title: CD19+, scRNA

description:
Library name: scMulti_BM_CD19_GEX
CD19_per_barcode_metrics.csv

data_processing:
Preprocessing of single cell multiome (sc-multiome) data was performed with cellranger-arc (v2.0.2) using mm10 version 2020-A (GENCODE vM23 /Ensembl 98). First rawdata for each modality (ATAC and Gene expression) in BCL format was demultiplexed and converted into fastq format using cellranger-arc mkfastq. Next cellranger-arc count (including alignment, filtering,barcode/feature quantification) was run for each individual sample. Finally, cellranger-arc aggr was used to aggregate all samples into one dataset. Aggregation was run with default settings except --normalize=none, as the dataset will be subjected to normalization in downstream analysis).
Assembly: mm10
Supplementary files format and content: Samples: per_barcode_metrics.csv, atac_fragments.tsv, gex_molecule_info.h5
Supplementary files format and content: Aggregated data (Bdev): Aggregation.csv, atac_fragments.tsv,  filtered_feature_bc_matrix.h5

molecule: nuclear RNA

extract_protocol:
Up to 100.000 ex vivo sorted BM progenitors (LSK, FLT3+, IL7Ra+ and CD19+) were spun down (300xg, 5 min 4 °C) and washed in PBS/0.4%BSA. . Nuclei were isolated according to Nuclei Isolation for Single Cell Multiome ATAC + GEX. Sequencing (CG000169, Rev C, 10x Genomics). Briefly, cells were resuspended in 100 µl chilled Lysis buffer (10 mM Tris-Hcl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.01 % Digitonin (Invitrogen, BN2006), 1% BSA, 1 mM DTT, 1 U/µl RNase inhibitor (Roche, 3335402001) and incubated 3 min on ice. Nuclei were washed 3x in 1 ml chilled Wash buffer (10 mM Tris-Hcl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1 % Tween-20, 1 mM DTT, 1 U/µl RNase inhibitor) before resuspension in 10-20 µl chilled diluted Nuclei buffer (1x Nuclei buffer (10x Genomics, 2000207), 1 mM DTT, 1U/µl RNase inhibitor). Nuclei concentrations were determined using TC20 automated cell counter (BioRad).
Single cell ATAC and Gene Expression libraries were constructed according to Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338, Rev F, 10x Genomics) using reagent from the Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression Reagent Bundle (10x Genomics, 1000285). Briefly, nuclei were transposed in bulk solution followed by subsequent GEM generation and barcoding in a Chromium Next GEM Chip J Single Cell (10x Genomics, 1000230) using a Chromium controller (10x Genomics). Post-GEM cleanup followed by Pre-Amplification of barcoded transposed DNA and cDNA were performed prior to ATAC and Gene Expression Library generation with Singel Index Kit N (10x Genomics, 1000212) and Dual Index Kit TT (10x Genomics, 1000215) respectively. Library quality control was performed with Qubit® dsDNA HS Assay Kit & assay tubes ThermoFisher Scientific, Q32854/Q32856) and Agilent 2100 Bioanalyser with the High Sensitivity DNA Kit (Agilent, 5067-4626). Libraries were subjected to paried-end dual-index sequencing (ATAC: Read 1N 50 cycles, i7 Index 8 cycles, i5 24 cycles, Read 2N 49 cycles, RNA: Read 1 28 cycles, i7 Index 10 cycles, i5 Index 10 cycles, Read 2 90 cycles) on a Nextseq 2000 (Illumina) using NextSeq2000 P3 100 cycles med PhiX (Illumina, 20040559) according to manufacturer’s instructions.

tag: library type

value: GEX


title: FLT3+, scRNA

status: Public on Nov 25 2025

type: SRA

city: Linköping

first: Mikael

last: Sigvardsson

address: Lab1, Level 13

department: Department of Biomedical and Clinical Sciences

country: Sweden

institute: Linköping University

description:
Library name: scMulti_BM_FLT3_GEX
FLT3_per_barcode_metrics.csv

library_source: transcriptomic single cell

organism: Mus musculus

tag: cell type

tag: strain


title: hPSCs_OTX2-OE-1 [RNA-Seq]

city: luzhou

last: Jiang

state: sichuan

address: 1st xianglinlu

country: China

institute: southwest medical university

description: Library name: pdox-prime1

library_source: transcriptomic

data_processing:
RNAseqv1
Adapter of sequence reads were trimmed and poor quality reads  were removed by TrimGalore(quality <20 or length <30),
Paired-end RNA-seq reads were trimmed and then mapped to hg38 genome by STAR (v.2.7.4a)
Raw count tables of genes were computed using featureCounts (v2.0.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: hPSCs

extract_protocol:
Total RNA was isolated using RNA isolater Total RNA Extraction Reagent (Vazyme, R401) according to the manufacturer’s instructions.
TRIzol was used to extract total RNA, and libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme, NR605) according to the manufacturer’s instructions. 500 ng total RNA was used to construct libraries. Library samples were subjected to the Illumina NovaSeq 6000 sequencing system.

tag: cell line

value: hPSCs

value: prime

tag: treatment


title: IL7RA+, scRNA

description:
Library name: scMulti_BM_IL7RA_GEX
IL7RA_per_barcode_metrics.csv


title: Dp16; Control diet; Sample_T4_534143

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

country: USA

institute: University of Colorado Anschutz Medical Campus

description: Library name: T4_534143

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 RTA3 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCm38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCm38 index with a Gencode M24 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode M24 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Counts: Tab-delimited text files containing per gene strand-specific fragment counts.
Supplementary files format and content: FPKMs: Tab-delimited text files containing per gene strand-specific normalized fragments-per-kilobase-per-million-mapped (FPKM).

molecule: polyA RNA

source_name: liver

extract_protocol:
Total RNA from tissue samples was extracted using TRIzol reagent (Invitrogen) following the manufacturer protocol. RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Tecan/Nugen Universal Plus mRNA Kit. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the University of Colorado Cancer Center Genomics Shared Resource.

tag: tissue

value: liver

tag: genotype

tag: Sex

value: Female

value: Control diet


title: BM Ebf1+/-Pax5+/- proB CD25+, RNA-seq, rep2

description: Library name: RNAseq_TH_BM_proB_CD25pos_rep2

data_processing:
RNA-seq data were preprocessed by trimming with TrimGalore (v0.6.4) –clip_R1/R2 15 –thre_prime_clip_R1/R2 3 (except for reanalysis of GSE122597 data: --length 20), followed by alignment to the mm10 mouse reference genome (GRCm38.p5.vM15) with STAR (v2.7.3) using the following options: --quantMode TranscriptomeSAM --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif. Transcript levels were generated with rsem-calculate-expression in RSEM (v1.3.0), with the following options: --paired-end --alignments --output-genome-bam --sampling-for-bam --estimate-rspd --calc-ci (--paired-end omitted for single-end data).
Assembly: mm10
Supplementary files format and content: *Aligned.toTranscriptome.rsem.out.genes.results

source_name: BM proB CD25+

extract_protocol:
Up to 50.000 ex vivo sorted WT, Ebf1+/-, Pax5+/- and Ebf1+/-Pax5+/- (CD25-, CD25+ and total proB cell population) and sorted cells were spun down (800 x g, 5 min, 4 °C). Pellets were resuspended in 350 µl RLT (Qiagen, 74004) supplemented with 3.5 µl β-mercaptoethanol (ThermoFischer Scientific, 35602BID) and snap frozen on dry ice. RNA purification was performed with RNAeasy micro kit (Qiagen, 74004) and samples were eluted in 14 µl RNase-free water. 1 µl of each sample was used for quality control on Agilent 2100 Bioanalyser using the RNA 6000 Pico kit (Agilent, 5067-1513). SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio) was used for cDNA synthesis, followed by DNA purification with Ampure XP (Beckman-Coulter, A63881) and concentration measurement using Qubit® dsDNA HS Assay Kit & assay tubes (ThermoFisher Scientific, Q32854/Q32856). Quality of amplified cDNA were evaluated by running 1 µl of each sample on Agilent 2100 Bioanalyser with the High Sensitivity DNA Kit (Agilent, 5067-4626).
Libraries for sequencing were generated with Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) using the Nextera XT Index Kit (Illumina, FC-131-1001) for indexing. Library quantification and quality control was performed with Qubit® dsDNA HS Assay Kit & assay tubes ThermoFisher Scientific, Q32854/Q32856) and Agilent 2100 Bioanalyser with the High Sensitivity DNA Kit (Agilent, 5067-4626). SMART-seq libraries were subject to 2x150 cycles of paired-end sequencing on a Nextseq2000 (Illumina) using NextSeq 2000 P3 Reagents (Illumina, 20040561).

value: BM proB CD25+


title: LSK, scRNA

description:
Library name: scMulti_BM_LSK_GEX
LSK_per_barcode_metrics.csv

source_name: LSK

value: LSK


title: naive_hPSCs_OTX2-KO-2 [RNA-Seq]

description: Library name: OTX2-KO-4CL2

source_name: naive hPSCs

value: naive hPSCs

value: naive


title: Dp16; Control diet; Sample_T4_531083

description: Library name: T4_531083


title: naive_hPSCs_OTX2-KO-1 [RNA-Seq]

description: Library name: OTX2-KO-4CL1


title: FLT3+, scATAC

description:
Library name: scMulti_BM_FLT3_ATAC
FLT3_per_barcode_metrics.csv

library_source: genomic single cell

molecule: genomic DNA

value: ATAC


title: CD19+, scATAC

description:
Library name: scMulti_BM_CD19_ATAC
CD19_per_barcode_metrics.csv


title: Dp16; Control diet; Sample_T5_531083

description: Library name: T5_531083


title: IL7RA+, scATAC

description:
Library name: scMulti_BM_IL7RA_ATAC
IL7RA_per_barcode_metrics.csv


title: hPSCs_OTX2-KO-2 [RNA-Seq]

description: Library name: OTX2-KO-prime2


title: LSK, scATAC

description:
Library name: scMulti_BM_LSK_ATAC
LSK_per_barcode_metrics.csv


title: Dp16; Control diet; Sample_T8_534135

description: Library name: T8_534135


title: LMPP_H_250123_L1

city: Edinburgh

first: Giuseppina

last: Camiolo

state: Edinburgh

address: EDINBURGH BIOQUARTER

country: United Kingdom

institute: CENTRE FOR REGENERATIVE MEDICINE - THE UNIVERSITYOF EDINBURGH

data_processing:
Raw reads were trimmed using TrimGalore
Raw ends were aligned with STAR (v2.7.1a) ( GRCm39 for mouse)
Aligned reads (BAM files) were then analysed in RStudio (2022.07.2+576 version). DESeq2 package was used to prefilter  (to exclude rows with zero or near zero data) and to normalize read counts. A results table with normalized read counts was obtained.
Assembly: GRCm39 for mouse
Supplementary files format and content: tab-delimited text includes raw counts for each sample

source_name: E14.5 foetal liver

extract_protocol:
cells were sorted from freshly isolated mouse E14.5 foetal livers from a mouse line that has doxycyline-inducible KMT2A-MLLT3 expression; DOX was given at E12.5 and embryos retireved 2 days later for foetal liver dissection; single cell preparations were stained with cell surface markers for LMPPs (Lin-Sca1+ckit+CD45+Flt3+) with or without CSF1R cell surface expression and the two LMPP populations (CSF1R+/-) directly sorted into lysis buffer. RNA was extracted with RNAeasy micro kit (Qiagen).  0.5ng of total RNA was used to prepare the libraries.
the libraries were prepared using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB #E6420) according to the provided protocol.

