run_metadata: 28573

This data as json

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28573	SRR26395047	SRX22100886	SRS19166012	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			1 cell RNA seq rep4		strain:AB x India\|age:0.5 hpf\|dev stage:1cell\|collection date:2018 12\|geo loc name:China:Beijing\|sex:N/A\|tissue:embryo\|source material identifier:SR 1 4\|BioSampleModel:Model organism or animal									Illumina RNA seq of zebrafish: 1 cell replicate4	DR 023	DR 023	mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	HiSeq X Ten		SRP466518			C1-4_1.fq.gz C1-4_2.fq.gz	fastq fastq	17516685480.0	62559591.0	C1 4 1.fq.gz	0:140 1:140	A:4618802699;C:4171295741;G:4210242921;T:4516296296;N:47823	140	140			4618802699	4171295741	4210242921	4516296296	47823	SRX22100886	SRS19166012	SRA1731898	University of Michigan\|Computational Medicine and Bioinformatics	University of Michigan	2	0.95994	0.96214	0.01942	0.01842	0.8421	0.84157	0.47848	0.47528	140	140	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown		United States	2023-10-16	Zygote	Embryo	Embryo Imprecise	All anatomical structures