title: H460-siRIC-Tot-RNA replicate 3

description: Library name: 7-H460-siRIC-Tot-RNA

growth_protocol: A549 and H460 cells were maintained in RPMI (Biowest) supplemented with 10% fetal bovie serum (FBS, Gibco), 1% L-glutamine (Gibco) and 1% antibiotics (Gibco) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested from the input (total RNA) or polysomal fractions using the TriPure isolation method (ref. 11667165001, Roche).
RNA was subjected to library preparation using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit (Cat# 20040525, Illumina) according to the manufacturer's protocols.

value: Lung

value: Lung cancer cell

value: Rictor knockdown

value: Replicate 3


title: patient133

status: Public on Jul 01 2026

type: other

city: Memphis

first: Kyle

middle: S

last: Smith

state: TN

address: 262 Danny Thomas Pl

country: USA

institute: St. Jude Children's Research Hospital

description: Brain tumor patient

hyb_protocol: Bisulphite converted DNA was amplified and hybridized to human MethylationHM450 BeadChip

scan_protocol: Array were imaged using BeadArray Reader (HiScan) and standard recommended illumina scanner setting

data_processing: Minfi R package (v1.58)

label: Cy3 and Cy5

molecule: other

organism: Homo sapiens

source_name: Brain tumor

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from samples using Qiagen Kit according to standard instructions

tag: Sex

value: Male

tag: age

tag: mstage

tag: risk group

value: Average

tag: subgroup

tag: shh subtype

tag: tissue

value: Brain tumor


title: Sample-38-24

type: SRA

city: Cologne

first: Philipp

last: Antczak

address: Robert-Koch-Strasse 21

department: Center for Molecular Medicine Cologne

country: Germany

institute: University Hospital Cologne

description: Library name: S38_24

library_source: transcriptomic

data_processing:
STAR v.2.7.5b with sjdbOverhang 100
Assembly: Ensembl Daphnia magna v2.4
Supplementary files format and content: CountData_Complete.csv was generated by compiling the count information from the STAR run and combining it with gene information from Ensembl Daphnia Magna v 2.4

molecule: total RNA

organism: Daphnia magna

source_name: whole organism

growth_protocol: We followed the methods outlined in ref. (Mathews et al., 2020) with a few differences. Every sampling day, we measured the length of each daphnid and noted the reproductive status (counts of eggs or embryos in the brood pouch and all free-swimming neonates) using a Leica dissecting scope (Leica M80), and we sacrificed individuals for transcriptomic analysis throughout the experiment.

extract_protocol:
We removed Daphnia for transcriptomic analyses from their treatments without being measured to minimize stress. We stored them individually in 500 μL of RNAlater and immediately flash froze them in liquid nitrogen. We then stored them at -80o F until RNA extraction. We extracted RNA from individual Daphnia using a RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions and the extracted RNA was stored in -80o F until sequencing by RNA-seq. The rRNA depletion procedure was used in RNA-Seq library preparation for total of 84 daphnia RNA samples.
Seven hundred ng of total RNA from each sample was subjected to library preparation using NEBNext Ultra II Directional RNA Library Prep with NEBNext rRNA Depletion Kit (New England Biolab, NEB, Ipswich, MA, USA) followed by the manufacturer’s protocol. Each library sample (total of 84) was individually barcoded with NEBNext Dual Index Primers (NEB, Ipswich, MA, USA). The QC of each library was validated by using Qubit fluorometer with Qubit dsDNA HS Assay Kit (Life Technologies, Grand Island, NY) and the Agilent Bioanalyzer 2100 system with Agilent DNA 1000 kit (Agilent Technologies, Santa Clara, CA).

treatment_protocol: We chose coal ash mixture exposure concentrations based on previous work (Mathews et al., 2020): 0.015, 0.06, 0.12, 0.25, 1.00, 4.00 nM Hg/L. We define the different concentrations in terms of their Hg concentration for simplicity; however, these concentrations represent a suite of coal ash constituents (Mathews et al., 2020). Similar to ref. (Mathews et al., 2020), we exposed the D. magna to coal ash through a dietary exposure route, since previous work found that coal ash is more toxic to zooplankton through a dietary exposure route compared to aqueous. We conducted dietary exposure by first exposing C. reinhardtii to the exposure concentrations of coal ash for two hours prior to feeding and then feeding the D. magna 25,000 cells/mL/day (0.026 mg C/individual/day).

value: whole organism

tag: day

tag: concentration

tag: treatment

value: coal ash


title: H460-siRIC-POLY replicate 3

city: Liège

first: Morgane

last: Paque

address: Quartier Hôpital, avenue de l'Hôpital 1

department: University of Liège

country: Belgium

institute: GIGA Institute

description: Library name: 7-H460-siRIC-POLY

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 97.
Assembly: Assembly: GRCh38
Supplementary files format and content: tab-delimited tsv file include raw counts for annotations for all Sample
Library strategy: Polysome-seq

molecule: polyA RNA

source_name: Lung

treatment_protocol: Transfection

tag: cell line

tag: cell type

tag: genotype

tag: batch


title: TatWT_RNAPII-Ser2p-ChIP_rep1

city: Jupiter

first: CHUAN

last: LI

state: FL

address: 130 Scripps Way

institute: University of Florida

description:
Library name: 903_17
ChIP-seq analysis of RNAPII-Ser2p in Jurkat T cell population infected with TatWT HIVgko under basal condition

library_source: genomic

data_processing:
Raw sequencing reads of ChIP_seq were quality-checked and adapter-trimmed prior to alignment. Reads were aligned to a combined human (hg38) and HIV reference genome, filtered to remove low-quality and duplicate reads, and normalized coverage tracks were generated. Processed data files consist of normalized bigWig signal tracks used for visualization and quantitative analyses. Raw sequencing reads of RNA_seq were quality-checked and adapter-trimmed prior to quantification. Reads were pseudo-aligned to a combined human (hg38) and HIV reference transcriptome using Salmon, and transcript-level abundances were summarized to gene-level counts using tximport. Raw gene counts and DESeq2-normalized counts were generated for downstream analyses and deposited as processed data files.
Assembly: Sequencing reads were processed using a combined reference consisting of the human genome assembly GRCh38 (hg38) and the HIV-1 proviral sequence corresponding to the integrated HIVGKO construct.
Supplementary files format and content: Processed ChIP-sequencing data are provided as normalized genome-wide signal tracks in bigWig format. Files contain read coverage normalized to counts per million (CPM) across the human (hg38) and HIV reference genomes and are suitable for visualization and quantitative analysis. Processed ChIP-sequencing data are provided as normalized genome-wide signal tracks in bigWig format. Files contain read coverage normalized to counts per million (CPM) across the human (hg38) and HIV reference genomes and are suitable for visualization and quantitative analysis.

molecule: genomic DNA

source_name: Cell line

growth_protocol: Jurkat CD4⁺ T cells were maintained in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) and penicillin-streptomycin-glutamine (100 U/mL penicillin, 100 µg/mL streptomycin, 2 mM L-glutamine) at 37 °C in a humidified incubator with 5% CO₂. Cells were routinely tested and confirmed negative for mycoplasma contamination.

extract_protocol:
Cells were crosslinked with formaldehyde, chromatin was fragmented by sonication, and immunoprecipitated DNA was purified following reversal of crosslinks prior to sequencing library preparation. Total RNA was isolated from harvested cells using a commercial silica column–based RNA purification kit according to the manufacturer’s instructions. RNA quality and concentration were assessed prior to RNA-sequencing library preparation.
Sequencing libraries were prepared using a commercial library preparation kit from New England Biolabs (NEB) according to the manufacturer’s instructions.

treatment_protocol: Jurkat HIVGKO-infected cells were maintained under basal (non-stimulated) conditions or stimulated to induce Tat accumulation and HIV transcription. For stimulated conditions, cells were treated with phorbol 12-myristate 13-acetate (PMA) and trichostatin A (TSA) for the indicated duration prior to harvesting. Non-stimulated controls were cultured in parallel under identical conditions without stimulation.

value: Cell line

value: Jurkat T

value: T cell

value: TatWT

value: Non-stimulation


title: patient132

description: Brain tumor patient

value: Female

value: High

tag: g34 subtype

value: VII


title: H460-siNT-Tot-RNA replicate 3

description: Library name: 7-H460-siNT-Tot-RNA

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 97.
Assembly: Assembly: GRCh38
Supplementary files format and content: tab-delimited tsv file include raw counts for annotations for all Sample

value: Lung

value: Wild type


title: Sample-36-17

description: Library name: S36_17


title: patient131

description: Brain tumor patient


title: H460-siNT-POLY replicate 3

description: Library name: 7-H460-siNT-POLY

value: Lung cancer cell


title: TatNull+Stim_TatChIP_rep1

description:
Library name: 903_39
ChIP-seq analysis of Tat in Jurkat T cell population infected with TatNull HIVgko under stimulated condition

value: TatNull

value: Stimulation (PMA+TSA)


title: TatNull+Stim_TatChIP_rep2

description:
Library name: 903_40
ChIP-seq analysis of Tat in Jurkat T cell population infected with TatNull HIVgko under stimulated condition


title: Sample-31-24

description: Library name: S31_24


title: Sample-27-10

description: Library name: S27_10


title: patient130

description: Brain tumor patient

value: Male

value: Average


title: H460-siRIC-Tot-RNA replicate 2

description: Library name: 6-H460-siRIC-Tot-RNA

value: Rictor knockdown

value: Replicate 2


title: TatNull_Tat-ChIP_rep2

description:
Library name: 903_38
ChIP-seq analysis of Tat in Jurkat T cell population infected with TatNull HIVgko under basal condition

value: Cell line


title: patient129

description: Brain tumor patient

value: V

value: Brain tumor


title: Sample-26-6

description: Library name: S26_6

value: whole organism

value: coal ash


title: H460-siRIC-POLY replicate 2

description: Library name: 6-H460-siRIC-POLY


title: TatNull_Tat-ChIP_rep1

description:
Library name: 903_37
ChIP-seq analysis of Tat in Jurkat T cell population infected with TatNull HIVgko under basal condition

value: Jurkat T

value: T cell

value: Non-stimulation


title: Sample-24-17

description: Library name: S24_17


title: patient128

description: Brain tumor patient

value: VI


title: H460-siNT-Tot-RNA replicate 2

description: Library name: 6-H460-siNT-Tot-RNA

value: Lung

value: Wild type


title: TatWT+Stim_Tat-ChIP_rep2

description:
Library name: 893_8
ChIP-seq analysis of Tat in Jurkat T cell population infected with TatWT HIVgko under stimulated condition

value: TatWT


title: patient127

description: Brain tumor patient

value: Female


title: TatWT+Stim_Tat-ChIP_rep1

description:
Library name: 893_7
ChIP-seq analysis of Tat in Jurkat T cell population infected with TatWT HIVgko under stimulated condition

value: Stimulation (PMA+TSA)


