metadata: run_metadata: 61 rows where experiment.library_selection = "size fractionation" and experiment.library

61 rows where experiment.library_selection = "size fractionation" and experiment.library_strategy = "OTHER"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
29739	29739	SRR27467672	SRX23139234	SRS20090275	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Dome mock R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 5 hpf mock rep2	EV04009	EV04009	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04009.R1.fastq.gz	fastq	609590940.0	4354221.0	EV04009.R1.fastq.gz	0:140	A:155062144;C:147628702;G:168099121;T:138772205;N:28768	140		155062144	147628702	168099121	138772205	28768	SRX23139234	SRS20090275	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29740	29740	SRR27467673	SRX23139233	SRS20090278	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			1K cell BS R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 3 hpf BS rep2	EV04008	EV04008	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04008.R1.fastq.gz	fastq	675505180.0	4825037.0	EV04008.R1.fastq.gz	0:140	A:178823976;C:121648962;G:198428643;T:176572292;N:31307	140		178823976	121648962	198428643	176572292	31307	SRX23139233	SRS20090278	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29741	29741	SRR27467674	SRX23139232	SRS20090272	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			1K cell DM R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 3 hpf DM rep2	EV04007	EV04007	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04007.R1.fastq.gz	fastq	702064440.0	5014746.0	EV04007.R1.fastq.gz	0:140	A:176719694;C:166467163;G:207893965;T:150951950;N:31668	140		176719694	166467163	207893965	150951950	31668	SRX23139232	SRS20090272	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	2e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29742	29742	SRR27467675	SRX23139231	SRS20090271	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			1K cell mock R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 3 hpf mock rep2	EV04006	EV04006	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04006.R1.fastq.gz	fastq	664790700.0	4748505.0	EV04006.R1.fastq.gz	0:140	A:172014219;C:146545691;G:200358431;T:145840649;N:31710	140		172014219	146545691	200358431	145840649	31710	SRX23139231	SRS20090271	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99993		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29743	29743	SRR27467676	SRX23139230	SRS20090273	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			4 cell DM R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 1 hpf DM rep2	EV04004	EV04004	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04004.R1.fastq.gz	fastq	895671560.0	6397654.0	EV04004.R1.fastq.gz	0:140	A:206443066;C:147067097;G:365386937;T:176734600;N:39860	140		206443066	147067097	365386937	176734600	39860	SRX23139230	SRS20090273	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Cleavage	Embryo	Whole Organism	All anatomical structures
29744	29744	SRR27467677	SRX23139229	SRS20090274	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			4 cell mock R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 1 hpf mock rep2	EV04003	EV04003	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04003.R1.fastq.gz	fastq	664112120.0	4743658.0	EV04003.R1.fastq.gz	0:140	A:163711695;C:142612940;G:211194350;T:146562626;N:30509	140		163711695	142612940	211194350	146562626	30509	SRX23139229	SRS20090274	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	2e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Cleavage	Embryo	Whole Organism	All anatomical structures
29745	29745	SRR27467678	SRX23139228	SRS20090268	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			eggs mock R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:activated eggs\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:activated eggs\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: eggs mock rep2	EV04001	EV04001	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04001.R1.fastq.gz	fastq	970037880.0	6928842.0	EV04001.R1.fastq.gz	0:140	A:258735538;C:237798398;G:268588390;T:204871983;N:43571	140		258735538	237798398	268588390	204871983	43571	SRX23139228	SRS20090268	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Undetermined	Embryo	Undetermined	Embryo Imprecise
29746	29746	SRR27467679	SRX23139227	SRS20090270	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			ovary BS R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: ovary BS rep2	EV02003	EV02003	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	NextSeq 500		SRP482074	EV02003.R1.fastq.gz EV02003.R2.fastq.gz	fastq fastq	1031891720.0	3416860.0	EV02003.R1.fastq.gz	0:151 1:151	A:264464363;C:153440613;G:408557241;T:205367487;N:62016	151	151	264464363	153440613	408557241	205367487	62016	SRX23139227	SRS20090270	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	2	0.0	0.00019	0.0	0.00015	1.0	0.99993		1.0	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Adult	Adult	Gonad	Reproductive System
