Project description:Observational, Multicenter, Post-market, Minimal risk, Prospective data collection of PillCam SB3 videos (including PillCam reports) and raw data files and optional collection of Eneteroscopy reports
Project description:This GEO submission contains processed single-cell RNA sequencing data generated using the Seq-Well platform from pleural mesothelioma tumors and comparator pleural specimens. Raw sequencing data are available through controlled access in dbGaP under accession phs004285. Processed expression matrices and cell-level metadata for the single-cell libraries are provided in this submission.
Project description:Single-cell RNA-seq libraries were generated from human PBMCs that were incubated with anti-HER2/CD3 TDB in the presence of KPL-4 cells. This dataset only contains the metadata and processed data. Raw data can be accessed via the EGA accession EGAS00001003734
Project description:We performed single-cell RNA sequencing (scRNA-seq) on thymocytes isolated from wild-type (WT) and CDC42 knockout (CDC42 KO) mice to investigate the role of CDC42 in thymocyte development. This dataset includes raw UMI counts, normalized expression data, and metadata for thousands of thymocytes across different developmental stages. Comparative analysis revealed transcriptional differences between WT and CDC42 KO thymocytes, highlighting CDC42’s role in T cell differentiation.
Project description:A novel one-dimensional on-line pH gradient-eluted strong cation exchange (SCX)-nano-ESI-MS/MS method was developed for protein identification and tested with mixture of six standard proteins, total lysate of HuH7 and N2a cells, as well as membrane fraction of N2a cells. This method utilized an on-line nano-flow SCX column in a nano-LC system coupled with a nano-electrospray high-resolution mass spectrometer. Protein digests were separated on a nano-flow SCX column with a pH gradient and directly introduced into a mass spectrometer through nano-electrospray ionization. SCXLC-MS/MS showed identification capability for higher proportion of basic peptides compared to RPLC-MS/MS method, especially for histidine-containing peptides. Our SCXLC-MS/MS method is an excellent alternative method to the RPLC-MS/MS method for analysis of standard proteins, total cell and membrane proteomes.
Project description:RAW-Rv3722c and RAW-Vector cells were collected for RNA extraction and subject to transcriptome sequencing. Expression levels of all genes in the two cell lines were determined by Next Generation Sequencing (NGS)
Project description:Raw data for Metabolomics Studies of Cell-Cell Interactions using Single Cell Mass Spectrometry Combined with Fluorescence Microscopy
Project description:<p>Raw data of both bulk and single-cell metabolomics. It includes all MS, LC-MS and LC-MS/MS raw data associated with the article 'Single-cell thiol profiling enabled by live-cell labeling reveals metabolic heterogeneity in ferroptosis'.</p>
Project description:Single-cell transcriptomic dataset comprising 41 patient-derived cell cultures (PDCs) established from pancreatic ductal adenocarcinoma (PDAC). The dataset was generated using Evercode™ technology with the Whole Transcriptome v2 kit (Parse Biosciences, ECW02130), based on Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq). For scRNA-seq, PDCs were processed in two batches, 14 samples in the first batch (R1) and 27 samples in the second batch (R2). Sequencing was performed separately for each batch using the Illumina NovaSeq X Plus platform. Paired-end reads were generated on a 10B flow cell with 200 sequencing cycles. FASTQ quality control (QC), barcode correction, alignment to the human reference genome (GRCh38.p13), multiplet detection, and raw count matrix generation were performed using the split-pipe pipeline (v1.1.1, Parse Biosciences) with default parameters. This single-cell collection of experimentally derived models reveals transcriptional heterogeneity both within and across PDCs. The submitted file consists of the count matrix along with the corresponding metadata.