{"database": "metadata", "table": "run_metadata", "rows": [[31778, "SRR28590150", "SRX24189492", "SRS20963515", "SRP500320", "PRJNA1097627", "GPI transamidase complex is required for primordial germ cell migration and development in zebrafish", "GSE263481", "Transcriptome Analysis", "Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However  it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study  we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk  both encoding essential GPIT complex subunits  resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably  a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore  expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence  we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation  we performed RNA seq of PGCs in wild type and pigu /  embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then  post genotyping of rest somatic cells  PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.", null, "pubmed:39741393", null, "pigu homo shield PGCs RNA rep1", "GSM8193369", null, "source name:embryo|tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:pigu homo|geo loc name:missing|collection date:missing", "pigu homo shield PGCs RNA rep1", "RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples", "embryo", "GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu /  zygotes  respectively  to label PGCs. Then  the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l  and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 204 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3\u2019UTR mRNA was injected into WT and pigu /  zygotes  respectively  to label PGCs. Then  the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 \u00b5l PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 \u00b5l  and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 \u00b5l tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN  74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas  EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol  as previously described  and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer\u2019s instructions. Notably  SMART seq2 of low input RNA seq relies on polyA based amplification.", "The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3\u2019UTR citation was described before. Unless stated  all embryos were raised in Holtfreter\u2019s solution at 28.5\u00b0C and staged as described previously.", "tissue:embryo|cell line:germ cell|cell type:PGCs|genotype:pigu homo", "GSM8193369", "GSM8193369: pigu homo shield PGCs RNA rep1; Danio rerio; RNA Seq", "GSM8193369 r1", "GSM8193369", "1", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN  74104 as recommended protocols. Total RNA 5 \u03bcg was DNase I Fermentas  EN0521 treated at 37\u00b0C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol  as previously described  and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably  SMART seq2 of low input RNA seq relies on polyA based amplification.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP500320", null, null, "pigu_homo_shield_PGCs_RNA_rep1_r2.fq.gz pigu_homo_shield_PGCs_RNA_rep1_r1.fq.gz", "fastq fastq", 2204383800.0, 7347946.0, "GSM8193369 r1", "0:150 1:150", "A:618947181;C:459789570;G:491705141;T:633938869;N:3039", 150, 150, null, null, 618947181, 459789570, 491705141, 633938869, 3039, "SRX24189492", "SRS20963515", "SRA1842063", "Tsinghua University", "Tsinghua University", 2, 0.91971, 0.9203, 0.0732, 0.07256, 0.77512, 0.77516, 0.53347, 0.53419, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2024-04-08", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["31778"], "units": {}, "query_ms": 9.398936002980918}