type: other

city: College Park

first: Gerald

last: Wilkinson

address: Biology-Psychology Building

department: Department of Biology

institute: University of Maryland

description: Eptesicus fuscus skin sample from bat ID EpFu.MJ220 (male)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

molecule: other

organism: Eptesicus fuscus

source_name: Wing skin biopsy

label_protocol: Standard Illumina protocol

extract_protocol: DNA extracted using Zymo DNA miniprep

treatment_protocol: Standard Illumina protocol

value: Wing skin biopsy

value: male


title: F6_AsIII_30uM

status: Public on Sep 30 2024

type: SRA

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

description:
F6_59
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

library_source: transcriptomic

data_processing:
raw sequencing reads were mapped to the current Atlantic salmon genome (GCF_905237065) downloaded from the NCBI genome database using the Hisat2 mapper and counted using FeatureCounts as part of the Subread package. Raw counts were further normalized using DESeq2 (1.40.2) Bioconductor package (V3.17), features that had lower count than 10 reads were filtered prior to normalization. Differentially expressed genes (DEGs) were determined using Wald test and corrected for multiple testing using the Benjamini and Hochberg test, as implemented in the DESeq2 package. Differentially expressed genes were used for further downstream pathway analysis. Due to the high number of differentially expressed genes in AsIII exposed cells, a 2-fold differential expression cut of was applied to these samples. Due to limited tools and databases for biological function of non-model species, DEG feature gene names were converted to human ortholog gene names using the BioDBnet database (https://biodbnet-abcc.ncifcrf.gov/db/dbOrtho.php) prior to pathway analysis. Pathway analysis were conducted using the open source Metascape software (https://metascape.org)
Assembly: GCF_905237065
Supplementary files format and content: The processed datafile contain a matrix of normalized gene counts in txt format.

molecule: total RNA

organism: Salmo salar

source_name: Liver

growth_protocol: Hepatocytes were isolated from six male Atlantic salmon (447–572g) with a two-step perfusion method. Briefly, a peristaltic pump (Miniplus 3, Gilson, USA) was used to clear the liver for blood (4 mL/min) via the hepatic vein followed by digestion with collagenase (1 mg/mL). When the digestion of the liver was complete, the organ was removed from the fish. The hepatocytes were gently shaken in PBS by using tweezers. Subsequently, the cell suspensions were filtered (100 μm nylon gauze) and the cells collected by centrifugation (50 × g for 5 min). The hepatocytes were washed twice with PBS. The cells were collected by centrifugation (50 × g for 5 min). The supernatant was decanted, and the final cell pellet was resuspended in L-15 medium (without phenol red) containing 10% fetal bovine serum (Sigma Aldrich), 1% glutamax (Invitrogen, Norway) and 1% penicillin-streptomycin-amphotericin (10000 units/mL potassium penicillin, 10000 μg/mL streptomycin sulphate and 25 μg/mL amphotericin B) (Lonzo, Medprobe, Oslo, Norway). Cell viability was determined following the manufacturer’s protocol of Trypan Blue exclusion methodology (Lonzo, Medprobe, Oslo, Norway). The different cell suspensions used in this study had hepatocyte cell viability >90%. Fish handling was approved by the Norwegian Animal Research Authority (FOTS ID, 19351). The hepatocytes were plated on 2 μg/cm2 laminin (L2020, Sigma-Aldrich, Oslo, Norway) coated 3D 6-well Alvetex® scaffolds (200 μm cross-linked polystyrene membranes, 42 μm mean void size, Reprocell, Glasgow, United Kingdom) in 6 well culture plates (Falcon, Corning, VWR, Bergen, Norway). The following cell concentrations were used; 7.2 × 106 cells per scaffold in 6-well plates (in 10 mL complete L15 medium) and 0.2 × 106 cells per well in 96-well plates (in 0.200 mL or 0.150 mL complete L-15 medium in 2D and 3D, respectively). the hepatocytes were kept at 10 °C in a sterile incubator without additional O2/CO2 (Sanyo, CFC FREE, Etten Leur, Netherland).

extract_protocol:
Hepatocytes for RNA extraction and sequencing were seeded on 6-well Alvetex® scaffolds. After 48 h exposure to arsenite, arsenate and arsenobetaine, 2 mL of cell medium from each well was taken and kept at -20ºC until further analysis (see section 2.6). The rest of the cell medium was discarded. Retrieval of cells from Alvetex® scaffolds for this analysis was performed according to manufacturer’s description (see protocol for retrieval of cells from Alvetex® scaffold's for metabolomic analysis). In summary, the well inserts with the hepatocyte cells were transferred to new 6-well plates. The cells were washed with PBS (1 mL) which was removed from the well before the next step. The Alvetex Scaffold membrane was removed with the aid of flat-ended forceps. To break down the cells, introduce 600 µL of the Qiagen RNeasy® kit lysis buffer RLT directly to the well where is Alvetex Scaffold membrane was left. Allow the plate on a rotating platform (100 rpm) for 10 min at room temperature. Conclude the process by adding 600 µL of 70% ethanol to the now-homogenized lysate. Ensure a proper mix by pipetting the combination up and down around 10 times. The cell suspension was transferred to centrifugation tubes and centrifuged at 1000×g for 5 min at 4 °C. Cell pellets were flash frozen and stored at −80 °C until RNA extraction was performed.Total RNA was extracted from Atlantic salmon Primary hepatocytes using a RNeasy Plus Mini Kit (Qiagen, Crawley, UK) as previously described (Søderstrøm et al 2023). Total RNA purity was evaluated using a nanodrop NanoDrop™ (Thermo Fisher Scientific™, MA, USA) Samples had a 260/230 and 260/280 ratio of 2.2 ± 0.1 and 2.09 ± 0.03 respectively. Integrity of RNA for each sample was investigated using RNA 6000 Nano LabChips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Although the integrity of the majority of the samples were assessed as good (RIN = 9.7 ± 0.12, N = 48), RNA from cells exposed to 250 µM AsSug showed a reduction in integrity (RIN 5.3 ± 0.5, N = 6).
Total RNA samples of arsenate and arsenobetaine were sent to Novogene Europe, Cambridge, UK, for cDNA library preparation and sequencing using the Illumina NovaSeq 6000 platform for 150 bp paired end reads. Enriched mRNA was prepared using Oligo(dT beads). cDNA libraries were prepared following manufacturer's instructions per the Novogen pipeline (Novogene Europe, Cambridge, UK)

treatment_protocol: Aqueous solutions of arsenite (Spectrascan, 1000ug/mL) were purchased from Teknolab (Ski, Norway). Arsenosugar glycerol was gently given by Jack Creed of the Environmental Protection Agency (EPA) National Exposure Research Laboratory in Cincinnati, OH, USA. Arsenite and arsenosugar glycerol used in the exposure experiments were dissolved individually to constitute a 1 mM stock solution from which dilutions were made. The stock solutions were diluted in Leibovitz L-15 medium w/o phenol red supplemented with 10% FBS and 1% antibiotic antimycotic solution. The primary cells were cultured for 36–40 h prior to chemical exposure. Liver cells from six fish (N = 6) were exposed for 24 h and 48 h to establish dose-response curves for arsenite (0.1, 1, 3, 10 and 30 μM), arsenate (10, 50, 100 and 500 μM), arsenobetaine (10, 50, 100 and 500 μM) and for arsenosugar glycerol (0.5, 5, 10, 50, 50, 100, 250 μM). The concentrations used were selected based on earlier in vitro toxicity assessments

tag: tissue

value: Liver

tag: cell line

value: Primary cells

tag: cell type

value: Primary hepatocytes

tag: FISH number

tag: treatment


title: patient E M(IL4,CGRP)

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

data_processing:
Basecalling and demultiplexing using Illumina's bcl2fastq v2.20.0.422
Pseudomapping to human NCBI RefSeq RNA dataset using Kallisto v0.48.0
Supplementary files format and content: tab delimited raw counts from kallisto

molecule: polyA RNA

organism: Homo sapiens

source_name: macrophage

extract_protocol:
NEBNext Ultra II Directional RNA Library Prep Kit
polyA tailed RNA capture and sequencing

tag: individual

value: patient E

value: macrophage


title: Rat synovium_Ad inj

city: Bunkyo-ku

first: Kentaro

last: Endo

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Institute of Science Tokyo

data_processing:
SOAPnuke v1.5.2
Remove the reads containing the adaptor, the reads whose N content is greater than 5%, and low-quality reads using SOAPnuke (parameter: -l 15 -q 0.2 -n 0.05).
Trimmed sequence reads were mapped to Rnor_6.0 using HISAT2 v2.0.4 (parameter: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF).
Read count extraction and normalization were performed using HISAT2.
Assembly: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: Tab-delimited text files include TPM values for each sample

organism: Rattus norvegicus

source_name: Synovium

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN, Hilden, German).
mRNA was isolated using oligo dT beads and fragmented. Single-strand cDNA was generated using random N6-primed reverse transcription, followed by a secondstrand cDNA with dUTP. After PCR amplification and DNA nanoball synthesis, the products were sequenced by BGISEQ-500.

