run_metadata: 36672

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
36672	SRR797917	SRX255753	SRS404584	SRP020090	PRJNA194542	Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish	GSE45532	Transcriptome Analysis	The basic helix loop helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets in particular fast twitch muscle differentiation genes thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast twitch muscle specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber type regulator Prdm1a a SET domain DNA binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype early and increased fast muscle differentiation is the opposite of the Pbx null phenotype delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes we used RNA seq analysis to globally assess gene expression in zebrafish embryos with single and double losses of function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4 MO;prdm1a / embryos suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program. Overall design: Total RNA samples were genotyped and pooled for 4 sample types: control MO;prdm1+/+; control MO;prdm1 / ; pbx2/4 MO;prdm1+/+; and pbx2/4 MO;prdm1 / embryos at the 10 somite s stage from three independent sets of egg collections/injections.		pubmed:23789105		pbx2/4 MO; prdm1 / rep1	GSM1108124		tissue:embryos\|developmental stage:10 somites\|strain:AB\|genotype:pbx2/4 MO; prdm1 /	pbx2/4 MO; prdm1 / rep1	Reads were aligned by tophat 1.4 gene counts are collected using Bioconductor Rsamtools package. Reads mapped to M locations are counted as 1/M at each occurrence. differentential gene expression detection was performed by edgeR. Genome build: Zv9 release 63 Supplementary files format and content: GSE45532 gene.counts.csv: Read counts extracted by Bioconductor packages for each ENSEMBL genes. Reads that mapped to M locations are counted as 1/M for each occurrence. The columns are: gene name ENSEMBL ID and read counts for all samples. Supplementary files format and content: GSE45532 double.genes.csv: Differential expressed genes between Double knockout pbx2/4 MO;prdm1 / vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name ENSEMBL gene.id edgeR pvalue edgeR log fold change. Supplementary files format and content: GSE45532 pbx.genes.csv: Differential expressed genes between pbx2/4 MO vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name ENSEMBL gene.id edgeR pvalue edgeR log fold change. Supplementary files format and content: GSE45532 prdm.genes.csv: Differential expressed genes between prom1 / vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name ENSEMBL gene.id edgeR pvalue edgeR log fold change.	embryos	Embryos were injected with pbx2/4 morpholinos or control morpholinos at the 1 cell stage.	Total RNA from individual embryos was isolated using the RNAqueous Micro Kit Ambion. Samples were genotyped pooled then further cleaned and concentrated using the RNeasy MinElute Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:10 somites\|strain:AB\|genotype:pbx2/4 MO; prdm1 /	GSM1108124	GSM1108124: pbx2/4 MO; prdm1 / rep1; Danio rerio; RNA Seq	GSM1108124 1		1		GEO Accession:GSM1108124	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP020090			LM8_prdm1pbx_ACTTGA_L006_R1_001.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_002.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_003.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_004.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_005.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_008.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_007.fastq.gz LM8_prdm1pbx_ACTTGA_L006_R1_006.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	2850641541.0	28794359.0	GSM1108124 r1	0:99	A:734323874;C:687104792;G:685405933;T:731354277;N:12452665	99				734323874	687104792	685405933	731354277	12452665	SRX255753	SRS404584	SRA071780	GEO	Tapscott, Human Biology, Fred Hutchison Cancer Research Center	1	0.94396		0.11137		0.72308		0.49037		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2013-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures