title: embryoE7.75, WT, bio rep1

city: Philadelphia

first: Naiara

last: Akizu

state: PA

address: 3501 Civic Center Blvd

department: Pathology And Lab Medicine

institute: Children's Hospital of Philadelphia

data_processing:
The demultiplexing, barcoded processing and gene counting were made using Cell Ranger v7.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryo

extract_protocol:
E7.75 embryos were isolated and placed in DMEM/10% FBS on ice. Once genotypes were confirmed, embryos were pooled and dissociated using trypsin for 5 minutes at 37°C. After dissociation, trypsin was neutralized with three times the amount of DMEM/10% FBS.
The 10x Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 was used to perform single cell and library preparations. Generation of gel beads in emulsion, barcoding, GEM-RT clean-up, complementary DNA amplification, and library construction were all performed as per the manufacturer’s protocol.

value: embryo

tag: age

value: female

value: WT


title: sdg701-Mi-H3K4me3-2

status: Public on May 10 2025

type: SRA

city: wuhan

first: zhu

last: bo

state: beijing

address: shi zi shan street

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

description: Library name: sdg701-Mi-H3K4me3-2

library_source: genomic

data_processing:
RNA-seq raw reads were filtered by fastp (v.0.23.4) to remove low quality reads and adapter. Clean reads were aligned to the MSU7.0 rice reference genome (Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/) by hisat2 (v.2.1.0). FeatureCounts (v.2.0.1) were used for quantitative analysis and the differentially expressed genes were calculated by DESeq2. For the single-cell RNA seq data of hybrid (SY63), fastp (v.0.23.4) was used to remove duplicate and low-quality reads, and then clean reads were matched with the reference genomes of parents ZS97 and MH63 (ZS97RS3 and MH63RS3, Rice Information GateWay [RIGW], http://rice.hzau.edu.cn/rice_rs3/) using hisat2 (v.2.1.0). Further use PP2PG65 software to isolate parental reads through SNPs of ZS97 and MH63.
Fastp (v.0.23.4) was used to remove low-quality reads and adapter from the CUT&Tag raw data. Clean reads were mapped to the MSU7.0 genome by Bowtie2 (v.2.4.1). SAMtools (v.1.20)  is used to convert between SAM and BAM formats, sort and deduplicate BAM files, and merge two biological replicates. MACS2 (v.2.2.7.1) was used to call histone modification peaks with the parameters (-f BAMPE -g 3.8e8 --broad -q 0.01 for H3K27me3, H3K36me3 and H3K9me2; -f BAMPE -g 3.8e8 -q 0.01 for H3K4me3), and H3 sample was used as control. The bigwig files were generated using bamCoverage with the parameters (-bam -binSize 10 –normalize Using BPM) in deepTools (v.2.5.3), which were visualized in the Integrated Genome Browser, draw heatmaps and metaplots.
BS-seq low-quality reads were filtered out from the raw data by TrimGalore (v.0.6.6; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Clean reads were mapped to the MSU7.0 rice genome. Bismark (v.0.23.1) was used to match, deduplicate and extract methylation sites. To obtain more loci for analysis, we combined the two biological replicates. Duplicates were removed and uniquely mapped reads were retained and each cytosine covered by at least five reads for further analysis. Density plots show the frequency distribution of DNA methylation differences between 50-bp window of two samples with at least 20 informative sequenced cytosines in both samples and 70% CG, 30% CHG, or 10% CHH methylation in either of the samples as previously described.
Assembly: MSU7.0
Supplementary files format and content: bigwig file
Supplementary files format and content: RNA-seq normalized counts file
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: Earl stage microspore

growth_protocol: For field cultivation, the plants were grown in Wuhan during summer seasons under standard agricultural practices. Seedlings were transplanted to the field in early May and harvested in October. For greenhouse experiments, germinated rice seedlings were planted in soil-filled containers and grown under controlled conditions with a 14-h light/10-h dark cycle at 32°C (light) and 26°C (dark). Tillers of rice plants at an appropriate developmental stage were harvested for collection of spikelets. The collected spikelets were used for phenotypic analysis and isolation of male germ cells.

extract_protocol:
For collection of tetrads and microspores, when tillers flag leaf collar and penultimate leaf collar aligned spikelets of 0.4-0.6 cm length were taken. Like extracting meiocytes, anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with tetrad shapes were collected as tetrads. Cells with single, free-floating state and have not formed cell walls were collected as microspores.For collection of mature unicellular microspores, when tillers flag leaf auricle was about 5 cm above the auricle of the penultimate leaf, fresh spikelets > 0.6 cm were collected. At this stage the color of the spikelets is still white. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with distinct germination pores and having formed cell walls are collected as unicellular microspores.For collection of bicellular microspores, spikelets turning greener in color were taken. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with distinct large vacuoles, two nuclei, and thickened pollen walls are collected as bicellular microspores.For collection of mature pollen, tillers green spikelets were taken. At this point, the anthers have developed into yellow color. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. The cells that are distinctly filled with starch are collected as pollen.A differential centrifugation isolation method was used to separate sperm from whole rice anthers.
Isolation and purification of mRNA from different types of cells were performed using the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat. # N712). The RNA-seq libraries were prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat. # TD502) and sequenced on Illumina HiSeq 6000. For rice in SY63 backgrounds, we used single male germ cell to construct the transcriptome library. We used approximately 100-200 male germ cells to construct the transcriptome library.BS-seq libraries were constructed using reported protocol Clark et al (2017). About 400–500 male germ cells were pooled for each replicate bisulfite seq library construction.The CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Cat. # TD903) and sequenced on Illumina HiSeq 6000. We used approximately 10,000 male germ cells to construct the CUT&Tag library by male germ cell isolation technology. The male germ cells were lysed with 200 µL Nuclear extraction buffer 2 (NEB2) (0.25 M sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 1% Triton X-100, 1× protease inhibitor), and the nuclei pellet was resuspended in 100 µL wash buffer (from the TD903 kit) for library construction. About 100,000 sperm cells were pooled for each replicate CUT&Tag library construction. About 100,000–200,000 seedling cell nuclei were pooled for each replicate CUT&Tag library construction.For ATAC-seq library construction, the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, Cat. # TD711) was used to prepare libraries for different types of cells. Using the same number of cells as for CUT&Tag, we isolated approximately 10,000 male germ cells to construct the ATAC-seq library. Approximately 100,000 sperm cells and 100,000–200,000 seedling cell nuclei were pooled for each replicate ATAC-seq library construction.

tag: cell type

value: Earl stage microspore

tag: genotype


title: Beas-2B-siSPRY2-wsp-4-1

city: Denver

first: Arnav

last: Gupta

state: CO

address: 1400 Jackson St. K720

department: Pulmonary and Critical Care

country: USA

institute: National Jewish Health

description: Library name: Beas-2B-siSPRY2-wsp-4-1

library_source: transcriptomic

data_processing:
Reads were trimmed for adapters, minimum length, and minimum quality using the bbduk tool from the BBMap Suite (v. 38.73) with arguments ‘ref=adapters.fa ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=20 ftr=36’
Trimmed reads were mapped to the human genome (hg38; downloaded from the UCSC genome browser on September 16, 2019, with corresponding hisat2 index files) using hisat2 (v. 2.1.0)
Resulting SAM files were converted to BAM format using samtools view (v. 1.9) with arguments ‘-S -b’, duplicates were removed using picard tools MarkDuplicates (v. 2.26.6) and then resulting BAM files were sorted and indexed using samtools sort and index, respectively.
Sorted BAM files were converted to bedGraph coverage format files using genomeCoverageBed from the BEDTools suite (v. 2.29.2) with arguments ‘-bg -ibam -g hg38 -strand +’.
Gene assignment and counting was performed using the featureCounts function from the Rsubread package (v 2.6.4) applied to sorted BAM files using the hg38 gtf annotation downloaded from the UCSC Genome Browser on September 26, 2019
Assembly: hg38
Supplementary files format and content: BedGraph files are non-normalized coverage files.
Supplementary files format and content: featureCounts file is a non-normalized count file including all experimental conditions

molecule: polyA RNA

organism: Homo sapiens

source_name: Lung

growth_protocol: Beas-2B airway epithelial cells were grown in standard submerged culture conditions in DMEM supplemented with 10% Fetal Bovine Serum

extract_protocol:
RNA extraction from lysates harvested in trizol was performed using the purelink RNA kit (Life Technologies).
RNA sequencing libraries were prepared according to the Watchmaker mRNA Library Build user guide. Briefly, mRNA from 200ng of total RNA was isolated using polyA, oligo-dT magnetic beads. The isolated mRNA was then subject to enzymatic fragmentation, resulting in ~200 bp fragments. The resulting RNA fragments underwent first and second strand cDNA synthesis. IDT xGen Stubby Adapters were then ligated to the cDNA. The ligated product was then PCR amplified for 10 cycles using the IDT xGen UDI Primers. The resulting libraries were quantified using the Qubit HSDNA assay and TapeStation DNA 1000 assay. Equal molar concentrations were pooled, diluted to 800pM, and sequenced using a 200 cycle NextSeq 2000 flow cell.

treatment_protocol: Cells were first transfected with scrambled control or SPRY2-targeting siRNA and then exposed to wood smoke particles (WSP) at 1 mg/ml or 0.26 mg/cm2 for 2 and 4 hours before harvested in trizol for RNA extraction.

tag: tissue

value: Lung

tag: cell line

value: Airway epithelial cell

tag: treatment

tag: batch


title: ZH11-Me-H3-1

description: Library name: ZH11-Me-H3-1

source_name: Meiocyte

value: Meiocyte


title: embryoE7.75, cYAPKO, bio rep1

description: 10x Chromium Next GEM Single Cell 3’ GEM

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: Sex

value: cYAPKO


title: Beas-2B-siSPRY2-wsp-4-2

description: Library name: Beas-2B-siSPRY2-wsp-4-2


title: EYE treated with 75% oxygen Postnatal day12(P12), Wild type

city: shantou

first: xiaoqiang

last: xiao

state: Guangdong

address: North dongxia road

institute: Joint Shantou International Eye Center,Shantou University and the Chinese University of Hong Kong

description: No

data_processing:
raw reads quality control by Q30,Q20 and GC Content analysis, filtered the adaptor -polluted reads and low quality reads
The filtered reads then were further mapped to the rRNAs database with SOAP2 (Li R, 2009) to eradicate the rRNA pollution. rRNA-free clean reads were then mapped to reference genome with BWA –MEM software
Using de novo circRNA prediction softeware CITI, basing on Back-spliced junctions, identified circRNA candidates
DEseq2 software was used to screen differentially expressed circRNAs.
CIRI-AS software was used for the identification of alternative splicing events and exon position of circRNAs.
Supplementary files format and content: CIRI identified circular RNA reads
Supplementary files format and content: text files include circular Back splice reads  and SRPBM values for each Sample

organism: Mus

source_name: Ocular tissue

extract_protocol:
new birth mice (postnatal day 7,P7 treated with 75% oxygen for five days P12,then placed into air feed, Ocular tissues were then taken at P12(immediately after put back into the air) and P13.Total RNAs were extracted from the tissues and send to company for high-throughput circular RNA sequencing
Total RNA was removed the rRNA,and linear RNA ,the resultant was then fragmented and used to sequencing
The modified cDNAs fragments with length ranging from 150 bp to 200 bp were used for library construction.  Following cluster generation, the paired-end sequencing was conducted on an Illumina Hiseq 4000 platform.

