loss, P53 loss and Tgfbr2 loss, Kras-G12D oncogenic allele)

value: Veh + PDL1


title: ADCKO male mice, DAPI+ NeuN-, replicate 3

value: neocortex

value: DAPI+ NeuN- nuclei

value: 6 months old


title: SH2_0pt5mM_1

description: Library name: SH2_0pt5mM_1

value: mouse pancreatic

value: GCN1 knockdown KRASG12D, TP53R172H

value: 0.5 mM Glutamine


title: 1021_2024-Veh

value: Veh


title: ADCKO male mice, DAPI+ NeuN-, replicate 2


title: 1023_2024-LY + PDL1

value: LY + PDL1


title: 1020_2024-Veh


title: NK cells, GFP-, week 2, replicate 2

description:
Library name: QNKC2026AH
QNKC2026AH_8_GFP_minus__NKw2.2

value: GFP-

value: NK cell differentiation


title: 1019_2024-Veh + PDL1


title: ADCKO male mice, DAPI+ NeuN-, replicate 1


title: NK cells, GFP-, week 1, replicate 3

description:
Library name: QNKC2021AB
QNKC2021AB_3_GFP_minus__NKw1.3

value: iPSC

value: iPSCs generated from human newborn foreskin fbroblasts (NuFF)

value: Week 1


title: 1018_2024-Veh + PDL1

value: liver metastasis


title: 1017_2024-Veh

value: liver metastatic cell originated from colorectal primary tumor


title: ADCKO male mice, DAPI+, replicate 3

value: DAPI+ nuclei


title: 1015_2024-LY

value: MTO129 cells are APKT (Apc loss, P53 loss and Tgfbr2 loss, Kras-G12D oncogenic allele)

value: LY


title: NK cells, GFP-, week 1, replicate 2

description:
Library name: QNKC2020A3
QNKC2020A3_2_GFP_minus__NKw1.2

value: NK progenitor cells derived from RSS-EGFP+/+


title: 1014_2024-LY + PDL1


title: 1013_2024-LY


title: 1010_2024-LY


title: AGS, sgSETD1A

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
Basecalls were performed using bcl2fastq.
Sequenced reads from RNA-seq experiments were aligned by using HISAT2.
FPKM was extracted using Cufflinks.
Assembly: hg19
Supplementary files format and content: tab-deliminated text file included TPM valuse for each sample

source_name: AGS

growth_protocol: RPMI1640, 10% fetal bovine serum, 1x penicillin/streptmycin. AGS cells were cultured in RPMI1640 containing additional 1% non-essential amino acid. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was extracted by using the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Doxycycline was prepared to a stock solution at a concentration of 1 mg/mL in PBS and used as 1:1000 dilution.

value: AGS

value: Human gastric cancer cell line

value: SETD1A knockout

value: Doxycycline 6 days


title: kd_sh2_2

description:
Library name: C2_S6
GCN1 knockout shRNA2 replicate 2

data_processing:
6 RNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing.
Basecalling was performed by RTA (version 3.9.2).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.20) allowing 1 mismatch.
Reads were filtered to retain reads with base quality Q30 and above (~92% retained)
Trimming of adapters and low-quality bases was performed using CutAdapt (v1.18).
STAR (version 2.5.2b) is run in twopass basic mode to align trimmed reads to mm10 genome
Gene-level expression quantificiation  was performed using RSEM (version 1.3.3) and the hg38 (Gencode 21)
differential expression was performed using DESeq2
Assembly: hg38
Supplementary files format and content: Tab-delimited text file contains RSEM gene-level counts output.

growth_protocol: Human pancreatic KLM1 control and GCN1 knockdown cells were grown in DMEM with 10% FBS and antibiotics

