title: MLS 1765-92 cells rep2

city: Gothenburg

first: Anders

last: Ståhlberg

address: Medicinaregatan 1F

department: Department of Laboratory Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
Adapters were trimmed from reads with TrimGalore v.0.6.1 and Cutadapt v.2.3
Unpaired reads were removed with BBMap repair.sh v.38.61b.
Reads were aligned to the ENSEMBL GRCh38 reference genome using Burrows Wheeler Aligner (BWA)
PCR duplicate reads were identified with picard markDuplicates and corrected for during peak calling
Reads of mitochondrial origin were removed with the python script removeChrom and ENCODE blacklisted regions were eliminated using BEDTools intersect.
The bam-files were sorted based on chromosome coordinates using samtools, before performing peak calling with the Model-based Analysis of ChIP-seq2 (MACS2) using an FDR cutoff of < 0.05.
BigWig files were created with deepTools by normalizing to reads per genetic content.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: Peak files (MACS2 output)

growth_protocol: Cells were cultured at 37°C in 5% CO2 in media supplemented with 100U/ml penicillin and 100mg/ml streptomycin; either RPMI 1640 GlutaMAX with 5% fetal bovine serum (MLS 1765 cells) or IMDM GlutaMAX with 10% fetal bovine serum (EWS TC-71 cells). Cell lines were passaged using 0.25% trypsin supplemented with 0.5mM EDTA. All media and supplements were obtained from Gibco (Thermo Fisher Scientific).

extract_protocol:
50 000 cells were harvested and lysed in a lysis buffer containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630. Transposition was performed by resuspending and incubating the nuclei in TD buffer with TDE1 Tagment DNA Enzyme from Illumina for 60 min at 37°C and 1000 rpm mixing. Transposed DNA was isolated with a MinElute PCR purification kit (Qiagen) and eluted in 15 µl 10 mM Tris buffer (pH 8, Qiagen). Purified DNA was stored at -20°C. Libraries were amplified in a 10 cycles PCR reaction. Double-sided size selection of libraries was performed with Agencourt AMPure XP (BD Biosciences).
ATAC-Seq experiments were performed  as previously described by Buenrostro et al.  Nat Methods 2013, 10, 1213-1218 doi: 10.1038/nmeth.2688

value: myxoid liposarcoma cell line


title: mRNAseq_Flower_b2_WTCol-0_rep1

status: Public on Sep 22 2025

type: SRA

city: La Jolla

first: Julie

middle: A

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: Plant Molecular and Cellular Biology

country: USA

institute: Salk Institute for Biological Studies

description:
Library name: sample60
experiment batch2

library_source: transcriptomic

data_processing:
Reads were mapped to the TAIR10 reference genome using STAR (v2.7.10a) allowing 2 mismatches and only uniquely mapped reads with the following options: --alignIntronMin 20 --alignIntronMax 6000 --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 and --alignMatesGapMax 7500. To facilitate expression quantification, Tag Directories were generated from the resulting bam files using the makeTagDirectory function of HOMER (v4.10) with the following options: -format sam -mis 2 and -unique. mRNA expression was quantified using the analyzeRepeats.pl function of HOMER (v4.10). A custom gtf file containing genes, transposons, and repeats was used for quantification with the option -condenseGenes to report the highest expressed transcript, and -noadj to report raw read count. UCSC format track files were generated using the makeUCSCfile function of HOMER (v4.10) with the following options: -fragLength given -norm 10000000 -style rnaseq and -strand both.
Assembly: TAIR10
Supplementary files format and content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: stage 12 and younger flower buds

growth_protocol: For wild-type plants (Col-0 ecotype), T-DNA insertion lines, rim-cr CRISPR deletion lines, and rim22-3 EMS lines, seeds were stratified in 0.1% agar (Phyto Agar, Cat# P1003) at 4˚C for 4 days before sowing directly onto soil and grown under Salk greenhouse conditions. Approximately five weeks after planting, stage 12 and younger flower buds were collected and frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from flower buds (stage 12 and younger) using the Zymo Quick-RNA Miniprep Kit (R1055).
1 μg of DNase I treated total RNA was used for mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Cat# E7490L). Library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit (NEB, Cat# E7770L). Pooled libraries were sequenced using a 50 bp single-end kit (SE50) or paired-end kit (PE50) on the Illumina Nextseq 2000 or Novaseq X plus platforms.

tag: tissue

value: stage 12 and younger flower buds

tag: cell type

value: Columbia

tag: genotype

value: WT


title: MLS 1765-92 cells rep1

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line


title: Induced_senescent_BJ_cells_Ctrl_rep1_KAS-seq

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
The Trim_Galore tool was employed to remove low-quality bases and adapter-containing reads from the raw KAS-seq data. Reads that were trimmed to shorter than 30 bp were discarded.
The remaining reads were aligned to the reference genome (hg19) using Bowtie2 (v2.3.3.1), with the alignment carried out under default parameters. The SAM files were then converted and sorted into BAM files using samtools sort (v1.9).
Duplicate reads were removed with the assistance of Picard MarkDuplicates (v1.141), and the deduplicated, uniquely mapped reads were extended to 150 bp to align with the average length of DNA fragments, a process executed using the awk command. The extended data, in BED file format, were converted to BedGraph files using bedtools genomecov, and subsequently transformed into BigWig files through bedGraphToBigWig, part of the University of California, Santa Cruz (UCSC) precompiled utilities.
Shell scripts for KAS-seq data mapping and quality control can be accessed at GitHub (https://github.com/Ruitulyu/KAS-Analyzer).
The metagene profile plots and heatmaps were constructed using deepTools plotProfile and plotHeatmap. For peak calling, MACS2 was utilized to identify broad KAS-seq peaks, and 2kb bins overlapping with KAS-seq peaks were used to detect differentially generated time-course KAS-seq signals. Finally, the k-means clustering method was applied to segregate the differential 2kb bins into 4 clusters.
Assembly: hg19
Supplementary files format and content: bigWig, KAS-seq read density
Supplementary files format and content: bed, KAS-seq peaks
Library strategy: KAS-seq

source_name: BJ cells

growth_protocol: BJ cells were grown in EMEM (Corning, 10009-CV) supplemented with penicillin and streptomycin (Gibco, 15070), 10% FBS (Sigma, F2442).

extract_protocol:
After treatment, cells were collected for genomic DNA (gDNA)purification using the PureLink genomic DNA mini kit (Thermo Fisher, K182002). In a 100 µL volume, around 1 µg gDNA was incubated with 1 mM DBCO-PEG4-biotin (Sigma, 760749) in 1× PBS at 37 °C for 1.5 h with gentle shake for biotinylation. gDNA was then purified by DNA Clean & Concentrator-5 kit (Zymo Research, D4013) and fragmented to around 250 bp by sonication. 10 µL Dynabeads MyOne Streptavidin C1 (Thermo Fisher, 65001) were then applied to pull-down biotinylated DNA fragments following the manufacturer’s protocol. DNA was eluted from the bead by heating the beads in 15 µL H2O at 95 °C for 10 min.
Library construction was performed using the xGen™ methyl-seq DNA library prep kit (IDT, 10009860).

treatment_protocol: Cells were treated with 5 mM N3-kethoxal in 6-well plates for 10 min under their normal culture condition.

value: BJ cells

value: Fibroblasts established from skin taken from normal foreskin from a neonatal male

tag: treatment

value: Vanadyl sulfate, 0 mins

tag: time

value: 0 minutes


title: ECIS57T_chip1

city: Houston

first: Nicholas

last: Navin

state: Texas

address: 6565 MD Anderson Blvd

department: Systems Biology

institute: MD anderson Cancer Center

description: Library name: ECIS57T_chip1

library_source: transcriptomic single cell

data_processing:
The scRNA-seq FASTQ files were trimmed with Trimmomatic to remove sequencing and library adaptors
The trimmed reads were alignment to the reference genomes of human (hg19 reference) with STARsolo
Assembly: hg19
Supplementary files format and content: Gene count

source_name: Breast

extract_protocol:
The genomic DNA and RNA was extract from isolated single nuclei
The in house nanowell based DNA-RNA sequencing (wellDA-seq) protocol; Single cell DNA-RNA coassay

value: Breast


title: ECIS57T_chip2

description: Library name: ECIS57T_chip2


title: IntestiCult™ OGM, Ileum, 10X, rep1

city: Vancouver

first: STEMCELL

last: Technologies

state: BC

address: 1618 Station st

department: RND

country: Canada

institute: STEMCELL Technologies

description:
Library name: OCM2-4-Ileum-OGM
scRNA-seq data from the ileum expanded in IntestiCult™ OGM

data_processing:
10X libraries: the barcoded processing, gene counting and aggregation were made using the 10X Genomics Cell Ranger software v3.1.0. Sequencing data was demultiplexed using Illumina's cellranger multi.
Illumina libraries: the barcoded processing, gene counting and aggregation were made using the Fluent BioSciences PIPSeeker software v3.3. Processed data at sensitivity 3 are provided.
Downstream analysis were performed with Seurat v5.2.1. Cells with gene count between 2,000 and 10,000 genes and less than 10% mitochondrial genes were retained for analysis. RPCA integration was performed in order to incorporate all samples under a single UMAP. Gene expression of key markers was used to identify cell types.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ileum

extract_protocol:
Intestinal organoids in matrigel domes were digested using gentle cell dissociation reagent for 10 minutes, followed by centrifugation at 300g for 5 minutes. The cell pellet is washed with DMEM-F12 + 0.5% BSA, and centrifuged at 300g for 5 minutes. After removal of the supernatant, the pellet is resuspended in 1mL of warmed (37°C) Trypsin-EDTA (0.05%), and incubated at 37°C for 5-10 minutes. The cell suspension is then mixed thoroughly until large fragments have dissociated into single cells. An equal volume of DMEM/F-12 + 1% BSA is added to the suspension to deactivate the trypsin. A pre-wet a 37um reversible strainer is used to remove any large fragments that remain. Cell concentration, viability and percent of clumps are determined using a Nucleocounter. Single cells are centrifuged at 200g for 5 mins (RT). The supernatant was removed, and 1mL of pre-warmed cell suspension buffer is added with a wide bore pipette and gentle mixing to resuspend the pellet. Cells are then centrifuged at 200g for 3 minutes (RT), followed by aspiration of the supernatant. 200-400uL of cold cell suspension buffer is added to the pellet and gently mixed 10-15 times to resuspend. The single cell concentration is determined using the laboratory’s preferred method. A suspension of 2,500 live cells/uL is prepared in a cell suspension buffer to achieve an input volume of 4uL (10,000 live cells/uL) into a PIP reaction.
10X libraries: Library was prepared using Chromium Single Cell 3ʹ v1 protocol with GEM-X Universal Multiplex technology (10x Genomics). Sample quality control was performed using the Agilent 2100 Bioanalyzer or the Agilent 4200 TapeStation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq 2000 with Paired End 59 bp × 59 bp reads. Illumina libraries: Library preparation was performed according to the manufacturer’s instructions (Illumina Single Cell 3′ RNA Prep, T10, Illumina). Briefly, single cells were combined with Particle-templated Instant Partitions (PIPs) and barcoded beads to generate emulsified partitions. Following chemical lysis, mRNA released from each partition was reverse transcribed into barcoded cDNA. The cDNA was then amplified by whole transcriptome amplification, isolated from PIPs, and purified using magnetic beads. Quality control included Qubit quantification and fragment analysis. For library construction, cDNA underwent fragmentation, end repair and A-tailing, adapter ligation, and sample index PCR to add Illumina P5, P7, and index sequences. Final libraries were cleaned with magnetic beads and prepared for sequencing on Illumina platforms.

