title: Gast_37_72h_120h_Ribo

description:
Library name: Gastr38-2-4_Ribo
Ribosome Profiling from 72h and 120h gastruloids, Replicate 3

data_processing:
Bioinformatic analysis of single-cell sequencing data: Raw sequencing data in the form of BCL files, were demultiplexed using Illumina bcl2fastq v2.20 with default settings. Up to one mismatch in the sample barcode sequences was allowed. Resulting fastq files were processed using the BD Rhapsody Pipeline (version 1.9.1) hosted at the Seven Bridges’ cloud platform (https://www.sevenbridges.com/). A custom mouse reference genome, based on Gencode vM25 (GRCm38.p6), was generated and combined with the 669 sgRNAs sequences. Based on STAR aligner, a custom STAR reference genome was created and the Refined Putative Cell Calling option was disabled during the pipeline execution. For downstream analysis, unique molecular identifier (UMI) count data was corrected by BD Genomics Recursive Substitution Error Correction (RSEC).  Bioinformatic analysis of dial-out data: PCR dial-out data was processed using an in-house custom Python script as previously described. Three 9-nucleotide cell barcodes were extracted from the 97 possible barcodes from Read 1. Up to one mismatch was allowed for each barcode (Hamming distance of 1). The script retrieved the 8-nucleotide UMI sequences from Read 1 as per the BD manual. For valid barcodes, sgRNAs were identified in Read 2 by performing an exact match search for the 20-nucleotide sgRNA sequence. Following UMI deduplication sgRNA UMI counts per cell were computed. In case of multiple sgRNAs detected for an individual cell, specific sgRNA assignment was only performed if the cells UMI count exceeded the 99th percentile.  Processing of single-cell RNA sequencing data: The Scrublet Python package was used for duplet detection and removal on each individual sample. Expected doublet rates were adjusted based on estimates by the BD Rhapsody scanner. Genes expressed at least 5 cells were retained. Following filtering, 4 datasets from 2 different screen replicates were combined in Seurat using the Harmony package. Data from Cnot8 KO, Cnot7 KO and Control organoids comes from a single cartridge/whole transcriptome assembly, with no need for integration. Only cells containing detected sgRNAs and classified as singlets were selected for further analysis. Cells were filtered based on the following criteria: UMI counts > 500, UMI counts lower than the 0.99 quantile (to remove outliers) and mitochondrial gene content < 20%. Filtered datasets were then processed using Seurat’s standard pipeline.
Bulk RNA sequencing data analysis: Paired-end RNA-seq data was processed using the Nextflow RNA-seq pipeline (https://github.com/nf-core/rnaseq) version 3.14.0 as previously described. In short, the FastQC program was used for quality control, followed by quality and adapter trimming using TrimGalore. Read alignment was performed to the Gencode vM25 (GRCm38.p6) reference by STAR. Reads were quantified using Salmon. Quality control of analysis pipelines was done by MultiQC.    Ribosome profiling data analysis: UMI- tools in combination with a custom “regular expression pattern” were used to extract ribosome footprints from fastq files. Footprints above minimal length cutoff of 20 nt were extracted, along with sample barcode 5 nt in length. For further processing adapter sequences (AGATCGGAAG) were moved to the 7 nt UMI sequence of the fastq header. Removal of reads aligning to rRNAs and tRNAs was performed using bowtie2 v2.2.5. All remaining reads were aligned to the Gencode vM25 (GRCm38.p6) reference genome by STAR v2.7.11a allowing up to one mismatch (--outFilterMismatchNmax 1) and a maximum of 20 multimappers (--outFilterMultimapNmax 20). UMI deduplication of the aligned bam files was performed using the UMI-tools dedup command. Reads mapping to the CDS regions of the genome in forward strand were counted by featureCounts program.
Nanopore data bioinformatic analysis and poly(A) length estimation: Raw nanopore reads in .pod5 format were basecalled and mapped to the reference mouse genome GRCm38 (primary assembly, obtained from the GENCODE website) using the Dorado software [https://github.com/nanoporetech/dorado] version 0.8.3 with the model rna004_130bps_sup@v5.1.0. Dorado is the software package developed and supported by Oxford Nanopore Technologies for the processing of raw nanopore data obtained on their platform. Dorado uses a deep learning-based algorithm for basecalling (transforming nanopore current data to nucleotide sequence), minimap2 aligner [PMID: 29750242] for read alignment to the genome, and a separate heuristic algorithm for estimating poly(A) tail length in each read. Importantly, successfully estimated tail lengths are stored as the “pt:i” tags in the output .bam files, while the basecalled sequences of reads contain only short fragments of poly(A) tails which are not informative for actual length of the poly(A) tails. Identification of the poly(A) tails in the reads was configured to tolerate non-adenine gaps up to 3 nt in length: tail_interrupt_length = 3. We further retained only uniquely mapped reads with mapping quality above or equal to one (in minimap2 output, quality=0 indicates that a read is a multimapper that aligns equally well to more than one genomic loci) and present “pt:i” tag. In total, ~8.1 mln reads were retrieved from four samples (two bioreplicates for each of the two conditions: Cnot8 KO and Control), with ~1.7 to ~2.5 mln reads per sample. Read counting was performed by featureCounts.
For a subset of analyses, the WTA reads were aligned and quantified with STARsolo (STAR v2.7.11b) against the Gencode vM25 (GRCm38.p6) genome, using the BD Rhapsody bead cell-barcode and UMI configuration (CB_UMI_Complex mode with single-mismatch whitelist matching).
Assembly: Gencode Mouse vM25 (GRCm38.p6)
Supplementary files format and content: Comma-separated value files and matrix files with count numbers, *_counts.csv.gz files contain Cell Barcode, Gene Symbol and RSEC adjusted counts.
Supplementary files format and content: Some single-cell WTA gene-expression matrices are provided in the standard STARsolo output format - three files per sample: *_matrix.mtx.gz (genes x cells, integer UMI counts) with *_barcodes.tsv.gz (composite cell barcodes) and _features.tsv.gz (Ensembl gene ID, gene symbol, feature type). Dial-out sgRNA files (_DO.csv.gz) give the per-cell sgRNA assignment with columns: cell_barcode, cell_index, sgRNA, umi_count, sgrna_detected.
Library strategy: Ribo-Seq


title: C3

status: Public on Jul 13 2026

type: SRA

city: Zhanjiang City

first: Xiao

last: Wang

state: Guangdong Province

address: No. 57 South Renmin Avenue

country: China

institute: Affiliated Hospital of Guangdong Medical University

description: Library name: C3

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count and FPKM value for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: elective abortion of natural pregnancy as the control group

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

tag: tissue

value: Endometrial Villi

tag: treatment


title: Gast_37_48h_96h_Ribo

city: Schlieren

first: Ataman

last: Sendoel

address: Wagistrasse 12

department: Institute of Regenerative Medicine

country: Switzerland

institute: University of Zurich

description:
Library name: Gastr38-1-3_Ribo
Ribosome Profiling from 48h and 96h gastruloids, Replicate 3

library_source: other

molecule: other

organism: Mus musculus

source_name: Gastruloids

growth_protocol: Mouse embryonic stem cell culture: The dual T/Brachyury-mCherry, SOX1-GFP reporter (SBR) mouse ES cell line was cultured in in tissue culture treated 6 well plates (Thermo Scientific, 140675), in DMEM with Glutamax (Gibco, 7001569) supplemented with 10% FCS (XXX), Penicillin-Streptomycin (100U/ml, 100µg/ml respectively), non-essential amino acids (0.1 mM, Gibco, 11140050), sodium pyruvate (1mM, Thermo Scientific, 11360070), , beta-mercaptoethanol (0.11 mM, Gibco, 21985023) , 3 µM CHIR99021 (SML1046), 1 µM PD0325901 (S1036), 100u/mL LIF (produced in house). Cells were split every 48-72h, by accutase treatment followed by centrifugation at 200 g, 4min and seeding between 75 000 and 150 000 cells per well.

