title: Tissue sample from Pt98_t4

type: RNA

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: Gene-level expression estimates from RMA analysis using the Transcriptome Analysis Console (TAC 4.0) software

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip Human Transcriptome 2.0 Arrays (HTA 2.0) according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: Gene-level expression signals were estimated according to the robust multi-array average (RMA) approach implemented in the Transcriptome Analysis Console (TAC 4.0) software (Affymetrix) with defult settings.

label: Biotin

source_name: Patient 98, tumor 4

label_protocol: 100 ng total RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

growth_protocol: Tumor organoids were cultured under standard organoid-forming conditions in Matrigel domes submerged in advanced DMEM/F12 medium supplemented with 10 mM HEPES, 2 mM GlutaMAX, 50 U/ml penicillin/streptomycin, 1x B27, 10 nM [Leu15]-Gastrin I, 1 mM N-acetyl-l-cysteine, 50 ng/mL EGF, 100 ng/mL Noggin, 500 nM A83-01, and 10 µM SB202190.

extract_protocol: Total RNA was extracted from tumor organoids and tumor tissue samples using the Allprep DNA/RNA/miRNA Universal kit according to the manufacturer’s instructions (Qiagen GmBH).

treatment_protocol: Tumor organoids were maintained under standard culture conditions without any additional treatments before RNA extraction.

value: tissue

tag: patient

tag: tumor

tag: samples from repeated resections


title: TN_CD_female_17w_113_heart

status: Public on Apr 20 2026

type: SRA

city: LAUSANNE

first: Johan

last: Auwerx

address: Station 15

department: SV-IBI

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne EPFL

description: Library name: HDP-018734_heart

library_source: transcriptomic

data_processing:
Bulk RNA barcoding and sequencing (BRB-seq) libraries were generated and sequenced by Alithea Genomics (Switzerland). The raw data was demultiplexed, cleaned, and aligned to the mouse reference genome GRCm39/mm39 using R (version 4.1.a) and START (version 2.7.9a). Count matrices were used for downstream analyses
Assembly: genome GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: heart

extract_protocol:
RNA was extracted from liver and heart tissues using Direct-zol-96 RNA kit (Zymo research)
The generation of bulk RNA Barcoding and sequencing (BRB-seq) libraries was performed using the MERCURIUSTM BRB-seq library preparation kit for Illumina and following the manufacturer’s manual

tag: tissue

value: heart


title: TN_WD_female_9w_112_heart

description: Library name: HDP-018837_heart


title: ESC-RA-0h-scRNA

city: Guangzhou

first: Weipeng

last: Mo

state: Guangdong

address: 58 Zhongshaner Rd

department: The First Affiliated Hospital

country: China

institute: Sun Yat-sen University

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software.
Assembly: mm10
Supplementary files format and content: Cell Ranger Feature Barcode Matrices (HDF5 Format).

source_name: ESC

growth_protocol: ESCs were grown in culture dishes coated with 0.1% gelatin (Sigma) in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 15% fetal bovine serum (FBS, AusGeneX), 1× nonessential amino acids (100×, Gibco), 1× L-glutamate (100×, Gibco), 1× penicillin-streptomycin (100×, Gibco), 50 μM β-mercaptoethanol (Sigma), 103 units /ml LIF (ESGRO), 1 μM PD0325901 (MedChemExpress) and 3 μM CHIR99021 (MedChemExpress). The medium was replaced daily when cells were not passaged. Cells are maintained at 37℃ in the 5% CO2 incubator.

extract_protocol:
1. Cell Counting & Quality Control: The prepared cell suspension was counted using TC20 Automated Cell Counter (Bio-Rad, USA) to obtain the information of cell size, concentration and viability, and to determine the sample loading volume. 2. GEM Generation and cDNA Amplification: Within the Chromium instrument, barcoded Single Cell 3' Gel Beads are mixed with cells or nuclei, enzymes, and partitioning oil to form tens of thousands of single cell emulsion droplets called "GEMs" (Gel Bead-in-emulsion). Immediately following GEM generation, the Gel Bead is dissolved and any co-partitioned cell is lysed. Oligonucleotides containing (i) an Illumina Read 1 (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 12 nt unique molecular identifier (UMI), and (iv) 30 nt poly(dT) sequence are released and mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents. Incubation of the GEMs produces 10x Barcoded, full length cDNA from poly-adenylated mRNA. Then, the first-strand cDNA of 10X Barcoded was purified by silane magnetic beads, and sufficient mass was obtained by PCR amplification. The PCR products were clean up by SPRI beads, and double-stranded cDNA was obtained. Then quantify and qualify the dsDNA by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), so as to confirm the final PCR cycle number for library construction.
Library Construction: The 1/4 of the dsDNA was then treated with Fragmentation Mix to fragment cDNA, End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by double sided size selection to recover ~300 bp of the cDNA. Each sample was then added adaptors to both ends by a T-A ligation. The purified Ligation was amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform Illumina bridge PCR. And P7 primers are a mixture of four primers, each carrying a eight-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: ESCs were induced to differentiate by removing LIF/2i or adding 2 μM RA (Sigma) for 12h and 24 h, respectively.

tag: cell line

value: ESC

tag: genotype

value: WT

tag: treatment


title: Tissue sample from Pt98_t1

organism: Homo sapiens

source_name: Patient 98, tumor 1

tag: group


title: TN_WD_female_17w_115_heart

description: Library name: HDP-018737_heart


title: ESC-RA24h-scRNA


title: RT_WD_female_17w_111_heart

description: Library name: HDP-018889_heart


title: cArg_IV_rep2

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

country: USA

institute: Cornell University

description: Library name: Sample_43

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Assembly: GRCh39.p13
Supplementary files format and content: tab-delimited text files including normalized read counts per codon on individual mRNAs for Ribo-seq.
Supplementary files format and content: comma-delimited text files including read counts mapped to each position on reporter mRNA Ribo-seq.
Library strategy: Ribo-Seq

extract_protocol:
For mRNA reporters, 8 μg of mRNA was transfected into HEK293-Kb cells (~80% confluence) in 10 cm dishes for 8 h. For plasmid reporters, 1 μg plasmid was transfected into 35 mm dishes for 24 h. Cells were washed with cold PBS and lysed in polysome lysis buffer (10 mM HEPES, pH 7.4; 100 mM KCl; 5 mM MgCl₂; 100 μg/mL cycloheximide; 1% Triton X-100). Lysates were cleared by centrifugation at 20,000 × g for 10 min at 4 °C and digested with RNase I (Ambion, 750 U per 100 A₂₆₀ units) at 4 °C for 1 h. Total RNA was extracted using TRIzol LS (Invitrogen) for cDNA library construction.
Ribosome-protected fragments (25–35 nt) or disome footprints (40-60 nt) were resolved on a 15% polyacrylamide TBE–urea gel (Invitrogen) and visualized with SYBR Gold. Excised RNA fragments were eluted overnight in RNA elution buffer (300 mM sodium acetate, pH 5.2; 1 mM EDTA; 0.1 U/μL SUPERase·In), cleared through Spin-X columns, and ethanol-precipitated. cDNA libraries were constructed using T4 PNK, Poly(A) polymerase, and custom Ezra enzyme, followed by ligation of 5' adapters, streptavidin bead-based purification, and reverse transcription following the previous study [28]. Final cDNA was amplified with barcoded primers, size-selected (180 bp), quantified, pooled, and sequenced on an Illumina MiniSeq or NextSeq 500.


title: Tissue sample from Pt99_t1

source_name: Patient 99, tumor 1


title: cArg_CGCCGC-CGGCGG

description: Library name: Sample_44


title: TN_CD_female_3d_110_heart

description: Library name: HDP-019118_heart


title: Tissue sample from Pt95_t2

source_name: Patient 95, tumor 2


title: RARX-WT-RA24h-scRNA


title: RARX-KO-RA24h-scRNA

value: DKO


title: Tissue sample from Pt9_t1

source_name: Patient 9, tumor 1


title: Tissue sample from Pt8_t1

source_name: Patient 8, tumor 1


title: Tissue sample from Pt93_t1

source_name: Patient 93, tumor 1


title: Ribo_cPro_GC7

description: Library name: Sample_42


title: cArg_rep6

description: Library name: Sample_41


title: Cyp26a1-KO-Rep3

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2. Expression levels of all genes were counted and expression profile matrix was constructed with stringtie.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include gene expression (FPKM, TPM) for each Sample.

molecule: polyA RNA

extract_protocol:
ESCs were lysed with Trizol reagent (Life Technologies), and RNA was extracted based on the manufacturer’s instructions.
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexes were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer's instructions.


title: TN_WD_female_3d_109_heart

description: Library name: HDP-019068_heart


title: Tissue sample from Pt7_t1

source_name: Patient 7, tumor 1


title: Cyp26a1-KO-Rep2

value: Cyp26a1 knockout


title: Cyp26a1-KO-Rep1


title: TN_WD_female_9w_108_heart

description: Library name: HDP-018838_heart


title: cArg_rep5

description: Library name: Sample_40


title: RT_CD_male_17w_107_heart

description: Library name: HDP-018953_heart


title: cArg_rep4

description: Library name: Sample_39


title: Tissue sample from Pt6.3_t2

source_name: Patient 6, tumor 2

value: third sampled resection


title: Cyp26a1-WT-Rep3

value: wildtype


title: TN_WD_female_27d_106_heart

description: Library name: HDP-018997_heart


title: cArg_rep3

description: Library name: Sample_38


title: RT_CD_male_17w_105_heart

description: Library name: HDP-018948_heart


title: Cyp26a1-WT-Rep2


title: cPhe_SAMD9_+Dox_rep1

description: Library name: Sample_37


title: Tissue sample from Pt6_t2

value: first sampled resection


title: TN_WD_female_17w_104_heart

description: Library name: HDP-018792_heart


title: Tissue sample from Pt6.3_t1

source_name: Patient 6, tumor 1


title: Cyp26a1-WT-Rep1


title: cPhe_SAMD9_-Dox_rep1

description: Library name: Sample_36


title: TN_CD_male_27d_103_heart

description: Library name: HDP-018979_heart


title: ESC-RA24h-bulkRNA-Rep3


title: cLys_-Lys

description: Library name: Sample_35


title: cLeu_-Leu

description: Library name: Sample_34


title: Tissue sample from Pt6.2_t2

value: second sampled resection


title: ESC-RA24h-bulkRNA-Rep2


title: Tissue sample from Pt6.2_t1


title: RT_WD_male_17w_101_heart

description: Library name: HDP-018888_heart


title: Tissue sample from Pt55_t2

source_name: Patient 55, tumor 2


title: TN_CD_male_9d_100_heart

description: Library name: HDP-019058_heart


title: TN_CD_male_17w_98_heart

description: Library name: HDP-018694_heart


title: ESC-NoRA24h-bulkRNA-Rep1


title: TN_CD_female_3d_102_heart

description: Library name: HDP-019119_heart


title: cArg_IV_rep1

description: Library name: Sample_29


title: ESC-RA24h-bulkRNA-Rep1


title: TN_CD_male_9w_96_heart

description: Library name: HDP-018824_heart


title: Tissue sample from Pt54.3_t1

source_name: Patient 54, tumor 1


title: ESC-RA12h-bulkRNA-Rep2


title: cPhe_-Phe

description: Library name: Sample_33


title: cMet_-Met

description: Library name: Sample_32


title: ESC-NoRA24h-bulkRNA-Rep3


title: TN_WD_female_9w_99_heart

description: Library name: HDP-018791_heart


title: ESC-RA12h-bulkRNA-Rep1


title: Tissue sample from Pt54.2_t3

source_name: Patient 54, tumor 3


title: Tissue sample from Pt55.3_t1

source_name: Patient 55, tumor 1


title: cArg_-Arg

description: Library name: Sample_31


title: ESC-NoRA24h-bulkRNA-Rep2


title: Ribo_Gly

description: Library name: Sample_27


title: cCys_-Cys

description: Library name: Sample_30


title: Tissue sample from Pt54_t1.1

source_name: Patient 54, tumor 1.1


title: TN_CD_male_27d_97_heart

description: Library name: HDP-018981_heart


title: Tissue sample from Pt54.2_t1


title: ESC-RA12h-bulkRNA-Rep3


title: Tissue sample from Pt54.2_t4

source_name: Patient 54, tumor 4


title: Ribo_Cys

description: Library name: Sample_25


title: Tissue sample from Pt50.2_t1

source_name: Patient 50, tumor 1


title: TN_CD_male_9d_91_heart

description: Library name: HDP-019072_heart

source_name: heart


title: Tissue sample from Pt55_t1


title: Ribo_Asp

description: Library name: Sample_24


title: ESC-RA-0h-bulkRNA-Rep3

source_name: ESC


title: ESC-NoRA12h-bulkRNA-Rep2


title: Ribo_His

description: Library name: Sample_23


title: cArg_rep2

description: Library name: Sample_28


title: ESC-NoRA12h-bulkRNA-Rep1


title: ESC-RA-0h-bulkRNA-Rep2


title: TN_CD_male_17w_90_heart

description: Library name: HDP-018805_heart


title: RT_WD_female_17w_95_heart

description: Library name: HDP-018850_heart


title: Tissue sample from Pt18_t4

source_name: Patient 18, tumor 4


title: ESC-RA-0h-bulkRNA-Rep1


title: Tissue sample from Pt22.2_t1

source_name: Patient 22, tumor 1


title: WT-RA24h-RXRA-Cut/tag

library_source: genomic

data_processing:
We used Bowtie2 to map the paired-end Illumina reads to mm10. bamCoverage was used to generates a coverage track (bigWig).
Assembly: mm10
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
DNA was extracted according to the instructions of the kit (NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit, N259-YH01, novoprotein).
DNA libraries were constructed according to the instructions of the kit (NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit, N259-YH01, novoprotein).

