title: fctx_HET5 snRNA-seq

description:
Library name: GEX_fctx_HET5
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds


title: AML_OCI3_24h_JIB04_2_H3K36me3

status: Public on Jun 03 2026

type: SRA

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

country: USA

institute: Baylor College of Medicine

description: Library name: AML_OCI3_24h_JIB04_2_H3K36me3

library_source: genomic

data_processing:
ChiP-seq reads were removed adaptor and low-quality reads based on the default threshold using cutadapt.
ChIP-seq reads were aligned to the hg38 genome using Bowtie version 2.3.4. After alignment, samtools was used to perform quality control checks on the alignment BAM files and allowed only the uniquely mapped reads to be retained. Then PCR duplicates were removed by Picard using the MarkDuplicates tool with the parameters “VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = true” for downstream analyses.
For H3K4me3 and H3K9me3, .narrowPeaks were called using the MACS2 with the significance cut-off p-value 1e-9. For H3K27me3 and H3K36me3, broadpeaks were called using SICER with the parameters “-s hg38 -w 200 -f 150 -fdr 0.01 -g 600 -e 1 --significant_reads”. The peaks were then filtered by the hg38 ENCODE blacklist (https://www.encodeproject.org/files/ENCFF356LFX/).
Signal intensities for each ChIP library were normalized to 1x, and bigwig files were generated from BAM files using deeptools.
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak and bed (except for input samples)

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: AML-OCI3 were cultured in RPMI with 10% FBS and 1% penicillin/streptomycin at 37ºC and 5% CO2

extract_protocol:
cells were fixed with 1% Formaldehyde for 10 min and further processed using the Covaris truChIP Chromatin Shearing Kit according to Covaris protocol. Chromatin was sheared to 200-500bp fragments using the Covaris M220 Focused-ultrasonicator
Libraries were prepared using the Takara ThruPLEX® DNA-seq 48D Kit (R400675) according to manufacturer instructions.

treatment_protocol: AML-OCI3 cells were treated with DMSO or 40nM JIB-04 for 24h and 48h

tag: cell line

tag: cell type

value: Acute Myeloid Leukemia

tag: treatment

tag: time


title: SW480, Tram, 8h, rep1

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

country: Germany

institute: Heidelberg University

description: Library name: Tram_8h_rep1

library_source: transcriptomic

data_processing:
Alignment to hg38 was performed using STAR v2.5.3a allowing a maximum of 10 mismatches and providing a gtf with exon coordinates of the Gencode Basic V38 transcript set.
Alignments were annotated and summarized at the gene level using featureCounts within the subread package v1.6.3.
Differential expression was tested by pair-wise comparison of each trametinib or CHIR-9901 time-point to its respective DMSO control using the DESeq2 package v1.46.0 with default settings.
Assembly: hg38
Supplementary files format and content: The file RNASeq_SW480_MEKi_DESeq2.csv contains read counts per gene (as determined by a common gene symbol in the Gencode Basic V38 transcript set), normalized read counts as generated by DESeq2 with the median of ratios method (columns ending with _norm), log2 fold-changes (_DESeq2log2FC), standard errors (_DESeq2lfcSE) and corresponding adjusted p-values (_DESeq2padj) for the pair-wise comparisons of the trametinib (Tram) or CHIR-99021 (Chir) time-points to their respective DMSO control.

molecule: polyA RNA

growth_protocol: SW480 cells were cultured in RPMI 1640 medium (Gibco), supplemented with 10% fetal bovine serum (FBS, Gibco), 1% Glutamax (Gibco), and 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA was isolated from cultured cells using the peqGOLD Total RNA Kit (VWR), following the manufacturer’s instructions. After lysis in TRK buffer and homogenization, lysates were applied to RNA Mini Columns. DNase I digestion was performed to remove genomic DNA. RNA was washed, eluted with preheated nuclease-free water (70 °C) and stored at −70 °C.
Libraries were prepared at the DKFZ Genomics & Proteomics Core Facility using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced on a NovaSeq 6000 (Illumina) as paired-end 100 nt long reads.

treatment_protocol: SW480 cells were treated with 100 nM trametinib (Tram), 10 µM CHIR-99021 (Chir) or DMSO for 8 h, 24 h or 72 h.


title: f1937

city: Chongqing

first: Ziwei

last: Wu

country: China

institute: Breast Disease Center, Southwest Hospital, Army Medical University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.
RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2  or DEGseq.
Assembly: Reference gene source: Homo_sapiens ; Reference genome version: GRCh38.p13; Reference Genome Source: http://asia.ensembl.org/Homo_sapiens/Info/Index.

molecule: total RNA

source_name: Human breast cancer

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using TRIzol.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

tag: tissue

value: Human breast cancer

value: TNBC

value: Huaier


title: e1937

address: Southwest Hospital, Army Medical University


title: SW480, Tram, 72h, rep1

description: Library name: Tram_72h_rep1


title: fctx_HET6 snRNA-seq

city: Toronto

first: Paul

middle: M

last: McKeever

state: ON

address: 60 Leonard Ave., 4th floor - 4KD481

department: Tanz CRND

country: Canada

institute: University of Toronto

description:
Library name: GEX_fctx_HET6
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds

library_source: transcriptomic single cell

data_processing:
Raw base call files were demultiplexed using Illumina software to generate FASTQ files.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
FASTQ files were processed using Cell Ranger ARC (10x Genomics) to perform alignment, barcode assignment, and generation of paired gene expression and chromatin accessibility count matrices.
Gene expression reads were aligned to the mouse reference genome mm10 using STAR within the Cell Ranger ARC pipeline.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
Assembly: mm10
Supplementary files format and content: Processed data files include filtered gene expression count matrices, chromatin accessibility peak count matrices, fragment files, and associated cell metadata generated from Cell Ranger ARC and downstream Seurat/Signac analyses.
Supplementary files format and content: Processed files are provided in standard formats including HDF5 (.h5), Matrix Market (.mtx), tab-delimited text (.tsv), and compressed fragment files (.tsv.gz) containing single-nucleus transcriptomic and chromatin accessibility measurements.

molecule: nuclear RNA

organism: Mus musculus

source_name: frontal cortex

growth_protocol: C9orf72 wild-type, heterozygous knockout, and homozygous knockout mice were maintained under standard laboratory housing conditions with ad libitum access to food and water on a 12 h light/dark cycle. Brain tissue was collected from approximately 3-month-old animals.

extract_protocol:
Nuclei were isolated from frozen hippocampus and frontal cortex tissue using region-specific nuclei isolation workflows optimized for each brain region. Hippocampal nuclei were isolated using an iodixanol density gradient purification protocol following mechanical homogenization and filtration to enrich for intact nuclei and reduce debris contamination. Frontal cortex nuclei were isolated using the 10x Genomics Nuclei Isolation Kit according to the manufacturer’s protocol. Purified nuclei were counted and assessed prior to loading onto the 10x Genomics Chromium platform. RNA and chromatin accessibility information were simultaneously captured from individual nuclei using the Chromium Single Cell Multiome ATAC + Gene Expression workflow.
Single-nucleus multiomic libraries were generated using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression platform according to the manufacturer’s instructions. Briefly, isolated nuclei were subjected to transposition using Tn5 transposase to generate ATAC fragments, followed by GEM generation for simultaneous barcoding of gene expression and chromatin accessibility molecules from individual nuclei. Gene expression and ATAC libraries were amplified separately and sequenced on Illumina NovaSeq 6000 and NovaSeq X Plus instruments.

treatment_protocol: No experimental treatments were applied prior to tissue collection. Hippocampus and frontal cortex tissues were rapidly dissected from frozen brain samples for downstream single-nucleus isolation.

value: frontal cortex

tag: genotype

value: C9orf72 heterozygous knockout


title: AML_OCI3_24h_JIB04_1_H3K36me3

description: Library name: AML_OCI3_24h_JIB04_1_H3K36me3


title: fctx_HET7 snRNA-seq

description:
Library name: GEX_fctx_HET7
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds


title: d1937


title: SW480, Tram, 24h, rep1

description: Library name: Tram_24h_rep1


title: AML_OCI3_24h_DMSO_2_H3K36me3

description: Library name: AML_OCI3_24h_DMSO_2_H3K36me3

value: DMSO


title: fctx_WT5 snRNA-seq

description:
Library name: GEX_fctx_WT5
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds

value: wild-type


title: SW480, DMSO, 8h, rep3

description: Library name: DMSO_8h_rep3


title: AML_OCI3_24h_DMSO_1_H3K36me3

description: Library name: AML_OCI3_24h_DMSO_1_H3K36me3


title: c1937

value: control


title: b1937


title: SMC, regular growth medium, biol rep 4

city: Madison

first: Bo

last: Liu

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin - Madison

description: Library name: Sample 12

data_processing:
Salmon (version 1.10.1)
Assembly: mm10
Supplementary files format and content: csv file

source_name: Primary aortic SMCs

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit (12183018A, ThermoFisher Scientific).
cDNA library was prepared using an Illumina Stranded mRNA Prep kit. The cDNA library was then subjected to Illumina NovaSeq X Plus sequencing with the settings of 2x150 bp and 50 million reads per sample.

treatment_protocol: Mouse primary aortic SMCs were serum-starved in DMEM containing 0.3% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin for 48 hours. In the meantime, BMDMs were first primed with 20 ng/mL IFNγ overnight, followed by a 4-hour LPS stimulation (100 ng/mL). The IFNγ/LPS treated and control BMDMs were then thoroughly washed with PBS 4 times. Fresh DMEM containing 0.3% FBS, 100 U/mL penicillin, 100 µg/mL streptomycin and 10ng/mL M-CSF were added to the BMDMs. After a 24-hour incubation period, the conditioned media was harvested and centrifuged at 1000 g for 5 minutes to remove any cell debris. Subsequently, the SMCs were exposed to the conditioned media for 24 hours.

value: Primary aortic SMCs

value: Regular growth medium


title: SW480, DMSO, 72h, rep3

description: Library name: DMSO_72h_rep3


title: SMC, regular growth medium, biol rep 3

description: Library name: Sample 11


title: a1937


title: SW480, DMSO, 24h, rep3

description: Library name: DMSO_24h_rep3


title: Input ChIPseq, activated CD4 cells

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

description: mapped to HG38

data_processing:
bcl conversion and demultiplexing (bcl2fastq), to fastq files
fastq mapping to hg38 reference (STAR, default parameters apart alignIntronMax flag set to 1 for end-to-end mapping)
quality control (MultiQC v.0.9dev0, default parameters)
peak calling (HOMER)
Assembly: HG38
Supplementary files format and content: xlsx file with 2 sheets containing matrix with peak location (chromosome, strand, start, stop), peak score

source_name: Primary activated CD4 cells from PBMC

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells, culture activated with ConA+LPS for 72h

extract_protocol:
MAFnify immmunoprecipitation system (Invitrogen, cat-no 49-2024)
ChIP-seq

treatment_protocol: ChIP with anti-survivin (ab192675, abcam), 1 microgram/mL or anti-histone anti-histone H3K27ac (C15410196-10, Diagenode)- 0.5 microg/mL