extract_protocol:
Gastruloids were generated as described previously. In short, murine embryonic stem cells (mESCs) are washed twice with PBS, followed by a detachment using Accutase (AT-104) for 4 min at 37C, 5% CO2. Cells were collected in 4.5 ml of embryonic stem cell medium with 10% fetal calf serum. Cells were centrifuged 200xg, 4min, 4°C and then resuspended in 10 ml PBS, followed by a second spin and PBS wash. Finally, cells were resuspended in 1 ml of N2B27 and counted using a hemocytometer. 40 µl of N2B27 with 300 cells per well were seeded in low adhesion 96 well plates (CLS7007-24EA) and incubated for 48h at 37C, 5% CO2. After 48 hours gastruloids were pulsed with 150uL of N2B27 supplemented with 3uM CHIR99021 (SML1046-5MG). Medium was refreshed using N2B27 every 24 hours for the extend of culture (between 120-144h). 120h gastruloids were harvested using P1000 cut-tips and subjected to single cell sequencing. In short gastruloids were collected in 15 ml tubes, washed once with PBS and incubated with accutase for 15 mins at 37C. Cell suspensions were resuspended using low adhesion tips and centrifuged 200xg, 4min, 4C. For sorting, cells were resuspended in FACS buffer (2% FCS and 0.5 ng/ul DAPI in PBS), passed through a 35 µm filter cap into 5 ml FACS tubes and sorted for GFP+ populations using a BD FACSAria III cell sorter using a 70 µM nozzel. Sorted cells were then spun down 15 min at 400xg, 4°C and then resuspended in BD sample buffer. Unsorted gastruloids were harvested and processed the same way, resuspended in sample buffer and then passed through 35 µm cell filters 3 times. Single cell suspensions were prepared for sequencing using the BD Rhapsody Single-Cell Analysis System with the BD Rhapsody Cartridge Kit (633733). Bead based reverse transcription, amplification and sequencing library production was performed following manufacturer’s instructions (BD Biosciences, doc ID: 210967 rev. 2.0).                                                                   Samples for Nanopore direct RNA-seq: Samples for Nanopore direct RNA-sequencing were harvested at 72 h of gastruloid development. Gastruloids were harvested using cut P1000 tips, collected in 15 ml tubes and washed 2 times in PBS+CHX. Supernatant was removed, and organoids were flash frozen in liquid nitrogen. Frozen organoids were then resuspended in ribosome lysis buffer (1x mammalian polysome buffer, 1mM DTT, 1% TritonX-100, 0.5%NP40, 25U/µL Turbo DNase, 100µg/mL CHX), incubated for 5 min on ice, followed by 5 min spin at 20 000 g at 4°C. Supernatant was collected and flash frozen in liquid nitrogen, before being stored at -80 °C before downstream processing.                    Samples for ribosome profiling: Ribosome profiling experiments were performed as previously described, with minor modifications for gastruloids. In short, gastruloids were harvested at indicated time points using cut P1000 tips and collected into 15 ml tubes. Gastruloids were washed 2 times in PBS+CHX, supernatant was removed, and organoids were flash frozen in liquid nitrogen. Frozen organoids were then resuspended in ribosome lysis buffer (1x mammalian polysome buffer, 1mM DTT, 1% TritonX-100, 0.5%NP40, 25U/µL Turbo DNase, 100µg/mL CHX), incubated for 5 min on ice, followed by 5 min spin at 20 000 g at 4°C. Supernatant was collected and flash frozen in liquid nitrogen, before being stored at -80 °C before downstream processing. Samples for RNA degradation: Gastruloids at 96 h of development were treated with 10 µM Actinomycin D (ThermoScientific, 11805017) in N2B27 and gastruloids were harvested after 0, 2 and 4 h of treatment. Gastruloids were harvested at indicated time points using cut P1000 tips and flash frozen. Frozen organoids were then resuspended in ribosome lysis buffer without cyclohexamide (1x mammalian polysome buffer, 1mM DTT, 1% TritonX-100, 0.5%NP40, 25U/µL Turbo DNase), incubated for 5 min on ice, followed by 5 min spin at 20 000 g at 4°C. Supernatant was collected and RNA was purified using the DirectZol RNA kit. Purified RNA was submitted for library preparation and sequencing to Novogene.
Reverse transcription from beads and sequencing library production was carried out according to the manufacturer’s instructions (BD Biosciences, doc ID: 210967 rev. 1.0). Library construction protocol for RNA-seq: RNA was isolated from lysates gastruloids at indicated time points as described in the Ribosome profiling section using TRIzol®  LS Reagent (Invitrogen, 10296028) and column purified with a Direct-zol RNA MiniPrep kit (Zymo Research, R2052). Libraries were prepared and sequenced at Novogene. Library construction protocol for Other:  As previously described, the sgRNA-containing region was amplified from the BD Rhapsody beads using a nested KAPA Polymerase reaction. In the first polymerase reaction (PCR1), the Rhapsody beads from each separate cartridges were resuspended and distributed into 4 separate 50 µL reactions  (100 µl KAPA HiFi HotStart ReadyMix (Roche 07958935001), 6 µl forward primer (5′-ACACGACGCTCTTCCGATCT-3′, 10 μM), 6 µl reverse primer (5′-TCTTGTGGAAAGGACGA-3′, 10 μM), 12 μl Bead RT/PCR Enhancer reagent from BD Biosciences and 72 μl nuclease-free water for a total volume of 200 μl). PCR1 conditions were as follows: initial denaturation at 95 °C for 5 min, followed by 25 cycles of denaturation 95 °C for 30 s, annealing 53 °C for 30 s, extension 72 °C for 20 s and a final extension of 10 min at 72 °C. The 4 x 50 µl PCR1 product was pooled, and beads were removed using a magnet. Amplicons were cleaned up using Agencourt AMPure XP beads (Beckman Coulter, A63881) following manufacturer’s instructions. 3 μl of cleaned up PCR1 was used as template for PCR 2 (25 µL KAPA HiFi HotStart Ready Mix, 2 μl forward primer (5′-ACACGACGCTCTTCCGATCT-3′, 10 μM), 2 μl reverse primer (CAGACGTGTGCTCTTCCGATCTCTTGTGGAAAGGACGAAACA*C*C*G-3′, 10 μM), 18 μl nuclease-free water) for a total volume of 50 μl. PCR2 conditions were as follows: initial denaturation at 95 °C for 3 min, followed by 10 cycles of denaturation 95 °C for 30 s, annealing 60 °C for 3 min, extension 72 °C for 60 s, and a final extension of 5 min at 72 °C. Agencourt AMPure XP beads were used to clean up PCR2 product according to the manufacturer’s instructions  before the indexing PCR. Indexing PCR was performed according to BD Biosciences ‘mRNA Targeted Library Preparation’ protocol (doc ID: 210968 rev. 3.0). Library construction protocol for Ribo-seq: Ribosome profiling was conducted with some adjustments of the original method (64, 65). For RNA digestion, cell lysates were incubated with 1 U/µg of RNase 1 (Epicentre/Lucigen, 10U/µL) for 45 minutes at room temperature. Reaction was stopped by adding 4 µL of SUPERase Inhibitor (20 U/µL, SUPERase-InTM RNase Inhibitor Thermo Scientific AM2694). To eliminate free nucleotides and isolate ribosome-protected fragments, the RNase I-treated samples were processed using Amersham MicroSpin S-400 HR columns (Cytiva, 27514001). RNA extraction was performed utilizing TRIzol® LS Reagent (Invitrogen 10296028) in combination with the Direct-zolTM RNA MiniPrep kit (Zymo Research, R2052). Total RNA concentration was measured using QubitTM RNA broad range kit (Invitrogen, Q10210). Ribosome footprints were excised and extracted from a 15% TBE-UREA gel (Invitrogen, EC68852BOX) using the 20nt, 22nt, 27nt, 30nt and 60nt oligonucleotides mix as markers (1 µL of 10 µM dilution in 19µL RNase-free H2O). Extraction was performed overnight with RNA extraction buffer (300mM NaOAc pH=5.5, 1mM EDTA, 0.25% v/v SDS). T4 PNK (NEB, M0201S) end-healing reaction was performed on the ribosome footprints for 1 hour at 37˚C. Linker ligation reaction followed using T4 RnI truncated K227Q (NEB, M0351L) in combination with 20 µM of preadenylated linker for 3 hours at 22˚C (50% w/v PEG-8000, 10X T4 RNA ligase, preadenylated linker, T4 RnI truncated K227Q). Ribosomal RNA was depleted using biotinylated rRNA depletion oligos (2 µM) by mixing 10 µL of sample with 10 µL of oligo mix and incubated for 2 minutes at 80˚C, followed by a gradual decrease in temperature to 25˚C. MyOne Streptavidin dynabeads (Life Technologies, 65001) were used to recover the samples. Reverse transcription was performed on the Ribosomal RNA-free samples using SuperScriptTM IV Reverse Transcriptase (Invitrogen, 18090050). Footprints were excised and extracted from a 15% TBE-UREA gel. Extraction was performed overnight with DNA extraction buffer (10mM Tris-HCl pH=8, 300mM NaCl, 1mM EDTA). cDNA was circularized using CircLigase II (100 U/µL, Biosearch, CL4115K) for 1 hour at 60˚C. cDNA was amplified using Phusion High-Fidelity DNA polymerase (Thermo Scientific, F530S) using an individual index per sample. 6-12 cycle amplicons were visualized using an 8% TBE non-denaturing polyacrylamide gel to determine optimal cycle number. PCR was carried out with 7-9 cycles and analyzed on an 8% TBE non-denaturing polyacrylamide gel (Invitrogen, EC61252BOX). DNA was excised from gel and extracted using DNA extraction buffer by incubating overnight with gentle shaking. DNA was recovered and precipitated in 10 mM Tris-HCl pH=8. DNA was quantified using Qubit TM 1X dsDNA High Sensitivity Assay (Invitrogen, Q33230) and quality was verified using the Bioanalyzer High Sensitivity DNA kit (Agilent, 5067-4626). Samples were pooled and prepared for sequencing.               Nanopore direct RNA-seq: RNA was isolated from ribosome profiling lysate buffer lysates using Direct-zol RNA Kit, according to manufacturer’s instruction. Nanopore direct RNA-sequencing library preparation was performed using the Direct RNA Sequencing Kit (SQK-RNA004) according to manufacturer’s instructions. Samples were loaded onto MinION flow cells (FLO-MIN114).

value: Gastruloids

tag: cell line

value: SBR

tag: cell type

value: mESCs/gastruloid cells


title: Gast_37_72h_120h_Ribo2

description:
Library name: Gastr37-2-4_Ribo2
Ribosome Profiling from 72h and 120h gastruloids, Replicate 2


title: C1

description: Library name: C1

value: elective abortion of natural pregnancy as the control group


title: Gast_37_48h_96h_Ribo2

description:
Library name: Gastr37-1-3_Ribo2
Ribosome Profiling from 48h and 96h gastruloids, Replicate 2


title: C2

description: Library name: C2


title: ICH5

city: Chongqing

first: yuhao

last: duan

address: No. 136 Zhongshan 2nd Road, Yuzhong District

department: School of Pediatrics

institute: Children's Hospital of Chongqing Medical University

description:
Library name: ICH5
ICH Brain group, replicate biosample 5

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: gene count for each Sample

source_name: brain

value: brain

value: ICH Brain


title: Gast_36_72h_120h_Ribo

description:
Library name: Gastr36-2-4_Ribo
Ribosome Profiling from 72h and 120h gastruloids, Replicate 1


title: Gast_36_48h_96h_Ribo

description:
Library name: Gastr36-1-3_Ribo
Ribosome Profiling from 48h and 96h gastruloids, Replicate 1


title: ICH4

description:
Library name: ICH4
ICH Brain group, replicate biosample 4


title: Ezh2 KO1

status: Public on Jul 15 2026

city: 合肥

first: 曹硕

last: 曹

state: 安徽

address: 九龙路

institute: 安徽大学

description:
Library name: SAMPLE7
Ezh2_KO_Ezh2_KO_FRAS200000130-1a

data_processing:
RNA Sequencing and Differentially Expressed Genes Analysis.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: mm10
Supplementary files format and content: tsv file of raw counts

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: stem cell


title: TAMs from AMPKfl/flLyz2cre/cre mice replicate 3

city: Beijing

first: Huan

address: 38 Life Science Park Road

institute: National Center for Protein Sciences, Beijing

description: Library name: KO-3

data_processing:
All samples passed quality control based on the results of FastQC.
Reads were aligned to the mouse genome assembly mm10.GRCm38 using HISAT2.
The aligned reads were counted using FeatureCounts.
Differentially expressed genes were determined with DESeq2 program
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tumor

extract_protocol:
Total RNA was isolated with RNeasy plus Mini Kit (Qiagen) according the manufacturer's protocol.
Library preparation was performed with Hieff NGS™ Ultima Dual-mode RNA Library Prep Kit according the manufacturer's protocol.

value: Tumor

value: TAM

tag: genotype

value: Non


title: Resistant,Panicle,high night temperature,inoculated B.glumae,rep 2

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

country: USA

institute: University of Nebraska-Lincoln

description: Library name: R_HT_P2

data_processing:
RNA-Seq reads were first trimmed with Trim Galore version 0.6.4 (Krueger, 2019; Martin, 2011) which includes filtering reads shorter than 30 bp and low-quality ends from reads (Phred score: <20) and the option of removing reads with Ns. The quality of reads before and after trimming was confirmed using FastQC version 0.12.1 (Andrews, 2019)
The filtered reads were then aligned to the Oryza sativa Japonica genome (EnsemblPlants IRGSP-1.0; GCA_001433935.1) using STAR version 2.7.10b (Dobin et al., 2013) with default parameters and --sjdbOverhang of 149. The alignment files generated by STAR were then used to generate gene counts using Subread version 2.0.0 (featureCounts), with default parameters (Liao et al., 2014). A data matrix of gene counts for all samples was created using a custom Python script, which was used for further differential gene expression analysis
Differential gene expression analysis was performed separately for the resistant and susceptible accessions using DESeq2 version 1.38.3 (Love et al., 2014). A Wald test was employed to calculate p-values, and genes with a Benjamini-Hochberg adjusted p-value less than 0.05 and a log2 fold change greater than 1 were considered differentially expressed
Assembly: EnsemblPlants IRGSP-1.0; GCA_001433935.1
Supplementary files format and content: A tab-delimited data matrix of raw feature counts with features (genes) in rows and sample names in columns.

organism: Oryza sativa

source_name: panicle

growth_protocol: The selected accessions were grown until heading stage in the greenhouse.

extract_protocol:
Panicles were ground using 1600 MiniG® automated tissue homogenizer (Spex Sample Prep, Metuchen NJ), and total RNA was extracted using Trizol reagent (Life Technologies, Carlsbad, CA). RNA was precipitated with 5M Potassium Acetate pH 5.2, and 100% ice-cold ethanol and air-dried. RNA pellets were resuspended in 20 µl of RNAse-free water
RNA purity and integrity was evaluated using the ExperionTM Automated Electrophoresis system (BioRad, Hercules, CA).  RNA sequencing was performed by Novogene (Davis, CA) for 150 bp paired-end read sequencing on the Illumina PE250 platform

treatment_protocol: Emerging panicles were inoculated with B. glumae (Pathogen, P) or treated with water (Mock, M) and maintained at normal night temperature (22C) and high night temperature (28C) conditions for 3 days.

value: panicle

value: B.glumae inoculation


title: TAMs from AMPKfl/flLyz2cre/cre mice replicate 2

description: Library name: KO-2


title: TAMs from AMPKfl/flLyz2cre/cre mice replicate 1

description: Library name: KO-1


title: ICH3

description:
Library name: ICH3
ICH Brain group, replicate biosample 3


title: ICH2

description:
Library name: ICH2
ICH Brain group, replicate biosample 2


title: ICH1

description:
Library name: ICH1
ICH Brain group, replicate biosample 1


title: Control5

description:
Library name: Control5
control group, replicate biosample 5

value: control


title: TAMs from AMPKfl/fl mice replicate 3

description: Library name: WT-3

value: AMPKfl/fl


title: TAMs from AMPKfl/fl mice replicate 2

description: Library name: WT-2


title: Control4

description:
Library name: Control4
control group, replicate biosample 4


title: Control3

description:
Library name: Control3
control group, replicate biosample 3


title: 60% HFD plus 0.25% HDCA

city: Chiba

first: Eunyoung

last: Lee

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

department: Department of Medical Physiology

country: Japan

institute: Chiba University, Graduate School of Medicine

description:
Library name: sample3
10× Genomics

library_source: transcriptomic single cell

data_processing:
The cDNA was enzymatically fragmented, end-repaired, size-selected, and ligated with adaptors. Libraries were indexed through PCR, size-selected again, and quality-assessed. Sequencing was performed on a NovaSeq 6000 (paired-end) to capture 10× barcodes and UMI (R1), sample indices (I7), and transcripts (R2).
The data were processed using 10× Genomics Cell Ranger software for demultiplexing, alignment to mm10, UMI counting, and quality control.
Assembly: Mouse mm10
Supplementary files format and content: features, matrix files

source_name: Primary hepatocytes

extract_protocol:
Single-cell hepatocytes were prepared using the collagenase perfusion method.
The scRNA-seq libraries were prepared using 10× Genomics Chromium Next GEM single-cell 3ʹ reagent kits. Cell suspensions were loaded onto the 10× Genomics Chromium Controller to generate gel beads in emulsion (GEM) for polyA cDNA synthesis with cell barcodes and unique molecular identifiers (UMI). GEMs were broken, and single-stranded cDNA was cleaned with DynaBeads, amplified, and assessed for quality using an Agilent TapeStation.

