title: HCT116 xenograft, Re3

city: guangzhou

first: wen

last: qing

state: State...

address: guangzhou

institute: jinan university

description:
Re3
Bev_Re

data_processing:
Sequencing data quality assessment
Tophat2, Hisat2 and STAR software can be used for comparative analysis of RNA-Seq sequencing data
We used Stringtie software to compare the results based on the alignment to the genome,     reads were spliced into transcripts and quantified
A network stream algorithm was applied to splice and quantify transcripts and genes
EdgeR software was used to analyze the significance of expression difference
Assembly: hg18
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: lncRNA.difftranscript.txt files represent differential transcripts
Supplementary files format and content: lncRNA.transcript_level.Differential_analysis_results.txt files represent all transcripts

source_name: HCT116 xenograft

growth_protocol: HCT116-luc cells were resuspended in Matrigel at a concentration of 1 × 10^7 cells/mL, and a total of 2 × 10^5 tumor cells in 20 μL were injected into the left main lobe of the mouse liver. Tumor-bearing mice were randomized into the vehicle and bevacizumab groups on the seventh day.

extract_protocol:
Total RNA was extracted using Tissue RNA Kit (Omega). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the method of ribosomal RNA removal.

treatment_protocol: The treatment group of HCT116-luc xenografts was injected intraperitoneally (i.p.) with 10 mg/kg bevacizumab (Roche) twice a week for 7 weeks, while the vehicle group received IgG.

value: HCT116 xenograft

value: Bevacizumab Day 42

tag: phenotype

value: bevacizumab-resistant


title: LigF_178

status: Public on Aug 30 2023

type: SRA

city: Chicago

first: Atieh

last: Hajirahimkhan

state: Illinois

address: 303 E Superior, 4-220

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
quality control of the raw sequence data was assessed using FASTQC
Sequence reads were mapped to the reference genome hg38 using STAR.
To evaluate the quality of the RNA-seq data, the number of reads falling into different annotated regions of the reference genes was determined with bamUtil
To analyze the data, low quality mapped reads were excluded and feature counts were used to quantify the gene level expression. Differential gene expression analysis was performed with edgeR
Assembly: hg 38
Supplementary files format and content: excell speadsheet containing raw counts

molecule: total RNA

organism: Homo sapiens

source_name: breast microstructure, liquritigenin, 24 h

extract_protocol:
RNA was harvested using Direct-Zol RNA prep kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Roche KAPA Hyperprep kit and QIAseq Fast Select rRNA removal kit following manufacturers' protocols.

tag: cell line

value: tissue

tag: cell type

value: high-risk human breast microstructures

tag: genotype

value: postmenopausal

tag: treatment

value: liquiritigenin

tag: time


title: HCT116 xenograft, Re2

country: China

description:
Re2
Bev_Re

tag: tissue


title: A32

city: Guangzhou

first: Qianjun

last: Li

email: qqjun8@yeah.net, qqjun8@163.com

state: Guangdong

address: No. 1838, North Guangzhou Avenue

department: Sleep Medicine Center

institute: Nanfang Hospital, Southern Medical University

library_source: genomic

data_processing:
Sequencing data were filtered to remove low-quality sequences.Sequence splicing was performed using FLASH (Fast Length Adjustment of Short reads, V1.2.11)
Remove the primer sequence from the Tags sequence using the software CUTADAPT (version 1.16).
Using UCHIME method in VSEARCH(V2.3.4) software and combined with Gold Database (V20110519) chimera database to remove chimera sequences to get high-quality Tags sequence.
The software VSEARCH (V2.3.4) was used to cluster high-quality Tags sequence into OTU, and the REPRESENTATIVE sequence of OTU was obtained.
Using RDP Classifer (V2.2) software combined with Silva (V128) database, species annotation was performed for OTU representative sequences.
Based on 16S data, Alpha(α) diversity index (Observed OTU richness and Shannon Diversity) and Beta(β) diversity index based on Principal Coordinate Analysis (PCoA) (unweighted-Unifrac distance, Adonis) was used to assess the differences between groups. Linear discriminant analysis (LDA) and LDA Effective Size (LEfSe) was used to assess the taxonomic differences among groups.The network was then utilized to present the relationship between intestinal microbiome, intestinal barrier biomarkers, and AHI (Cytoscape v3.7.2). Statistical analysis of data was conducted in SPSS (version 21.0) and R software (v3.5.1).
Genome_build: 16S rDNA Sequences were aggregated into operational taxonomic units (OTUs) using 97% identity of the Silva v128 database
Supplementary_files_format_and_content: ConnectTags_stat.txt
Supplementary_files_format_and_content: OTU_table_for_biom.txt
Supplementary_files_format_and_content: Genus.absolute_abundance.txt
Supplementary_files_format_and_content: Alpha_diversity_detail.txt
Supplementary_files_format_and_content: unweighted_unifrac_Beta_diversity.txt

molecule: genomic DNA

organism: human feces metagenome

source_name: Human feces

extract_protocol:
Bead beading isolation was done to extract genomic DNA using the QIAamp DNA Kit (QIAGEN, Hilden, Germany), following the manufacturer's protocol. The extracted DNA concentration was measured by Qubit 2.0 Fluorometer (Life Technology, Carlsbad, CA). DNA quality was detected by 1.0% agarose gel electrophoresis. Then, the 16S rDNA gene regions (V3 and V4) were amplified by PCR.
The 16S rDNA libraries were sequenced on the Illumina MiSeq platform PE300 mode (Illumina, USA)

treatment_protocol: One gram of fresh fecal samples was collected in a sterile fecal tube on the first day after admission and were immediately stored in the -20℃ refrigerator of the department, then sent to the -80℃ refrigerator of the central laboratory of Nanfang Hospital for cold storage within 4 hours by the researchers.

value: Fecal

tag: diagnosis

value: Mild-OSA

value: No


title: A31


title: dna2-md-7h-ChIP-repeat2

city: Jinan

first: liangran

last: zhang

state: Shandong

address: Jingshi Street

department: State Key Laboratory of Microbial Technology

institute: Shandong University

data_processing:
Adaptors and bases with a quality rating of less than 25 were trimmed by Trim-galore.
ChIP-Seq reads were mapped to the reference genome (SacCer3) by Bowtie2.
Peaks were called by MACS2 with default settings,and the folds enrichment ≥ 2.
Assembly: SacCer3
Supplementary files format and content: bigWig

organism: Saccharomyces cerevisiae SK1

source_name: Budding yeast

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 90 min. The reaction was quenched with glycine. The cells were broken with glass beads in lysis buffer and the chromatin was sheared by sonication.
The library was prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, Cat# ND607-01) according to the manufacturer’s manual.

value: Budding yeast

value: dna2-md (pCLB2-DNA2)

tag: antibody

tag: time point


title: HCT116 xenograft, Re1

description:
Re1
Bev_Re


title: A30

value: Moderate-OSA


title: HCT116 xenograft, CTL3

description:
CTL3
Bev_CTL

value: Bevacizumab Day 0

value: bevacizumab-sensitive


title: A29


title: dna2-md-4h-Input-repeat1


title: dna2-md-4h-Input-repeat2


title: A27


title: dna2-md-7h-ChIP-repeat1


title: HCT116 xenograft, CTL1

description:
CTL1
Bev_CTL


title: A26

value: Severe-OSA


title: A25


title: HCT116 xenograft, CTL2

description:
CTL2
Bev_CTL


title: A22


title: A24


title: A17


title: dna2-md-4h-ChIP-repeat2


title: A20


title: A18


title: dna2-md-4h-ChIP-repeat1


title: R18, HAoSMC cells, pH 6.8, sample group: 9

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

data_processing:
Read alignment (HISAT2 2.1.0)
Read counting (featureCounts - 2.0.0)
Annotation with biomaRt and Ensembl 104
Assembly: hg38
Supplementary files format and content: .csv file including annotation raw counts (output of featureCounts) for each sample

source_name: HAoSMC

growth_protocol: HK2 and CCD-1092SK were cultivated with DMEM medium (10% FCS, 1.5g/L NaHCO3), at 37°C, 5% CO2. HAoSMC were cultivated with supplemented "Smooth muscle cell growth Medium 2" (PromoCell, Germany), at 37°C, 5% CO2.

extract_protocol:
Total RNA was isolated with BluZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
polyA enrichment (performed by Novogene Europe)

treatment_protocol: Cells were synchronized for 24h with DMEM medium without FCS. HK2 and CCD-1092Sk cells were incubated at pH 7.4 or 6.4; HAoSMC were incubated at pH 7.4 and pH 6.8. The lower pH conditions were reached with HCl. All incubations were maintained for 48h.

value: HAoSMC

tag: Sex

value: male

value: vascular smooth muscle cells

tag: sample group


title: A16


title: A15


title: A9


title: R17, HAoSMC cells, pH 7.4, sample group: 9


title: R14, HAoSMC cells, pH 6.8, sample group: 8


title: A8


title: R13, HAoSMC cells, pH 7.4, sample group: 8


title: Wild type-7h-Input-repeat1

value: Wild type (Dna2)


title: A6


title: Wild type-7h-ChIP-repeat2


title: A7


title: R10, HAoSMC cells, pH 6.8, sample group: 7


title: Wild type-7h-ChIP-repeat1


title: A5


title: R09, HAoSMC cells, pH 7.4, sample group: 7


title: A2


title: Wild type-4h-Input-repeat1


title: Wild type-4h-Input-repeat2


title: R06, HAoSMC cells, pH 6.8, sample group: 6


title: A3


title: Wild type-7h-Input-repeat2


title: Wild type-4h-ChIP-repeat1


title: Wild type-4h-ChIP-repeat2


title: R05, HAoSMC cells, pH 7.4, sample group: 6


title: MIN6 cells, V10

city: Dasman

first: Fahd

last: Almulla

address: Jasim Mohamad Al Bahar St

country: Kuwait

institute: Dasman Diabetes Institute

data_processing:
bcl2fastq v.2.20
Sequence reads were trimmed and verys hort reads removed using Trimmomatic (v0.39).
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 (v2.1.0)
Read count extraction using htseq-count tool in HTSeq (v 0.9.1)
Normalization and Differential gene expression analysis using Bioconductor package edgeR, adopting the default setting
Assembly: mm10
Supplementary files format and content: RawCounts.csv

organism: Mus musculus

growth_protocol: Min6 cells were cultured in DMEM media with 5.6 mM glucose supplemented with 15% heat-inactivated fetal bovine serum (FBS), 2 mM l-glutamine, 1 mM sodium pyruvate, 10 mM HEPES, 50 μg/mL penicillin, 100 μg/mL streptomycin, and 70 mM β-mercaptoethanol at 37.0 °C, with 5% CO2. for 24 hours

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 SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with Verapamil (50 μM) or left untreated for another 24 hours.

value: beta cell

value: WT

value: Verapamil

value: 24 hours


title: MIN6 cells, V11


title: MIN6 cells, V12


title: MIN6 cells, V8


title: MIN6 cells, V9


title: MIN6 cells, V7


title: MIN6 cells, V6


title: R01, HAoSMC cells, pH 7.4, sample group: 5


title: A4

value: Fecal


title: A1


title: A092, CCDSK cells, pH 6.4, sample group: 4

source_name: CCDSK

value: CCDSK

value: fibroblast


title: 271

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description:
10X genomics
rna_cell_metadata.txt

library_source: transcriptomic single cell

data_processing:
Single-cell gene expression was quantified from raw reads using CellRanger 3.0.2 (10X Genomics), using a reference built from Chlorocebus_sabaeus (ChlSab1), with gene sequences annotated based on the complete gene sequence (including exons and introns).
Assembly: ChlSab1.1
Supplementary files format and content: *matrix.mtx.gz: Tab-delimited text of sparse matrix file (matrix market format)
Supplementary files format and content: *features.tsv.gz: Tab-delimited text of gene IDs for matrix file
Supplementary files format and content: *barcodes.tsv.gz: Tab-delimited text of cell barcodes for matrix file
Supplementary files format and content: rna_cell_metadata.txt: tab-delimited text file of cells used in analysis, originating sample IDs, treatment groups, cluster assignments, and cell type labels. Note that sample IDs were prepended to cell barcodes.

