metadata: run_metadata: 8 rows where devstage_curation = "Cleavage" and experiment.platform = "ION

8 rows where devstage_curation = "Cleavage" and experiment.platform = "ION_TORRENT"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	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.study_ref	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.Acount	run.Ccount	run.Gcount	run.Tcount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
41417	41417	SRR4423119	SRX2245303	SRS1745853	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development			Time course 1 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:64 cells\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal								RNA Seq of Zebrafish: 64 cells2 hpf	347 1	347 1	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534		S01large.fastq	fastq	406838773.0	3451573.0	S01large.fastq	0:117.87	A:90440106;C:114282886;G:115318720;T:86797061;N:0	117	90440106	114282886	115318720	86797061	SRX2245303	SRS1745853	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.9203	0.10547	0.93095	0.75003	158	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41432	41432	SRR4423104	SRX2245288	SRS1745853	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development			Time course 1 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:64 cells\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal								miRNA Seq of Zebrafish: 64 cells2 hpf	348 1	348 1	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534		S01small.fastq	fastq	91910627.0	1396009.0	S01small.fastq	0:65.84	A:21663404;C:25661192;G:25069267;T:19516764;N:0	65	21663404	25661192	25069267	19516764	SRX2245288	SRS1745853	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.56828	0.1715	0.92435	0.90047	34	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
59499	59499	SRR11924325	SRX8469997	SRS6770648	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.	pubmed:32912962	small RNA 32 cell	GSM4591064	source name:32 cell stage\|tissue:32 cell stage\|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt	small RNA 32 cell	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	32 cell stage		Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.	tissue:32 cell stage\|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt	GSM4591064	GSM4591064: small RNA 32 cell; Danio rerio; OTHER	GSM4591064		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.	GEO Accession:GSM4591064	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent S5	SRP265951		small_RNA_32_cell_stage.fastq	fastq	275040056.0	6091077.0	GSM4591064 r1	0:45.15	A:69136092;C:69806677;G:72527986;T:63569301;N:0	45	69136092	69806677	72527986	63569301	SRX8469997	SRS6770648	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.67676	0.30881	0.86636	0.63482	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	rrna_depletion	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Cleavage	Embryo	Undetermined	Embryo Imprecise
59509	59509	SRR11924311	SRX8469986	SRS6770637	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.	pubmed:32912962	32 cell 3	GSM4591054	source name:32 cell stage\|tissue:32 cell stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	32 cell 3	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	32 cell stage		Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	tissue:32 cell stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591054	GSM4591054: 32 cell 3; Danio rerio; OTHER	GSM4591054		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591054	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP265951	intentional duplicate	32_cell_3.bam GSE151797_Reference_sequence.fa	bam bam	306452866.0	9472058.0	GSM4591054 r1	0:32.35	A:62923439;C:99486553;G:78734118;T:65308756;N:0	32	62923439	99486553	78734118	65308756	SRX8469986	SRS6770637	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.69616	0.21356	0.91885	0.77399	44	B	usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Cleavage	Embryo	Undetermined	Embryo Imprecise
59510	59510	SRR11924310	SRX8469985	SRS6770636	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.	pubmed:32912962	32 cell 2	GSM4591053	source name:32 cell stage\|tissue:32 cell stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	32 cell 2	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	32 cell stage		Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	tissue:32 cell stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591053	GSM4591053: 32 cell 2; Danio rerio; OTHER	GSM4591053		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591053	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP265951	intentional duplicate	32_cell_2.bam GSE151797_Reference_sequence.fa	bam bam	231900531.0	6985149.0	GSM4591053 r1	0:33.20	A:46033127;C:77390842;G:61355372;T:47121190;N:0	33	46033127	77390842	61355372	47121190	SRX8469985	SRS6770636	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.83429	0.25864	0.9137	0.78928	39	B	usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Cleavage	Embryo	Undetermined	Embryo Imprecise
59511	59511	SRR11924308	SRX8469984	SRS6770635	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.	pubmed:32912962	32 cell 1	GSM4591052	source name:32 cell stage\|tissue:32 cell stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	32 cell 1	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	32 cell stage		Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	tissue:32 cell stage\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591052	GSM4591052: 32 cell 1; Danio rerio; OTHER	GSM4591052		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591052	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP265951	intentional duplicate	32_cell_1.bam GSE151797_Reference_sequence.fa	bam bam	252107732.0	7470443.0	GSM4591052 r1	0:33.75	A:53056857;C:79089015;G:65131744;T:54830116;N:0	33	53056857	79089015	65131744	54830116	SRX8469984	SRS6770635	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.78874	0.25062	0.89645	0.73533	48	B	usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Cleavage	Embryo	Undetermined	Embryo Imprecise
62961	62961	SRR13520380	SRX9931398	SRS8106883	SRP303129	PRJNA694577	Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes	GSE165422	Transcriptome Analysis	Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT–PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection and then when the embryos to develop ttwo xxx hpf 6 hpf and 12 hpf these groups was collected respectively by deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation mainly including isg15 foxo3b phlda3 cdkn1a zgc:136826 and si:dkey 204l11.1 compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf 6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group	pubmed:35690839	G8 1: pEGFP N1 injected at 1hpf	GSM5033115	source name:zebrafish embryos\|strain:TU\|developmental stage:1hpf\|tissue:embryo	G8 1: pEGFP N1 injected at 1hpf	Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10 genome using Mapsplice v2.1.8 with parameters s 22 p 15 ins 6 del 6 non canonical bam o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample	zebrafish embryos	In the 1 cell stage of zebrafish embryos 8ng/μL pEGFP N1 was injected and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf 6hpf and 12hpf. Add 1mL TRIzol Invitrogen USA store at 80℃	RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol	strain:TU\|developmental stage:1hpf\|tissue:embryo	GSM5033115	GSM5033115: G8 1: pEGFP N1 injected at 1hpf; Danio rerio; RNA Seq	GSM5033115		1	RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol	GEO Accession:GSM5033115	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP303129		G8-1.fastq.gz	fastq	2029634086.0	12394054.0	GSM5033115 r1	0:163.76	A:548662597;C:501840467;G:525047427;T:454083595;N:0	163	548662597	501840467	525047427	454083595	SRX9931398	SRS8106883	SRA1187495	GEO	Qingshun Zhao	1	0.81344	0.01015	0.78058	0.48067	90	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2021-01-25	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
62964	62964	SRR13520377	SRX9931395	SRS8106880	SRP303129	PRJNA694577	Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes	GSE165422	Transcriptome Analysis	Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT–PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection and then when the embryos to develop ttwo xxx hpf 6 hpf and 12 hpf these groups was collected respectively by deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation mainly including isg15 foxo3b phlda3 cdkn1a zgc:136826 and si:dkey 204l11.1 compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf 6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group	pubmed:35690839	C1: un injected at 1hpf	GSM5033112	source name:zebrafish embryos\|strain:TU\|developmental stage:1hpf\|tissue:embryo	C1: un injected at 1hpf	Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10 genome using Mapsplice v2.1.8 with parameters s 22 p 15 ins 6 del 6 non canonical bam o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample	zebrafish embryos	In the 1 cell stage of zebrafish embryos 8ng/μL pEGFP N1 was injected and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf 6hpf and 12hpf. Add 1mL TRIzol Invitrogen USA store at 80℃	RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol	strain:TU\|developmental stage:1hpf\|tissue:embryo	GSM5033112	GSM5033112: C1: un injected at 1hpf; Danio rerio; RNA Seq	GSM5033112		1	RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol	GEO Accession:GSM5033112	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP303129		C1.fastq.gz	fastq	2073298475.0	13102880.0	GSM5033112 r1	0:158.23	A:558146987;C:513562209;G:538130597;T:463458682;N:0	158	558146987	513562209	538130597	463458682	SRX9931395	SRS8106880	SRA1187495	GEO	Qingshun Zhao	1	0.83706	0.01172	0.77948	0.48172	233	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2021-01-25	Cleavage	Embryo	Embryo Imprecise	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;