Project description:The locations of mammalian recombination hotspots are determined by PRDM9, a zinc finger histone methyltransferase that locally trimethylates histone H3 at residues K4 and K36. We previously reported two hypomorphic catalytic mutations, Prdm9-EP and Prdm9-EK, with different phenotypic effects. Prdm9-EP, but not Prdm9-EK, is compatible with female sub-fertility, while both mutations phenocopy the Prdm9-null condition in males. Here we directly compare and contrast the enzymatic effects of the two mutations in vitro and in vivo. We previously performed two biological H3K4me3 ChIP-seq replicates in spermatocytes isolated from Prdm9-EP homozygous males (GSE144144; SRX8588740 and SRX8588741), and re-processed previously reported H3K4me3 ChIP-seq data from spermatocytes isolated from wild-type B6 males (GSE52628; SRX381465 and SRX381466). We used those raw and processed files for this study (GSE144144). We also previously performed one biological H3K4me3 replicate in spermatocytes isolated from Prdm9-EP homozygous males (GSE112110; SRX4136625). We report an additional replicate here, and merged the two replicates for analysis; raw and processed files are reported here. We also performed ChIP-seq for H3K36me3 in both Prdm9-EP and Prdm9-EK homozygous spermatocytes. Raw and processed files are available here. For comparison, we re-mapped and re-analyzed H3K36me3 ChIP-seq data we previously reported from wild-type B6 spermatocytes (GSE76416; SRX1508234); processed files are available here.
Project description:This GEO submission includes RNAseq raw data (fastq.gz) and processed data (using DESeq2) from samples obtained in the wild type and the pfd4 and 6x_pfd mutants
Project description:A549 cells were co-transfected with CRISPR/Cas9 (containing sgRNA and GFP) and HDR donor plasmids (containing RFP and puromycin). The genetic editing cells were selected by puromycin. And then, we performed RNA sequencing for transcription profiling of A549 RB1 RB1 wild-type/knockout cell lines. The raw data were processed with Tophat and cuffdiff for gene expression analysis.
Project description:This data set is made up of 4 experiments (batches) analysing chondrocytes from healthy and diseased knees in 12 patients with osteoarthritis. There are 6 samples (from 3 patients) for each batch, where diseased and control samples were extracted from each patient and compared within patient. The batches were necessary due to the maximum sample capacity (6) of the mass spectrometer. The raw data files were deposited at EBI PRIDE database under accession number PXD002014 ( http://www.ebi.ac.uk/pride/archive/projects/PXD002014 ). This ArrayExpress record contains sample meta-data and processed data in the form of ratios and the log2 fold changes. The ratios were calculated for each patient as diseased vs control (the reference). Please note that one patient (number 52) was excluded from the fold change analysis as no proteins showed any significant change which suggests the samples were not correct or something went wrong with them. There is also the median and standard deviation across the patients.
Project description:This ArrayExpress record contains meta-data and results of quantitative analysis of cell lines from the NCI-60 panel using pressure cycling technology (PCT) and SWATH-mass spectrometry. Each cell line was analyzed in duplicate. Raw data files are available at the EMBL-EBI protemics data archive (PRIDE) at accession PXD003539 (http://www.ebi.ac.uk/pride/archive/projects/PXD003539). Since the record here does not include the raw data files and hence there is no need to explicitly link individual replicate to a raw file, each sample is only listed once in the ArrayExpress samples table for clarity.