molecule: polyA RNA

organism: Chlorocebus sabaeus

source_name: retina/choroid

extract_protocol: 30 mg pulverized retina/choroid tissue was resuspended in 500 µL of nuclei permeabilization buffer (0.1% Triton-X-100 (Sigma-Aldrich, T8787), 1X protease inhibitor, 1 mM DTT, and 0.2 U/µL RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS). Sample was incubated on a rotator for 5 min at 4°C and then centrifuged at 500 rcf for 5 min (4°C, run speed 3/3). Supernatant was removed and pellet was resuspended in 400 µL of sort buffer (1 mM EDTA 0.2 U/µL RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS) and stained with DRAQ7 (1:100; Cell Signaling, 7406). 75,000 nuclei were sorted using a SH800 sorter (Sony) into 50 µL of collection buffer consisting of 1 U/µL RNase inhibitor in 5% BSA; the FACS gating strategy sorted based on particle size and DRAQ7 fluorescence. Sorted nuclei were then centrifuged at 1000 rcf for 15 min (4°C, run speed 3/3) and supernatant was removed. Nuclei were resuspended in 35 µL of reaction buffer (0.2 U/µL RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS) and counted on a hemocytometer. 12,000 nuclei were loaded onto a Chromium Controller (10x Genomics). Libraries were generated using the Chromium Single-Cell 3′ Library Construction Kit v3 (10x Genomics, 1000075) with the Chromium Single-Cell B Chip Kit (10x Genomics, 1000153) and the Chromium i7 Multiplex Kit for sample indexing (10x Genomics, 120262) according to manufacturer specifications. CDNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter, B23319) was used for size selection and clean-up steps. Final library concentration was assessed by Qubit dsDNA HS Assay Kit (Thermo-Fischer Scientific) and fragment size was checked using Tapestation High Sensitivity D1000 (Agilent) to ensure that fragment sizes were distributed normally about 500 bp.

tag: sample id

tag: note

value: this is a second capture from the same biological sample as 240

value: retina/choroid

value: treated


title: MIN6 cells, V4


title: MIN6 cells, V5


title: MIN6 cells, V3


title: MIN6 cells, V1


title: MIN6 cells, V2


title: R02, HAoSMC cells, pH 6.8, sample group: 5


title: 240

description:
10X genomics
rna_cell_metadata.txt


title: 270

description:
10X genomics
rna_cell_metadata.txt

value: this is a second capture from the same biological sample as 239

value: control


title: 239

description:
10X genomics
rna_cell_metadata.txt


title: MIN6 cells, C12

value: Untreated


title: A090, CCDSK cells, pH 6.4, sample group: 4


title: A089, CCDSK cells, pH 7.4, sample group: 4


title: 211

description:
10X genomics
rna_cell_metadata.txt


title: MIN6 cells, C10


title: MIN6 cells, C9


title: A088, CCDSK cells, pH 7.4, sample group: 4


title: A087, CCDSK cells, pH 7.4, sample group: 4


title: 210

description:
10X genomics
rna_cell_metadata.txt


title: A091, CCDSK cells, pH 6.4, sample group: 4


title: MIN6 cells, C5


title: B174

description:
10X genomics
atac_cell_metadata.txt
merged_regions.bed
merged_annotation.txt

data_processing:
Peak calling analysis was performed separately for all reads in each single-cell capture. Raw reads were aligned to the reference genome for Chlorocebus sabaeus (ChlSab1) with BWA MEM (Li, 2013), and cell barcodes were added as tags in the BAM file. Apparent PCR duplicates were removed using Picard MarkDuplicates (Wysoker et al., 2019), performed with respect to cell barcode using the BARCODE TAG option, so that duplicate reads were only removed if they came from the same cell barcode. Read alignments were first adjusted to account for TAC transposon binding: +4bp for + strand alignments, -5bp for - strand alignments. Open chromatin peaks were called using Macs2 (Zhang et al., 2008) with nomodel set and no background provided (flags “--nomodel --nolambda"); peaks with a score >5 (-log10 q-value) were retained.
A union set of peak calls from all captures was obtained using bedtools merge (Quinlan and Hall, 2010), and formatted as a reference file for featureCounts. Read-based annotations were obtained for each read using featureCounts (Liao et al., 2014) with “-R CORE” to obtain read-based peak assignments. Peak counts for individual cells was obtained through the combination of the cell barcode and peak assignment for each read in the peak assignment output from featureCounts.
Assembly: ChlSab1.1
Supplementary files format and content: *matrix.mtx.gz: Tab-delimited text of sparse matrix file (matrix market format)
Supplementary files format and content: *features.tsv.gz: Tab-delimited text of peak IDs for matrix file
Supplementary files format and content: *barcodes.tsv.gz: Tab-delimited text of cell barcodes for matrix file
Supplementary files format and content: atac_cell_metadata.txt: tab-delimited text file of cells used in analysis, originating sample IDs,  treatment groups, and cluster assignments. Note that sample IDs were prepended to cell barcodes.
Supplementary files format and content: merged_regions.bed: BED formatted file of merged peak calls across all samples, used for peak quantification
Supplementary files format and content: merged_annotation.txt: proximal, gene body, and distal gene annotations for each peak

extract_protocol: Combinatorial barcoding single-nucleus ATAC-seq was provided by the Center for Epigenomics, UC San Diego and performed as previously describe (Hocker et al., 2021; Preissl et al., 2018; Wang et al., 2020). Two laser-induced CNV monkey eyes were sequenced from each vehicle and EBIN-treated NHPs. 135,837,688 raw reads with an average alignment percent of 98.5723 were obtained an average from each eye. After quality control and peak calling, an average of 129,433 peaks were obtained (Fig. S7C). Briefly, for each sample, retina/choroid tissues were homogenized using mortar and pestle on liquid nitrogen. 1 ml nuclei permeabilization buffer (10 mM Tris-HCL [pH 7.5], 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20 [Sigma], 0.1% IGEPAL-CA630 [Sigma] and 0.01% Digitonin [Promega] in water; Corces et al., 2017) was added to 30 mg of ground retina/choroid tissue and tissue was resuspended by pipetting for 8–15 times. Nuclei suspension was incubated for 10 min at 4°C and filtered with 30 μm filter (CellTrics). Nuclei were pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf), resuspended in 500 µL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2000 nuclei/9 µL, and 2000 nuclei were dispensed into each well of one 96-well plate. For tagmentation, 1 µL barcoded Tn5 transposomes [4] was added using a BenchSmart 96 (Mettler Toledo), mixed five times and incubated for 60 min at 37°C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 µL of 40 mM EDTA were added to each well with a BenchSmart 96 (Mettler Toledo) and the plate was incubated at 37°C for 15 min with shaking (500 rpm). Next, 20 µL 2 x sort buffer (2% BSA, 2 mM EDTA in PBS) was added using a BenchSmart 96 (Mettler Toledo). All wells were combined into a FACS tube and stained with 3 µM Draq7 (Cell Signaling). Using a SH800 (Sony), 20 2 n nuclei were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 µL EB (25 pmol) primer i7, 25 pmol primer i5, 200 ng BSA (Sigma). Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1 µL 0.2% SDS, samples were incubated at 55°C for 7 min with shaking (500 rpm). 1 µL 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5 µL NEBNext High-Fidelity 2 × PCR Master Mix (NEB) were added, and samples were PCR-amplified (72°C 5 min, 98°C 30 s, (98°C 10 s, 63°C 30 s, 72°C 60 s)×12 cycles, held at 12°C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRI Beads (Beckmann Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent).


title: MIN6 cells, C4


title: MIN6 cells, C3


title: A079, CCDSK cells, pH 6.4, sample group: 3


title: A080, CCDSK cells, pH 6.4, sample group: 3


title: MIN6 cells, C11


title: A744


title: INA6_4h_Ancistrocladinium_A_treatment_V

type: RNA

city: Wuerzburg

first: Daniela

last: Bruennert

state: Bavaria

address: Josef-Schneider-Str. 4

department: Gynecology

institute: University Hospital Wuerzburg

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: 5.5 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom D human arrays for 16 h at 45°C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console v4.1.3 software.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Summarized probe set signals in the log2 scale were calculated using the GCCN-SST-RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 software. After exporting into Microsoft Excel, average signal values, comparison fold changes, and significance P values were calculated. Probe sets with a fold change above 2.0-fold and a student’s t-test P value lower than 0.05 was considered significantly regulated. Splicing expression changes were calculated using TAC4.0 software (Affymetrix; Thermo Fisher Scientific, Inc, Santa Clara, CA, USA). Filter criteria for splicing expression changes were that genes expressed in both conditions were considered as true, the exon splicing index had to be ≥ 2 or ≤ 2, the exon P value < 5% and the exon had to be expressed under at least one condition.

label: biotin

source_name: multiple myeloma cell line

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. Subsequently, synthesized cRNA (15 µg) was purified and reverse transcribed into sense-strand (ss) cDNA, at which unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/ apyrimidinic en-donuclease 1 (APE 1), followed by terminal labeling with biotin.

growth_protocol: INA6 cells were grown in RPMI-1640 medium supplemented with 10% FBS, 1% P/S, 1% L-Glutamine and 2 nM IL-6. 1x10^6 cells were seeded in 3 ml per well of a 6-well-plate.

extract_protocol: RNA was isolated from 1x10^6 INA6 cells using the PEQgold RNA extraction kit (Peqlab, Erlangen, Germany) according to the manufacturers’ guidelines.

treatment_protocol: 1x10^6 INA6 cells were treated for 4 h with PBS as solvent control or 3 uM Ancistrocladinium A in a 6-well plate followed by harvesting and PBS-washing of the cells.

tag: agent

value: Ancistrocladinium

value: multiple myeloma cell line derived from pleura


title: A077, CCDSK cells, pH 7.4, sample group: 3

value: male


title: MIN6 cells, C2


title: MIN6 cells, C1


title: INA6_4h_Ancistrocladinium_A_treatment_IV


title: A076, CCDSK cells, pH 7.4, sample group: 3


title: HepG2 CYP2C19 cells, compound 6, day 1

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

institute: University Medical Center - Mainz

data_processing:
Quality control on the sequencing data was performed with the FastQC tool (0.12.0, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Transcript abundance estimates were computed with Salmon (version 1.5.0) with a transcriptome index generated from the GENCODE (version 38), and subsequently summarized to gene level with the tximeta R package (version 1.16.0).
The exploration, modelling, and interpretation of the expression data followed previously described protocols (Ludt et al., 2022).
Exploratory data analysis was executed with the pcaExplorer package (version 2.24.0).
Differential expression analysis was performed with DESeq2 package (version 1.38.3) [31], setting the false discovery rate (FDR) cutoff to 0.05. Accurate estimation of the effect sizes (described as log2FoldChange) was finalized using the apeglm shrinkage estimator (version 1.20.0).
Subsequent analyses included Gene Ontology pathway enrichment by topGO (version 2.50.0) - using all expressed genes as background dataset and the ideal package (version 1.22.0) and clusterProfiler (version 4.6.0) with default settings.
The enrichment results were the foundation for visualization and summarization with the GeneTonic package (version 2.2.0).
Gene expression profiles were plotted as heatmaps (color-coded standardized Z scores for the expression values, after variance stabilizing transformation) to simplify comparison across samples.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file include the expression values for all genes as a count matrix, used for the statistical modeling