29747	29747	SRR27467680	SRX23139226	SRS20090267	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			24h BS R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 24 hpf BS rep2	EV03009	EV03009	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV03009.R1.fastq.gz	fastq	168931280.0	2222780.0	EV03009.R1.fastq.gz	0:76	A:49803604;C:36479774;G:37758990;T:44874154;N:14758	76		49803604	36479774	37758990	44874154	14758	SRX23139226	SRS20090267	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00034		0.0002		0.99965		0.5		76		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
29748	29748	SRR27467681	SRX23139225	SRS20090266	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			24h DM R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 24 hpf DM rep2	EV03008	EV03008	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV03008.R1.fastq.gz	fastq	200878792.0	2643142.0	EV03008.R1.fastq.gz	0:76	A:46955288;C:54746275;G:55887832;T:43270561;N:18836	76		46955288	54746275	55887832	43270561	18836	SRX23139225	SRS20090266	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.29408		0.00737		0.91823		0.54549		76		B		usable mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
29749	29749	SRR27467682	SRX23139224	SRS20090269	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			24h mock R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 24 hpf mock rep2	EV03007	EV03007	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV03007.R1.fastq.gz	fastq	175642840.0	2311090.0	EV03007.R1.fastq.gz	0:76	A:44745275;C:48908904;G:44862157;T:37111895;N:14609	76		44745275	48908904	44862157	37111895	14609	SRX23139224	SRS20090269	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.06887		0.00273		0.96623		0.48721		76		B		usable mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
29750	29750	SRR27467683	SRX23139223	SRS20090265	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Bud BS R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 10 hpf BS rep2	EV04014	EV04014	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04014.R1.fastq.gz	fastq	774901260.0	5535009.0	EV04014.R1.fastq.gz	0:140	A:193865579;C:138861953;G:251102013;T:191036071;N:35644	140		193865579	138861953	251102013	191036071	35644	SRX23139223	SRS20090265	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Gastrula	Embryo	Whole Organism	All anatomical structures
29751	29751	SRR27467684	SRX23139222	SRS20090264	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Bud DM R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 10 hpf DM rep2	EV04013	EV04013	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04013.R1.fastq.gz	fastq	666372840.0	4759806.0	EV04013.R1.fastq.gz	0:140	A:172923134;C:142243998;G:211584978;T:139591020;N:29710	140		172923134	142243998	211584978	139591020	29710	SRX23139222	SRS20090264	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99991		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Gastrula	Embryo	Whole Organism	All anatomical structures
29752	29752	SRR27467685	SRX23139221	SRS20090262	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Bud mock R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 10 hpf mock rep2	EV04012	EV04012	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04012.R1.fastq.gz	fastq	628769540.0	4491211.0	EV04012.R1.fastq.gz	0:140	A:160925901;C:143204697;G:183224867;T:141385307;N:28768	140		160925901	143204697	183224867	141385307	28768	SRX23139221	SRS20090262	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	1e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Gastrula	Embryo	Whole Organism	All anatomical structures
29753	29753	SRR27467686	SRX23139220	SRS20090263	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Dome BS R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 5 hpf BS rep2	EV04011	EV04011	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04011.R1.fastq.gz	fastq	720913200.0	5149380.0	EV04011.R1.fastq.gz	0:140	A:185414155;C:126110104;G:238649631;T:170706590;N:32720	140		185414155	126110104	238649631	170706590	32720	SRX23139220	SRS20090263	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29754	29754	SRR27467687	SRX23139219	SRS20090259	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Dome DM R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 5 hpf DM rep2	EV04010	EV04010	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04010.R1.fastq.gz	fastq	443650200.0	3168930.0	EV04010.R1.fastq.gz	0:140	A:114663509;C:102512276;G:135709753;T:90744641;N:20021	140		114663509	102512276	135709753	90744641	20021	SRX23139219	SRS20090259	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	1e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Blastula	Embryo	Whole Organism	All anatomical structures