value: Primary activated CD4 cells from PBMC

tag: stimulation

value: ConA+LPS

tag: chip antibody

value: Input


title: H3K27me3 ChIPseq, activated CD4 cells

description: mapped to HG38


title: SMC, regular growth medium, biol rep 2

description: Library name: Sample 10


title: SW480, DMSO, 8h, rep2

description: Library name: DMSO_8h_rep2


title: SMC, regular growth medium, biol rep 1

description: Library name: Sample 9


title: Survivin ChIPseq, activated CD4 cells

description: mapped to HG38

value: Survivin, ab192675, abcam


title: SW480, DMSO, 72h, rep2

description: Library name: DMSO_72h_rep2


title: UA44 fed on S. stutzeri, biol rep 2

city: LUCKNOW

first: SONIA

last: VERMA

state: UP

address: CSIR-Central Drug Research Institute

country: India

institute: CSIR-Central Drug Research Institute

description: Library name: Sample 4

data_processing:
RNA-Seq data was analyzed using the Galaxy platform.
Quality assessment (FastQC) and trimming (Trimmomatic) were followed by alignment to the C. elegans ce11 genome (HISAT2).
The tabular processed data files were generated using featureCounts on aligned files.
Differential expression analysis was conducted using the LIMMA package after voom normalization.
Assembly: ce11
Supplementary files format and content: tab delimited text file includes raw counts of each sample

organism: Caenorhabditis elegans

source_name: Whole worm

extract_protocol:
total RNA was extracted using the RNeasy Mini Kit (Qiagen)
Libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit

value: Whole worm


title: SMC, IFNγ/LPS BMDM-CM, biol rep 4

description: Library name: Sample 8

value: IFNγ/LPS BMDM-CM


title: SW480, DMSO, 24h, rep2

description: Library name: DMSO_24h_rep2


title: UA44 fed on S. stutzeri, biol rep 1

description: Library name: Sample 3


title: SMC, IFNγ/LPS BMDM-CM, biol rep 3

description: Library name: Sample 7


title: Wild type (cv M82) biological replicate 3 Full Ripe or Breaker+10 stage

type: RNA

city: rome

first: SARAH

last: FRUSCIANTE

state: Roma

address: via anguillarese 301

department: SSPT (Department for Sustainability)

country: Italy

institute: ENEA -  Italian National Agency for new Technologies, Energy and Sustainable Economic Development

description: not applicable

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. It contains mix for target dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Eu-TOM3 (custom exon) was then hybridized with each biotin-labeled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip® cartridges were washed and stained with GeneChip® Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0001 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 72 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.

scan_protocol: Image acquisition, processing: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner3000 7G using default parameters.

data_processing:
Data were processed using RobiNA v2.0 software. Normalization method: rma; P-value correction method: fdr; Multiple testing strategy: global; P-value cut-off value for significant differential expression: 0.05; Genes that showed a log2-fold change smaller than two ignored: yes
eutom3gene_v2_ucprobes
EUTOM3_funcion_GO.tsv

label: Biotin

organism: Solanum lycopersicum

source_name: mutant immature fruit

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with Ambion® WT Expression Kit (Ambion, Austin, TX). The sense strand cDNA was synthesized with the same kit, then it was fragmented and labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Plants were grown in a greenhouse under a long photoperiod (16-h light/24°C and 8-h dark/20°C) and irradiance (150 mmol m22 s21). Fruit were labeled at the Mature Green stage of ripening and collected at Mature Green, Breaker and 10 days later Breaker. Pericarps was frozen in liquid nitrogen and stored at -80°C for subsequent analyses.

extract_protocol: Briefly, total RNA isolation was performed using a Tris-Borate/phenol-chloroformisoamyl alcohol 25:24:1-based extraction followed by Potassium Acetate/Lithium Chloride/Sodium Chloride precipitation steps (Lopez-Gomez and Gomez-Lim, 1992) and DNAse I purification at 37°C for 20’. RNA quality was determined by using a Nanodrop ND-1000 (NanoDrop Technologies) and an Agilent 2100 Bioanalyzer: only RNAs showing A260/A280 and A260/230 ratios between, respectively, 1.8-2.0 and 2.0-2.2 and with a 28S/18S ratio between 1.5 and 2.0 were selected.

treatment_protocol: not applicable

value: pericarp


title: SW480, DMSO, 8h, rep1

description: Library name: DMSO_8h_rep1


title: Wild type (cv M82) biological replicate 1 Full Ripe or Breaker+10 stage

description: not applicable


title: Wild type (cv M82) biological replicate 2 Full Ripe or Breaker+10 stage

description: not applicable


title: UA44 fed on OP50, biol rep 2

description: Library name: Sample 2


title: Wild type (cv M82) biological replicate 3 Breaker stage

description: not applicable


title: SMC, IFNγ/LPS BMDM-CM, biol rep 2

description: Library name: Sample 6


title: SW480, DMSO, 72h, rep1

description: Library name: DMSO_72h_rep1


title: UA44 fed on OP50, biol rep 1

description: Library name: Sample 1


title: SMC, IFNγ/LPS BMDM-CM, biol rep 1

description: Library name: Sample 5


title: SW480, DMSO, 24h, rep1

description: Library name: DMSO_24h_rep1


title: TRAM, RPF, rep3

description: Library name: TRAM_RPF_rep3

library_source: other

data_processing:
Adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were reomoved with the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Sequences were aligned to human rRNA and tRNA sequences using Bowtie v1.2.2, allowing a maximum of two mismatches per read and reporting all alignments in the best stratum.
Reads that did not align to rRNA or tRNA were mapped to the basic set of Gencode V38.
Read counts were summarized at the gene level by counting all 25–35 nt long reads that align to annotated ORFs of one specific gene (as defined by a common gene symbol). Relative to the 5′ end of the read, an offset of -12 nt to the start codon and -15 nt for the stop codon was assumed.
Differentially translated mRNAs were identified with a likelihood ratio test followed by multiple testing correction with the Benjamini-Hochberg procedure in DESeq2 v1.46.0.
Assembly: Gencode V38
Supplementary files format and content: The file RiboSeq_HCT116_DESeq2_results.csv contains the read counts per gene for all samples, and normalized read counts as generated by DESeq2 with the median of ratios method (in columns ending with _norm). For identifying changes in mRNA abundance and translated mRNA upon Trametinib treatment, log2 fold-changes for input and footprint samples (IN_log2FC, FP_log2FC) are given with their corresponding adjusted p-values (IN_padj, FP_padj) as generated by DESeq2 with default settings. Changes in ribosome density are represented by log2 fold-changes (RD_log2FC) and corresponding adjusted p-values (RD_padj) as generated in DESeq2 with a likelihood ratio test. The column is_5TOP contains information whether we classified an mRNA as a 5'TOP mRNA based on Meyuhas et al. (PMID: 25234618), and the column is_stemness whether we classified a gene as a marker for instestinal stemness based on Merlos-Suarez et al. (PMID: 21419747).
Library strategy: Ribo-Seq

molecule: other

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium (Gibco), supplemented with 10% fetal bovine serum (FBS, Gibco), 1% Glutamax (Gibco), and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Before lysis, cells were incubated with 100 μg/ml cycloheximide (CHX) for 5 min at RT and washed with ice-cold PBS before harvesting by scraping in polysome lysis buffer (20 mM Tris-HCl pH 7.4, 5 mM MgCl2, 150 mM NaCl, 1 mM DTT, 1% Triton-X-100, EDTA-free complete protease inhibitors [Roche]). The lysates were rotated for 10 min at 4°C and cleared from cell debris by centrifugation at 10,000 × g for 10 min at 4°C. For generating ribosome protected fragments, lysates were digested with 240 U RNase I (Ambion) per A260 Unit for 20 min at 4°C. After 17.5–50% [w/v] sucrose-density gradient centrifugation, fractions of ~300 µl were collected during gradient elution and supplemented with 300 µl urea buffer (10 mM Tris, pH 7.5, 350 mM NaCl, 10 mM EDTA, 1% SDS, and 7 M urea) and 300 µl phenol:chloroform:isoamyl alcohol (25:24:1). By phase separation, RNA of the cytoplasmic lysates (inputs; IN) and the monosomal fractions (ribosome protected fragments; RPF) was isolated.
The input and RPF samples were depleted of ribosomal RNA (rRNA) using the Human-Mouse-Rat Ribo-Seq riboPOOL kit (siTOOLs Biotech). After random fragmentation of input RNA at 95°C for 12 min in alkaline fragmentation buffer (2 mM EDTA, 88 mM NaHCO3, 12 mM Na2CO3), both input and RPF samples were size-selected (25-35 nt) on 15% polyacrylamide Tris-borate-EDTA-urea gels. Following end-repair using T4 PNK, 1.65 ng per sample were used for library preparation using the NEBNext Multiplex Small RNA Library Prep Set according to the manufacturer’s instructions.

treatment_protocol: HCT116 cells were seeded at a density of 3 × 106 per dish in 10 cm dishes one day before treatment for 24 h with 100 nM trametinib (MEKi) or DMSO.

value: TRAM


title: Wild type (cv M82) biological replicate 2 Breaker stage

description: not applicable


title: SMC, naïve BMDM-CM, biol rep 4

description: Library name: Sample 4

value: naïve BMDM-CM


title: SW480, Chir, 8h, rep3

description: Library name: Chir_8h_rep3


title: TRAM, RPF, rep2

description: Library name: TRAM_RPF_rep2


title: SMC, naïve BMDM-CM, biol rep 3

description: Library name: Sample 3


title: SW480, Chir, 72h, rep3

description: Library name: Chir_72h_rep3


title: Wild type (cv M82) biological replicate 1 Breaker stage

description: not applicable


title: Wild type (cv M82) biological replicate 3 Mature Green stage

description: not applicable


title: TRAM, RPF, rep1

description: Library name: TRAM_RPF_rep1


title: SMC, naïve BMDM-CM, biol rep 2

description: Library name: Sample 2


title: Wild type (cv M82) biological replicate 2 Mature Green stage

description: not applicable


title: SW480, Chir, 24h, rep3

description: Library name: Chir_24h_rep3


title: TRAM, IN, rep3

description: Library name: TRAM_IN_rep3

data_processing:
Adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were reomoved with the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Sequences were aligned to human rRNA and tRNA sequences using Bowtie v1.2.2, allowing a maximum of two mismatches per read and reporting all alignments in the best stratum.
Reads that did not align to rRNA or tRNA were mapped to the basic set of Gencode V38.
Read counts were summarized at the gene level by counting all 25–35 nt long reads that align to annotated ORFs of one specific gene (as defined by a common gene symbol). Relative to the 5′ end of the read, an offset of -12 nt to the start codon and -15 nt for the stop codon was assumed.
Differentially translated mRNAs were identified with a likelihood ratio test followed by multiple testing correction with the Benjamini-Hochberg procedure in DESeq2 v1.46.0.
Assembly: Gencode V38
Supplementary files format and content: The file RiboSeq_HCT116_DESeq2_results.csv contains the read counts per gene for all samples, and normalized read counts as generated by DESeq2 with the median of ratios method (in columns ending with _norm). For identifying changes in mRNA abundance and translated mRNA upon Trametinib treatment, log2 fold-changes for input and footprint samples (IN_log2FC, FP_log2FC) are given with their corresponding adjusted p-values (IN_padj, FP_padj) as generated by DESeq2 with default settings. Changes in ribosome density are represented by log2 fold-changes (RD_log2FC) and corresponding adjusted p-values (RD_padj) as generated in DESeq2 with a likelihood ratio test. The column is_5TOP contains information whether we classified an mRNA as a 5'TOP mRNA based on Meyuhas et al. (PMID: 25234618), and the column is_stemness whether we classified a gene as a marker for instestinal stemness based on Merlos-Suarez et al. (PMID: 21419747).

