metadata: run_metadata: 27 rows where devstage_curation = "Zygote" and experiment.library

27 rows where devstage_curation = "Zygote" and experiment.library_selection = "unspecified"

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.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
51155	51155	SRR8552547	SRX5354343	SRS4345561	SRP184786	PRJNA521558	Brd4 and p300 confer transcriptional competency during zygotic genome activation	PRJNA521558	Other	The awakening of the genome post fertilization is a cornerstone of animal development. However the mechanisms that activate the silent genome post fertilization are poorly understood. Here we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.	RPF WT 0h Cycloheximide Ribo RPF	RPF WT 0h CHX R RPF AGN000073	strain:TU/AB\|age:0.0\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|treatment:cyclohex\|molecule:RNA\|selection:r \|condition:RPF\|sample ref:AGS000069\|replicate ref:AGN000073\|replicate order:1\|BioSampleModel:Model organism or animal	RPF WT 0h Cycloheximide Ribo RPF	AGR000135	AGR000135	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP184786	AGR000135_R1.fastq.gz	fastq	2161849320.0	30025685.0	AGR000135 R1.fastq.gz	0:72	A:645981607;C:467229372;G:514731353;T:527710797;N:6196191	72		645981607	467229372	514731353	527710797	6196191	SRX5354343	SRS4345561	SRA847217	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0		0.0		1.0				72		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-02-08	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51621	51621	SRR8788632	SRX5578491	SRS4540272	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.	Developmental timecourse WT 1c R0 B2	Developmental timecourse WT 1c R0 B2 AGN000663	strain:TU/AB\|age:0.2\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|sample ref:AGS000583\|replicate ref:AGN000663\|replicate order:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT 1c R0 B2	AGR000855	AGR000855	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP189512	AGR000855_R1.fastq.gz AGR000855_R2.fastq.gz	fastq fastq	2435568352.0	16023476.0	AGR000855 R1.fastq.gz	0:76 1:76	A:629791020;C:590108147;G:587059372;T:624338627;N:4271186	76	76	629791020	590108147	587059372	624338627	4271186	SRX5578491	SRS4540272	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.87561	0.86738	0.07392	0.07503	0.76266	0.76102	0.46339	0.46911	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51622	51622	SRR8788633	SRX5578490	SRS4540271	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.	Developmental timecourse WT 1c R0 B1	Developmental timecourse WT 1c R0 B1 AGN000662	strain:TU/AB\|age:0.2\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:r0\|sample ref:AGS000583\|replicate ref:AGN000662\|replicate order:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT 1c R0 B1	AGR000854	AGR000854	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP189512	AGR000854_R1.fastq.gz AGR000854_R2.fastq.gz	fastq fastq	2337549024.0	15378612.0	AGR000854 R1.fastq.gz	0:76 1:76	A:609210481;C:563729049;G:558514098;T:602041398;N:4053998	76	76	609210481	563729049	558514098	602041398	4053998	SRX5578490	SRS4540271	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.88449	0.87899	0.06047	0.0611	0.7601	0.75838	0.47133	0.47598	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51637	51637	SRR8788648	SRX5578475	SRS4540259	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.	Developmental timecourse WT 1c pA B1	Developmental timecourse WT 1c pA B1 AGN000636	strain:TU/AB\|age:0.2\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|sample ref:AGS000570\|replicate ref:AGN000636\|replicate order:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT 1c pA B1	AGR000828	AGR000828	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP189512	AGR000828_R1.fastq.gz AGR000828_R2.fastq.gz	fastq fastq	1778932000.0	11703500.0	AGR000828 R1.fastq.gz	0:76 1:76	A:473620191;C:414842330;G:414924231;T:473971099;N:1574149	76	76	473620191	414842330	414924231	473971099	1574149	SRX5578475	SRS4540259	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.93194	0.93539	0.02446	0.02342	0.81671	0.81696	0.48421	0.48694	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51638	51638	SRR8788649	SRX5578474	SRS4540258	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.	Developmental timecourse WT 1c pA B2	Developmental timecourse WT 1c pA B2 AGN000637	strain:TU/AB\|age:0.2\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|molecule:RNA\|selection:pA\|sample ref:AGS000570\|replicate ref:AGN000637\|replicate order:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT 1c pA B2	AGR000829	AGR000829	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP189512	AGR000829_R1.fastq.gz AGR000829_R2.fastq.gz	fastq fastq	2327471424.0	15312312.0	AGR000829 R1.fastq.gz	0:76 1:76	A:617481287;C:543018300;G:545498739;T:619434178;N:2038920	76	76	617481287	543018300	545498739	619434178	2038920	SRX5578474	SRS4540258	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.92019	0.92287	0.02435	0.02357	0.81426	0.8145	0.48095	0.48594	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51647	51647	SRR8788658	SRX5578465	SRS4540254	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.	