treatment_protocol: Primary hepatocytes were isolated from WT mice fed different diets (ND, HFD, or HFD+HDCA).

value: Primary hepatocytes

value: WT


title: TAMs from AMPKfl/fl mice replicate 1

description: Library name: WT-1


title: Control1

description:
Library name: Control1
control group, replicate biosample 1


title: Control2

description:
Library name: Control2
control group, replicate biosample 2


title: 60% HFD

description:
Library name: sample2
10× Genomics

value: 60% HFD


title: WSN13_3h

city: Xiamen

first: Xing

last: Xu

address: 422, Siming South Road

institute: Xiamen University

description:
Library name: WSN13_3h
expression matrix (txt) and original file (fastq)

data_processing:
The source code for the analysis of scBiopsy-seq is available on github (https://github.com/Linshiyan-Thea/scBiopsy-seq).
Assembly: GRCh38,GRCh38.105, GRCm38 and GRCm38.102
Supplementary files format and content: matrix files

molecule: polyA RNA

source_name: lung

extract_protocol:
The capillary tip was filled with 1.5 μL of mixed solution (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP (AD101–12, TransGen Biotech, Beijing, China), 0.4 U·μL−1 Murine RNase Inhibitor (GMP4102PA-01, Vazyme Biotech Co., Ltd., Nanjing, China)), and then connected to the work electrode of the ultra-micro extraction instrument (Rayme Biotechnology Co., Ltd., Jiangsu, China). The counter electrode and the reference electrode were immersed in the culture medium within the confocal dish. The cells to be extracted were visualized by microscope and the preloaded capillary was gradually moved downward until it touched the cytoplasm of the selected cell. The tip of the capillary was then inserted into the cytoplasm, with a deformation observed in the selected cell. By setting the applied voltages and the duration of current application, a precisely controlled volume was extracted from the cell. After that, the capillary was retracted out of the cell, taken out of the extraction instrument and placed at -80°C for RNA storage.
Once it was required to undergo the RNA library construction, the capillary was connected to the work electrode again. The cellular contents within the capillary were injected into the top plate of the DMF device, enabling the subsequent RNA library processing on the DMF system. The lysis buffer (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP, 0.4 U·μL−1 Murine RNase Inhibitor and 0.2% Triton-X-100(A110694, Sangon Biotech, Shanghai, China) was introduced and mixed with the cellular contents at 72°C for 3 minutes for complete RNA release. Then the reverse transcription (RT) mix (1.7 μM biotinylated-TSO oligo, 5 × HiScript II RT buffer (Vazyme Biotech Co., Ltd., Nanjing, China), 1.7 U·μL−1 Murine RNase Inhibitor, 19 U·μL−1 HiScript II Reverse Transcriptase (R201, Vazyme Biotech Co., Ltd., Nanjing, China) and 0.05% Pluronic F68 (24040032, ThermoFisher, America)) was introduced to initiate the RT reaction at 42°C for 90 minutes, which was stopped by heat at 70°C for 15 min. After that, the PCR mix (2 × KAPA HiFi HotStart ReadyMix (KK2602, KAPA, America), 0.06 μM Biotinylated-ISPCR oligo and 0.05% Pluronic F68) was introduced to amplify the cDNAs (95°C 3 minutes, 25 cycles of 98°C 30 s, 65°C 45 s and 72°C 6 minutes, followed by a final step at 72˚C for 5 min). The products were recovered from the DMF device into a 200-μL eppendorf tube, purified with 0.6 × DNA clean beads (Vazyme Biotech Co., Ltd., Nanjing, China) and quantified by qubit 3.0. Then 1 ng of the products were utilized and processed by sequencing-ready library construction kits (TD503, Vazyme). The library was purified twice with 0.6 × DNA clean beads (N411, Vazyme Biotech Co., Ltd., Nanjing, China) and sequenced by Novaseq500 according to the manufacturer’s instructions.

treatment_protocol: The cellular contents of SW480 cells were extracted initially prior to the ARV771 treatment, designated as the sample at 0 h. Immediately thereafter 250 nM ARV771 was added to the culture medium, and the cells were extracted at 1 h and 4 h.

value: lung

value: Non-small cell lung cancer cell lines


title: ND

description:
Library name: sample1
10× Genomics

value: ND


title: iNKT KO 60% HFD plus 0.25% HDCA TCRseq

description:
Library name: sample6
10× Genomics

data_processing:
The cDNA was enzymatically fragmented, end-repaired, size-selected, and ligated with adaptors. Libraries were indexed through PCR, size-selected again, and quality-assessed. Sequencing was performed on a NovaSeq 6000 (paired-end) to capture 10× barcodes and UMI (R1), sample indices (I7), and transcripts (R2).
The data were processed using 10× Genomics Cell Ranger software for demultiplexing, alignment to mm10, UMI counting, and quality control.
Assembly: GRCm39
Supplementary files format and content: features, matrix files
Supplementary files format and content: CSV files to analyse TCR repertoire
Library strategy: TCR-Seq

source_name: lymphocytes

extract_protocol:
For scRNA-seq analysis of liver-resident mononuclear cells (MNCs), CD45+ cells in MNCs were isolated from murine liver and were sorted using a BD FACS Aria III (10,000 cells each).
The scRNA-seq libraries were prepared using 10× Genomics Chromium Next GEM single-cell 3ʹ reagent kits. Cell suspensions were loaded onto the 10× Genomics Chromium Controller to generate gel beads in emulsion (GEM) for polyA cDNA synthesis with cell barcodes and unique molecular identifiers (UMI). GEMs were broken, and single-stranded cDNA was cleaned with DynaBeads, amplified, and assessed for quality using an Agilent TapeStation.

treatment_protocol: CD4+ lymphocytes were isolated from WT mice fed 60% HFD or 60% HFD plus 0.25% HDCA. For the control, CD4+ lymphocytes were also isolated from  Ja18-/-(iNKT KO) mice fed 60% HFD plus 0.25% HDCA.

value: lymphocytes

value: iNKT KO


title: WSN13_0h

description:
Library name: WSN13_0h
expression matrix (txt) and original file (fastq)


title: WT 60% HFD TCRseq

description:
Library name: sample4
10× Genomics


title: WT 60%HFD plus 0.25% HDCA TCRseq

description:
Library name: sample5
10× Genomics


title: WSN12_0h

description:
Library name: WSN12_0h
expression matrix (txt) and original file (fastq)


title: WSN12_3h

description:
Library name: WSN12_3h
expression matrix (txt) and original file (fastq)


title: iNKT KO 60% HFD plus 0.25% HDCA scRNAseq

description:
Library name: sample3
10× Genomics

data_processing:
The cDNA was enzymatically fragmented, end-repaired, size-selected, and ligated with adaptors. Libraries were indexed through PCR, size-selected again, and quality-assessed. Sequencing was performed on a NovaSeq 6000 (paired-end) to capture 10× barcodes and UMI (R1), sample indices (I7), and transcripts (R2).
The data were processed using 10× Genomics Cell Ranger software for demultiplexing, alignment to mm10, UMI counting, and quality control.
Assembly: GRCm39
Supplementary files format and content: features, matrix files
Supplementary files format and content: CSV files to analyse TCR repertoire


title: WSN11_3h

description:
Library name: WSN11_3h
expression matrix (txt) and original file (fastq)


title: WT 60%HFD plus 0.25% HDCA scRNAseq

description:
Library name: sample2
10× Genomics


title: WSN11_0h

description:
Library name: WSN11_0h
expression matrix (txt) and original file (fastq)


title: WSN10_0h

description:
Library name: WSN10_0h
expression matrix (txt) and original file (fastq)


title: WT 60% HFD scRNAseq

description:
Library name: sample1
10× Genomics


title: ovo_2

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

state: MO

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: Library name: L66523

data_processing:
FASTQs files were trimmed with bbduk.sh to remove contaminate and adapter
distict sequences were counted
Assembly: SchMedS3 (PRJNA885486)
Supplementary files format and content: all_counts.tsv.gz contains raw counts of each distinct sequence across all samples

organism: Schmidtea mediterranea

source_name: Evs from OVO RNAi treated whole animals replicate 2

extract_protocol:
EV isolation and concentration
Five hundred asexual planarians, 4-5mm long, were cultured in Ziploc containers in 0.1u filtered Montjuic water without antibiotics. The animals were cultured at 20°C for 2.5 days. Conditioned Montjuic water was collected and centrifuged at 3000 x g for 10 minutes. The supernatant was collected and centrifuged at 10000 x g for 15 minutes. The supernatant was transferred to a new tube and spun at 15800 x g for 30 minutes to obtain a pellet of large EVs. The supernatant was collected and transferred to a 100Kda cutoff Amicon filter tube. The tube was spun at 3000 x g for 15 minutes to concentrate the supernatant to 4ml as per the manufacturer’s instruction. The concentrate was then transferred to a 4ml ultracentrifuge tube and subjected to 120,000 x g for 90 minutes to obtain a pellet of small EVs.

value: OVO RNAi


title: WSN10_3h

description:
Library name: WSN10_3h
expression matrix (txt) and original file (fastq)


title: lung-derived CD45+ immune cells post control CAR T treatment #1 gene expression

status: Public on Jul 14 2026

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: Library name: Ctrl1_GEX

data_processing:
The Cell Ranger v6 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing, alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix and TCR filtered contig annotations for single cells in each sample

growth_protocol: CD45+ immune cells isolated from lung were used directly for experiments.

extract_protocol:
CD45+ immune cells were sorted and loaded onto the Chromium Controller according to their respective cell counts to target 10,000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 5’ v2 Library and Gel Bead Kit (10x Genomics)

value: CD45+ immune cells

value: wild type

value: Sort-purified CD45+ immune cells


title: WSN9_3h

description:
Library name: WSN9_3h
expression matrix (txt) and original file (fastq)


title: ago3_3

description: Library name: L66521

source_name: Evs from AGO3 RNAi treated whole animals replicate 3

value: Ago3 RNAi


title: WSN9_0h

description:
Library name: WSN9_0h
expression matrix (txt) and original file (fastq)


title: ovo_1

description: Library name: L66522

source_name: Evs from OVO RNAi treated whole animals replicate 1


title: WSN8_3h

description:
Library name: WSN8_3h
expression matrix (txt) and original file (fastq)


title: ago3_2

description: Library name: L66520

source_name: Evs from AGO3 RNAi treated whole animals replicate 2


title: ago3_1

description: Library name: L66519

source_name: Evs from AGO3 RNAi treated whole animals replicate 1


title: WSN7_3h

description:
Library name: WSN7_3h
expression matrix (txt) and original file (fastq)


title: WSN8_0h

description:
Library name: WSN8_0h
expression matrix (txt) and original file (fastq)


title: ago1_3

description: Library name: L66518

source_name: Evs from AGO1 RNAi treated whole animals replicate 3

value: Ago1 RNAi


title: ago1_2

description: Library name: L66517

source_name: Evs from AGO1 RNAi treated whole animals replicate 2


title: WSN7_0h

description:
Library name: WSN7_0h
expression matrix (txt) and original file (fastq)


title: WSN6_3h

description:
Library name: WSN6_3h
expression matrix (txt) and original file (fastq)


title: ago1_1

description: Library name: L66516

source_name: Evs from AGO1 RNAi treated whole animals replicate 1


title: WSN6_0h

description:
Library name: WSN6_0h
expression matrix (txt) and original file (fastq)


title: piwi1_1

description: Library name: L66513

source_name: Evs from PIWI1 RNAi treated whole animals replicate 1

value: Piwi1 RNAi


title: piwi1_2

description: Library name: L66514

source_name: Evs from PIWI1 RNAi treated whole animals replicate 2


title: unc22_3

description: Library name: L66512

source_name: Evs from UNC22 RNAi treated whole animals replicate 3

value: unc22 RNAi


title: WSN4_3h

description:
Library name: WSN4_3h
expression matrix (txt) and original file (fastq)


