run_metadata: 65727

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
65727	SRR15600957	SRX11898452	SRS9909634	SRP333957	PRJNA757460	Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish	GSE182714	Other	Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping together with RNA from their offspring at 16 cell 3.5 hpf and 5.3 hpf stages. For each time point at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf a separate batch of uninjected control as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. Paired end sequencing 2 × 75 bp reads was performed with NextSeq 500 Illumina USA.		pubmed:36127363		Adar MO 12h rep 3	GSM5535068		source name:whole zebrafish embryo\|strain:WT ABTL\|tissue:whole embryo\|developmental stage:12hpf	Adar MO 12h rep 3	Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10 using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options q 15 Q 20 were used i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10 Supplementary files format and content: tab delimited file format	whole zebrafish embryo	To assess the effect of Adar KD and OE uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.	Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. For the 7 dpf samples total RNA was subjected to mRNA enrichment using NEBNext PolyA mRNA Magnetic Isolation Module E7490 NEB. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer. For the 7 dpf samples library was constructed using TruSeq Stranded Total 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:WT ABTL\|tissue:whole embryo\|developmental stage:12hpf	GSM5535068	GSM5535068: Adar MO 12h rep 3; Danio rerio; RNA Seq	GSM5535068		1	Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific USA and cleaned up on the Qiagen Rneasy Mini column Qiagen USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al. 2018 total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human Mouse Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories USA as recommended by the manufacturer.	GEO Accession:GSM5535068	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP333957			C-12h-MO_S9_L004_R1_001.fastq.gz C-12h-MO_S9_L004_R2_001.fastq.gz	fastq fastq	775028848.0	5098874.0	GSM5535068 r4	0:76 1:76	A:188415416;C:196744039;G:203147300;T:186326840;N:395253	76	76			188415416	196744039	203147300	186326840	395253	SRX11898452	SRS9909634	SRA1283368	GEO	Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw	2	0.91249	0.92074	0.17336	0.17294	0.71965	0.72188	0.51754	0.52395	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	rrna_depletion	ribozero	bulk	bulk	bulk		Poland	2021-08-24	Segmentation	Embryo	Whole Organism	All anatomical structures