Developmental timecourse WT a Am 1c pA B2	Developmental timecourse WT a Am 1c pA B2 AGN000689	strain:TU/AB\|age:0.2\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:pA\|sample ref:AGS000596\|replicate ref:AGN000689\|replicate order:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am 1c pA B2	AGR000901	AGR000901	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP189512	AGR000901_R1.fastq.gz AGR000901_R2.fastq.gz	fastq fastq	2702532792.0	17779821.0	AGR000901 R1.fastq.gz	0:76 1:76	A:716369155;C:635020541;G:634097644;T:714669224;N:2376228	76	76	716369155	635020541	634097644	714669224	2376228	SRX5578465	SRS4540254	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.92422	0.92692	0.02266	0.02137	0.82481	0.82495	0.49869	0.50166	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51669	51669	SRR8788680	SRX5578443	SRS4540236	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.	Developmental timecourse WT a Am 1c pA B1	Developmental timecourse WT a Am 1c pA B1 AGN000688	strain:TU/AB\|age:0.2\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:pA\|sample ref:AGS000596\|replicate ref:AGN000688\|replicate order:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am 1c pA B1	AGR000900	AGR000900	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP189512	AGR000900_R1.fastq.gz AGR000900_R2.fastq.gz	fastq fastq	2460261056.0	16185928.0	AGR000900 R1.fastq.gz	0:76 1:76	A:657092605;C:573296643;G:571761179;T:655966705;N:2143924	76	76	657092605	573296643	571761179	655966705	2143924	SRX5578443	SRS4540236	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.91111	0.91731	0.02394	0.02269	0.8269	0.82747	0.4987	0.49478	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51671	51671	SRR8788682	SRX5578441	SRS4540219	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.	Developmental timecourse WT a Am 1c R0 B2	Developmental timecourse WT a Am 1c R0 B2 AGN000705	strain:TU/AB\|age:0.2\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:r0\|sample ref:AGS000604\|replicate ref:AGN000705\|replicate order:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am 1c R0 B2	AGR000919	AGR000919	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP189512	AGR000919_R1.fastq.gz AGR000919_R2.fastq.gz	fastq fastq	4296568800.0	28266900.0	AGR000919 R1.fastq.gz	0:76 1:76	A:1116113844;C:1001549711;G:1051044551;T:1119953961;N:7906733	76	76	1116113844	1001549711	1051044551	1119953961	7906733	SRX5578441	SRS4540219	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.61505	0.62079	0.11845	0.11395	0.7878	0.79273	0.52552	0.5261	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51694	51694	SRR8788705	SRX5578418	SRS4540219	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.	Developmental timecourse WT a Am 1c R0 B2	Developmental timecourse WT a Am 1c R0 B2 AGN000705	strain:TU/AB\|age:0.2\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:r0\|sample ref:AGS000604\|replicate ref:AGN000705\|replicate order:2\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am 1c R0 B2	AGR000918	AGR000918	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP189512	AGR000918_R1.fastq.gz AGR000918_R2.fastq.gz	fastq fastq	2356801040.0	15505270.0	AGR000918 R1.fastq.gz	0:76 1:76	A:645305534;C:504536913;G:529941536;T:671927563;N:5089494	76	76	645305534	504536913	529941536	671927563	5089494	SRX5578418	SRS4540219	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.66091	0.63258	0.1287	0.13224	0.78715	0.79109	0.53729	0.53151	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51695	51695	SRR8788706	SRX5578417	SRS4540217	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.	Developmental timecourse WT a Am 1c R0 B1	Developmental timecourse WT a Am 1c R0 B1 AGN000704	strain:TU/AB\|age:0.2\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:r0\|sample ref:AGS000604\|replicate ref:AGN000704\|replicate order:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am 1c R0 B1	AGR000917	AGR000917	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP189512	AGR000917_R1.fastq.gz AGR000917_R2.fastq.gz	fastq fastq	3129506568.0	20588859.0	AGR000917 R1.fastq.gz	0:76 1:76	A:805704877;C:741159058;G:771769886;T:805184484;N:5688263	76	76	805704877	741159058	771769886	805184484	5688263	SRX5578417	SRS4540217	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.57337	0.57983	0.13988	0.13406	0.79204	0.80105	0.51447	0.53836	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51696	51696	SRR8788707	SRX5578416	SRS4540217	SRP189512	PRJNA529241	Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse	PRJNA529241	Other	Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.	