run_metadata: 48308
This data as json
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| 48308 | SRR10368282 | SRX7076276 | SRS5592161 | SRP145615 | PRJNA471311 | Gene expression analysis of jam3b mutant embryos | GSE114416 | Transcriptome Analysis | Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction cell migration and cell polarization in many tissue including the epithelium endothelium and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells the role of Jam3 in hematopoietic or vascular development is still unknown. In this study a zebrafish jam3b mutant line jam3b sa37 was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500. | WT 12hpf 2 | GSM4144776 | source name:whole embryo|tissue:whole embryo|age:12 hpf type | WT 12hpf 2 | Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample. | whole embryo | Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker which includes the three nucleotide barcodes followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing | tissue:whole embryo|age:12 hpf type | GSM4144776 | GSM4144776: WT 12hpf 2; Danio rerio; RNA Seq | GSM4144776 | 1 | Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker which includes the three nucleotide barcodes followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing | GEO Accession:GSM4144776 | RNA-Seq | TRANSCRIPTOMIC | CAGE | SINGLE | ILLUMINA | NextSeq 500 | SRP145615 | S01.fastq.gz | fastq | 2235469804.0 | 29611055.0 | GSM4144776 r1 | 0:75.49 1:0 | A:582276989;C:546056334;G:609905170;T:497018748;N:212563 | 75 | 0 | 582276989 | 546056334 | 609905170 | 497018748 | 212563 | SRX7076276 | SRS5592161 | SRA703389 | GEO | Kanazawa University | 1 | 0.9362 | 0.12401 | 0.76857 | 0.48408 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cage | unknown | bulk | unknown | unknown | Japan | 2019-10-30 | Segmentation | Embryo | Whole Organism | All anatomical structures |