run_metadata: 10070

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
10070	ERR4844841	ERX4714623	ERS5338300	ERP125162	PRJEB41393	Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos	E-MTAB-9777	Transcriptome Analysis	Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis autophagy and cell cycle regulation among others. Here we employ targeted morpholino knockdown to deplete Foxk1 Fokx2 and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.	ENA FIRST PUBLIC:2020 12 01\|ENA LAST UPDATE:2020 11 17		Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011]	foxk MO rep2	SAMEA7579964	Garvan Institute of Medical Research	ENA first public:2020 12 01\|ENA last update:2020 11 17\|External Id:SAMEA7579964\|INSDC center alias:Garvan Institute of Medical Research\|INSDC center name:Garvan Institute of Medical Research\|INSDC first public:2020 12 01T04:12:08Z\|INSDC last update:2020 11 17T14:25:39Z\|INSDC status:public\|Submitter Id:E MTAB 9777:foxk MO rep2\|age:24hpf\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|organism part:whole organism\|sample name:E MTAB 9777:foxk MO rep2\|strain:AB / Tubingen									Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos	E MTAB 9777:foxk MO rep2 s	foxk MO rep2 s	Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos	Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011]	Experimental Factor: compound:morpholino against foxk1/foxk2/foxk2 1\|Experimental Factor: dose:9	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 1500		ERP125162	Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos	ENA FIRST PUBLIC:2020 12 01\|ENA LAST UPDATE:2020 11 17	foxk1-2_rep2.fastq.gz	fastq	3550070715.0	35149215.0	E MTAB 9777:foxk MO rep2	0:101 1:0	A:901160433;C:835963324;G:840839574;T:967604789;N:4502595	101	0			901160433	835963324	840839574	967604789	4502595	ERX4714623	ERS5338300	ERA3145932	European Nucleotide Archive	European Nucleotide Archive	1	0.94006		0.07603		0.69455		0.46867		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		Unknown	2020-11-17	Pharyngula	Embryo	Whole Organism	All anatomical structures