value: Synovium

tag: disease state

value: osteoarthritis

value: Injected with human AdMSCs


title: F6_AsIII_10uM

description:
F6_58
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


state: MD

country: USA

description: Eptesicus fuscus skin sample from bat ID EpFu.FAA81 (female)

tag: Sex

value: female


description: Eptesicus fuscus skin sample from bat ID EpFu.MD245 (male)


description: Eptesicus fuscus skin sample from bat ID EpFu.F663A (female)


description: Eptesicus fuscus skin sample from bat ID EpFu.FCCA8 (female)


title: F6_AsIII_100uM

description:
F6_60
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: PBS_Plate1.B1

city: Sendai

first: Kota

last: Sato

state: Miyagi

address: 1-1, Seiryo-machi, Aoba-ku

department: Ophthalmology

institute: Tohoku University

library_source: transcriptomic single cell

data_processing:
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software. Trimmed reads were then mapped to the mouse GRCm38.p6 (mm10) genome with STAR software (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

organism: Mus musculus

source_name: retina

extract_protocol:
Total RNA were directly extracted with lysis buffer inculding Rnase inhibitor from single cell sorted with FACS.
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). cDNA synthesis and amplification of RNA derived from lysed cell was sequentially conducted in a same PCR tube. After purification, amplified cDNA was validated and quantified. Following tagmentation of cDNA, adapter addition and PCR amplification were conducted using Nextera XT DNA Library Prep Kit (Illumina).

value: microglia

value: retina

tag: strain

tag: age

value: 10-14 weeks old

value: PBS treatment


title: patient E M(IL4)


title: PBS_Plate1.B2


title: F6_AsIII_3uM

description:
F6_57
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: PBS_Plate1.A6


description: Eptesicus fuscus skin sample from bat ID EpFu.F0D0A (female)


description: Eptesicus fuscus skin sample from bat ID EpFu.FFE5E (female)


description: Eptesicus fuscus skin sample from bat ID EpFu.F1684 (female)


title: patient E M(0)

value: control


description: Eptesicus fuscus skin sample from bat ID EpFu.FE5F7 (female)


title: F6_Control_AsIII

description:
F6_56
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: PBS_Plate1.A3


description: Eptesicus fuscus skin sample from bat ID EpFu.MD22C (male)


title: patient A M(IL4,CGRP)

value: patient A


title: PBS_Plate1.A5


title: PBS_Plate1.A4


title: F6_AsB_500uM

description:
F6_180
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: patient C M(IL4)

value: patient C


title: patient C M(0)


description: Eptesicus fuscus skin sample from bat ID EpFu.F113A (female)

value: Wing skin biopsy


title: PBS_Plate1.A2


title: patient A M(IL4)


title: F6_AsB_10uM

description:
F6_177
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Liver


title: patient A M(0)


description: Eptesicus fuscus skin sample from bat ID EpFu.M0E5C (male)

value: male


title: patient C M(IL4,CGRP)


title: scRNA-seq_keloid1

city: Shanghai

first: Jiayi

last: Mao

address: Zhi Zao Ju road

country: China

institute: shanghai ninth people's hospital

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells. We processed the unique molecular identifier (UMI) count matrix using the R package Seurat (version 3.1.1). To remove low quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, we applied a criteria to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations assuming a Guassian distribution of each cells' UMI/gene numbers. Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where >10% of the counts belonged to mitochondrial genes. Additionally, we applied DoubletFinder package (version 2.0.2) to identify potential doublet. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)
Library size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were logtransformed.
Differentially expressed genes(DEGs) were identified using the FindMarkers function(test.use = MAST) in Seurat[1]. P value < 0.05 and |log2foldchange| > 0.58 was set as the threshold for significantly differential expression. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Top variable genes across single cells were identified using the method described in Macosko et al
The most variable genes were selected using FindVariableGenes function(mean.function = FastExpMean, dispersion.function = FastLogVMR) in Seurat
Principal component analysis (PCA) was performed to reduce the dimensionality with RunPCA function in Seurat
Graph-based clustering was performed to cluster cells according to their gene expression profile using the FindClusters function in Seurat
Cells were visualized using a 2-dimensional t-distributed stochastic neighbor embedding (t-SNE) algorithm with the RunTSNE function in Seurat
Assembly: We used the FindAllMarkers function(test.use = bimod) in Seurat to identify marker genes of each cluster.
Supplementary files format and content: For a given cluster, FindAllMarkers identified positive markers compared with all other cells.
Supplementary files format and content: Then, we used the R package SingleR, a novel computational method for unbiased cell type recognition of scRNA-seq, with the reference transcriptomic datasets ‘Human Primary Cell Atlas’ (Mabbott et al. 2013) to infer the cell of origin of each of the single cells independently and identify cell types.

source_name: skin

extract_protocol: we used single-cell RNA sequencing (scRNA-seq) analysis to analyze intercellular communication networks and enrich fibroblast populations in two additional keloid and normal skin samples to study fibroblast diversity

value: skin

tag: genotype

value: WT


title: RPMS_CMV_344_S8_R1_001

city: Clayton

first: Daniel

middle: James

last: Gough

state: Victoria

address: 27-31 Wright Street

department: Centre for Cancer Research

country: Australia

institute: Hudson Institute of Medical Research

description: count matrix with gene names primary vs mets

data_processing:
FastQ files were aligned to GRCm38 using Hisat2
Transcripts per million were quantified using Stringtie/PrepDE
Assembly: GRCmm38
Supplementary files format and content: excel files including TPM values for each Sample

source_name: Small cell lung cancer cell line derived from the liver

growth_protocol: Cells were extracted from tissue and cultured in advanced RPMI supplemented with glutamax and 1%FCS

extract_protocol:
RNA was harvested using AccuPrep RNA exptraction Kit (Bioneer). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded RNA library kit (Illumina) following manufacturer's protocols.

value: lung epithelium


description: Eptesicus fuscus skin sample from bat ID EpFu.MWH80 (male)


title: RPMS_CMV_343_S7_R1_001

value: Small cell lung cancer cell line derived from the liver


description: Eptesicus fuscus skin sample from bat ID EpFu.F1B22 (female)


title: F6_AsB_100uM

description:
F6_179
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Primary cells

value: Primary hepatocytes


description: Eptesicus fuscus skin sample from bat ID EpFu.F13AB (female)

value: female


title: scRNA-seq_Ctrl1


title: F6_Control_AsB

description:
F6_176
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: F5_AsIII_100uM

description:
F5_55
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: F6_AsB_50uM

description:
F6_178
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: F5_AsIII_30uM

description:
F5_54
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: PBS_Plate1.A1

value: microglia


title: mRNA_keloid3

data_processing:
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the human genome (GRCh38) using HISAT2
FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq_x0002_count
Differential expression analysis was performed using the DESeq (2012) R package. P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression.
Assembly: Differentially expressed miRNAs were identified with the threshold of p value < 0.05. While the p value was calculated with DEG algorithm [5] in the R package for experiment with biological replicates, and with Audic Claverie statistic [6] for experiment without biological replicates.
Supplementary files format and content: Hierarchical cluster analysis of differentially expressed genes (DEGs) was performed to demonstrate the expression pattern of genes in different groups and samples. GO enrichment and KEGG pathway enrichment analysis of DEGs were performed respectively using R based on the hypergeometric distribution
Supplementary files format and content: After reads ressembled by StringTie, gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated  genes using Cuffcompare software. ASprofile was used to analyse the alternatively splicing of differentially regulated transcripts isoforms or exons. SNPs and InDels were called using SAMtools and BCFtools, and the details were shown on SAMtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then SnpEff  annotates and predicts the effects of variants on genes (such as amino acid changes).