treatment_protocol: No treatment

value: Pancreatic

value: KRASG12A, TP53M273I


title: NK cells, GFP+, week 1, replicate 1

description:
Library name: QNKC2022AJ
QNKC2022AJ_4_GFP_plus_NKw1.1

value: GFP+


title: ADCKO male mice, DAPI+, replicate 2

value: neocortex

value: 6 months old


title: kd_sh2_1

description:
Library name: C1_S5
GCN1 knockout shRNA2 replicate 1


title: 1011_2024-LY + PDL1

value: LY + PDL1


title: ADCon female mice, DAPI+ NeuN-, replicate 3

value: DAPI+ NeuN- nuclei


title: kd_sh1_1

description:
Library name: B1_S3
GCN1 knockout shRNA1 replicate 1


title: ADCon female mice, DAPI+ NeuN-, replicate 2


title: cntrl2

description:
Library name: A2_S2
Control Replicate 2


title: cntrl1

description:
Library name: A1_S1
Control Replicate 1


title: AGS, sgSETD1A, H3K36me3, ChIP

data_processing:
Basecalls were performed using bcl2fastq.
Data were mapped to the University of California Santa Cruz human genome assembly (hg19) using Bowtie2 and duplicated reads were removed using Picard tools.
bigwig files were generated using HOMER software.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: RPMI1640, 10% fetal bovine serum, 1x penicillin/streptmycin, 1% non-essential amino acid. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. For SETD1A, RNAP2, Ser2P and H3K36me3 ChIP, we fixed cells with 2 mM DSG for 30 min before formaldehyde fixation. After washing and cell lysis, nuclei pellets were sonicated by using Picoruptor (Diagenode)
Libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems).


title: DMNQ_rep4

description: Library name: LB01012

data_processing:
Data were processed using the ATAC-seq pipeline from the nf-core framework (nfcore/atacseq v2.0;  Ewels et al., 2020; https://zenodo.org/record/3965985#.YA8a8GRKjZk) in conjunction with Docker (version 20.10.8; Merkel, 2014).
The command used was " nextflow run nf-core/atacseq --input design.csv --genome GRCm38 -profile docker -r 2.0 --read_lenght 50 --macs_gsize 2913022398".
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/atacseq).
Assembly: hg38
Supplementary files format and content: Normalized genome-wide bigWig coverage files included in the mergedReplicate folder of the nfcore pipeline.
Supplementary files format and content: Microsoft Excel Spreadsheet (xlsx) files holding the name of every annotated differential accessible region (DAR) obtained from differential analysis (DiffBind) of M0 vs H2O2 datasets and the resulting fold change (fold),  p-value and FDR.
Supplementary files format and content: Microsoft Excel Spreadsheet (xlsx) files holding the name of every annotated differential accessible region (DAR) obtained from differential analysis (DiffBind) of M0 vs DMNQ datasets and the resulting fold change (fold),  p-value and FDR. In the second sheet are listed annotated STAT5 target genes.

source_name: primary human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from whole blood via density gradient centrifugation using lymphocyte separation medium (PromoCell). Monocytes were isolated via adherence to plastic treated tissue culture plates. Monocytes were differentiated into macrophages for 7 days in differentiation medium [RPMI 1640 medium (Sigma-Aldrich) supplemented with 100ng/ml human macrophage colony stimulating factor (M-CSF, Biolegend), 10% fetal bovine serum (FBS, Biochrome Millipore), 100U/ml penicillin, 100U/ml streptomycin, 0.25µg/ml fungizone and 2mM L-glutamine (all Gibco)] with 2 medium changes in between. Additionally, cells were stimulated with either H2O2 or DMNQ during the differentiation period.

extract_protocol:
100.000 cells were washed twice in 1 mL ice-cold PBS, by centrifugation at 500 g for 5 min. Pellets were resupended in 100 µL ice-cold ATAC Lysis Buffer and processed with the ATAC.seq kit (Cat # 53150; Active Motif) according to manufacturer's instructions.
33.5 µl tagmented DNA were mixed with 2.5 µl I7 index primer, 2.5 µl 2.5 uM I5 index primer (dual indexing), 1 µl dNTP, 10 µl 5x Q5 Reaction buffer and 0.5 µl Q5 Polymerase and processed accordingly to manufacturer's instructions.

treatment_protocol: hMDM were treated for 24h with either 100 µM H2O2 or 0.2 µM DMNQ or left untreated (M0).

tag: individual

value: DMNQ


title: AGS, sgSETD1A, Ser2P, ChIP


title: ADCon female mice, DAPI+, replicate 3


title: DMNQ_rep3

description: Library name: LB01009

value: primary human monocyte-derived macrophages


title: ADCon female mice, DAPI+, replicate 2

value: DAPI+ nuclei


title: DMNQ_rep2

description: Library name: LB01006


title: AGS, sgEmpty, Ser2P, ChIP

value: SETD1A wt


title: DMNQ_rep1

description: Library name: LB01003


title: ADCKO male mice, DAPI+, replicate 1


title: NK cells, GFP-, week 1, replicate 1

description:
Library name: QNKC2019A0
QNKC2019A0_1_GFP_minus__NKw1.1

value: iPSC

value: iPSCs generated from human newborn foreskin fbroblasts (NuFF)