value: Ileum

value: Primary Organoid Intestinal epithelial


title: MLS 1765-92 cells rep3


title: IntestiCult™ Plus, Duodenum, 10X, rep1

description:
Library name: OCM2-1-Duodenum-IntPlus
scRNA-seq data from the duodenum expanded in IntestiCult™ Plus

source_name: Duodenum

value: Duodenum


title: IntestiCult™ OGM, Colon, Illumina, rep1

description:
Library name: Illumina-5-Colon-OGM_S5
scRNA-seq data from the colon expanded in IntestiCult™ OGM

source_name: Colon

value: Colon


title: EWS TC-71 cells rep 2

source_name: EWS TC-71

value: EWS TC-71

value: Ewing's sarcoma cell line


title: EWS TC-71 cells rep 3


title: EWS TC-71 cells rep 1


title: Bulk ATAC seq, bone marrow, ISO, rep2

city: St. Louis

first: Douglas

last: Mann

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis

description: Library name: bonemarrow_ISO_rep2

data_processing:
ATAC-seq data were processed using a Snakemake (v7.32.4) pipeline designed for reproducibility and modular execution. Consensus peaks were identified across all samples using bedtools multiinter (v2.31.1), retaining regions shared by a minimum number of replicates as defined in the configuration file (default = 2). Read counts under consensus peaks were quantified per sample using bedtools multicov (v2.31.1). Normalization and differential accessibility analyses were performed in R (v4.4.3) using DESeq2 (v1.46.0).
Assembly: mm10
Supplementary files format and content: read counts per sample: counts.txt

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
50,000 bone marrow nuclei were isolated and DNA fragmented in situ using Tagment DNA Enzyme 1 (Illumina, cat. no. 20034197) at 37 °C for 30 minutes. Transposed DNA was purified using the Zymo DNA Clean and Concentrator-5 kit (Zymo Research, cat. no. D4014).
ATAC-seq libraries were prepared as previously described (Corces et al., Nat. Methods, 2017). Libraries were amplified by PCR using Nextera XT multiplex primers and NEBNext High-Fidelity 2X PCR Master Mix (NEB, cat. no. M0541) for 10 cycles. Post-amplification cleanup and size selection were performed using a two-sided selection with DINOMAG magnetic beads (Labscoop, cat. no. DN9004-75ML), applying a 0.55× and 1.55× bead-to-sample volume ratio to retain fragments in the desired size range.

treatment_protocol: Female 10-wk old wild-type (C57BL/6J) mice were injected intraperitoneally with lipopolysaccharide (LPS; 2.5 mg/kg), 1 ug recombinant interferon-b1/10 ug recombinant interferon-y (IFN), isoproterenol (ISO; 300 mg/kg), or diluent. Mice were then euthanized 7 days later (n=3/group) with bone marrow aspirates collected and used for bulk ATAC sequencing.

value: Bone marrow

value: Various

value: Wild-type

value: ISO


title: BCIS51T_chip1

description: Library name: BCIS51T_chip1


title: TEM6GFP-3

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

data_processing:
quality assessment: FastQC (0.11.9)
adapter removal: Cutadapt (3.5)
read quality trimming: Trimmomatic (0.39)
alignment to Ensembl Hs 107: STAR with GeneCounts (2.7.10a)
generation of RPKM and TMM: edgeR (3.40.1)
Assembly: Ensembl Genes 107 Homo sapiens GRCh38.p13
Supplementary files format and content: RPKM, TMM, Raw Counts, Annotation

molecule: total RNA

source_name: Brainstem (pons)

extract_protocol:
New England Biolabs NEBNext® Poly(A) mRNA Magnetic Isolation Module
IDT xGen Broad-Range RNA Library Preparation Kit

value: Brainstem (pons)

value: SU-DIPG-VI (RRID:CVCL_IT40)

value: Cancer cell

value: 3D culture (Co-culture of 3 cell types)


title: TEM6GFP-2


title: BCIS106T_chip1

description: Library name: BCIS106T_chip1


title: BCIS66T_chip2

description: Library name: BCIS66T_chip2


title: BCIS66T_chip1

description: Library name: BCIS66T_chip1


title: TEM6GFP-1


title: Bulk ATAC seq, bone marrow, IFN, rep3

description: Library name: bonemarrow_IFN_rep3

value: IFN


title: BCIS70T_chip1

description: Library name: BCIS70T_chip1


title: BCIS106T_chip2

description: Library name: BCIS106T_chip2


title: Bulk ATAC seq, bone marrow, ISO, rep1

description: Library name: bonemarrow_ISO_rep1


title: TEM-13-3

value: SU-DIPG-XIII (RRID:CVCL_IT41)


title: BCIS70T_chip2

description: Library name: BCIS70T_chip2

value: Breast


title: BL [CLG36]

type: protein

city: San Francisco

first: Jessica

last: Neely

state: California

address: 550 16th Street

department: Pediatrics

institute: UCSF

data_processing:
NPX values per Olink
Data is presented as NPX values. NPX is Olink's relative protein quantification unit on log2 scale. NPX  values are calculated from the number of matched counts, using NGS (Next Generation Sequencing) as  readout. The NPX values are presented in a separate results file. Data values for measurements below  limit of detection (LOD) are reported for all samples.

molecule: protein

source_name: plasma

extract_protocol: Olink Explore 3072

tag: site

value: CARRA

tag: disease status

value: BL

tag: age

tag: Sex

value: Female


title: Bulk ATAC seq, bone marrow, IFN, rep2

description: Library name: bonemarrow_IFN_rep2


title: BCIS51T_chip2

description: Library name: BCIS51T_chip2


title: Bulk ATAC seq, bone marrow, IFN, rep1

description: Library name: bonemarrow_IFN_rep1


title: Bulk ATAC seq, bone marrow, ISO, rep3

description: Library name: bonemarrow_ISO_rep3


title: TEM-13-2


title: BCIS74T_chip2

description: Library name: BCIS74T_chip2


title: Cellline_mixing_experiment_1_2

description: Library name: Cellline_mixing_experiment_1_2


title: TEM-13-1


title: BCIS74T_chip1

description: Library name: BCIS74T_chip1


title: Cellline_mixing_experiment_1_1

description: Library name: Cellline_mixing_experiment_1_1


title: wellDR3

description: Library name: wellDR3


title: T-2-6

value: 3D culture (Tumor cell only)


title: Cellline_mixing_experiment_2

description: Library name: Cellline_mixing_experiment_2


title: Bulk ATAC seq, bone marrow, LPS, rep2

description: Library name: bonemarrow_LPS_rep2

value: LPS


title: MDA_MB_231_3DE_Takara

description: Library name: MDA_MB_231_3DE_Takara


title: T-1-6


title: T-13-3


title: Bulk ATAC seq, bone marrow, PBS, rep3

description: Library name: bonemarrow_PBS_rep3

value: PBS


title: Bulk ATAC seq, bone marrow, PBS, rep2

description: Library name: bonemarrow_PBS_rep2

value: Bone marrow


title: Control Saline Mouse 3

city: Manhasset

first: Lior

last: Brimberg

state: NY

address: 350 Community Drive

institute: Feinstein Institutes for Medical Research

description:
Library name: 3_3_S9
10x Genomic

data_processing:
Sequencing data was mapped and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) with default settings.  Gene expression reads were aligned to the mouse reference genome version GRCm38 using GENCODE vM23/Ensembl 98 annotations (obtained from 10X Genomics, build "gex-mm10-2020-A").
Assembly: mouse reference genome version GRCm38
Supplementary files format and content: Tab sperated valuse Files  and

source_name: Hippocamous

extract_protocol:
Hippocampal tissue was manually dissociated on ice, then enzymatically dissociated using the Neural Tissue Dissociation Kit (Miltenyi, 130-092-628) per manufacturer instructions. Myelin was removed with Myelin Removal Beads (Miltenyi, 130-096-433). Cells were washed in FACS buffer (HBSS + 1% BSA) and stained in 100 uL FACS buffer with Live/Dead Fixable dye (1:500, Life Technologies L34964), FITC anti-mouse CD45 (1:100, BD 30-F11), and PE anti-mouse CD11b (1:100, BD M1/70) for 30 min at 4°C in the dark. After washing, cells were sorted on a BD FACSAria III.
Single-cell cDNA libraries were prepared according to the manufacturer’s instructions (Next GEM Single Cell 3′GEM v.3.1 protocol, 10x Genomics). Libraries were sequenced on a NextSeq2000 to a median read depth of ~38,000 reads per cell using the recommended read format (28x10x10x90bp).

value: Hippocamous

value: Brain macrophages/Microglia

tag: strain


title: Caspr2 Saline Mouse 2

description:
Library name: 3_5_S11
10x Genomic


title: Control Saline Mouse 2

description:
Library name: 3_2_S8
10x Genomic


title: Caspr2 Saline Mouse 1

description:
Library name: 3_4_S10
10x Genomic


title: T-13-1


title: Control Saline Mouse 1

description:
Library name: 3_1_S7
10x Genomic


title: Caspr2 Captopril Mouse 3

description:
Library name: 2_6_S6
10x Genomic


title: Bulk ATAC seq, bone marrow, PBS, rep1

description: Library name: bonemarrow_PBS_rep1

value: Various

value: Wild-type


title: Bulk ATAC seq, bone marrow, LPS, rep3

description: Library name: bonemarrow_LPS_rep3


title: Caspr2 Captopril Mouse 1

description:
Library name: 2_4_S4
10x Genomic


title: Caspr2 Captopril Mouse 2

description:
Library name: 2_5_S5
10x Genomic


title: RQC CRISPR sample2

city: shanghai

first: jingminjie

state: CN

address: shanghai

country: China

institute: Ruijin Hospital

data_processing:
Raw sequencing reads alignment to the human reference genome GRCh38 using Cell Ranger version 7.2.0, and UMI quantification and sgRNA identification and quantification were performed. Then, downstream analysis was performed using R Seurat 4.3.0.
1) Cell with nFeature < 500, nCount < 1000, mitochondrial ratio > 10%, and sgRNA UMIs < 5 were filtered; 2) And cell with 2 or more perturbations were filtered; 3) Target genes with the number of cells perturbed ≥50 were kept.
Cells which passed QC metrics were passed to Seurat 4.3.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreas

extract_protocol:
EndoC-βH1 cells were infected with lentivirus expressing Zim3 KRAB-dCas9-NLS-P2A-EGFP supplemented with 5 μg/mL polybrene. GFP+ cells were sorted for generating CRISPRi cell line. Then, CRISPRi EndoC-βH1 cells were transduced with a low multiplicity of infection (MOI) of lentivirus containing sgRNA library cassette in order that less than 20% of the cells were BFP+ to ensure the majority cells received only one lentivirus per cell. At 14 days post transduction, the treated cells were sorted using fluorescence activated cell sorting (FACS).
Briefly, the sorted cells with greater than 85% viability are qualified for 3’ digital gene expression by profiling ~100,000 individual cells per sample. Partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated cDNA share a common 10x Barcode. Dual Indexed libraries are generated and sequenced from the cDNA and 10x Barcodes are used to associate individual reads back to the individual partitions.
The detailed process according to 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 User Guide with Feature Barcode technology for CRISPR Screening.