title: unc22_2

description: Library name: L66511

source_name: Evs from UNC22 RNAi treated whole animals replicate 2


title: WSN4_0h

description:
Library name: WSN4_0h
expression matrix (txt) and original file (fastq)


title: unc22_1

description: Library name: L66510

source_name: Evs from UNC22 RNAi treated whole animals replicate 1


title: WSN3_3h

description:
Library name: WSN3_3h
expression matrix (txt) and original file (fastq)


title: WSN5_0h

description:
Library name: WSN5_0h
expression matrix (txt) and original file (fastq)


title: WSN3_0h

description:
Library name: WSN3_0h
expression matrix (txt) and original file (fastq)


title: TR_sEVs_3

description: Library name: L76879

source_name: small EVs (pellet from 120,000g centrifugation) from tail fragments replicate 3

value: wildtype


title: ovo_3

description: Library name: L66509

source_name: Evs from OVO RNAi treated whole animals replicate 3


title: WSN2_3h

description:
Library name: WSN2_3h
expression matrix (txt) and original file (fastq)

source_name: lung


title: TR_sEVs_2

description: Library name: L76878

source_name: small EVs (pellet from 120,000g centrifugation) from tail fragments replicate 2


title: TR_sEVs_1

description: Library name: L76877

source_name: small EVs (pellet from 120,000g centrifugation) from tail fragments replicate 1


title: WSN1_3h

description:
Library name: WSN1_3h
expression matrix (txt) and original file (fastq)


title: HR_sEVs_3

description: Library name: L76876

source_name: small EVs (pellet from 120,000g centrifugation) from head fragments replicate 3


title: HR_sEVs_2

description: Library name: L76875

source_name: small EVs (pellet from 120,000g centrifugation) from head fragments replicate 2


title: WSN1_0h

description:
Library name: WSN1_0h
expression matrix (txt) and original file (fastq)


title: S-27_4h

description:
Library name: S-27_4h
expression matrix (txt) and original file (fastq)

source_name: colon

value: colon

value: colon cancer cell line


title: HR_sEVs_1

description: Library name: L76874

source_name: small EVs (pellet from 120,000g centrifugation) from head fragments replicate 1


title: S-27_1h

description:
Library name: S-27_1h
expression matrix (txt) and original file (fastq)

value: WT


title: WT_sEVs_2

description: Library name: L76872

source_name: small EVs (pellet from 120,000g centrifugation) from whole animals replicate 2


title: S-27_0h

description:
Library name: S-27_0h
expression matrix (txt) and original file (fastq)


title: S-26_1h

description:
Library name: S-26_1h
expression matrix (txt) and original file (fastq)


title: KMD65_Post

type: genomic

city: Palo Alto

first: Shota

last: Nishitani

state: CA

address: 3165 Porter Dr.

department: Department of Psychiatry and Behavioral Sciences

institute: Stanford University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the human Infinium MethylationEPIC v2 BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using the BeadArray Scanner (iScan) under standard settings

data_processing: Raw IDAT files were processed using the minfi package (Bioconductor) in R, with EPIC v2 manifest and annotation (IlluminaHumanMethylationEPICv2manifest and IlluminaHumanMethylationEPICv2anno.20a1.hg38). Background correction was performed using the Noob method (preprocessNoob). Beta values, methylated signals, unmethylated signals, and detection p-values were extracted for each probe and sample.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: KMD Delirium

label_protocol: Bisulfite conversion

extract_protocol: QIAamp DNA Mini Kit (QIAGEN)

value: blood

tag: patient id

tag: group

value: non-POD

tag: gender

value: male

tag: age

tag: anesthesia type

value: spinal

tag: anesthesia duration (m)

tag: operative time (m)

tag: blood loss (ml)

tag: sampling day


title: WT_sEVs_1

description: Library name: L76871

source_name: small EVs (pellet from 120,000g centrifugation) from whole animals replicate 1


title: KMD65_Pre

value: Pre


title: S-26_0h

description:
Library name: S-26_0h
expression matrix (txt) and original file (fastq)


title: KMD64_Pre

value: general


title: S-25_4h

description:
Library name: S-25_4h
expression matrix (txt) and original file (fastq)


title: S-25_1h

description:
Library name: S-25_1h
expression matrix (txt) and original file (fastq)


title: KMD64_Post


title: S-24_4h

description:
Library name: S-24_4h
expression matrix (txt) and original file (fastq)


title: KMD63_Post

value: POD


title: S-24_1h

description:
Library name: S-24_1h
expression matrix (txt) and original file (fastq)


title: KMD62_Post

value: female


title: KMD62_Pre


title: S-23_4h

description:
Library name: S-23_4h
expression matrix (txt) and original file (fastq)


title: KMD61_Pre


title: S-24_0h

description:
Library name: S-24_0h
expression matrix (txt) and original file (fastq)


title: S-23_1h

description:
Library name: S-23_1h
expression matrix (txt) and original file (fastq)


title: KMD61_Post


title: S-23_0h

description:
Library name: S-23_0h
expression matrix (txt) and original file (fastq)


title: S-22_4h

description:
Library name: S-22_4h
expression matrix (txt) and original file (fastq)


title: KMD60_Post


title: S-22_1h

description:
Library name: S-22_1h
expression matrix (txt) and original file (fastq)


title: S-22_0h

description:
Library name: S-22_0h
expression matrix (txt) and original file (fastq)


title: KMD58_Post


title: KMD59_Pre


title: S-21_1h

description:
Library name: S-21_1h
expression matrix (txt) and original file (fastq)


title: S-21_4h

description:
Library name: S-21_4h
expression matrix (txt) and original file (fastq)


title: KMD58_Pre


title: S-21_0h

description:
Library name: S-21_0h
expression matrix (txt) and original file (fastq)


title: KMD57_Post


title: S-20_4h

description:
Library name: S-20_4h
expression matrix (txt) and original file (fastq)


title: KMD57_Pre


title: S-20_1h

description:
Library name: S-20_1h
expression matrix (txt) and original file (fastq)


title: KMD56_Post


title: KMD56_Pre


title: S-20_0h

description:
Library name: S-20_0h
expression matrix (txt) and original file (fastq)


title: SK-BR-3-6h-6

description:
Library name: SK-BR-3-6h-6
expression matrix (txt) and original file (fastq)

source_name: breast

value: breast

value: Breast cancer cell lines


title: KMD55_Post


title: KMD55_Pre


title: SK-BR-3-6h-4

description:
Library name: SK-BR-3-6h-4
expression matrix (txt) and original file (fastq)


title: SK-BR-3-6h-5

description:
Library name: SK-BR-3-6h-5
expression matrix (txt) and original file (fastq)


title: piwi1_3

description: Library name: L66515

source_name: Evs from PIWI1 RNAi treated whole animals replicate 3


title: KMD54_Pre


title: SK-BR-3-6h-3

description:
Library name: SK-BR-3-6h-3
expression matrix (txt) and original file (fastq)


title: KMD54_Post


title: WSN5_3h

description:
Library name: WSN5_3h
expression matrix (txt) and original file (fastq)

value: lung

value: Non-small cell lung cancer cell lines


title: SK-BR-3-6h-2

description:
Library name: SK-BR-3-6h-2
expression matrix (txt) and original file (fastq)


title: KMD53_Pre


title: SK-BR-3-6h-1

description:
Library name: SK-BR-3-6h-1
expression matrix (txt) and original file (fastq)


title: KMD53_Post


title: SK-BR-3-4h-6

description:
Library name: SK-BR-3-4h-6
expression matrix (txt) and original file (fastq)


title: KMD52_Pre


title: KMD52_Post


title: SK-BR-3-4h-5

description:
Library name: SK-BR-3-4h-5
expression matrix (txt) and original file (fastq)


title: SK-BR-3-4h-4

description:
Library name: SK-BR-3-4h-4
expression matrix (txt) and original file (fastq)


title: WSN2_0h

description:
Library name: WSN2_0h
expression matrix (txt) and original file (fastq)


title: KMD51_Post


title: KMD51_Pre


title: SK-BR-3-4h-3

description:
Library name: SK-BR-3-4h-3
expression matrix (txt) and original file (fastq)


title: SK-BR-3-4h-2

description:
Library name: SK-BR-3-4h-2
expression matrix (txt) and original file (fastq)


title: KMD50_Post


title: WT_sEVs_3

description: Library name: L76873

source_name: small EVs (pellet from 120,000g centrifugation) from whole animals replicate 3


title: SK-BR-3-4h-1

description:
Library name: SK-BR-3-4h-1
expression matrix (txt) and original file (fastq)


title: KMD50_Pre


title: S-26_4h

description:
Library name: S-26_4h
expression matrix (txt) and original file (fastq)


title: SK-BR-3-1h-6

description:
Library name: SK-BR-3-1h-6
expression matrix (txt) and original file (fastq)


title: KMD49_Post


title: SK-BR-3-1h-5

description:
Library name: SK-BR-3-1h-5
expression matrix (txt) and original file (fastq)


title: KMD49_Pre


title: KMD48_Post


title: SK-BR-3-1h-4

description:
Library name: SK-BR-3-1h-4
expression matrix (txt) and original file (fastq)


title: S-25_0h

description:
Library name: S-25_0h
expression matrix (txt) and original file (fastq)


title: KMD48_Pre


title: KMD47_Pre


title: SK-BR-3-1h-2

description:
Library name: SK-BR-3-1h-2
expression matrix (txt) and original file (fastq)


title: SK-BR-3-1h-3

description:
Library name: SK-BR-3-1h-3
expression matrix (txt) and original file (fastq)


title: SK-BR-3-1h-1

description:
Library name: SK-BR-3-1h-1
expression matrix (txt) and original file (fastq)


title: KMD47_Post


title: KMD46_Post


title: SK-BR-3-0h-6

description:
Library name: SK-BR-3-0h-6
expression matrix (txt) and original file (fastq)


title: KMD63_Pre


title: SK-BR-3-0h-5

description:
Library name: SK-BR-3-0h-5
expression matrix (txt) and original file (fastq)


title: KMD46_Pre


title: SK-BR-3-0h-4

description:
Library name: SK-BR-3-0h-4
expression matrix (txt) and original file (fastq)


title: KMD45_Pre


title: SK-BR-3-0h-3

description:
Library name: SK-BR-3-0h-3
expression matrix (txt) and original file (fastq)


title: KMD44_Post


title: SK-BR-3-0h-2

description:
Library name: SK-BR-3-0h-2
expression matrix (txt) and original file (fastq)


title: SK-BR-3-0h-1

description:
Library name: SK-BR-3-0h-1
expression matrix (txt) and original file (fastq)


title: KMD44_Pre


title: KMD45_Post


title: KMD60_Pre


title: KMD43_Pre


title: 8L, NRAS, Y, 4hr

city: Wilsonville

first: Srivathsan

middle: V

last: Ranganathan

state: OR

address: 30519 SW Ruth St

department: DOS

institute: OHSU

description: Library name: 139722

data_processing:
Fastq files assembled with Bcl2Fastq (Illumina Inc.)
Fastq files aligned with Ensembl v75 gene models (GRCh37 build of the human genome) using Kallisto (v0.46.2).
Salmon-produced transcript abundance estimates scaled using average transcript length (over all sequenced samples) and library size and converted to Ensembl-annotated gene-level count estimates (‘tximport’ Bioconductor package)
Differential expression of bulk RNAseq experiments involved filtering out Ensembl-identified genes with low counts (‘edgeR’ Bioconductor package), normalization of counts via trimmed mean of M-values method (‘edgeR’), surrogate variable analysis (‘sva’ Bioconductor package), and gene-wise modeling using empirical Bayesian limma-voom procedure (‘limma’ Bioconductor package)62,71,72. Heatmaps produced using ComplexHeatmap v2.6.2
Assembly: GRCh37
Supplementary files format and content: quant.sf format

source_name: cell line

growth_protocol: Human MOLM14 cells generously provided by Dr. Yoshinobu Matsuo (Fujisaki Cell Center, Hayashibara Biochemical Labs, Okayama, Japan). Gilteritinib resistant cultures were maintained as previously described4 in 100 nM of gilteritinib (Selleck Chemicals, Houston, TX) and RPMI (Life Technologies Inc., Carlsbad, CA) with 10% FBS (Atlanta Biologicals, Flowery Branch, GA), 2% L-glutamine, 1% penicillin/streptomycin (Life Technologies Inc.), and 0.1% amphotericin B (HyClone, South Logan, UT). Gilteritinib and media were replenished every 2-3 days.