source_name: liver

growth_protocol: Cells were grown in DMEM medium (DMEM, 31966021, Gibco™) at 37 °C and 5% CO2 in a humidified incubator. DMEM media were supplemented with 10% fetal bovine serum (FBS) and with 3 μg/mL blasticidin (ant-bl-05, InvivoGen)

extract_protocol:
RNA extraction was performed with the InviTrap® Spin Cell RNA Mini Kit (Invitek Molecular GmbH, Berlin, Germany), according to the manufacturer's instruction. The cell pellet was lysed with 350 μL Lysis Solution and treated with β-mercaptoethanol. After DNA removal, 350 μL 70% ethanol were added and the sample applied onto the RNA-RTA Spin Filter. After several washing steps, RNA was eluted with 60 μL of Elution Buffer R and the concentration and purity measured with NanoDrop.
Library preparation using the NEBNext© Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, MA, USA),

treatment_protocol: 24 h before treatment, 5×10^5 CYP2C19-overexpressing HepG2 cells were seeded into 6-well-plates. Cells were treated with the compounds of interest resulting in a final concentration of IC50 calculated beforehand

value: liver

value: cytochrome P450 2C19-overespressing HepG2

value: liver cell line

value: cyclohexil

value: day 1


title: HepG2 CYP2C19 cells, compound 5, day 2

value: tetrabut

value: day 2


title: INA6_4h_Ancistrocladinium_A_treatment_II


title: MIN6 cells, C6

value: beta cell

value: WT

value: 24 hours


title: HepG2 CYP2C19 cells, compound 5, day 1


title: MIN6 cells, C8


title: HepG2 CYP2C19 cells, compound 6, day 2


title: MIN6 cells, C7


title: HepG2 CYP2C19 cells, compound 4, day 1

value: metylcresol


title: HepG2 CYP2C19 cells, compound 4, day 2


title: INA6_4h_Ancistrocladinium_A_treatment_I


title: INA6_PBS_control_IV

value: PBS


title: HepG2 CYP2C19 cells, DMSO control, day 1

value: DMSO


title: A078, CCDSK cells, pH 6.4, sample group: 3

value: CCDSK

value: fibroblast


title: A074, HK2 cells, pH 6.4, sample group: 2

value: epithelial


title: INA6_PBS_control_II

value: multiple myeloma cell line derived from pleura

value: male


title: A073, HK2 cells, pH 6.4, sample group: 2


title: ge3_24h_test2_section_D

city: Bundoora

first: Mathew

middle: G

last: Lewsey

state: VIC

address: AgriBio, 5 Ring Rd

department: Animal, Plant and Soil Sciences

country: Australia

institute: La Trobe University

description: 10x Genomics

data_processing:
The demultiplexing were performed using bcltool (v2.20.0). Selection of spots and image alignment was performed in Loupe Browser (v. 6.2.0, 10x Genomics) to generate alignment files for each section. The sequencing data, bright field images and alignment files were used as input for the Space Ranger (v. 1.3.1, 10x Genomics) to generate gene-spot matrices. IBSCv2 barley genome assembly was used as the reference genome for Space Ranger. For each section, spots with a total UMI count less than 30 and less than 10 expressed genes were excluded from the following analysis.
Assembly: IBSCv2 barley genome assembly
Supplementary files format and content: SpaceRanger output files, including count matrix, web summary.

organism: Hordeum vulgare

source_name: germinating grain

growth_protocol: Barley grains (cv La Trobe) were surface sterilized using the chlorine-gas method in a fume hood, germinated on top of two layers of sterilized filter paper with 12 mL of sterile water added and wrapped with foil at 23°C. Seeds were harvested at 0, 1, 3, 6 and 24 HAI

extract_protocol:
Seeds were harvested at 0, 1, 3, 6 and 24 HAI. The seeds for the Visium experiment were collected at the indicated time-points and hand-dissected longitudinally. The seeds were immediately snap frozen in an isopentane bath (2-methylbutane, Sigma Aldrich, cat no. 270342-1L) for 1 min, subsequently embedded in Optimal Cutting Temperature (OCT, Tissue-Tek, cat no. 4583) and the blocks frozen in the isopentane bath and kept on dry-ice. The cryoblocks were cut on a cryostat (Leica Biosystems; MA, USA) to a thickness of 8 µm at -18°C. The sections were carefully place on a prechilled Tissue Optimization (TO) or Gene Expression (GE) slide and kept frozen at -80 °C until required. The slides were dried on a metal plate (PN-1000317, 10X Genomics) in the thermocycler at 37 °C for 1 min, fixed with chilled methanol at -20°C for 30 min, stained with 0.1% (wt/vol) Safranin O (Sigma-Aldrich, cat no. S8884-25G) in 50% (vol/vol) EtOH with 2U/μl RNase inhibitor at room temperature (RT) for 5 min and washed in increasing concentrations of EtOH until the discard liquid was clear. After drying at 37°C for 1 min, the slides were mounted in 85% (vol/vol) glycerol + 2U/μl RNase inhibitor, covered with a coverslip and images of sections were taken using Axio-Imager.M2 microscope (Zeiss). TO slides were fully recorded in one file meanwhile GE capture areas were imaged individually. Raw images were stitched together using Zen blue software v2.5 (Zeiss). Prior to imaging, the microscope settings were validated using the Visium Imaging Test Slide (PN-2000235). The slide contained the same 8 areas with fiducial frames that the TO slide. However, the test slide only contained 4 areas coated with fluorescent spots to set the boundaries of the capture areas, the focus, and the fluorescence conditions. The optimised settings were saved into the TO macro for following experiments. After imaging, the coverslip was removed immediately immersing the slide at 45° angle in 3x SSC buffer with the coverslip surface completely submerged and facing down. The coverslip slowly separated from the slide without damaging the samples nor the capture areas. The slide was immersed again in 3x SSC buffer to fully remove the mounting media and was let dry for a few seconds. To pre-permeabilize the tissue, the slides were mounted in a plastic cassette and sections incubated in pre-permeabilization solution (48 μl Exonuclease I buffer, NEB, cat no. B0293S; 4.5 µl of BSA, Sigma-Aldrich, cat no. A7039-100G; and 2% (w/v) PVP40, Sigma-Aldrich, cat no. PVP40-1KG) (PMID: 30353173) at 37°C for 30 min. This was followed with a wash with 0.1× SSC buffer (Sigma-Aldrich, cat no. S6639L). The sections were permeabilized with Permeabilization mix™ (10X Genomics) at 37°C for different times (1, 3, 6, 15, 30 min TO slides) or for 3 min (GE slides). Then, wells were washed with 0.1× SSC buffer. After permeabilization, Reverse transcription mixture™ (10X Genomics) was added to each section and incubated at 56°C for 45 min as described in the 10X Genomics User guide (PN-1000186, CG000239_VisiumSpatialGeneExpression_UserGuide_RevD).  To remove the tissue, a hydrolytic enzyme mixture was prepared by adding 70 µL of each enzyme; cellulase (Yakult -"ONOZUKA" R-10, cat no. YAKL0012), pectate lyase (Megazyme, cat no. E-PCLYAN2), xyloglucanase (Megazyme, cat no. E-XEGP), endo 1,4 β-xylanase (Megazyme, cat no. E-XYNACJ), endo 1,4 β-mannanase (Megazyme, cat no. E-BMACJ) and lichenase (Megazyme, cat no. E-LICHN) to 140 µl of 250 mM sodium citrate buffer (Sigma-Aldrich, cat. no. 71497-250 G), pH 6.6. The enzymatic mixture was added to the wells and incubated in a Thermo Mixer at 37 °C for 90 min with shaking (300 r.p.m.). The wells were washed with 0.1x SSC buffer.  Samples were incubated with 10% (v/v) Triton X-100 solution in a Thermo Mixer at 56 °C for 1 h with shaking (300 r.p.m.), followed by a wash with 0.1x SSC buffer. Next wash consisted in a mixture of RLT buffer (Qiagen ref.79216) with 1% β-mercaptoethanol, which was incubated in a Thermo Mixer at 56 °C for 1 h with shaking (300 r.p.m.) and followed by a wash with 0.1x SSC buffer. A final incubation with 70 µl proteinase K mixture (60 µl of proteinase K (Qiagen, cat no. 19131) and 420 µl of PKD buffer (Qiagen, cat no. 1034963) was performed in a Thermo Mixer at 56 °C for 1 h with shaking (300 r.p.m.).  Hybridization chamber was detached, and the slide washed in a petri dish with 50 °C pre-warmed wash buffer 1 (2× SSC/0.1% SDS) at 50 °C for 10 min with shaking (300 rpm). The slides were further washed with wash buffer 2 (0.2× SSC) and wash buffer 3 (0.1× SSC) at RT for 1 min with shaking (300 rpm). The slide was spin-dried in a swing-bucket centrifuge.
Following the Gene Expression workflow, libraries from the different capture areas were synthesized as described in 10X User guide (PN-1000190, CG000239_VisiumSpatialGeneExpression_UserGuide_RevD). Visium libraries were sequenced on an Illumina NextSeq 550 platform according to the 10X Genomics Visium manufacturer’s instructions (PN – XXXXXXXXXX, CG000239_VisiumSpatialGeneExpression_UserGuide_RevD), targeting 100 million reads using dual indexing kit TT set A (PN-1000215, 10X Genomics).
10x Genomics Visium gene expression

value: germinating grain

tag: age

value: 24 HAI


title: ge3_24h_test2_section_C

description: 10x Genomics


title: A072, HK2 cells, pH 6.4, sample group: 2


title: ge1_24h_test_section_D

description: 10x Genomics


title: INA6_PBS_control_V


title: A070, HK2 cells, pH 7.4, sample group: 2


title: A075, CCDSK cells, pH 7.4, sample group: 3


title: ge1_24h_test_section_B

description: 10x Genomics


title: ge1_24h_test_section_A

description: 10x Genomics


title: ge1_24h_test_section_C

description: 10x Genomics


title: ge10_24h_section_D

description: 10x Genomics


title: ge5_6h_section_D

description: 10x Genomics

value: 6 HAI


title: A062, HK2 cells, pH 6.4, sample group: 1


title: ge10_24h_section_A

description: 10x Genomics


title: A061, HK2 cells, pH 6.4, sample group: 1


title: ge5_6h_section_C

description: 10x Genomics


title: ge10_24h_section_B

description: 10x Genomics


title: Patient 18N

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Normal esophageal epithelia

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: Sections (100 μm) were prepared from FFPE samples and RNA samples were extracted using miRNesy mini kit (Qiagen).

value: Normal esophageal epithelia

value: 52 years

value: Male

tag: Stage

tag: relapus


title: ge5_6h_section_B

description: 10x Genomics


title: Patient 10N

value: 60 years

value: Female


title: A060, HK2 cells, pH 6.4, sample group: 1

tag: cell line


title: ge5_6h_section_A

description: 10x Genomics


title: A059, HK2 cells, pH 7.4, sample group: 1

tag: cell type


title: ge8_3h_section_D

description: 10x Genomics

value: 3 HAI


title: ge8_3h_section_C

description: 10x Genomics


title: A069, HK2 cells, pH 7.4, sample group: 2


title: ge8_3h_section_B

description: 10x Genomics


title: ge8_3h_section_A

description: 10x Genomics


title: ge10_24h_section_C

description: 10x Genomics


title: A058, HK2 cells, pH 7.4, sample group: 1


title: ge9_1h_section_D

description: 10x Genomics

value: 1 HAI


title: A057, HK2 cells, pH 7.4, sample group: 1


title: Patient 8N


title: Patient 7N

value: 64 years


title: Patient 6N

value: 54 years


title: ge9_1h_section_C

description: 10x Genomics


title: Patient 12N

value: 75 years


title: ge9_1h_section_B

description: 10x Genomics


title: LNCaP_NMyc_SP2509_48hr_3

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

description: LNCAP cell line 48h SP2509 rep 3

data_processing:
Sequencing was performed on Illumina HiSeq 2500 for MR42D and LASCPC-01 cell lines. For the rest, sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Paired-end alignments were obtained using STAR v2.5.2a as the aligner (Dobin et al. Bioinformatics. 2013.) using the following options (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMtype BAM Unsorted --outReadsUnmapped Fastx --outSAMstrandField intronMotif). Samtools (v 1.5) was used to sort and index the bam file. featureCounts function from the subread program (v1.6.1) was used to compute gene and isoform counts.
Differential expression was performed using DESeq2 v4.1.0 using ranked shrunkLFC (shrunk Log Fold Change) values
Assembly: hg38
Supplementary files format and content: The columns of the counts.txt files are: (1) refgeneGene; (2) entrez; (3) symbol; (4) gene  coordinates (5) sample read count

source_name: LNCAP

growth_protocol: LNcaP-NMyc cells were grown in RPMI with 10% FBS. MR42D cells were grown in RPMI with 10% FBS and 10µM Enzalutamide. LASCPC-01 cells were grown in modified HITES media as recommended by ATCC (CRL-3356).