value: Ocular tissue

tag: strain

value: Wild type

value: 75percent high oyxgen treatment through postnatal day 7 to postnatal day 12


title: Beas-2B-siSPRY2-wsp-4-3

description: Library name: Beas-2B-siSPRY2-wsp-4-3


title: ZH11-BM-H3-1

description: Library name: ZH11-BM-H3-1

source_name: Bicellular microspore

value: Bicellular microspore


title: sdg701-Mi-H3K4me3-1

description: Library name: sdg701-Mi-H3K4me3-1


title: Beas-2B-siSPRY2-wsp-2-4

description: Library name: Beas-2B-siSPRY2-wsp-2-4


title: ZH11-Mi-H3-1

description: Library name: ZH11-Mi-H3-1


title: ZH11-Sp-H3-1

description: Library name: ZH11-Sp-H3-1

source_name: Sperm

value: Sperm


title: Huh7 cells, shControl

city: Tianjin

first: 佳仪

last: 吴

address: No.94 Weijin Road

institute: Nankai University

description:
Library name: Samole1
Column name in raw_counts.txt:shCtrl

data_processing:
After library preparation and pooling of different samples, the samples were subjected for NGS platform by Berry Genomics Co., Ltd
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

growth_protocol: Huh7 cells were maintained in DMEM suppleented with 10% fetal bovine serum and antibiotics inhumidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library

value: Hepatocellular carcinoma cells


title: Beas-2B-siSPRY2-wsp-2-1

description: Library name: Beas-2B-siSPRY2-wsp-2-1


title: ZH11-Se-H3-1

description: Library name: ZH11-Se-H3-1

source_name: Seedling

value: Seedling


title: ZH11-UM-H3K9me2-2

description: Library name: ZH11-UM-H3K9me2-2

source_name: Unicellular microspore

value: Unicellular microspore


title: Beas-2B-siSPRY2-veh-3

description: Library name: Beas-2B-siSPRY2-veh-3

value: vehicle


title: ZH11-UM-H3K9me2-1

description: Library name: ZH11-UM-H3K9me2-1


title: Beas-2B-siSPRY2-veh-4

description: Library name: Beas-2B-siSPRY2-veh-4


title: Beas-2B-siSPRY2-veh-2

description: Library name: Beas-2B-siSPRY2-veh-2


title: Beas-2B-siSPRY2-veh-1

description: Library name: Beas-2B-siSPRY2-veh-1


title: ZH11-Sp-H3K9me2-1

description: Library name: ZH11-Sp-H3K9me2-1


title: Beas-2B-siCTRL-wsp-4-4

description: Library name: Beas-2B-siCTRL-wsp-4-4

value: control


title: ZH11-UM-H3-1

description: Library name: ZH11-UM-H3-1


title: ZH11-Se-H3K9me2-2

description: Library name: ZH11-Se-H3K9me2-2


title: Beas-2B-siSPRY2-wsp-2-3

description: Library name: Beas-2B-siSPRY2-wsp-2-3


title: Beas-2B-siSPRY2-wsp-4-4

description: Library name: Beas-2B-siSPRY2-wsp-4-4


title: ZH11-Mi-H3K9me2-1

description: Library name: ZH11-Mi-H3K9me2-1


title: ZH11-Me-H3K9me2-2

description: Library name: ZH11-Me-H3K9me2-2


title: Beas-2B-siCTRL-wsp-4-1

description: Library name: Beas-2B-siCTRL-wsp-4-1


title: Beas-2B-siCTRL-wsp-4-3

description: Library name: Beas-2B-siCTRL-wsp-4-3


title: Beas-2B-siCTRL-wsp-4-2

description: Library name: Beas-2B-siCTRL-wsp-4-2


title: Beas-2B-siSPRY2-wsp-2-2

description: Library name: Beas-2B-siSPRY2-wsp-2-2


title: ZH11-Mi-H3K9me2-2

description: Library name: ZH11-Mi-H3K9me2-2


title: ZH11-Se-H3K9me2-1

description: Library name: ZH11-Se-H3K9me2-1


title: Beas-2B-siCTRL-wsp-2-3

description: Library name: Beas-2B-siCTRL-wsp-2-3


title: ZH11-Me-H3K36me3-2

description: Library name: ZH11-Me-H3K36me3-2


title: Beas-2B-siCTRL-wsp-2-4

description: Library name: Beas-2B-siCTRL-wsp-2-4


title: ZH11-Me-H3K36me3-3

description: Library name: ZH11-Me-H3K36me3-3


title: ZH11-Me-H3K9me2-1

description: Library name: ZH11-Me-H3K9me2-1


title: Beas-2B-siCTRL-wsp-2-1

description: Library name: Beas-2B-siCTRL-wsp-2-1


title: ZH11-Me-H3K36me3-1

description: Library name: ZH11-Me-H3K36me3-1


title: Beas-2B-siCTRL-veh-4

description: Library name: Beas-2B-siCTRL-veh-4


title: ZH11-Sp-H3K9me2-2

description: Library name: ZH11-Sp-H3K9me2-2


title: ZH11-UM-H3K36me3-2

description: Library name: ZH11-UM-H3K36me3-2


title: Beas-2B-siCTRL-veh-3

description: Library name: Beas-2B-siCTRL-veh-3


title: ZH11-UM-H3K36me3-1

description: Library name: ZH11-UM-H3K36me3-1


title: ZH11-Sp-H3K36me3-3

description: Library name: ZH11-Sp-H3K36me3-3


title: Beas-2B-siCTRL-veh-1

description: Library name: Beas-2B-siCTRL-veh-1


title: ZH11-Sp-H3K36me3-2

description: Library name: ZH11-Sp-H3K36me3-2


title: TEAD4, RA-

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: Library name: TEAD4_RA_minus_S9

data_processing:
Sequenced reads were quality-tested using FASTQC and mapped to the hg19 reference genome using the STAR aligner with default parameters.
Peaks were identified with findPeaks in HOMER, using default parameters and input condition as background reference.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: H1 hESCs

growth_protocol: hESCs were mantained in mTeSR1 media on matrigel-covered plates.

extract_protocol:
Cells were double crosslinked with 2mM di (N-succinimidyl) glutarate (DSG) followed for 45 minutes at room temperature, followed by 1% formaldehyde for an additional 15 minutes at room temperature. Post-fixation, the cells were lysed and sonicated to fragment the chromatin. The non-sonicated chromatin was then precipitated, and the cell extract was subjected to overnight incubation with specific antibodies at 4°C. Subsequently, DNA purification was carried out using the Qiaquick PCR purification kit (QIAGEN, 28106). Library preparation was performed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. High-throughput sequencing using NextSeq1000.
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Chromatin was collected at Day 5, without treatment of RA 1uM for 24h.

value: H1 hESCs

value: YAP KO hESC-derived CPCs Day 5, RA 1uM 24h

tag: chip antibody

value: YAP KO hESC-derived CPCs Day 5


title: YAP, RA-

description: Library name: YAP_RA_minus_S7

value: WT hESC-derived CPCs Day 5, RA 1uM 24h

value: YAP

value: WT hESC-derived CPCs Day 5


title: ZH11-Se-H3K36me3-2

description: Library name: ZH11-Se-H3K36me3-2


title: Beas-2B-siCTRL-wsp-2-2

description: Library name: Beas-2B-siCTRL-wsp-2-2

value: Lung

value: Airway epithelial cell


title: Input, RA+

extract_protocol:
Cells were double crosslinked with 2mM di (N-succinimidyl) glutarate (DSG) followed for 45 minutes at room temperature, followed by 1% formaldehyde for an additional 15 minutes at room temperature. Post-fixation, the cells were lysed and sonicated to fragment the chromatin. The non-sonicated chromatin was then precipitated, and the cell extract was subjected to overnight incubation with specific antibodies at 4°C. Subsequently, DNA purification was carried out using the Qiaquick PCR purification kit (QIAGEN, 28106). Library preparation was performed using the NEBNext®Ultra™ II DNA Library Prep Kit for Illumina. High-throughput sequencing using NextSeq1000.
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Chromatin was collected at Day 5, following treatment of RA 1uM for 24h.


title: ZH11-Se-H3K36me3-1

description: Library name: ZH11-Se-H3K36me3-1


title: ZH11-Sp-H3K36me3-1

description: Library name: ZH11-Sp-H3K36me3-1


title: TEAD4, RA+


title: ZH11-Mi-H3K36me3-1

description: Library name: ZH11-Mi-H3K36me3-1

value: Earl stage microspore


title: ZH11-Mi-H3K36me3-2

description: Library name: ZH11-Mi-H3K36me3-2


title: LSCCP9, replicate 1, scRNAseq

city: Hangzhou

first: Zi-Ming

last: Fu

state: Zhejiang

address: Qingchun Road 79

department: Department of Otolaryngology

institute: The First Affiliated Hospital, School of Medicine, Zhejiang University

description:
Library name: LSCCP9
Adjacent normal tissue of LSCC9

data_processing:
Reads were processed using the Cell Ranger 7.1.0 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version GRCm38, using the STAR algorithm.Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat (v5) R toolkit for quality control and downstream analysis of our single cell RNAseq data.All functions were run with default parameters, unless specified otherwise.
We first filtered the matrices to exclude low-quality cells using a standard panel of three quality criteria: (1) numberof detected transcripts (number of uniquemolecular identifiers); (2) detected genes; and (3) percent of reads mapping to mitochondrial genes (Quartile threshold screening criteria). The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package. The normalized data (NormalizeData function in Seuratpackage) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression. Next, we integrated data from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the seurat package . Then we performed principal component analysis (PCA) and reduced the data to the top 50 PCA components after scaled the data. We visualized the clusters on a 2D map produced with tdistributed stochastic neighbor embedding (t-SNE)
Assembly: GRCh38.p13: http://asia.ensembl.org/Homo_sapiens/Info/Index;
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Adjacent normal tissue of LSCC9

extract_protocol:
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification
Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).

value: Adjacent normal tissue of LSCC9

value: male


title: NU-054, Mouse aorta cells, Postnatal age 20 (P20)

city: Chicago

first: Yogesh

last: Goyal

state: IL

address: 303 E Superior St

institute: Northwestern University

description:
Library name: NU-054
sequencing single-cell libraries

data_processing:
The approach to perform single cell analysis, including quality control steps and doublet removal was inspired from our previous studies. The Cellranger output expression matrices were merged for each sample.
The R package Seurat (v5.1.0) was used to cluster the cells in the merged matrix. Cells with less than 100 genes or more than 2e4 transcripts or 7.5% of mitochondrial expression were first filtered out as low-quality cells. The NormalizeData function was used to normalize the expression level for each cell with default parameters. The FindVariableFeatures function was used to select variable genes with default parameters. The ScaleData function was used to scale and center the counts in the dataset.
Principal component analysis (PCA) was performed on the variable genes. The RunHarmony function from the Harmony package was applied to remove potential batch effect among individual samples. Uniform Manifold Approximation and Projection (UMAP) dimensional reduction was performed using the RunUMAP function. The clusters were obtained using the FindNeighbors and FindClusters functions with the resolution set to 0.5. To ensure data quality, we first filtered out low-quality cell clusters by removing clusters with an average of fewer than 1,000 genes detected per cell (nFeature_RNA) and fewer than 2,000 total molecules detected per cell (nCount_RNA). Following this filtration, doublets were identified and removed.
Doublets were identified by evaluating the expression of specific markers - Pecam1, Dcn, Prox1, Tagln, and Cd3e - and determining whether each marker exceeded a defined threshold. Threshold levels were set based on a histogram analysis of gene expression data. Cells expressing two or more markers above these thresholds were classified as doublets.
Upon completing these quality control measures, we proceeded with data normalization and scaling, followed by the application of Harmony and UMAP, as described earlier. The cluster marker genes were found using the FindAllMarkers function. The cell types were annotated by overlapping the cluster markers with the published marker genes. Subsequently, we focused on isolating endothelial and proliferating cells by employing clusters that had been annotated using our previous mentioned methodology. For each subset of data, we repeated normalization, scaling, and the application of Harmony and UMAP to ensure consistency across analyses. Proliferating endothelial cells were identified by further clustering within the proliferating cell group and refining cell type annotations utilizing the aforementioned methodology. The dot plot was plotted using the DotPlot function. The violin plots were plotted using the VlnPlot function. The UMAP showing individual genes were plotted using the FeaturePlot function. Differential expression analysis between two group of cells was conducted using the FindMarkers function. Genes with adjusted p value smaller than 0.05 were considered significantly differentially expressed. The module scores were calculated based on genes in GO pathways downloaded from https://geneontology.org/.
Assembly: mm10
Supplementary files format and content: *.matrix.mtx: Sparse gene expression matrix; rows are features/genes, columns are 10x barcodes (what we call "cellID")
Supplementary files format and content: *.barcodes.tsv: Barcodes
Supplementary files format and content: *.features.tsv: Features/genes