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd.  (Shanghai, China)


title: RPMS_CMV_273_S5_R1_001


title: RPMS_CMV_341_S6_R1_001


title: F5_AsIII_10uM

description:
F5_53
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


description: Eptesicus fuscus skin sample from bat ID EpFu.F9AA4 (female)


title: mRNA_keloid2


title: F5_AsIII_3uM

description:
F5_52
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: RPMS_CMV_232_S3_R1_001

source_name: Small cell lung cancer cell line derived from the lung


title: RPMS_CMV_252_S4_R1_001

value: Small cell lung cancer cell line derived from the lung


title: F5_Control_AsIII

description:
F5_51
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: mRNA_keloid1


description: Eptesicus fuscus skin sample from bat ID EpFu.M4123 (male)


title: mRNA_Ctrl3


title: F5_AsB_500uM

description:
F5_175
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


description: Eptesicus fuscus skin sample from bat ID EpFu.M3DF6 (male)


title: RPMS_CMV_231_S2_R1_001


description: Eptesicus fuscus skin sample from bat ID EpFu.M6P23 (male)


description: Eptesicus fuscus skin sample from bat ID EpFu.F1176 (female)


title: RPMS_CMV_228_S1_R1_001

description: count matrix with gene names primary vs mets


title: F5_AsB_50uM

description:
F5_173
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: RPMS-CMV_252_S9_R1_001

description: count matrix with gene names primary RPM vs RPMS


title: RPMS-CMV_231_S6_R1_001


title: Untreated_0h_1

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

library_source: other

data_processing:
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using  bcl2fastq vv2.20.0.422 (Illumina)
10x cellranger/cellranger-arc 2.0 was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome. The output files for rna and atac were h5 files and fragments.tsv.gz respectively, which were utilized for downstream processing and quality control analysis.
HDF5 files (filtered) were then uploaded into R statistical programming language using the Seurat package (version 4.0) where normalization, scaling, integration and reference based label transfer was performed.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: Fragment TSVs (Tab separated)
Supplementary files format and content: Fragment Metadata CSVs (Comma separated)
Supplementary files format and content: HDF5 file (Hierarchical Data Format)
Supplementary files format and content: ADT counts (Comma seperated)

source_name: Blood

extract_protocol:
Cryopreserved PBMC samples were thawed into 40 mL of pre-warmed AIM V media (37°C) (GIBCO) and centrifuged for 10 minutes at 400g (4°C). Thawed cells were resuspended in 5 mL of cold AIM V (4°C), and 30 µL was removed to be counted on the Nexcelom Cellaca MX cell counter. Thawed cells were then washed with 25 mL of cold AIM V media (4°C) and centrifuged for 10 minutes at 400g (4°C). Individual samples were resuspended in Dulbeccos phosphate-buffered saline (DPBS) (Costar) at a concentration of 10 million cells per mL.
Samples were centrifuged at 400g for 5 minutes at 4C and resuspended in PBS. Each sample was then individually stained with a panel of 55 oligo-conjugated antibodies. Each sample was also stained with a unique Cell Hashing Antibody to enable sample pooling and reduce well-to-well effects. Following a 30 minute antibody incubation, each sample was washed 3 times with PBS + 2% BSA to remove unbound antibodies, counted, and pooled together. The hashed cell pool was then processed according to the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit User Guide with modification: HTO (hash tag-derived oligo) primers were added to the pre-amplification PCR mix, and HTO libraries were prepared from the captured cell hashing antibodies in the same way as the ADT libraries. Final libraries were sequenced to target 80,000 reads per cell for GEX, 70,000 for ATAC, 50,000 for ADT, and 10,000 for HTO libraries

treatment_protocol: T cells were centrifuged for 5 minutes at 400g and resuspended in growth medium (RPMI 1640 (Gibco), 20% FBS, 1X Pen/Strep, 50 ng/mL IL-2, 5 ng/mL IL-7, 5 ng/mL IL-15). Drugs were added to cells at the indicated concentrations in Nunc™ 96-well polystyrene round-bottom microwell plates (Thermo Fisher Scientific, Cat#262162) in a total volume of 200 µL/well. Plates were stored in tissue culture incubators at 37C with 5% CO2 for 4, 24, or 72 hours following drug or control treatment.

value: Blood

value: T cells

tag: time (hours)

value: Untreated


title: F5_AsB_100uM

description:
F5_174
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: DMSO_4h_1

value: DMSO


title: F5_AsB_10uM

description:
F5_172
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: PA14_NF_5m_2

city: Urbana

first: Joseph

last: Sanfilippo

state: IL

address: 600 S Matthews Ave

institute: University of Illinois

data_processing:
Preprocessed and quality checked fastq files were obtained from the Roy J. Carver Biotechnology Center. Reads were aligned using STAR (https://github.com/alexdobin/STAR) to the publicly available P. aeruginosa PA14 NCBI reference genome.
Aligned reads were output as BAM unsorted files, which were sorted and indexed using Samtools (https://www.htslib.org/).
Gene hit counts were then calculated using featureCounts (https://subread.sourceforge.net/featureCounts.html) with gene_id as the identifier
Raw read counts of genes were normalized using trimmed mean of M-values (TMM) implemented in edgeR package.
Differential expression was calculated using limma and the output was generated as an excel file displaying differential expression values.
Assembly: P. aeruginosa PA14 NCBI
Supplementary files format and content: text file contains raw counts for each sample

organism: Pseudomonas aeruginosa PA14

source_name: Bacteria

growth_protocol: Cells from overnight culture were back-diluted in a shaking incubator to reach mid-log (0.4-0.5 OD) phase.

extract_protocol:
RNA was harvested uding TRIzol® MaxTM Bacterial RNA Isolation Kit (ThermoFisher).
The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNAseq Sample Prep kit (Roche).

treatment_protocol: Mid-log P. aeruginosa cells were treated wiith  H2O2  for 5 minutes

value: Bacteria

value: WT PA14

value: 8 µM H2O2 for 5 mins


description: Eptesicus fuscus skin sample from bat ID EpFu.F0G50 (female)

value: Wing skin biopsy


title: PA14_NF_5m


title: PA14_NF_2

value: No treatment


title: Bortezomib_4h_1

value: Bortezomib


title: Lenalidomide_4h_1

value: Lenalidomide


title: F4_AsIII_100uM

description:
F4_50
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Liver


title: RPM-CMV_429_S8_R1_001

value: lung epithelium


title: RPM-CMV_428_S7_R1_001


title: F4_AsIII_30uM

description:
F4_49
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Primary cells

value: Primary hepatocytes


description: Eptesicus fuscus skin sample from bat ID EpFu.F004F (female)

value: female


title: Dexamethasone_4h_1

value: Dexamethasone


title: PA14_NF


title: RPM-CMV_427_S5_R1_001

value: Small cell lung cancer cell line derived from the lung


title: F4_AsIII_10uM

description:
F4_48
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: mRNA_Ctrl2

value: skin

value: WT


title: mRNA_Ctrl1


description: Eptesicus fuscus skin sample from bat ID EpFu.M1BAF (male)

value: male


title: 14d

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

data_processing:
Sequencing was performed on MGISeq2000 platform in a 28+100 or 28+120 base paired-end mode.
Raw sequencing data were converted to matrices of expression using Space Ranger (version spaceranger-1.3.0, 10X Genomics).
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcode
Supplementary files format and content: features.tsv.gz: list of gene ID
Supplementary files format and content: matrix.mtx.gz: non-zero gene expresion raw UMI count data in Matrix Market Exchange Formats
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcode and the cordinate specifying spot
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: tissue_hires_image.png: image of tissue
Library strategy: Spatial Transcriptomics

extract_protocol:
Mouse skin tissue slide gene expressions were detected by 10x Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared for sequencing using 10x Visium spatial protocols and standard MGI protocols.

value: wound

tag: time

value: 14 day


title: DMSO_24h_1

value: Blood

value: T cells

value: DMSO


title: RPM-CMV_426_S3_R1_001


title: F4_AsIII_3uM

description:
F4_47
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 7d

value: 7 day


title: RPMS-CMV_228_S4_R1_001


title: F5_Control_AsB

description:
F5_171
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 3d

value: 3 day


title: 29C_w1118_3

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: 29C w1118 replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to BDGP6/dm6 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include TPM values for all 54 samples

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strains

extract_protocol:
Samples for RNA sequencing were prepared with TRIzol (Ambion #15596018) from whole flies and the RNA was extracted by isopropanol precipitation from the aqueous phase
Sequencing libraries for each sample were prepared from 1 μg total RNA by using the Illumina TruSeq RNA Sample Prep v2 Kit per the manufacturer’s instructions

value: whole flies

value: males, 10-days-old


title: F4_Control_AsIII

description:
F4_46
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Liver

value: Primary cells


title: Dexamethasone_24h_1


title: Lenalidomide_24h_1

value: Lenalidomide


title: 29C_w1118_2

description: 29C w1118 replicate 2


title: 7d_wound

data_processing:
Sequencing was performed on MGISeq2000 platform in a 100+108 base or 28+100 base paired-end mode.
Generated reads were input into the cellranger count pipeline (Cell Ranger v.6.0.0, 10x Genomics) for alignment to the mm10 genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: comma-delimited text files include raw counts for all cells detected

extract_protocol:
Freshly collected skin wound tissues were dissociated using whole skin dissociation kit (Miltenyi Biotec Inc.), according to manufacturer’s instruction. In brief, skin tissues were incubated with enzyme mixture for 1 h at 37’C. After incubation, cell aggregates were dissociated using gentleMACS Dissociator (Mi Miltenyi Biotec Inc.) with gentleMACS program mode (h_skin_01). Red blood cells of collected single-cell suspensions were lysed by BD Pharm Lyse Lysing Buffer (BD Biosciences). Cell debris were removed by Debris Removal Solution (Miltenyi Biotech Inc.) as follows manufacturer’s guide. Obtained cells’ number and viability were measured using Countess II FL Automated Cell counter (Thermo Fischer) and Live/Dead Viability/Cytotoxicity kit for mammalian cells (Thermo Fischer).
Single-cell RNA library construction was processed according to the protocol outlined in the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) User Guide (10x Genomics). Briefly, to generate gel beads-in Emulsion (GEM), cell suspension, barcoded Gel Beads, and Partitioning Oil were loaded into the Chromium Chip. Then Single cell droplets were generated by Chromium Controller (10x Genomics). Every GEM was reverse-transcripted to full-length cDNAs with Unique Molecular Identifiers (UMIs) and the 10x Barcode at single-cell level. To construct the library, pooled barcoded cDNA was cleaned up with Dynabeads MyOne SilaneDynaBeads (Thermo Fisher), amplified by PCR and selected proper size of cDNA fragments using SPRIselect (Beckman Coulter). Quality and quantity of constructed libraries were evaluated using Bioanalyzer 2100 (Agilent).