value: GFP-

value: NK cell differentiation

value: Week 1


title: kd_sh1_2

description:
Library name: B2_S4
GCN1 knockout shRNA1 replicate 2


title: ADCon female mice, DAPI+, replicate 1

description: 10X Genomics Chromium Single Cell 3' Reagent Kits  v3.1


title: H2O2_rep4

description: Library name: LB01011


title: AGS, sgSETD1A, RNAP2, ChIP

value: AGS

value: Human gastric cancer cell line

value: SETD1A knockout

value: Doxycycline 6 days


title: ADCon female mice, DAPI+ NeuN-, replicate 1

value: neocortex


title: ADCon male mice, DAPI+ NeuN-, replicate 3

value: 6 months old


title: H2O2_rep3

description: Library name: LB01008


title: AGS, sgSETD1A, SETD1A, spikein ChIP


title: AGS, sgEmpty, RNAP2, ChIP


title: H2O2_rep2

description: Library name: LB01005


title: M0_rep4

description: Library name: LB01010

value: untreated


title: AGS, sgEmpty, SETD1A, spikein ChIP


title: M0_rep2

description: Library name: LB01004


title: M0_rep3

description: Library name: LB01007


title: Con male mice, DAPI+ NeuN-, replicate 4

value: DAPI+ NeuN- nuclei


title: ADCon male mice, DAPI+, replicate 3


title: M0_rep1

description: Library name: LB01001


title: ADCon male mice, DAPI+ NeuN-, replicate 1


title: U2940, IRF4-KO, replicate 2

city: Vancouver

first: Gerben

last: Duns

state: BC

address: 675 West 10th Ave

department: Lymphoid Cancer Research

country: Canada

institute: BC Cancer

description: Library name: U2940_KO21_2

data_processing:
libraries were aligned to the genome build GRCh37 using BWA MEM.
Deeptools v.3.5.111 was used to generate BigWig files for plotting and visualization, normalizing using reads per kilobases per million mapped reads (rpkm), with parameters of “ --ignoreDuplicates --samFlagExclude 1028 --minMappingQuality 5 --binSize 20 –extendReads”
Genome browser snapshots were visualized on the UCSC Genome Browser
MACS v.2.2.7.1 was used to call narrow peaks using the parameters “-f BAMPE --seed 1234 -B --extsize 120” and high confidence peak regions were selected using a q-value threshold of 0.1.
Assembly: GRCh37
Supplementary files format and content: bigWig, narrowPeak

source_name: cell line

growth_protocol: The U-2940 cells were cultured in Roswell Park Memorial Institute-1640 medium (RPMI-1640) supplemented with 10% Fetal Bovine Serum (FBS) (Corning, catalog no. 35-077-CV). Karpas-1106p cells were cultured in RPMI-1640 supplemented with 20% FBS. All cell lines were maintained at 37°C in a 5% CO₂ incubator.

extract_protocol:
libraries were prepared using the Active Motif ATAC Library Prep Kit (catalog no. 53150) according to the manufacturer’s instructions. Briefly, 200,000 cells per sample were pelleted and washed with cold PBS. The cells were lysed to release nuclei, which were immediately subjected to transposition reactions.
The transposition reaction was performed using the enzyme and buffer provided in the kit to tag and fragment accessible chromatin regions. After incubation at 37°C for 60 minutes, transposed DNA was purified using the purification columns included in the kit. The purified DNA was amplified using PCR to generate sequencing-ready libraries. The final libraries were purified, and their quality and size distribution were assessed using a Bioanalyzer 2100 (Agilent Technologies). Libraries were quantified using a Qubit fluorometer (Thermo Fisher Scientific) before being sequenced on an Illumina’s NexSeq 550 (75 nt reads, paired end).

