title: 25xGFA1 rep2, Copper treated, 45 min

description:
Library name: Sample 35
Column name in raw_counts.csv and row name in Samples.csv: 3662_45min

value: 45 min


title: 25xGFA1 rep2, Copper treated, 30 min

status: Public on Jul 24 2025

type: SRA

city: Davis

first: Ben

last: Montpetit

state: CA

address: One Shields Avenue

country: USA

institute: University of California, Davis

description:
Library name: Sample 34
Column name in raw_counts.csv and row name in Samples.csv: 3662_30min

library_source: transcriptomic

data_processing:
Sequences were trimmed of their UMIs,truseq adapters, and low quality sequences using Umi Tools v1.1.2 and bbduk (bbmap v38.79; k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Quality control checks were performed using Fastqc v0.11.9, before and after trimming steps
Assembly: The yeast genome was assembled using the STAR aligner v2.7.10a (--sjdbOverhang  99) and GCF_000146045.2_R64_genomics.fna hosted on the NCBI database
Trimmed sequences were aligned to the genome assembly using the STAR aligner v2.7.10a and output as Bam files(--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000)
Readcounts were extracted using samtools v1.10 and htseq v2.0.2
Supplementary files format and content: CSV file includes raw read count expression matrix for each sample (column) and gene (row); Sample.csv contains metadata required for downstream analysis

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Haploid, MAT A

growth_protocol: 5 mL of YPD media was inoculated from fresh grown plates and grown for ~8 hrs. Cultures were diluted to OD600 of 0.002 in 100 mL of YPD and grown overnight to reach OD600 of ~1.0. Cells were harvested, washed with copper-free minimal media (Formedium, CYN0901), and resuspended into 200 mL copper-free media such that OD600 = 0.25. Cells were grown for ~2 hrs, baseline samples were collected, and then cultures were induced with 500 mM CuSO4. Samples were collected 5, 10, 15, 20, 25, 30, 45, and 60 min post-CuSO4.

extract_protocol:
RNA was harvested using the Quick-RNA Fungal/Bacterial Miniprep kit (Zymo Research) excluding the kit's DNase I treatment process. RNA was treated with Turbo™ DNase for 30 min at 37°C and cleaned by RNA Clean & Concentrator-5 (Zymo Research).
Lexogen Quantseq 3' mRNA library seq kit

treatment_protocol: All samples were treated with 500 uM Copper Sulfate. 0 min samples are controls before treatment time course.

tag: strain background

tag: strain

tag: cell type

value: Haploid, MAT A

tag: genotype

value: GFA1 25x Gene array

tag: treatment

value: Copper Treatment

tag: time

value: 30 min


title: 25xGFA1 rep2, Copper treated, 25 min

description:
Library name: Sample 33
Column name in raw_counts.csv and row name in Samples.csv: 3662_25min

value: 25 min


title: TBB180

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

organism: Homo sapiens

source_name: lung biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human lung biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: rejection archetype cluster (nr, tcmr/mixed, nkrl, lowsft)

value: NR


title: TBB177


title: TBB178


title: 25xGFA1 rep2, Copper treated, 20 min

description:
Library name: Sample 32
Column name in raw_counts.csv and row name in Samples.csv: 3662_20min

value: 20 min


city: Bern

first: Irene

last: Paassen

address: Murtenstrasse 28

department: Biomedical Research

country: Switzerland

institute: Universität Bern

description: Library name: scRNA-seq part of multiome data AT-SHH15

library_source: transcriptomic single cell

data_processing:
Initial processing: cell-ranger arc (version 2.0.0), seurat (version 4.1.1) and signac (version 1.7.0)
Reads were mapped to GRCh38 and cell genotypes were annotated by sourorcell (Heaton et al., 2020)
ATAC peaks were merged using signac (version 1.7.0)
Good quality samples were filtered (ATAC counts < 50000 & > 800, RNA counts < 30000 & > 800, nucleosome signal < 1.5, TSS enrichment > 1, % of blacklist regions < 3%, % of mitochondrial genes < 20%)
Assembly: GRCh38
Supplementary files format and content: count matrix and metadata table

molecule: nuclear RNA

source_name: Brain

growth_protocol: ATRT tumoroids cultured in tumor stem medium

extract_protocol:
Organoids were mechanically dissociated into single cell and further homogenized using a douncer. After cell lysis,each organoid sample was filtered once using a 70 uM filter as well as a 40 uM filter. Intact single nuclei were sorted and two independent samples were mixed based on different gender (male with female). Between 10.000 and 40.000 nuclei were loaded on the ChipJ Chromatin Controller (10X Genomics).
Libraries were prepared followed naufacturere instruction (10X Genomics, protocol: CG000338 Rev D)

tag: tissue

value: Brain

tag: cell line

value: AT-SHH15 tumoroid


title: 25xGFA1 rep2, Copper treated, 10 min

description:
Library name: Sample 30
Column name in raw_counts.csv and row name in Samples.csv: 3662_10min

value: 10 min


description: Library name: scRNA-seq part of multiome data AT-SHH04

value: AT-SHH04 tumoroid


title: 25xGFA1 rep2, Copper treated, 15 min

description:
Library name: Sample 31
Column name in raw_counts.csv and row name in Samples.csv: 3662_15min

value: 15 min


title: ATRT SHH-9 patient tissue viably frozen

description: Library name: ATRT-SHH-9

library_source: genomic

data_processing:
Initial processing: cell-ranger arc (version 2.0.0), seurat (version 4.1.1) and signac (version 1.7.0)
Reads were mapped to GRCh38 and cell genotypes were annotated by sourorcell (Heaton et al., 2020)
ATAC peaks were merged using signac (version 1.7.0)
Good quality samples were filtered (ATAC counts < 50000 & > 800, RNA counts < 30000 & > 800, nucleosome signal < 1.5, TSS enrichment > 1, % of blacklist regions < 3%, % of mitochondrial genes < 20%)
Assembly: GRCh38
Supplementary files format and content: peak matrix and metadata table

molecule: genomic DNA

growth_protocol: Viably frozen tissue (10% DMSO, 90% FBS)

extract_protocol:
Tissue was minced into small pieces and further homogenized using a douncer. After cell lysis,each organoid sample was filtered once using a 70 uM filter as well as a 40 uM filter. Intact single nuclei were sorted and two independent samples were mixed based on different gender (male with female). Between 10.000 and 40.000 nuclei were loaded on the ChipJ Chromatin Controller (10X Genomics).
Libraries were prepared followed naufacturere instruction (10X Genomics, protocol: CG000338 Rev D)


title: 25xGFA1 rep1, Copper treated, 60 min

description:
Library name: Sample 28
Column name in raw_counts.csv and row name in Samples.csv: 3661_60min

value: 60 min


title: 25xGFA1 rep1, Copper treated, 5 min

description:
Library name: Sample 27
Column name in raw_counts.csv and row name in Samples.csv: 3661_5min

value: 5 min


title: 25xGFA1 rep2, Untreated, 0 min

description:
Library name: Sample 29
Column name in raw_counts.csv and row name in Samples.csv: 3662_0min

value: Untreated

value: 0 min(untreated)


title: TBB175


title: TBB176

value: NKRL


title: TBB174


title: 25xGFA1 rep1, Copper treated, 30 min

description:
Library name: Sample 25
Column name in raw_counts.csv and row name in Samples.csv: 3661_30min

value: Haploid, MAT A


title: TBB171


title: ATRT SHH-8 patient tissue viably frozen

description: Library name: ATRT-SHH-8


title: 25xGFA1 rep1, Copper treated, 25 min

description:
Library name: Sample 24
Column name in raw_counts.csv and row name in Samples.csv: 3661_25min

value: GFA1 25x Gene array


title: 25xGFA1 rep1, Copper treated, 20 min

description:
Library name: Sample 23
Column name in raw_counts.csv and row name in Samples.csv: 3661_20min

value: Copper Treatment


title: ATRT SHH-7 patient tissue viably frozen

description: Library name: ATRT-SHH-7


title: TBB170


title: ATRT MYC-4 patient tissue viably frozen

description: Library name: ATRT-MYC-4


title: 25xGFA1 rep1, Copper treated, 15 min

description:
Library name: Sample 22
Column name in raw_counts.csv and row name in Samples.csv: 3661_15min


title: TBB173


title: ATRT SHH-10 patient tissue viably frozen

description: Library name: ATRT-SHH-10


title: ATRT SHH-6 patient tissue viably frozen

description: Library name: ATRT-SHH-6


title: 25xGFA1 rep1, Copper treated, 10 min

description:
Library name: Sample 21
Column name in raw_counts.csv and row name in Samples.csv: 3661_10min


title: 25xGFA1 rep1, Untreated, 0 min

description:
Library name: Sample 20
Column name in raw_counts.csv and row name in Samples.csv: 3661_0min


title: TBB169

value: TCMR/Mixed


title: 25xGFA1rep1, Copper treated, 45 min

description:
Library name: Sample 26
Column name in raw_counts.csv and row name in Samples.csv: 3661_45min

value: 45 min


title: ATRT TYR-5 patient tissue viably frozen

description: Library name: ATRT-TYR-5


title: Wildtype rep2, Copper treated, 60 min

description:
Library name: Sample 18
Column name in raw_counts.csv and row name in Samples.csv: 1051_2_60min

value: WT


title: ATRT TYR-6 patient tissue viably frozen

description: Library name: ATRT-TYR-6


title: TBB168


title: Wildtype rep3, Untreated, 0 min

description:
Library name: Sample 19
Column name in raw_counts.csv and row name in Samples.csv: 1051_3_0min


title: Wildtype rep2, Copper treated, 45 min

description:
Library name: Sample 16
Column name in raw_counts.csv and row name in Samples.csv: 1051_2_45min


title: Wildtype rep2, Copper treated, 30 min

description:
Library name: Sample 15
Column name in raw_counts.csv and row name in Samples.csv: 1051_2_30min

value: 30 min


title: Wildtype rep2, Copper treated, 5 min

description:
Library name: Sample 17
Column name in raw_counts.csv and row name in Samples.csv: 1051_2_5min


title: AT-MYC08 tumoroid model treated with Thiostrepton replicate 2

description: Library name: AT08Thio_2

data_processing:
Initial processing: adapters trimmed with trim galore (version 0.65), reads aligned with STAR (version 2.7.2).
Read counts quantified with featureCounts (version 1.6.7).
RNA counts were merged using R (version 4.2.0) and analyzed using DESeq2 (version 1.36.0).
Assembly: GRCh38
Supplementary files format and content: unnormalized count matrix and metadata table

source_name: ATRT tumoroid model

growth_protocol: Tumoroid model

extract_protocol:
1xSHH (AT-SHH04) and 1xMYC (AT-MYC08) tumoroid models were treated with IC80 of different drugs for 48h. Cells treated with only DMSO of the same model were used as negative controls. One million cells were plated for each condition in 2ml TSM in one well of 6-well suspension plates (Greiner Bio-One). After 48h, cells were harvested and washed once with 10ml ice-cold DMEM, subsequently centrifuged at 200 × G for 5 min at 4 °C. Cell pallet was snap-frozen using liquid nitrogen and stored at -80 °C until Trizol extraction. Total RNA was extracted from tumoroid samples using Trizol reagent (Invitrogen). RNA quality and quantity were assessed using Bioanalyzer2100 RNA Nano 6000 chips (Agilent) and Qubit measurement.
Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s protocol. Standard paired-end (PE150) approach with the Illumina NovaSeq 6000 platform was performed at Novogene (Germany).