29755	29755	SRR27467688	SRX23139218	SRS20090261	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			ovary DM R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: ovary DM rep2	EV02002	EV02002	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	NextSeq 500		SRP482074	EV02002.R1.fastq.gz EV02002.R2.fastq.gz	fastq fastq	861320308.0	2852054.0	EV02002.R1.fastq.gz	0:151 1:151	A:205625519;C:162178974;G:334206312;T:159256900;N:52603	151	151	205625519	162178974	334206312	159256900	52603	SRX23139218	SRS20090261	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	2	2e-05	0.00049	0.0	0.00027	1.0	0.99947		0.44444	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Adult	Adult	Gonad	Reproductive System
29756	29756	SRR27467689	SRX23139217	SRS20090260	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			ovary mock R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: ovary mock rep2	EV02001	EV02001	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	NextSeq 500		SRP482074	EV02001.R1.fastq.gz EV02001.R2.fastq.gz	fastq fastq	520371066.0	1723083.0	EV02001.R1.fastq.gz	0:151 1:151	A:116107273;C:90896560;G:218652568;T:94682244;N:32421	151	151	116107273	90896560	218652568	94682244	32421	SRX23139217	SRS20090260	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	2	2e-05	0.00086	0.0	0.00078	0.99995	0.99981	0.0	0.61538	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Adult	Adult	Gonad	Reproductive System
29757	29757	SRR27437477	SRX23109820	SRS20064574	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			1K cell mock R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 3 hpf mock rep3	EV07007	EV07007	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07007.R1.fastq.gz	fastq	479994620.0	3428533.0	EV07007.R1.fastq.gz	0:140	A:124628886;C:116843590;G:123136721;T:115372734;N:12689	140		124628886	116843590	123136721	115372734	12689	SRX23109820	SRS20064574	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	6e-05		1e-05		0.99989		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29758	29758	SRR27437478	SRX23109819	SRS20064573	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			4 cell BS R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 1 hpf BS rep3	EV07006	EV07006	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07006.R1.fastq.gz	fastq	2584527680.0	18460912.0	EV07006.R1.fastq.gz	0:140	A:685107500;C:367766834;G:717359848;T:814224206;N:69292	140		685107500	367766834	717359848	814224206	69292	SRX23109819	SRS20064573	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	2e-05		1e-05		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Cleavage	Embryo	Whole Organism	All anatomical structures
29759	29759	SRR27437479	SRX23109818	SRS20064571	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			4 cell DM R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 1 hpf DM rep3	EV07005	EV07005	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07005.R1.fastq.gz	fastq	713829480.0	5098782.0	EV07005.R1.fastq.gz	0:140	A:183575304;C:168886779;G:213156258;T:148191838;N:19301	140		183575304	168886779	213156258	148191838	19301	SRX23109818	SRS20064571	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	5e-05		0.0		0.99989		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Cleavage	Embryo	Whole Organism	All anatomical structures
29760	29760	SRR27437480	SRX23109817	SRS20064572	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			4 cell mock R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 1 hpf mock rep3	EV07004	EV07004	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07004.R1.fastq.gz	fastq	517336680.0	3695262.0	EV07004.R1.fastq.gz	0:140	A:136783049;C:131207858;G:139873280;T:109458276;N:14217	140		136783049	131207858	139873280	109458276	14217	SRX23109817	SRS20064572	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	7e-05		0.0		0.99981		0.7		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Cleavage	Embryo	Whole Organism	All anatomical structures
29761	29761	SRR27437481	SRX23109816	SRS20064569	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			eggs BS R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:activated eggs\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:activated eggs\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: eggs BS rep3	EV07003	EV07003	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07003.R1.fastq.gz	fastq	688960160.0	4921144.0	EV07003.R1.fastq.gz	0:140	A:187831021;C:119362814;G:195214528;T:186533242;N:18555	140		187831021	119362814	195214528	186533242	18555	SRX23109816	SRS20064569	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Undetermined	Embryo	Undetermined	Embryo Imprecise
