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  • 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

  • Cell line transcriptome

    Cheng Cheng, , 2023.11.07

    Description

    mRNA expression data of Wilm's tumor cell line after knockdown of EHMT2. Each experiment has three replications.

    Analysis type

    Other

    OEZ014371