treatment_protocol: ESCs were induced to differentiate for 24 hours by withdrawal of LIF/2i and addition of 2 μM RA (Sigma).

tag: antibody

value: RXRA


title: Ribo_Thr

description: Library name: Sample_20


title: TN_CD_female_9w_87_heart

description: Library name: HDP-018829_heart


title: RT_WD_female_17w_94_heart

description: Library name: HDP-018893_heart


title: Tissue sample from Pt18_t3

source_name: Patient 18, tumor 3


title: WT-RA24h-RARA-Cut/tag

value: RARA


title: Ribo_Trp

description: Library name: Sample_18


title: Ribo_Gln

description: Library name: Sample_26


title: ESC-NoRA12h-bulkRNA-Rep3


title: RARX-WT-RA24h-H3K27ac-Cut/tag


title: Tissue sample from Pt50_t3

source_name: Patient 50, tumor 3


title: TN_CD_female_9d_84_heart

description: Library name: HDP-019112_heart


title: TN_WD_male_9w_85_heart

description: Library name: HDP-018827_heart


title: Tissue sample from Pt137_t3

source_name: Patient 137, tumor 3


title: RARX-KO-RA24h-ATAC

data_processing:
We used Bowtie2 to map the paired-end Illumina reads to mm10. bamCoverage was used to generates a coverage track (bigWig).
Assembly: mm10
Supplementary files format and content: bigwig files

extract_protocol:
DNA was extracted according to the instructions of the kit (High-Sensitivity Open Chromatin Profile Kit 2.0, N248, novoprotein).
DNA libraries were constructed according to the instructions of the kit (High-Sensitivity Open Chromatin Profile Kit 2.0, N248, novoprotein).


title: Ribo_Glu

description: Library name: Sample_15


title: Tissue sample from Pt134_t5

source_name: Patient 134, tumor 5


title: RARX-WT-RA24h-ATAC


title: TN_WD_male_17w_93_heart

description: Library name: HDP-018751_heart


title: RT_WD_female_17w_82_heart

description: Library name: HDP-018891_heart


title: RT_CD_male_17w_92_heart

description: Library name: HDP-018949_heart


title: Tissue sample from Pt3_t6

source_name: Patient 3, tumor 6


title: Tissue sample from Pt3_t1

source_name: Patient 3, tumor 1


title: Ribo_Phe

description: Library name: Sample_22


title: TN_WD_male_9w_89_heart

description: Library name: HDP-018826_heart


title: Ribo_Arg_rep1

description: Library name: Sample_21


title: PB_D12_Ctrl_Rep2

city: Fargo

first: Tadeu

middle: dos Reis de

last: Oliveira

state: ND

address: 1616 Albrecht Blvd. North

department: Edward T. Schafer Agricultural Research Center

institute: USDA-Agricultural Research Service

description: Library name: PPP2_30

data_processing:
Paired-end reads obtained from the Novaseq 6000 system were processed using Trimmomatic to trim low-quality bases and remove adapter sequences, applying the parameters HEADCROP:10, SLIDINGWINDOW:4:15, and MINLEN:36. Trimmed reads were aligned to the Solanum tuberosum genome assembly version 6.1 (DM1-3516 R44) using HISAT2 (--dta). The resulting SAM files were converted to BAM format, sorted, and indexed using SAMtools. Transcript abundance was quantified with StringTie (-e, -B flags) using the reference genome annotation in GFF3 format. Gene and transcript count matrices were generated with the prepDE.py3 script.
Assembly: The Solanum tuberosum genome assembly version 6.1 was used for read alignment and analysis. The genome assembly, annotation, and related resources are available in the SpudDB database (Pham et al., 2020; https://spuddb.uga.edu/).
Supplementary files format and content: The processed data files include tab-delimited text files containing gene and transcript count matrices (gene_count_matrix.csv and transcript_count_matrix.csv). These files provide quantified expression levels for differential expression analysis, generated using the prepDE.py3 script based on StringTie outputs.

organism: Solanum tuberosum

source_name: Primary Bud

extract_protocol:
RNA extraction and purification were performed using the Qiagen RNeasy Plant Mini Kit, following the method described by Rubio-Piña & Zapata-Pérez (2011) for plant tissues rich in polysaccharides and polyphenols. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer.
RNA-seq

value: Primary Bud

value: Russet Burbank (Solanum tuberosum L.)

value: Control


title: Tissue sample from Pt134_t2

source_name: Patient 134, tumor 2


title: RT_WD_male_17w_79_heart

description: Library name: HDP-018896_heart


title: Ribo_Pro

description: Library name: Sample_13


title: Ribo_Tyr

description: Library name: Sample_19


title: Tissue sample from Pt134_t1

source_name: Patient 134, tumor 1


title: PB_D12_Ctrl_Rep1

description: Library name: PPP2_29


title: TN_WD_male_9d_88_heart

description: Library name: HDP-018699_heart


title: Tissue sample from Pt18_t1

source_name: Patient 18, tumor 1


title: TN_WD_female_27d_86_heart

description: Library name: HDP-018977_heart


title: Ribo_Ile

description: Library name: Sample_11


title: RARX-KO-RA24h-H3K27ac-Cut/tag


title: TN_WD_female_27d_78_heart

description: Library name: HDP-018976_heart


title: Tissue sample from Pt17_t1

source_name: Patient 17, tumor 1


title: Ribo_Met

description: Library name: Sample_10


title: Ribo_Val

description: Library name: Sample_9


title: Ribo_Asn

description: Library name: Sample_17


title: Ribo_Lys

description: Library name: Sample_16


title: RARX-WT-RA0h-H3K27ac-Cut/tag


title: Tissue sample from Pt12_t4

source_name: Patient 12, tumor 4


title: Tissue sample from Pt15_t3

source_name: Patient 15, tumor 3


title: PB_D9_Eth_Rep2

description: Library name: PPP2_26

value: Ethylene


title: TN_WD_male_3d_83_heart

description: Library name: HDP-019020_heart

source_name: heart


title: Tissue sample from Pt12_t1

source_name: Patient 12, tumor 1


title: TN_CD_male_3d_75_heart

description: Library name: HDP-019026_heart


title: Ribo_Leu

description: Library name: Sample_14


title: Tissue sample from Pt134_t4

source_name: Patient 134, tumor 4


title: TN_CD_male_17w_81_heart

description: Library name: HDP-018701_heart


title: PB_D9_Ctrl_Rep4

description: Library name: PPP2_24


title: TN_CD_female_17w_80_heart

description: Library name: HDP-018716_heart


title: TMA

city: Atlanta

first: James

middle: Ricahrd

last: Rose

state: GA

address: 1750 Haygood Dr NE

department: Biomedical Engineering

institute: Emory University

description: coordinates provided for individual punches

hyb_protocol: TMA sections were processed according to the 10x Genomics manufacturer's protocol for Xenium Prime In Situ Gene Expression with optional Cell Segmentation Staining using a 5,006-gene pane

scan_protocol: Imaging processing, decoding, quality score generation, and 10x Xenium segmentation kit segmentation was performed by the Xenium Analyzer system. Analysis version 3.3.0.1

data_processing: Xenium Onboard Analysis (XOA) v3.3.0.1

label: Xenium probe set

source_name: multiple

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: C57BL/6J mice (8 weeks old) received a single retro-orbital injection of LNPs encapsulating β-Galactosidase mRNA (40 μg, 2 mg/kg) or vehicle (DPBS) control; 24 hours post-injection, animals were perfused with formalin fixative, tissues were harvested, fixed in 10% neutral buffered formalin for 24 hours, and paraffin embedded; 2 mm diameter cores were punched from selected regions of each tissue block and re-embedded into a single TMA block, which was sectioned and mounted onto Xenium slides.

value: multiple

tag: tissue preservation method

value: FFPE


title: RT_WD_female_17w_74_heart

description: Library name: HDP-018955_heart

value: heart


title: Tissue sample from Pt116_t3

source_name: Patient 116, tumor 3

value: tissue


title: PB_D9_Ctrl_Rep3

description: Library name: PPP2_23


title: Tissue sample from Pt116_t2

source_name: Patient 116, tumor 2


title: Tissue sample from Pt134_t3

source_name: Patient 134, tumor 3


title: TN_CD_female_17w_72_heart

description: Library name: HDP-018731_heart


title: Ribo_Ser

description: Library name: Sample_12

value: WT


title: Tissue sample from Pt116_t1

source_name: Patient 116, tumor 1


title: PB_D9_Eth_Rep4

description: Library name: PPP2_28


title: PB_D9_Eth_Rep3

description: Library name: PPP2_27


title: Tissue sample from Pt13_t1

source_name: Patient 13, tumor 1


title: TN_CD_male_9d_71_heart

description: Library name: HDP-019059_heart


title: PB_D9_Ctrl_Rep1

description: Library name: PPP2_21


title: TN_CD_male_17w_70_heart

description: Library name: HDP-018709_heart


title: TN_CD_female_17w_76_heart

description: Library name: HDP-018714_heart


title: TN_CD_male_3d_77_heart

description: Library name: HDP-019024_heart


title: Tissue sample from Pt112_t1

source_name: Patient 112, tumor 1


title: Ribo_Ala

description: Library name: Sample_8


title: TN_WD_male_9d_73_heart

description: Library name: HDP-019052_heart


title: PB_D9_Eth_Rep1

description: Library name: PPP2_25

source_name: Primary Bud


title: PB_D6_Eth_Rep3

description: Library name: PPP2_19


title: Tissue sample from Pt11_t1

source_name: Patient 11, tumor 1


title: E18.5 ureters, ΔNp63-cKO vs control, rep4

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 2500ng of each fluorescently labelled cRNA were used for hybridization.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE2_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values (for each channel independently) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:  normalized PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: control 4

label_protocol: 200 ng of total RNA were used to synthesize AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Thermo Fisher Scientific) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and reaction volumes were halved, and just one round of T7 amplification was conducted.

extract_protocol: Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from E18.5 embryos.

tag: strain

value: NMRI

tag: Sex

value: female

tag: developmental stage

value: ureter

source_name: ΔNp63-cKO 4

value: Pax2-cre/+; Trp63(dN-flox/dN-flox)


title: PB_D6_Eth_Rep2

description: Library name: PPP2_18


title: PB_D9_Ctrl_Rep2

description: Library name: PPP2_22


title: E15.5 ureters, ΔNp63-cKO vs control, rep4

treatment_protocol: Ureters were mechanically dissected from E15.5 embryos.

