title: Foxm1 siRNA RPTEC rep 3

city: St. Louis

first: Monica

last: Chang-Panesso

state: MO

address: 600 S. Euclid Ave CB 8126

department: Medicine / Nephrology

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a maximum of one mismatch in the indexing read for sample demultiplexing. RNA-seq reads were then aligned to the mm10 (for mouse) or GRCh38 (for human) with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Raw counts and RPKM were output for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Processed file represents the raw read counts in a comma-separated text format

source_name: primary RPTEC

growth_protocol: Primary human proximal tubular cells were purchased from Lonza (CC-2553) and cultured with Renal epithelium cell growth medium bullet kit (CC-3190 Lonza). Cells were maintained in a humidified 5% CO2 atmosphere at 37°C. Experiments were carried out on early passage cells.

extract_protocol:
Total mRNA were isolated from human RPTECs using a RNA kit from Qiagen (RNeasy Mini prep kit, Cat# 74104). Total RNA integrity was determined using Agilent 4200 Tapestation.
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: hRPTECs were grown to 50-60% confluency at which point they were transfected with 10 nmol/L of target siRNA (Foxm1 #5248 ) or negative control siRNA (Silencer Select Thermofisher) using Lipofectamine RNAiMAX (Life Technologies) following the manufacturer’s protocol. Cells were harvested at day 2 post-transfection for RNA isolation.

value: primary RPTEC

value: Epithelial cell

value: Foxm1 siRNA

value: 2 days


title: FC12024294

status: Public on Jul 10 2024

type: SRA

city: Rochester

first: Dongmei

last: Li

state: NY

address: 265 Crittenden Boulevard Cu 420708

department: Clinical and Translational Research

country: USA

institute: University of Rochester

library_source: other

data_processing:
Norgen uses an Advanced Pipeline for the processing of raw counts and alignment to endogenous genome and annotated transcriptome. We perform initial steps for adapter trimming, QC, filtering and mapping to contaminants. Then, the pipeline maps reads to endogenous and exogenous genomes. The pipeline provides detailed mapping of miRNA, tRNA and piRNA.
Assembly: human endogenous and exogenous genomes
Supplementary files format and content: CSV file include raw counts for each miRNA in each sample

molecule: other

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Norgen’s RNA isolation and library preparation is based on their patented RNA binding matrix, silicon carbide, which allows us to capture miRNAs without phenol/chloroform and without any bias to GC content. Norgen’s Plasma/Serum Exosome Purification and RNA Isolation Mini Kit (Cat. 58300)
We follow a standard library preparation workflow for all samples (Figure 1). The workflow includes 3' and 5' adapter ligation, followed by reverse transcription and then the indexing PCR. The target band is then excised from the PAGE gel and purified.

tag: tissue

value: Plasma

tag: age

tag: treatment

value: W1 Non-user

tag: batch


title: P. cristatum, f/20, Day 16, rep5

city: Selinsgrove

first: Sophie

last: Charvet

state: PA

address: 514 University Avenue

institute: Susquehanna University

description: significanlty increased ingestion of fluorescently labeled bacteria (compared to negative control and to other treatments)

library_source: transcriptomic

data_processing:
quality check FastQC, Rcorrector, TrimGalore, followed by Kraken to identify and remove prokaryote reads
Assembly: rnaSPAdes - using 3 replicates from each experimental condition. Followed by BLASTn to remove prokaryote transcripts and re-assembly and CD-HIT-EST
Read mapping and counts were performed using Salmon
Assembly: PcrisNIES626_rnaSPAdes.fsa
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

organism: Pterosperma cristatum

growth_protocol: P. cristatum cultures (monoprotistan, non-axenic) were grown at 17-18°C, in a 12h day/night cycle under an irradiance of 80 µE m-2 s-1

extract_protocol:
cells were harvested by filtration on 0/8 µm, RNA was extracted using Trizol reagent and the PureLink RNA mini kit  (Invotrogen). 0.2-1.6 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared for polyA selection with a TruSeq library preparation

treatment_protocol:
f/2 medium was prepared according to Guillard (1975), without adding silicate
f/20 medium was obtained with a 10x dilution of f/2 in artificial seawater.

tag: strain

value: aged culture in f/20 medium, nutrient depleted (ND)

tag: time

tag: format


title: FC12334418


title: P. cristatum, f/20, Day 16, rep4


title: Foxm1 siRNA RPTEC rep 2

molecule: total RNA

tag: cell line

tag: cell type


title: VAL_be_rep6

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned with the Cutadapt package (v3.4)  for trimming adaptors and low-quality bases with a quality phred-like score <20. Reads <75 pbs were excluded from RNA-seq analysis.
The Citrus clementia (v1.0_182) and Poncirus trifoliata (v1.3.1_565) genomes from JGI (Joint Genome Institute, Berkeley, CA) were used as reference sequences for RNA-seq analysis.  The cleaned reads of each sample were mapped independently to the individual reference genome.
The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2), samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates, choose and count uniquely mapped reads for gene expression analysis. PCA analysis (for detecting outlier samples) based on all identified genes in each analysis were performed with the R-package v4.1.3. The counted reads of each gene were analyzed by an in-house DESeq2-based R pipeline. The adjusted p-value was used to detect the false positive rate in each comparison. Significant up- and downregulated genes were selected using the p-value, log2 Fold Change (log2 FC), and the adjusted p-value (pAdj) for downstream analysis.
Assembly: Citrus clementina
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

organism: Citrus reticulata x Citrus trifoliata

source_name: stem vascular

growth_protocol: Seeds from both rootstocks were sown into 1.5" x 8.25” (3.8 cm x 21 cm) Ray Leach cone-tainers (Stuewe & Sons, Tangent, OR) containing Fafard 4P potting medium (Fafard, Agawam, MA) and transplanted into 5” x 9.5” (12.7 cm x 24.1 cm) tree pots (Stuewe & Sons) containing the same potting medium after 9 months.

extract_protocol:
The tissue was ground in liquid nitrogen using mortar and pestle and stored at -80 °C until use. Approximately 100 mg of ground tissue were used to extract RNA using the Qiagen RNeasy plant mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA quality and concentration were measured using the QUBIT RNA fluorometry method (Invitrogen, Waltham, MA) and an Agilent Bioanalyzer (Agilent, Santa Clara, CA).
An amount of 250 ng of high-quality total RNA with an RNA integrity number (RIN) of 7 or higher was used for the library construction using the reagents provided in the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA) and the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer's instructions. Briefly, 100 ng of total RNA were used for mRNA isolation using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The poly A enriched RNA was fragmented in NEBNext First Strand Synthesis Buffer. Synthesis of double stranded cDNA was done using the 2nd strand master mix provided in the kit, followed by end-repair and dA-tailing.  At this point, Illumina adaptors were ligated to the sample.  Finally, the library was amplified, and followed by purification with AMPure beads. Thirty-nine barcoded libraries were pooled equimolarly for sequencing simultaneously for 0.52 lanes of NavaSeq 6000 S4 2x150 cycles

treatment_protocol: Rootstock liners were grafted by the inverted T-bud method (Albrecht et al., 2021) with certified, disease-free budwood of ‘Valencia’ sweet orange (C. sinensis), and ‘Bearss’ lemon (C. limon). Buds were grafted 10 cm above the soil level.  Buds were unwrapped after 2-3 weeks when the unions had healed and produced callus. At this point, rootstocks liners were broken above the graft union and bent to force shoot growth. Rootstocks were cut off when scions had grown by at least 10 cm. Plants were grown in an enclosed temperature-controlled (13-33°C) greenhouse under natural light at the University of Florida, IFAS Southwest Florida Research and Education Center, Immokalee, FL

value: stem vascular


title: VAL_ab_rep6


title: P. cristatum, f/20, Day 11, rep4

description: low ingestion of fluorescently labeled bacteria (but not significant for negative control)

value: f/20 medium, nutrient reduced (NR)

value: Day 11


title: FC13124883


title: Foxm1 siRNA RPTEC rep 1


title: BL_be_rep6


title: Negative control  siRNA RPTEC rep3

value: Scrambled siRNA


title: FC14966956


title: Negative control  siRNA RPTEC rep2


title: FC13081493


title: P. cristatum, f/20, Day 11, rep2


title: BL_ab_rep6


title: P. cristatum, f/20, Day 11, rep1


title: BL_be_rep5


title: FC14275623

value: W1 Exclusive e-cig user


title: FC12753362


title: P. cristatum, f/20, Day 11, rep5


title: P. cristatum, f/2, Day 11, rep 5

description: no significant ingestion of fluorescently labeled bacteria

value: f/2 medium, nutrient replete (RR)


title: Negative control  siRNA RPTEC rep1


title: BL_ab_rep5


title: cut-and-run_IgG_rep2

library_source: genomic

data_processing:
Cut-and-run: Fastq files were trimmed with Trim Galore and aligned with Bowtie2 (parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700) using hg38. Peak calling was performed on each sample separately using MACS2 with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig format
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: primary hRPTEC

extract_protocol:
CUT&RUN assay libraries for primary renal proximal tubular epithelial cells  were generated with the CUTANA kit (EpiCypher, 14-1048). 500,000 cells were mixed and incubated with Concanavalin A (ConA) conjugated paramagnetic beads. Antibody to FOXM1 was added to target samples and IgG was added to negative controls. The remaining steps were performed according to manufacturer’s instructions.
Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645S) with manufacturer’s instructions, including minor modifications indicated by CUTANA described above.
cut-and-run with CUTANA kit (EpiCypher, 14-1048)

treatment_protocol: The primary RPTEC with early passages were seeded at 1 × 10^6 cells per 10 cm culture dish 24 h prior to the assay.

