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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
29025 SRR26974567 SRX22668017 SRS19663577 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–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR 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.   pubmed:38172511   samples in nlrc3 MO rep3 GSM7921554   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 nlrc3 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   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   tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture GSM7921554 GSM7921554: samples in nlrc3 MO rep3; Danio rerio; RNA Seq GSM7921554 r1 GSM7921554 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP474706   loader:fastq load.py Mo3_Clean_Data2.fq.gz Mo3_Clean_Data1.fq.gz fastq fastq 5520729146.0 19885310.0 GSM7921554 r1 0:138.82 1:138.81 A:1394113679;C:1363204261;G:1378651437;T:1384757621;N:2148 138 138     1394113679 1363204261 1378651437 1384757621 2148 SRX22668017 SRS19663577 SRA1759375 Zhejiang university Zhejiang university 2 0.9435 0.94469 0.05163 0.05105 0.7601 0.75958 0.46104 0.46669 141 141 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk bulk bulk   China 2023-11-28 Pharyngula Embryo Embryo Imprecise All anatomical structures