value: male


title: TN_WD_male_3d_68_heart

description: Library name: HDP-019021_heart


title: TN_CD_female_3d_67_heart

description: Library name: HDP-019090_heart


title: PB_D6_Eth_Rep4

description: Library name: PPP2_20


title: E18.5 ureters, ΔNp63-cKO vs control, rep2

source_name: control 2

source_name: ΔNp63-cKO 2


title: TN_CD_female_9d_66_heart

description: Library name: HDP-019084_heart


title: E15.5 ureters, ΔNp63-cKO vs control, rep2


title: TN_CD_male_27d_69_heart

description: Library name: HDP-018995_heart


title: Tissue sample from Pt104_t1

source_name: Patient 104, tumor 1


title: siControl, rep5

city: Philadelphia

first: Ricardo

middle: A

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

description: Library name: Scramble-p7-1

data_processing:
For Scramble libraries, raw fastq reads were aligned to the hg19 reference genome using STAR (Dobin et al. 2013). For all other libraries, raw fastq reads were aligned to the hg38 reference genome with RefSeq transcripts aligned by UCSC using STAR (Dobin et al. 2013)(v2.7.1a) with parameters: --outFilterMismatchNmax 3 --outFilterMultimapNmax 1.
For all libraries, gene-level read counts were obtained using featureCounts (Liao, Smyth, and Shi 2014).
For scramble libraries, raw counts were normalized to median library size using DESEQ2. For all other libraries, raw counts were normalized to transcripts per million (TPM) using gene length obtained from featureCounts.
Assembly: hg19 for scramble libraries, hg38 for all others
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: CSV files includes normalized counts (DESEQ2 normalized counts for Scramble libraries, TPM values for all other libraries)

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum, 2 mM l-glutamine, 100 U ml-1 penicillin, and 100 µg ml-1 streptomycin at 37°C with 5% CO2.

extract_protocol:
For Scramble libraries, Qiagen RNeasy mini kit for RNA purification. For all others, Maxwell RSC simple RNA Tissue kit using Automation Maxwell® RSC 48 Instrument.
For all Scramble libraries, as well as siNTC5-1, siNTC5-2, siHNRNPK-1, and siHNRNPK-2, libraries were prepared with Illumina TruSeq stranded mRNA kit. For siNTC5-3, siNTC5-4, siHNRNPK-3, and siHNRNPK-4, libraries were prepared with the Illumina Stranded mRNA, Ligation kit.

treatment_protocol: RNAiMAX transfection reagent (Thermo Fisher Scientific) was diluted in Opti-MEM reduced serum medium and pipetted onto siRNA (nontargeting control or HNRNPK). The mixture was incubated at room temperature for 20 minutes. HCT116 cells were harvested by trypsinization, resuspended in antibiotic-free medium, and plated onto siRNA duplexes for a final siRNA concentration of 25 nM. Cells were collected for extraction after 72 hours of RNAi treatment.

tag: cell type

value: Human colon cancer

value: Nontargeting control siRNA


title: E15.5 ureters, ΔNp63-cKO vs control, rep3

source_name: control 3

source_name: ΔNp63-cKO 3


title: PB_D6_Ctrl_Rep3

description: Library name: PPP2_15


title: Tissue sample from Pt12_t3

source_name: Patient 12, tumor 3


title: E15.5 ureters, ΔNp63-cKO vs control, rep1

source_name: control 1

source_name: ΔNp63-cKO 1


title: RT_WD_male_17w_64_heart

description: Library name: HDP-018962_heart

source_name: heart


title: Tissue sample from Pt10_t3

source_name: Patient 10, tumor 3


title: Tissue sample from Pt10_t2

source_name: Patient 10, tumor 2


title: siControl, rep6

description: Library name: Scramble-p7-2


title: E18.5 ureters, ΔNp63-cKO vs control, rep3


title: TN_WD_female_9d_62_heart

description: Library name: HDP-019087_heart


title: PB_D6_Eth_Rep1

description: Library name: PPP2_17


title: PB_D3_Eth_Rep4

description: Library name: PPP2_12


title: E18.5 ureters, ΔNp63-cKO vs control, rep1


title: Tissue sample from Pt1_t1

source_name: Patient 1, tumor 1


title: TN_WD_male_17w_61_heart

description: Library name: HDP-018729_heart


title: TN_CD_female_27d_63_heart

description: Library name: HDP-019005_heart


title: PB_D6_Ctrl_Rep4

description: Library name: PPP2_16


title: PDO from Pt99_t2

source_name: Patient 99, tumor 2

value: PDO cultured from resected liver metastases


title: THP1 cells, siCCR1, rep2

first: Jialiang

last: Chen

address: Tianhe Road 600

department: Urology

institute: Third Affiliated Hospital of Sun Yat-Sen University

description: Library name: S2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Monocyte


title: TN_CD_male_27d_60_heart

description: Library name: HDP-018994_heart


title: Human islets, donor 3

city: Farmington

first: Yuqi

last: Zhao

state: CT

address: 273 Main Street A4

institute: City Of Hope

description:
Library name: Donor COHP_33889_Hu-1231
COHP_33889_Hu-1231

data_processing:
Raw base call files were demultiplexed and converted to FASTQ format using Illumina bcl2fastq or 10x Genomics Cell Ranger mkfastq. Reads were aligned to the human reference genome using Cell Ranger. Unique molecular identifier (UMI) counts were quantified to generate gene-by-cell expression matrices.
Assembly: GRCh38
Supplementary files format and content: Processed data files are provided in Matrix Market format and include filtered feature-barcode matrices (`matrix.mtx.gz`), cell barcode files (`barcodes.tsv.gz`), and feature annotation files (`features.tsv.gz`).

source_name: Pancreatic islets

extract_protocol:
Human islets (2,000 IEQ/donor) were dissociated into sin-gle cells using TrypLE Express containing 1 mM EDTA(ThermoFisher Scientiﬁc, Cat. No. 12605028) at 37_x000E_C for 12–15 min. Cells were washed twice with PBS containing 0.1%human serum albumin (Baxalta, NDC 0944-0493-01). Five toseven thousand cells from each donor preparation were usedfor droplet-based single-cell mRNA sequencing analysis onthe 10x Genomics Chromium platform of 30 Library and Gelbead Kit V3.1
Single-cell gene expression libraries were generated using the 10x Genomics Chromium Single Cell Gene Expression kit following the manufacturer’s protocol. Single cells were encapsulated with barcoded gel beads in emulsion (GEMs), and mRNA molecules were captured and reverse transcribed using oligo-dT primers containing cell barcodes and UMIs. Barcoded cDNA was amplified by PCR, followed by fragmentation, adapter ligation, and index PCR to generate sequencing-ready libraries. Libraries were assessed for quality and sequenced on an Illumina sequencing platform.

value: Pancreatic islets


title: TN_CD_male_9d_65_heart

description: Library name: HDP-019057_heart


title: PB_D3_Eth_Rep2

description: Library name: PPP2_10

source_name: Primary Bud

value: Primary Bud

value: Russet Burbank (Solanum tuberosum L.)


title: PB_D6_Ctrl_Rep2

description: Library name: PPP2_14

value: Control


title: Human islets, donor 2

description:
Library name: Donor COHP_33887_Hu-1206
COHP_33887_Hu-1206


title: PB_D6_Ctrl_Rep1

description: Library name: PPP2_13


title: Human islets, donor 1

description:
Library name: Donor COHP_32762_Hu-1180
COHP_32762_Hu-1180


title: PDO from Pt99_t1

source_name: Patient 99, tumor 1


title: TN_WD_male_9d_59_heart

description: Library name: HDP-019075_heart


title: THP1 cells, normal, rep3

description: Library name: N3


title: PDO from Pt98_t6

source_name: Patient 98, tumor 6


title: TN_WD_female_17w_58_heart

description: Library name: HDP-018807_heart


title: PB_D3_Ctrl_Rep4

description: Library name: PPP2_8


title: PB_D3_Eth_Rep3

description: Library name: PPP2_11

value: Ethylene


title: THP1 cells, siCCR1, rep3

description: Library name: S3


title: PDO from Pt98_t5

source_name: Patient 98, tumor 5


title: THP1 cells, siCCR1, rep1

description: Library name: S1


title: THP1 cells, normal, rep1

description: Library name: N1


title: PB_D3_Eth_Rep1

description: Library name: PPP2_9


title: TN_CD_female_9d_57_heart

description: Library name: HDP-019111_heart

value: heart


title: TN_CD_female_17w_56_heart

description: Library name: HDP-018706_heart


title: TN_CD_female_27d_55_heart

description: Library name: HDP-019006_heart


title: PDO from Pt95_t2

source_name: Patient 95, tumor 2


title: TN_CD_female_3d_54_heart

description: Library name: HDP-019061_heart


title: ARID1A-HA ChIP in hES ARID1A-dTAG degron line, dTAG-13-treated, clone B

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

description: Library name: 10_hES_clone_B_dTAG_ChIP_ARID1A-HA

data_processing:
Processed through nfcore ChIPseq analysis pipeline.
Trimmed by TrimGalore, aligned with BWA, sequences filtered and duplicates marked.
Peak calling by macs2
Assembly: hg38
Supplementary files format and content: macs2 narrowPeak bed file

source_name: hES

growth_protocol: 20% IMDM with P/S, GlutaMax

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min in 37 C. The reaction was quenched with glycine. Nuclei were isolated with a Triton-X-100-containing buffer, and chromatin was subject to sonication with BioRuptor Pico (Diagenode). After immunoprecipitation and reversal of crosslinking, the DNA was isolated with the phenol-chloroform method, and subject to library preparation.
Ultra II DNA Library Prep Kit for Illumina, with dual indexes. Size distribution of the libarries was assessed by Agilent Bioanalyzer.