value: primary hRPTEC

value: Epithelial cells

tag: antibody

value: IgG (Epicypher, 13-0042)


title: FC12765152


title: VAL_be_rep5


title: cut-and-run_IgG_rep1


title: P. cristatum, f/2, Day 11, rep 4


title: P. cristatum, f/2, Day 11, rep 3


title: FC13291296


title: cut-and-run_FOXM1_rep2


title: P. cristatum, f/20, Day 11, rep3


title: VAL_be_rep4


title: VAL_ab_rep5


title: P. cristatum, f/2, Day 11, rep 2


title: FC13288350


title: cut-and-run_FOXM1_rep1


title: P. cristatum, f/2, Day 11, rep 1


title: FC14999672


title: HONE1 cells, input

city: Guangzhou

first: Yanping

last: Mao

state: Guangdong

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
The obtained ChIP-DNA and input DNA fragments were firstly end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (#E7442, NEB, USA) and then ligated adaptor using the NEBNext Ultra Ligation Module (#E7445, NEB). The DNA libraries were amplified for 15 cycles for obtaining more material and then subjected to high-throughput sequencing using Illumina NextSeq 500.
The sequencing adapters, short reads (length < 35 bp), and low-quality reads were removed to obtain high-quality clean reads, which were confirmed using FastQC.
The reads were aligned to a human genome (assembly GRCh38) using Bowtie2 software (v2.2.6). Peak detection was carried out using MACS (v2.1.1) and 0.01 was set as the cut-off value.
Annotation of peak sites to gene features was performed using the ChIPseeker R package
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: HONE1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum, and cultured at at 37 °C with 5% CO2

extract_protocol:
ChIP assay was performed using a pierceTM Magnetic ChIP Kit (#26157, ThermoFisher) according to its protocol. Briefly,  cells were crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine at room temperature. Then, the cell nuclei were isolated, lysed, and sonicated to yield 200-1000 bp chromatin fragments. The chromatin fragments were immunoprecipitated with 3 ul anti-HA antibody (#ab9110, Abcam) or anti-rabbit IgG antibody (#26157, ThermoFisher) overnight at 4 °C and then immobilized on protein A/G magnetic beads for 2 h at 4 °C. After washing, the enriched DNA was eluted, de-crosslinked, purified, and then subjected to ChIP-seq or qPCR analyses.
The obtained ChIP-DNA and input DNA fragmentsby ChIP assay were firstly end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (#E7442, NEB, USA) and then ligated adaptor using the NEBNext Ultra Ligation Module (#E7445, NEB). The DNA libraries were amplified for 15 cycles for obtaining more material

treatment_protocol: HONE1 cells were transiently transfected with ARNTL2 overexpression plasmids using NeofectTM DNA transfection reagent (#TF20121201, Neofect, China), and harvested after 36h

value: Nasopharyngeal carcinoma cell line

tag: chip antibody


title: FC12183568


title: BL_be_rep4


title: HONE1 cells, ARNTL2-HA, ChIP

value: anti-HA antibody (#ab9110, Abcam)


title: FC12351102


title: BL_ab_rep4


title: HONE1 cells, siCon rep3

data_processing:
Paired-end sequence files (fastq) were mapped onto a human reference genome (assembly GRCh38) using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Fragments per kilobase of exon million mapped reads (FPKM) were calculated to evaluate gene abundance. Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM value for each sample

growth_protocol: HONE1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA  from HONE1 cells transfected with siARNTL2 or control siRNA was extracted using TRIzol reagent kit (#15596018, Invitrogen) according to the manufacturer's instructions.
RNA sequencing libraries were constructed using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB). The sequencing was carried out on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: HONE1 cells were transfected with siARNTL2 or control siRNA using Lipofectamine 3000 reagent (#L3000015, Invitrogen). The cells were harvested after transfection at 36 h for assays.

tag: genotype

value: WT


title: VAL_be_rep1


title: FC15004682


title: VAL_ab_rep1


title: HONE1 cells, siCon rep1


title: BL_be_rep3


title: HONE1 cells, siARNTL2 rep3

value: ARNTL2 knockdown


title: VAL_ab_rep4


title: BL_ab_rep3


title: VAL_be_rep3


title: HONE1 cells, siARNTL2 rep2


title: FC12717255


title: VAL_ab_rep3


title: FC13290546


title: HONE1 cells, siARNTL2 rep1


title: HONE1 cells, siCon rep2


title: Saureus_control_Rep4

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

country: Germany

institute: Bielefeld University

data_processing:
mapping: bowtie2 2.4.1, default parameters
read trimming: trimmomatic 0.36, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:39
differential gene expression analysis: R 3.6.3 and DESeq2 1.26, default parameters
Assembly: ASM1467273v1, ASM1346v1
Supplementary files format and content: Table S2 RNAseq Ab in USA300 CFCM.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: Table S3 Main RNAseq pathways Ab.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: Table S4 RNAseq Sa in A118 CFCM.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: Table S5 Main RNAseq pathways Sa.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: ReadCounts_AbA118_in_CFCM_and_TSB.ods
Supplementary files format and content: ReadCounts_SaUSA_in_CFCM_and_TSB.ods

organism: Staphylococcus aureus subsp. aureus USA300

source_name: bacteria

extract_protocol:
peqGOLD Total RNA Kit, VWR Peqlab, Darmstadt, Germany
llumina® Stranded Total RNA Prep Kit

value: bacteria

value: TSB medium


title: NNI-42, SB202190-treated

city: Singapore

first: Hong Sheng

last: Cheng

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine,

country: Singapore

institute: Nanyang Technological University

data_processing:
The paired-end reads were aligned to the human reference genome (Homo sapiens GRCh38) using HISAT2 (v2.2.1)
Gene counts were quantified with featureCounts from the Subread package (v2.0.3)
Assembly: GRCh38
Supplementary files format and content: Raw gene counts of each sample in .csv format

growth_protocol: Mesenchymal glioma-propagating cells were cultured as neurosphere suspensions in serum-free growth medium supplemented with growth factors.

extract_protocol:
Total RNA was extracted using Pure-NA Fastspin Total RNA Extraction kit (Research Instruments, Singapore). The integrity and purity of the total RNA was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies), agarose gel electrophoresis and nanodrop.
mRNA was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. The library concentration was checked using Qubit 2.0 and qPCR while the insert size was examined with Agilent 2100 bioanalyzer.

treatment_protocol: 1*10^6 cells were seeded in a 10 cm dish overnight. The cells were treated the next day with either DMSO or 100 nM SB202190 daily for 72 h. At the end of the treatment, the cells from different treatment groups were collected for total RNA extraction.

tag: individual

value: patient NNI-42

tag: disease state

value: Glioblastoma neurospheres


title: FC13234748

value: Plasma

value: W1 Non-user


title: FC13221362


title: BL_be_rep2

value: stem vascular


title: NNI-42, DMSO-treated

value: DMSO


title: FC14990206


title: BL_ab_rep2


title: Saureus_control_Rep3


title: NNI-40, SB202190-treated

value: patient NNI-40


title: Saureus_control_Rep2


title: VAL_be_rep2


title: FC12735626


title: NNI-40, DMSO-treated


title: NNI-25, SB202190-treated

value: patient NNI-25


title: Control prostatic urethral tissue 4

type: RNA

city: GuiYang

first: XiaoHu

last: Tang

address: No. 83 Zhongshan East Road

institute: Guizhou Provincial People's Hospital

description:
Biological replicate 4 of 4.Control prostatic urethral tissue, untreated, harvested after 5 days after sham surgery.
sham4

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rat ceRNA Microarray 2019（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Rattus norvegicus

source_name: Prostatic urethral tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: SD rats were reared under standard laboratory conditions (12/12 hour light/dark cycle, 22±2°C with a relative humidity of 55±5%) and allowed to consume standard laboratory food pellets and water ad libitum.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: SD rats underwent simulating transurethral laser prostatectomy

tag: gender

value: male

value: SD rat

value: Urethral tissue

value: control


title: Saureus_Abaumannii_CFCM_Rep4

value: Abaumannii CFCM Medium


title: Prostatic urethral trauma tissue 4

description:
Biological replicate 4 of 4.Prostatic urethral trauma tissue, treated, harvested after 5 days after sham surgery.
TULP4

source_name: Prostatic urethral trauma tissue

value: Prostatic urethral trauma


title: NNI-25, DMSO-treated


title: Saureus_Abaumannii_CFCM_Rep3


title: Prostatic urethral trauma tissue 3

description:
Biological replicate 3 of 4.Prostatic urethral trauma tissue, treated, harvested after 5 days after sham surgery.
TULP3


title: Prostatic urethral trauma tissue 1

description:
Biological replicate 1 of 4.Prostatic urethral trauma tissue, treated, harvested after 5 days after sham surgery.
TULP1


title: BL_ab_rep1


title: FC12347256


title: BL_be_rep1


title: Control prostatic urethral tissue 3

description:
Biological replicate 3 of 4.Control prostatic urethral tissue, untreated, harvested after 5 days after sham surgery.
sham3


title: NNI-10, SB202190-treated

value: patient NNI-10


title: Control prostatic urethral tissue 2

description:
Biological replicate 2 of 4.Control prostatic urethral tissue, untreated, harvested after 5 days after sham surgery.
sham2


title: Saureus_Abaumannii_CFCM_Rep2

value: bacteria


title: Control prostatic urethral tissue 1

description:
Biological replicate 1 of 4.Control prostatic urethral tissue, untreated, harvested after 5 days after sham surgery.
sham1


title: Differentiated (day 61) - long reads -  rep 2

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: Quebec

address: 740 Dr. Penfield Avenue

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
The IsoSeq pipeline (Pacific Biosciences) was used to process the neuronal differentiation LR data and generate circular consensus sequence (CCS) reads, which were stored in uBAM (unaligned BAM) format.
Next, lima (PacBio) was used to remove primer sequences. IsoSeq3 ‘refine’ command was used to remove poly-A tails and concatemers (reads which are attached end-to-end), followed by the ‘cluster’ command to cluster reads that represent the same transcript (i.e. make them adjacent).
The ‘align’ command of pbmm2 (PacBio) was then used to align reads to the reference genome, followed by the Isoseq3 ‘collapse’ command to condense the data into a transcriptome (fasta + GFF) and provide an abundance file containing full length counts (FL counts).
The quality control script from SQANTI3 (sqanti3_qc.py) was used together with supporting data types (CAGE peak, polyA motif list, polyA peaks file, and Intropolis splice junctions), removing low-quality transcripts according to SQANTI’s quality criteria.
Next, the rules filter script (sqanti3_RulesFilter.py) was run to further filter transcripts based on the following criteria: if a transcript is a full splice match (FSM), then it is kept unless the 3' end is unreliable (intrapriming); if a transcript is not a FSM, then it is kept only if all of below are true: (a) 3' end is reliable; (b) the transcript does not have a junction that is labeled as RT Switching; and (c) all junctions are canonical.
Finally, the full-length (FL) LR counts from SQANTI3 output that had the same “associated_transcript” were combined, providing transcript counts.
Assembly: GRCh38.p13
Supplementary files format and content: count matrices, csv files

source_name: neurons

growth_protocol: The hESC line was maintained in feeder-free conditions with the E8 medium. Neural differentiation was initiated when the cells reached 90-100% confluency. From days 0-11, the cells were maintained in neural induction medium (10 µM SB431542 and 100 nM LDN193189 in E6 medium) with medium change every two days. From day 12, the cells were fed the cortical neuron medium (10 ng/mL GDNF, 100 µM ascorbic acid, 1x Glutagro, 1x N2 supplement, 1x B27 without vitamin A in neurobasal medium) with medium change every other day until rosette structures became visible. Then, neurons were detached using Accutase and replated on poly-L-ornithin/fibronection/laminin-coated plates. Neurons were maintained in cortical neuron medium with medium change every other day. On days 22-24, neurons were checked for the presence of axonal projections and 10 µM DAPT was included in the cortical neuron medium until the projections appeared. From day 30, neurons were considered mature with the medium feeding frequency reduced to 1-2 times per week

extract_protocol:
RNA extraction using Zymo Quick-RNA Microprep kit according to the manufacturer’s protocol. SIRV set 4 (Lexogen) was spiked at 1% in the hESC and differentiated neuron-derived RNA samples.
PacBio Iso-seq libraries from the same RNA samples were generated using the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, PacBio Iso-Seq Express Oligo Kit and SMRTbell express template prep kit 2.0 according to the manufacturer’s protocol. The libraries were sequenced on a PacBio Sequel Iie.