extract_protocol:
After the indicated treatments, RNA was extracted from cells using the RNeasy Plus Mini Kit (Qiagen cat# 74034) according to the manufacturer’s protocol.
Libraries were prepared using the Illumina TruSeq stranded kit.

treatment_protocol: LASCPC-01 cells were treated with 300 nM SP2509 for 24 hours. LNCaP-NMyc and MR42D cells were treated with 600 nM SP2509 fro 48hours.

value: LNCAP


title: Patient 5N

value: 65 years


title: ge6_0h_section_C

description: 10x Genomics

value: 0 HAI


title: ge9_1h_section_A

description: 10x Genomics


title: ge6_0h_section_D

description: 10x Genomics


title: LNCaP_NMyc_SP2509_48hr_2

description: LNCAP cell line 48h SP2509 rep 2


title: ge6_0h_section_B

description: 10x Genomics


title: Patient 3N

value: 72 years


title: LNCaP_NMyc_SP2509_48hr_1

description: LNCAP cell line 48h SP2509 rep 1


title: Patient 4N


title: C27.Q.M

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

description:
R27
Quail_RNAseq.xlsx

data_processing:
Quality of sequenced CAGE reads was checked by using FastQC v0.11.5 and then trimmed with fastx_trimmer -Q33 -l 75 (FASTX Toolkit 0.0.14). Moirai removeN script was applied to remove reads with “N” nucleotides. CAGE reads matching to adapters or rRNA (Moirai defined rRNA for galGal3) were removed with Trimmomatic-0.38 and RNAdust 1.06, respectively.
Trimmed CAGE reads were aligned with BWA 0.7.10-r789 and unmapped reads realigned with Hisat2 v2.1.0
Alignments were processed into CTSS (CAGE transcription start sites) and CAGE peaks with PromoterPipeline (https://github.com/Population-Transcriptomics/C1-CAGE-preview) with default threshold of at least 10 TPM (tags per million) in one of the samples.
CAGE peaks were associated with nearby transcripts located on the same strand by using ChIPseeker v1.32.0 package for R.
Quality of sequenced RNAseq reads was checked by using FastQC v0.11.5 and then trimmed with Trimmomatic-0.38
Trimmed RNAseq reads were aligned to reference genome assemblies by using Hisat2 v2.1.0, counted with HTSeq v2.0.1, and normalized by library size and exon length in edgeR v3.42.2.
Assembly: galGal6 (GCF_000002315.6)
Assembly: Coturnix_japonica_2.1 (GCF_001577835.2)
Assembly: MGAL_WU_HG_1.0 (GCA_905368555.1)
Assembly: GT_SO_6221 (http://gigadb.org/dataset/100559)
Assembly: ZJU1.0 (GCF_015476345.1)
Assembly: bTaeGut2.pat.W.v2 (GCF_008822105.2)
Assembly: ZJU1.0 (GCA_016128335.1)
Supplementary files format and content: xlsx files with CAGE peaks coordinates, TSS position, associated genes, tag per million normalized counts
Supplementary files format and content: xlsx files with RNAseq raw and FPKM counts

organism: Coturnix japonica

source_name: embryonic fibroblasts P5

growth_protocol: Embryonic fibroblast cells were isolated from eggs incubated for ~10 days at 38.5 °C to reach stage HH36. Embryos were then treated by resection of head and neck, limb, skin and fat deposit, and internal developing organs. The remained trunk portion was trypsinized at 37°C, followed by neutralization and centrifugation to obtain digested cell pellet. Cell pellet was resuspended with DMEM/10%FBS and seeded in DMEM/10%FBS or DMEM/F12/10%FBS for expansion.

extract_protocol:
Total RNA was prepared using commercial reagents (TRIzol, Invitrogen) from each sample of avian embryonic fibroblast cells at the fifth passage (P5).
5ug of RNA from each fibroblast sample was used for nAnTi-CAGE and polyA RNAseq libraries preparation and subsequent sequencing using the Illumina HiSeq2500 platform (K. K. DNAForm, Yokohama, Japan)

value: embryonic fibroblasts P5

value: male

tag: medium

value: DMEM/F12/10percent FBS


title: HepG2 CYP2C19 cells, DMSO control, day 2

value: liver

value: cytochrome P450 2C19-overespressing HepG2

value: liver cell line

tag: treatment

value: DMSO

value: day 2


title: LNCaP_NMyc_DMSO_48hr_3

description: LNCAP cell line 48h DMSO rep 3


title: QEF 2020-03 High P5 [C30]

description:
C30
Quail_CAGE.xlsx

value: female

value: DMEM/10percent FBS


title: QEF 2020-03 F12 P5 [C29]

description:
C29
Quail_CAGE.xlsx


title: LNCaP_NMyc_DMSO_48hr_2

description: LNCAP cell line 48h DMSO rep 2


title: QEF 2020-02 High P5 [C28]

description:
C28
Quail_CAGE.xlsx


title: QEF 2020-02 F12 P5 [C27]

description:
C27
Quail_CAGE.xlsx


title: QEF 2020-01 High P5 [C26]

description:
C26
Quail_CAGE.xlsx


title: QEF 2020-01 F12 P5 [C25]

description:
C25
Quail_CAGE.xlsx


title: Patient 1N

value: Normal esophageal epithelia

value: Male


title: Patient 18T

source_name: Esophageal neuroendocrine carcinoma

value: Esophageal neuroendocrine carcinoma

value: 52 years

value: IIB

value: presence


title: VAT_Control_12

city: Ulm

first: Ulrich

last: Stifel

address: Helmholtzstrasse 8/1

department: CME

institute: Universität Ulm

data_processing:
Reads were mapped using hisat2.
Differential analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Excel files contain raw read count values per sample

source_name: visceral adipose tissue

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene

value: visceral adipose tissue

tag: disease

value: Healthy


title: Patient 2N

tag: tissue

value: 70 years


title: Patient 8T

value: 60 years

value: IIA

value: absence


title: Patient 12T

value: 75 years

value: IB


title: 8wks_del_skm_4

city: La Jolla

first: Pamela

last: Duran

address: 2880 Torrey Pines Scenic Dr

institute: University of California, San Diego

hyb_protocol: Using a two-step magnetic beads purification, probe excess was removed in PrepStation and target/probe complexes were bound on the cartridge.

scan_protocol: Nanostring nCounter Digital Analyzer processed digital barcode reads.

data_processing: Barcode reads were analyzed by nSolver Analysis Software 4.0 and differential expression analysis was done with a custom R script.

label: Capture ProbeSet

organism: Rattus norvegicus

source_name: Sprague Dawley, 8 weeks after delayed injection, skm

label_protocol: RNA concentration was measured using a Qubit 3.0 Fluorometer with a Qubit™ RNA HS Assay kit. The hybridization buffer (70 µl) was then mixed with the Custom Reporter CodeSet solution, and 8 µl of this master mix was then added separately to 50-100 ng of RNA per tissue sample, and RNA-free water up to 13 µl total. Then, 2 µl of Capture ProbeSet was added to the mixture, thoroughly mixed and placed on a thermocycler at 65°C for 16-48 hours and then maintained at 4°C for less than 24 hours.

extract_protocol: Pubocaudalis muscle was harvested, submerged in RNAlater and stored at -80C. Samples were then thawed and RNA was isolated with RNAeasy Fibrous Tissue Mini Kit.

treatment_protocol: Simulated birth injury, saline or SKM injection as specified

tag: strain

value: Sprague Dawley

value: pubocaudalis rat skeletal muscle

tag: condition

value: 8 weeks after delayed injection, skm


title: 8wks_del_skm_5


title: C25.Q.F

description:
R25
Quail_RNAseq.xlsx

value: embryonic fibroblasts P5

value: female

value: DMEM/F12/10percent FBS


title: VAT_Control_11


title: ge6_0h_section_A

description: 10x Genomics

value: germinating grain

value: 0 HAI


title: Patient 6T

value: Esophageal neuroendocrine carcinoma

value: 64 years

value: Female

value: IA


title: VAT_Control_3

value: visceral adipose tissue

value: Healthy


title: 8wks_del_skm_6


title: VAT_Control_9


title: VAT_Control_2


title: LNCaP_NMyc_DMSO_48hr_1

description: LNCAP cell line 48h DMSO rep 1

value: LNCAP

value: DMSO

tag: time point


title: 8wks_del_skm_3


title: Patient 7T

value: 54 years

tag: Sex

value: IIIC

value: presence


title: 8wks_del_skm_1

value: Sprague Dawley

value: pubocaudalis rat skeletal muscle

value: 8 weeks after delayed injection, skm


title: 8wks_del_skm_2


title: VAT_Cushing_15

value: Cushing


title: Patient 10T

value: 60 years

value: IIB

value: absence


title: 8wks_del_sa_5

source_name: Sprague Dawley, 8 weeks after delayed injection, saline

value: 8 weeks after delayed injection, saline


title: Patient 5T

value: Esophageal neuroendocrine carcinoma

value: 65 years

value: Male


title: 8wks_del_sa_4


title: 8wks_del_sa_3


title: 8wks_del_sa_1


title: Patient 4T

value: 64 years


title: VAT_Cushing_14

value: visceral adipose tissue


title: VAT_Cushing_13


title: Patient 3T

value: 72 years

value: Female


title: VAT_Cushing_11


title: 84_SBI_4

source_name: Sprague Dawley, 84 days after simulated birth injury

value: 84 days after simulated birth injury


title: 84_SBI_3


title: INA6_PBS_control_I

value: PBS

value: multiple myeloma cell line derived from pleura

value: male


title: 84_SBI_2

value: Sprague Dawley

value: pubocaudalis rat skeletal muscle


title: Patient 1T

value: 70 years

value: IA

value: presence


title: Patient 2T

value: 54 years


title: 84_SBI_1


title: VAT_Cushing_10

value: Cushing


title: 7_del_skm_9

source_name: Sprague Dawley, 7  days after delayed injection, skm

value: 7  days after delayed injection, skm


title: 8wks_del_sa_2

value: 8 weeks after delayed injection, saline


title: A549_Input1

city: WuHan

first: Dong

last: Yang

address: No.5  HangKong Road

institute: Huazhong University of Science and Technology

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimgalore version 0.36, and masked for low-complexity or low-quality sequence.
The clean reads were mapped to human genome (GRCh38) using STAR software (version 2.5.3a).
The MACS2 software (Version 2.1.1) was used for peak calling the following setting -p 1E-10 --nomodel --keep-dup all --SPMR --extsize 147 --broad --broad-cutoff 1E-10
bigWig files were generated using the deeptools 3.1.3 bamCoverage with the following setting -p 10 --normalizeUsing RPKM
Assembly: GRCh38
Supplementary files format and content: bigWig

growth_protocol: DMEM/HG, 8% fetal bovine serum. Cells were cultured at 37°C at 5% CO2

extract_protocol:
A549 cells were fixed with 1% formaldehyde and stopped by adding glycine. Pellets were homogenized and resuspended in lysis buffer, and crosslinked chromatin was sheared into 200-500 bp fragments with Bioruptor Sonication System UCD-300 . 200 ug DNA from each sample were resuspended in digestion buffer containing H1.2 antibody plus protein G magnetic beads for overnight. Immune complexes were collected, washed, and eluted. The DNA-protein crosslinks were then incubated overnight at 65 °C for extracting DNA for qPCR analysis or high through-put sequencing.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for MGI（Catalog NO. NDM607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: epithelial cell

tag: chip antibody


title: A549_Input2


title: A549_H1C2


title: 7_del_skm_8


title: VAT_Cushing_8

value: visceral adipose tissue


title: VAT_Cushing_9


title: A549_H1C1


title: 7_del_skm_7


title: 7_del_skm_6


title: 7_del_skm_5


title: VAT_Cushing_6


title: 84_SBI_6


title: 84_SBI_5


title: 7_del_skm_3


title: MDA-MB-231 cells, miR-217 mimics, rep 2

city: zhengzhou

first: chenxi

last: ju

address: zhengzhou university, 100 science road

institute: zhengzhou university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the reference genome of Homo sapiens from ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/ using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: hg38
Supplementary files format and content: RPKM values of all samples

growth_protocol: MDA-MB-231 were grown in DMEM medium with 10% fetal bovine serum under appropriate conditions (37°C, 5% CO2).