title: Sample-22-6

description: Library name: S22_6


title: H460-siNT-POLY replicate 2

description: Library name: 6-H460-siNT-POLY

value: Lung cancer cell


title: patient126

description: Brain tumor patient

value: Average

value: VII


title: Sample-20-24

description: Library name: S20_24


title: H460-siRIC-Tot-RNA replicate 1

description: Library name: 4-H460-siRIC-Tot-RNA

value: Rictor knockdown

value: Replicate 1


title: TatWT_Tat-ChIP_rep2

description:
Library name: 893_6
ChIP-seq analysis of Tat in Jurkat T cell population infected with TatWT HIVgko under basal condition

value: Cell line


title: patient125

description: Brain tumor patient

value: Brain tumor


title: Sample-2-10

description: Library name: S2_10

value: whole organism

value: coal ash


title: H460-siRIC-POLY replicate 1

description: Library name: 4-H460-siRIC-POLY


title: patient124

description: Brain tumor patient

value: Male


title: TatWT_Tat-ChIP_rep1

description:
Library name: 893_5
ChIP-seq analysis of Tat in Jurkat T cell population infected with TatWT HIVgko under basal condition

value: Jurkat T

value: T cell

value: Non-stimulation


title: Sample-175-24

description: Library name: S175_24


title: H460-siNT-Tot-RNA replicate 1

description: Library name: 4-H460-siNT-Tot-RNA

value: Lung

value: Wild type


title: TatNll+Stim_input_rep1

description:
Library name: 893_4
Input DNA of Jurkat T cell population infected with TatNull HIVgko under stimulated condition

value: TatNull


title: patient123

description: Brain tumor patient

value: II


title: Sample-174-17

description: Library name: S174_17


title: H460-siNT-POLY replicate 1

description: Library name: 4-H460-siNT-POLY

value: Lung cancer cell


title: patient122

description: Brain tumor patient

value: Female

value: High

value: V


title: Sample-173-10

description: Library name: S173_10


title: TatNull_input_rep1

description:
Library name: 893_3
Input DNA of Jurkat T cell population infected with TatNull HIVgko under basal condition


title: A549-siRIC-Tot-RNA replicate 3

description: Library name: 6-A549-siRIC-Tot-RNA

value: Rictor knockdown

value: Replicate 3


title: TatWT+Stim_input_rep1

description:
Library name: 893_2
Input DNA of Jurkat T cell population infected with TatWT HIVgko under stimulated condition

value: Cell line

value: TatWT

value: Stimulation (PMA+TSA)


title: patient121

description: Brain tumor patient

value: Male

value: Average

value: VII

value: Brain tumor


title: A549-siRIC-POLY replicate 3

description: Library name: 6-A549-siRIC-POLY

value: Lung


title: Sample-170-24

description: Library name: S170_24

value: whole organism

value: coal ash


title: TatWT_input_rep1

description:
Library name: 893_1
Input DNA of Jurkat T cell population infected with TatWT HIVgko under basal condition

value: Jurkat T

value: T cell

value: Non-stimulation


title: patient120

description: Brain tumor patient

value: High

value: II


title: A5$49-siNT-Tot-RNA replicate 3

description: Library name: 6-A549-siNT-Tot-RNA

value: Lung cancer cell

value: Wild type


title: PC_UH_R4_P6

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: Library name: s576

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina BaseSpace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed March 2025), which manages workflows using Snakemake v8.0 (Mölder et al. 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al. 2018), STAR v2.7.8a (Dobin et al. 2013) to perform alignment of raw reads to the reference sequence and the qCount function of the QuasR R package (v1.30.0; (Gaidatzis et al. 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

source_name: Mammary

growth_protocol: MCF-7 cells (ATCC, Manassas, Virginia) were cultured in 10 cm dishes (Corning Falcon No. 353003, Corning, New York) with Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Thermo Fisher Scientific, Waltham, Massachusetts) containing 10% fetal bovine serum (FBS; Wisent Bioproducts, Saint-Jean Baptiste, QC, Canada), and 1% penicillin and streptomycin (P/S; Wisent), at 37°C in a humidified atmosphere (5% CO2).

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.1 kit (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

treatment_protocol: For the experiment, cells were washed with phosphate-buffered saline (PBS) and the media were replaced with phenol red-free DMEM supplemented with 5% charcoal-dextran stripped FBS (CD-FBS) to eliminate estrogens present in commercial media and serum (Atlas et al. 2003) for 24 h. Cells were then seeded into clear 96-well plates (Corning Falcon No. 353075) at a density of 2.0 x 104 cells per well in phenol red-free DMEM supplemented with 5% CD-FBS and 1% P/S. After 24 h, the medium was removed and replaced with phenol red-free DMEM containing 5% CD-FBS and 1% P/S and chemicals of interest. Cells were exposed for 48 h, in quadruplicates, to BPA, the 12 chemicals of interest at eight different concentrations (0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50 µM), 17β-estradiol (E2; 0.1, 1 nM) as a positive control, and at least four plate-matched solvent controls (0.1% DMSO).

value: Mammary

value: Epithelial

value: WT

value: technical control

tag: chemical

value: universal human RNA

tag: dose


title: patient119

description: Brain tumor patient

tag: Sex

value: Male

value: Average


title: Sample-168-17

description: Library name: S168_17


title: Sample-166-10

description: Library name: S166_10


title: A549-siNT-POLY replicate 3

description: Library name: 6-A549-siNT-POLY

value: Lung

value: Replicate 3


title: PC_B_R4_P6

description: Library name: s575

value: brain RNA


title: patient118

description: Brain tumor patient

value: Female

tag: age

value: Brain tumor


title: Sample-165-6

description: Library name: S165_6

value: whole organism

value: coal ash


title: A549-siRIC-Tot-RNA replicate 2

description: Library name: 4-A549-siRIC-Tot-RNA

value: Rictor knockdown

value: Replicate 2


title: Sample-161-17

description: Library name: S161_17


title: patient117

description: Brain tumor patient

tag: mstage

value: High

value: I


title: A549-siRIC-POLY replicate 2

description: Library name: 4-A549-siRIC-POLY

value: Lung cancer cell


title: DMSO_0-1_R16_P6

description: Library name: s574

value: Mammary

value: Epithelial

value: WT

value: vehicle control

value: dimethyl sulfoxide


title: patient116

description: Brain tumor patient

tag: risk group

value: Average


title: DMSO_0-1_R15_P6

description: Library name: s573


title: TatWT_RNAPII-Ser2p-ChIP_rep2

description:
Library name: 893_9
ChIP-seq analysis of RNAPII-Ser2p in Jurkat T cell population infected with TatWT HIVgko under basal condition

value: Cell line

value: Jurkat T

value: T cell

value: TatWT

value: Non-stimulation


title: Sample-16-10

description: Library name: S16_10

value: whole organism

value: coal ash


title: A549-siNT-Tot-RNA replicate 2

description: Library name: 4-A549-siNT-Tot-RNA

value: Lung

value: Wild type

value: Replicate 2


title: patient115

description: Brain tumor patient

value: Female

tag: subgroup

value: VII

value: Brain tumor


title: DMSO_0-1_R14_P6

description: Library name: s572

value: Mammary

value: Epithelial

value: WT


title: A549-siNT-POLY replicate 2

description: Library name: 4-A549-siNT-POLY

value: Lung cancer cell


title: Sample-158-6

description: Library name: S158_6


title: DMSO_0-1_R13_P6

description: Library name: s571

value: vehicle control

value: dimethyl sulfoxide


title: patient114

description: Brain tumor patient

value: High

tag: shh subtype


title: A549-siRIC-Tot-RNA replicate 1

description: Library name: 3-A549-siRIC-Tot-RNA

tag: tissue

value: Rictor knockdown

value: Replicate 1


title: patient113

description: Brain tumor patient

value: Male


title: Sample-156-24

description: Library name: S156_24

value: whole organism

tag: day

value: coal ash


title: E2_1_R4_P6

description: Library name: s570

value: chemical exposure


title: A549-siRIC-POLY replicate 1

description: Library name: 3-A549-siRIC-POLY

value: Lung


title: Sample-152-10

description: Library name: S152_10

tag: concentration


title: E2_0-1_R4_P6

description: Library name: s569

tag: treatment


title: patient112

description: Brain tumor patient

value: Average


title: Sample-151-6

description: Library name: S151_6


title: NC_R4_P6

description: Library name: s568

tag: cell line

value: technical control

value: lysis buffer


title: Sample-15-6

description: Library name: S15_6


title: patient111

description: Brain tumor patient

value: Brain tumor


title: A549-siNT-POLY replicate 1

description: Library name: 3-A549-siNT-POLY

tag: cell type

value: Wild type


title: NC_R3_P6

description: Library name: s567

value: Mammary

value: Epithelial

tag: genotype

value: WT


title: A549-siNT-Tot-RNA replicate 1

description: Library name: 3-A549-siNT-Tot-RNA

value: Lung cancer cell

tag: batch


title: patient110

description: Brain tumor patient

value: High

tag: g34 subtype

value: VII


title: Sample-149-17

description: Library name: S149_17


title: DMSO_0-1_R12_P6

description: Library name: s566

value: vehicle control

tag: chemical

value: dimethyl sulfoxide


title: DMSO_0-1_R11_P6

description: Library name: s565

tag: dose


title: TC202UI

city: Houston

first: Tajhal

middle: D

last: Patel

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Library name: TC202UI

library_source: transcriptomic single cell

data_processing:
The 10x Genomics Cellranger software (v6.0) was used to demultiplex cell barcodes and map sequencing reads to the human reference genome (GRCh38).
Assembly: human GRCh38
Supplementary files format and content: tab-separated values files and matrix files

source_name: Human Colon Organoid

extract_protocol:
HCO monolayers on chamber slides were washed with PBS containing 5 mM EDTA and dissociated with 200 µL/well Accutase (STEMCELL Technologies, 07920). Cells were mixed using wide-bore pipette tips and incubated at 37°C for ~55 min until fully digested. Wells from the same HCO donor line and treatment were pooled, neutralized with fetal bovine serum, and diluted with 1mL cold differentiation medium with ROCK inhibitor Y-27632. Then the cell suspensions were centrifuged at 300g for 5min at 4°C, resuspended in 100 µL differentiation medium with Y-27632, and passed through Flowmi Cell Strainers (Millipore Sigma, BAH136800040). The resulting single-cell suspension was adjusted to 1,000 cells/µL for sequencing.
Single-cell gene expression libraries were generated using the Chromium Single Cell 3′ v3.1 kit (10x Genomics). Briefly, HCO single cell suspensions were combined with reverse transcription reagents, Gel Beads containing barcoded oligonucleotides, and oil on a Chromium X instrument (10x Genomics) to form Gel Bead-In-Emulsions (GEMs), enabling barcoded cDNA synthesis from each individual cell. Subsequently, the GEMs were disrupted and cDNA from each single cell was pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA was amplified by PCR. The amplified cDNA was then fragmented, end-repaired, A-tailed, and ligated with sequencing adaptors. Final sequencing libraries were generated by amplification.

