title: RASMC, DAPT_plus_Cholesterol_treatment, H3K4me3, rep3(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K4me3_rep3, Cut_Tag
rat aortic smooth muscle cell


title: iSLK-WT Cells, 24 hour lytic induction, cytoplasmic RNA fraction, Bio Rep 2

status: Public on May 29 2025

type: SRA

city: Lausanne

first: Mandy

last: Muller

address: Rue du Bugnon 48

department: Institute of Microbiology

country: Switzerland

institute: University Hospital of Lausanne

description: Library name: 24BC

library_source: transcriptomic

data_processing:
Samples were sequenced using the Illumina PE150 sequencing platform. Raw data generated on the sequencing platform contained a small percentage of low-quality data. The base quality score is an important indicator of sequencing quality. Base quality (Q) is closely related to the sequencing error rate (P) and is influenced by factors such as the status of the sequencer, the quality of sequencing reagents, and the characteristics of the samples. The formula for calculating the quality score is as follows. Q=-10log(10)P
The raw data then filtered to get high-quality data. The raw data were processed as the following steps: a. Start searching for poly(A) sequences in the reads from the right side, with a length of 6A and a mismatch rate of 0.2. b. Search for poly(A) sequences from the left side, with a length of 9A and a mismatch rate of 0.1. c. Truncate the part of the poly(A) sequence that contains 4 consecutive non-A bases, keeping the longest portion of the poly(A) sequence. d. If the remaining part of the reads after truncating the poly(A) sequence has a length of at least 20, then such reads are classified as poly(A) clean reads, and the corresponding poly(A) length is equal to the length of poly(A) in the reads.
The retained poly(A) sequence lengths are greater than or equal to 11 nt, and the alignment was performed using Bowtie2. In the end, only one type of read was obtained, meaning that the length of the front part of the sequence is not less than 20 nt, and the length of the back part poly(A) sequence is not less than 11 nt.
RPKM (Reads per kilobase of a gene per million reads) indicates the number of reads from a specific gene per kilobase length among every million reads, and it characterizes the expression abundance of the gene (Mortazavi, Williams et al. 2008). By normalizing for mRNA length and sequencing depth (RPKM), the expression abundance between different sequencing samples can be compared, eliminating biases that may arise from variations in mRNA length and sequencing depth between different samples. RPKM = total exon reads / (uniquely mapped reads * exon length) - total exon reads: The number of reads mapped to all exons of a gene, counted in units. - uniquely mapped reads: The number of reads in a sample that have a unique mapping in the genome, counted in millions. - exon length: The length of the exon, measured in Kb. - RPKM indicates the number of reads falling within the range of every kilobase length of a specific gene among every million uniquely mapped reads. In this part of the analysis, we will statistically analyze the number of genes detected in this project with RPKM > 0 and RPKM ≥ 1.
Assembly: Hg38  and  AF148805.2 HHV8
Supplementary files format and content: Obtain_the_high_quality_clean_reads.xls - xls file containign the number of detected reads, polyA containing reads, and cleaned polyA reads
Supplementary files format and content: Tab-delimited text files containing the RPKM for each experimental condtion, lists of number of transcripts or genes associated with polyA tail length, lists of comparisons looking at the change of polyA tail length between experimental conditions, list of the differential statistics between conditions and polyA tail change

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: iSLK-WT (BAC16)

growth_protocol: iSLK-WT cells were grown in DMEM supplimented with 10% fetal bovine serum (FBS) and antibiotics (Penn/Strep) with humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cell pellets were washed with cold PBS, then resuspended and incubated in fractionation buffer A (50mM Tris pH8, 140mM NaCl, 1.5mM MgCl2, 0.2% NP40, 1mM DTT, and 200units RNAsin) for 5 minutes on ice. Solution was spun at 3000 x g. Supernatant was collected on ice as cytoplasmic fraction and pellet was kept as nuclear fraction. 1ml of TRIzol (invitrogen) reagent was added to each sample.
Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis. For each sample, ~5μg of total RNA was used for poly(A)-seq library preparation. Total RNA was digested by RNase T1 (Thermo, EN0541), polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Vazyme, N401-01) before directional poly(A)-seq library preparation. After 3' adaptor (Gnomegen, K02420-L) ligation, purified mRNAs were reverse transcripted to cDNA with RT primer that was complemented with the 3' adaptor. Then DNA was synthesized with Terminal-Tagging oligo cDNA and SMARTer® Stranded RNA-Seq Kit (TAKARA, 634837). Followed by purification and amplification, PCR products corresponding to 200-500 bps were purified, quantified, and stored at -80 °C before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Novaseq Xplus for 150 nt paired-end sequencing.

treatment_protocol: Lytic infection was induced by adding 0.2ug/ml doxycycline and 110ug/ml sodium butyrate for 24 hours

tag: cell line

value: iSLK-WT (BAC16)

tag: cell type

value: Epithelial/renal carcinoma

tag: genotype

value: WT

tag: treatment

value: Doxycycline induced lytic reactivation


title: PBMCs of SPF chicken 14 days after vaccination of inactivated AIV vaccine

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

country: China

institute: Xi'an Jiaotong University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://github.com/10XGenomics/cellranger)
Assembly: GRCg6a
Supplementary files format and content: Matrix file containing the transcription profiles of all single cells could be loaded to Seurat for further analysis.

molecule: total RNA

organism: Gallus gallus

source_name: blood

extract_protocol:
Seperated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina scRNA-seq and 10 × Chromium platform protocols (single cell 3’ v3 protocol, 10x Genomics).

tag: tissue

value: blood

tag: Sex

value: male

value: peripheral blood mononuclear cells

tag: age

value: 35-day old

value: inactivated AIV vaccine


title: iSLK-WT Cells, 24 hour lytic induction, nuclear RNA fraction, Bio Rep 1

description: Library name: 24AN

molecule: nuclear RNA


title: PBMCs of SPF chicken 7 days after vaccination of live AIV vaccine

description: 10x Genomics

value: live AIV vaccine


title: CONTROL_TE57_274

type: RNA

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

data_processing: Data were quantified by relative threshold cycles (Crt) methods and normalized on miR-16-5p as per the manufacturer’s instructions (Thermo Fisher Scientific). To further compensate for variability, we added additional normalizers by selecting the two miRNAs most correlating with miR-16-5p, from the list of six miRNAs previously described as housekeeping (doi:10.1093/jnci/djv063). Normalization was performed using the following procedure: a scaling factor (SF) was calculated for each sample, by subtracting the average of the three normalizers to a constant value (K=19.079)(doi:10.1093/jnci/djv063). Data were then normalized using the formula: Crt normalized=miRNA Crt raw – SF. Normalization was skipped for Crt=40. Batch bias was investigated through analysis of the miRNAs expression distribution across centers (FC analysis, Wilcoxon Rank Sum test).

label: FAM

source_name: plasma

label_protocol: Total RNA was reverse transcribed using the custom RT Primers and components supplied with the TaqMan MicroRNA Reverse Transcription Kit. The pre-amplified samples were assembled with TaqMan OpenArray Real-Time PCR Master Mix and loaded to OpenArray plates using the OpenArray Accufill System

growth_protocol: not applicable

extract_protocol: Plasma samples were thawed on ice, and RNA was extracted with the commercial miRNeasy mini-Kit (QIAgen™, Hilden, Germany) using the QIAcube™ robot, following the manufacturer´s instructions.

treatment_protocol: not applicable

tag: gender

value: M

tag: smocking status

value: CURRENT

tag: nodule density

value: solid

tag: nodule size

tag: molecule subtype

value: microRNA

tag: center

value: MUG


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K4me3, rep2(Cut&Tag)

city: Xiamen

first: Wei

last: Shen

state: Fujian

address: 2999 Jinshan Rd, Huli District

institute: Xiamen University

description:
Library name: RASMC_DAPT_Cholesterol_H3K4me3_rep2, Cut_Tag
rat aortic smooth muscle cell

library_source: genomic

data_processing:
raw reads was cleaned by fastp with default parameters
cleaned reads were mapped to rn7 genome downloaded from ensembl by bowtie2
duplicated reads were further removed by picard
narrowpeak files were generated by macs2
bigwig files were generated by deeptools
Assembly: rn7
Supplementary files format and content: narrowpeak
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Rattus norvegicus

source_name: aortic smooth muscle cell

extract_protocol:
cells were lysed and nucleus were extracted to incubate with primiary antibody, secondary antibody and pAG-Tn5
library was contructed by usingCUT&TAG 3.0 High-Sensitivity Kit for Illumina (Novoprotein N259-YH01)

value: aortic smooth muscle cell

tag: batch


title: RASMC, Cholesterol_treatment, H3K27ac, rep1(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K27ac_rep1, Cut_Tag
rat aortic smooth muscle cell


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K4me3, rep1(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K4me3_rep1, Cut_Tag
rat aortic smooth muscle cell


title: CONTROL_TE57_273


title: RASMC, Cholesterol_treatment, H3K27ac, rep2(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K27ac_rep2, Cut_Tag
rat aortic smooth muscle cell


title: PBMCs of SPF chicken 21 days after vaccination of live AIV vaccine

description: 10x Genomics


title: EBV-infected B Cells, STAT1 KO, day 7 (biol rep 3)

city: Durham

first: Nicolas

middle: Martin

last: Reinoso-Vizcaino

state: North Carolina

address: 213 Research Drive

department: Molecular Genetics & Microbiology

country: USA

institute: Duke University

description:
Library name: 1599_d7_STAT1
Column in Early_Infection_RAW_counts

data_processing:
Raw files were analyzed using FastQC(v0.12.1)
Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.39) with the following parameters: ILLUMINACLIP:IlluminaAdapterPE.fa:2:30:10, SLIDINGWINDOW:4:20, and MINLEN:36.
Trimmed reads were aligned to genomic reference constructed from the concatenation of human genome (hg38) with type 1 EBV genome (NC_007605), using Hisat2 (v2.1.0).
Gene counts were generated using featureCounrs from Rsubread package (v2.18.0)
Read counts were normalized using DESeq2 (v1.44.0)
Assembly: hg38 concatenated with type 1 EBV genome (NC_007605)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: Peripheral blood mononuclear cells

growth_protocol: EBV-infected B cells were growth on RPMI media supplemented with 20% fetal bovine serum (FBS) in humified athmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the RNeasy MicroKit (Qiagen), ), including on-column DNase digestion.
Poly(A) mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB). Libraries were quantified with Qubit dsDNA BR Assay (Invitrogen) and quality control was performed using High Sensitivity D1000 ScreenTape Assay on 4150 TapeStation System (Agilent).

treatment_protocol: Primary B cells were tranfected with Cas9-RNP complexes targeting gene of interest plus CD46 (used as a proxy) and then infected with EBV (B95.8 strain).

value: Peripheral blood mononuclear cells

value: Primary B cells

value: CD46 / STAT1 KO

value: EBV-infected

tag: time

value: Day 7


title: PBMCs of SPF chicken 7 days after vaccination of inactivated AIV vaccine

description: 10x Genomics

value: blood


title: PBMCs of SPF chicken 4 days after vaccination of live AIV vaccine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://github.com/10XGenomics/cellranger).
Assembly: GRCg6a
Supplementary files format and content: Matrix file containing the transcription profiles of all single cells could be loaded to Seurat for further analysis.

extract_protocol:
Separated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina scRNA-seq and 10 × Chromium platform protocols (single cell 3’ v3 protocol, 10x Genomics).

