run_metadata: 36993

This data as json

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
36993	SRR870737	SRX288477	SRS431103	SRP023492	PRJNA206070	Nanog SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition	GSE47558	Other	Upon fertilization maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT a universal step in animal development unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish ZGA is required for gastrulation and clearance of maternal mRNAs which is achieved in part by the conserved microRNA miR 430. However the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation and a failure to activate >75% of zygotic genes. Furthermore we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre and post MZT; ribosome profiling pre MZT		pubmed:24056933		Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling	GSM1152439		source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling\|tissue:Whole embryos\|strain:TUAB\|Stage:2hpf\|treatment:Nanog MO SoxB1 MO\|rna subtype:total RNA	Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling	Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded using Bowtie v0.12.9 with switches seedlen 25 n 3 k 1 y e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated normalizing against the non repetitive sum length of a gene’s introns and the total number of aligned exonic reads in the sample. For Ribosome Profiling reads were trimmed of 3’ adapter sequence and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments >=18nts for input mRNA. Reads were aligned as above retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling generated as described above.	Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling	Treated embryos were injected at 1 cell stage for all treatements except cycloheximide which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.	For mRNA Seq total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling 50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit RPHMR12126 Epicentre. For nuclease treatment 3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al. 2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit RPHMR12126 Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al. Science 2012.		tissue:Whole embryos\|strain:TUAB\|Stage:2hpf\|treatment:Nanog MO SoxB1 MO\|rna subtype:total RNA	GSM1152439	GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER	GSM1152439		1	For mRNA Seq total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling 50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit RPHMR12126 Epicentre. For nuclease treatment 3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al. 2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit RPHMR12126 Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al. Science 2012.	GEO Accession:GSM1152439	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP023492			NS2_RPrpf.run1_f0.fastq.gz	fastq	304000000.0	4000000.0	GSM1152439 r1	0:76	A:78867584;C:90953343;G:79555524;T:54616280;N:7269	76				78867584	90953343	79555524	54616280	7269	SRX288477	SRS431103	SRA082637	GEO	Giraldez Lab, Genetics, Yale University	1	0.87907		0.22745		0.87117		0.75368		76		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown		United States	2013-05-31	Cleavage	Embryo	Whole Organism	All anatomical structures