value: E14.5 foetal liver

value: haematopoietic cells (LMPPs)

tag: sample group

value: CSF1R+ FL LMPPs


title: LMPP_G_250123_L1


title: hPSCs_OTX2-KO-1 [RNA-Seq]

description: Library name: OTX2-KO-prime1


title: LMPP_E_250123_L1


title: LMPP_F_250123_L1


title: TLSCs_WT-2 [RNA-Seq]

description: Library name: H9-Cas9-toti2

source_name: TLSCs

value: TLSCs

value: totipotent


title: Wild-type C57BL/6J; High fat diet; Sample_T6_534137

description: Library name: T6_534137

value: wild-type C57/BL6

value: Male

value: High fat diet


title: LMPP_D_250123_L1

value: CSF1R- FL LMPPs


title: TLSCs_WT-1 [RNA-Seq]

description: Library name: H9-Cas9-toti1


title: LMPP_A_250123_L1


title: Wild-type C57BL/6J; High fat diet; Sample_T0_534141

description: Library name: T0_534141

value: liver


title: Wild-type C57BL/6J; High fat diet; Sample_T5_534137

description: Library name: T5_534137


title: RPMI 2650 CISTR KO clone 2 rep1

city: Toronto

first: Philipp

last: Maass

state: Ontario

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: Library name: RPMI 2650 CISTR KO clone 2 rep1

data_processing:
We aligned reads to hg38 using STAR aligner, version 2.7.0f. We used FeatureCounts to count reads aligning to genes in GENCODE v32 (human), vM33 (mouse).
Assembly: hg38, mm39
Supplementary files format and content: text files include RPKM values for each sample

source_name: RPMI 2650

extract_protocol:
RNA was harvested and purified using TRIzol (Invitrogen). 1 ug of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus following manufacturer's protocols.

value: RPMI 2650

value: nasal epithelial

value: CISTR KO


title: naive_hPSCs_WT-2 [RNA-Seq]

description: Library name: H9-Cas9-4CL2


title: RPMI 2650 WT clone 2 rep1

description: Library name: RPMI 2650 WT clone 2 rep1

value: WT


title: naive_hPSCs_WT-1 [RNA-Seq]

description: Library name: H9-Cas9-4CL1

value: naive hPSCs


title: LMPP_B_250123_L1


title: Dp16; Control diet; Sample_T2_532053

description: Library name: T2_532053

value: Control diet


title: Wild-type C57BL/6J; High fat diet; Sample_T4_534139

description: Library name: T4_534139


title: Wild-type C57BL/6J; High fat diet; Sample_T0_534139

description: Library name: T0_534139


title: ATACseq_T3M4_Rep2

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

description: Library name: Sample020

library_source: genomic

data_processing:
Paired end sequencing reads were filtered for adapter contamination with Trim Galore and mapped to the reference genome assembly hg38 using bowtie2 with --dovetail. BamTools Filter was used for removing low quality (mapQ >= 30) and mitochondrial reads. Resulting bam file was converted to a bed file with bedtools bamtobed. Peak calling and bedgraph generation was performed using macs3 callpeak using shift and extend method to center peaks at 5’ cut site (shift -100 extension size 200). The data was visualized by using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: Normalized bigwigs and bed file for each condition

source_name: cell line

growth_protocol: BxPC3 and T3M4 (RPMI, 10% FBS, 1% Pen-Strep) and L36pl and HPAFII (phenol red free MEM, 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol:
For ATAC-Seq library preparation, cells were harvested and libraries were produced using ATAC-Seq kit (Active Motif, 53150) following manufacturer’s instructions. Library concentration was determined via Qubit and fragment size was quantified with TapeStation.
For ATAC-Seq library preparation, cells were harvested and libraries were produced using ATAC-Seq kit (Active Motif, 53150) following manufacturer’s instructions. Library concentration was determined via Qubit and fragment size was quantified with TapeStation.

value: cell line

value: Pancreatic ductal adenocarcinoma


title: Wild-type C57BL/6J; High fat diet; Sample_T2_534139

description: Library name: T2_534139


title: hPSCs_WT-2 [RNA-Seq]

description: Library name: H9-Cas9-prime2

value: hPSCs

value: prime


title: ATACseq_T3M4_Rep3

description: Library name: Sample021


title: hPSCs_WT-1 [RNA-Seq]

description: Library name: H9-Cas9-prime1


title: ATACseq_HPAFII_Rep3

description: Library name: Sample018

value: HPAFII


title: RPMI 2650 WT clone 2 rep2

description: Library name: RPMI 2650 WT clone 2 rep2


title: ATACseq_HPAFII_Rep2

description: Library name: Sample017


title: Wild-type C57BL/6J; High fat diet; Sample_T5_534134

description: Library name: T5_534134


title: hPSCs_WT-2 [Cut&Tag]

description: Library name: ndox-prime2

data_processing:
cuttag_pipeline
The raw FASTQ files were preprocessed using Cutadapt (v1.18) with stringent parameters (-e 0.1 for maximum error rate and -m 5 for minimum read length)
High-quality reads were then aligned to the hg38 human reference genome using Bowtie2 (v2.2.2)
The resulting alignments were processed using SAMtools (v.1.7) to filter out low-quality mappings (Q < 30). The filtered reads were converted to BAM format and PCR duplicates were removed using Picard Tools (v.2.8.0) with the REMOVE_DUPLICATES = true.
For peak identification, we employed MACS2 (v.2.2.7.1)    with specific parameters: --narrow for narrow peak calling, --keep-dup all to retain all duplicates during model building, -B for storing fragment pileup information, and --SPMR for signal per million scaling.
Finally, genome-wide visualization profiles were generated using deepTools (v3.1.3) to facilitate comprehensive analysis of the sequencing data.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&TAG

extract_protocol:
Fresh cells were collected and washed with 500 μl wash buffer and centrifuged at 500×g for 5 min at room temperature. Cell pellets were resuspended with 100 μl wash buffer.
The CUT&Tag assay was performed according to the manual of the Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD904, Vazyme Biotech). 1 × 105 cells were used as starting material for every sample. Libraries were amplified using 12 cycles on the thermocysler. Post amplification libraries were size select at 250-450bp in length using DNA Clean Beads  (N411, Vazyme Biotech). Libraries were validated using the dsDNA HS Assay Kit (EQ121, Vazyme Biotech).


title: Wild-type C57BL/6J; High fat diet; Sample_T4_534134

description: Library name: T4_534134


title: hPSCs_WT-1 [Cut&Tag]

description: Library name: ndox-prime1


title: ATACseq_HPAFII_Rep1

description: Library name: Sample016


title: RPMI 2650 CISTR KO clone 2 rep2

description: Library name: RPMI 2650 CISTR KO clone 2 rep2


title: ATACseq_BxPC3_Rep2

description: Library name: Sample014


title: Wild-type C57BL/6J; High fat diet; Sample_T6_531358

description: Library name: T6_531358


title: ATACseq_cat_L36plClone2_dTAG_4h_Rep3

description: Library name: Sample012


title: ATACseq_BxPC3_Rep1

description: Library name: Sample013


title: TLSCs_WT-2 [Cut&Tag]

description: Library name: ndox-toti2

value: TLSCs

value: totipotent


title: Wild-type C57BL/6J; High fat diet; Sample_T2_531084

description: Library name: T2_531084

value: wild-type C57/BL6

value: Male


title: TLSCs_WT-1 [Cut&Tag]

description: Library name: ndox-toti1


title: Wild-type C57BL/6J; High fat diet; Sample_T10_534138

description: Library name: T10_534138

value: Female

value: High fat diet


title: ATACseq_cat_L36plClone2_dTAG_24h_Rep3

description: Library name: Sample009


title: ATACseq_cat_L36plClone2_dTAG_4h_Rep2

description: Library name: Sample011


title: naive hPSCs_WT-2 [Cut&Tag]

description: Library name: ndox-4cl2

value: naive


title: Wild-type C57BL/6J; High fat diet; Sample_T1_534138

description: Library name: T1_534138

value: liver


title: ATACseq_cat_L36plClone2_dTAG_1h_Rep3

description: Library name: Sample006


title: ATACseq_cat_L36plClone2_dTAG_24h_Rep1

description: Library name: Sample007


title: naive hPSCs_WT-1 [Cut&Tag]

description: Library name: ndox-4cl1


title: ATACseq_T3M4_Rep1

description: Library name: Sample019


title: Wild-type C57BL/6J; High fat diet; Sample_T0_534138

description: Library name: T0_534138


title: ATACseq_cat_L36plClone2_dTAG_24h_Rep2

description: Library name: Sample008


title: ATACseq_cat_L36plClone2_dTAG_1h_Rep2

description: Library name: Sample005


title: Wild-type C57BL/6J; High fat diet; Sample_T3_531085

description: Library name: T3_531085


title: ATACseq_cat_L36plClone2_dTAG_0h_Rep3

description: Library name: Sample003


title: ATACseq_cat_L36plClone2_dTAG_1h_Rep1

description: Library name: Sample004


title: hPSCs_OTX2-OE-1 [Cut&Tag]

description: Library name: pdox-prime1


title: ATACseq_cat_L36plClone2_dTAG_0h_Rep2

description: Library name: Sample002


title: Wild-type C57BL/6J; Control diet; Sample_T1_534136

description: Library name: T1_534136


title: ATACseq_cat_L36plClone2_dTAG_0h_Rep1

description: Library name: Sample001


title: Untransfected HEK cells replicate 3

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
Library name: Sample-12
column name in mature_counts.csv and hairpin_counts.csv: "UT3".

data_processing:
miRNA sequencing data were processed using the nf-core/smrnaseq pipeline2 on the HiPerGator high-performance computing cluster with Nextflow (version 25.04.4) and Singularity (version 3.10.4). Raw FASTQ files were quality-checked with FastQC (version 0.12.1) and trimmed using cutadapt3 (version 5.2) following the instruction of NEXTFLEX small RNA kit v4. Contamination was filtered with Bowtie2 (version 2.5.4). Reads were aligned to the miRbase mature miRNA and miRbase hairpin using Bowtie1 (version 1.3.1). Post-alignment processing of miRbase hairpin was done with SAMtools (version 1.2.1), edgeR (version 4.8.0), and mirtop (version 0.4.28). Alignment against human reference genome was performed with Bowtie1. MiRDeep2 (version 0.1.3) was used to perform novel and known miRNA discovery. Mirtrace (version 1.0.1) was adapted for miRNA quality control, and MultiQC (version 1.27.1) was used for raw read, alignment, and expression results present.
Assembly: GRCh37
Supplementary files format and content: comma-separated values file contains raw count of mature RNA in each sample obtained from edgeR
Supplementary files format and content: comma-separated values file contains raw count of hairpin RNA in each sample obtained from edgeR

source_name: HEK 293

growth_protocol: HEK293T cells were cultured as a monolayer in DMEM, supplemented with 10% v/v FBS, 100 U mL-1 penicillin, and 100 µg mL-1 streptomycin.

extract_protocol:
RNAs were extracted from cells using the RNeasy plus mini kit according to the manufacturer’s instructions.
The library preparation from the input RNA was conducted according to the NEXTFLEX small RNA kit v4 (Revvity, NOVA-5132-31). Briefly, the input RNA has been ligated to 3’ adenylated adapter and 5’ adapter. The RNA was then reverse transcribed to generate the first strand of cDNA. The synthesized product was cleaned up with beads and amplified with PCR (using 15 cycles) to incorporate a unique barcode and to generate final libraries. The libraries were purified using SPRI beads to remove any remaining primers and adaptors. The final libraries were validated on an Agilent 4200 TapeStation

treatment_protocol: Cells were transfected  with Lipo2000 to transiently express wt and mutant p53 construct 24 hr prior to collection. Cells were washed once with PBS and harvested with trypsin digestion.

value: HEK 293

value: epithelial cell

value: Wild type

value: Untransfected HEK cells, harvested at the same time with other samples


title: Wild-type C57BL/6J; Control diet; Sample_T3_534136

description: Library name: T3_534136

value: Control diet


title: ATACseq_cat_L36plClone2_dTAG_4h_Rep1

description: Library name: Sample010

value: cell line

value: Pancreatic ductal adenocarcinoma


title: TLSCs_OTX2-OE-1 [Cut&Tag]

description: Library name: pdox-toti1


title: Untransfected HEK cells replicate 1

description:
Library name: Sample-10
column name in mature_counts.csv and hairpin_counts.csv: "UT1".