value: male

value: 35 days


title: RASMC, DAPT_treatment, H3K4me3, rep3(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K4me3_rep3, Cut_Tag
rat aortic smooth muscle cell

value: WT


title: TUMOR_TE57_271

value: FORMER

tag: histology

value: adenocarcinoma

tag: Stage

value: IB


title: PBMCs of SPF chicken 4 days after vaccination of inactivated AIV vaccine

description: 10x Genomics

value: peripheral blood mononuclear cells

value: inactivated AIV vaccine


title: RASMC, DAPT_treatment, H3K4me3, rep2(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K4me3_rep2, Cut_Tag
rat aortic smooth muscle cell


title: EBV-infected B Cells, STAT1 KO, day 7 (biol rep 1)

description:
Library name: 1577_d7_STAT1
Column in Early_Infection_RAW_counts


title: EBV-infected B Cells, ISG15 KO, day 7 (biol rep 3)

description:
Library name: 1599_d7_ISG15
Column in Early_Infection_RAW_counts

value: CD46 / ISG15 KO


title: RASMC, DAPT_treatment, H3K4me3, rep1(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K4me3_rep1, Cut_Tag
rat aortic smooth muscle cell


title: RAW264.7 cells coculture 48h with TTJ cells, replicate C

city: Boston

first: Remi

last: Diesler

state: MA

address: 75 Francis Street

department: Pulmonary Division

institute: Brigham and Women's Hospital

description:
R836
NovaSeq X Plus Series (PE150)

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high qualit
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built 3 using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression lev
For DESeq2 with biological replicates: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package (1.20.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The corrected P-value ≤ 0.05 & |log2 (foldchange)| ≥ 1 was set as the threshold of significant differential expression. 4 For edgeR without biological replicates: Prior to differential gene expression analysis, for each sequencing library, read counts were adjusted using the edgeR R package (3.22.5) by scaling normalization factors to eliminate differences in sequencing depth between samples, followed by differential expression analysis. The resulting P value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The corrected P-value ≤ 0.05 & |log2 (foldchange)| ≥ 1 was set as the threshold of significant differential expression.
2.5 GO and KEGG enrichment analysis of differentially expressed genes Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways 5 with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway. 2.6 Gene Set Enrichment Analysis Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre-defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO、KEGG、 Reactome、DO and DisGeNET data sets were used for GSEA independently.
Assembly: mm10
Supplementary files format and content: raw counts
Supplementary files format and content: FPKM counts

organism: Mus musculus

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells and TTJ cells were maintained in DMEM + FBS 10% in atmosphere enriched in CO2 (5%) at 37C

extract_protocol:
Total RNA was extracted using RNA Mini Extraction Kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

tag: cell line

value: RAW264.7 cells

value: Macrophages

value: coculture 48h with TTJ cell


title: RAW264.7 cells coculture 48h with TTJ cells, replicate B

description:
R835
NovaSeq X Plus Series (PE150)

tag: cell type


title: EBV-infected B Cells, ISG15 KO, day 7 (biol rep 2)

description:
Library name: 1578_d7_ISG15
Column in Early_Infection_RAW_counts

value: Peripheral blood mononuclear cells

value: Primary B cells

tag: genotype


title: RASMC, Cholesterol_treatment, H3K4me3, rep3(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K4me3_rep3, Cut_Tag
rat aortic smooth muscle cell

value: aortic smooth muscle cell

tag: treatment


title: TUMOR_TE57_269

value: M

value: CURRENT

value: IA

value: part-solid

value: microRNA

value: MUG


title: EBV-infected B Cells, ISG15 KO, day 7 (biol rep 1)

description:
Library name: 1577_d7_ISG15
Column in Early_Infection_RAW_counts

tag: tissue

value: EBV-infected

value: Day 7


title: RASMC, Cholesterol_treatment, H3K4me3, rep2(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K4me3_rep2, Cut_Tag
rat aortic smooth muscle cell

value: WT


title: RAW264.7 cells coculture 48h with TTJ cells, replicate A

description:
R834
NovaSeq X Plus Series (PE150)


title: CONTROL_TE57_264

value: F

value: FORMER


title: EBV-infected B Cells, CD46 KO (control), day 7 (biol rep 3)

description:
Library name: 1599_d7_CD46
Column in Early_Infection_RAW_counts

value: CD46 KO


title: RAW264.7 cells, replicate C

description:
R833
NovaSeq X Plus Series (PE150)

value: RAW264.7 cells

value: Macrophages


title: CONTROL_TE57_263

value: solid


title: EBV-infected B Cells, STAT1 KO, day 7 (biol rep 2)

description:
Library name: 1578_d7_STAT1
Column in Early_Infection_RAW_counts

value: Peripheral blood mononuclear cells

value: Primary B cells

value: CD46 / STAT1 KO


title: CONTROL_TE57_270

value: M


title: RASMC, Cholesterol_treatment, H3K4me3, rep1(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K4me3_rep1, Cut_Tag
rat aortic smooth muscle cell

value: aortic smooth muscle cell


title: RAW264.7 cells, replicate B

description:
R832
NovaSeq X Plus Series (PE150)


title: RASMC, DMSO_treatment, H3K4me3, rep3(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K4me3_rep3, Cut_Tag
rat aortic smooth muscle cell

value: DMSO


title: EBV-infected B Cells, CD46 KO (control), day 7 (biol rep 2)

description:
Library name: 1578_d7_CD46
Column in Early_Infection_RAW_counts


title: EBV-infected B Cells, CD46 KO (control), day 7 (biol rep 1)

description:
Library name: 1577_d7_CD46
Column in Early_Infection_RAW_counts


title: CONTROL_TE57_262

value: CURRENT

value: part-solid

value: microRNA


title: CONTROL_TE57_272

value: MUG


title: RAW264.7 cells, replicate A

description:
R831
NovaSeq X Plus Series (PE150)

value: WT


title: RASMC, DMSO_treatment, H3K4me3, rep2(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K4me3_rep2, Cut_Tag
rat aortic smooth muscle cell


title: CONTROL_TE57_261


title: si_STAU1_3

city: Urumqi

first: Ling

last: Zhang

state: Xinjiang

address: No. 91 Tianchi Road

institute: People's Hospital of Xinjiang Uygur Autonomous Region

data_processing:
For high-throughput sequencing applications, libraries were prepared according to the manufacturer's guidelines and sequenced on an Illumina NovaSeq Xplus system utilizing 150 nt paired-end reads.
Initially, raw reads with more than 2 N bases were removed. Next, adaptors and low-quality bases were trimmed from the raw sequencing data via the FASTX-Toolkit (version 0.0.13).  Reads shorter than 16 nt were also excluded.  The cleaned reads were subsequently aligned to the GRCh38 genome via HISAT2, allowing for up to 4 mismatches20.
Only uniquely mapped reads were utilized for counting gene read numbers and calculating fragments per kilobase of transcript per million fragments mapped (FPKM) 21.
The R Bioconductor package DESeq2 was used to screen out the differentially expressed genes (DEGs). An adjusted P value <0.01 and a fold change ≥2 or ≤0.5 were set as the cutoff criteria for identifying DEGs.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) among the samples were identified and quantified via the ABLas pipeline. In summary, ABLs detect ten types of ASEs on the basis of splice junction reads, which include exon skipping (ES), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), intron retention (IR), mutually exclusive 5' UTRs (5pMXE), mutually exclusive 3' UTRs (3pMXE), cassette exons, A3SS & ES, and A5SS & ES. To evaluate RBP-regulated ASEs, Student’s t test was performed to evaluate the significance of the ratio alteration of AS events. Events that reached significance at a P value cutoff corresponding to a false discovery rate cutoff of 5% were classified as RBP-regulated ASEs.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted via TRIzol (15596-018; Ambion, USA). The RNA was further purified through two rounds of phenol‒chloroform extraction and subsequently treated with RQ1 DNase (M6101; Promega, Madison, WI, USA) to eliminate any DNA contamination. The quality and concentration of the purified RNA were assessed by measuring the absorbance at 260 nm and 280 nm (A260/A280) via an ultrafine spectrophotometer (N50 touch, IMPLEN, Germany). Additionally, the integrity of the RNA was confirmed via 1.0% agarose gel electrophoresis. For each sample, 1 μg of total RNA was treated with RQ1 DNase (M6101, Promega, USA) to eliminate DNA prior to the preparation of a directional RNA-seq library via the VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605, Vazyme, China).  mRNAs were isolated via VAHTS mRNA capture beads (N401, Vazyme, China).  The fragmented RNA was then converted into double-stranded cDNA.  After the end repair and A-tailing steps, the DNAs were ligated to VAHTS RNA Multiplex Oligos Set 1 for Illumina (N323, Vazyme, China), followed by amplification of the ligated products.  These products were purified and quantified before being stored at -80°C until sequencing.
For high-throughput sequencing, the libraries were prepared for following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

value: STAU1 knockdown


title: CONTROL_TE57_260

value: HUM


title: Fus+/+, 3 months, biol rep 4, control for KO

city: London

first: Pietro

last: Fratta

address: Queen Square

country: United Kingdom

institute: University College London

description:
Library name: KO_WT4
Column name in annotated_raw_counts.csv: KO_WT4

data_processing:
Sequence reads were trimmed for adapter sequences/low-quality sequences using fastp.
Trimmed reads were aligned to the reference mouse genome (GRCm38) using STAR (v2.7.0f). Gene expression levels were quantified by counting the reads that are mapped to each gene using FeatureCounts (v1.6.4). Differential gene expression analysis was performed using the DEseq2 package (v1.36.0).
Assembly: GRCm38
Supplementary files format and content: comma-delimited text file includes raw counts for all samples

source_name: spinal cord

extract_protocol:
Snap frozen spinal cord samples were crushed by a pestle and mortar on dry ice followed by lysis of half the sample in Qiazol (Qiagen). RNA was then extracted using the miRNeasy Mini Kit (Qiagen) as per manufacturer’s instructions. RNA quality was checked by the Agilent Tapestation system and RNAs were stored at -80°C. All sequenced samples had RIN scores higher than 8.
cDNA libraries were made using the KAPA RNA HyperPrep Kit with RiboErase (Roche).

value: spinal cord

value: Fus+/+


title: RASMC, DMSO_treatment, H3K4me3, rep1(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K4me3_rep1, Cut_Tag
rat aortic smooth muscle cell


title: si_STAU1_2


title: TUMOR_TE57_26

value: adenocarcinoma

value: IIB


title: si_STAU1_1


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K4me2, rep3(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K4me2_rep3, Cut_Tag
rat aortic smooth muscle cell