value: ATRT tumoroid model


title: Wildtype rep2, Copper treated, 25 min

description:
Library name: Sample 14
Column name in raw_counts.csv and row name in Samples.csv: 1051_2_25min

value: 25 min


title: Wildtype rep2, Copper treated, 20 min

description:
Library name: Sample 13
Column name in raw_counts.csv and row name in Samples.csv: 1051_2_20min

value: 20 min


title: AT-MYC08 tumoroid model treated with Thiostrepton replicate 1

description: Library name: AT08Thio_1


title: TBB166

value: lowSFT


title: Wildtype rep2 Copper treated, 10 min

description:
Library name: Sample 11
Column name in raw_counts.csv and row name in Samples.csv: 1051_2_10min

value: 10 min


title: TBB167

value: NR


title: Wildtype rep2, Untreated, 0 min

description:
Library name: Sample 10
Column name in raw_counts.csv and row name in Samples.csv: 1051_2_0min


title: AT-MYC08 tumoroid model treated with RO31-8220 mesylate replicate 2

description: Library name: AT08RO31_2


title: TBB163


title: AT-MYC08 tumoroid model treated with Entinostat replicate 2

description: Library name: AT08Enti_2


title: AT-MYC08 tumoroid model treated with RO31-8220 mesylate replicate 1

description: Library name: AT08RO31_1


title: Wildtype rep1, Copper treated, 5 min

description:
Library name: Sample 8
Column name in raw_counts.csv and row name in Samples.csv: 1051_1_5min

value: 5 min


title: Wildtype rep1, Copper treated, 45 min

description:
Library name: Sample 7
Column name in raw_counts.csv and row name in Samples.csv: 1051_1_45min


title: Wildtype rep1, Copper treated, 60 min

description:
Library name: Sample 9
Column name in raw_counts.csv and row name in Samples.csv: 1051_1_60min

value: 60 min


title: TBB162


title: AT-MYC08 tumoroid model treated with Entinostat replicate 1

description: Library name: AT08Enti_1


title: AT-MYC08 tumoroid model treated with DMSO replicate 1

description: Library name: AT08DMSO_1


title: TBB164


title: Wildtype rep1, Copper treated, 30 min

description:
Library name: Sample 6
Column name in raw_counts.csv and row name in Samples.csv: 1051_1_30min


title: Wildtype rep2, Copper treated, 15 min

description:
Library name: Sample 12
Column name in raw_counts.csv and row name in Samples.csv: 1051_2_15min

value: 15 min


title: TBB161


title: TBB165


title: Wildtype rep1, Copper treated, 25 min

description:
Library name: Sample 5
Column name in raw_counts.csv and row name in Samples.csv: 1051_1_25min


title: TBB160

value: NKRL


title: Wildtype rep1, Copper treated, 20 min

description:
Library name: Sample 4
Column name in raw_counts.csv and row name in Samples.csv: 1051_1_20min

value: Haploid, MAT A


title: AT-SHH04 tumoroid model treated with Thiostrepton replicate 1

description: Library name: AT04Thio_1


title: Wildtype rep1, Copper treated, 15 min

description:
Library name: Sample 3
Column name in raw_counts.csv and row name in Samples.csv: 1051_1_15min


title: TBB159


title: TBB158


title: Wildtype rep1, Copper treated, 10 min

description:
Library name: Sample 2
Column name in raw_counts.csv and row name in Samples.csv: 1051_1_10min


title: AT-SHH04 tumoroid model treated with RO31-8220 mesylate replicate 2

description: Library name: AT04RO31_2


title: TBB156


title: TBB157


title: AT-SHH04 tumoroid model treated with RO31-8220 mesylate replicate 1

description: Library name: AT04RO31_1


title: Wildtype rep1, Untreated, 0 min

description:
Library name: Sample 1
Column name in raw_counts.csv and row name in Samples.csv: 1051_1_0min

value: Untreated

value: 0 min(untreated)


title: WVGAS10_M92_cMLS_ERY_REP_2

city: Morgantown

first: Lei

last: Wang

state: West Virginia

address: 64 Medical Center Drive

department: Department of Microbiology, Immunology and Cell Biology

institute: west virginia university

description: Library name: Sample 5

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence with the QIAGEN CLC Genomics Workbench (version 23) "Rule-based" proprietary trimming tool in the transcriptomic analysis tools according to a quality score of 0.05 (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/801/index.php?manual=Sequencing_data_analyses.html)
Trimmed reads were mapped in pairs to the MGAS2221 genome (Bioproject accession PRJNA562873) and the pRW35-like plasmid sequence (GenBank accession NZ_CP032701) using the CLC genomic workbench proprietary CLC Mapper tool. (parameters were as follows: mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction 0.8)   (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/801/index.php?manual=Read_mapping.html)
The CLC genomics workbench proprietary RNA-Seq analysis pipeline was used to perform read count extraction and normalization. Normalization was done using median-of-ratios (DESeq2). (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/801/index.php?manual=Statistical_analysis_identifying_differential_expression.html)
Differential gene expression was determined using DESeq2 as part of the CLC genomics workbench proprietary RNA-Seq analysis pipeline. The analysis of erythromycin treatment versus control was done for each strain (cMLS vs iMLS phenotype) independently, resulting in two pairwise comparisons. DESeq2 uses a generalized linear model framework based on negative binomial distribution.
Assembly: the MGAS2221 genome
Supplementary files format and content: reads_count.txt
Supplementary files format and content: First colum: Name; second column: Chromosome; third column: region; columns thereafter: reads count  for each sample
Supplementary files format and content: WVGAS10_cMLS_NO_ERY_versus_WVGAS10_cMLS_ERY.txt,  and WVGAS15_iMLS_NO_ERY_versus WVGAS15_iMLS_ERY.txt
Supplementary files format and content: First colum: Name; second column: Chromosome; third column: region; fourth column: Max Group Mean; fifth group column: Log2 fold change; sixth column: fold change; seventh column: p-value; eight column: FDR p-value; nineth column Bonferroni

organism: Streptococcus pyogenes

extract_protocol:
Cells collected in RNA protect and total RNA was extracted using the the IBI Scientific rBAC Mini RNA Bacteria Kit protocol adapted for GAS. RNA was isolated from cells. DNAse treated.
RNA libraries of cDNA for RNA sequencing were prepared by Admera Health using the QIAseq FastSelect rRNA 5S/16S/23S (Bacteria) kit + NEB Ultra II and the Directional RNA Library Prep Kit 2x150, according to Manufactor Instructions.

treatment_protocol: Bacterial isolates were cultured overnight on brain heart infusion agar at 37°C with 5% CO2. Cultures were used to inoculate Todd Hewitt Yeast media at a starting OD600nm of 0.05. At log-phase (OD600nm 0.5) a final concentration of 10 g/mL erythromycin was added to half of the culture, followed by 1-hour of incubation.

tag: mlsb sub-phenotype

value: cMLS

value: 10 µg/mL erythromycin

value: 1 hour


title: TBB155


title: AT-SHH04 tumoroid model treated with Entinostat replicate 2

description: Library name: AT04Enti_2


title: Dec1(-/-) Week4 SC-islet

city: Philadelphia

first: Mai

last: Liu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: Sample 17

data_processing:
Raw FASTQ files were aligned to the human reference genome (hg19, February 2009 assembly) using STAR aligner with default parameters, generating sorted BAM files. Gene-level quantification was performed using HTSeq-count  in union mode.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files containing Htseq output for each sample

source_name: HUES 8 hESC line

growth_protocol: Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ºC 5% CO2 incubator. A six-stage differentiation protocol was applied next (Pollock et al., STAR protocols 2023)

extract_protocol:
Total RNA was isolated using the miRNeasy kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was depleted from total RNA using the Ribo-Zero Gold Kit (Epicentre, Madison, WI).
Directional cDNA libraries were prepared using a KAPA Biosystems Stranded RNA-seq Library Preparation kit, pooled, and sequenced on an Illumina HiSeq 2500 platform across multiple lanes.

value: HUES 8 hESC line


title: AT-SHH04 tumoroid model treated with Thiostrepton replicate 2

description: Library name: AT04Thio_2

value: ATRT tumoroid model


title: AT-SHH04 tumoroid model treated with Entinostat replicate 1

description: Library name: AT04Enti_1


title: TBB154


title: AT-SHH04 tumoroid model treated with DMSO replicate 2

description: Library name: AT04DMSO_2


title: Dec1(-/-) Week1 SC-islet

description: Library name: Sample 14


title: Dec1(-/-) Week2 SC-islet

description: Library name: Sample 15


title: WT Week4 SC-islet

description: Library name: Sample 13

value: WT


title: HUVECs, shRING1B, biol rep 3

city: Guangzhou

first: Jingyuan

last: Zhang

address: 190 Kaiyuan Avenue,Science Park

country: China

institute: Guangzhou National Labratory

data_processing:
The quality control was performed with TrimGalore (v0.6.10, https://github.com/FelixKrueger/TrimGalore)
Clean reads were subsequently aligned to the human genome (GRCh38) using STAR (v2.7.10b)18, and only uniquely mapped reads were retained.
Reads summarization was conducted using featureCounts (v2.0.6)19 to generate the raw count table.
Assembly: GRCh38
Supplementary files format and content: Microsoft EXCEL file includes FPKM values for each Samples

source_name: Endothelial cells

growth_protocol: HUVECs were maintained in EGM2 medium (Lonza) with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using RNeasy Mini Kit (QIAGEN), 1.0μg of total RNA was used for the construction sequencing librabies
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® （NR604-01/02）following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Endothelial cells

value: RING1B knockdown


title: WT Week3 SC-islet

description: Library name: Sample 12


title: HUVECs, shRING1B, biol rep 2


title: Dec1(-/-) Week3 SC-islet

description: Library name: Sample 16


title: WT Week2 SC-islet

description: Library name: Sample 11


title: WT Week1 SC-islet

description: Library name: Sample 10


title: AT-SHH04 tumoroid model treated with DMSO replicate 1

description: Library name: AT04DMSO_1


title: HUVECs, shRING1A, biol rep 3

value: RING1A knockdown


title: Dec1(-/-) Week2 CD49+ beta cells

description: Library name: Sample 9


title: TBB152

value: NR


title: KI-538_combination_rep1

city: Cleveland

first: Han

state: Ohio

address: 2109 Adelbert Rd, Wood Building, RT400

institute: Case Western Reserve University

description:
Library name: CPP-27
MCF-7 D538G ER knock-in cells treated with fulvestrant+MTO combination for 48h, replicate 1

data_processing:
Raw sequencing reads (75 bp single-end) were quality controlled using FastQC to trim adapter sequences and assess read quality. Trimmed reads were aligned to the human reference genome (GENCODE v38) using HISAT2. Aligned reads were processed for gene expression quantification to generate count matrices.
Assembly: Human genome GENCODE v38
Supplementary files format and content: FPKM (Fragments Per Kilobase of transcript per Million mapped reads) expression matrix for all samples. Rows represent genes (gene symbols or Ensembl IDs) and columns represent individual samples

growth_protocol: MCF-7 cells (wildtype, Y537S ER knock-in, and D538G ER knock-in) were cultured in DMEM supplemented with 10% FBS at 37°C with 5% CO2. Cells were maintained in exponential growth phase and passaged regularly. All cell cultures were routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted from treated cells using RNeasy Plus Mini Kit (Qiagen, #74134) according to manufacturer's instructions. RNA quality and quantity were assessed prior to library preparation.
cDNA libraries were generated at the on-campus Genomics Core Facility using standard RNA-seq library preparation protocols. Libraries were prepared for single-end sequencing on the Illumina NextSeq 550 platform.

treatment_protocol: Cells were treated with vehicle control (DMSO), fulvestrant (1 μM), MTO (1 μM) or combination treatment (fulvestrant + MTO) for 48 hours. All treatments were performed in biological duplicate.

value: breast cancer cell line

value: D538G ER knock-in

value: fulvestrant+MTO

tag: batch


title: KI-538_T4_rep1

description:
Library name: CPP-25
MCF-7 D538G ER knock-in cells treated with MTO 1μM for 48h, replicate 1

value: MTO 1μM


title: KI-538_ICI_rep2

description:
Library name: CPP-24
MCF-7 D538G ER knock-in cells treated with fulvestrant 1μM for 48h, replicate 2

value: fulvestrant 1μM


title: Icas9 Week2 CD49+ beta cells

description: Library name: Sample 8


title: HUVECs, shRING1A, biol rep 2


title: HUVECs, shRING1A, biol rep 1


title: HUVECs, shRING1B, biol rep 1


title: TBB153

value: NKRL


title: KI-538_DMSO_rep2

description:
Library name: CPP-22
MCF-7 D538G ER knock-in cells treated with DMSO control for 48h, replicate 2

value: DMSO


title: KI-538_ICI_rep1

description:
Library name: CPP-23
MCF-7 D538G ER knock-in cells treated with fulvestrant 1μM for 48h, replicate 1


title: HUVECs, shControl, biol rep 3


title: Dec1(-/-) Week1 CD49+ beta cells

description: Library name: Sample 6


title: TBB149


title: TBB146


title: TBB148


title: TBB150


title: KI-538_DMSO_rep1

description:
Library name: CPP-21
MCF-7 D538G ER knock-in cells treated with DMSO control for 48h, replicate 1


title: HUVECs, shControl, biol rep 2


title: Icas9 Week1 CD49+ beta cells

description: Library name: Sample 5


title: KI-537_combination_rep2

description:
Library name: CPP-18
MCF-7 Y537S ER knock-in cells treated with fulvestrant+MTO combination for 48h, replicate 2

value: Y537S ER knock-in


title: HUVECs, shControl, biol rep 1


title: WT Week1 CD49+ beta cells

description: Library name: Sample 4


title: WT Week2 CD49+ beta cells

description: Library name: Sample 7


title: KI-537_combination_rep1

description:
Library name: CPP-17
MCF-7 Y537S ER knock-in cells treated with fulvestrant+MTO combination for 48h, replicate 1


title: HUVECs, Control, CUT&Tag, biol rep 3

data_processing:
The sequencing data were analyzed using the Novozyme cloud platform (http://cloud.vazyme.com:83).
Read alignment was typically performed using Bowtie2 with the options: --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
For peak calling, the callpeak command from MACS2 was utilized with the parameters: -t KO-14.rmMT.bam -g mm -f BAMPE -n KO-14 --keep-dup=all --outdir.
Assembly: hg38
Supplementary files format and content: bigWig, narrow Peak (except for control samples)
Library strategy: CUT&Tag

extract_protocol:
The CUT&Tag process was conducted following the instructions provided in the CUT&Tag Kit (Vazyme).
Library construction involved the use of the CUT&Tag kit, and the library quality was assessed by Annoroad, and the libraries were sequenced using Illumina Novaseq.