value: cell line

value: primary mediastinal B-cell lymphoma-derived cells


title: Con male mice, DAPI+, replicate 4

value: DAPI+ nuclei


title: AGS, wt, E2F4, ChIP

value: wt


title: U2940, IRF4-KO, replicate 1

description: Library name: U2940_KO21_1


title: U2940, IRF4-WT, replicate 2

description: Library name: U2940_con3_2


title: AGS, wt, SETD1A, ChIP


title: ADCon male mice, DAPI+, replicate 1


title: AGS, sgEmpty

value: SETD1A wt


title: 120815_R2

description: 10X Chromium Single Cell 3' v3.1 Chemistry Dual Index

data_processing:
The sequenced reads were processed using the Cell Ranger analysis pipeline v.7.0.1 to generate FASTQ files and align sequencing reads to a pre-built human reference transcriptome version GRCh38-3.0.0 by 10x genomics. The raw binary format output with cell barcodes and unique molecular identifier count results were used for the downstream analysis.
Using the Scanpy tookit, the binary data in hierarchical data format (H5) from each sample were combined into an AnnData object. The basic filtering was performed on the number of genes expressed in the count matrix, total counts per cell and the percentage of counts in mitochondrial genes to reduce the number of poor-quality cells present in the data. The highly variable genes were identified using the built-in function from Scanpy. The doublets were identified using Scrublet and to make each cell comparable, the data is normalized to 10,000 reads per cell and corrected by regressing out using total counts, percentage of the mitochondrial genes expressed and the cell cycle scores. Lastly, the cells expressing high levels of immune cells and CD45+ were excluded from the downstream analysis. For embeddings analysis, the data is corrected using Harmony algorithm to reduce the effects of the sample specific effects, and then the mesenchymal and melanocytic marker expressions data is projected in UMAP.
Assembly: cellranger reference GRCh38-3.0.0
Supplementary files format and content: 10x-Genomics-formatted hdf5 file with observations/cells named by their barcode

extract_protocol:
Describe the protocols used to extract and prepare the material to be sequenced:  The 10x Genomics Chromium system was used for single-cell RNA sequencing. Cells were loaded onto a 10x Chromium Controller according to the manufacturer’s specifications to achieve a target of approximately 1000 - 3000 cells per sample. First-strand cDNA synthesis was performed in droplets using 10x Genomics reagents, then cDNA was amplified using a 15 cycle PCR to generate sufficient material for library construction.
Describe the library construction protocol: cDNA was fragmented, end-repaired, and A-tailed following the 10x Genomics protocol.  Adapters containing sequencing primers and sample indices were ligated to the prepared fragments. Size selection was performed using SPRIselect reagent (Beckman Coulter) to select fragments of approximately 400 bp. The quality and size distribution of the final library were assessed using an Agilent Tapestation using D5000 High Sensitivity reagents.
Single-cell RNA-seq (scRNA-seq) library prepared using 10x Genomics Chromium Single Cell 3' Solution. The libraries were sequenced on an Illumina NextSeq 2000 system, aiming for a depth of approximately 20,000 reads per cell, using paired-end sequencing.

value: melanoma


title: U2940, IRF4-C99R, replicate 2

description: Library name: U2940_C99R1_2


title: U2940, IRF4-C99R, replicate 1

description: Library name: U2940_C99R1_1


title: U2940, IRF4-WT, replicate 1

description: Library name: U2940_con3_1


title: CKO female mice, DAPI+ NeuN-, replicate 3


title: 120815_R1


title: Karpas-1106, IRF4-WT, replicate 2

description: Library name: Kar1106p_con26_2


title: CKO female mice, DAPI+ NeuN-, replicate 2


title: Karpas-1106, IRF4-C99R, replicate 1

description: Library name: Kar1106p_C99R13_1


title: Karpas-1106, IRF4-C99R, replicate 2

description: Library name: Kar1106p_C99R13_2


title: Karpas-1106, IRF4-WT, replicate 1

description: Library name: Kar1106p_con26_1


title: DTC110221_R1

value: dissociated tumor cells


title: CKO female mice, DAPI+ NeuN-, replicate 1


title: AGS, sgEmpty, H3K36me3, ChIP


title: DTC102119_R2


title: U2940, IRF4-KO, untreated, biol rep 18

description: Library name: U2940_IRF4KO_18

data_processing:
RNA-seq reads were aligned to the GRCh38 reference genome, and per-gene counts were generated using the STAR aligner.
Counts were normalized using the trimmed mean of M-values (TMM) method and scaled to log2-transformed counts per million (CPM)
Assembly: GRCh38
Supplementary files format and content: txt files include log2-transformed counts per million (CPM)

growth_protocol: The DOHH-2 and U-2940 cells were cultured in Roswell Park Memorial Institute-1640 medium (RPMI-1640) supplemented with 10% Fetal Bovine Serum (FBS) (Corning, catalog no. 35-077-CV). Karpas-1106p cells were cultured in RPMI-1640 supplemented with 20% FBS. All cell lines were maintained at 37°C in a 5% CO₂ incubator.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat no. 74104) according to the manufacturer’s instructions. Briefly, cells were lysed in RLT buffer supplemented with β-mercaptoethanol, and homogenized by pipetting. The lysate was then mixed with ethanol and loaded onto a silica column. Following a series of wash steps, RNA was eluted in RNase-free water. RNA concentration and purity were assessed using a spectrophotometer.
200 ng of RNA was used to construct libraries using the Illumina Stranded mRNA Prep Ligation Kit (Illumina, catalog no. 20040534)