molecule: cytoplasmic RNA


title: SMC, naïve BMDM-CM, biol rep 1

description: Library name: Sample 1


title: Tomato mutant Delta, Del (cv M82)  biological replicate 3 Full Ripe or Breaker+10 stage

description: not applicable


title: IVCs, DVT

description:
Library name: Sample 2
10x Genomics Chromium Single Cell 3’ v3.1 Reagent Kit

data_processing:
Raw Illumina sequencing reads were aligned to mm10 (GENCODE vM23/Ensembl 98) reference genome and, subsequently, genes were quantified as UMI counts using Simpleaf (alevin-fry pipline, V0.9.0).
Assembly: mm10
Supplementary files format and content: RDS files

source_name: Inferior vena cava

extract_protocol:
Mouse infrarenal IVCs were collected and sequentially digested in two digestion buffers (PBS containing 200 U/ml collagenase I (SCR103, Sigma Aldrich), 0.05 U/ml elastase (E1250, Sigma Aldrich), 5 U/ml neutral protease (LS02111, Worthington), and 0.3 U/ml deoxyribonuclease I (M6101, Promega) for 20 min, followed by DMEM containing 5 mg/ml collagenase type II [C6885, Sigma-Aldrich] and 0.5 mg/ml elastase [LS002292, Worthington Biochemistry]) for 2.5 min at 37 °C). The tissue suspension was filtered with a 40μm cell strainer, then centrifuged at 500 g for 5 min. Cells were resuspended with PBS containing 0.04% BSA. Single-cell suspensions from 6 DVT-adjacent IVCs were pooled to generate the experimental sample (DVT), and suspensions from 6 sham IVCs were pooled to generate the control sample (SHAM).
10,000 cells were loaded using the 10x Genomics Chromium platform with the Single Cell 3' v3.1 Reagent Kit to construct libraries. Libraries were then sequenced on an Illumina NovaSeq X Plus flowcell using a 2×150 bp sequencing reaction, targeting >90,000 reads per cell.

value: Inferior vena cava

value: DVT


title: SW480, Chir, 8h, rep2

description: Library name: Chir_8h_rep2


title: TRAM, IN, rep2

description: Library name: TRAM_IN_rep2


title: SW480, Chir, 72h, rep2

description: Library name: Chir_72h_rep2


title: Tomato mutant Delta, Del (cv M82)  biological replicate 2 Full Ripe or Breaker+10 stage

description: not applicable


title: TRAM, IN, rep1

description: Library name: TRAM_IN_rep1


title: IVCs, SHAM

description:
Library name: Sample 1
10x Genomics Chromium Single Cell 3’ v3.1 Reagent Kit

value: SHAM


title: Tomato mutant Delta, Del (cv M82) biological replicate 1 Full Ripe or Breaker+10 stage

description: not applicable


title: SW480, Chir, 24h, rep2

description: Library name: Chir_24h_rep2


title: DMSO, RPF, rep3

description: Library name: DMSO_RPF_rep3

value: DMSO


title: GastricMucosa_CR_biol rep_5

city: Dallas

first: Jeffrey

middle: Marc

last: Zigman

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: S_2487

data_processing:
Raw sequencing reads were subjected to quality control and filtering to remove low-quality reads and adapter sequences.
Filtered reads were aligned to the mouse genome assembly GRCm39 (Ensembl 104) using the STAR aligner software.
Gene abundance was quantified using featureCounts  to generate the aggregated raw count matrix.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file containing a matrix of raw read counts for all samples

source_name: Gastric Mucosa_C57BL/6N

extract_protocol:
Total RNA was extracted using RNA STAT-60 (AMSBio). After chloroform extraction and phase separation, the aqueous phase was mixed with ethanol and loaded onto RNeasy Mini Kit columns (Qiagen) for purification and washing following the manufacturer's protocol.
Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature. First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends, adenylated, and ligated with NEBNext Adaptors. The library fragments were purified with the AMPure XP system and PCR amplified. Finally, the libraries were sequenced on an Illumina NovaSeq X Plus platform to generate 150 bp paired-end reads

value: Gastric Mucosa_C57BL/6N

value: 7d 60% Calorie Restricted


title: Tomato mutant Delta, Del (cv M82)  biological replicate 3 Breaker stage

description: not applicable


title: SW480, Chir, 8h, rep1

description: Library name: Chir_8h_rep1


title: DMSO, RPF, rep2

description: Library name: DMSO_RPF_rep2


title: GastricMucosa_CR_biol rep_4

description: Library name: S_2486


title: SW480, Chir, 72h, rep1

description: Library name: Chir_72h_rep1


title: Tomato mutant Delta, Del (cv M82)  biological replicate 2 Breaker stage

description: not applicable


title: GastricMucosa_CR_biol rep_3

description: Library name: S_2482


title: DMSO, RPF, rep1

description: Library name: DMSO_RPF_rep1


title: SW480, Chir, 24h, rep1

description: Library name: Chir_24h_rep1


title: DMSO, IN, rep3

description: Library name: DMSO_IN_rep3


title: GastricMucosa_CR_biol rep_2

description: Library name: S_2481


title: Tomato mutant Delta, Del (cv M82)  biological replicate 3 Mature Green stage

description: not applicable


title: HCT116, Chir, 72h, rep3

description: Library name: Chir_72h_rep3

data_processing:
Alignment to hg38 was performed using STAR v2.5.3a allowing a maximum of 10 mismatches and providing a gtf with exon coordinates of the Gencode Basic V38 transcript set.
Alignments were annotated and summarized at the gene level using featureCounts within the subread package v1.6.3.
Differential expression was tested by pair-wise comparison of each trametinib or CHIR-9901 time-point to its respective DMSO control using the DESeq2 package v1.46.0 with default settings.
Assembly: hg38
Supplementary files format and content: The file RNASeq_HCT116_MEKi_DESeq2.csv contains read counts per gene (as determined by a common gene symbol in the Gencode Basic V38 transcript set), normalized read counts as generated by DESeq2 with the median of ratios method (columns ending with _norm), log2 fold-changes (_DESeq2log2FC), standard errors (_DESeq2lfcSE) and corresponding adjusted p-values (_DESeq2padj) for the pair-wise comparisons of the trametinib (Tram) or CHIR-99021 (Chir) time-points to their respective DMSO control.

treatment_protocol: HCT116 cells were treated with 100 nM trametinib (Tram), 10 µM CHIR-99021 (Chir) or DMSO for 8 h, 24 h or 72 h.

value: Chir, 72 h


title: DMSO, IN, rep2

description: Library name: DMSO_IN_rep2


title: GastricMucosa_CR_biol rep_1

description: Library name: S_2479


title: Tomato mutant Delta, Del (cv M82)  biological replicate 2 Mature Green stage

description: not applicable


title: HCT116, Tram, 72h, rep3

description: Library name: Tram_72h_rep3

value: Tram, 72 h


title: GastricMucosa_DIO_biol rep_5

description: Library name: S_2477

value: 4 wks HFD fed


title: DMSO, IN, rep1

description: Library name: DMSO_IN_rep1


title: Tomato mutant Delta, Del (cv M82) biological replicate 1 Mature Green stage

description: not applicable


title: HCT116, DMSO, 72h, rep3

description: Library name: DMSO_72h_rep3

value: DMSO, 72 h


title: RNA-Seq, MOCK-infected, input, rep1

city: Los Alamos

first: Taehyung

last: Kwon

email: ted3466@gmail.com, tae_kwon@lanl.gov

state: New Mexico

address: Los Alamos National Laboratory

department: Bioscience Division

institute: Los Alamos National Laboratory

description: Library name: VERO-MOCK-input-rep1

data_processing:
Read trimming and filtering were performed using FastP v0.23.2. The filtered reads were mapped against a combined reference sequence of Chlorocebus sabaeus and Vaccinia virus genomes using STAR v2.7.10b. Reads uniquely mapped to C. sabaeus were selected using Sambamba v1.0. Differential gene expression analysis was performed with input samples using DESeq2. Read count matrices were generated using featureCounts (Subread v2.0.3) and lowly expressed transcripts were excluded prior to DESeq2 analysis. Differential m6A modification analysis was performed between MOCK-infected samples and virus-infected samples using exomePeak2 v1.12.0. The exact locations of differentially m6A modified regions were annotated using Sambaba and HOMER v4.11.
Assembly: Chlorocebus sabaeus (GCF_015252025.1); Vaccinia virus (GCF_000860085.1)
Supplementary files format and content: "DESeq2.csv" files include the unfiltered results of differential gene expression analysis. "exomePeak2.csv" files include the unfiltered results of differential m6A modification analysis with zero-based coordinates. "annotated.txt" files include annotation of the differentially m6A modified regions.

organism: Chlorocebus sabaeus

source_name: epithelial kidney cells

growth_protocol: Vero cells were grown on Eagle's Minimum Essential Medium (EMEM) supplemented with 10% fetal bovine serum in 5% CO2 Incubator at 37C

extract_protocol:
Total RNA was collected via TRISOL-chloroform extraction and isopropanol precipitation, then fragmented to 200-300 base pairs with 10mM ZnCl2 buffered with 10mM TrisHCl, followed by rapid removal of Zn2+. For IP samples, they were incubated with protein A/G magnetic beads coated with anti-m6A antibodies for 4h at 8ºC with agitation in immunoprecipitation buffer. Beads were washed twice in IP buffer, followed by two washes in low-salt IP buffer and high-salt IP buffer. SMARTer Stranded Total RNA-Seq Kit v2 was used for preparation of Illumina sequencing libraries with 12 cycles PCR amplification for input samples and 16 cycles for IP samples.
250 ng of total RNA was depleted of ribosomal RNA and converted to cDNA. Adapters and indexes were added onto the ends of the fragments. Illumina libraries were prepared using the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat. Illumina libraries were eluted in DNA Elution Buffer. The concentration and average size of the library was obtained using the Tapestation D5000 Assay. Equimolar amounts of library were pooled together. The concentration of the library pool was obtained using the Qubit dsDNA HS Assay. The average size of the library pool was determined by the Agilent High Sensitivity DNA Kit. An accurate library quantification was determined using the Library Quantification Kit – Illumina/Universal Kit.