tag: chip antibody


title: Dec1(-/-) Week0 CD49+ beta cells

description: Library name: Sample 3


title: TBB147

value: TCMR/Mixed


title: KI-537_T4_rep2

description:
Library name: CPP-16
MCF-7 Y537S ER knock-in cells treated with MTO 1μM for 48h, replicate 2


title: KI-538_T4_rep2

description:
Library name: CPP-26
MCF-7 D538G ER knock-in cells treated with MTO 1μM for 48h, replicate 2


title: TBB145


title: HUVECs, Control, CUT&Tag, biol rep 2


title: HUVECs, Control, CUT&Tag, biol rep 1


title: KI-538_combination_rep2

description:
Library name: CPP-28
MCF-7 D538G ER knock-in cells treated with fulvestrant+MTO combination for 48h, replicate 2


title: HUVECs, RING1B, CUT&Tag, biol rep 3

value: RING1B(CST, 5694)


title: GSC4_KO404-4

city: Nantes

first: Julie

last: Gavard

address: 8 quai Moncousu

country: France

institute: INSERM

description:
Library name: sample 20
96_GSC4_KO404-4
GSC4-KO404.txt

data_processing:
FASTQ quality was assessed with FastQC and summarized using MultiQC (report linked in report.html). Read distribution per sample was visualized in four categories: Assigned, Aligned, Refseq_Total, and Refseq_UMI. Adequate coverage was defined as ≥200,000 Refseq_UMI reads and ≥5,000 detected genes per sample.
Séquençage paired-end 50 cycles (16-58)- OBCG (On-board Clustering Generation) - Hiseq Rapid SBS kit v2 50 cycles (ref #FC-402-4022) : RGT22886202; RGT22798176 - Hiseq Rapid PE cluster kit v2 (ref #GD-402-4002) : RGT22958484 - Flowcell : H2V7JBCX3 - Run : 190710_SNL149_0242_BH2V7JBCX3
Reads were demultiplexed by barcode to generate one FASTQ file per sample; unrecognized barcodes were stored in unknown.fastq. Reads were aligned to the species reference transcriptome using BWA. Aligned reads were counted to produce an expression matrix (DGE.unq.refseq.umi.dat) and summary statistics (DGE.unq.well_summary.dat). Unassigned read counts were stored in DGE.unknown_indexes.count.
Supplementary files format and content: log2FoldChange in txt format
Supplementary files format and content: expr*.tsv

source_name: brain, glioblastoma stem cell

growth_protocol: Patient-derived mesenchymal GSCs were maintained as non-adherent tumorspheres in NS34 serum-free media (DMEM/F12 with N2, G5, and B27 supplements, plus Glutamax and antibiotics, Life Technologies).

extract_protocol:
Total RNA was extracted using RNAesay kit Qiagen. Total RNA was extracted by the user. Quantity and purity were assessed using Nanodrop. RNA integrity was checked on Bioanalyzer (Agilent). Samples below 25ng/μL were re-diluted. RIN >9 for most samples.
Samples were diluted to 2.5 ng/μl, and 10 ng (4 μl) of each sample was randomly distributed on a 96-well plate. Barcodes were assigned and reverse transcription was performed. Samples were pooled and purified using the Zymo kit, followed by exonuclease treatment. Libraries were PCR-amplified (12 cycles), purified with magnetic beads, and double-stranded DNA was quantified. Tagmentation was performed using the Zymo kit, followed by a second PCR amplification (7 cycles) and magnetic bead purification. Final size selection of target fragments was done using magnetic beads.

treatment_protocol: WT and KO cells were grown similarly

value: brain, glioblastoma stem cell

value: glioblastoma stem like cell

value: KO JAM3

value: growing culture


title: GSC4_KO404-3

description:
Library name: sample 19
95_GSC4_KO404-3
GSC4-KO404.txt


title: HUVECs, RING1B, CUT&Tag, biol rep 2

value: Endothelial cells

value: WT


title: Icas9 Week0 CD49+ beta cells

description: Library name: Sample 2

value: HUES 8 hESC line


title: WT Week0 CD49+ beta cells

description: Library name: Sample 1


title: GSC4_KO404-2

description:
Library name: sample 18
94_GSC4_KO404-2
GSC4-KO404.txt


title: HUVECs, RING1B, CUT&Tag, biol rep 1


title: GSC4_KO404-1

description:
Library name: sample 17
93_GSC4_KO404-1
GSC4-KO404.txt


title: HUVECs, RING1A, CUT&Tag, biol rep 3


title: KI-537_DMSO_rep1

description:
Library name: CPP-11
MCF-7 Y537S ER knock-in cells treated with DMSO control for 48h, replicate 1

value: breast cancer cell line


title: KI-537_T4_rep1

description:
Library name: CPP-15
MCF-7 Y537S ER knock-in cells treated with MTO 1μM for 48h, replicate 1


title: KI-537_ICI_rep2

description:
Library name: CPP-14
MCF-7 Y537S ER knock-in cells treated with fulvestrant 1μM for 48h, replicate 2


title: KI-537_ICI_rep1

description:
Library name: CPP-13
MCF-7 Y537S ER knock-in cells treated with fulvestrant 1μM for 48h, replicate 1


title: KI-537_DMSO_rep2

description:
Library name: CPP-12
MCF-7 Y537S ER knock-in cells treated with DMSO control for 48h, replicate 2


title: KI-Ctrl_combination_rep2

description:
Library name: CPP-8
MCF-7 wildtype cells treated with fulvestrant+MTO combination for 48h, replicate 2

value: wildtype


title: AT-MYC08 tumoroid model treated with DMSO replicate 2

description: Library name: AT08DMSO_2

value: ATRT tumoroid model


title: GSC4_KO409-4

description:
Library name: sample 16
92_GSC4_KO409-4
GSC4-KO409.txt


title: HUVECs, RING1A, CUT&Tag, biol rep 2


title: KI-Ctrl_combination_rep1

description:
Library name: CPP-7
MCF-7 wildtype cells treated with fulvestrant+MTO combination for 48h, replicate 1

value: fulvestrant+MTO


title: HUVECs, RING1A, CUT&Tag, biol rep 1


title: GSC4_KO409-3

description:
Library name: sample 15
91_GSC4_KO409-3
GSC4-KO409.txt


title: KI-Ctrl_T4_rep2

description:
Library name: CPP-6
MCF-7 wildtype cells treated with MTO 1μM for 48h, replicate 2

value: MTO 1μM


title: HUVECs, H2AK119ub, CUT&Tag, biol rep 3


title: GSC4_KO409-2

description:
Library name: sample 14
90_GSC4_KO409-2
GSC4-KO409.txt


title: HUVECs, H2AK119ub, CUT&Tag, biol rep 2


title: KI-Ctrl_T4_rep1

description:
Library name: CPP-5
MCF-7 wildtype cells treated with MTO 1μM for 48h, replicate 1


title: KI-Ctrl_ICI_rep2

description:
Library name: CPP-4
MCF-7 wildtype cells treated with fulvestrant 1μM for 48h, replicate 2

value: fulvestrant 1μM


title: GSC4_NC1-4

description:
Library name: sample 12
88_GSC4_NC1-4
GSC4-KO404.txt
GSC4-KO409.txt


title: HUVECs, H2AK119ub, CUT&Tag, biol rep 1


title: KI-Ctrl_ICI_rep1

description:
Library name: CPP-3
MCF-7 wildtype cells treated with fulvestrant 1μM for 48h, replicate 1


title: pt9 and controls, sort 2 plate 18

city: Oxford

first: Sven

last: Turkalj

address: John Radcliffe Hospital/Headley Way, Oxford OX3 9DS

department: Radcliffe Department of Medicine

country: United Kingdom

institute: WIMM

description:
scRNA-seq data from TARGET-seq+ (pt9 and controls)
raw_counts_1.txt.gz
IVO_S2PL18

data_processing:
Transcriptome sequencing data were demultiplexed into fastq files for each plate with a unique i7-i5 index combination using bcl2fastq. These files contained reads from up to 384 cells with shared plate indexes. A custom python pipeline was used to further demultiplex and map the sequencing reads. First, reads from each plate were demultiplexed using the 14 bp single-cell barcode sequence in Read1 using cutadapt (v3.4). Concurrently, cDNA reads (Read2) were trimmed for polyA tails, Nextera adapters and low-quality reads. This generated individual fastq files with single-ended cDNA reads corresponding to each single-cell barcode. Reads were then mapped to the hg38 reference genome and ERCC92 transcripts with STARsolo (v2.7.10a) using the GENCODE v38 reference gene annotation (filtered to include protein coding genes and long non-coding RNAs), and counts for each gene were obtained using default parameters except the following: ‘--soloType SmartSeq --soloFeatures GeneFull_Ex50pAS’. Sequencing and mapping quality metrics were calculated with FastQC (v0.11.9), Samtools flagstat (v1.12), MultiQC (v1.11) and the outputs of STAR.
Assembly: hg38
Supplementary files format and content: Raw counts derived from pre-processing of raw FASTQ files
Library strategy: plate-based scRNA-Seq coupled to single-cell genotyping

source_name: bone marrow

extract_protocol:
NGS library preparation and purification
TARGET-seq+

value: bone marrow

value: primary sample

value: bone marrow mononuclear cells


title: GSC4_KO409-1

description:
Library name: sample 13
89_GSC4_KO409-1
GSC4-KO409.txt


title: GSC4_NC1-3

description:
Library name: sample 11
87_GSC4_NC1-3
GSC4-KO404.txt
GSC4-KO409.txt


title: KI-Ctrl_DMSO_rep2

description:
Library name: CPP-2
MCF-7 wildtype cells treated with DMSO control for 48h, replicate 2

value: DMSO


title: pt9 and controls, sort 2 plates 16-17

description:
scRNA-seq data from TARGET-seq+ (pt9 and controls)
raw_counts_1.txt.gz
IVO_S2PL16_17


title: KI-Ctrl_DMSO_rep1

description:
Library name: CPP-1
MCF-7 wildtype cells treated with DMSO control for 48h, replicate 1


title: GSC4_NC1-2

description:
Library name: sample 10
86_GSC4_NC1-2
GSC4-KO404.txt
GSC4-KO409.txt

value: brain, glioblastoma stem cell


title: GSC4_NC1-1

description:
Library name: sample 9
85_GSC4_NC1-1
GSC4-KO404.txt
GSC4-KO409.txt

value: glioblastoma stem like cell


title: pt9 and controls, plates 15-16

description:
scRNA-seq data from TARGET-seq+ (pt9 and controls)
raw_counts_1.txt.gz
IVO_S1PL15_16


title: pt9 and controls, plates 13-14

description:
scRNA-seq data from TARGET-seq+ (pt9 and controls)
raw_counts_1.txt.gz
IVO_S1PL13_14


title: GSC1_KO110-4

description:
Library name: sample 8
84_GSC1_KO110-4
GSC1-KO110.txt

value: KO JAM3


title: pt9 and controls, plates 11-12

description:
scRNA-seq data from TARGET-seq+ (pt9 and controls)
raw_counts_1.txt.gz
IVO_S1PL11_12


title: GSC1_KO110-3

description:
Library name: sample 7
83_GSC1_KO110-3
GSC1-KO110.txt

value: growing culture


title: pt9 and controls, plates 9-10

description:
scRNA-seq data from TARGET-seq+ (pt9 and controls)
raw_counts_1.txt.gz
IVO_S1PL09_10


title: GSC1_KO110-2

description:
Library name: sample 6
82_GSC1_KO110-2
GSC1-KO110.txt


title: Patient 409 PDOs, control, biological replicate 2

city: Boston

first: Christina

middle: S

last: Ennis

state: Massachusetts

address: 72 E Concord St, K520, K520

institute: Boston University

description:
Library name: 409C2
10X Genomics

data_processing:
Raw sequencing reads were processed using Cell Ranger v6.0.1 with default parameters to generate feature-barcode matrices aligned to the human reference genome GRCh38.p14. Seurat v5.0.1 was used for quality control (excluding cells with >20% mitochondrial reads or extreme gene counts), normalization (SCTransform), and clustering (PCA + Louvain).
Assembly: GRCh38.p14 (human)
Supplementary files format and content: tab-separated value files and matrix files.

molecule: polyA RNA

source_name: Breast tumor

growth_protocol: Breast tumor tissues were enzymatically digested and cultured as PDOs in Geltrex BME domes using a defined medium optimized to preserve stromal and immune cell populations. PDOs were maintained in 24-well plates at 37°C, 5% CO₂ for 3 days prior to downstream processing.

extract_protocol:
PDOs were enzymatically dissociated into single-cell suspensions using TrypLE Express. Cells were filtered through a 40 µm strainer, stained with DAPI, and live cells were sorted by FACS (FACSAria II). Cell suspensions were processed immediately for single-cell RNA-seq library preparation.
Single cells were loaded onto the 10X Genomics Chromium Controller and libraries were constructed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Libraries were sequenced on the Illumina NextSeq 2000 platform targeting ~30,000 reads per cell.

treatment_protocol: PDOs were treated with 5,000 exosome particles per estimated PDO cell. Exosomes were isolated from plasma of ND and T2D human donors using size-exclusion chromatography and added to the culture medium. PDOs were incubated for 3 days to allow exosome uptake.