treatment_protocol: Briefly, the culture plates were precoated with high glucose Dulbecco’s modified eagle medium (DMEM) supplemented with βCOAT (purchased from Human Cell Design), 100 U/ml penicillin and 100 µg/ml streptomycin 4 h at 37 ℃ in a humidified 5% CO2 atmosphere prior to cell plating. Cells were cultured in OPTIβ1 (purchased from Human Cell Design), passaged weekly with 0.05% Trypsin.

value: pancreatic beta cell

value: Pancreas


title: Control Captopril Mouse 2

description:
Library name: 2_2_S2
10x Genomic


title: Control Captopril Mouse 1

description:
Library name: 2_1_S1
10x Genomic


title: RQC CRISPR sample1


title: Control Captopril Mouse 3

description:
Library name: 2_3_S3
10x Genomic


title: Caspr2 Saline Mouse 3

description:
Library name: 3_6_S12
10x Genomic


title: rNLS8 2

first: Long-Jun

last: Wu

state: TX

address: 1825 Pressler Street

institute: University of Texas Health Science Center

description:
Library name: Sample 4
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv: spatial enrichment in csv format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
FFPE tissue block was sectioned by a microtome at 5µm
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagents kit according to manufacturer's construction

treatment_protocol: Dox withdrawal

value: brain

value: 11 weeks old

value: Male


title: GWAS CRISPR sample7


title: rNLS8 1

description:
Library name: Sample 3
FFPE Spatial transcriptome sequencing


title: Control 2

description:
Library name: Sample 2
FFPE Spatial transcriptome sequencing

value: Control


title: T-13-2

value: Brainstem (pons)

value: SU-DIPG-XIII (RRID:CVCL_IT41)

value: Cancer cell


title: GWAS CRISPR sample6


title: LAD + sham CM Day 1-56 snRNA-seq CMO

city: Würzburg

first: Andy

middle: Shing Fung

last: Chan

address: Gebäude E6,, Versbacher Str. 9

country: Germany

institute: Institute for Systems Immunology, University of Würzburg

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger softward v2.1.1. Seurat was used for CellPlex barcode demultiplexing
Assembly: mm10-2020-A
Supplementary files format and content: expdata_all_timepoints_LAD_Cryo_Sham.rds: gene expression matrix of filtered cells from all time points and surgery models
Supplementary files format and content: mdata_cells_timepoints_annotations_final.rds: annotation of filtered cells (cell types/states and time points/conditions)

source_name: heart left ventricles

extract_protocol:
Surgery / Cryo / LAD / Sham LV cryoinjury (Cryo), ischemia-reperfusion injury after left anterior descending artery (LAD) ligation, and sham surgery were applied to female wildtype C57BL/6J mice at 12 weeks of age. Surgery and cryoablation were performed as described previously (Simon-Chica et al. 2024). In brief, mice were anaesthetized by intraperitoneal injection of 80–100µL of anesthesia solution (20mg/mL ketamine (Ketaset; Zoetis, Parsippany-Troy Hills, NJ, USA), 1.4mg/mL xylazine hydrochloride (0.12% Rompun; Bayer, Leverkusen, Germany), in 114 mM NaCl (0.67% m/v; B. Braun Melsungen, Melsungen, Germany)). After induction of deep anesthesia, eye ointment (Bepanthen containing 50mg/mL dexpanthenol; Bayer) was applied, 500µL glucose solution (278mM glucose = 5% (m/v); B. Braun Melsungen) was injected intraperitoneally, and 250µL of analgesia solution (10µg/mL buprenorphine (Temgesic; Indivior Inc., North Chesterfield, VA, USA) in 154 mM NaCl (0.9% m/v, B. Braun Melsungen)) was injected subcutaneously in the neck. Mice were shaved at the left side of the thorax (precordial region) and on the right leg. Mice were placed on a warming platform of a small animal physiology monitoring system (Harvard Apparatus, Holliston, MA, USA), and the front extremities were fixed with tape. A rectal thermometer was inserted to allow regulation of the heating platform to ensure a body temperature of 37°C. Thermometer and tail were fixed with tape. Mice were intubated for positive pressure ventilation (Kent Scientific, Torrington, CT, USA; 40% O2, 120 breathing cycles per minute). Isoflurane was applied at 5% until the animal stopped spontaneous respiratory movements, and then reduced to 2.0–2.5%. An infrared blood oximeter was attached to the right leg to track haemoglobin oxygen saturation, which was used to adjust the ventilation if needed. The surgical field was disinfected using Softasept N (B. Braun Melsungen). Skin and muscles were cut along the third intercostal space, and a rib spreader was introduced. The pericardium was cut, and the epicardial surface was dry-blotted using a cellulose pad. For mice undergoing ventricular cryoablation, a hexagonal metal probe (stainless steel, 2.5 mm edge-normal distance) was pre-chilled in liquid nitrogen and applied for 8–10 s on the free LV mid-wall, positioned to avoid major coronary vessels. After retraction of the probe, the time until the tissue regained deep-red color was protocoled (consistently within 5–10 s). For mice in which the ischemia-reperfusion injury was introduced, the LAD was identified and ligated with an 8-0 suture, while a narrow plastic tubing was inserted below the suture. Successful ligation was indicated by a colour change of the infarcted area from red to grey. After 30–45 min, tubing and suture were removed. For sham surgery, application of the metal probe or ligation was skipped. The rib spreader was removed, and the thorax closed using a 6-0 silk suture around the third and fourth ribs (4–5 single knots). Before final closure, any remaining air was removed from the thorax using a small cannula. Isoflurane application was stopped, and the skin was closed with a 4-0 silk suture. Once the mouse started breathing spontaneously, intubation and fixation were terminated, and the mouse was transferred to a heated and oxygenated wake-up chamber. Analgesia was maintained for 72 h post-surgery by twice-daily subcutaneous injection of 250µl of buprenorphine (10µg/mL in 154 mM NaCl; morning and late afternoon). During the night, buprenorphine was also supplied via the drinking water (10µg/mL buprenorphine (Subutex lingual tablets, Indivior) in 20 mM glucose solution).  Tissue Processing and Cell Isolation The tissue collection and slicing protocol was adapted from a previously published protocol 52,53. In brief, mice received sodium-heparin solution (16units/g body weight) by intraperitoneal injection, before being sacrificed by cervical dislocation five min later. The chests were opened, and hearts were excised. To wash out the blood from the heart, hearts were cannulated and flushed with cold ‘cutting solution’ (in mM): NaCl 138, NaH2PO4 0.33, KCl 5.4, MgCl2 2, HEPES 10, glucose 10, CaCl2 0.5, 2,3-butanedione 2-monoxime (BDM) 30, pH adjusted to 7.3 with 1 M NaOH at 37°C, osmolality 330 ± 10mOsm/L. Tissue blocks of ventricular free wall containing the post-cryoablation or post-ischemia-reperfusion lesion centre (identified as a region appearing mostly white), BZ and adjacent myocardium (or corresponding tissue areas from sham animals) were excised and embedded in low-melting-point agarose (4% (m/v)) at 37°C, and then put on ice. Agarose blocks were glued to the stage of a precision vibratome and cut into 300µm thick slices (60Hz cutting frequency, 1.5Hz amplitude, model 7000smz-2; Campden Instruments, Loughborough, UK). Resulting tissue slices were subjected to chemical fixation, cryopreservation, or cell isolation. For chemical fixation, slices were exposed for 30min to 4 % paraformaldehyde (PFA)-containing phosphate-buffered saline (PBS) at room temperature (RT), washed three times in PBS, and then stored in PBS at 4°C. To cryopreserve tissue, each slice was placed flat in the bottom center of a cryo-mold (Tissue-Tek, 4566), immersed in a thin layer of optimal cutting temperature compound (OCT, Tissue-Tek, 4583). To fix the orientation and keep the slice flattened, an additional cryomold of the same size was placed on top of the tissue, before snap-freezing in liquid nitrogen. Frozen slices were stored at -80°C until cryosectioning. For cell isolation, tissue slices were stored at 4°C in cutting solution and warmed to RT before initiating cell isolation. Tissue slices were transferred to ‘enzymatic solution’ containing (in mM): KCl 20, KH2PO4 10, MgCl2 2, Taurin 20, glucose 10, l-glutamic acid potassium salt monohydrate 100, BDM 30, pH adjusted to 7.3 with KOH at 37°C. Tissue was digested for 12min with proteinase XXIV (concentration: 0.5mg/mL; Sigma-Aldrich, St. Louis, MO, USA) and further digested with Liberase TL Research Grade (concentration: 0.23mg/mL with 5μM CaCl2; Hoffmann-La Roche, Basel, Switzerland) for up to 45 min. To remove large tissue fragments, the cell suspension was filtered through a nylon mesh (pore size: 1mm x 1mm).  NM antibody labelling and FACS sorting FACS sorting was performed using a BD FACS Symphony S6 or FACSAria™ III Cell Sorter (BD BioSciences, Franklin Lakes, NJ, USA). The same gating and collection strategy was applied across all time points post-lesioning to ensure comparable cell type ratios. For each of the collected NM sample for 10x GEM generation, isolated cells were first blocked by the TruStain FcX™ Fc blocking antibody (Biolegend, 101319) for 15 min at 4°C. Cells were labeled for 30min at 4°C in dark with fluorophore-conjugated antibodies against various surface markers, including CD45-Pacific BlueTM (Biolegend, 103125), Ter119-APC/Cy7 (Biolegend, 116223), CD31-PE (Biolegend, 102507), CD146-PE (Biolegend, 134703), CD14-FITC (Biolegend, 123307) and CD11c-APC (Biolegend, 117309), together with the Zombie-NIR viability dye (BioLegend, 423105) which labels dead cells. All antibodies were diluted at 1:100 in FACS buffer [PBS with 10% fetal bovine serum (FBS, VWR, MDTC35-016-CV) containing 1% Penicillin-Streptomycin solution (P/S, 100U/mL, Gibco, 15140122)]. When performing FACS gating, half of the cells were collected from the Zombie-NIR and Ter119-negative gate (unbiased), and another half of the cells were collected from the enrichment gates (See Supplementary Figure 1a). Cells were sorted into FACS buffer-coated 1.5 mL tubes, each with 40μL of FACS buffer with 1:1000 diluted Murine RNase Inhibitor (New England Biolabs, M0314L). After collection. Cell counting was performed. In each sample, 10,000 cells from the unbiased tube and 10,000 cells from the enrichment tube were pooled together for 10x GEM generation.  Single nucleus isolation from mouse hearts For nucleus isolation, vibratome-cut cardiac slices were placed in MACS M-tubes (Miltenyi Biotec, 130-093-236), containing 1mL of nuclear staining buffer [PBS with 1% BSA (Miltenyi Biotec, 130-091-376) and 1:500 diluted (0.2U/μL) Murine RNase Inhibitor, pre-cooled to 4°C. The tube was placed into a gentleMACS Octo dissociator (Miltenyi Biotec, 130-096-427), and then dissociated with in-built protocol “Protein_01.01 M-tube”. The M-tubes then underwent pulse-spinning, were flushed with 1mL of nuclear staining buffer, and filtered through a 40-μm cell strainer (Falcon, 1172689). The eluates were collected in 50mL Falcon tubes, which were then centrifuged for 5 min in 500g, 4°C, break = 5. Supernatants were removed, and pellets were resuspended in 500μL of nuclear staining buffer.  Nuclei antibody labelling and FACS sorting Isolated nuclei from different time points were first labelled with 1:100 diluted PCM-1 antibody (MERCK, HPA023370) in nuclear staining buffer for 5 min at 4°C (NOT on ice), 1:100 diluted fluorophore-conjugated anti-Rabbit IgG secondary antibody (Biolegend, 406419) for additional 25 min, 4°C in dark. Samples then underwent centrifugation (5min, 500g, 4°C, break = 5), followed by multiplexing with CellPlex reagents according to the manufacturer’s instruction (10x Genomics, PN-1000261), resulting in time point specific labelling in each sample. After labelling, nuclei were washed with 2ml nuclear staining buffer and centrifuged (5min, 500g, 4°C, break = 5). Labelled nuclei from all time points were then pooled together in 1mL nuclear staining buffer containing 10μg/mL Hoechst 33,342 (Thermo Fisher Scientific, H3570), and underwent FACS sorting to enrich for Hoechst+ PCM-1+ nuclei. Enriched nuclei were collected in a 1.5mL tube pre-coated with nuclear staining buffer, containing 150μL of nuclear staining buffer with 1:100 diluted of Murine RNase Inhibitor. Within the collected nuclei, 10μL was stained with Trypan Blue solution (ThermoFisher, 15250061) at a ratio of 1:1, and was visually inspected under a light microscope (20x objective) to assess nuclei shape and morphology. If the majority of nuclei appeared to be intact (no visible disruption of nuclear membrane), this was followed by nuclear counting. 20,000 nuclei were used for 10x GEM generation.  Sample processing for sequencing In each sample, up to 20,000 sorted cells were loaded into GEM Chip (10x Genomics, PN-1000127) and encapsulated into emulsion droplets using the Chromium Controller (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instruction. cDNA library generation and amplification were performed with the protocol “Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)” according to manufacturer’s instructions (10x Genomics, PN-1000268 and PN-1000190). The prepared cDNA library was then sequenced on the Nextseq2000 platform (Illumina, San Diego, CA, USA). The CellRanger v6.1.1. pipeline was used to generate a digital gene expression matrix starting from raw data. For alignment and quantification of gene expression the reference transcriptome has been built using the mouse mm10-2020-A as reference genome. De-multiplexing of CellPlex barcodes into individual samples was performed by Seurat 46.
Library was performed according to the manufacter's instructions (single cell 3' v3.1 protocol, 10x Genomics). Briefly, cells/nuclei were resuspended in the maxter mix and loaded together with partitioning oil and gel beads inot the chip togenerate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to two cDNA samples, known as gene expression cDNA (GEX) and CellPlex cDNA (CMO), respectively, each contains and Illumina R1 primer sequence, unique molecular identifier (UMI) and the 10x Barcode. The pooled GEX cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and appropiate fragment size was selected with SPRIselect reagent for subsequent library construction. The CMO cDNA was directly amplifed by PCR and then was purified with SPRIselect reagent. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and sample index were added.