extract_protocol:
RNA was extrated using TRIzol (Invitrogen) from MDA-MB-231 after treated with miR-217 mimics and mimics negative control.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina®

value: breast cancer cell line

value: transfected miR-217 mimics


title: VAT_Cushing_5


title: 7_del_skm_2


title: 7_del_skm_1


title: MDA-MB-231 cells, miR-217 mimics, rep 1


title: 7_del_sa_10

source_name: Sprague Dawley, 7  days after delayed injection, saline

value: 7  days after delayed injection, saline


title: VAT_Cushing_4


title: 7_del_sa_9


title: VAT_Cushing_3


title: MDA-MB-231 cells, control, rep 2

value: transfected mimics negative control


title: VAT_Cushing_1


title: 7_del_skm_4


title: 7_del_sa_8


title: 7_del_sa_5


title: 7_del_sa_6


title: 7_del_sa_7


title: KO rep2 CD8+ T cells, 24 hr. stim.

city: Philadelphia

first: Paula

last: Oliver

state: PA

address: 816F ARC, 3615 Civic Center Blvd.

department: Department of Pathology, Perelman School of Medicine

institute: University of Pennsylvania

description: KO 2

data_processing:
Sequencing reads were quality checked using FASTQC.
Paired-end reads were pseudo-aligned to the GRCm38 (mm10) genome using Kallisto (V0.45.0) to give raw read counts.
Transcripts per million (TPM) were calculated from the raw read counts by obtaining gene lengths using MyGene in Python and calculating reads per kilobase (RPK) for each gene. The RPK values were summed per sample and divided by 1,000,000 to obtain each sample’s “per million” scaling factor; RPK divided by the scaling factor outputted TPM.
Assembly: GRCm38 / mm10
Supplementary files format and content: tab-delimited text files include log2TPM values for each sample

source_name: Spleen/Lymph node

growth_protocol: Naïve CD8 + T cells were isolated by magnetic separation using the Miltenyi Naïve CD8 + T cell isolation kit. Naïve CD8 + T cells were stimulated in vitro in complete RPMI (RPMI 1640 supplemented with 10% fetal bovine serum (Atlanta Biologicals), HEPES (Thermo Fisher Scientific), nonessential amino acids, sodium pyruvate (Thermo Fisher Scientific), 2mM-Glutamine, antibiotics and 2-mercaptoethanol) with plate bound anti-CD3 (Clone 17A2 Biolegend) and anti-CD28 (Clone 37.51 Biolegend) antibodies. The tissue culture plates were coated with the antibodies overnight at 4°C (5 μg/ml). Cells were cultured at 37°C with 10% CO 2 .

extract_protocol:
Total RNA was isolated using TRIzol reagent and poly-A selection was used to remove rRNA.
DNA library was quantified using Qubit and sequenced on a BGIseq500 platform.

treatment_protocol: Cells were stimulated for 24 hr with anti-CD3/CD28 mAbs

value: Spleen/Lymph node

value: CD8+ T cell

tag: genotype

value: Cul4b KO

value: 24 hr anti-CD3/28 mAbs


title: KO rep3 CD8+ T cells, 24 hr. stim.

description: KO 3


title: 7_del_sa_4

value: Sprague Dawley

value: pubocaudalis rat skeletal muscle


title: control41

city: Seoul

first: HyunKyung

last: Lee

address: 101, Daehak-ro

country: South Korea

institute: Seoul National University

data_processing:
Reads were mapped to the reference genome using Tophat (v2.0.13), and DEGs were derived from aligned results using Cuffdiff (v2.2.1).
A geometric method was applied to library normalization and a pooled method was applied to dispersion estimation.
Assembly: Human hg19
Supplementary files format and content: excel files include FPKM values for each sample

source_name: Blood

extract_protocol:
Mononuclear cells were isolated from peripheral blood using the Lymphocyte-separation medium (3 mL; MP Biomedicals, Solon, OH, USA). RNA was extracted from the mononuclear cells using the RiboPure RNA purification kit-blood (Thermo Fisher Scientific, Waltham, MA, USA).
mRNA-sequencing libraries were prepared using the Truseq stranded mRNA library prep kit (Illumina, San Diego, CA, USA) according to manufacturer instructions.

value: Blood

value: Peripheral Blood Mononuclear Cells


title: control40


title: 7_del_sa_1


title: 7_del_sa_2


title: KO rep1 CD8+ T cells, 24 hr. stim.

description: KO 1


title: WT rep3 CD8+ T cells, 24 hr. stim.

description: WT 3

value: WT


title: 7_del_sa_3


title: control39


title: 3_del_skm_9

source_name: Sprague Dawley, 3  days after delayed injection, skm

value: 3  days after delayed injection, skm


title: control38


title: 3_del_skm_7


title: 3_del_skm_8


title: MDA-MB-231 cells, control, rep 1


title: 3_del_skm_5


title: WT rep2 CD8+ T cells, 24 hr. stim.

description: WT 2


title: ifta41


title: control36


title: control37


title: WT rep1 CD8+ T cells, 24 hr. stim.

description: WT 1


title: control35


title: ifta40


title: pool 3 Squalene samples

city: Zaragoza

first: Roubi Hamid

middle: Ahmad

last: AbuObeid

state: Spain

address: calle de Miguel Servet, 177

country: Spain

institute: university of Zaragoza

data_processing:
low quality reads, reads with adaptors and reads with unknown bases are filtered to get the clean reads. Then clean reads are mapped onto reference genome, followed with novel gene prediction, SNP &INDEL calling and gene splicing detection. Finally, Differentially Expressed Genes between samples are identified
Assembly: (Ensembl Sus scrofa genome 11.1; www.ensembl.org)
Supplementary files format and content: Fragments Per Kilobase of transcript per Million (FPKM)  values for each Sample

organism: Sus scrofa

source_name: Liver

extract_protocol:
RNA was extracted from frozen livers   using  Quick-RNA MiniPrep kit (Cat.No:R1055, ZYMO Research, Irvine, CA, USA).
Quality control of total RNA sample is assessed by RNA concentration, RIN value,28S/18S and fragment length distribution using Bio analyzer (Agilent RNA 6000 Nano Kit). mRNA enrichment with poly A tail using oligo dT beads. RNA fragmentation and reverse transcription, the first-strand cDNA is generated using random N6-primed reverse transcription, followed by the second-strand cDNA synthesis. Synthesized cDNA is subjected to end-repair and then is 3’ adenylated. Adaptors are ligated to the ends of these 3’ adenylated cDNA fragments. Followed by several rounds of PCR amplification to enrich the purified cDNA template using PCR primer. Cyclization by denaturing PCR product then DNA is cyclized by splint oligo and DNA ligase. DNA nanoball synthesis and finally, Sequencing on DNBSEQ platform.

value: Liver

tag: breed

value: Large White x Landrace

value: steatosis diet squalene supplemented 0.5%

tag: time

value: Male


title: 3_del_sa_9

source_name: Sprague Dawley, 3  days after delayed injection, saline

value: 3  days after delayed injection, saline


title: pool1 Squalene samples


title: 3_del_skm_1


title: pool 4 Squalenesamples


title: 3_del_skm_3


title: pool 2 Squalene samples


title: 3_del_sa_7


title: 3_del_skm_2


title: 3_del_sa_3


title: 3_del_sa_5


title: 3_del_sa_6


title: 3_del_sa_4


title: 3_del_sa_2


title: pool 4 control samples

value: steatosis diet


title: ifta39


title: 3_del_skm_6


title: pool 3 control samples


title: 3_del_sa_1


title: 7_im_skm_8

source_name: Sprague Dawley, 7  days after immediate injection, skm

value: 7  days after immediate injection, skm


title: 7_im_skm_7


title: control34


title: 3_del_sa_8


title: 3_del_skm_4


title: control33


title: ifta38


title: 7_im_skm_5


title: pool1 control samples


title: 7_im_skm_6


title: ifta36


title: control32


title: 7_im_skm_4


title: ifta37


title: 121836R_Lung_ART

city: Québec

first: Jérôme

last: Estaquier

state: Québec

address: 2705 Boulevard Laurier

country: Canada

institute: Centre de Recherche du CHU de Québec-Université Laval

data_processing:
Reads were trimmed using fastp v0.20.0.
Quality check was performed on raw and trimmed data to ensure the quality of the reads using FastQC v0.11.8 and MultiQC v1.8.
The quantification was performed with Kallisto v0.46.2 against the Macaca mulata transcriptome (Mmul_10 downloaded from Ensemble release 103).
Assembly: Mmul_10
Supplementary files format and content: xlsx file includes TPM values for each sample

organism: Macaca mulatta

source_name: Lung

extract_protocol:
Total RNA were extracted from samples preserved in TRIzol, using the Qiagen RNeasy Micro kit with DNaseI treatment, following the manufacturer’s protocol.
The NEBNext Ultra II directional RNA library prep kit for Illumina (New England Biolabs Inc., Ipswich, MA, USA) was used to mRNA sequencing libraries, according to the manufacturer’s instructions

value: Lung

value: SIV-infected and ART-treated


title: R110562_Lung_ART


title: 7_im_skm_3


title: 7_im_skm_2


title: 131596R_Lung_SIVlow

value: SIV-infected (low viremic)


title: R110360_Lung_ART


title: ifta34


title: 7_im_sa_8

source_name: Sprague Dawley, 7  days after immediate injection, saline


title: 7_im_skm_1


title: ifta35


title: 7_im_sa_7

value: 7  days after immediate injection, saline


title: 7_im_sa_9

value: Sprague Dawley


title: 131054R_Lung_SIVlow


title: 7_im_sa_5

value: pubocaudalis rat skeletal muscle


title: 7_im_sa_6


title: pool 2 control samples


title: ifta33

value: Blood


title: 121688R_Lung_SIVlow


title: 7_im_sa_3


title: 7_im_sa_1


title: 7_im_sa_2


title: 7_im_sa_4


title: control31

value: Peripheral Blood Mononuclear Cells


title: control30


title: 122070R_Lung_SIVlow


title: PB044_Lung_SIVhigh

value: SIV-infected (high viremic)