value: neurons


title: FC13140667


title: NNI-10, DMSO-treated


title: Saureus_control_Rep1

value: TSB medium


title: ChIP-seq SW480 RNAPII Rep 2

city: Chicago

first: Mannan

last: Bhola

state: IL

address: 303 E Superior St

department: BMG

institute: Northwestern university

description:
ChIP-seq
ChIP_SW480_RNAPII_Merge.bw

data_processing:
The low-quality reads were removed using Trim_Galore (v0.6.10 with cutadapt v4.2) with the following parameters: --clip_R1 3 --clip_R2 3 --three_prime_clip_R1 3 --three_prime_clip_R2 3 for paired-end reads and --clip_R1 3 --three_prime_clip_R1 3 for single-end reads. Sequencing reads were mapped to the hg38 human genome (GCA_000001405.15_GRCh38_no_alt_analysis_set.fa) using bwa  v0.7.17 (mem for paired-end reads, aln and samse for single-end reads) and default parameters. SAMtools v1.14 was used for filtering the mapping quality and the duplicate reads. Only high-quality reads (uniquely mapped, pass quality check, no PCR duplicates, and with mapping quality score >= 30. For paired end reads, we further required properly paired and both ends uniquely mapped) were used for further analysis. Spike-in normalization was performed by mapping the reads to the Drosophila melanogaster genome (dm6) using bwa mem with the same parameters. Deeptools v3.5.1 was used to generate normalized bigwig files by combining reads from two replicas. The bins per million mapped normalized reads were used and the log2 ratio between the ChIP-seq signal over Input was calculated.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: SW480 Cells

growth_protocol: Human SW480 cells were grown at 37°C, supplied with 5% CO in Dulbeccos modified Eagle medium (DMEM, Gibco) medium supplemented with 10% FBS.

extract_protocol:
Cell resuspensions were next dounced ten times in a prechilled glass homogenizer. Nuclei were collected and resuspended in shearing buffer (0.1% SDS, 0.5% N-lauroylsarcosine, 1% Triton X-100, 10 mM Tris-HCl pH 8.1, 100 mM NaCl, 1 mM EDTA, 1 mM PMSF, PICs) and incubated on ice for 30 min. Chromatin was fragmented using an E220 Focused-Ultrasonicator (Covaris) to an average size of 200-600 bp.
ChIP-seq libraries for all samples were generated and sequenced by Admera Health. Briefly, immunoprecipitated DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA) and quality assessed by Tapestation genomic DNA Assay (Agilent Technologies, California, USA). Library preparation was performed using KAPA Hyper Prep (Roche, Basel, Switzerland) following the manufacturers recommendations. All samples were subjected to end-repair, adaptor ligation followed by indexed PCR using Illumina® 8-nt dual-indices. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay and Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA). Final libraries were quantified using QuantStudio ® 5 System (Applied Biosystems, California, USA) prior to equimolar pooling based on qPCR QC values. Sequencing was performed on an Illumina NovaSeq (Illumina, CA, USA) with aread length configuration of 150 PE for 40 M PE reads 20 M in eachdirection) per sample. For TOP1cc-seq and RNA PolII CHIP-seq, the read length configuration was 75 SE.

treatment_protocol: The cells were cross-linkedwith 2 mM disuccinimidylglutarate (ProteoChem) for 30 min, followed by cross-linkingwith1% formaldehyde for an additional 10 min at room temperature andquenched with 125 mM glycine (Thermo Fisher Scientific) for 5 min.Cell pellets were resuspended in lysis buffer [20 mM tris-HCl(pH 7.5),300 mM NaCl, 2 mM EDTA, 0.5% NP-40,1% Triton X-100,1 mMPMSF, and PICs] and incubated on ice for 30 min.

value: SW480 Cells

value: RNAPII (Santa Cruz, sc-899)


title: Differentiated (day 61) - long reads -  rep 1


title: Differentiated (day 41) - long reads -  rep 2


title: WT (NEM316), Replica 2

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.15. Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 1.2.1.1, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version v1.5.3 from Subreads package (parameters: -t locus_tag -g ID -s 1).
Count data were analyzed using R version 3.6.1 and the Bioconductor package DESeq2 version 1.26.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed with(out) applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the biological condition. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially  expressed.
Assembly: Streptococcus agalactiae NEM316 (from NCBI id=165229, NCBI RefSeq reference NC_004368)
Supplementary files format and content: DESeq 2 output matrix

organism: Streptococcus agalactiae

source_name: bacterial cell

growth_protocol: Bacterial cultures in rich media (THY) incubated at 37°C in static condition are harvested in exponential growth phase (OD600 = 0.5).

extract_protocol:
Total RNA are extracted after cell wall mechanical lysis with 0.1 µm beads (Precellys Evolution, Bertin Technologies) in RNApro reagent (MP Biomedicals), and purified by chloroform extraction and ethanol precipitation.
Depletion of rRNA (FastSelect Bacterial, Qiagen) and libraries construction ((TruSeq Stranded mRNA, Illumina) are done following manufacturer instructions.

treatment_protocol: Bacterial pellets are washed with cold PBS containing RNA stabilization reagents (RNAprotect, Qiagen) before flash freezing and storage at -80°C.

value: bacterial cell

value: WT (NEM316)


title: FC12344908

value: Plasma

value: W1 Exclusive e-cig user


title: WT (NEM316), Replica 3


title: Prostatic urethral trauma tissue 2

description:
Biological replicate 2 of 4.Prostatic urethral trauma tissue, treated, harvested after 5 days after sham surgery.
TULP2


title: Differentiated (day 41) - long reads -  rep 1


title: WT (NEM316), Replica 1


title: Saureus_Abaumannii_CFCM_Rep1


title: ChIP-seq SW480 Input Rep 1

description:
ChIP-seq
ChIP_SW480_input_Merge.bw


title: SaeS T133A, Replica 2

value: SaeS T133A


title: SaeS T133A, Replica 3


title: VAL_ab_rep2

value: stem vascular


title: Ribo_Ec_ribopools_2

city: Wako city

first: Shintaro

last: Iwasaki

address: 2-1, Hirosawa

department: CPR

country: Japan

institute: RIKEN

description:
Ribosome profiling_and_rRNA_depletion_with_ribopools
Ribo_Ec.csv

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38,mm10,SacCer-3,dm6,TAIR10,NC_000913.2
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Supplementary files format and content: csv files contain mapped reads and depleted reads information as indicated in the colunms
Library strategy: Ribo-seq

organism: Escherichia coli

extract_protocol:
HEK cells  were cultured in a 10 cm dish in preparation for the RocA treatment, and in a 6-well plate for the heat shock treatment. The cells were then lysed in 500 µl and 100 µl of lysis buffer. Human skin cells cultured in a well of 6-well plates were lysed in 100 μl of lysis buffer. The mouse forebrain was dissected on ice and disrupted using a loose fitting Dounce homogenizer in 3 mL ice-cold homogenizing buffer.The homogenate was treated with an equal volume of 2× lysis buffer and incubated for 10 min on ice. S2 cells, cultured for 3 days, were seeded in 10 cm dishes. To these cells, 10 μl of 100 mg/ml cycloheximide was added, followed by immediate centrifugation at 1,000 × g to collect the cell pellet. The pellet was then washed with PBS and treated with 400 μl of lysis buffer. E. coli MG1655 cells grown overnight at 37°C in LB media were diluted 1:100 in fresh LB media and grown at 37°C until the OD600 was 0.4-0.5. Cells were then collected by filtration and snap frozen in liquid nitrogen. The frozen cell pellet and lysis buffer were disrupted using a multi-beads shocker. For yeast, cells collected in ribosome profiling lysis buffer were pulverised using a Multi-Beads Shocker with a pre-cooled chamber and ball using liquid nitrogen.  0.2 g of frozen Arabidopsis wild-type (Col-0) seedlings were combined with 400 μl of Arabidopsis lysis buffer.This mixture was then subjected to grinding using a multi-bead shocker
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification..For RNA-Seq, TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMARTerseq (Illumina). For Escherichia coli, MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)


title: TOP1-seq SW480 TOP1 Rep 2

description:
ChIP-seq
TOPseq_SW480_TOP1_Merge.bw

value: Topoisomerase I (abcam, ab109374)


title: ChIP-seq SW480 RNAPII Rep 1

description:
ChIP-seq
ChIP_SW480_RNAPII_Merge.bw


title: TOP1-seq SW480 TOP1 Rep 1

description:
ChIP-seq
TOPseq_SW480_TOP1_Merge.bw


title: Ribo_Ec_ribopools_1


title: TOP1-seq SW480 Input Rep 2

description:
ChIP-seq
TOPseq_SW480_input_Merge.bw


title: SaeS T133A, Replica 1


title: ∆saeR, replica 3

value: {delta}saeR


title: TOP1-seq SW480 Input Rep 1

description:
ChIP-seq
TOPseq_SW480_input_Merge.bw


title: Ribo_Ec_CT_2

description:
Ribosome profiling_and_rRNA_depletion_with_None
Ribo_Ec.csv


title: ∆saeR, replica 2


title: ∆saeR, replica 1


title: Total RNA-seq Patient 1T

description:
Total RNA-seq Ribo-Depletion
COAD1.fwd.bw
COAD1.rev.bw

data_processing:
The reads were trimmed for adapter contaminations and quality using Trim_Galore (v0.6.10 with cutadapt v4.2) with the following parameters: --clip_R1 15 --clip_R2 15 --three_prime_clip_R1 5 --three_prime_clip_R2 5. Paired-end raw reads were mapped to the hg38 human genome with GENECODE v43 (primary_assembly) using STAR aligner v2.7.9a with the following parameters: --genomeLoad NoSharedMemory --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --sjdbScore 1 --limitBAMsortRAM 60000000000 --outWigType wiggle --outWigNorm None. Only high-quality reads (both ends were uniquely mapped, pass quality check, and with mapping quality score >= 255) were kept for the analysis. The gene expression was determined with featureCounts (subread v1.6.1) using GENECODE v43 (primary_assembly) gene annotation with the parameters: -s 2 -B -p -t exon -g gene_id The gene counts were used to determine the differential gene expression with DESeq2 v1.36 and q-value<0.05 and a log2 fold change of 0.58.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Tumor tissue Patient 1

growth_protocol: Human SW480 cells were grown in Dulbecco’s modified Eagle medium (DMEM, Gibco) medium supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted from samples using TRIzol reagent (Invitrogen) according to the manufacturers instructions. For Chipseq, DNA samples were purified using UPrep® Spin Columns (Genesee Scientific).
Total RNA-seq (ribo-depleted) libraries for all samples were generated and sequenced by Admera Health. Briefly, isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Libraries were constructed with KAPA RNA HyperPrep with RiboErase (Roche, Indiana, USA) and performed based on manufacturers recommendations. Final library quantity was measured by KAPA SYBR® FAST qPCR and library quality evaluated by TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). The final library size was about 430 bp with an insert size of about 200bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for 50 M PE reads per sample (25M in each direction).