Developmental timecourse WT a Am 1c R0 B1	Developmental timecourse WT a Am 1c R0 B1 AGN000704	strain:TU/AB\|age:0.2\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|treatment:alpha am\|molecule:RNA\|selection:r0\|sample ref:AGS000604\|replicate ref:AGN000704\|replicate order:1\|BioSampleModel:Model organism or animal	Developmental timecourse WT a Am 1c R0 B1	AGR000916	AGR000916	RNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP189512	AGR000916_R1.fastq.gz AGR000916_R2.fastq.gz	fastq fastq	2105467064.0	13851757.0	AGR000916 R1.fastq.gz	0:76 1:76	A:578198310;C:450780203;G:468988474;T:603073355;N:4426722	76	76	578198310	450780203	468988474	603073355	4426722	SRX5578416	SRS4540217	SRA866166	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	2	0.64483	0.60666	0.15301	0.15391	0.79091	0.79651	0.51017	0.51384	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2019-05-31	Zygote	Embryo	Embryo Imprecise	All anatomical structures
62534	62534	SRR13234650	SRX9666676	SRS7865613	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.	MZythdf2/3 mRNA pA & R0 background matched ythdf2 het; MZythdf3 control 0hpf ribo0	MZythdf2/3 mRNA pA & R0 bkgd match ythdf2 het; MZythdf3 0h r0 AGN002340	strain:TU/AB\|age:0.0\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|genotype:ythdf2 223/+ or 223/ 223; MZythdf3\|strain maternal:ythdf2 223/+; ythdf3 365/ 365\|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365\|molecule:mRNA\|selection:r0\|sample ref:AGS001769\|replicate ref:AGN002340\|replicate order:1\|BioSampleModel:Model organism or animal	MZythdf2/3 mRNA pA & R0 background matched ythdf2 het; MZythdf3 control 0hpf ribo0	AGR003028	AGR003028	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP297464	AGR003028_R1.fastq.gz	fastq	809198220.0	10647345.0	AGR003028 R1.fastq.gz	0:76 1:0	A:131548927;C:262799074;G:295723637;T:119078265;N:48317	76	0	131548927	262799074	295723637	119078265	48317	SRX9666676	SRS7865613	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.96134		0.02867		0.81138		0.85893		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-10	Zygote	Embryo	Embryo Imprecise	All anatomical structures
62535	62535	SRR13234651	SRX9666675	SRS7865612	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.	MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 0h ribo0	MZythdf2/3 mRNA pA & R0 WT 0h r0 AGN002339	strain:TU/AB\|age:0.0\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|strain maternal:unrelated TUAB wild type\|strain paternal:unrelated TUAB wild type\|molecule:mRNA\|selection:r0\|sample ref:AGS001768\|replicate ref:AGN002339\|replicate order:1\|BioSampleModel:Model organism or animal	MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 0h ribo0	AGR003027	AGR003027	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP297464	AGR003027_R1.fastq.gz	fastq	935971920.0	12315420.0	AGR003027 R1.fastq.gz	0:76 1:0	A:153283406;C:303473141;G:336325094;T:142833742;N:56537	76	0	153283406	303473141	336325094	142833742	56537	SRX9666675	SRS7865612	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.9604		0.02878		0.80628		0.79692		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-10	Zygote	Embryo	Embryo Imprecise	All anatomical structures
62536	62536	SRR13234652	SRX9666674	SRS7865610	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.	MZythdf2/3 mRNA pA & R0 MZythdf2; MZythdf3 0hpf ribo0	MZythdf2/3 mRNA pA & R0 MZythdf2; MZythdf3 0h r0 AGN002338	strain:TU/AB\|age:0.0\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|genotype:MZythdf2; MZythdf3\|strain maternal:ythdf2 223/ 223; ythdf3 365/ 365\|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365\|molecule:mRNA\|selection:r0\|sample ref:AGS001767\|replicate ref:AGN002338\|replicate order:1\|BioSampleModel:Model organism or animal	MZythdf2/3 mRNA pA & R0 MZythdf2; MZythdf3 0hpf ribo0	AGR003026	AGR003026	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP297464	AGR003026_R1.fastq.gz	fastq	1165630772.0	15337247.0	AGR003026 R1.fastq.gz	0:76 1:0	A:185914121;C:376601239;G:425671246;T:177374359;N:69807	76	0	185914121	376601239	425671246	177374359	69807	SRX9666674	SRS7865610	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.96047		0.02268		0.81377		0.84903		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-10	Zygote	Embryo	Embryo Imprecise	All anatomical structures
62537	62537	SRR13234653	SRX9666673	SRS7865611	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.	MZythdf2/3 mRNA pA & R0 background matched ythdf2 het; MZythdf3 control 0hpf polyA	MZythdf2/3 mRNA pA & R0 bkgd match ythdf2 het; MZythdf3 0h pA AGN002335	strain:TU/AB\|age:0.0\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|genotype:ythdf2 223/+ or 223/ 223; MZythdf3\|strain maternal:ythdf2 223/+; ythdf3 365/ 365\|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365\|molecule:mRNA\|selection:pA\|sample ref:AGS001764\|replicate ref:AGN002335\|replicate order:1\|BioSampleModel:Model organism or animal	MZythdf2/3 mRNA pA & R0 background matched ythdf2 het; MZythdf3 control 0hpf polyA	AGR003022	AGR003022	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP297464	AGR003022_R1.fastq.gz	fastq	607989056.0	7999856.0	AGR003022 R1.fastq.gz	0:76 1:0	A:153708086;C:142012326;G:138315448;T:173916462;N:36734	76	0	153708086	142012326	138315448	173916462	36734	SRX9666673	SRS7865611	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.92885		0.03117		0.78362		0.5405		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-09	Zygote	Embryo	Embryo Imprecise	All anatomical structures
62540	62540	SRR13234656	SRX9666670	SRS7865605	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.	MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 0hpf polyA	MZythdf2/3 mRNA pA & R0 WT 0h pA AGN002332	strain:TU/AB\|age:0.0\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|strain maternal:unrelated TUAB wild type\|strain paternal:unrelated TUAB wild type\|molecule:mRNA\|selection:pA\|sample ref:AGS001761\|replicate ref:AGN002332\|replicate order:1\|BioSampleModel:Model organism or animal	MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 0hpf polyA	AGR003019	AGR003019	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP297464	AGR003019_R1.fastq.gz	fastq	565381784.0	7439234.0	AGR003019 R1.fastq.gz	0:76 1:0	A:140209814;C:133250366;G:128677079;T:163209960;N:34565	76	0	140209814	133250366	128677079	163209960	34565	SRX9666670	SRS7865605	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.93741		0.04563		0.80144		0.5511		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-09	Zygote	Embryo	Embryo Imprecise	All anatomical structures
62544	62544	SRR13234660	SRX9666666	SRS7865603	SRP297464	PRJNA683902	Ythdf m6A readers function redundantly during zebrafish development	PRJNA683902	Other	During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.	MZythdf2/3 mRNA pA & R0 MZythdf2; MZythdf3 0hpf polyA	MZythdf2/3 mRNA pA & R0 MZythdf2; MZythdf3 0h pA AGN002329	strain:TU/AB\|age:0.0\|dev stage:1cell\|sex:pooled male and female\|tissue:embryo\|genotype:MZythdf2; MZythdf3\|strain maternal:ythdf2 223/ 223; ythdf3 365/ 365\|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365\|molecule:mRNA\|selection:pA\|sample ref:AGS001758\|replicate ref:AGN002329\|replicate order:1\|BioSampleModel:Model organism or animal	MZythdf2/3 mRNA pA & R0 MZythdf2; MZythdf3 0hpf polyA	AGR003016	AGR003016	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP297464	AGR003016_R1.fastq.gz	fastq	695309104.0	9148804.0	AGR003016 R1.fastq.gz	0:76 1:0	A:179833613;C:157023961;G:155652114;T:202756408;N:43008	76	0	179833613	157023961	155652114	202756408	43008	SRX9666666	SRS7865603	SRA1169659	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.93546		0.03548		0.80087		0.5919		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2020-12-09	Zygote	Embryo	Embryo Imprecise	All anatomical structures
68606	68606	SRR18052577	SRX14204750	SRS12026894	SRP360172	PRJNA807674	A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb	PRJNA807674	Other	The Balbiani body Bb is the first marker of polarity in vertebrate oocytes. The Bb is a conserved structure found in diverse animals including insects fish amphibians and mammals. During early zebrafish oogenesis the Bb assembles as a transient aggregate of mRNA proteins and membrane bound organelles at the presumptive vegetal side of the oocyte. As the early oocyte develops the Bb appears to grow slowly until at the end of stage I of oogenesis it disassembles and deposits its cargo of localized mRNAs and proteins. In fish and frogs this cargo includes the germ plasm as well as gene products required to specify dorsal tissues of the future embryo. We demonstrate that the Bb is a stable solid structure that forms a size exclusion barrier similar to other biological hydrogels. Despite its central role in oocyte polarity little is known about the mechanism behind the Bb's action. Analysis of the few known protein components of the Bb is insufficient to explain how the Bb assembles translocates and disassembles. We isolated Bbs from zebrafish oocytes and performed mass spectrometry to define the Bb proteome. We successfully identified 77 proteins associated with the Bb sample including known Bb proteins and novel RNA binding proteins. In particular we identified Cirbpa and Cirbpb which have both an RNA binding domain and a predicted self aggregation domain. In stage I oocytes Cirbpa and Cirbpb localize to the Bb rather than the nucleus as in somatic cells indicating that they may have a specialized function in the germ line. Both the RNA binding domain and the self aggregation domain are sufficient to localize to the Bb suggesting that Cirbpa and Cirbpb interact with more than just their mRNA targets within the Bb. We propose that