value: hES

value: Human embryonic stem cells

value: ARID1A-FKBP12(F36V) degron knock-in

tag: batch


title: PDO from Pt98_t3

source_name: Patient 98, tumor 3


title: PB_D3_Ctrl_Rep1

description: Library name: PPP2_5


title: PDO from Pt98_t1

source_name: Patient 98, tumor 1


title: PDO from Pt98_t2

source_name: Patient 98, tumor 2


title: PDO from Pt98_t4

source_name: Patient 98, tumor 4


title: ARID1A-HA ChIP in hES ARID1A-dTAG degron line, DMSO, clone D

description: Library name: 13_hES_clone_D_DMSO_ChIP_ARID1A-HA

value: DMSO


title: PB_D3_Ctrl_Rep2

description: Library name: PPP2_6


title: ARID1A-HA ChIP in hES ARID1A-dTAG degron line, DMSO, clone B

description: Library name: 07_hES_clone_B_DMSO_ChIP_ARID1A-HA


title: ARID1A-HA ChIP in hES ARID1A-dTAG degron line, dTAG-13-treated, clone D

description: Library name: 16_hES_clone_D_dTAG_ChIP_ARID1A-HA


title: THP1 cells, normal, rep2

description: Library name: N2


title: TN_CD_male_3d_52_heart

description: Library name: HDP-019025_heart


title: PB_D0_Ctrl_Rep2

description: Library name: PPP2_2


title: PDO from Pt95_t1

source_name: Patient 95, tumor 1


title: SMC3 ChIP in hES ARID1A-dTAG degron line, dTAG-13-treated, clone D

description: Library name: 15_hES_clone_D_dTAG_ChIP_SMC3


title: PB_D0_Ctrl_Rep4

description: Library name: PPP2_4


title: SMC3 ChIP in hES ARID1A-dTAG degron line, dTAG-13-treated, clone B

description: Library name: 12_hES_clone_D_DMSO_ChIP_SMC3


title: PB_D3_Ctrl_Rep3

description: Library name: PPP2_7


title: Flesh_D15+3wk_Rep3

description: Library name: PPP2_135

source_name: Flesh

value: Flesh


title: PDO from Pt93_t3

source_name: Patient 93, tumor 3


title: PDO from Pt94_t2

source_name: Patient 94, tumor 2


title: PDO from Pt94_t1

source_name: Patient 94, tumor 1


title: RT_CD_female_17w_53_heart

description: Library name: HDP-018895_heart

source_name: heart


title: PB_D0_Ctrl_Rep3

description: Library name: PPP2_3


title: PDO from Pt93_t1

source_name: Patient 93, tumor 1


title: TN_CD_male_27d_51_heart

description: Library name: HDP-018993_heart


title: CTCF ChIP in hES ARID1A-dTAG degron line, dTAG-13-treated, clone D

description: Library name: 14_hES_clone_D_dTAG_ChIP_CTCF


title: PB_D0_Ctrl_Rep1

description: Library name: PPP2_1

source_name: Primary Bud


title: Flesh_D15+3wk_Rep4

description: Library name: PPP2_136


title: SMC3 ChIP in hES ARID1A-dTAG degron line, DMSO, clone B

description: Library name: 06_hES_clone_B_DMSO_ChIP_SMC3


title: PDO from Pt93_t4

source_name: Patient 93, tumor 4


title: CTCF ChIP in hES ARID1A-dTAG degron line, DMSO, clone D

description: Library name: 11_hES_clone_D_DMSO_ChIP_CTCF


title: TN_WD_female_9d_49_heart

description: Library name: HDP-019113_heart


title: TN_WD_female_3d_50_heart

description: Library name: HDP-019012_heart


title: PDO from Pt93_t2

source_name: Patient 93, tumor 2


title: SMC3 ChIP in hES ARID1A-dTAG degron line, DMSO, clone D

description: Library name: 09_hES_clone_B_dTAG_ChIP_SMC3


title: PDO from Pt93_t6

source_name: Patient 93, tumor 6


title: Flesh_D18_Ctrl_Rep3

description: Library name: PPP2_131


title: TN_WD_male_9d_48_heart

description: Library name: HDP-019053_heart


title: Flesh_D15+3wk_Rep2

description: Library name: PPP2_134


title: Flesh_D15+3wk_Rep1

description: Library name: PPP2_133


title: Flesh_D18_Ctrl_Rep2

description: Library name: PPP2_130


title: PDO from Pt88_t2

source_name: Patient 88, tumor 2


title: CTCF ChIP in hES ARID1A-dTAG degron line, dTAG-13-treated, clone B

description: Library name: 08_hES_clone_B_dTAG_ChIP_CTCF

source_name: hES


title: PDO from Pt9_t1

source_name: Patient 9, tumor 1


title: PDO from Pt88_t3

source_name: Patient 88, tumor 3


title: Flesh_D18_Ctrl_Rep4

description: Library name: PPP2_132


title: TN_WD_female_17w_46_heart

description: Library name: HDP-018705_heart


title: PDO from Pt84_t1

source_name: Patient 84, tumor 1


title: Flesh_D15+2wk_Rep3

description: Library name: PPP2_127


title: TN_CD_female_3d_45_heart

description: Library name: HDP-019062_heart


title: Input ChIP in hES ARID1A-dTAG degron line, DMSO, clone D

description: Library name: 03_hES_clone_D_DMSO_ChIP_input


title: CTCF ChIP in hES ARID1A-dTAG degron line, DMSO, clone B

description: Library name: 05_hES_clone_B_DMSO_ChIP_CTCF


title: Input ChIP in hES ARID1A-dTAG degron line, dTAG-13-treated, clone D

description: Library name: 04_hES_clone_D_dTAG_ChIP_input


title: TN_WD_female_17w_44_heart

description: Library name: HDP-018793_heart


title: TN_CD_female_3d_47_heart

description: Library name: HDP-019091_heart


title: Input ChIP in hES ARID1A-dTAG degron line, DMSO, clone B

description: Library name: 01_hES_clone_B_DMSO_ChIP_input


title: TN_WD_female_3d_43_heart

description: Library name: HDP-019013_heart


title: Flesh_D18_Ctrl_Rep1

description: Library name: PPP2_129


title: TN_WD_male_17w_40_heart

description: Library name: HDP-018728_heart


title: Flesh_D15+2wk_Rep4

description: Library name: PPP2_128


title: Input ChIP in hES ARID1A-dTAG degron line, dTAG-13-treated, clone B

description: Library name: 02_hES_clone_B_dTAG_ChIP_input


title: PBRM1 ChIP in SUM159 ARID1A HET clone 45

description: Library name: 21_ChIP_PBRM1_SUM159_Het45

value: Triple-negative breast cancer

value: ARID1A HET


title: TN_WD_male_9w_42_heart

description: Library name: HDP-018828_heart


title: RT_WD_female_17w_41_heart

description: Library name: HDP-018890_heart


title: TN_WD_male_3d_39_heart

description: Library name: HDP-019060_heart


title: PDO from Pt79_t4

description: Gene-level expression estimates from RMA analysis using the Transcriptome Analysis Console (TAC 4.0) software

source_name: Patient 79, tumor 4


title: Flesh_D15+2wk_Rep2

description: Library name: PPP2_126


title: Flesh_D15+2wk_Rep1

description: Library name: PPP2_125


title: Flesh_D17_Ctrl_Rep4

description: Library name: PPP2_124


title: PBRM1 ChIP in SUM159 ARID1A HET clone 77

description: Library name: 20_ChIP_PBRM1_SUM159_Het77


title: PDO from Pt80_t1

source_name: Patient 80, tumor 1


title: PBRM1 ChIP in SUM159 ARID1A HET clone 66

description: Library name: 19_ChIP_PBRM1_SUM159_Het66


title: TN_WD_male_3d_38_heart

description: Library name: HDP-019002_heart


title: TN_WD_female_9w_37_heart

description: Library name: HDP-018810_heart


title: Flesh_D17_Ctrl_Rep3

description: Library name: PPP2_123

source_name: Flesh


title: PDO from Pt79_t3

source_name: Patient 79, tumor 3


title: PDO from Pt8_t1

source_name: Patient 8, tumor 1


title: PDO from Pt79_t2

source_name: Patient 79, tumor 2


title: PBRM1 ChIP in SUM159 WT FHD-286 rep2

description: Library name: 18_ChIP_PBRM1_SUM159_WT2_FHD286

value: WT


title: TN_WD_male_17w_36_heart

description: Library name: HDP-018702_heart

source_name: heart


title: PDO from Pt85_t3

source_name: Patient 85, tumor 3


title: PDO from Pt76_t3

source_name: Patient 76, tumor 3


title: PDO from Pt79_t1

source_name: Patient 79, tumor 1


title: PBRM1 ChIP in SUM159 WT FHD-286 rep1

description: Library name: 16_ChIP_PBRM1_SUM159_WT1_FHD286


title: Flesh_D17_Ctrl_Rep2

description: Library name: PPP2_122


title: Flesh_D15+1wk_Rep3

description: Library name: PPP2_119


title: RT_WD_female_17w_35_heart

description: Library name: HDP-018964_heart


title: Flesh_D15+1wk_Rep4

description: Library name: PPP2_120


title: Flesh_D17_Ctrl_Rep1

description: Library name: PPP2_121


title: TN_WD_male_17w_34_heart

description: Library name: HDP-018750_heart


title: PDO from Pt7_t1

source_name: Patient 7, tumor 1


title: PBRM1 ChIP in SUM159 WT DMSO rep2

description: Library name: 17_ChIP_PBRM1_SUM159_WT2_DMSO


title: TN_CD_male_17w_33_heart

description: Library name: HDP-018727_heart


title: PDO from Pt76_t1

source_name: Patient 76, tumor 1


title: TN_WD_female_9w_30_heart

description: Library name: HDP-018808_heart


title: Flesh_D16_Ctrl_Rep4

description: Library name: PPP2_116


title: ARID1A ChIP in SUM159 ARID1A HET clone 45

description: Library name: 14_ChIP_ARID1A_SUM159_Het45


title: PBRM1 ChIP in SUM159 WT DMSO rep1

description: Library name: 15_ChIP_PBRM1_SUM159_WT1_DMSO


title: Flesh_D15+1wk_Rep2

description: Library name: PPP2_118


title: TN_CD_male_9w_32_heart

description: Library name: HDP-018825_heart


title: TN_WD_male_9w_31_heart

description: Library name: HDP-018797_heart


title: ARID1A ChIP in SUM159 ARID1A HET clone 66

description: Library name: 12_ChIP_ARID1A_SUM159_Het66


title: ARID1A ChIP in SUM159 ARID1A HET clone 77

description: Library name: 13_ChIP_ARID1A_SUM159_Het77


title: Flesh_D15+1wk_Rep1

description: Library name: PPP2_117


title: PDO from Pt68_t1

source_name: Patient 68, tumor 1


title: PDO from Pt66_t3

source_name: Patient 66, tumor 3


title: PDO from Pt66_t1

source_name: Patient 66, tumor 1


title: PDO from Pt66_t2

source_name: Patient 66, tumor 2


title: PDO from Pt63_t2

source_name: Patient 63, tumor 2


title: ARID1A ChIP in SUM159 WT FHD-286 rep2

description: Library name: 11_ChIP_ARID1A_SUM159_WT2_FHD286


title: Flesh_D16_Ctrl_Rep3

description: Library name: PPP2_115


title: ARID1A ChIP in SUM159 WT FHD-286 rep1

description: Library name: 09_ChIP_ARID1A_SUM159_WT1_FHD286


title: Flesh_D16_Ctrl_Rep2

description: Library name: PPP2_114


title: ARID1A ChIP in SUM159 WT DMSO rep2

description: Library name: 10_ChIP_ARID1A_SUM159_WT2_DMSO


title: PDO from Pt63_t1

source_name: Patient 63, tumor 1


title: TN_WD_female_9d_28_heart

description: Library name: HDP-019078_heart


title: PDO from Pt6_t2

source_name: Patient 6, tumor 2

value: first sampled resection


title: Flesh_D15_Eth_Rep3

description: Library name: PPP2_111

source_name: Flesh


title: Flesh_D15_Eth_Rep4

description: Library name: PPP2_112


title: PDO from Pt6.3_t2

value: PDO cultured from resected liver metastases

value: third sampled resection


title: CTCF ChIP in SUM159 CTCF HET clone 77

description: Library name: 19_ChIP_CTCF_SUM159_Het_trunc_77

value: CTCF HET truncated


title: TN_WD_female_3d_25_heart

description: Library name: HDP-019014_heart


title: TN_CD_male_3d_27_heart

description: Library name: HDP-019023_heart


title: Flesh_D16_Ctrl_Rep1

description: Library name: PPP2_113


title: Flesh_D15_Eth_Rep2

description: Library name: PPP2_110


title: ARID1A ChIP in SUM159 WT DMSO rep1

description: Library name: 08_ChIP_ARID1A_SUM159_WT1_DMSO


title: Flesh_D15_Eth_Rep1

description: Library name: PPP2_109


title: CTCF ChIP in SUM159 WT rep3

description: Library name: 14_ChIP_CTCF_SUM159_WT_3


title: CTCF ChIP in SUM159 CTCF HET clone 45

description: Library name: 22_ChIP_CTCF_SUM159_Het_trunc_45


title: PDO from Pt6.2_t1

source_name: Patient 6, tumor 1

value: second sampled resection


title: TN_WD_male_17w_24_heart

description: Library name: HDP-018712_heart


title: TN_WD_male_17w_22_heart

description: Library name: HDP-018710_heart


title: CTCF ChIP in SUM159 CTCF HET clone 66

description: Library name: 18_ChIP_CTCF_SUM159_Het_trunc_66


title: PDO from Pt55_t1

description: Gene-level expression estimates from RMA analysis using the Transcriptome Analysis Console (TAC 4.0) software

source_name: Patient 55, tumor 1


title: RT_CD_female_17w_26_heart

description: Library name: HDP-018965_heart


title: TN_CD_male_17w_23_heart

description: Library name: HDP-018806_heart


title: Flesh_D15_Ctrl_Rep4

description: Library name: PPP2_108

value: Russet Burbank (Solanum tuberosum L.)