treatment_protocol: SW480 cells were transduced with viral supernatants containing 8 μg ml-1 polybrene (Sigma-Aldrich). After 8h infection, virus-containing medium was removed and replaced with fresh medium. After 48 h, the cells were selected using puromycin at a final concentration of 1.5 μg ml-1 before harvesting the cells for sequencing

value: Tumor


title: Ribo_Ec_CT_1


title: Total RNA-seq Patient 1N

description:
Total RNA-seq Ribo-Depletion
NT1.fwd.bw
NT1.rev.bw

source_name: Normal tissue Patient 1

value: Normal


title: Ribo_Ec_ribopools_Ribo-Filterout_1

description:
Ribosome profiling_and_rRNA_depletion_with_ribopools,Ribo-FilterOut
Ribo_Ec.csv


title: ChIP-seq SW480 Input Rep 2

description:
ChIP-seq
ChIP_SW480_input_Merge.bw


title: SaeR D53A, Replica 3

value: SaeR D53A


title: Ribo_Ec_ribopools_Ribo-Filterout_2


title: Ribo_Ec_Ribo-Filterout_2

description:
Ribosome profiling_and_rRNA_depletion_with_Ribo-FilterOut
Ribo_Ec.csv


title: SaeR D53A, Replica 2


title: hESC (day 0) - long reads -  rep 2

source_name: human embryonic stem cells

value: human embryonic stem cells


title: hESC (day 0) – long reads - rep 1


title: Total RNA-seq Patient 2T

description:
Total RNA-seq Ribo-Depletion
COAD2.fwd.bw
COAD2.rev.bw

source_name: Tumor tissue Patient 2


title: Ribo_Ec_Ribo-Filterout_1


title: SaeR D53A, Replica 1


title: Total RNA-seq Patient 2N

description:
Total RNA-seq Ribo-Depletion
NT2.fwd.bw
NT2.rev.bw

source_name: Normal tissue Patient 2


title: Total RNA-seq Patient 5N

description:
Total RNA-seq Ribo-Depletion
NT5.fwd.bw
NT5.rev.bw

source_name: Normal tissue Patient 5


title: RNA_F_O3

description: Ribosome profiling_and_rRNA_depletion_with_Ribo-Zero, Ribo-FilterOut_Ribo-Calibration

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38,mm10,SacCer-3,dm6,TAIR10,NC_000913.2
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Supplementary files format and content: csv files contain mapped reads and depleted reads information as indicated in the colunms

organism: Mus musculus

source_name: mouse forebrain

extract_protocol:
HEK cells  were cultured in a 10 cm dish in preparation for the RocA treatment, and in a 6-well plate for the heat shock treatment. The cells were then lysed in 500 µl and 100 µl of lysis buffer.
Human skin cells cultured in a well of 6-well plates were lysed in 100 μl of lysis buffer.
The mouse forebrain was dissected on ice and disrupted using a loose fitting Dounce homogenizer in 3 mL ice-cold homogenizing buffer.The homogenate was treated with an equal volume of 2× lysis buffer and incubated for 10 min on ice.
S2 cells, cultured for 3 days, were seeded in 10 cm dishes. To these cells, 10 μl of 100 mg/ml cycloheximide was added, followed by immediate centrifugation at 1,000 × g to collect the cell pellet. The pellet was then washed with PBS and treated with 400 μl of lysis buffer.
E. coli MG1655 cells grown overnight at 37°C in LB media were diluted 1:100 in fresh LB media and grown at 37°C until the OD600 was 0.4-0.5. Cells were then collected by filtration and snap frozen in liquid nitrogen. The frozen cell pellet and lysis buffer were disrupted using a multi-beads shocker.
For yeast, cells collected in ribosome profiling lysis buffer were pulverised using a Multi-Beads Shocker with a pre-cooled chamber and ball using liquid nitrogen.
0.2 g of frozen Arabidopsis wild-type (Col-0) seedlings were combined with 400 μl of Arabidopsis lysis buffer.This mixture was then subjected to grinding using a multi-bead shocker
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification..For RNA-Seq, TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMARTerseq (Illumina). For Escherichia coli, MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)

value: mouse forebrain

value: Aged

tag: Sex

value: male

tag: rrna depletion

value: Ribo zero and Ribo-Filterout


title: RNA_F_O2

description: RNAseq_and_rRNA_depletion_with_Ribo-Zero_Ribo-Calibration

tag: tissue


title: DEN 30W-Otud3 knockout-3

city: Beijing

first: Hongmiao

last: Dai

address: Changping District

department: National Center for Protein Sciences (Beijing)

institute: State Key Laboratory of Proteomics

data_processing:
The raw data obtained from sequencing were filtered using SOAPnuke to remove.
HISAT (v2.2.1) anchors partial sequences of each read to the genome using global FM indexing and utilizes local indexing of these alignment positions to align the remaining sequences of each read to extend the alignment region.
Clean data was aligned to the reference gene set using Bowtie2 (v2.3.4.3).Gene expression quantification was performed using RSEM (v1.3.1) software. DESeq2 (v1.4.5) was employed for differential gene detection, with criteria set as Q value ≤ 0.05 or FDR ≤ 0.001.
Assembly: NCBI GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: liver

growth_protocol: Otud3 knockout mice and littermate Wild type (WT) C57BL/6 mice were bred and housed at the animal facility under specific pathogen free conditions.

extract_protocol:
Total RNA was isolated using a Direct-zol RNA MiniPrep kit (Zymo, Irvine, CA), including a DNase I digestion step.
RNA-seq library preparation and sequencing were conducted by Beijing Genomics Institute (BGI; ShenZhen, China).

treatment_protocol: Hepatocellular carcinoma was induced in Otud3 knockout and littermate WT male mice by the administration of a single intraperitoneal (i.p.) injection of the hepatocarcinogen diethylnitrosamine (DEN, N0258, Sigma-Aldrich) (25 mg/kg of DEN dissolved in 0.9% saline) at 15 days after birth. Mice were euthanized at 30 weeks post-injection.

value: liver

value: Otud3 knockout

value: DEN 30W


title: DEN 30W-Otud3 knockout-2


title: Total RNA-seq SW480_shTOP1 Rep 2

description:
Total RNA-seq Ribo-Depletion
TOP1_KD_Merge.raw.fwd.bw
TOP1_KD_Merge.raw.rev.bw

source_name: SW480 Cells with shRNA TOP1

value: SW480 Cells

tag: shRNA


title: DEN 30W-Otud3 knockout-1

tag: treatment


title: DEN 30W-WT-3

value: WT


title: RNA_F_O1

tag: age


title: Total RNA-seq SW480_shCTL Rep 2

description:
Total RNA-seq Ribo-Depletion
SCR_Merge.raw.fwd.bw
SCR_Merge.raw.rev.bw

source_name: SW480 Cells with shRNA Control

value: Control


title: Total RNA-seq SW480_shTOP1 Rep 1


title: DEN 30W-WT-2


title: RNA_F_Y2

tag: strain

value: Young


title: RNA_F_Y3


title: Total RNA-seq SW480_shCTL Rep 1


title: Total RNA-seq HCT116 Rep 2

description:
Total RNA-seq Ribo-Depletion
HCT116M.raw.fwd.bw
HCT116M.raw.rev.bw

source_name: HCT116 Cells

value: HCT116 Cells


title: DEN 30W-WT-1


title: No DEN-Otud3 knockout-3

value: No DEN


title: Ribo_F_O3


title: Total RNA-seq HCT116 Rep 1


title: RNA_F_Y1


title: Ribo_F_O2


title: No DEN-Otud3 knockout-2


title: Ribo_F_O1


title: Total RNA-seq SW480 Rep 2

description:
Total RNA-seq Ribo-Depletion
SW480M.raw.fwd.bw
SW480M.raw.rev.bw


title: No DEN-Otud3 knockout-1


title: Total RNA-seq SW480 Rep 1


title: No DEN-WT-3


title: No DEN-WT-2


title: Ribo_F_Y3


title: No DEN-WT-1


title: Total RNA-seq FHC Rep 1

description:
Total RNA-seq Ribo-Depletion
FHCM_merge2.raw.fwd.bw
FHCM_merge2.raw.rev.bw

source_name: FHC Cells

value: FHC Cells


title: Ribo_F_Y2


title: Ribo_F_Y1


title: 206203800135_R07C01

status: Public on Jul 09 2024

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description:
gDNA from monocytes
D0

hyb_protocol: bisulphite converted DNA was amplified fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000)  using standard recommended Illumina scanner setting

data_processing:
Data were processed using R studio (R v4.2.0)
Normalized  Average Beta (Noob + Quantile Normalization)
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: D

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from cell samples using a salting-out protocol.

value: Male

value: freshly isolated monocytes

tag: preliminary stimulus (day 6)

value: Non-applicable

tag: secondary stimulus (day 8)

tag: day of collection


title: 206203800145_R05C01

description:
gDNA from monocytes
F0

source_name: F

tag: cell type


title: Total RNA-seq Patient 5T

description:
Total RNA-seq Ribo-Depletion
COAD5.fwd.bw
COAD5.rev.bw

source_name: Tumor tissue Patient 5

value: Tumor


title: 206203800145_R03C01

description:
gDNA from microglia-like cells
D4

value: microglia-like

value: 100 uM ATP

value: 100 ng/mL LPS


title: 206203800135_R06C01

description:
gDNA from microglia-like cells
C4

source_name: C


title: 206203800135_R05C01

description:
gDNA from microglia-like cells
B3

source_name: B


title: 206191200058_R02C01

description:
gDNA from microglia-like cells
B4


title: 206203800145_R07C01

description:
gDNA from microglia-like cells
C3


title: 206203800145_R02C01

description:
gDNA from microglia-like cells
A4

source_name: A


title: Patient 26 at (T1)

city: Riyadh

first: Abderrezak

last: Bouchama

address: Ahmad Ibn Hanbal Street, Ar Rimayah

department: Experimental Medicine

country: Saudi Arabia

institute: KAIMRC

description: Gene expression data from obese patient 2 months after the bariatric surgery

hyb_protocol: 11 µg of labeled and fragmented cRNA were hybridized for 16 hours at 54 C on Affymetrix Human Genome U133 Plus 2.0 Array. After that, washing and staining of the GeneChips were performed using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: We processed the raw CEL files using freely available updated chip definition files (CDF) for HG-U 133 Plus 2.0 arrays based on Entrez genes, which remaps every probe in the array, re-aligning to the sequences of the latest genome assembly. Specifically, we used three libraries of version 22, namely HG-U 133 Plus 2.0 Entrez gcdf, HG-U 133 Plus 2.0 Entrez gprobe, and HG-U 133 Plus 2.0 Entrez gdb (2) from http://mbni.org/customcdf/22.0.0.  We imported and converted the probe intensity data from the CEL files along with the above-mentioned CDF file into the probe level ‘AffyBatch’ object by ReadAffy function of the Affy R package in Bioconductor (3). We imported the phenotypic data using the pData function into the AffyBatch object. Finally, we used (4)the RMA function on this object for background correction, normalization of the multiple array data using the Robust Multiarray Average (RMA) method, and expression calculation for the entire probes available in the CDF file. This step produces an object containing probe level expression matrix. We populated the probe level feature data into this ‘Expression Set’ object using annotateEset function of the R package ‘affycoretools’ and chipDB object (hgu133plus2hsrefseq.db) from the brain array project. Then, we used the ‘exprs’ function in the Affy package to extract the expression matrix of the genes / probes for further downstream analyzes.