29762	29762	SRR27437482	SRX23109815	SRS20064568	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			eggs DM R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:activated eggs\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:activated eggs\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: eggs DM rep3	EV07002	EV07002	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07002.R1.fastq.gz	fastq	520725380.0	3719467.0	EV07002.R1.fastq.gz	0:140	A:138972126;C:125739732;G:142785467;T:113214166;N:13889	140		138972126	125739732	142785467	113214166	13889	SRX23109815	SRS20064568	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00014		1e-05		0.99969		0.5		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Undetermined	Embryo	Undetermined	Embryo Imprecise
29763	29763	SRR27437483	SRX23109814	SRS20064570	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			eggs mock R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:activated eggs\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:activated eggs\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: eggs mock rep3	EV07001	EV07001	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07001.R1.fastq.gz	fastq	684538960.0	4889564.0	EV07001.R1.fastq.gz	0:140	A:178906891;C:169237174;G:192342342;T:144034095;N:18458	140		178906891	169237174	192342342	144034095	18458	SRX23109814	SRS20064570	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0001		1e-05		0.99977		0.76923		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Undetermined	Embryo	Undetermined	Embryo Imprecise
29764	29764	SRR27437484	SRX23109813	SRS20064567	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			24h BS R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 24 hpf BS rep3	EV07018	EV07018	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07018.R1.fastq.gz	fastq	887731180.0	6340937.0	EV07018.R1.fastq.gz	0:140	A:204102176;C:148262233;G:350287017;T:185056779;N:22975	140		204102176	148262233	350287017	185056779	22975	SRX23109813	SRS20064567	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Pharyngula	Embryo	Whole Organism	All anatomical structures
29765	29765	SRR27437485	SRX23109812	SRS20064566	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			ovary BS R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: ovary BS rep3	EV04017	EV04017	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04017.R1.fastq.gz	fastq	576584540.0	4118461.0	EV04017.R1.fastq.gz	0:140	A:149516980;C:91163801;G:169046762;T:166831111;N:25886	140		149516980	91163801	169046762	166831111	25886	SRX23109812	SRS20064566	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Adult	Adult	Gonad	Reproductive System
29766	29766	SRR27437486	SRX23109811	SRS20064565	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			24h DM R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 24 hpf DM rep3	EV07017	EV07017	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07017.R1.fastq.gz	fastq	466089960.0	3329214.0	EV07017.R1.fastq.gz	0:140	A:117818387;C:108651920;G:144753443;T:94853810;N:12400	140		117818387	108651920	144753443	94853810	12400	SRX23109811	SRS20064565	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Pharyngula	Embryo	Whole Organism	All anatomical structures
29767	29767	SRR27437487	SRX23109810	SRS20064563	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			24h mock R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 24 hpf mock rep3	EV07016	EV07016	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07016.R1.fastq.gz	fastq	638674120.0	4561958.0	EV07016.R1.fastq.gz	0:140	A:159572532;C:147135537;G:186885553;T:145063254;N:17244	140		159572532	147135537	186885553	145063254	17244	SRX23109810	SRS20064563	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	4e-05		0.0		0.99993		0.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Pharyngula	Embryo	Whole Organism	All anatomical structures
29768	29768	SRR27437488	SRX23109809	SRS20064564	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Bud BS R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 10 hpf BS rep3	EV07015	EV07015	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07015.R1.fastq.gz	fastq	598389400.0	4274210.0	EV07015.R1.fastq.gz	0:140	A:150315140;C:106310211;G:186765596;T:154982225;N:16228	140		150315140	106310211	186765596	154982225	16228	SRX23109809	SRS20064564	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Gastrula	Embryo	Whole Organism	All anatomical structures
29769	29769	SRR27437489	SRX23109808	SRS20064562	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Bud DM R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 10 hpf DM rep3	EV07014	EV07014	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07014.R1.fastq.gz	fastq	739056780.0	5278977.0	EV07014.R1.fastq.gz	0:140	A:197948890;C:178761090;G:200265458;T:162060992;N:20350	140		197948890	178761090	200265458	162060992	20350	SRX23109808	SRS20064562	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99995		0.5		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Gastrula	Embryo	Whole Organism	All anatomical structures