title: CTCF ChIP in SUM159 WT rep2

description: Library name: 13_ChIP_CTCF_SUM159_WT_2


title: PDO from Pt6.2_t2


title: CTCF ChIP in SUM159 WT rep1

description: Library name: 12_ChIP_CTCF_SUM159_WT_1


title: Flesh_D15_Ctrl_Rep3

description: Library name: PPP2_107

value: Control


title: PDO from Pt55.3_t1


title: PDO from Pt55_t2

source_name: Patient 55, tumor 2


title: PDO from Pt6.3_t1


title: TN_CD_female_9w_21_heart

description: Library name: HDP-018823_heart

source_name: heart


title: Flesh_D15_Ctrl_Rep1

description: Library name: PPP2_105


title: Input to CTCF/SMC3 ChIP in SUM159 CTCF HET clone 45

description: Library name: 11_ChIP_input_SUM159_Het_trunc_45


title: Input to CTCF/SMC3 ChIP in SUM159 CTCF HET clone 77

description: Library name: 08_ChIP_input_SUM159_Het_trunc_77


title: Flesh_D15_Ctrl_Rep2

description: Library name: PPP2_106


title: TN_WD_female_17w_20_heart

description: Library name: HDP-018789_heart


title: TN_WD_female_17w_29_heart

description: Library name: HDP-018736_heart


title: TN_CD_female_17w_17_heart

description: Library name: HDP-018698_heart


title: RT_WD_female_17w_18_heart

description: Library name: HDP-018848_heart


title: TN_WD_male_27d_19_heart

description: Library name: HDP-018984_heart


title: PDO from Pt54_t1.1

source_name: Patient 54, tumor 1.1


title: Input to CTCF/SMC3 ChIP in SUM159 CTCF HET clone 66

description: Library name: 07_ChIP_input_SUM159_Het_trunc_66


title: Flesh_D12_Eth_Rep4

description: Library name: PPP2_104

value: Ethylene


title: Input to ARID1A/PBRM1 ChIP in SUM159 ARID1A HET clone 77

description: Library name: 06_input_ChIP_SUM159_Het77


title: Flesh_D12_Eth_Rep3

description: Library name: PPP2_103


title: PDO from Pt54_t1.2

source_name: Patient 54, tumor 1.2


title: PDO from Pt54.3_t1

source_name: Patient 54, tumor 1


title: RT_WD_female_17w_15_heart

description: Library name: HDP-018892_heart

value: heart


title: Input to ARID1A/PBRM1 ChIP in SUM159 ARID1A HET clone 45

description: Library name: 07_input_ChIP_SUM159_Het45


title: PDO from Pt54.2_t4

source_name: Patient 54, tumor 4


title: TN_WD_female_9d_16_heart

description: Library name: HDP-019077_heart


title: Flesh_D12_Eth_Rep1

description: Library name: PPP2_101


title: Flesh_D12_Eth_Rep2

description: Library name: PPP2_102


title: PDO from Pt54.2_t3

source_name: Patient 54, tumor 3


title: TN_CD_female_9d_14_heart

description: Library name: HDP-019083_heart


title: Flesh_D12_Ctrl_Rep4

description: Library name: PPP2_100


title: PDO from Pt54.2_t2

source_name: Patient 54, tumor 2


title: Input to ARID1A/PBRM1 ChIP in SUM159 WT FHD286 rep1

description: Library name: 02_input_ChIP_SUM159_WT1_FHD286


title: Input to ARID1A/PBRM1 ChIP in SUM159 WT DMSO rep1

description: Library name: 01_input_ChIP_SUM159_WT1_DMSO


title: Input to ARID1A/PBRM1 ChIP in SUM159 WT DMSO rep2

description: Library name: 03_input_ChIP_SUM159_WT2_DMSO


title: TN_WD_female_17w_13_heart

description: Library name: HDP-018696_heart


title: TN_CD_female_27d_11_heart

description: Library name: HDP-019008_heart


title: Input to CTCF/SMC3 ChIP in SUM159 WT rep3

description: Library name: 03_ChIP_input_SUM159_WT_3


title: Flesh_D12_Ctrl_Rep3

description: Library name: PPP2_99


title: Flesh_D12_Ctrl_Rep2

description: Library name: PPP2_98


title: TN_WD_male_17w_12_heart

description: Library name: HDP-018695_heart


title: Flesh_D12_Ctrl_Rep1

description: Library name: PPP2_97


title: RT_CD_female_17w_9_heart

description: Library name: HDP-018883_heart


title: Flesh_D9_Eth_Rep3

description: Library name: PPP2_95


title: TN_CD_female_9w_10_heart

description: Library name: HDP-018790_heart


title: Flesh_D9_Eth_Rep4

description: Library name: PPP2_96


title: PDO from Pt52_t2

source_name: Patient 52, tumor 2


title: Input to CTCF/SMC3 ChIP in SUM159 WT rep1

description: Library name: 01_ChIP_input_SUM159_WT_1


title: PDO from Pt32_t2

source_name: Patient 32, tumor 2


title: Input to CTCF/SMC3 ChIP in SUM159 WT rep2

description: Library name: 02_ChIP_input_SUM159_WT_2


title: PDO from Pt32_t3

source_name: Patient 32, tumor 3


title: TN_CD_female_17w_8_heart

description: Library name: HDP-018732_heart


title: PDO from Pt32_t1

source_name: Patient 32, tumor 1


title: PDO from Pt50.2_t1

source_name: Patient 50, tumor 1


title: PDO from Pt50_t3

source_name: Patient 50, tumor 3


title: TN_WD_male_9w_7_heart

description: Library name: HDP-018794_heart


title: RIVA_TQ2_ATAC_Rep1

description:
Library name: Darko_TQ2_CTCF_ATAC
Single cell ATAC data

library_source: genomic single cell

data_processing:
Cellranger Arc 2.0.0
Signac 1.5.0 Processing
MACS2 peak calling
Harmony correction of PCA and LSI
Slingshot 2.8.0 pseudotime
Assembly: GRCh38
Supplementary files format and content: batch1.msobj.rds Signac Object
Supplementary files format and content: b1.dq.atac_fragments.tsv.gz Cellranger Fragment File
Supplementary files format and content: b1.tq.atac_fragments.tsv.gz Cellranger Fragment File
Supplementary files format and content: batch2.msobj.rds Signac Object
Supplementary files format and content: b2.dq.atac_fragments.tsv.gz  Cellranger Fragment File
Supplementary files format and content: b2.tq.atac_fragments.tsv.gz Cellranger Fragment File
Supplementary files format and content: b2.dko.atac_fragments.tsv.gz Cellranger Fragment File

source_name: RIVA

extract_protocol:
Cell lines underwent the manufacturer's nuclear preparation procedure
20000 nuclei were loaded into the 10x Chromium Instrument and prepared according to the manufacturer's protocol for 10x multiome

value: RIVA

value: B-cell lymphoma ABC-DLBCL

value: ARID1A Het ARID2 KO


title: Flesh_D9_Eth_Rep1

description: Library name: PPP2_93

source_name: Flesh


title: PDO from Pt54.2_t1


title: Flesh_D9_Eth_Rep2

description: Library name: PPP2_94


title: Flesh_D9_Ctrl_Rep4

description: Library name: PPP2_92


title: Flesh_D9_Ctrl_Rep3

description: Library name: PPP2_91


title: RIVA_TQ2_RNA_Rep1

description:
Library name: Darko_TQ2_CTCF_RNA
Single cell RNA data


title: TN_CD_female_27d_6_heart

description: Library name: HDP-019007_heart


title: TN_WD_male_17w_5_heart

description: Library name: HDP-018711_heart


title: RIVA_DQ1_ATAC_Rep1

description:
Library name: Darko_DQ1_CTCF_ATAC
Single cell ATAC data


title: Flesh_D9_Ctrl_Rep1

description: Library name: PPP2_89


title: RIVA_DKO4_RNA

description:
Library name: KK-4511_03_GEX_DKO4
Single cell RNA data


title: RT_WD_male_17w_4_heart

description: Library name: HDP-018885_heart


title: Flesh_D9_Ctrl_Rep2

description: Library name: PPP2_90


title: RIVA_DQ1_RNA_Rep1

description:
Library name: Darko_DQ1_CTCF_RNA
Single cell RNA data


title: TN_WD_female_3d_3_heart

description: Library name: HDP-019069_heart


title: PDO from Pt30_t1

source_name: Patient 30, tumor 1


title: Input to ARID1A/PBRM1 ChIP in SUM159 WT FHD286 rep2

description: Library name: 04_input_ChIP_SUM159_WT2_FHD286


title: PDO from Pt29_t3

source_name: Patient 29, tumor 3


title: PDO from Pt3_t1

source_name: Patient 3, tumor 1


title: PDO from Pt30_t2

source_name: Patient 30, tumor 2


title: PDO from Pt3_t6

source_name: Patient 3, tumor 6


title: RIVA_TQ2_RNA_Rep2

description:
Library name: KK-4511_02_GEX_TQ2
Single cell RNA data

value: ARID1A Het ARID2 WT


title: TN_WD_female_9d_160_liver

description: Library name: HDP-019077_liver

source_name: liver

value: liver


title: Flesh_D6_Eth_Rep2

description: Library name: PPP2_86

value: Flesh


title: Flesh_D6_Eth_Rep4

description: Library name: PPP2_88


title: RT_CD_male_17w_2_heart

description: Library name: HDP-018919_heart

source_name: heart


title: RT_WD_female_17w_158_liver

description: Library name: HDP-018848_liver


title: Flesh_D6_Eth_Rep1

description: Library name: PPP2_85


title: RIVA_TQ2_ATAC_Rep2

description:
Library name: KK-4511_02_ATAC_TQ2
Single cell ATAC data


title: PDO from Pt29_t1

description: Gene-level expression estimates from RMA analysis using the Transcriptome Analysis Console (TAC 4.0) software

source_name: Patient 29, tumor 1


title: RIVA_DQ1_ATAC_Rep2

description:
Library name: KK-4511_01_ATAC_DQ1
Single cell ATAC data

value: ARID1A WT ARID2 WT


title: RT_CD_male_17w_1_heart

description: Library name: HDP-018950_heart


title: TN_CD_male_17w_157_liver

description: Library name: HDP-018709_liver


title: RIVA_DQ1_RNA_Rep2

description:
Library name: KK-4511_01_GEX_DQ1
Single cell RNA data


title: PDO from Pt28_t2

source_name: Patient 28, tumor 2


title: RIVA_DKO4_ATAC

description:
Library name: KK-4511_03_ATAC_DKO4
Single cell ATAC data


title: TN_CD_male_27d_159_liver

description: Library name: HDP-018993_liver


title: PDO from Pt29_t2

source_name: Patient 29, tumor 2


title: Flesh_D6_Eth_Rep3

description: Library name: PPP2_87


title: RIVA ARID1A Het rep 3

description: Library name: 06_ATAC_RIVA_TQ2_rep3

data_processing:
Trimming by TrimGalore
Alignment by BWA
Filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Assembly: hg38 / mm10
Supplementary files format and content: bed files of MACS2 narrowPeaks

source_name: cell line

extract_protocol:
Omni ATAC-Seq protocol (Corces et al., 2017; Nature Methods)
Amplification with Q5® High-Fidelity 2X Master Mix and Illumina dual indexes.

treatment_protocol: Inhibitor or DMSO treatment for 24h.