label: biotin

source_name: Peripheral Blood Mononuclear Cells (PBMCs) 2 months after bariatric surgery

label_protocol: 500 ng of total RNA were used to synthesis cDNA and preparing biotinylated cRNA according to the Affymetrix protocol

extract_protocol: The total RNA was extracted from PBMCs using the SV Total RNA Isolation Kit from Promega following the manufacturer's instructions.

tag: type of surgery

value: Roux en Y gastric Bypass

tag: phenotype

value: Responder

value: PBMCs


title: 206203800135_R08C01

description:
gDNA from microglia-like cells
A3


title: Patient 24 at (T2)

description: Gene expression data from obese patient one year after the bariatric surgery

source_name: Peripheral Blood Mononuclear Cells (PBMCs) 12 months after bariatric surgery

value: Sleeve Gastrectomy


title: Patient 26 at (T2)


title: Patient 26 at (T0)

description: Gene expression data from obese patient before the bariatric surgery

source_name: Peripheral Blood Mononuclear Cells (PBMCs) before surgery


title: 206203800135_R03C01

description:
gDNA from monocytes
E0

source_name: E


title: Patient 25 at (T1)

value: Female

value: Non-Responder


title: Patient 24 at (T1)


title: Total RNA-seq FHC Rep 2

tag: cell line


title: 206203800145_R06C01

description:
gDNA from monocytes
C0


title: 206203800145_R08C01

description:
gDNA from microglia-like cells
D2


title: 206203800135_R01C01

description:
gDNA from microglia-like cells
C2


title: Patient 23 at (T2)


title: Patient 25 at (T2)


title: 206203800145_R04C01

description:
gDNA from microglia-like cells
B2


title: Patient 23 at (T1)


title: 206191200058_R03C01

description:
gDNA from microglia-like cells
A2


title: 206191200058_R01C01

description:
gDNA from microglia-like cells
D3


title: Patient 23 at (T0)


title: Patient 22 at (T2)


title: Patient 22 at (T1)


title: 206203800135_R02C01

description:
gDNA from microglia-like cells
D1


title: 206191200058_R04C01

description:
gDNA from microglia-like cells
C1


title: Patient 24 at (T0)


title: 206203800145_R01C01

description:
gDNA from microglia-like cells
B1


title: Patient 21 at (T2)


title: 206203800135_R04C01

description:
gDNA from microglia-like cells
A1


title: Patient 21 at (T1)


title: Control mouse 4

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

data_processing:
The raw reads were processed with Ion Torrent RNASEQAnalysis pipeline (Torrent Suite version 5.0.4)
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
Assembly: AmpliSeq Mouse Transcriptome v1
Supplementary files format and content: htseq normalized count

source_name: skin

extract_protocol:
Collected tissue samples were snap-frozen in liquid nitrogen and stored at -80°C  prior to analysis. For RNA isolation, the samples were homogenized in Fenozol (A&A Biotechnology, Gdansk, Polska) using a tissue homogenizer (OMNI International, Kennesaw, GA, USA).
Library was prepared using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit according to the manufacturer’s protocol (Thermo Fisher Scientific)

value: skin

tag: genotype


title: Control mouse 3


title: Mcpip1(MKO) mouse 4


title: Control mouse 2


title: Mcpip1(MKO) mouse 3


title: Mcpip1(MKO) mouse 1


title: Patient 20 at (T2)


title: Patient 20 at (T0)


title: Mcpip1(MKO) mouse 2


title: Patient 19 at (T2)


title: Patient 20 at (T1)


title: Patient 22 at (T0)


title: Patient 18 at (T2)


title: Patient 19 at (T0)


title: Mcpip1(EMdKO) mouse 4


title: Patient 18 at (T0)


title: Patient 18 at (T1)


title: Patient 21 at (T0)


title: Mcpip1(EMdKO) mouse 3


title: Patient 19 at (T1)


title: Patient 17 at (T2)


title: Patient 17 at (T0)


title: Mcpip1(EMdKO) mouse 2


title: Control mouse 1


title: Mcpip1(EMdKO) mouse 1


title: Patient 16 at (T1)


title: Mcpip1(EKO) mouse 4


title: Patient 16 at (T2)


title: Patient 16 at (T0)


title: Mcpip1(EKO) mouse 3


title: Patient 15 at (T2)


title: Mcpip1(EKO) mouse 2


title: Mcpip1(EKO) mouse 1


title: Patient 25 at (T0)


title: Patient 15 at (T0)


title: DamID-Seq control stat rep3

first: Guilhem

last: Janbon

address: 25 rue du Dr Roux

data_processing:
150 bases were sequenced from both ends using an Illumina Novaseq6000  instrument according to the manufacturer’s instructions (Illumina).
After triming of illumina adaptors, the DamID adaptor containing reads were selected and aligned to the C. neoformans reference genome using Minimap2. Adenine residues of genomic GATC sequences positionned at the extremities of these reads were considered as potential methylated positions.

organism: Cryptococcus neoformans

growth_protocol: Cells were grown on YPD at 30°C in early stationnary phase

extract_protocol: Genomic DNA was digested with DpnII (NEB, R0543S) and dephosphorylated before being by DpnI (Takara, 1235A). Ligation of DamID adaptor (GGTCGCGGCCGAG+GATC) was followed by 8 cycles PCR reaction. The resulting samples were sent for Illumina sequencing (Novogene).

value: WT


title: Patient 14 at (T2)


title: Patient 15 at (T1)


title: DamID-Seq control expo rep2

growth_protocol: Cells were grown on YPD at 30°C in exponential phase


title: DamID-Seq control expo rep3


title: DamID-Seq control stat rep1


title: Patient 14 at (T1)


title: DamID-Seq control expo rep1


title: DamID-Seq stat rep3


title: Patient 13 at (T1)


title: Patient 14 at (T0)


title: Patient 13 at (T2)


title: DamID-Seq expo rep3


title: Patient 13 at (T0)


title: DamID-Seq expo rep2


title: Patient 12 at (T1)


title: DamID-Seq control stat rep2


title: DamID-Seq expo rep1


title: Patient 12 at (T2)


title: Chip Tur1 expo imput rep 6

data_processing:
150 bases were sequenced from both ends using an Illumina Novaseq6000  instrument according to the manufacturer’s instructions (Illumina).
The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. neoformans H99 genome with Minimap2. Peak calling was performed using MACS2 using default settings using default settings.

growth_protocol: Cells were grown on YPD at 30°C in early stationnary phase and crosslinked by addition formaldehyde (1% final concentration)

extract_protocol: Chromatin was fragmented using a Bioruptor Pico (diagenode). 20 µL of each chromatin extract were kept aside for “input” samples.


title: Patient 11 at (T2)


title: Patient 12 at (T0)


title: Chip Tur1 expo imput rep 4


title: Chip Tur1 expo imput rep 5


title: DamID-Seq stat rep2


title: Chip Tur1 expo imput rep 2

growth_protocol: Cells were grown on YPD at 30°C in exponential phase and crosslinked by addition formaldehyde (1% final concentration)


title: Chip Tur1 expo imput rep 3


title: DamID-Seq stat rep1


title: Chip Tur1 expo imput rep 1


title: Patient 11 at (T0)


title: Chip Tur1 stat rep 2

extract_protocol: Chromatin was fragmented using a Bioruptor Pico (diagenode). Chromatin extracts were incubated overnight at 4°C with anti-Flag M2 magnetic beads suspension (Millipore, Merck M8823). The day after, beads were washed  anddDecrosslink was achieved by adding proteinase K to eluates at 65°C. The day after, DNA was recovered using Phenol-Chloroform method, quantified by QuBit.

tag: chip antibody

value: anti-Flag M2 (Millipore, Merck M8823)


title: Chip Tur1 stat rep 3


title: Chip Tur1 expo rep 3


title: Patient 10 at (T0)

tag: gender


title: Patient 10 at (T1)


title: Chip Tur1 expo rep 2


title: Chip Tur1 expo rep 1


title: Patient 8 at (T1)

value: Biliopacreatic Diversion without duodenal switch


title: Patient 9 at (T0)

value: Gastric Resection


title: Patient 7 at (T1)


title: Patient 10 at (T2)

value: Male


title: Chip Tur1 stat rep 1


title: Patient 8 at (T0)


title: Patient 6 at (T2)


title: Patient 7 at (T0)


title: Patient 5 at (T0)

value: laparascopic mini gastric bypass


title: Patient 6 at (T0)


title: Patient 5 at (T2)


title: Patient 7 at (T2)


title: Patient 9 at (T1)


title: Patient 5 at (T1)


title: Patient 4 at (T2)


title: Whole heart (TAC-R) 2

city: Saitama

first: Manabu

last: Shiraishi

address: Omiya

institute: Jichi Medical University

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

hyb_protocol: 1. Total RNA QC check was performed using an Agilent 2100 Bioanalyzer. 2. 100 ng of Total RNA was aliquoted. 3. the GeneChipTM WT PLUS Reagent Kit was used and the kit protocol (GeneChipTM WT PLUS Reagent Kit User Manual) was followed. WT PLUS Reagent Kit User Manual), prepare Fragmented and Labeled cDNA samples, and then prepare 100 μL of the following hybridization solution. 4. the array was incubated in a GeneChipTM Hybridization Oven 645 at 45°C, temperature of 1.5 °C, and humidity of 1.5 °C, according to the protocol supplied with the kit.Incubate the array at 45°C for 16 hours (60 rpm) using GeneChipTM Hybridization Oven 645 according to the protocol supplied with the kit. 5. Wash the array with GeneChipTM Fluidics Station 450 according to the kit protocol. Wash the arrays with GeneChipTM Fluidics Station 450 according to the protocol supplied with the kit.

scan_protocol: The GeneChipTM Scanner 3000 7G was used to scan the arrays according to the accompanying manual <GeneChipTM Command Console (AGCC) 4.0 User Manual>.  Command Console (AGCC) 4.0 User Manual. at Filgen, Inc.