Cirbp proteins crosslink mRNA cargo and proteinaceous components of the Bb as it grows. Beyond Cirbpa and Cirbpb our proteomics dataset presents many candidates for further study making it a valuable resource for building a comprehensive mechanism for Bb function at a p…	Oocyte development Oocyte stage 1.3 40 70μm 7/14/14 Biorep2	Oocyte development Oocyte I.3 B2 AGN001112	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:pA\|sample ref:AGS000972\|replicate ref:AGN001112\|replicate order:2\|project label long:Zebrafish oocyte development from Mullins Lab sorted cells\|project label short:Oocyte development\|sample label short:Oocyte I.3\|replicate label short:Oocyte I.3 B2\|BioSampleModel:Model organism or animal	Oocyte development Oocyte stage 1.3 40 70m 7/14/14 Biorep2	AGR001536	AGR001536	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP360172	AGR001536_R1.fastq.gz	fastq	467635448.0	6153098.0	AGR001536 R1.fastq.gz	0:76 1:0	A:123171986;C:108126001;G:105088073;T:125086357;N:6163031	76	0	123171986	108126001	105088073	125086357	6163031	SRX14204750	SRS12026894	SRA1373771	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.96741		0.02607		0.7763		0.49394		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
68607	68607	SRR18052578	SRX14204749	SRS12026893	SRP360172	PRJNA807674	A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb	PRJNA807674	Other	The Balbiani body Bb is the first marker of polarity in vertebrate oocytes. The Bb is a conserved structure found in diverse animals including insects fish amphibians and mammals. During early zebrafish oogenesis the Bb assembles as a transient aggregate of mRNA proteins and membrane bound organelles at the presumptive vegetal side of the oocyte. As the early oocyte develops the Bb appears to grow slowly until at the end of stage I of oogenesis it disassembles and deposits its cargo of localized mRNAs and proteins. In fish and frogs this cargo includes the germ plasm as well as gene products required to specify dorsal tissues of the future embryo. We demonstrate that the Bb is a stable solid structure that forms a size exclusion barrier similar to other biological hydrogels. Despite its central role in oocyte polarity little is known about the mechanism behind the Bb's action. Analysis of the few known protein components of the Bb is insufficient to explain how the Bb assembles translocates and disassembles. We isolated Bbs from zebrafish oocytes and performed mass spectrometry to define the Bb proteome. We successfully identified 77 proteins associated with the Bb sample including known Bb proteins and novel RNA binding proteins. In particular we identified Cirbpa and Cirbpb which have both an RNA binding domain and a predicted self aggregation domain. In stage I oocytes Cirbpa and Cirbpb localize to the Bb rather than the nucleus as in somatic cells indicating that they may have a specialized function in the germ line. Both the RNA binding domain and the self aggregation domain are sufficient to localize to the Bb suggesting that Cirbpa and Cirbpb interact with more than just their mRNA targets within the Bb. We propose that Cirbp proteins crosslink mRNA cargo and proteinaceous components of the Bb as it grows. Beyond Cirbpa and Cirbpb our proteomics dataset presents many candidates for further study making it a valuable resource for building a comprehensive mechanism for Bb function at a p…	Oocyte development Oocyte stage I.3 40 70μm 7/14/14 Biorep1	Oocyte development Oocyte I.3 B1 AGN001111	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:pA\|sample ref:AGS000972\|replicate ref:AGN001111\|replicate order:1\|project label long:Zebrafish oocyte development from Mullins Lab sorted cells\|project label short:Oocyte development\|sample label short:Oocyte I.3\|replicate label short:Oocyte I.3 B1\|BioSampleModel:Model organism or animal	Oocyte development Oocyte stage I.3 40 70m 7/14/14 Biorep1	AGR001535	AGR001535	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP360172	AGR001535_R1.fastq.gz	fastq	495577380.0	6520755.0	AGR001535 R1.fastq.gz	0:76 1:0	A:128639721;C:114539094;G:112745153;T:133122222;N:6531190	76	0	128639721	114539094	112745153	133122222	6531190	SRX14204749	SRS12026893	SRA1373771	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.96355		0.02609		0.76694		0.47874		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