value: cell line


title: TN_WD_female_9d_156_liver

description: Library name: HDP-019078_liver


title: RIVA ARID1A Het rep 2

description: Library name: 05_ATAC_RIVA_TQ2_rep2


title: Flesh_D6_Ctrl_Rep4

description: Library name: PPP2_84


title: Flesh_D6_Ctrl_Rep1

description: Library name: PPP2_81


title: Flesh_D6_Ctrl_Rep2

description: Library name: PPP2_82


title: Flesh_D3_Eth_Rep4

description: Library name: PPP2_80


title: RIVA ARID1A Het rep 1

description: Library name: 04_ATAC_RIVA_TQ2_rep1


title: PDO from Pt28_t4

source_name: Patient 28, tumor 4


title: RIVA ARID1A Het ISWI KO rep 2

description: Library name: 02_ATAC_RIVA_ISWI_KO_TQ2AA6_rep2


title: PDO from Pt26_t2

source_name: Patient 26, tumor 2


title: TN_CD_female_9d_154_liver

description: Library name: HDP-019054_liver


title: RIVA ARID1A Het ISWI KO rep 3

description: Library name: 03_ATAC_RIVA_ISWI_KO_TQ2AA6_rep3


title: PDO from Pt26_t1

source_name: Patient 26, tumor 1


title: TN_CD_female_27d_155_liver

description: Library name: HDP-019007_liver


title: PDO from Pt24_t1

source_name: Patient 24, tumor 1


title: Flesh_D3_Eth_Rep3

description: Library name: PPP2_79


title: TN_CD_male_27d_153_liver

description: Library name: HDP-018995_liver


title: PDO from Pt25_t1

source_name: Patient 25, tumor 1


title: RIVA ARID1A Het ISWI KO rep 1

description: Library name: 01_ATAC_RIVA_ISWI_KO_TQ2AA6_rep1


title: PDO from Pt23_t5

source_name: Patient 23, tumor 5


title: PDO from Pt23_t4

source_name: Patient 23, tumor 4


title: TN_WD_male_17w_151_liver

description: Library name: HDP-018711_liver


title: SKMEL cells treated with FHD286 rep 2

description: Library name: 8_SKMEL_FHD286_100nM_24h_ATAC_R2

value: SKMEL

value: Skin

value: WT


title: TN_WD_female_9w_152_liver

description: Library name: HDP-018837_liver


title: SKMEL cells treated with FHD286 rep 3

description: Library name: 9_SKMEL_FHD286_100nM_24h_ATAC_R3


title: Flesh_D3_Eth_Rep1

description: Library name: PPP2_77

source_name: Flesh


title: PDO from Pt24_t2

source_name: Patient 24, tumor 2

value: PDO cultured from resected liver metastases


title: Flesh_D3_Ctrl_Rep4

description: Library name: PPP2_76


title: SKMEL cells treated with FHD286 rep 1

description: Library name: 7_SKMEL_FHD286_100nM_24h_ATAC_R1


title: TN_CD_male_9d_150_liver

description: Library name: HDP-019056_liver


title: Flesh_D3_Eth_Rep2

description: Library name: PPP2_78


title: TN_CD_female_27d_149_liver

description: Library name: HDP-019017_liver


title: Flesh_D3_Ctrl_Rep2

description: Library name: PPP2_74


title: Flesh_D3_Ctrl_Rep1

description: Library name: PPP2_73


title: Flesh_D3_Ctrl_Rep3

description: Library name: PPP2_75


title: SKMEL cells treated with DMSO rep 2

description: Library name: 11_SKMEL_DMSO_24h_ATAC_R2

value: DMSO


title: SKMEL cells treated with DMSO rep 1

description: Library name: 10_SKMEL_DMSO_24h_ATAC_R1


title: TN_CD_male_9d_148_liver

description: Library name: HDP-019057_liver


title: TN_WD_male_27d_147_liver

description: Library name: HDP-019015_liver


title: PDO from Pt23_t1

source_name: Patient 23, tumor 1


title: PDO from Pt22.2_t1

source_name: Patient 22, tumor 1


title: PDO from Pt21_t1

source_name: Patient 21, tumor 1


title: PDO from Pt20_t1

source_name: Patient 20, tumor 1


title: TN_CD_male_9w_146_liver

description: Library name: HDP-018825_liver

source_name: liver


title: PDO from Pt23_t2

source_name: Patient 23, tumor 2


title: Jurkat cells treated with DMSO rep 3

description: Library name: 18_Jurkat_DMSO_24h_ATAC_R3

value: Jurkat

value: T cell


title: PDO from Pt23_t3

source_name: Patient 23, tumor 3


title: TN_CD_male_9d_144_liver

description: Library name: HDP-019059_liver


title: Flesh_D0_Ctrl_Rep4

description: Library name: PPP2_72

value: Russet Burbank (Solanum tuberosum L.)

value: Control


title: Flesh_D0_Ctrl_Rep2

description: Library name: PPP2_70


title: Flesh_D0_Ctrl_Rep1

description: Library name: PPP2_69


title: Jurkat cells treated with DMSO rep 2

description: Library name: 17_Jurkat_DMSO_24h_ATAC_R2

source_name: cell line


title: TN_WD_female_17w_145_liver

description: Library name: HDP-018705_liver


title: Jurkat cells treated with FHD286 rep 3

description: Library name: 15_Jurkat_FHD286_100nM_24h_ATAC_R3


title: PB_D15+3wk_Rep3

description: Library name: PPP2_67

source_name: Primary Bud

value: Primary Bud


title: Jurkat cells treated with DMSO rep 1

description: Library name: 16_Jurkat_DMSO_24h_ATAC_R1


title: TN_CD_male_27d_141_liver

description: Library name: HDP-018979_liver


title: TN_WD_male_3d_142_liver

description: Library name: HDP-019020_liver


title: PB_D15+3wk_Rep4

description: Library name: PPP2_68


title: Flesh_D0_Ctrl_Rep3

description: Library name: PPP2_71


title: Jurkat cells treated with FHD286 rep 2

description: Library name: 14_Jurkat_FHD286_100nM_24h_ATAC_R2


title: PDO from Pt18_t4

source_name: Patient 18, tumor 4


title: PDO from Pt18_t1

source_name: Patient 18, tumor 1


title: TN_CD_female_9w_140_liver

description: Library name: HDP-018829_liver


title: PDO from Pt18_t3

source_name: Patient 18, tumor 3


title: SUM159 ARID1AKO cells clone 3

description: Library name: 12_ATAC_rep_SUM159_KO_94

value: Breast

value: ARID1A KO


title: TN_CD_male_27d_143_liver

description: Library name: HDP-018994_liver


title: Jurkat cells treated with FHD286 rep 1

description: Library name: 13_Jurkat_FHD286_100nM_24h_ATAC_R1


title: TN_CD_male_17w_139_liver

description: Library name: HDP-018694_liver


title: PB_D15+3wk_Rep1

description: Library name: PPP2_65


title: PB_D15+3wk_Rep2

description: Library name: PPP2_66


title: TN_WD_male_27d_137_liver

description: Library name: HDP-019009_liver


title: SUM159 ARID1AKO cells clone 2

description: Library name: 11_ATAC_rep_SUM159_KO_42


title: SUM159 ARID1AKO cells clone 1

description: Library name: 10_ATAC_rep_SUM159_KO_20


title: PB_D18_Ctrl_Rep4

description: Library name: PPP2_64


title: SUM159 ARID1AHet cells clone 3

description: Library name: 09_ATAC_rep_SUM159_Het_trunc_77

value: ARID1A Het


title: PB_D18_Ctrl_Rep3

description: Library name: PPP2_63


title: TN_WD_male_3d_138_liver

description: Library name: HDP-019060_liver

value: liver


title: PDO from Pt17_t3

description: Gene-level expression estimates from RMA analysis using the Transcriptome Analysis Console (TAC 4.0) software

source_name: Patient 17, tumor 3


title: PDO from Pt137_t5

source_name: Patient 137, tumor 5

value: first sampled resection


title: PDO from Pt137_t4

source_name: Patient 137, tumor 4


title: PDO from Pt15_t3

source_name: Patient 15, tumor 3


title: TN_WD_male_3d_136_liver

description: Library name: HDP-019022_liver


title: PDO from Pt137_t3

source_name: Patient 137, tumor 3


title: PDO from Pt17_t1

source_name: Patient 17, tumor 1


title: TN_CD_male_27d_135_liver

description: Library name: HDP-018981_liver


title: PB_D18_Ctrl_Rep1

description: Library name: PPP2_61


title: SUM159 ARID1AHet cells clone 2

description: Library name: 08_ATAC_rep_SUM159_Het_trunc_66


title: PB_D15+2wk_Rep3

description: Library name: PPP2_59


title: PB_D18_Ctrl_Rep2

description: Library name: PPP2_62


title: SUM159 WT cells clone 1

description: Library name: 01_ATAC_rep_SUM159_WT_1


title: TN_CD_male_9w_134_liver

description: Library name: HDP-018821_liver


title: PDO from Pt17_t2

source_name: Patient 17, tumor 2


title: SUM159 ARID1AHet cells clone 1

description: Library name: 07_ATAC_rep_SUM159_Het_trunc_45


title: PB_D15+2wk_Rep2

description: Library name: PPP2_58


title: SUM159 WT cells clone 2

description: Library name: 02_ATAC_rep_SUM159_WT_2


title: SKMEL cells treated with DMSO rep 3

description: Library name: 12_SKMEL_DMSO_24h_ATAC_R3


title: PB_D15+2wk_Rep4

description: Library name: PPP2_60


title: TN_CD_female_3d_132_liver

description: Library name: HDP-019062_liver


title: PDO from Pt134_t2

source_name: Patient 134, tumor 2


title: PB_D15+2wk_Rep1

description: Library name: PPP2_57


title: SUM159 WT cells clone 3

description: Library name: 03_ATAC_rep_SUM159_WT_3


title: TN_CD_female_17w_133_liver

description: Library name: HDP-018706_liver


title: PDO from Pt134_t4

source_name: Patient 134, tumor 4


title: SUM159 cells treated with DMSO rep 2

description: Library name: 5_SUM159_DMSO_24h_ATAC_R2


title: TN_CD_male_3d_130_liver

description: Library name: HDP-019024_liver

source_name: liver


title: TN_WD_female_27d_129_liver

description: Library name: HDP-018977_liver


title: TN_CD_male_27d_131_liver

description: Library name: HDP-018982_liver


title: PB_D17_Ctrl_Rep1

description: Library name: PPP2_53


title: PB_D17_Ctrl_Rep3

description: Library name: PPP2_55


title: PB_D17_Ctrl_Rep2

description: Library name: PPP2_54


title: PB_D17_Ctrl_Rep4

description: Library name: PPP2_56


title: PDO from Pt134_t1

source_name: Patient 134, tumor 1


title: TN_WD_female_9w_128_liver

description: Library name: HDP-018810_liver


title: TN_WD_female_17w_127_liver

description: Library name: HDP-018807_liver


title: PDO from Pt13_t1

source_name: Patient 13, tumor 1


title: SUM159 cells treated with FHD286 rep 2

description: Library name: 2_SUM159_FHD286_100nM_24h_ATAC_R2

source_name: cell line


title: SUM159 cells treated with FHD286 rep 1

description: Library name: 1_SUM159_FHD286_100nM_24h_ATAC_R1


title: TN_CD_male_3d_126_liver

description: Library name: HDP-019023_liver


title: PDO from Pt137.2_t1

source_name: Patient 137, tumor 1

value: second sampled resection


title: PDO from Pt125_t3

source_name: Patient 125, tumor 3


title: SUM159 cells treated with DMSO rep 1

description: Library name: 4_SUM159_DMSO_24h_ATAC_R1

value: cell line


title: PDO from Pt134_t3

source_name: Patient 134, tumor 3


title: PB_D15+1wk_Rep4

description: Library name: PPP2_52

source_name: Primary Bud


title: PDO from Pt124_t2

source_name: Patient 124, tumor 2


title: hES ARID1Adegron cells treated with dTAG at 24 hours clone 2

description: Library name: 11_ATAC_hES_ARID1Adegron_24h_dTAG_clone_D

value: Human Embryonic Stem Cells

value: ARID1A degron

value: dTAG


title: PB_D15+1wk_Rep3

description: Library name: PPP2_51


title: PDO from Pt125_t1

source_name: Patient 125, tumor 1

value: PDO cultured from resected liver metastases


title: hES ARID1Adegron cells treated with dTAG at 24 hours clone 1

description: Library name: 10_ATAC_hES_ARID1Adegron_24h_dTAG_clone_B


title: TN_WD_male_27d_125_liver

description: Library name: HDP-018984_liver


title: TN_WD_male_9w_124_liver

description: Library name: HDP-018827_liver


title: PB_D15+1wk_Rep1

description: Library name: PPP2_49


title: SUM159 cells treated with FHD286 rep 3

description: Library name: 3_SUM159_FHD286_100nM_24h_ATAC_R3

value: WT


title: PB_D15+1wk_Rep2

description: Library name: PPP2_50


title: hES ARID1Adegron cells treated with DMSO at 24 hours clone 2

description: Library name: 08_ATAC_hES_ARID1Adegron_24h_DMSO_clone_D

value: DMSO


title: TN_CD_male_3d_123_liver

description: Library name: HDP-019026_liver


title: PDO from Pt134_t5

source_name: Patient 134, tumor 5


title: hES ARID1Adegron cells treated with DMSO at 24 hours clone 1

description: Library name: 07_ATAC_hES_ARID1Adegron_24h_DMSO_clone_B


title: RT_WD_male_17w_122_liver

description: Library name: HDP-018961_liver


title: TN_CD_male_9w_121_liver

description: Library name: HDP-018788_liver


title: PDO from Pt121_t2

source_name: Patient 121, tumor 2


title: PB_D16_Ctrl_Rep3

description: Library name: PPP2_47


title: PB_D16_Ctrl_Rep4

description: Library name: PPP2_48


title: hES ARID1Adegron cells treated with dTAG at 6 hours clone 2

description: Library name: 05_ATAC_hES_ARID1Adegron_6h_dTAG_clone_D


title: PDO from Pt121_t3

source_name: Patient 121, tumor 3


title: PDO from Pt124_t1

source_name: Patient 124, tumor 1


title: hES ARID1Adegron cells treated with dTAG at 6 hours clone 1

description: Library name: 04_ATAC_hES_ARID1Adegron_6h_dTAG_clone_B


title: hES ARID1Adegron cells treated with DMSO at 6 hours clone 2

description: Library name: 02_ATAC_hES_ARID1Adegron_6h_DMSO_clone_D


title: PDO from Pt121_t1

source_name: Patient 121, tumor 1


title: TN_CD_male_3d_119_liver

description: Library name: HDP-019025_liver


title: PB_D16_Ctrl_Rep1

description: Library name: PPP2_45


title: PB_D16_Ctrl_Rep2

description: Library name: PPP2_46


title: TN_CD_female_3d_120_liver

description: Library name: HDP-019119_liver


title: PDO from Pt12_t4

source_name: Patient 12, tumor 4


title: hES ARID1Adegron cells treated with DMSO at 6 hours clone 1

description: Library name: 01_ATAC_hES_ARID1Adegron_6h_DMSO_clone_B


title: PB_D15_Eth_Rep4

description: Library name: PPP2_44

value: Ethylene


title: Human LC snRNA-seq, Caudal section, reaction B

city: New York

first: Fahrunisa Meryem Betul

last: Erol Gulsen

address: 1150 St Nicholas Ave

department: Pediatrics

institute: Columbia University

description:
Library name: LC002B
10x Genomics Chromium Single-Cell 3' v3

data_processing:
Raw gene–barcode matrices were generated using Cell Ranger v6.1.2 (10x Genomics). Reads were aligned to the GRCh38-2020-A human reference transcriptome with intronic reads excluded (--include-introns false).
Filtered feature–barcode matrices were imported into R v4.3.2 and processed with Seurat v5.0.1. QC filtering retained 2,071 of 2,347 nuclei (88.2%). Four Chromium reactions were integrated using Seurat's reciprocal PCA (RPCA)-based workflow.
The four Basak LC snRNA-seq reactions were integrated with published human LC snRNA-seq datasets (Weber et al., eLife 2024, DOI: 10.7554/eLife.84628; Siletti et al., Science 2023, DOI: 10.1126/science.add7046) into a single Seurat object using SCTransform normalization followed by RPCA-based multi-sample integration.
Assembly: GRCh38 (GRCh38-2020-A, 10x Genomics reference)
Supplementary files format and content: Cell Ranger filtered feature–barcode matrix files (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz)
Supplementary files format and content: Seurat objects in RDS format (basak_snRNA_seurat.rds, meta_snRNA_allcells_seurat.rds, meta_snRNA_neurons_seurat.rds)