value: heart left ventricles

value: cardiomyocytes

value: wild type

value: LAD / sham


title: LAD + sham CM Day 1-56 snRNA-seq GEX

description: 10x Genomics


title: LAD + sham nonmyocytes Day56 scRNA-seq CMO

description: 10x Genomics

value: non-myocytes


title: GWAS CRISPR sample5


title: GWAS CRISPR sample4


title: LAD + sham nonmyocytes Day56 scRNA-seq GEX

description: 10x Genomics


title: LAD + sham nonmyocytes Day28 scRNA-seq CMO

description: 10x Genomics


title: LAD + sham nonmyocytes Day28 scRNA-seq GEX

description: 10x Genomics


title: Bulk ATAC seq, bone marrow, LPS, rep1

description: Library name: bonemarrow_LPS_rep1

value: Bone marrow

value: LPS


title: GWAS CRISPR sample3


title: GWAS CRISPR sample2


title: LAD + sham nonmyocytes Day7 scRNA-seq CMO

description: 10x Genomics


title: LAD + sham nonmyocytes Day3 scRNA-seq CMO

description: 10x Genomics


title: LAD + sham nonmyocytes Day7 scRNA-seq GEX

description: 10x Genomics


title: LAD + sham nonmyocytes Day1 scRNA-seq CMO

description: 10x Genomics


title: GWAS CRISPR sample1


title: LAD + sham nonmyocytes Day1 scRNA-seq GEX

description: 10x Genomics


title: Control 1

description:
Library name: Sample 1
FFPE Spatial transcriptome sequencing

value: Female


title: Vehicle-5

city: Guangzhou

first: Yijun

last: Zhu

state: Guangdong

address: Zhongshan Er Lu

institute: The First Affiliated Hospital of Sun Yat-sen University

description: Library name: sample11

data_processing:
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, sequencing was performed with an Illumina Novaseq 6000 /MGISEQ-T7 instrument.
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Use HISAT2 software to match data to the reference genome
The expression levels of the transcripts were quantified using FeatureCounts
The differential expression analysis of genes was performed using the differential analysis software DESeq2
Functional annotations and enrichment analysis use  GSEA(Gene Set Enrichment Analysis), GO (gene ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes)
Assembly: mm10
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted from the XXX(tissue) using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA).

value: colon


title: Zmiz1-KO-nd-4

type: RNA

city: Research Triangle Park

first: Francesco

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

description: Gene expression from Zmiz1-f/f uterus with no decidual striumulus

hyb_protocol: Five and one-half micrograms (5.5 ìg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using TAC Software.

label: biotin

label_protocol: One hundred nanograms (100 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

growth_protocol: Ovaries were removed and mice held for 10-14 days to allow endogenous hormones to clear.

extract_protocol: Trizol (Thermo Fisher) was used to isolate RNA from  uterine tissue according to the manufacturer’s protocol. Following chloroform extraction, RNA was prepared from the aqueous layer using the Direct-zol RNA Miniprep Kit (Zymo Research).

treatment_protocol: Mice were injected subcutaneously (sc) daily for 3 days with estradiol (Steraloids; 100 µl of 1 µg/ml estradiol in Sesame Oil (Sigma)), followed by 2 days with no injections, then daily sc injections of progesterone

value: no decidual strimulus


title: Zmiz1-KO-d-1

description: Gene expression from Zmiz1-f/f uterus 20 hours after decidual stimulus (intraluminal oil injection)

value: decidual strimulus


title: Zmiz1-KO-d-3

source_name: Zmiz1-f/f uterus 20 hours after decidual stimulus (intraluminal oil injection)


title: Zmiz1-KO-nd-5

source_name: Zmiz1-f/f uterus with no decidual striumulus


title: Zmiz1-flox-d-2


title: Zmiz1-KO-nd-3


title: Zmiz1-KO-d-2


title: Cryoablation CM batch1 Day 1-56 snRNA-seq CMO

description: 10x Genomics

value: Cryoablation


title: Cryoablation CM batch1 Day 1-56 snRNA-seq GEX

description: 10x Genomics


title: HBCx10 untreated, chemonaive tumor, biological rep 8

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description: Gene expression data from PDX untreated, chemonaive tumor

hyb_protocol: 15 µg of fragmented, biotin-labeled cRNA were hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array for 16 hours at 45°C in a GeneChip Hybridization Oven 640 (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: After hybridization, arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned with the Affymetrix GeneChip Scanner 3000 following the manufacturer’s standard protocols.

data_processing:
Raw Affymetrix CEL files were processed using the GCRMA (GC Robust Multi-array Average) algorithm implemented in the Bioconductor R package `gcrma`. The method performs background correction, quantile normalization, and summarization at the probe set level using the Affymetrix Human Genome U133 Plus 2.0 annotation. The resulting log2-transformed expression values were then exponentiated (2^value) and rounded to the nearest integer to obtain approximate transcript abundance values.
Integer values obtained by applying round(2^x) to log2-transformed GCRMA-normalized signal intensities, resulting in pseudo-counts approximating transcript abundance.

source_name: PDX untreated, chemonaive tumor

label_protocol: 500 ng of total RNA were used for cDNA synthesis and biotin labeling using the Affymetrix 3’ IVT Express Kit, according to the manufacturer's protocol.

growth_protocol: For PDX model, female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific-pathogen-free conditions. Mouse care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). In this study, we used a xenograft model generated from two primary triple-negative breast cancer  (HBCx10 and HBCx33) established previously at Institut Curie with informed consent from the patient.

extract_protocol: Total RNA was extracted from tumor samples using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent Bioanalyzer and samples with RIN > 7 were selected for downstream processing.

treatment_protocol: Mice were treated with various methods (Table S2): capecitabine (Xeloda; Roche Laboratories) at a dose of 540 mg/kg, orally 5 d/week, for 25 to 51 days (i.e. pCR); adriamycine (Accord) at 2 mg/kg, intraperitoneal (i.p.)  1×/21 days; cyclophosphamide (Baxter) at 100 mg/kg, i.p. 1×/21 days; cisplatin (Mylan) at 6 mg/kg, i.p. 1×/21 days; or carboplatine (Accord) at 90 mg/kg, i.p. 1x/21 days. Relative tumor volumes (mm3) were measured as described previously. Before downstream analysis, cell suspensions were prepared as previously described (7).