value: Breast tumor

tag: subject id

value: Patient 409

value: Control


title: Patient 409 PDOs, type 2 diabetic exosome treated, biological replicate 2

description:
Library name: 409T2
10X Genomics

value: T2D exosomes


title: Patient 409 PDOs, nondiabetic exosome treated, biological replicate 2

description:
Library name: 409N2
10X Genomics

value: ND exosomes


title: Patient 409 PDOs, type 2 diabetic exosome treated, biological replicate 1

description:
Library name: 409T1
10X Genomics


title: pt9 and controls, plates 7-8

description:
scRNA-seq data from TARGET-seq+ (pt9 and controls)
raw_counts_1.txt.gz
IVO_S1PL07_08


title: GSC1_KO110-1

description:
Library name: sample 5
81_GSC1_KO110-1
GSC1-KO110.txt


title: Patient 409 PDOs, nondiabetic exosome treated, biological replicate 1

description:
Library name: 409N1
10X Genomics


title: pt9 and controls, plates 5-6

description:
scRNA-seq data from TARGET-seq+ (pt9 and controls)
raw_counts_1.txt.gz
IVO_S1PL05_06


title: GSC1_NC1-4

description:
Library name: sample 4
80_GSC1_NC1-4
GSC1-KO110.txt

value: WT


title: Patient 409 PDOs, control, biological replicate 1

description:
Library name: 409C1
10X Genomics


title: pt9 and controls, plates 3-4

description:
scRNA-seq data from TARGET-seq+ (pt9 and controls)
raw_counts_1.txt.gz
IVO_S1PL03_04


title: GSC1_NC1-3

description:
Library name: sample 3
79_GSC1_NC1-3
GSC1-KO110.txt


title: Patient 377 PDOs, type 2 diabetic exosome treated

description:
Library name: 377T
10X Genomics

value: Patient 377


title: pt9 and controls, plates 1-2

description:
scRNA-seq data from TARGET-seq+ (pt9 and controls)
raw_counts_1.txt.gz
IVO_S1PL01_02


title: GSC1_NC1-2

description:
Library name: sample 2
78_GSC1_NC1-2
GSC1-KO110.txt


title: TBB144

value: NR


title: Patient 377 PDOs, nondiabetic exosome treated

description:
Library name: 377N
10X Genomics


title: pt14 and controls, plate 13

description:
scRNA-seq data from TARGET-seq+ (pt14 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S4PL13


title: TBB172


title: TBB133


title: TBB136


title: TBB141


title: TBB151

value: NKRL


title: TBB126


title: TBB124


title: GSC1_NC1-1

description:
Library name: sample 1
77_GSC1_NC1-1
GSC1-KO110.txt


title: Patient 377 PDOs, control

description:
Library name: 377C
10X Genomics


title: TBB143


title: pt14 and controls, plates 11-12

description:
scRNA-seq data from TARGET-seq+ (pt14 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S3PL11-PL12

value: bone marrow


title: TBB134


title: TBB130

value: lowSFT


title: TBB140

value: TCMR/Mixed


title: B6_Hprx_Lung_rep6

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

institute: University of California, San Diego (UCSD)

description:
Library name: Sample 77
Lung.B6.set2.TPM.txt
mouse_C57Bl6_M_Lungtissue_RNA_Hprx2wk_rep3

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.
RNA sequencing reads were aligned to the mm10 mouse reference genome using STAR using default parameters.  Gene expression levels were calculated using HOMER by counting all strand specific reads within exons.  Only the most abundant transcripts, including multiple alternative variants, were selected for each gene, and the genes with a length smaller than 250 bp were removed.  Transcripts per million (TPM) were used to evaluate the correlation among replicates.
For ChIP-seq, Only read 1 (R1) was used for analysis. FASTQ files were mapped to the mm10 mouse reference genome with Bowtie2 using default parameters. Alignment files were processed using HOMER. Peaks were called by combining replicate conditions and using HOMER (findPeaks) using parameters “-style factor -size 200”.
Assembly: mm10
Supplementary files format and content: Tab-delimited Text of TPM for RNA-seq, ChIP-seq peak locations in BED format

organism: Mus musculus

source_name: Whole lung

growth_protocol: Trem2 knockout (Strain #: 027197) and DBA (Strain #: 000671) mice were purchased from Jackson Laboratory. Mice were maintained under a 12 hr light/12 hr dark cycle at constant temperature (20-23°C) with free access to food and water.  Animals were fed a normal chow diet (T8604, Envigo).

extract_protocol:
Mice were euthanized with CO2. After respiratory movements have ceased, mice were transferred to a dissection area, the abdomen and chest were opened through a midline incision. The aorta was cut and the lungs were perfused with ice cold PBS through the right ventricle until the lungs were cleared of blood. Lungs were gently removed from the thorax, the lobes were dissected from the trachea, placed in sterile tubes and snap frozen in liquid nitrogen. Tissue was stored at -80°C until used for downstream RNA-seq, ChIP-seq analysis and protein measurements. Total RNA was isolated from lung tissue or culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) as described by the manufacture.  mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB).  For ChIP-seq, frozen mouse lung tissues were pulverized on dry ice and the tissue powder was cross-linked with 2 mM disuccinimidyl glutarate (DSG) (ProteoChem) in PBS for 30 min at room temperature, and then directly a second crosslinking was performed by the addition of 1% (vol/vol) formaldehyde in PBS for 10 min. The crosslinking reaction was quenched by 0.125 M glycine (Sigma-Aldrich). The tissue powder was washed once with ice-cold PBS and pelleted at 1000 g for 5 min at 4°C. Crosslinked cells were resuspended in 100 l of PIPA-NR buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 0.1% SDS, 1% NP-40, 0.5 mM DTT, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail). Chromatin DNA was sonicated in a 96-well plate (Costar) using PIXUL™ Multi-Sample Sonicator (Active Motif) with the following setting: Process Time, 90 min; Pulse, 50 N; PRF, 1.00 kHz; Burst Rate, 20 Hz. Samples were centrifuged at 15000 rpm for 10 min at 4C, and the supernatant was used for immunoprecipitation.
For RNA-seq, to fragment Poly A-enriched mRNA, mRNAs were incubated in 2X Superscript III first-strand buffer (Invitrogen) with 10 mM DTT at 94°C for 9 minutes.  The 10 µ l of fragmented mRNAs were incubated with 0.5 µl of Random primers (3 µg/µl) (Invitrogen), 0.5 µl of Oligo dT primer (50 µM) (Invitrogen), 0.5 µl of SUPERase-In (Ambion), and 1 µl of dNTPs (Invitrogen) at 50°C for 1 min.  After the incubation, 5.8 µl of water, 1 µl of DTT (100 mM), 0.1 µl of Actinomycin D (2 µg/µL), 0.2 µl of 1% Tween-20 and 0.5 µl of Superscript III (Invitrogen) were added and incubated on the following conditions: 25°C for 10 min, 50°C for 50 min, and 4°C hold.  The mixture was purified with RNAClean XP beads (Beckman Coulter) as described by the manufacture and eluted with 10 µl of water.  For second-strand synthesis with dUTP, the RNA/cDNA double-stranded hybrid was then added to 1.5 µl of Blue Buffer (Enzymatics), 1.1 µl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µl of RNAse H (5 U/µl) (Enzymatics), 1.05 µl of water, 1 µl of DNA polymerase I (Enzymatics), and 0.15 µl of 1% Tween-20.  The mixture was incubated at 16°C for 2.5 hr.  The resulting dUTP-marked dsDNA was purified with 2 µl of SpeedBeads (GE Healthcare) in 20% PEG 8000/2.5M NaCl (final 13% PEG 8000), and eluted with 40 µl of EB (Zymo Research).  The eluted dsDNA was carried out end repair by blunting, A-tailing and adapter ligation as previously described (Heinz et al., 2010) using barcoded adapters (Bioo Scientific).  The end repaired dsDNA was amplified for 16 cycles using 0.05 U/µl KAPA High Fidelity HotStart (Kapa Biosystems) and 1 µM each of primers Solexa 1GA and Solexa 1GB.  The amplified libraries were selected using PAGE/TBE gel (Invitrogen) for 225-325 bp fragments by gel extraction. Chromatin immunoprecipitation (ChIP) was performed as previously described (Heinz et al., 2018).

treatment_protocol: For hyperoxia experiments (Hprx), neonatal mice were exposed within 24 hr of birth to 75% oxygen until postnatal day 14 (P14). The control (Nx) pups were raised in room air.

value: Whole lung

value: Hyperoxia

value: 14 days


title: Patient 318 PDOs, type 2 diabetic exosome treated

description:
Library name: 318T
10X Genomics

value: Patient 318


title: pt14 and controls, plates 9-10

description:
scRNA-seq data from TARGET-seq+ (pt14 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S3PL09-PL10

value: primary sample

value: bone marrow mononuclear cells


title: B6_Hprx_Lung_rep5

description:
Library name: Sample 76
Lung.B6.set2.TPM.txt
mouse_C57Bl6_M_Lungtissue_RNA_Hprx2wk_rep2


title: TBB142


title: TBB122


title: Patient 318 PDOs, nondiabetic exosome treated

description:
Library name: 318N
10X Genomics

value: Breast tumor


title: TBB123


title: pt14 and controls, plates 7-8

description:
scRNA-seq data from TARGET-seq+ (pt14 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S3PL07-PL08


title: TBB127


title: TBB137


title: TBB121


title: TBB131


title: B6_Hprx_Lung_rep4

description:
Library name: Sample 75
Lung.B6.set2.TPM.txt
mouse_C57Bl6_M_Lungtissue_RNA_Hprx2wk_rep1


title: Patient 318 PDOs, control

description:
Library name: 318C
10X Genomics

value: Control


title: TBB132


title: pt14 and controls, plates 5-6

description:
scRNA-seq data from TARGET-seq+ (pt14 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S3PL05-PL06


title: B6_Nx_Lung_rep6

description:
Library name: Sample 74
Lung.B6.set2.TPM.txt
mouse_C57Bl6_M_Lungtissue_RNA_Nx2wk_rep2

value: Nx


title: NL_02-06-0047-0

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description:
Library name: NL_02-06-0047-0
10X Chromium Flex RNA protocol

data_processing:
Single-cell RNA-sequencing (scRNA-seq) 10x dataset preprocessing including cell demultiplexing and alignment were performed using Cell Ranger Single-Cell Software Suite (version 7.0.0, 10x Genomics Inc). We used the human reference genome (GRCh38, Ensembl 91) for alignment and generated raw and filtered cell by gene count matrix files.
Assembly: Human GRCh38
Supplementary files format and content: Sparse matrix HDF5 file with UMI counts per barcode per gene ID for all barcodes

source_name: Nasal Lavage

extract_protocol:
Nasal lavage samples were collected using a previously established protocol. Briefly, 240ml of sterile sodium bicarbonate buffered normal saline in a sinus rinse bottle (NeilMed Sinus Rinse) was used to rinse the sinuses and collect lavage material. After collection, the lavage was centrifuged, resuspended, strained and homogenized. The sample was split into 3 aliquots to be used for 1) histology assessed by cytospin and manual differentials, 2) bulk RNA-sequencing by pelleting and preserving in 1ml of RNAprotect Saliva Reagent (Qiagen), and 3) single cell RNA-sequencing by pelleting and immediately fixing the cell pellet (within 60 minutes of sample collection) using the 10X Chromium Flex RNA protocol (10x Genomics), according to the manufacturer’s instructions, using a 1 hour fixation.
Fixed samples were shipped to a central facility where they were thawed and hybridized overnight to one of four probe sets (10x Genomics). Samples were pooled in groups of four, washed, and loaded onto the Chromium X (10x Genomics) for probe capture. Sequencing libraries were generated using the Chromium Fixed RNA Profiling Reagent Kit for Multiplexed Samples. Gene expression libraries were pooled and treated with Illumina Free Adapter Blocking Reagent (Illumina). Sequencing was carried out on a NextSeq 2000 sequencer (Illumina) using NextSeq P3 flowcells (Illumina) with a target depth of 10,000 reads/cell.