source_name: aorta

extract_protocol:
Animals were sacrificed through CO2 inhalation before perfusion through the left ventricle with warm Versene solution (0.2g EDTA, 8g sodium chloride, 0.2g potassium chloride, 1.15g anhydrous sodium phosphate, 0.2g anhydrous potassium phosphate, dissolved in distilled water, pH 7.5) The aorta was dissected from the body and adventitia removed before being cut open to expose the endothelium. For the P5 and P10 timepoints, whole aortas were pooled into digestion solution (Liberase TH 70ug/mL, Sigma-Aldrich; DNase I, Qiagen; 10mM HEPES, Corning) and incubated at 37°C for 20 minutes while pipetting up and down every 2 minutes to generate a single-cell suspension. For P20 and P30 timepoints, aortas were cut open and pinned down with the endothelium facing up. After adding warm 1X trypsin (Gibco) for 5 minutes, a microfeather blade was used to gently scrape the endothelium of the aorta, as in previously established methods 17. The samples were incubated in 1X trypsin for an additional 5 minutes while pipetting up and down to generate a single-cell suspension. After neutralizing the digestion solution with DMEM containing 10% FBS, the cell suspension was filtered through a 20 uM cell strainer. Post-digestion cleanup was done prior to cell counting and viability assessment. Cell suspensions were loaded onto a Chromium Next GEM Chip G and run using the Chromium Controller iX (10X Genomics) to generate gel beads in emulsion (GEMs).
Single-cell RNA sequencing libraries were constructed using the Chromium Next GEM Single Cell 3’ v3.1 (Dual Index). Sequencing was performed on a NextSeq2000 Sequencing System (Illumina).

value: aorta

value: Mouse aorta cells

tag: time

value: Postnatal age 20 (P20)


title: YAP, RA+


title: NU-053, Mouse aorta cells, Postnatal age 10 (P10)

description:
Library name: NU-053
sequencing single-cell libraries

value: Postnatal age 10 (P10)


title: LSCCP10, replicate 1, scRNAseq

description:
Library name: LSCCP10
Adjacent normal tissue of LSCC10

source_name: Adjacent normal tissue of LSCC10

value: Adjacent normal tissue of LSCC10


title: LSCCP6, replicate 1, scRNAseq

description:
Library name: LSCCP6
Adjacent normal tissue of LSCC6

source_name: Adjacent normal tissue of LSCC6

value: Adjacent normal tissue of LSCC6


title: ZH11-Me-H3K27me3-1

description: Library name: ZH11-Me-H3K27me3-1

value: Meiocyte


title: Beas-2B-siCTRL-veh-2

description: Library name: Beas-2B-siCTRL-veh-2

value: vehicle

value: control


title: NU-050, Mouse aorta cells, Postnatal age 5 (P05)

description:
Library name: NU-050
sequencing single-cell libraries

value: Postnatal age 5 (P05)


title: ZH11-BM-H3K27me3-1

description: Library name: ZH11-BM-H3K27me3-1

value: Bicellular microspore


title: ZH11-Me-H3K27me3-2

description: Library name: ZH11-Me-H3K27me3-2


title: LSCCP4, replicate 1, scRNAseq

description:
Library name: LSCCP4
Adjacent normal tissue of LSCC4

source_name: Adjacent normal tissue of LSCC4

value: Adjacent normal tissue of LSCC4


title: LSCCP5, replicate 1, scRNAseq

description:
Library name: LSCCP5
Adjacent normal tissue of LSCC5

source_name: Adjacent normal tissue of LSCC5

value: Adjacent normal tissue of LSCC5


title: LSCCP1, replicate 1, scRNAseq

description:
Library name: LSCCP1
Adjacent normal tissue of LSCC1

source_name: Adjacent normal tissue of LSCC1

value: Adjacent normal tissue of LSCC1


title: NU-049, Mouse aorta cells, Postnatal age 30 (P30)

description:
Library name: NU-049
sequencing single-cell libraries

value: Postnatal age 30 (P30)


title: LSCCP2, replicate 1, scRNAseq

description:
Library name: LSCCP2
Adjacent normal tissue of LSCC2

source_name: Adjacent normal tissue of LSCC2

value: Adjacent normal tissue of LSCC2


title: ZH11-UM-H3K27me3-2

description: Library name: ZH11-UM-H3K27me3-2

value: Unicellular microspore


title: LSCCP7, replicate 1, scRNAseq

description:
Library name: LSCCP7
Adjacent normal tissue of LSCC7

source_name: Adjacent normal tissue of LSCC7

value: Adjacent normal tissue of LSCC7

value: male


title: LSCCP8, replicate 1, scRNAseq

description:
Library name: LSCCP8
Adjacent normal tissue of LSCC8

source_name: Adjacent normal tissue of LSCC8

value: Adjacent normal tissue of LSCC8


title: LSCC10, replicate 1, scRNAseq

description:
Library name: LSCC10
Moderately differentiated squamous cell carcinoma

source_name: laryngeal squamous cell carcinoma

value: laryngeal squamous cell carcinoma


title: Placenta, Young_11_5, Rep20

city: Burnaby

first: Julian

last: Christians

state: BC

address: 8888 University Drive

department: Biological Sciences

country: Canada

institute: Simon Fraser University

data_processing:
Read sequences were aligned to the Mus musculus (mm10) reference sequence using DRAGEN RNA app on Basespace Sequence Hub.
Assembly: mm10
Supplementary files format and content: tab-delimited quant.sf files include TPM values for each sample

source_name: placenta

extract_protocol:
We homogenized placental tissue using zirconium oxide beads (0.5 mm, ZROB05, Next Advance) and a mechanical shaker (MM300, Retsch). Placental mRNA was extracted using the Qiagen RNeasy Plus kit, including gDNA Eliminator columns to remove genomic DNA, according to manufacturer instructions.
Samples were prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq2000 with Paired End 59bp × 59bp reads, with 20 million paired end reads per sample.

value: placenta

tag: group

tag: gestational day

value: Female

tag: librarypreparationbatch

tag: sequencingbatch

tag: transcriptpercent

tag: inputreads

tag: uniquereads

tag: mappedreads

tag: totalbases

tag: mappedbases

tag: uniquereadsscaled


title: ZH11-UM-H3K27me3-1

description: Library name: ZH11-UM-H3K27me3-1

tag: cell type

tag: genotype


title: LSCC7, replicate 1, scRNAseq

description:
Library name: LSCC7
Moderately to poorly differentiated squamous cell carcinoma

tag: tissue

tag: Sex

tag: age


title: LSCCP3, replicate 1, scRNAseq

description:
Library name: LSCCP3
Adjacent normal tissue of LSCC3

source_name: Adjacent normal tissue of LSCC3

value: Adjacent normal tissue of LSCC3


title: Placenta, Young_11_5, Rep18

value: Male


title: LSCC8, replicate 1, scRNAseq

description:
Library name: LSCC8
Well to moderately differentiated squamous cell carcinoma


title: LSCC9, replicate 1, scRNAseq

description:
Library name: LSCC9
Moderately differentiated squamous cell carcinoma


title: LSCC5, replicate 1, scRNAseq

description:
Library name: LSCC5
Moderately to poorly differentiated squamous cell carcinoma


title: HCT116 cells, Rab27B KO, rep 3

city: Lawrence

first: Dan

last: Dixon

state: Kansas

address: 1200 Sunnyside Ave

department: Molecular Biosciences

institute: University of Kansas

data_processing:
Sequencing length- PE100
fastq files were aligned to version GCF_000001405.38_GRCh38.P12 of human reference genome using HISAT
Used Bowtie2 to align the clean reads to the reference genes
Data processing was conducted by BGI genomics
Processed data was analyzed using Dr. Tom Data Visualisation Solution
Assembly: version GCF_000001405.38_GRCh38.P12 of human reference genome
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values of upregulated genes (Rab27BKO / HCT116)
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values of downregulated genes (Rab27BKO / HCT116)

growth_protocol: 5x105 cells/well were plated in 6-well tissue culture-treated dishes with DMEM supplemented with 10% FBS and placed in a 5% CO2 37 °C incubator for 48 hours

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the DNBSeqTM by BGI Genomics

treatment_protocol: Cells were left untreated

tag: cell line

value: Colon cancer cell line

value: Rab27B KO

tag: treatment

value: Untreated


title: LSCC6, replicate 1, scRNAseq

description:
Library name: LSCC6
Moderately differentiated squamous cell carcinoma


title: ZH11-Sp-H3K27me3-2

description: Library name: ZH11-Sp-H3K27me3-2

source_name: Sperm

value: Sperm


title: ZH11-Sp-H3K27me3-1

description: Library name: ZH11-Sp-H3K27me3-1


title: LSCC4, replicate 1, scRNAseq

description:
Library name: LSCC4
Moderately differentiated squamous cell carcinoma


title: Placenta, Young_11_5, Rep17

tag: group

tag: gestational day


title: HCT116 cells, Rab27B KO, rep 2


title: HCT116 cells, Rab27B KO, rep 1


title: ZH11-Se-H3K27me3-1

description: Library name: ZH11-Se-H3K27me3-1

source_name: Seedling

value: Seedling


title: Placenta, Young_11_5, Rep16

tag: librarypreparationbatch

tag: sequencingbatch


title: LSCC2, replicate 1, scRNAseq

description:
Library name: LSCC2
Squamous cell carcinoma


title: ZH11-Se-H3K27me3-2

description: Library name: ZH11-Se-H3K27me3-2


title: LSCC3, replicate 1, scRNAseq

description:
Library name: LSCC3
Moderately differentiated squamous cell carcinoma


title: LSCC1, replicate 1, scRNAseq

description:
Library name: LSCC1
Moderately differentiated squamous cell carcinoma


title: HCT116 cells, wt control, rep 3

value: WT


title: HCT116 cells, wt control, rep 2


title: Placenta, Young_11_5, Rep14

tag: transcriptpercent

tag: inputreads


title: ZH11-Mi-H3K27me3-1

description: Library name: ZH11-Mi-H3K27me3-1

source_name: Earl stage microspore

value: Earl stage microspore


title: Placenta, Young_11_5, Rep13

tag: uniquereads

tag: mappedreads


title: ZH11-Mi-H3K4me3-2

description: Library name: ZH11-Mi-H3K4me3-2


title: HCT116 cells, wt control, rep 1


title: Placenta, Aged, Rep18

value: Aged

tag: totalbases

tag: mappedbases


title: VCL9, replicate 1, scRNAseq

description:
Library name: VCL9
Moderate to severe dysplasia

source_name: vocal cord leukoplakia

value: vocal cord leukoplakia


title: ZH11-Mi-H3K4me3-1

description: Library name: ZH11-Mi-H3K4me3-1

tag: cell type


title: Placenta, Aged, Rep17

tag: genotype

tag: uniquereadsscaled


title: ATAD3A Ast KO-4

city: Hefei

first: Li

last: Wang

address: No. 443, Mount Huangshan Road, Shushan District

institute: University of Science and Technology of China

description:
Library name: Sample 7
10x Genomics

data_processing:
For scRNA-seq data processing, raw reads were aligned to mouse reference genome GRCm39 using the Cell Ranger software (v8.0.0) to generate cell × gene matrices. The FASTQ files were processed using the standard workflow of cellranger to generate gene expression count matrices for each sample. The raw count matrices from all samples were merged using Scanpy (V1.9.6), followed by quality control.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor cells

extract_protocol:
Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion).
ScRNA-seq libraries were subsequently prepared following the manufacturer’s protocol of Chromium Next GEM Single Cell 3’ Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode.

