run_metadata: 28565
This data as json
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| 28565 | SRR26395039 | SRX22100894 | SRS19166020 | SRP466518 | PRJNA1028258 | Zygotic activation of transposable elements during zebrafish early embryogenesis | PRJNA1028258 | Other | Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age. | pubmed:40246845 | 1k cell Iso seq | strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 4|BioSampleModel:Model organism or animal | PacBio Iso seq of zebrafish: 1k cell | DR 004 | DR 004 | Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN CA USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies CA USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies CA USA. RNA samples with a RIN 8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA Inc. Mountain View CA USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems Wilmington MA USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently two cDNA libraries <3 kb >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences Menlo Park CA USA and sequenced on the PacBio sequel II platform. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | PACBIO_SMRT | Sequel II | SRP466518 | 1k.ccs.fq.gz | fastq | 8036121763.0 | 2087907.0 | 1k.ccs.fq.gz | 0:3848.89 | A:2152838341;C:1873567602;G:1863627936;T:2146087884;N:0 | 3848 | 2152838341 | 1873567602 | 1863627936 | 2146087884 | 0 | SRX22100894 | SRS19166020 | SRA1731898 | University of Michigan|Computational Medicine and Bioinformatics | University of Michigan | 1 | 0.43117 | 0.00077 | 0.86352 | 0.48891 | 2071 | T | long read | pacbio | pacbio_modern | full_length | poly_a | unknown | bulk | unknown | unknown | United States | 2023-10-16 | Blastula | Embryo | Embryo Imprecise | All anatomical structures |