run_metadata: 41449

This data as json

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41449	SRR4423750	SRX2245912	SRS1746318	SRP091576	PRJNA348537	Polysome seq in zebrafish early embryonic development	GSE88776	Transcriptome Analysis	We followed the polysomal association of maternal and early zygotic transcriptome over the first few hours of embryonic development prior to and post MBT. We isolated polysome associated bound and non polysome associated unbound mRNAs using sucrose gradient centrifugation followed by size fractionation. Using next generation sequencing RNA seq we profiled the transcriptome in polysome bound and unbound fractions. Our analysis revealed distinct dynamics of polysome association of cytoplasmically polyadenylated maternal mRNAs. Overall design: rRNA depleted RNA was extracted from pooled embryos of desired stages Egg 1 cell 16 cells 128 cells 3.5hpf and 5.3hpf and subjected to polysome profiling to separate between polysome free and polysome associated fragments. Unfractionated rRNA depleted samples at corresponding stages were used as background control. One RNA seq library was generated for each sample.		pubmed:29229769		1 cell polysome unbound	GSM2345434		source name:whole zebrafish embryo\|strain:wild type AB\|developmental stage:1cell\|tissue:whole embryo	1 cell polysome unbound	Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. For the RNA Seq data analysis sequencing reads were aligned to the GRCz10 zebrafish genome using STAR v2.4.2a Dobin et al. 2012. For the novel transcript discovery sequencing reads were trimmed using cutadapt 1.9.1 e 0.1; q 20; O 3; m 20; a AGATCGGAAGAGC. Subsequently the reads were aligned to the GRCz10 zebrafish genome using GSNAP version 2015 12 31 filter chastity=both; max mismatches=5; novelsplicing=1. Transcriptome was assembled using cufflinks 2.2.1 multi read correct; library type fr secondstrand with Ensembl release 83 genome annotation. Cuffcompare was run to compare and annotate the newly assembled transcripts. Transcript level abundances were generated using Salmon 0.6.0 algorithm Patro et al. 2015. The abundances were summarized to gene level and imported to DESeq2 using tximport 1.0.2. Subsequently data was normalized to library size using DESeq2 „median ratio method” Anders and Huber 2010. Genome build: GRCz10 Supplementary files format and content: Salmon's quantification files tab delimited text files contain abundance measurements for each sample. normalizedCounts.txt tab delimited text file contains counts for all the samples normalized using DESeq2.	whole zebrafish embryo		rRNA depletion was performed using RiboZero Magnetic Gold Kit Epicentre unfractionated polysome associated and non associated RNA were subsequently isolated using Qiagen RNAeasy kit Qiagen USA. Sequencing library was constructed using Stranded RNA seq libraries were generated using ScriptSeq v2 RNA Library Preparation Kit Illumina USA.	Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.	strain:wild type AB\|developmental stage:1cell\|tissue:whole embryo	GSM2345434	GSM2345434: 1 cell polysome unbound; Danio rerio; RNA Seq	GSM2345434		1	rRNA depletion was performed using RiboZero Magnetic Gold Kit Epicentre unfractionated polysome associated and non associated RNA were subsequently isolated using Qiagen RNAeasy kit Qiagen USA. Sequencing library was constructed using Stranded RNA seq libraries were generated using ScriptSeq v2 RNA Library Preparation Kit Illumina USA.	GEO Accession:GSM2345434	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP091576			unbound_1Cell.fq.gz	fastq	4132524225.0	55100323.0	GSM2345434 r1												SRX2245912	SRS1746318	SRA485192	GEO	Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw	1	0.83821		0.13815		0.75682		0.5164		75		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown		Poland	2016-10-14	Zygote	Embryo	Whole Organism	All anatomical structures