molecule: nuclear RNA

source_name: locus coeruleus

extract_protocol:
Postmortem human brainstem tissue containing the locus coeruleus was dissected using a 2 mm diameter punch from cryosectioned transverse slices. Nuclei were isolated using a protocol adapted from 10x Genomics: tissue was homogenized in Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute; Millipore-Sigma), centrifuged, and washed twice in Nuclei Wash & Resuspension Buffer (0.04% BSA in PBS). The nuclei suspension was filtered through a 40 µm Flowmi Cell Strainer and loaded onto the 10x Chromium instrument at the Single Cell Analysis Core, Columbia University.
Sequencing libraries were generated using the 10x Genomics Chromium Single-Cell 3' Reagent Kit v3 and sequenced on an Illumina NovaSeq 6000.

value: locus coeruleus

tag: age

value: female

tag: donor id

tag: disease state

value: neurotypical

tag: lc region

value: caudal


title: PDO from Pt12_t3

data_processing: Gene-level expression signals were estimated according to the robust multi-array average (RMA) approach implemented in the Transcriptome Analysis Console (TAC 4.0) software (Affymetrix) with defult settings.

source_name: Patient 12, tumor 3

extract_protocol: Total RNA was extracted from tumor organoids and tumor tissue samples using the Allprep DNA/RNA/miRNA Universal kit according to the manufacturer’s instructions (Qiagen GmBH).

tag: patient

tag: tumor

tag: samples from repeated resections


title: TN_WD_female_9d_117_liver

description: Library name: HDP-019117_liver

data_processing:
Bulk RNA barcoding and sequencing (BRB-seq) libraries were generated and sequenced by Alithea Genomics (Switzerland). The raw data was demultiplexed, cleaned, and aligned to the mouse reference genome GRCm39/mm39 using R (version 4.1.a) and START (version 2.7.9a). Count matrices were used for downstream analyses
Assembly: genome GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: liver

extract_protocol:
RNA was extracted from liver and heart tissues using Direct-zol-96 RNA kit (Zymo research)
The generation of bulk RNA Barcoding and sequencing (BRB-seq) libraries was performed using the MERCURIUSTM BRB-seq library preparation kit for Illumina and following the manufacturer’s manual

tag: tissue


title: TN_WD_female_27d_118_liver

description: Library name: HDP-018986_liver


title: PB_D15_Eth_Rep3

description: Library name: PPP2_43

value: Primary Bud

tag: genotype

value: Russet Burbank (Solanum tuberosum L.)

tag: treatment


title: Human LC snRNA-seq, Caudal section, reaction A

description:
Library name: LC002A
10x Genomics Chromium Single-Cell 3' v3


title: PDO from Pt116_t3

source_name: Patient 116, tumor 3

tag: group


title: Human LC snRNA-seq, Rostral section, reaction B

description:
Library name: LC001B
10x Genomics Chromium Single-Cell 3' v3

value: rostral


title: RT_CD_female_17w_115_liver

description: Library name: HDP-018920_liver

value: liver


title: PB_D15_Eth_Rep2

description: Library name: PPP2_42


title: PB_D15_Eth_Rep1

description: Library name: PPP2_41


title: TN_WD_female_3d_116_liver

description: Library name: HDP-019012_liver


title: PDO from Pt116_t2

description: Gene-level expression estimates from RMA analysis using the Transcriptome Analysis Console (TAC 4.0) software

source_name: Patient 116, tumor 2


title: PB_D15_Ctrl_Rep4

description: Library name: PPP2_40

value: Control


title: PB_D15_Ctrl_Rep3

description: Library name: PPP2_39


title: PDO from Pt12_t1

source_name: Patient 12, tumor 1


title: Human LC snRNA-seq, Rostral section, reaction A

description:
Library name: LC001A
10x Genomics Chromium Single-Cell 3' v3


title: TN_WD_male_9d_113_liver

description: Library name: HDP-019081_liver


title: PDO from Pt112_t2

source_name: Patient 112, tumor 2


title: PDO from Pt112_t1

source_name: Patient 112, tumor 1


title: Sample3 of Run6, Fetal hippocampal tissue section

city: Amsterdam

first: Dilara

last: Ayyildiz

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute For Neuroscience

description:
Library name: S3R6
10x Genomics

data_processing:
Paired-end FASTQ files were aligned and quantified with STARsolo123 from STAR v2.7.10b_alpha_230301(--soloFeatures Gene GeneFull_Ex50pAS Velocyto, --soloType CB_UMI_Simple, --soloCBwhitelist 3M-february-2018.txt, --soloUMIlen 12, --soloCellFilter EmptyDrops_CR, --soloMultiMappers EM) using the human reference genome GRCh38 (GENCODE v32/Ensembl98). All downstream steps were performed using the count matrix of GeneFull_Ex50pAS option, unless specified otherwise.
Assembly: GRCh38
Supplementary files format and content: Seurat Object as RDS file

source_name: Hippocampus

extract_protocol:
Nuclei were isolated from the frozen punched tissue or sections using an optimized isolation protocol. Briefly, samples were homogenized using a glass Dounce homogenizer (15 gentle strokes) in 1 ml of ice-cold Homogenization Buffer (HB), which contained mM sucrose, 5 mM calcium chloride, 3 mM magnesium acetate, 10 mM Tris, 0.1 mM EDTA, 0.1% Igepal, 0.1 mM PMSF, 1 mM 2-mercaptoethanol, and UltraPure water, along with 5 μl RNasin Plus (Promega, Benelux, Belgium). The homogenate was filtered using a 70 μm strainer and washed with 1.65 mL HB, bringing the final volume to 2.65 ml. An additional 2.65 ml of Gradient Medium (containing 5 mM calcium chloride, 50% OptiPrep (Sigma-Aldrich, Belgium), 3 mM magnesium acetate, 10 mM Tris, 0.2 mM PMSF, and 1 mM 2-mercaptoethanol) was added to achieve a final volume of 5.3 ml. To isolate the nuclei, OptiPrep Diluent Medium (ODM) consisting of 150 mM potassium chloride, 30 mM magnesium chloride, 60 mM Tris, and 250 mM sucrose was prepared. The sample was layered onto a 4 ml 29% cushion (29% Optiprep, ODM) using a P1000 pipette, and the weight was balanced with HB. Centrifugation was carried out at 7,700 rpm for 30 min at 4°C using a SW41Ti rotor. After centrifugation, the  supernatant was removed with a plastic Pasteur pipette, and the lower supernatant was aspirated using a P200 pipette. The nuclei were resuspended in 200 μl of resuspension buffer (1x PBS, 1% BSA, and 0.2 U/μl RNasin Plus), transferred to a fresh tube, and washed again with 100-200 μl of the same buffer. The resuspended solution was pooled, and any clumps were disrupted by pipetting with a P200. The sample was then filtered through a 0.35 μm strainer using a Falcon tube. A 9 μl-aliquot of the sample was mixed with 1 μl of propidium iodide (PI) stain, loaded onto a LUNA-FL slide, and left to settle for 30 seconds. The nuclei were examined under a LUNA-FL Automated Cell Counter to assess numbers and morphology.
Post cDNA amplification cleanup and construction of sample-indexed libraries and their amplification followed manufacturer’s directions (10x Genomics, CG000183_Rev_A), with the amplification step directly dependent on the quantity of input cDNA. In order to reach sequencing saturation of ~65% (~45,000 reads/nucleus), single nucleus libraries were run using paired-end sequencing with single indexing on the NovaSeq6000 platform, following manufacturer’s instructions (10x Genomics, CG000204_Rev_A). To avoid lane bias, multiple uniquely indexed samples were mixed and distributed over several lanes.

value: Hippocampus

value: Gestational week 24

value: Fetal

value: Run 6


title: TN_WD_female_9w_114_liver

description: Library name: HDP-018791_liver


title: PDO from Pt116_t1

source_name: Patient 116, tumor 1

value: PDO cultured from resected liver metastases


title: Sample6 of Run6, Fetal hippocampal tissue section

description:
Library name: S6R6
10x Genomics


title: PB_D15_Ctrl_Rep2

description: Library name: PPP2_38

source_name: Primary Bud


title: TN_WD_female_9d_110_liver

description: Library name: HDP-019085_liver


title: PB_D15_Ctrl_Rep1

description: Library name: PPP2_37


title: Sample4 of Run6, Fetal hippocampal tissue section

description:
Library name: S4R6
10x Genomics


title: Sample2 of Run6, Moderate Alzheimer's Disease,  Dentate gyrus punch

description:
Library name: S2R6
10x Genomics

source_name: Dentate gyrus

value: Dentate gyrus

value: F

value: MAD


title: PDO from Pt104_t3

source_name: Patient 104, tumor 3


title: Sample5 of Run6, Resillient,  Dentate gyrus punch

description:
Library name: S5R6
10x Genomics

value: M

value: RES


title: PB_D12_Eth_Rep4

description: Library name: PPP2_36

value: Ethylene


title: TN_WD_female_3d_112_liver

description: Library name: HDP-019013_liver


title: TN_CD_male_3d_109_liver

description: Library name: HDP-019001_liver


title: PDO from Pt104_t1

source_name: Patient 104, tumor 1


title: PB_D12_Eth_Rep3

description: Library name: PPP2_35


title: PDO from Pt104_t4

source_name: Patient 104, tumor 4


title: PDO from Pt11_t1

source_name: Patient 11, tumor 1


title: Sample2 of Run3, Non-demented control,  Dentate gyrus punch

description:
Library name: S2R3
10x Genomics

value: CTRL

value: Run 3


title: RT_WD_male_17w_108_liver

description: Library name: HDP-018886_liver


title: Sample1 of Run6, Resillient,  Dentate gyrus punch

description:
Library name: S1R6
10x Genomics


title: PB_D12_Eth_Rep1

description: Library name: PPP2_33

value: Primary Bud

value: Russet Burbank (Solanum tuberosum L.)