68630	68630	SRR18054176	SRX14206224	SRS12028356	SRP360207	PRJNA807702	Stage specific transcriptomic analysis and database for zebrafish oogenesis	PRJNA807702	Other	Oogenesis produces functional eggs and is essential for fertility embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates and recent studies have identified multiple regulators in oocyte development through forward genetics screens as well as reverse genetics by CRISPR mutagenesis. However many developmental steps in oogenesis in zebrafish and other species remain poorly understood and their underlying mechanisms are unknown. Here we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish which we deposit online as a resource for the community. Further the presence of multiple gene isoforms in zebrafish and the exclusive curation of the single isoforms present in humans by many bioinformatic tools challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.	Oocyte development Oocyte stage III >300μm 7/18/14 Biorep2	Oocyte development Oocyte III B2 AGN001118	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:pA\|sample ref:AGS000976\|replicate ref:AGN001118\|replicate order:2\|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells\|project label short:Oocyte development\|sample label short:Oocyte III\|replicate label short:Oocyte III B2\|BioSampleModel:Model organism or animal	Oocyte development Oocyte stage III >300m 7/18/14 Biorep2	AGR001530	AGR001530	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP360207	AGR001530_R1.fastq.gz	fastq	517403516.0	6807941.0	AGR001530 R1.fastq.gz	0:76 1:0	A:130410978;C:120266868;G:121067507;T:138839131;N:6819032	76	0	130410978	120266868	121067507	138839131	6819032	SRX14206224	SRS12028356	SRA1373868	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.96922		0.02991		0.75519		0.46295		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
68631	68631	SRR18054177	SRX14206223	SRS12028357	SRP360207	PRJNA807702	Stage specific transcriptomic analysis and database for zebrafish oogenesis	PRJNA807702	Other	Oogenesis produces functional eggs and is essential for fertility embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates and recent studies have identified multiple regulators in oocyte development through forward genetics screens as well as reverse genetics by CRISPR mutagenesis. However many developmental steps in oogenesis in zebrafish and other species remain poorly understood and their underlying mechanisms are unknown. Here we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish which we deposit online as a resource for the community. Further the presence of multiple gene isoforms in zebrafish and the exclusive curation of the single isoforms present in humans by many bioinformatic tools challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.	Oocyte development Oocyte stage III >300μm 7/18/14 Biorep1	Oocyte development Oocyte III B1 AGN001117	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:pA\|sample ref:AGS000976\|replicate ref:AGN001117\|replicate order:1\|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells\|project label short:Oocyte development\|sample label short:Oocyte III\|replicate label short:Oocyte III B1\|BioSampleModel:Model organism or animal	Oocyte development Oocyte stage III >300m 7/18/14 Biorep1	AGR001529	AGR001529	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP360207	AGR001529_R1.fastq.gz	fastq	533176860.0	7015485.0	AGR001529 R1.fastq.gz	0:76 1:0	A:134362652;C:123935022;G:124704799;T:143147744;N:7026643	76	0	134362652	123935022	124704799	143147744	7026643	SRX14206223	SRS12028357	SRA1373868	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.96834		0.02909		0.75666		0.46022		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
68632	68632	SRR18054178	SRX14206222	SRS12028355	SRP360207	PRJNA807702	Stage specific transcriptomic analysis and database for zebrafish oogenesis	PRJNA807702	Other	Oogenesis produces functional eggs and is essential for fertility embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates and recent studies have identified multiple regulators in oocyte development through forward genetics screens as well as reverse genetics by CRISPR mutagenesis. However many developmental steps in oogenesis in zebrafish and other species remain poorly understood and their underlying mechanisms are unknown. Here we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish which we deposit online as a resource for the community. Further the presence of multiple gene isoforms in zebrafish and the exclusive curation of the single isoforms present in humans by many bioinformatic tools challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.	Oocyte development Oocyte stage II 100 300μm 7/19/14 Biorep2	Oocyte development Oocyte II B2 AGN001114	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:pA\|sample ref:AGS000974\|replicate ref:AGN001114\|replicate order:2\|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells\|project label short:Oocyte development\|sample label short:Oocyte II\|replicate label short:Oocyte II B2\|BioSampleModel:Model organism or animal	Oocyte development Oocyte stage II 100 300m 7/19/14 Biorep2	AGR001538	AGR001538	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP360207	AGR001538_R1.fastq.gz	fastq	506265108.0	6661383.0	AGR001538 R1.fastq.gz	0:76 1:0	A:130859707;C:117220375;G:114714386;T:136798614;N:6672026	76	0	130859707	117220375	114714386	136798614	6672026	SRX14206222	SRS12028355	SRA1373868	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.96292		0.03541		0.75605		0.47042		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