title: 14d_wound


title: 29C_w1118_1

description: 29C w1118 replicate 1


title: F4_AsB_100uM

description:
F4_169
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Primary hepatocytes


title: F4_AsB_50uM

description:
F4_168
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: DMSO_72h_1


title: 3d_wound


title: 25C_w1118_2

description: 25C w1118 replicate 2


title: 25C_w1118_3

description: 25C w1118 replicate 3


title: 25C_w1118_1

description: 25C w1118 replicate 1


title: Bortezomib_72h_1

value: Bortezomib


title: Lenalidomide_72h_1


title: F4_Control_AsB

description:
F4_166
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: Bortezomib_24h_1


title: F3_AsIII_100uM

description:
F3_45
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 18C_w1118_3

description: 18C w1118 replicate 3


title: 18C_w1118_2

description: 18C w1118 replicate 2


title: Human corneal epithelial cells, Treatment of BAC and hAdMSC-CM 3

city: Kizugawa

first: Tsutomu

last: Imaizumi

state: Kyoto

address: 6-5-4 Kunimidai

department: Basic Research Development Division

institute: Rohto Pharmaceutical Co., Ltd

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 system in 150-base two paired-end mode.
Sequence reads were trimmed using Trimmomatic v.0.38.
Trimmed sequence reads were mapped to the human reference genome sequences (hg38) using HISAT2 v.2.1.0.
The number of raw reads mapped to the exon regions was calculated using FeatureCounts v.1.6.3.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Text file includes matrix table with raw gene counts for every gene and every sample.

source_name: Human corneal epithelium

growth_protocol: Human corneal epithelial cells were maintained in DMEM/F12 containing 2% B-27 supplement, 20 ng/mL KGF, 10 μM Y-27632 in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using QIAzol Lysis Reagent (QIAGEN).
cDNA library was prepared using NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs).

treatment_protocol: One day after cultivation of human corneal epithelial cells, they were cultured in the hAdMSC-CM one day before and immediately after stimulating hCECs with BAC (Sigma).

value: Human corneal epithelium

value: Human corneal epithelial cells

value: BAC and hAdMSC-CM


title: Human corneal epithelial cells, Treatment of BAC and hAdMSC-CM 2


title: HAESC 3D spheroids maintained in Placental Epithelial Cell Basal Medium_rep2

type: RNA

city: TSUKUBA

first: ELDA NURAFNIE

last: IBNU RASID

state: IBARAKI

address: 1-1-1 TENNODAI

institute: UNIVERSITY OF TSUKUBA

description:
Gene expression data from HAESC 3D spheroids maintained in Placental Epithelial Cell Basal Medium for 7 days
Control 2

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Human; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files) filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space).
Signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4).

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: hAESCs were isolated from the term placenta. Firstly, the amnion was aseptically separated from the chorion and then washed with 200 mL of Hank's Basic Salt Solution - Calcium and Magnesium Free (CMF-HBSS). The amnion was cut into smaller pieces using surgical scissors and placed in 50 mL conical tubes. A total of 20 mL pre-digestion buffer containing CMF-HBSS and 0.5 mM EGTA was added to the tubes. The amnion was gently rocked in the solution for 30 seconds and then transferred to new 50 mL conical tubes. Again 20 mL pre-digestion buffer was added to the tubes and was incubated at 37oC for 10 minutes. Next, the pre-digestion buffer was discarded, and 20 mL of 0.05% trypsin-EDTA was added to the tubes, incubated for 40 minutes at 37oC, and then placed on ice. Next, Dulbecco's Modified Eagle Medium (DMEM, 10% FBS, 1% Penn-Strep) was added to the trypsin digest and centrifuged at 200 g for 10 minutes at 4oC. After discarding the supernatant, the pellet was resuspended in 10 mL of DMEM and filtered through a 100 μm filter.   Cells were maintained in Placental Epithelial Cell Basal Medium (PromoCell, Cat. # C-26140) and were constantly monitored with media change every 2-4 days. The cells were cultured in 3D culture plates (ElplasiaTM, Kuraray Co., Ltd., Cat # RB 500 400 NA 24) coated with LipidureTM solution (NOF Corporation, Cat. # CMS206; 400 μL) (50 mg in 10 mL absolute ethanol) as described previously. hAESC spheroids were formed by seeding 1 × 106 cells into each well of the 24-well plates. Cells were seeded in the Placental Basal Epithelial Cell Medium and cultured for 24 h.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: After 24 hours of initial culture, cells were treated with 1/1000 of dilution of 200mg/ml of Tsuru. Control samples were maintained in the Placental medium. The medium was changed every 2 days during the 7 days treatment. Finally, we collected the treatment and control samples from the one-week culture.

value: Human Amniotic Epithelial Stem Cells

value: HAESC 3D spheroids

value: control


title: F4_AsB_500uM

description:
F4_170
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: HAESC 3D spheroids maintained in Placental Epithelial Cell Basal Medium_rep1

description:
Gene expression data from HAESC 3D spheroids maintained in Placental Epithelial Cell Basal Medium for 7 days
Control 1


title: F3_AsIII_30uM

description:
F3_44
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 18C_w1118_1

description: 18C w1118 replicate 1


title: F3_AsIII_10uM

description:
F3_43
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: Human corneal epithelial cells, Treatment of BAC and hAdMSC-CM 1


title: Human corneal epithelial cells, Treatment of BAC 3

value: BAC


title: F4_AsB_10uM

description:
F4_167
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 84_MO_10uM_rep3_24h

city: Beijing

first: Yihan

last: Lin

address: No.5 Yiheyuan Road, Haidian

institute: Peking University

data_processing:
Trimmomatic 0.39 was used to remove the 5' end 15-bp low quality sequence of the FASTQ file. BWA 0.7.17-r1188 was employed to map the resulting cleaned reads to the reference sequence. The resulting bam files were processed using a command mpileup from samtools to generate bcf file. To precisely profile the mutational frequency, nucleotides with sequencing quality score below Q30 were discarded. Then, custom Bash and Python scripts were used to extract the mutation information and calculate the mutation frequency. The mutation frequency at each specific position within the target gene is calculated by dividing the number of mutated bases (transversion and transition) at that position by the total number of bases sequenced at the specific position.
Assembly: Coding sequence of EGFP
Supplementary files format and content: The processed files in csv format contain the total mutation frequency for each sample.

organism: Mesocricetus auratus

source_name: kidney

growth_protocol: BHK-21 cells were cultivated in Minimum Essential Medium with Earle's Balanced Salts (MEM/EBSS) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, 100 μg/ml streptomycin, and 1% MEM Non-Essential Amino Acids Solution (Gibco, #11140050) in a humidified 37℃ incubator with 5% CO2.

extract_protocol:
The cells were harvested, and total RNA was extracted using TRIzol™ Reagent (Thermo Fisher Scientific, #15596018). Subsequently, approximately 3 μg of total RNA was reverse transcribed using the HiScript III 1st Strand cDNA Synthesis Kit (Vazyme, #R312-02) with a primer (SINDBIS_GSPR2: TGCGCCTCCTCGGAAATACG) located in the 3′ untranslated region of the replicative RNA.
EGFP region was amplified from the cDNA samples via 28 rounds of PCR using KOD OneTM PCR Master Mix and specific primers(For a 50 μl PCR reaction, 5 μl cDNA was used as template). The PCR product was purified using the HiPure Gel Pure DNA Micro Kit (Magen, #D2110-03). The gel-purified PCR product (approximately 1 μg) was subjected to sequencing using Tsingke Biotechnology's Fast NGS service. In brief, the experimental workflow provided by Tsingke Biotechnology involved the following steps: Firstly, DNA was enzymatically digested using Tn5 with sequence adaptors. Secondly, the digested products were subjected to PCR amplification using indexed sequencing primers. Finally, the resulting PCR products were recovered and subjected to sequencing using an Illumina MiSeq platform, ensuring a sequencing depth exceeding 500× on the target gene for accurate estimation of mutation frequency.