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K4me2, rep2(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K4me2_rep2, Cut_Tag
rat aortic smooth muscle cell


title: CONTROL_TE57_259


title: Fus+/+, 3 months, biol rep 2, control for KO

description:
Library name: KO_WT2
Column name in annotated_raw_counts.csv: KO_WT2


title: NC_3

value: control plasmid


title: BENIGN_TE57_258

value: F

value: FORMER

value: solid


title: RASMC, DMSO_treatment, H3K27ac rep3(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K27ac_rep3, Cut_Tag
rat aortic smooth muscle cell

value: aortic smooth muscle cell


title: Fus+/+, 3 months, biol rep 3, control for KO

description:
Library name: KO_WT3
Column name in annotated_raw_counts.csv: KO_WT3


title: Fus+/+, 3 months, biol rep 1, control for KO

description:
Library name: KO_WT1
Column name in annotated_raw_counts.csv: KO_WT1


title: Fus-/-, 3 months, biol rep 4

description:
Library name: KO_HOM4
Column name in annotated_raw_counts.csv: KO_HOM4

value: Fus-/-


title: NC_2


title: RASMC, DAPT_treatment, H3K4me2, rep3(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K4me2_rep3, Cut_Tag
rat aortic smooth muscle cell


title: NC_1


title: Fus-/-, 3 months, biol rep 3

description:
Library name: KO_HOM3
Column name in annotated_raw_counts.csv: KO_HOM3


title: RASMC, DAPT_treatment, H3K4me2, rep2(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K4me2_rep2, Cut_Tag
rat aortic smooth muscle cell


title: BENIGN_TE57_257

value: M

value: CURRENT


title: BENIGN_TE57_256

value: microRNA


title: Fus-/-, 3 months, biol rep 2

description:
Library name: KO_HOM2
Column name in annotated_raw_counts.csv: KO_HOM2


title: Subject11_trametinib

city: Dallas

first: Jonathan

last: Rios

state: TX

address: 2222 Welborn Street

institute: Scottish Rite for Children

data_processing:
Sequence reads were mapped to the human reference genome (hg38) using STAR (v2.7.8). Alignments were filtered to remove duplicates, singleton reads, and unaligned reads. Gene expression was quantified using the Ensembl database (release 109). Expression levels of protein-coding transcripts were normalized using the Median Ratio method for DESeq2 analysis.Processed files with FPKM normalization are also included.
Assembly: hg38
Supplementary files format and content: Gene expression matrix normalized by Median Ratio method for DESeq2 analysis
Supplementary files format and content: Gene expression matrix normalized by FPKM

source_name: fracture pseudarthrosis bone

growth_protocol: MEM-alpha with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was extracted using the Rneasy Plus minikit (Qiagen)
Ribosomal RNA was removed using the RiboErase kit (Kapa Biosystems). Remaining RNA was fragmented and reverse-transcribed using SuperScript III RT enzyme (Life Technologies). Following second strand synthesis, dual indexes were ligated and the library amplified prior to sequencing on an Illumina NovaSeq X Plus to generate paired-end 150bp reads.

treatment_protocol: vehicle (dmso), 2.5nM trametinib, or 5uM selumetinib

value: fracture pseudarthrosis bone

value: primary cell

value: trametinib


title: TUMOR_TE57_253

value: part-solid

value: HUM


title: RASMC, DAPT_treatment, H3K4me2, rep1(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K4me2_rep1, Cut_Tag
rat aortic smooth muscle cell

value: WT


title: Subject11_selumetinib

value: selumetinib


title: Fus-/-, 3 months, biol rep 1

description:
Library name: KO_HOM1
Column name in annotated_raw_counts.csv: KO_HOM1

value: spinal cord


title: RASMC, Cholesterol_treatment, H3K4me2, rep3(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K4me2_rep3, Cut_Tag
rat aortic smooth muscle cell


title: Fus d14/d14, 3 months, biol rep 5

description:
Library name: D14_HOM3_5
Column name in annotated_raw_counts.csv: D14_HOM3_5

value: Fus d14/d14


title: RASMC, Cholesterol_treatment, H3K4me2, rep2(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K4me2_rep2, Cut_Tag
rat aortic smooth muscle cell


title: Fus d14/d14, 3 months, biol rep 4

description:
Library name: D14_HOM3_4
Column name in annotated_raw_counts.csv: D14_HOM3_4


title: Subject10_trametinib


title: RASMC, Cholesterol_treatment, H3K4me2, rep1(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K4me2_rep1, Cut_Tag
rat aortic smooth muscle cell


title: CONTROL_TE57_250

value: F

value: MUG


title: Subject11_DMSO

value: vehicle


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K4me2, rep1(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K4me2_rep1, Cut_Tag
rat aortic smooth muscle cell

value: aortic smooth muscle cell


title: Subject10_selumetinib


title: CONTROL_TE57_252

value: solid


title: Fus d14/d14, 3 months, biol rep 3

description:
Library name: D14_HOM3_3
Column name in annotated_raw_counts.csv: D14_HOM3_3


title: RASMC, DMSO_treatment, H3K4me2, rep3(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K4me2_rep3, Cut_Tag
rat aortic smooth muscle cell

value: DMSO


title: Fus d14/d14, 3 months, biol rep 2

description:
Library name: D14_HOM3_2
Column name in annotated_raw_counts.csv: D14_HOM3_2


title: Subject10_DMSO


title: RASMC, DMSO_treatment, H3K4me2, rep2(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K4me2_rep2, Cut_Tag
rat aortic smooth muscle cell


title: TUMOR_TE57_25

value: M

value: CURRENT

value: adenocarcinoma

value: IA


title: CONTROL_TE57_249

value: FORMER

value: microRNA


title: RASMC, DMSO_treatment, H3K4me2, rep1(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K4me2_rep1, Cut_Tag
rat aortic smooth muscle cell


title: TUMOR_TE57_247

value: IIB

value: part-solid


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K4me1, rep3(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K4me1_rep3, Cut_Tag
rat aortic smooth muscle cell

value: WT


title: CONTROL_TE57_248


title: Subject9_trametinib

value: fracture pseudarthrosis bone

value: primary cell

value: trametinib


title: Fus d14/d14, 3 months, biol rep 1

description:
Library name: D14_HOM3_1
Column name in annotated_raw_counts.csv: D14_HOM3_1

value: spinal cord

value: Fus d14/d14


title: TUMOR_TE57_246

value: F

value: carcinoma planoepitheliale

value: MUG


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K4me1, rep2(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K4me1_rep2, Cut_Tag
rat aortic smooth muscle cell

value: aortic smooth muscle cell


title: Subject9_selumetinib

value: selumetinib


title: CONTROL_TE57_251

value: M


title: Fus+/+, 3 months, biol rep 4

description:
Library name: D14_WT3_4
Column name in annotated_raw_counts.csv: D14_WT3_4

value: Fus+/+


title: Subject8_trametinib


title: Fus+/+, 3 months, biol rep 3

description:
Library name: D14_WT3_3
Column name in annotated_raw_counts.csv: D14_WT3_3


title: Fus+/+, 3 months, biol rep 2

description:
Library name: D14_WT3_2
Column name in annotated_raw_counts.csv: D14_WT3_2


title: RASMC, DAPT_plus_Cholesterol_treatment, H3K4me1, rep1(Cut&Tag)

description:
Library name: RASMC_DAPT_Cholesterol_H3K4me1_rep1, Cut_Tag
rat aortic smooth muscle cell


title: Fus+/+, 3 months, biol rep 1

description:
Library name: D14_WT3_1
Column name in annotated_raw_counts.csv: D14_WT3_1


title: Subject8_selumetinib


title: RASMC, DAPT_treatment, H3K4me1, rep3(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K4me1_rep3, Cut_Tag
rat aortic smooth muscle cell


title: Subject8_DMSO

value: vehicle


title: Fus d14/d14, 1 month, biol rep 5

description:
Library name: D14_HOM1_5
Column name in annotated_raw_counts.csv: D14_HOM1_5


title: TUMOR_TE57_241

value: CURRENT

value: large-cell neuroendocrine

value: IA

value: solid

value: microRNA

value: HUM


title: RASMC, DAPT_treatment, H3K4me1, rep2(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K4me1_rep2, Cut_Tag
rat aortic smooth muscle cell

value: WT


title: CONTROL_TE57_240


title: Fus d14/d14, 1 month, biol rep 4

description:
Library name: D14_HOM1_4
Column name in annotated_raw_counts.csv: D14_HOM1_4

value: spinal cord


title: Subject7_trametinib

value: fracture pseudarthrosis bone

value: primary cell

value: trametinib


title: CONTROL_TE57_245


title: RASMC, DAPT_treatment, H3K4me1, rep1(Cut&Tag)

description:
Library name: RASMC_DAPT_H3K4me1_rep1, Cut_Tag
rat aortic smooth muscle cell


title: CONTROL_TE57_244

value: F

value: FORMER


title: Subject9_DMSO


title: Fus d14/d14, 1 month, biol rep 3

description:
Library name: D14_HOM1_3
Column name in annotated_raw_counts.csv: D14_HOM1_3

value: Fus d14/d14


title: CONTROL_TE57_24

value: MUG


title: Subject7_selumetinib

value: selumetinib


title: CONTROL_TE57_239


title: Subject7_DMSO

value: vehicle


title: RASMC, Cholesterol_treatment, H3K4me1, rep3(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K4me1_rep3, Cut_Tag
rat aortic smooth muscle cell

value: aortic smooth muscle cell


title: Subject6_trametinib


title: RASMC, Cholesterol_treatment, H3K4me1, rep1(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K4me1_rep1, Cut_Tag
rat aortic smooth muscle cell


title: RASMC, Cholesterol_treatment, H3K4me1, rep2(Cut&Tag)

description:
Library name: RASMC_Cholesterol_H3K4me1_rep2, Cut_Tag
rat aortic smooth muscle cell


title: Fus d14/d14, 1 month, biol rep 1

description:
Library name: D14_HOM1_1
Column name in annotated_raw_counts.csv: D14_HOM1_1


title: Fus d14/d14, 1 month, biol rep 2

description:
Library name: D14_HOM1_2
Column name in annotated_raw_counts.csv: D14_HOM1_2


title: CONTROL_TE57_238

value: M

value: CURRENT


title: Fus+/+, 1 month, biol rep 5

description:
Library name: D14_WT1_5
Column name in annotated_raw_counts.csv: D14_WT1_5

value: Fus+/+


title: CONTROL_TE57_237

value: solid

value: microRNA


title: RASMC, DMSO_treatment, H3K4me1, rep2(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K4me1_rep2, Cut_Tag
rat aortic smooth muscle cell

value: WT

value: DMSO


title: Fus+/+, 1 month, biol rep 3

description:
Library name: D14_WT1_3
Column name in annotated_raw_counts.csv: D14_WT1_3

value: spinal cord


title: Subject5_trametinib

value: fracture pseudarthrosis bone

value: primary cell


title: RASMC, DMSO_treatment, H3K4me1, rep1(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K4me1_rep1, Cut_Tag
rat aortic smooth muscle cell


title: CONTROL_TE57_235

value: HUM


title: RASMC, DMSO_treatment, H3K4me1, rep3(Cut&Tag)

description:
Library name: RASMC_DMSO_H3K4me1_rep3, Cut_Tag
rat aortic smooth muscle cell


title: Subject6_DMSO


title: TUMOR_TE57_236

value: F

value: adenocarcinoma

value: IA


title: CONTROL_TE57_234


title: Subject5_selumetinib

value: selumetinib


title: Fus+/+, 1 month, biol rep 2

description:
Library name: D14_WT1_2
Column name in annotated_raw_counts.csv: D14_WT1_2


title: rat VSMC_DAPT_Cholesterol_rep3

data_processing:
ATAC-Seq reads were trimmed from 3' end until the final base had a quality score >30, using sickle version 1.33, discarding reads left with < 30bp
Trimmed reads were aligned to Rn7 genome using bowtie version 2.4.5 with default parameters
Duplicated reads were removed by using picard version 2.27.1 with default parameters
Peaks were called using MACS version 2.2.7.1 with significance cutoff as q <= 0.05
bigwig files were generated by using deeptools version 3.5.1 with setting as: --binSize 1 --skipNonCoveredRegions --normalizeUsing RPKM; narrowPeak files were exported from the MACS2 (version 2.2.7.1)  peak calling result
Assembly: rn7
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: aoric smooth muscle cell