value: Human Colon Organoid

value: Control uninfected


title: patient108

description: Brain tumor patient

tag: Sex

value: Male


title: TC202042

description: Library name: TC202042

value: EAEC 042 infected


title: Sample-147-6

description: Library name: S147_6

value: whole organism

value: coal ash


title: C103UI

description: Library name: C103UI


title: DMSO_0-1_R10_P6

description: Library name: s564


title: patient107

description: Brain tumor patient

tag: age

value: VIII


title: patient109

description: Brain tumor patient

value: Female

tag: mstage

value: Average

value: Brain tumor


title: Sample-145-24

description: Library name: S145_24


title: C103042

description: Library name: C103042


title: DMSO_0-1_R9_P6

description: Library name: s563

value: Mammary

value: Epithelial


title: patient106

description: Brain tumor patient

tag: risk group


title: Sample-143-17

description: Library name: S143_17


title: patient105

description: Brain tumor patient

tag: subgroup


title: ASC204UI

description: Library name: ASC204UI


title: Sample-141-10

description: Library name: S141_10


title: ASC204042

description: Library name: ASC204042


title: E2_0-1_R3_P6

description: Library name: s561

value: WT

value: chemical exposure


title: E2_1_R3_P6

description: Library name: s562


title: Sample-140-6

description: Library name: S140_6


title: patient104

description: Brain tumor patient

value: High

value: V


title: BTL_50_R4_P6

description: Library name: s544

value: bithionol


title: scRNA-seq of primary colon tumor from patient S12

city: Zhengzhou

first: Yukang

last: Chen

state: Henan

address: No. 1 Jianshe East Road, Erqi District

department: Department of Interventional Radiology

country: China

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: S12

data_processing:
The raw sequencing data was processed by fastp (Chen, Zhou et al. 2018) to trim primer sequences and low-quality bases. Subsequently, Seeksoul tools (SeekGene) was used to process the remaining data, demultiplex cellular barcodes and map reads to the human GRCh38 reference genome to generate feature-barcode matrices. The resulting matrix was used for downstream analyses, including converting into a Seurat object using the R package Seurat.
Assembly: GRCh38
Supplementary files format and content: Matrix Market (MEX) format files (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) generated by Seeksoul, containing raw unique molecular identifier (UMI) counts for each gene in each valid cell

source_name: colon adenocarcinoma

extract_protocol:
After harvested, tissues were washed in ice-cold PBS (Hyclone, SH30256.01) and dissociated using SeekMate Tissue Dissociation Reagent Kit A Pro (SeekGene, K01801301) or SeekMate Tissue Dissociation Kit C (SeekGene, K01501) from SeekGene as instructions. DNase I (Sigma, 9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using Fluorescence Cell Analyzer (Countstar® Rigel, S2) or SeekMate Tinitan Fluorescence Cell Counter (SeekGene, M002C) with AO/PI reagent after removal of erythrocytes (Solarbio, R1010) and then debris and dead cells removal was performed if needed (Miltenyi, 130-109-398/130-090-101). Finally, fresh cells were washed twice in the RPMI1640 (Gibco, 11875119) and then resuspended at 1x10^6 cells per ml in RPMI1640 and 2% FBS (Gibco, 10100147C).
Single-cell RNA-Seq libraries were prepared using SeekOne® Digital Droplet Single Cell 3' library preparation kit (SeekGene, Catalog No. K00202). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeekOne® chip S3. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip S3. After emulsion droplet generation, reverse transcription was performed at 42°C for 90 minutes and inactivated at 85°C for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR was performed to amplify the DNA representing 3' polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were cleanup with VAHTS DNA Clean Beads (Vazyme, N411-01), analyzed by Qubit (Thermo Fisher Scientific, Q33226) and Bio-Fragment Analyzer (Bioptic, Qsep400). The libraries were then sequenced on Illumina NovaSeq 6000 with PE150 read length.

value: colon adenocarcinoma

tag: patient id

value: male

tag: disease state

value: primary tumor

tag: tnm stage


title: patient147

description: Brain tumor patient

value: Male

value: III

tag: tissue


title: Sample-148-10

description: Library name: S148_10

value: whole organism

tag: day

tag: concentration

tag: treatment

value: coal ash


title: Sample-137-24

description: Library name: S137_24


title: patient103

description: Brain tumor patient


title: scRNA-seq of primary colon tumor from patient S11

description: Library name: S11

value: female


title: BTL_10_R4_P6

description: Library name: s543

tag: cell line

tag: cell type

tag: genotype


title: patient102

description: Brain tumor patient

value: Female

value: Average

tag: g34 subtype

value: I


title: scRNA-seq of primary colon tumor from patient S10

description: Library name: S10


title: Sample-130-24

description: Library name: S130_24


title: BTL_5_R4_P6

description: Library name: s542

value: Mammary

value: Epithelial

tag: chemical

tag: dose

tag: batch


title: Sample-13-24

description: Library name: S13_24


title: patient101

description: Brain tumor patient

tag: Sex

tag: age

tag: mstage

tag: shh subtype

value: Brain tumor


title: BTL_1_R4_P6

description: Library name: s541

value: WT

value: chemical exposure


title: scRNA-seq of primary colon tumor from patient S9

description: Library name: S9

tag: patient id

tag: disease state


title: patient100

description: Brain tumor patient

tag: risk group

tag: subgroup

tag: tissue


title: Sample-129-17

description: Library name: S129_17

tag: day

tag: concentration

tag: treatment


title: scRNA-seq of primary colon tumor from patient S8

description: Library name: S8

tag: tnm stage


title: BTL_0-5_R4_P6

description: Library name: s540

tag: cell line

tag: cell type

tag: genotype

value: bithionol


title: Sample-127-10

description: Library name: S127_10


title: BTL_0-1_R4_P6

description: Library name: s539

tag: chemical

tag: dose

tag: batch


title: patient99

description: Brain tumor patient

tag: Sex

tag: age

tag: mstage


title: scRNA-seq of primary colon tumor from patient S7

description: Library name: S7

value: colon adenocarcinoma

tag: patient id

tag: disease state


title: patient98

description: Brain tumor patient

tag: risk group

tag: subgroup

tag: shh subtype


title: Sample-126-6

description: Library name: S126_6

tag: tissue

tag: day

tag: concentration


title: scRNA-seq of primary colon tumor from patient S6

description: Library name: S6

tag: tnm stage


title: Sample-125-24

description: Library name: S125_24

tag: treatment


title: BTL_0-01_R4_P6

description: Library name: s538

tag: cell line

tag: cell type

tag: genotype


title: scRNA-seq of primary colon tumor from patient S5

description: Library name: S5

value: male


title: patient97

description: Brain tumor patient


title: BTL_0-001_R4_P6

description: Library name: s537

tag: chemical

tag: dose

tag: batch


title: Sample-124-17

description: Library name: S124_17


title: patient96

description: Brain tumor patient

tag: Sex

tag: age

tag: mstage


title: AO2246_10_R4_P6

description: Library name: s536

value: antioxidant 2246


title: patient95

description: Brain tumor patient

value: Male

tag: risk group

tag: g34 subtype

value: VII


title: scRNA-seq of primary colon tumor from patient S4

description: Library name: S4

tag: patient id

tag: disease state

value: primary tumor


title: Sample-123-10

description: Library name: S123_10

tag: tissue

value: whole organism

tag: day

value: coal ash


title: scRNA-seq of primary colon tumor from patient S3

description: Library name: S3

value: female

tag: tnm stage


title: patient94

description: Brain tumor patient

value: Female

value: Average

tag: subgroup

value: II


title: AO2246_5_R4_P6

description: Library name: s535

value: Mammary

tag: cell line

value: Epithelial

tag: treatment


title: scRNA-seq of primary colon tumor from patient S2

description: Library name: S2


title: Sample-122-6

description: Library name: S122_6

tag: concentration


title: AO2246_1_R4_P6

description: Library name: s534

tag: cell type

tag: genotype

value: WT

tag: chemical


title: patient93

description: Brain tumor patient

tag: Sex

value: Brain tumor


title: Sample-120-24

description: Library name: S120_24


title: MDA-MB-231 M3 cells, PRMT1 knockdown, biological replicate 2

city: nanjing

first: li

last: shang

address: longmian road 101

institute: nanjing medcial university

description:
Library name: C_2
Column name in genes.reads.count.AC.hg38.tsv.gz: C_2

data_processing:
Raw reads were filtered using fastp v0.23.2.
Unique molecular identifiers (UMIs) were processed using umikit v1.0, and reads were aligned to the human hg38 genome using STAR v2.7.6a.
Reads mapped to exonic regions were retained. UMI-based deduplication and sequencing/PCR error correction were performed using gencore v1.0.
Gene-level read counts were calculated using featureCounts from Subread v1.5.1.
Differential expression analysis was performed using edgeR v3.40.2.
Assembly: hg38
Supplementary files format and content: Tab-delimited gzip-compressed text file containing gene-level raw read counts for A_1, A_2, A_3, C_1, C_2, and C_3. B-group samples were removed.

source_name: breast

growth_protocol: MDA-MB-231 M3 human breast cancer bone-metastatic cells were cultured under standard cell culture conditions before RNA collection.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Thermo Scientific, Cat. 15596026). Genomic DNA was removed with DNase I (NEB, Cat. M0303L). RNA purity was assessed using a Nanodrop One spectrophotometer; RNA integrity was assessed using a LabChip GX Touch; RNA concentration was quantified using Qubit 3.0 with the Qubit RNA Broad Range Assay kit.
RNA-seq libraries were prepared using the KC-Digital stranded mRNA-seq Library Prep Kit for Illumina (Seqhealth Ltd., Wuhan, China, Cat. DR09202). Library fragments of 200-500 bp were enriched, quantified, and sequenced as paired-end 150 bp reads on an Illumina NovaSeq 6000 platform.

treatment_protocol: Control samples were collected from untreated/control MDA-MB-231 M3 cells. PRMT1 knockdown samples were generated by siPRMT1-mediated knockdown of PRMT1.