title: TLSCs_OTX2-OE-2 [Cut&Tag]

description: Library name: pdox-toti2


title: HEK cells expressing R273H p53 replicate 3

description:
Library name: Sample-09
column name in mature_counts.csv and hairpin_counts.csv: "273H_3".

value: R273H p53 transient expression

value: HEK cells were transfected with Lipo2000 to transiently express R273H p53 construct 24 hr prior to collection


title: ATACseq_BxPC3_Rep3

description: Library name: Sample015


title: HEK cells expressing R273H p53 replicate 1

description:
Library name: Sample-07
column name in mature_counts.csv and hairpin_counts.csv: "273H_1".


title: HEK cells expressing G245S p53 replicate 3

description:
Library name: Sample-06
column name in mature_counts.csv and hairpin_counts.csv: "245S_3".

value: G245S p53 transient expression

value: HEK cells were transfected with Lipo2000 to transiently express G245S p53 construct 24 hr prior to collection


title: naive hPSCs_OTX2-OE-2 [Cut&Tag]

description: Library name: pdox-4cl2

value: naive hPSCs


title: HEK cells expressing R273H p53 replicate 2

description:
Library name: Sample-08
column name in mature_counts.csv and hairpin_counts.csv: "273H_2".


title: hPSCs_OTX2-OE-2 [Cut&Tag]

description: Library name: pdox-prime2

value: hPSCs

value: prime


title: Wild-type C57BL/6J; Control diet; Sample_T3_532053

description: Library name: T3_532053

value: wild-type C57/BL6

value: Male


title: Wild-type C57BL/6J; Control diet; Sample_T4_532053

description: Library name: T4_532053

value: liver


title: naive hPSCs_OTX2-OE-1 [Cut&Tag]

description: Library name: pdox-4cl1

value: naive


title: TLSCs_OTX2-KO-2

description: Library name: OTX2-KO-toti2

data_processing:
ENCODE-DCC ATAC-seq protocol
Raw sequencing reads underwent adapter trimming and quality filtering using Cutadapt (v1.18) [7] was used to auto-detect adapters with the parameters to ‘‘-e 0.1 –m 5’’
Processed reads were then aligned to the reference genome using Bowtie2 (v2.2.2) with optimized parameters (-X 2000 for maximum fragment length and -mm --local for local alignment)
Duplicate removal was performed using Picard MarkDuplicates, retaining only high-quality alignments with mapping quality scores >10 (MAPQ > 10).
For visualization and downstream analysis, we generated normalized BigWig files using bamCoverage from deepTools (v3.1.3)
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Fresh cells were collected and washed with 500 μl wash buffer and centrifuged at 500×g for 5 min at 4℃. Cell pellets were washed with 50 μl pre-cooled TW Buffer for twice.Re-suspended the cell pellets  with 50 μl precooled lysis buffer, placed on ice for 5 min, centrifuged at 500×g for 10 min at 4°C, and the supernatant was discarded.
The ATAC-seq library was performed according to the manual of the Hyperactive ATAC-Seq Library Prep Kit for Illumina (TD711, Vazyme Biotech). 1 × 105 cells were used as starting material for every sample. Libraries were amplified using 12 cycles on the thermocysler. Post amplification libraries were size select at 250-450bp in length using DNA Clean Beads  (N411, Vazyme Biotech). Libraries were validated using the dsDNA HS Assay Kit (EQ121, Vazyme Biotech).

value: TLSCs

value: totipotent


title: HEK cells expressing G245S p53 replicate 2

description:
Library name: Sample-05
column name in mature_counts.csv and hairpin_counts.csv: "245S_2".

value: HEK 293

value: epithelial cell


title: Wild-type C57BL/6J; Control diet; Sample_T3_531357

description: Library name: T3_531357

value: Control diet


title: TLSCs_OTX2-KO-1

description: Library name: OTX2-KO-toti1


title: HEK cells expressing G245S p53 replicate 1

description:
Library name: Sample-04
column name in mature_counts.csv and hairpin_counts.csv: "245S_1".


title: HEK cells expressing wt p53 replicate 2

description:
Library name: Sample-02
column name in mature_counts.csv and hairpin_counts.csv: "WT2".

value: wt p53 transient expression

value: HEK cells were transfected with Lipo2000 to transiently express wt p53 construct 24 hr prior to collection


title: Wild-type C57BL/6J; Control diet; Sample_T3_534142

description: Library name: T3_534142

value: Female


title: HEK cells expressing wt p53 replicate 1

description:
Library name: Sample-01
column name in mature_counts.csv and hairpin_counts.csv: "WT1".


title: HEK cells expressing wt p53 replicate 3

description:
Library name: Sample-03
column name in mature_counts.csv and hairpin_counts.csv: "WT3".


title: naive hPSCs_OTX2-KO-2

description: Library name: OTX2-KO-4CL2


title: minusUV

description: Library name: Sample-07

library_source: other

data_processing:
Reads were quality-filtered, demultiplexed, trimmed to remove 5′ and 3′ linker sequences, and collapsed to eliminate PCR duplicates. Filtered reads were then aligned to the human genome (hg38) using BWA. Mapped reads were further collapsed using fastq2collapse.pl from the CTK toolkit with default parameters. The genomic distribution of uniquely mapped CLIP reads was determined using bed2annotation.pl. Uniquely mapped CLIP tags from all samples were pooled, and peaks were identified using tag2peak.pl (CTK) with a significance cutoff of p < 0.05. For each sample, tag counts within significant peaks were quantified using the countOverlaps function in R.
Assembly: hg38
Supplementary files format and content: Text files including peak counts for each sample

molecule: other

growth_protocol: Stable HEK293T cells expressing mutant and wt p53 were cultured as a monolayer in DMEM, supplemented with 10% v/v FBS, 100 U mL-1 penicillin, 100 µg mL-1 streptomycin, and 1.5 µg/mL Puromycin.

extract_protocol:
Cell pellets were resuspended in 1 mL of lysis buffer (1× PBS, 0.1% SDS, 0.5% sodium deoxycholate, 0.5% NP-40, supplemented with freshly added protease inhibitors), and immunoprecipitations were performed 2 h at 4 °C using a mouse monoclonal anti-FLAG antibody (8 μg conjugated to 100 μL of Protein A Dynabeads). Subsequent radiolabeling, RNA extraction, reverse transcription, and qPCR steps were performed to obtain input cDNA
Purified RNA samples were subjected to reverse transcription using barcoded RT primers, enabling the subsequent pooling of samples. To increase the overall yield, cDNA from each replicate of the wild-type and mutant conditions was pooled together following the reverse transcription step. The resulting cDNA was then immunoprecipitated using a BrdU-specific antibody, followed by circularization with CircLigase. The circularized product was then amplified via qPCR. This amplification utilized the KAPA enzyme supplemented with SYBR Green dye and specific Illumina indexing primers, DP5-PE and SP3-PE. Amplification continued until the fluorescence reached 400 Relative Fluorescence Units (RFU). The resulting amplicons were purified using AMPure magnetic beads. Finally, the pooled libraries were sequenced on the Illumina NextSeq 2000 platform.

treatment_protocol: Cells were washed twice with 1× PBS and UV-crosslinked on ice with one pulse of 400 mJ/cm² followed by one pulse of 200 mJ/cm². Cells were immediately scraped in fresh ice-cold 1× PBS and centrifuged at 5300 × g for 5 min at 4 °C.

value: wt p53 overexpression


title: Untransfected HEK cells replicate 2

description:
Library name: Sample-11
column name in mature_counts.csv and hairpin_counts.csv: "UT2".

value: Wild type

value: Untransfected HEK cells, harvested at the same time with other samples


title: Mut273_2

description: Library name: Sample-06

value: R273H p53 overexpression


title: Wild-type C57BL/6J; Control diet; Sample_T2_534136

description: Library name: T2_534136


title: Mut273_1

description: Library name: Sample-05


title: naive hPSCs_OTX2-KO-1

description: Library name: OTX2-KO-4CL1

value: naive hPSCs


title: Wild-type C57BL/6J; Control diet; Sample_T5_534143

description: Library name: T5_534143

value: wild-type C57/BL6


title: Mut245_2

description: Library name: Sample-04

value: G245S p53 overexpression


title: hPSCs_OTX2-KO-2

description: Library name: OTX2-KO-prime2

value: hPSCs

value: prime


title: Wild-type C57BL/6J; Control diet; Sample_T7_534135

description: Library name: T7_534135

value: liver


title: Mut245_1

description: Library name: Sample-03


title: Wild-type C57BL/6J; Control diet; Sample_T3_531083

description: Library name: T3_531083


title: hPSCs_OTX2-KO-1

description: Library name: OTX2-KO-prime1


title: WT_2

description: Library name: Sample-02


title: TLSCs_WT-1

description: Library name: H9-Cas9-toti1

value: TLSCs

value: totipotent


title: WT_1

description: Library name: Sample-01

value: HEK 293

value: epithelial cell


title: Dp16; Sample_Dp16_194_13427_Lv

description: Library name: Dp16_194_13427_Lv


title: TLSCs_WT-2

description: Library name: H9-Cas9-toti2


title: Lupus20_NonSjogren

city: Framingham

first: Shuran

last: Xing

state: MA

address: 16 Chubb Rd

institute: Bio-Techne

description: Library name: SAMPLE111

data_processing:
Sequencing reads (2 × 75 bp, paired end) were aligned to the human reference genome (GRCh38) using STAR (v2.7.9a), guided by Ensembl GTF release 106 annotations [43]. The resulting alignments were processed with Salmon (v1.9.0) to quantify transcript abundance, incorporating both sequence-specific and GC bias corrections to compute transcript-level read counts and transcripts per million (TPM) values [89]. Transcript-level quantifications were aggregated to the gene level using the tximport package in Bioconductor.
Assembly: GRCh38, GTF release 106
Supplementary files format and content: csv file containing raw count matrix gene*sample

source_name: saliva

extract_protocol:
Stimulated whole saliva was collected by instructing participants to chew on paraffin wax (Cat no. 3978-289, Benco Dental,) for up to 10 minutes and deposit saliva into a vial treated with RNase inhibitor (Cat no. NC1081844, Fisher Scientific). After samples were collected, they were centrifuged at 2,600 x g for 15 minutes to remove cells. Subsequently, all de-identified samples were stored at −80 °C until further processing. 0.5 mL of patient’s saliva was diluted with 0.5 mL of PBS prior to filtering with 0.8µm syringe filters (catalog no. SLAAR33SB, Fisher Scientific) to exclude extracellular vesicles larger than 800 nm in diameter. Salivary EVs, including exosomes, were isolated, and their total RNAs were extracted by Exosome Diagnostics (Waltham, MA, USA) using the ExoLution™ isolation platform
Exosome Diagnostics (Waltham, MA) conducted the construction and sequencing of Total RNA-Seq libraries using their exclusive EV long RNA-Seq platform. Briefly, EV RNA samples extracted from saliva underwent DNase treatment to eliminate any residual DNA. Following DNA digestion, synthetic RNA spike-in controls (ERCC spike-in mix, catalog no. 4456740, Thermo Fisher Scientific) were introduced into each sample. The EV RNA/ERCC blend was then fragmented for an optimal insert size and reverse transcribed using random priming. Then, second strand synthesis and A-Tailing were performed to facilitate adapter ligation. This was followed by two rounds of purification utilizing AMPureXP® beads (catalog no. A63881, Beckman Coulter). The final libraries were then amplified using a high-fidelity polymerase to a desired concentration for sequencing and purified once more using AMPure-XP® to remove any primer dimers. The Agilent Tape Station High Sensitivity D1000 Screen Tape Assay (catalog no. 5067-5584, Agilent Technologies) and Qubit 1X dsDNA HS Assay Kit (catalog no. Q33231, Thermo Fisher Scientific) were used to quantify libraries. Finally, libraries were normalized and pooled for target enrichment.