value: Breast

tag: disease

value: TNBC

tag: model

value: patient-derived xenograft (PDX)


title: Zmiz1-flox-d-4


title: Zmiz1-flox-d-5


title: Cryoablation CM batch2 Day 1-56 snRNA-seq CMO

description: 10x Genomics


title: Vehicle-2

description: Library name: sample8


title: Vehicle-3

description: Library name: sample9


title: Zmiz1-KO-nd-2


title: Cryoablation nonmyocytes Day56 scRNA-seq CMO

description: 10x Genomics


title: HBCx10 untreated, chemonaive tumor, biological rep 7


title: Cryoablation CM batch2 Day 1-56 snRNA-seq GEX

description: 10x Genomics


title: Vehicle-1

description: Library name: sample7


title: HA-9

description: Library name: sample6


title: HBCx10 untreated, chemonaive tumor, biological rep 6


title: Cryoablation nonmyocytes Day56 scRNA-seq GEX

description: 10x Genomics


title: Vehicle-4

description: Library name: sample10


title: Zmiz1-flox-d-1


title: Cryoablation nonmyocytes Day28 scRNA-seq CMO

description: 10x Genomics


title: Zmiz1-flox-nd-5


title: Zmiz1-flox-nd-4


title: HBCx10 untreated, chemonaive tumor, biological rep 5


title: Cryoablation nonmyocytes Day28 scRNA-seq GEX

description: 10x Genomics


title: NGO treated aGVHD patient's PBMC 4, CD3/28, IL-2 activated, 48h

city: Seoul

first: Aaron

last: Yu

address: Gwanak-ro 1

country: South Korea

institute: Seoul national university

description:
Library name: aGVHDNGO4
aGVHDNGO4

data_processing:
Differentially expressed genes were subjected to gene enrichment analysis with the R package clusterProfiler
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each example

source_name: peripheral blood

growth_protocol: hPBMCs were incubated with RPMI containing 10% FBS, 1X Antibiotic-Antimycotic

extract_protocol:
Total RNA was extracted and purified from hPBMCs studied in vitro using the TRIzol reagent. 100ng of total RNA was used to construct sequencing library
Libraries were generated using the SMARTer Stranded RNA-Seq Kit (Takara Bio USA, Mountain View, CA, USA) according to the manufacturer's protocol.

treatment_protocol: To evaluate the effect of NGO, 20 μg/mL of NGO were added to PBMCs for 48hr

value: peripheral blood

value: peripheral blood mononuclear cell

value: 20μg/mL of NGO, CD3/28 dynabead, 30U/mL of IL-2 for 48h


title: NGO treated aGVHD patient's PBMC 5, CD3/28, IL-2 activated, 48h

description:
Library name: aGVHDNGO5
aGVHDNGO5


title: HA-7

description: Library name: sample4


title: HBCx10 untreated, chemonaive tumor, biological rep 2


title: HBCx10 untreated, chemonaive tumor, biological rep 3


title: HA-8

description: Library name: sample5


title: NGO treated aGVHD patient's PBMC 3, CD3/28, IL-2 activated, 48h

description:
Library name: aGVHDNGO3
aGVHDNGO3


title: NGO treated nonGVHD patient's PBMC 4, CD3/28, IL-2 activated, 48h

description:
Library name: nonGVHDNGO4
nonGVHDNGO4


title: Cryoablation nonmyocytes Day7 scRNA-seq GEX

description: 10x Genomics

value: heart left ventricles


title: HBCx10 untreated, chemonaive tumor, biological rep 1


title: NGO treated nonGVHD patient's PBMC 5, CD3/28, IL-2 activated, 48h

description:
Library name: nonGVHDNGO5
nonGVHDNGO5


title: Cryoablation nonmyocytes Day7 scRNA-seq CMO

description: 10x Genomics

value: wild type


title: HA-11

description: Library name: sample2


title: Cryoablation nonmyocytes Day3 scRNA-seq CMO

description: 10x Genomics


title: NGO treated nonGVHD patient's PBMC 3, CD3/28, IL-2 activated, 48h

description:
Library name: nonGVHDNGO3
nonGVHDNGO3


title: HBCx10 treated with Anthracyclines, relapse tumor, biological rep 8

description: Gene expression data from PDX treated with Anthracyclines, relapse tumor


title: Cryoablation nonmyocytes Day3 scRNA-seq GEX

description: 10x Genomics


title: HBCx10 treated with Anthracyclines, relapse tumor, biological rep 6

source_name: PDX treated with Anthracyclines, relapse tumor


title: Cryoablation nonmyocytes Day1 batch2 scRNA-seq GEX

description: 10x Genomics


title: Cryoablation nonmyocytes Day1 batch2 scRNA-seq CMO

description: 10x Genomics


title: aGVHD patient's PBMC 4, CD3/28, IL-2 activated, 48h

description:
Library name: aGVHD4
aGVHD4

value: CD3/28 dynabead, 30U/mL of IL-2 for 48h


title: HBCx10 treated with Anthracyclines, relapse tumor, biological rep 7


title: HA-6

description: Library name: sample3


title: aGVHD patient's PBMC 3, CD3/28, IL-2 activated, 48h

description:
Library name: aGVHD3
aGVHD3


title: HBCx10 treated with Anthracyclines, relapse tumor, biological rep 5


title: Cryoablation nonmyocytes Day1 batch 1 scRNA-seq CMO

description: 10x Genomics

value: non-myocytes


title: Kidney, healthy, tamoxifen control (normoxia), SM1763

city: Zürich

first: Olga

middle: Maria

last: Lempke

address: Winterthurerstrasse 190

country: Switzerland

institute: Univeristy of Zurich

description:
Library name: tam5x_SM1763_ctrl
Fresh frozen tissue for Spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger to generate FASTQ files from BCL files.
Sequences were aligned to the mouse reference genome (mm10) using Space Ranger’s default settings.
Gene expression counts for RefSeq-annotated coding genes were quantified per cell using Space Ranger’s default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in matrix market exchange format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: aligned_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_impage.png: high-resolution image of tissue
Supplementary files format and content: tissue_lowres_impage.png: low-resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol:
Fixed kidney tissues were OCT embedded and frozen, 10 μm cryosections were cut using crytostat
Spatial transriptomics of mouse kidneys was performed according to the manufacturer's recommendations (Visium CytAssist for fixed frozen tissue; 10x Genomics, Pleasanton, CA, USA).

value: Kidney

tag: condition

value: Healthy

value: Normoxia


title: HA-10

description: Library name: sample1

value: colon


title: HBCx10 treated with Anthracyclines, relapse tumor, biological rep 4


title: nonGVHD patient's PBMC 5, CD3/28, IL-2 activated, 48h

description:
Library name: nonGVHD5
nonGVHD5


title: Kidney, healthy, 0.1% CO 4hrs (hypoxia), SO4157

description:
Library name: Exp45_SO4157
Fresh frozen tissue for Spatial transcriptomics sequencing

value: Hypoxia


title: Kidney, healthy, tamoxifen control (normoxia), SM1758

description:
Library name: tam5x_SM1758_ctrl
Fresh frozen tissue for Spatial transcriptomics sequencing


title: HBCx10 treated with Anthracyclines, relapse tumor, biological rep 3


title: RPS27A_2

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: QC

address: 3201 Jean-Mignault

institute: Université de Sherbrooke

description: NEBNext Single Cell/Low input RNA library Prep Kit

data_processing:
Reads were trimmed using fastp v0.23.2 with the following parameters "--qualified_quality_phred 30 --length_required 20 --cut_window_size 1 --cut_mean_quality 30 --cut_front --cut_tail" to remove adapters and low-quality reads.
The quality of the reads was assessed before and after trimming using FastQC v0.11.5.
The human transcriptome was generated from the human genome (GRCh38 assembly, v107 in Ensembl) using gffread (available from Cufflinks v2.2.1).
An index was created from this transcriptome using the "index" mode of Kallisto v0.48.3 and the following parameter "--kmer-size=31"
Trimmed reads were then pseudoaligned to this human transcriptome and quantified using the "quant" mode of Kallisto with the following parameters "--bias --bootstrap-samples=50"
Differential expression analyses were finally conducted at the gene-level using tximport v1.22.0 and DESeq2 v1.34.0, using the RPS27A condition as control.
Assembly: hg38
Supplementary files format and content: Comma-separated value (.csv) file containing the id, name, biotype, log2 fold change (with regards to the RPS27A condition), p-value, adjusted p-value and abundance in each sample (in TPM) for all the genes detected in the RNA-Seq.

source_name: HeLa

growth_protocol: HeLa cells (ATCC, USA) were grown in Dulbecco's Modified Eagle Medium (DMEM)

extract_protocol:
After immunoprecitipation, beads were then resuspended in 300 µl RLT buffer (Qiagen RNeasy kit, Qiagen, Germany) and the RNA was recovered using Qiagen RNeasy kit (Qiagen, Germany).
Each of the RNAseq libraries was generated from 50 ng of total RNA free of genomic DNA using the NEBNext Single Cell/Low input RNA Library Prep kit for Illumina (E6420S) and following the protocol for Low input
The resulting libraries were subjected to a total of 11 amplification cycles and then purified using Ampure XP 0.9X beads.

treatment_protocol: HeLa cells were transfected with HA-RPS27A-Myc or HA-RPS27AP5-Myc constructs and were incubated for 48 h.

value: HeLa

value: Epithelial

value: Transfected


title: nonGVHD patient's PBMC 3, CD3/28, IL-2 activated, 48h

description:
Library name: nonGVHD3
nonGVHD3


title: Kidney, healthy, 0.1% CO 4hrs (hypoxia), SK4156

description:
Library name: Exp45_SK4156
Fresh frozen tissue for Spatial transcriptomics sequencing


title: aGVHD patient's PBMC 5, CD3/28, IL-2 activated, 48h

description:
Library name: aGVHD5
aGVHD5


title: HBCx10 treated with Anthracyclines, relapse tumor, biological rep 2

value: Breast

value: TNBC


title: RPS27A_1


title: Kidney, healthy, FG-4592/roxadustat, SK9682

description:
Library name: Exp42_SK9682
Fresh frozen tissue for Spatial transcriptomics sequencing

value: roxadustat


title: HBCx10 treated with Anthracyclines, relapse tumor, biological rep 1

value: patient-derived xenograft (PDX)


title: NGO treated aGVHD patient's PBMC 2, CD3/28, IL-2 activated, 48h

description:
Library name: aGVHDNGO2
aGVHDNGO2

value: peripheral blood

value: peripheral blood mononuclear cell

value: 20μg/mL of NGO, CD3/28 dynabead, 30U/mL of IL-2 for 48h


title: Kidney, healthy, FG-4592/roxadustat, SK7543

description:
Library name: Exp42_SK7543
Fresh frozen tissue for Spatial transcriptomics sequencing


title: RPS27AP5_3


title: NGO treated aGVHD patient's PBMC 1, CD3/28, IL-2 activated, 48h

description:
Library name: aGVHDNGO1
aGVHDNGO1


title: HBCx10 treated with Anthracyclines, residual tumor, biological rep 8

description: Gene expression data from PDX treated with Anthracyclines, residual tumor


title: Cryoablation nonmyocytes Day1 batch 1 scRNA-seq GEX

description: 10x Genomics

value: heart left ventricles

value: wild type

value: Cryoablation


title: RPS27AP5_2


title: HBCx10 treated with Anthracyclines, residual tumor, biological rep 7

source_name: PDX treated with Anthracyclines, residual tumor


title: RPS27AP5_1


title: HBCx10 treated with Anthracyclines, residual tumor, biological rep 6


title: RPS27A_3


title: NGO treated nonGVHD patient's PBMC 1, CD3/28, IL-2 activated, 48h

description:
Library name: nonGVHDNGO1
nonGVHDNGO1


title: aGVHD patient's PBMC 2, CD3/28, IL-2 activated, 48h

description:
Library name: aGVHD2
aGVHD2

value: CD3/28 dynabead, 30U/mL of IL-2 for 48h


title: HBCx10 treated with Anthracyclines, residual tumor, biological rep 5


title: MLS 402-91

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

institute: University of Gothenburg

data_processing:
Data was processed using pipseeker (Fluent Biosciences)
Assembly: GRCh38
Supplementary files format and content: Files containing cell barcodes (barcodes.tsv), feature/gene names (genes.tsv), and raw gene counts for every gene and every cell (matrix.mtx). These files were output files from pipseeker.