extract_protocol:
RNA isolated with miRNeasy Mini Kit (Qiagen Inc.) according to the manufacturer’s protocol
Libraries prepared using TruSeq Stranded mRNA Kit (Illumina Inc.)

treatment_protocol: Cell lines were treated with 5 µM NRAS or control ASO or media alone every other day for 96 hours and then treated with 100 nM gilteritinib. Cell pellets were collected at timepoint 0, 4, and 24 hours after treatment.

value: cell line

value: AML cell line

value: NRAS G12S

value: NRAS

tag: aso dose_(um)

tag: gilteritinib

value: Y

tag: gilt concentration_(um)

tag: time -_gilteritinib_treatment


title: 8L, NRAS, Y, 24hr

description: Library name: 139721

tag: tissue


title: KMD42_Post

value: blood


title: 5L, NRAS, N, 0hr

description: Library name: 139719

tag: cell line

value: N


title: KMD41_Post

value: male


title: 10L, Control, Y, 24hr

description: Library name: 139723

tag: cell type

value: NRAS G12D

value: Control


title: 10L, No ASO, Y, 4hr

description: Library name: 139720

tag: genotype

value: No ASO


title: 5L, Control, Y, 4hr

description: Library name: 139718


title: KMD41_Pre

tag: patient id

value: POD

value: spinal

value: Pre


title: 5L, No ASO, N, 0hr

description: Library name: 139716


title: KMD40_Post

tag: group

value: general


title: 4X-H2Av-NC13-1

city: Denton

first: Fanju

last: Meng

state: TX

address: 1155 Union Circle #305220

department: Biological Sciences

institute: University of North Texas

description: Library name: 4X-H2Av-NC13-1

data_processing:
RNA-seq reads were trimmed for adaptors using TrimGalore (version 0.6.10), and then mapped to the D. melanogaster reference genome (dm6) or zebrafish genome (GRCz11) using STAR (version 2.7.11b)
The transcript-level abundance was quantified with Salmon and then aggregated using tximport to obtain gene-level quantification.
Subsequent differential expression analysis was done using DESeq2
Statistical tests and plots for data visualization were generated in R and GraphPad
Assembly: dm6 and GRCz11
Supplementary files format and content: txt files with TPM count table and DEseq2 results

organism: Drosophila melanogaster

source_name: whole embryo

growth_protocol: Drosophila embryos of roughly the correct stage were observed by confocal imaging until they reached the desired timepoint and then flash frozen.

extract_protocol:
Embryos were then macerated in TRIzol with a needle to extract RNA and purified using Direct-Zol™ RNA MiniPrep Kit (Zymo Research) according to manufacturer’s protocol.
RNA libraries for batch 1, 2 and 5 were prepared with Illumina total RNA with rRNA depletion, and RNA libraries for batch 3 and 4 were prepared with SMART-Seq Total RNA Pico Input with UMIs according to user manual.

value: whole embryo

tag: developmental stage

tag: batch


title: KMD40_Pre

tag: gender

tag: age

tag: anesthesia type


title: KMD39_Post

value: non-POD

value: female

tag: anesthesia duration (m)

tag: operative time (m)

tag: blood loss (ml)


title: KMD39_Pre

tag: sampling day


title: 8L, Control, Y, 4hr

description: Library name: 139713

value: cell line

value: AML cell line

tag: aso dose_(um)

tag: gilteritinib

tag: gilt concentration_(um)


title: KMD38_Pre

tag: tissue


title: KMD38_Post


title: 11L, Control, N, 0hr

description: Library name: 139711

tag: cell line

tag: cell type

tag: time -_gilteritinib_treatment


title: KMD37_Pre

tag: patient id

tag: group


title: 7L, Control, Y, 24hr

description: Library name: 139714

tag: genotype

value: NRAS G12S


title: 7L, No ASO, N, 0hr

description: Library name: 139709


title: KMD37_Post

tag: gender


title: KMD36_Post

tag: age


title: 6L, Control, Y, 24hr

description: Library name: 139712

value: Y


title: 11L, NRAS, Y, 24hr

description: Library name: 139710

value: NRAS


title: KMD36_Pre

value: blood

tag: anesthesia type


title: KMD35_Pre

tag: anesthesia duration (m)


title: 11L, NRAS, N, 0hr

description: Library name: 139707

value: N


title: KMD35_Post

tag: operative time (m)


title: 11L, Control, Y, 24hr

description: Library name: 139706

value: NRAS G12D


title: 7L, No ASO, Y, 4hr

description: Library name: 139705


title: KMD34_Pre

tag: blood loss (ml)


title: 8L, Control, N, 0hr

description: Library name: 139704

value: Control


title: KMD34_Post

tag: sampling day


title: 5L, No ASO, Y, 4hr

description: Library name: 139703

value: No ASO

tag: aso dose_(um)


title: KMD33_Post

value: POD

value: male


title: KMD33_Pre

value: Pre


title: 12L, Control, N, 0hr

description: Library name: 139701

tag: gilteritinib


title: 5L, NRAS, Y, 24hr

description: Library name: 139702

tag: gilt concentration_(um)


title: KMD32_Post

tag: tissue

value: spinal


title: 8L, No ASO, N, 0hr

description: Library name: 139700

tag: cell line


title: KMD32_Pre


title: U2OS, BrdU-IP-seq, aphidicolin G2M, rep2

city: Kobe

first: Jothivanan

last: Elumalai

state: Hyogo

address: 2-2-3, Minatojima Minamimachi, Chuo-ku

department: Biosystems Dynamics Research (BDR)

institute: RIKEN

description: Library name: Sample 347

library_source: genomic

data_processing:
We used only one end of the paired-end sequenced reads for our analysis. Raw fastq files were subjected to quality assessment with FastQC v0.11.5 , and the cutadapt program v1.15 was used to eliminate SEQXE and Illumina adapters. Mapping to the hg19 or mm9 genome was carried out using bwa v0.7.17-r1188 (bwa-aln command). The resulting mapped reads were sorted using samtools v1.7, and duplicate reads were flagged using picard-tools v2.8.1.
For BrdU-IP Repli-seq: After removing duplicate reads and filtering blacklist regions, we counted the reads and calculated reads per million for each 100-kb non-overlapping window in early- and late-S fractions. Then, RT is determined by calculating log2(early/late) for each 100-kb window. All the BrdU-IP RT profiles were quantile normalized before downstream analysis.
For BrdU-IP G2M-seq: After removing duplicate reads and filtering blacklist regions, we counted the reads and calculated reads per million for each 100-kb non-overlapping window in untreated and aphidicolin-treated conditions. Then, aphidicolin-induced G2/M replication is determined by calculating log2(aphidicolin/untreated) for each 100-kb window.
Assembly: hg19
Supplementary files format and content: log2(aphidicolin/untreated) G2M replication (.bedGraph)

source_name: Bone

growth_protocol: Human osteosarcoma cells (U2OS) were cultured in DMEM (Nacalai, 08459-64) supplemented with 10% FBS (Sigma, 172012) and maintained at 37°C with 5% CO2. CBMS1 mouse embryonic stem cells (mESCs) have been described (Murakami et al, Development, 2011) and grown in 2i/LIF medium as described (Hayashi et al, Nat. Protoc. 2013).

extract_protocol:
75% ethanol fixed cells were stained with Propidium iodide (Nacalai tesque, 29037), then early- and late-S phase cell population (at least 10,000 cells/fraction) were sorted by a Sony SH800 or MA900 cell sorter. Extracted DNA was sonicated by a Bioruptor UCD-250 (Sonic Bio). BrdU-incorporated DNA was immunoprecipitated using anti-BrdU antibody (BD Biosciences Pharmingen, #555627).
BrdU-immunoprecipitated DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed from early- and late-replicating DNA after WGA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions

treatment_protocol: Cells were subjected to treatment with or without 0.4 μM aphidicolin for 24 hours and labelled with 50 μM BrdU for 30 minutes before harvesting.

value: Bone

tag: cell type

value: Sarcoma-derived

tag: treatment

value: Aphidicolin


title: 10L, NRAS, N, 0hr

description: Library name: 139699

value: cell line

tag: time -_gilteritinib_treatment


title: U2OS, BrdU-IP-seq, untreated G2M, rep2

description: Library name: Sample 346

value: Untreated


title: KMD31_Pre

tag: patient id

tag: group

value: female

value: general


title: 5L, Control, N, 0hr

description: Library name: 139698

value: AML cell line

tag: genotype

value: NRAS G12S


title: KMD31_Post

value: blood

tag: gender

tag: age


title: U2OS, BrdU-IP-seq, aphidicolin G2M, rep1

data_processing:
We used only one end of the paired-end sequenced reads for our analysis. Raw fastq files were subjected to quality assessment with FastQC v0.11.5 , and the cutadapt program v1.15 was used to eliminate SEQXE and Illumina adapters. Mapping to the hg19 or mm9 genome was carried out using bwa v0.7.17-r1188 (bwa-aln command). The resulting mapped reads were sorted using samtools v1.7, and duplicate reads were flagged using picard-tools v2.8.1.
For BrdU-IP Repli-seq: After removing duplicate reads and filtering blacklist regions, we counted the reads and calculated reads per million for each 100-kb non-overlapping window in early- and late-S fractions. Then, RT is determined by calculating log2(early/late) for each 100-kb window. All the BrdU-IP RT profiles were quantile normalized before downstream analysis.
For BrdU-IP G2M-seq: After removing duplicate reads and filtering blacklist regions, we counted the reads and calculated reads per million for each 100-kb non-overlapping window in untreated and aphidicolin-treated conditions. Then, aphidicolin-induced G2/M replication is determined by calculating log2(aphidicolin/untreated) for each 100-kb window.
Assembly: hg19, mm9
Supplementary files format and content: log2(early/late) RT (.bedGraph)
Supplementary files format and content: log2(aphidicolin/untreated) G2M replication (.bedGraph)
Library strategy: BrdU-IP-seq


title: U2OS, BrdU-IP-seq, untreated LateS, rep2


title: U2OS, BrdU-IP-seq, untreated EarlyS, rep2


title: 5L, Control, Y, 24hr

description: Library name: 139697

value: Y


title: KMD30_Post

tag: anesthesia type

tag: anesthesia duration (m)


title: 10L, NRAS, Y, 4hr

description: Library name: 139695

value: NRAS G12D

value: NRAS


title: 12L, No ASO, Y, 4hr

description: Library name: 139694

value: No ASO


title: KMD29_Pre

value: POD

tag: operative time (m)

tag: blood loss (ml)


title: U2OS, 10-cell Repli-seq, aphidicolin S12, rep2

data_processing:
We used only one end of the paired-end sequenced reads for our analysis. Raw fastq files were subjected to quality assessment with FastQC v0.11.5 , and the cutadapt program v1.15 was used to eliminate SEQXE and Illumina adapters. Mapping to the hg19 or mm9 genome was carried out using bwa v0.7.17-r1188 (bwa-aln command). The resulting mapped reads were sorted using samtools v1.7, and duplicate reads were flagged using picard-tools v2.8.1.
For single-G1 karyotype analysis: After marking the duplicate reads, copy number analysis was conducted using the AneuFinder package v1.22.0 within R v4.1.3. Initially, duplicate reads, blacklist regions (available at https://github.com/Boyle-Lab/Blacklist) and reads with a mapping quality (MAPQ) below 10 were filtered out. Uniquely mapped reads were counted within each 500-Kb genomic window, adjusted for GC content (GC.BSgenome=BSgenome.Hsapiens.UCSC.hg19 for humans and BSgenome.Mmusculus.UCSC.mm9 for mouse, method="loess"), and copy number segmentation was executed using the "findCNVs" function (method='edivisive', R=50) of the AneuFinder package. For quality control (QC), multivariate clustering was applied, and clusters with a spikiness value exceeding 1 were eliminated.
For Log2percentile RT: We followed our established procedure to generate binarized replication timing (RT) profiles for each of the 14 fractions of S-phase or single-cells under analysis, along with their respective percentage replication scores (Miura et al, Nat. Protoc. 2020). The percentage replication score of each S-phase fraction or single-cells was utilized to compute their raw, non-binarized replication timing profile, termed as "log2repliscore RT".
Assembly: hg19, mm9
Supplementary files format and content: CNV states (.txt)
Supplementary files format and content: log2percentile RT (.txt)
Library strategy: scRepli-seq

extract_protocol:
Single cells were sorted with a Sony SH800 or MA900 cell sorter. Sample preparations were performed as described (Miura et al, Nat. Protoc. 2020). DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE).
NGS libraries were constructed for amplied DNA using an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions.

treatment_protocol: Cells were subjected to treatment with or without 0.4 μM aphidicolin for 24 hours and labelled with 10 μM EdU for 60 and 15 minutes before harvesting, respectively.


title: KMD29_Post

tag: sampling day


title: U2OS, 10-cell Repli-seq, aphidicolin S10, rep2


title: 9L, Control, Y, 24hr

description: Library name: 139693

value: Control

tag: aso dose_(um)

tag: gilteritinib


title: U2OS, 10-cell Repli-seq, aphidicolin S13, rep2

tag: tissue


title: U2OS, 10-cell Repli-seq, aphidicolin S9, rep2

tag: cell line


title: KMD28_Pre

value: spinal

value: Pre


title: U2OS, 10-cell Repli-seq, aphidicolin S7, rep2

value: Bone

tag: cell type

value: Sarcoma-derived


title: KMD28_Post


title: U2OS, 10-cell Repli-seq, aphidicolin S6, rep2

tag: treatment

value: Aphidicolin


title: 5L, No ASO, Y, 24hr

description: Library name: 139692

value: cell line

tag: gilt concentration_(um)

tag: time -_gilteritinib_treatment


title: 7L, NRAS, Y, 4hr

description: Library name: 139691


title: U2OS, 10-cell Repli-seq, aphidicolin S5, rep2


title: MOLM14, No ASO, N, 0hr

description: Library name: 139690

value: WT

value: N


title: U2OS, 10-cell Repli-seq, aphidicolin S3, rep2


title: KMD27_Pre

tag: patient id

tag: group

value: male

value: general


title: U2OS, 10-cell Repli-seq, aphidicolin S2, rep2


title: 10L, Control, N, 0hr

description: Library name: 139689

value: AML cell line

tag: genotype


title: U2OS, 10-cell Repli-seq, aphidicolin S1, rep2


title: U2OS, 10-cell Repli-seq, aphidicolin G1, rep2


title: MOLM14, No ASO, Y, 4hr

description: Library name: 139688

value: Y


title: KMD26_Post

value: blood

value: non-POD

tag: gender

value: female

tag: age


title: U2OS, 10-cell Repli-seq, aphidicolin S13, rep1


title: U2OS, 10-cell Repli-seq, aphidicolin S12, rep1


title: KMD25_Pre

tag: anesthesia type

tag: anesthesia duration (m)


title: U2OS, 10-cell Repli-seq, aphidicolin S11, rep1


title: 12L, NRAS, N, 0hr

description: Library name: 139686

value: NRAS G12D

value: NRAS


title: U2OS, 10-cell Repli-seq, aphidicolin S10, rep1


title: KMD25_Post

tag: operative time (m)

tag: blood loss (ml)


title: U2OS, 10-cell Repli-seq, aphidicolin S9, rep1


title: 11L, No ASO, N, 0hr

description: Library name: 139685

value: No ASO

tag: aso dose_(um)


title: U2OS, 10-cell Repli-seq, aphidicolin S8, rep1


title: 6L, No ASO, Y, 24hr

description: Library name: 139687

value: NRAS G12S

tag: gilteritinib


title: U2OS, 10-cell Repli-seq, aphidicolin S7, rep1

tag: tissue

value: Bone


title: KMD43_Post

value: spinal

tag: sampling day


title: 6L, NRAS, N, 0hr

description: Library name: 139684

tag: cell line

tag: cell type


title: KMD42_Pre

value: POD

value: Pre


title: 10L, Control, Y, 4hr

description: Library name: 139717

value: cell line

value: Control

tag: gilt concentration_(um)


title: U2OS, 10-cell Repli-seq, aphidicolin S6, rep1

value: Sarcoma-derived

tag: treatment

value: Aphidicolin


title: 6L, No ASO, Y, 4hr

description: Library name: 139715

value: AML cell line

tag: time -_gilteritinib_treatment


title: KMD24_Pre

tag: patient id

tag: group


title: U2OS, 10-cell Repli-seq, aphidicolin S5, rep1


title: 8L, No ASO, Y, 24hr

description: Library name: 139683

tag: genotype

value: Y


title: U2OS, 10-cell Repli-seq, aphidicolin S4, rep1


title: KMD23_Post

value: blood

tag: gender

value: male

tag: age

value: general


title: 12L, Control, Y, 24hr

description: Library name: 139708

value: NRAS G12D


title: U2OS, 10-cell Repli-seq, aphidicolin S3, rep1


title: 6L, No ASO, N, 0hr

description: Library name: 139682

value: N


title: U2OS, 10-cell Repli-seq, aphidicolin S2, rep1


title: KMD23_Pre

tag: anesthesia type

tag: anesthesia duration (m)


title: U2OS, 10-cell Repli-seq, aphidicolin S1, rep1


title: 7L, No ASO, Y, 24hr

description: Library name: 139681

value: No ASO


title: U2OS, 10-cell Repli-seq, aphidicolin G1, rep1


title: U2OS, 10-cell Repli-seq, untreated S14, rep2

value: Untreated


title: KMD22_Post

value: non-POD

value: female

tag: operative time (m)

tag: blood loss (ml)


title: 6L, Control, Y, 4hr

description: Library name: 139680

value: NRAS G12S

tag: aso dose_(um)

tag: gilteritinib


title: U2OS, 10-cell Repli-seq, untreated S13, rep2

tag: tissue

value: Bone


title: U2OS, BrdU-IP-seq, untreated G2M, rep1

tag: cell line


title: KMD22_Pre

value: spinal

tag: sampling day

value: Pre


title: U2OS, 10-cell Repli-seq, untreated S12, rep2

tag: cell type

value: Sarcoma-derived


title: KMD24_Post


title: U2OS, BrdU-IP-seq, untreated LateS, rep1

tag: treatment


title: 9L, No ASO, Y, 4hr

description: Library name: 139679

value: cell line

tag: gilt concentration_(um)

tag: time -_gilteritinib_treatment


title: KMD21_Pre

tag: patient id

tag: group


title: KMD30_Pre

value: POD

tag: gender


title: U2OS, BrdU-IP-seq, untreated EarlyS, rep1


title: 8L, No ASO, Y, 4hr

description: Library name: 139696

value: AML cell line

tag: genotype

value: Y


title: U2OS, 10-cell Repli-seq, untreated S11, rep2


title: U2OS, 10-cell Repli-seq, untreated S10, rep2


title: 9L, No ASO, Y, 24hr

description: Library name: 139678


title: U2OS, 10-cell Repli-seq, aphidicolin S14, rep2

value: Aphidicolin


title: U2OS, 10-cell Repli-seq, untreated S9, rep2


title: KMD21_Post

value: blood

value: male

tag: age

tag: anesthesia type


title: U2OS, 10-cell Repli-seq, aphidicolin S11, rep2


title: U2OS, 10-cell Repli-seq, untreated S8, rep2


title: U2OS, 10-cell Repli-seq, untreated S7, rep2


title: 10L, No ASO, Y, 24hr

description: Library name: 139677

value: NRAS G12D


title: KMD20_Post

value: general

tag: anesthesia duration (m)

tag: operative time (m)


title: U2OS, 10-cell Repli-seq, untreated S6, rep2

value: Untreated


title: U2OS, 10-cell Repli-seq, untreated S4, rep2


title: U2OS, 10-cell Repli-seq, untreated S5, rep2


title: KMD20_Pre

value: non-POD

tag: blood loss (ml)


title: 12L, NRAS, Y, 24hr

description: Library name: 139676

value: NRAS

tag: aso dose_(um)

tag: gilteritinib


title: 9L, NRAS, Y, 24hr

description: Library name: 139675

tag: tissue

tag: cell line


title: U2OS, 10-cell Repli-seq, untreated S3, rep2

tag: cell type


title: KMD19_Pre

value: female

tag: sampling day


title: U2OS, 10-cell Repli-seq, untreated S2, rep2

value: Bone

tag: treatment


title: 11L, No ASO, Y, 4hr

description: Library name: 139674

value: No ASO

tag: gilt concentration_(um)

tag: time -_gilteritinib_treatment


title: U2OS, 10-cell Repli-seq, aphidicolin S8, rep2


title: U2OS, 10-cell Repli-seq, untreated S1, rep2


title: KMD19_Post

tag: patient id

tag: group


title: U2OS, 10-cell Repli-seq, untreated G1, rep2


title: MOLM14, No ASO, Y, 24hr

description: Library name: 139673

tag: genotype

value: WT


title: U2OS, 10-cell Repli-seq, untreated S14, rep1

value: Sarcoma-derived


title: U2OS, 10-cell Repli-seq, untreated S13, rep1


title: 12L, No ASO, N, 0hr

description: Library name: 139672

value: cell line

value: N


title: KMD18_Post

tag: gender

tag: age

value: spinal


title: KMD18_Pre

tag: anesthesia type

tag: anesthesia duration (m)

value: Pre


title: U2OS, 10-cell Repli-seq, untreated S11, rep1


title: U2OS, 10-cell Repli-seq, untreated S12, rep1


title: 9L, NRAS, N, 0hr

description: Library name: 139671

value: AML cell line


title: U2OS, 10-cell Repli-seq, untreated S10, rep1


title: KMD17_Pre

value: blood

tag: operative time (m)

tag: blood loss (ml)


title: U2OS, 10-cell Repli-seq, untreated S9, rep1


title: U2OS, 10-cell Repli-seq, aphidicolin S4, rep2

value: Aphidicolin


title: 6L, NRAS, Y, 24hr

description: Library name: 139670

value: NRAS G12S

tag: aso dose_(um)

tag: gilteritinib

value: Y


title: KMD17_Post

tag: tissue


title: U2OS, 10-cell Repli-seq, untreated S8, rep1

tag: cell line

tag: cell type

value: Untreated


title: U2OS, 10-cell Repli-seq, untreated S7, rep1

tag: treatment


title: U2OS, 10-cell Repli-seq, untreated S6, rep1


title: KMD27_Post

value: POD

value: male

value: general

tag: sampling day


title: 7L, Control, Y, 4hr

description: Library name: 139669

value: Control

tag: gilt concentration_(um)

tag: time -_gilteritinib_treatment


title: KMD16_Pre

tag: patient id

tag: group

value: female


title: U2OS, 10-cell Repli-seq, untreated S5, rep1

value: Bone


title: 9L, Control, Y, 4hr

description: Library name: 139668

tag: genotype

value: NRAS G12D


title: KMD16_Post

tag: gender

tag: age


title: U2OS, 10-cell Repli-seq, untreated S4, rep1

value: Sarcoma-derived


title: U2OS, 10-cell Repli-seq, untreated S3, rep1


title: U2OS, 10-cell Repli-seq, untreated S2, rep1


title: 12L, No ASO, Y, 24hr

description: Library name: 139667

value: cell line

value: No ASO


title: U2OS, 10-cell Repli-seq, untreated S1, rep1


title: KMD15_Post

value: non-POD

tag: anesthesia type

value: spinal

tag: anesthesia duration (m)


title: 9L, Control, N, 0hr

description: Library name: 139666

value: AML cell line

value: N


title: KMD15_Pre

value: blood

tag: operative time (m)

tag: blood loss (ml)

value: Pre


title: U2OS, 10-cell Repli-seq, untreated G1, rep1

value: Untreated


title: U2OS, scRepli-seq, aphidicolin singleG1 043

value: Aphidicolin


title: 7L, NRAS, N, 0hr

description: Library name: 139665

value: NRAS G12S

value: NRAS

tag: aso dose_(um)

tag: gilteritinib


title: KMD14_Pre

tag: tissue

value: POD


title: U2OS, scRepli-seq, aphidicolin singleG1 040

tag: cell line

tag: cell type


title: KMD14_Post

value: female

tag: sampling day


title: U2OS, scRepli-seq, aphidicolin singleG1 039

value: Bone

tag: treatment


title: U2OS, scRepli-seq, aphidicolin singleG1 038


title: KMD13_Post


title: 11L, No ASO, Y, 24hr

description: Library name: 139663

value: NRAS G12D

value: Y

tag: gilt concentration_(um)