value: tumor cells


title: Placenta, Young_11_5, Rep19

tag: tissue

tag: Sex


title: ZH11-Me-H3K4me3-2

description: Library name: ZH11-Me-H3K4me3-2

source_name: Meiocyte

value: Meiocyte


title: VCL8, replicate 1, scRNAseq

description:
Library name: VCL8
Epithelial hyperplasia with hyperkeratosis

value: male

tag: age


title: VCL7, replicate 1, scRNAseq

description:
Library name: VCL7
Epithelial hyperplasia with dysplasia


title: ZH11-Me-H3K4me3-1

description: Library name: ZH11-Me-H3K4me3-1


title: Placenta, Aged, Rep16


title: ATAD3A Ast KO-3

description:
Library name: Sample 6
10x Genomics


title: Placenta, Young_11_5, Rep15


title: ZH11-Mi-H3K27me3-2

description: Library name: ZH11-Mi-H3K27me3-2


title: ZH11-BM-H3K4me3-2

description: Library name: ZH11-BM-H3K4me3-2

source_name: Bicellular microspore

value: Bicellular microspore


title: VCL10, replicate 1, scRNAseq

description:
Library name: VCL10
Moderate to severe dysplasia


title: ATAD3A Ast KO-1

description:
Library name: Sample 4
10x Genomics


title: Placenta, Aged, Rep14

value: placenta


title: ATAD3A Ast KO-2

description:
Library name: Sample 5
10x Genomics


title: Placenta, Aged, Rep15

value: Female


title: Placenta, Aged, Rep13


title: VCL5, replicate 1, scRNAseq

description:
Library name: VCL5
Epithelial hyperplasia with dysplasia


title: ZH11-UM-H3K4me3-2

description: Library name: ZH11-UM-H3K4me3-2

source_name: Unicellular microspore

value: Unicellular microspore


title: ATAD3A fl/fl-2

description:
Library name: Sample 2
10x Genomics


title: VCL3, replicate 1, scRNAseq

description:
Library name: VCL3
Severe dysplasia


title: ZH11-Sp-H3K4me3-2

description: Library name: ZH11-Sp-H3K4me3-2


title: VCL4, replicate 1, scRNAseq

description:
Library name: VCL4
Mild to moderate dysplasia


title: ZH11-UM-H3K4me3-1

description: Library name: ZH11-UM-H3K4me3-1


title: ZH11-BM-H3K4me3-1

description: Library name: ZH11-BM-H3K4me3-1


title: ATAD3A fl/fl-3

description:
Library name: Sample 3
10x Genomics


title: VCL2, replicate 1, scRNAseq

description:
Library name: VCL2
Severe dysplasia


title: Placenta, Aged, Rep11

value: Male


title: ZH11-Sp-H3K4me3-1

description: Library name: ZH11-Sp-H3K4me3-1


title: Placenta, Aged, Rep10


title: Placenta, Aged, Rep12


title: WT- Naive-N2

city: Nanning

first: Pengcheng

last: Cui

address: Da-Xue-Dong Road No.100

institute: Guangxi University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using TopHat(version:2.0.9).
Hisat2（version:2.0.4） software used for basecalling.
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene was calculated.
Differentially expressed genes were identified using edgeR [4]. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
The fold-changes were also estimated according to the FPKM in each sample. The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Assembly: hg38
Supplementary files format and content: Excel file include FPKM values for each Sample.

source_name: Renal Tissue

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were collected and stored at -80˚C until required for further use.

value: Renal Tissue

tag: cell line

value: Primary Cell

tag: treatment

value: Intraperitoneal injection of saline


title: VCP10, replicate 1, scRNAseq

description:
Library name: VCP10
Vocal cord polyp

source_name: vocal cord polyps

value: vocal cord polyps


title: WT- Naive-N3


title: VCL6, replicate 1, scRNAseq

description:
Library name: VCL6
Mild dysplasia


title: VCL1, replicate 1, scRNAseq

description:
Library name: VCL1
Moderate to severe dysplasia


title: ATAD3A fl/fl-1

description:
Library name: Sample 1
10x Genomics


title: ZH11-Se-H3K4me3-2

description: Library name: ZH11-Se-H3K4me3-2

value: Seedling


title: Placenta, Aged, Rep9

tag: group

tag: gestational day


title: Placenta, Aged, Rep8

tag: librarypreparationbatch

tag: sequencingbatch


title: Dsba-l-ko-Naive-N3

value: Dsbal knockout


title: ZH11-Se-H3K4me3-1

description: Library name: ZH11-Se-H3K4me3-1


title: VCP9, replicate 1, scRNAseq

description:
Library name: VCP9
Vocal cord polyp


title: WT- Naive-N1

value: WT


title: Placenta, Aged_Exercise, Rep17

tag: transcriptpercent

tag: inputreads


title: Dsba-l-ko-Naive-N2


title: Placenta, Aged_Exercise, Rep16

tag: uniquereads

tag: mappedreads


title: sdg725-Mi-3

description: Library name: sdg725-Mi-3

data_processing:
RNA-seq raw reads were filtered by fastp (v.0.23.4) to remove low quality reads and adapter. Clean reads were aligned to the MSU7.0 rice reference genome (Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/) by hisat2 (v.2.1.0). FeatureCounts (v.2.0.1) were used for quantitative analysis and the differentially expressed genes were calculated by DESeq2. For the single-cell RNA seq data of hybrid (SY63), fastp (v.0.23.4) was used to remove duplicate and low-quality reads, and then clean reads were matched with the reference genomes of parents ZS97 and MH63 (ZS97RS3 and MH63RS3, Rice Information GateWay [RIGW], http://rice.hzau.edu.cn/rice_rs3/) using hisat2 (v.2.1.0). Further use PP2PG65 software to isolate parental reads through SNPs of ZS97 and MH63.
Fastp (v.0.23.4) was used to remove low-quality reads and adapter from the CUT&Tag raw data. Clean reads were mapped to the MSU7.0 genome by Bowtie2 (v.2.4.1). SAMtools (v.1.20)  is used to convert between SAM and BAM formats, sort and deduplicate BAM files, and merge two biological replicates. MACS2 (v.2.2.7.1) was used to call histone modification peaks with the parameters (-f BAMPE -g 3.8e8 --broad -q 0.01 for H3K27me3, H3K36me3 and H3K9me2; -f BAMPE -g 3.8e8 -q 0.01 for H3K4me3), and H3 sample was used as control. The bigwig files were generated using bamCoverage with the parameters (-bam -binSize 10 –normalize Using BPM) in deepTools (v.2.5.3), which were visualized in the Integrated Genome Browser, draw heatmaps and metaplots.
BS-seq low-quality reads were filtered out from the raw data by TrimGalore (v.0.6.6; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Clean reads were mapped to the MSU7.0 rice genome. Bismark (v.0.23.1) was used to match, deduplicate and extract methylation sites. To obtain more loci for analysis, we combined the two biological replicates. Duplicates were removed and uniquely mapped reads were retained and each cytosine covered by at least five reads for further analysis. Density plots show the frequency distribution of DNA methylation differences between 50-bp window of two samples with at least 20 informative sequenced cytosines in both samples and 70% CG, 30% CHG, or 10% CHH methylation in either of the samples as previously described.
Assembly: MSU7.0
Supplementary files format and content: bigwig file
Supplementary files format and content: RNA-seq normalized counts file

value: Earl stage microspore


title: Dsba-l-ko-Naive-N1


title: Placenta, Aged_Exercise, Rep15

tag: totalbases

tag: mappedbases


title: sdg725-Mi-2

description: Library name: sdg725-Mi-2

tag: cell type

tag: genotype


title: VCP7, replicate 1, scRNAseq

description:
Library name: VCP7
Vocal cord polyp

tag: tissue


title: WT-AKI-13

value: Intraperitoneal injection of LPS


title: VCP6, replicate 1, scRNAseq

description:
Library name: VCP6
Vocal cord polyp

tag: Sex

value: female


title: sdg723-Mi-3

description: Library name: sdg723-Mi-3

value: mutant


title: VCP5, replicate 1, scRNAseq

description:
Library name: VCP5
Vocal cord polyp

value: male

tag: age


title: Placenta, Aged_Exercise, Rep13

tag: uniquereadsscaled


title: sdg725-Mi-1

description: Library name: sdg725-Mi-1


title: WT-AKI-12

tag: cell line

tag: treatment


title: sdg723-Mi-2

description: Library name: sdg723-Mi-2


title: WT-AKI-319


title: VCP4, replicate 1, scRNAseq

description:
Library name: VCP4
Vocal cord polyp


title: Placenta, Aged_Exercise, Rep14

tag: group

tag: gestational day


title: sdg723-Mi-1

description: Library name: sdg723-Mi-1


title: WT-AKI-317


title: VCP3, replicate 1, scRNAseq

description:
Library name: VCP3
Vocal cord polyp


title: Placenta, Aged_Exercise, Rep12

tag: librarypreparationbatch

tag: sequencingbatch


title: VCP2, replicate 1, scRNAseq

description:
Library name: VCP2
Vocal cord polyp


title: Placenta, Aged_Exercise, Rep11

tag: transcriptpercent

tag: inputreads


title: sdg708-Mi-3

description: Library name: sdg708-Mi-3


title: Dsba-l-ko-AKI-381


title: Placenta, Aged_Exercise, Rep10

tag: uniquereads

tag: mappedreads


title: VCP8, replicate 1, scRNAseq

description:
Library name: VCP8
Vocal cord polyp


title: VCP1, replicate 1, scRNAseq

description:
Library name: VCP1
Vocal cord polyp


title: sdg708-Mi-2

description: Library name: sdg708-Mi-2


title: Dsba-l-ko-AKI-156


title: iHeps_EMTi2

city: Hong Kong

first: yangyang

last: yuan

address: William MW Mong Block, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Adaptor sequence and low-quality sequence were trimmed by trim_galore.
Sequence reads were mapped to hg38 genome using STAR.
TPMCaculator was used to quanlify gene expression.
Assembly: hg38
Supplementary files format and content: CSV file includes raw counts for each sample

source_name: M0061 iPSC

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Thermo Fisher). Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using mRNA-seq library kit following manufacturer’s protocol.

