run_metadata: 49501
This data as json
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| 49501 | SRR7909906 | SRX4746023 | SRS3826020 | SRP162761 | PRJNA493632 | Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [Bulk RNA seq] | GSE120578 | Transcriptome Analysis | To characterize the distinct features of HSPCs and relevant niche cells we performed RNA seq with sorted zebrafish HSPCs and niche cells based on fluorescent protein labeling from distinct regions at six relatively discrete stages. Overall design: We used double transgenic line Tg kdrl:mCherry/CD41:GFP and sorted HSCs ECs and NCs from embryonic tails at 36 hpf 52 hpf 3 dpf and 4 dpf. And we sorted HSPCs and NCs from CD41: GFP kidney marrow at 3 mpf. | parent bioproject:PRJNA493631 | pubmed:31042481;pubmed:33785593 | 52 hpf CHT NC rep2 | GSM3403645 | source name:zebrafish embryos|tissue:zebrafish embryos|cell type:double negative cells|Stage:52 hpf | 52 hpf CHT NC rep2 | Reads quality were first checked by "Fastqc" And then clean reads were mapped to the reference genome by HISAT Uniquely mapped reads were utilized to calculate the counts of each gene by HTSeq Reads counts matrix was then normalized to library size by DESeq2 with default parameters and normalized reads were then used to calculate the FPKM Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by FPKM | zebrafish embryos | The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina. | tissue:zebrafish embryos|cell type:double negative cells|Stage:52 hpf | GSM3403645 | GSM3403645: 52 hpf CHT NC rep2; Danio rerio; RNA Seq | GSM3403645 | 1 | The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit Cat. No. 74104. The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina. | GEO Accession:GSM3403645 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP162761 | NC-2_HNJNLCCXX_L6_1.clean.fq.gz NC-2_HNJNLCCXX_L6_2.clean.fq.gz | fastq fastq | 9365683800.0 | 31218946.0 | GSM3403645 r1 | 0:150 1:150 | A:2345549529;C:2328220975;G:2350758892;T:2339854432;N:1299972 | 150 | 150 | 2345549529 | 2328220975 | 2350758892 | 2339854432 | 1299972 | SRX4746023 | SRS3826020 | SRA785160 | GEO | Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB) | 2 | 0.92542 | 0.92647 | 0.07392 | 0.07341 | 0.72681 | 0.7305 | 0.48431 | 0.49202 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | nebnext | bulk | bulk | bulk | China | 2018-09-27 | Hatching | Embryo | Embryo Imprecise | All anatomical structures |