title: 3_im_skm_7

source_name: Sprague Dawley, 3  days after immediate injection, skm

value: 3  days after immediate injection, skm


title: 3_im_skm_9


title: ifta32


title: control29


title: 3_im_skm_8


title: PB013_Lung_SIVhigh


title: 3_im_skm_6


title: PB028_Lung_SIVhigh


title: ifta31


title: control28


title: 3_im_skm_5


title: 3_im_skm_4


title: PB023_Lung_SIVhigh


title: 3_im_skm_3


title: 3_im_skm_1


title: 3_im_sa_9

source_name: Sprague Dawley, 3  days after immediate injection, saline


title: 3_im_skm_2


title: PB069_Lung_healthy

value: Healthy


title: 3_im_sa_7

value: 3  days after immediate injection, saline


title: PB061_Lung_healthy


title: 3_im_sa_6


title: control27


title: PB057_Lung_healthy


title: 3_im_sa_5


title: 3_im_sa_4


title: ifta29


title: 121836R_Liver_ART

value: Liver


title: control26


title: R110562_Liver_ART


title: ifta28


title: 3_im_sa_8


title: R110360_Liver_ART


title: 35_SBI_6

source_name: Sprague Dawley, 35 days after simulated birth injury

value: 35 days after simulated birth injury


title: 35_SBI_5


title: control25


title: 3_im_sa_1


title: 131596R_Liver_SIVlow


title: 131054R_Liver_SIVlow


title: control24


title: ifta30


title: 35_SBI_2


title: 35_SBI_4


title: 31_SBI_6

source_name: Sprague Dawley, 31 days after simulated birth injury

value: 31 days after simulated birth injury


title: 35_SBI_1


title: 35_SBI_3


title: 31_SBI_5


title: ifta27


title: 31_SBI_4


title: control23


title: 121688R_Liver_SIVlow


title: 3_im_sa_2


title: 3_im_sa_3


title: 31_SBI_3


title: 122070R_Liver_SIVlow


title: 31_SBI_2


title: 31_SBI_1


title: PB044_Liver_SIVhigh


title: PB013_Liver_SIVhigh


title: ifta25


title: ifta24


title: PB028_Liver_SIVhigh


title: ifta23


title: 10_SBI_2

source_name: Sprague Dawley, 10 days after simulated birth injury

value: 10 days after simulated birth injury


title: PB023_Liver_SIVhigh


title: 10_SBI_3


title: 10_SBI_1


title: ifta22


title: 7_SBI_7

source_name: Sprague Dawley, 7 days after simulated birth injury

value: 7 days after simulated birth injury


title: 7_SBI_6


title: PB069_Liver_healthy


title: 7_SBI_5


title: control22


title: 7_SBI_4


title: 7_SBI_3


title: 7_SBI_1


title: ifta21


title: ifta26


title: 3_SBI_9

source_name: Sprague Dawley, 3 days after simulated birth injury

value: 3 days after simulated birth injury


title: PB057_Liver_healthy


title: 3_SBI_7


title: 3_SBI_8


title: control21


title: 3_SBI_5


title: 7_SBI_8


title: ifta20


title: 7_SBI_2


title: 3_SBI_4


title: 3_SBI_3


title: ifta19


title: 3_SBI_2


title: 1_SBI_3

source_name: Sprague Dawley, 1 day after simulated birth injury

value: 1 day after simulated birth injury


title: cre_AA14_2

city: jinan

first: Jun-Yan

last: Wang

state: Select one...

address: No. 44, West Culture Road, Lixia District, Jinan City, Shandong Province

institute: shandong university

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: pituitary

extract_protocol:
The collected pituitary cells are quickly put into liquid nitrogen and stored at low temperature. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from pituitary cells according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA). Library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated, which were mapped to the mouse genome using hisat2 (v2.0.0) after quality control filtering.

value: pituitary

value: AA14 for one week


title: cre_AA14_1


title: cre_AA14_3


title: PB061_Liver_healthy


title: control19


title: 1_SBI_2

value: Sprague Dawley


title: 1_SBI_1

value: pubocaudalis rat skeletal muscle


title: cre_Vehicle_2

value: control vehicle for one week


title: ifta18

value: Blood

value: Peripheral Blood Mononuclear Cells


title: cre_Vehicle_1


title: B152

city: Chicago

source_name: retina/choroid

tag: sample id

value: retina/choroid

value: control


title: ifta17

source_name: Blood


title: B054

value: treated


title: uninjured_3

source_name: Sprague Dawley, uninjured

value: uninjured


title: uninjured_2


title: uninjured_1


title: 3_SBI_6


title: ctrl_AA14_3


title: control20


title: control18


title: cre_Vehicle_3


title: MhCT08 E_2

city: Bangalore

first: Nehanjali

last: Dwivedi

state: Karnataka

address: MSCTR, 8th floor A block

country: India

institute: MSCTR

data_processing:
Reads obtained form the sequencer were quality-checked and filtered using fastp and were aligned to genome using STAR pipeline. From the alignment map, counts for each gene were obtained using featureCounts.
Assembly: Genome Reference Consortium Human Build 38 (GRCh38)
Supplementary files format and content: csv files include gene-wise raw counts for each sample.

source_name: from tongue

growth_protocol: Patient-derived epithelial and fibroblast cells used in the study were maintained in RPMI- 1640 media with 20% Fetal Bovine Serum (FBS), 1X penicillin- streptomycin and sub cultured every 48 hours.

extract_protocol:
RNA was harvested using TRIzol method as per the manufacturer's instructions
Library for RNAseq was prepared using illumina TruSeq library preparation kit.

treatment_protocol: No treatment was given to the cells

tag: disease state

value: tongue squamous cell carcinoma

value: from tongue

value: MhCT08 E

value: Epithelial Cells

value: WT

value: No Treatment


title: MhCT08 E_1


title: control17


title: 3_SBI_1

value: 3 days after simulated birth injury


title: MhCT08 F_2

value: MhCT08 F

value: Fibroblast Cells


title: ctrl_AA14_2

value: pituitary

value: AA14 for one week


title: ctrl_AA14_1


title: MhCT12 E_1

value: MhCT12 E


title: ifta16

value: Blood

value: Peripheral Blood Mononuclear Cells


title: MhCT12 F_2

value: MhCT12 F


title: MhCT08 F_1


title: MhCT12 F_1


title: control16


title: ifta15


title: Library prepared from human serum cfDNA extracted with TACS-TOPO scheme

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

description: The serum used was purchased from Kohjin Bio Co., Ltd (Cat#12181201)

library_source: other

data_processing:
The paired-end reads were preprocessed with fastp to trimm low-quality data, fixed adaptor sequence, and merge the paired reads into a single read.
The proprocessed reads were mapped on human reference genome with bowtie2.
Mapped reads in BAM format were separated into four BAM files with insert size (short: 37-75 nt, long: 147-190 nt) and strand(forward and reverse strand of reference) with samtools.
Finally, the four bam files were converted to bedgraph files using bedtools genomecov.
Assembly: hg19
Supplementary files format and content: bedgraph

molecule: other

source_name: serum

extract_protocol:
To a 1.5 mL microcentrifuge tube (Eppendorf), 50 µL of human serum, 100 µL of 10 mM Tris-HCl, pH 8.0, 2.5 µL of 500 mM EDTA, 0.75 µL of 5 M NaCl, 5 µL of 10% (w/v) SDS, and 5 µL of 20 mg/ml proteinase K (Qiagen) were added and incubated at 50 °C for 1 h. After the protease digestion, extractions were performed twice with TE Saturated Phenol (Nippon Gene) and once with phenol-chloroform-isoamyl alcohol (25:24:1) (Nacalai Tesque). Then, the aqueous phase was transferred to a new tube, supplemented with 25 µL of 3 M sodium acetate, pH 5.4, and 550 µL of isopropanol. The mixture was centrifuged at 15,000 × g for 5 min, and the supernatant was discarded by decantation. Then, the DNA pellet was rinsed with 70% (v/v) ethanol and dissolved in 10 µL of 10 mM Tris-HCl, pH 8.0.
[TACS ligation] A solution containing the target ssDNA was mixed with 2.5 µL of 10x TACS buffer [500 mM HEPES-KOH, pH 7.5, 50 mM MgCl2, 5% (v/v) Triton X-100] and 1 µL of rSAP (New England Biolabs, Ipswich, MA); the total volume was then adjusted to 11 µL with ddH2O. The reaction mixture was incubated at 37 °C for 15 min and 95 °C for 5 min. Next, 10 µL of 50% (w/v) PEG6000, 1 µL each of 10 mM ATP, 25 µM adaptor ([PHO]AGA[U]CGGAAGAGCGT*C*G*T*G[NH2]), 1 µL of 15 U/μL TdT (Takara Bio Inc, Shiga Japan), and 1 µL of 2 mg/ml TS2126 RNA ligase were added. TS2126 RNA ligase was prepared as described previously (Hisano O. et al., 2021). Note that TS2126 RNA ligase can be substituted with CircLigase II ssDNA ligase from Lucigen (Middleton, WI). The reaction was incubated at 37 °C for 15 min, 65 °C for 30 min, and 95 °C for 5 min.   [Replication of adaptor-tagged ssDNA] The adaptor-tagged ssDNA solution was mixed with 14 µL of ddH2O, 5 µL of 10x ExTaq buffer (Takara Bio), 4 µL of 2.5 mM dNTPs, 1 µL of 50 µM replicating primer ([PHO]ACACTCTTTCCCTACACGACGCTCTTCCGATCTTT), and 1 µL of 5 unit/µL hot start GeneTaq (Nippon Gene) followed by incubation at 95 °C for 3 min, 45 °C for 5 min, 55 °C for 5 min, and 65°C for 5 min.  [VOC-mediated second adaptor tagging] After complementary strand synthesis, 5 µL of 500 mM EDTA (Nacalai Tesque, Kyoto, Japan) and 1 µL of 150 mg/ml VOC (TA type) were added to the reaction mixture and incubated at 25 °C for 15 min.   [Purification of the library] After the second adaptor tagging, the reaction mixture was supplemented with 35 µL of Buffer B2 (3 M guanidine hydrochloride, 20% Tween 20) and 5 µL of Proteinase K (Qiagen) and incubated at 50 °C for 15 min. Then, 2 µL of Sera-Mag Carboxylate Magnetic Beads (Cytiva, Marlborough, MA) and 100 µL of isopropanol were mixed. After incubation at room temperature for 5 min, the magnetic particles were collected on a magnetic stand, and the supernatant was removed. The beads were washed twice with 200 µL of a solution containing 32% (v/v) PEG400, 1 M NaCl, and 50 mM Tris-HCl, pH 8.0. Finally, the beads were rinsed with 70% (v/v) ethanol, and the purified DNA was eluted with 25 µL of 10 mM Tris-Acetate, pH 8.0.   [UDG and APE 1 treatment, nick filling, and PCR amplification] To the purified library, 5 µL of 10×ExTaq Buffer, 4 µL of 2.5 mM dNTPs, 1 µL of 20 µM Amplification Univ (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT), 1 µL of 20 µM Amplification Index-1 (CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC), 1 µL of UDG (New England Biolabs), and 1 µL of APE 1 (New England Biolabs) were added. After adjusting the reaction volume to 50 µL with water, the reaction was incubated at 37 °C for 15 min, 72 °C for 5 min, and 95 °C for 1 min, followed by two cycles of 3-step incubations at 95 °C for 15 s, 55 °C for 30 s, and 72 °C for 1 min. The reaction mixture was purified with 90 µL of AxyPrep Mag PCR clean according to the manufacturer's instructions. The purified DNA was eluted in 21 µL of 10 mM Tris-Acetate, pH 8.0.