value: epithelial kidney cells

value: Vero E6

value: Total mRNA sequencing of MOCK-treated sample


title: GastricMucosa_DIO_biol rep_4

description: Library name: S_2476


title: Wild type (cv M82) biological replicate 1 Mature Green stage

description: not applicable


title: HCT116, Chir, 24h, rep3

description: Library name: Chir_24h_rep3

value: Chir, 24 h


title: RNA-Seq, VV-infected, 2 hpi, input, rep1

description:
Library name: VERO-VV-2hpi-input-rep1
2hpi_DESeq2.csv

value: Total mRNA sequencing of VV-WR infected (MOI 1) sample at 6 hpi


title: Tomato mutant yellow flash, r (cv AC)  biological replicate 3 Mature Green stage

description: not applicable

value: pericarp


title: Tomato mutant Delta, Del (cv M82) biological replicate 1 Breaker stage

description: not applicable


title: GastricMucosa_DIO_biol rep_3

description: Library name: S_2475


title: HCT116, Tram, 24h, rep3

description: Library name: Tram_24h_rep3

value: Tram, 24 h


title: RNA-Seq, VV-infected, 6 hpi, input, rep1

description:
Library name: VERO-VV-6hpi-input-rep1
6hpi_DESeq2.csv


title: GastricMucosa_DIO_biol rep_2

description: Library name: S_2471


title: Tomato mutant yellow flash, r (cv AC)  biological replicate 2 Mature Green stage

description: not applicable


title: HCT116, DMSO, 24h, rep3

description: Library name: DMSO_24h_rep3

value: DMSO, 24 h


title: RNA-Seq, VV-infected, 24 hpi, input, rep1

description:
Library name: VERO-VV-24hpi-input-rep1
24hpi_DESeq2.csv

value: Total mRNA sequencing of VV-WR infected (MOI 1) sample at 24 hpi


title: GastricMucosa_DIO_biol rep_1

description: Library name: S_2470


title: Tomato mutant yellow flash, r (cv AC)  biological replicate 1 Mature Green stage

description: not applicable


title: HCT116, Tram, 8h, rep3

description: Library name: Tram_8h_rep3

value: Tram, 8 h


title: MeRIP-Seq, VV-infected, 2 hpi, IP, rep1

description:
Library name: VERO-VV-2hpi-IP-rep1
exomePeak2.csv file contains zero-based coordinates
2hpi_exomePeak2.csv
2hpi_annotated.txt

data_processing:
*library strategy: MeRIP-seq
Read trimming and filtering were performed using FastP v0.23.2. The filtered reads were mapped against a combined reference sequence of Chlorocebus sabaeus and Vaccinia virus genomes using STAR v2.7.10b. Reads uniquely mapped to C. sabaeus were selected using Sambamba v1.0. Differential gene expression analysis was performed with input samples using DESeq2. Read count matrices were generated using featureCounts (Subread v2.0.3) and lowly expressed transcripts were excluded prior to DESeq2 analysis. Differential m6A modification analysis was performed between MOCK-infected samples and virus-infected samples using exomePeak2 v1.12.0. The exact locations of differentially m6A modified regions were annotated using Sambaba and HOMER v4.11.
Assembly: Chlorocebus sabaeus (GCF_015252025.1); Vaccinia virus (GCF_000860085.1)
Supplementary files format and content: "DESeq2.csv" files include the unfiltered results of differential gene expression analysis. "exomePeak2.csv" files include the unfiltered results of differential m6A modification analysis with zero-based coordinates. "annotated.txt" files include annotation of the differentially m6A modified regions.

value: m6A immunoprecipitated mRNA sequencing of VV-WR infected (MOI 1) sample at 2 hpi


title: HCT116, Chir, 8h, rep3

description: Library name: Chir_8h_rep3

value: Chir, 8 h


title: Tomato mutant apricot, at (cv AC)  biological replicate 3 Mature Green stage

description: not applicable


title: MeRIP-Seq, MOCK-infected, IP, rep1

description: Library name: VERO-MOCK-IP-rep1

value: m6A immunoprecipitated mRNA sequencing of MOCK-treated sample


title: GastricMucosa_Lean_biol rep_3

description: Library name: S_2463

value: Gastric Mucosa_C57BL/6N

value: ad lib chow fed


title: HCT116, DMSO, 8h, rep3

description: Library name: DMSO_8h_rep3

value: DMSO, 8 h


title: MeRIP-Seq, VV-infected, 6 hpi, IP, rep1

description:
Library name: VERO-VV-6hpi-IP-rep1
exomePeak2.csv file contains zero-based coordinates
6hpi_exomePeak2.csv
6hpi_annotated.txt

value: m6A immunoprecipitated mRNA sequencing of VV-WR infected (MOI 1) sample at 6 hpi


title: GastricMucosa_Lean_biol rep_2

description: Library name: S_2460


title: Tomato mutant apricot, at (cv AC)  biological replicate 2 Mature Green stage

description: not applicable


title: Tomato mutant apricot, at (cv AC)  biological replicate 1 Mature Green stage

description: not applicable


title: MeRIP-Seq, VV-infected, 24 hpi, IP, rep1

description:
Library name: VERO-VV-24hpi-IP-rep1
exomePeak2.csv file contains zero-based coordinates
24hpi_exomePeak2.csv
24hpi_annotated.txt

value: epithelial kidney cells

value: m6A immunoprecipitated mRNA sequencing of VV-WR infected (MOI 1) sample at 24 hpi


title: HCT116, Chir, 72h, rep2

description: Library name: Chir_72h_rep2

value: Chir, 72 h


title: GastricMucosa_Lean_biol rep_1

description: Library name: S_2459


title: HCT116, Tram, 72h, rep2

description: Library name: Tram_72h_rep2

value: Tram, 72 h


title: RNA-Seq, MOCK-infected, input, rep2

description: Library name: VERO-MOCK-input-rep2

value: Vero E6

value: Total mRNA sequencing of MOCK-treated sample


title: F10020_Mouse ABC dataset_HTO

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA97202_vx0179

data_processing:
Sequencing was performed on NovaSeq 6000 or NovaSeq X Plus platform in 28+90, 101+101 or 151+151 base paired-end mode.
Illumina Real Time Analysis RTA3 v3.4.4 or RTA4 v4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-7.1.0 or 9.0.1, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and B cell receptor repertoire profiling.
Assembly: mm10, GRCh38 or GRCm39
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format files including filtered counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format files including raw counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the BCR clonotype information
Library strategy: CITE-seq

molecule: protein

source_name: Spleen

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Hashtag oligonucleotides (HTO) or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits v2 or v3 with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping User Guide.

value: Spleen

tag: strain

value: Resiquimod; Tamoxifen

tag: library type

value: HTO

tag: hto

value: TotalSeq-C0301 anti-mouse Hashtag 1 (uMT:Rosa26CreERT2/+Commd3flox/+); TotalSeq-C0303 anti-mouse Hashtag 3 (uMT:Rosa26CreERT2/+Commd3flox/flox)


title: RNA-Seq, VV-infected, 2 hpi, input, rep2

description:
Library name: VERO-VV-2hpi-input-rep2
2hpi_DESeq2.csv

value: Total mRNA sequencing of VV-WR infected (MOI 1) sample at 6 hpi


title: HCT116, DMSO, 72h, rep2

description: Library name: DMSO_72h_rep2

value: DMSO, 72 h


title: F10020_Mouse ABC dataset_GEX

description: Library name: GA97200_vx0179

value: mRNA


title: HCT116, Chir, 24h, rep2

description: Library name: Chir_24h_rep2

value: Chir, 24 h


title: NE

city: Shanghai

first: Jieyuan

last: Xue

address: 280 South Chongqing Road

institute: Shanghai Jiao Tong University

description: Library name: 2

data_processing:
Basecalls were performed using bcl2fastq (v2.17) for Novaseq output.
FastQC (Version 0.12.1) was used for quality control of FastQ.gz files.
Seqtk subsample (Version 1.4) was used for specifying seed values to ensure that the extracted sequence pairs can maintain pairing relationships.
Trim Galore (Version 0.6.7) was used for quality control and low-quality data pruning of sequencing data.
The clean reads were then aligned to reference mm39 genome sequences by Bowtie2 (Version 2.5.3) used for comparing reads and producing BAM files.
Assembly: mm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
C3H 10T1/2 were harvested by 0.05% trypsin. 10000 cells per sample were used as starting material. Libraries were amplified using 13 cycles on the thermocycler. Post amplificationlibraries were size selected at 250-450bp in length using Agencourt AMPure XP beads fromBeckman Coulter.
Cut&Tag libraries were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903). DNA was subjected to PCR amplification by universal barcoded i5 and i7 primers from TruePrep Index Kit V2 for Illumina (Vazyme, TD202) with 14 cycles on the thermocycler.

value: 10 μM NE for 6 hrs

tag: cut &tag_antibody

value: p-CREB


title: RNA-Seq, VV-infected, 6 hpi, input, rep2

description:
Library name: VERO-VV-6hpi-input-rep2
6hpi_DESeq2.csv


title: HCT116, Tram, 24h, rep2

description: Library name: Tram_24h_rep2

value: Tram, 24 h


title: RNA-Seq, VV-infected, 24 hpi, input, rep2

description:
Library name: VERO-VV-24hpi-input-rep2
24hpi_DESeq2.csv

value: epithelial kidney cells

value: Total mRNA sequencing of VV-WR infected (MOI 1) sample at 24 hpi


title: Ctrl

description: Library name: 1

value: vehicle for 6 hrs


title: HCT116, DMSO, 24h, rep2

description: Library name: DMSO_24h_rep2

value: DMSO, 24 h


title: MeRIP-Seq, MOCK-infected, IP, rep2

description: Library name: VERO-MOCK-IP-rep2

value: Vero E6

value: m6A immunoprecipitated mRNA sequencing of MOCK-treated sample


title: Day3_IgG_control

city: washington dc

first: Shaoqi

last: Zhu

state: WASHINGTON

address: 725 21st st nw

institute: the george washington university

data_processing:
The sequencing quality of Cut&Run libraries was assessed by FastQC (v0.11.8)(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Low-quality bases and adapters were removed through Trim Galore (v0.6.7)(MAPQ > 30)
Bowtie2 v2.3.4.1 was used to align the sequencing reads to the mm10 mouse genome, and only uniquely mapped reads were retained with PCR duplicates removal using MarkDuplicate from Picard(picard-2.25.5-0)
MACS2( V2.1.1.20160309) as used for calling CUT&Run peaks, with IgG as control. Stringent criteria of FDR < 1e-5, --fe-cutoff 4 and --llocal 7500 were used.
Assembly: mm10
Supplementary files format and content: narrowPeak, bigWig
Library strategy: Cut&Run

source_name: splenocytes

extract_protocol:
hCD2-Cre, Rosa26-lsl-GFP, and CTCF wild-type or floxed P14 CD8+ T cells were adoptively transferred into CD45-disparate recipients followed by infection with LCMV-Clone 13. At 72 hours (day 3) post-infection, GFP+ P14 cells were sorted and purified for pSer5 RNA polymerase II CUT&RUN analysis.
The DNA segments from pSer5 RNAPII Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina HiseqX platform.

value: splenocytes

value: P14 CD8+ T cells

value: IgG


title: HCT116, Chir, 8h, rep2

description: Library name: Chir_8h_rep2

value: Chir, 8 h


title: MeRIP-Seq, VV-infected, 2 hpi, IP, rep2

description:
Library name: VERO-VV-2hpi-IP-rep2
exomePeak2.csv file contains zero-based coordinates
2hpi_exomePeak2.csv
2hpi_annotated.txt

value: m6A immunoprecipitated mRNA sequencing of VV-WR infected (MOI 1) sample at 2 hpi


title: Day3_RNA_poly_II_WT-3

value: WT


title: HCT116, Tram, 8h, rep2

description: Library name: Tram_8h_rep2

value: Tram, 8 h


title: GastricMucosa_Lean_biol rep_4

description: Library name: S_2467

value: Gastric Mucosa_C57BL/6N

value: ad lib chow fed


title: MeRIP-Seq, VV-infected, 6 hpi, IP, rep2

description:
Library name: VERO-VV-6hpi-IP-rep2
exomePeak2.csv file contains zero-based coordinates
6hpi_exomePeak2.csv
6hpi_annotated.txt

value: m6A immunoprecipitated mRNA sequencing of VV-WR infected (MOI 1) sample at 6 hpi


title: Day3_RNA_poly_II_WT-2


title: MeRIP-Seq, VV-infected, 24 hpi, IP, rep2

description:
Library name: VERO-VV-24hpi-IP-rep2
exomePeak2.csv file contains zero-based coordinates
24hpi_exomePeak2.csv
24hpi_annotated.txt

value: m6A immunoprecipitated mRNA sequencing of VV-WR infected (MOI 1) sample at 24 hpi