68633	68633	SRR18054179	SRX14206221	SRS12028354	SRP360207	PRJNA807702	Stage specific transcriptomic analysis and database for zebrafish oogenesis	PRJNA807702	Other	Oogenesis produces functional eggs and is essential for fertility embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates and recent studies have identified multiple regulators in oocyte development through forward genetics screens as well as reverse genetics by CRISPR mutagenesis. However many developmental steps in oogenesis in zebrafish and other species remain poorly understood and their underlying mechanisms are unknown. Here we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish which we deposit online as a resource for the community. Further the presence of multiple gene isoforms in zebrafish and the exclusive curation of the single isoforms present in humans by many bioinformatic tools challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.	Oocyte development Oocyte stage II 100 300μm 7/16/14 Biorep1	Oocyte development Oocyte II B1 AGN001113	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:pA\|sample ref:AGS000974\|replicate ref:AGN001113\|replicate order:1\|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells\|project label short:Oocyte development\|sample label short:Oocyte II\|replicate label short:Oocyte II B1\|BioSampleModel:Model organism or animal	Oocyte development Oocyte stage II 100 300m 7/16/14 Biorep1	AGR001537	AGR001537	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP360207	AGR001537_R1.fastq.gz	fastq	450099360.0	5922360.0	AGR001537 R1.fastq.gz	0:76 1:0	A:117120225;C:103500083;G:101671751;T:121875501;N:5931800	76	0	117120225	103500083	101671751	121875501	5931800	SRX14206221	SRS12028354	SRA1373868	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.96171		0.03386		0.75635		0.47167		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
68634	68634	SRR18054180	SRX14206220	SRS12028352	SRP360207	PRJNA807702	Stage specific transcriptomic analysis and database for zebrafish oogenesis	PRJNA807702	Other	Oogenesis produces functional eggs and is essential for fertility embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates and recent studies have identified multiple regulators in oocyte development through forward genetics screens as well as reverse genetics by CRISPR mutagenesis. However many developmental steps in oogenesis in zebrafish and other species remain poorly understood and their underlying mechanisms are unknown. Here we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish which we deposit online as a resource for the community. Further the presence of multiple gene isoforms in zebrafish and the exclusive curation of the single isoforms present in humans by many bioinformatic tools challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.	Oocyte development Oocyte stage I.2 20 40μm 7/11/14 Biorep2	Oocyte development Oocyte I.2 B2 AGN001110	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:pA\|sample ref:AGS000970\|replicate ref:AGN001110\|replicate order:2\|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells\|project label short:Oocyte development\|sample label short:Oocyte I.2\|replicate label short:Oocyte I.2 B2\|BioSampleModel:Model organism or animal	Oocyte development Oocyte stage I.2 20 40m 7/11/14 Biorep2	AGR001534	AGR001534	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP360207	AGR001534_R1.fastq.gz	fastq	522974164.0	6881239.0	AGR001534 R1.fastq.gz	0:76 1:0	A:136675382;C:120732318;G:119005486;T:139668537;N:6892441	76	0	136675382	120732318	119005486	139668537	6892441	SRX14206220	SRS12028352	SRA1373868	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.96408		0.02945		0.7781		0.48418		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
68635	68635	SRR18054181	SRX14206219	SRS12028353	SRP360207	PRJNA807702	Stage specific transcriptomic analysis and database for zebrafish oogenesis	PRJNA807702	Other	Oogenesis produces functional eggs and is essential for fertility embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates and recent studies have identified multiple regulators in oocyte development through forward genetics screens as well as reverse genetics by CRISPR mutagenesis. However many developmental steps in oogenesis in zebrafish and other species remain poorly understood and their underlying mechanisms are unknown. Here we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish which we deposit online as a resource for the community. Further the presence of multiple gene isoforms in zebrafish and the exclusive curation of the single isoforms present in humans by many bioinformatic tools challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.	