value: Nasal Lavage

value: Immune+epithelial

tag: donor group

value: highEOS


title: pt14 and controls, plates 3-4

description:
scRNA-seq data from TARGET-seq+ (pt14 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S3PL03-PL04


title: B6_Nx_Lung_rep5

description:
Library name: Sample 73
Lung.B6.set2.TPM.txt
mouse_C57Bl6_M_Lungtissue_RNA_Nx2wk_rep1


title: TBB120


title: pt14 and controls, plates 1-2

description:
scRNA-seq data from TARGET-seq+ (pt14 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S3PL01-PL02


title: TBB117


title: TBB139


title: TBB129

value: NR


title: TBB114


title: NL_02-06-0063-1

description:
Library name: NL_02-06-0063-1
10X Chromium Flex RNA protocol


title: TBB125


title: TBB116


title: NL_02-06-0003-7

description:
Library name: NL_02-06-0003-7
10X Chromium Flex RNA protocol


title: TBB128

value: NKRL


title: TBB112


title: pt11 and controls, plates 15-16

description:
scRNA-seq data from TARGET-seq+ (pt11 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S5PL15-PL16

value: bone marrow


title: TBB135


title: TBB111


title: TBB138


title: TBB118


title: NL_02-06-0048-1

description:
Library name: NL_02-06-0048-1
10X Chromium Flex RNA protocol

value: lowEOS


title: T2KO_Nx_BMDM_ChIP_p53_rep1

source_name: Bone marrow-derived macrophages

value: Bone marrow-derived macrophages

tag: antibody

value: anti-p53 Cell Signaling Technology #2524S / 1C12


title: pt11 and controls, plates 13-14

description:
scRNA-seq data from TARGET-seq+ (pt11 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S5PL13-PL14


title: TBB119


title: T2KO_Hprx_BMDM_ChIP_p53_rep2

value: Hyperoxia


title: pt11 and controls, plates 11-12

description:
scRNA-seq data from TARGET-seq+ (pt11 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S5PL11-PL12


title: NL_02-06-0039-1

description:
Library name: NL_02-06-0039-1
10X Chromium Flex RNA protocol


title: T2KO_Nx_BMDM_ChIP_p53_rep2


title: TBB115


title: T2KO_Hprx_BMDM_ChIP_p53_rep1


title: TBB109


title: NL_02-06-0014-7

description:
Library name: NL_02-06-0014-7
10X Chromium Flex RNA protocol


title: TBB113


title: pt11 and controls, plates 9-10

description:
scRNA-seq data from TARGET-seq+ (pt11 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S5PL09-PL10


title: B6_Nx_BMDM_ChIP_p53_rep2


title: TBB110


title: TBB108


title: TBB107


title: B6_Nx_BMDM_ChIP_p53_rep1


title: BM Sample

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: BRAFi/MEKi treated

data_processing:
Preprocessing of scRNA-seq data was done using CellRanger Suite (v3.1.0, https://support.10xgenomics.com) with refdata-cellranger-hg38-3.0.0 transcriptome as a reference
Assembly: hg38
Supplementary files format and content: standard cellranger output

source_name: PDX

extract_protocol:
Single cell droplets were generated using the Chromium next gem single cell 3' kit v3.1 (10x Genomics)
cDNA synthesis and amplification, library preparation and indexing were done using the 10x Genomics Library Preparation kit (10x Genomics)

value: PDX

tag: sample

value: BM

value: naive


title: cleavage_mitoxantrone_rep3_MTX_INPUT

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

description: 50 bp PE

data_processing:
Reads were trimmed using  Trimmomatic version 0.36
Reads were aligned to the T2T-CHM13v2.0 genome assembly using BWA version 0.7.17
Reads aligning to centromere/satellite  locations were counted using htseq-count from HTSeq version 2.7.13
Assembly: T2T-CHM13v2.0 genome assembly from the Telomere-to-telomere consortium CHM13 project.
Supplementary files format and content: Tab-delimted text file containing counts of reads aligning to centromere/satellite  locations, based on comprehensive centromere/satellite repeat annoation file provided by the Telomere-to-telomere consortium CHM13 project.

growth_protocol: KG1 cells were maintained in Iscove’s Modified Dulbecco’s Modified Eagle’s Medium (IDMEM) containing 25mM HEPES, 2mM L-glutamine and supplemented with 20% (v/v) FBS and 1% penicillin and streptomycin.

extract_protocol:
Sonication conditions were 5x10 second cycles at 20% power, 4μg and 5μg of TOP2A (3116) and TOP2B (3535) antibodies were incubated with protein A magnetic beads for 16 hours at 4°C and samples were eluted with 60μl TE buffer. Eluted DNA was treated with 8μl (1.12μg) of TDP2 (Abnova) for 40 minutes at 37°C to release DNA 5’ ends that may be blocked for ligation by TOP2. DNA was digested with type 1 restriction enzyme BsmAI to optimise library construction. Samples were heat deactivated at 80°C for 10 minutes and DNA was purified using spin columns. Samples were eluted in 60μl TE buffer.
Illumina Truseq

treatment_protocol: KG1 cells (~9x105/mL) were incubated with 100μM etoposide or 20 μM mitoxantrone or vehicle for 1 hour.

tag: order number/project_number

tag: replica

value: mitoxantrone replica 3

value: myelogenous leukaemia

value: AML

value: mitoxantrone


title: pt11 and controls, plates 7-8

description:
scRNA-seq data from TARGET-seq+ (pt11 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S5PL07-PL08

value: primary sample

value: bone marrow mononuclear cells


title: pt11 and controls, plates 1-2

description:
scRNA-seq data from TARGET-seq+ (pt11 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S5PL01-PL02


title: B6_Hprx_BMDM_ChIP_p53_rep2


title: B6_Nx_BMDM_ChIP_Input_rep2

value: Nx


title: pt11 and controls, plates 5-6

description:
scRNA-seq data from TARGET-seq+ (pt11 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S5PL05-PL06


title: pt11 and controls, plates 3-4

description:
scRNA-seq data from TARGET-seq+ (pt11 and controls)
raw_counts_1.txt.gz
AJ03_IVO-S5PL03-PL04


title: B6_Nx_BMDM_ChIP_Input_rep1


title: cleavage_mitoxantrone_rep3_nodrug_INPUT

description: 50 bp PE

value: no drug


title: TBB106

value: NR


title: pt4 and controls, plate 15

description:
scRNA-seq data from TARGET-seq+ (pt4 and controls)
raw_counts_1.txt.gz
AJ01_IVO-S2P15

value: bone marrow


title: BMD Sample

description: BRAFi/MEKi + Dasatenib treated

value: BMD


title: pt4 and controls, plates 13-14

description:
scRNA-seq data from TARGET-seq+ (pt4 and controls)
raw_counts_1.txt.gz
AJ01_IVO-S2P13-S2P14


title: B6_Hprx_BMDM_ChIP_Input_rep2

value: Bone marrow-derived macrophages


title: pt4 and controls, plates 11-12

description:
scRNA-seq data from TARGET-seq+ (pt4 and controls)
raw_counts_1.txt.gz
AJ01_IVO-S2P11-S2P12


title: B6_Hprx_BMDM_ChIP_Input_rep1


title: TBB101


title: cleavage_mitoxantrone_rep3_MTX_beta

description: 50 bp PE


title: B6_Hprx_BMDM_ChIP_p53_rep1

value: anti-p53 Cell Signaling Technology #2524S / 1C12


title: TBB102

value: NKRL


title: cleavage_mitoxantrone_rep3_MTX_alpha

description: 50 bp PE


title: cleavage_mitoxantrone_rep3_nodrug_alpha

description: 50 bp PE


title: TBB105


title: cleavage_mitoxantrone_rep2_MTX_INPUT

description: 50 bp PE

value: mitoxantrone replica 2


title: TBB103


title: cleavage_mitoxantrone_rep2_MTX_beta

description: 50 bp PE


title: DBA_Nx_Lung_ChIP_p53_rep1

value: Whole lung

value: 14 days


title: TBB100


title: DBA_Hprx_Lung_ChIP_p53_rep2

value: Hyperoxia


title: pt4 and controls, plates 5-6

description:
scRNA-seq data from TARGET-seq+ (pt4 and controls)
raw_counts_1.txt.gz
AJ01_IVO-S2P5-S2P6


title: TBB99

value: TCMR/Mixed


title: pt4 and controls, plates 7-8

description:
scRNA-seq data from TARGET-seq+ (pt4 and controls)
raw_counts_1.txt.gz
AJ01_IVO-S2P7-S2P8


title: DBA_Hprx_Lung_ChIP_p53_rep1


title: cleavage_mitoxantrone_rep3_nodrug_beta

description: 50 bp PE

value: mitoxantrone replica 3

value: myelogenous leukaemia

value: AML


title: TBB98


title: cleavage_mitoxantrone_rep2_MTX_alpha

description: 50 bp PE

value: mitoxantrone


title: TBB97

value: lowSFT


title: pt4 and controls, plates 3-4

description:
scRNA-seq data from TARGET-seq+ (pt4 and controls)
raw_counts_1.txt.gz
AJ01_IVO-S2P3-S2P4

value: primary sample

value: bone marrow mononuclear cells


title: cleavage_mitoxantrone_rep2_nodrug_INPUT

description: 50 bp PE

value: no drug


title: pt4 and controls, plates 9-10

description:
scRNA-seq data from TARGET-seq+ (pt4 and controls)
raw_counts_1.txt.gz
AJ01_IVO-S2P9-S2P10

value: bone marrow


title: DBA_Nx_Lung_ChIP_Input_rep2

value: Nx


title: pt4 and controls, plates 1-2

description:
scRNA-seq data from TARGET-seq+ (pt4 and controls)
raw_counts_1.txt.gz
AJ01_IVO-S2P1-S2P2


title: TBB96

value: NR


title: cleavage_mitoxantrone_rep2_nodrug_beta

description: 50 bp PE


title: DBA_Nx_Lung_ChIP_Input_rep1


title: Hela_500K_R2

city: Miami

first: Pradeep

middle: Reddy

last: Cingaram

state: FL

address: 1501 N.W. 10th Avenue

department: Human genetics

institute: University of Miami

data_processing:
Raw fastq PRO-seq data were processed as described previosly (Beckedorff, Blumenthal et al. 2020). Briefly PRO-seq reads were trimmed by Cutadapt 1.14 (Martin, 2011) and Trimmomatic v0.32 (Bolger etal., 2014), and aligned to the human genome (hg19) genome or the drosophila genome (dm3) by bowtie 1.1.2 (Langmead etal., 2009). PRO-seq signalwas normalized by the number of reads mapped to spike-in dm3 genome, and then converted to bigwig data, which were used for downstream analyses.Quantification of nascent transcription per region was generated with an in-house script based on pyBigWig [Devon Ryan, B. G. F. R., doi:10.5281/zenodo.45238 (2016)] used to extract the normalized reads (CPM) per position from the bigwig files with a bin size of 1 bp upon merging the signal across two replicates.
Assembly: hg19 and mm10
Supplementary files format and content: The processed data files are in bigWig format : PRO-seq and rPRO-seq: bigwigs were normalized by Count Per Million produced from DeepTools2. PRO-seq and rPRO-seq: bigwigs were with Bedtools v2.26 with genomecov.

source_name: HeLa (ATCC#CCL-2)

growth_protocol: HeLa  cell lines were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations.

extract_protocol:
To investigate hematopoietic stem and progenitor cells (HSPC), we employed an inducible whole-body knockout model. This involved crossing our animal model with Rosa26-CreERT2 (Cre recombinase-estrogen receptor T2) mice obtained from Jackson Laboratory (Stock No: 008463). Both control and Ints11 floxed mice received intraperitoneal injections of tamoxifen (75mg/Kg per day) for five consecutive days to induce the deletion of Ints11. To isolate HSPC cells, we utilized the Direct Lineage Cell Depletion Kit and cKit (CD117) MicroBeads from Miltenyi Biotec, following the manufacturer's instructions. In brief, BM cells were initially stained with a cocktail of lineage marker antibodies directly coupled to MicroBeads and then passed through a column. Subsequently, the cells were further purified using cKit MicroBeads to enrich hematopoietic stem and progenitor cell populations.
For rPRO-seq experiments were conducted following established protocols (see detailed protocol in supplementary file 1). Initially, a mixture of HeLa nuclei and Drosophila S2 cell nuclei as spike-ins was prepared. Nuclear run-on assays were executed by incubating nuclei at 30°C for 3 minutes with 25 μM Biotin-11-ATP/UTP/CTP/GTP (PerkinElmer). Subsequently, total RNA was extracted using Direct-zol RNA Miniprep and fragmented with 0.2 M NaOH for 10 minutes on ice, followed by purification of biotinylated nascent RNAs using streptavidin beads M-280 (Invitrogen). The 3’ RNA adaptor ligation process employs pre-adenylated single-stranded DNAs (P-3’ App-DNA), and T4 RNA ligase 2, truncated KQ, is utilized, incubated at 25°C for 1 hour. Additionally, on-bead 5’ RNA end repair involved using RppH (NEB) to remove the 5' cap and repair the triphosphate, followed by PNK-mediated repair of the 5' hydroxyl. The hybridization of DBO involves incorporating the dimer blocking oligonucleotide (DBO) into the RNA within the DBO mix. This is followed by a thermocycler program and subsequent combination with the 5’ adaptor ligation mixes in the RNA DBO mix, with a 1-hour incubation at 25°C. After adapter ligation, SuperScript III reverse transcription was employed. PCR amplification generated 140–350 bp libraries, which were size-selected using AMpure XP beads and sequenced using single-read runs on a NovaSeq 6000.

value: HeLa (ATCC#CCL-2)

value: cervical adenocarcinoma

tag: fraction

value: rPROseq RNA


title: cleavage_mitoxantrone_rep2_nodrug_alpha

description: 50 bp PE

value: mitoxantrone replica 2

tag: cell type


title: DBA_Hprx_Lung_ChIP_Input_rep2

value: Whole lung

tag: genotype

value: Hyperoxia

value: 14 days


title: Hela_500K_R1


title: TBB95

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).


