Project IDOEP004015
Project Name16S rRNA gene diversity during DOES incubation under different HHP
Experiment TypeMetagenomic
OEX022552
Project IDOEP004042
Project NameMetagenomics during DOES incubation under different HHP
Experiment TypeMetagenomic
ProtocolThe extracted microbial DNA was processed to construct metagenome shotgun sequencing libraries following the standard Illumina TruSeq DNA Sample Preparation Guide. Each library was sequenced by Illumina NovaSeq 6000 platform (Illumina, USA) with PE150 strategy at Shanghai Personal Biotechnology (Shanghai, China).
OEX022859
Project IDOEP004045
Project NameMetatranscriptomics during DOES incubation under different HHP
Experiment TypeMetatranscriptomic
ProtocolTo ensure DNA removal, the RNA extracts are treated with TURBO DNase (Invitrogen, Waltham, MA, USA) as directed by the manufacturer.
OEX022922
Project IDOEP004102
Project NameHeterologous expression and activity assay of clade I and II N2O reductase genes using WP3 strain at 0.1, 20 and 40 MPa
Experiment TypeTranscriptomic
OEX023021
Project IDOEP005097
Project NameDifferentiation of islet organoids (S5D3)
Experiment TypeTranscriptomic
ProtocolAll experiments were performed according to Trizol nucleic acid extraction, GEO seq transcriptome amplification, and TruePrep® DNA Library Prep Kit V2 for Illumina® instruction manual. The experiments were carried out to extract RNA using Trizol method from organoids. Smart II and KAPA amplification were used, BGI P100 was sequenced, and sheared to approximately 300-500 bp using Q-sep instrument.
OEX027384
Project IDOEP005036
Project NameICC WES
Experiment TypeGenomic
OEX027276
Project IDOEP001350
Project NameNewly-designed primers for hadal ecosystem
Experiment TypeMetagenomic
ProtocolPCR amplification of full-length 16S rRNA gene
OEX010862
Project IDOEP001350
Project NameNewly-designed primers for hadal ecosystem
Experiment TypeMetagenomic
ProtocolPCR amplification of multiple 16S rRNA gene hypervariable regions
OEX010861
Project IDOEP004811
Project NameLoss of Setd2 induces systemic inflammation via embryo-derived Kupffer-like cell differentiation to drive malignant transformation
Experiment TypeTranscriptomic
ProtocolFor 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
Project IDOEP004811
Project NameLoss of Setd2 induces systemic inflammation via embryo-derived Kupffer-like cell differentiation to drive malignant transformation
Experiment TypeTranscriptomic single cell
ProtocolBM 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