Oocyte development Oocyte stage I.2 20 40μm 7/11/14 Biorep1	Oocyte development Oocyte I.2 B1 AGN001109	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:pA\|sample ref:AGS000970\|replicate ref:AGN001109\|replicate order:1\|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells\|project label short:Oocyte development\|sample label short:Oocyte I.2\|replicate label short:Oocyte I.2 B1\|BioSampleModel:Model organism or animal	Oocyte development Oocyte stage I.2 20 40m 7/11/14 Biorep1	AGR001533	AGR001533	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP360207	AGR001533_R1.fastq.gz	fastq	454518152.0	5980502.0	AGR001533 R1.fastq.gz	0:76 1:0	A:120919123;C:103646258;G:100584120;T:123378628;N:5990023	76	0	120919123	103646258	100584120	123378628	5990023	SRX14206219	SRS12028353	SRA1373868	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.96396		0.03175		0.79019		0.51458		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
68636	68636	SRR18054182	SRX14206218	SRS12028351	SRP360207	PRJNA807702	Stage specific transcriptomic analysis and database for zebrafish oogenesis	PRJNA807702	Other	Oogenesis produces functional eggs and is essential for fertility embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates and recent studies have identified multiple regulators in oocyte development through forward genetics screens as well as reverse genetics by CRISPR mutagenesis. However many developmental steps in oogenesis in zebrafish and other species remain poorly understood and their underlying mechanisms are unknown. Here we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish which we deposit online as a resource for the community. Further the presence of multiple gene isoforms in zebrafish and the exclusive curation of the single isoforms present in humans by many bioinformatic tools challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.	Oocyte development Oocyte stage I.1 10 20μm 7/9/14 Biorep2	Oocyte development Oocyte I.1 B2 AGN001108	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:pA\|sample ref:AGS000968\|replicate ref:AGN001108\|replicate order:2\|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells\|project label short:Oocyte development\|sample label short:Oocyte I.1\|replicate label short:Oocyte I.1 B2\|BioSampleModel:Model organism or animal	Oocyte development Oocyte stage I.1 10 20m 7/9/14 Biorep2	AGR001532	AGR001532	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP360207	AGR001532_R1.fastq.gz	fastq	482678432.0	6351032.0	AGR001532 R1.fastq.gz	0:76 1:0	A:125959724;C:109945632;G:110752110;T:129659869;N:6361097	76	0	125959724	109945632	110752110	129659869	6361097	SRX14206218	SRS12028351	SRA1373868	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.9545		0.05008		0.75158		0.49904		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
68637	68637	SRR18054183	SRX14206217	SRS12028350	SRP360207	PRJNA807702	Stage specific transcriptomic analysis and database for zebrafish oogenesis	PRJNA807702	Other	Oogenesis produces functional eggs and is essential for fertility embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates and recent studies have identified multiple regulators in oocyte development through forward genetics screens as well as reverse genetics by CRISPR mutagenesis. However many developmental steps in oogenesis in zebrafish and other species remain poorly understood and their underlying mechanisms are unknown. Here we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish which we deposit online as a resource for the community. Further the presence of multiple gene isoforms in zebrafish and the exclusive curation of the single isoforms present in humans by many bioinformatic tools challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.	Oocyte development Oocyte stage I.1 10 20μm 7/9/14 Biorep1	Oocyte development Oocyte I.1 B1 AGN001107	strain:TU/AB\|age:not applicable\|sex:pooled male and female\|tissue:embryo\|molecule:mRNA\|selection:pA\|sample ref:AGS000968\|replicate ref:AGN001107\|replicate order:1\|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells\|project label short:Oocyte development\|sample label short:Oocyte I.1\|replicate label short:Oocyte I.1 B1\|BioSampleModel:Model organism or animal	Oocyte development Oocyte stage I.1 10 20m 7/9/14 Biorep1	AGR001531	AGR001531	mRNA	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP360207	AGR001531_R1.fastq.gz	fastq	495339804.0	6517629.0	AGR001531 R1.fastq.gz	0:76 1:0	A:130381117;C:112367825;G:112982326;T:133080550;N:6527986	76	0	130381117	112367825	112982326	133080550	6527986	SRX14206217	SRS12028350	SRA1373868	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.94462		0.05195		0.7486		0.51364		76		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures

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