title: HCT116, DMSO, 8h, rep2

description: Library name: DMSO_8h_rep2

value: DMSO, 8 h


title: Day3_RNA_poly_II_WT-1


title: HCT116, Chir, 72h, rep1

description: Library name: Chir_72h_rep1

value: Chir, 72 h


title: Wild type (cv Ailsa Craig, AC) biological replicate 3 Mature Green stage

description: not applicable

source_name: wild type immature fruit

value: pericarp


title: RNA-Seq, MOCK-infected, input, rep3

description: Library name: VERO-MOCK-input-rep3

value: epithelial kidney cells

value: Total mRNA sequencing of MOCK-treated sample


title: Day3_RNA_poly_II_CTCF-KO-3

value: CTCFKO


title: HCT116, Tram, 72h, rep1

description: Library name: Tram_72h_rep1

value: Tram, 72 h


title: RNA-Seq, VV-infected, 2 hpi, input, rep3

description:
Library name: VERO-VV-2hpi-input-rep3
2hpi_DESeq2.csv

value: Vero E6

value: Total mRNA sequencing of VV-WR infected (MOI 1) sample at 6 hpi


title: Day3_RNA_poly_II_CTCF-KO-2

value: splenocytes

value: P14 CD8+ T cells


title: Tomato mutant apricot, at (cv AC)  biological replicate 2 Full Ripe or Breaker+10 stage

description: not applicable


title: Tomato mutant tangerine, t (cv AC)  biological replicate 1 Breaker stage

description: not applicable


title: HCT116, DMSO, 72h, rep1

description: Library name: DMSO_72h_rep1

value: DMSO, 72 h


title: Tomato mutant tangerine, t (cv AC)  biological replicate 2 Breaker stage

description: not applicable


title: Tomato mutant apricot, at (cv AC)  biological replicate 1 Full Ripe or Breaker+10 stage

description: not applicable


title: RNA-Seq, VV-infected, 6 hpi, input, rep3

description:
Library name: VERO-VV-6hpi-input-rep3
6hpi_DESeq2.csv


title: Tomato mutant apricot, at (cv AC)  biological replicate 3 Full Ripe or Breaker+10 stage

description: not applicable


title: Wild type (cv Ailsa Craig, AC) biological replicate 2 Mature Green stage

description: not applicable


title: Tomato mutant yellow flash, r (cv AC)  biological replicate 2 Breaker stage

description: not applicable


title: Tomato mutant yellow flash, r (cv AC)  biological replicate 3 Breaker stage

description: not applicable


title: Tomato mutant yellow flash, r (cv AC)  biological replicate 1 Breaker stage

description: not applicable


title: Tomato mutant apricot, at (cv AC)  biological replicate 3 Breaker stage

description: not applicable


title: Day3_RNA_poly_II_CTCF-KO-1


title: Tomato mutant tangerine, t (cv AC)  biological replicate 3 Breaker stage

description: not applicable


title: HCT116, Chir, 24h, rep1

description: Library name: Chir_24h_rep1

value: Chir, 24 h


title: RNA-Seq, VV-infected, 24 hpi, input, rep3

description:
Library name: VERO-VV-24hpi-input-rep3
24hpi_DESeq2.csv

value: Total mRNA sequencing of VV-WR infected (MOI 1) sample at 24 hpi


title: Astrocytes, APP-NLGF, rep5

city: Zwijnaarde

first: Roosmarijn

middle: E.

last: Vandenbroucke

state: Gent

address: Technologiepark-Zwijnaarde 71

department: VIB Center for Inflammation Research

country: Belgium

institute: VIB-UGent

description:
Library name: X41_A22_APP_C3WT_5_astro_S53
Bulk_RNA_seq_PieterD_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Astrocytes_no_outliers.txt

data_processing:
Element Biosciences software was used for basecalling.
Sequenced reads were inspected with FastQC v0.11.8, trimmed for adaptor sequences with Trimmomatic v0.39, then mapped to mm10 whole genome using STAR v2.7.3a, converted to BAM-files with Samtools v1.9 and finally counted with HTSeqCount v0.11.2
An edgeR (v3.32.1) - limma (v3.46.0) workflow was used to normalize the count data.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (one file for microglia samples and another file for astrocyte samples)
Supplementary files format and content: Matrix table with log-CPM values for all biologically meaningfully expressed genes for each sample (one file for microglia samples and another file for astrocyte samples)

source_name: Astrocytes

extract_protocol:
After euthanasia using an overdose of ketamine (87.5 mg/kg) and xylazine (12.5 mg/kg), mice were perfused transcardially using 10 ml 0.2 % heparin in ice-cold D‐PBS per mouse  at a flow rate of 4.50 ml/min. Whole brain samples were isolated from the skull, weighed and collected in 1.5 mL ice-cold 1x HBSS -/- . Brains were cut into pieces using spring scissors and slurry was dissociated into single cell suspensions using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec). Cells were enzymatically dissociated using activated enzyme (P) for 15 min at 37 °C and enzyme (A) for 2x10 min at 37 °C under continuous nutation, with mechanical dissociation by trituration 10 times with a 5 ml serological pipet in between enzymatic dissociation steps. Subsequently, samples were passed through a 70 µM cell strainer. Myelin was removed by centrifugation (300g, 11 min, room temperature, low acceleration/break) of samples in 24 % Percoll PLUS and 75 U/ml DNase. After aspiration of the myelin layer and supernatant, cell pellet was resuspended in 50 µL of FACS buffer (0.5% BSA in D‐PBS). This process was repeated twice. Single cell suspensions were pre-incubated with Fc Block (1/100; BD Biosciences, 553142) for 10 min at 4 °C and stained with appropriate antibodies diluted at 4 °C in the dark for 30 min. After washing and centrifugation (400g, 7min, 4°C), supernatans was removed and pellets were resuspended in FACS buffer and transferred through a 35 µm mesh into a 5 ml Falco®Round‐Bottom Polystyrene Test Tube with Cell Strainer Snap Cap. Cell viability was assessed using DAPI 1/200, added immediately prior to sorting. Cell sorting was performed on the FACSymphony S6 using the 85 µm nozzle.  Cells were sorted into 2 ml Eppendorf tubes containing 450 µL RLT Plus lysis buffer (QIAGEN) containing 1% β-mercaptoethanol. The samples were extensively vortexed and stored at ‐80 °C until RNA isolation. Total RNA from sorted cells was extracted using the RNeasy ®Plus Micro Kit (QIAGEN, 74034) according to the manufacturer’s instructions. The concentration and purity of the RNA was determined using the Nanodrop ND-1000 (Nanodrop Technologies, Thermo Scientific) and the Agilent 2100 Bio-Analyzer.
RNA libraries were prepared for sequencing according to Element Biosciences protocols with the following parameters: AVITI 150 cycles Cloudbreak Freestyle sequencing kit single-end reads (101-10-10-0), 1% PhiX.

treatment_protocol: Not treated

tag: Sex

value: Female

value: Astrocytes


title: Tomato mutant apricot, at (cv AC)  biological replicate 2 Breaker stage

description: not applicable


title: HCT116, Tram, 24h, rep1

description: Library name: Tram_24h_rep1

value: Tram, 24 h


title: MeRIP-Seq, MOCK-infected, IP, rep3

description: Library name: VERO-MOCK-IP-rep3

value: m6A immunoprecipitated mRNA sequencing of MOCK-treated sample


title: Astrocytes, APP-NLGF, rep4

description:
Library name: X39_A20_APP_C3WT_4_astro_S51
Bulk_RNA_seq_PieterD_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Astrocytes_no_outliers.txt


title: HCT116, DMSO, 24h, rep1

description: Library name: DMSO_24h_rep1

value: DMSO, 24 h


title: Astrocytes, APP-NLGF, rep3

description:
Library name: X37_A17_APP_C3WT_3_astro_S49
Bulk_RNA_seq_PieterD_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Astrocytes_no_outliers.txt


title: MeRIP-Seq, VV-infected, 2 hpi, IP, rep3

description:
Library name: VERO-VV-2hpi-IP-rep3
exomePeak2.csv file contains zero-based coordinates
2hpi_exomePeak2.csv
2hpi_annotated.txt

value: m6A immunoprecipitated mRNA sequencing of VV-WR infected (MOI 1) sample at 2 hpi


title: HCT116, Chir, 8h, rep1

description: Library name: Chir_8h_rep1

value: Chir, 8 h


title: MeRIP-Seq, VV-infected, 6 hpi, IP, rep3

description:
Library name: VERO-VV-6hpi-IP-rep3
exomePeak2.csv file contains zero-based coordinates
6hpi_exomePeak2.csv
6hpi_annotated.txt

value: epithelial kidney cells

value: m6A immunoprecipitated mRNA sequencing of VV-WR infected (MOI 1) sample at 6 hpi


title: Astrocytes, APP-NLGF, rep2

description:
Library name: X34_A14_APP_C3WT_2_astro_S46
Bulk_RNA_seq_PieterD_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Astrocytes_no_outliers.txt


title: Tomato mutant apricot, at (cv AC)  biological replicate 1 Breaker stage

description: not applicable

value: pericarp


title: Tomato mutant Beta, B (cv AC)  biological replicate 3 Mature Green stage

description: not applicable


title: Tomato mutant Beta, B (cv AC)  biological replicate 2 Mature Green stage

description: not applicable


title: HCT116, Tram, 8h, rep1

description: Library name: Tram_8h_rep1

value: Tram, 8 h


title: Tomato mutant Beta, B (cv AC)  biological replicate 1 Mature Green stage

description: not applicable


title: MeRIP-Seq, VV-infected, 24 hpi, IP, rep3

description:
Library name: VERO-VV-24hpi-IP-rep3
exomePeak2.csv file contains zero-based coordinates
24hpi_exomePeak2.csv
24hpi_annotated.txt

value: Vero E6

value: m6A immunoprecipitated mRNA sequencing of VV-WR infected (MOI 1) sample at 24 hpi


title: Astrocytes, APP-NLGF, rep1

description:
Library name: X31_A11_APP_C3WT_1_astro_S43
Bulk_RNA_seq_PieterD_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Astrocytes_no_outliers.txt

value: Male


title: HCT116, DMSO, 8h, rep1

description: Library name: DMSO_8h_rep1

value: DMSO, 8 h


title: Astrocytes, WT, rep4

description:
Library name: X30_A10_C3WT_5_astro_S42
Bulk_RNA_seq_PieterD_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Astrocytes_no_outliers.txt

value: WT


title: Pr5_uninfected_male_rep3

city: Stillwater

first: Clinton

last: Jones

state: Oklahoma

address: 250 McElroy Hall

department: Veterinary Pathobiology

institute: Oklahoma State University

description:
OCJ4140_Male_Pr5_HSVvsControl.txt
OCJ4140_Male_Pr5_dLATvsControl.txt

hyb_protocol: Samples were submitted to NanoString Technologies for RNA isolation and subsequent sample processing

data_processing: Quality control, normalization, and between-group comparisons for differential gene expression were done using the nSolver Analysis Software from NanoString Technologies

label: NanoString target-specific fluorescent barcodes

source_name: Pr5, uninfected

extract_protocol: Serial coronal sections (60 µm thick) of brainstem were obtained on super frost plus slides using a cryostat (Leica CM3050S). The principal sensory nucleus (Pr5) of the spinal trigeminal tract and locus coeruleus (LC) were microdissected by Palkovit’s punch technique, using a mouse brain stereotaxic atlas as a reference (Paxinos and Franklin, 2019). Bilateral micropunches were collected from 60-µm thick coronal sections based on stereotaxic coordinates. Punches collected from Pr5 and LC were preserved in RNAlater at -20°C until shipped.

value: male

tag: infection

value: uninfected


title: WGBS, space, SSCLCs

city: Fuzhou

first: Ying

last: Li

state: Fujian

address: No. 2, Xueyuan Road, University Town

institute: Fuzhou University

description:
Library name: Sample6
SSCLCs differentiated from H1 human embryonic stem cells under spaceflight microgravity conditions. Cells were differentiated aboard the spacecraft over 15 days using SSC-specific medium. Integrated automated systems enabled remote culture and in-orbit preservation. This sample provides a genome-wide methylation map of male germline precursors developed in space.