treatment_protocol: After 24 hours of electroporation, cells were subjected to continuous puromycin treatment (10 µg/ml) with regular passages. After another 5-7 days, a relatively stable and homogeneous population of cells carrying replicative RNA with EGFP expression was generated. These cells were then treated with nucleoside analogues at specified concentrations and durations.

value: kidney

value: fibroblast cells

value: repRNA-v4 based

value: molnupiravir


title: 29C_Mito-FLucDM-GFP_2copies_3

description: 29C Mito-FLucDM-GFP 2copies replicate 3

value: whole flies

value: males, 10-days-old

value: 29C Mito-FLucDM-GFP 2copies


title: HAESC 3D spheroids treated with Tsuru_rep2

description:
Gene expression data from HAESC 3D spheroids treated with Tsuruazuki extract for 7 days
Tsuru 2

source_name: HAESC 3D spheroids were treated with Tsuru for 7 days

value: Tsuru


title: F3_AsIII_3uM

description:
F3_42
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Liver

value: Primary cells

value: Primary hepatocytes


title: 29C_Mito-FLucDM-GFP_2copies_2

description: 29C Mito-FLucDM-GFP 2copies replicate 2


title: F3_Control_AsIII

description:
F3_41
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: Human corneal epithelial cells, Treatment of BAC 2

value: Human corneal epithelium

value: Human corneal epithelial cells


title: 82_MO_10uM_rep1_24h


title: 81_MO_10uM_rep3_48h


title: Human corneal epithelial cells, Treatment of BAC 1


title: HAESC 3D spheroids treated with Tsuru_rep1

description:
Gene expression data from HAESC 3D spheroids treated with Tsuruazuki extract for 7 days
Tsuru 1

value: Human Amniotic Epithelial Stem Cells


title: 29C_Mito-FLucDM-GFP_2copies_1

description: 29C Mito-FLucDM-GFP 2copies replicate 1


title: 80_MO_10uM_rep2_48h


title: DDX_12

city: Lyon

first: Cyril

middle: F

last: Bourgeois

address: 46 Allée d'Italie

department: LBMC

country: France

institute: ENS de Lyon

data_processing:
Nextflow pipeline
Sequence reads were trimmed for adapter sequence/low-quality sequence using fastp (--qualified_quality_phred 30, --length_required 25, --detect_adapter_for_pe)
Trimmed reads were mapped using hisat2, then the results were binarized, sorted and indexed using samtools.
Read counts were obtained using htseq (-r pos -a 10 -s “yes” -t exon -i gene_id) and differentially expressed genes were identified using DESeq2.
Assembly: GRCH38.99/hg38
Supplementary files format and content: htseq raw count files (.tsv)
Supplementary files format and content: DESeq normalized counts file (.csv)

growth_protocol: SH-SY5Y cells (ECACC) were grown and transfected essentially as recommended by the supplier

extract_protocol:
Total RNA were isolated using TriPure Isolation Reagent (Roche)
Directional RNA libraries were prepared from total RNA after removal of ribosomal RNA (lncRNA library, Novogene).

treatment_protocol: cells were transfected with 60 nM siRNA targeting DDX17, or with a control siRNA (siGL2, targeting luciferase) and harvested for RNA extraction 48h post-transfection

value: SH-SY5Y cell line

value: Neuroblastoma

value: siRNA anti-DDX17


title: F3_AsB_500uM

description:
F3_165
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 79_MO_10uM_rep1_48h

value: kidney


title: 25C_Mito-FLucDM-GFP_2copies_3

description: 25C Mito-FLucDM-GFP 2copies replicate 3

value: 25C Mito-FLucDM-GFP 2copies


title: 25C_Mito-FLucDM-GFP_2copies_2

description: 25C Mito-FLucDM-GFP 2copies replicate 2


title: F3_AsB_100uM

description:
F3_164
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 78_MO_20uM_rep3_72h

value: fibroblast cells

value: repRNA-v4 based


title: DDX_7


title: F3_AsB_50uM

description:
F3_163
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 25C_Mito-FLucDM-GFP_2copies_1

description: 25C Mito-FLucDM-GFP 2copies replicate 1

value: whole flies


title: 83_MO_10uM_rep2_24h

value: molnupiravir


title: F3_AsB_10uM

description:
F3_162
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 77_MO_10uM_rep3_72h


title: 18C_Mito-FLucDM-GFP_2copies_3

description: 18C Mito-FLucDM-GFP 2copies replicate 3

value: males, 10-days-old

value: 18C Mito-FLucDM-GFP 2copies


title: F3_Control_AsB

description:
F3_161
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Liver


title: 18C_Mito-FLucDM-GFP_2copies_2

description: 18C Mito-FLucDM-GFP 2copies replicate 2


title: F3_AsV_100uM

description:
F3_104
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Primary cells


title: HCT116 shALKBH5_2

city: Guangzhou

first: Dingcheng

last: Shen

address: 26 Yuancun Erheng Road

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

data_processing: none provided by the submitter

growth_protocol: HCT116 cells were maintained Mc5A supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NovaSeq mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: ALKBH5 knockdown


title: 76_MO_5uM_rep3_72h


title: 18C_Mito-FLucDM-GFP_2copies_1

description: 18C Mito-FLucDM-GFP 2copies replicate 1


title: HCT116 shALKBH5_1


title: F3_AsV_50uM

description:
F3_103
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

data_processing:
raw sequencing reads were mapped to the current Atlantic salmon genome (GCF_905237065) downloaded from the NCBI genome database using the Hisat2 mapper and counted using FeatureCounts as part of the Subread package. Raw counts were further normalized using DESeq2 (1.40.2) Bioconductor package (V3.17), features that had lower count than 10 reads were filtered prior to normalization. Differentially expressed genes (DEGs) were determined using Wald test and corrected for multiple testing using the Benjamini and Hochberg test, as implemented in the DESeq2 package. Differentially expressed genes were used for further downstream pathway analysis. Due to the high number of differentially expressed genes in AsIII exposed cells, a 2-fold differential expression cut of was applied to these samples. Due to limited tools and databases for biological function of non-model species, DEG feature gene names were converted to human ortholog gene names using the BioDBnet database (https://biodbnet-abcc.ncifcrf.gov/db/dbOrtho.php) prior to pathway analysis. Pathway analysis were conducted using the open source Metascape software (https://metascape.org)
Assembly: GCF_905237065
Supplementary files format and content: The processed datafile contain a matrix of normalized gene counts in txt format.

extract_protocol:
Hepatocytes for RNA extraction and sequencing were seeded on 6-well Alvetex® scaffolds. After 48 h exposure to arsenite, arsenate and arsenobetaine, 2 mL of cell medium from each well was taken and kept at -20ºC until further analysis (see section 2.6). The rest of the cell medium was discarded. Retrieval of cells from Alvetex® scaffolds for this analysis was performed according to manufacturer’s description (see protocol for retrieval of cells from Alvetex® scaffold's for metabolomic analysis). In summary, the well inserts with the hepatocyte cells were transferred to new 6-well plates. The cells were washed with PBS (1 mL) which was removed from the well before the next step. The Alvetex Scaffold membrane was removed with the aid of flat-ended forceps. To break down the cells, introduce 600 µL of the Qiagen RNeasy® kit lysis buffer RLT directly to the well where is Alvetex Scaffold membrane was left. Allow the plate on a rotating platform (100 rpm) for 10 min at room temperature. Conclude the process by adding 600 µL of 70% ethanol to the now-homogenized lysate. Ensure a proper mix by pipetting the combination up and down around 10 times. The cell suspension was transferred to centrifugation tubes and centrifuged at 1000×g for 5 min at 4 °C. Cell pellets were flash frozen and stored at −80 °C until RNA extraction was performed.Total RNA was extracted from Atlantic salmon Primary hepatocytes using a RNeasy Plus Mini Kit (Qiagen, Crawley, UK) as previously described (Søderstrøm et al 2023). Total RNA purity was evaluated using a nanodrop NanoDrop™ (Thermo Fisher Scientific™, MA, USA) Samples had a 260/230 and 260/280 ratio of 2.2 ± 0.1 and 2.09 ± 0.03 respectively. Integrity of RNA for each sample was investigated using RNA 6000 Nano LabChips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Although the integrity of the majority of the samples were assessed as good (RIN = 9.7 ± 0.12, N = 48), RNA from cells exposed to 250 µM AsSug showed a reduction in integrity (RIN 5.3 ± 0.5, N = 6).
Total RNA samples of arsenate and arsenobetaine were sent to Novogene Europe, Cambridge, UK, for cDNA library preparation and sequencing using the Illumina NovaSeq 6000 platform for 150 bp paired end reads. Enriched mRNA was prepared using Oligo(dT beads). cDNA libraries were prepared following manufacturer's instructions per the Novogen pipeline (Novogene Europe, Cambridge, UK)

