run_metadata: 74098
This data as json
| 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 |
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| 74098 | SRR23433708 | SRX19347584 | SRS16745102 | SRP422577 | PRJNA934472 | Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] | GSE225136 | Other | The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates | parent bioproject:PRJNA934075 | pubmed:38605226 | mt IP rep2 | GSM7039975 | source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing | mt IP rep2 | Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample | trunk region of zebrafish embryos | Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq | tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A | GSM7039975 | GSM7039975: mt IP rep2; Danio rerio; RIP Seq | GSM7039975 r1 | GSM7039975 | 1 | Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq | RIP-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP422577 | loader:fastq load.py | mt2_IP_R1.fastq.gz mt2_IP_R2.fastq.gz | fastq fastq | 10153956215.0 | 38248544.0 | GSM7039975 r1 | 0:132.74 1:132.73 | A:2745473943;C:2337991849;G:2337827470;T:2732618213;N:44740 | 132 | 132 | 2745473943 | 2337991849 | 2337827470 | 2732618213 | 44740 | SRX19347584 | SRS16745102 | SRA1590470 | Huazhong University of Science and Technology | Huazhong University of Science and Technology | 2 | 0.91716 | 0.92124 | 0.17169 | 0.17213 | 0.69057 | 0.69092 | 0.45478 | 0.4582 | 133 | 133 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-02-12 | Undetermined | Embryo | Trunk | Surface Structure |