value: M0061 iPSC

value: pluripotent stem cells

value: hALB-mCherry gene editing

value: hepatocytes differentiation


title: Placenta, Aged, Rep7

value: placenta

value: Aged

value: Female

tag: totalbases

tag: mappedbases


title: Dsba-l-ko-AKI-320

value: Renal Tissue

value: Primary Cell

tag: cell type

tag: genotype


title: sdg708-Mi-1

description: Library name: sdg708-Mi-1


title: Placenta, Aged, Rep6

tag: tissue

tag: Sex

value: Male


title: iHeps_EMTi1

source_name: M0060 iPSC

value: M0060 iPSC


title: Mus musculus Testis Cre_single-cell RNA-seq

city: Stockholm

first: Masomeh

last: Askari

address: Svante Arrhenius väg 20C

country: Sweden

institute: Stockholm University

description: Library name: Cre_scWTA_lib1

data_processing:
Cell barcode annotation
Valid cell barcodes were downloaded from BD Biosciences. For scRNA-seq, read 1 (R1) contains the information of barcodes and unique molecular indices (UMIs), while read 1 (R2) are from complementary DNA (cDNA). R1 retains 35 to 38 nucleotides cell barcodes followed by 8 nucleotide UMIs. For scATAC-seq, read I1 (Rl1) marked barcode and UMIs, while R1 and R2 are paired DNA sequences. The construction of Rl1 is 35 nucleotides cell barcodes followed by 8 nucleotides UMIs in reverse complemented. Allowing 0 mismatch, raw reads without valid cell barcodes were filtered. For the remaining reads, information of cell barcodes and UMIs were assigned to the read names of the cDNA end (scRNA-seq) or the paired DNA end (scATAC-seq).
Read alignment
We used STAR (v2.7.10b 24.0; {Dobin et al., 2013 #17514}) to align scRNA-seq reads to the mouse reference genome (mm10) using parameters --outFilterIntronMotifs RemoveNoncanonicalUnannotated –outFilterMultimapNmax 1. PCR duplications with the same UMIs and same alignment coordinates from the same cells were removed. Afterwards, a cell-by-gene sparse matrix was made for each sample.
We used bwa-mem  (v0.7.12; {Heng Li, 26.05.2013 #226945}) to align scATAC-seq reads to the mouse reference genome (mm10) using default parameters. The aligned files were converted to bed format using bedtools (v2.27.1), with +4/–5 coordinate shift for plus/minus strand reads to account for the 9 bp apart cuts by Tn5 transposase. PCR duplications with the UMIs and alignment coordinates from the same cells are removed. A fragment file was then generated for each sample.
Cell type annotation
Cell type annotation was done using the Seurat (v5.2.1; {Hao et al., 2021, #248943}) R package for scRNA-seq. We first removed cells with <500 expressed genes or ≥5% UMIs from mitochondrial genes. The gene UMI counts for each of the remaining cell were log normalized with a factor equals to 10,000. Top 5,000 variable genes were then extracted for principal component analysis (PCA). Top 20 PCs were further used for clustering (resolution = 0.8) and uniform manifold approximation and projection (UMAP) analysis. For each sample, we then used the DoubletFinder R package (v2.0.4; {McGinnis et al., 2019 #127124}) to remove doublets and multiplets using the top 10 PCs and default parameters. A total of 33 cell clusters were identified. We assigned cell-type to each cell cluster using the expression of marker genes (Figure S9B; Table S4B). Clusters without clear marker gene expression were removed from downstream analysis.
Cell-type annotation for scATAC-seq was performed using ArchR R package (v1.0.3; {Granja et al., 2021, #164955}). We filtered cells with <1,000 fragments or a TSS score <4. Doublets/multiplets were removed using ArchR for each sample with default parameters. Genome-wide tile matrix of 500 bp and UMAP analysis with default parameters were used for clustering. A total of 25 cell clusters were identified. We then assigned cell-type for each cluster based on the cell-type annotation generated from scRNA-seq analysis for those cells with both open chromatin and transcriptome captured along with the chromatin accessibility of marker genes.
Pseudo-bulk analysis
According to the cell-type annotation, we generated pseudo-bulks by merging all aligned reads/fragments for each cell type for scRNA-seq and scATAC-seq, respectively. We then normalized each pseudo-bulks to reads/fragments per million mapped reads/fragments and generated bigwig tracks. Chromatin accessibility of gene promoters is defined by the average normalized coverage at ±200 bp from TSS.
Assembly: mm10
Supplementary files format and content: Meta table txt format
Supplementary files format and content: Matrix txt format

source_name: Testis

extract_protocol: We performed BD Rhapsody Single-Cell Analysis System to simultaneously analyze the profile of mRNA expression and accessible chromatin state in cells from the testis of 11, 17 and 25 dpp wild-type mice and 8-weeks-old Cre/+ and Nfya-CKO mice.

value: Testis

value: CRE


title: Placenta, Aged_Exercise, Rep9

tag: uniquereadsscaled


title: iHeps_control2

source_name: M0059 iPSC

tag: cell line

value: M0059 iPSC


title: Mus musculus Testis NFYA_CKO_single-cell RNA-seq

description: Library name: NFYA_CKO_scWTA_lib1

value: CKO


title: sdg701-Mi-2

description: Library name: sdg701-Mi-2

value: Earl stage microspore


title: Placenta, Aged_Exercise, Rep8


title: Mus musculus Testis Cre_single-cell ATAC-seq

description: Library name: Cre_scATAC_lib1

library_source: genomic single cell


title: sdg701-Mi-1

description: Library name: sdg701-Mi-1


title: Placenta, Aged_Exercise, Rep7


title: K512R-AS input rep2

city: Shanghai

first: Jianxiu

address: Shanghai, China

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong universIty

library_source: other

data_processing:
For RIP-seq data, paired-end reads were harvested from illumina Novaseq 6000 sequencer, and were quality controlled by Q30.
3’ adaptor-trimming and low quality reads were removing by cutadapt software (v1.9.3).
Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4)
Genes were identified by MACS software with every pair.
Differentially sites were identified by diffReps
Assembly: hg19
Supplementary files format and content: Excel file includes RIP RNA sites
Supplementary files format and content: bed file includes RIP RNA sites

molecule: other

extract_protocol:
H1299 cells stably expressing Myc-PABPC1-WT or PABPC1-K512R were treated with or without 500 µM sodium arsenite, then RNA immunoprecipitation assay was carried out with GenSeq® RIP kit using anti-Myc antibody.
rRNAs were removed from the immunoprecipitated RNA and input RNA samples by using GenSeq® rRNA Removal Kit (GenSeq, Inc.). RNA libraries were constructed by using rRNA-depleted RNAs with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions.


title: ZH11-BM-3

description: Library name: ZH11-BM-3

value: Bicellular microspore


title: Mus musculus Testis NFYA_CKO_single-cell ATAC-seq

description: Library name: NFYA_CKO_scATAC_lib1


title: Placenta, Aged_Exercise, Rep6


title: ZH11-BM-2

description: Library name: ZH11-BM-2


title: K512R-AS input rep1


title: K512R-AS IP rep2


title: Mus musculus Testis 25dpp single-cell ATAC-seq

description: Library name: 25dpp_scATAC_lib1

value: WT


title: Placenta, Aged_Exercise, Rep5


title: ZH11-BM-1

description: Library name: ZH11-BM-1


title: Placenta, Aged, Rep5


title: K512R-AS IP rep1


title: Mus musculus Testis 17dpp single-cell ATAC-seq

description: Library name: 17dpp_scATAC_lib1


title: ZH11-UM-3.

description: Library name: ZH11-UM-3

value: Unicellular microspore


title: Mus musculus Testis 11dpp single-cell ATAC-seq

description: Library name: 11dpp_scATAC_lib1


title: sdg701-Mi-3

description: Library name: sdg701-Mi-3


title: Placenta, Aged, Rep4


title: K512R input rep2


title: Placenta, Aged_Exercise, Rep4


title: ZH11-UM-1.

description: Library name: ZH11-UM-1


title: ZH11-UM-2.

description: Library name: ZH11-UM-2


title: Mus musculus Testis 17dpp single-cell RNA-seq

description: Library name: 17dpp_scWTA_lib1


title: Placenta, Aged, Rep3


title: iHeps_control1

source_name: M0058 iPSC

value: M0058 iPSC

value: pluripotent stem cells

value: hALB-mCherry gene editing

tag: treatment


title: K512R IP rep2


title: Mus musculus Testis 11dpp single-cell RNA-seq

description: Library name: 11dpp_scWTA_lib1


title: ZH11-Te-3

description: Library name: ZH11-Te-3

source_name: Tetrad

value: Tetrad


title: Chip3_input

city: Fuzhou

first: zhaofeng

last: zhang

address: No. 29 Xinquan Road

institute: Fujian Medical University Union Hospital

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: ileum

extract_protocol: genomic DNA extraction

value: ileum


title: K512R IP rep1


title: Placenta, Aged, Rep2

source_name: placenta

value: placenta

tag: group

value: Aged

value: Female


title: ZH11-Te-1

description: Library name: ZH11-Te-1


title: Placenta, Aged_Exercise, Rep3

tag: gestational day

value: Male


title: WT-AS input rep2


title: Chip2_input


title: WT-AS input rep1


title: ZH11-Te-2

description: Library name: ZH11-Te-2


title: ZH11-Sp-2

description: Library name: ZH11-Sp-2

source_name: Sperm

value: Sperm


title: Chip1_input


title: Placenta, Aged_Exercise, Rep1

tag: librarypreparationbatch


title: Chip3_ip_FXR


title: ZH11-Sp-1

description: Library name: ZH11-Sp-1


title: WT-AS IP rep1


title: Mus musculus Testis 25dpp single-cell RNA-seq

description: Library name: 25dpp_scWTA_lib1

value: Testis


title: ZH11-Mi-3

description: Library name: ZH11-Mi-3

source_name: Earl stage microspore


title: Placenta, Young_11_5, Rep12

tag: sequencingbatch


title: K512R input rep1


title: Chip2_ip_FXR


title: Placenta, Young_11_5, Rep11

tag: transcriptpercent


title: Chip1_ip_FXR


title: Placenta, Young_11_5, Rep10

tag: inputreads


title: ZH11-Mi-2

description: Library name: ZH11-Mi-2


title: WT input rep1


title: WT input rep2


title: ZH11-Mi-1

description: Library name: ZH11-Mi-1


title: Placenta, Aged_Exercise, Rep2

tag: uniquereads


title: Placenta, Young_11_5, Rep9

tag: mappedreads


title: Placenta, Young_11_5, Rep8

tag: totalbases


title: WT-AS IP rep2


title: ZH11-Me-3

description: Library name: ZH11-Me-3

value: Meiocyte


title: WT IP rep2


title: female_tbg_male_dmt

city: Davis

first: Ethan

last: Fenton

address: 1544 Newton Court

department: Neuroscience

institute: UC Davis

description: 10X Genomics

data_processing:
Reads were mapped, assigned cell barcodes, and the UMIs were collapsed using Cell Ranger V8.0.1 to generate a count matrix. Cells were filtered based on total UMI count, unique genes expressed, and mitochondrial fraction and signal from burst and cytosolic reads removed with SoupX v1.5. Gene counts were normalized using SCTransform, cells were integrated using reciprocal principal components analysis in Seurat v5 and cell types were called by performing PCA on all integrated genes and running a de-novo Louvain clustering algorithm using the top 40 principal components with resolution set to 1.
Assembly: mm39
Supplementary files format and content: tab separated values files and matrix files from raw_feature_bc_matrix from Cell Ranger V8.0.1

molecule: nuclear RNA

source_name: Medial Prefrontal Cortex

extract_protocol:
RNA was prepared from isolated/sorted nuclei using 10X Genomics protocol (CG000286)
Libraries were prepared using the 10X Genomics protocol (CG000286)

