run_metadata: 62955
This data as json
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| 62955 | SRR13519935 | SRX9930983 | SRS8106457 | SRP303120 | PRJNA694557 | Slc20a1b is essential for hematopoietic stem/progenitor cell expansion in zebrafish | GSE165415 | Transcriptome Analysis | Hematopoietic stem and progenitor cells HSPCs are able to self renew and can give rise to all blood lineages throughout their lifetime yet the mechanisms regulating HSPC development have yet to be discovered. In this study we characterized a hematopoiesis defective zebrafish mutant line named smu07 which was obtained from our previous forward genetic screening and found the HSPC expansion deficiency in the mutant. Positional cloning identified that slc20a1b which encodes a sodium phosphate cotransporter contributed to the smu07 blood phenotype. Further analysis demonstrated that mutation of slc20a1b affects HSPC expansion through cell cycle arrest at G2/M phases in a cell autonomous manner. Our study shows that slc20a1b is a vital regulator for HSPC proliferation in zebrafish early hematopoiesis and provides valuable insights into HSPC development. Overall design: A mini bulk RNA Seq analysis to compare the expression profiles of wild type HSPCs and smu07 mutant HSPCs | pubmed:33751369 | Mutant HSPCs sample2 | GSM5033015 | tissue:Hematopoietic Stem/Progenitor Cell|strain:AB|genotype:Smu07 mutant|age:4 dpf|facs gate:cd41:eGFP low | Mutant HSPCs sample2 | Clean fastq files were applied to FASTQC for quality control. post quality control the clean reads were mapped to the zebrafish GRCz11 reference genome using STAR. The mapped reads were then counted using FeatureCounts from Rsubread. The counts matrix was applied to DESeq2 for normalization differentially expressed genes identification and sample to sample distance analysis. GO terms enrichment was performed using the online resource Metascape. Genome build: GRCz11 Supplementary files format and content: Normalized counts TPM matrix | Hematopoietic Stem/Progenitor Cell | The embryos underwent no further treatment. | The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500 cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme N711 03 for cell lysis reverse transcription amplification and library construction. | Zebrafish embroys were maintained in egg water in 28 °C till 4 dpf for sacrification. | strain:AB|genotype:Smu07 mutant|age:4 dpf|facs gate:cd41:eGFP low | GSM5033015 | GSM5033015: Mutant HSPCs sample2; Danio rerio; RNA Seq | GSM5033015 | 1 | The 4 dpf larvae were grind and enzyme digested into single cells. The cells were then applied to FACS to sort the HSPCs. Approximately 500 cells from each group were collected and applied to the Discover sc WTA v2 kit Vazyme N711 03 for cell lysis reverse transcription amplification and library construction. | GEO Accession:GSM5033015 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP303120 | mut_s2_1.fq.gz mut_s2_2.fq.gz | fastq fastq | 26776953600.0 | 89256512.0 | GSM5033015 r1 | 0:150 1:150 | A:6950803865;C:6328522725;G:6423534554;T:7073865657;N:226799 | 150 | 150 | 6950803865 | 6328522725 | 6423534554 | 7073865657 | 226799 | SRX9930983 | SRS8106457 | SRA1187446 | GEO | South China University of Technology | 2 | 0.94573 | 0.94677 | 0.11184 | 0.11217 | 0.77546 | 0.77644 | 0.55902 | 0.56264 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | China | 2021-01-25 | Larval | Larval | Blood | Hematopoietic System |