value: saliva

value: Lupus


title: Lupus22_NonSjogren

description: Library name: SAMPLE113


title: Lupus21_NonSjogren

description: Library name: SAMPLE112


title: Lupus19_NonSjogren

description: Library name: SAMPLE110


title: naive hPSCs_WT-2

description: Library name: H9-Cas9-4CL2

value: naive


title: Dp16; Sample_Dp16_193_13427_Lv

description: Library name: Dp16_193_13427_Lv


title: Lupus18_NonSjogren

description: Library name: SAMPLE109


title: Rheumatoid_Arthritis17_NonSjogren

description: Library name: SAMPLE108


title: Rheumatoid_Arthritis16_NonSjogren

description: Library name: SAMPLE107


title: Rheumatoid_Arthritis15_NonSjogren

description: Library name: SAMPLE106


title: Dp16; Sample_Dp16_183_13425_Lv

description: Library name: Dp16_183_13425_Lv


title: hPSCs_WT-2

description: Library name: H9-Cas9-prime2


title: Rheumatoid_Arthritis13_NonSjogren

description: Library name: SAMPLE104


title: hPSCs_WT-1

description: Library name: H9-Cas9-prime1


title: 412_8_SSA_Neg

description: Library name: SAMPLE102


title: Dp16; Sample_Dp16_175_13423_Lv

description: Library name: Dp16_175_13423_Lv


title: Wild-type C57BL/6J; Sample_WT_203_13429_Lv

description: Library name: WT_203_13429_Lv

value: wild-type


title: 561_18_SSA_Neg

description: Library name: SAMPLE103


title: 411_4_SSA_Neg

description: Library name: SAMPLE100


title: rv1_sgDNMT_rep3

city: Boston

first: Varadha Balaji

last: Venkadakrishnan

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: VBV96

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

source_name: prostate

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

value: prostate

value: cell line


title: 560_26_SSA_Neg

description: Library name: SAMPLE99


title: Dp16; Sample_Dp16_202_13429_Lv

description: Library name: Dp16_202_13429_Lv


title: rv1_sgDNMT_rep1

description: Library name: VBV94


title: Wild-type C57BL/6J; Sample_WT_192_13427_Lv

description: Library name: WT_192_13427_Lv


title: 560_20_SSA_Neg

description: Library name: SAMPLE96


title: Wild-type C57BL/6J; Sample_WT_184_13425_Lv

description: Library name: WT_184_13425_Lv


title: 561_19_SSA_Neg

description: Library name: SAMPLE98


title: rv1_sgDNMT_rep2

description: Library name: VBV95


title: 561_24_SSA_Neg

description: Library name: SAMPLE97


title: Wild-type C57BL/6J; Sample_WT_195_13427_Lv

description: Library name: WT_195_13427_Lv


title: 560_27_SSA_Neg

description: Library name: SAMPLE94


title: Wild-type C57BL/6J; Sample_WT_179_13423_Lv

description: Library name: WT_179_13423_Lv


title: naive hPSCs_WT-1

description: Library name: H9-Cas9-4CL1


title: Rheumatoid_Arthritis14_NonSjogren

description: Library name: SAMPLE105


title: rv1_sgGFP_rep3

description: Library name: VBV93

value: sgGFP


title: 561_28_SSA_Neg

description: Library name: SAMPLE95


title: rv1_sgGFP_rep2

description: Library name: VBV92


title: PF044_SSA_Neg

description: Library name: SAMPLE92


title: 560_21_SSA_Neg

description: Library name: SAMPLE93


title: Wild-type C57BL/6J; Sample_WT_173_13422_Lv

description: Library name: WT_173_13422_Lv


title: Dp16; Sample_Dp16_188_13426_Lv

description: Library name: Dp16_188_13426_Lv


title: 561_25_SSA_Neg

description: Library name: SAMPLE101


title: rv1_sgGFP_rep1

description: Library name: VBV91


title: PF038_SSA_Neg

description: Library name: SAMPLE89


title: PF039_SSA_Neg

description: Library name: SAMPLE90


title: 22Rv1_sgGFP_H3K27me3_rep2

description: Library name: 20221107_CR22_078_VV10481_S102

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

extract_protocol: CUT&RUN Epicypher kit was used.

value: WT


title: PF037_SSA_Neg

description: Library name: SAMPLE88


title: PF041_SSA_Neg

description: Library name: SAMPLE91


title: Hippocampal CA1 of 4m_Erbb4_WT_3

city: Daejeon

first: Se Young

last: Lee

address: Daehakro 291

country: South Korea

institute: KAIST

description:
Library name: 4m_Erbb4_WT_3
10X Genomics

data_processing:
snRNAseq data were analysed using Cell Ranger v8.0.1. Briefly, raw BCL files from Illumina HiSeq were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’. FASTQ files were further processed with ‘cellranger count’, involving mapping to the mouse reference genome (mm10-2020-A), quantifying gene expression via unique molecular identifiers (UMI) and cell barcodes, cell clustering, and differential gene expression analysis. Multiple sequencing runs were combined using ‘cellranger aggr’.
Assembly: mm10-2020-A for 2- or 3-month-old WT and 5XFAD. GRCm39-2024-A for 4-month-old WT and 5XFAD
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Isolated cells were counted by LUNA-FLTM Automated Fluorescence Cell Counter (logos biosystems) and processed following the manufacturer’s instruction; 10x Genomics Single Cell Protocols Cell Preparation Guide and the Guidelines for Optimal Sample Preparation flowchart (Documents CG00053 and CG000126, respectively). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’ v3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
Libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol (CG000204)

treatment_protocol: AAVs were injected into the CA1 of 4-month-old WT and 5XFAD unilaterally

value: Hippocampus


title: Hippocampal CA1 of 4m_Erbb4_WT_2

description:
Library name: 4m_Erbb4_WT_2
10X Genomics


title: PF035_SSA_Neg

description: Library name: SAMPLE86


title: 22Rv1_sgGFP_H3K27me3_rep1

description: Library name: 20221107_CR22_077_VV10481_S101


title: PF036_SSA_Neg

description: Library name: SAMPLE87


title: PF034_SSA_Neg

description: Library name: SAMPLE85


title: PF032_SSA_Neg

description: Library name: SAMPLE83


title: 22Rv1_sgGFP_H3K4me3_rep2

description: Library name: 20221107_CR22_076_VV10481_S100


title: Hippocampal CA1 of 4m_Erbb4_WT_1

description:
Library name: 4m_Erbb4_WT_1
10X Genomics


title: Hippocampal CA1 of 4m_HA_WT_3

description:
Library name: 4m_HA_WT_3
10X Genomics

value: HA-AAV


title: PF029_SSA_Neg

description: Library name: SAMPLE81


title: 22Rv1_sgGFP_H3K4me3_rep1

description: Library name: 20221107_CR22_075_VV10481_S99


title: PF030_SSA_Neg

description: Library name: SAMPLE82


title: Hippocampal CA1 of 4m_HA_WT_2

description:
Library name: 4m_HA_WT_2
10X Genomics


title: 22Rv1_sgGFP_IgG_rep1

description: Library name: 20221107_CR22_073_VV10481_S97


title: Hippocampal CA1 of 4m_HA_WT_1

description:
Library name: 4m_HA_WT_1
10X Genomics


title: 22Rv1_sgGFP_IgG_rep2

description: Library name: 20221107_CR22_074_VV10481_S98


title: PF024_SSA_Neg

description: Library name: SAMPLE78


title: 22Rv1_sgDNMT1_H3K27me3_rep2

description: Library name: 20221107_CR22_070_VV10481_S94

value: DNMT1 knockout


title: Hippocampal CA1 of 4m_sgErbb4_5XFAD_3

description:
Library name: 4m_sgErbb4_5XFAD_3
10X Genomics


title: PF022_SSA_Neg

description: Library name: SAMPLE76


title: 22Rv1_sgDNMT1_H3K27me3_rep1

description: Library name: 20221107_CR22_069_VV10481_S93


title: PF021_SSA_Neg

description: Library name: SAMPLE75


title: 22Rv1_sgDNMT1_H3K4me3_rep2

description: Library name: 20221107_CR22_068_VV10481_S92


title: PF020_SSA_Neg

description: Library name: SAMPLE74


title: Hippocampal CA1 of 4m_sgErbb4_5XFAD_1

description:
Library name: 4m_sgErbb4_5XFAD_1
10X Genomics


title: PF018_SSA_Neg

description: Library name: SAMPLE72


title: PF033_SSA_Neg

description: Library name: SAMPLE84


title: Hippocampal CA1 of 4m_sgControl_5XFAD_3

description:
Library name: 4m_sgControl_5XFAD_3
10X Genomics

value: sgControl-AAV


title: PF016_SSA_Neg

description: Library name: SAMPLE70


title: Hippocampal CA1 of 4m_sgControl_5XFAD_2

description:
Library name: 4m_sgControl_5XFAD_2
10X Genomics


title: 22Rv1_sgDNMT1_IgG_rep2

description: Library name: 20221107_CR22_066_VV10481_S90


title: PF028_SSA_Neg

description: Library name: SAMPLE80


title: PF014_SSA_Neg

description: Library name: SAMPLE68


title: PF015_SSA_Neg

description: Library name: SAMPLE69


title: 411_3_SSA_Pos

description: Library name: SAMPLE67


title: PF026_SSA_Neg

description: Library name: SAMPLE79


title: 561_7_SSA_Pos

description: Library name: SAMPLE66


title: Hippocampus of 3m_5XFAD_2

description:
Library name: 3m_5XFAD_2
10X Genomics


title: 411_24_Healthy_NonSjogren

description: Library name: SAMPLE65


title: Hippocampal CA1 of 4m_sgErbb4_5XFAD_2

description:
Library name: 4m_sgErbb4_5XFAD_2
10X Genomics


title: Hippocampal CA1 of 4m_sgControl_5XFAD_1

description:
Library name: 4m_sgControl_5XFAD_1
10X Genomics


title: Hippocampus of 3m_5XFAD_1

description:
Library name: 3m_5XFAD_1
10X Genomics


title: 22Rv1_sgDNMT1_IgG_rep1

description: Library name: 20221107_CR22_065_VV10481_S89


title: PF023_SSA_Neg

description: Library name: SAMPLE77


title: WCM154_sgDNMT1_H3K27me3_rep1

description: Library name: 20221107_CR22_061_VV10481_S85

value: pateint-dervied organoids


title: 412_12_SSA_Pos

description: Library name: SAMPLE62


title: 560_32_Sicca_NonSjogren

description: Library name: SAMPLE64


title: PF013_SSA_Neg

description: Library name: SAMPLE63


title: PF019_SSA_Neg

description: Library name: SAMPLE73


title: WCM154_sgDNMT1_H3K4me3_rep2

description: Library name: 20221107_CR22_060_VV10481_S84


title: Hippocampus of 3m_WT_2

description:
Library name: 3m_WT_2
10X Genomics


title: 22Rv1_sgDNMT1_H3K4me3_rep1

description: Library name: 20221107_CR22_067_VV10481_S91


title: 561_40_Healthy_NonSjogren

description: Library name: SAMPLE60


title: PF017_SSA_Neg

description: Library name: SAMPLE71


title: Hippocampus of 3m_WT_1

description:
Library name: 3m_WT_1
10X Genomics


title: 561_55_Sicca_NonSjogren

description: Library name: SAMPLE61


title: 561_15_SSA_Pos

description: Library name: SAMPLE59


title: 412_30_Healthy_NonSjogren

description: Library name: SAMPLE58


title: 560_5_SSA_Pos

description: Library name: SAMPLE57


title: Hippocampus of 2m_5XFAD_2

description:
Library name: 2m_5XFAD_2
10X Genomics


title: WCM154_sgDNMT1_H3K27me3_rep2

description: Library name: 20221107_CR22_062_VV10481_S86


title: WCM154_sgDNMT1_IgG_rep2

description: Library name: 20221107_CR22_058_VV10481_S82


title: 560_17_SSA_Pos

description: Library name: SAMPLE55


title: PF012_SSA_Neg

description: Library name: SAMPLE56


title: WCM154_sgDNMT1_IgG_rep1

description: Library name: 20221107_CR22_057_VV10481_S81


title: Hippocampus of 2m_5XFAD_1

description:
Library name: 2m_5XFAD_1
10X Genomics


title: 411_27_Healthy_NonSjogren

description: Library name: SAMPLE53


title: WCM154_sgGFP_H3K27me3_rep2

description: Library name: 20221107_CR22_046_VV10481_S70


title: PRNE_NEPC_M5358

city: New York City

first: Richa

last: Singh

state: NY

address: 413 East, 69th street

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

description: Library name: Sample 4

data_processing:
Single-end bisulfite-converted reads were aligned using Bismark following trimming and adapter removal by TrimGalore. Methylkit was used for identifying differentially methylated sites (DMSs). Sites covered by at least 10 reads, at least 25% difference in methylation between conditions and 5% False Discovery Rate (FDR) were considered as significantly differentially methylated.
DMRcate was used to analyze differentially methylated regions (DMRs). CpG files generated by methylkit were normalized for coverage and sites covered by at least 10 reads were used for differential analysis. The comparison was made between two pairs of PRN NEPC Vs. PRN adeno tumors and between NEPC PDOs (n=3) Vs. CRPC PDOs (n=2). A minimum of 5 consecutive CpGs were used to define a DMR and 5% FDR was used to identify significant DMRs. Homer was used to annotating the significant DMRs to promoters/TSS (±2000 bp from TSS and TSS), gene body (exons, introns, 5’-UTR and 3’-UTR), intergenic regions and CpG islands.
Assembly: Genome_build: mm10 for mouse and hg38 for human data
Supplementary files format and content: CpG count files in tab-delimited txt

source_name: prostate primary tumor

growth_protocol: NEPC patient-derived organoids were grown in human organoid media as per published protocol. The cells were grown in RPMI 1640 medium (Gibco, 11875-093) supplemented with 10% fetal bovine serum (Gemini, 900–108) and 1% penicillin/streptomycin (Gibco, 15140-122).

extract_protocol:
DNA methylation profiling was performed on biopsy punched tumor tissues of histopathologically confirmed foci of adenocarcinomas and NEPC from mouse primary tumor. DNA was extracted using Nucleospin Tissue kit (Macherey Nagel, 740952). For DNA methylation profile from patient-derived organoids, DNA was extracted from cell pellets of each. For EZH2 knockout lines, DNA was extracted from cell pellets after 14 days of nucleofection and validating the knockout.
Library preparation for single-end 100 base-pairs(SE 100) RRBS libraries, sequencing, and post-processing of the raw data was performed at Epigenomics Core at Weill Cornell Medicine. The resulting libraries were normalized, pooled, multiplexed, and clustered on flow cells and sequenced for 100 cycles of single-end reads on an Illumina NovaSeq 6000 instrument.

treatment_protocol: NEPC patient-derived organoids were treated wth 5µM  of tazemetostat for 14 days followed by DNA extraction.

value: prostate primary tumor

value: NEPC tumor

value: PRNE (PbCre/+; Ptenf/f; Rb1f/f; EZH2f/f; MYCN+/+)

value: Intact mice

tag: age

value: 12 weeks old


title: PF011_SSA_Neg

description: Library name: SAMPLE52

value: saliva


title: 561_10_SSA_Pos

description: Library name: SAMPLE51


title: PRNE_NEPC_M4851

description: Library name: Sample 3


title: WCM154_sgGFP_H3K27me3_rep1

description: Library name: 20221107_CR22_045_VV10481_S69


title: 412_9_SSA_Pos

description: Library name: SAMPLE50


title: PRN_NEPC_M4943

description: Library name: Sample 2

value: PRN (PbCre/+; Ptenf/f; Rb1f/f; MYCN+/+)

value: 10 weeks old


title: WCM154_sgGFP_H3K4me3_rep2

description: Library name: 20221107_CR22_044_VV10481_S68

value: prostate


title: PRN_Adeno_M4943

description: Library name: Sample 1

value: Adenocarcinoma tumor


title: 411_2_SSA_Pos

description: Library name: SAMPLE47


title: PF009_SSA_Neg

description: Library name: SAMPLE45


title: 560_33_Sicca_NonSjogren

description: Library name: SAMPLE46


title: WCM154_sgGFP_H3K4me3_rep1

description: Library name: 20221107_CR22_043_VV10481_S67


title: WCM154_sgGFP_IgG_rep2

description: Library name: 20221107_CR22_042_VV10481_S66


title: PRNE-NEPC_M5358

description:
Library name: Sample 2
12 weeks old

data_processing:
Quality control of raw sequencing reads was performed using FastQC
Low-quality reads were removed using Trimmomatic with a sliding window of 4bp and quality threshold of 20
Reads passing QC were aligned to mm10 using STAR
BAM file creation, sorting, and indexing were performed using SAMtools
Transcript abundances in FPKM were caluculated using Cufflinks
Assembly: Genome_build: mm10
Supplementary files format and content: Raw count files by HTseq in tab delimited txt

extract_protocol:
RNA extraction from GEM prostate tumors was performed using the Maxwell 16 LEV simplyRNA Tissue Kit (Promega, AS1280). Regions of the cryopreserved tumor samples that were identified by a blinded pathologist were excised with a biopsy punch and processed as described.
Paired-end 50 base pairs (PE50) libraries were generated using the TruSeq RNA Library Prep Kit [Non-stranded, polyA+] (Illumina) following the manufacturer's recommended protocol.


title: 411_26_Healthy_NonSjogren

description: Library name: SAMPLE44


title: PRNE-NEPC_M4851

description:
Library name: Sample 1
12 weeks old


title: WCM154_sgGFP_IgG_rep1

description: Library name: 20221107_CR22_041_VV10481_S65


title: 411_1_SSA_Pos

description: Library name: SAMPLE42


title: MLS17-03798-A1

city: New York

first: Dusan

last: Bogunovic

institute: Columbia Univesity

description: Library name: MLS17-03798-A1

data_processing:
Sequencing output and the histology images were processed using space ranger software (10X Genomics).  The space ranger mkfastq function was used for sample demultiplexing and to converting spatial barcodes and reads into FASTQ format.
The space ranger count function was used to align reads from FATSQ files to human genome (hg38) and then align microscopic slide image and transcriptome to generate barcode/UMI counts, feature spot matrices, cluster data, and perform gene expression analysis.
Assembly: hg38
Supplementary files format and content: Filtered feature-barcode matrices (filtered_feature_bc_matrix) containing only spot barcodes in MEX format for each sample. Spatial folder output from space ranger count function containing QC images for aligned fiducials and detetected tissue in jpg format, scalefactors_json.json, high and low resolution versions of the input image in png format, and tissue_positions_list.csv
Library strategy: Spatial Transcriptomics

source_name: Active Skin Lesion At collection time

growth_protocol: Three to four millimeter skin punch biopsies were obtained from lesional patient skin and non-lesional skin of healthy controls.

extract_protocol: Tissues were embedded in OCT and frozen in liquid nitrogen-chilled isopentane within 5 minutes of devascularization. 10-µm cryosections were mounted onto the ST arrays (10X Visium)  where reverse transcription of cellular transcripts took place in situ after tissue permeabilization.

treatment_protocol: Subjects were biologic-naïve (untreated)

value: Skin punch biopsy

value: Patient 1:Skin Lesion 3 (ISG15 Deficiency)


title: 411_25_Healthy_NonSjogren

description: Library name: SAMPLE54


title: 560_8_SSA_Pos

description: Library name: SAMPLE40


title: PRN_NEPC_M3733_H3K4me3

description:
Library name: Sample 35
H3K4me3 IP

data_processing:
Quality of raw sequencing reads was assessed by FastQC (Babraham Bioinformatics). Adapters and low-quality reads (Phred score <20) were removed using TrimGalore. Good quality reads were aligned to mm10 or hg38 genome using Bowtie2. Reads with mapping quality score <20 was removed from downstream analysis. PCR duplicates were removed using Picard MarkDuplicates. Peak calling was performed using the sonicated input DNA as control by MACS2 algorithm with a q-value of <0.05. For H3K27me3, broad peak module of MACS2 was used. Enriched ChIP-seq peak regions were annotated to mm10/hg38 genomic features using HOMER annotatePeak.pl. Known or de novo transcription factor motifs were identified using HOMER findMotifs.pl +/−100 bp from each peak. Unique and overlapping peaks between conditions were defined using BEDTools, keeping atleast 1bp overlap for overlapping peaks. For each condition, two replicates were used and normalized to its input control before merging. The combined signal from both replicates were used to generate enrichment profile plots and heatmap using deepTools.
Assembly: Genome_build: mm10 for mouse and hg38 for human data
Supplementary files format and content: Bedgraph files

growth_protocol: NEPC patient-derived organoid cells (1 × 106 cells diluted in 100ul of 1:1 PBS and Matrigel) were injected subcutaneously in the flanks of nude (NU/J) mice (Jackson Laboratories, #002019, RRID: IMSR_JAX:002019). Treatment was started after the tumor reached 150mm3.

extract_protocol:
Adenocarcinoma and NEPC foci were identified from hematoxylin-eosin stained slides of OCT blocks of primary tumors, reviewed by pathologist. The corresponding foci in OCT blocks were cored using 2mm biopsy punch and tissues were dissociated using pestle and motor homogenizer, followed by syringes in cold PBS.  Cryosections of xenograft tumors were homogenized in a similar protocol. Dissociated cells were crosslinked in 1% methanol-free formaldehyde (Thermo Scientific, 28908) for 15 min at 37 °C. Crosslinking was quenched with 2.5 M glycine for 5 min at room temperature. Washed cell pellets were resuspended in 1 mL of lysis buffer (50 mM Tris HCl pH 8, 0.5% SDS, 10 mM EDTA with protease and phosphatase inhibitors; Thermo Fisher Scientific, 78428/78430) and lysed for 20 minutes at 4°C. Collected nuclei were resuspended in a second lysis buffer (10 mM Tris HCl pH 7.5, 150 mM NaCl, 0.1% SDS, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate, with protease and phosphatase inhibitors; Thermo Fisher Scientific, 78428/78430) and sonicated in Bioruptor Pico, Diagenode for 12mins. To the sheared chromatin, equal volumes of specific antibody and respective IgG control antibody was added and incubated overnight at 4°C. The immunoprecipitated chromatin was washed with several buffers and eluted in 300 µL of fresh elution buffer (100 mM NaHCO3 and 1% SDS). Reverse crosslinking was performed with 45 mM Tris pH 7, 170 mM NaCl at 65°C overnight, followed by RNase and proteinase K treatment and DNA was purified using the NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel, 740609) as per manufacturer’s recommendation.
Libraries with purified immunoprecipitated DNA fragments were generated using the Hyper Prep Kit (Kapa Biosystems, KK8502). Library quality and fragment size distribution was checked in DNA High Sensitivity Bioanalyzer (Agilent, 5067-4626). Equimolar concentration of immunoprecipitated and input DNA fragments were pooled and sequenced in Illumina NovaSeq 6000 instrument at Weill Cornell Medicine Genomics core facility.

treatment_protocol: Decitabine (0.8mg/kg) was administered to mice in treated group by intraperitoneal injection once daily for 7 days. Equal volume of PBS was injected to mice in vehicle groups.