value: breast

value: MDA-MB-231 M3

value: breast cancer cell

value: siPRMT1-mediated PRMT1 knockdown


title: patient92

description: Brain tumor patient

value: Male

tag: age

value: High

value: VI


title: Sample-12-24

description: Library name: S12_24

value: whole organism


title: AO2246_0-1_R4_P6

description: Library name: s532

value: chemical exposure

value: antioxidant 2246

tag: dose

tag: batch


title: patient91

description: Brain tumor patient

tag: mstage

tag: risk group

tag: g34 subtype


title: MDA-MB-231 M3 cells, PRMT1 knockdown, biological replicate 3

description:
Library name: C_3
Column name in genes.reads.count.AC.hg38.tsv.gz: C_3

tag: tissue


title: AO2246_0-05_R4_P6

description: Library name: s531


title: scRNA-seq of primary colon tumor from patient S1

description: Library name: S1

value: colon adenocarcinoma

tag: patient id

value: female

tag: disease state

value: primary tumor


title: AO2246_0-5_R4_P6

description: Library name: s533

value: Mammary


title: Sample-118-17

description: Library name: S118_17

tag: day

value: coal ash


title: patient90

description: Brain tumor patient

tag: subgroup

value: VIII


title: MDA-MB-231 M3 cells, control, biological replicate 2

description:
Library name: A_2
Column name in genes.reads.count.AC.hg38.tsv.gz: A_2

tag: cell line

tag: treatment

value: control


title: Sample-108-6

description: Library name: S108_6

tag: concentration


title: MDA-MB-231 M3 cells, control, biological replicate 1

description:
Library name: A_1
Column name in genes.reads.count.AC.hg38.tsv.gz: A_1

value: breast

tag: cell type


title: MDA-MB-231 M3 cells, control, biological replicate 3

description:
Library name: A_3
Column name in genes.reads.count.AC.hg38.tsv.gz: A_3

value: MDA-MB-231 M3


title: Sample-111-17

description: Library name: S111_17


title: AO425_10_R4_P6

description: Library name: s528

value: Epithelial

tag: genotype

value: WT

tag: chemical

value: antioxidant 425


title: Sample-109-10

description: Library name: S109_10


title: MDA-MB-231 M3 cells, PRMT1 knockdown, biological replicate 1

description:
Library name: C_1
Column name in genes.reads.count.AC.hg38.tsv.gz: C_1

value: breast cancer cell

value: siPRMT1-mediated PRMT1 knockdown


title: AO2246_0-001_R4_P6

description: Library name: s529


title: Sample-11-17

description: Library name: S11_17

value: whole organism


title: patient89

description: Brain tumor patient

tag: Sex

value: Male

tag: age

value: Average

value: Brain tumor


title: AO2246_0-01_R4_P6

description: Library name: s530

value: chemical exposure

value: antioxidant 2246

tag: dose

tag: batch


title: AO425_5_R4_P6

description: Library name: s527

value: Mammary


title: patient88

description: Brain tumor patient

tag: mstage

tag: risk group


title: patient87

description: Brain tumor patient

value: Female

tag: g34 subtype

value: VI

tag: tissue


title: patient85

description: Brain tumor patient

value: VIII


title: Sample-106-24

description: Library name: S106_24

value: coal ash


title: Sample-103-10

description: Library name: S103_10


title: OE3

city: Lanzhou

first: Jiajing

last: He

address: No. 1 Dong Gang Xi Road, Chengguan District

department: The Reproductive Medicine Center

institute: The First Hospital of Lanzhou University

description:
Library name: OE3
THBS1 overexpression group, replicate biosample 3

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

source_name: KGN

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

value: KGN

value: cell culture

value: THBS1 overexpression


title: AO425_1_R4_P6

description: Library name: s526

value: Epithelial

value: WT

value: antioxidant 425


title: patient86

description: Brain tumor patient

value: High


title: patient84

description: Brain tumor patient

value: Male


title: OE2

description:
Library name: OE2
THBS1 overexpression group, replicate biosample 2


title: AO425_0-5_R4_P6

description: Library name: s525


title: Sample-101-6

description: Library name: S101_6

value: whole organism


title: AO425_0-1_R4_P6

description: Library name: s524


title: patient83

description: Brain tumor patient

value: I

value: Brain tumor


title: Ctrl3

description:
Library name: Ctrl3
control group, replicate biosample 3

value: wt


title: OE1

description:
Library name: OE1
THBS1 overexpression group, replicate biosample 1


title: AO425_0-05_R4_P6

description: Library name: s523

value: Mammary

value: chemical exposure


title: Control sib 406

type: genomic

city: Istanbul

first: Elif

last: ÖNEL

address: Buyukdere Street

country: Turkey

institute: Istanbul Technicial University

description: DNA is isolated from peripheral blood samples via salting-out procedure is genotyped using GSA MG v2.

hyb_protocol: Allele-specific staining was performed for chips.

scan_protocol: BeadArray Reader (Illumina) is used after bead chips are stained.

data_processing:
GenomeStudio v2.0 is used for deriving genotypes.
value definition: Genotype:  AA,AB,BB,or 00 (no call)

label: biotin

source_name: Blood

label_protocol: DNA fragmentation is applied.

extract_protocol: DNA is isolated from peripheral blood samples via salting-out procedure.

value: Blood


title: patient82

description: Brain tumor patient

value: Average


title: Patient 404

description: DNA is isolated from peripheral blood samples via salting-out procedure is genotyped using Infinium Global Screening Array with Cytogenetics-24.

value: Female


title: Patient 403


title: AO425_0-01_R4_P6

description: Library name: s522


title: patient81

description: Brain tumor patient

value: II


title: Ctrl2

description:
Library name: Ctrl2
control group, replicate biosample 2

value: KGN

value: cell culture


title: Ctrl1

description:
Library name: Ctrl1
control group, replicate biosample 1


title: BTL_50_R3_P6

description: Library name: s504

value: Epithelial

value: bithionol


title: patient80

description: Brain tumor patient

value: IV


title: Inflamed small intestine, Crohn's disease

type: RNA

city: Seoul

first: Yoonho

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: University of Ulsan College of Medicine

hyb_protocol: The Xenium custom probes were treated on the section slide for hybridization at 50℃ overnight. After slide washing,  ligation was performed at 37°C for 30 minutes. Amplification was immediately processed on the thermal cycler (C1000 96-well, Bio-Rad).  After slide washing, autofluorescence quenching and nuclei staining were performed on the sectioned slide. Subsequently, the sectioned slide was loaded onto the Xenium analyzer (XOA v1.7.6, 10x Genomics) to begin fluorescence signal detection.

scan_protocol: Xenium In Situ Analyzer

data_processing: Raw data were preprocessed with XeniumRanger v1.7.1 (10x Genomics)

label: Xenium Human Probe Set

source_name: 10 µm section Inflamed small intestine

label_protocol: Xenium Human Probe Set

extract_protocol: The OCT embedded frozen tissue blocks were carefully sectioned as 10μm thickness at –18°C cryostat. The sections were mounted onto a Xenium slide. Fixation and Permeabilization followed the manufacturer’s instructions(CG000581, 10x Genomics).

tag: disease state

value: Crohn's disease

value: small intestine


title: patient79

description: Brain tumor patient

value: VIII


title: AO425_0-001_R4_P6

description: Library name: s521

value: antioxidant 425


title: GPCRGSNO3

city: Bunkyo-ku

first: Rivo

middle: Yudhinata Brian

last: Nugraha

state: Tokyo

address: 7-3-1 Hongo

department: Biomedical Chemistry

country: Japan

institute: The University of Tokyo

description:
Library name: Sample 6
Column name in CPM_expression_data.tsv: GPCRGSNO3

data_processing:
Total RNA of psAP2-EhGPCRgs and psAP2-mock control trophozoites was subjected to directional library preparation and sequenced on an Illumina NovaSeq 6000 platform (Veritas Genetics, China; Fujifilm, Japan). For sequence read analysis, fastp (version 0.23.2) was used to assess the quality of all reads and remove those of low quality. Each read obtained after filtering was mapped to the reference genome AmoebaDB-EhistolyticaHM1IMSS-Genome using STAR (version 2.7.10a). Mapping reads was done using the default parameter values. Additionally, featureCount (version 2.0.1) was used to calculate the number of counts for each gene, as defined by its gene ID. In this case, counting reads was performed for the gene ID defined by AmoebaDB‒Ehistolytica HM1:IMSS release‒54 (https://amoebadb.org/amoeba/app/downloads). Genes which have no count in all samples were removed. After filtering, the total number of reads was normalized to 1 million per sample (CPM, count per million). Normalized read counts were analyzed using edgeR (version 3.40.2) to identify Differentially Expressed Genes (DEGs) between the control and silencing groups.
Assembly: AmoebaDB‒Ehistolytica HM1:IMSS release‒54
Supplementary files format and content: tab-delimited text file includes raw data in count per million unit

organism: Entamoeba histolytica

source_name: HM1:IMSS G3

growth_protocol: Trophozoites of Entamoeba histolytica strains HM-1:IMSS G3 were axenically cultured in 6 ml screw-capped Pyrex glass tubes containing Diamond’s BI-S-33 (BIS) medium at 35.5°C. All trophozoites used for the experiment were prepared during the logarithmic phase at 24 hours of cultivation.

extract_protocol:
RNA of E. histolytica was extracted from ~1x10^6 cells using Trizol reagent (Ambion; Life Technologies, Grand Islands, NY, USA) based on the manufacturer’s protocol. Genomic DNA was removed after treatment with DNase I (Invitrogen). At least 3.5 μg of total RNA was used for RNA-seq.
cDNA was synthesized using the SuperScript III First-Strand Synthesis System (Invitrogen) according to the manufacturer’s protocol.

value: HM1:IMSS G3

value: Single cell amoebazoa

value: EhGPCR (CL6EHI_096680) silencing

tag: developmental stage

value: Trophozoite


title: HepG2.batch2.SMET.rep3.G03

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

institute: McGill University

description: Library name: HepG2_Batch2_SMET_3_G03

library_source: other

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

source_name: cell lysate

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to various concentrations of 6ppd-quinone for 24 hours after seeding at 35,000 cells per well

value: liver

value: hepatocyte

value: cell line


title: HepG2.batch2.SMET.rep3.H03

description: Library name: HepG2_Batch2_SMET_3_H03


title: BTL_10_R3_P6

description: Library name: s503

value: Mammary

value: WT

value: chemical exposure


title: patient78

description: Brain tumor patient

value: Male

value: Average

tag: subgroup

value: Brain tumor


title: GPCRGSNO2

description:
Library name: Sample 5
Column name in CPM_expression_data.tsv: GPCRGSNO2

tag: cell line


title: HepG2.batch2.SMET.rep3.F03

description: Library name: HepG2_Batch2_SMET_3_F03

tag: treatment


title: BTL_5_R3_P6

description: Library name: s502

value: Epithelial

value: bithionol


title: patient77

description: Brain tumor patient

value: High

value: V


title: HepG2.batch2.SMET.rep3.E03

description: Library name: HepG2_Batch2_SMET_3_E03


title: GPCRGSNO1

description:
Library name: Sample 4
Column name in CPM_expression_data.tsv: GPCRGSNO1

value: HM1:IMSS G3


title: PSAP2NO3

description:
Library name: Sample 3
Column name in CPM_expression_data.tsv: PSAP2NO3

value: Single cell amoebazoa


title: BTL_0-5_R3_P6

description: Library name: s500


title: HepG2.batch2.SMET.rep3.D03

description: Library name: HepG2_Batch2_SMET_3_D03


title: BTL_1_R3_P6

description: Library name: s501


title: patient75

description: Brain tumor patient

value: Female

value: VII


title: HepG2.batch2.SMET.rep3.C03

description: Library name: HepG2_Batch2_SMET_3_C03

value: liver


title: patient76

description: Brain tumor patient

value: I


title: PSAP2NO2

description:
Library name: Sample 2
Column name in CPM_expression_data.tsv: PSAP2NO2

value: Trophozoite


title: BTL_0-1_R3_P6

description: Library name: s499

value: Mammary


title: HepG2.batch2.SMET.rep3.B03

description: Library name: HepG2_Batch2_SMET_3_B03

value: hepatocyte

value: cell line


title: patient74

description: Brain tumor patient


title: BTL_0-01_R3_P6

description: Library name: s498

value: chemical exposure


title: patient73

description: Brain tumor patient

value: Male

value: VIII


title: PSAP2NO1

description:
Library name: Sample 1
Column name in CPM_expression_data.tsv: PSAP2NO1

value: WT


city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

description:
Library name: pmr4_3H_R3
pmr4-1 P. brassicae pathotype 3H-infected R3, Day14