data_processing:
Bisulfite sequencing reads were trimmed by 9 nt and processed with Trim Galore (v0.6.10).
Cleaned reads were aligned to the in silico bisulfite-converted hg38 genome using Bismark (v0.24.1) in non-directional mode.
Duplicate removal employed deduplicate_bismark, and methylation levels at CpG sites were extracted via bismark_methylation_extractor. Global methylation levels were computed in 1 Mb genomic bins (requiring ≥5 CpG sites/bin), with methylation calculated as methylated C / (C + T).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

source_name: human embryonic stem cell

growth_protocol: The H9 human embryonic stem cell line (WiCell, Inc.) was propagated on γ-irradiated mouse embryonic fibroblast (MEF) feeder layers in KnockOut™ DMEM (Gibco, 10829018) supplemented with 20% KnockOut™ Serum Replacement (Gibco, A3181502), 25 μg/mL recombinant human basic fibroblast growth factor (R&D Systems, 233-FB/CF), 1% penicillin-streptomycin (Gibco, 15140163), 1 mM GlutaMAX (Gibco, 35050061), and 1% Non-Essential Amino Acids (NEAA; Gibco, 11140076). Cultures were maintained at 37°C in a humidified atmosphere with 5% CO₂. The H1 human embryonic stem cell line (WiCell, Inc.) was cultured on Matrigel-coated plates (Corning, 365230) using E8 medium (Gibco, A1517001) containing 1% penicillin-streptomycin. Cultures were incubated at 37°C in a humidified 5% CO₂ environment. For subculturing, H1 hESCs were rinsed twice with DPBS (Yeasen, 60152ES76), detached into single cells using EDTA (Cellapy, CA1023100) incubated at 37°C for 2 minutes, and subsequently replated onto fresh Matrigel-coated plates. The culture medium was replaced daily, and cells were passaged every four days.

extract_protocol:
Based on post-flight processing of germ cell derivatives (PGCLCs, FLCs, SSCLCs) preserved in RNALater. WGBS Library Preparation: Genomic DNA was isolated using TRIzol Reagent. Bisulfite conversion used the EpiArt DNA Methylation Bisulfite Kit. Converted DNA was purified via spin columns and processed with the VAHTS Universal Pro DNA Library Prep Kit.
For WGBS libraries, bisulfite-converted DNA was processed using the VAHTS Universal Pro DNA Library Prep Kit, with library quantification via Qubit fluorometry and Agilent Bioanalyzer prior to 150-bp paired-end sequencing on the Illumina NovaSeq 6000.

treatment_protocol: PGCLC Differentiation Protocol (from H9 hESCs) H9 hESCs were seeded onto Matrigel-coated chambers at 30–40% confluency and propagated for 24 hours. Differentiation was initiated using PGC-specific medium (KnockOut™ DMEM supplemented with 10% FBS, 1 mM GlutaMAX, 1% NEAA, 1% penicillin-streptomycin, and 50 ng/mL recombinant human BMP4. Cultures were maintained at 37℃/5% CO₂ with complete medium replacement every 48 hours for 6 days. FLC Differentiation Protocol (from H9 hESCs) 5 × 10⁴ undifferentiated H9 hESCs (50% confluency) were seeded onto Matrigel-coated 6-well plates. Cells were treated with induction medium (KnockOut™ DMEM + 10% FBS, 1 mM GlutaMAX, 1% NEAA, 50 ng/mL BMP4, and 50 ng/mL BMP8a for 1 hour at 37°C/5% CO₂. Subsequently, cells were transduced with lentiviral vectors expressing DAZL and BOLL for 24 hours, followed by 24-hour recovery and 72-hour blasticidin selection (2 μg/mL). At day 7, cells were treated with differentiation medium containing 5 ng/mL GDF9:BMP15 heterodimer (purified per established protocol) and 10 ng/mL EGF for 24 hours, followed by medium refresh every 48 hours with 50 ng/mL GDF9 + 25 ng/mL BMP15. SSCLC Differentiation Protocol (from H1 hESCs) H1 hESCs were seeded onto Matrigel-coated vessels at 30–40% confluency and propagated for 48 hours. Differentiation was initiated using SSC-specific medium (MEMα supplemented with 3% KnockOut Serum Replacement, 1 mM GlutaMAX, 1× ITS-X, 0.2 mg/mL vitamin C, 1× Chemically Defined Lipid Concentrate, 1 ng/mL bFGF, and 20 ng/mL recombinant human GDNF). Medium was refreshed every 36 hours for 15 days.

value: human embryonic stem cell

value: SSCLCs differentiaton under spaceflight enviroment were subjected to WGBS


title: Tomato mutant tangerine, t (cv AC)  biological replicate 3 Mature Green stage

description: not applicable


title: Astrocytes, WT, rep3

description:
Library name: X28_A8_C3WT_4_astro_S40
Bulk_RNA_seq_PieterD_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Astrocytes_no_outliers.txt

value: Astrocytes


title: Pr5_uninfected_male_rep2

scan_protocol: Samples were submitted to NanoString Technologies for RNA isolation and subsequent sample processing


title: Tomato mutant tangerine, t (cv AC)  biological replicate 2 Mature Green stage

description: not applicable


title: WGBS, ground, SSCLCs

description:
Library name: Sample5
Spermatogonia stem-like cells (SSCLCs) differentiated from H1 human embryonic stem cells under ground control conditions. Cells were harvested at day 15 of differentiation and processed for WGBS to assess methylation status in male germ cell precursors.

value: SSCLCs differentiaton under ground condition were subjected to WGBS


title: Pr5_uninfected_male_rep1

label_protocol: Samples were submitted to NanoString Technologies for RNA isolation and subsequent sample processing


title: Tomato mutant tangerine, t (cv AC)  biological replicate 1 Mature Green stage

description: not applicable


title: Astrocytes, WT, rep2

description:
Library name: X25_A5_C3WT_3_astro_S37
Bulk_RNA_seq_PieterD_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Astrocytes_no_outliers.txt


title: Astrocytes, WT, rep1

description:
Library name: X23_A3_C3WT_2_astro_S35
Bulk_RNA_seq_PieterD_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Astrocytes_no_outliers.txt

value: Female


title: WGBS, space, FLCs

description:
Library name: Sample4
FLCs differentiated under microgravity conditions. Cells underwent the same differentiation protocol as ground controls but in a spaceflight environment. Post-flight, cells were recovered and processed for DNA extraction and whole-genome bisulfite sequencing to identify spaceflight-induced alterations in the DNA methylome of developing ovarian follicle cells.

value: FLCs differentiaton under spaceflight enviroment were subjected to WGBS


title: Wild type (cv Ailsa Craig, AC) biological replicate 1 Mature Green stage

description: not applicable


title: Pr5_uninfected_female_rep3

description:
OCJ4140_Female_Pr5_HSVvsControl.txt
OCJ4140_Female_Pr5_dLATvsControl

value: female


title: WGBS, ground, FLCs

description:
Library name: Sample3
Follicle-like cells (FLCs) differentiated from H9 human embryonic stem cells under ground control conditions (1g). Cells were harvested following a second stage-7-day differentiation protocol involving lentiviral transduction of DAZL/BOLL, and GDF9/BMP15 treatment. Genomic DNA was isolated for whole-genome bisulfite sequencing to establish baseline methylation profiles of in vitro derived ovarian follicle cells.

value: FLCs differentiaton under ground condition were subjected to WGBS


title: Wild type (cv Ailsa Craig, AC) biological replicate 3 Breaker stage

description: not applicable

value: pericarp


title: Microglia, APP-NLGF, rep5

description:
Library name: X20_M22_APP_C3WT_5_micro_S32
Bulk_RNA_seq_PieterD_raw_counts_Microglia_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Microglia_no_outliers.txt

source_name: Microglia

value: Microglia


title: Pr5_uninfected_female_rep2


title: WGBS, space, PGCLCs

description:
Library name: Sample2
PGCLCs differentiated under microgravity conditions. Cells were fixed in orbit and returned to Earth for DNA extraction and whole-genome bisulfite sequencing. Comparison with ground controls reveals spaceflight-induced alterations in DNA methylation.

value: PGCLCs differentiaton under spaceflight enviroment were subjected to WGBS


title: Microglia, APP-NLGF, rep4

description:
Library name: X18_M20_APP_C3WT_4_micro_S30
Bulk_RNA_seq_PieterD_raw_counts_Microglia_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Microglia_no_outliers.txt


title: Pr5_uninfected_female_rep1


title: Wild type (cv Ailsa Craig, AC) biological replicate 2 Breaker stage

description: not applicable


title: Pr5_dLAT2903_male_rep3

source_name: Pr5, dLAT2903


title: sextuple_monosome_rep3

city: Kaifeng

first: Xiaohong

address: Jinming Street

institute: Henan University

data_processing:
Library strategy: Ribo-seq
illumina Novaseq6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seedlings were grown vertically on 1/2 MS medium with 1% sucrose and 1.2% agar.

extract_protocol:
Total RNA of polysome or monosome fractions was precipitated and pooled for RNA-seq analysis. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ten day old Col-0, 2OX and sextuple seedlings grown vertically on 1/2 MS agar plates were collected for monosomal and polysomal RNA isolation. Ten day old Col-0 seedlings were transferred from MS plates to 9-well plate containing 1mL 1/2 liquid MS medium per well and treated with 50uM antimycin for 5 hours (sample named as Col_AA), or treated with DMSO (sample named as Col_CK)

value: whole seedling

tag: age

value: ten day old

value: sextuple mutant

tag: molecule subtype

value: monosomal RNA


title: C42B Enz 20 + Tala 10 A

city: Sacramento

first: Alan

last: Lombard

state: CA

address: 4500 2nd Avenue, Rm 4674

institute: University of California, Davis

description: Library name: LLG055

data_processing:
Raw sequencing data were processed using the nf-core/rnaseq pipeline (version 3.14.0, DOI 10.5281/zenodo.10471647), which includes quality control, alignment, and quantification steps
Reads were trimmed using Trim Galore
reads were mapped to the Homo sapiens reference genome (GRCh38) using STAR (Dobin et al., 2013). Gene-level quantification was performed using Salmon (Patro et al., 2017) against the GENCODE v45 gene annotation
Raw counts were extracted from the Salmon file outputs
Assembly: GRCh38 and GENCODE v45 gene annotation
Supplementary files format and content: tab-delimited text file contains raw counts for each sample and associated Ensembl gene id from the GENCODE v45 gene annotation.

growth_protocol: Cells are maintained in RPMI 1640 supplemented with 10% FBS and 1% pen/strep in humidified incubator at 5% CO2.

extract_protocol:
RNA was isolated from cultured cells using Trizol reagent (Thermofisher) following manufacturer’s instructions and further purified using the RNeasy kit (Qiagen) with the optional on-column DNase step according to the manufacturer’s protocols. Total RNA was eluted from the columns in nuclease-free water and stored at -80°C
Indexed, stranded mRNA-seq libraries were prepared from total RNA (1000 ng) using the KAPA Stranded mRNA-Seq Kit (Roche) according to the manufacturer’s standard protocol for mRNA capture, fragmentation, random-primed first strand synthesis, second strand synthesis with dUTP marking, A-tailing, adaptor ligation, and library amplification. Libraries were pooled and multiplex sequenced on an Illumina NovaSeqX Plus System

treatment_protocol: Cells were plated in 60mm and treated as indicated the following day. For LLG001-LLG018, treatment duration is indicated. For LLG037-LLG057, treatment was for 5-days.