title: DBA_Hprx_Lung_ChIP_Input_rep1

tag: treatment


title: Hela_100K_R2


title: cleavage_mitoxantrone_rep1_MTX_INPUT

description: 100bp PE

value: mitoxantrone replica 1

value: myelogenous leukaemia


title: TBB94

value: TCMR/Mixed


title: cleavage_mitoxantrone_rep1_MTX_beta

description: 100bp PE

value: AML

value: mitoxantrone


title: T2KO_Nx_Lung_ChIP_p53_rep2

value: Trem2 knock out

tag: time

value: anti-p53 Cell Signaling Technology #2524S / 1C12


title: Hela_100K_R1


title: cleavage_mitoxantrone_rep1_nodrug_INPUT

description: 100bp PE

value: no drug


title: T2KO_Nx_Lung_ChIP_p53_rep1

value: Nx


title: TBB93

tag: rejection archetype cluster (nr, tcmr/mixed, nkrl, lowsft)

value: NR


title: Hela_50K_R2

value: HeLa (ATCC#CCL-2)


title: cleavage_mitoxantrone_rep1_nodrug_beta

description: 100bp PE


title: T2KO_Hprx_Lung_ChIP_p53_rep2

tag: tissue


title: T2KO_Hprx_Lung_ChIP_p53_rep1


title: cleavage_mitoxantrone_rep1_nodrug_alpha

description: 100bp PE

tag: cell line


title: TBB92

value: NKRL


title: cleavage_mitoxantrone_rep1_MTX_alpha

description: 100bp PE


title: T2KO_Nx_Lung_ChIP_Input_rep2


title: Hela_50K_R1

value: cervical adenocarcinoma

value: rPROseq RNA


title: T2KO_Nx_Lung_ChIP_Input_rep1

value: Whole lung


title: TOP2B null undifferentiated iPSC cells, biol rep4

data_processing:
Reads were quantified against Gencode version 45 transcripts using Salmon (version 1.10.0)
Low quality bases were trimmed and adapter sequences removed using trimmomatic (version 0.36)
Gene level counts were obtained from transcript level counts using the R package tximport (version 1.26.1)
Assembly: GRC38
Supplementary files format and content: Tab delimited text file including raw counts for each Sample
Supplementary files format and content: Tab delimited text file including TPM values for each Sample

source_name: iPSC

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen)
RNA libraries for RNS-seq were prepard using Illumina Stranded mRNA Prep, Ligation library preparation protocol

treatment_protocol:
Undifferentiated iPSC cells were maintained in Geltrex (Thermo-Fisher)-coated wells of 6-well plates in mTesR medium (StemCell Technologies). For the first 24 hours after plating the medium contained 10mM ROCK inhibitor (Y27632, StemCell Technologies), after which the medium was replaced with mTesR without ROCKi.
iPSC cells were induced to differentiate into cardiomyocytes essentially as in PMID: 23257984: Once iPSC cells reached 60-70% confluence (day 0), medium was replaced with RPMI 1640 supplemented with B27 minus insulin (Thermo-Fisher) containing 10µM GSK-3 inhibitor (CHIR 99021) and 10ng/ml Activin A. On day 1 medium was replaced with RPMI 1640 supplemented with B27 minus insulin. On day 3 medium was replaced with RPMI 1640 supplemented with B27 minus insulin, containing 5mM GSK-3 inhibitor IWP2. On day 5 medium was replaced with RPMI 1640 supplemented with B27 minus insulin. On day 7 medium was replaced with RPMI 1640 supplemented with B27 with insulin, and medium was replaced every two days with the same medium until the cells formed sheets of beating cardiomyocytes, at which time RNA was isolated for library preparation.

value: iPSC

value: TOP2B knockout

value: utreated


title: TBB88


title: TBB89


title: cleavage_etoposide_rep4_VP16_beta

description: 50 bp PE

value: etoposide replica 4

value: myelogenous leukaemia

value: etoposide


title: TOP2B null undifferentiated iPSC cells, biol rep3


title: TBB87

value: TCMR/Mixed


title: TBB91


title: T2KO_Hprx_Lung_ChIP_Input_rep2

value: Trem2 knock out

value: Hyperoxia

value: 14 days


title: TOP2B null undifferentiated iPSC cells, biol rep2


title: T2KO_Hprx_Lung_ChIP_Input_rep1


title: Hela_25K_R2


title: cleavage_etoposide_rep4_VP16_alpha

description: 50 bp PE

value: AML


title: TBB90

value: NR


title: TBB86


title: TOP2B null undifferentiated iPSC cells, biol rep1


title: Hela_25K_R1

value: HeLa (ATCC#CCL-2)


title: B6_Nx_Lung_ChIP_p53_rep2

value: Nx

value: anti-p53 Cell Signaling Technology #2524S / 1C12


title: cleavage_etoposide_rep4_nodrug_beta

description: 50 bp PE

value: no drug


title: WT undifferentiated iPSC cells, biol rep4

value: WT


title: B6_Nx_Lung_ChIP_p53_rep1

value: Whole lung


title: TBB85


title: WT undifferentiated iPSC cells, biol rep3

value: iPSC


title: cleavage_etoposide_rep4_nodrug_alpha

description: 50 bp PE


title: B6_Hprx_Lung_ChIP_p53_rep2


title: cleavage_etoposide_rep4_nodrug_INPUT

description: 50 bp PE


title: TBB84


title: B6_Hprx_Lung_ChIP_p53_rep1


title: WT undifferentiated iPSC cells, biol rep1

value: utreated


title: cleavage_etoposide_rep3_VP16_beta

description: 50 bp PE

value: etoposide replica 3


title: B6_Nx_Lung_ChIP_Input_rep3


title: cleavage_etoposide_rep3_VP16_alpha

description: 50 bp PE

value: myelogenous leukaemia


title: WT iPSC-derived cardiomyocytes, JM-437, biol rep4

source_name: iPSC-derived cardiomyocyte

value: iPSC-derived cardiomyocyte

value: topobexin, 10mM, 3 hr


title: TBB83

value: lowSFT


title: TBB81


title: cleavage_etoposide_rep3_nodrug_INPUT

description: 50 bp PE


title: WT iPSC-derived cardiomyocytes, JM-437, biol rep3


title: B6_Nx_Lung_ChIP_Input_rep1


title: TBB79


title: TBB78


title: cleavage_etoposide_rep3_nodrug_beta

description: 50 bp PE


title: cleavage_etoposide_rep3_VP16_INPUT

description: 50 bp PE

value: etoposide


title: TBB104


title: TBB80


title: cleavage_etoposide_rep3_nodrug_alpha

description: 50 bp PE


title: WT iPSC-derived cardiomyocytes, JM-437, biol rep2


title: B6_Hprx_Lung_ChIP_Input_rep2

value: Hyperoxia

value: 14 days


title: WT iPSC-derived cardiomyocytes, JM-437, biol rep1


title: TBB82

value: NR


title: B6_Hprx_Lung_ChIP_Input_rep1


title: B6_Nx_Lung_ChIP_Input_rep2


title: cleavage_etoposide_rep2_VP16_beta

description: 50 bp PE

value: etoposide replica 2

value: AML


title: cleavage_etoposide_rep2_VP16_INPUT

description: 50 bp PE


title: T2KO_Hprx_BMDM_rep2

description: BMDM.TPM.txt

value: Bone marrow-derived macrophages

value: Trem2 knock out


title: TBB77


title: TBB75


title: T2KO_Hprx_BMDM_rep1

description: BMDM.TPM.txt


title: TBB76


title: TBB74

value: TCMR/Mixed


title: cleavage_etoposide_rep2_VP16_alpha

description: 50 bp PE


title: TOP2B null iPSC-derived cardiomyocytes, untreated, biol rep2

value: TOP2B knockout


title: TBB73


title: T2KO_Nx_BMDM_rep2

description: BMDM.TPM.txt

value: Nx


title: cleavage_etoposide_rep2_nodrug_INPUT

description: 50 bp PE

value: no drug


title: TOP2B null iPSC-derived cardiomyocytes, untreated, biol rep1

value: utreated


title: T2KO_Nx_BMDM_rep1

description: BMDM.TPM.txt


title: cleavage_etoposide_rep2_nodrug_alpha

description: 50 bp PE

value: myelogenous leukaemia


title: WT iPSC-derived cardiomyocytes, Dexrazoxane, biol rep3

value: iPSC-derived cardiomyocyte

value: WT

value: Dexrazoxane, 100mM, 3 hr


title: TOP2B null iPSC-derived cardiomyocytes, untreated, biol rep3


title: cleavage_etoposide_rep2_nodrug_beta

description: 50 bp PE


title: WT iPSC-derived cardiomyocytes, Dexrazoxane, biol rep2


title: cleavage_etoposide_rep1_VP16_INPUT

description: 38 bp PE

value: NGS_ZSONDKA_BB_140411 Project S016130

value: etoposide replica 1

value: etoposide


title: DBA_Hprx_BMDM_rep1

description: BMDM.TPM.txt

value: Hyperoxia


title: WT iPSC-derived cardiomyocytes, Dexrazoxane, biol rep4


title: DBA_Hprx_BMDM_rep2

description: BMDM.TPM.txt


title: TBB71

value: NR


title: TOP2B null iPSC-derived cardiomyocytes, untreated, biol rep4


title: DBA_Nx_Lung_ChIP_p53_rep2

value: Whole lung

value: 14 days

value: anti-p53 Cell Signaling Technology #2524S / 1C12


title: TBB69


title: cleavage_etoposide_rep1_VP16_beta

description: 38 bp PE

value: AML


title: TBB72


title: WT iPSC-derived cardiomyocytes, Dexrazoxane, biol rep1


title: DBA_Nx_BMDM_rep2

description: BMDM.TPM.txt

value: Bone marrow-derived macrophages


title: TBB70

value: lowSFT


title: DBA_Nx_BMDM_rep1

description: BMDM.TPM.txt

value: Nx


title: cleavage_etoposide_rep1_VP16_alpha

description: 38 bp PE


title: TBB68


title: WT iPSC-derived cardiomyocytes, untreated, biol rep4

value: utreated


title: WT iPSC-derived cardiomyocytes, untreated, biol rep3


title: cleavage_etoposide_rep1_nodrug_INPUT

description: 38 bp PE

value: myelogenous leukaemia

value: no drug


title: B6_Hprx_BMDM_rep2

description: BMDM.TPM.txt


title: TBB67


title: cleavage_etoposide_rep1_nodrug_beta

description: 38 bp PE


title: B6_Hprx_BMDM_rep1

description: BMDM.TPM.txt


title: B6_Nx_BMDM_rep2

description: BMDM.TPM.txt


title: WT iPSC-derived cardiomyocytes, untreated, biol rep2

value: iPSC-derived cardiomyocyte

value: WT


title: TBB66


title: cleavage_etoposide_rep1_nodrug_alpha

description: 38 bp PE

value: NGS_ZSONDKA_BB_140411 Project S016130


title: B6_Nx_BMDM_rep1

description: BMDM.TPM.txt


title: WT iPSC-derived cardiomyocytes, untreated, biol rep1


title: B5.R, miRNA-seq

city: Cádiz

first: Fernando

last: Bonet

address: Plaza Falla 9

country: Spain

institute: University of Cádiz

description: KGK3D_B5R_22s002844-1-1_TORO_lane122s002844_sequence.txt.gz

data_processing:
European version of the Galaxy platform (https://usegalaxy.eu/)
Reads were trimmed with the Trim Galore software (Galaxy Version 0.6.7+galaxy0)
Trimmed sequences reads were aligned to the built-in human reference genome Dec. 2013 (GRCh38/hg38) with the RNA STAR Gapped-read mapper (Galaxy Version 2.7.10b+galaxy3)
For gene expression analyses, bam files were downloaded from the Galaxy server and further analyzed with the different RStudio packages downloaded from the Bioconductor website (http://bioconductor. org).
Reads were assigned to genes by means of the “featureCounts” function of the “Rsubread” package, version 2.10.5. and annotation files Chromosomal coordinates of Homo sapiens microRNAs (https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3)
Assembly: hg38
Supplementary files format and content: Excel file contents RAW counts for each sample

source_name: Myocardium

extract_protocol:
RNA was isolated using Trizol and RNA Clean & Concentrator Kits (Zymo Research). 1.5 ug of total RNA was used for the construction of sequencing libraries
Standard miRNA libraries were generated using the NEXTFLEX small RNA-seq kit v3 (Perkin Elmer, Waltham, MA, USA), and single-end libraries were sequenced on an Illumina SE75 Platform

value: Myocardium

value: ACM


title: B3.R, miRNA-seq

description: KGK3D_B3R_22s002843-1-1_TORO_lane122s002843_sequence.txt.gz


title: T2KO_Hprx_Lung_rep4

value: Trem2 knock out

value: Hyperoxia


title: Hypoxia, smooth muscle cell differentiated, replicate 3

city: Erlangen

first: Matthias

last: Weider

address: Glückstr. 11

department: Department of Orthodontics and Orofacial Orthopedics

country: Germany

institute: Universitätsklinikum Erlangen

description:
Hypo_SM3
norm_counts_Hypo_SMvsHypo_Prolif.csv
norm_counts_Hypo_SMvsNorm_SM.csv
rawcts_prefilt2.csv