value: Medial Prefrontal Cortex

tag: time after_treatment

tag: age

value: 8 weeks

tag: strain

value: wt


title: ZH11-Me-2

description: Library name: ZH11-Me-2

extract_protocol:
For collection of tetrads and microspores, when tillers flag leaf collar and penultimate leaf collar aligned spikelets of 0.4-0.6 cm length were taken. Like extracting meiocytes, anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with tetrad shapes were collected as tetrads. Cells with single, free-floating state and have not formed cell walls were collected as microspores.For collection of mature unicellular microspores, when tillers flag leaf auricle was about 5 cm above the auricle of the penultimate leaf, fresh spikelets > 0.6 cm were collected. At this stage the color of the spikelets is still white. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with distinct germination pores and having formed cell walls are collected as unicellular microspores.For collection of bicellular microspores, spikelets turning greener in color were taken. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with distinct large vacuoles, two nuclei, and thickened pollen walls are collected as bicellular microspores.For collection of mature pollen, tillers green spikelets were taken. At this point, the anthers have developed into yellow color. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. The cells that are distinctly filled with starch are collected as pollen.A differential centrifugation isolation method was used to separate sperm from whole rice anthers.
Isolation and purification of mRNA from different types of cells were performed using the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat. # N712). The RNA-seq libraries were prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat. # TD502) and sequenced on Illumina HiSeq 6000. For rice in SY63 backgrounds, we used single male germ cell to construct the transcriptome library. We used approximately 100-200 male germ cells to construct the transcriptome library.BS-seq libraries were constructed using reported protocol Clark et al (2017). About 400–500 male germ cells were pooled for each replicate bisulfite seq library construction.The CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Cat. # TD903) and sequenced on Illumina HiSeq 6000. We used approximately 10,000 male germ cells to construct the CUT&Tag library by male germ cell isolation technology. The male germ cells were lysed with 200 µL Nuclear extraction buffer 2 (NEB2) (0.25 M sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 1% Triton X-100, 1× protease inhibitor), and the nuclei pellet was resuspended in 100 µL wash buffer (from the TD903 kit) for library construction. About 100,000 sperm cells were pooled for each replicate CUT&Tag library construction. About 100,000–200,000 seedling cell nuclei were pooled for each replicate CUT&Tag library construction.For ATAC-seq library construction, the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, Cat. # TD711) was used to prepare libraries for different types of cells. Using the same number of cells as for CUT&Tag, we isolated approximately 10,000 male germ cells to construct the ATAC-seq library. Approximately 100,000 sperm cells and 100,000–200,000 seedling cell nuclei were pooled for each replicate ATAC-seq library construction.

tag: cell type

tag: genotype


title: Placenta, Young_11_5, Rep7

tag: tissue

tag: Sex

tag: mappedbases

tag: uniquereadsscaled


title: AS-6h-K512R-repeat2

data_processing:
For RNA-seq data, paired-end reads were harvested from illumina Novaseq 6000 sequencer, and were quality controlled by Q30.
3’ adaptor-trimming and low quality reads were removing by cutadapt software (v1.9.3).
The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Assembly: hg19
Supplementary files format and content: Excel file includes lncRNA expression profiling
Supplementary files format and content: Excel file includes mRNA expression profiling

extract_protocol:
To study the influence of PABPC1 SUMOylation on mRNA stability, we performed 4sU pulse-chase sequencing in H1299 cells under normal or stress condition to detect RNA stability. Briefly, H1299 cells stably expressing PABPC1-WT or PABPC1-K512R were labeled with 200 mM 4-thio-uridine for 2 h, after which medium was replaced with fresh medium with or without 500 µM sodium arsenite. The total RNA was extracted at indicated time point, then 4sU labeled RNAs were converted to biotinylated RNAs using HPDP-Biotin and isolated using DynabeadsTM MyOneTM Streptavidin C1.
4sU-labeled RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions.
mRNA-Seq and LncRNA-Seq

tag: cell line


title: ZH11-Me-1

description: Library name: ZH11-Me-1


title: Old 72h fasted biol rep 4

city: Cologne

first: Kazuto

last: Kawamura

address: Joseph-Stelzmann-Str. 9b

department: Molecular Genetics of Ageing

country: Germany

institute: Max Planck Institute for Biology of Ageing

description: Library name: Oldfasted4

data_processing:
After removing rRNA and tRNAs, reads were pseudo-aligned to the reference genome (Nfu_20140520) using Kallisto (0.45.0). Pair-wise differential gene expression was performed using DESeq2 (1.24.0).
Assembly: Nfu_20140520
Supplementary files format and content: Tab separated values of DESeq2 normalised counts

organism: Nothobranchius furzeri

source_name: adipose

growth_protocol: Adult fish were single-housed in 2.8 L tanks from the second week of life. Water parameters were pH 7-8, kH 3-5, and T 27.5 °C, 12 hours of light and 12 hours of darkness and fed with 10 mg of the dry pellet (BioMar INICIO Plus G) and Premium Artemia Coppens® twice a day.

extract_protocol:
Harvested tissues were snap-frozen in liquid nitrogen and stored at –80 °C. RNA extraction of all samples was done at the same time.
About 1 μg of total RNA was used per sample for library preparation. The ribosome removal step was conducted using the RiboZero rRNA removal kit (Illumina).

treatment_protocol: Fasted samples were fasted for 3 days. Refed samples were refed for 1 day.

value: adipose

value: WT (GRZ-AD)


title: WT IP rep1


title: Placenta, Aged, Rep1

tag: group

tag: gestational day

tag: librarypreparationbatch


title: female_veh_male_tbg

description: 10X Genomics

tag: treatment


title: Old 72h fasted biol rep 3

description: Library name: Oldfasted3


title: Placenta, Young_10_5, Rep6

tag: sequencingbatch

tag: transcriptpercent

tag: inputreads

tag: uniquereads


title: AS-3h-K512R-repeat2


title: D6_100X_rep1

city: Xuzhou

first: Cen

middle: Ai

last: Zhang

state: Jiangsu

address: No.2 Kunpeng

institute: Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District

data_processing:
Raw reads of all sequencing data were trimmed using fastp (Chen et al., 2018b) based on the  read length (≥50 bp).
The trimmed reads RNA-seq data were mapped to the rice reference genome with Hisat2 (Kim et al., 2015a).
Aligned reads with mapping quality (MapQ) less than 20 were removed using samtools (Li et al., 2009).
Read counts for all annotated genes in the rice reference genome were extracted using FeatureCounts (v1.6.4) (-g gene_id) (Liao et al. 2014).
Assembly: MSU V7.0
Supplementary files format and content: tab-delimited text files of FPKM files

organism: Oryza sativa

source_name: root

extract_protocol:
Total RNA was extracted from the aforementioned rice roots using TRIzol reagent (ThermoFisher Scientific, Cat # 15596026). 30 µg total RNA was used for DNase I treatment followed by mRNA enrichment using oligo d(T) beads.
The enriched mRNA was subsequently used for RNA-seq library preparation following the  standard protocol for preparing Illumina RNA-seq libraries.

value: root

value: 100X  CD


title: Old 72h fasted biol rep 2

description: Library name: Oldfasted2


title: AS-6h-K512R-repeat1


title: Placenta, Young_10_5, Rep5

tag: mappedreads

tag: totalbases


title: AS-3h-K512R-repeat1


title: D6_CK_rep2

value: normal


title: female_dmt_male_veh

description: 10X Genomics

tag: time after_treatment

tag: age

tag: strain


title: D6_CK_rep1

tag: tissue


title: 6h-K512R-repeat2

tag: genotype


title: Old 24h refed biol rep 4

description: Library name: Oldrefed4


title: 6h-K512R-repeat1


title: Placenta, Young_11_5, Rep5

tag: Sex

tag: mappedbases

tag: uniquereadsscaled


title: Old 24h refed biol rep 3

description: Library name: Oldrefed3


title: D4_100X_rep1


title: Old 24h refed biol rep 2

description: Library name: Oldrefed2


title: Placenta, Young_11_5, Rep4

tag: group

tag: gestational day


title: 3h-K512R-repeat2

tag: cell line


title: D6_100X_rep2

tag: treatment


title: D4_CK_rep2


title: D4_100X_rep2


title: 0h-K512R-repeat2


title: Placenta, Young_11_5, Rep3

tag: librarypreparationbatch

tag: sequencingbatch

tag: transcriptpercent


title: Young 72h fasted biol rep 4

description: Library name: Youngfasted4


title: 0h-K512R-repeat1


title: D4_CK_rep1


title: AS-6h-WT-repeat2


title: Placenta, Young_10_5, Rep2

tag: inputreads

tag: uniquereads

tag: mappedreads


title: Young 72h fasted biol rep 3

description: Library name: Youngfasted3


title: Placenta, Young_10_5, Rep3

tag: totalbases


title: AS-6h-WT-repeat1


title: Placenta, Young_10_5, Rep4


title: Old 72h fasted biol rep 1

description: Library name: Oldfasted1


title: Young 72h fasted biol rep 2

description: Library name: Youngfasted2


title: Placenta, Young_10_5, Rep1


title: Placenta, Young_11_5, Rep6


title: Young 72h fasted biol rep 1

description: Library name: Youngfasted1


title: Old 24h refed biol rep 1

description: Library name: Oldrefed1


title: 3h-K512R-repeat1


title: AS-3h-WT-repeat2


title: Young 24h refed biol rep 4

description: Library name: Youngrefed4


title: Patient 12, NF, 4723

city: Galway

first: Barry

last: Digby

address: University Road

country: Ireland

institute: University of Galway

description: Library name: Sample24

data_processing:
nf-core/rnaseq 3.1
STAR aligner v2.6.1d
Salmon quantification v1.4.0
Assembly: GRCh38
Supplementary files format and content: Comma delimited file containing raw counts.
Supplementary files format and content: Gene symbols as row names

source_name: Breast

growth_protocol: CAFs/NFs were grown in CAF media (MEM-α medium supplemented with 10% fetal bovine serum, 1% Penicillin/Streptomycin and 1 ng/ml human fibroblast growth factor 2 ) and incubated in a humidified atmosphere (37 ℃, 5% CO2).

extract_protocol:
Total RNA was isolated using MagnaPure Compact RNA Isolation Kit (Roche, 04802993001) and Roche Magnapure system (Roche, MPCC1593). RNA concentration was determined by DeNovix DS-11.
RNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit

value: Breast

tag: cell type

value: Fibroblasts

value: WT


title: Placenta, Young_11_5, Rep2

tag: tissue

value: placenta


title: AS-3h-WT-repeat1

tag: genotype


title: flox-IR3h-3

city: shanghai

last: qigen

address: Pujian Road 160

institute: Shanghai Jiao Tong University

description: Library name: SAMPLES6

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence / low - quality sequence using CLC genomic benchwork ( parameter - Quality limit :0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork ( parameters - mismath cost :2 insertion cost :3 deletion cost :3 length fraction :0.8 similarity fraction :0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
mm10
Assembly: hg38
Supplementary files format and content: tab - delimited text file includes raw counts for each Sample
Supplementary files format and content: Csv files include FPKM values for each Sample

source_name: liver

growth_protocol: C57BL/6 mice were housed in a room at 25℃ with a 12-hour lingh/dark cycle and understricted access to chow food and water

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

value: liver

value: Liver ischemia-reperfusion treatment


title: Young 24h refed biol rep 3

description: Library name: Youngrefed3


title: Placenta, Young_11_5, Rep1

tag: Sex

value: Female


title: Patient 12, CAF, 4722

description: Library name: Sample23


title: flox-IR3h-2

description: Library name: SAMPLES5


title: 6h-WT-repeat1


title: 3h-WT-repeat2


title: flox-IR3h-1

description: Library name: SAMPLES4


title: 03 MHT at 42°C for 90 min only

type: RNA

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin, and scanned with a probe array scanner (Thermo Fisher Scientific Inc.).