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Filtered reads were mapped to TAIR10 complete reference genome.
Reads quantification was performed by Salmon.
Normalized counts were obtained from R tximport and DESeq2 package.
Assembly: Arabidopsis thaliana (thale cress) genome assembly TAIR10 from The Arabidopsis Information Resource (TAIR) [GCA_000001735.1 GCF_000001735.3]
Supplementary files format and content: Matrix table files include normalized counts for each sample

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Arabidopsis thaliana wild type (Col-0) and pmr4-1 seeds were sowed and grown in the soil Sunshine® Mix #5 Natural & Organic (Sun Gro Horticulture Canada Ltd). Arabidopsis and B. napus plants were grown at 22 °C under 16 h ~125 mE m-2 s-1 light and 8 h dark photoperiod conditions.

extract_protocol:
Total RNA was extracted using  RNeasy® Plant Mini kit (Qiagen) kit. 500 ng of total RNA was used for the construction of sequencing libraries.
Libraries were generated with the TruSeq UD V1.5 Kit following the instruction manual. Samples were loaded on the Illumina NovaSeq 6000 platform for pair-end sequencing with 150 cycles at the Omics and Precision Agriculture Laboratory.

treatment_protocol: 1 ml of Plasmodiophora brassicae pathotype 3H resting spore inoculum at a final density at 1 x 10^7 spores/ml was applied to 14-day-old seedling, while 1 ml ddH2O was applied to to 14-day-old seedling for mock control.

value: root

value: P. brassicae pathotype 3H resting spore inoculation

value: Day 14


title: HepG2.batch2.SMET.rep3.A03

description: Library name: HepG2_Batch2_SMET_3_A03


title: WT_Tm_RNA_SET4_rep3

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

institute: Yonsei University College of Medicine

description: Library name: WT_Tm_RNA_SET4_rep3

data_processing:
Paired-end sequencing reads were trimmed using TrimGalore (v0.6.4)
The trimmed reads were aligned to the human reference genome hg19 using STAR (v2.6.0c)61 with the parameters --chimSegmentMin 20 --twopassMode Basic --quantMode TranscriptomeSAM.
Reads counts at gene-levels are quantified using RSEM (v1.3.1)62 and normalized to transcripts per million (TPM).
Strand specific reads were selected using SAMtools (v1.3.1), and genome-wide coverage tracks were generated using deepTools (v3.4.3).
hg19
Assembly: RSEM output files including raw counts, TPM values
Supplementary files format and content: normalized bigwig

growth_protocol: The human colorectal cancer cell line HCT116 was cultured in RPMI-1640 medium (Welgene) supplemented with 10% fetal bovine serum (FBS; HyClone) and 1% penicillin–streptomycin (Welgene) at 37 ℃ in a humidified incubator containing 5% CO2. Cells were subcultured every 48–72 h.

extract_protocol:
Total RNA was extracted from wild-type HCT116 and transcription factor knockout cells using RiboEx (GeneAll Biotechnology)
Sequencing libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7760) following the manufacturer’s protocol.

treatment_protocol: Cells were treated with tunicamycin (Sigma-Aldrich) at a final concentration of 0.5 µg ml-1 for 6 h. Cells treated with 0.1% DMSO for the same duration served as vehicle controls.

value: Human colorectal cancer

value: 0.5 μg ml tunicamycin

tag: time


title: BTL_0-001_R3_P6

description: Library name: s497

tag: cell type

value: Epithelial

value: bithionol


title: patient72

description: Brain tumor patient

value: Average

value: VI

value: Brain tumor


title: HepG2.batch2.SMET.rep2.H03

description: Library name: HepG2_Batch2_SMET_2_H03

value: liver

tag: genotype


title: patient71

description: Brain tumor patient

value: Female

value: High

tag: shh subtype


description:
Library name: pmr4_3H_R2
pmr4-1 P. brassicae pathotype 3H-infected R2, Day14


title: AO2246_10_R3_P6

description: Library name: s496

value: Mammary

value: chemical exposure

tag: chemical

value: antioxidant 2246


title: HepG2.batch2.SMET.rep2.G03

description: Library name: HepG2_Batch2_SMET_2_G03

value: hepatocyte

value: cell line


description:
Library name: pmr4_3H_R1
pmr4-1 P. brassicae pathotype 3H-infected R1, Day14

value: root

value: P. brassicae pathotype 3H resting spore inoculation


title: AO2246_5_R3_P6

description: Library name: s495

value: WT


title: patient70

description: Brain tumor patient

tag: Sex

value: Male

tag: age


title: patient69

description: Brain tumor patient

value: VII


title: AO2246_1_R3_P6

description: Library name: s494

value: Epithelial

tag: dose

tag: batch


title: pmr4-1 Mock control, R3, Day14

description:
Library name: pmr4_Mock_R3
pmr4-1 Mock control, R3, Day14

value: Mock control

value: Day 14


title: HepG2.batch2.SMET.rep2.F03

description: Library name: HepG2_Batch2_SMET_2_F03


title: HepG2.batch2.SMET.rep2.E03

description: Library name: HepG2_Batch2_SMET_2_E03


title: pmr4-1 Mock control, R2, Day14

description:
Library name: pmr4_Mock_R2
pmr4-1 Mock control, R2, Day14


title: AO2246_0-5_R3_P6

description: Library name: s493


title: patient68

description: Brain tumor patient

tag: mstage

tag: risk group

value: VI

value: Brain tumor


title: pmr4-1 Mock control, R1, Day14

description:
Library name: pmr4_Mock_R1
pmr4-1 Mock control, R1, Day14

tag: tissue


title: HepG2.batch2.SMET.rep2.D03

description: Library name: HepG2_Batch2_SMET_2_D03

value: liver


title: AO2246_0-1_R3_P6

description: Library name: s492


title: patient67

description: Brain tumor patient

value: Average


description:
Library name: WT_3H_R3
Col-0 P. brassicae pathotype 3H-infected, R3, Day14


title: AO2246_0-05_R3_P6

description: Library name: s491

value: Mammary


title: HepG2.batch2.SMET.rep2.C03

description: Library name: HepG2_Batch2_SMET_2_C03


title: patient66

description: Brain tumor patient

value: High

tag: g34 subtype

value: II


description:
Library name: WT_3H_R2
Col-0 P. brassicae pathotype 3H-infected, R2, Day14


description:
Library name: WT_3H_R1
Col-0 P. brassicae pathotype 3H-infected, R1, Day14


title: AO2246_0-01_R3_P6

description: Library name: s490

value: chemical exposure

value: antioxidant 2246


title: HepG2.batch2.SMET.rep2.B03

description: Library name: HepG2_Batch2_SMET_2_B03

value: hepatocyte

value: cell line


title: patient65

description: Brain tumor patient


title: AO2246_0-001_R3_P6

description: Library name: s489

value: WT


title: patient64

description: Brain tumor patient

value: Female

value: V


title: ATRT patient tumor, RNA070_17_206

city: Paris

first: Franck

last: Bourdeaut

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Library name: RNA070_17_206
Column name in raw counts and TPM matrixes : RNA070_17_206
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt

data_processing:
Raw data were processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility, following standard analysis in the field and available at https://github.com/bioinfo-pf-curie/RNA-seq.
Sequencing adaptors were trimmed using TrimGalore!
read QC were performed using fastqc
read mapping on GRCh39/hg19 reference genome were performed using STAR (version 2.5.3a) and the refFlat gene annotation downloaded from UCSC
duplicated reads were marked with picard and then removed
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: a single tab-delimited text file includes matrix of TPM values with sample in columns and genes on rows

source_name: tumor

growth_protocol: I2A cells were maintained in RPMI containing 10% fetal bovine serum (FBS) and supplemented with 50 ng/mL doxycycline, 50 μg/mL hygromycin B and 300 μg/mL geneticin. G401-i cells were maintained in RPMI containing 10% FBS and supplemented with 50 ng/mL doxycycline. For both inducible cell lines, medium was changed every 3-4 days to renew drugs and cells were washed three times in Phosphate Buffer Saline (PBS) to completely remove doxycycline in order to induce SMARCB1 expression.

extract_protocol:
Total RNAs from cell line samples were extracted using the Nucleospin II kit (Macherey-Nagel). Total RNAs from frozen human tumors were extracted using the QIAamp RNAeasy kit (Qiagen)
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.,).

treatment_protocol: For low-dose decitabine (DAC) experiments, I2A cells were treated with DAC at 100 nM or DMSO as a control for 21 days.

value: tumor

value: Rhabdoid tumor

tag: patient id


title: HepG2.batch2.SMET.rep1.H03

description: Library name: HepG2_Batch2_SMET_1_H03


title: HepG2.batch2.SMET.rep2.A03

description: Library name: HepG2_Batch2_SMET_2_A03


title: patient63

description: Brain tumor patient

data_processing: Minfi R package (v1.58)

value: Male

tag: subgroup


title: AO425_10_R3_P6

description: Library name: s488

tag: cell line

value: Epithelial

value: antioxidant 425


title: Col-0 Mock control, R2, Day14

description:
Library name: WT_Mock_R2
Col-0 Mock control, R2, Day14

value: root

tag: treatment

value: Mock control

value: Day 14


title: Col-0 Mock control, R3, Day14

description:
Library name: WT_Mock_R3
Col-0 Mock control, R3, Day14


title: HepG2.batch2.SMET.rep1.G03

description: Library name: HepG2_Batch2_SMET_1_G03

value: liver


title: AO425_5_R3_P6

description: Library name: s487

value: Mammary


title: patient62

description: Brain tumor patient

value: Average

value: VII

value: Brain tumor


title: Col-0 Mock control, R1, Day14

description:
Library name: WT_Mock_R1
Col-0 Mock control, R1, Day14


title: HepG2.batch2.SMET.rep1.F03

description: Library name: HepG2_Batch2_SMET_1_F03

value: hepatocyte

value: cell line


title: patient61

description: Brain tumor patient

value: VIII


title: BMSC wild-type 3

city: Beijing

first: Fu

state: Changping District

address: No. 68 North Huinan Street

department: Department of Nephrology

institute: Beijing Jishuitan Hospital

description:
Library name: MSC-cb6p5
con3

data_processing:
Processed data files in this project were generated through a comprehensive bioinformatics pipeline. Raw sequencing reads were first quality-filtered using Fastp (v0.20.1) with a minimum length threshold of 50 bp, followed by quality assessment using FastQC (v0.11.9). High-quality reads (CleanReads) were then aligned to the reference genome (mRatBN7.2) using HISAT2 (v2.1.0) with parameters --rna-strandness rf -fr to account for strand-specific RNA-seq. Post-alignment, SAMtools (v1.9) was employed for processing BAM files. Quantification of gene expression was performed with HTSeq-count (v0.11.2) using -s reverse to generate counts per gene. Differential expression analysis was conducted using DESeq2 (v1.22.2) for biological replicates and DESeq (v1.34.1) for non-replicates, with significance thresholds set at q-value < 0.05 and |log2FoldChange| > 1. Additional analyses, including GO, KEGG, and Reactome enrichment, were carried out using hypergeometric distribution tests, and data quality was further evaluated using RSeQC (v4.0.0) .
Assembly: mRatBN7.2
Supplementary files format and content: The file CKD-vs-con-all.gene.xls contains a complete dataset of all protein-coding genes analyzed during the differential expression comparison between CKD and control samples, without filtering for statistical significance. It includes each gene's identifier, average normalized expression across all samples as calculated by DESeq2, and group-specific averages for both CKD and control conditions. The file also reports the fold change and log2 fold change in expression between the two groups, along with associated p-values and adjusted q-values to assess statistical relevance. Additionally, it details the direction of regulation, whether a gene is upregulated, downregulated, or not significantly changed, as well as FPKM values for each sample and a description of each gene’s annotated function.