tag: batch


title: PRN_NEPC_M3733_H3K4me3-Input

description:
Library name: Sample 34
Input


title: SS18-870-bA

description: Library name: SS18-870-bA

source_name: Active lesion but substantial healing

value: Patient 1:Skin Lesion 2 (ISG15 Deficiency)


title: PRN_NEPC_M3733_H3K27me3

description:
Library name: Sample 33
H3K27me3 IP


title: 561_50_Sicca_NonSjogren

description: Library name: SAMPLE38


title: SS18-870-aA

description: Library name: SS18-870-aA

value: Patient 1:Skin Lesion 1 (ISG15 Deficiency)


title: PRN_NEPC_M3733_H3K27me3-Input

description:
Library name: Sample 32
Input


title: 561_36_Sicca_NonSjogren

description: Library name: SAMPLE36


title: PF007_SSA_Neg

description: Library name: SAMPLE35


title: 560_58_SSA_Pos

description: Library name: SAMPLE34


title: 411_28_Healthy_NonSjogren

description: Library name: SAMPLE49


title: Control-Abdomen-Skin

description: Library name: Control-Abdomen-Skin

source_name: Normal / Healthy Control sample

value: Healthy Control


title: Input, 293T

city: Shanghai

first: Yang

last: Ming

address: No.2005,Songhu Road

institute: Fudan Universitry

description: Library name: Input

data_processing:
Sequencing was carried out on the Illumina Novaseq 6000. For the bioinformatics analysis, firstly, raw sequencing reads were quality-controlled and filtered using Trimmomatic to remove low-quality reads and adapter sequences. The high-quality reads were then aligned to the reference genome containing the rDNA sequence using Bowtie2. Next, the binding peaks were called and identified by MACS2. The reads number of RNA species with peaks called was calculated by the FeatureCount.
Assembly: hg19
Supplementary files format and content: BED file containing the peak information.

growth_protocol: cells were cultured in High Glucose Dulbecco’s modified Eagle’s medium (DMEM)（Hyclone, #SH30243.01）with 10% fetal bovine serum (ExCell, #FSP500), 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco, #15140122) and in high-humidity incubators at 5% (v/v) CO2 and 37℃.

extract_protocol:
The released RNA was extracted using an RNA extraction kit (R4130, MagenBio) . The mechanism is that RNA is adsobed onto silica spi columns under chaotropic reagents.
library preparation was performed using a small RNA library preparation kit (RK20312, Abclonal)

treatment_protocol: Steady state

value: Immortalized Human Embryonic Kidney Cell 293T

value: WT

value: Steady State

tag: RIP antibody= none


title: PRN_NEPC_M3713_H3K27me3

description:
Library name: Sample 30
H3K27me3 IP

value: prostate primary tumor

value: NEPC tumor


title: 560_14_SSA_Pos

description: Library name: SAMPLE43


title: 561_37_Sicca_NonSjogren

description: Library name: SAMPLE33


title: 561_54_Healthy_NonSjogren

description: Library name: SAMPLE41


title: 560_29_Sicca_NonSjogren

description: Library name: SAMPLE32


title: 412_32_Healthy_NonSjogren

description: Library name: SAMPLE48


title: 561_3_SSA_Pos

description: Library name: SAMPLE30


title: PRN_NEPC_M2266-2_Input

description:
Library name: Sample 29
Input

value: Intact mice


title: WCM154_sgDNMT1_H3K4me3_rep1

description: Library name: 20221107_CR22_059_VV10481_S83

value: pateint-dervied organoids

value: DNMT1 knockout


title: 412_29_Healthy_NonSjogren

description: Library name: SAMPLE39

value: saliva


title: MED19-CLIP, 293T

description: Library name: MED19-CLIP

tag: RIP antibody= MED19


title: PF008_SSA_Neg

description: Library name: SAMPLE37


title: PRN_NEPC_M2266-2_H3K4me3

description:
Library name: Sample 28
H3K4me3 IP

value: PRN (PbCre/+; Ptenf/f; Rb1f/f; MYCN+/+)


title: 560_4_SSA_Pos

description: Library name: SAMPLE29


title: WT 293T cells, IgG ChIP-IP

description: Library name: Wild-Type Cell-IgG

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.01.
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bio Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Wild-Type

tag: chip antibody

value: IgG


title: 561_49_Sicca_NonSjogren

description: Library name: SAMPLE27


title: PF005_SSA_Neg

description: Library name: SAMPLE26


title: WT 293T cells, H3K4Me3 ChIP-IP

description: Library name: Wild-Type Cell-ChIP


title: PRN_Adeno_M5217_Input

description:
Library name: Sample 27
Input

value: Adenocarcinoma tumor


title: 561_47_Healthy_NonSjogren

description: Library name: SAMPLE24


title: PRN_NEPC_M3713_Input

description:
Library name: Sample 31
Input


title: EM2_Visium_v1

city: Houston

first: Hussein

last: Abbas

state: Texas

address: 1515 Holcombe Blvd

institute: The University of Texas at MD Anderson Cancer cent

description: Visium v1 on FFPE

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences aligned to the human reference genome GRCh38, utilizing the count function to map barcoded spots to individual slides using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: spatial.tar.gz: Spatial informations of slides including aligned_fiducials.jpg (aligned fiducials of the tissue image), cytassist_image.tiff (Image of the tissue captured by CytAssist machine; available only for v2 samples), detected_tissue_image.jpg (image of tissue and spots), scalefactors_json.json (scalefactors in json format), spatial_enrichment.csv (Table of Moran's I values for each feature), tissue_hires_image.png (high resolution image of tissue), tissue_lowres_image.png (Low resolution image of tissue), tissue_positions.csv (list of spatial barcodes and the coordinates specifying spots)
Supplementary files format and content: filtered_feature_bc_matrix.h5: Feature Barcode Matrix
Library strategy: Spatial Transcriptomics

source_name: Mediastinal Lymph Node

extract_protocol:
4µm sections cut from FFPE tissues
Spatial transcriptome libraries prepared according to the standard Visium-Cytassist Spatial Gene Expression protocol (CytAssist-enabled) for the v2 assay using Visium CytAssist Reagent Kit, and standard Visium Spatial Gene Expression protocol (Direct placement) for the v1 assay (10X Genomics).

value: Mediastinal Lymph Node

tag: disease state

value: AML

tag: timepoint

value: Newly diagnosed


title: PRN_Adeno_M5217_H3K27me3

description:
Library name: Sample 26
H3K27me3 IP


title: 560_39_Sicca_NonSjogren

description: Library name: SAMPLE23


title: PF006_SSA_Neg

description: Library name: SAMPLE31


title: EM1_Visium_v1

description: Visium v1 on FFPE

source_name: Skin

value: Skin


title: PRN_Adeno_M2266-2_Input

description:
Library name: Sample 25
Input


title: EM2_Visium_CytAssist_v2

description: Visium v2 on FFPE


title: 560_52_Healthy_NonSjogren

description: Library name: SAMPLE22


title: PF003_SSA_Neg

description: Library name: SAMPLE20


title: 412_31_Healthy_NonSjogren

description: Library name: SAMPLE21


title: PRN_Adeno_M2266-2_H3K4me3

description:
Library name: Sample 24
H3K4me3 IP


title: BM2_Visium_CytAssist_v2

description: Visium v2 on FFPE

source_name: Bone Marrow

value: Bone Marrow


title: 412_7_SSA_Pos

description: Library name: SAMPLE28


title: 561_57_Healthy_NonSjogren

description: Library name: SAMPLE18


title: PRN_Adeno_M2266-2_H3K27me3

description:
Library name: Sample 23
H3K27me3 IP


title: 560_16_SSA_Pos

description: Library name: SAMPLE17


title: BM1_Visium_CytAssist_v2

description: Visium v2 on FFPE


title: EM1_Visium_CytAssist_v2

description: Visium v2 on FFPE


title: 560_38_Sicca_NonSjogren

description: Library name: SAMPLE16


title: 561_43_Healthy_NonSjogren

description: Library name: SAMPLE13


title: PF002_SSA_Neg

description: Library name: SAMPLE19


title: 561_42_Sicca_NonSjogren

description: Library name: SAMPLE25


title: PRN_Adeno_M2229_Input

description:
Library name: Sample 22
Input


title: 412_11_SSA_Pos

description: Library name: SAMPLE14


title: PRN_Adeno_M2229_H3K4ME3

description:
Library name: Sample 21
H3K4me3 IP


title: 561_56_Sicca_NonSjogren

description: Library name: SAMPLE12


title: EMT6 cells, shISG20, 1% O2 (biol rep 3)

city: Baltimore

first: YONGKANG

last: YANG

state: Maryland

address: Room 673, MRB, 725 North Broadway

department: ICE

institute: Johns Hopkins University

description: Library name: Sample 12

data_processing:
RNA-seq data were processed and interpreted using Genialis Expressions software (https://www.genialis.com). Sequence quality checks were performed on raw and trimmed reads (FastQC), trimming and quality filtering of reads (BBDuk), mapping to reference human genome Ensembl v.92 (STAR), expression quantification (featureCounts), and expression normalisation (RNA.norm).
Assembly: GRCh38
Supplementary files format and content: Excel tables containing detailed information on TPM values for each Sample

source_name: breast

growth_protocol: EMT6 cells were maintained in Waymouth's MB 752/1 medium that were supplemented with 15% (vol/vol) fetal bovine serum (FBS), 2mM L-glutamine and 1% (vol/vol) penicillin-streptomycin (P/S).

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and treated with DNase (Qiagen).
Library preparation and sequencing using the NovaSeq 6000 platform (Illumina) were performed by the Johns Hopkins Genetics Resources Core Facility High-Throughput Sequencing Center.

treatment_protocol: ISG20 knockdown or control subclones of EMT6 cells were exposed in 20% or 1% oxygen condition for 48 hours.

value: breast

value: EMT6 cells

value: breast cancer cells

value: ISG20 knockdown

value: 1% O2, 48 hours


title: SW620, normoxia 4 hours, DMSO, rep3

city: San Diego

first: Peter

last: Croucher

state: CA

address: 11055 Flintkote Avenue

institute: Cardiff Oncology Inc

description:
SW620_Nx_DMSO_4h_R3
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq software (version 2.20)
Gene expression was quantified using Salmon v1.9.0 with GRCh38 (GENCODE release 44)
Genes were library size factor normalized and filtered using DESeq2 (v1.42.1)
Differential gene expression was assessed using DESeq2 (v1.42.1). Log2 fold-changes (LFC) were shrunken using the ashr algorithm and p-values were adjusted using independent hypothesis weighting against the ‘baseMean’ counts and the Benjamini-Hochberg method.
Gene set enrichment analyses used fGSEA (v1.28.0) on genes ranked by their LFC
Assembly: hg38
Supplementary files format and content: Comma delimited text file (.csv) containing size-factor normalized gene counts for each sample

growth_protocol: Human KRAS-mutant colorectal cancer cell lines HCT116 and SW620 were cultured in RPMI supplemented with 10% FBS and 1X penicillin-streptomycin solution. The cells were incubated at 37°C in a humidified chamber containing 5% CO2 and 20% O2. Hypoxic conditions were achieved by culturing cells at 1%O2 and 5% CO2.

extract_protocol:
Cells were lysed in 700 µL of Trizol LS Reagent and total RNA isolated using the PureLinkTM RNA Mini Kit.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina and paired-end sequenced (2 x 150 bp) on an Illumina NovaSeq.

treatment_protocol: Cell lines were dosed with either DMSO (vehicle) or onvansertib. Onvansertib was adminsitsred at two doses. After 20h in normoxia cell lines were either subject to hypoxia or kept at normoxia for 4h. Experiments were performed in triplicate.