data_processing:
Data were mapped onto the Mus musculus reference genome mm10 using hisat2 (version 2.0.5),
assembled via Stringtie (version 1.3.3b)
and quantified using featureCounts (version 1.5.0-p3) by the sequencing company
Assembly: mm10
Supplementary files format and content: norm_counts_Norm_ChondrvsNorm_Prolif.csv normalised counts of comparison of chondrocyte differentiated vs proliferating cells under normoxic conditions
Supplementary files format and content: norm_counts_Norm_OsteovsNorm_Prolif.csv normalised counts of comparison of osteoblast differentiated vs proliferating cells under normoxic conditions
Supplementary files format and content: norm_counts_Norm_SMvsNorm_Prolif.csv normalised counts of comparison of smooth muscle differentiated vs proliferating cells under normoxic conditions
Supplementary files format and content: norm_counts_Hypo_ChondrvsHypo_Prolif.csv normalised counts of comparison of chondrocyte differentiated vs proliferating cells under hypoxic conditions
Supplementary files format and content: norm_counts_Hypo_OsteovsHypo_Prolif.csv normalised counts of comparison of osteoblast differentiated vs proliferating cells under hypoxic conditions
Supplementary files format and content: norm_counts_Hypo_SMvsHypo_Prolif.csv normalised counts of comparison of smooth muscle differentiated vs proliferating cells under hypoxic conditions
Supplementary files format and content: norm_counts_Hypo_ProlifvsNorm_Prolif.csv normalised counts of proliferating cells under hypoxic vs normoxic conditions
Supplementary files format and content: norm_counts_Hypo_ChondrvsNorm_Chondr.csv normalised counts of chondrocyte differentiated cells under hypoxic vs normoxic conditions
Supplementary files format and content: norm_counts_Hypo_OsteovsNorm_Osteo.csv normalised counts of osteoblast differentiated cells under hypoxic vs normoxic conditions
Supplementary files format and content: norm_counts_Hypo_SMvsNorm_SM.csv normalised counts of smooth muscle differentiated cells under hypoxic vs normoxic conditions

growth_protocol: O9-1 cranial neural crest cells were maintained in prolferation/ chondrocyte differentiation/ osteoblast differentiation/ smooth muscle cell differentiation medium under 21% O2 or 0.5% O2, 37°C, 5% CO2

extract_protocol:
RNA was extracted with the RNeasy plus kit (Qiagen) according to manufacturer’s instructions.
400ng of RNA per sample was used for library preparation (Novogene NGS Stranded RNA Library Prep Set (PT044))

value: smooth muscle cell differentiated cranial neural crest cells

value: Smooth muscle differentiation medium (DMEM (Gibco) with 10% FCS and 1% Penicillin/Streptomycin), 3 days, cultivated in 0.5% O2


title: Hypoxia, smooth muscle cell differentiated, replicate 2

description:
Hypo_SM2
norm_counts_Hypo_SMvsHypo_Prolif.csv
norm_counts_Hypo_SMvsNorm_SM.csv
rawcts_prefilt2.csv


title: T2KO_Hprx_Lung_rep3

value: Whole lung

value: 14 days


title: Hypoxia, smooth muscle cell differentiated, replicate 1

description:
Hypo_SM1
norm_counts_Hypo_SMvsHypo_Prolif.csv
norm_counts_Hypo_SMvsNorm_SM.csv
rawcts_prefilt2.csv


title: T2KO_Hprx_Lung_rep2


title: B2.R, miRNA-seq

description: KGK3D_B2R_22s002842-1-1_TORO_lane122s002842_sequence.txt.gz


title: TBB62

value: NR


title: TBB63

value: TCMR/Mixed


title: TBB65


title: cleavage_etoposide_rep4_VP16_INPUT

description: 50 bp PE

value: etoposide replica 4

value: AML

value: etoposide


title: B1.R, miRNA-seq

description: KGK3D_B1R_22s002841-1-1_TORO_lane122s002841_sequence.txt.gz


title: T2KO_Hprx_Lung_rep1


title: Hypoxia, osteoblast differentiated, replicate 3

description:
Hypo_Osteo3
norm_counts_Hypo_OsteovsHypo_Prolif.csv
norm_counts_Hypo_OsteovsNorm_Osteo.csv
rawcts_prefilt2.csv

value: osteoblast differentiated cranial neural crest cells

value: Osteoblast differentiation medium (alpha-MEM (Gibco) containing 10% FCS, 1% Penicillin/Streptomycin, 10mM beta-glycerophosphate, 0.1µM dexamethasone and 100ng/ml BMP-2), 10 days, cultivated in 0.5% O2


title: A6.R, miRNA-seq

description: KGK3D_A6R_22s002840-1-1_TORO_lane122s002840_sequence.txt.gz

value: Control


title: TBB61


title: TBB64


title: TBB60

value: lowSFT


title: T2KO_Nx_Lung_rep4

value: Nx


title: Hypoxia, osteoblast differentiated, replicate 2

description:
Hypo_Osteo2
norm_counts_Hypo_OsteovsHypo_Prolif.csv
norm_counts_Hypo_OsteovsNorm_Osteo.csv
rawcts_prefilt2.csv


title: A4.R, miRNA-seq

description: KGK3D_A4R_22s002839-1-1_TORO_lane122s002839_sequence.txt.gz

value: Myocardium


title: TBB58

value: NKRL


title: Hypoxia, osteoblast differentiated, replicate 1

description:
Hypo_Osteo1
norm_counts_Hypo_OsteovsHypo_Prolif.csv
norm_counts_Hypo_OsteovsNorm_Osteo.csv
rawcts_prefilt2.csv


title: A2.R, miRNA-seq

description: KGK3D_A2R_22s002838-1-1_TORO_lane122s002838_sequence.txt.gz


title: T2KO_Nx_Lung_rep3

value: Trem2 knock out


title: T2KO_Nx_Lung_rep2


title: TBB57


title: A1.R, miRNA-seq

description: KGK3D_A1R_22s002837-1-1_TORO_lane122s002837_sequence.txt.gz


title: Hypoxia, chondrocyte differentiated, replicate 3

description:
Hypo_Chondr3
norm_counts_Hypo_ChondrvsHypo_Prolif.csv
norm_counts_Hypo_ChondrvsNorm_Chondr.csv
rawcts_prefilt2.csv

value: chondrocyte differentiated cranial neural crest cells

value: Osteoblast differentiation medium for three days, followed by micro mass culture on matrigel-coated plastic ware in chondrogenic differentiation medium for seven days. This medium consisted of alpha-MEM with 5% FCS, 1% Penicillin/Streptomycin, 1x Insulin-Transferrin-Selenium (Gibco), 0.1µM dexamethasone, 10ng/ml TGF-beta3 and 50ng/ml BMP-2, cultivated in 0.5% O2


title: Hypoxia, chondrocyte differentiated, replicate 2

description:
Hypo_Chondr2
norm_counts_Hypo_ChondrvsHypo_Prolif.csv
norm_counts_Hypo_ChondrvsNorm_Chondr.csv
rawcts_prefilt2.csv


title: T2KO_Nx_Lung_rep1

value: Whole lung


title: TBB59


title: Hypoxia, chondrocyte differentiated, replicate 1

description:
Hypo_Chondr1
norm_counts_Hypo_ChondrvsHypo_Prolif.csv
norm_counts_Hypo_ChondrvsNorm_Chondr.csv
rawcts_prefilt2.csv


title: Hypoxia, proliferating, replicate 3

description:
Hypo_Prolif3
norm_counts_Hypo_ChondrvsHypo_Prolif.csv
norm_counts_Hypo_OsteovsHypo_Prolif.csv
norm_counts_Hypo_SMvsHypo_Prolif.csv
norm_counts_Hypo_ProlifvsNorm_Prolif.csv
rawcts_prefilt2.csv

value: proliferating cranial neural crest cells

value: Proliferation medium (STO-conditioned DMEM (Gibco) containing 15% fetal calf serum (FCS), 1% Penicillin/Streptomycin, 0.1 mM non-essential amino acids and 55 µM beta-mercaptoethanol to which 25ng/ml bFGF and 5ng/ml LIF had been added), cultivated in 0.5% O2


title: pt5 and controls, sort 7 plate 11

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL11_S15

value: bone marrow

value: primary sample

value: bone marrow mononuclear cells


title: DBA_Hprx_Lung_rep3

value: Hyperoxia

value: 14 days


title: pt5 and controls, sort 7 plate 10

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL10_S14


title: WT undifferentiated iPSC cells, biol rep2

value: iPSC

value: WT

value: utreated


title: DBA_Hprx_Lung_rep2


title: DBA_Hprx_Lung_rep1


title: Hypoxia, proliferating, replicate 1

description:
Hypo_Prolif1
norm_counts_Hypo_ChondrvsHypo_Prolif.csv
norm_counts_Hypo_OsteovsHypo_Prolif.csv
norm_counts_Hypo_SMvsHypo_Prolif.csv
norm_counts_Hypo_ProlifvsNorm_Prolif.csv
rawcts_prefilt2.csv


title: pt5 and controls, sort 7 plate 9

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL9_S13


title: TBB53

value: lowSFT


title: pt5 and controls, sort 7 plate 8

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL8_S12


title: Normoxia, smooth muscle cell differentiated, replicate 4

description:
Norm_SM4
norm_counts_Norm_SMvsNorm_Prolif.csv
norm_counts_Hypo_SMvsNorm_SM.csv
rawcts_prefilt2.csv

value: smooth muscle cell differentiated cranial neural crest cells

value: Smooth muscle differentiation medium (DMEM (Gibco) with 10% FCS and 1% Penicillin/Streptomycin), 3 days, cultivated in 21% O2


title: DBA_Nx_Lung_rep4

value: Nx


title: DBA_Hprx_Lung_rep4


title: pt5 and controls, sort 7 plate 12

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL12_S16


title: Normoxia, smooth muscle cell differentiated, replicate 3

description:
Norm_SM3
norm_counts_Norm_SMvsNorm_Prolif.csv
norm_counts_Hypo_SMvsNorm_SM.csv
rawcts_prefilt2.csv


title: DBA_Nx_Lung_rep3


title: TBB55

value: NR


title: TBB52


title: pt5 and controls, sort 7 plate 6

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL6_S10


title: Hypoxia, proliferating, replicate 2

description:
Hypo_Prolif2
norm_counts_Hypo_ChondrvsHypo_Prolif.csv
norm_counts_Hypo_OsteovsHypo_Prolif.csv
norm_counts_Hypo_SMvsHypo_Prolif.csv
norm_counts_Hypo_ProlifvsNorm_Prolif.csv
rawcts_prefilt2.csv


title: TBB56


title: TBB54


title: Normoxia, smooth muscle cell differentiated, replicate 2

description:
Norm_SM2
norm_counts_Norm_SMvsNorm_Prolif.csv
norm_counts_Hypo_SMvsNorm_SM.csv
rawcts_prefilt2.csv


title: DBA_Nx_Lung_rep2


title: TBB51


title: Normoxia, smooth muscle cell differentiated, replicate 1

description:
Norm_SM1
norm_counts_Norm_SMvsNorm_Prolif.csv
norm_counts_Hypo_SMvsNorm_SM.csv
rawcts_prefilt2.csv


title: TBB50


title: DBA_Nx_Lung_rep1


title: TBB47

value: NKRL


title: pt5 and controls, sort 7 plate 7

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL7_S11


title: TBB49


title: pt5 and controls, sort 7 plate 4

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL4_S8


title: Normoxia, osteoblast differentiated, replicate 4

description:
Norm_Osteo4
norm_counts_Norm_OsteovsNorm_Prolif.csv
norm_counts_Hypo_OsteovsNorm_Osteo.csv
rawcts_prefilt2.csv

value: osteoblast differentiated cranial neural crest cells

value: Osteoblast differentiation medium (alpha-MEM (Gibco) containing 10% FCS, 1% Penicillin/Streptomycin, 10mM beta-glycerophosphate, 0.1µM dexamethasone and 100ng/ml BMP-2), 10 days, cultivated in 21% O2


title: B6_Hprx_Lung_rep2

value: Whole lung


title: pt5 and controls, sort 7 plate 3

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL3_S7

value: bone marrow


title: B6_Hprx_Lung_rep3


title: Normoxia, osteoblast differentiated, replicate 3

description:
Norm_Osteo3
norm_counts_Norm_OsteovsNorm_Prolif.csv
norm_counts_Hypo_OsteovsNorm_Osteo.csv
rawcts_prefilt2.csv


title: B6_Hprx_Lung_rep1


title: Normoxia, osteoblast differentiated, replicate 2

description:
Norm_Osteo2
norm_counts_Norm_OsteovsNorm_Prolif.csv
norm_counts_Hypo_OsteovsNorm_Osteo.csv
rawcts_prefilt2.csv


title: pt5 and controls, sort 7 plate 2

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL2_S6

value: primary sample


title: pt5 and controls, sort 7 plate 1

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL1_S5

value: bone marrow mononuclear cells


title: TBB48


title: pt5 and controls, sort 6 plate 5

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S6PL5_S4


title: B6_Nx_Lung_rep3


title: B6_Nx_Lung_rep4


title: pt5 and controls, sort 7 plate 5

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S7PL5_S9


title: Normoxia, osteoblast differentiated, replicate 1

description:
Norm_Osteo1
norm_counts_Norm_OsteovsNorm_Prolif.csv
norm_counts_Hypo_OsteovsNorm_Osteo.csv
rawcts_prefilt2.csv