title: U2940, IRF4-C99R, untreated, biol rep 16

description: Library name: U2940_C99R_16


title: U2940, IRF4-KO, untreated, biol rep 21

description: Library name: U2940_IRF4KO_21


title: U2940, IRF4-KO, untreated, biol rep 19

description: Library name: U2940_IRF4KO_19


title: CKO female mice, DAPI+, replicate 3


title: CKO female mice, DAPI+, replicate 2


title: DTC102119_R1


title: DTC110221_R2


title: U2940, IRF4-C99R, untreated, biol rep 11

description: Library name: U2940_C99R_11


title: U2940, IRF4-C99R, untreated, biol rep 1

description: Library name: U2940_C99R_1


title: U2940, WT, biol rep 4

description: Library name: U2940_WT_con4


title: DTC81621MM_R1


title: DTC81621MM_R2


title: CKO male mice, DAPI+ NeuN-, replicate 3


title: CKO male mice, DAPI+ NeuN-, replicate 2


title: U2940, IRF4-C99R, untreated, biol rep 8

description: Library name: U2940_C99R_8


title: 990922_STK11_R2

value: STK11 knockout


title: U2940, WT, biol rep 3

description: Library name: U2940_WT_con3


title: Karpas1106p, IRF4-C99R, untreated, biol rep 14

description: Library name: Kar1106-C99R-14


title: 990922_STK11_R1


title: CKO male mice, DAPI+ NeuN-, replicate 1


title: Karpas1106p, IRF4-C99R, untreated, biol rep 13

description: Library name: Kar1106-C99R-13


title: U2940, IRF4-C99R, untreated, biol rep 14

description: Library name: U2940_C99R_14


title: CKO male mice, DAPI+, replicate 3


title: 990922_SCR_R2

value: scrambled


title: Karpas1106p, IRF4-C99R, untreated, biol rep 2

description: Library name: Kar1106-C99R-2


title: Karpas1106p, WT, untreated, biol rep 27

description: Library name: Kar1106-con27


title: 990922_SCR_R1


title: U2940, WT, biol rep bulk_2

description: Library name: U2940_WT_bulk_2


title: Karpas1106p, WT, untreated, biol rep B

description: Library name: Kar1106-conB


title: CKO male mice, DAPI+, replicate 2


title: Karpas1106p, WT, untreated, biol rep 26

description: Library name: Kar1106-con26


title: SkMel28_Ctrl_HCL_R2


title: Karpas1106p, WT, untreated, biol rep 8

description: Library name: Kar1106-con8


title: Karpas1106p, IRF4-C99R, untreated, biol rep B

description: Library name: Kar1106-C99R-B


title: Con female mice, DAPI+ NeuN-, replicate 3


title: SkMel28_Ctrl_HCL_R1


title: Hippocampus,  sustained hypoxia group (SH) (10% oxygen, 8 hours/day), rep2

description: Library name: Sample 11

value: hippocampus

value: WT

value: 10% oxygen, 8 hours/day


title: SkMel28_Tgfb_R2

value: TGF-β


title: experiment5_Uextract 7d_rep3

city: Hang Zhou

first: Wenya

last: Zhang

address: No. 600 Dunyu Road

institute: Westlake University

description:
Library name: Sample 89
column name in extract experiments counts.xlsx: Uex7d_3

data_processing:
kallisto 0.46.2. R 4.0.5 and tximport 1.18.0 were used for alignment
Assembly: GCA_000572305.1 S. mediterranea reference transcriptome (smed_20140614)
Supplementary files format and content: csv files incude raw counts for each sample

organism: Schmidtea mediterranea

source_name: planarian SiRNeoblast

growth_protocol: The culture medium, comprising KnockOut DMEM (ThermoFisher, 10829018), 100× non-essential amino acid solution (Gibco, 11140050), 100× vitamin solution (Gibco, 11120052), 100× sodium pyruvate (Gibco, 11360070), 100× Pen/Strep (Gibco, 15070063), and 20% heat-inactivated FBS (Sigma, F8318). 22℃, 5% CO2

extract_protocol:
2× lysis buffer (Plastech, XR2301) supplemented with RNase inhibitor (Vazyme, R301).
Reverse transcription was performed using 1M Betaine and LNA-modified TSO (template switching oligo). PCR amplification was performed with KAPA HiFi HotStart polymerase (Roche, KK2601) and ISPCR primers. The resulting PCR products were purified with AMPure XP bead (Beckman, A63881). Tagmentation was performed with Tn5 transposase (Vazyme, TD501), followed by indexing PCR with dual barcodes (i5/i7).

treatment_protocol: experiment1,  SiRNeoblasts were cultured on the flat substrate; experiment2,  SiRNeoblasts were cultured in the aggrewell plate or flat plate conditions for 1 day; experiment3, SiRNeoblasts were cultured in U-bottom plate or 100Pa PA gel or flat plate conditions for 1 day/2 days/3 days; experiment4, SiRNeoblasts were cultured in HFF1 feeder or MEF feeder or flat plate conditions for 1 day/3 days; experiment5, SiRNeoblasts were cultured in U-bottom plate-extract or U-bottom plate+extract  or flat -extract conditions for 1 day/3 days/7 days.