29770	29770	SRR27437490	SRX23109807	SRS20064561	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Bud mock R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 10 hpf mock rep3	EV07013	EV07013	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07013.R1.fastq.gz	fastq	844338040.0	6030986.0	EV07013.R1.fastq.gz	0:140	A:217780710;C:182517044;G:251974206;T:192043675;N:22405	140		217780710	182517044	251974206	192043675	22405	SRX23109807	SRS20064561	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	4e-05		0.0		0.99993		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Gastrula	Embryo	Whole Organism	All anatomical structures
29771	29771	SRR27437491	SRX23109806	SRS20064560	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Dome BS R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 5 hpf BS rep3	EV07011	EV07011	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07011.R1.fastq.gz	fastq	893528580.0	6382347.0	EV07011.R1.fastq.gz	0:140	A:240101890;C:155985797;G:262065322;T:235351334;N:24237	140		240101890	155985797	262065322	235351334	24237	SRX23109806	SRS20064560	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29772	29772	SRR27437492	SRX23109805	SRS20064559	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Dome DM R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 5 hpf DM rep3	EV07012	EV07012	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07012.R1.fastq.gz	fastq	797662600.0	5697590.0	EV07012.R1.fastq.gz	0:140	A:201908589;C:182656132;G:249672167;T:163404182;N:21530	140		201908589	182656132	249672167	163404182	21530	SRX23109805	SRS20064559	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99991		0.75		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29773	29773	SRR27437493	SRX23109804	SRS20064558	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Dome mock R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 5 hpf mock rep3	EV07010	EV07010	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07010.R1.fastq.gz	fastq	467593280.0	3339952.0	EV07010.R1.fastq.gz	0:140	A:122604957;C:118747514;G:124074466;T:102153374;N:12969	140		122604957	118747514	124074466	102153374	12969	SRX23109804	SRS20064558	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	4e-05		0.0		0.99993		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29774	29774	SRR27437494	SRX23109803	SRS20064557	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			1K cell BS R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 3 hpf BS rep3	EV07008	EV07008	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07008.R1.fastq.gz	fastq	705682040.0	5040586.0	EV07008.R1.fastq.gz	0:140	A:194506527;C:127442743;G:192893716;T:190818958;N:20096	140		194506527	127442743	192893716	190818958	20096	SRX23109803	SRS20064557	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29775	29775	SRR27437495	SRX23109802	SRS20064556	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			1K cell DM R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 3 hpf DM rep3	EV07009	EV07009	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV07009.R1.fastq.gz	fastq	380716280.0	2719402.0	EV07009.R1.fastq.gz	0:140	A:95351632;C:89558330;G:115625953;T:80169603;N:10762	140		95351632	89558330	115625953	80169603	10762	SRX23109802	SRS20064556	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	6e-05		1e-05		0.99991		0.75		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Blastula	Embryo	Whole Organism	All anatomical structures
29776	29776	SRR27437496	SRX23109801	SRS20064555	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			ovary DM R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: ovary DM rep3	EV04016	EV04016	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04016.R1.fastq.gz	fastq	635752880.0	4541092.0	EV04016.R1.fastq.gz	0:140	A:160072248;C:143996869;G:189137330;T:142516059;N:30374	140		160072248	143996869	189137330	142516059	30374	SRX23109801	SRS20064555	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	1e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Adult	Adult	Gonad	Reproductive System
29777	29777	SRR27437497	SRX23109800	SRS20064554	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			ovary mock R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: ovary mock rep3	EV04015	EV04015	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV04015.R1.fastq.gz	fastq	489700680.0	3497862.0	EV04015.R1.fastq.gz	0:140	A:126641754;C:126582886;G:130564204;T:105889815;N:22021	140		126641754	126582886	130564204	105889815	22021	SRX23109800	SRS20064554	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	6e-05		0.0		0.99983		0.55555		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Adult	Adult	Gonad	Reproductive System