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.

source_name: Heart released from TAC

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).

growth_protocol: Whole hearts were isolated from the Sprague-Dawley rats.

extract_protocol: RNA was isolated from cultured fibroblasts with the Gene Jet PCR purification Kit (Thermo Scientific), according to the manufacturer’s instructions.

treatment_protocol: Animals were male Sprague Dawleys (10 weeks old). Food and water were withheld 6 hours prior to surgery. Surgical instruments were sterilized in an autoclave. The surgical field was disinfected with 75% isopropyl alcohol. During surgery, the heating pad was set at an appropriate temperature (37℃) to avoid rapid changes in heart rate and respiratory rate, maintaining normal body temperature. Inhalation anesthesia was administered with a mixture of 2% isoflurane and 100% oxygen at 0.5 to 1.0 L/min. The hairs on the anterior neck and chest were removed with depilatory cream. Rats were positioned supine on a heating pad, with anterior teeth over fixed silk strings, the neck stretched, and limbs secured with surgical paper tape. Anesthesia was maintained with 1.5-2% isoflurane and 0.5-1.0 L/min 100% oxygen during surgery, confirmed by the toe-pinch reflex. The surgical field was sterilized with 70% alcohol, using sterile drapes and gloves for each rat. Skin incisions were made with a scalpel at the midline of the rat's neck and chest. The muscular layer over the trachea was separated bilaterally. A partial sternal incision was made up to the second rib, expanding the sternum with a chest retractor. Thymus and adipose tissue were gently detached from the aortic arch. After identifying the transverse aorta, a 3-0 silk string was passed between the brachiocephalic artery and the left common carotid artery using sharp forceps. A loop of about 10 mm in diameter was created with 5-0 monofilament thread, with a 3-0 silk thread passed through it (to indicate where to cut the silk thread in aortic stenosis later). A 21-gauge blunt needle was placed parallel to the aorta, tying the 3-0 silk thread quickly to ensure no loosening, and the needle removed to create aortic stenosis. In control rats, all procedures were similar except for aortic ligation. The chest traction device was removed, the sternum closed with 4-0 silk thread, and the skin closed with continuous sutures using 6-0 monofilament suture. Postoperative analgesia was provided with intraperitoneal buprenorphine injections. Anesthesia was gradually lowered, and rats allowed to recover on a heating pad upon signs of spontaneous respiration. After full recovery, they returned to the room on a 12-hour light/dark cycle and fed soft food. For pain relief, rats received intraperitoneal buprenorphine (0.1 mg/kg) every 12 hours for 3 days. Four weeks after transverse aorta ligation, skin incisions were made at the neck and chest midline under inhalation anesthesia. Adhesive scar tissue was dissected, and the silk thread ligating the aorta was identified by the loop created with 5-0 monofilament thread. The 3-0 silk thread was cut, releasing the stenosis, taking care to avoid aorta damage. All procedures in control and TAC rats were performed similarly, except for aortic ligature dissection. The chest was closed as in the initial surgery, and postoperative pain management was provided as before.

value: Heart


title: Tet1, Cortex, bACE, KO Rep7

city: Philadelphia

first: Yee Hoon

last: Foong

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

hyb_protocol: Bisulfite and bACE converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Mouse285 Methylation BeadChip 12v1-0 using standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe R Package
Beta values of individual probe for each individual sample. Probes that did not pass SeSAMe quality control pOOBAH approach is maksed with NA
Processed data file:  Tet1_array_betas.csv

label: Cy3 and Cy5

source_name: Adult Cortex

extract_protocol: genomic DNA was extracted using standard Phenol:Chloform extraction

treatment_protocol: Bisulfite treated followed by Bisulfite-assisted APOBEC3A-coupled epigenetic (bACE) protocol

value: Adult Cortex

value: KO


title: Tet1, Cortex, bACE, KO Rep6


title: Tet1, Cortex, bACE, KO Rep8


title: Patient 4 at (T0)


title: Patient 3 at (T2)


title: Patient 6 at (T1)


title: Whole heart (TAC) 2

source_name: TAC-subjected heart


title: Patient 3 at (T1)


title: Whole heart (normal) 1

source_name: Healty heart


title: Whole heart (TAC) 1


title: Whole heart (normal) 2


title: Whole heart (TAC-R) 1


title: Tet1, Cortex, bACE, KO Rep5


title: Patient 2 at (T2)


title: Patient 3 at (T0)


title: Patient 4 at (T1)


title: Tet1, Cortex, bACE, KO Rep4


title: Patient 2 at (T0)


title: Tet1, Cortex, bACE, KO Rep3


title: Tet1, Cortex, bACE, KO Rep1


title: 7_NJ_MOR_F

city: Boston

first: Camron

middle: D

last: Bryant

state: MA

address: 140 The Fenway

department: Department of Pharmaceutical Sciences - Center for Drug Discovery

institute: Northeastern University

data_processing:
Reads were trimmed for quality using Trimmomatic
Reads were aligned to the mm10 mouse reference genome using STAR
featureCounts program was used to cout reads mapping to the exon feature
Assembly: mm10
Supplementary files format and content: text file including reads from each sample

source_name: Brainstem

extract_protocol:
RNA was extracted using Trizol (Qiagen), ethanol precipitation, filtering columns (Qiagen), DNAse digestion (Qiagen), and elution with RNAse and nucleotide-free water.
poly-A selection

value: Brainstem

value: Morphine

tag: Sex


title: Tet1, Cortex, bACE, HxD Rep8

value: HxD


title: Patient 2 at (T1)

value: PBMCs


title: 6_NJ_SAL_F

value: Saline


title: 8_NJ_MOR_F

value: Female


title: 5_NJ_SAL_M


title: Tet1, Cortex, bACE, HxD Rep4


title: Tet1, Cortex, bACE, HxD Rep7


title: Patient 1 at (T0)

value: Responder


title: 2_NJ_MOR_M


title: Patient 1 at (T2)


title: Tet1, Cortex, bACE, HxD Rep6


title: Tet1, Cortex, bACE, HxD Rep5


title: 4_NJ_MOR_M


title: 3_NJ_SAL_M


title: Tet1, Cortex, bACE, HxD Rep3


title: Tet1, Cortex, bACE, HxD Rep2


title: Tet1, Cortex, bACE, HxD Rep1


title: Tet1, Cortex, bACE, WT Rep8


title: Tet1, Cortex, bACE, WT Rep7


title: Tet1, Cortex, bACE, KO Rep2


title: Tet1, Cortex, bACE, WT Rep6


title: 1_NJ_SAL_F


title: Tet1, Cortex, bACE, WT Rep5


title: Tet1, Cortex, bACE, WT Rep4


title: Tet1, Cortex, bACE, WT Rep3


title: 008 W12 NL

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

country: Australia

institute: Liverpool Hospital

description: Fibrosis Panel v2.0

hyb_protocol: as per standard protocol for Nanostring Ncounter

scan_protocol: nCounter with stadard protocol

data_processing: Processed using Nanostring Nsolver 4.0. Quality control conducted in Nsolver using negative threshold with negative controls.

source_name: PG8 Week 12 Non-Lesional

label_protocol: Nanostring Codeset

extract_protocol: RNA Extracted using Qiagen Rneasy kit as per astandard protocol.

treatment_protocol: Patients with clinican diagnosed Pyoderma Gangrenosum were administered subcutanoeus injections of tildrakizumab 200mg week 0,4,8 and 12.

value: skin biopsy

tag: disease state

value: Pyoderma Gangrenosum, Week 12

value: tildrakizumab


title: 007 W12 L

description: Fibrosis Panel v2.0

source_name: PG7 Week 12 Lesional

tag: tissue


title: 008 W12 L

description: Fibrosis Panel v2.0

source_name: PG8 Week 12 Lesional


title: Tet1, Cortex, bACE, WT Rep1

value: WT


title: Tet1, Cortex, bACE, WT Rep2


title: Tet1, Cortex, BS, KO Rep8

treatment_protocol: Bisulfite treated


title: 006 W12 NL

description: Fibrosis Panel v2.0

source_name: PG6 Week 12 Non-Lesional


title: 005 W12 L

description: Fibrosis Panel v2.0

source_name: PG5 Week 12 Lesional


title: 005 W12 NL

description: Fibrosis Panel v2.0

source_name: PG5 Week 12 Non-Lesional


title: Tet1, Cortex, BS, KO Rep6


title: 006 W12 L

description: Fibrosis Panel v2.0

source_name: PG6 Week 12 Lesional


title: Tet1, Cortex, BS, KO Rep4


title: 004 W12 NL

description: Fibrosis Panel v2.0

source_name: PG4 Week 12 Non-Lesional


title: Tet1, Cortex, BS, KO Rep7


title: Tet1, Cortex, BS, KO Rep5


title: Tet1, Cortex, BS, KO Rep2


title: 003 W12 NL

description: Fibrosis Panel v2.0

source_name: PG3 Week 12 Non-Lesional


title: Tet1, Cortex, BS, KO Rep3


title: 003 W12 L

description: Fibrosis Panel v2.0

source_name: PG3 Week 12 Lesional


title: 007 W0 NL

description: Fibrosis Panel v2.0

source_name: PG7 Week 0 Non-Lesional

value: Pyoderma Gangrenosum, Baseline


title: 008 W0 L

description: Fibrosis Panel v2.0

source_name: PG8 Week 0 Lesional


title: 006 W0 L

description: Fibrosis Panel v2.0

source_name: PG6 Week 0 Lesional


title: 006 W0 NL

description: Fibrosis Panel v2.0

source_name: PG6 Week 0 Non-Lesional


title: Tet1, Cortex, BS, HxD Rep7

source_name: Adult Cortex


title: Tet1, Cortex, BS, HxD Rep6


title: 002 W12NL

description: Fibrosis Panel v2.0

source_name: PG2 Week 12 Non-Lesional


title: 005 W0 L

description: Fibrosis Panel v2.0

source_name: PG5 Week 0 Lesional


title: 004 W12 L

description: Fibrosis Panel v2.0

source_name: PG4 Week 12 Lesional


title: Tet1, Cortex, BS, HxD Rep8


title: Tet1, Cortex, BS, HxD Rep5


title: Tet1, Cortex, BS, HxD Rep2


title: Tet1, Cortex, BS, HxD Rep3


title: Tet1, Cortex, BS, WT Rep8


title: 002 W0 NL

description: Fibrosis Panel v2.0

source_name: PG2 Week 0 Non-Lesional


title: 007 W0 L

description: Fibrosis Panel v2.0

source_name: PG7 Week 0 Lesional


title: Tet1, Cortex, BS, KO Rep1


title: Tet1, Cortex, BS, WT Rep6


title: 003 W0 L

description: Fibrosis Panel v2.0

source_name: PG3 Week 0 Lesional


title: Tet1, Cortex, BS, WT Rep5


title: 001 W0 NL

description: Fibrosis Panel v2.0

source_name: PG1 Week 0 Non-Lesional


title: VCaP_input_ML792-DHT_rep5

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Corresponding input sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: VCaP

growth_protocol: VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
For ChIP-seq, after 1% formaldehyde crosslinking, cells were harvested, chromatin was sonicated to 100-300 bp fragments, and protein-DNA complexes were isolated with specified antibody.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit according to instructions.

treatment_protocol: VCaP cells were treated either with vehicle (EtOH) or 100 nM of dihydrotestosterone (DHT) for 1 h before the start of ChIPs. Before EtOH or DHT treatment, the cells were treated either with vehicle (DMSO) or SAE inhibitor (ML792) for 24 h prior ChIPs.