value: planarian SiRNeoblast

value: cells cultured in U plate with planarian extract for 7d

tag: batch


title: experiment5_Uextract 3d_rep3

description:
Library name: Sample 86
column name in extract experiments counts.xlsx: Uex3d_3

value: cells cultured in U plate with planarian extract for 3d


title: experiment5_Uextract 7d_rep2

description:
Library name: Sample 88
column name in extract experiments counts.xlsx: Uex7d_2


title: Con female mice, DAPI+ NeuN-, replicate 1

value: neocortex

value: DAPI+ NeuN- nuclei

value: 6 months old


title: experiment5_Uextract 3d_rep2

description:
Library name: Sample 85
column name in extract experiments counts.xlsx: Uex3d_2


title: CKO male mice, DAPI+, replicate 1

value: DAPI+ nuclei


title: experiment5_Uextract 3d_rep1

description:
Library name: Sample 84
column name in extract experiments counts.xlsx: Uex3d_1


title: experiment5_Uextract 1d_rep3

description:
Library name: Sample 83
column name in extract experiments counts.xlsx: Uex1d_3

value: cells cultured in U plate with planarian extract for 1d


title: SkMel28_Vem_R2

value: vemurafenib


title: Con female mice, DAPI+, replicate 3


title: experiment5_Uextract 1d_rep2

description:
Library name: Sample 82
column name in extract experiments counts.xlsx: Uex1d_2


title: Con female mice, DAPI+, replicate 2


title: Karpas1106p, WT, untreated, biol rep 7

description: Library name: Kar1106-con7

value: cell line

value: primary mediastinal B-cell lymphoma-derived cells


title: experiment5_Uextract 1d_rep1

description:
Library name: Sample 81
column name in extract experiments counts.xlsx: Uex1d_1


title: SkMel28_Vem_R1

value: melanoma


title: SkMel28_Ctrl_DMSO_R2


title: experiment5_U 7d_rep1

description:
Library name: Sample 78
column name in extract experiments counts.xlsx: U7d_1

value: cells cultured in U plate for 7d


title: experiment5_U 7d_rep2

description:
Library name: Sample 79
column name in extract experiments counts.xlsx: U7d_2


title: H2O2_rep1

description: Library name: LB01002

value: primary human monocyte-derived macrophages


title: Con female mice, DAPI+, replicate 1


title: experiment5_U 3d_rep3

description:
Library name: Sample 77
column name in extract experiments counts.xlsx: U3d_3

value: WT

value: cells cultured in U plate for 3d


title: Con female mice, DAPI+ NeuN-, replicate 2


title: Con male mice, DAPI+ NeuN-, replicate 3


title: experiment5_Uextract 7d_rep1

description:
Library name: Sample 87
column name in extract experiments counts.xlsx: Uex7d_1


title: experiment5_U 3d_rep2

description:
Library name: Sample 76
column name in extract experiments counts.xlsx: U3d_2


title: SkMel28_Ctrl_DMSO_R1


title: SkMel28_Tgfb_R1

value: TGF-β


title: experiment5_U 1d_rep3

description:
Library name: Sample 74
column name in extract experiments counts.xlsx: U1d_3

value: planarian SiRNeoblast

value: cells cultured in U plate for 1d


title: A375_Vem_R2


title: Con male mice, DAPI+ NeuN-, replicate 1


title: experiment5_U 7d_rep3

description:
Library name: Sample 80
column name in extract experiments counts.xlsx: U7d_3


title: experiment5_U 3d_rep1

description:
Library name: Sample 75
column name in extract experiments counts.xlsx: U3d_1


title: A375_Vem_R1

description: 10X Chromium Single Cell 3' v3.1 Chemistry Dual Index


title: experiment5_U 1d_rep2

description:
Library name: Sample 73
column name in extract experiments counts.xlsx: U1d_2


title: experiment5_U 1d_rep1

description:
Library name: Sample 72
column name in extract experiments counts.xlsx: U1d_1


title: experiment5_0d_rep3

description:
Library name: Sample 71
column name in extract experiments counts.xlsx: POS_3

value: non cultured cells


title: A375_Ctrl_NAK_R2


title: experiment5_0d_rep1

description:
Library name: Sample 69
column name in extract experiments counts.xlsx: POS_1


title: experiment5_flat 7d_rep3

description:
Library name: Sample 68
column name in extract experiments counts.xlsxv: flat7d_3