value: colorectal cancer cell line

value: DMSO (vehicle) and 20 hours normoxia followed by 4 hours in normoxia


title: SW620, normoxia 4 hours, DMSO, rep2

description:
SW620_Nx_DMSO_4h_R2
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: 412_10_SSA_Pos

description: Library name: SAMPLE11

value: saliva


title: EMT6 cells, shISG20, 1% O2 (biol rep 2)

description: Library name: Sample 11


title: SW620, normoxia 4 hours, DMSO, rep1

description:
SW620_Nx_DMSO_4h_R1
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: 561_2_SSA_Pos

description: Library name: SAMPLE9


title: 560_44_Sicca_NonSjogren

description: Library name: SAMPLE10


title: SW620, hypoxia 4 hours, 75nM Onvansertib, rep3

description:
SW620_Hx_ONV2_4h_R3
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv

value: Onvansertib (75 nM) and 20 hours normoxia followed by 4 hours in hypoxia


title: 560_41_Healthy_NonSjogren

description: Library name: SAMPLE7


title: 560_51_Sicca_NonSjogren

description: Library name: SAMPLE8


title: EMT6 cells, shISG20, 1% O2 (biol rep 1)

description: Library name: Sample 10


title: SW620, hypoxia 4 hours, 75nM Onvansertib, rep2

description:
SW620_Hx_ONV2_4h_R2
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: 560_46_Sicca_NonSjogren

description: Library name: SAMPLE6


title: 560_1_SSA_Pos

description: Library name: SAMPLE3


title: 411_6_SSA_Pos

description: Library name: SAMPLE4


title: 560_12_SSA_Pos

description: Library name: SAMPLE5


title: 561_9_SSA_Pos

description: Library name: SAMPLE15


title: PF001_SSA_Neg

description: Library name: SAMPLE2


title: EMT6 cells, shISG20, 20% O2 (biol rep 2)

description: Library name: Sample 8


title: SW620, hypoxia 4 hours, 75nM Onvansertib, rep1

description:
SW620_Hx_ONV2_4h_R1
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: 561_30_Sicca_NonSjogren

description: Library name: SAMPLE1


title: SW620, hypoxia 4 hours, 25nM Onvansertib, rep3

description:
SW620_Hx_ONV1_4h_R3
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv

value: Onvansertib (25 nM) and 20 hours normoxia followed by 4 hours in hypoxia


title: EMT6 cells, shNTC, 1% O2 (biol rep 3)

description: Library name: Sample 6

value: wild type


title: EMT6 cells, shISG20, 20% O2 (biol rep 1)

description: Library name: Sample 7


title: RNAu2 (control)  sample analyzed with ToS kit

city: Valencia

first: Antonio

last: Fernandez-Serra

address: Profesor Beltran Baguena, 8

country: Spain

institute: Fundacion Instituto Valenciano de Oncologia

description: Library name: RNA2_TOS

data_processing:
HTG parser v5.3 and TempOSeqR v1.0
Assembly: hg38 (HTG) and HWT_2_1_BrCa_22575plex (ToS)
Supplementary files format and content: csv file includes read counts for HTG and TempOSeq analysis

source_name: Control RNA sample

extract_protocol:
HTG and TempOSeq are targeted RNA-seq methods without FFPE sample RNA extraction
HTG edgeseq HTP panel and TempOSeq Human Whole Transcriptome Assay

value: Control RNA sample

value: ToS


title: SW620, hypoxia 4 hours, 25nM Onvansertib, rep2

description:
SW620_Hx_ONV1_4h_R2
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: RNAu3 (control)  sample analyzed with ToS kit

description: Library name: RNA3_TOS


title: RNAu1 (control) sample analyzed with ToS kit

description: Library name: RNA1_TOS


title: HTP92 sample analyzed with ToS kit

description: Library name: HTP92_TOS

source_name: Endometrial Cancer

value: Endometrial Cancer


title: SW620, hypoxia 4 hours, 25nM Onvansertib, rep1

description:
SW620_Hx_ONV1_4h_R1
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: HTP93 sample analyzed with ToS kit

description: Library name: HTP93_TOS


title: HTP91 sample analyzed with ToS kit

description: Library name: HTP91_TOS


title: EMT6 cells, shNTC, 1% O2 (biol rep 1)

description: Library name: Sample 4


title: SW620, hypoxia 4 hours, DMSO, rep3

description:
SW620_Hx_DMSO_4h_R3
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv

value: DMSO (vehicle) and 20 hours normoxia followed by 4 hours in hypoxia


title: HTP90 sample analyzed with ToS kit

description: Library name: HTP90_TOS


title: HTP89 sample analyzed with ToS kit

description: Library name: HTP89_TOS


title: HTP88 sample analyzed with ToS kit

description: Library name: HTP88_TOS


title: SW620, hypoxia 4 hours, DMSO, rep2

description:
SW620_Hx_DMSO_4h_R2
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: EMT6 cells, shNTC, 20% O2 (biol rep 3)

description: Library name: Sample 3


title: HTP84 sample analyzed with ToS kit

description: Library name: HTP84_TOS


title: HCT116, normoxia 4 hours, DMSO, rep3

description:
HCT116_Nx_DMSO_4h_R3
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: EMT6 cells, shNTC, 20% O2 (biol rep 1)

description: Library name: Sample 1


title: EMT6 cells, shNTC, 20% O2 (biol rep 2)

description: Library name: Sample 2


title: HTP82 sample analyzed with ToS kit

description: Library name: HTP82_TOS


title: HTP81 sample analyzed with ToS kit

description: Library name: HTP81_TOS


title: HTP87 sample analyzed with ToS kit

description: Library name: HTP87_TOS


title: SW620, hypoxia 4 hours, DMSO, rep1

description:
SW620_Hx_DMSO_4h_R1
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: HTP80 sample analyzed with ToS kit

description: Library name: HTP80_TOS


title: EMT6 cells, shNTC, 1% O2 (biol rep 2)

description: Library name: Sample 5


title: EMT6 cells, shISG20, 20% O2 (biol rep 3)

description: Library name: Sample 9


title: HTP79 sample analyzed with ToS kit

description: Library name: HTP79_TOS


title: HCT116, normoxia, 4 hours, DMSO, rep2

description:
HCT116_Nx_DMSO_4h_R2
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: Vestibule, 10 weeks, Bio rep 4

city: Omaha

first: David

middle: Z

last: He

state: NE

address: 2500 California Plaza

department: Biomedical Science

institute: Creighton University

description:
Library name: CBA/J 10 weeks  Vestibular Bio rep 4
10X Genomics

data_processing:
Standard 10x Genomics CellRanger pipeline (version 6.1.2) was used for demultiplexing, alignment (10x reference genome mm10), barcode processing, and UMI counting to obtain the filtered count matrices. Processing and visualization of the scRNA-seq data from cochlear and vestibular were performed in R. Filtered count matrices obtained from the biological replicates of cochlear and vestibular samples were loaded into R, converted to Seurat Objects, and pre-processed to eliminate the poor-quality cells using parameters such as counts, features, percentage of mitochondria, ribosomes, and blood gene content. Cells with at least 200 features, 1000 UMI counts, and less than 25% mitochondrial genes were included for the downstream analysis. Individual Seurat Objects were integrated into a single Seurat Object for cochlea and vestibule.
Assembly: Mouse mm10
Supplementary files format and content: Filtered barcode, matrix and features(genes) files

source_name: Vestibular Sensory Epithelium

extract_protocol:
Whole cochlear and vestibular organs were microdissected from the inner ears of 10-weeks-old CBA/J mice in petri dishes containing cold L-15 media (Gibco). The sensory epithelia were subjected to enzymatic digestion by transferring into 1.5 ml eppendorf tubes containing 1 ml/mg collagenase IV (Sigma) in L-15 medium for 10 minutes at room temperature. Then the cells were resuspended in 400 µL of enzyme-free DMEM containing 10% FBS and single-cell suspensions were obtained by trituration using a trimmed 200 ul pipette tip followed by filtering with a 40 uM strainer. The cells were pelleted by centrifuging at 300 xg for 5 mins at 4°C, then resuspended in media and subsequently quantified the number of cells. 7-8 mice were used for each biological replicate, and 6 and 4 biological replicates were obtained for cochlea and vestibule respectively.
Single-cell capture and library preparation were performed using droplet-based microfluidic technology, following the manufacturer’s instructions for the Chromium Next GEM Single Cell 3ʹ v3.1 dual index kit. The quality of the obtained libraries was assessed via high-sensitivity DNA kits (Agilent Technologies) using Agilent 2100 Bioanalyzer prior to sequencing with Illumina NovaSeq 6000.

treatment_protocol: Animals were bred and aged to assess the biological aging

value: Vestibular Sensory Epithelium

value: Wild-type


title: HTP78 sample analyzed with ToS kit

description: Library name: HTP78_TOS


title: Vestibule, 10 weeks, Bio rep 2

description:
Library name: CBA/J 10 weeks  Vestibular Bio rep 2
10X Genomics


title: Vestibule, 10 weeks, Bio rep 3

description:
Library name: CBA/J 10 weeks  Vestibular Bio rep 3
10X Genomics


title: HCT116, normoxia 4 hours, DMSO, rep1

description:
HCT116_Nx_DMSO_4h_R1
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: HTP83 sample analyzed with ToS kit

description: Library name: HTP83_TOS


title: HTP77 sample analyzed with ToS kit

description: Library name: HTP77_TOS


title: HCT116, hypoxia 4 hours, 200nM Onvansertib, rep3

description:
HCT116_Hx_ONV2_4h_R3
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv

value: Onvansertib (200 nM) and 20 hours normoxia followed by 4 hours in hypoxia


title: HTP75 sample analyzed with ToS kit

description: Library name: HTP75_TOS


title: Vestibule, 10 weeks, Bio rep 1

description:
Library name: CBA/J 10 weeks  Vestibular Bio rep 1
10X Genomics


title: HTP74 sample analyzed with ToS kit

description: Library name: HTP74_TOS


title: HTP73 sample analyzed with ToS kit

description: Library name: HTP73_TOS


title: HCT116, hypoxia 4 hours, 200nM Onvansertib, rep2

description:
HCT116_Hx_ONV2_4h_R2
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: HTP72 sample analyzed with ToS kit

description: Library name: HTP72_TOS


title: HTP71 sample analyzed with ToS kit

description: Library name: HTP71_TOS


title: HCT116, hypoxia 4 hours, 75nM Onvansertib, rep3

description:
HCT116_Hx_ONV1_4h_R3
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: RNAu3 (control)  sample analyzed with HTG kit

description: Library name: RNA3_HTP

value: HTG


title: HCT116, hypoxia 4 hours, 75nM Onvansertib, rep2

description:
HCT116_Hx_ONV1_4h_R2
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: RNAu1 (control) sample analyzed with HTG kit

description: Library name: RNA1_HTP


title: Cochlea, 10 weeks, Bio rep 4

description:
Library name: CBA/J 10 weeks  Cochlear Bio rep 4
10X Genomics

source_name: Cochlear Sensory Epithelium

value: Cochlear Sensory Epithelium


title: HTP70 sample analyzed with ToS kit

description: Library name: HTP70_TOS


title: HCT116, hypoxia 4 hours, 75nM Onvansertib, rep1

description:
HCT116_Hx_ONV1_4h_R1
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: HTP92 sample analyzed with HTG kit

description: Library name: HTP92_HTP


title: RNAu2 (control)  sample analyzed with HTG kit

description: Library name: RNA2_HTP


title: Cochlea, 10 weeks, Bio rep 2

description:
Library name: CBA/J 10 weeks  Cochlear Bio rep 2
10X Genomics


title: Cochlea, 10 weeks, Bio rep 5

description:
Library name: CBA/J 10 weeks  Cochlear Bio rep 5
10X Genomics


title: HTP93 sample analyzed with HTG kit

description: Library name: HTP93_HTP


title: Cochlea, 10 weeks, Bio rep 3

description:
Library name: CBA/J 10 weeks  Cochlear Bio rep 3
10X Genomics


title: HCT116, hypoxia 4 hours, DMSO, rep3

description:
HCT116_Hx_DMSO_4h_R3
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: Cochlea, 10 weeks, Bio rep 6

description:
Library name: CBA/J 10 weeks  Cochlear Bio rep 6
10X Genomics


title: Cochlea, 10 weeks, Bio rep 1

description:
Library name: CBA/J 10 weeks  Cochlear Bio rep 1
10X Genomics


title: HCT116, hypoxia 4 hours, DMSO, rep2

description:
HCT116_Hx_DMSO_4h_R2
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: HTP84 sample analyzed with HTG kit

description: Library name: HTP84_HTP


title: HTP89 sample analyzed with HTG kit

description: Library name: HTP89_HTP


title: HCT116, hypoxia 4 hours, 200nM Onvansertib, rep1

description:
HCT116_Hx_ONV2_4h_R1
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv


title: HTP83 sample analyzed with HTG kit

description: Library name: HTP83_HTP


title: wild type ZT20 rep3

city: Irvine

first: Kousha

last: Changizi

state: California

address: Donald Bren Hall

department: ICS/IGB

institute: University of California, Irvine

data_processing:
Reads aligned to mm10 assembly and RefSeq genes using TopHat release 2.1.1
Gene expression results (FPKM) obtained using Cufflinks release 2.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Samples

source_name: Colon

extract_protocol:
Total RNA was extracted from the colon with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
RNA libraries for each group were prepared as described in the Illumina TruSeq mRNA stranded protocol.

