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  • EXPR Old_RNA-seq

    Yuanliang  Zhang, Shanghai Institute of Hematology, 2024.01.26

    Project ID

    OEP004811

    Project Name

    Loss of Setd2 induces systemic inflammation via embryo-derived Kupffer-like cell differentiation to drive malignant transformation

    Experiment Type

    Transcriptomic

    Protocol

    For bulk RNA-seq, total RNA samples were extracted, and ribosomal RNA (rRNA) was removed using the Ribo-Zero rRNA Removal Kit (MRZMB126, Illumina). Subsequently, rRNA-depleted samples were fragmented, then subjected to first and second strand cDNA synthetization. cDNAs were ligated with sequencing adapters according to standard Novaseq 6000 platform (Illumina) manuscripts.

    OEX027260

  • EXPR Old_c-Kit+_scRNA-seq

    Yuanliang  Zhang, Shanghai Institute of Hematology, 2024.01.26

    Project ID

    OEP004811

    Project Name

    Loss of Setd2 induces systemic inflammation via embryo-derived Kupffer-like cell differentiation to drive malignant transformation

    Experiment Type

    Transcriptomic single cell

    Protocol

    BM cells separated from old WT and Setd2-MDS mice were stained with biotin-c-Kit antibody on ice for 20 minutes, then washed with MojoSort™ Buffer (480017, BioLegend) at 3,000rpm for 5 minutes. Subsequently, samples labelled with biotin-c-Kit antibody were isolated through MACS assay, then the c-Kit+ BM cells were purified with BD FACSAria™ III. After purification, the BD Rhapsody system (BD Biosciences) was used to capture the transcriptomic information of single cells. Then, a limiting dilution approach was performed to randomly sediment and capture the single cell. Beads with oligonucleotide barcodes were then added to reach a saturated state, ensuring that each cell can be paired with one bead. Cells subjected with beads were captured and used for scRNA-seq. Whole transcriptome libraries were constructed following the BD Rhapsody single-cell whole-transcriptome amplification workflow. Single-cell libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA Assay Kit (Thermo Fisher Scientific). The library was sequenced by HiSeq Xten (Illumina) on a 150 bp paired-end run.

    OEX027261

  • EXPR Old_LSK_ATAC_seq

    Yuanliang  Zhang, Shanghai Institute of Hematology, 2024.01.26

    Project ID

    OEP004811

    Project Name

    Loss of Setd2 induces systemic inflammation via embryo-derived Kupffer-like cell differentiation to drive malignant transformation

    Experiment Type

    Transcriptomic

    Protocol

    A total of 1×105 BM LSKs from WT and KO-MDS mice were sorted, washed in DPBS, and lysed in 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) for the follow-up process, which was performed by TruePrepTM DNA Library Prep Kit V2 for Illumina (TD501, Vazyme) according to the manufacturer’s instructions. Subsequently, the library fragments were purified by VAHTS DNA clean beads (Vazyme, N411-01) for future sequencing according to standard illumina HiSeq/NextSeq platform manuscripts.

    OEX027259

  • EXPR scRNAseq001

    boya  zhang, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 2024.02.27

    Project ID

    OEP004177

    Project Name

    OEP004177

    Experiment Type

    Transcriptomic single cell

    OEX027323

  • EXPR scRNAseq006

    boya  zhang, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 2024.02.27

    Project ID

    OEP004177

    Project Name

    OEP004177

    Experiment Type

    Transcriptomic single cell

    OEX027324

  • EXPR scRNAseq002

    Boya  Zhang, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 2023.06.02

    Project ID

    OEP004177

    Project Name

    OEP004177

    Experiment Type

    Transcriptomic single cell

    OEX024220

  • EXPR scRNAseq003

    Boya  Zhang, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 2023.06.02

    Project ID

    OEP004177

    Project Name

    OEP004177

    Experiment Type

    Transcriptomic single cell

    OEX024221

  • EXPR scRNAseq004

    Boya  Zhang, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 2023.06.02

    Project ID

    OEP004177

    Project Name

    OEP004177

    Experiment Type

    Transcriptomic single cell

    OEX024222

  • EXPR scRNAseq005

    Boya  Zhang, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 2023.06.02

    Project ID

    OEP004177

    Project Name

    OEP004177

    Experiment Type

    Transcriptomic single cell

    OEX024223

  • EXPR WES004

    Boya  Zhang, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 2023.06.15

    Project ID

    OEP004193

    Project Name

    OEP004193

    Experiment Type

    Genomic

    OEX024236