tag: time -_gilteritinib_treatment


title: 9L, No ASO, N, 0hr

description: Library name: 139662

value: cell line


title: U2OS, scRepli-seq, aphidicolin singleG1 036

value: Sarcoma-derived


title: KMD13_Pre

tag: patient id

tag: group

value: non-POD


title: 8L, Control, Y, 24hr

description: Library name: 139661

tag: genotype

value: Control


title: KMD12_Pre

tag: gender

value: male

tag: age

value: spinal


title: U2OS, scRepli-seq, aphidicolin singleG1 034


title: U2OS, scRepli-seq, aphidicolin singleG1 035


title: U2OS, scRepli-seq, aphidicolin singleG1 032


title: 12L, NRAS, Y, 4hr

description: Library name: 139660

value: AML cell line


title: U2OS, scRepli-seq, aphidicolin singleG1 031


title: 6L, Control, N, 0hr

description: Library name: 139659

value: N


title: U2OS, scRepli-seq, aphidicolin singleG1 030


title: 11L, Control, Y, 4hr

description: Library name: 139658


title: KMD11_Post

value: blood

tag: anesthesia type

tag: anesthesia duration (m)


title: U2OS, scRepli-seq, aphidicolin singleG1 028

value: Aphidicolin


title: U2OS, scRepli-seq, aphidicolin singleG1 027


title: 7L, Control, N, 0hr

description: Library name: 139657

value: NRAS G12S


title: U2OS, scRepli-seq, aphidicolin singleG1 026


title: 9L, NRAS, Y, 4hr

description: Library name: 139656

value: NRAS


title: U2OS, scRepli-seq, aphidicolin singleG1 024


title: KMD10_Pre

value: POD

value: general

tag: operative time (m)

tag: blood loss (ml)

value: Pre


title: U2OS, scRepli-seq, aphidicolin singleG1 023

value: Bone


title: U2OS, scRepli-seq, aphidicolin singleG1 025


title: 7L, NRAS, Y, 24hr

description: Library name: 139655

tag: aso dose_(um)

tag: gilteritinib

value: Y


title: KMD09_Pre

tag: tissue

value: female


title: U2OS, scRepli-seq, aphidicolin singleG1 022

tag: cell line

tag: cell type

value: Sarcoma-derived


title: U2OS, scRepli-seq, aphidicolin singleG1 020

tag: treatment


title: U2OS, scRepli-seq, aphidicolin singleG1 019


title: 5L, NRAS, Y, 4hr

description: Library name: 139653

value: cell line

tag: gilt concentration_(um)


title: KMD08_Pre

tag: sampling day


title: U2OS, scRepli-seq, aphidicolin singleG1 018


title: U2OS, scRepli-seq, aphidicolin singleG1 017


title: 8L, NRAS, N, 0hr

description: Library name: 139652

tag: time -_gilteritinib_treatment


title: KMD08_Post

tag: patient id

tag: group


title: U2OS, scRepli-seq, aphidicolin singleG1 016


title: U2OS, scRepli-seq, aphidicolin singleG1 014


title: KMD07_Pre

value: non-POD

tag: gender


title: 6L, NRAS, Y, 4hr

description: Library name: 139650

tag: genotype


title: U2OS, scRepli-seq, aphidicolin singleG1 012


title: KMD07_Post

tag: age

tag: anesthesia type


title: U2OS, scRepli-seq, aphidicolin singleG1 011


title: 12L, Control, Y, 4hr

description: Library name: 139649

value: NRAS G12D

value: Control


title: U2OS, scRepli-seq, aphidicolin singleG1 010


title: KMD06_Post

tag: anesthesia duration (m)

tag: operative time (m)


title: MB2141 xenograft, decitabine treated biol rep 2

city: Aurora

first: Kasey

middle: L.

last: Couts

state: CO

institute: University of Colorado Anschutz Medical Campus

description:
Library name: 2141D21HI2
Column name in Raw_Counts_All_Samples.txt: 2141D21HI2

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.2.
Trimmed reads were mapped to the Homo sapiens hg38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: csv files include TPM values for each sample

source_name: Mouse xenograft tumor

growth_protocol: MB2141 cells were maintained in RPMI with l-glutamine supplemented with 10% FBS and antibiotics (pen-strep and Normocin) in a humidified atmosphere with 5% CO2 at 37C. MB2141 xenograft tumors were generated by injecting 5M cells in a 1:1 mix of complete media and Cultrex into both flanks of 8-10 week old female athymic nude mice.

extract_protocol:
Total RNA was harvested using the Rneasy Plus Mini Kit (Qiagen) with on-column DNAse digest.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: MB2141 cells were pulsed with 500nM decitabine daily for 3 days, followed by drug withdrawal for 4 days prior to RNA harvest. MB2141 xenografts were treated with decitabine which was co-administered with tetrahydrouridine (THU) to inhibit cytidine deaminase and improve systemic exposure. THU was administered at 4 mg/kg via subcutaneous injection 30 minutes prior to decitabine. Decitabine was administered subcutaneously at 10 µg per mouse (~0.4 mg/kg) for three consecutive days only to reflect the clinical schedule of 3-5 days per 28-day cycle, and tumors were harvested for RNA purification at 21 days post first decitabine treatment.

value: Mouse xenograft tumor

value: Decitabine

tag: time

value: 21 days


title: U2OS, scRepli-seq, aphidicolin singleG1 008

value: Aphidicolin


title: KMD06_Pre

value: blood

tag: blood loss (ml)


title: MB2141 xenograft, decitabine treated biol rep 1

description:
Library name: 2141D21HI1
Column name in Raw_Counts_All_Samples.txt: 2141D21HI1

tag: tissue


title: U2OS, scRepli-seq, aphidicolin singleG1 006

tag: cell line


title: KMD05_Pre

value: male


title: KMD11_Pre

value: spinal


title: U2OS, scRepli-seq, aphidicolin singleG1 009

tag: cell type


title: U2OS, scRepli-seq, aphidicolin singleG1 005

tag: treatment


title: MB2141 xenograft, vehicle treated biol rep 2

description:
Library name: 2141D21V2
Column name in Raw_Counts_All_Samples.txt: 2141D21V2

value: Vehicle


title: U2OS, scRepli-seq, aphidicolin singleG1 004


title: KMD05_Post

value: POD

value: general


title: U2OS, scRepli-seq, aphidicolin singleG1 003

value: Bone


title: U2OS, scRepli-seq, aphidicolin singleG1 007


title: U2OS, scRepli-seq, aphidicolin singleG1 041


title: MB2141 xenograft, vehicle treated biol rep 1

description:
Library name: 2141D21V1
Column name in Raw_Counts_All_Samples.txt: 2141D21V1


title: U2OS, scRepli-seq, aphidicolin singleG1 042


title: 10L, NRAS, Y, 24hr

description: Library name: 139664

value: AML cell line

value: NRAS

tag: aso dose_(um)

tag: gilteritinib

value: Y

tag: gilt concentration_(um)


title: U2OS, scRepli-seq, aphidicolin singleG1 002

value: Sarcoma-derived


title: KMD04_Pre

tag: patient id

value: female

tag: sampling day

value: Pre


title: U2OS, scRepli-seq, aphidicolin singleG1 037


title: U2OS, scRepli-seq, aphidicolin singleG1 033


title: MB2141 cells, decitabine treated biol rep 2

description:
Library name: 2141DEC2
Column name in Raw_Counts_All_Samples.txt: 2141DEC2

value: Human melanoma cells

value: 1 week


title: KMD04_Post

tag: group

tag: gender


title: KMD12_Post

value: non-POD

tag: age


title: U2OS, scRepli-seq, untreated singleG1 043

value: Untreated


title: U2OS, scRepli-seq, untreated singleG1 044


title: MB2141 cells, decitabine treated biol rep 1

description:
Library name: 2141DEC1
Column name in Raw_Counts_All_Samples.txt: 2141DEC1

value: Decitabine


title: U2OS, scRepli-seq, untreated singleG1 042


title: KMD03_Post

value: blood

tag: anesthesia type


title: U2OS, scRepli-seq, aphidicolin singleG1 029

value: Aphidicolin


title: U2OS, scRepli-seq, untreated singleG1 041


title: MB2141 cells, untreated biol rep 2

description:
Library name: 2141UNT2
Column name in Raw_Counts_All_Samples.txt: 2141UNT2


title: KMD03_Pre

value: spinal

tag: anesthesia duration (m)


title: U2OS, scRepli-seq, untreated singleG1 040


title: U2OS, scRepli-seq, untreated singleG1 039


title: U2OS, scRepli-seq, untreated singleG1 038


title: KMD02_Post

value: POD

value: male

tag: operative time (m)


title: MB2141 cells, untreated biol rep 1

description:
Library name: 2141UNT1
Column name in Raw_Counts_All_Samples.txt: 2141UNT1

tag: time


title: U2OS, scRepli-seq, untreated singleG1 037

value: Bone


title: KMD10_Post

value: general

tag: blood loss (ml)


title: U2OS, scRepli-seq, untreated singleG1 036

tag: tissue


title: Cell-line resistance replicate 3

city: Hefei

first: Jun

state: Anhui

address: 17 Lujiang Road

institute: The First Affiliated Hospital of USTC, Anhui Provincial Hospital

description:
Library name: figure3_cell_line_resistance_rep3
Column name in Fig3_cell_line_FPKM_matrix_GEO.csv: figure3_cell_line_resistance_rep3

data_processing:
Raw sequencing reads were filtered to remove adapters and low-quality reads.
Clean reads were aligned to the human reference genome.
Gene expression values were calculated and reported as FPKM values for all samples.
Assembly: GRCh38
Supplementary files format and content: Fig3_cell_line_FPKM_matrix_GEO.csv is a comma-separated gene-level FPKM matrix for all 6 cell-line RNA-seq samples.

growth_protocol: Human breast cancer cell-line samples were cultured under standard in vitro conditions.

extract_protocol:
Total RNA was extracted from cell-line samples according to the manufacturer's protocol.
RNA-seq libraries were prepared from total RNA and sequenced using paired-end sequencing.

treatment_protocol: Samples were grouped according to treatment response status as sensitive or resistant.

value: breast

tag: cell line

value: breast cancer cell line

value: epithelial cancer cell

tag: genotype

value: breast cancer

value: resistant

tag: batch

value: cell line


title: KMD02_Pre

value: Pre


title: U2OS, scRepli-seq, untreated singleG1 035

tag: cell type

value: Sarcoma-derived

tag: treatment


title: Cell-line resistance replicate 2

description:
Library name: figure3_cell_line_resistance_rep2
Column name in Fig3_cell_line_FPKM_matrix_GEO.csv: figure3_cell_line_resistance_rep2


title: U2OS, scRepli-seq, aphidicolin singleG1 021


title: U2OS, scRepli-seq, untreated singleG1 034

value: Untreated


title: KMD01_Pre

value: non-POD

value: female


title: 11L, NRAS, Y, 4hr

description: Library name: 139654

value: AML cell line

value: NRAS G12D

value: NRAS

tag: aso dose_(um)

tag: gilteritinib

value: Y

tag: gilt concentration_(um)

tag: time -_gilteritinib_treatment


title: U2OS, scRepli-seq, untreated singleG1 033

value: Bone


title: Cell-line resistance replicate 1

description:
Library name: figure3_cell_line_resistance_rep1
Column name in Fig3_cell_line_FPKM_matrix_GEO.csv: figure3_cell_line_resistance_rep1


title: KMD01_Post

value: blood

tag: patient id

tag: group

tag: gender

value: spinal

tag: sampling day


title: U2OS, scRepli-seq, untreated singleG1 032


title: KMD09_Post

value: POD

tag: age

tag: anesthesia type

tag: anesthesia duration (m)

tag: operative time (m)


title: U2OS, scRepli-seq, untreated singleG1 031

tag: tissue

tag: cell line


title: U2OS, scRepli-seq, untreated singleG1 030


title: U2OS, scRepli-seq, untreated singleG1 029


title: UTI89/pRRK1_2019 biol rep 3

city: Salt Lake City

first: Matthew

middle: A

last: Mulvey

state: Utah

address: 1390 Presidents' Circle

department: Biology

institute: University of Utah

description:
Library name: Sample 14
all.counts_KO.tsv

data_processing:
Sequences were processed using BBduk v37.10 to trim adapters
Samtools v1.20 was used to read features
Differential gene expression was analyzed using DESeq2 in R v4.4.0
Assembly: Reads were mapped to the UTI89 reference strain GCF_000013265 using bowtie2 v2.5.3
Supplementary files format and content: txt file contains raw counts for each sample
Supplementary files format and content: csv contains l2fc for each gene

organism: Escherichia coli

source_name: whole cell

growth_protocol: Overnight cultures of UTI89/pRRK1, UTI89ΔmicC/pRRK1, and UTI89ΔmicC/pMicC were back diluted 1:100 into 5 mL LB and grown for 3 hours 15 min at 37°C, shaking 225 rpm.