value: Enzalutamide 20μM + Talazoparib 10nM


title: SOX17KO_cloneE3_E2_Rep2

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

description: Library name: Sample 6

data_processing:
Sequencing reads were aligned to hg19 build of the human genome using HISAT2
SAMtools was used to convert SAM files to BAM files
Read counts were normalized and analyzed for differential expression via the DESeq2 package in R
Genes were defined by the University of California Santa Cruz (UCSC) Known Genes and reads that mapped to known genes were assigned with featureCounts
Assembly: hg19
Supplementary files format and content: Gene counts (raw) in a text file

source_name: Ishikawa

growth_protocol: Cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. 3 days prior to 17beta-estradiol (E2) treatments, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific) with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
Following treatment, cells were lysed with buffer RLT Plus (Qiagen) containing 1% beta-mercaptoethanol (Sigma-Aldrich). RNA was extracted and purified using a Quick RNA Mini Prep kit (Zymo Research).
NEBNext Ultra II Directional RNA Library Prep kit with poly(A) mRNA isolation was used to construct RNA-seq libraries according to the manufacturer’s instructions (NEB).

treatment_protocol: Cells were treated with either 10 nm 17beta-estradiol (E2) or 0.1% DMSO for 8 hours

value: Ishikawa

value: endometrioid adenocarcinoma

value: SOX17 KO

value: 10 nm 17beta-estradiol


title: Microglia, APP-NLGF, rep3

description:
Library name: X16_M17_APP_C3WT_3_micro_S28
Bulk_RNA_seq_PieterD_raw_counts_Microglia_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Microglia_no_outliers.txt


title: WGBS, ground, PGCLCs

description:
Library name: Sample1
Primordial germ cell-like cells (PGCLCs) differentiated from H9 human embryonic stem cells under ground control conditions (1g). Cells were harvested at day 6 of differentiation and processed for whole-genome bisulfite sequencing to assess DNA methylation patterns.

value: human embryonic stem cell

value: PGCLCs differentiaton under ground condition were subjected to whole genome bisulfite sequencing (WGBS)


title: patient 6B human aortic valve leaflet tissue, female, diseased

city: La Jolla

first: Talia

last: Baddour

state: California

address: 9500 Gilman Dr.

department: Bioengineering

institute: University of California San Diego

description:
Library name: Patient 6B
Fresh Frozen Spatial Transcriptome sequencing

data_processing:
For single cell RNA sequencing: The Homo Sapiens genome and gene annotations (assembly: GRCh38) were used to align data via the Cell Ranger 8.0.0 (10X Genomics) “count” command to generate expression matrices. Downstream analysis on patient gene expression matrices was performed using the Seurat32 v4.4.0 pipeline in R.  Matrices were filtered from dead cells and cells with high (> 7000) and low (< 200) feature counts. Normalization was performed using Seurat’s SCT transform v.2 which applies a negative binomial regression model to correct for technical artifacts such as sequencing depth variation while maintaining highly variable biological features. The normalized data was then integrated using Pearson’s residuals via the functions PrepSCTIntegration() followed by FindIntegrationAnchors() and IntegrateData() in Seurat. Dimensional reduction was performed on the integrated data set with the RunPCA() and RunUMAP() functions with 30 principal components. Graph-based clustering was performed using k-nearest neighbor FindNeighbors() and transformed into clusters using FindClusters() at a resolution of 0.01 on the data set. Wilcoxon rank sum testing was used to identify differentially expressed genes between different patient groups.
For spatial transcriptomics: The sequencing data was aligned to images using SpaceRanger v.3.0.0 (10X Genomics) to generate gene expression matrices for subsequent analysis and processing. Spatial transcriptomics analysis was performed using the Seurat v4.4.0 pipeline in R. Gene expression matrices were initially filtered from high or low feature counts and regions of dead cells. Regions of calcification were confirmed via Von Kossa staining on tissue serial sections. Normalization was performed using Seurat’s SCT transform v.2 and merged our male and female replicates (N = 2) data into a single Seurat object and applied dimensional reduction and principal component analysis on the merged group. Then, male and female groups were integrated for comparison using Pearson residuals, FindIntegrationAnchors(), followed by PrepSCTIntegration(), and IntegrateData(). Graph-based clustering using k-nearest neighbor function FindNeighbors() and transformed into clusters using FindClusters() at a resolution of 0.1 on the entire integrated dataset. Wilcoxon rank-sum testing was used to identify differentially expressed genes between male and female samples.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz; scRNA seq = cell barcodes, spatial = spatial barcodes
Supplementary files format and content: features.tsv.gz; gene IDs
Supplementary files format and content: matrix.mtx.gz; gene expression count data
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: aortic valve leaflet

extract_protocol:
For single cell RNA sequencing: Aortic valve leaflets were excised from the aortic valve by cutting along the valve base and rinsed with Earle’s Balanced Salt Solution (EBSS) (Gibco, Cat. No. 24010043). All 3 leaflets per specimen were cut in half with 3 halves placed on ice for spatial transcriptomics protocols and three halves digested for single cell isolation and sequencing. Tissues were minced in Liberase TM (Sigma-Aldrich, Cat. No. 5401119001) in EBSS at 0.25 WU/mL and digested on an orbital shaker at 175 RPM for 30 mins at 37°C. DNAse I (Sigma Aldrich, Cat. No. DN25) was added to digestion medium at 100 µg/µL to prevent cell aggregation from genomic DNA. After digestion cells were immediately quenched with 10% Fetal Bovine Serum (FBS, Thermo Scientific, Cat. No. 16000069) in Medium 199 (Thermo Fisher Scientific, Cat. No. 11043023). Cells were strained in 3 successive straining steps with 100 µm, 70 µm, and 30 µm strainers and centrifuged at 400 rcf for 10 minutes. The cell pellet was resuspended in red blood cell lysis buffer (Thermo Scientific, Cat. No. 00433357) and rinsed using 10% FBS in media. After a final centrifugation step, cells were resuspended in 200 µL of 10% FBS media and counted using a cell hemacytometer prior to cell encapsulation in gel-beads for single cell RNA sequencing.
For spatial transcriptomics: Aortic valve leaflets embedded in OCT medium were cryosectioned at 10 μm in thickness at -20°C. Spatial transcriptomics protocols (10X Genomics) were performed on tissue sections with an RNA Integrity Number (RIN) > 7 measured on the Agilent TapeStation for all samples.
For single cell RNA sequencing: Following the manufacturer’s protocol (Single Cell 3′ v2, 10x Genomics), human aortic valve cells isolated from valve leaflets were suspended in master mix and inserted into a microfluidic chip together with partitioning oil and gel beads to form gel bead-in-emulsions (GEMs). Within each GEM, poly-A RNA from the cell lysate was reverse transcribed into cDNA incorporating an Illumina R1 primer sequence, a Unique Molecular Identifier (UMI), and the 10x barcode. The barcoded cDNA was then purified with Silane DynaBeads, PCR-amplified, and size-selected using SPRIselect reagent. During library assembly, the Illumina R2 primer sequence was added, along with paired-end constructs containing P5 and P7 sequences and a sample index.
For spatial transcriptomics: Spatial gene expression libraries were prepared using the Visium Spatial Gene Expression Kit (10x Genomics) following the manufacturer’s instructions for fresh frozen tissue. Briefly, cryosectioned tissue was placed on Visium Gene Expression Slides, fixed, and stained with hematoxylin and eosin (H&E) for imaging. Permeabilization released mRNA, which hybridized to spatially barcoded capture oligonucleotides on the slide. Reverse transcription generated spatially barcoded cDNA, which was then collected, purified, and amplified by PCR. The amplified cDNA was enzymatically fragmented, end-repaired, A-tailed, and ligated to sequencing adapters containing sample indices. Final libraries were amplified, quantified, and assessed for quality prior to sequencing.

value: aortic valve leaflet

tag: disease state

value: diseased


title: Wild type (cv Ailsa Craig, AC) biological replicate 1 Breaker stage

description: not applicable

data_processing:
Data were processed using RobiNA v2.0 software. Normalization method: rma; P-value correction method: fdr; Multiple testing strategy: global; P-value cut-off value for significant differential expression: 0.05; Genes that showed a log2-fold change smaller than two ignored: yes
eutom3gene_v2_ucprobes
EUTOM3_funcion_GO.tsv


title: Microglia, APP-NLGF, rep2

description:
Library name: X13_M14_APP_C3WT_2_micro_S25
Bulk_RNA_seq_PieterD_raw_counts_Microglia_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Microglia_no_outliers.txt

value: Female


title: Pr5_dLAT2903_male_rep2

value: male


title: patient 6A human aortic valve leaflet tissue, female, diseased

description:
Library name: Patient 6A
Fresh Frozen Spatial Transcriptome sequencing

value: female


title: Microglia, APP-NLGF, rep1

description:
Library name: X11_M11_APP_C3WT_1_micro_S23
Bulk_RNA_seq_PieterD_raw_counts_Microglia_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Microglia_no_outliers.txt

value: Male

value: Microglia


title: Pr5_dLAT2903_male_rep1


title: Tomato mutant tangerine, t (cv AC)  biological replicate 3 Full Ripe or Breaker+10 stage

description: not applicable

value: pericarp


title: Pr5_dLAT2903_female_rep3


title: Tomato mutant tangerine, t (cv AC)  biological replicate 1 Full Ripe or Breaker+10 stage

description: not applicable


title: patient 1B human aortic valve leaflet tissue, male, diseased

description:
Library name: Patient 1B
Fresh Frozen Spatial Transcriptome sequencing


title: Microglia, WT, rep4

description:
Library name: X10_M10_C3WT_5_micro_S22
Bulk_RNA_seq_PieterD_raw_counts_Microglia_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Microglia_no_outliers.txt

value: WT


title: Microglia, WT, rep3

description:
Library name: X08_M8_C3WT_4_micro_S20
Bulk_RNA_seq_PieterD_raw_counts_Microglia_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Microglia_no_outliers.txt


title: patient 1A human aortic valve leaflet tissue, male, diseased

description:
Library name: Patient 1A
Fresh Frozen Spatial Transcriptome sequencing


title: Pr5_dLAT2903_female_rep2


title: patient 22 human aortic valve leaflet cells, male, healthy

description:
Library name: Patient 22
10X Genomics

data_processing:
For single cell RNA sequencing: The Homo Sapiens genome and gene annotations (assembly: GRCh38) were used to align data via the Cell Ranger 8.0.0 (10X Genomics) “count” command to generate expression matrices. Downstream analysis on patient gene expression matrices was performed using the Seurat32 v4.4.0 pipeline in R.  Matrices were filtered from dead cells and cells with high (> 7000) and low (< 200) feature counts. Normalization was performed using Seurat’s SCT transform v.2 which applies a negative binomial regression model to correct for technical artifacts such as sequencing depth variation while maintaining highly variable biological features. The normalized data was then integrated using Pearson’s residuals via the functions PrepSCTIntegration() followed by FindIntegrationAnchors() and IntegrateData() in Seurat. Dimensional reduction was performed on the integrated data set with the RunPCA() and RunUMAP() functions with 30 principal components. Graph-based clustering was performed using k-nearest neighbor FindNeighbors() and transformed into clusters using FindClusters() at a resolution of 0.01 on the data set. Wilcoxon rank sum testing was used to identify differentially expressed genes between different patient groups.
For spatial transcriptomics: The sequencing data was aligned to images using SpaceRanger v.3.0.0 (10X Genomics) to generate gene expression matrices for subsequent analysis and processing. Spatial transcriptomics analysis was performed using the Seurat v4.4.0 pipeline in R. Gene expression matrices were initially filtered from high or low feature counts and regions of dead cells. Regions of calcification were confirmed via Von Kossa staining on tissue serial sections. Normalization was performed using Seurat’s SCT transform v.2 and merged our male and female replicates (N = 2) data into a single Seurat object and applied dimensional reduction and principal component analysis on the merged group. Then, male and female groups were integrated for comparison using Pearson residuals, FindIntegrationAnchors(), followed by PrepSCTIntegration(), and IntegrateData(). Graph-based clustering using k-nearest neighbor function FindNeighbors() and transformed into clusters using FindClusters() at a resolution of 0.1 on the entire integrated dataset. Wilcoxon rank-sum testing was used to identify differentially expressed genes between male and female samples.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz; scRNA seq = cell barcodes, spatial = spatial barcodes
Supplementary files format and content: features.tsv.gz; gene IDs
Supplementary files format and content: matrix.mtx.gz; gene expression count data
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots

value: healthy


title: Tomato mutant tangerine, t (cv AC)  biological replicate 2 Full Ripe or Breaker+10 stage

description: not applicable


title: Tomato mutant yellow flash, r (cv AC)  biological replicate 3 Full Ripe or Breaker+10 stage

description: not applicable


title: Pr5_dLAT2903_female_rep1


title: Tomato mutant yellow flash, r (cv AC)  biological replicate 2 Full Ripe or Breaker+10 stage

description: not applicable


title: Microglia, WT, rep1

description:
Library name: X03_M3_C3WT_2_micro_S15
Bulk_RNA_seq_PieterD_raw_counts_Microglia_no_outliers.txt
Bulk_RNA_seq_PieterD_normalized_counts_Microglia_no_outliers.txt


title: patient 10 human aortic valve leaflet cells, male, healthy

description:
Library name: Patient 10
10X Genomics


title: Tomato mutant Beta, B (cv AC)  biological replicate 3 Breaker stage

description: not applicable


title: patient 5 human aortic valve leaflet cells, male, diseased

description:
Library name: Patient 5
10X Genomics


title: primary rat astrocytes, H2O2, MItoCoat-mRNA 3

city: Charlestown

first: Kazuhide

last: Hayakawa

state: Massachusetts

address: MGH149 13th street, Room 2401

department: Radiology

institute: Massachusetts General Hospital

description: Library name: Stress-MRC3

data_processing:
by GENEWIZ (New Jersey, USA).
Assembly: Alignment files (BAM) were generated for downstream analysis. Gene-level counts were quantified using featureCounts from the Subread package (v1.5.2), counting uniquely mapped reads overlapping annotated exons (strand-specific when applicable).

organism: Rattus norvegicus

source_name: Primary

growth_protocol: Astrocytes were plated in poly-D-lysine-coated 75-cm2 flasks, and maintained in Dulbecco’s Modified Eagle’s medium containing 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA, including mitochondrial mRNA, was extracted from mitochondria-enriched fractions using the RNeasy Micro Kit (QIAGEN) according to the manufacturer’s protocol.
Library preparation and sequencing were performed by GENEWIZ (New Jersey, USA). Raw reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic (v0.36) and aligned to the Rattus norvegicus reference genome (Rnor6.0, Ensembl annotation) using the splice-aware aligner STAR aligner (v2.5.2b).

treatment_protocol: Cells were treated with H₂O₂ at a final concentration of 100 µM for 30 min at 37 °C in a humidified 5% CO₂ incubator by adding plate-specific volumes of the 10 mM H₂O₂ stock (1 µL, 10 µL, and 20 µL to 96-well, 12-well, and 6-well plates, respectively), while vehicle control wells received the same volume of sterile distilled water.

value: Primary

tag: cell line

value: astrocyte

value: ATP restoration

tag: batch

value: polyA RNA


title: Pr5_wtHSV1_male_rep2

source_name: Pr5, wt HSV-1


title: patient 2 human aortic valve leaflet cells, male, healthy

description:
Library name: Patient 2
10X Genomics


title: Pr5_wtHSV1_male_rep1


title: Tomato mutant Beta, B (cv AC)  biological replicate 2 Breaker stage

description: not applicable

source_name: mutant immature fruit


title: patient 1 human aortic valve leaflet cells, male, diseased

description:
Library name: Patient 1
10X Genomics


title: Pr5_wtHSV1_female_rep3


title: Tomato mutant Beta, B (cv AC)  biological replicate 1 Breaker stage

description: not applicable


title: FGF stimulated epicardial cell EVs, FGF-EVs, rep 4

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

institute: University of Toronto

description: Library name: FGF4

data_processing:
Libraries were sequenced using a NovaSeq 6000 S4 (Illumina) at  2× 150 (bp) and an average depth of 12 million reads.
R1 reads were trimmed to 75 bp before analysis and these were the files used for further analyses.
The Qiagen RNA- seq Analysis Portal 3.0 (workflow version 1.2) was used to align trimmed R1 sequencing data to the human genome (GRCh38.103) via the miRbase v22 database and generate raw miRNA count files for each sample (see EpiEV_rawcounts.txt).
Biological replicates with fewer than 100 total aligned miRNA counts were considered to have failed sequencing and not included in further analyses (NT2, FGF1).
Publicly available ComBat-seq R code was used to perform batch effect adjustment of raw miRNA count data based on RNA extraction cell culture batches according to a published protocol: https://doi.org/10.1093/nargab/lqaa078 (see EpiEV_Adjustedcounts.txt). RNA extraction batches: 1 (all groups reps 1 and 2), 2 (all groups reps 3 and 4); Culture batches = biological replicate numbers (1 to 4, for each group)
Assembly: GRCh38.103/miRbase v22
Supplementary files format and content: EpiEV_rawcounts.txt: tab-delimited text file including raw counts for each sample
Supplementary files format and content: EpiEV_Adjustedcounts.txt: tab-delimited text file including ComBat-seq adjusted counts for each sample along with calculated counts per million (CPM) mapped miRNA transcripts for each sample and average CPM for each group.

extract_protocol:
miRNA was isolated from lysed EV pellets using the miRNeasy Micro Kit (Qiagen, 217084) according to the manufaturer's protocol.
Library preparation was performed using the QIAseq miRNA Library Kit (Qiagen, catalog no. 331502).

treatment_protocol: To prepare epicardial cells for EV isolation, cryopreserved non-GFP pro-epicardial cells were seeded on 6 well plates using the same density and protocol as described above. Four different culture stimulation conditions were applied to different subsets of pro-epicardial cells. The ‘SB’ epicardial cell group was cultured in the same supplemented StemPro media formulation as outlined above from the time of plating (day 0) for the full duration of culture. Cells in the ‘TGF-b’ stimulation group were grown in the same supplemented StemPro media, but with no SB-431542 and with the addition of 5 ng/ml TGF-b1 (PeproTech, 100-21-10UG) starting one day after plating (considered day 0) for 4 days total. The ‘FGF’ stimulation group was grown in supplemented StemPro media with no SB-431542 and with the addition of 10 ng/ml bFGF (R&D Systems, 233-FB-025) starting one day after plating (day 0) for the full duration of culture. ‘No treatment’ (NT) cells were cultured in supplemented StemPro media with no SB-431542 and no other additives from the time of plating (day 0) for the full duration of culture. Culture media was changed every 2 days. On day 4, culture media (following the formulations specified above for each stimulation group) was ultrafiltered via centrifugation in Amicon Ultra-15 100kDa centrifugal filters (MilliporeSigma, UFC910024) at 4000g for 30 minutes at room temperature to deplete supplemented media of background EVs. Cells from each stimulation group were cultured in their respective formulations of ultrafiltered media for two 48-hour periods (day 4 to day 6 and day 6 to day 8). Conditioned media collected from cells on days 6 and 8 was frozen at -20C until EV isolation. Thawed conditioned media was centrifuged at 3200g for 10min to pellet cell debris. Supernatant was collected. The PEG-based miRCURY exosome isolation kit (Qiagen, 76743) was utilized for EV isolation.  PEG-media solutions were rotated overnight at 4C then centrifuged for 30min at 3200g and 21C to pellet EVs. Pellets were rinsed superficially with PBS without resuspension. EV pellets were resuspended directly in Qiazol lysis buffer for total RNA extraction.

tag: cell type

value: epicardial-derived cell

tag: treatment

value: 10 ng/ml bFGF, 8 days


title: primary rat astrocytes, H2O2, MitoCoat-mRNA 1

description: Library name: Stress-MRC1

tag: tissue


title: primary rat astrocytes, H2O2, MitoCoat3

description: Library name: Stress-MC3

tag: genotype


title: Pr5_wtHSV1_female_rep2


title: FGF stimulated epicardial cell EVs, FGF-EVs, rep 3

description: Library name: FGF3


title: Tomato mutant Beta, B (cv AC)  biological replicate 2 Full Ripe or Breaker+10 stage

description: not applicable

extract_protocol: Briefly, total RNA isolation was performed using a Tris-Borate/phenol-chloroformisoamyl alcohol 25:24:1-based extraction followed by Potassium Acetate/Lithium Chloride/Sodium Chloride precipitation steps (Lopez-Gomez and Gomez-Lim, 1992) and DNAse I purification at 37°C for 20’. RNA quality was determined by using a Nanodrop ND-1000 (NanoDrop Technologies) and an Agilent 2100 Bioanalyzer: only RNAs showing A260/A280 and A260/230 ratios between, respectively, 1.8-2.0 and 2.0-2.2 and with a 28S/18S ratio between 1.5 and 2.0 were selected.


title: Tomato mutant yellow flash, r (cv AC)  biological replicate 1 Full Ripe or Breaker+10 stage

description: not applicable


title: primary rat astrocytes, H2O2, MitoCoat 2

description: Library name: Stress-MC2


title: Pr5_wtHSV1_female_rep1


title: FGF stimulated epicardial cell EVs, FGF-EVs, rep 2

description: Library name: FGF2


title: LC_uninfected_male_rep3

description:
OCJ4140_Male_LC_HSVvsControl.txt
OCJ4140_Male_LC_dLATvsControl.txt

source_name: LC, uninfected

value: LC

value: uninfected


title: primary rat astrocytes, H2O2, MitoCoat 1

description: Library name: Stress-MC1


title: TGF-beta stimulated epicardial cell EVs, TGFb-EVs, rep 4

description: Library name: TGFb4

value: 5 ng/ml TGF-b1, 4 days; no treatment, 4 days


title: Tomato mutant Beta, B (cv AC)  biological replicate 1 Full Ripe or Breaker+10 stage

description: not applicable


title: LC_uninfected_female_rep3

description:
OCJ4140_Female_LC_HSVvsControl.txt
OCJ4140_Female_LC_dLATvsControl.txt


title: Wild type (cv Ailsa Craig, AC) biological replicate 3 Full Ripe or Breaker+10 stage

description: not applicable


title: TGF-beta stimulated epicardial cell EVs, TGFb-EVs, rep 3

description: Library name: TGFb3


title: Wild type (cv Ailsa Craig, AC) biological replicate 2 Full Ripe or Breaker+10 stage

description: not applicable


title: TGF-beta stimulated epicardial cell EVs, TGFb-EVs, rep 2

description: Library name: TGFb2


title: primary rat astrocytes, H2O2, Mitochondria treatment 1

description: Library name: Stress-mito1


title: LC_dLAT2903_female_rep3

source_name: LC, dLAT2903


title: LC_dLAT2903male_rep3


title: Wild type (cv Ailsa Craig, AC) biological replicate 1 Full Ripe or Breaker+10 stage

description: not applicable