extract_protocol:
Chromatin regions accessible by tn5 transposase were cut, tagged and amplified
Library was constructed by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502)

value: aoric smooth muscle cell

tag: strain

value: Sprague-Dawley

value: DAPT+Cholesterol 48h


title: Fus+/+, 1 month, biol rep 1

description:
Library name: D14_WT1_1
Column name in annotated_raw_counts.csv: D14_WT1_1


title: CONTROL_TE57_233

tag: age

value: M

value: FORMER


title: rat VSMC_DAPT_Cholesterol_rep2


title: CONTROL_TE57_232

tag: gender

value: CURRENT


title: Subject5_DMSO

value: vehicle


title: Subject4_Fracture_DMSO


title: rat VSMC_DAPT_Cholesterol_rep1


title: BENIGN_TE57_231

tag: smocking status

value: solid

value: microRNA


title: Muscle, 24 mon, spleen, islated cells, TIGIT-PD1-CD4-2

city: Beijing

first: fang

last: wu

address: Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

description: Library name: 24m-neg2

data_processing:
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM45 was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DEGseq46. DEGs with |log2FC| ≧ 1 and FDR ≤ 0.001 were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including KEGG were performed to identify which DEGs were significantly enriched in metabolic pathways. KEGG pathway analysis were carried out by KOBAS47.
Assembly: GRCm39
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: islated cells

extract_protocol:
Total RNA was extracted from the sorted cell cluster using TRIzol®Reagent. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies), high-quality RNA sample (OD260/280= 1.8-2.2, OD260/230≥ 2.0, RIN≥ 6.5, 28S:18S≥ 1.0) was used to construct sequencing library.
The synthesized cDNA was subjected to end-repair and phosphorylation, ccording to Illumina’s library construction protocol. Libraries were size selected for 300 bp cDNA target fragments to PCR amplified for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2× 150 bp read length). Quality control and Read mapping by fastp42, HISAT243, and StringTie44 software.

value: islated cells

value: spleen islated cells


title: Muscle, 24 mon, spleen, islated cells, TIGIT-PD1-CD4-3

description: Library name: 24m-neg3


title: Subject4_Fracture_selumetinib

value: fracture pseudarthrosis bone

value: primary cell


title: rat VSMC_Cholesterol_rep3

value: Cholesterol 48h


title: rat VSMC_Cholesterol_rep2


title: Subject6_selumetinib


title: Muscle, 24 mon, spleen, islated cells, TIGIT-PD1-CD4-1

description: Library name: 24m-neg1


title: Subject4_Fracture_trametinib

value: trametinib


title: Fus+/+, 1 month, biol rep 4

description:
Library name: D14_WT1_4
Column name in annotated_raw_counts.csv: D14_WT1_4

value: spinal cord

value: Fus+/+


title: TUMOR_TE57_230

value: adenocarcinoma

value: IIB

tag: nodule density

value: HUM


title: CONTROL_TE57_23

value: F

tag: nodule size

value: MUG


title: Muscle, 24 mon, spleen, islated cells, TIGIT+PD1+CD4-3

description: Library name: 24m-dpos3


title: Subject4_Control_trametinib

source_name: control bone

value: control bone


title: Muscle, 24 mon, spleen, islated cells, TIGIT+PD1+CD4-1

description: Library name: 24m-dpos1


title: Subject4_Control_selumetinib

value: selumetinib


title: rat VSMC_Cholesterol_rep1

value: aoric smooth muscle cell

value: Sprague-Dawley


title: CONTROL_TE57_228

value: M

value: FORMER

value: solid

tag: molecule subtype

value: microRNA


title: rat VSMC_DAPT_rep2

value: DAPT 48h


title: Subject4_Control_DMSO

value: primary cell

value: vehicle


title: Subject3_Fracture_DMSO

value: fracture pseudarthrosis bone


title: rat VSMC_DAPT_rep1


title: CONTROL_TE57_227

value: CURRENT

tag: center


title: CONTROL_TE57_226


title: Subject3_Fracture_selumetinib


title: rat VSMC_DMSO_rep3

value: DMSO 48h


title: Muscle, 3 mon, spleen, islated cells, TIGIT-PD1-CD4-2

description: Library name: 3m-neg2

value: islated cells

value: spleen islated cells


title: Muscle, 3 mon, spleen, islated cells, TIGIT-PD1-CD4-1

description: Library name: 3m-neg1


title: CONTROL_TE57_225

value: MUG


title: Subject3_Fracture_trametinib

value: trametinib


title: Subject3_Control_DMSO

value: control bone


title: CONTROL_TE57_224


title: rat VSMC_DMSO_rep1

value: aoric smooth muscle cell


title: Muscle, 3 mon, spleen, islated cells, TIGIT+PD1+CD4-2

description: Library name: 3m-dpos2


title: Subject3_Control_selumetinib

value: selumetinib


title: TUMOR_TE57_229

value: M

value: adenocarcinoma

value: IV

value: HUM


title: Muscle, 24 mon, spleen, islated cells, TIGIT+PD1+CD4-2

description: Library name: 24m-dpos2


title: rat VSMC_DAPT_rep3

value: Sprague-Dawley

value: DAPT 48h


title: Muscle, 3 mon, spleen, islated cells, TIGIT+PD1+CD4-1

description: Library name: 3m-dpos1


title: Muscle,  3 mon, spleen, islated cells, TIGIT-PD1-CD4-3

description: Library name: 3m-neg3


title: Subject3_Control_trametinib

value: primary cell


title: Subject2_Fracture_DMSO

value: fracture pseudarthrosis bone

value: vehicle


title: Pig oocyte, scBS-Seq, in-vivo, cell AB

city: Murcia

first: Francisco

last: Huertas

address: C/ Campus Universitario de Espinardo Nº7 (Edificio CEEIM)

country: Spain

institute: Marbyt - Smart Solutions for Biotechnology

data_processing:
Demultiplexed samples were derived to a quality control and adapter trimming using TrimGalore!
Sscrofa11.1 genome were converted to its bisulfite versions using Bismark.
Trimmed reads were aligned to Sscrofa11.1 converted genome using Bismark.
Finally, a methylation extraction with Bismark was performed to obtain processed files.
Assembly: Sscrofa11.1
Supplementary files format and content: Bismark coverage report table
Library strategy: scBS-seq

organism: Sus scrofa

source_name: In vivo

extract_protocol:
Matured oocytes were individually lysed and flash-frozen in 5 μL of RLT Plus buffer (Qiagen) at −80°C until further use. Both DNA and RNA from lysate were separated using the G&T-seq and Smartseq2 protocol (Angermueller et al., 2016). Magnetic beads (MyOne C1, Life Technologies) were washed and then annealed to oligo dTs. These were employed to capture polyadenylated mRNA from cell lysates
Single-cell BS-seq libraries were prepared based on a previous method described by Clark et al. (2017).  The lysate containing the DNA was purified using a 0.9:1 ratio of Ampure XP Beads (Beckman Coulter) and eluted into 10 μl of water to use for scBS-seq library preparation. DNA purified from single cells was treated using the EZ Methylation Direct Kit (Zymo) for bisulfite-conversion following the manufacturer's instructions

treatment_protocol: In vitro versus in vivo matured porcine oocytes

value: Oocyte

value: WT

value: in-vivo


title: rat VSMC_DMSO_rep2

value: DMSO 48h


title: Pig oocyte, scBS-Seq, in-vivo, cell AA


title: Subject2_Fracture_selumetinib


title: BENIGN_TE57_220

value: CURRENT

value: part-solid

value: microRNA


title: Single-cell RNA-seq of VSIR WT post-radiation timepoint 2

city: Palo Alto

first: Dhanya

last: Nambiar

state: CA

address: 269 campus drive, CCSR building, 1230

department: Radiation Oncology

institute: Stanford University

description:
Library name: vsir_wt1rt2
10X Genomics scRNA-seq using v3 chemistry

data_processing:
Feature and count matrices were extracted as H5 files using Cell Ranger software. Data was processed using Seurat. Cells with fewer than 200 features or genes present in fewer than 3 cells were filtered. Gene expression was log normalized and scaled for top 2000 highly variable features. Principal component analysis was performed and datasets were integrated with Harmony.
Assembly: Mouse mm10-2020-A
Supplementary files format and content: H5 files from Cell Ranger 7.0.1

source_name: mouse tumour tissue

extract_protocol:
Single-cell suspensions were prepared by enzymatic digestion of finely minced tumors in RPMI-1640 medium (supplemented with 0.1 mg/mL DNase I and 1 mg/mL Collagenase at 37 °C with gentle agitation (100 rpm) for 30–45 minutes. The digested material was passed through 40 μm cell strainers) to obtain a single-cell suspension. Red blood cells were removed using Red Blood Cell Lysis Solution following the manufacturer’s instructions. Cells were washed and counted using a hemocytometer prior to loading onto the 10x Genomics Chromium Controller.
Single-cell suspensions were loaded onto the 10x Genomics Chromium Controller using the Chromium Single Cell 3’ v3.1 reagent kit according to the manufacturer’s protocol. Following droplet generation and cell lysis, mRNA was reverse transcribed and barcoded within individual gel beads in emulsion (GEMs). Barcoded cDNA was amplified, fragmented, end-repaired, A-tailed, adaptor-ligated, and indexed for sequencing. Final libraries were quantified, quality-checked, and sequenced on an Illumina NovaSeq 6000 platform with paired-end reads.