organism: Rattus

source_name: BMSC

growth_protocol: Bone marrow mesenchymal stem cells (BMSCs) were isolated from the femurs and tibias of Sprague Dawley rats and cultured in α-MEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were maintained at 37°C in a humidified atmosphere with 5% CO₂ and passaged upon reaching 80–90% confluence. BMSCs were validated by flow cytometry (CD29⁺, CD90⁺, CD34⁻, CD45⁻) and used at passages 3–5 for experiments. Osteogenic and adipogenic differentiation capacity was confirmed through Alizarin Red and Oil Red O staining, respectively.

extract_protocol:
Total RNA was extracted from exosome samples using TRIzol Reagent (Invitrogen) according to the manufacturer’s protocol. RNA quality and concentration were assessed using a Qubit®2.0 Fluorometer and Agilent 2200 TapeStation RNA integrity was verified, and samples with OD260/OD280 ratios between 1.8–2.0 were used for sequencing.
RNA libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit. Poly-A mRNA was purified from total RNA using oligo(dT) magnetic beads and fragmented. First and second strand cDNA synthesis was performed, followed by end repair, A-tailing, adapter ligation, and PCR amplification. The resulting libraries were quality-checked using the Agilent 2100 Bioanalyzer and quantified before sequencing on an Illumina platform.

value: BMSC

value: wild-type

tag: disease model

value: Ctrl


title: HepG2.batch2.SMET.rep1.E03

description: Library name: HepG2_Batch2_SMET_1_E03

tag: cell type


title: AO425_0-5_R3_P6

description: Library name: s485

tag: genotype

value: WT

value: chemical exposure


title: patient60

first: Kyle

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

description: Brain tumor patient

value: Female


title: AO425_1_R3_P6

description: Library name: s486

value: Epithelial

value: antioxidant 425


title: HepG2.batch2.SMET.rep1.D03

description: Library name: HepG2_Batch2_SMET_1_D03


title: patient59

description: Brain tumor patient

value: Male


title: BMSC CKD 1

description:
Library name: CKD4-1
CKD1


title: AO425_0-05_R3_P6

description: Library name: s483


title: patient58

description: Brain tumor patient


title: HepG2.batch2.SMET.rep1.C03

description: Library name: HepG2_Batch2_SMET_1_C03

value: liver


title: SHAL2

city: Bundoora

first: Quynh Nhu

last: Dinh

state: VIC

address: Kingsbury Drive & Plenty Rd

country: Australia

institute: La Trobe University

data_processing:
High-throughput sequencing was conducted using the HiSeqTM2500 platform
The results were mapped to the Ensembl-released mouse genome sequence and annotation.
Differential expression analysis was conducted using the DESeq R Package V.1.10.1 and P-values were adjusted using the Banjamini and Hochberg’s approach for controlling the false discovery rate
Genes were considered differentially expressed if the adjusted P-value was less than 0.05.
Supplementary files format and content: tab-delimited text files fpkm gene counts

organism: Mus musculus

source_name: Cerebral artery

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene

treatment_protocol: Mice underwent ad libitum eating or intermittant fasting for 3 months. After 3 months, chronic cerebral hypoperfusion was induced by the bilateral carotid arterys stenosis (BCAS) surgery. Control mice underwent sham surgery. Mice were culled at days 1, 14, 21 and 30 days post-surgery and cerebral arteries were collected.

value: Cerebral artery

tag: strain

tag: disease state

value: Control


title: BMSC wild type 2

description:
Library name: con9-2
con2

value: CKD


title: BMSC CKD 2

description:
Library name: CKD2
CKD2


title: HepG2.batch2.SMET.rep1.B03

description: Library name: HepG2_Batch2_SMET_1_B03


title: AO425_0-01_R3_P6

description: Library name: s482

value: Mammary

tag: chemical


title: patient57

city: Memphis

last: Smith

description: Brain tumor patient

source_name: Brain tumor

extract_protocol: DNA was extracted from samples using Qiagen Kit according to standard instructions

tag: Sex

tag: age

value: Average

value: II

value: Brain tumor


title: ATRT patient tumor, RNA371_23_009

description:
Library name: RNA371_23_009
Column name in raw counts and TPM matrixes : RNA371_23_009
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt

value: tumor

value: Rhabdoid tumor


title: WT_Con_RNA_SET4_rep1

description: Library name: WT_Con_RNA_SET4_rep1

value: Human colorectal cancer

value: 0.1% DMSO

tag: time


title: AO425_0-001_R3_P6

description: Library name: s481

value: WT

value: chemical exposure

tag: dose

tag: batch


title: HepG2.batch2.SMET.rep1.A03

description: Library name: HepG2_Batch2_SMET_1_A03

tag: tissue

value: hepatocyte

value: cell line


title: BMSC wild-type 1

description:
Library name: con9-1
con1

value: BMSC

value: wild-type

value: Ctrl


title: patient56

description: Brain tumor patient

value: Male

tag: mstage

tag: risk group

value: High

tag: g34 subtype

value: V


title: BMSC CKD 4

description:
Library name: CKD4-2
CKD3

value: CKD


title: HepG2.batch2.PER.rep3.H02

description: Library name: HepG2_Batch2_PER_3_H02

value: liver

tag: cell line


title: CHOP_KO_Tm_RNA_SET3_rep3

description: Library name: CHOP_KO_Tm_RNA_SET3_rep3

tag: treatment

value: 0.5 μg ml tunicamycin


title: patient55

description: Brain tumor patient

value: Average

tag: subgroup

tag: shh subtype

value: Brain tumor


title: PC_B_R4_P5

description: Library name: s479

value: Mammary

tag: cell type

value: Epithelial

tag: genotype

value: technical control

value: brain RNA


title: HepG2.batch2.PER.rep3.G02

description: Library name: HepG2_Batch2_PER_3_G02

value: hepatocyte


title: RDY327 ChEC-seq, 25 min IAA, rep C

city: Oklahoma City

first: John

middle: B

last: Ridenour

state: OK

address: 825 NE 13th St.

department: Cell Cycle and Cancer Biology Research Program

institute: Oklahoma Medical Research Foundation

description: Library name: RDHTS1033

data_processing:
Paired-end 150 bp reads were preprocessed using bbduk (BBMap version 39.06) and aligned using Bowtie 2 (version 2.5.0). BAM files were created, sorted, and indexed using Samtools (version 1.18). Genome coverage was calculated and normalized by counts per million (CPM) using deepTools2 (version 3.5.4). Average genome coverage across replicates was calculated using BEDTools (version 2.30.0) and bedGraphToBigWig. Preprocessing and processing steps were implemented as a Snakemake workflow (https://github.com/DonczewLab/ChEC-Seq_Analysis).
Assembly: Saccharomyces cerevisiae strain S288C version R64-3-1 (RefSeq Assembly GCF_000146045.2)
Supplementary files format and content: Processed data (counts per million [CPM] normalized genome coverage) are provided in bigwig (.bw) format.
Library strategy: ChEC-seq

organism: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae cells were grown in YPD medium (10 g/l yeast extract, 20 g/l peptone, 20 g/l glucose, 20 mg/ml adenine sulfate) at 30°C with shaking at 220 rpm.

extract_protocol:
DNA was purified using a ChIP DNA Clean and Concentrator kit (Zymo Research). Cleaved DNA was selected based on size using Sera-Mag Speedbeads (Cytiva) prepared as described (dx.doi.org/10.17504/protocols.io.x54v9p7b1g3e/v2).
Libraries were constructed using a Next Ultra II DNA Library Prep kit (New England Biolabs) as described (https://doi.org/10.1371/journal.pgen.1010945) and sequenced on an Illumina NovaSeq 6000 at the Oklahoma Medical Research Foundation Clinical Genomics Center.

treatment_protocol: Saccharomyces cerevisiae cells were grown to an OD600 of ~0.5. Cultures were treated with 1 mM 3-indoleacetic acid (IAA) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 25 min. The final OD600 of the cultures was ~0.7. Cells were pelleted at 3,000 g then resuspended in Buffer A, permeabilized, and treated with calcium chloride to induce DNA cleavage.