data_processing: GeneChip Analysis Suite was used.

label: biotin

source_name: human OSCC HSC-3 cells

label_protocol: Five hundred nanograms (ng) of total RNA was used to synthesize cRNA with a GeneChip 3' IVT Express Kit (Thermo Fisher Scientific Inc.).

growth_protocol: Human OSCC HSC-3 cells were cultured in E-MEM medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin mixed solution at 37°C in a humidified environment with 5% CO2.

extract_protocol: Total RNA was extracted from cells using a NucleoSpin RNA isolation kit (MACHEREY-NAGEL GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >9.5 were considered acceptable.

treatment_protocol: Mild hyperthermia (MHT) treatments were performed by immersing plastic culture dishes, sealed with Parafilm M film, in a 42 °C water bath for 90 min, followed by incubation at 37 °C in a CO2 incubator for 3 h. Chloroquine (CQ) was dissolved in sterilized water and added to the culture medium 30 min prior to MHT treatment.

value: human oral squamous cell carcinoma cell line

tag: gender

value: male

tag: age

value: tongue

tag: life span

value: infinite

tag: morphology

value: epithelial-like

value: HSC-3 cells were treated with MHT at 42°C for 90 min, followed by incubation at 37°C for 3 h.


title: MC38 cells, ERM, NonLabel_Enrich, 12G, Rep3

city: Beijing

first: Ruixiang

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

data_processing:
Cutadapt (v.1.18) was utilized firstly for adaptor sequence removal.
Then the reads were mapped by hisat2 (v.2.1.0) against the genome assembly downloaded from Ensembl.
Using the gene annotation (v.87) downloaded from Ensembl, the mapped reads were counted by HTSeq (v0.7.2) with the option “–stranded no”.
Then, differential expression analysis was carried out by DESeq2(v.1.16.1).
Assembly: GRCh38 (hg38), GRCm39 (mm39)
Supplementary files format and content: XLSX format includes raw counts for each sample

growth_protocol: HEK293T and MC38 cells were cultured in complete medium consisting of Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum at 37°C with 5% CO2.

extract_protocol:
RNAs were extract following the TRIzol Reagent manufacturer’s instructions, digested with 1-2 μL DNaseI at 37°C for 30 min, and then incubated with click reagents consisting of 0.1 mM biotin-azide, 2 mM THPTA, 0.5 mM CuSO4 and 5 mM sodium ascorbate. After 10 min of CuAAC reaction at room temperature, RNAs were purified with RNA Clean&Concentrator kit and eluted with pre-warmed nuclease-free water. The RNA integrity was detected by Fragment Analyzer. Approximately 1 μg RNA was kept as pre-enrichment samples, while the remaining was purified with streptavidin beads and the post-enrichment samples were purified by TRIzol Reagent.
Total RNAs were used for library construction and libraries were constructed by NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) following the manuyfacturer's instructions.

treatment_protocol: Cells stably expressing ERM located LAP were seeded to 100-mm cell culture dishes, then labeled at around 90% confluence. Cells were incubated with 10 mM PA and 50 μM furimazine in DMEM medium supplemented with 10% fetal bovine serum at 37 °C for 15-60 min. Then, the cells were washed with cold PBS thrice.

tag: cell line


title: Patient 11, NF, 4300

description: Library name: Sample22


title: flox-sham3

description: Library name: SAMPLES3

tag: treatment

value: Sham operated


title: 3h-WT-repeat1


title: 02 CQ 30 μM only

value: HSC-3 cells were treated with CQ 30 μM at 37°C for 30 min, and cultured at 37°C for 90 min, followed by incubation at 37°C for 3 h.


title: MC38 cells, ERM, NonLabel_Enrich, 12G, Rep2


title: Patient 10, NFF, 3537

description: Library name: Sample20


title: 04 MHT at 42°C for 90 min, CQ 30 μM

value: HSC-3 cells were treated with CQ 30 μM at 37°C for 30 min, and treated with MHT at 42°C for 90 min, followed by incubation at 37°C for 3 h.


title: 01 Control

value: HSC-3 cells were cultured at 37°C for 90 min, followed by incubation at 37°C for 3 h.


title: flox-sham2

description: Library name: SAMPLES2


title: 0h-WT-repeat2


title: 6h-WT-repeat2


title: Patient 10, CAF, 3536

description: Library name: Sample19

value: Breast


title: flox-sham1

description: Library name: SAMPLES1


title: 0h-WT-repeat1


title: MC38 cells, ERM, Label_Input, 12G, Rep3


title: Young 24h refed biol rep 2

description: Library name: Youngrefed2

value: adipose

value: WT (GRZ-AD)


title: NcoR1-IR0h-3

description: Library name: SAMPLES6

growth_protocol: NcoR1fl/fl and NcoR1ΔHep mice were housed in a room at 25℃ with a 12-hour lingh/dark cycle and understricted access to chow food and water

value: knockdown NcoR1


title: Patient 9, NF, 3533

description: Library name: Sample18

value: Fibroblasts

value: WT


title: MC38 cells, ERM, Label_Input, 12G, Rep2


title: NcoR1-IR0h-2

description: Library name: SAMPLES5

value: liver

value: Liver ischemia-reperfusion treatment


title: Patient 9, CAF, 3532

description: Library name: Sample17


title: Patient 11, CAF, 4299

description: Library name: Sample21


title: Young 24h refed biol rep 1

description: Library name: Youngrefed1


title: Patient 8, NF, 4344

description: Library name: Sample16


title: MC38 cells, ERM, Label_Input, 12G, Rep1


title: SY63-um-2

city: wuhan

first: zhu

last: bo

address: shi zi shan street

institute: Huazhong Agricultural University

description: Library name: SY63-um-2

organism: Oryza sativa Indica Group

source_name: Unicellular microspore

value: Unicellular microspore


title: SY63-um-1

description: Library name: SY63-um-1


title: NcoR1-IR0h-1

description: Library name: SAMPLES4


title: SY63-Te-3

description: Library name: SY63-Te-3

value: Tetrad


title: flox-IR0h-3

description: Library name: SAMPLES3


title: MC38 cells, ERM, NonLabel_Enrich, 12G, Rep1


title: MC38 cells, ERM, Label_Enrich, 12G, Rep3


title: MC38 cells, ERM, Label_Enrich, 12G, Rep2


title: Patient 7, NF, 4341

description: Library name: Sample14


title: SY63-um-3

description: Library name: SY63-um-3


title: SY63-Te-2

description: Library name: SY63-Te-2


title: MC38 cells, ERM, Label_Enrich, 12G, Rep1


title: flox-IR0h-2

description: Library name: SAMPLES2


title: Patient 7, CAF, 4340

description: Library name: Sample13


title: SY63-Te-1

description: Library name: SY63-Te-1


title: flox-IR0h-1

description: Library name: SAMPLES1


title: MC38 cells, ERM, NonLabel_Enrich, 3G, Rep3


title: MC38 cells, ERM, NonLabel_Enrich, 3G, Rep2


title: SY63-pooled-pollen-2

description: Library name: SY63-pooled-pollen-2

source_name: Pollen

value: Pollen


title: Patient 6, CAF, 4315

description: Library name: Sample11


title: SY63-pooled-pollen-1

description: Library name: SY63-pooled-pollen-1


title: Patient 6, NF, 4316

description: Library name: Sample12


title: MC38 cells, ERM, NonLabel_Enrich, 3G, Rep1


title: Patient 5, NF, 4215

description: Library name: Sample10


title: MC38 cells, ERM, Label_Input, 3G, Rep3


title: Patient 8, CAF, 4344

description: Library name: Sample15


title: SY63-Pollen-3

description: Library name: SY63-Pollen-3


title: YAP KO, RA+, Day 5

city: La Jolla

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Sequence reads were aligned to hg19 and preprocessed using SnapTools.
After alignment, the pair-end reads were converted into fragment. Only the paired fragments with MAPQ>30 and fragment length< 1000bp were kept. After alignment and filtration, a snap-format (Single-Nucleus Accessibility Profiles) file was generated, which contained meta data, cell-by-bin count matrices of a variety of resolutions, cell-by-peak count matrix.
Assembly: hg19
Supplementary files format and content: A structured hdf5 file in snap (Single Nucleus Accessibility Profile) format

source_name: H1 hESCs

extract_protocol:
Nuclei were isolated and permeabilized using OMNI buffer (0.1% NP40, 0.1% Tween-20, 0.01% Digitonin; Corces et al., Nat. methods 2017).
Nuclei were counted and 2k nuclei were dispensed per well; 96 wells per sample for tagmentation. After tagmentation nuclei from individual samples were pooled. 20 nuclei from each sample were sorted per well (768 wells total; 2n/4n mix in 672 wells (plates 1-7) and 48 wells each for 2n and 4n, respectively (plate 8). Method adapted from: Cusanovich et al., Science, 2015

treatment_protocol: Day 5 samples were untreated or treated with RA 1uM for 24h (from day 4 to day 5).

value: H1 hESCs

value: YAP KO hESC-derived CPCs Day 5, RA 1uM 24h

value: YAP KO

value: RA 1uM 24h (D4 to D5)


title: YAP KO, RA-, Day 5

value: YAP KO hESC-derived CPCs Day 5, untreated


title: Patient 4, NF, 4117

description: Library name: Sample8


title: SY63-Pollen-2

description: Library name: SY63-Pollen-2


title: MC38 cells, ERM, Label_Input, 3G, Rep2


title: WT, RA+, Day 5

value: WT hESC-derived CPCs Day 5, RA 1uM 24h


title: Patient 4, CAF, 4116

description: Library name: Sample7

value: Breast


title: SY63-Pollen-1

description: Library name: SY63-Pollen-1


title: MC38 cells, ERM, Label_Input, 3G, Rep1


title: WT, RA-, Day 5

value: WT hESC-derived CPCs Day 5, untreated


title: SY63-Mi-5

description: Library name: SY63-Mi-5

value: Earl stage microspore


title: MC38 cells, ERM, Label_Enrich, 3G, Rep2


title: shPRP4K

city: Halifax

first: Graham

last: Dellaire

state: Nova Scotia

address: 5850 College Street

department: Department of Pathology

institute: Dalhousie University

description: Library name: Dal171MCF7shPRP4KplusDox

data_processing:
Sequencing reads were mapped and aligned using HISAT2 on Galaxy (version 2.2.1 + galaxy1) to the human reference genome (hg19).
The penalty for non-canonical splice sites were set to 12. Long introns containing splice sites had a natural logarithm penalty function [f(x) = B + A * log(x)]. The constant terms B and A were set to -8 and 1, respectively. The remainder of the settings, such as minimum and maximum intron lengths, were kept at default.
Data was visualized using Broad Institute Integrated Genomics Viewer (IGV version 2.19) via a sashimi plot using the aligned BAM files.
Assembly: hg19
Supplementary files format and content: *Novel_Splice_Sites.tabular files contain the HISAT output for the location of newly detected splice juntions

growth_protocol: Human MCF7 breast cancer cells were cultured using Eagle’s Minimal Essential Medium (MEM; Sigma) in T-75 flasks, supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, 10 μg/mL human recombinant insulin, and 100X GlutaMAX™ (ThermoFisher Scientific). Cultures were maintained at 37°C in an incubator with 5% CO₂. For cells stably expressing shRNAs, the culture medium additionally contained 1 μg/mL puromycin.