value: Vertebral Cancer of the Prostate

value: VCaP

value: ML792 + DHT

tag: concentration

tag: time


title: Tet1, Cortex, BS, HxD Rep4

value: Adult Cortex


title: Normal 1

description: Fibrosis Panel v2.0

source_name: Healthy Control

value: Healthy Control

tag: treatment


title: 001 W0 L

description: Fibrosis Panel v2.0

source_name: PG1 Week 0 Lesional


title: Normal 2

description: Fibrosis Panel v2.0


title: 004 W0 L

description: Fibrosis Panel v2.0

source_name: PG4 Week 0 Lesional


title: 003 W0 NL

description: Fibrosis Panel v2.0

source_name: PG3 Week 0 Non-Lesional


title: Tet1, Cortex, BS, WT Rep7


title: Tet1, Cortex, BS, HxD Rep1


title: VCaP_input_DMSO-DHT_rep4

value: DMSO + DHT


title: 002 W12 L

description: Fibrosis Panel v2.0

source_name: PG2 Week 12 Lesional


title: DkdpE_AK

city: Namur

first: Regis

last: Hallez

address: 61 Rue de Bruxelles

country: Belgium

institute: UNamur

description: gDNA

data_processing:
Around 2 x 10^7 paired-end sequence reads (2 x 75) were first mapped on the genome of C. crescentus NA1000 (NC_011916.1) and converted to SAM using BWA and SAM tools from the sourceforge server (https://sourceforge.net/)
MACS2 algorithm was used to model the length of DNA fragment as well as the shift size.
The number of reads overlapping each genomic position was computed using custom Python scripts and the previously modeled DNA fragment and shift sizes.
A peak was defined as the genomic region where each position has more reads than the 97th percentile. The candidate peaks were annotated using custom Python scripts.
Assembly: NC_011916.1
Supplementary files format and content: The xls files report KdpE ChIP-Seq peaks in Caulobacter. The  different columns are organized as follows: column 1: Start_Coord (coordinates for the start of the peak); column 2: End_Coord (coordinates for the end of the peak); column 3: Summit (highest number of reads of peak); column 4:  Summit_Coord (coordinates for the highest number of reads of peak); column 5: Reads (number of reads in the peak); column 6: Reads Norm (number of reads / total number of alignedreads ); column 7: GeneUp (CCNA_number of gene upstream of the peak based on the summit); column 8: GeneUpName (name of gene upstream of the peak); column 9: GeneDown ( CCNA_number of gene downstream of the peak based on the summit); column 10: GeneDownName (name of gene downstream of the peak); column 11: OperonUp (Operon in which gene upstream of the peak belongs); column 12: OperonDown (Operon in which gene downstream of the peak belongs).

organism: Caulobacter vibrioides

source_name: mid-exponential phase

growth_protocol: C. crescentus strains grown overnight at 30°C in synthetic medium (M2G) to saturation before being diluted in fresh M2G-K medium supplemented with 0.025 mM K+ or 0.5 mM K+ and grown at 30°C to mid-exponential phase (OD660~0.5-0.6).

extract_protocol:
Resuspended pellets were lysed with 2 µl of Ready-lyse lysozyme solution (Epicentre)  for 5 min at RT. Protease inhibitors (Roche) was added and incubated for 10 min. Then, 550 µl of ChIP buffer (1.1% triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, plus protease inhibitors) was added to the lysate and incubated at 37 °C for 10 min before sonication (2 x 8 bursts of 30 sec on ice using a Diagenode Bioruptor) to shear DNA fragments to a length of 300 to 500 bp. Lysate was cleared by centrifugation for 10 min at 12,500 rpm at 4 °C and protein content was evaluated by measuring OD280. Then, 7.5 mg of proteins were diluted in ChIP buffer supplemented with 0.01% SDS and precleared 1 h at 4 °C with 50 µl of protein A magneticbeads (BioRad) and 100 µg BSA. One µl of polyclonal anti-KdpE antibodies, produced by rabbits (CER Groupe, Marloie, Belgium) immunised with purified His6-KdpE protein, were added to the supernatant before overnight incubation at 4 °C under gentle agitation. Eighty µl of BSA pre-saturated protein A magnetic beads were added to the solution for 2 h at 4 °C with rotation, washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), once with LiCl buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), once with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA) at 4 °C and a second wash with TE buffer at RT. The DNA-protein complexes were eluted twice in 250 µl freshly prepared elution buffer (0.1 M NaHCO3, 1% SDS). NaCl was added at a concentration of 300 mM to the combined eluates (500 µl) before overnight incubation at 65 °C to reverse the crosslink. The samples were treated with 20 µg of proteinase K in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5) for 2 h at 45 °C. DNA was extracted using Nucleospin PCR clean-up kit (Macherey-Nagel) and resuspended in 50 µl elution buffer (5 mM Tris-HCl pH 8.5).
ChIP-Seq libraries were prepared at the Seqalis company (Belgium) using the Illumina TruSeq DNA library (Roche-KapaHyperPrep)  according to the manufacturer's instructions.

treatment_protocol: 80 ml of mid-log phase cells (OD660~ 0.5-0.6) were cross-linked in 1% formaldehyde and 10 mM sodium phosphate (pH 7.6) at room temperature for 10 min and 30 min on ice thereafter. Crosslinking was stopped by addition of 125 mM glycine and incubated for 5 min on ice. Cells were washed thrice in PBS resuspended in 450 µl in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl)

value: mid-exponential phase

value: deltakdpE

value: Mid-exponential phase in synthetic minimal medium (M2G-K) with 0.025 mM K+


title: VCaP_input_DMSO-DHT_rep3


title: VCaP_HOXB13_ML792_DHT_rep3

value: HOXB13 (Cell Signaling, 90944S)


title: VCaP_HOXB13_ML792_DHT_rep2


title: Tet1, Cortex, BS, WT Rep4


title: Tet1, Cortex, BS, WT Rep3


title: DkdpE_LK

description: gDNA


title: 002 W0 L

description: Fibrosis Panel v2.0

source_name: PG2 Week 0 Lesional


title: VCaP_HOXB13_DMSO_DHT_rep3


title: VCaP_HOXB13_ML792_DHT_rep1


title: Tet1, Cortex, BS, WT Rep1


title: VCaP_HOXB13_DMSO_DHT_rep2


title: WT_LK

description: gDNA


title: VCaP_HOXB13_DMSO_DHT_rep1


title: VCaP_FOXA1_ML792_DHT_rep3

value: FOXA1 (Abcam, ab23738)


title: VCaP_FOXA1_ML792_DHT_rep2


title: WT_AK

description: gDNA


title: VCaP_FOXA1_ML792_DHT_rep1


title: DC3K1

city: Bangkok

first: Arnatchai

last: Maiuthed

state: Bangkok

address: 447 Thanon Si Ayutthaya, Thung Phaya Thai, Ratchathewi

department: Pharmacology

country: Thailand

institute: Faculty of Pharmacy, Mahidol University

data_processing:
Reference genome was pre-defined for the analysis. Version information of the reference genome is: Mesocricetus_auratus.MesAur1.0.genome.fa. HISAT2 is a highly efficient system for mapping RNA-seq reads, which is a more advanced version of TopHat2/Bowtie2.HISAT2 uses a Burrows-Wheeler Transform and Ferragina-Manzini（FM）index based search. HISAT2 uses one global graph FM index (GFM) to represent general population, as well as small indexes (local indexes) combined with several alignment strategies in order to achieve more efficient alignment.
Assembly: Version information of the reference genome is: Mesocricetus_auratus.MesAur1.0.genome.fa.
Supplementary files format and content: All_gene_fpkm.xls contains all FPKM values for all genes in all groups. Samples are in columns and genes are in rows. Each value represents FPKM for a specific gene in a specific sample.
Supplementary files format and content: All_gene_counts.xls contains all count values for all genes in all groups. Samples are in columns and genes are in rows. Each value represents the count for a specific gene in a specific sample.

organism: Mesocricetus auratus

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 2 mL/kg/day vehicle (dimethyl sulfoxide) euthanized 3 days post-inoculation, biol rep 1

growth_protocol: Male, 8-week-old, Golden Syrian Hamsters were kept for 7 days in a temperature-controlled room (20–22 °C) with 12:12 h light/dark cycles for quarantine and acclimatization. The animals were group-housed in an HEPA-filtered cage system and were provided with commercial diet and chlorinated water ad libitum.

extract_protocol:
Extraction of RNA was performed using the AllPrep DNA/RNA Mini Kit (Qiagen). In short, hamster kidney tissues were homogenized in 350 μL of RLT buffer and then applied to a DNA spin column. The homogenized lysate was centrifuged to extract DNA, and the resulting supernatant containing RNA and protein was collected. Next, absolute ethanol was added, gently mixed with a pipette, transferred to an RNeasy® spin column, and centrifuged to remove proteins from the mixture. The RNA portion was washed with 700 μL of RW1 buffer and 500 μL of RPE buffer, respectively. Finally, the RNA was eluted with 50 μL of RNase-free water and stored at -80°C until use.
(1) mRNA was isolated by Oligo(dT)-attached magnetic beads.  (2) mRNA was then randomly fragmented in fragmentation buffer.  (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads.  (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp.  (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step (4).

treatment_protocol: Hamsters were split into 5 groups, which were: 1. SARS-CoV-2-infected, orally received vehicle treatment (2 mL/kg/day dimethyl sulfoxide), and sacrificed 1 day post inoculation (Delta control day 1), 2. Delta control day 3, 3. SARS-CoV-2-infected, orally administered 1000 mg/kg/day AP 95% ethanol standardized extract, and sacrificed 1 day post inoculation (Delta AP day 1), 4. Delta AP day 3, and 5. Delta AP day 7.

