run_metadata: 64261
This data as json
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| 64261 | SRR14376444 | SRX10728749 | SRS8816980 | SRP318111 | PRJNA726733 | SMARTseq data of zebrafish sox10+ cells | GSE173696 | Transcriptome Analysis | The goals of this study are to compare transcriptome profiling mRNA level and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups and the stem markers of nueral crest progenitors were upregulated in mutants. Overall design: sox10+ cells from slc30a1 mutant zebrafish and their siblings at 2 dpf and 2.5 dpf were sorting out by FACS machine whole RNA were extraced and performed SMARTseq analysis. | pubmed:34977877 | sox10+ cells Con2 2 | GSM5277050 | source name:sox10+ cells|genotype:control|age:2 dpf|tissue:neural crest|cell type:sox10+ cells | sox10+ cells Con2 2 | Illumina Novaseq 6000 were used for basecalling Reads of samples were aligned to Ensembl Danio rerio zebrafish genome GRCz11 http://www.ensembl.org/ using HISAT package. The mapped reads of each sample were assembled using StringTie and all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts StringTie and edgeR were used to estimate the expression levels of all transcripts StringTie was used to calculate FPKM for quantification of mRNAs Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample | sox10+ cells | Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050 Zymo Research. Library construction started from fragmented cDNA and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq | genotype:control|age:2 dpf|tissue:neural crest|cell type:sox10+ cells | GSM5277050 | GSM5277050: Con2 2; Danio rerio; RNA Seq | GSM5277050 | 1 | Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050 Zymo Research. Library construction started from fragmented cDNA and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq | GEO Accession:GSM5277050 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP318111 | loader:fastq load.py | con2_Clean_Data1.fq.gz con2_Clean_Data2.fq.gz | fastq fastq | 6562017327.0 | 22133886.0 | GSM5277050 r1 | 0:148.23 1:148.24 | A:1768000404;C:1519120771;G:1524128982;T:1750730516;N:36654 | 148 | 148 | 1768000404 | 1519120771 | 1524128982 | 1750730516 | 36654 | SRX10728749 | SRS8816980 | SRA1226391 | GEO | Zhejiang University School of Medicine | 2 | 0.94243 | 0.9414 | 0.03946 | 0.03954 | 0.73904 | 0.74105 | 0.4702 | 0.46577 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2021-05-01 | Hatching | Embryo | Brain | Nervous System |