29778	29778	SRR27435863	SRX23108233	SRS20063070	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			1K cell mock R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 3 hpf mock rep4	EV08010	EV08010	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08010.R1.fastq.gz	fastq	678729520.0	4848068.0	EV08010.R1.fastq.gz	0:140	A:170672553;C:182320916;G:171865707;T:153824163;N:46181	140		170672553	182320916	171865707	153824163	46181	SRX23108233	SRS20063070	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0006		4e-05		0.99878		0.79069		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29779	29779	SRR27435864	SRX23108232	SRS20063068	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			4 cell BS R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 1 hpf BS rep4	EV08009	EV08009	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08009.R1.fastq.gz	fastq	756964460.0	5406889.0	EV08009.R1.fastq.gz	0:140	A:191381054;C:111783194;G:185694475;T:268052883;N:52854	140		191381054	111783194	185694475	268052883	52854	SRX23108232	SRS20063068	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	1e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Cleavage	Embryo	Whole Organism	All anatomical structures
29780	29780	SRR27435865	SRX23108231	SRS20063069	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			4 cell DM R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 1 hpf DM rep4	EV08008	EV08008	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08008.R1.fastq.gz	fastq	751794680.0	5369962.0	EV08008.R1.fastq.gz	0:140	A:194845808;C:197389162;G:194749636;T:164756481;N:53593	140		194845808	197389162	194749636	164756481	53593	SRX23108231	SRS20063069	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00124		0.00029		0.99853		0.77083		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Cleavage	Embryo	Whole Organism	All anatomical structures
29781	29781	SRR27435866	SRX23108230	SRS20063066	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			4 cell mock R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:1 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 1 hpf mock rep4	EV08007	EV08007	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08007.R1.fastq.gz	fastq	761961760.0	5442584.0	EV08007.R1.fastq.gz	0:140	A:194053323;C:191169414;G:194452160;T:182234253;N:52610	140		194053323	191169414	194452160	182234253	52610	SRX23108230	SRS20063066	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00242		0.00062		0.99803		0.81818		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Cleavage	Embryo	Whole Organism	All anatomical structures
29782	29782	SRR27435867	SRX23108229	SRS20063067	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			eggs BS R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:activated eggs\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:activated eggs\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: eggs BS rep4	EV08006	EV08006	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08006.R1.fastq.gz	fastq	501745580.0	3583897.0	EV08006.R1.fastq.gz	0:140	A:124242793;C:76040623;G:131428076;T:170000220;N:33868	140		124242793	76040623	131428076	170000220	33868	SRX23108229	SRS20063067	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	4e-05		0.0		0.99993		0.66666		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Undetermined	Embryo	Undetermined	Embryo Imprecise
29783	29783	SRR27435868	SRX23108228	SRS20063063	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			eggs DM R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:activated eggs\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:activated eggs\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: eggs DM rep4	EV08005	EV08005	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08005.R1.fastq.gz	fastq	740147520.0	5286768.0	EV08005.R1.fastq.gz	0:140	A:192131338;C:198130943;G:182616631;T:167216834;N:51774	140		192131338	198130943	182616631	167216834	51774	SRX23108228	SRS20063063	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00052		8e-05		0.99922		0.92537		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Undetermined	Embryo	Undetermined	Embryo Imprecise
29784	29784	SRR27435869	SRX23108227	SRS20063065	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			eggs mock R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:activated eggs\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:activated eggs\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: eggs mock rep4	EV08004	EV08004	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08004.R1.fastq.gz	fastq	761663140.0	5440451.0	EV08004.R1.fastq.gz	0:140	A:194684966;C:192212418;G:196372829;T:178340184;N:52743	140		194684966	192212418	196372829	178340184	52743	SRX23108227	SRS20063065	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00151		0.00037		0.99884		0.82352		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Undetermined	Embryo	Undetermined	Embryo Imprecise
29785	29785	SRR27435870	SRX23108226	SRS20063064	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			24h BS R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 24 hpf BS rep4	EV08021	EV08021	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08021.R1.fastq.gz	fastq	747571860.0	5339799.0	EV08021.R1.fastq.gz	0:140	A:185666613;C:121868156;G:181153824;T:258830310;N:52957	140		185666613	121868156	181153824	258830310	52957	SRX23108226	SRS20063064	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Pharyngula	Embryo	Whole Organism	All anatomical structures
29786	29786	SRR27435871	SRX23108225	SRS20063062	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			ovary BS R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: ovary BS rep4	EV08003	EV08003	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08003.R1.fastq.gz	fastq	571689580.0	4083497.0	EV08003.R1.fastq.gz	0:140	A:141414131;C:88722455;G:138790445;T:202723075;N:39474	140		141414131	88722455	138790445	202723075	39474	SRX23108225	SRS20063062	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99991		0.75		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Adult	Adult	Gonad	Reproductive System
29787	29787	SRR27435872	SRX23108224	SRS20063061	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			24h DM R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 24 hpf DM rep4	EV08020	EV08020	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08020.R1.fastq.gz	fastq	775090400.0	5536360.0	EV08020.R1.fastq.gz	0:140	A:198131068;C:205114604;G:198783890;T:173006366;N:54472	140		198131068	205114604	198783890	173006366	54472	SRX23108224	SRS20063061	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00056		4e-05		0.9989		0.71052		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Pharyngula	Embryo	Whole Organism	All anatomical structures
29788	29788	SRR27435873	SRX23108223	SRS20063060	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			24h mock R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:24 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 24 hpf mock rep4	EV08019	EV08019	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08019.R1.fastq.gz	fastq	763233240.0	5451666.0	EV08019.R1.fastq.gz	0:140	A:189362337;C:199268270;G:198509945;T:176040551;N:52137	140		189362337	199268270	198509945	176040551	52137	SRX23108223	SRS20063060	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00036		6e-05		0.99939		0.85365		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Pharyngula	Embryo	Whole Organism	All anatomical structures
29789	29789	SRR27435874	SRX23108222	SRS20063057	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Bud BS R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 10 hpf BS rep4	EV08018	EV08018	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08018.R1.fastq.gz	fastq	809203080.0	5780022.0	EV08018.R1.fastq.gz	0:140	A:209714496;C:130623600;G:197912909;T:270895413;N:56662	140		209714496	130623600	197912909	270895413	56662	SRX23108222	SRS20063057	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Gastrula	Embryo	Whole Organism	All anatomical structures
29790	29790	SRR27435875	SRX23108221	SRS20063059	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Bud DM R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 10 hpf DM rep4	EV08017	EV08017	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08017.R1.fastq.gz	fastq	722137500.0	5158125.0	EV08017.R1.fastq.gz	0:140	A:176408094;C:195907583;G:188487109;T:161283055;N:51659	140		176408094	195907583	188487109	161283055	51659	SRX23108221	SRS20063059	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00053		3e-05		0.999		0.70422		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Gastrula	Embryo	Whole Organism	All anatomical structures
29791	29791	SRR27435876	SRX23108220	SRS20063058	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Bud mock R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:10 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 10 hpf mock rep4	EV08016	EV08016	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08016.R1.fastq.gz	fastq	827605660.0	5911469.0	EV08016.R1.fastq.gz	0:140	A:204173663;C:224596562;G:206999037;T:191779555;N:56843	140		204173663	224596562	206999037	191779555	56843	SRX23108220	SRS20063058	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00037		2e-05		0.99908		0.7037		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Gastrula	Embryo	Whole Organism	All anatomical structures