value: cells cultured in flat plate for 7d


title: Con male mice, DAPI+, replicate 3

description: 10X Genomics Chromium Single Cell 3' Reagent Kits  v3.1

value: neocortex


title: Con male mice, DAPI+, replicate 2

value: 6 months old


title: Con male mice, DAPI+, replicate 1

value: DAPI+ nuclei


title: Con male mice, DAPI+ NeuN-, replicate 2

value: DAPI+ NeuN- nuclei


title: experiment5_flat 7d_rep2

description:
Library name: Sample 67
column name in extract experiments counts.xlsx: flat7d_2


title: experiment5_flat 7d_rep1

description:
Library name: Sample 66
column name in extract experiments counts.xlsx: flat7d_1


title: Tumor microenvironment sample 3 control c

value: liver metastasis

value: tumor microenvironment

value: Control


title: Tumor microenvironment sample 3 control b


title: experiment5_flat 3d_rep2

description:
Library name: Sample 64
column name in extract experiments counts.xlsx: flat3d_2

value: cells cultured in flat plate for 3d


title: experiment5_flat 3d_rep3

description:
Library name: Sample 65
column name in extract experiments counts.xlsx: flat3d_3


title: 170123_2_R1

value: melanoma


title: 991104_R2


title: experiment5_flat 3d_rep1

description:
Library name: Sample 63
column name in extract experiments counts.xlsx: flat3d_1


title: experiment5_flat 1d_rep3

description:
Library name: Sample 62
column name in extract experiments counts.xlsx: flat1d_3

value: cells cultured in flat plate for 1d


title: experiment5_0d_rep2

description:
Library name: Sample 70
column name in extract experiments counts.xlsx: POS_2

value: WT


title: 991104_R1


title: A375_Ctrl_NAK_R1


title: experiment5_flat 1d_rep1

description:
Library name: Sample 60
column name in extract experiments counts.xlsx: flat1d_1


title: 170314_R2


title: Tumor microenvironment sample 2 hashed library 2

description: multiplexed

value: hashed


title: experiment5_flat 1d_rep2

description:
Library name: Sample 61
column name in extract experiments counts.xlsx: flat1d_2


title: experiment4_0d_rep3

description:
Library name: Sample 59
column name in feeder experiments counts.xlsx: 064-POS-3


title: 170123_2_R2

description: 10X Chromium Single Cell 3' v3.1 Chemistry Dual Index


title: experiment4_0d_rep2

description:
Library name: Sample 58
column name in feeder experiments counts.xlsx: 064-POS-2


title: experiment4_MEF 3d_rep3

description:
Library name: Sample 56
column name in feeder experiments counts.xlsx: 064-MEF3d-3

value: cells cultured on MEF feeder for 3d


title: T cells &TCR anti-PD-L1

value: T cells


title: Tumor microenvironment sample 2 hashed library 1

description: multiplexed


title: experiment4_0d_rep1

description:
Library name: Sample 57
column name in feeder experiments counts.xlsx: 064-POS-1

value: planarian SiRNeoblast


title: 170314_R1


title: 150922_R2


title: experiment4_MEF 3d_rep1

description:
Library name: Sample 54
column name in feeder experiments counts.xlsx: 064-MEF3d-1


title: T cells &TCR galunisertib

value: Galunisertib


title: Tumor microenvironment sample 3 control a


title: experiment4_MEF 1d_rep3

description:
Library name: Sample 53
column name in feeder experiments counts.xlsx: 064-MEF1d-3

value: cells cultured on MEF feeder for 1d


title: 150922_R1


title: experiment4_MEF 1d_rep2

description:
Library name: Sample 52
column name in feeder experiments counts.xlsx: 064-MEF1d-2


title: experiment4_MEF 1d_rep1

description:
Library name: Sample 51
column name in feeder experiments counts.xlsx: 064-MEF1d-1


title: 130107_R2


title: T cells &TCR dual treatment

value: anti-PD-L1 + Galunisertib


title: T cells &TCR  control


title: experiment4_HFF1 3d_rep2

description:
Library name: Sample 49
column name in feeder experiments counts.xlsx: 064-HFF13d-2

value: cells cultured on HFF1 feeder for 3d


title: 130107_R1


title: experiment4_HFF1 3d_rep1

description:
Library name: Sample 48
column name in feeder experiments counts.xlsx: 064-HFF13d-1


title: experiment4_HFF1 1d_rep3

description:
Library name: Sample 47
column name in feeder experiments counts.xlsx: 064-HFF11d-3

