Project description:This project contains raw data, intermediate files and results used to create the integrated map of protein expression in human cancer (including data from cell lines and tumours). The map is based on joint reanalysis of 11 large-scale quantitative proteomics studies. The datasets were primarily retrieved from the PRIDE database, as well as MassIVE database and CPTAC data portal. The raw files were manually curated in order to capture mass spectrometry acquisition parameters, experimental design and sample characteristics. The raw files were jointly processed with MaxQuant computational platform using standard settings (see Data Processing Protocol). Due to size of the data, the processing was done in two batches denoted as “celllines” and “tumours” analysis. In total, using a 1% peptide spectrum match and protein false discovery rates, the analysis allowed identification of 21,580 protein groups in the cell lines dataset (MQ search results available in ‘txt-celllines’ folder), and 13,441 protein groups in the tumours dataset (MQ search results available in ‘txt-tumours’ folder).
Project description:10x Genomics Xenium in situ targeted gene expression was performed on FFPE mouse brain tissue using the Xenium Mouse Brain Gene Expression panel (mBrain_v1.1). The staged dataset contains adult and aged cohorts with control and heat-stress sample annotations. Heat-stress mice received periodic heat exposure at approximately 40 deg C for 3 hours/day for 14-15 days. Raw files include high-resolution morphology images and decoded transcripts; processed files include transcript count matrices, cell summaries, and cell and nucleus segmentation boundaries.
Project description:This data set contains ChEC-seq binding profiles of various TF in yeast strains deleted of other TFs. Each sample has a pair-end sequencing file and a processed file (.out) is a genomic signal track after alignment to S.cerevisiae (R64) reference genome. Mapping was done using the read end. This dataset also contains raw and processed MNase-seq data files for nucleosome occupancy. Data related to manuscript: The architecture of binding cooperativity between densely bound transcription factors.
Project description:This dataset contains mass spectrometry raw data (.d and wiff files) of primary and metastatic tumors of 16 localized colon cancer patients
Project description:This dataset contains bulk RNA sequencing data from paired aganglionic and ganglionic colonic tissue specimens obtained from three pediatric patients diagnosed with Hirschsprung disease (HSCR, OMIM 142623). RNA was extracted and sequenced to investigate transcriptomic alterations and signaling pathway dysregulation associated with HSCR pathogenesis. Raw paired-end FASTQ files generated by Illumina NovaSeq 6000 sequencing are provided for each sample, enabling downstream analyses of differential gene expression between diseased and unaffected intestinal segments.
Project description:Conducted chromatin accessibility by ATAC-seq in tubule-specific Acly knockout and WT mice. The dataset includes raw sequencing files.
Project description:This dataset contains mass spectrometry raw files and identification results from intact N-glycoproteomic analysis of extracellular vesicles (EVs) isolated from human seminal plasma. Intact N-glycopeptides were enriched and analyzed using an Orbitrap Fusion Lumos mass spectrometer coupled to an Easy-nLC 1200 system. The uploaded dataset includes: (1) Data-dependent acquisition (DDA) LC-MS/MS files acquired via stepped collision energy higher-energy collision dissociation (StepHCD) across discovery cohort samples; and (2) StepHCD-based parallel reaction monitoring (PRM) targeted LC-MS/MS files across validation cohort samples. Raw data files were searched against the human UniProt reviewed database using Glyco-Decipher software with a 1% false discovery rate (FDR).
Project description:This dataset contains mass spectrometry raw files and identification results from intact N-glycoproteomic analysis of extracellular vesicles (EVs) isolated from human seminal plasma. Intact N-glycopeptides were enriched and analyzed using an Orbitrap Fusion Lumos mass spectrometer coupled to an Easy-nLC 1200 system. The uploaded dataset includes: (1) Data-dependent acquisition (DDA) LC-MS/MS files acquired via stepped collision energy higher-energy collision dissociation (StepHCD) across discovery cohort samples; and (2) StepHCD-based parallel reaction monitoring (PRM) targeted LC-MS/MS files across validation cohort samples. Raw data files were searched against the human UniProt reviewed database using Glyco-Decipher software with a 1% false discovery rate (FDR).
Project description:This dataset contains RNA-seq profiles from the posterior explants of Xenopus laevis embryos at stage 26. Explants were sectioned posterior to the otic vesicle and treated with 0.5 mM picrotoxin for 3 h to inhibit Gamma-Aminobutyric Acid (GABA) signaling, followed by removal of the ventral yolk. Two biological replicates were prepared for each condition, with each replicate pooling explants from three embryos. RNA-seq was performed to identify transcriptional changes associated with GABA signaling during tailbud-stage body axial elongation. The dataset includes raw FASTQ files and metadata, enabling the analysis of differential gene expression patterns under GABA inhibition.