{"database": "metadata", "table": "run_metadata", "rows": [[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.", null, "pubmed:29229769", null, "1 cell  polysome unbound", "GSM2345434", null, "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 \u201emedian ratio method\u201d 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", null, "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", null, "SRP091576", null, null, "unbound_1Cell.fq.gz", "fastq", 4132524225.0, 55100323.0, "GSM2345434 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX2245912", "SRS1746318", "SRA485192", "GEO", "Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw", 1, 0.83821, null, 0.13815, null, 0.75682, null, 0.5164, null, 75, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Poland", "2016-10-14", "Zygote", "Embryo", "Whole Organism", "All anatomical structures"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["41449"], "units": {}, "query_ms": 9.604085003957152}