growth_protocol: Cells were cultured in RPMI Glutamax cell culture media  supplemented with 5% fetal bovine serum, 100U/ml penicillin and 100 mg/ml streptomycin. Cells were kept in 37°C and 5% CO2

extract_protocol:
Cells were detached using StemPro Accutase and resuspended in cell media. Cells were further processed according to the PIPseq T2 protocol (Fluent Biosciences) where cells were resuspended in cell suspension buffer, counted and 5000 cells were forwarded to library construction.
Library construction was performed according to the PIPseq T2 protocol (Fluent Biosciences). Briefly, cells were mixed with template particles and PIPs (particle-templated instant partitions) were formed by vortexing. After lysis on a PIPseq dry bath and breaking of the formed emulsion, RNA was synthesized into cDNA and amplified according to Fluent Biosciences’ instructions. Subsequently, amplified cDNA was isolated from the PIPs before library preparation and 10 ng of amplified and purified cDNA was used. Fragmentation, end repair and A-tailing was performed according to Fluent Biosciences’ instructions followed by adapter ligation. After clean-up, index PCR was performed using dual illumna indexes. An addiotional clean-up step followed and quantification and quality control was assessed with Qubit and Agilent TapeStation analyses.

value: Myxoid liposarcoma cells


title: HBCx10 untreated, chemonaive tumor, biological rep 4


title: MLS 2645-94 p6

data_processing:
Alignment was performed using STAR version 2.7.9A using the ENSEMBL GRCh38 assembly reference genome
Gene expression was quantified using HTseq version 0.13.5
Assembly: GRCh38
Supplementary files format and content: counts.txt contains raw read counts generated by HTseq

growth_protocol: Myxoid liposarcoma cell lines (1765-92, 402-91 and 2645-94) were cultured in RPMI 1640 GlutaMAX with 5% fetal bovine serum and Ewing sarcoma cell lines (6647 and TC-71) were cultured in IMDM GlutaMAX with 10% fetal bovine serum, both media supplemented with 100 U/ml penicillin and 100 ug/ml streptomycin. Cells were passaged using 0.25% trypsin supplemented with 0.5 mM EDTA and maintained at 37°C and 5% CO2. EWS cells were cultured on collagen-coated T25 culture flasks while MLS cells were grown on non-coated flasks, all with cell culture media containing 0.0025% DMSO for 24h.

extract_protocol:
RNA was extracted using Qiagen miRNeasy micro kit including DNase treatment, according to the manufacturer’s instructions.
Library preparation was performed according to the Smart-seq2 protocol (Picelli et al., 2014) with some modifications.

value: Myxoid liposarcoma


title: HBCx10 treated with Anthracyclines, residual tumor, biological rep 4


title: aGVHD patient's PBMC 1, CD3/28, IL-2 activated, 48h

description:
Library name: aGVHD1
aGVHD1


title: nonGVHD patient's PBMC 4, CD3/28, IL-2 activated, 48h

description:
Library name: nonGVHD4
nonGVHD4


title: MLS 2645-94 p4


title: nonGVHD patient's PBMC 2, CD3/28, IL-2 activated, 48h

description:
Library name: nonGVHD2
nonGVHD2


title: HBCx10 treated with Anthracyclines, residual tumor, biological rep 3


title: C2_Spleen

city: Hong Kong SAR

first: Yating

last: XU

state: Hong Kong SAR

address: Tat Chee Avenue, Kowloon, Hong Kong SAR

institute: City University of Hong Kong

description: Library name: C2_Spleen

data_processing:
Sequencing reads alignment was performed by using HISAT2. Count aligned reads and quantification were calculated based on exon regions using FeatureCounts.
Assembly: Sequencing reads alignment was performed by using HISAT2. Count aligned reads and quantification were calculated based on exon regions using FeatureCounts.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Spleen

extract_protocol:
Total RNA was extracted from spleen and SI samples by homogenization in TRIzol reagent, followed by chloroform extraction and isopropanol precipitation. DNA was removed by DNase treatment (TURBO DNA-freeTM Kit).
Routine procedures of mRNA purification and library generation were performed by Novogene.

value: Spleen

value: control


title: C3_Spleen

description: Library name: C3_Spleen


title: MLS 2645-94 p3


title: nonGVHD patient's PBMC 1, CD3/28, IL-2 activated, 48h

description:
Library name: nonGVHD1
nonGVHD1


title: HBCx10 treated with Anthracyclines, residual tumor, biological rep 2


title: C1_Spleen

description: Library name: C1_Spleen


title: NGO treated nonGVHD patient's PBMC 2, CD3/28, IL-2 activated, 48h

description:
Library name: nonGVHDNGO2
nonGVHDNGO2


title: Whole blood, Male, Ctrl, rep6 [22-146]

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

description:
22-146
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt

data_processing:
*library strategy: Enzymatic methyl-seq (EM-seq)
Reads were filtered, trimmed, and deduplicated using fastp version 0.23.1 with default parameters.
Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104) and methyl calling were performed using Bismark. This process was implemented in the DRAGEN Methylation Pipeline,  which was run on an Illumina DRAGEN server using default parameters.
Differential methylation analysis was performed using MethylKit R package (version 1.20.0). Methylation calls were only retained if CpG sites had a minimum depth of 6 reads and were in at least 5 animals per group. Tiles were analyzed using 500 bp sliding windows with an overlap of 250 bp and a minimum of 5 CpGs per window. For each tile (i.e., region), a logistic regression model was fitted to calculate p-values. These p-values were then adjusted to q-values using the SLIM method, without correcting for overdispersion. Lambda methylation level in CpG context was added as covariate in the analysis to account for conversion rate disparity among samples, as well as age at sampling, dam and sire ID. Methylation differences were calculated as average methylation of choline treated calves minus average methylation of vehicle treated calves. Tiles were annotated using the AnnotePeak function on ChipSeeker R package (version 1.32.1).
Assembly: ARS-UCD1.2.104
Supplementary files format and content: A tab-delimited text file includes information about differential methylated regions, methylation level for each sample and annotation.

organism: Bos indicus

source_name: whole blood

growth_protocol: Whole blood samples were collected from the jugular vein of cows derieved from two groups of embyo

extract_protocol:
One mL of blood was sent to the Génome Québec sequencing platform for DNA extraction
DNA conversion step involves in three primary enzymes: TET2 and T4-BGT detect and transform 5mC and 5hmC into a product that cannot be deaminated by the APOBEC3A enzyme. Subsequently, APOBEC3A deaminates unmodified cytosines by converting them to uracils. As a result, unmethylated cytosines are transformed into uracils and then to thymines during PCR amplification, while methylated cytosines remain as cytosines

treatment_protocol: A control group of embryo cultured in 1.8mM sodium chloride and a treatment group of embryo cultured in 1.8mM choline chloride

value: whole blood

value: Male

value: Ctrl


title: HBCx10 treated with Anthracyclines, residual tumor, biological rep 1

value: Breast

value: TNBC


title: MLS 402-91 p5


title: HBCx33 untreated, chemonaive tumor, biological rep 7

value: patient-derived xenograft (PDX)


title: Whole blood, Male, Ctrl, rep5 [22-131]

description:
22-131
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: Vv3_4_Spleen

description: Library name: Vv3_4_Spleen

value: Vv3 infection


title: Vv3_3_Spleen

description: Library name: Vv3_3_Spleen


title: MLS 402-91 p4


title: Zmiz1-flox-nd-1

value: no decidual strimulus


title: HBCx33 untreated, chemonaive tumor, biological rep 6


title: Whole blood, Male, Ctrl, rep4 [22-103]

description:
22-103
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: Vv3_2_Spleen

description: Library name: Vv3_2_Spleen


title: HBCx33 untreated, chemonaive tumor, biological rep 5


title: Whole blood, Male, Ctrl, rep3 [22-095]

description:
22-095
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: C3_SI

description: Library name: C3_SI

source_name: Small intestine

value: Small intestine


title: MLS 402-91 p3


title: Whole blood, Male, Ctrl, rep2 [22-149]

description:
22-149
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: MLS 402-91 p2


title: HBCx33 untreated, chemonaive tumor, biological rep 4


title: C2_SI

description: Library name: C2_SI


title: MLS 2645-94 p2


title: Whole blood, Male, Ctrl, rep1 [22-171]

description:
22-171
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: HBCx33 untreated, chemonaive tumor, biological rep 3


title: MLS 1765-92 p6


title: MLS 1765-92 p5


title: Zmiz1-flox-nd-3

description: Gene expression from Zmiz1-f/f uterus with no decidual striumulus


title: Whole blood, Male, Choline, rep6 [22-145]

description:
22-145
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt

value: Choline


title: C1_SI

description: Library name: C1_SI


title: HBCx33 untreated, chemonaive tumor, biological rep 2

description: Gene expression data from PDX untreated, chemonaive tumor


title: HBCx33 untreated, chemonaive tumor, biological rep 1


title: Vv3_3_SI

description: Library name: Vv3_3_SI


title: Vv3_2_SI

description: Library name: Vv3_2_SI


title: MLS 1765-92 p3


title: Whole blood, Male, Choline, rep5 [22-138]

description:
22-138
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: MLS 1765-92 p4


title: Whole blood, Male, Choline, rep4 [22-096]

description:
22-096
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: HBCx33 treated with Cisplatin, relapse tumor, biological rep 7

description: Gene expression data from PDX treated with Cisplatin, relapse tumor


title: HBCx33 treated with Cisplatin, residual tumor, biological rep 7

description: Gene expression data from PDX treated with Cisplatin, residual tumor


title: EWS TC-71 p6

value: Ewing sarcoma


title: EWS TC-71 p4


title: HBCx33 treated with Cisplatin, relapse tumor, biological rep 6

source_name: PDX treated with Cisplatin, relapse tumor


title: Vv3_1_SI

description: Library name: Vv3_1_SI


title: Whole blood, Male, Choline, rep2 [22-177]

description:
22-177
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: Whole blood, Male, Choline, rep3 [22-129]

description:
22-129
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: Whole blood, Male, Choline, rep1 [22-162]

description:
22-162
Vehicle-male_vs_Choline-male_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: EWS TC-71 p3


title: HBCx33 treated with Cisplatin, residual tumor, biological rep 6

source_name: PDX treated with Cisplatin, residual tumor


title: Organoid_ATEM_2

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

description:
Library name: LX851_TX1025
ATEM_PTEM_organoid_validation_set.rds

data_processing:
Cellranger count v6.1.1
Assembly: mm10
Supplementary files format and content: 10X seurat objects containing raw and filtered counts

source_name: Tongue

growth_protocol: Tongues were collected from 20 BL/6 mice. CvP and FoP were collected using tweezers under stereomicroscope. Tissues were minced and treated with TrypLE containing 10 μM Y-27538 for up to 30 minutes. During the enzymatic digestion process, every 5 minutes, tissues were pipetted several times using a 1000 uL pipette tip. Single cells and small tissue clumps were collected in cold medium and fresh TrypLE + 10 uM Y-27538 was added to further digest the remaining tissues. In brief, 300 – 400 μL of 1 mg/mL collagenase/dispase solution was injected under the lingual epithelium using a 27G needle and tongues were incubated at 37°C for 20 to 25 minutes. Then, the epithelium was peeled off and digested with TrypLE containing 10 µM Y-27538 in the same manner as CvP and FoP tissues. ATEM and ATDM were collected and processed in the similar manner as the tissues. Single cells were washed twice with cold FACS buffer containing 1% FBS, 0.1 mM EDTA, and PBS. Cell pellets were resuspended in 500 μL cold FACS buffer, filtered through a 70 μm cell strainer and then through a 40 μm FACS tube. Cells were stained with 5 μM Draq5 (424101; Biolegend) and 1 μM 4′,6-diamidino-2-phenylindole (DAPI, D9542; Sigma-Aldrich) according to the manufacturer’s protocols. Viable single cells (Draq5+/DAPI-) were collected in PBS containing 1% BSA and 10 μM Y-27538 using the SH800S Cell Sorter (Sony Biotechnology, CA, USA). Cell numbers were counted using a hemocytometer before and after cells were washed with PBS containing 1% BSA and 10 μM Y-27538.