value: mouse tumour tissue

value: tumour/ immune cells

value: Wild type


title: CONTROL_TE57_221

value: M

value: FORMER


title: Subject2_Fracture_trametinib

value: trametinib


title: Pig oocyte, scBS-Seq, in-vivo, cell X


title: Pig oocyte, scBS-Seq, in-vivo, cell Z


title: Single-cell RNA-seq of VSIR KO sample replicate 2

description:
Library name: vsir_ko2
10X Genomics scRNA-seq using v3 chemistry

value: VSIR KO


title: CONTROL_TE57_216

value: solid

value: MUG


title: Pig oocyte, scBS-Seq, in-vivo, cell V


title: Single-cell RNA-seq of VSIR WT post-radiation timepoint 1

description:
Library name: vsir_wt1rt1
10X Genomics scRNA-seq using v3 chemistry


title: Single-cell RNA-seq of VSIR KO post-radiation timepoint 2

description:
Library name: vsir_ko1rt2
10X Genomics scRNA-seq using v3 chemistry


title: Subject2_Control_DMSO

value: control bone

value: primary cell

value: vehicle


title: Subject2_Control_selumetinib

value: selumetinib


title: Pig oocyte, scBS-Seq, in-vivo, cell U

value: Oocyte

value: WT

value: in-vivo


title: CONTROL_TE57_222

value: microRNA

value: HUM


title: TUMOR_TE57_223

value: CURRENT

value: adenocarcinoma

value: IIB


title: CONTROL_TE57_215

value: F


title: Single-cell RNA-seq of VSIR WT sample replicate 2

description:
Library name: vsir_wt2
10X Genomics scRNA-seq using v3 chemistry

value: mouse tumour tissue

value: tumour/ immune cells

value: Wild type


title: Single-cell RNA-seq of VSIR KO post-radiation timepoint 1

description:
Library name: vsir_ko1rt1
10X Genomics scRNA-seq using v3 chemistry

value: VSIR KO


title: Subject2_Control_trametinib

value: control bone

value: trametinib


title: Pig oocyte, scBS-Seq, in-vivo, cell T


title: TUMOR_TE57_22

value: FORMER

value: IA

value: part-solid

value: MUG


title: Pig oocyte, scBS-Seq, in-vivo, cell AC

value: Oocyte

value: WT

value: in-vivo


title: CONTROL_TE57_214

value: M

value: CURRENT

value: non-solid

value: microRNA


title: Single-cell RNA-seq of VSIR KO sample replicate 1

description:
Library name: vsir_ko1
10X Genomics scRNA-seq using v3 chemistry

value: mouse tumour tissue


title: Subject1_Fracture_DMSO

value: fracture pseudarthrosis bone

value: primary cell

value: vehicle


title: Single-cell RNA-seq of VSIR WT sample replicate 1

description:
Library name: vsir_wt1
10X Genomics scRNA-seq using v3 chemistry

value: tumour/ immune cells

value: Wild type


title: Pig oocyte, scBS-Seq, in-vivo, cell S


title: Subject1_Fracture_selumetinib

value: selumetinib


title: Subject1_Fracture_trametinib

value: trametinib


title: hepAGT +/+ liver, 42d WD, #37

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

description: Library name: L_37

data_processing:
Raw read data in FASTQ format were processed through fastp to remove adaptor sequences and low-quality sequences.
Trimmed sequence reads were mapped to the mouse genome mm10 using STAR (v2.6.1d, mismatch=2) and quantified using FeatureCounts (v1.5.0-p3).
Assembly: mm10
Supplementary files format and content: Comma-separated values files including read counts of genes for each sample

source_name: Liver

growth_protocol: Mice were maintained in a barrier facility on a light:dark cycle of 14:10 hours (ambient temperature of 21°C) and fed a normal mouse laboratory diet (Fat 6.2% wt/wt; Diet #2918; Envigo). Littermates were used for all experiments.

extract_protocol:
After euthanasia, liver samples were snap-frozen in a homogenization solution (#Z305H, Promega) containing 1-thioglycerol (#A208B, Promega). Subsequently, mRNA was extracted using Maxwell RSC simplyRNA Tissue Kits (#AS1340, Promega) according to the manufacturer’s protocol.
RNA samples were shipped to Novogene (CA) for bulk mRNA sequencing. The sequencing library was generated from total mRNA (1 µg) using NEBNext UltraTM RNA Library Prep Kits for Illumina (New England BioLabs, MA). cDNA libraries were then sequenced by a Next Generation NovaSeq platform, (HWI-ST1276, Illumina), in a pair-end fashion to reach more than 1,500,000 reads.

treatment_protocol: To induce hypercholesterolemia, male mice at 7 weeks of age were fed a diet supplemented with saturated fat (milk fat 21% wt/wt) and cholesterol (0.2% wt/wt; Diet #TD.88137, Envigo, termed “Western diet”) for 5, 14, or 42 days.

value: Liver

value: hepAGT +/+

value: Western diet

tag: time on_diet_(days)

tag: Sex

value: male

tag: background strain


title: CONTROL_TE57_212

value: solid

value: MUG


title: Pig oocyte, scBS-Seq, in-vivo, cell R

value: Oocyte

value: WT

value: in-vivo


title: hepAGT +/+ liver, 42d WD, #36

description: Library name: L_36


title: Pig oocyte, scBS-Seq, in-vivo, cell Q


title: Subject1_Control_DMSO

value: control bone


title: hepAGT +/+ liver, 42d WD, #33

description: Library name: L_33


title: Subject1_Control_selumetinib


title: TUMOR_TE57_21

value: F

value: CURRENT

tag: histology

value: typical carcinoid

tag: Stage

value: IA

value: microRNA


title: hepAGT +/+ liver, 42d WD, #32

description: Library name: L_32


title: Pig oocyte, scBS-Seq, in-vivo, cell O

tag: cell type


title: Subject1_Control_trametinib

value: primary cell


title: hepAGT +/+ liver, 42d WD, #30

description: Library name: L_30

tag: genotype


title: hepAGT +/+ liver, 14d WD, #27

description: Library name: L_27

tag: treatment


title: BENIGN_TE57_208

value: M

value: HUM


title: CONTROL_TE57_213


title: ZPRV2BRU

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

data_processing:
Bru-seq reads were aligned to human genome (hg19) by Bowtie 2 version 2.4.4 with default parameters [41]. The aligned reads were counted in each gene body of hg19 downloaded from UCSC Table Browser. Gene with a read count exceeding 20 in each replicate of one condition were retained for differential analysis using DESeq2 [44]. Significantly differential genes were defined by a false discovery rate (FDR) threshold of < 0.05.
Assembly: hg19
Supplementary files format and content: ZMR_vs_Mock_DESeq2.xls and ZPRV_vs_Mock_DESeq2.xls are comparing differential genes between MR_vs_Mock and PRV_vs_Mock separately.
Library strategy: Bru-Seq

growth_protocol: The human glioblastoma SNB-19 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS, GibcoTM, #10437028) at 37 °C in 5% CO2.

extract_protocol:
For Bru-seq, the experiments were conducted following the Bru-seq protocol [29]. Briefly, cells were cultured in T-75 flasks for 24 h prior to the experiment. For Bromouridine labeling, 6-10 ml of medium of each flask was transferred to clean falcon tubes and BrU was added to a final concentration of 2 mM. The remaining medium was discarded and BrU containing medium was added back to flasks and cells were incubated at 37 °C for 30 min. Cells were collected by trypsinization and pelleting. Trizol was then added to the pellet to lyse cells. For total RNA isolation, we added 0.2 ml chloroform per 1 ml Trizol used initially. After dissolving RNA in the nuclease free water, we applied TURBO DNA-freeTM Kit (InvitrogenTM, #AM1907) to remove any isolated DNA content. The goat anti-mouse IgG magnetic Dynabeads (InvitrogenTM, #11033) were conjugated with anti-BrdU antibodies (BD Pharmingen, #555627). For isolating BrU-labeled DNA, the total RNA was heated to 80 °C for 10 min and was cooled on ice before being incubated with prepared Dynabeads at room temperature for 1 h. Next, the bead pellet was incubated in nuclease free water at 95 °C for 10 min to elute BrU-RNA from the beads.
The cDNA library preparation was done by following the steps in the Bru-seq protocol.

tag: cell line

value: Human Glioblastoma Cell Lines

value: PR


title: Pig oocyte, scBS-Seq, in-vivo, cell L

tag: tissue


title: BENIGN_TE57_207

tag: age

value: FORMER


title: Pig oocyte, scBS-Seq, in-vivo, cell M


title: Pig oocyte, scBS-Seq, in-vivo, cell K


title: Pig oocyte, scBS-Seq, in-vivo, cell N


title: CONTROL_TE57_210

tag: gender


title: TUMOR_TE57_211

tag: smocking status

value: adenocarcinoma

value: part-solid


title: ZMR2BRU

value: MR


title: Pig oocyte, scBS-Seq, in-vivo, cell J

value: Oocyte

value: WT


title: ZMR1BRU


title: hepAGT -/- liver, 14d WD, #24

description: Library name: L_24

value: Liver

value: hepAGT -/-

value: Western diet

value: male


title: M2BRU

value: Mock


title: CONTROL_TE57_209

value: CURRENT

value: microRNA


title: Pig oocyte, scBS-Seq, in-vivo, cell B

value: in-vivo


title: M1BRU


title: hepAGT +/+ liver, 14d WD, #22

description: Library name: L_22

value: hepAGT +/+


title: hepAGT +/+ liver, 14d WD, #23

description: Library name: L_23


title: CONTROL_TE57_202

value: M

tag: nodule density

value: solid

value: MUG


title: hepAGT -/- liver, 14d WD, #21

description: Library name: L_21


title: Pig oocyte, scBS-Seq, in-vivo, cell A


title: U251_WT_ZV2

data_processing:
DRIP-seq reads were aligned to human genome (hg19) by Bowtie 2 version 2.4.4 with default parameters [41]. The aligned reads were sorted by genomic coordinates using Samtools [42]. Peaks for DRIP-seq were identified by MACS2 version 2.2.6 with their corresponding input BAM file [43]. Identified peaks were merged and reads were re-counted in the merged peak regions. Peaks with a read count exceeding 20 in each replicate of one condition were retained for differential analysis using DESeq2 [44]. Significantly differential peaks were defined by a false discovery rate (FDR) threshold of < 0.05. All peaks and differential peaks were annotated to genes using annotatePeaks.pl from HOMER (version 4.11) [45].
Assembly: hg19
Supplementary files format and content: KO_DESeq.xls and WT_DESeq.xls are comparing differential DRIP-seq peak between ZIKV and Mock treatment in IFNAR1 KO and WT line, separately
Library strategy: DRIP-seq

growth_protocol: The human glioblastoma U-251 MG cells were cultured in Eagle’s minimum essential medium (EMEM) supplemented with 10% FBS at 37 °C in 5% CO2.

extract_protocol:
For DRIP-seq, the experiments were conducted following the DRIP-seq protocol [28]. Briefly, cells were cultured in T-75 flasks for 24 h prior to the experiment. For IFN-β treatment, 10 ng/ml of IFN-β was added for 18 h. Cells were collected by trypsinization and pelleting followed by DPBS washes. Cells were resuspended in TE buffer containing 20% (wt/vol) SDS and 20 mg/ml proteinase K and incubated at 37 °C overnight. On the next day, DNA was extracted and then fragmentated using a cocktail of restriction enzymes at 37 °C overnight. Prior to S9.6 immunoprecipitation, digested DNA was diluted in TE buffer, and 10% of each tube was saved as input for later qPCR. For S9.6 immunoprecipitation, 1 x DRIP binding buffer (10 x DRIP binding buffer: 100 mM sodium phosphate, pH 7, 1.4 M NaCl and 0.5% (vol/vol) Triton X-100) and S9.6 antibody (1 mg/ml) were added to the diluted DNA followed by incubation at 4 °C on a rotator for 14 to 17 h. Next, DNA from last step was added to the prepared agarose beads and gently rotated at 4 °C for 2 h followed by two washes with 1 x DRIP binding buffer. DNA was eluted in DRIP elution buffer (50 mM Tris, pH 8, 10 mM EDTA, pH 8, and 0.5% SDS) containing proteinase K followed by rotation at 55 °C for 45 min. After DNA was purified, the immunoprecipitation efficiency was checked by qPCR.
The DNA libraries were constructed for S9.6 antibody immunoprecipitated DNA samples.

treatment_protocol: To generate IFNAR1 KO cells, the sgRNA construct targeting IFNAR1 inserted in a pLentiCRISPRv2 backbone was purchased from GenScript (sgRNA target sequence GATCTAATGTTAAAGACTGG). Lentivirus particles containing the CRISPR/Cas9 system was produced by co-transfecting HEK293-T cells with the plasmid and the packaging plasmids. Supernatants containing lentiviruses were harvested 72 h post transfection and filtered through 0.2 μm filters prior to storage at -80 °C. For transduction of glioblastoma cells to generate IFNAR1-KO cells, cells were seeded at a confluency of 30% to 40% before transduction with the lentiviral particles. After 72 h of transduction, cells were selected with 2 μg/mL puromycin for 2 weeks, followed by single cell cloning in U-251 MG KO cells.

