{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Tamoghna Chowdhury"],"organism":["Mus musculus"],"software":["bismark, trim_galore"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14862"],"description":["In the male mouse germline, PIWI-interacting RNAs (piRNAs), bound by the PIWI protein MIWI2 (PIWIL4), guide the DNA methylation of young active transposable elements (TEs) through SPOCD1. We find that SPOCD1 interacts with the nuclear pore protein TPR, and that this interaction is required to prevent SPOCD1 and its known binding partners SPIN1 and C19ORF84 from being incorporated into constitutive heterochromatin. We perform enzymatic methylation sequencing of undifferentiated spermatogonia from wild-type mice and mice carrying the K464A mutation in SPOCD1, which prevents interaction with TPR. The mutant mice display a stochastic failure of young LINE1 methylation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - FACS-purified P14 undifferentiated spermatogonia (DAPI -ve, CD45 -ve, CD51-ve, c-Kit -ve, CD9 +ve)","Library Construction - Methyl-seq libraries were prepared using the NEBnext Enzymatic Methyl-seq kit (NEB E7120) according to the manufacturer’s instructions","Nucleic Acid Extraction - DNA from spermatogonia was isolated by Proteinase K digest (10 mM Tris-HCl pH 8, 5 mM EDTA , 1% SDS, 0.3 M Na-acetate, 0.2 mg/ml proteinase K) overnight, followed by 2x phenol/chloroform/isoamylalcohol (25:24:1, buffered at pH 8, Sigma-Aldrich) extraction and 2x chloroform extraction. The DNA was precipitated at -20˚C after addition of 1/10 volume 3M Na-acetate, 10µg linear acrylamide (Invitrogen) and 1 volume of isopropanol, washed 2x with 70% ethanol, and solubilized in 5mM Tris pH8.","Sequencing - Methyl-seq libraries were sequenced paired-end 150bp on an Illumina Nextseq2000 sequencer with the P3 flowcell."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Raw sequence reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.7,www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 1.18, parameters: --paired --length 25 --trim-n --clip_R2 5). Trimmed reads were aligned to the mouse genome (mm10) in paired-end mode to be able to use overlapping parts of the reads only once. Alignments were carried out with Bismark v0.23.0 (Krueger and Andrews, 2011) with the following set of parameters: paired-end. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor (v0.23.0).","Data Transformation - 50 adjacent CpG running window probes were generated and percentage methylation determined for probes containing at least 10 reads on the pooled replicate data."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["methylation profiling by high throughput sequencing"],"species":["Mus musculus"],"pubmed_authors":["Xinyu Xiang","Tamoghna Chowdhury","Donal O'Carroll"],"additional_accession":[]},"is_claimable":false,"name":"Whole genome DNA methylation of undifferentiated spermatogonia of postnatal day 14 (P14) wild-type and Spocd1-K464A (does not interact with TPR) homozygous mutant mice","description":"In the male mouse germline, PIWI-interacting RNAs (piRNAs), bound by the PIWI protein MIWI2 (PIWIL4), guide the DNA methylation of young active transposable elements (TEs) through SPOCD1. We find that SPOCD1 interacts with the nuclear pore protein TPR, and that this interaction is required to prevent SPOCD1 and its known binding partners SPIN1 and C19ORF84 from being incorporated into constitutive heterochromatin. We perform enzymatic methylation sequencing of undifferentiated spermatogonia from wild-type mice and mice carrying the K464A mutation in SPOCD1, which prevents interaction with TPR. The mutant mice display a stochastic failure of young LINE1 methylation.","dates":{"release":"2025-11-12T00:00:00Z","modification":"2025-11-12T02:02:36.089Z","creation":"2025-02-21T15:41:05.808Z"},"accession":"E-MTAB-14862","cross_references":{"ENA":["ERP169390"],"Biostudies":["E-MTAB-11612","E-MTAB-7997","E-MTAB-12713"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002761","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}