extract_protocol:
10X RNA sequencing
GEX 3'

value: Tongue

value: ATEM

value: various


title: HBCx33 treated with Cisplatin, relapse tumor, biological rep 5


title: Organoid_PTEM_2

description:
Library name: LX851_TX1026
ATEM_PTEM_organoid_validation_set.rds

value: PTEM


title: EWS 6647 p6


title: Whole blood, Female, Ctrl, rep5 [22-098]

description:
22-098
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt

value: Female


title: EWS TC-71 p2


title: HBCx33 treated with Cisplatin, residual tumor, biological rep 5


title: Organoid_PTEM_3

description:
Library name: LX851_TX1027
ATEM_PTEM_organoid_validation_set.rds


title: HBCx33 treated with Cisplatin, relapse tumor, biological rep 4


title: EWS 6647 p5


title: Whole blood, Female, Ctrl, rep4 [22-081]

description:
22-081
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: Organoid_PTEM_1

description:
Library name: LX649
ATEM_PTEM_organoid_discovery_set.rds


title: HBCx33 treated with Cisplatin, residual tumor, biological rep 4


title: Whole blood, Female, Ctrl, rep3 [22-163]

description:
22-163
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: Organoid_ATDM_1

description:
Library name: LX761
ATDM_organoid.rds
ATEM_ATDM_organoid.rds

value: ATDM


title: Organoid_ATEM_1

description:
Library name: LX650
ATEM_PTEM_organoid_discovery_set.rds
ATEM_ATDM_organoid.rds


title: Tissue_AT

description:
Library name: LX109
AT_PT_tissue_allcelltypes.rds
AT_PT_tissue_epithelialcells.rds
AT_tabula_tissue_epithelialcells_validation_set.rds


title: EWS 6647 p2


title: HBCx33 treated with Cisplatin, relapse tumor, biological rep 3


title: Whole blood, Female, Ctrl, rep2 [22-140]

description:
22-140
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt

value: whole blood


title: CreERT2 rep4

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

description:
Library name: Sample 8
6-8 weeks

data_processing:
Reads were mapped to mm10 using STAR v2.5.3.
Gene counts were generated using featureCounts v1.5.1.
Reads per kilo base per million (RPKM) normalised counts were calculated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values per sample

source_name: bone marrow

growth_protocol: Cells were cultured in Iscove’s modified Dulbecco’s medium with GlutaMAX containing 20% FBS, 50 μmol ml-1 2-mercaptoethanol, 100 IU ml-1 penicillin, 100 μg ml-1 streptomycin .

extract_protocol:
RNA was isolated using Machery Nagel RNA extraction kit according to manufacturer’s instructions.  Library construction of 280 ng total RNA for each sample was made using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) (Kapa Biosystems) using 10 cycles of PCR amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with tamoxifen(0.5 μmol/L) for 1 day.

value: bone marrow

value: primary murine pre-B

value: BCR-ABL1 transformed pre-B

value: Ctnnb1ex3fl/+ (C57BL/6)

value: Tamoxifen (0.5 μmol/L) for 1 day.


title: HBCx33 treated with Cisplatin, residual tumor, biological rep 3

value: Breast

value: TNBC

value: patient-derived xenograft (PDX)


title: CreERT2 rep3

description:
Library name: Sample 7
6-8 weeks


title: Cyp51_heart_rep1

city: Nanjing

first: Jimiao

last: Gao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

description:
Library name: Sample 3
10x Genomics

data_processing:
The raw FASTQ files were de-multiplexed and mapped to the mouse genome (mm10) using Cell Ranger (v.6.1.1) pipeline with default parameters. Cell filter, data normalization, and unsupervised analysis were carried out using the R package Seurat (v4.1.0) following its recommended steps34. In brief, genes expressed in less than 10 cells, and cells meeting any of the following criteria, were filtered out: mitochondrial genes >20%, unique molecular identifiers (<500 or >50000), and gene count (<500 or >6000). Doublets were detected and removed using the R package DoubletFinder (v2.0.3). The remaining data were then normalized and scaled using the SCT method. A subset of 30 significant PCs was selected using the Seurat ElbowPlot and JackStrawPlot functions. To correct for technical batch effects, we applied the Seurat integration method. Cell clustering and t-Distributed Stochastic Neighbor Embedding (tSNE) visualization were performed using the Seurat FindClusters (algorithm= Leiden) and RunTSNE functions. To identify specific genes for each cell cluster, we applied the Seurat FindAllMarkers function using the default parameters. The annotation of cell identities in each cluster was defined by the expression of known marker genes.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
E10.5 wild-type and homozygous CYP51A1I383V mouse embryos were isolated and dissected to obtain hearts. The hearts were washed for 2-3 times with DPBS pre-cooled at 4℃ and then was transferred to a new 1.5 mL centrifuge tube containing Collagenase II. Cell dissociation solution was transferred to a C tube containing enzymatic cell dissociation solution, and a gentleMACS Dissociator (Miltenyi Biotec) was used to digest the tissue. The resulting suspension was filtered using 70 or 40 µm Cell Strainer and centrifuged at 4℃. After removing the supernatant, the cell pellet was resuspended in 1 mL cell resuspension solution. Subsequently, 3 mL red blood cell lysis buffer was added, and the sample was incubated on ice for 2-10 min. To stop lysis, 6 mL DMEM containing 5% weight/volume FBS was added. Finally, after centrifugation at 4℃, the supernatant was discarded, and the pellet was resuspended in 1 mL of the abovementioned mixture for the first subsequent cell quality inspection. If any additional processing steps were performed, cell quality inspection was conducted again. After staining with AO/PI double fluorescent dye, cell quality was assessed using Countstar Rigel S2 to determine cell concentration, cell viability and cell clump. At the same time, Trypan blue staining was performed to evaluate cell morphology, cell concentration, cell fragments and impurities.
Follwing quality inspection, the concentration of single-cell suspensions was adjusted to 700-1500 cells/μL, and single cell capture and library construction were performed according to the instructions of the Chromium Next GEM Chip G Single Cell Kit (10x Genomics, PN-1000120) and Chromium Next GEM Single Cell 3ʹ GEM (Library & Gel Bead Kit v3.1, 10x Genomics, PN-1000121), respectively. For the single-cell suspensions, single-cell separation and cDNA synthesis were performed using the Chromium Controller (10x Genomics, GCG-SR-1). Next, cDNA was recovered using magnetic beads, followed by amplification and purification. Subsequently, cDNA quality inspection was conducted using Qubit 4.0% & dsDNA HS Assay (Thermo, Q32854) and Agilent 4150 & High Sensitivity D5000 Tape station to determine cDNA concentration and integrity, respectively. The 3′ Gene Expression Library was constructed using the quality-qualified cDNA based on Chromium Next GEM Single-Cell 3′ GEM protocol. The library was quantitatively examined after fragmentation, adaptor ligation and sample index PCR. Finally, the library pool was sequenced on the Illumina NovaSeq 6000 instrument using 150-bp paired-end reads.

value: heart

tag: developmental stage


title: Cyp51_heart_rep2

description:
Library name: Sample 4
10x Genomics


title: HBCx33 treated with Cisplatin, relapse tumor, biological rep 2


title: Whole blood, Female, Choline, rep6 [22-132]

description:
22-132
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt

value: Choline


title: Whole blood, Female, Ctrl, rep6 [22-206]

description:
22-206
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt

value: Ctrl


title: HBCx33 treated with Cisplatin, residual tumor, biological rep 2

description: Gene expression data from PDX treated with Cisplatin, residual tumor


title: CreERT2 rep2

description:
Library name: Sample 6
6-8 weeks


title: Whole blood, Female, Choline, rep5 [22-198]

description:
22-198
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: Wt_heart_rep2

description:
Library name: Sample 2
10x Genomics

value: wild-type


title: LAD + sham nonmyocytes Day3 scRNA-seq GEX

description: 10x Genomics

source_name: heart left ventricles

value: heart left ventricles

value: non-myocytes

value: wild type

value: LAD / sham


title: HBCx33 treated with Cisplatin, relapse tumor, biological rep 1

description: Gene expression data from PDX treated with Cisplatin, relapse tumor


title: Whole blood, Female, Choline, rep4 [22-082]

description:
22-082
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt

value: whole blood

value: Female


title: EWS 6647 p3

value: Ewing sarcoma


title: Wt_heart_rep1

description:
Library name: Sample 1
10x Genomics


title: Multiome, heart, ISO, ATAC

city: St. Louis

first: Douglas

last: Mann

address: 660 S Euclid Ave

institute: Washington University in St. Louis

description: Library name: Heart_ISO_ATAC

library_source: genomic single cell

data_processing:
Raw fastq files were aligned using CellRanger ARC to generate fragment files and aligned count matrices
Assembly: mm10
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz

source_name: Heart

extract_protocol:
Nuclei were extracted from hearts using the Chromium Nuclei Isolation kit (10x Genomics). For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns PN-1000283, Chromium Next GEM Chip J Single Cell Kit, 48 rxns PN-1000234, Single Index Kit N Set A, 96 rxns PN-1000212 (ATAC), Dual Index Kit TT Set A, 96 rxns PN-1000215 (3v3.1 GEX), were used.
Multiome 3v3.1 GEX and ATAC libraries were prepared as recommended by 10x Genomics (ChromiumNextGEM Multiome_ATAC_GEX_User_Guide_RevD). The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.