value: Human Glioblastoma Cell Lines

value: ZIKV


title: ZPRV1BRU

value: PR


title: TUMOR_TE57_201

value: adenocarcinoma

value: IB

tag: nodule size


title: Pig oocyte, scBS-Seq, in-vitro, cell 26

source_name: In vitro

value: Oocyte

value: WT

value: in-vitro


title: hepAGT -/- liver, 14d WD, #26

description: Library name: L_26

value: Liver

value: hepAGT -/-

value: Western diet

value: male


title: U251_WT_ZV1


title: TUMOR_TE57_200

value: F

value: FORMER

value: IA

value: part-solid

tag: molecule subtype

value: microRNA


title: hepAGT -/- liver, 14d WD, #20

description: Library name: L_20


title: Pig oocyte, scBS-Seq, in-vivo, cell C

value: in-vivo


title: hepAGT +/+ liver, 5d WD, #18

description: Library name: L_18

value: hepAGT +/+


title: hepAGT +/+ liver, 14d WD, #25

description: Library name: L_25


title: Pig oocyte, scBS-Seq, in-vitro, cell 22


title: CONTROL_TE57_199

value: M

tag: center

value: HUM


title: U251_WT_Mock

value: Human Glioblastoma Cell Lines

value: Mock


title: CONTROL_TE57_204

value: CURRENT

value: solid

value: MUG


title: Pig oocyte, scBS-Seq, in-vitro, cell 25

value: Oocyte

value: WT

value: in-vitro


title: hepAGT +/+ liver, 14d WD, #19

description: Library name: L_19

value: Liver

value: Western diet

tag: time on_diet_(days)

value: male


title: CONTROL_TE57_20

value: F


title: Pig oocyte, scBS-Seq, in-vitro, cell 24


title: Pig oocyte, scBS-Seq, in-vitro, cell 21


title: U251_KO_ZV2

value: IFNAR1 KO

value: ZIKV


title: CONTROL_TE57_197

value: microRNA


title: CONTROL_TE57_203


title: U251_KO_Mock


title: Pig oocyte, scBS-Seq, in-vitro, cell 19


title: U251_KO_ZV1plusH


title: U251_KO_ZV1


title: CONTROL_TE57_191

value: M


title: hepAGT +/+ liver, 5d WD, #16

description: Library name: L_16

value: hepAGT +/+

tag: Sex


title: hepAGT +/+ liver, 5d WD, #14

description: Library name: L_14

tag: background strain


title: prv_zika2

data_processing:
DRIP-seq reads were aligned to human genome (hg19) by Bowtie 2 version 2.4.4 with default parameters [41]. The aligned reads were sorted by genomic coordinates using Samtools [42]. Peaks for DRIP-seq were identified by MACS2 version 2.2.6 with their corresponding input BAM file [43]. Identified peaks were merged and reads were re-counted in the merged peak regions. Peaks with a read count exceeding 20 in each replicate of one condition were retained for differential analysis using DESeq2 [44]. Significantly differential peaks were defined by a false discovery rate (FDR) threshold of < 0.05. All peaks and differential peaks were annotated to genes using annotatePeaks.pl from HOMER (version 4.11) [45].
Assembly: hg19
Supplementary files format and content: DENV.DESeq.xls, IFN.DESeq.xls, MR.DESeq.xls and PRV.DESeq.xls are comparing differential DRIP-seq peak between DENV_vs_Mock, IFN_vs_Mock, MR_vs_Mock and PR_vs_Mock treatment separately.
Library strategy: DRIP-seq

value: Human Glioblastoma Cell Lines

value: PR


title: Pig oocyte, scBS-Seq, in-vitro, cell 20


title: CONTROL_TE57_192

value: FORMER


title: hepAGT +/+ liver, 5d WD, #13

description: Library name: L_13


title: hepAGT +/+ liver, 0d WD, #7

description: Library name: L_07

value: Normal diet


title: Pig oocyte, scBS-Seq, in-vitro, cell 16


title: prv_Zika_RNaseH


title: prv_zika1


title: hepAGT +/+ liver, 5d WD, #10

description: Library name: L_10


title: mr_Zika_RNaseH

value: MR


title: TUMOR_TE57_190

tag: histology

value: adenocarcinoma

value: IA

value: solid

value: MUG


title: CONTROL_TE57_189

value: CURRENT


title: CONTROL_TE57_19

value: HUM


title: CONTROL_TE57_198


title: Pig oocyte, scBS-Seq, in-vitro, cell 14

value: Oocyte

value: WT

value: in-vitro


title: hepAGT +/+ liver, 0d WD, #6

description: Library name: L_06

value: Liver

value: male


title: Pig oocyte, scBS-Seq, in-vitro, cell 13


title: mr_Zika1


title: TUMOR_TE57_188

value: M

tag: Stage

value: microRNA


title: Pig oocyte, scBS-Seq, in-vitro, cell 9

tag: cell type


title: TUMOR_TE57_187

value: IIB


title: Notch1+/-;Gata5-/- , rep4

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

description: Library name: N1hetG5null_4

data_processing:
FASTQ files were trimmed using Trim Galore!` to remove Illumina adapter sequences and low quality reads. High-quality trimmed reads
trimmed reads were aligned with STAR (v2.7.10b)37 to mouse reference genome version GRCm39, GENCODE110
Gene expression was quantified using RESM (v1.3.1)
differential expression analysis was performed with DESeq2 (v1.34.0)
Assembly: mouse reference genome version GRCm39, GENCODE110
Supplementary files format and content: raw_counts.csv   csv file containing counts for each genotype replicate
Supplementary files format and content: DEG_all_genotypes_L2FC0.58_padjust0.1.csv   csv file containing differentially expressed genes (DESeq2 output) of Notch1+/-;Gata5-/- vs wildtype p10 aortic valves

source_name: Aortic valve

extract_protocol:
Aortic valve tissue samples were collected in an RNase-free setting from wildtype, Notch1+/-;Gata5+/- and Notch1+/;Gata5-/- mice at P10. Aortic valve tissues were harvested in Trizol, snap frozen and homogenized using TissueLyser II. Three aortic valves tissue were pooled to form one biological replicate for each genotype. Total RNA was isolated using Norgen Bioteck total RNA isolation kit, and DNase treatment was performed post RNA purification.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Aortic valve

tag: genotype


title: Input1

value: Human Glioblastoma Cell Lines

tag: treatment

value: Mock


title: Pig oocyte, scBS-Seq, in-vitro, cell 17


title: hepAGT +/+ liver, 0d WD, #4

description: Library name: L_04

value: hepAGT +/+

value: Normal diet


title: hepAGT +/+ liver, 0d WD, #3

description: Library name: L_03


title: Notch1+/-;Gata5-/- , rep3

description: Library name: N1hetG5null_3


title: CONTROL_TE57_186

data_processing: Data were quantified by relative threshold cycles (Crt) methods and normalized on miR-16-5p as per the manufacturer’s instructions (Thermo Fisher Scientific). To further compensate for variability, we added additional normalizers by selecting the two miRNAs most correlating with miR-16-5p, from the list of six miRNAs previously described as housekeeping (doi:10.1093/jnci/djv063). Normalization was performed using the following procedure: a scaling factor (SF) was calculated for each sample, by subtracting the average of the three normalizers to a constant value (K=19.079)(doi:10.1093/jnci/djv063). Data were then normalized using the formula: Crt normalized=miRNA Crt raw – SF. Normalization was skipped for Crt=40. Batch bias was investigated through analysis of the miRNAs expression distribution across centers (FC analysis, Wilcoxon Rank Sum test).


title: prv_mock

tag: cell line


title: Notch1+/-;Gata5-/- , rep2

description: Library name: N1hetG5null_2

tag: tissue


title: CONTROL_TE57_185

tag: age

value: F


title: mr_Mock


title: Pig oocyte, scBS-Seq, in-vitro, cell 7


title: Pig oocyte, scBS-Seq, in-vitro, cell 6


title: BENIGN_TE57_184

tag: gender

value: solid


title: mr_Zika2

value: MR


title: Notch1+/-;Gata5+/- , rep4

description: Library name: N1hetG5het_4


title: BENIGN_TE57_183

tag: smocking status

value: CURRENT

value: HUM


title: IFNB2

value: IFN


title: Pig oocyte, scBS-Seq, in-vitro, cell 4

value: Oocyte

value: WT

value: in-vitro


title: Notch1+/-;Gata5+/- , rep3

description: Library name: N1hetG5het_3


title: CONTROL_TE57_180

tag: nodule density

value: MUG


title: Pig oocyte, scBS-Seq, in-vitro, cell 3


title: Pig oocyte, scBS-Seq, in-vitro, cell 8


title: IFN2


title: Notch1+/-;Gata5+/- , rep2

description: Library name: N1hetG5het_2


title: CONTROL_TE57_18

value: M

value: microRNA


title: Pig oocyte, scBS-Seq, in-vitro, cell 2


title: IFN1


title: Notch1+/-;Gata5+/- , rep1

description: Library name: N1hetG5het_1

value: Aortic valve


title: TUMOR_TE57_178

value: adenocarcinoma

value: IA

value: part-solid

tag: nodule size


title: Pig oocyte, scBS-Seq, in-vitro, cell 1


title: DENV2

value: Human Glioblastoma Cell Lines

value: DENV


title: WT,rep4

description: Library name: WT_4

value: Wildtype


title: CONTROL_TE57_179

value: F

value: FORMER

value: solid

tag: molecule subtype


title: DENV1


title: Notch1+/-;Gata5-/- , rep1

description: Library name: N1hetG5null_1


title: IFN_Mock

value: Mock


title: mut_I_2

city: Belgrade

first: Mirjana

last: Novkovic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetic and Genetic Engineering

data_processing:
fastp v0.23.4, STAR v2.7.0, RSEM v1.3.3
Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 (qualified_quality_phred=20, nqualified_percent_limit=30, average_qual=25, low_complexity_filter=True, complexity_threshold=30)
passing filter reads were mapped to the genome reference (Danio rerio GRCz11v110, Ensembl v110 ) using STAR v2.7.10 with standard parameters, except for the sjdbOverhang option set on read length
Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3, to estimate transcript and gene abundances. Subsequently, the sample-specific gene-level abundances were merged into a single raw expression matrix applying a dedicated RSEM command (rsem-generate-data-matrix).
Assembly: Danio rerio GRCz11v110, Ensembl v110
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

organism: Danio rerio

source_name: skeletal muscle

growth_protocol: Wild-type (wt) fish AB (Oregon) and ankrd1abns502 (mut) were maintained under standard conditions, in circulating water system, under 14 h light/10 h dark cycle and at 28.5 ◦C.

extract_protocol:
Skeletal muscle tissue dissected out from the region around the injury and complementary region of non-injured wt and ankrd1a-/- fish was homogenized in TRIzol Reagen (Invitorgen, Thermo Fisher Scientific, USA) and total RNA was extracted using RNA Clean and concentrator kit (ZYMO Research, USA), according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase-free water and its quantity and purity were measured promptly after isolation, using BioSpec-nano (Shimadzu, Japan) and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM (Thermo Scientific Fisher, USA).
cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit (Illumina, California, USA)

treatment_protocol: Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail, in line with the anal opening. Immediately, after the injury, fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle, just behind the anal opening and containing the injury area anterior and posterior to the needle lesion, was dissected by a razor blade and used for RNA isolation.

