{"database": "metadata", "table": "run_metadata", "rows": [[29028, "SRR26974570", "SRX22668014", "SRS19663574", "SRP474706", "PRJNA1046144", "Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates", "GSE248871", "Transcriptome Analysis", "Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish  to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted  which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows\u2013Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT\u2013PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow  we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and  Nlrc3 morphants  with a fold change =1.5 and p value <0.05. Based on the results of RNA seq  some signaling pathways essential for  the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch  WNT  NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq  we performed  experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.", null, "pubmed:38172511", null, "samples in control MO rep3", "GSM7921551", null, "source name:zebrafish embryos|tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture|geo loc name:missing|collection date:missing", "samples in control MO rep3", "Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.", "zebrafish embryos", null, "Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture", "GSM7921551", "GSM7921551: samples in control MO rep3; Danio rerio; RNA Seq", "GSM7921551 r1", "GSM7921551", "1", "Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474706", null, "loader:fastq load.py", "S3_Clean_Data1.fq.gz S3_Clean_Data2.fq.gz", "fastq fastq", 5643732705.0, 20272868.0, "GSM7921551 r1", "0:139.20 1:139.19", "A:1466198749;C:1349499199;G:1367008013;T:1461024521;N:2223", 139, 139, null, null, 1466198749, 1349499199, 1367008013, 1461024521, 2223, "SRX22668014", "SRS19663574", "SRA1759375", "Zhejiang university", "Zhejiang university", 2, 0.95103, 0.95208, 0.07142, 0.07068, 0.73428, 0.73371, 0.47064, 0.47197, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-11-28", "Pharyngula", "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": ["29028"], "units": {}, "query_ms": 8.263318999524927}