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD73:TRP1 TAF1-MNase::HYG

value: 25 min IAA treatment


title: PC_UH_R4_P5

description: Library name: s480

value: WT

value: universal human RNA


title: HepG2.batch2.PER.rep3.F02

description: Library name: HepG2_Batch2_PER_3_F02

value: cell line


title: patient53

description: Brain tumor patient

value: Male

value: VIII


title: RDY327 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS1031


title: patient54

description: Brain tumor patient


title: DMSO_0-1_R8_P5

description: Library name: s478

value: vehicle control

value: dimethyl sulfoxide


title: RDY327 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS1029


title: HepG2.batch2.PER.rep3.E02

description: Library name: HepG2_Batch2_PER_3_E02

value: liver


title: patient52

description: Brain tumor patient

value: Female

value: Average

value: Brain tumor


title: RDY327 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS1032

value: 25 min DMSO treatment


title: DMSO_0-1_R6_P5

description: Library name: s476

value: Mammary

value: Epithelial


title: patient51

description: Brain tumor patient


title: HepG2.batch2.PER.rep3.C02

description: Library name: HepG2_Batch2_PER_3_C02

value: hepatocyte


title: HepG2.batch2.PER.rep3.D02

description: Library name: HepG2_Batch2_PER_3_D02


title: patient50

description: Brain tumor patient

value: High

value: VII


title: RDY327 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS1028

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD73:TRP1 TAF1-MNase::HYG


title: RDY327 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS1030


title: patient49

description: Brain tumor patient


title: HepG2.batch2.PER.rep3.A02

description: Library name: HepG2_Batch2_PER_3_A02

value: cell line


title: E2_0-1_R2_P5

description: Library name: s473

value: WT

value: chemical exposure


title: AO425_0-1_R3_P6

description: Library name: s484

value: antioxidant 425


title: BCIF45

value: Cerebral artery

tag: strain

value: Male

tag: disease state

value: Chronic cerebral hypoperfusion


title: patient47

description: Brain tumor patient

tag: Sex

value: Average

value: III


title: RDY322 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS1023

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD32:TRP1 TAF1-MNase::HYG

value: 25 min IAA treatment


title: patient48

description: Brain tumor patient

value: Female

tag: age

value: I

value: Brain tumor


title: NC_R2_P5

description: Library name: s472

value: Mammary

value: Epithelial

value: technical control

tag: chemical

value: lysis buffer


title: patient46

description: Brain tumor patient

value: High


title: HepG2.batch2.PER.rep2.G02

description: Library name: HepG2_Batch2_PER_2_G02

value: liver

value: hepatocyte

value: cell line


title: DMSO_0-1_R4_P5

description: Library name: s470

value: WT

value: vehicle control

value: dimethyl sulfoxide

tag: dose


title: NC_R1_P5

description: Library name: s471

tag: batch


title: HepG2.batch2.PER.rep2.F02

description: Library name: HepG2_Batch2_PER_2_F02

tag: tissue


title: HepG2.batch2.PER.rep2.H02

description: Library name: HepG2_Batch2_PER_2_H02


title: RDY322 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS1025

value: yeast cell


title: patient44

description: Brain tumor patient

value: Male

tag: mstage

value: Average

value: VIII


title: RDY322 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS1022

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD32:TRP1 TAF1-MNase::HYG

value: 25 min DMSO treatment


title: patient45

description: Brain tumor patient

tag: risk group

value: II

value: Brain tumor


title: patient41

description: Brain tumor patient


title: RDY337 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS1037

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD28:TRP1 TAF1-MNase::HYG

value: 25 min IAA treatment


title: HepG2.batch2.PER.rep2.A02

description: Library name: HepG2_Batch2_PER_2_A02


title: E2_0-1_R1_P5

description: Library name: s465

value: Mammary

value: Epithelial

value: chemical exposure


title: DMSO_0-1_R3_P5

description: Library name: s469


title: RDY322 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS1024


title: patient39

description: Brain tumor patient


title: RDY337 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS1036


title: E2_1_R1_P5

description: Library name: s466


title: patient43

description: Brain tumor patient

tag: g34 subtype


title: RDY337 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS1039

tag: cell line


title: HepG2.batch2.PER.rep2.C02

description: Library name: HepG2_Batch2_PER_2_C02

value: liver

value: hepatocyte

value: cell line

tag: treatment


title: HepG2.batch2.PER.rep1.G02

description: Library name: HepG2_Batch2_PER_1_G02


title: HepG2.batch2.PER.rep3.B02

description: Library name: HepG2_Batch2_PER_3_B02


title: RDY322 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS1027


title: BTL_10_R2_P5

description: Library name: s447

value: WT

value: bithionol


title: patient38

description: Brain tumor patient

value: Female

tag: subgroup

value: VII


title: RDY337 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS1034

value: yeast cell


title: HepG2.batch2.PER.rep1.F02

description: Library name: HepG2_Batch2_PER_1_F02


title: DMSO_0-1_R7_P5

description: Library name: s477

value: vehicle control

value: dimethyl sulfoxide


title: RDY337 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS1038

value: 25 min DMSO treatment


title: DMSO_0-1_R5_P5

description: Library name: s475


title: E2_1_R2_P5

description: Library name: s474


title: HepG2.batch2.PER.rep1.H02

description: Library name: HepG2_Batch2_PER_1_H02


title: BTL_5_R2_P5

description: Library name: s446


title: RDY226 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS794

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD21:TRP1


title: BTL_1_R2_P5

description: Library name: s445


title: HepG2.batch2.PER.rep1.D02

description: Library name: HepG2_Batch2_PER_1_D02


title: RDY226 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS792


title: DMSO_0-1_R2_P5

description: Library name: s468


title: patient42

description: Brain tumor patient

value: Average

value: Brain tumor


title: HepG2.batch2.PER.rep2.B02

description: Library name: HepG2_Batch2_PER_2_B02


title: BTL_0-5_R2_P5

description: Library name: s444

value: Mammary


title: patient35

description: Brain tumor patient

value: Male

value: High

value: VIII


title: HepG2.batch2.PER.rep1.C02

description: Library name: HepG2_Batch2_PER_1_C02

value: liver

value: hepatocyte


title: HepG2.batch2.PER.rep2.E02

description: Library name: HepG2_Batch2_PER_2_E02

value: cell line


title: BTL_0-1_R2_P5

description: Library name: s443

value: Epithelial

value: WT

value: chemical exposure

value: bithionol


title: patient34

description: Brain tumor patient

tag: shh subtype


title: RDY337 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS1035

tag: cell type

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD28:TRP1 TAF1-MNase::HYG

value: 25 min IAA treatment


title: BTL_0-01_R2_P5

description: Library name: s442

tag: genotype


title: RDY322 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS1026

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD32:TRP1 TAF1-MNase::HYG

value: 25 min DMSO treatment


title: patient37

description: Brain tumor patient

value: Average

value: VII

value: Brain tumor


title: patient32

description: Brain tumor patient

value: Male


title: BTL_0-001_R2_P5

description: Library name: s441

value: Mammary


title: HepG2.batch2.PER.rep1.A02

description: Library name: HepG2_Batch2_PER_1_A02

value: liver


title: HepG2.batch2.MBZ.rep3.H08

description: Library name: HepG2_Batch2_MBZ_3_H08

value: hepatocyte


title: AO2246_5_R2_P5

description: Library name: s439

value: antioxidant 2246


title: AO2246_1_R2_P5

description: Library name: s438

value: Epithelial


title: BTL_50_R2_P5

description: Library name: s448

value: WT


title: RDY283 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS682

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD9:TRP1


title: RDY283 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS680


title: HepG2.batch2.PER.rep2.D02

description: Library name: HepG2_Batch2_PER_2_D02

value: cell line


title: patient36

description: Brain tumor patient

value: Female


title: AO2246_0-5_R2_P5

description: Library name: s437

value: chemical exposure


title: HepG2.batch2.MBZ.rep3.E08

description: Library name: HepG2_Batch2_MBZ_3_E08


title: patient207

description: Brain tumor patient


title: NALM6_CART22_Rep2

city: Philadelphia

first: Rawan

last: Shraim

state: PA

address: 3501 Civic Center Blvd

department: Oncology

institute: Children's Hospital of Philadelphia

description: Library name: HTS114_23_D5_NALM6_CART22_Rep2_S23

data_processing:
Bulk RNA-sequencing - Fastq files were aligned to the human reference genome (GRCh38) using the STAR aligner (v2.7.11b). Per gene read counts for Ensembl gene annotations were computed using the subread package in R. Gene counts were normalized for library sizes, voom transformed and represented as log2CPM( counts per million)  using the edgeR R package (v 4.2.2).
scRNA-sequencing - Samples were processed using cellranger-7.1.0. For non-multiplexed samples, cellranger count was used to obtain the single-cell matrix and .h5 file. For multiplexed samples, cellranger multi was used in additional to supplementary files corresponding to the sample names. After obtaining the .h5 file, Seurat was used for downstream analyses.
Assembly: HG38
Supplementary files format and content: scRNA-sequencing - Files are in .h5 format and can be read into R using Seurat library.
Supplementary files format and content: Bulk RNA-sequencing - csv files with voom transformed log2 CPM per sample

growth_protocol: Bulk RNA-sequencing - NALM6 or UOCB cell lines transduced to express GFP were co-cultured with CART cells at an effector:target ratio of 1:8 in RPMI supplemented with 20% fetal bovine serum (FBS) and 1% penicillin/streptomycin, 1% HEPES, 1% non-essential amino acids, and 1% L-glutamine.

extract_protocol:
Bulk RNA-sequencing  -  Pellets were transformed to total RNA using Qiagen’s QiaShredder (Cat no. 79656) and RNeasy Mini RNA extraction kit
scRNA-sequencing - Cryopreserved peripheral blood mononuclear cells (PBMCs) or bone marrow mononuclear cells (BMMC) were thawed and resuspended in media. Suspensions were centrifuged at 300 x g for 5 minutes at 4°C and resuspended in Dulbecco's phosphate-buffered saline (DPBS, Gibco, PN 14190-144) with 1% bovine serum albumin (BSA, Miltenyi Biotec, PN 130-091-376). Cell suspensions were then centrifuged at 500 x g for 5 minutes at 4°C and resuspended in 50 µL of cell staining buffer (Biolegend Inc, PN 420201) followed by addition of 5 µL of Human TruStain FcX™ blocking reagent (Biolegend Inc, PN 422301) if the cell count per sample in DPBS + 1% BSA was > 200,000 cells. Cells were incubated in Fc block for 10 minutes at 4°C. During incubation, hashtag antibodies were prepared by adding 2.2 µL (1.5 µg) of each of the TotalSeq™ anti-human Hashtag to 52.8 µL cell staining buffer and centrifuged at 14000 x g for 10 minutes at 4°C. At the end of incubation in Fc block, each cell suspension was labelled with 50 µL TotalSeq™ anti-human Hashtag antibody and incubated for 30 minutes at 4°C. Cells were then washed thrice in cell staining buffer at 500 x g for 5 minutes at 4°C and resuspended in DPBS + 0.04% BSA. If cell counts in DPBS + 1% BSA were < 200, 000 cells, cells were centrifuged at 300 x g for 5 minutes at 4°C and resuspended in DPBS + 0.04% BSA.
Bulk RNA-sequencing - Complementary DNA libraries were prepared with Illumina’s Stranded mRNA poly-A enrichment kit following the standard protocol. Individual library QC was performed on Agilent TapeStation prior to pooling. Pooled libraries were sequenced on NextSeq2000 on a P4 XLEAP SBS flow cell to collect 20 million reads per sample.
scRNA-sequencing - Hashed and pooled cell suspensions or individual cell suspensions were subsequently processed to generate single cell RNA-seq libraries using chromium Next GEM single cell 3’ reagent kits v3.1 Dual Index (10x Genomics, PN-1000268) with 3’ feature barcode technology (10x Genomics, PN-1000262) for cell surface protein using chromium controller as per manufacturer’s instructions. Library fragment size was determined using the Bioanalyzer Agilent 2100 with the High Sensitivity DNA chip (Agilent Technologies, 5067-4626) and libraries were quantified using Kapa qPCR quantification kit (Roche Diagnostics, PN 501965234). After pooling, libraries were sequenced on an Illumina NovaSeq 6000 using sequencing parameters read1: i7: i5: read2 :: 28:10:10:90 bp at an average sequencing depth of 50,000 read pairs per cell.

treatment_protocol: Bulk RNA-sequencing - Cells were incubated with or without IL-10 added at a concentration of 15 ng/mL.

value: without IL10


title: HepG2.batch2.MBZ.rep3.D08

description: Library name: HepG2_Batch2_MBZ_3_D08


title: PBMC, DENV1, P3, biol rep 2

city: Syracuse

first: Celine

last: Hardy

address: 750 East Adams Street

institute: SUNY Upstate Medical University

description: Library name: Sample 8

data_processing:
FASTQs generated using bcl2fastq
Kallisto (v0.46.2) was used to pseudoalign samples to the GRCh38 human transcriptome without bootstraps
Transcript-level counts and abundance data were imported into R using the TxImport package and TMM normalized using the package EdgeR
Assembly: GRCh38
Supplementary files format and content: abundance.tsv file containing transcripts per million (TPM)

source_name: PBMC

extract_protocol:
RNA was extracted with the Qiagen RNeasy Plus Mini kit
RNA quality and quantity were assessed with the Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit. Sequencing libraries were prepared with the Illumina Stranded Total RNA Ribo-Zero Plus library prep kit, using 20-50ng RNA as input. Libraries were assessed with the D1000 assay on the Agilent 4150 TapeStation and quantified with Qubit dsDNA High Sensitivity assay. A paired end 2x150bp sequencing run was performed on the Illumina NextSeq 2000 instrument.

