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  • Processed_CUT&Tag-seq data

    Yifei Cheng, , 2023.12.18

    Description

    To process raw data, reads containing adapter or ploy-N were removed to generate clean reads. Further filtration according to the calculated Q20, Q30 and GC content resulted in high-quality clean reads, which were then aligned to reference human genome GRCh38 using the BWA program (version 0.7.15). The MACS2 package(version 2.2.9.1)was used for peak-calling from the BAM files with q-value < 0.05. HOMER (version 4.11) was applied to the generated peak file and the genome fasta for motif analysis. Peaks were annotated using the annotatePeaks.pl function. For defining differentially accessible peaks, peak files of each sample were first merged using BEDTools (version 2.28.0). The counts of the reads over the bed were then determined for each sample using the multicov function from BEDTools. Finally, differentially accessible peaks were assessed using DESeq2 (version v1.42.0).

    Analysis type

    Other

    OEZ014525

  • Processed spatial transcriptomics data at bin50-level

    Yifei Cheng, , 2023.05.12

    Description

    The raw reads were decoded by ST_BarcodeMap (version 0.0.1), filtered adapter sequence by Fastp, and then aligned to the reference genome GRCh38.p12(Human) via STAR. Mapped reads were annotated, then calculated by HandleBam(version 1.0.0). The raw matrix was converted into the bin50-level matrix (i.e., 25*25um) by the Seurat R package(version 4.2.0). For quality control, the median number of gene types per bin50 for all chips should be over 500.

    Analysis type

    Other

    OEZ013918

  • Processed single-cell spatial transcriptomics

    Yifei Cheng, , 2023.05.12

    Description

    The raw reads were decoded by ST_BarcodeMap (version 0.0.1), filtered adapter sequence by Fastp, and then aligned to the reference genome GRCh38.p12(Human) via STAR. Mapped reads were annotated, then calculated by HandleBamz(version 1.0.0). Single-cell segmentation of Stereo-seq data is performed by a self-written algorithm.

    Analysis type

    Other

    OEZ013917

  • Processed_snATAC-seq

    Yifei Cheng, , 2023.05.11

    Description

    Data were aligned to the human genome (hg38), and the fragment files were achieved using the default parameters of DNBelab C4 snATAC-seq (version v3.0, BGI). Doublet removal, iterative latent semantic indexing (LSI) dimensionality reduction, initial clustering, and snATAC-se-snRNA-seq data integration were performed using ArchR(v1.0).

    Analysis type

    Other

    OEZ013916

  • Processed shotgun proteomic profiles

    Yifei Cheng, , 2023.04.16

    Description

    Missing quantitative values were imputed using the K-nearest neighbor (KNN) algorithm in the DreamAI R package (v0.1.0).

    Analysis type

    Other

    OEZ013907

  • Whole genome sequecing analysis of IRD families

    Xin Li, , 2023.12.18

    Description

    A total of 271 unresolved IRD patients and their available family members (n=646) were screened using WGS technology to identify pathogenic SVs and intronic variants in 792 known ocular disease genes. The pathogenicity of all identified variants was evaluated through a combination of factors including allele frequencies (AFs) in the general population, functional annotation, and inheritance pattern analysis.

    Analysis type

    De Novo Assembly

    OEZ014524

  • xQTL analysis

    Chunchun Yuan, , 2023.11.27

    Description

    xQTL summary data for SNPs associated with selected M3S markers from methylation, metabolite and microbiota data

    Analysis type

    Other

    OEZ014452

  • PDAC_Proteomics_Library

    Chenxu Gao, , 2023.03.31

    Analysis type

    Other

    OEZ013891

  • Standard Genome Reference (Mock-Ref)

    Yu Zhang, , 2023.02.23

    Description

    This is the pooled reference genomes composed of 10 selected strains (Mock-Ref) used in MT-Enviro.

    Analysis type

    Reference Alignment

    OEZ013255

  • TMT6_Label_to_Sample_Mapping_File

    cheng cheng, Shanghai Jiaotong University School of Medicine affiliated Xinhua Hospital, 2023.11.10

    Analysis type

    Other

    OEZ014373