value: Primary hepatocytes


title: DDX_6

source_name: Ctrl

value: Control siRNA anti-GL2


title: HCT116 shNC_2

value: WT


title: 74_MO_0.1uM_rep3_72h


title: 73_DMSO_rep6_72h

value: DMSO


title: DDX_11

value: SH-SY5Y cell line

value: Neuroblastoma


title: F3_AsV_10uM

description:
F3_102
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: HCT116 shNC_1


title: 29C_Mito-FLucDM-GFP_1copy_3

description: 29C Mito-FLucDM-GFP 1copy replicate 3

value: 29C Mito-FLucDM-GFP 1copy


title: F3_Control_AsV

description:
F3_101
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 29C_Mito-FLucDM-GFP_1copy_2

description: 29C Mito-FLucDM-GFP 1copy replicate 2


title: F2_AsV_100uM

description:
F2_99
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: muscle, control, A144

city: chengdu

first: Li

last: Zeng

state: sichuan

address: 32# W. Sec 2, 1st Ring Rd

department: neurology

institute: sichuan provincial people's hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 30 )were removed .software trimmomatic-0.39,parameters PE -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Read alignment software,software HISAT ,version 2.2.1 ,parameters -1 <m1> -2 <m2>  -p 20
perform expression level for mRNAs by calculating Counts.stimate the expression levels of all transcripts.software featureCounts ,version 2.0.0,parameters -p -T 20 a GTF_file -t exon -g gene_name
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary files format and content: tab-delimited text file includes Count values for each Sample

source_name: muscle

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).  Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

value: muscle

value: control


title: 71_MO_10uM_rep2_72h

value: kidney

value: fibroblast cells

value: repRNA-v4 based


title: muscle, control, A143


title: 25C_Mito-FLucDM-GFP_1copy_3

description: 25C Mito-FLucDM-GFP 1copy replicate 3

value: whole flies

value: males, 10-days-old

value: 25C Mito-FLucDM-GFP 1copy


title: F2_AsV_50uM

description:
F2_98
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Liver

value: Primary cells


title: 70_MO_5uM_rep2_72h

value: molnupiravir


title: 75_MO_1uM_rep3_72h


title: muscle, control, A119


title: F2_AsV_10uM

description:
F2_97
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Primary hepatocytes


title: 25C_Mito-FLucDM-GFP_1copy_2

description: 25C Mito-FLucDM-GFP 1copy replicate 2


title: 69_MO_1uM_rep2_72h


title: muscle, control, A100


title: F2_Control_AsV

description:
F2_96
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 25C_Mito-FLucDM-GFP_1copy_1

description: 25C Mito-FLucDM-GFP 1copy replicate 1


title: 68_MO_0.1uM_rep2_72h


title: muscle, control, A097


title: muscle, control, A066


title: 29C_Mito-FLucDM-GFP_1copy_1

description: 29C Mito-FLucDM-GFP 1copy replicate 1


title: F2_AsIII_100uM

description:
F2_40
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 72_MO_20uM_rep2_72h


title: 18C_Mito-FLucDM-GFP_1copy_3

description: 18C Mito-FLucDM-GFP 1copy replicate 3

value: 18C Mito-FLucDM-GFP 1copy


title: 67_DMSO_rep5_72h

value: DMSO


title: 18C_Mito-FLucDM-GFP_1copy_1

description: 18C Mito-FLucDM-GFP 1copy replicate 1


title: 18C_Mito-FLucDM-GFP_1copy_2

description: 18C Mito-FLucDM-GFP 1copy replicate 2


title: F2_AsIII_30uM

description:
F2_39
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 66_MO_20uM_rep1_72h


title: F2_AsIII_10uM

description:
F2_38
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 65_MO_10uM_rep1_72h


title: muscle, control, A060


title: muscle, control, A042


title: 29C_NLS-FLucDM-GFP_2copies_2

description: 29C NLS-FLucDM-GFP 2copies replicate 2

value: 29C NLS-FLucDM-GFP 2copies


title: 29C_NLS-FLucDM-GFP_2copies_3

description: 29C NLS-FLucDM-GFP 2copies replicate 3


title: F2_AsIII_3uM

description:
F2_37
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: muscle, control, A056


title: F2_Control_AsIII

description:
F2_36
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 63_MO_1uM_rep1_72h


title: 64_MO_5uM_rep1_72h


title: F2_AsB_500uM

description:
F2_160
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 29C_NLS-FLucDM-GFP_2copies_1

description: 29C NLS-FLucDM-GFP 2copies replicate 1


title: F2_AsB_100uM

description:
F2_159
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 62_MO_0.1uM_rep1_72h


title: muscle, IMNM, A171

value: IMNM


title: 25C_NLS-FLucDM-GFP_2copies_3

description: 25C NLS-FLucDM-GFP 2copies replicate 3

value: 25C NLS-FLucDM-GFP 2copies


title: 25C_NLS-FLucDM-GFP_2copies_2

description: 25C NLS-FLucDM-GFP 2copies replicate 2


title: muscle, IMNM, A152

value: muscle


title: F2_AsB_50uM

description:
F2_158
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 25C_NLS-FLucDM-GFP_2copies_1

description: 25C NLS-FLucDM-GFP 2copies replicate 1


title: F2_Control_AsB

description:
F2_156
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 18C_NLS-FLucDM-GFP_2copies_3

description: 18C NLS-FLucDM-GFP 2copies replicate 3

value: 18C NLS-FLucDM-GFP 2copies


title: F2_AsB_10uM

description:
F2_157
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 18C_NLS-FLucDM-GFP_2copies_2

description: 18C NLS-FLucDM-GFP 2copies replicate 2


title: muscle, IMNM, A137


title: 59_FA_100uM_rep2_24h

value: kidney

value: favipiravir


title: 58_FA_100uM_rep1_24h

value: fibroblast cells

value: repRNA-v4 based


title: muscle, control, A029

value: control


title: muscle, IMNM, A134


title: F1_AsV_100uM

description:
F1_94
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 18C_NLS-FLucDM-GFP_2copies_1

description: 18C NLS-FLucDM-GFP 2copies replicate 1

value: whole flies

value: males, 10-days-old


title: muscle, IMNM, A122


title: 57_FA_100uM_rep3_48h


title: 56_FA_100uM_rep2_48h


title: 61_DMSO_rep4_72h


title: F1_AsV_50uM

description:
F1_93
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Liver

value: Primary cells


title: muscle, IMNM, A165


title: 60_FA_100uM_rep3_24h


title: 29C_NLS-FLucDM-GFP_1copy_2

description: 29C NLS-FLucDM-GFP 1copy replicate 2

value: 29C NLS-FLucDM-GFP 1copy


title: 55_FA_100uM_rep1_48h


title: 54_FA_200uM_rep3_72h


title: F1_Control_AsV

description:
F1_91
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

value: Primary hepatocytes


title: 29C_NLS-FLucDM-GFP_1copy_1

description: 29C NLS-FLucDM-GFP 1copy replicate 1


title: F1_AsIII_100uM

description:
F1_35
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: muscle, IMNM, A148


title: 53_FA_100uM_rep3_72h


title: muscle, IMNM, A073


title: muscle, IMNM, A068


title: 25C_NLS-FLucDM-GFP_1copy_3

description: 25C NLS-FLucDM-GFP 1copy replicate 3

value: 25C NLS-FLucDM-GFP 1copy


title: 52_FA_50uM_rep3_72h


title: 25C_NLS-FLucDM-GFP_1copy_2

description: 25C NLS-FLucDM-GFP 1copy replicate 2


title: F1_AsIII_30uM

description:
F1_34
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: muscle, IMNM, A065


title: F1_AsIII_10uM

description:
F1_33
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 29C_NLS-FLucDM-GFP_1copy_3

description: 29C NLS-FLucDM-GFP 1copy replicate 3


title: 51_FA_10uM_rep3_72h


title: 25C_NLS-FLucDM-GFP_1copy_1

description: 25C NLS-FLucDM-GFP 1copy replicate 1


title: muscle, IMNM, A057


title: F1_AsV_10uM

description:
F1_92
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: muscle, IMNM, A064


title: F1_AsIII_3uM

description:
F1_32
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 18C_NLS-FLucDM-GFP_1copy_3

description: 18C NLS-FLucDM-GFP 1copy replicate 3

value: 18C NLS-FLucDM-GFP 1copy


title: muscle, IMNM, A075

value: IMNM


title: 49_DMSO_rep3_72h

value: DMSO


title: 18C_NLS-FLucDM-GFP_1copy_2

description: 18C NLS-FLucDM-GFP 1copy replicate 2


title: muscle, IMNM, A045

value: muscle


title: F1_AsB_500uM

description:
F1_155
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 18C_NLS-FLucDM-GFP_1copy_1

description: 18C NLS-FLucDM-GFP 1copy replicate 1


title: 47_FA_100uM_rep2_72h


title: muscle, IMNM, A041


title: 29C_Cyto-FLucDM-GFP_1copy_3

description: 29C Cyto-FLucDM-GFP 1copy replicate 3

value: 29C Cyto-FLucDM-GFP 1copy


title: 50_FA_1uM_rep3_72h

value: kidney


title: F1_AsB_50uM

description:
F1_153
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: muscle, IMNM, A022


title: F1_Control_AsIII

description:
F1_31
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: F1_AsB_10uM

description:
F1_152
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.