value: serum


title: control15


title: eye disc,replicate2, scRNA

city: Houston

first: Komal Kumar

last: Bollepogu Raja

state: TX

address: One Baylor plaza

department: Pathology and Immunology

institute: baylor college of medicine

description:
10X Genomics
Larval_eye_scRNA.rds

data_processing:
scRNA-seq- The demultiplexing, barcode processing and initial QC was done using CellRanger aggr pipeline. Cell Ranger 6.01
snATAC-seq- The demultiplexing, barcode processing and initial QC was done using CellRanger ATAC count pipeline. Cell Ranger ATAC 2.01
Assembly: Dm6
Supplementary files format and content: scRNA-seq:Seurat object .rds file from R
Supplementary files format and content: snATAC-seq:Seurat object .rds file from R

organism: Drosophila melanogaster

source_name: eye disc

extract_protocol:
Eye discs from Drosophila late larvae were dissected in 1X PBS on ice and dissociated using collagenase and dispase for ~40min. The dissociated cells were washed once with 1X PBS with 0.05% BSA. The cell pellet was resuspended in 1xPBS+0.05% BSA and viability was asayed using Hoechst-PI
Library was prepaed as per the manufacture's instructions. Single Cell 3' Reagent Kit v3.1 from 10x Genomics. Drosohila larval eye single cells were resuspended on master mix and GEMs were generated by loading the cells with partioning oil and gel beads with primers. The poly-A RNA was captured on the beads and reverse transcribed to generate cDNA which contains Illumina R1 primer sequence,10X barcode and a unique molecular identifier. The cDNA was purified and amplified by PCR. Illumina R2 primer sequence, paired-end constructs with P5 and P7 and sample index were added during library construction. For snATACseq, single cells were first incubated with Tn5 transposase which fragments and introduces adapter sequences into chromatin. Single cell ATAC kit v2 was used to generate libraries.The transposed nuclei were then loaded into the 10x Chromium Controller along with barcoded Gel Beads and partitioning oil to generate GEMs. The Gel Beads were then dissolved and the barcoded DNA fragments pooled to generate libraries. We generated libraries from three independent biological replicates and sequenced them separately with a NovaSeq 6000

value: eye disc

value: Wild type


title: eye disc,replicate3, snATAC

description:
10X Genomics
Larval_eye_snATAC.rds

library_source: genomic single cell


title: eye disc,replicate1, snATAC

description:
10X Genomics
Larval_eye_snATAC.rds


title: eye disc,replicate2, snATAC

description:
10X Genomics
Larval_eye_snATAC.rds


title: ifta14


title: eye disc,replicate1, scRNA

description:
10X Genomics
Larval_eye_scRNA.rds


title: control14


title: CTPS-Ri, 48hour, larval fat body 3

city: Shanghai

first: Ji-Long

last: Liu

address: 230 Haike Road

institute: ShanghaiTech University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw data (raw reads) were processed using Trimmomatic.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count
FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress
DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest
Assembly: Release_6_plus_ISO1_MT
Supplementary files format and content: The excel files include FPKM values for each Sample

source_name: fat body

growth_protocol: second instar larvae were fed with the normal food.

extract_protocol:
total RNA was isolated from 50–100 2nd instar larvae of dissected fat bodies using TRIzol reagent (Invitrogen) according to the manufacturer’s recommendations.
The libraries were constructed using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: fat body

value: CTPS-Ri

value: CTPS knockdown


title: MhCT12 E_2

value: tongue squamous cell carcinoma

value: from tongue

value: Epithelial Cells

value: WT


title: myh6-transgenic heart, P90, biol rep 2

city: Changsha

first: Yongcheng

last: Pan

state: Hunan

address: 87 Xiangya Rd

institute: Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Hisat2 (v2.0.4) was used to map with reference genome (--dta -p 6 --max-intronlen 5000000); StringTie (v2.2.1) was applied to assemble the mapped reads (--merge -F 0.1 -T 0.1).
Quantification of gene expression levels was estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis was performed using the DESeq2.
Assembly: GRCm39/mm10
Supplementary files format and content: TXT files include FPKM values for each Sample
Supplementary files format and content: TXT files include CPM values for each Sample

source_name: heart

growth_protocol: The loxP-stop-loxP-NOTCH2NLC-(GGC)98 was inserted into the Rosa26 site to obtain the conditional transgenic NOTCH2NLC-(GGC)98 mice. The homozygous conditional transgenic mice were crossed with heterozygous E2a-Cre mice or homozygous Myh6-creERT2 mice to express NOTCH2NLC-(GGC)98 ubiquitously (E2a-tg) or specifically in cardiomyocytes (myh6-tg).

extract_protocol:
Total RNA was extracted from mice brain tissue using Trizol reagent (Invitrogen) according to the manufacturer's protocol.
An amount of 1 ug total RNA per sample was processed for library preparation using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations

treatment_protocol: The heart of postnatal 30 days (P30) E2a-tg and littermates control (without E2a-cre expression) were collected.  The P60 Myh6-tg mice were administered tamoxifen (20mg/ml, dissolved in corn oil) or corn oil via intraperitoneal injection (injection dose: 75mg/kg body weight) once every other day for a total of 3 injections. The heart tissues were collected at P90.

value: heart

value: injected with tamoxifen


title: CTPS-Ri, 48hour, larval fat body 2


title: myh6-transgenic heart, P90, biol rep 3


title: ctrl_Vehicle_3

value: pituitary

value: control vehicle for one week


title: myh6-transgenic heart, P90, biol rep 1


title: ctrl_Vehicle_2


title: CTPS-Ri, 48hour, larval fat body 1


title: ifta13

value: Blood


title: myh6-control heart, P90, biol rep 3

value: injected with corn oil


title: w1118, 48hour, larval fat body 2


title: w1118, 48hour, larval fat body 3


title: ifta12

value: Peripheral Blood Mononuclear Cells


title: control13


title: myh6-control heart, P90, biol rep 2


title: ctrl_Vehicle_1


title: w1118, 48hour, larval fat body 1


title: DLBCL5

city: West Lafayette

first: Nelly

last: Elshafie

state: Indiana

address: 625 Harrison St

institute: Purdue University

data_processing:
The small RNA sequences were mapped to the reference sequence using Bowtie 0.12.9 (35). For known miRNAs, miRBase20.0 and modified software miRDeep2_0_0_5 was used as a reference. Small RNA tags were mapped to RepeatMasker open-4.0.3 and Rfam (37) databases to remove tags originating from repetitive sequences, rRNA, tRNA, snRNA, and snoRNA. The software package miRDeep2 (36) and the characteristics of the hairpin structure of miRNA precursor were integrated to predict potential novel miRNAs.
Expression levels were assessed as transcripts per million (TPM)
Differential expression analysis of the two groups (DLBCL vs. healthy) is displayed (Supplementary Table 6) and was achieved using the DESeq2 v1.12.0 and R package (1.8.3)
The False Discovery Rate (FDR) rate was controlled by adjusting the P-values using the Benjamini & Hochberg (BH) method implemented in DESeq2. The adjusted P-values of <0.05 and the fold change of > 2 were used as the threshold for significantly differential expression. Predicting the target gene of miRNA was performed by miRanda3.3a
To graphically visualize the enrichment pathway, ShinyGO 0.75
Assembly: Canis_lupus_familiaris.CanFam3.1.dna

organism: Canis lupus familiaris

source_name: Fresh frozen lymphnodes

extract_protocol:
using the Monarch® Total RNA Miniprep Kit (NEB, Ipswich, MA, USA)
NEBNext® Multiplex Small RNA Library Prep Set (NEB, Ipswich, MA, USA) for Illumina®

value: Fresh frozen lymphnodes

value: Canine Diffuse Large B-Cell Lymphoma


title: DLBCL6


title: ifta11


title: DLBCL4


title: myh6-control heart, P90, biol rep 1


title: Dyskeratosis fibroblast, TERT expression, passage 10 TNF2_Tert_GACTAG

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to hg19 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
Assembly: hg19
Supplementary files format and content: read counts (.txt)

source_name: Primary skin fibroblasts

growth_protocol: DMEM, 10% FBS, Pen/Strep

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Primary skin fibroblasts

value: Primary fibroblast

value: Fibroblast

value: TERT overexpression


title: control12


title: E2a-transgenic heart, P30, biol rep 2


title: E2a-transgenic heart, P30, biol rep 3


title: DLBCL3


title: control11


title: DLBCL2


title: E2a-transgenic heart, P30, biol rep 1


title: Dyskeratosis fibroblast, shp53 expression, passage 10 TNF2_shp53_GCCAAG

value: shp53 Expression


title: DLBCL1


title: E2a-control heart, P30, biol rep 3


title: Healthy5

value: Healthy


title: E2a-control heart, P30, biol rep 2


title: Dyskeratosis fibroblast, shp53 expression, passage 13 TM2_shp53_GATGAA


title: ifta9


title: ifta10


title: ifta8


title: E2a-control heart, P30, biol rep 1


title: Dyskeratosis fibroblast, control treatment, passage 13 TM2_p13_ATTGGC

value: Control


title: Dyskeratosis fibroblast, shp53 expression, passage 10 DT_TCCGTC


title: Healthy4


title: Dyskeratosis fibroblast, TERT expression, passage 10 DKC_Tert_GAGTTA


title: young seurm infusion, chorolid plexus, 34

city: Pittsburgh

first: Iliya

last: Lefterov

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

description:
C440
YS-infusion-CP.xlsx

data_processing:
FASTQ TO BAM
FEATURECOUNTS
EDGER
Assembly: mm10
Supplementary files format and content: raw expresison counts from featurecounts

source_name: choroid plexus

growth_protocol: All animal experiments were performed in accordance with the NIH Guide for Care and Use of Animals and approved by the University of Pittsburgh Institutional Animal Care and Use Committee.

extract_protocol:
Mice were anesthetized by intraperitoneal injection using Avertin (250 mg/kg of body weight). Blood was collected from the right ventricle, followed by trans-cardiac perfusion through the left ventricle with 20 mL of cold 0.1 M phosphate buffered saline (PBS), pH 7.4. Brain was removed and divided into hemispheres. One hemisphere was dissected into the hippocampus and choroid plexus and flash frozen on dry ice for bulk RNA-seq.
RNA was isolated from cortex and purified using RNeasy mini kit (Qiagen) per the manufacturer’s protocol. RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies) and samples with RIN > 8 were further used for sequencing. Sequencing libraries were generated by Novogene.

treatment_protocol: Mice were anesthetized by isoflurane and blood was collected via cardiac puncture of the right ventricle with 25-gauge 5/8-inch 1 mL needle. Blood was incubated at room temperature for 60 min and centrifuged for 20 min at 16,000 g. The serum was aliquoted into 1.5 mL centrifuge tubes and stored at -20°C. For the young serum infusion, aged WT male mice received 100µL of young serum. Animals were injected every three days over a 25-day period.