value: Colon

value: ad libitum normal chow diet


title: HTP88 sample analyzed with HTG kit

description: Library name: HTP88_HTP


title: HTP87 sample analyzed with HTG kit

description: Library name: HTP87_HTP


title: wild type ZT20 rep2


title: HCT116, hypoxia 4 hours, DMSO, rep1

description:
HCT116_Hx_DMSO_4h_R1
HCT116_SW620_RNASeq_samples_normalized_counts_4hr.csv

value: colorectal cancer cell line


title: HTP82 sample analyzed with HTG kit

description: Library name: HTP82_HTP


title: PE_placenta

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description: FFPE spatial transcriptome sequencing

data_processing:
The Visium sequencing data were processed by Space Ranger.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducial.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: placenta

extract_protocol:
Formalin-fixed paraffinembedded (FFPE) placental tissues were used. Maternal side of the placenta (5μm) was mounted into each capture area of Visium CytAssist for FFPE (11mm × 11mm).
Library construction was performed according to the standard Visium for the FFPE workflow.

value: placenta

tag: condition

value: Preeclampsia


title: HTP90 sample analyzed with HTG kit

description: Library name: HTP90_HTP


title: Streptavidin_pulldown_rep2

city: Chicago

first: Rui

last: Yi

state: IL

address: 303 E. Chicago Avenue

institute: Northwestern University

description: Library name: Streptavidin_2

data_processing:
The 5' and 3' adapter sequences were removed using CutAdapt. Reads were mapped using BLAST to a Fasta file containing the mouse miRNA database. Reads containing an miRNA at the 5' end of the reads were futher mapped to the mouse genome using Novoalign.
Assembly: mm10
Supplementary files format and content: tab delimited file with microRNA count

molecule: cytoplasmic RNA

growth_protocol: Mouse keratinocytes from skin were cultured in homemade E low Calcium medium

extract_protocol:
After lysis and Dnase and Rnase treatment, biotinated proteins together with RNAs were pulled down by streptavidin conjugated Dynabeads. After ligation, RNA was purified by phenol/choloform extraction.
3' and 5' RNA linkers were added to the RNA by direct ligation, followed by RT-PCR to amplify the cDNA and add indexes.

treatment_protocol: Dsp-BirA fusion protein was expressed exogenously and cells were treated with biotin

value: Skin

value: Keratinocyte from skin

value: Epithelial cell

value: Dsp-BirA exogenous expression

value: biotin treated


title: HTP91 sample analyzed with HTG kit

description: Library name: HTP91_HTP

value: Endometrial Cancer


title: wild type ZT16 rep3

value: wild type


title: Normal_placenta

description: FFPE spatial transcriptome sequencing

value: Normal


title: Streptavidin_pulldown_rep1

description: Library name: Streptavidin_1


title: HTP80 sample analyzed with HTG kit

description: Library name: HTP80_HTP


title: wild type ZT16 rep2


title: HUVEC_LIMCH-EV_rep2

data_processing:
Expression levels for each gene were quantified from the sequencing data by Kallisto software.
The tximport package (ver. 1.18.0) was used to summarize the data.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: a tsv file includes TPM counts of each sample

source_name: HUVEC

growth_protocol: Human choriocarcinoma cell line (JAR) was cultured in DMEM (4500 mg/L glucose, Nacalai Tesque, Japan) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37 ℃ in 5% CO2. Human umbilical vein endothelial cell (HUVEC) was cultured in endothelial cell growth medium (EGM-2 added with bullet kit; cat no. CC-3162; Lonza, USA) at 37 ℃ in 5% CO2.

extract_protocol:
The total RNA was extracted using the miRNeasy Mini Kit (QIAGEN, Hilden, Germany).
The library construction and pair-end sequencing were conducted by Novogene, Inc. (Beijing, China).

treatment_protocol:
Full-length LIMCH1 was PCR-amplified with forward (5’-actgatgaattcaccATGGCTTGTCCCGCTCTCGG-3’) and reverse (5’-tacgatgcggccgctaTCACAATGTTGTAGGCTGCC-3’) primers from JAR complementary DNA (cDNA). The amplification product was excised via NotⅠ and EcoRⅠ digestion, separated on a 1.0% Agarose gel in 1 × TAE buffer, and the band was extracted from the gel using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany). The product was inserted into the FLAG-tagged pQCXIP retroviral vector (TaKaRa Bio, Japan) pre-digested with NotⅠ and EcoRⅠ. The resultant plasmid was introduced into competent high DH5α (cat no. DNA-903, TOYOBO Co., Ltd., Osaka, Japan), and transformants were selected on LB broth agar plate containing 100 μg/mL ampicillin. Positive clones were expanded by growth in LB broth medium containing 100 μg/mL ampicillin, and the plasmid was extracted using the QIAprep spin Miniprep Kit (Qiagen). Resultant pQCXIP-LIMCH1 clones were confirmed with sequencing. FLAG-tagged pQCXIP without the LIMCH1 insert was used as transfection control.
To extract EVs, the JAR cells were washed with phosphate buffered saline (PBS) and the culture medium was replaced with advanced DMEM medium (Thermo Fisher Scientific Inc., USA). After incubation for 48 h, the conditioned medium (CM) was collected and centrifuged at 2,000 × g for 10 min at 4 ℃. To thoroughly remove cellular debris, the supernatant was filtered through a 0.22 μm filter (Corning, USA). Then, the supernatant was ultracentrifuged at 45,000 rpm using a MLS-50 rotor (Beckman Coulter Inc., USA) for 70 min at 4 ℃; CM was ultracentrifuged at 32,000 rpm using a SW 32 Ti rotor (Beckman Coulter) for 120 min at 4 ℃. The pellet was again washed with PBS, ultracentrifuged at same conditions, and resuspended in PBS.
HUVECs were seeded in a 12-well plate, at a density of 100,000 cells/ well. Six hours after seeding, 30 μg of JAR-FLAG-EVs (Control-EVs) or JAR-LIMCH1-EVs (LIMCH1-EVs) were added and incubated for 24 hours.

value: HUVEC

value: LIMCH1-OE vector transfected JAR cell-derived EV


title: wild type ZT16 rep1


title: SEU-GFP seu inflorescences, Input, replicate 2

city: Berlin

first: Cezary

last: Smaczniak

address: Philippstr. 13

department: Institute for Biology

institute: Humboldt-Universität zu Berlin

description: Library name: SEU-GFP seu Input rep2

data_processing:
Adapter sequences were removed from the sequencing reads using Trimmomatic and the quality of sequencing data was evaluated by FastQC. Trimmed reads were mapped to the Arabidopsis TAIR10 genome using Bowtie2. Unmapped reads and reads with MAPQ score lower than 40 were removed using Samtools. Peak calling was performed using MACS2 against the Input control samples. Peaks called from two biological replicates were processed using the Irreproducibility Discovery Rate (IDR) framework with 0.05 threshold to generate a peak list consistent between the two replicates. For data visualization, genome alignment tracks (BigWig files) were generated with bamCoverage tool.
Assembly: TAIR10
Supplementary files format and content: .bw bigWig

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plant seeds were sterilized, stratified and grown on soil at 22 °C in a 16/8 h light/dark cycles with light intesity at 150 μmol m-2 s-1.

extract_protocol:
Inflorescences were fixed in 2.5 mM DSG and in 1% formaldehyde each time for 20 min at room temperature in the vacuum. Fixed tissue was ground to a fine powder in liquid nitrogen and nuclei were isolated. The crude nuclei were sonicated using Covaris S220 and centrifuged. The input sample was collected at this step. The rest of the supernatant was incubated with the μMACS Anti-GFP MicroBeads (Miltenyi Biotec) for immunoprecipitation. Bound chromatin was eluted from the beads. ChIP and Input samples were de-crosslinked and purified.
The DNA sequencing libraries for both ChIP and Input samples were prepared using ThruPLEX DNA-Seq Kit (Takara Bio) and SMARTer DNA Unique Dual Index Kit (Takara Bio) following manufacturer’s instructions. DNA double size selection 100-700 bp was performed using AMPure XP beads (Beckman Coulter).

value: inflorescence

value: pSEU:SEU-GFP seu-1

value: Input


title: SEU-GFP seu inflorescences, Input, replicate 1

description: Library name: SEU-GFP seu Input rep1


title: HUVEC_LIMCH-EV_rep3


title: HTP79 sample analyzed with HTG kit

description: Library name: HTP79_HTP

value: HTG


title: HUVEC_LIMCH-EV_rep1


title: SEU-GFP seu inflorescences, ChIP, replicate 2

description: Library name: SEU-GFP seu ChIP rep2

value: μMACS Anti-GFP MicroBeads


title: HTP77 sample analyzed with HTG kit

description: Library name: HTP77_HTP


title: HUVEC_control-EV_rep3

value: Control vector transfected JAR cell-derived EV


title: HTP78 sample analyzed with HTG kit

description: Library name: HTP78_HTP


title: wild type ZT12 rep2

value: Colon

value: ad libitum normal chow diet


title: wild type ZT12 rep3


title: HTP75 sample analyzed with HTG kit

description: Library name: HTP75_HTP


title: SEU-GFP seu inflorescences, ChIP, replicate 1

description: Library name: SEU-GFP seu ChIP rep1


title: wild type ZT12 rep1


title: HUVEC_control-EV_rep2


title: FIS x luh 8DAI rep3

description: Library name: FISxluh_8DAI_rep3

data_processing:
Adapter sequences were removed from the sequencing reads using Trimmomatic and the quality of sequencing data was evaluated by FastQC. Trimmed reads were mapped to the Arabidopsis TAIR9 genome using STAR. Unmapped reads were removed using Samtools. Reads that map to genomic features were counted using featureCounts. DESeq2 was used to generate gene normalized counts and identify differentially expressed genes across the four developmental stages in a pairwise comparison between genotypes.
Assembly: TAIR9
Supplementary files format and content: Deseq2NormCounts.csv; DeSeq2 gene normalized counts

extract_protocol:
Three biological replicates for each genotype in 4 different time points were prepared. Flowers were collected and immediately frozen in liquid nitrogen. The tissue was homogenized with the Precellys Homogenizer and the RNA was isolated with the QIAwave RNA Mini Kit (Qiagen). DNA was removed by DNase I digestion followed by LiCl precipitation. The RNA concentration was measured using the Qubit 4 (Invitrogen) and the RNA integrity was assessed on a 4200 TapeStation (Agilent). Samples with an RNA integrity number equivalent (RINe) higher than 6 were considered for further processing.
Total RNA (300 ng) served as input for library preparation using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). After library preparation, samples were run on the 4200 TapeStation (Agilent) for quality control.

treatment_protocol: When pLUH:LUH-GFP pAP1:AP1-GR ap1 cal plants (FIS) had developed a stem of 3-5 cm height, the DEX induction solution (2 μM dexametasone, 0.015% Silwet L-77) was pipetted onto the main shoot until the inflorescence turned dark green.  The first induction was applied at 10:00 and subsequent inductions were applied approximately every 24 h. Tissue was collected at 16:00 on the day of interest.

value: pAP1:AP1-GR ap1 cal luh

tag: ecotype

value: Landsberg

value: Dexamethasone

tag: time

value: 8 days


title: HUVEC_control-EV_rep1


title: wild type ZT20 rep1


title: HTP81 sample analyzed with HTG kit

description: Library name: HTP81_HTP

value: Endometrial Cancer


title: HTP74 sample analyzed with HTG kit

description: Library name: HTP74_HTP


title: wild type ZT8 rep3

value: wild type


title: FIS x luh 8DAI rep2

description: Library name: FISxluh_8DAI_rep2