title: 29C_Cyto-FLucDM-GFP_1copy_2

description: 29C Cyto-FLucDM-GFP 1copy replicate 2


title: 29C_Cyto-FLucDM-GFP_1copy_1

description: 29C Cyto-FLucDM-GFP 1copy replicate 1


title: 45_FA_10uM_rep2_72h

value: favipiravir


title: muscle, IMNM, A021


title: F1_Control_AsB

description:
F1_151
Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations (5, 10, 50 and 250 µM) in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations (0.1, 1, 3 µM) in addition to control on individual plates for each compound.


title: 44_FA_1uM_rep2_72h

value: fibroblast cells


title: AB27: HUVEC Borr 72h - rep3

city: Sackville

first: Anne

last: Berthold

state: New Brunswick

address: 62 York Street

department: Biology

institute: Mount Allison University

data_processing:
adapter trimming with BaseSpace™ Sequence Hub Prep platform was followed by trimming with Trim Galore (v.0.4.4, Krueger, 2016) with default settings.
pseudo alignment  and quantification was performed with Salmon (v.1.4.0, Patro et al., 2017) in reference to the human transcriptome from Gencode (Release 37 - GRCh38.p13).
Low-expressed genes were filtered out, and only genes with at least more than 1 read in at least 2 samples in one of the groups were considered for further analysis.
normalization and differential expression of the count matrix was performed with DESeq2 (v.1.28.1, Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: HUVEC_rawcounts.csv: Matrix table with raw counts for every gene and every HUVEC sample
Supplementary_files_format_and_content: HEK-293_rawcounts.csv: Matrix table with raw counts for every gene and every HEK-293 sample
Supplementary_files_format_and_content: BOTH_rawcounts.csv: Matrix table with raw counts for every gene and every cell type HUVEC and HEK-293

source_name: HUVEC Borr 72h - rep3

growth_protocol: All human cells were grown at 37°C with 5% CO2. HUVECs required optimized endothelial cell growth media EGMTM BulletKitTM (Lonza, CC-3124). HEK-293 cells were grown in DMEM media (Lonza, 12-733F) supplemented with 10% v/v heat-inactivated FBS (Rockland, FBS.02-0500), each 1% v/v L-glutamine (Lonza, 17-605E), sodium pyruvate (Lonza, 13-115E), and penicillin/streptomycin (Sigma-Aldrich, P4333). Borrelia burgdorferi strain B31 was cultured in Barbour-Stoenner-Kelly medium including 6% rabbit serum (BSK-H, Darlynn biologicals, BB83-500), supplemented with antibiotics (Sigma-Aldrich) at the final concentration of 50 µg/ml Rifampicin (R3501), 20 µg/ml Phosphomycin (P5396), and 2.5 µg/ml Amphotericin B (A9528) in glass culture tubes.

extract_protocol:
RNA extraction was performed with the RNeasy Mini Kit (74104, Qiagen) including DNase I on-column digestion (1010395, Qiagen) and elution in 50 µl RNase-free water.
The library for RNA-seq was prepared with 200 ng RNA input and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs (NEB), E7760L). First, mRNA was enriched using the NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, E7490L) and following the manufacturer’s instructions. Briefly, after isolation, samples were fragmented for 15 min at 94°C for a target insert size of 200 bp. Next, the first and the second cDNA strand were synthetized, followed by an Ampure XP bead (Beckman Coulter, A63881) clean up. Then the samples were end-prepped and the adaptor was ligated. The adaptor was diluted following the manufacturer’s instructions. The adaptor-ligated samples were purified with Ampure XP beads before amplification. A different Unique Dual Index Primer Pair (NEB, E6440S) was added to each sample and 11 cycles were used for the PCR enrichment. Purification using Ampure XP beads was used to obtain the final library. The quality and quantity of the library was assessed with the D1000 assay on the Tapestation (Agilent, 5067-5582 and 5067-5583) and the dsDNA HS assay from Qubit (Thermo Fisher, Life Technologies, Q32851).

treatment_protocol: Adherent human cells were exposed to Borrelia burgdorferi strain B31 for 72 h in antibiotic free media. The multiplicity of infection (MOI) was 50:1 bacteria cells: human cells.

value: HUVEC

value: Human umbilical vein endothelial  cells

value: exposed to Borrelia burgdorferi B31 for 72h


title: 43_DMSO_rep2_72h

value: repRNA-v4 based


title: F2-AsIII 3 uM 48h

city: Bergen

first: Kai

last: Lie

address: Pobox 2029 Nordnes

institute: Institute of Marine research

description: Hepatocyte isolated from individual fish were exposed to either arsenosugar (AsSug) at different concentrations in addition to control (AsSugControl) or arsenite (AsIII) at different concentrations in addition to control on individual plates for each compound.

extract_protocol:
Hepatocytes for RNA extraction and sequencing were seeded on 6-well Alvetex® scaffolds. After 48 h exposure to arsenite, arsenate and arsenobetaine, 2 mL of cell medium from each well was taken and kept at -20ºC until further analysis (see section 2.6). The rest of the cell medium was discarded. Retrieval of cells from Alvetex® scaffolds for this analysis was performed according to manufacturer’s description (see protocol for retrieval of cells from Alvetex® scaffold's for metabolomic analysis). In summary, the well inserts with the hepatocyte cells were transferred to new 6-well plates. The cells were washed with PBS (1 mL) which was removed from the well before the next step. The Alvetex Scaffold membrane was removed with the aid of flat-ended forceps. To break down the cells, introduce 600 µL of the Qiagen RNeasy® kit lysis buffer RLT directly to the well where is Alvetex Scaffold membrane was left. Allow the plate on a rotating platform (100 rpm) for 10 min at room temperature. Conclude the process by adding 600 µL of 70% ethanol to the now-homogenized lysate. Ensure a proper mix by pipetting the combination up and down around 10 times. The cell suspension was transferred to centrifugation tubes and centrifuged at 1000×g for 5 min at 4 °C. Cell pellets were flash frozen and stored at −80 °C until RNA extraction was performed.Total RNA was extracted from Atlantic salmon Primary hepatocytes using a RNeasy Plus Mini Kit (Qiagen, Crawley, UK) as previously described (Søderstrøm et al 2023). Total RNA purity was evaluated using a nanodrop NanoDrop™ (Thermo Fisher Scientific™, MA, USA) Samples had a 260/230 and 260/280 ratio of 2.2 ± 0.1 and 2.09 ± 0.03 respectively. Integrity of RNA for each sample was investigated using RNA 6000 Nano LabChips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Although the integrity of the majority of the samples were assessed as good (RIN = 9.7 ± 0.12, N = 48), RNA from cells exposed to 250 µM AsSug showed a reduction in integrity (RIN 5.3 ± 0.5, N = 6).
RNAseq of arsenite and arsenosugar 328 samples was conducted by a commercial company (Azenta Life Sciences, Leipzig, Germany). RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA). The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated using DNA Kit on the Agilent 5600 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA). The sequencing libraries were multiplexed and clustered onto a flow-cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

value: Liver


title: 25C_Cyto-FLucDM-GFP_1copy_3

description: 25C Cyto-FLucDM-GFP 1copy replicate 3

value: whole flies

value: males, 10-days-old

value: 25C Cyto-FLucDM-GFP 1copy


title: AB26: HUVEC Borr 72h - rep2

source_name: HUVEC Borr 72h - rep2


title: 42_FA_200uM_rep1_72h


title: F2-AsIII 1 uM 48h

source_name: Liver

value: Primary cells

value: Primary hepatocytes


title: muscle, IMNM, A044

value: IMNM


title: 25C_Cyto-FLucDM-GFP_1copy_2

description: 25C Cyto-FLucDM-GFP 1copy replicate 2


title: AB25: HUVEC Borr 72h - rep1

source_name: HUVEC Borr 72h - rep1


title: F2-AsIII Control 48h


title: 40_FA_50uM_rep1_72h


title: 48_FA_200uM_rep2_72h


title: 25C_Cyto-FLucDM-GFP_1copy_1

description: 25C Cyto-FLucDM-GFP 1copy replicate 1


title: 46_FA_50uM_rep2_72h


title: F2-AsIII 0.1 uM 48h


title: AB33: HUVEC control 72 h - rep3

source_name: HUVEC control 72 h - rep3

value: unexposed


title: S2_cells_H3K4me3_IP_SNAP_Spike_in_BRWD3_dsRNA2

city: Nashville

first: Jared

last: Nordman

address: 465 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

library_source: genomic

data_processing:
Base-calling and Quality Control (QC): The deepTools/3.3.1-Python-3.7.2 module was utilized for base-calling and performing quality control on the data.
Read alignment: The Bowtie2/2.3.5.1 module was employed for aligning the reads to a reference genome.
Conversion of SAM to BAM format and sorting: The SAMtools/1.9 module was used to convert the alignment results from SAM to BAM format, followed by sorting the BAM files.
Indexing of sorted BAM file: The SAMtools/1.9 module was also used for indexing the sorted BAM files, enabling efficient access to specific regions of interest.
To create a bigWig file with a bin size of 50bp using bamCoverage and a scaling factor, deepTools/3.3.1-Python-3.7.2 was used.
Assembly: dm6
Supplementary files format and content: bigwig for coverage visualization

molecule: genomic DNA

growth_protocol: S2 cells are maintained in Schneider's Drosophila medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin solution.