title: TN_WD_female_17w_107_liver

description: Library name: HDP-018736_liver

value: liver


title: PB_D12_Ctrl_Rep4

description: Library name: PPP2_32

value: Control


title: TN_CD_female_9d_106_liver

description: Library name: HDP-019083_liver


title: Sample1 of Run3, Severe Alzheimer's Disease,  Dentate gyrus punch

description:
Library name: S1R3
10x Genomics

value: SAD


title: PB_D12_Eth_Rep2

description: Library name: PPP2_34


title: Tolerant-LPS-C2

city: jinan

first: zhang

middle: jia

last: min

address: 山东省济南市平阴县

institute: jinan central hospital

description: Library name: Tolerant-LPS-C2

data_processing:
Raw reads were quality-controlled and adapter-trimmed using fastp.
Trimmed reads were aligned to the hg38 (human) reference genome using Bowtie2.
PCR duplicates were removed using Picard tools.
Peak calling was performed using MACS2 to identify open chromatin regions (ATAC-seq peaks).
Identified peaks were annotated, and transcription factor binding motif analysis was performed using HOMER.
Assembly: hg38
Supplementary files format and content: BAM: Aligned reads after quality control and duplicate removal BED: Called ATAC-seq peaks bigWig: Normalized signal tracks for visualization HOMER output: Peak annotation and motif analysis results

source_name: peripheral blood

growth_protocol:
Isolation, Sorting, and Culture of Primary Human Immune Cells
Peripheral blood mononuclear cells (PBMCs) were isolated from the peripheral blood of healthy volunteers and patients using Polymorphprep density gradient centrifugation. To obtain CD14⁺ monocytes, PBMCs were cultured in medium for 2 hours, and the adherent cells were subsequently collected. CD14⁺ cells were induced to differentiate into macrophages by treatment with M-CSF (50 ng/mL) for 5 days. Cell purity was assessed by flow cytometry. An in vitro model of immune paralysis was established by treating monocytes with 10–100 ng/mL LPS for 24 hours, followed by washing and culturing in RPMI medium supplemented with 10% human serum for 5 days in the presence of M-CSF (50 ng/mL) to allow differentiation into immune-paralyzed macrophages.

extract_protocol:
RNA Extraction and Transcriptome Sequencing
Total RNA was extracted from isolated and purified CD14⁺ monocytes using TRIzol reagent. Following ribosomal RNA (rRNA) depletion, sequencing libraries were constructed according to the Illumina library preparation protocol and subsequently sequenced on the Illumina Genome Analyzer II platform.
ATAC‑seq
A total of 1×10⁵ fresh cells were used for each assay. Libraries were constructed using Tn5 transposase treatment and sequenced on an Illumina platform. Raw reads were subjected to quality control using fastp and aligned to the reference genome with Bowtie2. PCR duplicates were removed using Picard, and MACS2 was used for peak calling to identify open chromatin regions (ATAC‑seq peaks). Identified peaks were annotated with HOMER, followed by transcription factor binding motif analysis.
Chromatin Immunoprecipitation (ChIP)
Log-phase cells were washed with PBS, cross-linked with 1% formaldehyde at room temperature for 10 min, and quenched with glycine. After lysis, chromatin was sonicated to 200–500 bp fragments. Chromatin was incubated with anti-RNA polymerase II antibody or control IgG pre-bound to Protein A/G magnetic beads at 4℃ overnight. After washing, elution, cross-link reversal and proteinase K digestion, DNA was purified and analyzed by qPCR for target region enrichment.

value: peripheral blood

value: monocytes


title: PDO from Pt10_t3

source_name: Patient 10, tumor 3


title: Tolerant-LPS-C1

description: Library name: Tolerant-LPS-C1


title: TN_CD_male_3d_105_liver

description: Library name: HDP-019000_liver


title: RT_CD_male_17w_104_liver

description: Library name: HDP-018953_liver


title: Sample6 of Run5, Moderate Alzheimer's Disease,  Dentate gyrus punch

description:
Library name: S6R5
10x Genomics

value: Run 5


title: PB_D12_Ctrl_Rep3

description: Library name: PPP2_31


title: Sample8 of Run5, Non-demented control,  Dentate gyrus punch

description:
Library name: S8R5
10x Genomics


title: PDO from Pt10_t2

source_name: Patient 10, tumor 2

value: PDO cultured from resected liver metastases


title: Sir_Root_Ctrl_Bulk_R3

city: Stanford

first: Guannan

last: Wang

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

description: Roots from 4-6-day-old seedlings for bulk RNA-seq

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using Cell Ranger (v5.0.1, 10X Genomics)
Assembly: Arabidopsis (TAIR10) from The Arabidopsis Information Resource (TAIR; https://www.arabidopsis.org/), C. sativa (v2) from Brassicaceae Database (BRAD; http://brassicadb.cn), E. salsugineum (v1.0) and S. parvula (v2.2) from Phytozome 12 (https://phytozome-next.jgi.doe.gov/) (Phytozome ID 574 and 173, respectively), reference genome for S. irio (v1.0) from Brassicaceae Database (BRAD; http://brassicadb.cn) with the updated gene model annotation (Sun et al., 2022) from the CoGe database (https://genomevolution.org/) with the Genome ID 57216.
Supplementary files format and content: tab-separated value files and matrix files; rds files

organism: Sisymbrium irio

source_name: Root

extract_protocol:
Primary root tips of seedlings from different species were cut and placed into a 35 mm petri dish containing a 70 um strainer and 4 mL enzyme solution (1.25% [w/v] Cellulase [“ONOZUKA” R-10, Yakult], 0.1%[w/v] Pectolyase [P-3026, Sigma-Aldrich], 0.4 M Mannitol, 20 mM MES [pH 5.7], 20 mM KCl, 10 mM CaCl2, 0.1% [w/v] bovine serum albumin). The sample dish was rotated at 85 rpm for 50 min at 25°C. The root tips were then transferred to a slide glass and gently pressed with a cover glass using a pencil rubber to release protoplasts. The tissues were transferred back to the enzyme solution and incubated for another 10 minutes. Then, the protoplast solution was filtered through a 70 μm filter, and then through a 40 μm filter twice using 50 mL conical tubes. The filtered solution was centrifuged at 500g for 10 min at 22°C using a swinging bucket rotor and the supernatant was discarded. Protoplasts were resuspended using 500 μL Solution A (0.4 M Mannitol, 20 mM MES [pH 5.7], 20 mM KCl, 10 mM CaCl2, 0.1% [w/v] bovine serum albumin) and transferred to a 2 mL round bottom tube. After centrifugation at 200g for 6 min, the pelleted protoplasts were resuspended with 30–50 μL Solution A to achieve the desired cell concentration (~1,000 protoplasts/μL).
The protoplast suspension was loaded into Chromium microfluidic chips (Next GEM Single Cell 3’ kit) and barcoded with a 10X Chromium Controller (10X Genomics). mRNA from the barcoded cells were subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ reagent kit v3.1 chemistry dual index (10X Genomics) according to the manufacturer’s instructions.

value: Root

value: 4-6-day-old seedlings


title: Tolerant-LPS-B2

description: Library name: Tolerant-LPS-B2


title: PDO from Pt1_t1

source_name: Patient 1, tumor 1


title: TN_CD_female_9d_103_liver

description: Library name: HDP-019084_liver

source_name: liver


title: Sample7 of Run5, Resillient,  Dentate gyrus punch

description:
Library name: S7R5
10x Genomics

value: Dentate gyrus


title: Sample5 of Run5, Severe Alzheimer's Disease,  Dentate gyrus punch

description:
Library name: S5R5
10x Genomics

value: F


title: Tolerant-LPS-B1

description: Library name: Tolerant-LPS-B1


title: TN_WD_female_27d_102_liver

description: Library name: HDP-018996_liver


title: Tolerant-LPS-A2

description: Library name: Tolerant-LPS-A2


title: Sir_Root_Ctrl_Bulk_R1


title: Sir_Root_Ctrl_Bulk_R2


title: Tolerant-LPS-A1

description: Library name: Tolerant-LPS-A1


title: Sample4 of Run2, Non-demented control,  Dentate gyrus punch

description:
Library name: S4R2
10x Genomics

value: M

value: Run 2


title: TN_WD_male_17w_100_liver

description: Library name: HDP-018728_liver


title: RT_WD_female_17w_101_liver

description: Library name: HDP-018889_liver


title: Sample4 of Run5, Non-demented control,  Dentate gyrus punch

description:
Library name: S4R5
10x Genomics

value: CTRL


title: Sir_Root_ABA_scRNAseq_R2

description: Roots from 4-6-day-old seedlings for scRNA-seq

value: 5 M ABA treatment


title: TN_WD_male_3d_98_liver

description: Library name: HDP-019002_liver


title: Sample4 of Run4, Non-demented control,  Dentate gyrus punch

description:
Library name: S4R4
10x Genomics

value: Run 4


title: Naive-PBS-B2

description: Library name: Naive-PBS-B2


title: TN_CD_female_3d_99_liver

description: Library name: HDP-019090_liver


title: Naive-PBS-C2

description: Library name: Naive-PBS-C2


title: Sample3 of Run4, Resillient,  Dentate gyrus punch

description:
Library name: S3R4
10x Genomics

value: RES


title: Sir_Root_NaCl_scRNAseq_R1

value: 100 mM NaCl treatment


title: TN_CD_female_9d_111_liver

description: Library name: HDP-019111_liver

value: liver


title: Sir_Root_ABA_scRNAseq_R1


title: Naive-PBS-C1

description: Library name: Naive-PBS-C1


title: Sample3 of Run2, Resillient,  Dentate gyrus punch

description:
Library name: S3R2
10x Genomics


title: Naive-PBS-B1

description: Library name: Naive-PBS-B1


title: Sir_Root_Ctrl_scRNAseq_R2

value: Control


title: Sample3 of Run5, Resillient,  Dentate gyrus punch

description:
Library name: S3R5
10x Genomics


title: RT_CD_male_17w_97_liver

description: Library name: HDP-018948_liver


title: TN_CD_female_3d_96_liver

description: Library name: HDP-019091_liver


title: Naive-PBS-A2

description: Library name: Naive-PBS-A2

value: peripheral blood


title: Naive-PBS-A1

description: Library name: Naive-PBS-A1

value: monocytes


title: Csa_Root_Ctrl_Bulk_R3

description: Roots from 3-day-old seedlings for bulk RNA-seq

organism: Camelina sativa

value: 3-day-old seedlings


title: Sir_Root_Ctrl_scRNAseq_R1


title: Naive-LPS-C2

description: Library name: Naive-LPS-C2


title: RT_WD_male_17w_94_liver

description: Library name: HDP-018875_liver


title: Sample2 of Run5, Severe Alzheimer's Disease,  Dentate gyrus punch

description:
Library name: S2R5stored
10x Genomics

value: SAD

value: Run 5


title: Sir_Root_NaCl_scRNAseq_R2

value: Root

value: 4-6-day-old seedlings


title: Sample2 of Run2, Moderate Alzheimer's Disease, Dentate gyrus punch

description:
Library name: S2R2
10x Genomics

value: Dentate gyrus

value: MAD


title: Csa_Root_Ctrl_Bulk_R1


title: TN_WD_male_9d_92_liver

description: Library name: HDP-019074_liver


title: Csa_Root_Ctrl_Bulk_R2


title: TN_WD_female_27d_95_liver

description: Library name: HDP-018997_liver


title: Naive-LPS-C1

description: Library name: Naive-LPS-C1


title: Sample1 of Run4, Severe Alzheimer's Disease,  Dentate gyrus punch

description:
Library name: S1R4
10x Genomics

value: F


title: Naive-LPS-B1

description: Library name: Naive-LPS-B1


title: Csa_Root_NaCl_scRNAseq_R2

description: Roots from 3-day-old seedlings for scRNA-seq


title: TN_WD_female_27d_91_liver

description: Library name: HDP-018998_liver


title: TN_CD_female_17w_93_liver

description: Library name: HDP-018731_liver


title: Csa_Root_NaCl_scRNAseq_R1


title: Sample2 of Run5, Moderate Alzheimer's Disease,  Dentate gyrus punch

description:
Library name: S2R5
10x Genomics

value: M


title: RT_WD_female_17w_90_liver

description: Library name: HDP-018951_liver


title: Naive-LPS-A2

description: Library name: Naive-LPS-A2


title: Csa_Root_ABA_scRNAseq_R2

value: 5 M ABA treatment


title: Naive-LPS-B2

description: Library name: Naive-LPS-B2


title: Sample1 of Run5, Non-demented control,  Dentate gyrus punch

description:
Library name: S1R5stored
10x Genomics

value: CTRL


title: Sample1 of Run2, Severe Alzheimer's Disease,  Dentate gyrus punch

description:
Library name: S1R2
10x Genomics

value: Run 2


title: Sample2 of Run4, Moderate Alzheimer's Disease,  Dentate gyrus punch

description:
Library name: S2R4
10x Genomics

value: Run 4


title: Csa_Root_ABA_scRNAseq_R1


title: Sample1 of Run1, Severe Alzheimer's Disease, Dentate gyrus punch

description:
Library name: S1R1
10x Genomics

value: Run 1


title: TN_CD_female_27d_88_liver

description: Library name: HDP-019018_liver

value: liver