treatment_protocol: Female 10-wk old wild-type (C57BL/6J) mice were injected intraperitoneally with LPS (2.5 mg/kg), b-glucan (1 mg/mouse), 1 ug recombinant interferon-b1/10 ug recombinant interferon-y, or diluent. Mice were then euthanized 7 days later (n=3/group) with hearts collected and used for nuclei isolation and Multiome sequencing (10x Genomics).

value: Heart

value: Various

value: Wild-type

value: ISO


title: ERT2 rep4

description:
Library name: Sample 4
6-8 weeks

value: bone marrow

value: primary murine pre-B

value: BCR-ABL1 transformed pre-B

value: Ctnnb1ex3fl/+ (C57BL/6)

value: Control treated


title: HBCx33 treated with Cisplatin, residual tumor, biological rep 1

value: Breast

value: TNBC

value: patient-derived xenograft (PDX)


title: Whole blood, Female, Choline, rep3 [22-170]

description:
22-170
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt

value: Choline


title: Multiome, heart, ISO, GEX

description: Library name: Heart_ISO_RNA


title: HBCx33 treated with Capecitabine, relapse tumor, biological rep 7

description: Gene expression data from PDX treated with Capecitabine, relapse tumor


title: ERT2 rep3

description:
Library name: Sample 3
6-8 weeks


title: Whole blood, Female, Choline, rep2 [22-185]

description:
22-185
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt


title: Whole blood, Female, Ctrl, rep1 [22-139]

description:
22-139
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt

value: Ctrl


title: Multiome, heart, IFN, ATAC

description: Library name: Heart_IFN_ATAC

value: IFN


title: Whole blood, Female, Choline, rep1 [22-175]

description:
22-175
Vehicle-fem_vs_Choline-fem_CG_6r_tiles500_step250_migrp5_covariates_methdiff_tiles_methpercent_annot.txt

value: whole blood

value: Female


title: HBCx33 treated with Capecitabine, residual tumor, biological rep 7

description: Gene expression data from PDX treated with Capecitabine, residual tumor


title: mRNAseq_Flower_b3_rim-cr_rep2

city: La Jolla

first: Julie

last: Law

address: 10010 North Torrey Pines Rd

institute: Salk Institute for Biological Studies

description:
Library name: sample72
experiment batch3

data_processing:
Reads were mapped to the TAIR10 reference genome using STAR (v2.7.10a) allowing 2 mismatches and only uniquely mapped reads with the following options: --alignIntronMin 20 --alignIntronMax 6000 --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 and --alignMatesGapMax 7500. To facilitate expression quantification, Tag Directories were generated from the resulting bam files using the makeTagDirectory function of HOMER (v4.10) with the following options: -format sam -mis 2 and -unique. mRNA expression was quantified using the analyzeRepeats.pl function of HOMER (v4.10). A custom gtf file containing genes, transposons, and repeats was used for quantification with the option -condenseGenes to report the highest expressed transcript, and -noadj to report raw read count. UCSC format track files were generated using the makeUCSCfile function of HOMER (v4.10) with the following options: -fragLength given -norm 10000000 -style rnaseq and -strand both.
Assembly: TAIR10
Supplementary files format and content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

source_name: stage 12 and younger flower buds

extract_protocol:
Total RNA was extracted from flower buds (stage 12 and younger) using the Zymo Quick-RNA Miniprep Kit (R1055).
1 μg of DNase I treated total RNA was used for mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Cat# E7490L). Library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit (NEB, Cat# E7770L). Pooled libraries were sequenced using a 50 bp single-end kit (SE50) or paired-end kit (PE50) on the Illumina Nextseq 2000 or Novaseq X plus platforms.

value: stage 12 and younger flower buds

value: Columbia

value: rim-cr


title: Multiome, heart, LPS and b glucan, ATAC

description: Library name: Heart_LPSandbglucan_ATAC

value: Heart

value: Various

value: Wild-type

value: LPS and b glucan


title: ERT2 rep1

description:
Library name: Sample 1
6-8 weeks

value: bone marrow

value: primary murine pre-B

value: BCR-ABL1 transformed pre-B

value: Ctnnb1ex3fl/+ (C57BL/6)


title: mRNAseq_Flower_b3_rim-cr_rep1

description:
Library name: sample71
experiment batch3


title: Blood neutrophil, 0h, Healthy control, TNFalpha treated, replicate4

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

description:
Library name: TNF_4
Donor_5

data_processing:
Reads were aligned to the human genome (hg38) using Tophat (v2.04)
Counts were generated using featureCounts in R (v3.6.3) profiving the hg38 GTF file (iGenomes)
Assembly: hg38
Supplementary files format and content: Raw gene counts

source_name: Neutrophil

growth_protocol: Neutrophils were isolated from whole blood by centrifugation through density-gradient reagent (Polymorphprep). Erythrocytes were removed by hypotonic lysis with ammonium chloride buffer.

extract_protocol:
Trizol:chloroform extraction followed by Qiagen RNAeasy cleanup including on-column DNase digest
50bp Single-end reads

treatment_protocol: Neutrophils were suspended in RPMI 1640 media and processed immediately

value: Neutrophil

value: Healthy

value: 1h TNFalpha (10ng/mL)


title: HBCx33 treated with Capecitabine, residual tumor, biological rep 6

source_name: PDX treated with Capecitabine, residual tumor

value: Breast

value: TNBC

value: patient-derived xenograft (PDX)


title: CreERT2 rep1

description:
Library name: Sample 5
6-8 weeks

value: Tamoxifen (0.5 μmol/L) for 1 day.


title: Blood neutrophil, 0h, Healthy control, TNFalpha treated, replicate3

description:
Library name: TNF_3
Donor_4


title: Multiome, heart, LPS and b glucan, GEX

description: Library name: Heart_LPSandbglucan_RNA


title: HBCx33 treated with Capecitabine, relapse tumor, biological rep 5

source_name: PDX treated with Capecitabine, relapse tumor


title: mRNAseq_Flower_b3_WTco-seg_rep1

description:
Library name: sample69
experiment batch3

value: stage 12 and younger flower buds

value: Columbia

value: WT


title: HBCx33 treated with Capecitabine, residual tumor, biological rep 5


title: Blood neutrophil, 0h, Healthy control, TNFalpha treated, replicate2

description:
Library name: TNF_2
Donor_3


title: HBCx33 treated with Capecitabine, relapse tumor, biological rep 4


title: Blood neutrophil, 0h, Healthy control, TNFalpha treated, replicate1

description:
Library name: TNF_1
Donor_6


title: ERT2 rep2

description:
Library name: Sample 2
6-8 weeks

value: Control treated


title: mRNAseq_Flower_b1_rim22-3_rep2

description:
Library name: sample59
experiment batch1


title: HBCx33 treated with Capecitabine, residual tumor, biological rep 4


title: Blood neutrophil, 0h, Healthy control, IL-8 treated, replicate3

description:
Library name: IL8_3
Donor_3


title: mRNAseq_Flower_b1_rim22-3_rep1

description:
Library name: sample58
experiment batch1


title: HBCx33 treated with Capecitabine, relapse tumor, biological rep 3


title: Multiome, heart, IFN, GEX

description: Library name: Heart_IFN_RNA

value: Heart

value: Various

value: Wild-type

value: IFN


title: Multiome, heart, PBS, ATAC

description: Library name: Heart_PBS_ATAC

value: PBS


title: mRNAseq_Flower_b1_WTCol-0_rep2

description:
Library name: sample57
experiment batch1


title: HBCx33 treated with Capecitabine, relapse tumor, biological rep 6


title: Multiome, heart, PBS, GEX

description: Library name: Heart_PBS_RNA


title: HBCx33 treated with Capecitabine, residual tumor, biological rep 3


title: Blood neutrophil, 0h, Healthy control, IL-8 treated, replicate1

description:
Library name: IL8_1
Donor_1


title: mRNAseq_Flower_b1_WTCol-0_rep1

description:
Library name: sample56
experiment batch1


title: mRNAseq_Flower_b3_WTco-seg_rep2

description:
Library name: sample70
experiment batch3


title: Blood neutrophil, 0h, Healthy control, IL-1beta treated, replicate3

description:
Library name: IL1B_3
Donor_4

value: 1h IL-1beta (10ng/mL)


title: HBCx33 treated with Capecitabine, relapse tumor, biological rep 2


title: smRNAseq_Flower_b6_WT_rep3

library_source: other

data_processing:
For each sample, fastq files were trimmed using cutadapt (v1.18) with the -a AGATCGGAAGAGC option to remove the adapter sequence and the -m 15 option to discard reads shorter than 15 nt. Clean reads were then mapped to the TAIR10 reference genome using ShortStack (v3.8.5) allowing one mismatch (--mismatches 1). The --mmap f option was also included to assign multiple-mapped reads to a specific locus using the fractional-seeded algorithm. The resulting bam files were then filtered to keep perfectly mapped reads or reads with a single mismatch at the 3’ end using bamtools (v2.5.1) together with an in-house script (JSON_findPerfectMatches_and_TerminalMisMatches_v3) to meet the characteristics of Pol-IV transcription. To facilitate downstream analyses, the filtered bam files were used to generate Tag Directories using the makeTagDirectory function of HOMER (v4.10) with the following options: -format sam -mis 1 -keepAll. To quantify the expression of smRNAs with specific sizes, the tag directories were split by size (20nt-25nt) using a custom perl script (splitTagDirectoryByLength.dev2.pl) and all subsequent analyses utilized the Tag Directories corresponding to 24nt siRNAs.
Assembly: TAIR10
Supplementary files format and content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

molecule: other

growth_protocol: For transgenic lines that required drug selection, seeds were sterilized in sterilization buffer (70% ethanol, 0.05% SDS) for 10 minutes, followed by plating on half strength Linsmaier and Skoog medium (1/2 LS; Caisson Labs, Cat# LSP03) supplemented with 0.6% agar (Phyto Agar, Cat# P1003). The plates were placed in a 4˚C cold room for 4 days before growing in a growth chamber with 16h-light and 8h-dark cycles for 7 days. The seedlings were transplanted and grown under Salk greenhouse conditions. For HEM EMS lines, T-DNA insertion lines, and their corresponding control lines, seeds were stratified in 0.1% agar (Phyto Agar, Cat# P1003) at 4˚C for 4 days before sowing directly onto soil and grown under Salk greenhouse conditions. Approximately five weeks after planting, stage 12 and younger flower buds were collected and frozen in liquid nitrogen.

extract_protocol:
Total RNA extraction and smRNA enrichment was performed following a previously reported protocol. Briefly, 10 μg of total RNA extracted from flower buds (stage 12 and younger) were used for each smRNA library prep.
The smRNA-seq libraries were constructed using the NEBNext Small RNA Library Prep Kit (NEB, Cat# E7330L). The smRNA libraries were further purified using an 8% acrylamide gel and size selected (130-160 bp) relative to the O'RangeRuler 10 bp DNA Ladder (Thermo Scientific, Cat# SM1313). The size selected smRNA libraries were pooled for sequencing with single-end 50 bp kit (SE50) on Illumina Nextseq 2000 or Novaseq X plus platforms.

tag: cultivar

tag: batch

value: experiment batch6