value: choroid plexus

value: WT


title: Healthy2


title: young seurm infusion, chorolid plexus, 33

description:
C439
YS-infusion-CP.xlsx


title: Dyskeratosis fibroblast, control treatment, passage 10 TNF2_p10_CACTTC


title: young seurm infusion, chorolid plexus, 32

description:
C438
YS-infusion-CP.xlsx


title: Dyskeratosis fibroblast, control treatment, passage 10 DKC_p10_GAGCTG


title: control10


title: control9


title: Dyskeratosis fibroblast, TERT expression, passage 13 TM2_Tert_AGCAGG


title: young seurm infusion, chorolid plexus, 31

description:
C437
YS-infusion-CP.xlsx


title: ifta6


title: ifta7


title: control7


title: Liver_CCL4.siLuc_rep4

city: Moscow

first: Noreen

last: Halimani

address: Bol'shoy Bul'var, 30, стр 1

department: Faculty of Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

description:
CCl4+siLuc.4
_raw_counts.csv.gz

data_processing:
Raw reads were preprocessed as follows: trimmed with Trimmomatic (v0.39) to remove the adapters. The processed reads were aligned to the Mus musculus genome (assembly GRCm39.105) using the HISAT2 algorithm. Following analysis was performed in R version 3.4.2. Gene read counts were calculated using Rsubread package, function featureCounts (with parameters count MultiMap-pingReads = F, isPairedEnd = TRUE) Genes with less than 10 reads on average for per sample were filtered out. To check the data for self-consistency, the following analysis was carried out: correlation analysis and MDS using the Spearman correlation and PCA using normalised gene counts as CPM (count per million). DEGs were identified using DESeq2 R package in comparisons between samples. Gene ontology analysis of DEGs was performed using the ClusterProfiler package with all significant genes as background. Pathway enrichment analyses were done across Bioplanet 2019, GO Molecular function, MSigDB_Hellmark_2020 and KEGG_Pathways_2019 CHEA 2016 databases were used to annotate differences in molecular functions, biological processes, and signalling pathways between experimental groups with Enrich
Supplementary files format and content: _raw_counts.csv.gz : a tab delineated txt file containing raw counts for each sample

source_name: CCL4-induced fibrosis_total liver homogenate

extract_protocol:
PolyA mRNA was isolated from liver samples using Trizol(15596018, Thermo Fisher Scientific), following manufacturer's protocol
A measure of 1 μg RNA was reverse-transcribed to cDNA using the QuantiTect Reverse Transcription Kit (Qiagen, Hilden, Germany). Illumina cDNA libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, MA, USA) following the manufacturer’s protocol. cDNA libraries were sequenced using the NextSeq500 (Illumina, San Diego, CA USA) instrument. Sequencing was carried out with a read length of at least 85bp in the paired-end mode, with an average number of reads per sample not less than 30 million

value: Female

value: Balb/c

value: liver

value: CCL4-induced fibrosis

value: IP CCL4 injection plus siLuc tail vein injection


title: Control fibroblast, TERT expression, passage 14 AT_ACGCTC

value: Normal


title: control8

value: Blood

value: Peripheral Blood Mononuclear Cells


title: Liver_CCL4.siLuc_rep3

description:
CCl4+siLuc.3
_raw_counts.csv.gz


title: young seurm infusion, chorolid plexus, 30

description:
C436
YS-infusion-CP.xlsx


title: young seurm infusion, chorolid plexus, 29

description:
C435
YS-infusion-CP.xlsx


title: Healthy3

value: Fresh frozen lymphnodes


title: control6


title: Liver_siLuc_rep3

description:
siLuc.3
_raw_counts.csv.gz

source_name: Healthy_total liver homogenate

value: IP olive oil injection plus siLuc tail vein injection


title: Liver_CCL4.siLuc_rep1

description:
CCl4+siLuc.1
_raw_counts.csv.gz


title: young seurm infusion, chorolid plexus, 28

description:
C434
YS-infusion-CP.xlsx


title: Liver_siLuc_rep2

description:
siLuc.2
_raw_counts.csv.gz


title: young seurm infusion, chorolid plexus, 27

description:
C433
YS-infusion-CP.xlsx


title: control4


title: Dyskeratosis fibroblast, TERT expression, passage 10 DKC_shp53_AAACAT

value: Primary skin fibroblasts

value: Primary fibroblast

value: Fibroblast


title: Dyskeratosis fibroblast, control treatment, passage 10 D_CTCAAT


title: young seurm infusion, chorolid plexus, 26

description:
C432
YS-infusion-CP.xlsx


title: Liver_siLuc_rep1

description:
siLuc.1
_raw_counts.csv.gz

value: Healthy


title: Control fibroblast, control treatment, passage 14 ALDC_p14_ATGCCT

value: Control


title: Control fibroblast, shp53 expression, passage 14 ALDC_shp53_GAATCT

value: shp53 Expression


title: ifta5


title: Liver_CCL4.siHAS2_ rep4

description:
CCl4+siHAS2.4
_raw_counts.csv.gz

value: IP CCL4 injection plus siHAS2 tail vein injection


title: young seurm infusion, chorolid plexus, 25

description:
C431
YS-infusion-CP.xlsx

value: choroid plexus

value: WT


title: Control fibroblast, control treatment, passage 14 A_ATAGCG


title: Liver_CCL4.siLuc_rep2

description:
CCl4+siLuc.2
_raw_counts.csv.gz

value: Female

value: Balb/c

value: liver


title: young seurm infusion, chorolid plexus, 24

description:
C430
YS-infusion-CP.xlsx


title: control2


title: Liver_CCL4.siHAS2_ rep2

description:
CCl4+siHAS2.2
_raw_counts.csv.gz

value: CCL4-induced fibrosis


title: MR42D_170922_Veh_2

city: Ann Arbor

first: Karan

last: Bedi

address: 1600 Huron Pkwy

institute: University of Michigan

description: MR42D cell line 24h Vehicle rep 2

data_processing:
Sequencing was performed on Illumina HiSeq 2500 for MR42D and LASCPC-01 cell lines. For the rest, sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Paired-end alignments were obtained using STAR v2.5.2a as the aligner (Dobin et al. Bioinformatics. 2013.) using the following options (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMtype BAM Unsorted --outReadsUnmapped Fastx --outSAMstrandField intronMotif). Samtools (v 1.5) was used to sort and index the bam file. featureCounts function from the subread program (v1.6.1) was used to compute gene and isoform counts.
Differential expression was performed using DESeq2 v4.1.0 using ranked shrunkLFC (shrunk Log Fold Change) values
Assembly: hg38
Supplementary files format and content: The columns of the counts.txt files are: (1) refgeneGene; (2) entrez; (3) symbol; (4) gene  coordinates (5) sample read count

extract_protocol:
After the indicated treatments, RNA was extracted from cells using the RNeasy Plus Mini Kit (Qiagen cat# 74034) according to the manufacturer’s protocol.
Libraries were prepared using the Illumina TruSeq stranded kit.

tag: agent

value: Veh


title: Liver_CCL4.siHAS2_ rep1

description:
CCl4+siHAS2.1
_raw_counts.csv.gz


title: MR42D_170922_Veh_3

description: MR42D cell line 24h Vehicle rep 3

tag: cell line


title: control3

value: Blood

tag: cell type

value: Peripheral Blood Mononuclear Cells


title: Control fibroblast, TERT expression, passage 14 ALDC_Tert_AACGTG

value: Normal

value: TERT overexpression


title: Liver_CCL4.siHAS2_ rep3

description:
CCl4+siHAS2.3
_raw_counts.csv.gz


title: young seurm infusion, chorolid plexus, 23

description:
C429
YS-infusion-CP.xlsx


title: MR42D_170922_Veh_1

description: MR42D cell line 24h Vehicle rep 1


title: ifta4


title: Liver_siHAS2_rep3

description:
siHAS2.3
_raw_counts.csv.gz

value: IP olive oil injection plus siHAS2 tail vein injection


title: MR42D_170922_SP2509_3

description: MR42D cell line 24h SP2509 rep 3


title: control5


title: ifta3


title: ifta2


title: MR42D_170922_SP2509_2

description: MR42D cell line 24h SP2509 rep 2


title: ifta1


title: young seurm infusion, chorolid plexus, 20

description:
C426
YS-infusion-CP.xlsx


title: Liver_siHAS2_rep2

description:
siHAS2.2
_raw_counts.csv.gz


title: Liver_siHAS2_rep1

description:
siHAS2.1
_raw_counts.csv.gz


title: Liver_CCL4.4MU_rep4

description:
CCl4+4MU.4
_raw_counts.csv.gz

value: IP CCL4 injection plus 4MU gavage


title: young seurm infusion, chorolid plexus, 19

description:
C425
YS-infusion-CP.xlsx


title: LASPC_Veh_24h_3

description: LASCPC01 cell line 24h Vehicle rep 3


title: control1


title: Liver_CCL4.4MU_rep3

description:
CCl4+4MU.3
_raw_counts.csv.gz


title: LASPC_Veh_24h_2

description: LASCPC01 cell line 24h Vehicle rep 2


title: young seurm infusion, chorolid plexus, 22

description:
C428
YS-infusion-CP.xlsx


title: young seurm infusion, chorolid plexus, 18

description:
C424
YS-infusion-CP.xlsx


title: Liver_CCL4.4MU_rep2

description:
CCl4+4MU.2
_raw_counts.csv.gz


title: ccRCC_OpioidNaive_7

city: Rockville

first: Alexis

middle: L

last: Norris

state: MD

address: 7500 Standish Place

institute: US FDA

data_processing:
Base calling with bcl2fastq2 version 2.19.0
Sequencing reads were trimmed using trimmomatic (version 0.36.6; parameters: SLIDINGWINDOW:4:20 MINLEN:50)
Trimmed reads were aligned to GRCh38/hg38 using HISAT2 (version 2.1.0; parameters: --n-ceil L,0.0,0.15 --mp 6,2 --no-softclip --np 1 --rdg 5,3 --rfg 5,3 --sp 2,1 --score-min L,0.0,-0.2 --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000).
Gene counts were estimated using featureCounts (version 1.6.3; parameters: -s 1 -t 'exon' -g 'gene_id' -J -Q 12 --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0) with GENCODE gene annotation (GENCODE version 33; Ensembl version 99).
Assembly: hg38
Supplementary files format and content: tab-delimited text file include gene counts for each Sample

source_name: Advanced clear cell renal cell carcinoma - tumor FFPE

extract_protocol:
Total RNA was extracted using the RNeasy FFPE Kit from Qiagen according to the manufacturer instructions and assessed for quality using the Agilent Bioanalyzer Total RNA Nano Chip. Samples with DV200 > 20 were selected to proceed for the RNA-Seq.
100 ng of total RNA was used to generate the RNA-seq paired end library through the Illumina RNA Prep with Enrichment Kit. RNA was reverse-transcribed into cDNA, followed by fragmentation, probes hybridization, and individual indexing. The indexed cDNAs were enriched by exome probes and followed by 14 PCR cycles amplification. After obtaining the sequencing libraries, 0.6 nM of the pooled library was subjected to sequencing on an Illumina NovaSeq instrument with SP capacity. Following the instruction provided by the manufacturer, paired end 2x75 cycles sequencing was performed.

value: Opioid naive


title: ccRCC_OpioidNaive_6

value: Advanced clear cell renal cell carcinoma - tumor FFPE


title: young seurm infusion, chorolid plexus, 17

description:
C423
YS-infusion-CP.xlsx


title: LASPC_SP2509_24h_3

description: LASCPC01 cell line 24h SP2509 rep 3


title: ccRCC_OpioidNaive_5


title: young seurm infusion, chorolid plexus, 15

description:
C421
YS-infusion-CP.xlsx


title: young seurm infusion, chorolid plexus, 16

description:
C422
YS-infusion-CP.xlsx


title: ccRCC_ExtendedOpioid_5

value: Extended opioid exposure


title: LASPC_SP2509_24h_2

description: LASCPC01 cell line 24h SP2509 rep 2


title: Liver_CCL4.4MU_rep1

description:
CCl4+4MU.1
_raw_counts.csv.gz


title: Liver_CCL4only_rep2

description:
CCl4.2
_raw_counts.csv.gz

value: IP CCL4 injection


title: young seurm infusion, chorolid plexus, 14

description:
C419
YS-infusion-CP.xlsx

value: choroid plexus


title: LASPC_SP2509_24h_1

description: LASCPC01 cell line 24h SP2509 rep 1


title: ccRCC_OpioidNaive_4


title: Liver_4MU_rep3

description:
4MU.3
_raw_counts.csv.gz

value: Healthy

value: IP olive oil injection plus 4MU gavage

value: 4MU gavage everyday for a fortnight


title: ccRCC_ExtendedOpioid_4


title: Liver_CCL4only_rep1

description:
CCl4.1
_raw_counts.csv.gz

value: Female

value: Balb/c

value: liver


title: young seurm infusion, chorolid plexus, 21

description:
C427
YS-infusion-CP.xlsx

value: WT


title: MR42D_170922_SP2509_1

description: MR42D cell line 24h SP2509 rep 1