title: Normoxia, chondrocyte differentiated, replicate 4

description:
Norm_Chondr4
norm_counts_Norm_ChondrvsNorm_Prolif.csv
norm_counts_Hypo_ChondrvsNorm_Chondr.csv
rawcts_prefilt2.csv

value: chondrocyte differentiated cranial neural crest cells

value: Osteoblast differentiation medium for three days, followed by micro mass culture on matrigel-coated plastic ware in chondrogenic differentiation medium for seven days. This medium consisted of alpha-MEM with 5% FCS, 1% Penicillin/Streptomycin, 1x Insulin-Transferrin-Selenium (Gibco), 0.1µM dexamethasone, 10ng/ml TGF-beta3 and 50ng/ml BMP-2, cultivated in 21% O2


title: TBB46


title: Normoxia, chondrocyte differentiated, replicate 3

description:
Norm_Chondr3
norm_counts_Norm_ChondrvsNorm_Prolif.csv
norm_counts_Hypo_ChondrvsNorm_Chondr.csv
rawcts_prefilt2.csv


title: B6_Nx_Lung_rep2

value: 14 days


title: Normoxia, chondrocyte differentiated, replicate 2

description:
Norm_Chondr2
norm_counts_Norm_ChondrvsNorm_Prolif.csv
norm_counts_Hypo_ChondrvsNorm_Chondr.csv
rawcts_prefilt2.csv


title: TBB44


title: B6_Nx_Lung_rep1


title: TBB41


title: pt5 and controls, sort 6 plate 2

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S6PL2_S1


title: TBB42

value: TCMR/Mixed


title: Normoxia, chondrocyte differentiated, replicate 1

description:
Norm_Chondr1
norm_counts_Norm_ChondrvsNorm_Prolif.csv
norm_counts_Hypo_ChondrvsNorm_Chondr.csv
rawcts_prefilt2.csv


title: Pool rep4 [Pool-ID-1_S1_L004]

city: Perugia

first: Elisabetta

last: Albi

state: Italy

address: Via Romana

department: Department of Pharmaceutical Sciences

country: Italy

institute: Università degli studi di Perugia

data_processing:
Reads were demultiplexed, according to the following barcodes, from all the Pool-ID-1 fastq files (B02: CATTCGCGTC, C02: GAGAGCTACT, D02: TGACAGCGTG, E02: ATGTAGGCCT, F02: CCGATGGTTG, G02:GCTTCCATTC)
Reads were mapped to the reference genome (mm10)
The number of mapped reads to each gene or miRNA was quantified
CPM, TPM and RPKM was computed to normalize the number of mapped reads in each gene or miRNA
All steps have been perfomed using the RAP software, GeneGlobe, Quiagen
Assembly: mm10
Supplementary files format and content: miRNA expression (Count, miRNA name and CPM)
Supplementary files format and content: Gene expression (TPM, RPKM, Total exons, Gene name, EnsemblID, Biotype, CPM)

growth_protocol: Immortalized hippocampal neurons HN9.10e (kind gift of Kieran Breen, Ninewells Hospital, Dundee, UK) were grown in DMEM supplemented with 10% FBS, 2 mMl-glutamine, 100 IU/mL penicillin, 100 μg/mL streptomycin, and 2.5 μg/mL amphotericin B

extract_protocol:
For nuclei extraction,Triton X-100  (1% in the above buffer) was added to homogenate (0.5:1 v/v). Sample was stirred on a vortex mixer for 30 s and the 1.5 M sucrose in the above buffer was added (0.25:1 v/v). After centrifugation at 2000g × 10 min, the pellet containing the nuclei was washed twice with 0.1M Barnes solution containing 0.085 M KCl, 0.0085 NaCl, 0.0025 M MgCl2, trichloroacetic acid-HCl 0.005 M. For nuclei lipid microdomain extraction, HN9.10 cell nuclei were washed in 10 mM Tris, containing 0.25 M sucrose, 2.5 mM MgCl2, 0.5 mM PMSF, and 1% Triton X-100, pH 7.5, at 0 °C, in order to remove the external nuclear membrane preserving the inner nuclear membrane, and were centrifuged at 1000g for 15 min at 4 °C. The pellet was re-suspended in 0.1 M Barnes solution  at pH 7.4, and was digested with DNase I (120 μg/ml) and RNase cocktail (500 μg/ml) for 15 min at 37 °C. The reaction was stopped on ice with Barnes solution (1:1 by vol.). After centrifugation at 5000 rpm for 5 min, the pellet was resuspended in 30 mM Tris containing 0.4 M ammonium sulphate, which facilitated the RNA precipitation, and 1 mM PMSF, pH 8.4, and then was centrifuged at 10,000 rpm for 15 min.
Paired-end

treatment_protocol: To test the effect of SM and Chol on NM composition, 500x10^3 cells were incubated with 5, 10, 15, 20μM SM-Chol prepared in equimolar ratio as liposomes for 6hrs. The NMs were purified and analyzed.

value: Immortalized hippocampal neurons


title: TBB43

first: Jessica

address: 250 Heritage Medical Research Centre

institute: University of Alberta


title: pt5 and controls, sort 6 plate 4

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S6PL4_S3


title: Hela_10M_R2

value: HeLa (ATCC#CCL-2)

value: cervical adenocarcinoma

value: PROseq RNA


title: Normoxia, proliferating, replicate 4

description:
Norm_Prolif4
norm_counts_Norm_ChondrvsNorm_Prolif.csv
norm_counts_Norm_OsteovsNorm_Prolif.csv
norm_counts_Norm_SMvsNorm_Prolif.csv
norm_counts_Hypo_ProlifvsNorm_Prolif.csv
rawcts_prefilt2.csv

value: proliferating cranial neural crest cells

value: Proliferation medium (STO-conditioned DMEM (Gibco) containing 15% fetal calf serum (FCS), 1% Penicillin/Streptomycin, 0.1 mM non-essential amino acids and 55 µM beta-mercaptoethanol to which 25ng/ml bFGF and 5ng/ml LIF had been added), cultivated in 21% O2


title: Hela_10M_R1


title: TBB45


title: Pool rep3 [Pool-ID-1_S1_L003]


title: Pool rep2 [Pool-ID-1_S1_L002]


title: Normoxia, proliferating, replicate 3

description:
Norm_Prolif3
norm_counts_Norm_ChondrvsNorm_Prolif.csv
norm_counts_Norm_OsteovsNorm_Prolif.csv
norm_counts_Norm_SMvsNorm_Prolif.csv
norm_counts_Hypo_ProlifvsNorm_Prolif.csv
rawcts_prefilt2.csv


title: WT-rep5

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

description: Library name: WT-rep5

data_processing:
Reads were mapped to the mm10 reference genome via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Normalized coverage tracks were generated by STAR v2.5 with parameters "--runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Unstranded --outWigNorm RPM", then converted to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: Counts per gene per sample in tab-delimited text format.
Supplementary files format and content: Normalized coverage tracks in bigWig format.

source_name: testis

extract_protocol:
TRIzol was used for RNA preparation, followed by RNA collection via Qiagen RNA Easy kit.
RNA libraries were prepared using the Illumina Total RNA Prep Ligation with Ribo-Zero Plus protocol.

value: testis

value: WT


title: Pool rep1 [Pool-ID-1_S1_L001]


title: Normoxia, proliferating, replicate 2

description:
Norm_Prolif2
norm_counts_Norm_ChondrvsNorm_Prolif.csv
norm_counts_Norm_OsteovsNorm_Prolif.csv
norm_counts_Norm_SMvsNorm_Prolif.csv
norm_counts_Hypo_ProlifvsNorm_Prolif.csv
rawcts_prefilt2.csv


title: TBB40

city: Edmonton

last: Chang

source_name: lung biopsy

value: NR


title: WT-rep4

description: Library name: WT-rep4


title: TBB39


title: pt5 and controls, sort 6 plate 3

description:
scRNA-seq data from TARGET-seq+ (pt5 and controls)
raw_counts_2.txt.gz
S6PL3_S2


title: TBB36


title: Nuclei rep3 [n3_S3]

tag: rna source

value: Nuclei


title: TBB37

value: lowSFT


title: TBB38


title: TBB35

value: NKRL


title: HeLa_dTAG-13_20K_rPRO-seq_R2

description: Library name: Sample 12

library_source: other

data_processing:
*library strategy: rPRO-seq
Raw fastq PRO-seq data were processed as described previosly (Beckedorff, Blumenthal et al. 2020). Briefly PRO-seq reads were trimmed by Cutadapt 1.14 (Martin, 2011) and Trimmomatic v0.32 (Bolger et al., 2014), and aligned to the human genome (hg19) genome or the drosophila genome (dm3) by bowtie 1.1.2 (Langmead et al., 2009). PRO-seq signal was normalized by the number of reads mapped to spike-in dm3 genome, and then converted to bigwig data, which were used for downstream analyses. Quantification of nascent transcription per region was generated with an in-house script based on pyBigWig [Devon Ryan, B. G. F. R., doi:10.5281/zenodo.45238 (2016)] used to extract the normalized reads (CPM) per position from the bigwig files with a bin size of 1 bp upon merging the signal across two replicates.
Assembly: hg19 and mm10
Supplementary files format and content: The rPRO-seq processed data files are in bigWig format, bigwigs were normalized by Count Per Million produced from DeepTools2. bigwigs were with Bedtools v2.26 with genomecov.

molecule: other

growth_protocol:
HeLa  cell lines were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations.
Mouse E14 embryonic stem cells (ESCs) were acquired from ATCC. These cells were consistently cultured on plates coated with 0.1% gelatin (Stemcell Technologies) in DMEM (high glucose with GlutaMAX Supplement) medium (Thermo Fisher Scientific) that was further supplemented with 1 mM sodium pyruvate, 100 U/mL penicillin and 100 U/mL streptomycin, 1X MEM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 15% embryonic stem-cell FBS (all from Thermo Fisher Scientific), and 1000 U/mL recombinant leukemia inhibitory factor (LIF) from Stemcell Technologies. The cells were maintained in a controlled environment at 37°C with 5% CO2. For the non-directed differentiation of the ESCs into embryoid bodies, the medium was adjusted to contain 10% serum and was devoid of LIF.

extract_protocol: For rPRO-seq experiments were conducted following established protocols (see detailed protocol in supplementary file 1). Initially, a mixture of HeLa or mESC nuclei and Drosophila S2 cell nuclei as spike-ins was prepared. Nuclear run-on assays were executed by incubating nuclei at 30°C for 3 minutes with 25 μM Biotin-11-ATP/UTP/CTP/GTP (PerkinElmer). Subsequently, total RNA was extracted using Direct-zol RNA Miniprep and fragmented with 0.2 M NaOH for 10 minutes on ice, followed by purification of biotinylated nascent RNAs using streptavidin beads M-280 (Invitrogen). The 3’ RNA adaptor ligation process employs pre-adenylated single-stranded DNAs (P-3’ App-DNA), and T4 RNA ligase 2, truncated KQ, is utilized, incubated at 25°C for 1 hour. Additionally, on-bead 5’ RNA end repair involved using RppH (NEB) to remove the 5' cap and repair the triphosphate, followed by PNK-mediated repair of the 5' hydroxyl. The hybridization of DBO involves incorporating the dimer blocking oligonucleotide (DBO) into the RNA within the DBO mix. This is followed by a thermocycler program and subsequent combination with the 5’ adaptor ligation mixes in the RNA DBO mix, with a 1-hour incubation at 25°C. After adapter ligation, SuperScript III reverse transcription was employed. PCR amplification generated 140–350 bp libraries, which were size-selected using AMpure XP beads and sequenced using single-read runs on a NovaSeq X.

treatment_protocol: For the depletion of INTS11-dTAG, cells were treated with 500 nm of dTAG-13 and 1 µl/ml DMSO as the control. The treatment duration was predetermined.


title: Nuclei rep2 [n2_S2]


title: WT-rep1

description: Library name: WT-rep1

tag: batch


title: Nuclei rep1 [n1_S1]


title: HeLa_dTAG-13_20K_rPRO-seq_R1

description: Library name: Sample 11


title: WT-rep2

description: Library name: WT-rep2


title: HeLa_dTAG-13_10K_rPRO-seq_R2

description: Library name: Sample 10


title: Normoxia, proliferating, replicate 1

description:
Norm_Prolif1
norm_counts_Norm_ChondrvsNorm_Prolif.csv
norm_counts_Norm_OsteovsNorm_Prolif.csv
norm_counts_Norm_SMvsNorm_Prolif.csv
norm_counts_Hypo_ProlifvsNorm_Prolif.csv
rawcts_prefilt2.csv


title: Nuclear lipid microdomains rep3 [c3_S6]

value: Nuclear lipid microdomains


title: Nuclear lipid microdomains rep2 [c2_S5]


title: KO-rep5

description: Library name: KO-rep5

value: Mta3 mutant (lacking BAH domain)


title: HeLa_dTAG-13_5K_rPRO-seq_R2

description: Library name: Sample 8


title: HeLa_dTAG-13_10K_rPRO-seq_R1

description: Library name: Sample 9