extract_protocol:
MCF7 cells were lysed and homogenized using Trizol reagent (ThermoFisher Scientific) immediately upon harvesting. RNA extraction was subsequently performed using the Ambion PureLink RNA Mini Kit (ThermoFisher Scientific), following the manufacturer's protocol, with the inclusion of an on-column DNase I digestion step to eliminate genomic DNA contamination. RNA quality and purity were verified with a Nanodrop 2000 spectrophotometer, accepting RNA samples with A260/A280 and A260/A230 absorbance ratios around 2.0 as sufficiently pure for downstream applications. RNA integrity numbers were determined using an Agilent Bioanalyzer 2100 and typically were above 9 and were used for cDNA production.
One microgram of total RNA was used for isolating polyA-purified mRNA and subsequently used for cDNA-library construction with the Illumina TruSeq RNA Preparation Kit.  Strand specificity was performed with 2’-deoxyuridine 5’-triphosphate during second-strand synthesis. All samples were indexed with Illumina adapters.

treatment_protocol: Human MCF7 cells expressing doxycycline-inducible control (shCtrl) and shRNAs targeting PRP4K (shPRP4K) were treated with 5 μg/mL doxycycline for 72 hours, with media refreshed every 24 hours, to induce knockdown of PRP4K expression.

value: Human adenocarcinoma cells

tag: shRNA


title: shControl

description: Library name: Dal181MCF7shCtrlplusDox

value: shControl


title: Patient 3, CAF, 4112

description: Library name: Sample5

value: Fibroblasts

value: WT


title: MC38 cells, ERM, Label_Enrich, 3G, Rep3


title: WT, RA+, Day 30

data_processing:
For the snRNA-seq libraries, CellRanger (v.2.1.1) was used to perform sample-demultiplexing, barcode processing and single-nuclei gene-UMI counting.
An expression matrix was obtained for each experiment by aligning to the hg19 reference genome using CellRanger with default parameters.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
GEMx
Chromium single-cell

treatment_protocol: Day 5 samples were untreated or treated with RA 1uM for 24h (from day 4 to day 5). Day 30 samples were untreated or treated with RA 1uM full-treatment of 3 days (From day 4 to day 7).

value: WT hESC-derived CMs Day 30, RA 1uM D4-D7

value: RA 1uM 72h (D4 to D7)


title: SY63-Mi-4

description: Library name: SY63-Mi-4


title: Patient 3, NF, 4113

description: Library name: Sample6


title: MC38 cells, ERM, Label_Enrich, 3G, Rep1


title: SY63-Mi-2

description: Library name: SY63-Mi-2


title: SY63-Mi-3

description: Library name: SY63-Mi-3


title: Patient 2, NF, 4028

description: Library name: Sample4


title: YAP KO, RA+, Day 30

value: YAP KO hESC-derived CMs Day 30, RA 1uM D4-D8


title: Patient 2, CAF, 4027

description: Library name: Sample3


title: Patient 5, CAF, 4214

description: Library name: Sample9


title: WT3

city: Chongqing

first: rui

last: Liu

address: No. 1 Medical College Road, Yuzhong District

institute: CHONGQING MEDICAL UNIVERSITY

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: The diethylnitrosamine (DEN)-induced HCC of WT mice

extract_protocol:
Total RNA was extracted from animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse model

value: diethylnitrosamine (DEN)-induced HCC

value: liver


title: YAP KO, RA-, Day 30

value: H1 hESCs

value: YAP KO hESC-derived CMs Day 30, untreated


title: SY63-Mi-1

description: Library name: SY63-Mi-1

data_processing:
RNA-seq raw reads were filtered by fastp (v.0.23.4) to remove low quality reads and adapter. Clean reads were aligned to the MSU7.0 rice reference genome (Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/) by hisat2 (v.2.1.0). FeatureCounts (v.2.0.1) were used for quantitative analysis and the differentially expressed genes were calculated by DESeq2. For the single-cell RNA seq data of hybrid (SY63), fastp (v.0.23.4) was used to remove duplicate and low-quality reads, and then clean reads were matched with the reference genomes of parents ZS97 and MH63 (ZS97RS3 and MH63RS3, Rice Information GateWay [RIGW], http://rice.hzau.edu.cn/rice_rs3/) using hisat2 (v.2.1.0). Further use PP2PG65 software to isolate parental reads through SNPs of ZS97 and MH63.
Fastp (v.0.23.4) was used to remove low-quality reads and adapter from the CUT&Tag raw data. Clean reads were mapped to the MSU7.0 genome by Bowtie2 (v.2.4.1). SAMtools (v.1.20)  is used to convert between SAM and BAM formats, sort and deduplicate BAM files, and merge two biological replicates. MACS2 (v.2.2.7.1) was used to call histone modification peaks with the parameters (-f BAMPE -g 3.8e8 --broad -q 0.01 for H3K27me3, H3K36me3 and H3K9me2; -f BAMPE -g 3.8e8 -q 0.01 for H3K4me3), and H3 sample was used as control. The bigwig files were generated using bamCoverage with the parameters (-bam -binSize 10 –normalize Using BPM) in deepTools (v.2.5.3), which were visualized in the Integrated Genome Browser, draw heatmaps and metaplots.
BS-seq low-quality reads were filtered out from the raw data by TrimGalore (v.0.6.6; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Clean reads were mapped to the MSU7.0 rice genome. Bismark (v.0.23.1) was used to match, deduplicate and extract methylation sites. To obtain more loci for analysis, we combined the two biological replicates. Duplicates were removed and uniquely mapped reads were retained and each cytosine covered by at least five reads for further analysis. Density plots show the frequency distribution of DNA methylation differences between 50-bp window of two samples with at least 20 informative sequenced cytosines in both samples and 70% CG, 30% CHG, or 10% CHH methylation in either of the samples as previously described.
Assembly: MSU7.0
Supplementary files format and content: bigwig file
Supplementary files format and content: RNA-seq normalized counts file


title: WT, RA-, Day 30

value: WT hESC-derived CMs Day 30, untreated


title: Patient 1, NF, 4034

description: Library name: Sample2


title: SY63-Meiocytes-3

description: Library name: SY63-Meiocytes-3

source_name: Meiocyte

value: Meiocyte


title: YAP KO, RA+, Day 5

value: YAP KO hESC-derived CPCs Day 5, RA 1uM 24h

value: YAP KO

value: RA 1uM 24h (D4 to D5)


title: WT2


title: WT1838


title: SY63-Meiocytes-2

description: Library name: SY63-Meiocytes-2


title: WT1359


title: YAP KO, RA-, Day 5

value: YAP KO hESC-derived CPCs Day 5, untreated


title: Patient 1, CAF, 4033

description: Library name: Sample1

value: Breast


title: SY63-Meiocytes-1

description: Library name: SY63-Meiocytes-1


title: WT1


title: B. velezensis cells, coculture, 13h, biol rep 2, C13_2

city: Cuernavaca

first: Leobardo

last: Serrano Carreón

state: Morelos

address: Av Universidad 2001

department: Ingenieria Celular y Biocatálisis

country: Mexico

institute: Instituto de Biotecnología - UNAM

data_processing:
RNA-seq data was aligned and quantified by Salmon (v0.14.1)
The differential gene expression analysis was performed by edge R (Bioconductor package) using RPM as response variable.
To study the effect of time or microbial interaction, two comparisons were analyzed: 1) Samples from co-culture (treatment) vs axenic (control), regardless of time and 2) Samples from 13 h (treatment) vs 8 h (control), regardless of if it comes from of axenic or co-cultivation.
An orthology assignment was performed by eggNOG-Mapper (Version 4.5)
Assembly: Genome of B. velezensis 83 (NCBI accession No. CP034203) was used as reference.
Supplementary files format and content: Tab-delimited text files include  NumReads values for each sample

organism: Bacillus velezensis

growth_protocol: Axenic (B.velensis 83) and co-cultures (B.velezensis 83 and C.gloeosporioides) were carried out in a stirred tank type bioreactor using potato dextrose mineral medium. 29 °C, pH6.8 and DOT>30%.

extract_protocol:
RNA was isolated by RNeasy Mini Kit (74104, QUIAGEN). Remotion of rRNA was performed by Ribominus™ Transcriptome Isolation Kit.
Hi Seq4000 Sequencing Systems (Ilumina Inc., CA, USA) was used for RNA-seq.

treatment_protocol: Bacterial RNA from axenic and co-cultures was isolated. Sampling (8h and 13h) was done before glucose limitation.

value: vegetative

value: Coculture with C. gloeosporioides 13 h


title: B. velezensis cells, coculture, 13h, biol rep 3, C13_3

value: WT


title: WT, RA-, Day 5

value: WT hESC-derived CPCs Day 5, untreated


title: SY63-BM-4

description: Library name: SY63-BM-4

source_name: Bicellular microspore

value: Bicellular microspore


title: B. velezensis cells, coculture, 13h, biol rep 1, C13_1


title: SY63-BM-3

description: Library name: SY63-BM-3


title: ko1937

source_name: The diethylnitrosamine (DEN)-induced HCC of KO mice


title: KP5


title: HEK293T cells, ERM, NonLabel_Enrich, 3G, Rep2


title: HEK293T cells, ERM, NonLabel_Enrich, 3G, Rep3


title: B. velezensis cells, coculture, 8h, biol rep 3, C8_3

value: Coculture with C. gloeosporioides 8 h


title: HEK293T cells, ERM, NonLabel_Enrich, 3G, Rep1


title: SY63-BM-2

description: Library name: SY63-BM-2


title: B. velezensis cells, coculture, 8h, biol rep 2, C8_2


title: ko1828

value: diethylnitrosamine (DEN)-induced HCC


title: ko1831

value: liver


title: B. velezensis cells, coculture, 8h, biol rep 1, C8_1


title: HEK293T cells, ERM, Label_Input, 3G, Rep3


title: miRNC_3

city: shijiazhuang

first: LuSha

address: 12 Jiankang Road

department: Deportment of Gynecology

institute: The Fourth hospital of hebei medical research

data_processing:
The expression levels of genes and transcripts were quantified separately using the software RSEM for subsequent analysis of differential gene/transcript expression among different samples, and the regulatory mechanisms of genes can be revealed by combining sequence function information.
The software used for differential expression was DESeq2 (with biological replicates, used by default) or DEGseq (without biological replicates, used by default), the default screening criteria for significantly differentially expressed genes are: FDR < 0.05 & |log2FC| ≧ 1, and when a gene satisfies both conditions, it will be regarded as a differentially expressed gene (DEG).
This analysis was performed using the software Goatools for enrichment analysis using Fisher's exact test. Four multiple tests (Bonferroni, Holm, Sidak and false discovery rate) were used to correct the p-value to control for the calculated false positive rate, and in general, significant enrichment was considered to exist for this GO function when the corrected p-value (p_fdr) was < 0.05
Assembly: hg38
Supplementary files format and content: gene.count.matrix.annot.xlsx

source_name: Endometrial cancer

extract_protocol:
TOTAL RNA was extracted from the tissue samples, the concentration and purity of the extracted RNA was examined using Nanodrop2000, RNA integrity was examined by agarose gel electrophoresis, and the Agilent5300 determined the RQN values were determined by Agilent5300. For single library construction, the total RNA amount was 1 μg, the concentration was ≥ 30 ng/μL, the RQN was > 6.5, and the OD260/280 was between 1.8 and 2.2.
Total RNA was first extracted and mRNA was enriched by Oligo dT, then fragmented mRNA was synthesized into cDNA by reverse transcription, ligated into adapter, and sequenced by NovaSeq X Plus platform after fragment screening and library enrichment.

value: Endometrial cancer

value: Ishikawa

tag: transfection

value: control mimics-NC