value: skeletal muscle

value: ankrd1a mutant

value: injured


title: mut_I_3


title: CONTROL_TE57_177

extract_protocol: Plasma samples were thawed on ice, and RNA was extracted with the commercial miRNeasy mini-Kit (QIAgen™, Hilden, Germany) using the QIAcube™ robot, following the manufacturer´s instructions.

value: CURRENT

tag: center

value: MUG


title: WT, rep2

description: Library name: WT_2


title: CONTROL_TE57_176

value: M

value: microRNA


title: Pig oocyte, scBS-Seq, in-vitro, cell 5

value: Oocyte

value: WT

value: in-vitro


title: WT, rep3

description: Library name: WT_3

value: Aortic valve


title: CONTROL_TE57_175


title: mut_I_4


title: WT, rep1

description: Library name: WT_1


title: mut_I_1


title: TUMOR_TE57_174

value: carcinoma planoepitheliale

value: IB


title: Microglia, vehicle

city: St. Louis

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

description:
Library name: veh
10X Genomics 3'GEX

data_processing:
The off-sequencer data was demultiplexed, aligned, and quantified with CellRanger v6.
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: Brain

extract_protocol:
10x Genomics Chromium single-cell preparation
NGS Illumina Next Seq

value: Brain

value: vehicle


title: Microglia, acetazolamide

description:
Library name: acz
10X Genomics 3'GEX

value: Acetazolamide


title: mut_NI_4

value: non-injured


title: Response of the thermally adapted ECL45 strain during the late temperature upshift exposure

city: Cuernavaca

first: Gilberto

last: Pérez Morales

state: Morelos

address: Avenida Universidad 2001, Colonia Chamilpa

department: Cellular Engineering Department

country: Mexico

institute: Instituto de Biotecnología - Universidad Nacional Autónoma de México

description: Analysis was performed using the experimental samples of the thermally adapted strain ECL45 after three residences times of the temperature upshift to 45 degrees Celcius compared with the control samples of the same strain at the optimal temperature of 37 degrees Celcius as reference .

hyb_protocol: Incorporation of fluorophore was analyzed by using the absorbance at 555 nm and 647 respectively. Equal quantities of labeled cDNA were hybridized using hybridization solution HybIT2 (TeleChem International INC). The arrays were incubated for 14 h at 42 °C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images were performed in GenePix 4100-A reader with its accompanying software. For each spot, the mean density, mean background, and mean normalized signal values were calculated with the Array-Pro Analyzer software from Media Cybernetics.

data_processing: Microarray data analysis was performed as follows. The data obtained from the quantification of the images were analyzed with Genarise in SWAP mode. The free software genArise, was developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean.

label: Alexa647, Alexa555

organism: Escherichia coli

source_name: Control samples of the thermally adapted strain ECL45 at the optimal ancestral temperature of 37 degrees Celsius in a chemostat culture

label_protocol: 10 ug of total RNA were used for cDNA synthesis, incorporating dUTP-Alexa555 or dUTP-Alexa647, employing the SuperScript Plus direct labeling kit (Invitrogen).

growth_protocol: The parental JU15 and the thermally adapted ECL45 strains were grown individually in a continuous culture in a 1 L bioreactor (Applikon ADI 1010—Ez-control, Delft, NL). For this purpose, the seed inocula were obtained from mid-exponential phase batch cultures in AM1 medium The bioreactor was operated with 750 mL of working volume at 400 rpm, pH 7 maintained by the automatic addition of 8 N KOH, and without aeration. Batch startup at 37 °C began with an OD600 of 0.1 (0.037 g-DCW/L). After reaching the stationary phase the chemostat culture operation was set at a dilution rate (D) of 0.09 h−1. The feeding solution contained AM1 medium with 40 g/L of glucose, 0.1 g/L of sodium citrate, 0.1 g/L of tryptone, and 0.05 g/L of yeast extract.

extract_protocol: 10 mL of culture were mixed with 500 µL of RNAlaterTM (Thermo Fisher Scientific, Baltics, UAB), then gently mixed by inversion. The samples were centrifugated at 5,000 rpm for 5 minutes, the supernatant was discarded, and the pellet was frozen at -70 °C until further analysis. Total RNA was isolated using the hot phenol method (Flores et al. 2005). Chromosomal DNA was removed with the turbo-DNA free kit (cat no. AM1907, Thermo Fisher Scientific, Baltics, UAB).

treatment_protocol: The strains were grown in a continuous culture for temperature upshift experiments. For this, cultures were transitioned to 45 °C after reaching the steady state at 37 °C.

value: ECL45 (MG1655:{delta}pflB, {delta}frdA, {delta}adhA {delta}xylFGH, {delta}midarpA, {delta}reg 27.3 kpb, gatCS184L, dxr c.475A>C , sapD c.704G>C , cysJ c.1378C>A, spoT c.829 C>G c.1367C>T, argE c.744C>A, yqgE c258delG, IGR  (gadB- pqqL )(A)6→5)

value: bacterial cell

tag: temperature

value: 37 °C

tag: time

value: late

label: Alexa555, Alexa647

source_name: Experimental samples of the thermally adapted strain ECL45 after three residences times of the temperature upshift to 45 degrees Celsius in a chemostat culture

value: 45 °C


title: mut_NI_3

value: skeletal muscle

value: ankrd1a mutant


title: genomic DNA, Day 1, Rep 2

city: Huddinge

first: Christian

middle: Günter

last: Riedel

state: Stockholm

address: Blickagången 16 (Neo Building, 6th floor)

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description: input.bw

data_processing:
The analysis of raw ATAC-seq and mRNA-seq data was conducted using Cactus v0.8.4 (Salignon et al, Genomics, 2024), using default parameters and the following custom parameters: species = 'worm', chromatin_state = 'iHMM.M1K16.worm_L3', use_input_control = true, diffbind__summits = 'TRUE', diffbind__design = 'FALSE', diffbind__edger_tagwise = 'FALSE', diffbind__min_count = 1, diffbind__background = 'FALSE', diffbind__library_size = 'DBA_LIBSIZE_FULL', diffbind__scale_control = 'FALSE', diffbind__score = 'DBA_SCORE_TMM_READS_FULL_CPM', split__peak_assignment = [ 'all', 'prom', 'distNC' , '3pUPR' ] and pwms_motifs = hughesCePWMSForHomerLO9.motif'. The latter custom motif file contained experimentally defined C. elegans TF binding motifs and was created by the Brunet lab and used in (Daugherty et al, Genome Research, 2017). Two replicates of a genomic DNA control, taken from the strain GR1373, were used in all analyses to remove peaks located in hotspot regions.
Assembly: ce11/WBcel235, Ensembl release 107
Supplementary files format and content: *.bw: BigWig files.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C. elegans were grown on the Escherichia coli strain OP-50 using standard methods (Stiernagle, 2006). In the case of RNAi experiments, animals were grown on the Escherichia coli strain HT115 transformed with L4440-based plasmids expressing double-stranded RNA targeting the genes of interest.

extract_protocol:
ATAC-seq was conducted as described in (Daugherty et al., 2017), using duplicates for every condition. In brief, day 1 adults were washed off the plates with M9, washed in PBS, and frozen in liquid nitrogen. Nuclei were released by mechanical homogenization(Haenni et al., 2012), counted by measuring optical density, and then processed as described in (Buenrostro et al., 2013).
ATAC-seq libraries were constructed by following the protocol described in (Buenrostro et al., 2013). 10 ng of genomic DNA were used as the input control.

treatment_protocol: C. elegans were synchronized at the L1 stage by bleaching and hedging in M9 and seeded onto plates pre-seeded with either OP-50 or RNAi bacteria (E. coli strain HT115 containing dsRNA-expressing plasmids that target a specific gene of interest). HT115 with the empty plasmid L4440 was used as the control. The RNAi clone targeting daf-16 was obtained from the Ahringer library (Kamath et al., Nature 2003), while the clone targeting lin-39 was obtained from the Vidal library (Reboul et al., Nature Genetics 2003). Plates were incubated at 15°C until the animals reached the late L4 stage. FUDR was added to a final concentration of 50 µM to prevent progeny production, and plates were shifted to 20°C (mRNA-seq) or 25°C (ATAC-seq) for the remainder of the assays. Worms were collected and harvested at indicated timepoints.

value: whole organism


title: Response of the thermally adapted ECL45 strain during the early temperature upshift exposure

description: Analysis was performed using the experimental samples of the thermally adapted strain ECL45 after 15 minutes of the temperature upshift to 45 degrees Celcius compared with the control samples of the same strain at the optimal temperature of 37 degrees Celcius as reference .

value: early

source_name: Experimental samples of the thermally adapted strain ECL45 after 15 minutes of the temperature upshift to 45 degrees Celsius in a chemostat culture


title: TUMOR_TE57_173

city: San Giovanni Rotondo (FG)

last: Bianchi

address: Viale Padre Pio 7

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

source_name: plasma

value: M

value: CURRENT

value: IIA

value: solid

value: microRNA

value: MUG


title: CONTROL_TE57_172


title: mut_NI_1


title: V5-CTER-E13-5

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Paired-end reads were trimmed using TrimmomaticPE to remove Illumina universal adapters. For data analysis, trimmed reads were mapped to mouse genome mm10 using Bowtie2 with default parameters for paired-end sequencing. Duplicate reads were removed with MarkDuplicates tools (Picard suite). Peaks were called with the callpeak tool from MACS2 package with following parameters: -f BAMPE -g mm -q 0.05 – nomodel –call-summits -B –SPMR. For visualisation, deeptools package was used to generate bigwig files
Assembly: mm10
Supplementary files format and content: Bigwig

source_name: E13-5 DRG

extract_protocol:
The spinal cord with attached DRG of E12.5 embryos (10 embryos/condition) or isolated DRG of E13.5 (18 embryos/condition) were collected in ice cold PBS and fixed in 1% Formaldehyde in Phosphate Buffer Saline (PBS, pH 7.5) for 15 minutes at room temperature in a shaking plate. The samples were quenched by adding a final concentration of 125 mM Glycine.
Library preparation was performed for histone modifications  and transcription factors using TruSeq ChIP library Preparation kit

value: E13-5 DRG

tag: developmental stage

tag: antibody


title: Response of the parental JU15 strain during the late temperature upshift exposure

description: Analysis was performed using the experimental samples of the parental strain JU15 after three residences times of the temperature upshift to 45 degrees Celcius compared with the control samples of the same strain at the optimal temperature of 37 degrees Celcius as reference .

source_name: Control samples of the parental strain JU15 at the optimal ancestral temperature of 37 degrees Celsius in a chemostat culture

value: JU15 (MG1655:{delta}pflB, {delta}frdA, {delta}adhA {delta}xylFGH, {delta}reg 27.3 kpb, gatCS184L)

source_name: Experimental samples of the parental strain JU15 after three residences times of the temperature upshift to 45 degrees Celsius in a chemostat culture


title: IgG-CTER-E13-5

value: IgG


title: mut_NI_2

value: non-injured


title: TUMOR_TE57_171

first: Fabrizio

value: F

tag: histology

value: carcinoma planoepitheliale

tag: Stage

value: IB


title: genomic DNA, Day 1, Rep 1

description: input.bw

tag: genotype


title: CTL-V5-E13-5


title: BENIGN_TE57_17

value: HUM


title: Response of the parental JU15 strain during the early temperature upshift exposure

description: Analysis was performed using the experimental samples of the parental strain JU15 after 15 minutes of the temperature upshift to 45 degrees Celcius compared with the control samples of the same strain at the optimal temperature of 37 degrees Celcius as reference .