extract_protocol:
H3K4me3 ChIP was performed using ~50 million S2 cells harvested after RNAi treatment and centrifuged at 600 rcf for 5 minutes. Cells were washed twice with PBS and fixed with 1% paraformaldehyde (PFA) for 10 minutes at room temperature. Crosslinking was quenched by adding glycine to a final concentration of 125mM and incubating at room temperature for 5 minutes. Cells were then centrifuged and resuspended in RIPA buffer supplemented with 2X cOmplete TM Protease Inhibitor Cocktail EDTA-free. Chromatin shearing was performed using a Diagenode Bioruptor. To facilitate accurate normalization, 10 µl of sheared chromatin was decrosslinking overnight and purified and DNA concentration was measured. 1µl of spike-in SNAP-ChIP K-MetStat mononucleosomes (EpiCypher, Cat. 19-1001) was added to 20 µg of sonicated chromatin. 3µg of H3K4me3 antibody (Active Motif, Cat. 39060) was added to the chromatin extract and incubated for 2 hours at 4°C. Pre-washed Protein A beads were added to the extract and incubated for one hour at 4°C. The beads were then washed twice with RIPA buffer, twice with high-salt RIPA buffer (500 mM NaCl), twice again with RIPA buffer and finally with TE buffer.
Libraries contructed following NEBNext Ultra II Library Prep Kit for Illumina

treatment_protocol: Cells were treated with dsRNAs to induce specific changes or knockdowns in gene expression.

value: late embryogenisis

value: brwd3 dsRNA2


title: 18C_Cyto-FLucDM-GFP_1copy_3

description: 18C Cyto-FLucDM-GFP 1copy replicate 3

value: 18C Cyto-FLucDM-GFP 1copy


title: AB32: HUVEC control 72 h - rep2

source_name: HUVEC control 72 h - rep2


title: 18C_Cyto-FLucDM-GFP_1copy_2

description: 18C Cyto-FLucDM-GFP 1copy replicate 2


title: F1-AsIII 3 uM 48h


title: S2_cells_H3K4me3_IP_SNAP_Spike_in_WT2

value: no dsRNA


title: 39_FA_10uM_rep1_72h

value: kidney

value: fibroblast cells

value: favipiravir


title: AB31: HUVEC control 72 h - rep1

source_name: HUVEC control 72 h - rep1

value: HUVEC

value: Human umbilical vein endothelial  cells


title: 18C_Cyto-FLucDM-GFP_1copy_1

description: 18C Cyto-FLucDM-GFP 1copy replicate 1


title: F6-AsIII 0.1 uM 48h

value: Liver


title: F1-AsIII 1 uM 48h


title: repRNA_v4_post_day7_rep3

extract_protocol:
The cells were harvested, and total RNA was extracted using TRIzol™ Reagent (Thermo Fisher Scientific, #15596018). Subsequently, approximately 3 μg of total RNA or IVT RNA was reverse transcribed using the HiScript III 1st Strand cDNA Synthesis Kit (Vazyme, #R312-02) with a primer (SINDBIS_GSPR2: TGCGCCTCCTCGGAAATACG) located in the 3′ untranslated region of the replicative RNA.
EGFP region was amplified from the cDNA or DNA samples via 28 rounds of PCR using KOD OneTM PCR Master Mix and specific primers(For a 50 μl PCR reaction, 5 μl cDNA was used as template). The PCR product was purified using the HiPure Gel Pure DNA Micro Kit (Magen, #D2110-03). The gel-purified PCR product (approximately 1 μg) was subjected to sequencing using Tsingke Biotechnology's Fast NGS service. In brief, the experimental workflow provided by Tsingke Biotechnology involved the following steps: Firstly, DNA was enzymatically digested using Tn5 with sequence adaptors. Secondly, the digested products were subjected to PCR amplification using indexed sequencing primers. Finally, the resulting PCR products were recovered and subjected to sequencing using an Illumina MiSeq platform, ensuring a sequencing depth exceeding 500× on the target gene for accurate estimation of mutation frequency.

treatment_protocol: After 24 hours of electroporation, cells were subjected to continuous puromycin treatment (10 µg/ml) with regular passages.

value: repRNA-v4 based

value: no


title: F6-AsIII Control 48h


title: S2_cells_H3K4me3_IP_SNAP_Spike_in_WT1


title: AB35: HEK-293 control 72 h - rep2

source_name: HEK-293 control 72 h - rep2

value: human embryonic kidney cells


title: AB30: HEK-293 Borr 72h - rep3

source_name: HEK-293 Borr 72h - rep3

value: exposed to Borrelia burgdorferi B31 for 72h


title: 38_FA_1uM_rep1_72h


title: F6-AsIII 3 uM 48h

value: Primary cells

value: Primary hepatocytes


title: 37_DMSO_rep1_72h

value: DMSO


title: F5-AsIII 3 uM 48h


title: 41_FA_100uM_rep1_72h


title: AB29: HEK-293 Borr 72h - rep2

source_name: HEK-293 Borr 72h - rep2


title: F6-AsIII 1 uM 48h


title: S2_cells_H3K4me3_IP_SNAP_Spike_in_BRWD3_dsRNA1

value: late embryogenisis

value: brwd3 dsRNA1


title: AB28: HEK-293 Borr 72h - rep1

source_name: HEK-293 Borr 72h - rep1


title: repRNA_v4_post_day7_rep2


title: repRNA_v4_post_day7_rep1


title: AB36: HEK-293 control 72 h - rep3

source_name: HEK-293 control 72 h - rep3

value: unexposed


title: Leaf of Rhodendron ‘xiaotaohong’, 40℃, melatonin-applied, rep3

city: Zhuji

first: Yanxia

last: Xu

state: Zhejiang

address: 66 Puyang Road

institute: Jiyang College, Zhejiang A&F University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Rhododendron reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Rhododendron simsii
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rhododendron

source_name: leaf

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

tag: variety

value: xiaotaohong

value: leaf


title: Bos taurus, m6A-Seq, pre_4_IP RNA

city: Changchun

first: Xiaorui

last: Yang

address: Xincheng Street

institute: Jilin Agricultural University

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: BOVINE(ensemble V107)
Supplementary files format and content: bigWig
Library strategy: m6A-seq

organism: Bos taurus

source_name: pituitary

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: pituitary


title: Bos taurus, m6A-Seq, pre_2_IP RNA


title: AB34: HEK-293 control 72 h - rep1

source_name: HEK-293 control 72 h - rep1


title: repRNA_v4_post_day3_rep3

source_name: kidney

value: kidney

value: fibroblast cells


title: F5-AsIII Control 48h


title: repRNA_v4_post_day3_rep2


title: F5-AsIII 1 uM 48h


title: Leaf of Rhodendron ‘xiaotaohong’, 40℃, melatonin-applied, rep1


title: F5-AsIII 0.1 uM 48h


title: Bos taurus, m6A-Seq, pre_1_IP RNA


title: F1-AsIII 0.1 uM 48h


title: repRNA_v4_post_day21_rep3


title: Bos taurus, m6A-Seq, pre_2_input RNA


title: Bos taurus, m6A-Seq, pre_4_input RNA


title: Bos taurus, m6A-Seq, pre_1_input RNA


title: F4-AsIII 3 uM 48h


title: Leaf of Rhodendron ‘xiaotaohong’, 35℃, melatonin-applied, rep2


title: repRNA_v4_post_day21_rep1


title: repRNA_v4_post_day21_rep2


title: repRNA_v4_post_day3_rep1


title: Leaf of Rhodendron ‘xiaotaohong’, 35℃, melatonin-applied, rep1


title: F4-AsIII 1 uM 48h