29792	29792	SRR27435877	SRX23108219	SRS20063056	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Dome BS R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 5 hpf BS rep4	EV08015	EV08015	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08015.R1.fastq.gz	fastq	804598200.0	5747130.0	EV08015.R1.fastq.gz	0:140	A:215467427;C:134937180;G:189531758;T:264604493;N:57342	140		215467427	134937180	189531758	264604493	57342	SRX23108219	SRS20063056	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	2e-05		0.0		0.99995		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29793	29793	SRR27435878	SRX23108218	SRS20063055	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Dome DM R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 5 hpf DM rep4	EV08014	EV08014	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08014.R1.fastq.gz	fastq	662443740.0	4731741.0	EV08014.R1.fastq.gz	0:140	A:164941700;C:167025964;G:177255084;T:153175163;N:45829	140		164941700	167025964	177255084	153175163	45829	SRX23108218	SRS20063055	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00069		0.0001		0.9992		0.83076		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29794	29794	SRR27435879	SRX23108217	SRS20063052	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			Dome mock R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:5 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 5 hpf mock rep4	EV08013	EV08013	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08013.R1.fastq.gz	fastq	794760540.0	5676861.0	EV08013.R1.fastq.gz	0:140	A:197361776;C:210230329;G:205734036;T:181380205;N:54194	140		197361776	210230329	205734036	181380205	54194	SRX23108217	SRS20063052	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00066		9e-05		0.99894		0.78378		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29795	29795	SRR27435880	SRX23108216	SRS20063054	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			1K cell BS R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:BS\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 3 hpf BS rep4	EV08012	EV08012	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08012.R1.fastq.gz	fastq	722593200.0	5161380.0	EV08012.R1.fastq.gz	0:140	A:188475497;C:119550806;G:173208825;T:241306038;N:52034	140		188475497	119550806	173208825	241306038	52034	SRX23108216	SRS20063054	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29796	29796	SRR27435881	SRX23108215	SRS20063053	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			1K cell DM R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:3 hpf\|collection date:2022\|geo loc name:Austria\|sex:mixed\|tissue:whole embryo\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: embryo 3 hpf DM rep4	EV08011	EV08011	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08011.R1.fastq.gz	fastq	753783380.0	5384167.0	EV08011.R1.fastq.gz	0:140	A:190029713;C:193734250;G:194752855;T:175212145;N:54417	140		190029713	193734250	194752855	175212145	54417	SRX23108215	SRS20063053	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00076		5e-05		0.99859		0.70873		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Blastula	Embryo	Whole Organism	All anatomical structures
29797	29797	SRR27435882	SRX23108214	SRS20063050	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			ovary DM R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:DM\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: ovary DM rep4	EV08002	EV08002	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08002.R1.fastq.gz	fastq	668593800.0	4775670.0	EV08002.R1.fastq.gz	0:140	A:164584224;C:175789134;G:175538168;T:152637106;N:45168	140		164584224	175789134	175538168	152637106	45168	SRX23108214	SRS20063050	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00525		2e-05		0.99192		0.63501		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Adult	Adult	Gonad	Reproductive System
29798	29798	SRR27435883	SRX23108213	SRS20063051	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other			ovary mock R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:mock\|BioSampleModel:Model organism or animal	tRAM seq of zebrafish: ovary mock rep4	EV08001	EV08001	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.	OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP482074	EV08001.R1.fastq.gz	fastq	753247460.0	5380339.0	EV08001.R1.fastq.gz	0:140	A:183862675;C:196453674;G:197604061;T:175275086;N:51964	140		183862675	196453674	197604061	175275086	51964	SRX23108213	SRS20063051	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00754		4e-05		0.98957		0.51048		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Adult	Adult	Gonad	Reproductive System
40707	40707	SRR3502888	SRX1760541	SRS1436386	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.	Zebrafish tRNA at 6hpf	tRNA AB 6h	strain:TUAB\|age:6hpf\|dev stage:Shield\|sex:pooled male and female\|tissue:Whole animal\|collected by:Ariel Bazzini\|genotype:WT\|BioSampleModel:Model organism or animal	Zebrafish tRNAs at 6hpf	tRNA 6hpf zebrafish	TGIRT tRNA Library	1	OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296	AB-tRNA_S9_R1_001.fastq.gz AB-tRNA_S9_R2_001.fastq.gz	fastq fastq	7860522000.0	26201740.0	tRNA zebrafish 6hpf	0:150 1:150	A:1945184302;C:2012637521;G:2171934357;T:1730625218;N:140602	150	150	1945184302	2012637521	2171934357	1730625218	140602	SRX1760541	SRS1436386	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.04186	0.04313	0.00633	0.00639	0.96834	0.96913	0.53967	0.5329	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	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");;