tag: cell type

value: bacterial cell

value: 37 °C

source_name: Experimental samples of the parental strain JU15 after 15 minutes of the temperature upshift to 45 degrees Celsius in a chemostat culture

value: 45 °C


title: wt_I_4

value: skeletal muscle

value: wt

tag: treatment

value: injured


title: Wild-Type, Day 1, Rep 1

tag: tissue

value: whole organism

value: eri-1(mg366); control(RNAi)


title: daf-2 mutant, B, Day 1, Rep 2

description: daf-2 samples used to compare with the daf-2;lin-39 condition


title: input-E13-5-CTER

value: input


title: CONTROL_TE57_167

tag: age

value: M

value: FORMER

value: microRNA

value: MUG


title: input-E13-5-CTL

value: E13-5 DRG


title: wt_I_3


title: Wild-Type, Day 1, Rep 2


title: daf-2 mutant, Day 1, Rep 2

description: daf-2 samples used to compare with the WT and daf-2;daf-16 conditions


title: CONTROL_TE57_166

tag: gender

value: CURRENT


title: Input-CTER-E12-5

source_name: E12-5 spinal cord with attached DRG

value: E12-5 spinal cord with attached DRG

value: Input


title: wt_I_1


title: wt_I_2


title: Input-CTL-E12-5


title: CONTROL_TE57_165

value: F

tag: smocking status


title: daf-2 mutant, Day 1, Rep 1


title: CONTROL_TE57_164


title: V5-CTER-E12-5


title: daf-2 mutant; lin-39 RNAi, Day 1, Rep 2


title: V5-CTL-E12-5


title: CONTROL_TE57_163

value: HUM


title: wt_NI_2

value: non-injured


title: wt_NI_3

value: skeletal muscle


title: IgG-CTER-E12-5

value: IgG


title: daf-2 mutant; lin-39 RNAi, Day 1, Rep 1


title: wt_NI_4

value: wt


title: Ad-Dyrk1b-3

city: Shanghai

first: Lianju

last: Li

state: China

address: Xujiahui Road

institute: Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases

data_processing:
Raw reads were processed to obtain high quality clean reads. Bowtie2[2] (version 2.2.8) was used to align the clean reads against the reference genome. The shifted, concordantly aliged pairs were used for peak calling by MACS[3]. Peak-related genes were confirmed using ChIPseeker[4] according to the genomic location and gene annotation of peaks. Significantly differential peaks (|log2(FC)| > 1, P < 0.05) were identified using DiffBind[5].
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

extract_protocol:
Livers were lysed to obtain the nuclear suspension.
Nuclei suspensions are incubated in a Transposition Mix that includes a Transposase. The
Transposase enters the nuclei and preferentially fragments the DNA in open regions of the chromatin.
Simultaneously, adapter sequences are added to the ends of the DNA fragments. Incubate the
transposition reaction at 37°C for 30 min. Immediately following transposition, the products are
purified using a QIAGEN minielute kit and sequenced using Illumina

value: Liver

value: Dyrk1b overexpression


title: wt_NI_1


title: TUMOR_TE57_205

value: adenocarcinoma

value: IIB

tag: nodule density

value: solid


title: daf-2 mutant, B, Day 1, Rep 1

value: whole organism


title: IgG-CTL-E12-5


title: Ad-Dyrk1b-2


title: daf-2 mutant; daf-16 RNAi, Day 1, Rep 2


title: TUMOR_TE57_157

value: M

value: squamous cell carcinoma

value: IIIA

tag: nodule size

value: microRNA


title: KO-HFD - TEN_025_16 (GE)

city: Noda

first: Yoshikazu

last: Higami

state: Chiba

address: 2641, Ymazaki

department: Faculty of Pharmaceutical Science

country: Japan

institute: Tokyo University of Science

description: Library name: LAB_312_24_S16

data_processing:
CLC Genomics Workbench v10.1.1
Reads mapped to reference with gene and transcript annotation using ENSEMBLE
Assembly: mm10
Supplementary files format and content: Processed data file was provided as in matrix table and CLC files.
Supplementary files format and content: tab-delimited excel files include RPKM values, the result of pairwise using edgeR and the result of ANOVA analysis for each sample.

source_name: epididymal white adipose tissue

extract_protocol:
RNA was harvested using TRIZOL (ThermoFisher/Invitrogen, 15596026 or 10296028) according to the manufacturer’s protocol.
Standard: 500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420). Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420).

value: epididymal white adipose tissue

value: Wwp1 Knockout mice

value: High fat diet


title: daf-2 mutant; daf-16 RNAi, Day 1, Rep 1


title: CONTROL_TE57_155

value: F

value: FORMER

tag: molecule subtype

value: MUG


title: Ad-Dyrk1b-1


title: CONTROL_TE57_156

value: CURRENT

value: part-solid

tag: center


title: lung cells, LPS+DMH1, 8weeks, rep1

city: shenzhen

first: Jiang

last: Yamei

address: longfei

institute: The Chinese University of Hong Kong-Shenzhen

data_processing:
FASTQ files were run through CellRanger (v7.1.0) software with default parameters for de-multiplexing, aligning reads with STAR software to mm10, and counting unique molecular identifiers (UMIs).
Assembly: mm10
Supplementary files format and content: filtered feature barcode matrix

source_name: lung

extract_protocol:
RNA was harvesd according to the instuction of Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, 1000268)
scRNA-seq libraries were constructed according to the instuction of Library Construction Kit (10x Genomics, 1000190)

value: lung

value: whole lung cells

value: WT


title: Ad-EGFP-3

source_name: Liver

value: Liver

value: control


title: CONTROL_TE57_154

value: M

value: solid


title: KO-HFD - TEN_025_15 (GE)

description: Library name: LAB_312_23_S15


title: lung cells, LPS, 8weeks, rep1

value: LPS


title: lung cells, LPS, 8weeks, rep2


title: lung cells, untreated, 8weeks, rep1

value: untreated


title: CONTROL_TE57_153

value: microRNA


title: lung cells, untreated, 8weeks, rep2


title: Ad-EGFP-1


title: lung cells, LPS+DMH1, 8weeks, rep2


title: Reascent, FosLow-MPP, replicate4, DNA methylation

city: Tianjin

first: Peng

last: Wu

address: 288 Nanjing Road

institute: IHCAMS

data_processing:
Reads quality control by Trimgalore and reads alignment by Bismark
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: Bone marrow

extract_protocol:
FACS-sorted Fos+ and Fos- MPPs from bone marrow
Genome-wide bisulfite sequencing library

treatment_protocol: hypoxia exposure

value: Bone marrow

tag: cell line

value: MPP

value: Hypoxia


title: WT-HFD - TEN_025_10 (GE)

description: Library name: LAB_312_18_S10

value: epididymal white adipose tissue

value: Wild type

value: High fat diet


title: WT-HFD - TEN_025_12 (GE)

description: Library name: LAB_312_20_S12


title: CONTROL_TE57_149

value: F

value: CURRENT

value: HUM


title: D1-OE1-1-IP

first: Liwen

last: Yang

address: Zhongguancun sourth no.12

department: Biotechnology Research Institute

data_processing:
RNA-seq: The fastq was used to remove adapter and filter out low-quality reads with more than 20% low-quality bases (quality <20), The clean reads were mapped to rice reference genome MSU7 by HISAT2. The gene expression level was calculated by featureCounts using default parameters. The DEseq package was used for identification and analysis of differential genes, and gene functional enrichment analysis was performed using agriGO v2.0 online software.
Assembly: MSU7
Supplementary files format and content: txt, narrowpeak
RNA m5C IP-seq:  The fastq was used to remove adapter and filter out low-quality reads with more than 20% low-quality bases (quality <20), The clean reads were mapped to rice reference genome MSU7 by the BWA with MEN algorithm.Then, MACS was introduced to locate enriched regions to call m5C peaks by comparing reads from the IP sample with the input sample.

organism: Oryza sativa

source_name: seedlings

growth_protocol:
RNA-seq: ZH11 and DRW1-OE plants were growth in rice paddies at Chinese Academy of Agricultural Sciences Langfang Experiment Station, China.
RNA m5C IP-seq:  ZH11 and DRW1-OE plants were growth in chamber at Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, China.

extract_protocol:
RNA-seq: Total RNA was extracted using a Plant RNA Kit (RP3302; Bioteke, Beijing, China), 1 μg total RNA was used for library construction.
RNA-seq: RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) following manufacturer's protocols
RNA m5C IP-seq:  Total RNA was extracted using a Plant RNA Kit (RP3302; Bioteke, Beijing, China), ~300 μg total RNA was used for library construction.
RNA m5C IP-seq:  RNA libraries for RNA m5C IP-seq were prepared using NEB Next® Ultra™ RNA Library Prep Kit (New England Biolabs) following manufacturer's protocols

value: seedlings

value: 3 weeks after germination


title: BENIGN_TE57_162


title: Ad-EGFP-2

value: Liver

value: control


title: CONTROL_TE57_152

value: M

value: solid

value: MUG


title: KO-HFD - TEN_025_13 (GE)

description: Library name: LAB_312_21_S13

value: Wwp1 Knockout mice


title: CONTROL_TE57_151

value: microRNA


title: D1-OE1-3-IP

institute: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences


title: CONTROL_TE57_150

value: FORMER


title: CONTROL_TE57_148


title: WT-HFD - TEN_025_11 (GE)

description: Library name: LAB_312_19_S11


title: KO-ND - TEN_025_08 (GE)

description: Library name: LAB_312_16_S8

value: Normal diet


title: BENIGN_TE57_147


title: D1-OE1-2-IP


title: ZH11-1-IP

value: WT


title: Reascent, FosLow-MPP, replicate3, DNA methylation

value: Bone marrow

value: MPP

value: Hypoxia


title: KO-ND - TEN_025_07 (GE)

description: Library name: LAB_312_15_S7

value: epididymal white adipose tissue


title: Reascent, FosHi-MPP, replicate3, DNA methylation


title: CONTROL_TE57_142

value: non-solid


title: D1-OE1-2-input

value: seedlings


title: KO-ND - TEN_025_05 (GE)

description: Library name: LAB_312_13_S5


title: WT-HFD - TEN_025_09 (GE)

description: Library name: LAB_312_17_S9

value: Wild type

value: High fat diet


title: D1-OE1-1-input

value: 3 weeks after germination


title: Reascent, FosLow-MPP, replicate2, DNA methylation


title: WT-ND - TEN_025_03 (GE)

description: Library name: LAB_312_11_S3


title: Hypoxia12wNormoxia5w, FosLow-MPP, replicate3, DNA methylation


title: ZH11-3-input


title: ZH11-3-IP


title: Hypoxia12wNormoxia5w, FosLow-MPP, replicate2, DNA methylation


title: Hypoxia12wNormoxia5w, FosLow-MPP, replicate1, DNA methylation


title: ZH11-2-IP


title: Reascent, FosLow-MPP, replicate1, DNA methylation


title: Reascent, FosHi-MPP, replicate4, DNA methylation


title: BENIGN_TE57_136

value: F

value: HUM


title: CONTROL_TE57_144

value: CURRENT

value: solid

value: MUG