value: cells cultured on HFF1 feeder for 1d


title: Fibroblasts sample 2 anti-PD-L1

value: Fibroblasts


title: F: CD22 CAR+SLP-76 5h stimulation

city: New York

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Raw Novaseq BCLs were demultiplexed with cellranger mkfastq v7.0.2
Sequencing reads were aligned to the human hg38 reference genome with CellRanger v7.0.2
Cell x gene counts matrices in h5 format were produced using the default parameters in CellRanger count
Assembly: hg38
Supplementary files format and content: Gene expression counts matrices (h5) from CellRanger pipeline

source_name: T cell

growth_protocol: At day 0, PBMCs or isolated T cells were thawed and activated with Human T-Activator αCD3/CD28 Dynabeads (Gibco) at a 3:1 bead to cell ratio, in AIM-V media (Gibco) supplemented with 5% FBS, 10 mM HEPES, 1X penicillin-streptomycin-glutamine solution (Gibco) and 100 U/mL recombinant human IL-2 (Peprotech). Retroviral transduction was performed on days three and four post-activation. Twelve-well non-tissue culture treated plates were coated with RetroNectin (Takara Bio) and blocked with 2% BSA prior to incubation and centrifugation with the retroviral supernatant for at least two hours at 32 °C at 3,200 rpm. The co-expression of CAR and proximal signaling molecules was achieved by co-administration of two separate viral vectors. The supernatant was then removed and 0.5x106 T cells were added to each well in 1 mL of complete AIM-V media. Dynabeads were removed on day five post-activation by magnetic separation and the T cells were maintained in culture in complete AIM-V at a density of 0.3x106/ml until day 10-14, with media changes every 2-3 days.

extract_protocol: 10x Genomics NextGEM 5' scRNA-seq

treatment_protocol: Cells were restimulated and the profiled after 0hr, 5hr, or 24hr to study heterogenity in CAR response as a function of MT-SLP-76

value: T cell

value: CD22 targeted CAR T


title: Fibroblasts sample 2 galunisertib

value: liver metastasis


title: experiment4_flat 3d_rep3

description:
Library name: Sample 44
column name in feeder experiments counts.xlsx: 064-flat3d-3

value: cells cultured in flat plate for 3d


title: experiment4_HFF1 1d_rep1

description:
Library name: Sample 45
column name in feeder experiments counts.xlsx: 064-HFF11d-1


title: experiment4_flat 3d_rep2

description:
Library name: Sample 43
column name in feeder experiments counts.xlsx: 064-flat3d-2


title: Fibroblasts sample 2 dual treatment


title: experiment4_flat 3d_rep1

description:
Library name: Sample 42
column name in feeder experiments counts.xlsx: 064-flat3d-1


title: Fibroblasts sample 2 control

value: Control


title: C: CD22 CAR 5h stimulation

value: MTSLP76 -


title: experiment4_flat 1d_rep2

description:
Library name: Sample 40
column name in feeder experiments counts.xlsx: 064-flat1d-2

value: WT

value: cells cultured in flat plate for 1d


title: Fibroblasts sample 1 anti-PD-L1


title: experiment4_flat 1d_rep1

description:
Library name: Sample 39
column name in feeder experiments counts.xlsx: 064-flat1d-1


title: Fibroblasts sample 1 galunisertib


title: B: CD22 CAR 24h stimulation


title: experiment3_U 3d_rep2

description:
Library name: Sample 37
column name in raw_counts_U_PA.xlsx: U_3d_2

value: cells cultured in U plate for 3d


title: experiment3_U 3d_rep3

description:
Library name: Sample 38
column name in raw_counts_U_PA.xlsx: U_3d_3


title: A: CD22 CAR unstimulated

value: unstim


title: CKO female mice, DAPI+, replicate 1

description: 10X Genomics Chromium Single Cell 3' Reagent Kits  v3.1

value: neocortex

value: DAPI+ nuclei

value: 6 months old


title: experiment3_U 3d_rep1

description:
Library name: Sample 36
column name in raw_counts_U_PA.xlsx: U_3d_1

value: planarian SiRNeoblast


title: Fibroblasts sample 1 dual treatment

value: anti-PD-L1 + Galunisertib


title: experiment4_HFF1 3d_rep3

description:
Library name: Sample 50
column name in feeder experiments counts.xlsx: 064-HFF13d-3

value: cells cultured on HFF1 feeder for 3d


title: experiment3_U 1d_rep3

description:
Library name: Sample 35
column name in raw_counts_U_PA.xlsx: U_1d_3

value: cells cultured in U plate for 1d


title: experiment3_U 1d_rep2

description:
Library name: Sample 34
column name in raw_counts_U_PA.xlsx: U_1d_2


title: Fibroblasts sample 1 control

value: Fibroblasts