Genomic differences among Sphingobium hydrophobicum strains with different cell surface hydrophobicityExperiment Type
Nuclei from formaldehyde crosslinked (1%; 10min at room temperature) embryos were isolated and chromatin was fragmented using sonicator (Branson). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and Dynabeads. DNA fragments were purified and libraries were prepared by NEBnext DNA Library Prep Kit (NEB, E7370L). Adapter ligated DNA was purified using AMPure XP beads (Beckman Coulter, A63881) and sequenced by illumina HiSeq 2500. NEBnext DNA Library Prep Kit
multiregion proteomics from Human liver MS-DIAExperiment Type
The resulting spectra from each fraction were searched separately against the homo_sapiens_uniprot_2021_3_9.fasta (194557 sequences) database by the search engine Proteome Discoverer 2.2 (PD 2.2, Thermo). The results of the search and identification by PD2.2 software were imported into Spectronaut (version 14.0, Biognosys) software to generate a library. The eligible peptides and product ions were selected from the spectrum by setting peptides and ion pair selection rules to generate a target list. The DIA data were imported, and ion-pair chromatographic peaks were extracted according to the Target List. The ions were matched, and the peak areas were calculated to qualitatively and quantitatively analyze the peptides. iRT was added to the sample to correct the retention time, and the precursor ion Q value cutoff was set to 0.01. The quantitative values were visualized with Bionic Visualizations Proteomaps (https://proteomaps.net/). Differentially expressed proteins (DEPs; tumor vs. adjacent nontumor, p<0.05, |logFC|>1) underlying enrichment analyses. Gene Ontology and KEGG pathways with adjusted p<0.05 (Benjamini‒Hochberg method) were considered significantly enriched.
Haplotype-resolved assemblies and variant benchmark of a Chinese QuartetExperiment Type
Mangrove plastisphere MAGsExperiment Type
Mangrove plastisphere 16S+18S+ITSExperiment Type
Bacterial community diversity of lake sediments in ChinaExperiment Type
PCR amplification of 16S rRNA gene V4 hypervariable region
Spatial and single-cell transcriptomics landscape of adenomyosisExperiment Type
Transcriptomic single cellProtocol
Samples from TNBC patients were isolated and transported rapidly to the research facility. Each sample was subsequently minced on ice to <1 mm cubic piece, followed by enzymatic digestion, centrifuged at 300 rcf for 30 sec at room temperature, and the supernatant was removed without disturbing the cell pellet. Next, 1× PBS containing 0.04% weight/volume BSA (400 µg/ml) was added and then the sample was centrifuged at 300 rcf for 5 min. The cell pellet was resuspended in 1 ml red blood cell lysis buffer and incubated for 10 min at 4°C, followed by resuspension in 1 ml PBS containing 0.04% BSA. Next, samples were filtered over Scienceware Flowmi 40-µm cell strainers (VWR). Finally, the cell concentration and viability were determined by hemocytometer and Trypan Blue staining.