treatment_protocol: Whole blood was collected from a healthy human donor, from which PBMC were freshly isolated and plated at 100,000 PBMC per well. PBMCs were inoculated with DENV-1 45AZ5 or DENV-3 CH53489 at 0 (uninfected control), 1 X 102, 103, or 104 PFU (triplicate for each condition). Cells were incubated at 37oC , 5% CO2 for 24 hours, following which cells were harvested, washed, and resuspended in RLT plus buffer with b-mercaptoethanol (BMF) and supernatants were discarded.

value: PBMC


title: AO2246_0-1_R2_P5

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

institute: Government of Canada

description: Library name: s436

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina BaseSpace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed March 2025), which manages workflows using Snakemake v8.0 (Mölder et al. 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al. 2018), STAR v2.7.8a (Dobin et al. 2013) to perform alignment of raw reads to the reference sequence and the qCount function of the QuasR R package (v1.30.0; (Gaidatzis et al. 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.1 kit (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions


title: AO2246_0-05_R2_P5

description: Library name: s435


title: RDY283 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS679

value: yeast cell

value: 25 min DMSO treatment


title: HepG2.batch2.MBZ.rep3.B08

description: Library name: HepG2_Batch2_MBZ_3_B08


title: DMSO_0-1_R1_P5

description: Library name: s467

value: vehicle control

value: dimethyl sulfoxide


title: HepG2.batch2.MBZ.rep3.G08

description: Library name: HepG2_Batch2_MBZ_3_G08


title: patient31

description: Brain tumor patient

value: Average

value: Brain tumor


title: RDY226 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS791

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD21:TRP1


title: HepG2.batch2.PER.rep1.B02

description: Library name: HepG2_Batch2_PER_1_B02

value: liver

value: hepatocyte


title: AO2246_10_R2_P5

description: Library name: s440

value: Mammary

value: Epithelial

value: antioxidant 2246


title: RDY283 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS684

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD9:TRP1

value: 25 min IAA treatment


title: RDY226 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS793


title: patient33

description: Brain tumor patient

value: Female


title: RDY226 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS790


title: patient40

description: Brain tumor patient

value: Male

value: VII


title: RDY226 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS789

value: yeast cell


title: AO2246_0-01_R2_P5

description: Library name: s434

value: WT

value: chemical exposure


title: RDY282 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS678

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD8:TRP1


title: HepG2.batch2.MBZ.rep3.A08

description: Library name: HepG2_Batch2_MBZ_3_A08

value: cell line


title: patient24

description: Brain tumor patient

value: High

value: III

value: Brain tumor


title: HepG2.batch2.MBZ.rep2.H08

description: Library name: HepG2_Batch2_MBZ_2_H08

value: liver

value: hepatocyte


title: HepG2.batch2.MBZ.rep2.F08

description: Library name: HepG2_Batch2_MBZ_2_F08


title: patient23

description: Brain tumor patient

value: Average

value: VIII


title: AO425_1_R2_P5

description: Library name: s430

value: Mammary

value: Epithelial

value: antioxidant 425


title: AO2246_0-001_R2_P5

description: Library name: s433

value: antioxidant 2246


title: AO425_5_R2_P5

description: Library name: s431


title: patient30

description: Brain tumor patient

value: Male

value: VII


title: patient28

description: Brain tumor patient


title: patient21

description: Brain tumor patient


title: HepG2.batch2.MBZ.rep3.F08

description: Library name: HepG2_Batch2_MBZ_3_F08


title: patient25

description: Brain tumor patient

value: Female


title: patient29

description: Brain tumor patient


title: RDY282 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS676

value: yeast cell

value: 25 min IAA treatment


title: HepG2.batch2.MBZ.rep2.G08

description: Library name: HepG2_Batch2_MBZ_2_G08

value: cell line


title: HepG2.batch2.MBZ.rep3.C08

description: Library name: HepG2_Batch2_MBZ_3_C08


title: RDY282 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS677

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD8:TRP1

value: 25 min DMSO treatment


title: patient22

description: Brain tumor patient

value: High

value: V

value: Brain tumor


title: RDY283 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS681

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD9:TRP1


title: patient27

description: Brain tumor patient

value: Average


title: RDY283 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS683


title: patient26

description: Brain tumor patient


title: AO425_10_R2_P5

description: Library name: s432

value: Mammary

value: WT

value: chemical exposure


title: RDY282 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS674


title: patient19

description: Brain tumor patient

value: VIII


title: RDY282 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS675


title: patient20

description: Brain tumor patient


title: AO425_0-1_R2_P5

description: Library name: s428

value: Epithelial

value: antioxidant 425


title: RDY225 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS788

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD7:TRP1


title: HepG2.batch2.MBZ.rep2.B08

description: Library name: HepG2_Batch2_MBZ_2_B08

value: liver

value: hepatocyte


title: AO425_0-01_R2_P5

description: Library name: s426


title: HepG2.batch2.MBZ.rep2.C08

description: Library name: HepG2_Batch2_MBZ_2_C08

value: cell line


title: RDY282 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS673

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD8:TRP1


title: AO425_0-5_R2_P5

description: Library name: s429


title: HepG2.batch2.MBZ.rep1.H08

description: Library name: HepG2_Batch2_MBZ_1_H08


title: HepG2.batch2.MBZ.rep2.E08

description: Library name: HepG2_Batch2_MBZ_2_E08


title: RDY225 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS787

value: 25 min DMSO treatment


title: RDY225 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS784

value: 25 min IAA treatment


title: RDY225 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS785


title: SEV,Alzheimer'sDisease,AD19

city: Pavia

first: Rosalinda

last: Di Gerlando

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

description: Library name: AD19

data_processing:
FastQ files were generated via Illumina bcl2fastq2 (Version 2.17.1.14 http://support.illumina.com/downloads/bcl2fastq-conversion-software-v217.html).
Quantification of miRNAs was done as described in the literature [13]. The workflow, including quality control filter, trimming of adapters, and reads mapping against miRNA precursors, is implemented in Docker4Seq package
Assembly: HG19
Supplementary files format and content: fastq.gz

source_name: Small Extracellular Vesicles from plasma

growth_protocol: Venus blood from AD patients, FTD patients and CTRL subjects was collected in sodium citrate tubes and then plasma was retrieved. Differential centrifugation method was applied to separate SEVs from LEVs.

extract_protocol:
RNA was extracted from SEVs fractions using miRNeasy Mini kit (Qiagen, Germany) according to manufacturer’s instructions.
Libraries for miRNA sequencing have been prepared using the Small RNA-Seq Library Prep kit (Lexogen) according to the user manual. Sequencing steps have been carried out on the Illumina NextSeq 500.


title: AO425_0-001_R2_P5

description: Library name: s425


title: HepG2.batch2.MBZ.rep2.D08

description: Library name: HepG2_Batch2_MBZ_2_D08


title: patient16

description: Brain tumor patient

value: Female

value: IV

value: Brain tumor


title: BTL_50_R1_P5

description: Library name: s408

value: Mammary

value: bithionol


title: SEV,Alzheimer'sDisease,AD12

description: Library name: AD12

value: Small Extracellular Vesicles from plasma


title: HepG2.batch2.MBZ.rep1.G08

description: Library name: HepG2_Batch2_MBZ_1_G08


title: BTL_10_R1_P5

description: Library name: s407

value: WT

value: chemical exposure


title: HepG2.batch2.MBZ.rep2.A08

description: Library name: HepG2_Batch2_MBZ_2_A08


title: patient17

description: Brain tumor patient

value: Male

value: Average

value: VIII


title: BCAL73

value: Cerebral artery

tag: strain

value: Chronic cerebral hypoperfusion


title: patient18

description: Brain tumor patient


title: RDY225 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS786

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD7:TRP1


title: patient15

description: Brain tumor patient


title: BTL_5_R1_P5

description: Library name: s406

value: Epithelial


title: RDY281 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS782

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD5:TRP1

value: 25 min IAA treatment


title: patient13

description: Brain tumor patient

value: Female


title: HepG2.batch2.MBZ.rep1.E08

description: Library name: HepG2_Batch2_MBZ_1_E08

value: liver

value: hepatocyte

value: cell line


title: HepG2.batch2.MBZ.rep1.D08

description: Library name: HepG2_Batch2_MBZ_1_D08


title: patient11

description: Brain tumor patient

value: High

value: IV

value: Brain tumor


title: BTL_1_R1_P5

description: Library name: s405

value: Mammary

value: WT

value: chemical exposure

value: bithionol


title: patient14

description: Brain tumor patient

value: Male

value: VIII


title: HepG2.batch2.MBZ.rep1.F08

description: Library name: HepG2_Batch2_MBZ_1_F08


title: RDY281 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS780

value: yeast cell


title: HepG2.batch2.MBZ.rep1.C08

description: Library name: HepG2_Batch2_MBZ_1_C08


title: RDY225 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS783

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD7:TRP1

value: 25 min DMSO treatment


title: patient12

description: Brain tumor patient

value: Average

value: VII


title: HepG2.batch2.MBZ.rep1.B08

description: Library name: HepG2_Batch2_MBZ_1_B08

value: liver


title: patient8

description: Brain tumor patient

value: Female

value: III


title: RDY281 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS777

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD5:TRP1


title: BTL_0-01_R1_P5

description: Library name: s402

value: Epithelial


title: BTL_0-1_R1_P5

description: Library name: s403


title: BTL_0-5_R1_P5

description: Library name: s404


title: patient10

description: Brain tumor patient

value: Brain tumor


title: SEV,HealthyControl,HC6

description: Library name: HC6

value: Small Extracellular Vesicles from plasma


title: HepG2.batch2.MBZ.rep1.A08

description: Library name: HepG2_Batch2_MBZ_1_A08

value: hepatocyte

value: cell line


title: RDY281 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS778

value: 25 min IAA treatment


title: patient9

description: Brain tumor patient

value: Male


title: RDY281 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS779


title: BTL_0-001_R1_P5

description: Library name: s401

value: Mammary

value: WT

value: chemical exposure

value: bithionol


title: RDY281 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS781

value: yeast cell

value: 25 min DMSO treatment


title: HepG2.batch2.DIQ.rep3.H01

description: Library name: HepG2_Batch2_DIQ_3_H01

value: liver


title: AO2246_10_R1_P5

description: Library name: s400

value: antioxidant 2246


title: patient7

description: Brain tumor patient

value: High

value: VII


title: HepG2.batch2.DIQ.rep3.G01

description: Library name: HepG2_Batch2_DIQ_3_G01


title: RDY280 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS776

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD5:TRP1


title: patient6

description: Brain tumor patient

value: Average

value: Brain tumor


title: AO2246_1_R1_P5

description: Library name: s398

value: Epithelial


title: HepG2.batch2.DIQ.rep3.F01

description: Library name: HepG2_Batch2_DIQ_3_F01

value: hepatocyte

value: cell line


title: RDY280 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS774

value: 25 min IAA treatment