value: Kidney


title: DC3K2

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 2 mL/kg/day vehicle (dimethyl sulfoxide) euthanized 3 days post-inoculation, biol rep 2


title: shzmat2-2-1

city: Changsha

first: Jiong

last: Li

address: No.138, Tongzipo Road

department: Department of Radiology

institute: The Third Xiangya Hospital, Central South University

data_processing:
The reference genome and its annotatton ffles were downloaded from a speciffed website. HISAT was used to build an index, and clean reads were aligned to the reference genome.
Gene expression levels were quanttffed using featureCounts to calculate gene alignment stattsttcs. Subsequently, FPKM (Fragments Per Kilobase Million) values for each gene were computed based on gene length. FPKM is currently the most used method for esttmattng gene expression levels.
DESeq2 was used for differenttal gene expression analysis between two groups, and Benjamini & Hochberg correctton was applied to P-values. Corrected P-values and log2 fold change were used as thresholds for signiffcant differenttal expression.
Enrichment analysis was performed based on the hypergeometric test, with pathway-based hypergeometric distributton testtng for KEGG and GO term-based analysis for GO.
rMATS was used to analyze alternattve splicing events, including SE (skipped exon), RI (retained intron), MXE (mutually exclusive exons), A5SS (alternattve 5' splice site), and A3SS (alternattve 3' splice site).
Assembly: ftp://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/dna/
Supplementary files format and content: fpkm.annot.txt

source_name: Liver

extract_protocol:
RNA was were extracted by Trizol method
1) By utilizing the structural characteristic that most eukaryotic mRNAs carry a polyA tail, mRNAs with polyA tails  were enriched by Oligo(dT) magnetic beads; 2) The purified mRNAs were cleaved into small fragments with fragmentation buffer at a suitable temperature; 3) First-strand cDNAs were produced by reverse transcription using a random hexamer primer; 4) Second-strand cDNAs are synthesized (strand-specific library: dUTPs were used instead of dTTPs in the  second-strand synthesis to incorporate dUTPs in the second-strand cDNAs, while the high-fidelity DNA  polymerase used in this method could not amplify uracil-containing DNA templates, thus realizing the  strand-specificity), while simultaneously performing end repair and dA-Tailing; 5) Sequencing adapter ligation was performed, followed by DNA magnetic bead purification and fragment selection  after ligation was completed to yield a library with 250-350 bp insert fragments; 6) The ligated products were amplified by PCR and purified again using DNA magnetic beads, where the products  were solubilized with nuclear-free water; 7) After the initial library was constructed, a Qubit fluorescence quantifier was used for concentration detection,  followed by a Qsep400 high-throughput biofragment analyzer for fragment size detection，Finally, the  effective concentration of the library was accurately quantified using Q-PCR;

value: Liver

value: Hepatocellular carcinoma cells


title: VCaP_FOXA1_DMSO_DHT_rep2


title: VCaP_FOXA1_DMSO_DHT_rep3


title: shzmat2-2-2


title: shzmat2-1-3


title: DC1K3

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 2 mL/kg/day vehicle (dimethyl sulfoxide) euthanized 1 day post-inoculation, biol rep 3


title: VCaP_input_ML792-EtOH_rep1

description: P2 100SE

value: ML792 + EtOH


title: VCaP_FOXA1_DMSO_DHT_rep1


title: DC1K2

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 2 mL/kg/day vehicle (dimethyl sulfoxide) euthanized 1 day post-inoculation, biol rep 2


title: VCaP_input_ML792-DHT_rep3

description: P2 100SE


title: VCaP_input_DMSO-DHT_rep2

description: P2 100SE


title: Tet1, Cortex, BS, WT Rep2

source_name: Adult Cortex

value: WT


title: shzmat2-1-2


title: VCaP_IgG_ML792-DHT_rep1

description: P2 100SE

value: Normal rabbit IgG (Millipore, 12-370)


title: DC1K1

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 2 mL/kg/day vehicle (dimethyl sulfoxide) euthanized 1 day post-inoculation, biol rep 1


title: VCaP_IgG_ML792-EtOH_rep1

description: P2 100SE

value: Vertebral Cancer of the Prostate


title: shzmat2-2-3


title: shzmat2-1-1


title: DA7K3

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 1000 mg/kg/day Andrographis paniculata extract euthanized 7 days post-inoculation, biol rep 3


title: DC3K3

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 2 mL/kg/day vehicle (dimethyl sulfoxide) euthanized 3 days post-inoculation, biol rep 3


title: huh7-control-3


title: VCaP_H3K27ac_ML792-DHT_rep2

description: P2 100SE

source_name: VCaP

value: VCaP

value: H3K27ac (Active Motif, 39133)


title: VCaP_IgG_DMSO-DHT_rep1

description: P2 100SE


title: DA7K2

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 1000 mg/kg/day Andrographis paniculata extract euthanized 7 days post-inoculation, biol rep 2


title: VCaP_H3K27ac_ML792-DHT_rep1

description: P2 100SE

value: ML792 + DHT


title: huh7-control-1


title: VCaP_H3K27ac_ML792-EtOH_rep1

description: P2 100SE


title: DA7K1

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 1000 mg/kg/day Andrographis paniculata extract euthanized 7 days post-inoculation, biol rep 1


title: VCaP_H3K27ac_DMSO-DHT_rep2

description: P2 100SE


title: DA3K3

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 1000 mg/kg/day Andrographis paniculata extract euthanized 3 days post-inoculation, biol rep 3


title: LNCaP, Vehicle_CFS, 0, 24 hours, Input, Rep2

city: Durham

first: Xiaodi

last: Qin

address: 2424 Erwin Road

institute: Duke Cancer Institute

data_processing:
ChIP-seq reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39.
Trimmed ChIP-seq reads were aligned to GRCh38/hg38 using BWA v0.7.17. Reads that were unaligned, multi-mapped, failed platform quality checks or had mapping quality less than 30 were removed.
Peaks were called and narrowPeak files were generated using MACS v2.2.7.1 with --pvalue 0.01, --keep-dup all, --call-summits, and -f BAMPE
BigWig files were generated using bamCoverage v3.5.1 from Deeptools suite, with --normalizeUsing RPGC, --binSize 10, --minFragmentLength 40, --effectiveGenomeSize 2701495761.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: Prostate

growth_protocol: LNCaP cells (2,000,000 cells/dish) were seeded in 15 cm tissu culture dish in RPMI 1640  supllemented with 8% charcoal dextran treated FBS(CFS). 5 millions cells were collected per condition. For VCaP cell line (5,000,000 cells/dish), cells were seeded in 15 cm tissu culture dish  in DMEM (8% CFS). 48 hrs later, cells were treated with R1881 for an additional 24 hrs

extract_protocol:
Cells were fixed using a final concentration of 1% methanol-free formaldehyde in PBS at for 10 min and quenched with 125mM glycine for 5 min. Cells were then washed twice in PBS Wash Buffer (Active Motif #53046), pelleted, and stored at -80˚C. For sonication, cells were thawed and resuspended in ice cold Buffer LB1 (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) containing 1x Halt™ 100X Protease and Phosphatase Inhibitor Cocktail (ThermoFisher #78446) on a rotator at 4˚C for 10 minutes. Cells were then centrifuged, liquid decanted, and resuspended in Buffer LB2 (10mM Tris-HCL pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) containing 1x Halt™ 100X Protease and Phosphatase Inhibitor Cocktail. Cells were then centrifuged, liquid decanted and resuspended in ice cold Buffer LB3 (10mM Tris-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-laurylsarcosine) containing 1x Halt™ 100X Protease and Phosphatase Inhibitor Cocktail. This nuclear resuspension was transferred into Covaris microtube 130 AFA Fiber pre-Slit snap-cap tubes (Covaris #520045) at a maximum concentration of 3 million cells per 130µL and sonicated using the following parameters on a Covaris ME220 according to the manufacturer’s recommendations (Duration (s) = 360, Peak Power = 75, Duty Factor = 5.0, Cycles/Burst = 1000). Following sonication, 10µL of chromatin was removed for analysis of resulting DNA size and concentration. Briefly, 10µL of sonicated chromatin was incubated with 20µg RNase A (Thermo Scientific #EN0531) in TE pH 8 for 30 minutes at 37˚C in a thermal cycler. 20µg of Proteinase K (Thermo Scientific #EO0491) in Active Motif Elution Buffer AM4 (Active Motif #103926) was then added and the sample was incubated for 30 minutes at 55˚C followed by 90 minutes at 65˚C in a thermal cycler. Samples were then cooled to room temperature and DNA was purified using SPRIselect beads (Beckman #B23318) at a bead:sample ratio of 1.4:1 and eluted in 10µL of 10 mM Tris, 0.1 mM EDTA.
Chromatin corresponding to 1 million cells was diluted with 200µL in Active Motif ChIP Buffer and incubated with pre-clearing Protein G agarose beads. After pre-clearing, agarose beads were pelleted and transferred to a new microcentrifuge tube containing 4µg of antibody specific to the target protein (AR: Abcam ab236225). IPs were then incubated overnight on a rotator at 4˚C. Protein G Agarose beads prepared the previous day according to Active Motif’s Low Cell ChIP kit were added to the antibody-bound chromatin and incubated for 4 hours on a rotator at 4˚C. IPs were then transferred to ChIP filtration columns, washed, and eluted in 80µL according to Active Motif’s Low Cell ChIP kit and DNA purified using SPRIselect beads at a bead:sample ratio of 1.4:1. After SPRI cleanup, ChIP samples and reverse crosslinked input DNA was made into sequencing Illumina libraries using Swift NGS 2S Plus (Swift Biosciences #21096) and indexed using Single Indexed Adapters with MIDs (Swift Biosciences #279384).  ChIP-seq libraries were prepared using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit with UMIs.

treatment_protocol: LNCaP and VCaP cells were tretaed with either vehicle, or increasing concentrations of low-dose (0.01, 0.03, 0.06, 0.1 nM R1881) or High-Dose (10nM R1881) androgens for 24 hours

value: Prostate

value: LNCaP

value: epithelial

value: Input

tag: compound

tag: dose

value: 24 hours


title: VCaP_H3K27ac_ML792-EtOH_rep2

description: P2 100SE


title: VCaP_H3K27ac_DMSO-EtOH_rep2

description: P2 100SE

value: DMSO + EtOH


title: VCaP_H3K27ac_DMSO-DHT_rep1

description: P2 100SE

value: DMSO + DHT


title: DA3K1

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 1000 mg/kg/day Andrographis paniculata extract euthanized 3 days post-inoculation, biol rep 1

value: Kidney


title: VCaP_input_DMSO-EtOH_rep1

description: P2 100SE


title: VCaP_H3K27ac_DMSO-EtOH_rep1

description: P2 100SE


title: DA3K2

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 1000 mg/kg/day Andrographis paniculata extract euthanized 3 days post-inoculation, biol rep 2


title: LNCaP, Vehicle_CFS, 0, 24 hours, Input, Rep1


title: DA1K2

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 1000 mg/kg/day Andrographis paniculata extract euthanized 1 day post-inoculation, biol rep 2


title: huh7-control-2

value: Liver


title: DA1K3

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 1000 mg/kg/day Andrographis paniculata extract euthanized 1 day post-inoculation, biol rep 3


title: LNCaP, Vehicle_CFS, 0, 24 hours, AR, Rep1

value: AR


title: LNCaP, R1881, 10 nM, 24 hours, Input, Rep2

value: 10 nM


title: lyz+, regeneration, scRNAseq

city: Atlanta

first: Elizabeth

middle: A

last: Peterson

state: GA

address: 1760 Haygood Dr NE

institute: Emory University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
All processing was performed in 10X Genomics CellRanger v3.1.0 using default parameters
Assembly: Danio_rerio_GRCz11
Supplementary files format and content: Cell Ranger outputs a .mtx file with the feature-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cell Ranger. The matrix is in market exchange format while the row (gene or feature) and columns (cell barcodes) are provided as TSV files. File formats are documented in the Cell Ranger software manual

organism: Danio rerio

source_name: heart

extract_protocol:
Hearts were dissected from adult lyz:EGFP zebrafish, and ventricles were digested with Liberase TM (0.26 U/ml ). Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics )

value: heart

tag: strain

value: neutrophil

tag: age

value: 6 months

value: 1 dpa


title: DA1K1

source_name: Golden hamster kidney tissue, Delta variant SARS-CoV-2-infected, 1000 mg/kg/day Andrographis paniculata extract euthanized 1 day post-inoculation, biol rep 1


title: LNCaP, R1881, 10 nM, 24 hours, Input, Rep1

tag: cell type


title: LNCaP, R1881, 10 nM, 24 hours, AR, Rep2