extract_protocol:
RNA was extracted using a PureLinkTM RNA Mini Kit (Invitrogen)
Libraries constructed using the Nugen Ovation Prokaryotic RNA-seq kit as per manufacturer instructions

treatment_protocol: At the two-hour growth mark IPTG was added to each culture to a final concentration of 0.1 mM.

value: whole cell

tag: strain

value: Gram negative rod, bacteria

tag: genotype

value: WT with empty vector


title: Cell-line sensitive replicate 3

description:
Library name: figure3_cell_line_sensitive_rep3
Column name in Fig3_cell_line_FPKM_matrix_GEO.csv: figure3_cell_line_sensitive_rep3

value: breast

value: breast cancer cell line

tag: cell type

value: epithelial cancer cell

value: breast cancer

tag: treatment

value: sensitive

tag: batch

value: cell line


title: Cell-line sensitive replicate 2

description:
Library name: figure3_cell_line_sensitive_rep2
Column name in Fig3_cell_line_FPKM_matrix_GEO.csv: figure3_cell_line_sensitive_rep2


title: UTI89/pRRK1_2019 biol rep 2

description:
Library name: Sample 13
all.counts_KO.tsv


title: U2OS, scRepli-seq, untreated singleG1 027

value: Sarcoma-derived

value: Untreated


title: U2OS, scRepli-seq, untreated singleG1 026


title: Cell-line Treatment replicate 3

description: Library name: figure7_cell_line_treatment_rep3

value: treated


title: U2OS, scRepli-seq, untreated singleG1 024


title: UTI89/pMicC biol rep 4

description:
Library name: Sample 11
all.counts_OE.tsv

value: micC overexpressor


title: U2OS, scRepli-seq, untreated singleG1 023

value: Bone


title: Cell-line Treatment replicate 2

description: Library name: figure7_cell_line_treatment_rep2


title: U2OS, scRepli-seq, untreated singleG1 022


title: UTI89/pMicC biol rep 3

description:
Library name: Sample 10
all.counts_OE.tsv


title: Cell-line Treatment replicate 1

description: Library name: figure7_cell_line_treatment_rep1


title: U2OS, scRepli-seq, untreated singleG1 021


title: U2OS, scRepli-seq, untreated singleG1 020


title: U2OS, scRepli-seq, untreated singleG1 019


title: UTI89/pMicC biol rep 2

description:
Library name: Sample 9
all.counts_OE.tsv


title: Cell-line Control replicate 3

description: Library name: figure7_cell_line_control_rep3

value: control


title: UTI89/pMicC biol rep 1

description:
Library name: Sample 8
all.counts_OE.tsv


title: U2OS, scRepli-seq, untreated singleG1 017


title: Cell-line Control replicate 2

description: Library name: figure7_cell_line_control_rep2


title: U2OS, scRepli-seq, untreated singleG1 016


title: UTI89/pRRK1 biol rep 4

description:
Library name: Sample 7
all.counts_OE.tsv


title: U2OS, scRepli-seq, untreated singleG1 014


title: U2OS, scRepli-seq, untreated singleG1 015


title: Cell-line Control replicate 1

description: Library name: figure7_cell_line_control_rep1


title: U2OS, scRepli-seq, untreated singleG1 013


title: Cell-line LRIG1 plus EGFR L747A replicate 3

description: Library name: figure6_cell_line_lrig1_plus_egfr_l747a_rep3

data_processing:
Raw sequencing reads were filtered to remove adapters and low-quality reads.
Clean reads were aligned to the human reference genome.
Gene expression values were calculated and reported as FPKM values for all samples.
Assembly: GRCh38
Supplementary files format and content: Fig6_cell_line_FPKM_matrix_GEO.csv is a comma-separated gene-level FPKM matrix for all 12 cell-line RNA-seq samples.

treatment_protocol: Samples were grouped according to LRIG1 and EGFR L747A manipulation status.

value: LRIG1 plus EGFR L747A


title: U2OS, scRepli-seq, untreated singleG1 012


title: U2OS, scRepli-seq, untreated singleG1 011


title: UTI89/pRRK1 biol rep 2

description:
Library name: Sample 5
all.counts_OE.tsv


title: U2OS, scRepli-seq, untreated singleG1 010


title: U2OS, scRepli-seq, untreated singleG1 009


title: U2OS, scRepli-seq, untreated singleG1 008


title: Cell-line LRIG1 plus EGFR L747A replicate 1

description: Library name: figure6_cell_line_lrig1_plus_egfr_l747a_rep1


title: U2OS, scRepli-seq, untreated singleG1 007


title: UTI89ΔmicC/pRRK1 biol rep 3

description:
Library name: Sample 3
all.counts_KO.tsv

value: micC knockout


title: Cell-line LRIG1 replicate 3

description: Library name: figure6_cell_line_lrig1_rep3


title: U2OS, scRepli-seq, untreated singleG1 006


title: U2OS, scRepli-seq, untreated singleG1 005


title: UTI89ΔmicC/pRRK1 biol rep 2

description:
Library name: Sample 2
all.counts_KO.tsv

value: whole cell


title: Cell-line LRIG1 replicate 2

description: Library name: figure6_cell_line_lrig1_rep2


title: U2OS, scRepli-seq, untreated singleG1 004


title: UTI89ΔmicC/pRRK1 biol rep 1

description:
Library name: Sample 1
all.counts_KO.tsv

value: Gram negative rod, bacteria


title: U2OS, scRepli-seq, untreated singleG1 002


title: Standard WGBS, 50 ng Arabidopsis leaf DNA, replicate 3

city: München

first: Jie

last: Yang

state: Bavaria

address: Karlsfelder Str. 38a

country: Germany

institute: Technical University of Munich (TUM)

description:
Library name: S45_3
WGBS protocol, 50 ng input (standard control)

data_processing:
Raw paired-end reads were trimmed with fastp using a two-step procedure to remove adapter contamination and the 10-bp random-primer/Adaptase-derived 5' sequence bias.
Trimmed reads were aligned to the TAIR10 Arabidopsis thaliana reference genome using Bismark (--local mode, non-directional, bowtie2).
Aligned reads were deduplicated with deduplicate_bismark, sorted, and filtered to retain properly paired reads with MAPQ >= 30 using samtools.
Cytosine methylation calls were extracted from filtered alignments using bismark_methylation_extractor (--CX) and converted to per-cytosine CX reports with coverage2cytosine.
Missing cytosine methylation states were imputed from the CX reports using METHimpute (HMM-based binomial test); the complete workflow is implemented in MethylStar (https://github.com/jlab-code/MethylStar).
Assembly: TAIR10
Supplementary files format and content: Tab-separated genome-wide cytosine reports (Bismark coverage2cytosine --CX_context output) for each library. Columns: chromosome (TAIR10); position (TAIR10); strand; count methylated; count unmethylated; methylation context (CpG/CHG/CHH); trinucleotide context. No processed file is provided for P10pg_3 and P50pg_3, which were excluded from downstream methylation analyses due to low bisulfite conversion rate (see Table S1).

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Arabidopsis thaliana plants were grown at 23°C under long-day conditions (16 h light / 8 h dark).

extract_protocol:
Flash-frozen Arabidopsis thaliana leaf tissue was cryo-milled using a TissueLyser II and lysed with Proteinase K. A serial dilution series of the extracted genomic DNA (5 pg-50 ng) was processed using the EZ DNA Methylation-Direct kit (Zymo Research), which performs bisulfite conversion directly from the digested lysate without a separate DNA purification step.
Bisulfite-converted DNA was processed using a post-bisulfite adapter tagging (PBAT) workflow adapted from the single-cell methyl-seq (snmC-seq) protocol: random priming with a P5L-indexed primer (Klenow Fragment exo-), enzymatic removal of excess primer (Exonuclease I / rSAP), single-stranded adapter ligation to the 3' end using the xGen Adaptase module, and indexing PCR (KAPA HiFi HotStart, 19-21 cycles) to introduce P5/P7 indexes. Standard bulk WGBS libraries (50 ng input, samples S45_1-3) were prepared conventionally for comparison.

treatment_protocol: No treatment was applied.

value: leaf


title: U2OS, scRepli-seq, untreated singleG1 001


title: Cell-line LRIG1-minus replicate 3

description: Library name: figure6_cell_line_lrig1_minus_rep3

value: breast


title: HV0060_HSP_24h_rep3

city: Heidelberg

first: Ralph

last: Grand

address: Im Neunheimer feld 345

institute: Heidelberg University

description: Library name: HV0060_HSP_24h_rep3_R1.fastq.gz

data_processing:
RNA-seq data were processed using the snakePipes mRNA-seq workflow. Raw sequencing reads in FASTQ format were aligned to the human reference genome  with default settings, including adapter and quality trimming.
Gene-level quantification was performed with featureCounts
Assembly: hg38
Supplementary files format and content: tsv

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVECs) (Promo Cell, C-12203 and Innoprot, #P2020) were cultured in endothelial cell basal medium 2 (ECGM2, PromoCell, #C-22216) with supplement mix (PromoCell, #C-39216) under standard cell culture conditions. HUVECs were split when the confluency reached 80% using TrypLE (Thermo Fisher, 12605028). For experiments cells were passaged at 1:3 or 1:4 into T-75 flasks 2-3 days prior to heat shock treatment. All HUVECs were used between passage four and six.

extract_protocol:
Cells were isolated 0 hours and 24 hours post seeding, snap frozen and stored at -80°C.  RNA was isolated using a RNeasy UCP Micro Kit (Qiagen, RNeasy UCP Micro Kit, #73934). RNA concentration was measured using a NanoDrop 200c.
Sequencing libraries were generated from 100 ng of total RNA using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Cells in T75 flasks were heat shocked at 42°C for 1h in either a water bath placed inside a tissue culture incubator or a standard water bath, then returned to standard culturing conditions for recovery. Cells recovered between 3 hours in a 37°C cell culture incubator prior to the respective experiments.

value: HUVEC

value: Entothelial

value: Heatshock+Printed


title: U2OS, scRepli-seq, untreated singleG1 018


title: Standard WGBS, 50 ng Arabidopsis leaf DNA, replicate 2

description:
Library name: S45_2
WGBS protocol, 50 ng input (standard control)


title: U2OS, scRepli-seq, aphidicolin singleG1 001

value: Aphidicolin


title: HV0059_HS_24h_rep3

description: Library name: HV0059_HS_24h_rep3_R1.fastq.gz

value: Heatshock


title: Cell-line LRIG1-minus replicate 2

description: Library name: figure6_cell_line_lrig1_minus_rep2

value: epithelial cancer cell

value: breast cancer


title: UTI89/pRRK1 biol rep 3

description:
Library name: Sample 6
all.counts_OE.tsv

value: WT with empty vector


title: HV0058_P_24h_rep3

description: Library name: HV0058_P_24h_rep3_R1.fastq.gz

value: Printed


title: Standard WGBS, 50 ng Arabidopsis leaf DNA, replicate 1

description:
Library name: S45_1
WGBS protocol, 50 ng input (standard control)


title: HV0057_C_24h_rep3

description: Library name: HV0057_C_24h_rep3_R1.fastq.gz

value: Control


title: Cell-line LRIG1 plus EGFR L747A replicate 2

description: Library name: figure6_cell_line_lrig1_plus_egfr_l747a_rep2


title: UTI89/pRRK1 biol rep 1

description:
Library name: Sample 4
all.counts_OE.tsv


title: Cell-line LRIG1-minus replicate 1

description: Library name: figure6_cell_line_lrig1_minus_rep1


title: HV0048_HSP_24h_rep2

description: Library name: HV0048_HSP_24h_rep2_R1.fastq.gz


title: Low-input WGBS, 50 ng Arabidopsis leaf DNA, replicate 2

description:
Library name: P50ng_2
low_input protocol, 50 ng input


title: HV0047_HS_24h_rep2

description: Library name: HV0047_HS_24h_rep2_R1.fastq.gz


title: Cell-line Control replicate 3

description: Library name: figure6_cell_line_control_rep3


title: HV0046_P_24h_rep2

description: Library name: HV0046_P_24h_rep2_R1.fastq.gz